title: 223989

city: Hamar

first: Maren

last: van Son

address: Storhamargata 44

country: Norway

institute: Norsvin

data_processing:
Fastqc v.0.10.1 for quality control of raw sequence data
TopHat v.2.0.12 for read alignment
Samtools v.1.1 for sorting and indexing of mapped reads, mpileup and bcftools call and filter for variant detection and variant filtering
HTSeq to calculate number of reads aligned to each transcript
Integrative Genomics Viewer (IGV) for visual inspection of reads
R packages edgeR v.3.2.4 and goseq for analyzing for differential expression and gene ontology enrichments
SnpEff v.4.1, VEP and SnpSift to annotate and filter variants
Genome_build: Sus scrofa 10.2
Supplementary_files_format_and_content: txt file with raw counts of sequence reads

organism: Sus scrofa

source_name: Testis

extract_protocol:
Total RNA for RNA sequencing was extracted from testicle tissue using the RNeasy Midi Kit from Qiagen according to the manufacturer’s instruction (Qiagen, CA, USA). Concentrations were measured using a NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies, DE, USA) and the RNA quality was examined by the 28S:18S rRNA ratio using the RNA 6000 Nano LabChip® Kit on 2100 Bioanalyzer (Agilent Technologies, CA, USA). All samples displayed a 260/280 ratio >1.8 and RNA integrity numbers (RIN) >8.5.
TruSeq RNA v2 (Illumina). 2 µg RNA was used as input, and 4 mins fragmentation at 94 oC was employed.

value: Norsvin Duroc

tag: sperm dna fragmentation index

tag: group

value: high


title: 223984

status: Public on Sep 01 2017

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: breed


title: 226260

value: low


title: 202517


title: 225577


title: 216352


title: 221066


title: 222375


title: 219433


title: Tobacco_Mock inoculated

city: Hangzhou

first: Xiaowei

last: Wang

address: 866 Yuhangtang Road

department: Insect Sciences

country: China

institute: Zhejiang University

description: 25 days post mock-inoculation

data_processing: The adapter-ligated tags are fixed on the Solexa Sequencing Chip to form single-molecule cluster, and then sequencing by synthesis is performed to generate millions of raw data with sequencing length of 35bp. Raw sequences were transformed into clean tags through removing adaptor sequence, low quality sequences. For annotation, all tags were mapped to the reference sequences and only allowed no more than 1 nucleotide mismatch. For gene expression analysis, the number of unambiguous clean tags for each gene was calculated and then normalized to TPM.

organism: Nicotiana tabacum

source_name: Tobacco leaves

growth_protocol: Clones of TYLCCNV with its satellite DNA, also known as DNA-beta, were used as inocula. To obtain virus-infected tobacco, plants at the 3-4 true-leaf stage were inoculated with TYLCCNV and its DNA-beta by agroinoculation. The control tobacco plants were mock inoculated using the same Agrobacterium strain. TYLCCNV inoculated and mock inoculated tobacco plants were cultivated to the 6-7 true-leaf stage at 22 days post-inoculation.

extract_protocol: Total RNA was isolated using the SV total RNA isolation system (Promega) according to the manufacturerâs protocol. We constructed the library for the above four samples according to Illumina's instructions.

treatment_protocol: Six tobacco plants were used in each treatment. For the whitefly feeding treatment, approximately 6,000 adult whiteflies that emerged from the tobacco plants were allowed to distribute randomly onto the leaves of six mock inoculated plants in one cage, and 6,000 adult whiteflies that emerged from the tobacco plants were released onto the leaves of six virus infected plants in another cage. After 72 h of feeding, all the adult whiteflies were discarded. Then the comparable leaves from the six plants in each of four treatments were harvested, flash-frozen in liquid N2 and stored at -80 °C.

tag: cultivar

tag: tissue

value: leaves

tag: inocula

value: mock


title: 217000


title: 214807

value: Norsvin Landrace


title: 212051


title: 224396


title: in vitro sclerotinia 3

city: Winnipeg

first: Michael

middle: G.

last: Becker

state: Manitoba

address: 66 Chancellors Circle

department: Biological Sciences

country: Canada

institute: University of Manitoba

description: Sclerotinia grown on PDA media for 72 hours

data_processing:
Trimmomatic adapter removal, headcrop, and quality filtering
TopHat2 alignment to UF70
Cuffnorm generation of FPKM table
Genome_build: UF70
Supplementary_files_format_and_content: Table of FPKM values

organism: Sclerotinia sclerotiorum

source_name: Sclerotinia sclerotiorum hyphae

growth_protocol: PDA media, growth for 72 hours at room temperature in dark (21 deg. C)

extract_protocol:
Trizol RNA Isolation. mRNA isolated from total RNA pool using NEBNext Magnetic isolation module.
Kumar et al. 2012 library preparation protocol

tag: cell type

value: hyphae


title: 325516


title: in vitro sclerotinia 2


title: in vitro sclerotinia 1


title: 325511


title: 325513


title: 2227493_TimePoint7_WholeBlood

city: Atlanta

first: Mary

last: Galinski

state: GA

address: 954 Gatewood Road

department: Vaccine Center at Yerkes

country: USA

institute: Emory University

description: Note that raw counts are provided for the parasite processed files. Normalized abundance measurements are provided for the host processed files.

data_processing:
Bases were called with Illumina RTA (Real-Time Analysis, v2.7.7) with default parameters. Illumina bcl2fastq v2.17.1.14 was used for demultiplexing. FASTQC (v0.10.1) was used to assess data quality, but the data were not filtered at this stage.
Reads were mapped to a composite reference assembly consisting of host, parasite, and ERCC control references with STAR (v2.5.2b) with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the algorithm of htseq-count.
Normalized expression (normalized read counts) was performed with DESeq2 (v1.10.1)
Genome_build: RNA-Seq reads were mapped to both a host and parasite genome.  Host: An early version of a new  assembly (as of 5/2014) of the rhesus macaque (MacaM assembly, v4.0, created by Aleksey Zimin at the University of Maryland, Rob Norgren at the University of Nebraska Medical Center and their colleagues.  The MacaM assembly has been deposited in GenBank under accession  PRJNA214746. Parasite: Plasmodium coatneyi strain Hackeri genome assembly was used. The assembly has been deposited in GenBank under the accession PRJNA329102.
Supplementary_files_format_and_content: Excel files contain normalized transcript abundances at the gene level, for each individual. Abundances are further classified by experimental Time Point (1-7), and Specimen Type (Whole Blood). Gene expression normalization is performed using the gene level expression files withby using the DESeq2 standard library size normalization method (estimateSizeFactors) with default parameters. See standard operating procedures provided in supplementary files for details. Note that raw counts are also provided as supplementary files.
Supplementary_files_format_and_content: Host DESeq2Normalized Counts Column headers are defined as follows:    'Gene ID':  Identifiers of all Genes in the annotation.     'Gene Symbol': Symbols of all Genes in the annotation.    'Raw File 1 / Raw File 2 / Sample Identifier / Abundances': DESeq2 normalized read counts of all genes, from the raw files listed in the column header. The raw file names and sample identifer both contain information regarding Specimen Type, NHP ID, and Time Point.      Notes:  There are 35 columns representing 5 animals for Time Points T01-T07    There is an read count entry per sample for every gene that appears in the annotation. For genes where there was no detection of expression by reads that mapped to their loci, the raw count is 0.
Supplementary_files_format_and_content: Host Parasite Raw Read Counts Column headers are defined as follows:    'Gene ID':  Identifiers of all Genes in the annotation.     'Gene Symbol': Symbols of all Genes in the annotation.    'Raw File 1 / Raw File 2 / Sample Identifier / Abundances': Raw read counts of all genes, from the raw files listed in the column header. The raw file names and sample identifer both contain information regarding Specimen Type, NHP ID, and Time Point.      Notes:  There are 35 columns representing 5 animals for Time Points T01-T07    There is an read count entry per sample for every gene that appears in the annotation. For genes where there was no detection of expression by reads that mapped to their loci, the raw count is 0.

organism:
Macaca mulatta
Plasmodium coatneyi

source_name: Whole blood

growth_protocol: Animals approved for use were moved into experimental housing 10 days prior to the start of the experiment.

extract_protocol:
Whole blood (3 ml) was collected in Tempus tubes (Applied Biosystems) that also preserve mRNA; these samples include erythrocytes, platelets and granulocytes in addition to mononuclear lymphocytes.  RNA was extracted using Tempus-Spin RNA isolation kits. The quality of all RNA samples was confirmed using a Bioanalyzer, with an RNA Integrity Number (RIN) greater than 8 recorded for all samples.
Approximately 1 μg of total RNA per sample was converted to double-stranded cDNA using poly-A beads to enrich for mRNA, and Illumina TruSeq Stranded mRNA Sample Prep kits to generate strand-specific libraries.   As a quality control, 92 spike-in RNAs of known concentration and GC proportions (ERCC Spike-In Control, Life Technologies) were added to constitute approximately 1% of the total RNA for each library.  Adapters were ligated to facilitate 3-plex sequencing on an Illumina HiSeq2000 at the Yerkes Genomics Core, aiming for 80 million paired-end 100 base pair (bp) reads per library.

treatment_protocol: The NHPs were given sub-curative treatment with Artemether during the experiment. After the 101-day experimental period, NHPs were treated with blood-stage curative doses of Artemether.

value: Whole blood

tag: time point

tag: gender

value: Male

tag: mahpic non human primate individual id

tag: parasite strain

value: P. coatneyi strain Hackeri


title: 2231894_TimePoint7_WholeBlood


title: 325509


title: 325510


title: 221522


title: post larvae [PL-3]

city: Qingdao

first: Hao

last: Song

state: Shandong

address: 7 Nanhai Road

institute: Institute of Oceanology,Chinese Academy of Sciences

description: y-3; PL-3

data_processing:
Raw data was obtained by base calling on the original image, and subsequently processed into clean reads by removing reads containing ploy-N or poly-A/T/C/G, with 5’ adapter contaminants, without 3’ adapter or the insert tag, and the low quality reads.
Other RNAs (tags originating from protein-coding genes, repeat sequences, rRNA, tRNA, snRNA, and snoRNA) were further removed after blasting against the RepeatMasker (www.repeatmasker.org/), the GenBank database (http://blast.ncbi.nlm.nih.gov) and the Rfam database (http://sanger.ac.uk/software/Rfam). Depending on the fact that no miRNA information of rapa whelk is included in miRBase21.0, the remaining clean reads were aligned to miRBase 21.0 with ≤2 mismatches in order to look for all known precursor/mature miRNAs. The miRNA with the highest expression for each mature miRNA family were selected as the temporary miRNA reference. Clean data were aligned to the above temporary miRNA reference and its expression level was calculated by summing the reads counts aligned to the temporary miRNA database with ≤2 mismatches. Besides, the precursor of the identified miRNAs were predicted, and molecules without a hairpin structure were identified as pseudo-miRNA. Finally, according to previous study, the potentially novel miRNAs were identified by using MIREAP (http://sourceforge.net/projects/mireap/) with stem-loop structure prediction.
By pairwise comparison the miRNA expression among pre-competent, competent and post larval samples, the differentially expressed miRNAs were identified and estimated. This procedures fit the BGI standard: (1) Normalize the expression of miRNA in each sample to determine the TPM (transcript per million). Normalization formula: TPM = Actual miRNA count / Total count of clean reads ∗ 106. (2) The final TPM in each larval stage was calculated by averaging these three biological replicates. (3) Fold-change and P-value were further calculated based on the normalized expression, as described in previous study.
Supplementary_files_format_and_content: "clean_FQ.stat.txt" is the statistics of clean reads and "annotation.stat.txt" is the statistics of annotation of clean reads. "all_mirna.exp_profile.txt" is the expression profile of all identified miRNAs. "association-mirna-mrna.txt" includes the informations of all the group differential expressed miRNAs and their target mRNAs.

organism: Rapana venosa

source_name: post larvae

growth_protocol: Parent Rapana venosa were naturally from Laizhou Bay (37°11′4.78″N, 119°41′3.75″E), China. Parent culture, spawning, larvae incubation and rearing were performed in the Blue Ocean Co. Limited (Laizhou, Shandong, China) according to previously published methods (Pan et al. 2013). Briefly, planktonic larvae were cultured in 3m×5m×1.5m cement pools at 24–26°C, at a density of 0.5/ml. Isochrysis galbana, Platymonas subcordiformis, and Chlorella vulgaris were mixed as a daily diet (15×104 cell/ml in three or four times) for the Planktonic larvae.

extract_protocol:
Total RNA was extracted from an individual intestine using the RNeasyMini Kit (Qiagen, USA) according to the manufacturer's instructions. The quality and concentration of RNA were measured using a NanoDrop 1000 spectrophotometer (Thermo).
After total RNA extraction, the RNA molecules in a size range of 18–30nt were enriched by polyacrylamide gel electrophoresis (PAGE). Then the 3’adapters were added and the 36-44nt RNAs were enriched. The 5’adapters were then ligated to the RNAs as well. The ligation products were reverse transcripted by PCR amplification and the 140-160bp size PCR products were enriched to generate a cDNA library and sequenced using Illumina HiSeqTM 2500 by Gene Denovo Biotechnology Co. Limited (Guangzhou, China).

treatment_protocol: Larval samples from pre-competent larval stage (the three spiral whorls stage), competent larval stage (the four spiral whorls stage) and the post larval stage (juveniles) were collected with three biological replicates (each replicate contains 40~100 individuals). The samples were monitored under a microscope to ensure that over 95% individuals have developmental synchrony. Each replicate was then washed with ddH2O and snap frozen in liquid nitrogen till use.

tag: developmental stages

value: post larvae


title: bam rep2

city: Kweishan, Taoyuan

first: Shu Yuan

last: Yang

address: Wenhua 1st Rd, No. 259

country: Taiwan

institute: Chang Gung University

description: oligo-dT selected RNA

data_processing:
The Fastq files were converted to Sanger Fastq files using Fastq Groomer on the Galaxy platform.
The RNAseq reads were mapped to the Drosophila genome (dm3) with Tophat2 on the Galaxy platform using default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks on the Galaxy platform using default parameters.
Genes with significant expression differences between the two genotypes were determined with Cuffdiff on the Galaxy platform using 0.05 as the false discovery rate.
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: *.tabular.txt: Tab-delimited text files include RPKM values for each sample.

organism: Drosophila melanogaster

source_name: Testis, bam-

growth_protocol: Fruit flies were grown at 25⁰C on standard medium.

extract_protocol:
Testes were dissected into cold PBS, extracted with RNABee (TelTest), and selected with oligo-dT beads (Thermo Fisher Scientific).
RNA libraries were prepared with the NEXTflex Directional RNAseq Kit (Bioo Scientific).

tag: genotype/variation

value: bam-

value: Testis

tag: age

value: Within 3 days of eclosion


title: 2231905_TimePoint6_WholeBlood


title: post larvae [PL-2]

description: y-2; PL-2


title: competent larvae [CL-3]

description: J-3; CL-3

source_name: competent larvae

value: competent larvae


title: competent larvae [CL-1]

description: J-1; CL-1


title: 2227542_TimePoint7_WholeBlood


title: 2227544_TimePoint7_WholeBlood


title: 2231898_TimePoint5_WholeBlood


title: 2231880_TimePoint6_WholeBlood


title: 325515


title: pre-competent larvae [Pre-CL-1]

description: F-1; Pre-CL-1

source_name: pre-competent larvae

value: pre-competent larvae


title: 2227488_TimePoint6_WholeBlood


title: pre-competent larvae [Pre-CL-3]

description: F-3; Pre-CL-3


title: 2231900_TimePoint6_WholeBlood


title: competent larvae [CL-2]

description: J-2; CL-2


title: pre-competent larvae [Pre-CL-2]

description: F-2; Pre-CL-2


title: 2227489_TimePoint5_WholeBlood


title: 2227478_TimePoint5_WholeBlood


title: 2231884_TimePoint4_WholeBlood


title: post larvae [PL-1]

description: Y-1; PL-1


title: 2231891_TimePoint4_WholeBlood


title: 2227471_TimePoint7_WholeBlood


title: 2227477_TimePoint4_WholeBlood


title: 2227476_TimePoint4_WholeBlood


title: 2227470_TimePoint4_WholeBlood


title: 2227467_TimePoint6_WholeBlood


title: 2231908_TimePoint5_WholeBlood


title: 2231909_TimePoint5_WholeBlood


title: 2231903_TimePoint3_WholeBlood


title: 7thday-postpinfection-rep1

city: Riverside

first: Heba

middle: A. H. M.

last: Zaghloul

state: CA

address: 900 University Ave

department: Entomology

institute: University of California, Riverside

data_processing:
Adapter sequences were trimmed and low quality reads filtered using Trimmomatic
Ribosomal contaminants were removed using SortMeRNA
Sequences were mapped to the SFAV-1a genome using bowtie2, only sequences mapping to this genome were retained
Genome_build: NC_008361
Supplementary_files_format_and_content: [.txt] Log2 RPKM values for SfAV-1a ORFs in the different time points post-infection.

organism: Spodoptera frugiperda ascovirus 1a

source_name: SfAV-1a 7 days infected 3rd instar Spodoptera frugiperda caterpillar

extract_protocol:
Total RNA was isolated from the entire body of each healthey or SfAV-1a infected Spodoptera frugiperda larva and homogenized separately by mechanical trituration in TRIzol (Invitrogen), followed by DNase-treatment using the RNA Clean and Concentrator TM-5 kit (ZYMO RESEARCH) and eluted in ultra pure distilled water (Invitrogen).
The NEBNextPoly(A) mRNA magnetic isolation module kit (New England Biolabs) was used to enrich the mRNA first from the DNase-treated total RNA samples.The libraries were then prepared following the manufacturer’s instructions of the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs)

tag: genotype

value: wild type

tag: host

value: Spodoptera frugiperda caterpillars

value: whole insect body

tag: developmental stage

value: 3rd instar larvae

tag: time


title: 2227474_TimePoint3_WholeBlood


title: 2231902_TimePoint3_WholeBlood


title: 2231877_TimePoint3_WholeBlood


title: 4thday-post-infection-rep1

source_name: SfAV-1a 4 days infected 3rd instar Spodoptera frugiperda caterpillar


title: 2227473_TimePoint3_WholeBlood


title: 48hpi-rep2

source_name: SfAV-1a 48h infected 3rd instar Spodoptera frugiperda caterpillar


title: 2227472_TimePoint2_WholeBlood


title: 24hpi-rep1

source_name: SfAV-1a 24h infected 3rd instar Spodoptera frugiperda caterpillar


title: 2227475_TimePoint2_WholeBlood


title: 2227468_TimePoint2_WholeBlood


title: 4thday-post-infection-rep2


title: 2231879_TimePoint2_WholeBlood


title: 24hpi-rep2


title: 12hpi-rep2

source_name: SfAV-1a 12h infected 3rd instar Spodoptera frugiperda caterpillar


title: 2227543_TimePoint2_WholeBlood


title: 48hpi-rep1


title: 12hpi-rep1


title: 2231897_TimePoint1_WholeBlood


title: Control-rep2

source_name: Uninfected, 3rd instar Spodoptera frugiperda caterpillar

value: Control


title: 6hpi-rep1

source_name: SfAV-1a 6h infected 3rd instar Spodoptera frugiperda caterpillar


title: 2231906_TimePoint1_WholeBlood


title: 2231907_TimePoint1_WholeBlood


title: 2227479_TimePoint1_WholeBlood


title: WSH1105-PH7-0

city: Wuxi

first: Ningzi

last: Guan

state: Jiangsu

address: No.1800 Lihu street

institute: Propionibacterium acidipropionici

data_processing:
fastx (version:0.0.13) software used to filter the data
The aligment of clean reads were mapped against Propionibacterium acidipropionici CGMCC 1.2230 using bowtie2 (version: 2-2.0.5)
To quantity the reads mapped using BEDTools (version:2.16.1)

organism: Acidipropionibacterium acidipropionici

source_name: WSH1105 (acid-tolerant)

extract_protocol:
The bacterial total RNA extracted using the RNeasy Mini Kit (QIAGEN, Hilden, Germany) following the manufacturer’s instructions and adding lysozyme (Sinopharm, Shanghai, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: genome shuffled mutant

tag: strain

tag: ph


title: WSH1105-PH5-5


title: 1-2230-PH7-0


title: 1-2230-PH5-5


title: mel_vir rep2

city: Berlin

first: Nikos

last: Karaiskos

address: Hannoversche Str. 28

country: Germany

institute: Max Delbrück Center for Molecular Medicine

description:
Sample 2
single-cell transcriptomics

data_processing:
Sequenced reads were converted to SAM files to couple them with the cell and molecular barcodes using Drop-seq_tools v1.12. They were further trimmed for SMART adapter and poly(A) remnants.
The filtered reads were mapped with STAR. The Drop-seq_tools v.1.12 were used to add gene annotations, detect bead synthesis errors and calculate the Digital Gene Expression matrices.
Bulk mRNA reads were mapped with STAR. Gene counts were computed with htseq-count.
Genome_build: Drosophila_melanogaster.BDGP6 & Drosophila_virilis.GCA_000005245.1
Supplementary_files_format_and_content: Digital Gene Expression matrices contain UMI counts per cell and per gene. Htseq-counts measure gene abundances in mRNA samples (read counts)

molecule: polyA RNA

organism:
Drosophila melanogaster
Drosophila virilis

source_name: Drop-seq of whole embryo

growth_protocol: Egg lays occurred in 1 hour intervals; embryos were aged for 2:30 hours (D. melanogaster) or 3:30 hours (D. virilis) at room temperature.

extract_protocol:
Embryos were dissociated first in a Dounce homogenizer and then further using a syringe with 22G x 2" needle, followed by filtering through 20 um cell strainer and fixation in 80% methanol/PBS
Captured transcriptomes were reverse transcribed while bound on barcoded oligo dT beads; PCR handles added by template switching; cDNA PCR-amplified (4 + 9 cycles); 600 pg cDNA library fragmented and amplified with Nextera XT v2 DNA sample preparation kit using custom primers for 3'-targeted amplification (Macosko et al. 2015 Cell 161)
Drop-seq single-cell transcriptome profiling according to Macosko et al. 2015 Cell 161

treatment_protocol: Dechorionated embryos were staged and stage 6 embryos hand-picked into ice-cold PBS-Triton 0.1%.

value: stage 6

value: dissociated cells

value: D.mel [y1 w1118 ; P{st.2::Gal4} ; P{vnd::dsRED}]  D.vir. [we]

tag: fixation

value: 80% methanol/PBS


title: mpo_RNAseqnuclear_+Mm1_3

status: Public on Aug 31 2017

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

description: mpo BAC driving biotin ligase

data_processing:
Reads were mapped using STAR (v.2.4.2a) to danRer10 and read counts were obtained using subreads FeatureCounts
Genome_build: danRer10
Supplementary_files_format_and_content: read counts

organism: Danio rerio

extract_protocol:
For nuclei isolation, zebrafish embryos were anaesthetised with 0.01% Tricaine 0.01% and aggregates of mycobacterium dissected based on tdTomato fluorescence. Embryos were washed in hypotonic buffer H (20 mM HEPES (pH 7.9), 15 mM MgCl2, 10 mM KCl, 1 mM DTT, and 1 X Complete protease inhibitor) and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B, every 5 minutes for 15 minutes. Nuclei were collected by centrifugation (2000 g, 4 °C) and resuspended in 1 mL buffer NDP (10 mM HEPES (pH 7.9), 40 mM NaCl, 90 mM KCl, 0.5 mM EDTA, 0.5 mM spermidine, 0.15 mM spermine, 1 mM dithiothreitol and 1 X Complete protease inhibitor). For nuclei purification, nuclei were incubated with 5 mg of M-280 streptavidin-coated dynabeads with rotation for 30 minutes at 4 °C. A flow-based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette (VWR, cat # 8913-898) attached to a 1 mL micropipette tip (Rainin reach pipet tip, cat # RT-L1000S), both pre-treated with NPB/BSA for 30 minutes, and added to a MiniMACS separator magnet (OctoMACS Separator, Miltenyl Biotec, cat # 130-042-109). A two-way stopcock (Biorad cat # 732-8102) was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing (Fisher Scientific, cat # 8220) and the flow-rate set to ~0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X-100 (NPBt) and added to the slow-flow setup. The tip was subsequently removed from the stand and the nuclei-beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow-flow setup. Nuclei-beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand (DynaMag TM-2 magnet, Invitrogen, cat # 12321D). Nuclei-beads were then processed for RNA extraction.
RNA extraction and DNAse treatment were carried out using the RNAqueous®-Micro Kit (Life Technologies, cat # AM1931). RNA integrity was checked with a RNA pico chip (Agilent Technologies, cat # 5067-1513) using the Agilent 2100 Bioanalyzer.
cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART-seqTMv4 ultra low input kit for RNA (Clontech laboratories, cat #’s 634888, 634889, 634890, 634891, 634892, 634893, and 634894). Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads (150 cycles) (Illumina, cat # FC-404-1002).

treatment_protocol: For M. marinum infection, embryos were injected at the 32-512 cell stage with M. marinum

tag: development

value: 3 days post fertilization

tag: tissue

value: neutrophil

value: InVivoBiotinylatedNuclei

tag: treatment

value: M. marinum 32-512 cell stage

tag: amplification

tag: strand

value: reverse


title: mel_vir rep1

description:
Sample 1
single-cell transcriptomics

tag: cell type


title: Mixed adult females and males

city: Sainte-Anne-de-Bellevue

first: Lucienne

last: Tritten

state: QC

address: 21111 Lakeshore Road

department: Institute of Parasitology

institute: McGill University

data_processing:
basecall using illumina CASAVA v1.8
The 3' adaptor was removed from raw reads and reads with the length less than 10 were excluded to constitute the mappable reads.
The mappable reads were aligned against the mouse genome and miRbase using Bowtie.
Genome_build: Trichuris muris 2b; miRbase v21; Mus musculus mm9;
Supplementary_files_format_and_content: Table S1 T. muris miRNAs.xls: summary of miRNA candidates identified in Trichuris muris
Supplementary_files_format_and_content: Table S2 mouse miRNAs in T. muris preparations.xls: summary of mouse miRNAs identified in T. muris preparations

organism:
Mus musculus
Trichuris muris

source_name: Worm secretions, culture media

growth_protocol: Live whole worms in culture

extract_protocol:
RNA extraction kit (Norgen Biotek #24100) from pelletted microvesicles.
Illumina Truseq Small RNA Preparation

treatment_protocol: Culture media subjected to Exoquick-TC for microvesicle precipitation

value: live worms


title: mpo_RNAseqnuclear_+Mm1_2

description: mpo BAC driving biotin ligase


title: mpo_RNAseqnuclear_+Mm1_1

description: mpo BAC driving biotin ligase


title: DT_T3_PEG

city: Giessen

first: Birgit

last: Samans

address: Heinrich-Buff-Ring 26-28

institute: University of Giessen

data_processing:
Preprocessing:   Removing putative adapter sequences applying the cutadapt package (https://cutadapt.readthedocs.org/en/stable/)  Trimming the first 11 base pairs  and removing low-quality reads using the fastx _trimmer and fastq _quality _filter (-q 28 -p 95) algorithms from the fastx _toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)
Alignment: The sequencing reads were aligned to the precompiled B. rapa cv. Chiifu reference genome v1.5  genome using the software tophat2 which applies the short read aligner Bowtie2
Quantify FPKM values by using cufflinks (http://cole-trapnell-lab.github.io/cufflinks/). The Brassica rapa identifier are accessible via the 'Brassica database' BRAD on the webside http://brassicadb.org. Additionally you have entries on http://www.uniprot.org and http://plants.ensembl.org.
Genome_build: B. rapa cv. Chiifu reference genome v1.5
Supplementary_files_format_and_content: FPKM values

organism: Brassica rapa

source_name: shoot tissue

growth_protocol: Ninety-six seeds of each genotype were germinated in 1% agar gel at 10˚C in the dark before transferring into a 50 mL Falcon tube which is containing MS liquid medium. The tubes were inserted into 15 cm deep 10 L rectangular plant containers in a controlled environment chamber (16 h day length, 60% relative humidity, 16 ˚C/12 ˚C day/night temperature and 216-257 μmol m-2 s-1 photosynthetically active radiation).

extract_protocol:
Total RNA from shoot samples was extracted using the RNeasy Mini Kit and treated with DNase. The quantity and quality of all RNA samples were checked using the Fragment AnalyzerTM Automated Capillary Electrophoresis system (Advanced Analytical) before being pooled for cDNA synthesis.
cDNA libraries were prepared with the TruSeq Stranded Total RNA with Ribo-ZeroTM Plant kit from Illumina using the manufacturer’s protocol. The libraries were quantified using the KAPA library quantification kit (KAPA Biosystems, Wilmington, MA, USA).
The libraries were randomized and mixed into three independent multiplexes from different sampling time-points.Each multiplex was freshly prepared and diluted before sequencing on the MiSeq Illumina sequencing platform with paired-end sequencing of 2 x 150 bp reads.

treatment_protocol: The treatment started when the seedlings had 4-5 true leaves. For each accession, half of the seedlings were exposed to osmotic stress by adding PEG 6000 to a final concentration of 2.5% (w/w), while the other half remained with MS medium as control. Whole shoots were sampled after 4 h, 8 h and 12 h imposition of stress with at least three replicate samples.


title: DS_T3_Ctrl


title: DS_T3_PEG


title: DT_T3_Ctrl


title: mpo_RNAseqnuclear_-Mm1_3

description: mpo BAC driving biotin ligase


title: mpo_RNAseqnuclear_-Mm1_2

description: mpo BAC driving biotin ligase


title: 2227466_TimePoint1_WholeBlood

value: Whole blood

tag: time point

tag: gender

value: Male

tag: mahpic non human primate individual id

tag: parasite strain

value: P. coatneyi strain Hackeri


title: KK43

city: Seoul

first: Yong-Joon

last: Cho

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

description: 15 min induction by 10 mM L-arabinose

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using Trimmomatic 0.35 as default parameter, then mapped to Salmonella enterica serovar Typhimurium 14028s whole genome using bowtie v. 2.2.4 with parameters -t --very-sensitive
The mapped reads were counted by featureCounts (http://bioinf.wehi.edu.au/featureCounts/) and Reads Per Kilobase of exon per Megabase of library size (RPKM) and Transcripts per Million (TPM) was calculated.
Genome_build: NCBI accession - PRJNA33067, assembly ID - GCA_000022165.1
Supplementary_files_format_and_content: Tab-delimited text files including TPM values and locus_tags for genes of Salmonella enterica serovar Typhimurium 14028s

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028s Wu

source_name: RNA from Salmonella Typhimurium 14028s harboring pBAD113 which contains mgtC leader

growth_protocol: The strains were grown in N-minimal media to exponential phase, and harvested after arabinose treatment.

extract_protocol:
After cell harvest, RNA samples were prepared using RNeasy kit. Genomic DNA was eliminated by DNaseI treatment.
To remove rRNA in total RNA, Ribo-Zero rRNA Removal Kits (Bacteria) (MRZMB126, Illumina, USA) was used. Illumina Stranded TruSeq Total RNA Sample Prep Kit (Cat#FC-122-2201) was used with 1 ug of rRNA depleted RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: 10 mM L-arabinose was added to the media for 15 min.

value: N-minimal media

tag: growth medium

tag: growth phase

value: exponential phase


title: 6hpi-rep2

tag: genotype

value: wild type

tag: host

value: Spodoptera frugiperda caterpillars

value: whole insect body

tag: developmental stage

value: 3rd instar larvae


title: mpo_RNAseqnuclear_-Mm1_1

description: mpo BAC driving biotin ligase

tag: strain


title: DT_T2_Ctrl

tag: time

value: Control


title: DS_T2_PEG


title: Control-rep1


title: DS_T1_Ctrl


title: DS_T2_Ctrl


title: DT_T1_Ctrl


title: RNAP2 Dex+KLF15_9e

city: Aurora

first: Tzu Lip

last: Phang

state: CO

address: 12700 East 19th Avenue

department: Medicine

institute: University of Colorado, Denver

description: Barcode: GCACTA

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 2 with the default setting.
Mapped reads were compressed, sorted and indexed using Samtools
Peaks were called using MACS version 2 with the default setting
Genome_build: mm9
Supplementary_files_format_and_content: .narrowPeak (BED file)

molecule: genomic DNA

organism: Homo sapiens

source_name: Human airway smooth muscle 2 (HASM2)

growth_protocol: Human ASM cells were derived from a normal deceased donor (PMID: 27371733) as described (PMID:20670427) and cultured in Ham’s F-12 medium with L-glutamine (Corning) supplemented with 10% FBS

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed as described previously (PMID: 23508109, 27371733), with the following modifications: cross-linking was performed by adding methanol-free 16% formaldehyde directly to the culture media to a final concentration of 1% and incubating for 5 minutes at room temperature with gentle rocking; samples were subsequently sonicated with a Diagenode Bioruptor at high power in 30-second bursts separated by 30-second incubations in ice water for a total of 25 cycles.
A minimum of 1 ng DNA from ChIP samples were used to prepare libraries using the Nugen Ovation Ultralow System V2 1-16 Part No. 0344 according to the manufacturer’s instructions. Samples were run on an Illumina HiSeq using 1X50 bp end reads

treatment_protocol: Anti GR antibody is a gift of Miles Pufall and was custom-made by Covance. It was raised against in rabbits against the epitope  QPDLSKAVSLSMGLYMGETETKVMGNDLG  and affinity purified.  RNAPII ChIP antibody came from Biolegend, Clone 8WG16, Catalog #920102

value: Human airway smooth muscle 2 (HASM2)

tag: transduction

value: Dex

tag: chip antibody

value: RNAPII (Biolegend, Clone 8WG16, Catalog #920102)


title: DT_T2_PEG

tag: treatment


title: RNAP2 KLF15_8B

description: Barcode: AACCAG

tag: tissue

value: EtOH


title: RNAP2 Dex+GFP_7c

description: Barcode: CACAGT

value: Ad-GFP


title: RNAP2 Dex+GFP_7e

description: Barcode: TTGGCA


title: RNAP2 KLF15_8D

description: Barcode: TGGTGA


title: RNAP2 Dex+KLF15_9b

description: Barcode: AGTGAG


title: RNAP2 EtOH_5E

description: Barcode: GAGTCA


title: RNAP2 EtOH_5b

description: Barcode: AGCATG


title: GR Dex+KLF15_4C

description: Barcode: GGAGAA

value: GR (gift of Miles Pufall)


title: RNAP2 Dex_6d

description: Barcode: CGTAGA


title: RNAP2 Dex_6e

description: Barcode: TCAGAG


title: DN345

description: 15 min induction by 10 mM L-arabinose

source_name: RNA from Salmonella Typhimurium 14028s harboring pBAD18, the empty vector


title: GR Dex_2A_Input

description: Barcode: GTGCTT


title: GR Dex+GFP_3E

description: Barcode: GTCGTA


title: DS_T1_PEG


title: GR Dex+KLF15_4B

description: Barcode: AAGAGG


title: GR EtOH_1E

description: Barcode: GCACTA


title: GR Dex+GFP_3D

description: Barcode: AAGCCT


title: GR EtOH_1D_Input

description: Barcode: ACCTCA


title: GR Dex_2E

description: Barcode: GTGCTT


title: 827 Mibefradil treatment RNAseq [SL129398]

city: Charlottesville

first: Stephen

last: Turner

state: VA

address: 1670 Discovery Drive

institute: Signature Science, LLC

description:
RNAseq for 827 patient dervived cells Mibefrail treated samples
SL129398

data_processing:
align to genome with STAR
count reads mapping to genes with featureCounts
Genome_build: grch37
Supplementary_files_format_and_content: gene counts, csv

source_name: GBM stem cells

growth_protocol: GSCs 827 were isolated from patient surgical specimens and characterized for in vivo tumorigenesis, pluripotency, self-renewal, stem cell markers, and neurosphere formation

extract_protocol:
RNA extraction according to manufactor's instructions
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: GSCs were treated with mibefradil (5 µM) or vehicle control for 24 h

value: patient dervied GBM stem cells

tag: passage


title: DT_T1_PEG


title: GR Dex_2A

description: Barcode: ACCTCA


title: 827 con RNAseq [SL129394]

description:
RNAseq for 827 patient dervived cells control samples
SL129394

tag: cell type


title: 827 Mibefradil treatment RNAseq [SL129397]

description:
RNAseq for 827 patient dervived cells Mibefrail treated samples
SL129397


title: 827 con RNAseq [SL129395]

description:
RNAseq for 827 patient dervived cells control samples
SL129395


title: 827 con RNAseq [SL129393]

description:
RNAseq for 827 patient dervived cells control samples
SL129393


title: GR EtOH_1D

description: Barcode: AGTGAG


title: Patient_03

city: Kuala Lumpur

first: Amir Feisal

last: Merican

state: Kuala Lumpur

address: University of Malaya

department: Institute of Biological Science

country: Malaysia

institute: University of Malaya

data_processing:
The RNA libraries were sequenced on Illumina HiSeq 2000 Platform
The qualities of all sequences in fastq format were assessed using FASTQC . The adaptors and low quality bases were trimmed from the sequence using Trimmomatic. Readwith a phred quality (Q > 20) were used for further alignment and assembly.
Quality trimmed raw reads from 3 samples were aligned to the human reference genome sequence (GRCh38.79 assembly) separately using HISAT (v 0.1.4) with GENCODE junctions as a guided reference annotation
The aligned reads for each sample was assembled separately into transcripts by StringTie (v1.3.3) using a GENCODE reference annotation (version 22) The transcripts abundance was estimated as fragments per kilobases of exon per million fragments mapped (FPKM)
Genome_build: GRCh38.79
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Monocyte Cells

extract_protocol:
CD14-Positive Monocytes cells were isolated from PBMC by negative selection method using Miltenyi Monocyte Isolation kit II (Miltenyi biotec). Total RNA was extracted from monocytes cells using the RNesasy mini kit (QIAGEN)
Messenger RNA isolation and sequencing libraries preparation was performed using TruSeq RNA Sample Preparation Kit and SuperScript II Reverse Transcriptase.

value: CD14-Positive Monocytes cells

tag: age

tag: disease status

value: XLA Patient


title: Patient_01


title: Hi-C H1 replicate 4

city: Cleveland

first: Fulai

last: Jin

state: OH - OHIO

address: 10900 Euclid Avenue

institute: Case Western Reserve University

data_processing:
Library strategy: HiC-Seq
The paired-end Hi-C reads were mapped to human genome hg18 using BOWTIE. Only first 36 bases were used for mapping when reads is longer. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed.
We focus on cis-interactions and therefore only kept Hi-C paired-end reads which both ends are mapped to the same chromosome. Out of all the intra-chromosome paired-end reads, we also discard the reads with both ends mapped to the same HindIII fragments. Since cut-and-ligation events are expected to generate reads within 500bp upstream of HindIII cutting sites due to the size selection (“+” strand reads should be within 500bp upstream of a HindIII site, and “-“ strand reads should be within 500bp downstream a HindIII site), we only keep reads pairs with both ends satisfying this criteria.
We next split all these reads into three classes based on their strand orientations (“same-strand”, “inward”, or “outward”), and generated the resulting lists of fragment pairs (with Hi-C read counts) from each class of reads.
There are total ~840k fragments in human genome. They are assembled into ~518k anchors after short fragments (<2kb) are merged into neighboring anchors. For every anchor, we first count Hi-C reads from the anchor to every fragment within 2Mb range.
We estimated a background frequency between any two fragments based on the average reads count of all fragment pairs that have similar lengths, similar gap distance, GC content. The fragment-to-fragment data can be then converted to anchor-to-anchor data by adding the read counts and background frequencies together based on the assignment of fragments to anchors. P values of the enrichment of Hi-C reads over the background frequency can be calculated using a negative binomial model. The statistical method has been described in previous publication (Jin, F. et al. Nature 2013, 503:290-294)
Genome_build: hg18
Supplementary_files_format_and_content: For each Hi-C replicate, the fragment-to-fragment frequency are provided in the txt file. The location of each fragment are provided in bed file.

source_name: embroynic stem cells

growth_protocol: Human H1 ES cells were cultured on the hESC-qualified Matrigel coated plates or coverslips in mTeSR1 medium for 5 days.

extract_protocol:
Hi-C experiments were conducted in biological replicates using HindIII according to previous publication (Lieberman-Aiden, E. et al. Science 326, 289-93 (2009).).
Libraries were prepared according to Illumina's instruction or cited literatures.

value: no treat

tag: experiment

value: Hi-C

tag: antibody

value: no

tag: restriction enzyme

value: HindIII


title: DMS114_Control

city: Columbus

first: Eric

last: Samorodnitsky

state: Ohio

address: 460 West 12th Avenue, Room 595

department: Comprehensive Cancer Center

institute: The Ohio State University

data_processing:
TopHat2 (version 2.0.10) was used for aligning the FASTQ files to the human reference genome UCSC build hg19 assembly. A UCSC gene annotation file in GTF format was also used during the alignment.
The aligned BAM file from TopHat2 was fed into RNASeqQC (version 1.1.7) [https://www.broadinstitute.org/cancer/cga/rnaseqc_download] to generate alignment metrics
Gene expression for known genes was calculated as FPKM (Fragments per Kilobase per Million Mapped Reads) using CuffLinks (version 2.1.1) from the Tuxedo suite, while the differentially significant genes from a parent and resistant cell line comparison were found using Cuffdiff (version 2.1.1). The gene annotation file from UCSC was provided to keep the gene format consistent throughout the pipeline.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM_TRACKING, DIFF files

source_name: Small cell lung cancer cell line

growth_protocol:
DMS114 cell line was cultured in Waymouth’s medium supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% penicillin (100 U/mL) and streptomycin (100 µg/mL). Similarly, RT112 cells were grown in RPMI-1640 and 2mmol/L Lglutamine. Cells were grown as monolayer cultures and maintained in a humidified atmosphere of 5% CO2 in air at 37°C. Cell morphology was monitored using an EVOS XL Core
Cell Imaging System under a phase-contrast microscope (Life Technologies, Pittsburgh, PA, USA). Cells were routinely tested for mycoplasma contamination monthly using the MycoAlert Plus Mycoplasma detection kit (Lonza, Walkersville, MD, USA) following manufacturer’s protocol. Cells were tested last during May 2016.

extract_protocol:
Trizol extraction, Invitrogen
We used 4 μg of each cell line’s total RNA and prepared the libraries following Illumina’s TruSeq Stranded mRNA Sample Preparation HS (high sample) protocol without modification. We performed 15 cycles of PCR for amplification of the adapter ligated DNA library and assessed the quality of the final DNA library using the High Sensitivity D1K ScreenTape (TapeStation 2200; Agilent Technologies, Santa Clara, CA). Per manufacturer’s protocol, library peak size was approximately at 260 bp. We prepared indexed libraries and sent them for 100-bp paired-end sequencing (2×100 bp) on an Illumina HiSeq 2000 at Beijing Genomics Institute (BGI, China). All four (DMS114, RT112 controls and respective resistant cells) libraries were pooled and sequenced in one lane.

treatment_protocol: Control cells were treated with vehicle DMSO. Resistant cells were maintained in media containing BGJ398 a pan FGFR inhibitor.

tag: cell line

value: DMS114 small cell lung cancer cell line

tag: tissue of origin

value: Lung

value: control

tag: treatment conditions

value: parental


title: DMS114_Resistant

tag: dose

value: resistant to BGJ398


title: RT112_Resistant

source_name: Urothelial carcinoma cell line

value: RT112 urothelial carcinoma cell line

value: Bladder


title: Hi-C H1 replicate 6


title: RT112_Control


title: DGM-10922_LA-BC (OSGIN1)

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description:
DGM-10922
Basal cells cultured from airway epithelium samples.
Re-accessioned GSM1155385

data_processing:
HiSeq Control Software (Illumina) was used to perform image analysis, base calling and sequence analysis on HiSeq generated sequence images resulting in fastq files.
Expression analysis was performed using Bowtie (v0.12.8.0, http://bowtie-bio.sourceforge.net), Tophat (v2.0.4, http://tophat.cbcb.umd.edu) and Cufflinks (v2.0.2, http://cufflinks.cbcb.umd.edu).
To correct for transcript length and depth of coverage, raw paired-end sequenced reads were converted into fragments per kilobase of exon per million fragments sequenced (FPKM) resulting in the fpkm_tracking files.
Resultant fragments were aligned (mapped) to the reference genome build UCSC hg19 using Bowtie.
Non-aligned reads were segmented using Tophat and re-aligned to the genome, aligning reads that span introns and determining junction splice sites. Cufflinks assembled reads into transcripts and assembled reads merged using Cuffmerge; the reads generated from a transcript are directly proportional to the transcripts relative abundance. For the analysis, Tophat (which automatically runs Bowtie) was run for each read pair in a given lane.
For each read pair, Tophat produced one file which contained all reads mapped to the human_g1k_v37 genome and RefSeq (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz) transcriptome.
This process was carried out independently for each sample lane. Before running Cufflinks, Samtools (v0.1.18.0, http://samtools.sourceforge.net) was used to merge each sample's independent Tophat results into one file. This file contains all of the aligned reads for each read pair. Finally, Cufflinks was run on the merged Tophat output to produce a file with FPKM values for each sample.
Data was analyzed using Tuxedo pipeline software.
Genome_build: GRCh37
Supplementary_files_format_and_content: fpkm_tracking files are text files that include the RefSeq gene and location, the FPKM value, high and low confidence and status.

source_name: airway basal cells, smoker

growth_protocol: Airway epithelial cells collected by brushing were cultured supplemented with growth factors according to the manufacturer's instructions. Media was changed every 2 days until time of harvest at day 7, when the cells had reached 70 to 80% confluence.

extract_protocol:
Total RNA from harvested nonsmoker and smoker basal cells was extracted with TRIzol with subsequent RNA clean-up using the RNeasy MinElute RNA purification kit to remove residual DNA.
The TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) was utilized as per protocol to generate cDNA that was then purified with QIAquick PCR purification kit (Qiagen, Valencia, CA).
Samples were loaded onto an Illumina flowcell for paired-end 101 x 2 sequencing reactions using the Illumina HiSeq 2000, using a single flow cell with 4 samples multiplexed per lane of flow cell.

value: airway basal cells

tag: smoking status

value: smoker


title: DGM-10907_LA-BC (OSGIN1)

description:
DGM-10907
Basal cells cultured from airway epithelium samples.
Re-accessioned GSM1155382


title: DGM-10638_LA-BC (OSGIN1)

description:
DGM-10638
Basal cells cultured from airway epithelium samples.
Re-accessioned GSM1155380


title: DGM-01774_LA-BC (OSGIN1)

description:
DGM-01774
Basal cells cultured from airway epithelium samples.
Re-accessioned GSM1155379

source_name: airway basal cells, nonsmoker

value: nonsmoker


title: DGM-11066_LA-BC (OSGIN1)

description:
DGM-11066
Basal cells cultured from airway epithelium samples.
Re-accessioned GSM1155384


title: 827 Mibefradil treatment RNAseq [SL129396]

description:
RNAseq for 827 patient dervived cells Mibefrail treated samples
SL129396

value: patient dervied GBM stem cells


title: DGM-10565_LA-BC (OSGIN1)

description:
DGM-10565
Basal cells cultured from airway epithelium samples.
Re-accessioned GSM1155377


title: DGM-10906_LA-BC (OSGIN1)

description:
DGM-10906
Basal cells cultured from airway epithelium samples.
Re-accessioned GSM1155381


title: DGM-11016_LA-BC (OSGIN1)

description:
DGM-11016
Basal cells cultured from airway epithelium samples.
Re-accessioned GSM1155383


title: DGM-10503_LA-BC (OSGIN1)

description:
DGM-10503
Basal cells cultured from airway epithelium samples.
Re-accessioned GSM1155378


title: DGM-10194_LA-BC (OSGIN1)

description:
DGM-10194
Basal cells cultured from airway epithelium samples.
Re-accessioned GSM1155375


title: DGM-10284_LA-BC (OSGIN1)

description:
DGM-10284
Basal cells cultured from airway epithelium samples.
Re-accessioned GSM1155374


title: DGM-10568_LA-BC (OSGIN1)

description:
DGM-10568
Basal cells cultured from airway epithelium samples.
Re-accessioned GSM1155376


title: DGM-11852_LA-BC (OSGIN1)

description:
DGM-11852
Basal cells cultured from airway epithelium samples.
Re-accessioned GSM1155372


title: DGM-01657_LA-BC (OSGIN1)

description:
DGM-01657
Basal cells cultured from airway epithelium samples.
Re-accessioned GSM1155373


title: Patient_02

value: CD14-Positive Monocytes cells


title: DGM-01620_LA-BC (OSGIN1)

description:
DGM-01620
Basal cells cultured from airway epithelium samples.
Re-accessioned GSM1155371


title: DGM-11374_LA-BC (OSGIN1)

description:
DGM-11374
Basal cells cultured from airway epithelium samples.
Re-accessioned GSM1155370


title: DGM-11111_LA-BC (OSGIN1)

description:
DGM-11111
Basal cells cultured from airway epithelium samples.
Re-accessioned GSM1155386


title: DIPG012_IgG

city: Copenhagen

first: Faizaan

last: Mohammad

state: Choose A State

address: Ole Maaloøs vej 5 Fourth Floor

country: Denmark

institute: BRIC

data_processing:
For pre-processing and reads mapping, ChIP-seq libraries were sequenced using the Illumina Genome Analyzer platform, producing single-end 42 bp reads after removal of multiplex index sequence tags. Reads were mapped to the human (UCSC hg38) or mouse (UCSC mm10) genome assemblies using the bowtie short read aligner (version 0.12.7) and excluding all haplotype variants and random or unknown chromosomal sequences. We used the default bowtie parameters except concerning multi-mapping reads which were discarded using option "-m1".
For representation of H3K27me3 ChIP-seq profiles on selected loci, mapped reads were de-duplicated by keeping a single read in each group of reads mapping to the exact same genomic sequence. Reads were extended to a total length of 250 bp starting from the 5' end and genomic coverage was computed at base pair resolution using the UCSC Kent utilities. Coverage values were scaled according to sequencing depth and immuno-precipitation yield.
For identification of genes and CGIs associated with H3K27me3 peaks, regions locally enriched for H3K27me3 were established by the SPP peak calling program using default parameters with a z-threshold value of 8 and a custom normalization factor between H3K27me3 ChIP and IgG libraries. This normalization factor was defined according to sequencing depth and immuno-precipitation yield.

source_name: DIPG012 IgG

growth_protocol: The mouse cells  as well as three human DIPG cell lines (DIPG007, DIPG012 and SF7761) were cultured on poly-D-lysine (PDL, Sigma) and laminin (Sigma) coated plates in neural stem cell medium (50% DMEM-F12, 50% neurobasal medium, N2 and B27 supplements, sodium pyruvate, glutamax, HEPES, β−mercaptoethanol, non-essential amino acids, bovine serum albumin, heparin, 100U/ml penicillin, 100 μg/ml streptomycin, human recombinant epidermal and basic fibroblast growth factors). Another human DIPG cell line (SF8628) was cultured in DMEM with 10% FBS.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature. Glycine was added at a final concentration of 125 mM to quench the formaldehyde. Cells were then washed twice with PBS and harvested in SDS buffer (50 mM Tris at pH 8.1, 0.5% SDS, 100 mM NaCl, 5 mM EDTA). Cells were pelleted down, resuspended in Triton-X IP buffer (100 mM Tris at pH 8.6, 0.3% SDS, 1.7% Triton X-100, and 5 mM EDTA) and the chromatin was sonicated to get the DNA fragments of <1000 bp with average DNA fragment size of 300 bp. 500 μg chromatin was used to perform chromatin immunoprecipitation (ChIP)
10 ng of ChIP DNA was used to make library using NEBNext Ultra DNA library kit for illumine (E7370; New England Biolabs) according to supplier’s instructions and the libraries were sequenced using Illumina HiSeq2500 sequencer.

value: IgG


title: DIPG007_me3

source_name: DIPG007 me3


title: SF8628_IgG

source_name: SF8628 IgG


title: DIPG007_IgG

source_name: DIPG007 IgG


title: DIPG012_me3

source_name: DIPG012 me3


title: SF7761_me3


title: SF7761_IgG

source_name: SF7761 IgG


title: SF8628_me3


title: S21DAP2

city: Yongin

first: Yeon-Ki

last: Kim

state: Kyonggido

address: 38-2 Namdong

department: GreenGene Biotech Inc.

institute: GreenGene Biotech Inc.

data_processing:
The Illumina Hiseq generates raw images utilizing HCS (HiSeq Control Software v2.2) for system  control and base calling through an integrated primary analysis software called RTA (Real Time  Analysis. v1.18). The BCL (base calls) binary is converted into FASTQ utilizing illumina package  bcl2fastq (v1.8.4). Adapters are trimmed away from the reads.
Programs such as TopHat, Cufflinks and HTSeq were used to process sequence reads. Differential exon usage was examined with the DEXseq package in Bioconductor. Briefly, the rice genome sequence (IRGSP-1.0_2014-06-25) in the RAP database (http://rapdb.lab.nig.ac.jp) was indexed using Bowtie 2 with an FM Index based on the Burrows-Wheeler transform (Langmead et al., 2009). Reads in FASTQ files were aligned using TopHat (v2.0.4) with default parameters (Kim et al., 2013). TopHat aligned the RNA-Seq reads to genomes using the short read aligner Bowtie 2 and then analyzed the mapping results to identify splice junctions between exons. In the program, samtools (version 1.2) was used for indexing and sorting of bam and sam files.
To extract exons among transcripts, non-overlapping exonic regions were defined with dexseq_prepare_annotation.py, and then the per-exon read counts were extracted with the script dexseq_count.py in the DEXSeq package (Anders et al., 2012). For each exon of each gene, the data contain the number of reads in each sample that overlap with the exon. If an exon’s boundary is not the same in all transcripts, the exon is separated into two or more parts, referred to as ‘‘counting bin’’. A read that overlaps with several counting bins of the same gene is counted for each of these. The program returned one file for each biological replicate with the exon counts. Finally, differential exon usage was assessed with the DEXseq package in Bioconductor (http://bioconductor.org). In the package, generalized linear models (GLMs) for model read counts and parameters are calculated from a negative binomial (NB) distribution of these count data (McCullagh and Nelder 1989).
Genome_build: the rice genome sequence (IRGSP-1.0_2014-06-25) in the RAP database (http://rapdb.lab.nig.ac.jp) was indexed
Supplementary_files_format_and_content: tab-delimited exon counts are generated in Exoncount file. To extract exons among transcripts, non-overlapping exonic regions were defined with dexseq_prepare_annotation.py, and then the per-exon read counts were extracted with the script dexseq_count.py in the DEXSeq package (Anders et al., 2012)

organism: Oryza sativa

source_name: Seeds at 20-30 days after pollination (S21DAP) were collected at the internal ripening stage of the grains.

extract_protocol:
mRNA was purified using the TruSeq RNA sample preparation kit (http://www.illumina.com/) following the company’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

value: Ilmi

value: Seeds at 20-30 days after pollination


title: P1cm2

source_name: Flowers before pollination were collected in the range of 0.5-1.5-cm panicles (P1cm)

value: Flowers in the range of 0.5-1.5-cm panicles (P1cm)


title: S21DAP1


title: Leaf2

source_name: Leaf at 14 days

value: Leaf


title: Th17 with IL-23+IL-1b rep2 (QZ3)

city: Cambridge

first: Raivo

last: Kolde

address: 415 Main St

institute: Broad Institute

description: number of cells: 542021

data_processing:
Alignment with Tophat+Bowtie
Counting of transcripts with htseq-count
QC with RSeqC
Normalization with cpm command in EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: 2017-04-07_ce_counts.txt (Counts), 2017-04-07_ce_norm.txt (CPM normalization)

organism: Mus musculus

source_name: Spleen

growth_protocol: cultured for 4 days in RPMI + 5% FBS

extract_protocol:
total volume 100ul
straight in Dynabeads polyA buffer
SmartSeq2
full length cDNA libraries were prepared using template switching and whole transcriptome amplification in a slight variation of the SmartSeq2 protocol described in PMID: 24056875

treatment_protocol: anti-CD3/CD28, anti-IL-4, anti-IFNg, IL-6, IL-23, IL-1b

tag: strain

tag: gender

value: male

value: Spleen

value: 11 weeks old


title: Gli1-R4-R6-unbound

city: St. Louis

first: Basab

last: Roy

state: MO

address: 4515 Mckinley avenue

department: Department of Genetics

institute: Washington University School of Medicine

data_processing:
Library strategy: Methyl-Spec-seq
Methylation property identification: For any particular DNA variant inside library, it carries particular barcode to indicate its methylation property, i.e., unmethylated, top hemimethylated, bottom hemimethylated, duplex methylated. Thus acording to the unique methylation barcode information, each read was identified and sorted to its methylation type.
Variant reads counting and sorting: For each randomized binding site, its number in Bound and Unbound portions were counted separately. The Bound/Unbound ratio was supposedly porportional to its relative binding affinity, and the negative logarithm of this ratio indicates the relative binding energy in kT unit.
Energy logo visualization: Based on the binding energy for particular reference and all its single variants, an energy logo can be generated to indicate the specificity of particular protein-DNA interactions. Futhermore, besides conventional G-T-A-C bases, we used two extra “M" and ”W" to represent methylated cytosine on upper and lower strand of DNA respectively, in which the height of M or W indicate the extra binding energy contribution between methylated and unmethylated base.
Supplementary_files_format_and_content: All processed data were saved in .txt files, including the methylation property, bound reads, unbound reads, Bound/Unbound ratio, relative binding energy for each variant.

source_name: In vitro protein-DNA binding reactions

extract_protocol:
After EMSA, DNA fragments were cut and extracted by gel extraction buffer at 50C for 30mins.
For each portion of DNA fragment, PE1 and PE2 PCR primers were used to PCR amplify extracted DNA by at least 8 cycles (95C 15s, 52C 15s, 72C 30s)
For each particular sample, there are two raw data files, i.e., bound reads and unbound reads with different Illumina Index. The processed data file was based on analysis of Bound and Unbound data together.

treatment_protocol: All EMSA reactions were done in 9% Tris-glycine gel, 200V, 30mins

tag: dna library composition

value: Including unmethylated dsDNA library CTCF-R1-R5, and M.sssI methylated dsDNA library CTCF-R1-R5-M.sssI

tag: recombinant protein

value: Mouse Gli


title: Root1

source_name: Root at 14 days

tag: tissue

value: Root


title: Gli1-R1-R5-unbound

value: Including barcoded unmethylated dsDNA libraries Gli-R1U, Gli-R2U, Gli-R33U, Gli-R4U, Gli-R5U, Gli-R6U; barcoded M.SssI methylated library Gli-R1M, Gli-R2M, Gli-R33M, Gli-R4M, Gli-R5M, Gli-R6M


title: Gli1-R1-R5-bound


title: CD4+CD25- cells from spleen of WT B6 mice (CE12)

description: sorted spleen cells - Cell lysates - cell number 2300000

source_name: naïve spleen - sorted cells

extract_protocol:
straight in Dynabeads polyA buffer
SmartSeq2
full length cDNA libraries were prepared using template switching and whole transcriptome amplification in a slight variation of the SmartSeq2 protocol described in PMID: 24056875

tag: genotype/variation

value: WT

tag: cell type

value: CD4+CD25- splenocytes

value: 8 weeks old


title: CD4+hCD2+ cells of CT Immunized IgA-/- mice (CE2)

description: sorted LP cells - Cell lysates - cell number 920628

source_name: Mice were orally immunized with CT - small intestine - sorted LP cells

tag: treatment

value: CT induction

value: CD4+IL-17A+ LP cells (following CT induction)

tag: age

value: 12-16 weeks old


title: Leaf1

value: Ilmi


title: Gli1-R4-R6-bound


title: Gli1-R6-unbound

value: Including barcoded unmethylated dsDNA libraries Gli-R6U, Top-hemimethylated Gli-R6U, duplex methylated Gli-R6U and M.SssI methylated Gli-R6U


title: Gli1-R6-bound


title: CD4+hCD2+ cells of IgA-/- mice (CE6)

description: sorted LP cells - Cell lysates - cell number 1800000

source_name: naïve small intestine - sorted LP cells

value: pooled male and female

value: IgAKO

value: CD4+IL-17A+ LP cells

value: 1 year old


title: naïve CD4+CD25- (QZ1)

description: number of cells: ~2.5x10^6

value: male

value: Spleen

value: 11 weeks old


title: CD4+hCD2+ cells of CT Immunized IgA-/- mice (CE1)

description: sorted LP cells - Cell lysates - cell number 686867


title: H3.3 L126A-L130A rep1

city: Madison

first: Peter

middle: W

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

data_processing:
RNA-seq data was aligned using bowtie and gene level expression was estimated using RSEM with default parameters as mentioned in (Li and Dewey, BMC, 2011).
Data was normalized using the median normalization approach based on the library size factor using EBSeq (Leng et al, Bioinformatics, 2013).
EBSeq was used to identify differentially expressed genes with a posterior probability of differential expression > 0.95 and FDR < 0.05 (Leng et al, Bioinformatics, 2013).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include TPM value for each sample

source_name: mESC

growth_protocol: Cells were maintained under 2i+LIF conditions in a medium containing a 1:1 mix of DMEM/F12 (Life Technologies 11330-033) and Neurobasal medium (Life Technologies 21103-049) with the addition of N2 and B27 supplements (Life Technologies 17502-048 and 17502-044, 1:100 dilutions), penicillin/streptomycin (100 U/mL and 100 µg/mL, respectively; Life Technologies 15140-122), 0.1 mM 2-mercaptoethanol, 1X GlutaMAXTM-I (Life Technologies 35050-061), 1X MEM NEAA (non-essential amino acids; Life Technologies 11140-050), Leukemia inhibitory factor (LIF), CHIR99021 at 3 μM (TOCRIS) and PD0325901 at 1 μM (Selleckchem). All experiments were performed under feeder-free conditions on dishes coated with 0.1% bovine gelatin. Cells were tested regularly for mycoplasma using the e-MycoTM Mycoplasma PCR Detection Kit (iNtRON Biotechnology).

extract_protocol:
RNA was harvested using Trizol reagent followed by column purification via Quick-RNA™ MiniPrep kit (Zymo), off-column DNase I digestion, and subsequent second column purification. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (Cat#E7530L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype

value: embryonic stem cells


title: H3.3KO rep2

value: H3.3 KO


title: H3.3 WT rep2


title: DaxxWT rep1

value: Daxx -/- + Daxx WT


title: H3.3 WT rep1


title: DaxxKO rep1

value: Daxx -/-


title: H3.3KO rep1


title: Plasmablast ChIP-Seq, rep1

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description:
genomic DNA, ChIP-ed
ChIP from 1.0x10^6 cells

data_processing:
All reads were processed with the trim_galore program (Trim Galore! version 0.3.7 and cutadapt 1.7.1) using the "-a ATCACCGACTGCCACGCCTTGGCCGTACAGCA GCCT" and "-q 20" options to remove the SOLiD adaptor (P1-T adaptor) sequence and low quality reads, respectively. The processed reads with 20 bases and longer were mapped on the mouse genome mm10 by Bowtie v1.1.2 with the "-n 3", "-best" and "-M 1" options.
Tdf files are made using igvtools v2.3.52 with "-w 25 -e 250" options.
BLIMP1 enrichment peaks was detected by MACS2_v2.1 with default parameter.
Genome_build: mm10

source_name: PB

growth_protocol: Purified B cells were  cultured in RPMI-1640 medium (Wako) supplemented with 10% FBS, 55 mM 2- mercaptoethanol, 10 mM HEPES, 1 mM sodium pyruvate, 100 units/mL penicillin, and 100 μg/mL streptomycin (GIBCO)

extract_protocol:
After 3 days of stimulation, cells were harvested and incubated with rat anti-CD138 (Syndecan-1) antibody conjugated with APC. BLIMP1 and CD138 positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015).
Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction.

treatment_protocol: Purified B cells were  stimulated with recombinant IL-4 (2 ng/mL; Peprotech) and LPS (10 ng/mL; Sigma) for 3 days

tag: chip antibdy

value: anti-GFP, Rb polyclonal, ab290

value: Homozygous EGFP-knocked-in at the N terminus of BLIMP1 (EGFP-BLIMP1)

tag: cell sorting

value: FACS (GFP+, CD138+)


title: Th17 with IL-23+IL-1b rep1 (QZ2)

description: number of cells: 725152

value: female

value: anti-CD3/CD28, anti-IL-4, anti-IFNg, IL-6, IL-23, IL-1b

value: 8 weeks old


title: Photoreceptor precursor ChIP-Seq, rep2

description:
genomic DNA, ChIP-ed
ChIP from 9.2x10^5 cells

source_name: PRP

extract_protocol:
Retinal tissues (P4) were dissociated from eye balls of EGFP-BLIMP1 mice and the incubation with 0.1 % trypsin and 1 mM EDTA in PBS at 37 °C for 10 min.  Trypsin was then inactivated by adding equal volume of PBS/10% FBS supplemented with 0.1mg/mL DNaseI (Sigma). BLIMP1 positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015).
Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction.

value: FACS (GFP+)


title: CD4+CD25- cells from spleen of WT B6 mice (CE13)

value: WT

value: CD4+CD25- splenocytes


title: Plasmablast ChIP-Seq, rep2

description:
genomic DNA, ChIP-ed
ChIP from 1.1x10^6 cells


title: E12.5_PGC_Male ChIP-Seq, input

description: genomic DNA, Input

source_name: E12.5_PGCM, input

extract_protocol:
EGFP-BLIMP1 embryos were obtained with intracytoplasmic sperm injection (ICSI) to oocytes (Kimura, 1995 #3053) and transfer of two-cell-stage embryos into oviducts of the surrogate mother mice. The embryonic male gonads at E12.5 were collected, for which sex was determined with the morphological features, and dissociated into single cells by incubating with 0.05 % trypsin and 0.5 mM EDTA (GIBCO) in PBS at 37 °C for 5 min. The cell suspension was then incubated with mouse anti-SSEA1 antibody conjugated with Alexa Fluor 647 (BioLegend). SSEA1 positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015).
Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction.

value: Input

value: FACS (SSEA1+)


title: H3.3 L126A-L130A rep2


title: E12.5_PGC_Ｍale ChIP-Seq

description:
genomic DNA, ChIP-ed
ChIP from 3.3x10^5 cells


title: d6 PGCLC ChIP-Seq, rep1

description:
genomic DNA, ChIP-ed
ChIP from 3.0x10^5 cells

source_name: d6 PGCLC

growth_protocol: EGFP-Blimp1 knock-in ESC lines were induced into EpiLCs as described for 36 hrs.

extract_protocol:
SSEA1 and  INTEGRINβ-3 positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015).
Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction.

treatment_protocol: The EpiLCs were then cultured under a floating condition by plating 2-3×10^3 cells per well of lipidure-coated U-bottom 96-well plate (Thermo Scientific) in the GK15 medium containing LIF, BMP4, BMP8a (500ng /mL), SCF (100 ng/mL), and EGF (50 ng/mL) for d6 PGCLCs.

value: FACS (SSEA1+, INTEGRINβ-3+)


title: d2 PGCLC ChIP-Seq, rep2

description:
genomic DNA, ChIP-ed
ChIP from 3.0x10^6 cells

source_name: d2 PGCLC

extract_protocol:
KIT positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015).
Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction.

treatment_protocol: The EpiLCs were then cultured under a floating condition by plating 2-3×10^3 cells per well of lipidure-coated U-bottom 96-well plate (Thermo Scientific) in the GK15 medium containing LIF and BMP4 (500 ng/mL) for d2 PGCLCs.

value: FACS (KIT+)


title: Embryonic intestinal epithelium ChIP-Seq, rep1

source_name: emIE

extract_protocol:
Intestinal epithelium were isolated as described (Gracz et al., 2012) with minor modifications.  The intestine (E16.5) from caudal half of duodenum to the ileocecal junction of EGFP-BLIMP1 mice were dissected, and the surrounding connective tissues and vessels were gently removed.  The isolated intestine were placed in the 1.5 ml eppendorf tube containing ice-cold PBS and cut into small pieces as fine as possible.  The intestine fragments were then transferred to 10 ml Falcon tube containing dissociation reagent ♯1 [47 mL PBS, 3 mL of 0.5 M (30 mM) EDTA, 75 μL of 1 M (1.5 mM) DTT] and placed on ice for 20min.  After the incubation, dissociation reagent ♯1 was replaced with dissociation reagent ♯2 [47 mL PBS, 3 mL of 0.5 M (30 mM) EDTA].  After 10 min incubation at 37 °C, the tube that contained intestine was shaken by hand for 30 sec to release epithelium from the basement membrane.  Dissociated cells were washed by removing supernatant and re-suspending cells in 10 mL PBS with 10% FBS.  The cells were collected by centrifugation and then re-suspended in 10 mL DMEM containing 8-mg Dispase (GIBCO), which digested cell–cell junction proteins and dissociated the whole epithelium to single cells.  The cells were then incubated in a water bath for 10 min at 37°C with vigorous shaking every 2 min.  After adding 10 % FBS, the cell suspension was passed through the cell strainer to remove large undissociated clumps of cells and connective tissues. BLIMP1 and EpCAM positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015).
Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction.

value: FACS (GFP+, EPCAM+)


title: C57-3

city: Newark

first: Melinda

middle: K.

last: Duncan

state: DE

address: 327 Wolf Hall

institute: University of Delaware

description:
75 C57Bl/6 E15.5 Biological replicate 3
This is duplicated sample record of GSM1210569  for the convenient retrieval of the complete raw data from SRA

data_processing:
Reads were trimmed using the CLC Genomics Workbench 5.5.1 with the following parameters: Max ambiguous bases:0; Minimum Q>0.01; minimum length 35bp
Reads were aligned to the Mus musculus genome using CLC Genomics Workbench 5.5.1
Unique gene counts were determined using CLC Genomics Workbench 5.5.1
Counts were normalized (CPM and RPKM) using R BioConductor EdgeR
Genome_build: Mus musculus GRCm38.77
Supplementary_files_format_and_content: tab-delimited: mgc gene symbol, ensembl gene ID, MGID, ensembl gene description, cpm, rpkm, raw count

source_name: C57Bl/6 mouse lens

extract_protocol:
RNA was extracted from pooled samples of 75 (C57BI/6) or 30 (β1-cKO) mouse lenses, using the SV total RNA isolation System (Promega, Madison, WI) according to the manufacturer's recommended protocol.
mRNA was purified from the total RNA samples using poly-T oligo attached magnetic beads. Then, it was converted to a library of template molecules for cluster generation and DNA sequencing according to the Illumina® TruSeq™ RNA Sample Preparation Kit v2. Afterwards, RNAseq was performed on Illumina® HiSeq 2000 (Illumina Inc., Madison, Wisconsin), with 50-cycle single-end (50bp) reads.

tag: strain background

value: lens

tag: number of lenses per replicate


title: d2 PGCLC ChIP-Seq, rep1


title: C57-2

description:
75 C57Bl/6 E15.5 Biological replicate 2
This is duplicated sample record of GSM1210568  for the convenient retrieval of the complete raw data from SRA


title: C57-1

description:
75 C57Bl/6 E15.5 Biological replicate 1
This is duplicated sample record of GSM1210567  for the convenient retrieval of the complete raw data from SRA


title: Embryonic intestinal epithelium ChIP-Seq, rep2

description:
genomic DNA, ChIP-ed
ChIP from 8.8x10^5 cells


title: E12.5_PGC_Ｆemale ChIP-Seq

description:
genomic DNA, ChIP-ed
ChIP from 3.6x10^5 cells

extract_protocol:
EGFP-BLIMP1 embryos were obtained with intracytoplasmic sperm injection (ICSI) to oocytes (Kimura, 1995 #3053) and transfer of two-cell-stage embryos into oviducts of the surrogate mother mice. The embryonic female gonads at E12.5 were collected, for which sex was determined with the morphological features, and dissociated into single cells by incubating with 0.05 % trypsin and 0.5 mM EDTA (GIBCO) in PBS at 37 °C for 5 min. The cell suspension was then incubated with mouse anti-SSEA1 antibody conjugated with Alexa Fluor 647 (BioLegend). SSEA1 positive cells were purified with FACS. Chromatin immunoprecipitation was performed as described previously(Kurimoto et al., 2015).
Libraries for ChIP_seq were prepared as described (Kurimoto, 2015 Cell Stem Cell) with a modification for application to the Illumina systems. Briefly, ChIP-ed and input DNAs were sheared to an average size of 150 bp by ultra-sonication (Covaris S2). The sheared DNAs were end-repaired, dA-tailed, ligated to an amplification adaptor (P1-T Adaptor/F and Barcode-Internal+12-mer/R), amplified with a 10-cycle PCR using Library PCR primer 1 (Life technologies) and Library PCR primer Barcode001 + Internal adaptor. For sequencing on the Illumina systems, we then added an adaptor and index to the amplified library with two rounds of additional PCRs. The 1st round additional PCR was performed for 6 cycles with Read1-P1 and Read2-internal-adaptor primers. The 2nd round PCR was performed for 4 cycles with Illumina P5-Read1 primer and P7-index N-Read2 primer to produce the index-tagged library DNAs. To exclude the initial constant region consisted of the amplification adaptor sequence (P1-T Adaptor) and maximize the efficient sequencing reads, we designed a custom sequencing primer, Custom-primer-29mer (Supplementary Table S2 of the manuscript), which met sequencing on Illumina platform (Caporaso, 2011 PNAS) in terms of the length, GC content, and melting temperature. The DNAs were then sequenced on the HiSeq 2500 platform (Illumina) in high throughput mode to generate single-end 100-bp reads, as the manufacturer's instruction.


title: DaxxKO rep2

value: embryonic stem cells


title: d6 PGCLC ChIP-Seq, rep2


title: β1-cKO-1

description: 30 β1-cKO E15.5 Biological replicate 1

source_name: β1-cKO mouse lens

value: mix

value: beta1-cKO (beta1 Flox/Flox MLR10 Cre+)


title: DaxxWT rep2

value: Daxx -/- + Daxx WT


title: β1-cKO-2

description: 30 β1-cKO E15.5 Biological replicate 2


title: Photoreceptor precursor ChIP-Seq, rep1

value: anti-GFP, Rb polyclonal, ab290

value: Homozygous EGFP-knocked-in at the N terminus of BLIMP1 (EGFP-BLIMP1)


title: P1cm1

source_name: Flowers before pollination were collected in the range of 0.5-1.5-cm panicles (P1cm)

value: Ilmi

value: Flowers in the range of 0.5-1.5-cm panicles (P1cm)


title: WT2_Input

city: Coventry

first: Andrew

middle: Christopher

last: Nelson

address: Gibbet Hill Campus

department: School of Life Sciences

institute: University of Warwick

data_processing:
ChIP-seq reads were mapped to mm9 using Stampy with default parameters
Peaks were called using MACS1.4.2 with default parameters with .wig files generated for data visualization.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files for visualization of ChIP and input data for both mutant and wild type samples.

source_name: Differentiated trophoblast stem cells

growth_protocol: Trophoblast stem cells differentiated to trophoblast giant cells by withdrawal of FGF4, TGFbeta1 and heparin sulfate.

extract_protocol:
Lysates were precleared with Protein G Dynabeads. Complexes were then isolated with 7µg anti-Blimp1 monoclonal antibody (Novus, clone 3H2-E8) linked to Protein G Dynabeads.
Sequencing libraries were prepared using the Illumina ChIP-seq DNA Sample Prep Kit. Libraries were size selected at ~200bp and four libraries were multiplexed per lane on a HiSeq 2500.

value: Day 2 trophoblast giant cells


title: MUT_ChIP

data_processing:
ChIP-seq reads were mapped to mm9 using Stampy with default parameters
Peaks were called using MACS1.4.2 with default parameters with .wig files generated for data visualization.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files for visualization of ChIP and input data for both mutant and wild type samples.

mm10.bedgraph and peaks_mm10.txt
ChIP-seq reads were mapped to mm10 using Bowtie2 with default parameters except -k 2.
Peaks were called against paired input samples with MACS2.1.0 using default parameters.
Genome_build:mm10
Supplementary_files_format_and_content:Bedgraph files for visualization of ChIP data for both mutant and wild type samples, and table of peak coordinates with associated MACS2 scores.


title: WT1_ChIP

data_processing:
ChIP-seq reads were mapped to mm9 using Stampy with default parameters.
Peaks were called using MACS1.4.2 with default parameters with .wig files generated for data visualization.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files for visualization of ChIP and input data for both mutant and wild type samples.

mm10.bedgraph and peaks_mm10.txt
ChIP-seq reads were mapped to mm10 using Bowtie2 with default parameters except -k 2.
Peaks were called against paired input samples with MACS2.1.0 using default parameters.
Genome_build:mm10
Supplementary_files_format_and_content:Bedgraph files for visualization of ChIP data for both mutant and wild type samples, and table of peak coordinates with associated MACS2 scores.

growth_protocol: Trophoblast stem cells differentiated by withdrawal of FGF4, TGFbeta1 and heparin sulfate.

value: Day 2 differentiated trophoblast stem cells


title: WT2_ChIP


title: Control rep2

city: Xi'an

first: Erfei

last: Chen

address: 229# North Taibai Road

institute: Northwest University

description: All.Counts.txt

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.2.0 mapping to reference genome
count counting
Genome_build: GRCh38_year_2014
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: HT-29 cells

growth_protocol: HT-29 cells were cultured with DMEM F12 medium

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
Ion  Proton Sequencing Protocol

treatment_protocol: Cells were transfected with pEF-BOS-EX vector or pEF-BOS-BMP5 using Roche X-tremeGENE HP DNA Transfection Reagent for 72h

value: colon

value: female

tag: transfection

value: pEF-BOS-EX vector


title: Control rep3

description: All.Counts.txt


title: BMP5 rep3

description: All.Counts.txt


title: Control rep1

description: All.Counts.txt


title: WT1_Input


title: rdd 3 DAI rep2

city: Tsukuba

first: Taiji

last: Kawakatsu

state: Ibaraki

address: 3-1-3 Kan-nondai

institute: National Agriculture and Food Research Organization

data_processing:
Methylated cytosine calls were made using the pipeline described in Lister et al. Human DNA methylomes at base resolution show widespread epigenomic differences. 2009. Nature
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab separated file of methylated cytosine positions. Column 1: chromosome, Column 2: position, Column 3: strand, Column 4: class, Column 5: # of C basecalls, Column 6: # of C+T basecalls.

organism: Arabidopsis thaliana

source_name: imbibed seed

growth_protocol: Col-0 and rdd dry seeds were sterilized with bleach and plated on half strength Linsmaier and Skoog medium supplemented with 1% agar. After 4 days stratification in the dark at 4ºC, plants were grown under long day condition at 22ºC.

extract_protocol:
DNA was extracted from dry and germinating seeds using modified CTAB method (Piskurewicz et al., Methods Mol Biol 2011).
One micrograms of genomic DNA was sonicated to 200 bp using the Covaris S2 System using the following parameters: cycle number = 6, duty cycle = 20%, intensity = 5, cycles/burst = 200 and time = 60 seconds. Sonicated DNA was purified using SPRI beads. Each sequencing library was constructed similar to genomic DNA libraries except the ligation was performed with methylated adapters provided by Illumina. Ligation products were purified with AMPure XP beads (Beckman) at a ratio of 1.8X of beads to sample. Up to 450 ng of ligated DNA was bisulfite treated using the MethylCode Kit (Invitrogen, Carlsbad, CA) following the manufacturer’s guidelines and then PCR amplified using KAPA HIFI Uracil+ (KAPA Biosystems, Wilmington, MA) using the following PCR conditions (2 minutes at 95C, 6 cycles of 15 seconds at 98C, 30 seconds at 60C, 4 minutes at 72C and 10 minutes at 72C).

value: rdd (ros1 dml2 dml3)

tag: developmental stage

value: 3 days after 4-day imbibition

value: seed


title: wt dry seed

data_processing:
Sequenced reads were mapped to TAIR10 whole genome using tophat 2.0.8 with a parameter (--library-type=fr-firststrand).
FPKM ( fragments per kilobase of exon per million fragments mapped) were quantified using Cufflinks 2.0.2 with parameters --library-type fr-unstranded
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM ( fragments per kilobase of exon per million fragments mapped) for all genes in the TAIR10 reference annotation as defined by Cufflinks

source_name: dry seed

extract_protocol:
RNA was extracted from dry seed and germinating seed using modified phenol-SDS methods (Takaiwa et al., MGG 1987).
RNA-seq library preparation was performed using the Illumina TruSeq RNA Library Prep kit from polyA+ selected mRNA as per manufacturer’s instructions.

value: Col-0 (wild type)

value: dry seed


title: rdd 4 DAI rep1

value: 4 days after 4-day imbibition


title: wt 0 DAI

value: 0 day after 4-day imbibition


title: BMP5 rep1

description: All.Counts.txt


title: rdd 4 DAI rep2


title: rdd 2 DAI rep2

value: 2 days after 4-day imbibition


title: rdd 1 DAI rep2

value: 1 days after 4-day imbibition


title: MUT_Input


title: rdd 1 DAI rep1


title: β1-cKO-3

description: 30 β1-cKO E15.5 Biological replicate 3

value: mix

value: beta1-cKO (beta1 Flox/Flox MLR10 Cre+)

value: lens


title: rdd 2 DAI rep1


title: rdd 3 DAI rep1


title: wt 4 DAI rep1


title: rdd 0 DAI rep1


title: rdd 0 DAI rep2


title: BMP5 rep2

description: All.Counts.txt


title: wt 4 DAI rep2


title: wt 3 DAI rep2


title: rdd dry seed rep1


title: rdd dry seed rep2


title: wt 2 DAI


title: wt 3 DAI rep1


title: wt 1 1DAI


title: wt 2 DAI rep1


title: wt 2 DAI rep2


title: 7thday-postpinfection-rep2

city: Riverside

first: Heba

last: Zaghloul

state: CA

address: 900 University Ave

institute: University of California, Riverside

data_processing:
Adapter sequences were trimmed and low quality reads filtered using Trimmomatic
Ribosomal contaminants were removed using SortMeRNA
Sequences were mapped to the SFAV-1a genome using bowtie2, only sequences mapping to this genome were retained
Genome_build: NC_008361
Supplementary_files_format_and_content: [.txt] Log2 RPKM values for SfAV-1a ORFs in the different time points post-infection.

source_name: SfAV-1a 7 days infected 3rd instar Spodoptera frugiperda caterpillar

extract_protocol:
Total RNA was isolated from the entire body of each healthey or SfAV-1a infected Spodoptera frugiperda larva and homogenized separately by mechanical trituration in TRIzol (Invitrogen), followed by DNase-treatment using the RNA Clean and Concentrator TM-5 kit (ZYMO RESEARCH) and eluted in ultra pure distilled water (Invitrogen).
The NEBNextPoly(A) mRNA magnetic isolation module kit (New England Biolabs) was used to enrich the mRNA first from the DNase-treated total RNA samples.The libraries were then prepared following the manufacturer’s instructions of the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs)

value: wild type

tag: host

value: Spodoptera frugiperda caterpillars

value: whole insect body

value: 3rd instar larvae

tag: time


title: wt 1 DAI rep2

tag: strain


title: wt 0 DAI rep2


title: wt 1 DAI rep1


title: wt 0 DAI rep1


title: wt dry seed rep2


title: wt dry seed rep1


title: F71_WT_4hr

city: Worcester

first: Alper

last: Kucukural

state: MA

address: 364 Plantation Street

department: Program in Molecular Medicine

institute: UMass Medical School

data_processing:
Because of their lower quality, the first and last base of all reads was trimmed, we then used trimmomatic-0.32 to trim by quality, removing 5’ or 3’ stretches of bases having average quality of less than 20 in a window size 10
Only reads longer than 36 bases were kept for further analysis. After quality trimming reads were aligned to the human ribosomal RNA using Bowtie2 v 2.2.3 with parameters -p 2 -N 1 --no-unal
All reads mapped to rRNA were discarded from further analysis. To estimate gene and isoform expression in Transcripts per Million (TPM) units and raw counts (expected_count), we used RSEM v1.2.28
Genome_build: hg19
Supplementary_files_format_and_content: tsv, read counts and tpm normalized counts

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by gradient centrifugation on Histopaque-1077 and CD14+ mononuclear cells were enriched via positive selection using anti-CD14 antibody MicroBead conjugates, according to the manufacturer’s protocol. CD14+ cells were then plated at a density of 1 to 2 x 106 cells/ml in RPMI-1640 supplemented with 5% heat inactivated human AB+ serum, 20 mM L-glutamine, 75 mM HEPES pH 7.2, 1 mM sodium pyruvate, and 1 x MEM non-essential amino acids. Differentiation of the CD14+ monocytes into dendritic cells (MDDCs) was promoted by addition of recombinant human GM-CSF and human IL-4; cytokines were produced from HEK293 cells stably transduced with pAIP-hGMCSF-co or pAIP-hIL4-co, respectively, as previously described (C. Reinhard et al., Retrovirology, 2014) with each cytokine supernatant added at a dilution of 1:100.

extract_protocol:
Qiagen RNeasy Miniplus
Nugen Ovation FFPE RNA-seq

treatment_protocol: MDDCs were seeded at 5x10^5 cells per well in 24-well plates and incubated with 100ul HIV-derived lentiviral vector pseudotyped with M-EBOV founder or A82V-containing Ebola virus glycoprotein. These challenges were performed in a total volume of 250ul culture medium. Cells were harvested at times indicated postinnoculation with virus.

tag: donor id

value: healthy donor #F71

value: monocyte-derived dendritic cells (MDDCs)

tag: stimulation

value: 4 hour stimulation with founder M-EBOV


title: F71_WT_2hr

value: 2 hour stimulation with founder M-EBOV