title: Vehicle replicate 1, GFP+ cells from 3 mice [Kentucky assay: whiskey lactone]

description: mRNA abundance data


title: Vehicle replicate 3, GFP- cells from 3 mice [Kentucky assay: whiskey lactone]

status: Public on Jun 01 2019

type: RNA

city: Lexington

first: Timothy

middle: S

last: McClintock

state: Kentucky

address: 508 Medical Science Buildi

department: Physiology

country: USA

institute: University of kentucky

description: mRNA abundance data

hyb_protocol: after fragmentation cRNA was hybridized for 16 hr at 45C on Clariom S Arrays. These were washed and stained in an Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix GCS3000 7G Scanner

data_processing: The data were analyzed with Affymetrix Gene Expression Console software using default analysis settings and global scaling as normalization method.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Olfactory mucosa; Vehicle-stimulated

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 50 - 100 ng of total RNA.

growth_protocol: 24 mice of both sexes, ages 7 - 12 weeks, were placed individuallly in clean air chambers for 40 hrs under air flow of 3.1L/min

extract_protocol: Mice were euthanized, olfactory mucosa were dissected, dissociated, and subjected to FACS.

treatment_protocol: After 26 hrs, half the mice were intermittently stimulated with vehicle (filtered air) or odorant for 10 sec every 20 min.

tag: strain

tag: tissue

value: Olfactory mucosa

tag: agent

value: Vehicle

tag: cell type

value: FACS sample, GFP+


title: Vehicle replicate 1, GFP- cells from 3 mice [Kentucky assay: whiskey lactone]

description: mRNA abundance data


title: wt2 vs. Dpep2

city: Berlin

first: Hans-Joachim

last: Mollenkopf

address: Charitéplatz 1

country: Germany

institute: Max-Planck-Institute for Infection Biology

description: biol. replicate 2, (+) polarity

hyb_protocol: Labeled samples was mixed and hybridized using Agilent Technologies habridization chambers according the supplier's recommendation. Washing of the hybridized arrays was done with a SSC protocol.

scan_protocol: Scanning of all microarrays was performed with 5µm resolution using a DNA microarray laser scanner (DNA Microarray Scanner BA, Agilent Technologies) according the manufacturers’ instructions.

data_processing: Raw microarray images were analyzed with the Image Analysis / Feature Extraction software G2567AA (Version A.9.5, Agilent Technologies) using local background without spacial detrend with a grid file and GE2-NonAT_95_Feb07 (Agilent Technologies) setting. Intensities were normalized by local background correction and by rank consistency filtering with LOWESS normalization. The intensity ratios were calculated by using the most conservative estimate of error between Universal Error Model and propagated error.

organism: Escherichia coli BL21(DE3)

source_name: broth culture

label_protocol: RNA labeling was performed with the two color Quick Amp Labeling Kit (Agilent Technologies) using FullSpectrum MultiStart Primer for T7 IVT RNA Amplification (BioCat GmbH, Heidelberg, Germany) as random T7 labeling.

growth_protocol: A single colony from a freshly striped plate was picked up and inoculated 20 ml LB broth in a 50 ml tube. The cells were grown in an orbital shaker at 37°C, 220 rpm for 4 hours.  3 ml of the cultures were used to inoculate 100 ml of LB broth in a 200 ml flask and grown to the cell density of A600=0.6.

extract_protocol: The total RNA was isolated from cells for microarray analysis using the SV Total RNA Isolation kits (Promega) with modifications. Culture aliquots were removed and mixed with 1 ml of stop solution (5% water-saturated phenol (pH: 4.5), 95% ethanol). The cultures were snap-frozen in liquid nitrogen and stored at -80°C.  After thawing on ice, bacteria were pelleted by centrifugation at 8000 g at 4°C for 20 min. The cell pellets were resuspended in 100 µl distilled H2O containing 50 mg/ml lysozyme, and the suspensions incubated at room temperature for 4 min. 75 µl lysis reagents (from Promega SV total RNA purification kit) was mixed with each sample, and then 350 µl RNA dilution buffer (from kit) was added. The mixtures were heated at 70 °C for 3 min and then centrifuged at 11,580 g for 10 min at room temperature. The supernatant from each sample was mixed with 200 µl of RNase-free 95% ethanol. The mixture was transferred to a spin column (from kit) and centrifuged for 1 min at max speed. The column was washed with 600 µl wash buffer (from kit). 50 µl of DNase mix (5 µl 90 mM MnCl2, 40 µl DNase core buffer, 5 µl DNase I (from kit)) was applied to the column matrix and incubated at room temperature for 15 min, and then 200 µl DNase stop mix (from kit) was added and centrifuge 11,580 g for 1 min. The column was washed twice with 600 µl and 250 µl wash buffer, respectively. Finally, RNA was eluted into 100 µl RNase-free distilled H2O. The purified RNA was quantified on a Nanodrop machine (Nano Drop Technologies).

treatment_protocol: In the phosphosugar stress condition, the cells were grown to a density of A600=0.5. 25% glucose or α-methylglucoside was added to the cultures to a final concentration of 1% and the incubation continued for 20 min. The same procedure above-mentioned was used to isolate total RNA from cells.

tag: genotype

value: wildtype

value: rne-∆EBS-FLAG


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_C9

type: SRA

city: Cambridge

first: Aviv

last: Regev

state: MA

address: 415 Main Street

department: Klarman Cell Observatory

institute: Broad Institute

description:
Sex: Female for HEK293 and Male for NIH3T3
scRNA-seq
3'-end
mixture_hg19_mm10_count_matrix.mtx, mixture_hg19_mm10_gene.tsv, mixture_hg19_mm10_cell.tsv

library_source: transcriptomic

data_processing:
For scRNA-seq and snRNA-seq data, scumi v0.1.0 (https://bitbucket.org/jerry00/scumi-dev/src/master/) was used to produce cell by gene sparse matrices (UMI count matrices for 3'-end methods and read count matrices for Smart-seq2). More specifically, STAR v2.6.1a was used for alignment except for Smart-seq2 and CEL-Seq2 data where HISAT v2.0.5 was used. featureCounts from the Subread package, v1.6.2 was used to tag each alignment with a gene tag. For bulk RNA-Seq data, reads were mapped to the reference genomes using Bowtie v0.12.9, and further quantified by RSEM v1.3.0 to generate transcripts per million values.
Genome_build: scRNA-seq data: a merged hg19 and mm10 geome for human and mouse mixture datasets, hg38 (GRCh38) for human PBMCs, and mm10 for mouse cortex data; bulk RNA-Seq data, hg38 (GRCh38) for human data and mm10 for mouse data
Supplementary_files_format_and_content: scRNA-seq data: mtx, a gene by cell count matrix in the sparse matrix market format
Supplementary_files_format_and_content: scRNA-seq data: cell.tsv, cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: scRNA-seq data: gene.tsv, gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: Bulk RNA-Seq data: TPM_bulk.tsv, tab-delimited text files of transcripts per million measurements of genes in each sample
Supplementary_files_format_and_content: mixture_hg19_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: mixture_hg19_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: mixture_hg19_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: pbmc_hg38_count_matrix.mtx :A gene by cell count matrix in the matrix market format
Supplementary_files_format_and_content: pbmc_hg38_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_cell.tsv :Cell names (colname names of the sparse count matrix)
Supplementary_files_format_and_content: cortex_mm10_count_matrix.mtx :A gene by cell count sparse matrix in the matrix market format
Supplementary_files_format_and_content: cortex_mm10_gene.tsv :Gene names (row names of the sparse count matrix)
Supplementary_files_format_and_content: HEK293_PBMC_TPM_bulk.tsv :A matrix of transcripts per million measurements
Supplementary_files_format_and_content: NIH3T3_cortex_TPM_bulk.tsv :A matrix of transcripts per million measurements

organism:
Homo sapiens
Mus musculus

source_name: Mixture of human HEK293 and murine NIH3T3 cell lines

extract_protocol:
Total RNA from bulk samples was extracted using Quick-RNA Mini Prep (Zymo Research) following the vendor protocol with a DNase treatment step
For library construction methods, see SAMPLES, description: Library Construction field. For details see the Methods section in the manuscript

tag: Sex

value: Pooled male and female

tag: library construction

value: sci-RNA-seq


title: 2 colorectal adjacent normal tissues [2N]

city: Guangzhou

first: Ri-Xin

last: Chen

state: Guangdong

address: No. 106, Zhongshan Er Road

country: China

institute: Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences

description: circRNA microarray in  Human colorectal adjacent normal tissues

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C)

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction.

organism: Homo sapiens

source_name: 2 colorectal adjacent normal tissues

label_protocol: Total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000

extract_protocol: RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis

treatment_protocol: All specimens were snap frozen in liquid nitrogen upon collection and were treated with Trizol reagent for further RNA extraction.

tag: tissues

value: adjacent normal tissues

tag: molecule subtype

value: circRNA


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_C8


title: Odor replicate 4, GFP+ cells from 3 mice [Kentucky assay: whiskey lactone]

description: mRNA abundance data

source_name: Olfactory mucosa; whiskey lactone-stimulated

value: whiskey lactone

value: FACS sample, GFP-


title: 2 colorectal carcinoma tissues [2T]

description: circRNA microarray in  Human colorectal carcinoma tissues

source_name: 2 colorectal carcinoma tissues

value: carcinoma tissues


title: TSWV_5dpi_30_rep3

city: Seoul

first: JOUNGHO

last: LEE

address: Gwanak-ro

country: South Korea

institute: Seoul National University

data_processing:
FastQC v0.10.0 and trimmomatic (v0.36) for trimming illumina reads
Mapping using TopHat v2.0.13 with default options including parameter -p 8
DEG analysis were done by DESeq2 R package
FPKM value was obtained using TopHate 2 and cufflinks 2
Supplementary_files_format_and_content: comma (,) limited text files of DEGs in different conditions

organism: Capsicum chinense

source_name: inoculated leaf of 'PI152225'

extract_protocol:
Inoculated leaves were extracted using RNA extraction kit(MG MED, Inc. Seoul, Korea)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RNA samples were obtained from 1 and 5 dpi TSWV- and mock-inoculated PI152225 plants. To ensure that clear differences in resistance breakdown at different temperatures were detected, leaf samples with local necrosis were harvested at 5 dpi.

tag: dpi

value: inoculated leaf


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_C7


title: rne flag2  vs. pept2

description: biol. replicate 2, (+) polarity

value: rne-FLAG


title: wt1 vs. Dpep1

description: biol. replicate 1, (+) polarity


title: rne pept2 vs. flag2

description: biol. replicate 2, (-) polarity


title: rne pept1 vs. flag1

description: biol. replicate 1, (-) polarity


title: Odor replicate 3, GFP+ cells from 3 mice [Kentucky assay: whiskey lactone]

description: mRNA abundance data


title: Odor replicate 4, GFP- cells from 3 mice [Kentucky assay: whiskey lactone]

description: mRNA abundance data


title: 1 colorectal carcinoma tissues [1T]

source_name: 1 colorectal carcinoma tissues


title: 1 colorectal adjacent normal tissues [1N]

source_name: 1 colorectal adjacent normal tissues


title: Odor replicate 2, GFP+ cells from 3 mice [Kentucky assay: whiskey lactone]

description: mRNA abundance data


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_C6


title: ssx_0351_mutant_Rep4

city: Richmond

first: Fadi

middle: Elias

last: El-Rami

state: VA

address: 521 N 11th Str, wood bldg, room 424

department: Microbiology & Immunology

institute: Virginia Commonwealth University

description: replicate 4

data_processing:
Standard Illumina pipeline. Real Time Analysis (RTA v. 1.18.66.3) software used for image processing, intesity extraction and basecalling based on intensities. CHASTITY software used for quality filter of basecalling.
Reads obtained from RNA-sequencing were aligned against the Streptococcus sanguinis SK36 genome using BasePairtech software.
Analyses were run on default parameter settings to obtain expression data of the ssx_0351 mutant compared to wild-type SK36. Significance was represented by fold change, p-value ≤ 0.05 and padj (multiple hypothesis adjusted p-value using Benjamini-Hochberg) for all the transcripts.
Genome_build: Streptococcus sanguinis reference genome; GCF_000014205.1
Supplementary_files_format_and_content: tab-delimited text file includes gene number, gene description, normalized expression count data for each replicate, base mean, log base 2 fold change,  log base 2 fold change, log fold change SE, p-value, and padj value for the mutant expression vs. the wild-type SK36 expression

organism: Streptococcus sanguinis

source_name: ssx_0351 deletion mutant

growth_protocol: Cells were incubated at 37°C under anaerobic conditions in brain-heart infusion media and harvested at late-log phase. The ssx_0351 mutant was supplemented with kanamycin (500 µg/ml) for selection of the antibiotic resistance cassette.

extract_protocol:
Cells were lysed and RNA was extracted by FastPrep lysing matrix beads. Clean-up and DNase I treatment was conducted by QIAGEN RNeasy mini kit, according to the manufacterer's protocol. Illlumina RiboZero Magnetic Kit for bacteria was used to deplete ribosomal RNA from 2 µg of total RNA.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs) was used for the RNA-seq library preparation according to the manufacturer’s protocol. Briefly, ribosomal-depleted RNA was fragmented followed by first-strand cDNA synthesis from random primers using ProtoScript II Reverse Transcriptase (New England BioLabs). Second strand cDNA was synthesized and purified. End repair was performed on the double-stranded cDNA and primed with the addition of 5’-phosphorylated dA-tailed ends using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase (New England BioLabs). This was immediately followed by adaptor ligation (New England BioLabs) and purified. Samples were PCR-amplified for 12 cycles with Phusion HiFi polymerase (New England Biolabs) with paired-end primers and a randomly chosen unique barcode (NEB Next Multiplex Oligs for Illumina - Index Primers 2, 11, 12, 13, 15, 16, 18, 20, 21, 22). Agencourt AMPure XP Beads (Beckman Coulter) were used for all purification steps.

tag: strain background

value: parent strain:SK36

tag: genotype/variation

value: ssx_0351 deletion mutant

tag: growth phase

value: late-log


title: Odor replicate 3, GFP- cells from 3 mice [Kentucky assay: whiskey lactone]

description: mRNA abundance data

value: Olfactory mucosa


title: TSWV_5dpi_30_rep2


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_C5


title: TSWV_1dpi_30_rep3


title: TSWV_5dpi_30_rep1


title: Odor replicate 1, GFP- cells from 3 mice [Kentucky assay: whiskey lactone]

description: mRNA abundance data


title: Odor replicate 1, GFP+ cells from 3 mice [Kentucky assay: whiskey lactone]

description: mRNA abundance data


title: ssx_0351_mutant_Rep3

description: replicate 3


title: ssx_0351_mutant_Rep2

description: replicate 2


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_C4


title: TSWV_1dpi_30_rep2


title: Odor replicate 2, GFP- cells from 3 mice [Kentucky assay: whiskey lactone]

description: mRNA abundance data


title: ssx_0351_mutant_Rep1

description: replicate 1


title: rne flag1 vs. pept1

description: biol. replicate 1, (+) polarity


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_C3


title: Vehicle replicate 4, GFP+ cells from 3 mice [Kentucky assay: isoamyl acetate]

description: mRNA abundance data

value: Vehicle


title: TSWV_1dpi_30_rep1


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_C2


title: Mock_5dpi_30_rep3


title: Wild-type_SK36_Rep4

description: replicate 4

source_name: Wild-type SK36

value: wild type


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_C12


title: Wild-type_SK36_Rep2

description: replicate 2


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_C1


title: Vehicle replicate 4, GFP- cells from 3 mice [Kentucky assay: isoamyl acetate]

description: mRNA abundance data

value: FACS sample, GFP+


title: Mock_5dpi_30_rep2


title: Vehicle replicate 3, GFP+ cells from 3 mice [Kentucky assay: isoamyl acetate]

description: mRNA abundance data


title: Wild-type_SK36_Rep1

description: replicate 1


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_C11


title: Mock_1dpi_30_rep3


title: Vehicle replicate 3, GFP- cells from 3 mice [Kentucky assay: isoamyl acetate]

description: mRNA abundance data


title: Mock_1dpi_30_rep2


title: Vehicle replicate 2, GFP+ cells from 3 mice [Kentucky assay: isoamyl acetate]

description: mRNA abundance data


title: Vehicle replicate 2, GFP- cells from 3 mice [Kentucky assay: isoamyl acetate]

description: mRNA abundance data


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_B8


title: Mock_1dpi_30_rep1


title: Mock_5dpi_30_rep1


title: TSWV_5dpi_25_rep3


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_B7


title: Vehicle replicate 1, GFP- cells from 3 mice [Kentucky assay: isoamyl acetate]

description: mRNA abundance data


title: Vehicle replicate 1, GFP+ cells from 3 mice [Kentucky assay: isoamyl acetate]

description: mRNA abundance data


title: TSWV_5dpi_25_rep2


title: Wild-type_SK36_Rep3

description: replicate 3


title: Odor replicate 4, GFP- cells from 3 mice [Kentucky assay: isoamyl acetate]

description: mRNA abundance data

source_name: Olfactory mucosa; isoamyl acetate-stimulated

value: isoamyl acetate


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_B6

value: Pooled male and female


title: TSWV_5dpi_25_rep1


title: MLV gRNA RNA-seq 1

city: Durham

first: Bryan

middle: R

last: Cullen

state: NC

address: 213 Research Drive

department: Molecular Genetics & Microbiology

institute: Duke University

description: RNA-seq of purified gRNA from virions isolated from MLV infected 3T3 cells

data_processing:
CASAVA 1.8.2
fastx toolkit
Bowtie (1)
Aligned to mm10 genome to remove mouse reads
Aligned remainder of the reads to the MLV genome
Genome_build: Moloney Murine Leukaemia Virus NCBI-NC_001501.1
Supplementary_files_format_and_content: bed files, aligned to the MLV genome

organism: Moloney murine leukemia virus

extract_protocol:
PAR-CLIP
All samples were processed with the Illumina Tru-seq small RNA-seq kit

tag: virus

value: MLV

tag: technique

value: RNA-seq

tag: par-clip antibody

tag: transfection

value: virion RNA


title: MLV gRNA RNA-seq 2

source_name: RNA-seq of purified gRNA from virions isolated from MLV infected 3T3 cells


title: MLV gRNA RNA-seq 3


title: Odor replicate 3, GFP+ cells from 3 mice [Kentucky assay: isoamyl acetate]

description: mRNA abundance data

tag: strain


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_B9

value: sci-RNA-seq


title: MLV 3T3 mut PA-m5C-seq

description: PA-m5C-seq of mutant RNA from MLV infected 3T3 cells

value: anti-m5C, Diagenode, Cat No C15200081, Lot No, RD-004

value: polyA RNA


title: TSWV_1dpi_25_rep3

tag: tissue

value: inoculated leaf


title: TSWV_1dpi_25_rep2


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_C10


title: MLV 3T3 virion PA-m5C-seq

description: PA-m5C-seq of virion RNA from MLV infected 3T3 cells


title: Odor replicate 3, GFP- cells from 3 mice [Kentucky assay: isoamyl acetate]

description: mRNA abundance data

tag: agent


title: Odor replicate 2, GFP+ cells from 3 mice [Kentucky assay: isoamyl acetate]

description: mRNA abundance data

tag: cell type

value: FACS sample, GFP-


title: smn-1(ok355); uaf-1(n4588) rep1

city: Changsha

first: Long

last: Ma

address: 110 Xiangya Road, Kaifu District

institute: Central South University

data_processing:
Base-calling was performed using CASAVA software.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows: 1) Remove the adaptor-polluted reads (Reads containing more than 5 adaptor-polluted bases were regarded as adaptor-polluted reads and would be filtered out). 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads. 3) Remove reads with number of N bases accounting for more than 5 %. As for paired-end sequencing data, both reads would be filtered out if any read of the paired-end reads are adaptor-polluted.
Bowtie/Bowtie2 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
Fragments Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM was calculated to estimate the expression level of genes in each sample.
Genome_build: WBcel235
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: worms

growth_protocol: Mutants or wild-type animals were synchronized by bleaching and allowed to grow for 2 days post the L1 larval stage at 20℃.

extract_protocol:
Total RNAs were extracted using TRI Reagent Solution according to manufacturer’s instructions (Invitrogen).
mRNA was enriched with oligo(dT) beads. RNA libraries were prepared using standard illumina protocols.The constructed libraries were sequenced as 150 bp paired-ends on Illumina platform.

treatment_protocol: Animals were washed with M9 three times and left in M9 for three hours to remove intestinal bacteria.

tag: developmental stage

value: day 2 post the L1 larval stage at 20C


title: MLV 3T3 cell PA-m5C-seq

description: PA-m5C-seq of cellular RNA from MLV infected 3T3 cells


title: TSWV_1dpi_25_rep1


title: Odor replicate 4, GFP+ cells from 3 mice [Kentucky assay: isoamyl acetate]

description: mRNA abundance data


title: uaf-1(n4588) rep3


title: MLV 3T3 mut PA-m6A-seq

description: PA-m6A-seq of mutant RNA from MLV infected 3T3 cells

value: anti-m6A, Synaptic Systems, Cat No 202111, Lot No, 202111/4


title: TGF-β1-3

city: Changchun

first: bao

last: yuan

address: 5333 Xi'an Road

institute: Jilin University

data_processing:
An AMPure XP system was used to purify the library fragments for screening cDNA fragments of 150 to 200 bp in length. An Agilent 2100, a Qubit 2.0and Q-PCR were used to assess the cDNA library qualityand quantity.
Sus scrofa 10.2 (ftp://ftp.ncbi.nlm.nih.gov/genomes/Sus_scrofa/ARCHIVE/ANNOTATION_RELEASE.105/)   was downloaded from the Ensembl genome browser and was used as the genome reference for isoform expression levelquantifications, splice junction searching and alignment.
The FPKM values of each transcript were calculated using StringTie 1.3.1
Supplementary_files_format_and_content: xlsx files  include FPKM values for each Sample …

organism: Sus scrofa

source_name: Junmu No. 6 white pigs

extract_protocol:
Six samples of total RNA were extracted using the TRIzolmethod (Roche,USA) according to standard protocols
The Illumina HiSeqXten platform was used to sequence and constructlibraries at BioMarkerTechnologies (Beijing, China) following the manufacturer’s recommended protocol.

value: Subcutaneous adipose tissue

value: porcine preadipocytes

tag: age

value: Five-day-old


title: Mock_5dpi_25_rep2


title: MLV 3T3 virion PA-m6A-seq

description: PA-m6A-seq of virion RNA from MLV infected 3T3 cells


title: MLV 3T3 cell PA-m6A-seq

description: PA-m6A-seq of cellular RNA from MLV infected 3T3 cells


title: Mock_5dpi_25_rep1


title: Mixture2.CBU1CANXX.103117_SciSeq-p1_B5

tag: Sex

tag: library construction


title: smn-1(ok355); uaf-1(n4588) rep2


title: Odor replicate 2, GFP- cells from 3 mice [Kentucky assay: isoamyl acetate]

description: mRNA abundance data

value: Olfactory mucosa


title: TGF-β1-2

source_name: Junmu No. 5 white pigs


title: Odor replicate 1, GFP+ cells from 3 mice [Kentucky assay: isoamyl acetate]

description: mRNA abundance data


title: uaf-1(n4588) rep1


title: Mock_5dpi_25_rep3


title: Mock_1dpi_25_rep3


title: smn-1(ok355) rep3


title: TGF-β1-1

source_name: Junmu No. 4 white pigs


title: NC-3

source_name: Junmu No. 3 white pigs


title: Odor replicate 1, GFP- cells from 3 mice [Kentucky assay: isoamyl acetate]

description: mRNA abundance data

value: FACS sample, GFP+


title: 33Psyn

city: Newcastle upon Tyne

first: Katherine

last: James

address: Urban Sciences Building

department: School of Computing

country: United Kingdom

institute: Newcastle University

data_processing:
Prinseq-lite  was used to filter and trim raw read data by quality using the following parameters: –min_qual_mean 20 -min_len 50 -ns_max_p 5 -trim_qual_left 20 -trim_qual_right 20 -trim_ns_left 1 -trim_ns_right 1 -trim_qual_type min -trim_qual_rule lt -trim_tail_left 10 -trim_tail_right 10 –lc_method dust –lc_threshold 7 -out_format 3
Trinity v2.2.0 was used to assemble a single reference assembly using both paired, and unpaired data 165 which passed QC, default kmer value (k=25), and retaining all contigs with a minimum length of 300bp.
DETONATE v1.11 and Transrate v1.0.0  were applied to filter chimeric, fragmented, or locally misassembled transcripts.
The cd-hit-est algorithm to cluster isoforms at a similarity threshold of 95% over at least 50% length of the shortest sequence (-c 0.95 –aS 50).
Annotation was carried out with the Trinotate pipeline v 3.0.1 using a chordate-only subset of the Uniprot/Swiss-Prot (UPSP_chord) database for all blastx and blastp steps. Blastx searches were thenrun against seven NCBI Refseq proteomes;Homo sapiens, Mus musculus, Latimeria chalumnae, Danio rerio and Lepisosteus oculatus, Callorhinchus milii, and Rhincodon typus). Contigs with blast e-values < 1 x 10-10 against either UPSP_chord or one of the 7 Refseq proteomes were retained.
Expression analyses were conducted via the pipeline packaged with Trinity v2.2.0; preprocessed read data for the 28Syn, 28Psyn, 33Syn and 33Psyn reads were aligned to the reference Ler_Trinity_CRBB transcriptome using the bowtie2 option, and the RSEM option was used to estimate transcript abundance.
Genome_build: Ler_Trinity_CRBB.fasta
Supplementary_files_format_and_content: Text files of tab-delimited TPM and FPKM files for each transcript, matrix file of raw counts for all samples, and fasta file of the de novo assembled contigs produced by Trinity.

organism: Leucoraja erinaceus

source_name: Post-synarcual

extract_protocol:
The synarcual and post-synarcual regions of the axial skeleton of two males at stage 28 and stage 33 respectively  were dissected in PBS at 4°C.  The central nervous system and axial musculature was removed and the remaining skeletal tissue was flash frozen in liquid N2 in aluminum foil envelopes.   Frozen tissue was pulverized with a hammer and total RNA was extracted using the Trizol® method employing a Qiagen TissueLyser II to complete the dissociation.   The resulting total RNA was further purified using the Qiagen RNeasy kit.  Quality and quantity were assessed with the Agilent Tapestation High Sensitivity RNA Screen Tape and only samples with RIN values > 8.0 were processed for sequencing.
Libraries were prepared using the Truseq RNA library preparation kit v2 (2 x 100bp, unstranded) and sequenced in a pooled lane on a HiSeq2000 sequencer on high-throughput mode generating 132,470,224 reads and 12.32Gbp (average read length = 93bp).

value: post-synarcual


title: Oxy_Mutant_SMRTseq_replABCpooled

city: New York

first: Leslie

last: Beh

state: NY

department: Biochemistry & Molecular Biophysics

institute: Columbia University

description: Biological replicates A,B,C

library_source: genomic

data_processing:
All Illumina sequencing data were quality trimmed (minimum quality score = 20) and length-filtered (minimum read length = 40 nt) using Galaxy. MNase-seq and 6mA IP-seq reads were mapped to the Oxytricha trifallax JRB310 (August 2013 build) macronuclear reference genome using Bowtie 2 with default settings, while poly(A)+ RNA-seq and TSS-seq reads were mapped using TopHat2 with August 2013 Oxytricha gene models.
Reads from all biological replicates from each dataset were merged before downstream processing. The per-basepair coverage of Oxytricha MNase-seq read pair centers (termed “nucleosome occupancy”) and full 6mA IP-seq reads were respectively computed across the genome.  Subsequently, the per-basepair coverage values were normalized by the average coverage within each chromosome to account for differences in DNA copy number (and hence, read depth) between Oxytricha chromosomes. The per-bp coverage values were then smoothed using a Gaussian filter of standard deviation = 15 . For RNA-seq data, the number of reads per kilobase of chromosome per million mapped reads (RPKM) was calculated for each chromosome without normalization by DNA copy number since there is no known correlation between Oxytricha DNA and transcript levels. Oxytricha TSS-seq data were processed using CAGEr; with clusterCTSS parameters (threshold = 1.6, thresholdIsTpm = TRUE, nrPassThreshold = 1, method = "paraclu", removeSingletons = TRUE, keepSingletonsAbove = 5). Only TSSs with tags per million counts > 0.1 were used for downstream analysis. All processed data files (.txt) format were generated using these normalization procedures.
Genome_build: Oxytricha trifallax JRB310 macronuclear genome (August 2013 build)
SMRT-seq data were processed with SMRTPipe v1.87.139483 in the SMRT Analysis 2.3.0 environment using, in order, the P_Fetch, P_Filter (with minLength = 50, minSubreadLength = 50, readScore = 0.75, and artifact = -1000), P_FilterReports, P_Mapping (with gff2Bed = True, pulsemetrics = DeletionQV, IPD, InsertionQV, PulseWidth, QualityValue, MergeQV, SubstitutionQV, DeletionTag, and loadPulseOpts = byread), P_MappingReports, P_GenomicConsensus (with algorithm = quiver, outputConsensus = True, and enableMapQVFilter = True), P_ConsensusReports, and P_ModificationDetection (with identifyModifcations = True, enableMapQVFilter = False, and mapQvThreshold = 10) modules. All other parameters were set to the default. Tetrahymena SMRT-seq reads were mapped to the June 2014 reference genome build.
Genomic coordinates of all epigenetic modifications are listed in "L920_allminus_020318_m6A_modifications.gff", "L920_allplus_012918_m6A_modifications.gff","Tth_PacBio_modifications_all_021716.gff". Only "m6A" calls were used for downstream analysis.
Genome_build: SMRT-seq - Tetrahymena thermophila SB210 macronuclear genome (June 2014 build).

molecule: genomic DNA

organism: Oxytricha trifallax

source_name: Whole cells

extract_protocol:
Oxytricha cells were washed twiced with Pringsheim media and genomic DNA was isolated using a Nucleospin Tissue kit (Macherey-Nagel).
SMRT-seq; Standard Pacific Biosicences SMRT-seq library construction protocol

value: Vegetative

tag: presence of n6-methyladenine on dna template

value: No

tag: source of histones used for chromatin assembly

tag: amount of histones used for chromatin assembly

tag: extent of mnase digestion


title: NC-2

source_name: Junmu No. 2 white pigs


title: smn-1(ok355) rep2


title: WT rep2


title: NC-1

source_name: Junmu No. 1 white pigs


title: 28Psyn


title: smn-1(ok355) rep1


title: uaf-1(n4588) rep2


title: 33Syn

source_name: Synarcual

value: synarcual


title: Vehicle replicate 4, GFP- cells from 3 mice [Kentucky assay: whiskey lactone]

description: mRNA abundance data

source_name: Olfactory mucosa; Vehicle-stimulated

value: Vehicle


title: Oxy_WT_SMRTseq_replABCpooled

description: Biological replicates A,B,C

value: Yes


title: WT rep1


title: 28Syn


title: Mock_1dpi_25_rep2

source_name: inoculated leaf of 'PI152225'

tag: dpi


title: wild type rep1

status: Public on May 31 2019

city: Wernigerode

first: Samuel

last: Hauf

address: Burgstr. 37

department: Division of Enteropathogenic Bacteria and Legionella (FG11)

institute: Robert Koch-Institute

description: depletion of bacterial rRNA using Illumina Ribo-ZeroTM

data_processing:
Quantification of transcript abundancy via quasi-mapping of raw reads using salmon-0.8.2_linux_x86_64 (https://github.com/COMBINE-lab/salmon)
For statistical significance a two-sided t-test was performed on log-transformed TPM values obtained from salmon output (quant.sf files) assuming heteroscedastic data
Significant hits were selected as having p < 0.01, an expression ratio > 2 and at least 10 TPM detected in all three replicates for wildtype or mutant
Genome_build: L. monocytogenes EGDe cDNA (ftp://ftp.ensemblgenomes.org/pub/bacteria/release-38/fasta/bacteria_0_collection/listeria_monocytogenes_egd_e/cdna/Listeria_monocytogenes_egd_e.ASM19603v1.cdna.all.fa.gz)
Supplementary_files_format_and_content: The *_quant.sf files contain the quantification output of salmon as tab delimited txt, the csv file contains a summary of the raw data as well as the statistics calculated from it.

organism: Listeria monocytogenes EGD-e

source_name: bacterial cells

growth_protocol: Strains were grown in BHI broth to an OD600 of ~0.5 (mid exponential phase).

extract_protocol:
RNA extraction followed the protocol of Völker et al. 1995 (01 April 1994, Microbiology 140: 741-752, doi: 10.1099/00221287-140-4-741) with modifications. Cell pellets were resuspended in 1 ml Lysis Buffer I (25% sucrose; 20 mM Tris-HCl pH 8, 0.25 mM EDTA) and 2 µl of lysozyme (100 mg/ml) was added. After incubation for 5 min on ice, the samples were pelleted (15,000 x g for 30 s at 4°C) and resuspended in 300 µl Lysis Buffer II (3 mM EDTA, 200 mM NaCl). This solution was then mixed with 300 µl Lysis Buffer III (3 mM EDTA, 200 mM NaCl, 1% SDS) that had been pre-incubated at 95°C and the mixture was incubated at 95°C for five more minutes. 600 µl phenol/chloroform/isoamylalcohol (25:24:1) was added and vigorously mixed at room temperature for 5 min. Phases were separated by centrifugation (15,000 x g, 5 min), the aqueous upper phase was collected and the phenol/chloroform extraction was repeated. Afterwards, the aqueous phase was mixed with 600 µl chloroform/isoamylalcohol (25:1), shaken vigorously for 5 min and phases were separated by centrifugation (5 min at 15,000 x g). The chloroform extraction was repeated. Finally, RNA was precipitated by addition of 0.1 x volume 3 M sodium acetate (pH 5.2) and 1.5 volumes 96% ethanol and incubation at -20°C overnight and pelleted by centrifugation (15,000 x g for 15 min at 4°C). The pellet was washed with 70% ethanol and resuspended in 100 µl DEPC treated water. 10 µg total RNA were digested with DNAse using the RNase-Free DNase Set (Qiagen). RNA was then purified using RNA clean & concentrator columns (Zymo Research) for purification for RNA molecules longer than 200 nucleotides. RNA quality was assessed using Agilent Bioanalyzer RNA Nano chips.
rRNA depletion was performed using the Ribo-Zero Bacteria Kit (Illumina) following the manufacturer's instructions. A total of approximately 2 µg purified RNA was trestedtreated with 10 µl Ribo-ZeroRemoval Solution and RNA concentrations were determined using a Qubit® fluorometer. After rRNA removal the remaining RNA was pelleted by ethanol precipitation following the recommendations in the Ribo-Zero protocol. RNA libraries were prepared using the TruSeq® Stranded mRNA Kit, starting with 19.5 µl Fragment, Prime, Finish Mix being added to the dried RNA pellet after rRNA depletion and ethanol precipitation. From this point on the manufacturers protocol was strictly followed (Illumina Part # 15031047 Rev. E). The RNA libraries were sequenced in paired-end mode with 2 times 76 cycles on the Illumina MiSeq (MiSeq® Reagent Kit v3; 150 cycles).

treatment_protocol: 25 ml of the culture was collected and quenched by adding of 25 ml ice cold killing buffer (20 mM Tris-HCl pH 7.5, 5 mM MgCl2, 20 mM NaN3). After 5 min incubation on ice, cells were harvested by centrifugation.

tag: genotype

value: wildtype


title: wild type rep3


title: Δlmo01408 replicate3


title: wild type replicate3


title: delta_lmo0422 rep1


title: delta_lmo0599 replicate1


title: delta_lmo0422 rep2


title: delta_lmo0599 replicate3


title: wild type replicate2


title: Δlmo01408 replicate2


title: wild type replicate1


title: delta_lmo0599 replicate2


title: WT replicate3


title: WT replicate2


title: WT replicate1


title: Δlmo01408 replicate1


title: delta_lmo0422 rep3


title: Rmh_Nfs

city: Cuernavaca

first: Luis

middle: Fernando

last: Lozano

state: Morelos

address: Av. Universidad 2001

country: Mexico

institute: Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México

data_processing:
Rna samples were sent to BGI Americas for Illumina HiSeq 2000h high throughput sequencing
The quality of the raw reads was assessed with FastQC software and trimmed with Trim Galore v0.3.7
Reads were aligned to the Oryza sativa CDS collection (Os-Nipponbare-Reference genome V 7.1) using Bowtie aligner with he following parameters: bowtie -aS -X 800 –ofrate 1 transcripts
Differential expression analysis between samples was determined with the NOISeq version 2.6.0 using Noiseq-sim method, which simulates technical replicates from a multinomial distribution to estimate DE probabilities, with the recommended q value of 0.9 (Tarazona et al. 2015), Noiseq-sim was used with the following parameters: size of simulated sample (pnr) = 0.2, number of simulated replicates (nss) = 5, allowed variability (v) = 0.02. Enrichment analysis of Gene Ontology (GO) terms was based on the TopGO v. 3.0.2. (Alexa and Rahnenführer 2016), and a p-value of 0.05 was used to define the most significant GO terms. DEGs were analyzed with the KEGG PATHWAY database (https://www.genome.jp/kegg/pathway.html) to determine the presence and distribution of all the up and down regulated genes in different pathways (Tanabe and Kanehisa 2012).
Genome_build: Oryza sativa CDS collection (Os-Nipponbare-Reference genome V 7.1)
Supplementary_files_format_and_content: Tab delimited txt files include RPKM values for each sample

organism: Oryza sativa

source_name: root

growth_protocol: Surface disinfected F2 seeds from PhL and vector control plants were germinated, and grown in 80 mL culture tubes containing Yoshida medium for two months in sterile conditionsin growth room at 28oC and 16 h/8 h light/dark cycle;

extract_protocol:
total RNA was isolated from 50 mg of liquid nitrogen frozen roots of RMh and PhL transgenic plants using Spectrum Plant Total RNA Kit (Sigma-Aldrich, USA).
Quality of RNA samples was evaluated using Nanodrop 2000 Spectrophotometer (Thermo Scientific, USA).

treatment_protocol: roots were covered with aluminum foil. Later the plants were taken out, roots thoroughly rinsed with sterile Yoshida medium lacking nitrogen and transferred to the same N-deprived medium, and treated  for 24 h with S. meliloti NFs (1x10-9M) or medium just supplemented with CHAPS (control)

tag: genotype/variation

value: RMh transgenic plant

tag: treatment

value: S. meliloti NFs (1x10-9M)

value: root


title: wild type rep2


title: PhL

value: PhL transgenic plant

value: control


title: PhL_Nfs


title: Control_rep1

city: Gifu

first: Kumiko

last: Tanabe

address: Yanagido 1-1

country: Japan

institute: Gifu University School of Medicine

hyb_protocol: The labeled cRNA was hybridized with a microarray slide (SurePrint G3 Mouse GE Microarray 8x60K Ver. 2.0; Agilent) for 17 h at 65℃ in Agilent G2545A hybridization oven.

scan_protocol: The microarray slide was then washed with Gene Expression Wash Buffer (Agilent Technologies), and scanned with Agilent Array scan G2565CA.

data_processing: The scanned image was processed for digitization with Feature Extraction software (Agilent Technologies).

source_name: mouse astrocyte cell line, no-treatement

label_protocol: Cy3-labeled cRNA probes were prepared from the total RNA using Low Input Quick Amp Labeling Kit (Agilent Technologies), following the manufacturer’s instructions.

growth_protocol: Mouse cloned astrocyte C8D1A cells obtained from the American Type Culture Collection (Rockville, MD), were seeded into 12 wells/plate (15 x 104 cells/well), and maintained in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum at 37oC in a humidified atmosphere of 5% CO2/95% air.  After 6 days, the medium was exchanged for serum-free DMEM.  The cells were then used for experiments after 24 h.

extract_protocol: Total RNA was extracted from PRF-treated C8D1A cells and untreated control cells using Maxwell RSC simplyRNA Tissue kit (Promega Corp., Fitchburg, Wisconsin, USA) and quantified with spectrophotometer (BioSpectrometer basic; Eppendorf, Hamburg, Germany).  RNA quality was confirmed using BioAnalyzer 2100 wit RNA 6000 nano kit (Agilent Technologies, Santa Clara, California, USA).  The qualified total RNA (RIN value with 9.5 or above) was used for microarray analysis.

value: astrocyte


title: PRF_rep3

source_name: mouse astrocyte cell line, PRF-treatement


title: 1_0294_009KGenen_s1_tnbc_control_H3K27Ac

city: South San Francisco

first: Suchit

last: Jhunjhunwala

state: CA

address: 1 DNA Way, MS-444A

institute: Genentech

data_processing:
Sequencing reads were aligned to human genome build hg19 with BWA using default parameters (Li 2013).
Alignments were filtered to extract only reads that belonged to matching pairs; pairs of reads that spanned on the average ~350-400 nt and were in the correct orientation. Read pairs with mapping quality 0 (high quality mappings to multiple locations) were not used for further analysis; in addition, presumptive PCR duplicates and reads that did not pass Illumina’s purity filter were removed.
Total number of reads was normalized according to the total number of reads that map to the Drosophila dm3 genome from each sample.
H3K27Ac ChIPseq peaks were called with SICER using input files as control (Zang et al., 2009).
Genome_build: hg19
Supplementary_files_format_and_content: Coverage files in bigWig format were generated by extending reads to 380 nt in silico and counting tags for 50-nt bins over the genome. Tab delimited text files report the genomic location along with the average number of tags for each H3K9me3-enriched regions (ChIPseq peaks).

source_name: MDSC

growth_protocol: Age-matched 6–8 week old female SCID.beige mice were injected with TNBC cell line were inoculated subcutaneously (right unilateral flank) with 5 million tumor cells (MDA.MB.231-X1.1 or CT26) in a final volume of 100 ul in HBSS plus matrigel. Immune cells were isolated from digested tumors [collagenase D (2 mg/ml, Roche) and DNAse (40 U/ml, Roche)] followed by dissociation using gentleMACSTM dissociator (Miltenyi Biotec). Single cell suspensions were stained and total MDSC (CD45+CD11b+Ly6C+Ly6G+/-F4-80-)  were sorted on the BD FACS Aria.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. ChIP reactions were performed in the presence of a constant amount of Drosophila chromatin, corresponding to a minor fraction of the total ChIP DNA, and the Drosophila-specific H2A.v antibody as a means of spike-in normalization amongst different samples.
Illumina sequencing libraries were prepared from the ChIP and input DNAs following standard enzymatic steps consisting of end-polishing, dA-addition, and adaptor ligation. The resulting DNA libraries were quantified and sequenced as 150 bp paired-end reads using Illumina’s HiSeq 2500. The average size of the sequenced fragments were around 380 bp.

treatment_protocol: When tumors reached a mean of 150-200 mm3, mice were grouped out (day 0) and treated with MCT, as vehicle, or 25 mg/kg of CBP/EP300-BRDi (GNE-781), a dose previously determined to have 24-hour IC90 target coverage 36, BID x 7 days, via oral gavage beginning day 1. Animals were dosed for 7 days before tumor digestions and MDSC cell sorting.

tag: chip antibody

value: vehicle


title: PRF_rep2


title: 3_0295_009KGenen_s3_tnbc_treated_H3K27Ac

value: CBP bromodomain inhibitor


title: PRF_rep1


title: Control_rep2


title: Control_rep3


title: 5_029J_009KGenen_Pooled_Input


title: gMDSC-8

data_processing:
Pre-processing: Sequenced reads were pre-processed to remove rRNA and low base quality reads.
Alignment: Reads were aligned to GRcm38 using GSNAP.
Expression: Mouse gene expression was quantified by counting number of uniquely mapped mouse-specific reads to any exon of any transcript isoform from the gene.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab separated tabular files, containing gene expression values (in absolut counts of uniquely mapped genes, and RPKM), and gene widths. Only the coding sequence region (CDS) of the gene was considered for counting mapped reads.

source_name: gMDSC

growth_protocol: Age-matched 6–8 week old female SCID.beige mice were injected with TNBC cell line were inoculated subcutaneously (right unilateral flank) with 5 million tumor cells (MDA.MB.231-X1.1 or CT26) in a final volume of 100 ul in HBSS plus matrigel. Immune cells were isolated from digested tumors [collagenase D (2 mg/ml, Roche) and DNAse (40 U/ml, Roche)] followed by dissociation using gentleMACSTM dissociator (Miltenyi Biotec). Single cell suspensions were stained and mMDSC (CD45+CD11b+Ly6C+Ly6G-F4-80-)   and gMDSC(CD45+CD11b+Ly6C+Ly6G+F4-80-)  were sorted on the BD FACS Aria.

extract_protocol:
Total RNA was isolated from above samples using Illumina TruSeq V2 kit.
Libraries were generated from poly-A-selected RNA

value: gMDSC


title: mMDSC-7

source_name: mMDSC

value: mMDSC


title: gMDSC-6


title: mMDSC-3


title: gMDSC-5


title: gMDSC-4


title: gMDSC-9


title: mMDSC-9


title: mMDSC-8


title: mMDSC-10


title: gMDSC-1


title: gMDSC-10


title: Rmh


title: gMDSC-2


title: gMDSC-7


title: mMDSC-5


title: gMDSC-3


title: iPSC-Vγ9Vδ2 T cells

city: Singapore

first: Jieming

last: Zeng

address: 31 Biopolis Way, The Nanos, #06-01

country: Singapore

institute: Institute of Bioengineering and Nanotechnology

description: Gene expression data from iPSC-derived Vγ9Vδ2 T cells

hyb_protocol: fragmented and labeled 2.3 ug ss cDNA was hybridized for 16 hr on 45 degree C on Hugene ST 2.0 array. It was washed on fluidics station 450

scan_protocol: Genechip were scanned on affymetrix genechip scanner 3000 7G

data_processing:
Data was processed using expression console software from Affymetrix and acoording to RMA
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: iPSC-derived Vγ9Vδ2 T cells

label_protocol: biotinylated and fragmentaed ss-cDNA was prepared as per (Affymetrix WT plus) protocol from 150ug of total RNA

growth_protocol: γδ T-iPSCs were differentiated into mimetic γδ T cells using our previously establised protocol (Stem Reports, 9: 1796, 2017).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: iPSC-derived mimetic γδ T cells were harvested on day 47 of differentiation.

tag: source cell type

value: iPSCs

value: iPSCs were differentiated for 47 days to derive Vγ9Vδ2 T cells


title: mMDSC-4


title: PBC-iPSC#9-NK cells

description: Gene expression data from iPSC-derived NK cells

source_name: iPSC-derived NK cells

value: iPSCs were differentiated for 47 days to derive NK cells


title: mMDSC-1


title: mMDSC-2


title: mMDSC-6


title: TOR1LM_control_ rep2

city: London

first: Patrick

last: Lajoie

state: Ontario

address: 1151 Richmond street

department: Anatomy and Cell Biology

country: Canada

institute: University of Western Ontario

description: Gene expression data from S.cerevesiae carrying wild-type TOR1 or hyperactive TOR1LM following treatment with tunicamycin

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G and AGCC.

data_processing: The data were analyzed with Partek Genomics Suite using the RMA normalization method and ANOVA to generate p-values.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae cells, mid-log phase

label_protocol: Biotinylated cRNA was prepared according to the Affymetrix GeneChip 3' IVT Plus protocol from 100 ng total RNA (Document Number 703210).

growth_protocol: S.cerevisiae cells expressing either a wild-type TOR1 or hyperactive TOR1LM allelle were cultured overnight at 30 degrees (with constant agitation) in YPD media. The next day the cells were diluted to an OD600 =0.2 and grown to log phase (OD600 =0.3)

extract_protocol: RNA extraction was performed using the MasterPure Yeast RNA purification kit (Epicentre) according to the manufacturer's instructions

treatment_protocol: Cultures were either untreated (control) or  treated with 2.5 μg/mL tunicamcyin for 2 hrs

tag: background strain

tag: growth phase

value: mid-log phase

value: untreated control


title: Wild-type_TOR1_tunicamycin_rep2

value: WT

value: tunicamycin


title: Wild-type_TOR1_tunicamycin_rep1


title: Wild-type_TOR1_control_rep1


title: TOR1LM_tunicamycin_ rep1


title: TOR1LM_control_ rep1


title: Wild-type_TOR1_control_rep2


title: TOR1LM_tunicamycin_ rep2


title: P62_wt_1423_2-8_3

city: Saarbrucken

first: Sonja

middle: M.

last: Kessler

address: Campus C2 3

institute: Saarland University

hyb_protocol: Hybridization to Mouse Genome 430 2.0 Affymetrix GeneChips (Santa Clara, CA, USA) was conducted for 16 h at 45°C according to the manufacturer’s instructions.

scan_protocol: Microarrays were scanned with an Affymetrix scanner controlled by Affymetrix Microarray Suite software.

data_processing: Robust Multi-array Average (RMA) algorithm was used for normalization of the gene expression array data

source_name: wildtype

label_protocol: The Gene Chip IVT Labeling kit (Affymetrix, High Wycombe, UK) was used to generate biotinylated cRNA. Purification and fragmentation was performed according to Affymetrix’s protocol.

growth_protocol: Animals were 5 weeks old.

extract_protocol: Total RNA was purified with the RNeasy Mini kit (Qiagen, Hilden, Germany). 2 µg of RNA was used for labeling procedures.

treatment_protocol: Livers were exised after cervical dislocation. Tissues were snap-frozen in liquid nitrogen and stored in -80°C until analysis.

tag: tissue

value: liver

value: wildtype

value: 5 weeks-old


title: P62_wt_1420_6


title: P62_wt_1420_1


title: P62_tg_1423_2-8_4

source_name: p62/IMP2-2 transgenic

value: p62 transgenic


title: P62_tg_1420_4


title: P62_wt_1386_4


title: P62_wt_1420_7


title: P62_tg_1407_3


title: P62_wt_1423_2-8_9


title: P62_tg_1386_9


title: P62_tg_1420_14


title: P62_wt_1371_4


title: P62_wt_1407_5


title: P62_wt_14231_2


title: P62_tg_1407_9


title: P62_tg_1423_2-8_1


title: P62_tg_14231_6


title: P62_tg_1420_12


title: P62_tg_1371_2


title: P62_wt_1407_2


title: Tcell_S1R1D14_CD19CAR_antibody_Donor2

city: Seattle

first: Suzie

last: Pun

state: WA

department: Bioengineering

institute: University of Washington

hyb_protocol: 1.5uL of each cell lysate was hybridized with the nCounter Immunology Panel (Human V2) Reporter CodeSet and Capture ProbeSet at 65C for 16 hours, according to the manufacturer's instructions. The hybridizatoin reactions were loaded onto a nCounter SPRINT Cartridge according to the manufacturer's instructions (maximum of 12 samples per cartridge), which purifies and prepares the hybridized samples for scanning via automated microfluidics.

scan_protocol: The cartridges were scanned by a nCounter SPRINT Profiler, which uses a three-channel epifluorescence scanner and digital analysis system to count the number of each fluorescent reporter tag in each sample lane.

data_processing: The raw data (RCC files) were imported and analyzed in nSolver Analysis Software 4.0 (Nanostring). The data were normalized in groups by day and cell type (D0, S1R1D14 mocks, S1R1D14 CD19 CAR). Two types of normalization were used. First, technical variance (e.g. lane-to-lane variation) was corrected by positive control normalization, which compares the geometric mean of positive controls within a single sample to the global geometric mean of the group of samples being analyzed. Second, differences in RNA input and sample quality were corrected by housekeeping normalization, which compares the geometric mean of mRNA counts from a select group of housekeeping genes within a single sample to the global geometric mean of the group of samples being analyzed. The Advanced Analysis 2.0 software (NanoString) was used to select the housekeeping genes that minimize the pairwise variation statistic.

source_name: CD8+ T cells, S1R1D14 CD19 CAR, antibody-isolated, Donor 2

label_protocol: Standard NanoString protocol.

growth_protocol: On the day of isolation (D0), a 10^6 cell pellet of CD8+ T cells from each isolation method and donor was flash frozen for downstream NanoString nCounter analysis whereas the remaining cells were banked for dowstream CAR T cell production. The CD8+ T cells of both isolation methods from each donor were then later thawed and 3.3 × 10^6 cells for both mock and CD19 CAR T cell groups were stimulated 1:1 with Dynabeads Human T-Activator CD3/CD28 (Invitrogen) in 4 mL complete RPMI with 50 U/μL rhIL-2 (Miltenyi) and 0.5 ng/mL rhIL-15 (Miltenyi) in a 12-well plate. After two days (S1D2), cells designated for CAR T cell production were transduced with clinical-grade PLAT-02 CD19 CAR lentiviral vector (a gift from the City of Hope) at a multiplicity of infection (MOI) of 0.3 with 40 μg/mL protamine sulfate via spinoculation for 30 min at 800xg at 32 oC. Thereafter, media exchanges were conducted every 2-3 days to replenish cytokines, and cells were moved to larger culture vessels when cell concentrations reached 1.5-2 × 106 cells/mL. The activator beads were removed 9-days post-stimulation, termed S1D9. CAR+ cells were magnetically enriched 12-days post-stimulation (S1D12) using biotinylated Erbitux antibody and Anti-Biotin Microbeads per the manufacturer’s instructions. On day 14 post-stimulation (S1D14), the 2-week stimulated T cells were further expanded using a 2-week rapid expansion protocol (REP). Briefly, 1.5 × 10^6 CD19 CAR T cells were co-incubated with 10.5 × 10^6 irradiated CD19+ TM-LCL feeder cells in 25 mL complete RPMI supplemented with the aforementioned cytokine concentrations in T-25 flasks (Corning). Similarly, 1.5 × 10^6 mock T cells were co-incubated with 10 × 10^6 irradiated CD19+ TM-LCL feeder cells and 50 × 10^6 irradiated donor-mismatched PBMC feeder cells in 25 mL complete RPMI supplemented with the same cytokines and 30 ng/mL OKT3 in T-25 flasks (Corning). Cells were maintained as was done over the 2-week activator bead expansion, except OKT3 was replaced only on Day 2. On day 14 post-REP (S1R1D14), a 10^6 cell pellet of each cell lot was flash frozen for downstream NanoString nCounter analysis.

extract_protocol: Thawed cell pellets were resuspended in RLT lysis buffer with β-mercaptoethanol at 3,500 cells/μL.

treatment_protocol: CD8+ T cells isolated from PBMCs using regular antibody-based CD8 Microbeads (Miltenyi) for enrichment. As CAR T cells, they were then transduced with a clinical-grade PLAT-02 CD19 CAR lentiviral vector and expanded using a sequential 2-week stimulation bead outgrowth from days S1D0 to S1D14 and 2-week rapid expansion protocol (REP) with irradiated feeder cells from days S1R1D0 to S1R1D14.

tag: individual

value: Donor 2

tag: cell type

value: CD8+ T Cells

tag: isolation method

value: Antibody

tag: culture time

value: 28 days

tag: bead stim

value: Days 0-9 On, Days 9-14 Off

tag: transduction

value: Clinical-grade PLAT-02 CD19 CAR lentiviral vector on Day 2

tag: post-transduction macs sort

value: EGFRt on Day 12

tag: feeder cells

value: Irradiated CD19+ TM-LCL cells on Day 14, grown until Day 28


title: Tcell_S1R1D14_CD19CAR_antibody_Donor1

source_name: CD8+ T cells, S1R1D14 CD19 CAR, antibody-isolated, Donor 1

value: Donor 1


title: Tcell_S1R1D14_CD19CAR_antibody_Donor3

source_name: CD8+ T cells, S1R1D14 CD19 CAR, antibody-isolated, Donor 3

value: Donor 3


title: Tcell_S1R1D14_CD19CAR_aptamer_Donor1

source_name: CD8+ T cells, S1R1D14 CD19 CAR, aptamer-isolated, Donor 1

treatment_protocol: CD8+ T cells tracelessly isolated from PBMCs using a biotinylated CD8-specific DNA aptamer attached onto Anti-Biotin Microbeads (Miltenyi) for enrichment and complementary reversal agent for label-free release. As CAR T cells, they were then transduced with a clinical-grade PLAT-02 CD19 CAR lentiviral vector and expanded using a sequential 2-week stimulation bead outgrowth from days S1D0 to S1D14 and 2-week rapid expansion protocol (REP) with irradiated feeder cells from days S1R1D0 to S1R1D14.

value: Aptamer


title: UDI48

city: Ghent

first: Celine

last: Everaert

address: De Pintelaan 185

country: Belgium

institute: University Ghent

description: cDNA

data_processing:
Alligment with STAR v2.5.3 :STAR --runThreadN 10 --outFileNamePrefix outdir --readFilesIn sample.fastq --genomeDir star_index --sjdbGTFfile gtf_index --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --twopassMode Basic --outSAMmultNmax 1 --outSAMprimaryFlag AllBestScore --outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 0
Quantification with Kallisto v0.43.1. For polyA: kallisto quant -t 10 -i kallisto_index --single -l 200 -s 20 -o outdir sample.fastq; For total: kallisto quant -t 10 -i kallisto_index –rf-stranded --single -l 200 -s 20 -o outdir sample.fastq
Genome_build: hg38
Supplementary_files_format_and_content: abundance.tsv output for kallisto

source_name: cell line

extract_protocol:
Cells were lysed and cDNA synthesised using the SMART-Seq Stranded Kit (Takara, 634444) or the SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara, 634413) reagents according to the manufacturer’s instructions with some modifications that were also implemented in the C1 SMARTer single cell total RNA sequencing protocol on script hub (Fluidigm).
Total RNA libraries were generated using the SMART-Seq Stranded Kit (Takara, 634444) or the SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara, 634413) reagents according to the manufacturer’s instructions with some modifications that were also implemented in the C1 SMARTer single cell total RNA sequencing protocol on script hub (Fluidigm).

tag: cell line

tag: library preparation kit


title: Tcell_S1R1D14_CD19CAR_aptamer_Donor3

source_name: CD8+ T cells, S1R1D14 CD19 CAR, aptamer-isolated, Donor 3


title: Tcell_S1R1D14_CD19CAR_aptamer_Donor2

source_name: CD8+ T cells, S1R1D14 CD19 CAR, aptamer-isolated, Donor 2


title: Tcell_S1R1D14_mock_antibody_Donor3

source_name: CD8+ T cells, S1R1D14 mock, antibody-isolated, Donor 3

treatment_protocol: CD8+ T cells isolated from PBMCs using regular antibody-based CD8 Microbeads (Miltenyi) for enrichment. As mock cells, they were then expanded using a sequential 2-week stimulation bead outgrowth from days S1D0 to S1D14 and 2-week rapid expansion protocol (REP) with irradiated feeder cells from days S1R1D0 to S1R1D14.

value: Irradiated CD19+ TM-LCL and donor-mismatched PBMC cells on Day 14, grown until Day 28


title: Tcell_S1R1D14_mock_antibody_Donor2

source_name: CD8+ T cells, S1R1D14 mock, antibody-isolated, Donor 2


title: UDI46

description: cDNA


title: Tcell_S1R1D14_mock_aptamer_Donor3

source_name: CD8+ T cells, S1R1D14 mock, aptamer-isolated, Donor 3

treatment_protocol: CD8+ T cells tracelessly isolated from PBMCs using a biotinylated CD8-specific DNA aptamer attached onto Anti-Biotin Microbeads (Miltenyi) for enrichment and complementary reversal agent for label-free release. As mock cells, they were then expanded using a sequential 2-week stimulation bead outgrowth from days S1D0 to S1D14 and 2-week rapid expansion protocol (REP) with irradiated feeder cells from days S1R1D0 to S1R1D14.


title: Tcell_S1R1D14_mock_antibody_Donor1

source_name: CD8+ T cells, S1R1D14 mock, antibody-isolated, Donor 1


title: Patient 2 derived cell line

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

hyb_protocol: Hybridization was conducted at 65C for 17 hours

scan_protocol: An Agilent SureScan Feature Extraction protocol was used to calculate spot-wise intensity and associate intensities with feature locations.

data_processing: Scanned intensities were background corrected and quantile normalized using the limma package in R.

source_name: Derived from Patient 2

label_protocol: RNA was labeled using Agilent Low Input Quick Amp Labeling Kit, following manufacturer specifications for one-color labeling.

growth_protocol: Cells were grown using Conditionally Reprogram technique

extract_protocol: RNA was extracted from samples using Qiagen RNeasy with on-column DNA digestion following manufacturer specfications.

treatment_protocol: P1-n-PTX-R7 and P2-n-PTX-R4 were treated with increasing doses of nab-PTX in order to allow the drug resistance development. They were passed and expanded for analysis in absence of drug. Patient 1 and Patient 2 were grown without special treatment.

value: Pancreas

tag: tumor type

value: Pancreatic ductal Adenocarcinoma

value: Gemcitabine


title: Patient 2 parental sample

source_name: Patient 2

tag: treatment


title: Tcell_S1R1D14_mock_aptamer_Donor2

source_name: CD8+ T cells, S1R1D14 mock, aptamer-isolated, Donor 2


title: Tcell_S1R1D14_mock_aptamer_Donor1

source_name: CD8+ T cells, S1R1D14 mock, aptamer-isolated, Donor 1


title: Patient 1 parental sample

source_name: Patient 1

value: Gemcitabine+ nab-PTX


title: Patient 1 derived cell line

source_name: Derived from Patient 1


title: Tcell_D0_antibody_Donor2

source_name: CD8+ T cells, D0, antibody-isolated, Donor 2

treatment_protocol: CD8+ T cells isolated from PBMCs using regular antibody-based CD8 Microbeads (Miltenyi) for enrichment.

value: 0 days


title: Tcell_D0_antibody_Donor3

source_name: CD8+ T cells, D0, antibody-isolated, Donor 3


title: UDI43

description: cDNA


title: UDI44

description: cDNA


title: Tcell_D0_antibody_Donor1

source_name: CD8+ T cells, D0, antibody-isolated, Donor 1


title: UDI45

description: cDNA


title: UDI42

description: cDNA


title: UDI47

description: cDNA


title: Tcell_D0_aptamer_Donor3

source_name: CD8+ T cells, D0, aptamer-isolated, Donor 3

treatment_protocol: CD8+ T cells tracelessly isolated from PBMCs using a biotinylated CD8-specific DNA aptamer attached onto Anti-Biotin Microbeads (Miltenyi) for enrichment and complementary reversal agent for label-free release.


title: Tcell_D0_aptamer_Donor1

source_name: CD8+ T cells, D0, aptamer-isolated, Donor 1


title: Tcell_D0_aptamer_Donor2

source_name: CD8+ T cells, D0, aptamer-isolated, Donor 2

value: Donor 2


title: UDI35

description: cDNA

source_name: cell line


title: UDI36

description: cDNA


title: UDI39

description: cDNA


title: Tmprss3_D25-KO

city: Miami

first: Pei-Ciao

last: Tang

state: FL

address: 1501 NW 10th Avenue, Miami, FL 33136, 926 F2

department: Otolayrngology

institute: University of Miami

description: scRNA-seq

data_processing:
Single cell 3’ RNA-seq experiment is conducted using the Chromium single cell system (10x Genomics, Inc) and the NovaSeq 6000 sequencer (Illumina, Inc).
Cell Ranger 2.1.0 was utilized to process the raw sequence data generated. Briefly, Cell Ranger used bcl2fastq to demultiplex raw base sequence calls generated from the sequencer into sample-specific FASTQ files.
Processed data were analyzed with the R package Seurat (version 2.3.1) with RStudio version 1.1.453 and R version 3.5.1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx files.

source_name: 3D inner ear organoid

extract_protocol:
Dissociated organoids in TrypLE. Dissociated cells were filtered through 40µM cell strainer followed by three washes in 2% BSA/DPBS. Finally, suspended in 2%BSA/DPBS.
The single cell suspension was first counted on the Countess II FL for cell number, cell viability, and cell size.
Appropriate number of cells were loaded on a multiple-channel micro-fluidics chip of the Chromium Single Cell Instrument (10x Genomics) with a targeted cell recovery of 10,000.
Single cell gel beads in emulsion containing barcoded oligonucleotides and reverse transcriptase reagents were generated with the v2 single cell reagent kit (10X Genomics).
Following cell capture and cell lysis, cDNA was synthesized and amplified. Illumina sequencing library was then prepared with the amplified cDNA. The resulting library was sequenced using a custom program on Illumina NovaSeq 6000.

value: Inner ear organoid

tag: developmental stage

value: Day 25

tag: derived strain

tag: genotype/variation


title: UDI31

description: cDNA


title: UDI30

description: cDNA


title: R1E_D25-WT

description: scRNA-seq


title: UDI34

description: cDNA


title: UDI37

description: cDNA


title: Tmprss3_D35-KO

description: scRNA-seq

value: Day 35


title: R1E_D35-WT

description: scRNA-seq


title: UDI20

description: cDNA


title: UDI22

description: cDNA


title: UDI38

description: cDNA


title: UDI26

description: cDNA


title: UDI21

description: cDNA


title: UDI27

description: cDNA


title: UDI40

description: cDNA


title: UDI29

description: cDNA


title: UDI28

description: cDNA


title: UDI23

description: cDNA


title: UDI15

description: cDNA


title: UDI18

description: cDNA


title: UDI16

description: cDNA


title: UDI14

description: cDNA


title: UDI32

description: cDNA


title: UDI12

description: cDNA


title: UDI24

description: cDNA


title: UDI11

description: cDNA


title: UDI07

description: cDNA


title: UDI05

description: cDNA


title: UDI10

description: cDNA


title: UDI96

description: cDNA

value: Jurkat


title: UDI19

description: cDNA


title: UDI93

description: cDNA


title: UDI94

description: cDNA


title: UDI02

description: cDNA


title: UDI04

description: cDNA


title: UDI86

description: cDNA


title: UDI95

description: cDNA


title: UDI87

description: cDNA


title: UDI92

description: cDNA


title: UDI85

description: cDNA


title: UDI90

description: cDNA


title: UDI79

description: cDNA


title: UDI80

description: cDNA


title: UDI88

description: cDNA


title: UDI13

description: cDNA


title: UDI77

description: cDNA


title: UDI76

description: cDNA


title: EB_8d_RA_TKO_228

city: Mainz

first: Emil

last: Karaulanov

address: Ackermannweg 4

institute: Institute of Molecular Biology

data_processing:
Sample demultiplexing and FastQ file generation was performed using Illumina's bcl2fastq Conversion Software v1.8.4.
The raw sequence reads were quality assessed with FastQC and then aligned to the mouse reference genome (NCBIM37/mm9 build from Illumina iGenomes) using TopHat v.1.4.1 with a GTF transcript annotation file from Illumina iGenomes, Ensembl release 66.
The mapped reads were quality assessed with RSeQC v.2.3.2, sorted with SamTools (v.0.1.19) and summarised on the gene level using htseq-count (HTSeq package v.0.6.1) with option "-s reverse".
Pairwise differential expression analyses were performed using the Bioconductor package edgeR v.3.4.2 following the classic (exactTest) analysis workflow.
Genome_build: NCBIM37/mm9
Supplementary_files_format_and_content: Tab-delimited text file with summarised read counts per gene from htseq-count.

source_name: Gadd45 TKO RA treated embryoid bodies

growth_protocol: 60.000 ESCs per cm^2 were plated on non-adherent cell culture dishes in DMEM supplemented with 10% ESC-grade FBS, 2mM L-Glutamine, 50U/ml Penicillin/Streptomycin, 1xNEAA, 1mM sodium pyruvate, 100µM β-mercaptethanol; including 5µM retinoic acid from differentiation day 5 until day 8 when the cells were harvested

extract_protocol:
RNeasy Mini Kit (Qiagen)
NGS lbrary prep was performed using Illumina's TruSeq Stranded mRNA HT Sample Prep Kit with dual-indexing following Illumina’s standard protocol (Part # 15031047 Rev. D). Libraries were profiled with a DNA 1000 chip on an Agilent 2100 Bioanalyzer and quantified using the Qubit dsDNA HS Assay Kit on a Qubit 2.0 Fluorometer (Life Technologies). All 36 samples were pooled in equimolar ratio and sequenced on 8 HiSeq 2000 lanes for 35 cycles plus additional 16 cycles for the i7 and i5 index reads.

tag: genotype

value: Gadd45 TKO

tag: strain

value: ESCs induced to undergo neuronal differentiation by application of retinoic acid during EB differentiation


title: UDI82

description: cDNA


title: UDI03

description: cDNA


title: UDI06

description: cDNA


title: EB_8d_RA_TKO_227


title: UDI08

description: cDNA


title: UDI72

description: cDNA


title: UDI71

description: cDNA


title: UDI74

description: cDNA


title: EB_8d_RA_Control_283

source_name: Control RA treated embryoid bodies

value: control


title: EB_8d_RA_TKO_36


title: UDI70

description: cDNA


title: UDI66

description: cDNA


title: N2B27_6d_TKO_36

source_name: Gadd45 TKO serum-free monolayer differentiated

growth_protocol: 5.000 ESCs per cm^2 were plated on gelatinized cell culture vessels in regular ESC medium overnight, then cells were washed twice with PBS to remove remaining LIF, and cultured in N2B27 medium (50% Advanced DMEM/F12, 50% Neurobasal, 2mM L-Glutamine, 50U/ml Penicillin/Streptomycin, 50µg/ml BSA, 0.5x N2-supplement, 0.5x B27-supplement) for 6 days

value: ESCs induced to undergo neuronal differentiation by culture in serum-free conditions


title: N2B27_6d_TKO_228


title: N2B27_6d_TKO_227


title: UDI64

description: cDNA


title: N2B27_6d_Control_282

source_name: Control serum-free monolayer differentiated


title: UDI63

description: cDNA


title: UDI62

description: cDNA


title: EB_8d_RA_Control_282


title: N2B27_6d_Control_281


title: UDI60

description: cDNA


title: EB_8d_untreated_TKO_228

source_name: Gadd45 TKO embryoid bodies

growth_protocol: 60.000 ESCs per cm^2 were plated on non-adherent cell culture dishes in DMEM supplemented with 10% ESC-grade FBS, 2mM L-Glutamine, 50U/ml Penicillin/Streptomycin, 1xNEAA, 1mM sodium pyruvate, 100µM β-mercaptethanol

value: ESCs differentiated for 8 days as embryoid bodies


title: UDI58

description: cDNA


title: EB_8d_untreated_TKO_36


title: UDI84

description: cDNA


title: EB_8d_untreated_Control_283

source_name: Control embryoid bodies


title: UDI69

description: cDNA


title: UDI55

description: cDNA


title: EB_8d_untreated_Control_282


title: UDI53

description: cDNA


title: UDI54

description: cDNA


title: UDI56

description: cDNA


title: EB_8d_RA_Control_281


title: mESC_72h_2i_TKO_228

source_name: 2i treated Gadd45 TKO mESCs

growth_protocol: 50% Advanced DMEM/F12, 50% Neurobasal, 2mM L-Glutamine, 50U/ml Penicillin/Streptomycin, 50µg/ml BSA, 0.5x N2-supplement, 0.5x B27-supplement, 1µM PD0325901, 3µM CHIR99021, 4% homemade LIF

value: ESCs cultured for 72h in 2i medium


title: N2B27_6d_Control_283


title: UDI50

description: cDNA


title: mESC_72h_2i_TKO_36


title: mESC_72h_2i_TKO_227


title: UDI52

description: cDNA


title: EB_8d_untreated_TKO_227


title: mESC_72h_VitC_TKO_228

source_name: Vitamin C treated Gadd45 TKO mESCs

growth_protocol: DMEM supplemented with 15% ESC-grade FBS, 2mM L-Glutamine, 50U/ml Penicillin/Streptomycin, 1xNEAA, 1mM sodium pyruvate, 100µM β-mercaptethanol and 4% homemade LIF; treated for 72h before harvest with L-ascorbic acid 2-phosphate sesquimagnesium salt at a final concentration of 100µg/ml

value: Regular serum cultured ESCs treated for 72h with Vitamin C


title: mESC_72h_VitC_TKO_227


title: mESC_72h_VitC_TKO_36


title: mESC_72h_2i_Control_283

source_name: 2i treated control mESCs


title: mESC_72h_2i_Control_281


title: UDI61

description: cDNA


title: mESC_72h_VitC_Control_283

source_name: Vitamin C treated control mESCs


title: mESC_72h_2i_Control_282


title: mESC_untreated_TKO_228

source_name: untreated Gadd45 TKO mESCs

growth_protocol: DMEM supplemented with 15% ESC-grade FBS, 2mM L-Glutamine, 50U/ml Penicillin/Streptomycin, 1xNEAA, 1mM sodium pyruvate, 100µM β-mercaptethanol and 4% homemade LIF

value: Regular serum cultured ESCs


title: EB_8d_untreated_Control_281


title: mESC_72h_VitC_Control_282


title: mESC_72h_VitC_Control_281


title: mESC_untreated_TKO_227


title: mESC_untreated_Control_283

source_name: untreated control mESCs


title: mESC_untreated_Control_282


title: mESC_untreated_Control_281


title: mESC_untreated_TKO_36


title: 4082 2

city: Cologne

first: Aleksandra

last: Trifunovic

address: Joseph-Stelzmann-Str. 26

institute: Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases

data_processing:
The ChIP-Seq workflow takes advantage of BWA for genomic alignment of the reads. Reads was mapped to the caenorhabditis_elegans (Ensembl database version 93).
Quality check of sequencing data were performed with FastQC version0.10.1.
For peak calling used MACS2 version 2.0.10.
QuickNGS pipeline identifies all genes which are 2000 bp up- or downstream from the MACS2 peaks.
The peak sequences are analyzed for enrichment of transcription factor binding motifs using MEME-ChIP Version 4.10.0.
Genome_build: Ensembl 93
Supplementary_files_format_and_content: The results comprise lists of significant peaks and reports for motif enrichment.

source_name: Whole organism

growth_protocol: Worms were synchronized by treating with alkaline hypochlorite solution.

extract_protocol:
Lysates were sonicated and cleared by centrifugation. Protein-DNA complexes were pulled-down using GFP-TRAP (Chromotek).
Libraries were prepared by using the Illumina TruSeq DNA Nano Kit with some modifications. The preparation was started with the end repair step of the protocol. Up to 100ng ChIP/Input DNA was used as starting material. After end repair and A-tailing dual indexing adapters were ligated. The products were then purified and amplified (12 PCR cycles for the Input Samples and 15 cycles for the ChIP Samples) to create the final libraries. After validation (Agilent 4200 TapeStation) each single library was quantified by using the Roche KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System. The libraries were then pooled equimolar. Finally the pool was sequenced on one Illumina HiSeq4000 lane 1x51bp (51+8+8).

treatment_protocol: Worms were plated as eggs on plates seeded with HT115 bacterial strain, carrying L4440 plasmid.

value: First day of adulthood

tag: tissue

value: Whole body

tag: antibody

value: GFP-TRAP (Chromotek; Cat. #gtma-20; Lot. 81025001MA)


title: 4082 3


title: Input 4082 3


title: 4082 1


title: 4081 2


title: Input 4082 1


title: 4081 1


title: 4081 3


title: Input 4082 2


title: Input 4081 3


title: Input 4081 2


title: RNA-Seq_C59D2, rep2

status: Public on May 30 2019

city: Berkeley

first: Robert

last: Tjian

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

description:
Homozygote cell line with endogenously tagged CTCF and Rad21 loci; CTCF RNA binding region deleted.
Total RNA (ribosomal RNA depleted).
processed data file: C59D2_1_2_RNAseq_coverage.bw
processed data file: C59D2_vs_C59_edgeR.txt
processed data file: C59D2_vs_C59_DeSeq2.txt

data_processing:
Base-calling performed with CASAVA by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley.
RNA-Seq reads quality control performed with FastQC (version 0.10.1).
RNA-Seq reads were aligned to the mm10 genome assembly using STAR RNA-Seq aligner (version 2.7) with the following options: --outSJfilterReads Unique --outFilterMultimapNmax 1 --outFilterIntronMotifs RemoveNoncanonical --outSAMstrandField intronMotif
We used Samtools (version 1.9) to convert STAR output .sam files into .bam files, and to sort and index them.
We used HTSeq (version 0.11.1) to count how many reads overlapped an annotated gene (GENECODE vM19 annotations) with the following options: htseq-count --stranded=no -f bam --additional-attr=gene_name -m union).
bigWig coverage files were generated with deepTools (version 2.4.1) with the following configurations: bamCoverage -of bigwig --binSize 50 --normalizeTo1x 2150570000 --extendReads 300 --ignoreDuplicates
Genome_build: mm10
Supplementary_files_format_and_content: *_RNAseq_coverage.bw: bigWig files containing the number of reads per 50 bp bins normalized to 1x sequencing depth (Reads Per Genomic Content).
Supplementary_files_format_and_content: *_htseq_counts.txt: Text files containing HTSeq raw read counts for Ensembl transcripts (GENECODE vM19 annotations).
Supplementary_files_format_and_content: C59D2_vs_C59_DeSeq2.txt: Text file containing edgeR differential expression analysis output (C59D2 vs. C59; GeneID, EnsGeneID, logFoldChange, logCPM, F, PValue, FDR, FoldChange, CHANGE).
Supplementary_files_format_and_content: C59D2_vs_C59_edgeR.txt: Text file containing DeSeq2 differential expression analysis output (C59D2 vs. C59; GeneID, EnsGeneID, Base mean, log2(FoldChange), StdErr, Wald-Stats, P-value, P-adj, FoldChange, CHANGE).

source_name: embryonic stem cells

growth_protocol: JM8.N4 mouse embryonic stem cells were grown on plates pre-coated with a 0.1% autoclaved gelatin solution (Sigma-Aldrich, G9391) under feeder free condition in knock-out DMEM with 15% FBS and LIF (full recipe: 500 mL DMEM (ThermoFisher#10829018), 6 mL MEM NEAA (ThermoFisher #11140050), 6 mL GlutaMax (ThermoFisher#35050061), 5 mL Penicillin-streptomycin (ThermoFisher #15140122), 4.6 μL 2-mercapoethanol (Sigma-Aldrich M3148), 90 mL fetal bovine serum (HyClone FBS SH30910.03 lot #AXJ47554)). mES cells were fed by replacing half the medium with fresh medium daily and passaged every two days by trypsinization.

extract_protocol:
RNA was extracted with the QIAGEN RNeasy Mini Kit according to manufacturer’s instructions, lysing cells directly into 6-well plates with buffer RTL plus. 5 µg of the eluted RNA were treated with DNase I in a 25-µl reaction at 37 °C for 30' (Invitrogen DNA-free™ DNA Removal Kit). DNA-free RNA was quantified by nanodrop and quality checked by Bioanalyzer and 2.5 µg were subjected to ribosomal RNA depletion following Illumina Ribo-zero rRNA Removal Kit's instructions. Precipitated RNA was resuspended to 17 µl End Repair Mix (ERP) from the TruSeq RNA Sample Preparation v2 Kit (Illumina RS-122-2001) and stored overnight at -80 °C until library preparation.
RNA fragmentation, first and second strand cDNA synthesis were performed according to the TruSeq RNA Sample Preparation v2 Kit but using Superscript III for reverse transcription instead of Superscript II (50 °C for 50' incubation time). cDNA was purified with AMPure XP beads diluted 1:2 with 20% PEG, 1.25M NaCl, and eluted in 38.5 μl 10 mM Tris-HCl pH 8.0, 36.5 μl of which were transferred to a new tube and subjected to the ChIP-Seq Solexa rapid library protocol (see linked manuscript).

value: FLAG-Halo-CTCF/Rad21-SNAPf-V5 Knock-in

tag: ctcf protein


title: RNA-Seq_C59D2, rep1


title: RNA-Seq_C59, rep2

description:
Homozygote cell line with endogenously tagged CTCF and Rad21 loci.
Total RNA (ribosomal RNA depleted).
processed data file: C59_1_2_RNAseq_coverage.bw
processed data file: C59D2_vs_C59_edgeR.txt
processed data file: C59D2_vs_C59_DeSeq2.txt

value: wild type


title: Input 4081 1


title: RNA-Seq_C59, rep1


title: Micro-C_C59D2_RBRd-CTCF_QC_rep2 (RTTH011)

description: Homozygote cell line with endogenously tagged CTCF and Rad21 loci; CTCF RNA binding region deleted

data_processing:
Library strategy: Micro-C
Base-calling performed with CASAVA by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley
ChIP-seq reads quality control performed with FastQC (version 0.10.1)
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie (version 0.12.8) with the following configurations: -n 2 -m 1
ChIP-seq reads for spike-in normalization were aligned to the sacCer3 genome assembly using bowtie (version 0.12.8) with the following configurations: -n 2 -m 1
We used samtools (version 1.9) to remove duplicates from mapped reads (rmdup -s), merge ChIP-seq replicates, and sort and index .bam files
ChIP-Seq peaks were called using MACS2 (version 2.1.0.20140616) with the following configurations: -t <sample.bam>  -c <input.bam> -f BAM -g mm --nomodel --extsize 300
bigWig coverage files were generated with deepTools (version 2.4.1) with the following configurations: bamCoverage -of bigwig --binSize 50 --normalizeTo1x 2150570000 --extendReads 300 --ignoreDuplicates
Spike-in normalized, bigWig files were generated with deepTools (version 2.4.1) with the following configurations: bamCoverage -of bigwig --binSize 50 --scaleFactor n --extendReads 300 --ignoreDuplicates, where n is calculated using unique alignments to S. cerevisiae genome
allValidPairs were generated by HiC-Pro package (>2.10 version)
mcool files were converted from allValidPairs by Cooler package
hic file were converted from allValidPairs by Juicer tools
Genome_build: mm10, sacCer3
Supplementary_files_format_and_content: text files containing ChIP-Seq peak genomic coordinates (mm10), length, summit, pileup, pvalue, qvalue and fold enrichment over input as determined by MACS2
Supplementary_files_format_and_content: bigWig files containing the number of reads per 50 bp bins normalized to 1x sequencing depth (Reads Per Genomic Content)
Supplementary_files_format_and_content: Spike-in normalized bigWig files
Supplementary_files_format_and_content: allValidParis file contains 1) read name, 2) chromosome of first locus, 3) read position of first locus,  4) strand of first locus, 5) chromosome of second locus, 6) read position of second locus, 7) strand of second locus, 8) DNA fragment lengh, 9) name of first restriction fragment, 10) name of second restiction fragment, 11) mapping quality of first read, 12) mapping quality of second read.
Supplementary_files_format_and_content: mcool file contains all valid Micro-C pairs stored in HDF5 format with mutiple resolutions
Supplementary_files_format_and_content: hic file contains all valid Micro-C pairs with mutiple resolutions

extract_protocol:
Micro-C protocol was performed as the following steps: 1) digest crosslinked chromatin by MNase; 2) Repair fragment ends with biotin-dNTP; 3) Proximal ligation and purge unligated ends; 4) Purify ligated dinucleosomal DNA.
Purified DNA with biotin-dNTPs was captured by Dynabeads® MyOne™ Streptavidin C1. Standard library preparation protocol including end-repair, A-tailing, and adapter ligation was performed on beads with individual enzymes purchased from Lucigen or NEBnext UltraII kit. Sequencing library was amplified by Kapa HiFi PCR enzyme with lowest possible cycles to reduce PCR duplicates. Sequencing library was sequenced paired-end 50x50 in Illumina HiSeq 4000 sequencer.

treatment_protocol: Cells were crosslinked by 1% formaldehyde for 10 min at room temperature. Formaldehyde reaction was quenched by 0.75M Tris. After two times of PBS washes, cells were then crosslinked by 3mM DSG for 45 min at room temperature. After two times of PBS washed, cell pellets were snap frozen or subjected to the following protocols.

value: JM8.N4 mouse embryonic stem cell line

value: ΔRBR (N576_D611del::GDGAGLINS-3xHA)


title: Micro-C_C59D2_RBRd-CTCF_highCov (RTTH020B)


title: Micro-C_C59D2_RBRd-CTCF_QC_rep1 (RTTH010)


title: Micro-C_C59_wt-CTCF_QC_rep2 (RTTH009)

description: Homozygote cell line with endogenously tagged CTCF and Rad21 loci


title: Micro-C_C59_wt-CTCF_QC_rep1 (RTTH008)


title: C59D2_CTCF_ChIPSeq (RTCC27H)

data_processing:
Base-calling performed with CASAVA by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley
ChIP-seq reads quality control performed with FastQC (version 0.10.1)
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie (version 0.12.8) with the following configurations: -n 2 -m 1
ChIP-seq reads for spike-in normalization were aligned to the sacCer3 genome assembly using bowtie (version 0.12.8) with the following configurations: -n 2 -m 1
We used samtools (version 1.9) to remove duplicates from mapped reads (rmdup -s), merge ChIP-seq replicates, and sort and index .bam files
ChIP-Seq peaks were called using MACS2 (version 2.1.0.20140616) with the following configurations: -t <sample.bam>  -c <input.bam> -f BAM -g mm --nomodel --extsize 300
bigWig coverage files were generated with deepTools (version 2.4.1) with the following configurations: bamCoverage -of bigwig --binSize 50 --normalizeTo1x 2150570000 --extendReads 300 --ignoreDuplicates
Spike-in normalized, bigWig files were generated with deepTools (version 2.4.1) with the following configurations: bamCoverage -of bigwig --binSize 50 --scaleFactor n --extendReads 300 --ignoreDuplicates, where n is calculated using unique alignments to S. cerevisiae genome
allValidPairs were generated by HiC-Pro package (>2.10 version)
mcool files were converted from allValidPairs by Cooler package
hic file were converted from allValidPairs by Juicer tools
Genome_build: mm10, sacCer3
Supplementary_files_format_and_content: text files containing ChIP-Seq peak genomic coordinates (mm10), length, summit, pileup, pvalue, qvalue and fold enrichment over input as determined by MACS2
Supplementary_files_format_and_content: bigWig files containing the number of reads per 50 bp bins normalized to 1x sequencing depth (Reads Per Genomic Content)
Supplementary_files_format_and_content: Spike-in normalized bigWig files
Supplementary_files_format_and_content: allValidParis file contains 1) read name, 2) chromosome of first locus, 3) read position of first locus,  4) strand of first locus, 5) chromosome of second locus, 6) read position of second locus, 7) strand of second locus, 8) DNA fragment lengh, 9) name of first restriction fragment, 10) name of second restiction fragment, 11) mapping quality of first read, 12) mapping quality of second read.
Supplementary_files_format_and_content: mcool file contains all valid Micro-C pairs stored in HDF5 format with mutiple resolutions
Supplementary_files_format_and_content: hic file contains all valid Micro-C pairs with mutiple resolutions

extract_protocol:
Cells were washed twice with ice-cold PBS, scraped, centrifuged for 10 min at 4000 rpm, resuspended in cell lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, and 0.5% NP-40, 1 ml/15 cm plate) and incubated for 10 min on ice. Lysates were then centrifuged for 10 min at 4000 rpm.  Nuclear pellets were resuspended in 6 volumes of sonication buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 0.1% SDS), incubated on ice for 10 min, and sonicated to obtain DNA fragments below 2000 bp in length (Covaris S220 sonicator, 20% Duty factor, 200 cycles/burst, 100 peak incident power, 50 cycles of 30" on and 30" off).  Sonicated lysates were cleared by centrifugation and 400-800 μg of chromatin was diluted in RIPA buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl) to a final concentration of 0.8 μg/μl, precleared with Protein A sepharose (GE Healthcare) for 2 hours at 4°C and immunoprecipitated overnight with 4-8 μg of antibodies.  About 15% of the precleared chromatin was saved as input.  Immunoprecipitated DNA was purified with the Qiagen QIAquick PCR Purification Kit, eluted in 60 μl of water and used for library preparation.
Solexa rapid prep (see linked manuscript)

treatment_protocol: Cells were cross-linked for 5 minutes at room temperature with 1% formaldehyde-containing medium; cross-linking was stopped by PBS-glycine (0.125 M final).

tag: chip antibody

value: CTCF (Abcam ab128873)


title: Micro-C_C59_wt-CTCF_highCov (RTTH020A)


title: C59D2_Smc1a_ChIPSeq (RTCC27G)

value: Scm1a (Bethyl Laboratories Inc. A300-055A)


title: C59D2_IgG_ChIPSeq (RTCC27F)

value: Rabbit normal IgG (Jackson ImmunoResearch 011-000-002)


title: C59D2_input (RTCC27E)


title: C59_input (RTCC27A)


title: C59_Smc1a_ChIPSeq (RTCC27C)


title: C59_CTCF_ChIPSeq (RTCC27D)


title: C59_IgG_ChIPSeq (RTCC27B)


title: UDI68

description: cDNA

value: Jurkat


title: PB9 D3 16562

status: Public on May 29 2019

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

institute: Genome institute of Singapore

description: Flavivirus

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Genome Studio (Illumina) was used to subtract background from raw gene expression intensity data. Standard normalization procedures for 1-color array data and data analysis to identify differentially expressed genes were performed using the GeneSpring GX software, version 12.5 (Agilent Technologies). Significantly regulated genes (p<0.05 with a cutoff of 1.5-fold change in treated compared to untreated samples) were analyzed with IPA and GSEA.

source_name: pathogenic DENV-3 16562, MOI=1

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit for Illumina arrays

extract_protocol: Total RNA isolated with Trizol following manufacturer's recommendations

treatment_protocol: Human PBMCs isolated from healthy donors (10^7 per condition) were treated for 48 hours with the indicated flaviviruses or adjuvants

tag: cell type

value: PBMC

tag: donor

value: donor 4

value: pathogenic DENV-3 16562, 10^6 PFUS


title: PB9 R848

description: TLR7/8 agonist

value: TLR7/8 agonist


title: PB9 PolyIC

description: TLR3 agonist

source_name: 5µg/ml PolyI:C

value: TLR3 agonist


title: PB9 ODN 2006

description: TLR9 agonist

source_name: 5µg/ml ODN2006

value: TLR9 agonist


title: PB9 D3 PGMK

description: Flavivirus

source_name: live-attenuated DENV-3 PGMK30Fh3, MOI=1

value: live-attenuated DENV-3 PGMK30Fh3, 10^6 PFUs


title: PB9 Mock

description: Untreated

source_name: Untreated

value: Untreated


title: PB9 LPS

description: TLR4 agonist

source_name: 1µg/ml LPS

value: TLR4 agonist


title: PB9 D2 PDK53

description: Flavivirus

source_name: live-attenuated DENV-2 PDK53, MOI=1

value: live-attenuated DENV-2 PDK53, 10^6 PFUs


title: PB8 Pam3SCK4

description: TLR2 agonist

source_name: 2.5µg/ml Pam3CSK4

value: donor 1

value: TLR2 agonist


title: PB8 LPS

description: TLR4 agonist


title: PB8 ODN 2006

description: TLR9 agonist


title: PB9 D2 16681

description: Flavivirus

source_name: pathogenic DENV-2 16681, MOI=1

value: pathogenic DENV-2 16681, 10^6 PFUs


title: PB8 D3 PGMK

description: Flavivirus


title: PB8 Mock

description: Untreated


title: PB8 D2 PDK53

description: Flavivirus


title: PB7 D2 PDK53

description: Flavivirus

value: donor 3


title: PB7 D3 PGMK

description: Flavivirus


title: PB9 YFV17D

description: Flavivirus

source_name: live-attenuated YFV-17D, MOI=1

value: live-attenuated YFV-17D, 10^6 PFUs


title: PB9 Pam3SCK4

description: TLR2 agonist


title: PB9 Alum

description: Aluminium hydroxide

source_name: Alhydrogel 2%

value: Aluminium hydroxide


title: PB8 YFV17D

description: Flavivirus


title: PB8 D2 16681

description: Flavivirus


title: PB8 D3 16562

description: Flavivirus


title: PB8 R848_donor1

description: TLR7/8 agonist


title: PB8 PolyIC

description: TLR3 agonist


title: PB7 ODN 2006

description: TLR9 agonist


title: PB8 Alum

description: Aluminium hydroxide


title: PB7 D2 16681

description: Flavivirus


title: PB7 YFV17D

description: Flavivirus


title: hcr1-delta HCR1-CTD DY139F

status: Public on May 23 2019

city: Bethesda

first: Nicholas

last: Guydosh

state: MD

address: 8 Center Dr, Bldg 8, 220

department: NIDDK

institute: National Institutes of Health

description:
hcr1-delta HCR1-CTD
Ribosome-protected RNA 25-34 nt

data_processing:
Base calling and demultiplexing was performed at the NIDDK Genomics Core at the NIH Intramural program, Bethesda, MD.
Files were demultiplexed and filtered to remove low-quality reads. They were then trimmed to the start of the linker sequence. Contaminating sequences that corresponded to gel markers were eliminated.
Reads were aligned to a library of RNA genes and those not matching were retained.
Reads were then aligned to the genome and those not matching to a custom library of splice junctions by using Bowtie (Langmead et al., 2009). For footprints, reads that did not match in these steps were trimmed of consecutive 3' As and realigned. The aligned reads from all alignment rounds were pooled and normalized to units of reads per million (rpm) (by dividing by the total number of million mapped reads in a sample) to generate wig files.
Replicates or multiple sequencing lanes for a given sample were pooled together to create a single wig file for each condition to be used in downstream analysis.
Genome_build: R64-1-1
Supplementary_files_format_and_content: All files are fixedStep wig files (text format, each line representing one position in the genome).

source_name: Whole cells

growth_protocol: Cells were generally grown to an OD of ~0.6 and harvested.

extract_protocol:
Ribosome profiling lysates were clarified, RNase treated, and run over sucrose gradients to extract the monosome peak. RNA was then extracted using SDS/hot phenol/chloroform and footprints of the specified size were retained by gel purification.
Briefly, RNAs were ligated to a universal DNA linker followed by reverse transcription. cDNAs were then circularized and PCR amplified. Ribosome profiling circularized cDNA was subject to ribosomal RNA subtraction using custom biotinylated oligos in some cases. In others, Ribo-Zero was used. RNA-Seq samples were prepared with the Illumina Truseq Stranded ribo-zero kit.

treatment_protocol: Cells were rapidly vacuum filtered and flash frozen. Ribosome profiling samples were lysed in a freezer mill with lysis buffer. Total RNA for mRNA-Seq was extracted from whole cells.

value: hcr1-delta HCR1-CTD


title: PB7 D3 16562

description: Flavivirus

value: PBMC


title: tma64-deltatma20-delta hcHCR1 DY145F

description:
tma64-deltatma20-delta hcHCR1
Ribosome-protected RNA 25-34 nt

value: tma64-deltatma20-delta hcHCR1


title: UDI78

description: cDNA

source_name: cell line

value: Jurkat


title: PB7 PolyIC

description: TLR3 agonist


title: PB7 LPS

description: TLR4 agonist


title: hcr1-delta HCR1-NTD DY138F

description:
hcr1-delta HCR1-NTD
Ribosome-protected RNA 25-34 nt

value: hcr1-delta HCR1-NTD


title: tma64-deltatma20-delta YEplac195 DY144F

description:
tma64-deltatma20-delta YEplac195
Ribosome-protected RNA 25-34 nt

value: tma64-deltatma20-delta YEplac195


title: PB6 R848

description: TLR7/8 agonist

value: donor 2

value: TLR7/8 agonist


title: hcr1-delta DY115F

description:
hcr1-delta
Ribosome-protected RNA 25-34 nt
Biological replicate of DY114F. Wig files composed of combination of two biological replicates (DY114F and DY115F).


title: PB6 D3 16562

description: Flavivirus

value: pathogenic DENV-3 16562, 10^6 PFUS


title: PB7 Mock

description: Untreated

value: Untreated


title: PB6 D3 PGMK

description: Flavivirus

value: live-attenuated DENV-3 PGMK30Fh3, 10^6 PFUs


title: PB6 Alum

description: Aluminium hydroxide


title: PB6 LPS

description: TLR4 agonist

value: TLR4 agonist


title: PB6 YFV17D

description: Flavivirus


title: PB6 PolyIC

description: TLR3 agonist

value: TLR3 agonist


title: PB7 Pam3SCK4

description: TLR2 agonist

value: TLR2 agonist


title: PB6 D2 PDK53

description: Flavivirus

value: live-attenuated DENV-2 PDK53, 10^6 PFUs


title: PB6 Pam3SCK4

description: TLR2 agonist