title: Methylation_MDA-MB-231-6

type: genomic

description: Methylation data

hyb_protocol: The resultant bisulfite-converted DNA was processed and hybridized to the Illumina Infinium Methylation EPIC Bead Chip.

scan_protocol: Subsequently, it was fluorescently stained and scanned on an Illumina iScan according to the Infinium HD Assay Methylation Protocol Guide provided by Illumina.

data_processing:
DNA methylation data was preprocessed and normalized using Bioconductor packages minfi and watermelon (ref ). Briefly, the function “preprocessNoob” (minfi) was used to correct for background fluorescence and dye biases within an array. Next, probes and samples with poor quality were identified and removed. Therefore, samples with more than 10% of probes that had detection p-values >1x10-5 or samples whose intensity distributions demonstrated irregularities were excluded (ref ). Furthermore, Illumina removed 1031 CpG probes when transitioning to their B1 version of the MethylationEPIC v1.0 manifest due to poor performance and additional probes in the transition from their B2 to their B3 version (ref ). In addition to probes flagged by Illumina, we also excluded probes with a median detection p-value >0.05 from the subsequent statistical analysis. Next, we corrected the type II probe bias using the function “BMIQ” (wateRmelon) to achieve a comparable methylation distributions of type I and II probes (ref ). All single nucleotide polymorphism (SNP)-CpG interaction or cross-reactive probes were flagged and excluded from the downstream analyses in order to reduce the bias of the results. The DNA -methylation data were analyzed using the R statistical programming language (version 3.6).
Processed data provided as M values and comparisons

label_protocol: not provided

extract_protocol: Genomic DNA (500 ng) was bisulfite treated and purified using the EZ DNA Methylation-Gold kit (Zymo Research, Irvine, CA) according to the manufacturer’s protocol (Bibikova et al).

value: breast cancer


title: HCC1937-1

status: Public on Jul 01 2021

type: SRA

city: Little Rock

first: Allen

last: Gies

state: AR

address: 4301 W. Markham

department: Biochemistry and Molecular Biology

country: USA

institute: University of Arkansas for Medical Sciences

library_source: transcriptomic

data_processing:
Fastq reads Trimmed with Trimmomatic 0.39
Trimmed reads aligned with STAR 2.7.1a
RNAseq Counts obtained by featureCounts 2.0.0
Genome_build: GRCh38 Ensemble release 99 Homo sapiens
Supplementary_files_format_and_content: txt feature counts

molecule: total RNA

organism: Homo sapiens

source_name: ATCC CRL-2336: established from a grade III infiltrating ductal primary breast tumor from a patient with a germ-line BRCA1 mutation

growth_protocol: MCF10A cells were cultured in DMEM/F12 supplemented with 20ng/mL hEGF, 100ng/mL cholera toxin, 10ug/mL bovine insulin, 500ng/mL hydrocortisone, 5% horse serum, and 1% Penicillin/Streptomycin. MDA-MB-231 cells were cultured in DMEM and supplemented with 10% FBS and 1% Penicillin/Streptomycin. HCC1937 cells were cultured in RPMI supplemented with 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol:
RNAseq #74101 (RNAseq)
Illumina TruSeq Stranded mRNA Sample Preparation Kit v2

tag: cell type

value: BRCA1-wild-type ductal primary breast tumor

tag: cell line


title: HTR-8 shNC_rep3

type: RNA

city: Guangzhou

first: Chonghui

last: Hu

state: Guangdong

address: 106 Zhongshan Er Road

department: Department of General Surgery

country: China

institute: Guangdong Provincial People's Hospital

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing:
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
affymetrix-array-type = PrimeView
program-name = Expression Console
program-version = 1.4.1.46

label: biotin

source_name: HTR-8 shNC

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was extracted using TRIzol reagent (Life technology, Carlsbad, CA, USA) according to the manufacturer's instruction. The RNA concentration was measured and complementary DNA was synthesized using reverse transcriptase kit (Takara, Dalian, China) according to the instruction.

tag: tissue

value: placenta

value: human extravillous trophoblast

tag: genotype/variation

value: control


title: HTR-8 shCSRP2BP_rep3

source_name: HTR-8 shCSRP2BP

value: CSRP2BP knockdown by specific shRNA (CSRP2BP-shRNA)


title: MDA-231-1

source_name: ATCC HTB-26;  isolated from a pleural effusion of a patient with invasive ductal carcinoma.

value: Triple-Negative Breast Cancer


title: Developing mouse embryo sections G12G01_S276

city: Seattle

first: Sanjay

middle: R

last: Srivatsan

state: WA

address: 3720 15TH Ave NE Genome Sciences S Foefe Bldg

department: Genome Sciences

institute: University of Washington

description:
Developing mouse embryo sections
sci-Space Slides 1-6
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell

data_processing:
Basecalls performed using bcl2fastq version 2.20
Poly-dT adapters were trimmed using Trimmomatic and aligned to mm10 using STAR. Mapped reads were then deduplicated and assigned to a gene (GENCODE vM15 - mouse). UMIs were enumerated for each cell/gene combination and finally a count matrix was made.
Count matrix was loaded into Monocle3 for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: Count Matrix (matrix marker file- .mtx), Cell Metadata (tab separated values- .tsv), Gene Metadata (tab separated values- .tsv)

molecule: polyA RNA

organism: Mus musculus

source_name: E14 saggital sections 8-10um thick

extract_protocol:
Nuclei were extracted with a permeabilization buffer, sonicated and fixed. cDNA molecules within nuclei are extracted after tagmentation through the use of denaturants.
3' end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis, tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it, a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.

tag: genotype

value: E14 Mouse Embryo

tag: sample type

value: Sagigital section


title: F3LHplus7

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

description:
Paired with corresponding F3LHplus2
counts_exp2.txt.gz

data_processing:
Low quality reads and Illumina adapters were trimmed using Trimmomatic (version 0.36)
Retained reads were mapped to the reference human genome, GRCh38, using STAR (version 2.5.3a)
Uniquely mapped reads were assigned to the corresponding genes using the featureCounts function in the Rsubread R package. Only reads mapped to exons were considered in the counting procedure. Genomic features were annotated according to Gencode basic annotations (Gencode version 26 for samples 1-20;  Gencode version 27 for samples 21-93)
Genome_build: UCSC hg38
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

source_name: Uterine fluid derived Extracellular Vesicles

extract_protocol:
Endometrial tissue biopsies were obtained with the use of a Pipelle, immediately after UF sampling. Uterine fluid samples were obtained by lavage of the endometrial cavity with 2.5 of physiologic solution using a balloon hysterosonosonography catheter to avoid vaginal contamination. Extracellular vesicles were isolated- after mucus disgregation by vortexing- using standard ultracentrifugation protocol.  RNA was harvested using  RNase micro KIT of QIAGEN with DNAse treatment step in coloumn.
To compare the transcriptomic profile of tissues and UF-Evs (samples 1-20), cDNA libraries were generated from total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen GmbH, Vienna, Austria). To perform transcriptome sequencing on UF-EVs collected from fertile women and ART patients during the window of implantation (samples 21-93), cDNA libraries were prepared using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio Inc., Otsu, Shiga, Japan)

tag: population

value: Provenly fertile control women

tag: menstrual cycle phase

value: secretory

tag: mentrual cycle day (counted from the first day of menstrual bleeding and expressed as n or from the day of urinary lh surge detection and expressed an lh+n)

value: LH+7 (within window of implantation)


title: REB057: MG1655 wt stat rep 3

city: Singapore

first: Swaine

middle: L

last: Chen

state: Singapore

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

department: Medicine

country: Singapore

institute: National University of Singapore and Genome Institute of Singapore

data_processing:
Raw sequencing reads were mapped to their respective reference genomes: RefSeq accession GCF_000013265.1 for E. coli UTI89, GCF_000005845.2 for E. coli MG1655 and GCF_000007445.1 for E. coli CFT073 using BWA-MEM (version 0.7.10) with default parameters, then the resulting bam files were sorted and deduplicated using PicardTools v.2.2.2
HTseq was used to quantify sequencing reads mapping to predicted open reading frames (ORFs)
Ribosomal RNA (rRNA) and transfer RNA (tRNA) sequences (based on the corresponding Genbank RefSeq annotation) were filtered out of the data set.
R (version 2.15.1) was used for differential expression analysis, using the edgeR package (samples were normalized by TMM (trimmed median of means), common and tagwise dispersion factors were estimated using a negative binomial model, and then fold change values were calculated from these normalized counts)
Genome_build: RefSeq accession GCF_000013265.1 for E. coli UTI89, GCF_000005845.2 for E. coli MG1655 and GCF_000007445.1 for E. coli CFT073
Supplementary_files_format_and_content: Tab-delimited text files with normalized expression values, fold change, P-values, and FDR values.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: MG1655 wt

growth_protocol: Stationary phase cells were obtained by propagating strains statically for two serial 24 hour passages at 37°C, with a 1:1000 dilution between passages (identical to the inoculum used for mouse infections). Log phase cells were obtained by diluting overnight cultures 1:100 in LB and growing to log phase (OD600 = 0.4 – 0.5) at 37°C with shaking.

extract_protocol:
RNA extraction with the Qiagen RNAEasy Mini Kit; ribosomal depletion with the Ribo Zero rRNA removal kit
RNA libraries were prepared using the ScriptSeq v2 RNA-seq library preparation kit

tag: strain

tag: growth condition

value: stationary phase

value: wt


title: Developing mouse embryo sections G11G05_S83


title: F3LHplus2

description:
Paired with corresponding F3LHplus7
counts_exp2.txt.gz

value: Uterine fluid derived Extracellular Vesicles

value: LH+2 (pre-receptive phase)


title: Methylation_MDA-MB-231-5

description: Methylation data

molecule: genomic DNA


title: F2LHplus7

description:
Paired with corresponding F2LHplus2
counts_exp2.txt.gz


title: porcine lung_treated_rep2

city: Leipzig

first: Bruno

last: Christ

state: Saxony

address: Liebigstraße 21

department: Department of Surgery

country: Germany

institute: University of Leipzig

description: Gene expression data from lung biopsy

hyb_protocol: Following fragmentation, biotynilated cDNA were hybridized to Affymetrix Porcine Gene 1.0 ST arrays for 16 h at 45° C in a GeneChip hybridization oven 640. Hybridized arrays were washed and stained in an Affymetrix Fluidics Station FS450.

scan_protocol: Signals were measured with an Affymetrix GeneChip Scanner 3000 7G

data_processing: Summarized probe set signals in log2 scale were calculated by using the RMA (1) algorithm with Affymetrix GeneChip Expression Console v1.4 Software. (1) Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data, Biostatistics, April 2003; Vol. 4; Number 2: 249–264.

organism: Sus scrofa

source_name: porcine lung biopsy after extended partial hepatectomy_treated with mesenchymal stromal cells

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol

extract_protocol: Sample preparation for microarray hybridization was carried out as described in the Affymetrix GeneChip WT PLUS Reagent Kit User Manual.

value: lung

tag: msc treatment

value: treated


title: Developing mouse embryo sections G11G02_S371


title: porcine lung_untreated_rep3

description: Gene expression data from lung biopsy

source_name: porcine lung biopsy after extended partial hepatectomy_vehicle control

value: untreated


title: porcine lung_untreated_rep2

description: Gene expression data from lung biopsy


title: porcine lung_treated_rep3

description: Gene expression data from lung biopsy


title: Developing mouse embryo sections G11G01_S275


title: Methylation_MDA-MB-231-4

description: Methylation data

value: breast cancer


title: Methylation_MDA-MB-231-3

description: Methylation data


title: Developing mouse embryo sections G10G06_S178


title: Methylation_MDA-MB-231-2

description: Methylation data


title: Methylation_MDA-MB-231-1

description: Methylation data


title: F2LHplus2

description:
Paired with corresponding F2LHplus7
counts_exp2.txt.gz


title: F1LHplus2

description:
Paired with corresponding F1LHplus7
counts_exp2.txt.gz


title: F1LHplus7

description:
Paired with corresponding F1LHplus2
counts_exp2.txt.gz


title: Methylation_HCC1937-6

description: Methylation data


title: Developing mouse embryo sections G09G06_S177


title: Developing mouse embryo sections G10G02_S370


title: Developing mouse embryo sections G10G05_S82


title: Methylation_HCC1937-4

description: Methylation data


title: Developing mouse embryo sections G09G05_S81


title: Developing mouse embryo sections G09G02_S369


title: 6H_L5_LPS

city: Barcelona

first: Laia

last: Ribas

address: Passeig Maritim 37-49

country: Spain

institute: Institut de Ciencies del Mar

description: Phenol-Chlorofrom DNA extraction

library_source: genomic

data_processing:
raw reads were quality trimmed by the Trim Galore! software (v. 0.4.5) with the following parameters  --nextera, --quality 20, and --phred64
adapters, the number and quality of the reads were checked using the FastQC software (v. 0.11.6)
the alignments of the pair-end reads were performed using the function “bismark”: --bowtie2, --non-directional, and --score_min 0 + (−0.6 x read length). Bismark software (v. 16.0)
methylation calling  bismark_methylation_extractor”: --bedGraph
Supplementary_files_format_and_content: tab-delimited files (sample_name.txt) contain the coverage and the frequency of Cs (methylated cytosines) and of Ts (unmethylated cytosines) per CpG (chromosome, base, strand) covered
Genome_build: GRCz11 Danio rerio https://www.ncbi.nlm.nih.gov/assembly/GCF_000002035.5/

organism: Danio rerio

source_name: LPS treatment

growth_protocol: Zebrafish were raised following:  Westerfield, M. (2000). The zebrafish book. A guide for the laboratory use of zebrafish (Danio rerio). 4th ed., Univ. of Oregon Press, Eugene.

extract_protocol:
library preparation following protocol as in Anastasiadi et al 2018
Gonads were extracted, flash frozen in nitrogen liquid. DNA was extracted  following  the Phenol-Chlorofrom DNA extraction. Bisulfite conversion was carried out using D5020, Zymo Research from 1000 ng of genomic DNA in each sample. Illumina Miseq 2500 wasused for sequencing the library.
Library was constructed following the Illumina’s protocol: “16S metagenomic library preparation” using Nextera XT Index Kit V2 set A, FC-131–2001 kit.

treatment_protocol: zebrafish larva were treated with LPS for P. aeruginosa. Methylation Bisulfite sequencing was performed as described in Anastasiadi el al., 2018

value: AB

tag: FISH origin

value: laboratory (reared in aquarium facilities)

tag: age

value: 90 days old


title: Methylation_HCC1937-2

description: Methylation data


title: Methylation_HCC1937-5

description: Methylation data


title: 6H_L4_LPS

description: Phenol-Chlorofrom DNA extraction


title: Developing mouse embryo sections G10G01_S274


title: 6H_L5_CT

description: Phenol-Chlorofrom DNA extraction

source_name: Control


title: 6H_L4_CT

description: Phenol-Chlorofrom DNA extraction


title: Developing mouse embryo sections G08G06_S176


title: porcine liver_treated_rep1

description: Gene expression data from liver biopsy

source_name: porcine liver biopsy after extended partial hepatectomy_treated with mesenchymal stromal cells

value: liver

tag: cell treatment


title: porcine liver_untreated_rep3

description: Gene expression data from liver biopsy

source_name: porcine liver biopsy after extended partial hepatectomy_vehicle control


title: porcine liver_treated_rep3

description: Gene expression data from liver biopsy


title: porcine liver_treated_rep2

description: Gene expression data from liver biopsy


title: Developing mouse embryo sections G09G01_S273

value: E14 Mouse Embryo


title: 6H_L3_LPS

description: Phenol-Chlorofrom DNA extraction


title: Developing mouse embryo sections G08G05_S80

value: Sagigital section


title: porcine liver_untreated_rep2

description: Gene expression data from liver biopsy


title: Methylation_HCC1937-1

description: Methylation data


title: porcine lung_untreated_rep1

description: Gene expression data from lung biopsy


title: Methylation_MCF10A-5

description: Methylation data

source_name: ATCC CRL-10317; derived from benign proliferative breast tissue

value: benign proliferative breast tissue


title: Methylation_MCF10A-6

description: Methylation data


title: 6H_L3_CT

description: Phenol-Chlorofrom DNA extraction


title: Methylation_HCC1937-3

description: Methylation data


title: porcine liver_untreated_rep1

description: Gene expression data from liver biopsy


title: Developing mouse embryo sections G08G02_S368


title: Methylation_MCF10A-3

description: Methylation data


title: Methylation_MCF10A-4

description: Methylation data


title: 6H_L2_LPS

description: Phenol-Chlorofrom DNA extraction


title: EUF10

description:
Excluded from analysis due to low coverage/quality
counts_exp2.txt.gz

value: Women undergoing ART and transfer of an euploid blastocyst

value: secretory


title: porcine lung_treated_rep1

description: Gene expression data from lung biopsy


title: 6H_L1_CT

description: Phenol-Chlorofrom DNA extraction


title: Developing mouse embryo sections G07G01_S271


title: Developing mouse embryo sections G07G05_S79


title: Breast Cancer cells - MD-MBA-453 - DMSO treated rep. 3

city: Pittsburgh

first: Megan

middle: E.

last: Yates

state: PA

address: 5051 Centre Ave

institute: University of Pittsburgh

description: Sample B3

data_processing:
Basecalls performed using Alta-Cyclic version v1.7.0.
Transcript counts were quantified using Salmon v1.3.0 with parameters --seqBias --gcBias -p 8 -o and index hg38
Gene-level counts were generated using tximport (Soneson et al., 2015) verison 1.18.0
Differential gene expression analysis was performed using the DESeq2 package verison 1.30.1
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file including tximport abundance, count and lengths for each gene in each sample

source_name: ATCC breast cancer cell line

growth_protocol: All cell lines were grown in RPMI-1640 (#SH30027.FS, GE Healthcare Hyclone, Logan, UT) media at 37 °C and 5% CO2. 150,000 cells/well of each cell line were seeded into 6 well plates and allowed to adhere overnight before the 6 hour treatment.

extract_protocol:
RNA extracted with Qiagen RNeasy Kit following manufacter's instructions.
RNA sequencing library construction, quality control, and PE150 sequencing were performed by Novogene Co., Ltd. according to their protocol.

treatment_protocol: Biological triplicates of each cell line were treated with 12µM MAL3-101 (Fewell et al., 2004) dissolved in DMSO or equal volume DMSO for 6 hours.

value: Triple negative breast cancer cell line

tag: treatment

value: DMSO

tag: treatment duration

value: 6 hr


title: Developing mouse embryo sections G07G06_S175


title: 3H_L5_LPS

description: Phenol-Chlorofrom DNA extraction


title: UF34

description:
Paired with corresponding T34
counts_exp1.txt.gz

value: Uterine fluid derived Extracellular Vesicles

value: Regularly cycling control women

value: between 19 and 23


title: UF35

description:
Paired with corresponding T35
counts_exp1.txt.gz

value: prolipherative

value: between 8 and 13


title: Breast Cancer cells - MD-MBA-453 - DMSO treated rep. 1

description: Sample B1

tag: cell type


title: 6H_L1_LPS

description: Phenol-Chlorofrom DNA extraction

value: AB


title: 6H_L2_CT

description: Phenol-Chlorofrom DNA extraction

value: laboratory (reared in aquarium facilities)


title: UF31

description:
Paired with corresponding T31
counts_exp1.txt.gz


title: 3H_L4_CT

description: Phenol-Chlorofrom DNA extraction

value: 90 days old


title: 3H_L5_CT

description: Phenol-Chlorofrom DNA extraction


title: Developing mouse embryo sections G06G02_S366


title: 3H_L4_LPS

description: Phenol-Chlorofrom DNA extraction


title: Breast Cancer cells - MD-MBA-453 - MAL3-101 treated rep. 3

description: Sample B7

tag: cell line

tag: treatment dosage


title: Breast Cancer cells - MD-MBA-231 - MAL3-101 treated rep. 3

description: Sample A6


title: Developing mouse embryo sections G06G05_S78

tag: tissue


title: Developing mouse embryo sections G08G01_S272

tag: genotype


title: Breast Cancer cells - MD-MBA-453 - MAL3-101 treated rep. 1

description: Sample B4


title: UF33

description:
Paired with corresponding T33
counts_exp1.txt.gz


title: UF32

description:
Paired with corresponding T32
counts_exp1.txt.gz


title: Breast Cancer cells - MD-MBA-453 - DMSO treated rep. 2

description: Sample B2


title: 3H_L3_CT

description: Phenol-Chlorofrom DNA extraction


title: Developing mouse embryo sections G05G06_S173

tag: sample type


title: Developing mouse embryo sections G05G05_S77


title: UF25

description:
Paired with corresponding T25
counts_exp1.txt.gz

tag: population


title: Developing mouse embryo sections G06G06_S174


title: Breast Cancer cells - MD-MBA-231 - DMSO treated rep. 2

description: Sample A2


title: Developing mouse embryo sections G05G02_S365


title: 3H_L2_CT

description: Phenol-Chlorofrom DNA extraction


title: Developing mouse embryo sections G07G02_S367


title: 3H_L1_CT

description: Phenol-Chlorofrom DNA extraction


title: Breast Cancer cells - MD-MBA-231 - MAL3-101 treated rep. 2

description: Sample A5


title: Developing mouse embryo sections G06G01_S270


title: Developing mouse embryo sections G04G05_S76


title: 3H_L3_LPS

description: Phenol-Chlorofrom DNA extraction


title: Unjammed_ipf_D14_3

city: Aurora

first: Ivana

last: Yang

state: CO

institute: University of Colorado Anschutz Medical Campus

description: ***Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects.***

data_processing:
RNA paired-end reads were aligned at the transcript level to Ensembl GRCh38 using Kallisto with the average mapping rate 90.1%. 120,425 transcripts were detected in the mRNA dataset using Gencode v27
Differential expression was assessed using the DESeq2 package in R
Benjamini-Hochberg false discovery rate (FDR)-adjusted p-values <0.05 were considered significant
Genome_build: GRCh38
Supplementary_files_format_and_content: RNA-seq counts quantified by kallisto are transcript-level pseudo-counts in comma-delimited format

source_name: epithelial-culture

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit
mRNA libraries were prepared from 500 ng total RNA with TruSeq stranded mRNA library preparation kits
sequenced at the averaged depth of 92.4M reads on the Illumina NovaSeq 6000

tag: diagnosis

value: ipf

value: Y

tag: timepoint

value: unjammed

tag: Sex

value: Male

value: epithelial-culture


title: G18_F

description: Phenol-Chlorofrom DNA extraction

source_name: Ovaries

extract_protocol:
Gonads were extracted, flash frozen in nitrogen liquid. DNA was extracted  following  the Phenol-Chlorofrom DNA extraction. Bisulfite conversion was carried out using D5020, Zymo Research from 1000 ng of genomic DNA in each sample. Illumina Miseq 2500 wasused for sequencing the library.
Library was constructed following the Illumina’s protocol: “16S metagenomic library preparation” using Nextera XT Index Kit V2 set A, FC-131–2001 kit.

treatment_protocol: control reared conditions

tag: strain


title: UF26

description:
Paired with corresponding T26
counts_exp1.txt.gz

tag: menstrual cycle phase

tag: mentrual cycle day (counted from the first day of menstrual bleeding and expressed as n or from the day of urinary lh surge detection and expressed an lh+n)


title: UF22

description:
Paired with corresponding T22
counts_exp1.txt.gz

value: secretory


title: Developing mouse embryo sections G04G01_S268

description:
Developing mouse embryo sections
sci-Space Slides 1-6
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell

value: E14 Mouse Embryo

value: Sagigital section


title: 3H_L1_LPS

description: Phenol-Chlorofrom DNA extraction

tag: FISH origin

tag: age


title: Breast Cancer cells - MD-MBA-231 - MAL3-101 treated rep. 1

description: Sample A4

value: Triple negative breast cancer cell line

tag: treatment

value: 6 hr


title: Breast Cancer cells - MD-MBA-231 - DMSO treated rep. 3

description: Sample A7

value: DMSO

tag: treatment duration


title: 3H_L2_LPS

description: Phenol-Chlorofrom DNA extraction


title: G16_M

description: Phenol-Chlorofrom DNA extraction

source_name: Testis


title: T34

description:
Paired with corresponding UF34
counts_exp1.txt.gz

source_name: Endometrial tissue

value: Endometrial tissue

value: Regularly cycling control women

value: between 19 and 23


title: Breast Cancer cells - MD-MBA-453 - MAL3-101 treated rep. 2

description: Sample B5

tag: cell type


title: Breast Cancer cells - MD-MBA-231 - DMSO treated rep. 1

description: Sample A1

tag: cell line


title: UF27

description:
Paired with corresponding T27
counts_exp1.txt.gz

value: Uterine fluid derived Extracellular Vesicles

value: prolipherative

value: between 8 and 13


title: Developing mouse embryo sections G03G06_S171


title: T30

description:
Paired with corresponding UF30
counts_exp1.txt.gz


title: T35

description:
Paired with corresponding UF35
counts_exp1.txt.gz


title: Unjammed_ipf_D14_4

value: ipf

value: N


title: G19_M

description: Phenol-Chlorofrom DNA extraction

value: AB

value: laboratory (reared in aquarium facilities)

value: 90 days old


title: UF30

description:
Paired with corresponding T30
counts_exp1.txt.gz

value: secretory


title: Developing mouse embryo sections G03G02_S363

value: E14 Mouse Embryo


title: T27

description:
Paired with corresponding UF27
counts_exp1.txt.gz


title: Unjammed_ipf_D14_2

value: unjammed

value: Male

value: epithelial-culture


title: T32

description:
Paired with corresponding UF32
counts_exp1.txt.gz


title: Jammed_control_D14_1

value: control

value: Y

value: jammed


title: G14_M

description: Phenol-Chlorofrom DNA extraction


title: T33

description:
Paired with corresponding UF33
counts_exp1.txt.gz

value: Endometrial tissue

value: Regularly cycling control women


title: Developing mouse embryo sections G04G06_S172

value: Sagigital section


title: Developing mouse embryo sections G05G01_S269


title: Unjammed_ipf_D8_4


title: Developing mouse embryo sections G03G01_S267


title: T25

description:
Paired with corresponding UF25
counts_exp1.txt.gz

value: between 19 and 23


title: T31

description:
Paired with corresponding UF31
counts_exp1.txt.gz


title: Unjammed_ipf_D14_1

value: ipf

value: Female


title: G15_F

description: Phenol-Chlorofrom DNA extraction

value: AB


title: T22

description:
Paired with corresponding UF22
counts_exp1.txt.gz


title: G17_F

description: Phenol-Chlorofrom DNA extraction

value: laboratory (reared in aquarium facilities)


title: Unjammed_ipf_D8_2

value: N


title: G13_F

description: Phenol-Chlorofrom DNA extraction

value: 90 days old


title: Jammed_control_D14_3


title: Unjammed_ipf_D8_1


title: Developing mouse embryo sections G03G05_S75

value: E14 Mouse Embryo


title: Developing mouse embryo sections G02G01_S266


title: Developing mouse embryo sections G02G05_S74


title: Unjammed_ipf_D8_3

value: unjammed


title: Developing mouse embryo sections G02G02_S362


title: Jammed_control_D8_2

value: Male


title: Jammed_control_D14_2

value: epithelial-culture


title: Jammed_control_D8_3

value: control


title: Cerebral Organoids KO/WWOX 2

city: Jerusalem

first: Daniel

middle: Jacob

last: Steinberg

address: Hebrew University-Hadassah Medical School - Ein Karem Campus

department: Lautenberg Center for Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem Israel

data_processing:
Base calling with Illumina bcl2fatsq.
Adapter removal and low base quality (Q=20) trimming with trim_galore versio 0.6.1. Filtering for read lengths longer than 20 bp. Testing quality with fastqc version 0.11.8.
Mapping to transcriptome with salmon version 1.2.1 in its mapping-based mode. Validate mapping mode and gc Bias correction are turned on. Salmon index is based on GRCh38 CDNA release 99 .
Differential gene analysis with R packages tximport (ver.1.16.1) followed by DEeq2 (ver.1.28.1).
Gene set enrichment analysis performed with Broad Institute GSEA software (ver.4.0.3) and WebGestaltR (ver.0.4.3).
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file with Salmon based gene counts for every gene and every sample.
Supplementary_files_format_and_content: Tab-delimited text file with upregulated differential gene list including Fold Change, p-value, p-adjusted and description.
Supplementary_files_format_and_content: Tab-delimited text file with downregulated differential gene list including Fold Change, p-value, p-adjusted and description.

source_name: Cerebral Organoids

growth_protocol: hESCs were grown on mitotically inactive MEF-feeder plates, in KOSR/FGF-2 based medium. Cerebral organoids were generated according to previously published protocols (Lancaster and Knoblich, Nature protocols, 2014)

extract_protocol:
Total RNA was extracted from homogenized organoids using Trizol reagent and standard phenol-chloroform isolation technique. RNA quality was assessed by using RNA ScreenTape kit, D1000 ScreenTape kit, Qubit(r) RNA HS Assay kit and Qubit(r) DNA HS Assay kit.
For mRNA library preparation, 1ug of RNA per sample was processed using KAPA Stranded mRNA-Seq Kit with mRNA Capture Beads. Library was eluted in 20µl of elution buffer, adjusted to 10mM, then 10µl (50%) from each sample was collected and pooled in one tube. Multiplex samples Pool (1.5pM including PhiX 1.5%) was loaded in NextSeq 500/550 High Output v2 kit (75 cycles) cartridge and loaded on NextSeq 500 System machine, with 75 cycles and single-read sequencing conditions.

treatment_protocol: hESCs were genetically engineered using the CRISPR/Cas9 technology, by electroporating a px330 plasmid, containing sgRNA targeting WWOX and the Cas9 sequence.

value: Knock out  of WWOX

value: 15 weeks

value: hESCs line:WiBR3


title: G12_M

description: Phenol-Chlorofrom DNA extraction


title: G7_M

description: Phenol-Chlorofrom DNA extraction


title: Developing mouse embryo sections G01G05_S73


title: G8_M

description: Phenol-Chlorofrom DNA extraction


title: Cerebral Organoids KO/WWOX 4


title: T26

description:
Paired with corresponding UF26
counts_exp1.txt.gz

value: Endometrial tissue

value: Regularly cycling control women

value: prolipherative

value: between 8 and 13


title: Cerebral Organoids untreated 2

value: Untreated


title: G11_F

description: Phenol-Chlorofrom DNA extraction

value: AB


title: G10_M

description: Phenol-Chlorofrom DNA extraction

value: laboratory (reared in aquarium facilities)


title: Developing mouse embryo sections G01G02_S361

value: Sagigital section


title: Developing mouse embryo sections G02G06_S170


title: Cerebral Organoids KO/WWOX 1


title: Unjammed_ipf_D4_4

value: ipf

value: N


title: G5_F

description: Phenol-Chlorofrom DNA extraction

value: 90 days old


title: G9_M

description: Phenol-Chlorofrom DNA extraction


title: Developing mouse embryo sections G01G06_S169

value: E14 Mouse Embryo


title: Unjammed_ipf_D4_2

value: unjammed

value: Male

value: epithelial-culture


title: hESC_Naive_BRM_ChIP

city: New York

first: Jianlong

last: Wang

state: New York

department: Department of Medicine

institute: Columbia University Irving Medical Center

description: BRM ChIP in naive hESCs

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality
Reads were aligned to the human genome hg38 using the bowtie2 (v2.3.4) program, with parameters -X 1000 --no-mixed --no-discordant.
The mapped reads were sorted and converted to a binary bam file using samtools (v0.1.19)
ChIP-seq peaks were determined by the MACS program (v.2.0.10), using input as the control data, and all other parameters followed the default settings. Board peaks were called from ChIP of BAF subunits, and narrow peaks were call from transcription factors.
Genome_build: hg38
Supplementary_files_format_and_content: Bed file of MACS called peaks.

source_name: Embryonic stem cells

growth_protocol: Conventional (primed) human ESCs were maintained on mitomycin C inactivated mouse embryonic ﬁbroblast (MEF) feeder layers and passaged using Collagenase (1 mg/mL) or manual methods. Primed human ESCs were cultured in human ESC medium (hESM) [DMEM/F12 (Invitrogen) supplemented with 15% fetal bovine serum (Gibco HI FBS, 10082-147), 5% KnockOut Serum Replacement (Invitrogen), 2 mM L-glutamine (MPBio), 1% nonessential amino acids (Invitrogen), 1% penicillin-streptomycin (Lonza), 0.1 mM β-mercaptoethanol (Sigma) and 4 ng/ml FGF2 (R&D systems)]. Naive human ESCs were cultured on mitomycin C-inactivated MEF feeder cells, and were passaged by a brief PBS wash followed by single-cell dissociation using 3-5 minute treatment with Accutase (Gibco) and centrifugation in fibroblast medium [DMEM (Invitrogen) supplemented with 10% FBS (Gibco HI FBS, 10082-147), 2 mM L-glutamine (MPBio), 1% nonessential amino acids (Invitrogen), 1% penicillin-streptomycin (Lonza) and 0.1 mM β-mercaptoethanol (Sigma)]. For conversion of pre-existing primed human ESC lines, we seeded 2 x 105 trypsinized single cells on a MEF feeder layer in hESM supplemented with ROCK inhibitor Y-27632 (Stemgent, 10 μM). 2 days later medium was switched to 5i/L/A or 4i/L/A (no IM12)-containing naive human ESC medium. Following an initial wave of cell death, naive colonies appeared within 10 days and were expanded polyclonally using Accutase (Gibco) on a MEF feeder layer. Naive human pluripotent cells were derived and maintained in serum-free N2B27-based media supplemented with inhibitors and cytokines. 500 mL of medium was generated by including: 240 mL DMEM/F12 (Invitrogen; 11320), 240 mL Neurobasal (Invitrogen; 21103), 5 mL N2 supplement (Invitrogen; 17502048), 10 mL B27 supplement (Invitrogen; 17504044), 10 μg recombinant human LIF (made in-house), 2 mM L-glutamine (MPBio), 1% nonessential amino acids (Invitrogen), 0.1 mM β-mercaptoethanol (Sigma), 1% penicillin-streptomycin (Lonza), 50 µg/ml BSA (Gibco Fraction V, 15260), and the following small molecules and cytokines: PD0325901 (Stemgent, 1 μM), IM-12 (Enzo, 1 μM or 0 µM), SB590885 (R&D systems, 0.5 μM), WH4-023 (A Chemtek or Selleckchem, 1 μM), Y-27632 (Stemgent, 10 μM) and Activin A (Peprotech, 10 ng/mL). All naïve hESC experiments were conducted in 5% O2, 5% CO2.

extract_protocol:
ChIP was performed following the standard protocol of Millipore (#17-371).
For ChIP of KLF4, SOX2, and SNF2L, about 5 million hESCs were used for each ChIP experiment. Sonication was performed on a Bioruptor system, with 30s ON, 30s OFF, 30 cycles, high amplitude. ChIP libraries were prepared using the NEBNext Ultra II DNA library prep kit and index primers sets (NEB, #7645S, #E7335S) followed the standard protocol. Sequencing was performed by Novogene with the Illumina HiSeq 4000 Sequencer. Data with 150 bp paired-end reads were obtained. For BRG1, BRM, and BAF155, about 20 million hESCs were used for each ChIP experiment. Library prep and sequencing was performed on Illumina NextSeq 500 in the Molecular Biology Core Facilities at the Dana-Farber Cancer Institute. Data with 75-bp single-end reads were obtained.

value: Embryonic stem cells

tag: culture condition

value: Naive (5i/L/A)

tag: chip antibody

value: BRM (Cell Signaling, #11966)


title: G4_M

description: Phenol-Chlorofrom DNA extraction


title: hESC_Primed_BAF155_ChIP

description: BAF155 ChIP in primed hESCs

value: Primed (conventional)

value: Homemade in Kadoch’s lab, cat#fx-3


title: Developing mouse embryo sections F12G05_S72

source_name: E14 saggital sections 8-10um thick

tag: genotype

tag: tissue


title: G6_F

description: Phenol-Chlorofrom DNA extraction


title: Jammed_control_D8_1

value: control

value: Y

value: jammed


title: Developing mouse embryo sections F12G06_S168

tag: sample type


title: G2_F

description: Phenol-Chlorofrom DNA extraction

value: AB

value: laboratory (reared in aquarium facilities)


title: hESC_Naive_BAF155_ChIP

description: BAF155 ChIP in naive hESCs


title: Developing mouse embryo sections F12G01_S264

value: Sagigital section


title: G3_M

description: Phenol-Chlorofrom DNA extraction


title: Unjammed_ipf_D4_1

tag: diagnosis

value: ipf

value: Female


title: Cerebral Organoids untreated 1

value: Untreated

value: 15 weeks

value: hESCs line:WiBR3


title: Unjammed_control_D4_3

tag: timepoint

value: unjammed

value: Male

value: epithelial-culture


title: Unjammed_control_D4_1

tag: Sex


title: Developing mouse embryo sections F12G02_S360

value: E14 Mouse Embryo


title: hESC_Naive_BRG1_ChIP

description: BRG1 ChIP in naive hESCs

value: Embryonic stem cells

value: Naive (5i/L/A)

value: BRG1 (Abcam, ab110641)


title: hESC_Primed_BRG1_ChIP

description: BRG1 ChIP in primed hESCs

value: Primed (conventional)


title: hESC_Naive_BAF_Input

description: ChIP Input in naive hESCs (for BAF subunits)


title: Developing mouse embryo sections G01G01_S265


title: si eIF2alpha #2 HEK293T RNA-seq replicate 1

city: Higashi-ku, Fukuoka

first: Kazuya

last: Ichihara

address: 3-1-1, Maidashi

country: Japan

institute: Kyushu University

data_processing:
Adaptor sequences were trimmed from raw reads with the use of cutadapt.
Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit.
Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCh38.p13) and human genome (hg38) also with the use of STAR.
Read counting was performed with the use of featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: Counts per transcript

source_name: HEK293T cells

growth_protocol: The cells were cultured under an atmosphere of 5% CO2 at 37°C in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (Life Technologies) and antibiotics.

extract_protocol:
The medium was aspirated, and the cells were immediately placed on ice, washed once with ice-cold phosphate-buffered saline (PBS), and lysed with lysis buffer [50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, and EDTA-free protease inhibitor] supplemented with either CHX (100 μg/ml) for Ribo-seq or 50 μM LTM for GTI-seq. The lysates were then incubated with TURBO DNase on ice for 10 min and centrifuged at 15,000 rpm for 10 min at 4°C, and the resulting supernatants were collected carefully, assayed for RNA concentration with a Qubit RNA BR assay kit, incubated with RNase I (20 U per 10 μg of RNA, Epicentre) for 45 min at 25°C, and placed on ice before the addition of SUPERase•In RNase inhibitor (Invitrogen). The samples were then loaded on a 1 M sucrose cushion buffer [20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, SUPERase•In (10 U/ml), 1 mM DTT, and either CHX (100 μg/ml) for Ribo-seq or 50 μM LTM for GTI-seq], and the gradients were centrifuged at 100,000 rpm for 1 h at 4°C in a Beckman TLA110 rotor. The resulting pellets were suspended in ribosome splitting buffer [20 mM Tris-HCl (pH 7.5), 300 mM NaCl, 5 mM EDTA, SUPERase•In (20 U/ml), 1 mM DTT, 1% Triton X-100] and subjected to purification with the use of an Amicon Ultra filtration device (100-kDa cutoff, Millipore) to deplete rRNAs.
The purified RNA was subjected to selection on the basis of a size range of 17 to 34 nt by electrophoresis through a 15% polyacrylamide and Tris-borate-EDTA (TBE)–urea gel (SuperSep RNA, Fujifilm). The footprint fragments were treated with T4 PNK to repair the 2x-3x cyclic phosphates, a DNA linker including barcode sequences (NI-810 to NI-817) was ligated with the use of T4 RNA Ligase 2, truncated K227Q (New England Biolabs), and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. Ribosomal RNAs were further depleted with the use of RiboZero Gold (Illumina). Reverse transcription was performed with the NI-802 primer, and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. The purified cDNAs were circularized with circLigase II (Lucigen), and index sequences were then added by amplification in a PCR reaction with the common primer (NI-798) and primers including index sequences (NI-799 and NI-822 to NI-826). Products of the desired size were purified on a 15% polyacrylamide nondenaturing gel (SuperSep DNA, Fujifilm), and the libraries were sequenced with a NovaSeq 6000 system (Illumina).

treatment_protocol: For arsenite treatment and GTI-seq, 40 μM sodium arsenite or 50 μM LTM was added to the medium either 60 or 30 min, respectively, before cell lysis.

tag: protocol

value: RNA-seq

value: si eIF2alpha


title: G1_F

description: Phenol-Chlorofrom DNA extraction

tag: strain

value: AB

value: laboratory (reared in aquarium facilities)

value: 90 days old


title: Unjammed_ipf_D4_3

description: ***Raw data disclaimer: Unable to provide raw sequencing files due to conflict with privacy protection for human subjects.***

value: ipf

value: Y


title: Developing mouse embryo sections F11G05_S71

value: Sagigital section


title: Developing mouse embryo sections F11G02_S359


title: si eIF2alpha #2 HEK293T RNA-seq replicate 2


title: Longissimus dorsi, late batch, low protein diet, individual 2

city: Zafra

first: María

middle: Muñoz

last: Muñoz

state: Badajoz

address: Centro I+D en Cerdo Ibérico, carretera Ex-101, km 4.7

institute: INIA

description: Gene expression data from Longissimus dorsi tissue

data_processing:
FastQC was used to evaluate the quality of the raw sequencing data
The sequences were trimmed to remove the sequencing adaptor and poly A and T tails with Trim Galore setting default values (stringency of 6bp) and paired-end reads where kept when both pairs were longer than 40 bp.
Filtered reads were mapped against the pig reference genome (Sscrofa11.1) using TopHat v2.1.0 applying default settings, except the reads were aligned first to the ENSEMBLE (Sscrofa11.1) transcriptome annotation (-G option) and the distance between pairs was set to 50 bp. (inner-mean distance) and the standard deviation at 150 bp.
Transcripts were assembled and quantified in FPKM using Cufflinks v2.2.1
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Longissimus dorsi, castrated male

growth_protocol: Differential diet treatment with ad libitum access to free and water

extract_protocol:
RiboPure RNA isolation kit
Paired-end libraries were prepared using TruSeq SBS Kit v3-(Illumina, San Diego CA) for each sample. Multiplex sequencing of the libraries was carried out on a HiSeq2000 sequence analyzer (Illumina, Inc) with four samples per lane, according to the manufacturer’s instruction at Centro Nacional de Análisis Genómico. Paired-end reads of 76 bp were generated.

treatment_protocol: Liver and longissimus dorsii muscle were manteined at -80 ºC

value: Longissimus dorsi

tag: diet

value: low protein

tag: time period

value: Late batch


title: Developing mouse embryo sections F11G01_S263


title: si eIF2alpha #1 HEK293T RNA-seq replicate 2


title: Longissimus dorsi, late batch, low protein diet, individual 1


title: Cerebral Organoids KO/WWOX 3

value: Knock out  of WWOX

tag: age

value: 15 weeks

value: hESCs line:WiBR3


title: Longissimus dorsi, late batch, low protein diet, individual 3


title: Developing mouse embryo sections F11G06_S167

value: E14 Mouse Embryo


title: Developing mouse embryo sections F10G06_S166


title: hESC_Primed_BAF_Input

description: ChIP Input in primed hESCs (for BAF subunits)

value: Embryonic stem cells


title: EKHT7_ROW34_17: Reads from single cell RNA-seq of the S1 injection site of either pup 3, cell 258

city: Geneva

first: Julien

last: Prados

address: Rue Michel Servet 1

department: SCMU

country: Switzerland

institute: University of Geneva

data_processing:
bulk RNA-seq reads were parsed to extract: sindbis barcode (nucleotide 1-32), sinbis index (nuceodite 89-94), and umi sequence (nucleotide 95-106).
RNA-seq reads are deduplicated on the base of the UMI sequence
RNA-seq reads are tagged as viral, spike or unknown depending on their barcode sequence
Single-cell gene expression are quantifyied using summarizeOverlaps() method of the R package GenomicsAlignments(). Only exonic reads are considered in the quantification and this includes 5' and 3' UTRs.
Barcodes found in the single cell of the injection site are clustered to correct for sequencing errors
Barcodes from the target regions are mapped to the error-corrected barcodes found in the injection sites
Counts are normalized with the number of spike found in the same target region
Genome_build: Single cell reads are mapped to mm10 genome (no mapping for bulk reads because it is a barcode sequencing protocol)
Supplementary_files_format_and_content: connectID_links.tsv.gz contains the result of the parsing of the sindbis reads. The file report the amount of unique umi sequence of a target that was associated to a barcode of the injection site. It also report include the number of spike in the region and te number of time the barcode was seen in the injection site.
Supplementary_files_format_and_content: connectID_S1_cells_metadata.tsv.gz contains meta-data for each single-cell, together with connection information extracted from the barcodes
Supplementary_files_format_and_content: connectID_S1_cells_count_matrix.tsv.gz contains the gene expression count matrix of every single cell

source_name: cortex S1

extract_protocol:
The primary somatosensory cortex was microdissected as aforementioned. Cells were further dissociated by incubating micro-dissected samples in 0.5 mg/mL pronase (Sigma, #P5147) at 37°C for 10 minutes, followed by incubation in 5% bovine serum albumin for 3 minutes and manual trituration in ACSF using pulled glass pipettes. Cells were then centrifuged for 10 minutes at 600 rpm and resuspended before filtration using a 70 mm cell strainer (ClearLine, # 141379C). Cells were then incubated for 10 minutes at 37°C with Hoechst (0.1 mg/mL) and isolated using a Beckman Coulter Moflo Astrios FAC-sorter. Singlet Hoechst+cells were sorted according to their Forward and Side scattering properties (FSC and SSC), and their negativity for Draq7TM (Viability dye, Far red DNA intercalating agent, Beckman Coulter, #B25595). 5000 to 10 000 cells were FACsorted for each experiment. Three microliters of C1 Suspension Reagent (Fluidigm) was added to 10 ml of FAC-sorted cells GFP+ cells, yielding a 300-500 cells / ml suspension. 12 ml of this suspension mix were loaded on a C1 Single-Cell AutoPrep integrated fluidic circuit (IFC) designed for 10 to 17 mm diameter-cells (Fluidigm, #100-5780). RNA was extracted using an RNeasy kit (Qiagen, #74034), and quality control was done using 2001 Bioanalyzer from Agilent. cDNA libraries were obtained using SMARTseq v4 kit (Clontech, # 634888) and sequenced using HiSeq 2500 sequencer.
SMARTseq v4 kit (Clontech, # 634888)

value: cortex S1

tag: dissection


title: Developing mouse embryo sections F10G05_S70

description:
Developing mouse embryo sections
sci-Space Slides 1-6
single Cell RNA sequencing library containing hash molecules denoting where a nucleus originated from and the transcriptome measured for each cell


title: RNA-seq circulating T follicular helper cells DSA+ ABMR+ [8TFH_S3]

first: Uma

last: Chandran

address: 5150 Center Ave

department: BioMedical Informatics

data_processing:
Alignment using HISAT2 2.1.0 build of Ensembl GRCh38 89 version of primary assembly with default paired-end unstranded parameters and converting to sorted bam files using Samtools 1.9
Counts were generated using HT-Seq 0.11.2 using Ensembl GRCh38 89 version as GTF file and using unstranded strandedness, gene_id GFF attribute, union mode, and exon feature type as parameters
edgeR in Rstudio using R version 3.5.1 including CPM values for each sample
Genome_build: HISAT2 GRCh38 DNA primary assembly fasta version 89
Supplementary_files_format_and_content: Raw Counts text files in tab-delimited format of each sample combining R1 and R2 generated by Htseq

growth_protocol: unstimulated cells

extract_protocol:
Total RNA was extracted from cells sorted directly into lysis buffer. RNA was isolated using miRNeasy Mini Kit (Qiagen).
cDNA synthesis and amplification were performed with strand specific/SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Takara).   Libraries were sequenced on an Illumina NextSeq 500.  The data are paired-end reads with expected read length of 75-bp.

tag: subject status

value: adult kidney transplant recipients

tag: patient status

value: with donor-specific HLA antibodies and antibody-mediated rejection (DSA+ ABMR+)

value: circulating T follicular helper cells


title: Longissimus dorsi, late batch, low protein diet, individual 5


title: Longissimus dorsi, late batch, control diet, individual 4

value: control


title: Developing mouse embryo sections F10G02_S358


title: Unjammed_control_D4_2

value: N

value: unjammed

value: Male

value: epithelial-culture


title: si eIF2alpha #2 HEK293T Ribo-seq replicate 2

value: Ribo-seq

value: si eIF2alpha

tag: treatment


title: Longissimus dorsi, late batch, control diet, individual 3

value: Longissimus dorsi

value: Late batch


title: si control HEK293T RNA-seq replicate 1

value: RNA-seq

value: si control


title: RNA-seq circulating T follicular helper cells DSA+ ABMR- [6TFH_S10]

value: with donor-specific HLA antibodies without antibody-mediated rejection (DSA+ ABMR-)

tag: cell type


title: RNA-seq circulating T follicular helper cells DSA+ ABMR+ [9TFH_S12]


title: Developing mouse embryo sections G04G02_S364

value: E14 Mouse Embryo

value: Sagigital section


title: si eIF2alpha #1 HEK293T RNA-seq replicate 1


title: Developing mouse embryo sections F09G06_S165


title: si eIF2alpha #2 HEK293T Ribo-seq replicate 1


title: Longissimus dorsi, late batch, low protein diet, individual 4

value: low protein


title: RNA-seq circulating T follicular helper cells DSA+ ABMR+ [10TFH_S2]

value: adult kidney transplant recipients

value: with donor-specific HLA antibodies and antibody-mediated rejection (DSA+ ABMR+)


title: Longissimus dorsi, late batch, control diet, individual 1

value: control


title: Longissimus dorsi, late batch, control diet, individual 5


title: Longissimus dorsi, early batch, low protein diet, individual 5

value: Early batch


title: si eIF2alpha #1 HEK293T Ribo-seq replicate 1


title: RNA-seq circulating T follicular helper cells DSA+ ABMR- [5TFH_S11]

value: circulating T follicular helper cells


title: Developing mouse embryo sections F10G01_S262


title: RNA-seq circulating T follicular helper cells DSA- [4TFH_S17]

value: without donor-specific HLA antibodies (DSA-)


title: RNA-seq circulating T follicular helper cells DSA+ ABMR- [7TFH_S14]


title: si control HEK293T RNA-seq replicate 2


title: si control HEK293T Ribo-seq replicate 1


title: sc-PC_GFP_2 L3

first: Shuibing

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

description:
Dropseq
PC-pool2.dge.txt.gz

data_processing:
Illumina bcl2fastq2 v2.19 was used for basecalling.
All single-cell RNA-seq samples were processed according to the Drop-seq Computational Protocol with the Drop-seq Toolkit v1.2 created by the McCarroll Lab (http://mccarrolllab.com/dropseq/). Sequences were first tagged with their corresponding cell and molecular barcodes (unique molecular identifiers, UMI) using dropseq TagBamWithReadSequenceExtended. Cell and molecular barcodes were required to have a minimum base quality of 10 across their lengths, otherwise they were discarded. SMART adapter sequences were trimmed from the 5’ end of each read whenever there were at least five continuous bases exactly matching the SMART adapter (dropseq TrimStartingSequence). Putative poly(A) tails were trimmed from the 3’ end whenever there were stretches of at least 6 adenosines with zero mismatches (dropseq PolyATrimmer).
Barcode-tagged and cleaned reads were aligned with default parameters of STAR (v.2.4.2a) after conversion of the unaligned BAM file to FASTQ format (Picard's SamToFastq tool). The final file containing alignment information plus the cell and UMI tags were generated using Picard MergeBamAlignment merging the unaligned and aligned BAM files to restore the XC and XM barcodes. Sequences that mapped to more than one locus were excluded from further analysis by filtering reads with a mapping quality lower than 10.
To determine the numbers of detected transcripts per gene and cell, the overlaps of the aligned reads with gene annotation (Ensembl release 76) were counted and summarized using dropseq TagReadWithGeneExon and dropseq DigitalExpression. Individual gene expression matrices from each sample were combined in R to create a single gene count matrix for all cells and genes.
Genome_build: GRCh38
Supplementary_files_format_and_content: excel file including gene name, Ensembl gene id, RPKM value for each each gene in each sample

source_name: embryonic

growth_protocol: Differentiation was initiated 72 hours after plating when the culture was approximately 80% confluent. Step 1: Cells were differentiated with 1.5 μM CHIR99021, 20 ng/mL BMP4 and 20 ng/mL Activin A in RPMI supplemented with B27 minus insulin, 2 mM GlutaMAX, 1x NEAA and 1x Pen/Strep for 3 days . Step 2: For cardiomyocyte differentiation, cells were treated for an additional 3 days with 5 µM XAV939 . For hPSC-SAN differentiation, Step 1 was followed by addition of 0.1 μM cucurbitacin, 1 μM retinoic acid, 5 μM SU5402  in RB27-INS from day 3-6. 5 µM XAV939 was added from day 5-6. From day 6 onward, both cardiomyocyte and hPSC-SAN differentiation were carried out in RPMI supplemented with B27, 2 mM GlutaMAX, 1x NEAA and 1x Pen/Strep (RB27+INS). Step 3: hPSC-SAN differentiation included additional treatment with 5 µM Tyrphostin AG 490 (Sigma Aldrich) from day 6-9 in RB27+INS. The HDAC inhibitor, chidamide, was added to the differentiation cocktail from day 7-9 with a final concentration 5 µM.

extract_protocol:
scRNA-seq libraries were prepared following the Dropseq protcol (Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas AR, Kamitaki N, Martersteck EM, Trombetta JJ, Weitz DA, Sanes JR, Shalek AK, Regev A, and McCarroll SA. Highly Parallel Genome- wide Expression Profiling of Individual Cells Using Nanoliter Droplets. Cell, 161(5):1202–1214, 2015. doi: 10.1016/j.cell.2015.05.002.)
Nextera XT Library Prep Kit

tag: gfp

value: GFP+

tag: mcherry

value: mCherry+


title: RNA-seq circulating T follicular helper cells DSA- [3TFH_S4]


title: Longissimus dorsi, early batch, low protein diet, individual 1

tag: tissue


title: Developing mouse embryo sections F08G02_S356

tag: genotype

tag: sample type


title: si eIF2alpha #1 HEK293T Ribo-seq replicate 2

value: Ribo-seq

value: si eIF2alpha


title: Developing mouse embryo sections F09G02_S357


title: sc-PC_GFP_2 L1

description:
Dropseq
PC-pool2.dge.txt.gz


title: eIF2A, eIF2D DKO HEK293T #2 arsenite RNA-seq replicate 1

value: eIF2A, eIF2D DKO

value: arsenite


title: Developing mouse embryo sections F09G05_S69


title: eIF2A, eIF2D DKO HEK293T #2 arsenite Ribo-seq replicate 2


title: Longissimus dorsi, early batch, low protein diet, individual 4

value: Longissimus dorsi


title: RNA-seq circulating T follicular helper cells DSA- [1TFH_S6]


title: sc-PC_GFP_1 L3

description:
Dropseq
PC-pool1.dge.txt.gz


title: Developing mouse embryo sections F08G05_S68


title: Longissimus dorsi, early batch, low protein diet, individual 3


title: sc-PC_GFP_2 L4

description:
Dropseq
PC-pool2.dge.txt.gz


title: si control HEK293T Ribo-seq replicate 2

value: si control


title: Longissimus dorsi, late batch, control diet, individual 2

value: Late batch


title: eIF2A, eIF2D DKO HEK293T #2 arsenite RNA-seq replicate 2

value: RNA-seq


title: Longissimus dorsi, early batch, control diet, individual 2


title: Longissimus dorsi, early batch, control diet, individual 3


title: sc-PC_GFP_2 L2

description:
Dropseq
PC-pool2.dge.txt.gz


title: eIF2A, eIF2D DKO HEK293T #1 arsenite RNA-seq replicate 2


title: Developing mouse embryo sections F09G01_S261

value: E14 Mouse Embryo

value: Sagigital section


title: Longissimus dorsi, early batch, control diet, individual 5


title: eIF2A, eIF2D DKO HEK293T #1 arsenite RNA-seq replicate 1


title: Developing mouse embryo sections F08G06_S164


title: sc-PC_GFP_1 L1

description:
Dropseq
PC-pool1.dge.txt.gz


title: Developing mouse embryo sections F08G01_S260


title: sc-PC_GFP_1 L4

description:
Dropseq
PC-pool1.dge.txt.gz


title: Developing mouse embryo sections F06G06_S162


title: Longissimus dorsi, early batch, control diet, individual 4


title: sc-mCherry_2 L3

description:
Dropseq
mCherry-pool2.dge.txt.gz

value: GFP-


title: Liver, late batch, low protein diet, individual 5

description: Gene expression data from liver tissue

source_name: Liver, castrated male

value: liver

value: low protein


title: Longissimus dorsi, early batch, control diet, individual 1

value: control

value: Early batch


title: Developing mouse embryo sections F07G06_S163


title: sc-PC_GFP_1 L2

description:
Dropseq
PC-pool1.dge.txt.gz

value: GFP+


title: eIF2A, eIF2D DKO HEK293T #1 arsenite Ribo-seq replicate 2


title: eIF2D KO HEK293T #2 arsenite RNA-seq replicate 1

value: eIF2D KO


title: Developing mouse embryo sections F07G01_S259


title: Developing mouse embryo sections F06G01_S258


title: Developing mouse embryo sections F06G02_S354


title: Developing mouse embryo sections F07G02_S355


title: Liver, late batch, low protein diet, individual 4

description: Gene expression data from liver tissue


title: Developing mouse embryo sections F07G05_S67


title: eIF2A, eIF2D DKO HEK293T #2 arsenite Ribo-seq replicate 1

value: Ribo-seq


title: sc-mCherry_2 L1

description:
Dropseq
mCherry-pool2.dge.txt.gz

value: mCherry+


title: eIF2A, eIF2D DKO HEK293T #1 arsenite Ribo-seq replicate 1

value: eIF2A, eIF2D DKO


title: eIF2D KO HEK293T #2 arsenite Ribo-seq replicate 1

value: arsenite


title: eIF2D KO HEK293T #2 arsenite Ribo-seq replicate 2


title: Liver, late batch, low protein diet, individual 3

description: Gene expression data from liver tissue


title: Developing mouse embryo sections F06G05_S66


title: Liver, late batch, low protein diet, individual 2

description: Gene expression data from liver tissue


title: sc-mCherry_2 L4

description:
Dropseq
mCherry-pool2.dge.txt.gz


title: Liver, late batch, control diet, individual 4

description: Gene expression data from liver tissue


title: Liver, late batch, low protein diet, individual 1

description: Gene expression data from liver tissue


title: Longissimus dorsi, early batch, low protein diet, individual 2

value: Longissimus dorsi


title: sc-mCherry_1  L3

description:
Dropseq
mCherry-pool1.dge.txt.gz


title: Developing mouse embryo sections F05G05_S65


title: eIF2D KO HEK293T #1 arsenite RNA-seq replicate 1


title: sc-mCherry_1  L4

description:
Dropseq
mCherry-pool1.dge.txt.gz


title: sc-mCherry_1  L2

description:
Dropseq
mCherry-pool1.dge.txt.gz


title: eIF2D KO HEK293T #1 arsenite RNA-seq replicate 2


title: Liver, late batch, control diet, individual 3

description: Gene expression data from liver tissue


title: eIF2D KO HEK293T #1 arsenite Ribo-seq replicate 2


title: sc-mCherry_1  L1

description:
Dropseq
mCherry-pool1.dge.txt.gz


title: Developing mouse embryo sections F05G01_S257


title: eIF2D KO HEK293T #2 arsenite RNA-seq replicate 2


title: Developing mouse embryo sections F05G06_S161


title: Developing mouse embryo sections F04G06_S160


title: Liver, late batch, control diet, individual 2

description: Gene expression data from liver tissue


title: The miRNA profile of exosomes from HCT29-derived spheres.

city: Taichung

first: Wei-Chung

last: Cheng

address: No.91, Hsueh-Shih Road

country: Taiwan

institute: China Medical University

data_processing:
Initially, the sequences generated went through a filtering process to obtain quality reads (Phred Score >20). Trimmomatics was implemented to trim or remove the reads according to the quality score.
Qualified reads were analyzed using our in-house pipeline (YM500) to clip the 3' adapter sequence and discarding reads shorter than 18 nucleotides. Reads were then aligned  to hg19 genome and MiRBase (version 21).
Expression values were normalized as reads-per-million (RPM).
Genome_build: hg19
Supplementary_files_format_and_content: miRNA_ID represents miRNA identity; RPM value represents the normalized expression value.

growth_protocol: The HCT15 spheres were expanded from the defined stem cell medium cultivation (10 ng/ml bFGF, 10 ng/ml EGF, N2 supplements in DMEM/F12 medium) for 3 weeks. Atmosphere: air, 95%; Carbon dioxide (CO2), 5%. Temperature, 37.0°C.

extract_protocol:
Small RNAs were isolated by miRNeasy kit (Quiagene).
RNA samples were prepared using Illumina sample preparation kit (Illumina, San Diego, CA) according to the TruSeq Small RNA Sample Preparation Guide. The 3′ and 5′ adaptors were ligated to total RNA and reverse transcribed followed by PCR amplification. The enriched cDNA was size-fractionated and purified on a 6% polyacrylamide gel electrophoresis.  Bands containing the 18-40 nucleotide RNA fragments (140-155 nucleotides in length with both adapters) were excised as the small RNA library.

treatment_protocol: Exosome isolation: The condition medium from cancer spheres was collected for exosome purification by differential untracentrifugation.

tag: cell line

value: colon cancer cells

tag: cell subtype

value: HCT29-derived spheres

tag: cellular component

value: Secreted microvesicles

tag: molecule subtype

value: Small RNA


title: eIF2A KO HEK293T #2 arsenite RNA-seq replicate 2

tag: protocol

value: RNA-seq

value: eIF2A KO


title: The miRNA profile of exosomes from parental HCT29 cells.

growth_protocol: The parental HCT15 cells were cultured under complete RPMI medium. Atmosphere: air, 95%; Carbon dioxide (CO2), 5%. Temperature, 37.0°C.

treatment_protocol: Exosome isolation: The exosome-depleted complete RPMI medium was used to collect condition medium for exosome purification by differential ultracentrifugation.

value: parental HCT29 cells


title: The miRNA profile of exosomes from HCT15-derived spheres.

value: HCT15-derived spheres


title: sc-mCherry_2 L2

description:
Dropseq
mCherry-pool2.dge.txt.gz

value: GFP-


title: Liver, late batch, control diet, individual 1

description: Gene expression data from liver tissue

value: liver

tag: diet

value: control

tag: time period

value: Late batch


title: Developing mouse embryo sections F05G02_S353

value: E14 Mouse Embryo

value: Sagigital section


title: Liver, late batch, control diet, individual 5

description: Gene expression data from liver tissue


title: Liver, early batch, low protein diet, individual 5

description: Gene expression data from liver tissue

value: low protein

value: Early batch


title: The miRNA profile of exosomes from parental HCT15 cells.

value: parental HCT15 cells


title: Developing mouse embryo sections F04G02_S352


title: Developing mouse embryo sections F04G01_S256


title: eIF2A KO HEK293T #2 arsenite Ribo-seq replicate 2

value: Ribo-seq

value: arsenite


title: Liver, early batch, low protein diet, individual 4

description: Gene expression data from liver tissue


title: eIF2D KO HEK293T #1 arsenite Ribo-seq replicate 1

value: eIF2D KO


title: Liver, early batch, low protein diet, individual 2

description: Gene expression data from liver tissue


title: Liver, early batch, low protein diet, individual 3

description: Gene expression data from liver tissue


title: Developing mouse embryo sections F03G05_S63


title: eIF2A KO HEK293T #1 arsenite RNA-seq replicate 2


title: eIF2A KO HEK293T #1 arsenite RNA-seq replicate 1


title: Liver, early batch, low protein diet, individual 1

description: Gene expression data from liver tissue


title: eIF2A KO HEK293T #2 arsenite Ribo-seq replicate 1


title: eIF2A KO HEK293T #2 arsenite RNA-seq replicate 1


title: Developing mouse embryo sections F04G05_S64


title: Developing mouse embryo sections F03G06_S159


title: P2_rep1

city: Bronx

first: Thomas

last: Meier

address: 1300 Morris Park Avenue

department: Department of Anatomy & Structural Biology

institute: Albert Einstein College of Medicine, INC

data_processing:
RNA-seq reads were aligned to the HG19 genome assembly using STAR aligner version 2.4.2a (STAR --runThreadN 10 --outSAMtype BAM   SortedByCoordinate --outSAMstrandField intronMotif   --outSAMattributes All --outFilterMultimapNmax 1--outFilterScoreMinOverLread 0.51   --outFilterMatchNminOverLread 0.51   --outFilterMismatchNmax 3   --seedSearchStartLmax 25 --alignIntronMax 50000 --sjdbGTFfile Homo_sapiens.GRCh37.75.gtf --quantMode TranscriptomeSAM  GeneCounts --twopassMode Basic)
Splicing analysis rMATs version 3.2.5
Differential analysis was performed by DESeq2 bioconductor package
Raw counts for gene was counted by featureCounts from subread packageCufflinks (version : 2.2.1 ) was used to calculate FPKM's
Genome_build: hg19
Supplementary_files_format_and_content: Combined FPKM file for all the samples as well as individual FPKM files for each sample in txt format

source_name: HeLa

extract_protocol:
RNA from the different cell lines was extracted using 500 µl TRIzol Reagent (Ambion) directly on 10-cm dishes (cell confluency ∼80%, ∼1,000,000 cells). Lysed cells in TRIzol were scraped into tubes, extracted twice with chloroform, the RNA was precipitated with 0.7 volume isopropanol after addition of 20 µg glycogen, and resuspended in UltraPure distilled water. RNA concentration and quality were determined by Nanodrop (ratio 260/230 and 260/280 above 1.8) and Agilent 2100 BioAnalyzer (RIN above 8). Total RNA was used for northern blot analysis, RiboMethSeq, and RT-PCR and RNase H analysis.
For deep sequencing, total RNA was prepared from 3 separate dishes for each sample and shipped to Novogene Corporation Inc. (Sacramento, CA) for cDNA library preparation (250~300 bp inserts) and Illumina sequencing (PE150). The RNA was prepared and sequenced one year apart in the USA and in China in two batches, one for the P1, KD1a, and KD1b cells and one for the P2 and KD2 cells.

value: HeLa


title: P2_rep2


title: P2_rep3


title: Developing mouse embryo sections F03G02_S351

extract_protocol:
Nuclei were extracted with a permeabilization buffer, sonicated and fixed. cDNA molecules within nuclei are extracted after tagmentation through the use of denaturants.
3' end capture of polyAdenylated transcripts. In situ reverse transcription with barcoded RT primers followed by second strand synthesis, tagmentation and index PCR gives each nucleus and all the RNA molecules contained within it, a unique combination of barcode sequences. These barcodes are then demultiplexed to create single cells in silico.


title: Developing mouse embryo sections F03G01_S255


title: Developing mouse embryo sections F02G06_S158


title: Zebrafish_Control_24hpf_rep1

city: Kunming

first: Junjie

last: Wu

address: No. 66 Gaoyao Village

institute: Yunnan Institute of Fishery Sciences Research

description: Gene expression after morpholino mediated knock down at 24hpf

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Zebrafish Gene Expression Microarray（4*44K，Design ID: 026437） for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: whole body, 24hpf

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Zebrafish was fed in recirculating aquacultural system.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit(Applied Biosystem p/n AM1556) following the manufacturer's instrctions.

treatment_protocol: 1nL morpholino of igf2bp1 was injected into each of embroy at 1-cell stage.

value: whole body

tag: age

tag: genotype/variation


title: WT HEK293T arsenite RNA-seq replicate 2

value: RNA-seq

value: WT


title: Liver, early batch, control diet, individual 5

description: Gene expression data from liver tissue


title: Developing mouse embryo sections F02G02_S350

first: Sanjay

data_processing:
Basecalls performed using bcl2fastq version 2.20
Poly-dT adapters were trimmed using Trimmomatic and aligned to mm10 using STAR. Mapped reads were then deduplicated and assigned to a gene (GENCODE vM15 - mouse). UMIs were enumerated for each cell/gene combination and finally a count matrix was made.
Count matrix was loaded into Monocle3 for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: Count Matrix (matrix marker file- .mtx), Cell Metadata (tab separated values- .tsv), Gene Metadata (tab separated values- .tsv)


title: eIF2A KO HEK293T #1 arsenite Ribo-seq replicate 2

value: eIF2A KO


title: Developing mouse embryo sections F02G05_S62


title: Zebrafish_Knock down_24hpf_rep1

value: knock down


title: P1_rep3


title: Developing mouse embryo sections F02G01_S254


title: eIF2A KO HEK293T #1 arsenite Ribo-seq replicate 1


title: WT HEK293T arsenite Ribo-seq replicate 2


title: Liver, early batch, control diet, individual 3

description: Gene expression data from liver tissue

value: liver


title: Developing mouse embryo sections F01G06_S157


title: WT HEK293T arsenite Ribo-seq replicate 1


title: eIF2A, eIF2D DKO HEK293T #2 RNA-seq replicate 2

value: eIF2A, eIF2D DKO


title: WT HEK293T arsenite RNA-seq replicate 1


title: KD2_rep1

value: Nopp140 knockdown


title: Liver, early batch, control diet, individual 2

description: Gene expression data from liver tissue

value: control


title: P1_rep1


title: KD1b_rep3


title: Liver, early batch, control diet, individual 4

description: Gene expression data from liver tissue


title: KD2_rep2


title: Liver, early batch, control diet, individual 1

description: Gene expression data from liver tissue


title: eIF2A, eIF2D DKO HEK293T #2 RNA-seq replicate 1


title: Developing mouse embryo sections F01G05_S61

value: E14 Mouse Embryo

value: Sagigital section


title: P1_rep2


title: Developing mouse embryo sections E12G06_S156


title: eIF2A, eIF2D DKO HEK293T #1 RNA-seq replicate 2


title: KD2_rep3


title: Developing mouse embryo sections E12G02_S348


title: Developing mouse embryo sections F01G02_S349


title: Developing mouse embryo sections E12G01_S252


title: eIF2A, eIF2D DKO HEK293T #1 RNA-seq replicate 1


title: Developing mouse embryo sections F01G01_S253


title: eIF2A, eIF2D DKO HEK293T #2 Ribo-seq replicate 1


title: KD1a_rep2


title: KD1a_rep1


title: eIF2A, eIF2D DKO HEK293T #1 Ribo-seq replicate 2


title: KD1b_rep2


title: Developing mouse embryo sections E12G05_S60


title: eIF2A, eIF2D DKO HEK293T #1 Ribo-seq replicate 1


title: eIF2D KO HEK293T #2 RNA-seq replicate 2


title: Developing mouse embryo sections E11G05_S59


title: KD1b_rep1


title: Developing mouse embryo sections E11G06_S155


title: eIF2A, eIF2D DKO HEK293T #2 Ribo-seq replicate 2


title: Turner syndrome rep2

city: Xiamen

first: zhiwei

last: zeng

address: Jimei

institute: huaqiao university

description: TS.narrowPeak.txt

data_processing:
Basecalls performed using CASAVA
ATAC-seq reads were aligned to the hg38 genome assembly using BWA
peaks were called using Genrich  with the following setting:  -j -y -r -e chrM -v -q 0.01
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using deeptools with the following setting: -bs 10 –normalized Using CPM –extend Reads –ignore Duplicates
Supplementary_files_format_and_content: peak text files

source_name: Amniotic fluid cells

extract_protocol:
Amniotic fluid cells were cultured and harvested to prepare a single-cell suspension.
First, use transposase for interruption. After the interruption is completed, use VAHTS DNA Clean Beads for purification.

value: Amniotic fluid cells

tag: disease state

value: Turner syndrome


title: NFKB1-Null_Carbocyanine_rep3_P-4_H12

city: Research Triangle Park

first: Christopher

last: Corton

state: NC

address: 109 TW Alexander Dr.

institute: US-EPA

data_processing:
TempO-Seq data are analyzed using the Tempo-SeqR software package which uses the statistical computing language R. The input data analyzed was taken from the FASTQ files. Each file was aligned to a pseudo-transcriptome input using the Bowtie algorithm. The data analysis output is a table of counts with each column representing a sample and each row representing a gene.
Supplementary_files_format_and_content: a table of counts with each column representing a sample and each row representing a gene.

source_name: HeLa cells

growth_protocol: Wild-type and the NFKB1-null HeLa cells were cultured in DMEM media (GIBCO) supplemented with 10% FBS (Omega Scientific, Australia) and 1x penicillin/streptomycin/glutamine. Cells were plated at 8 x10^5 cells per well in 24-well plates and cultured for 20 hours then exposed to test chemicals for 6 hours.

extract_protocol: Following cell lysis in Trizol, total RNA was extracted from each lysate and prepared for gene expression analysis using the human 1500+ Tempo-Seq platform (BioSpyder, Inc, Carlsbad, CA).

treatment_protocol: Chemicals, purchased from Sigma-Aldrich, were ≥ 95% pure. All chemical stock solutions were made in DMSO. After 20 hours of exposure, media was replaced with dosing media containing  IL1beta (1 ng/mL), TNFalpha (5 ng/mL), chlorhexidine diacetate (50 µM), or carbocyanine (50 µM) in DMSO (0.05%). Cells were treated for 6 hours then media was removed and cells lysed with 0.3 mL Trizol.

tag: agent

value: Carbocyanine

tag: concentration

value: 50 uM


title: NFKB1-Null_Carbocyanine_rep2_P-4_H11


title: Turner syndrome rep1

description: TS.narrowPeak.txt


title: KD1a_rep3

tag: treatment


title: Developing mouse embryo sections E11G02_S347

city: Seattle

last: Srivatsan

address: 3720 15TH Ave NE Genome Sciences S Foefe Bldg

institute: University of Washington


title: eIF2D KO HEK293T #2 RNA-seq replicate 1

value: eIF2D KO


title: Developing mouse embryo sections E11G01_S251


title: Developing mouse embryo sections E10G05_S58


title: eIF2D KO HEK293T #2 Ribo-seq replicate 2

value: Ribo-seq


title: eIF2D KO HEK293T #2 Ribo-seq replicate 1


title: NFKB1-Null_Carbocyanine_rep1_P-4_H10

value: HeLa


title: eIF2D KO HEK293T #1 RNA-seq replicate 2

value: RNA-seq


title: WT_Carbocyanine_rep2_P-4_H08

value: Wild type


title: Sample 23_genomic DNA from stomach tissue 23

city: Shillong

first: Srimoyee

last: Ghosh

state: Meghalaya

address: Umshing-Mawkynroh

department: Zoology

country: India

institute: North Eastern Hill University

description: Cancer stomach tissue sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: cancer_stomach tissue

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from Stomach tissue samples using Qiagen DNeasy Kit according to standard instructions

value: Stomach tissue

tag: tissue type

value: cancer

tag: histopathology

value: Adenocarcinoma


title: eIF2D KO HEK293T #1 RNA-seq replicate 1

tag: genotype


title: WT_Carbocyanine_rep3_P-4_H09


title: Developing mouse embryo sections E10G02_S346

tag: tissue

tag: sample type


title: Developing mouse embryo sections E10G01_S250


title: eIF2D KO HEK293T #1 Ribo-seq replicate 2


title: Sample 19_genomic DNA from stomach tissue 19

description: Cancer stomach tissue sample


title: Sample 15_genomic DNA from stomach tissue 15

description: Cancer stomach tissue sample


title: Sample 24_genomic DNA from stomach tissue 24

description: normal stomach tissue sample

source_name: normal_stomach tissue

value: normal

value: Normal stomach tissue


title: Developing mouse embryo sections E09G06_S153


title: Sample 16_genomic DNA from stomach tissue 16

description: normal stomach tissue sample


title: Sample 21_genomic DNA from stomach tissue 21

description: Cancer stomach tissue sample


title: WT_Carbocyanine_rep1_P-4_H07

tag: cell line


title: Developing mouse embryo sections E09G05_S57


title: NFKB1-Null_B2_rep2_P-4_H05

value: Chlorhexidine diacetate


title: NFKB1-Null_B2_rep3_P-4_H06


title: Developing mouse embryo sections E09G02_S345

value: E14 Mouse Embryo


title: Sample 20_genomic DNA from stomach tissue 20

description: normal stomach tissue sample


title: eIF2A KO HEK293T #2 RNA-seq replicate 2

value: eIF2A KO


title: NFKB1-Null_B2_rep1_P-4_H04


title: Sample 22_genomic DNA from stomach tissue 22

description: normal stomach tissue sample


title: Developing mouse embryo sections E10G06_S154

value: Sagigital section


title: eIF2A KO HEK293T #2 RNA-seq replicate 1


title: eIF2D KO HEK293T #1 Ribo-seq replicate 1


title: Sample 18_genomic DNA from stomach tissue 18

description: normal stomach tissue sample


title: Developing mouse embryo sections E09G01_S249


title: eIF2A KO HEK293T #2 Ribo-seq replicate 2


title: Developing mouse embryo sections E08G06_S152


title: WT_B2_rep2_P-4_H02


title: eIF2A KO HEK293T #2 Ribo-seq replicate 1


title: WT_B2_rep3_P-4_H03


title: Developing mouse embryo sections E08G05_S56


title: Sample 11_genomic DNA from stomach tissue 11

description: Cancer stomach tissue sample


title: eIF2A KO HEK293T #1 RNA-seq replicate 2


title: eIF2A KO HEK293T #1 RNA-seq replicate 1


title: NFKB1-Null_TNFa_rep3_P-4_G12

value: TNFa

value: 0.5 ng/mL


title: Sample 17_genomic DNA from stomach tissue 17

description: Cancer stomach tissue sample


title: Developing mouse embryo sections E08G01_S248


title: eIF2A KO HEK293T #1 Ribo-seq replicate 2


title: WT_B2_rep1_P-4_H01

value: 50 uM


title: Developing mouse embryo sections E07G06_S151


title: Developing mouse embryo sections E08G02_S344


title: NFKB1-Null_TNFa_rep1_P-4_G10


title: Sample 13_genomic DNA from stomach tissue 13

description: Cancer stomach tissue sample


title: eIF2A KO HEK293T #1 Ribo-seq replicate 1


title: Sample 12_genomic DNA from stomach tissue 12

description: normal stomach tissue sample


title: WT_TNFa_rep3_P-4_G09


title: Sample 10_genomic DNA from stomach tissue 10

description: normal stomach tissue sample


title: Developing mouse embryo sections E07G02_S343


title: WT_TNFa_rep2_P-4_G08


title: WT

city: Jongro-gu

first: Dongjin

last: Jeong

state: Seoul

address: 103 Daehak-ro

country: South Korea

institute: Seoul National University

description: WT

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Raw data were extracted using Illumina GenomeStudio v2011.1 and all data analysis and visualization of differentially expressed genes was conducted using R 2.14.0
a higher signal value was required to obtain a detection p-value < 0.05. Selected gene signal values were transformed by logarithm and statistical significance of the expression data determined using fold change

source_name: Mouse joint tissue

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion)

growth_protocol: Each mice was injected sera of K/BxN mice to induce AIA. Mice were sacrificed for

extract_protocol: Used RNeasy Mini kit (Qiagen)

value: Joint


title: Sample 6_genomic DNA from stomach tissue 6

description: normal stomach tissue sample


title: WT HEK293T RNA-seq replicate 3

value: WT


title: Sample 9_genomic DNA from stomach tissue 9

description: Cancer stomach tissue sample


title: Developing mouse embryo sections E07G05_S55


title: gld

description: gld


title: WT HEK293T RNA-seq replicate 4


title: Sample 7_genomic DNA from stomach tissue 7

description: Cancer stomach tissue sample

value: Mucinous Adenocarcinoma


title: Developing mouse embryo sections E07G01_S247


title: WT HEK293T Ribo-seq replicate 2

value: RNA-seq


title: Sample 8_genomic DNA from stomach tissue 8

description: normal stomach tissue sample


title: hiPSC line_44

last: Chen

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Genotyping was performed using the default parameters in the Birdseed v2 algorithm of Genotyping Console (GTC) 4.2 software (Affymetrix). As a quality control for the genotyping, Contrast QC values were calculated as implemented in the GTC 4.2, and samples used passed the recommended values. Genome annotations applied in data analysis referred to the human reference assembly GRCh37/hg19 as provided by the Affymetrix annotation file
primary data description: Genotype-matrix_42_hPSC_lines.txt contains Genotype Call (SNP call, Forward Strand Base Calls): AA, AT, AC, AG, TT, TC, TG, CC, CG, GG, and NoCall; 'Signal' = Summarized signal

label: cy3, cy5

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: cells were culture in mTESR medium and passaged every 5 days.

extract_protocol: Genomic DNA was extracted from mononuclear cell preparations of leukemic blasts obtained from peripheral blood or bone marrow at diagnosis using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: cell type

value: induced pluripotent stem cell (iPSC) line


title: Developing mouse embryo sections E06G06_S150


title: hiPSC line_43


title: WT_TNFa_rep1_P-4_G07

value: Wild type

value: HeLa


title: Sample 5_genomic DNA from stomach tissue 5

description: Cancer stomach tissue sample

value: Stomach tissue

value: cancer

value: Adenocarcinoma


title: hiPSC line_40


title: WT HEK293T Ribo-seq replicate 1


title: hiPSC line_42


title: Developing mouse embryo sections E06G05_S54


title: WT HEK293T CHX replicate 2

value: Ribo-seq


title: NFKB1-Null_IL-1B_rep1_P-4_G04

value: 0.1 ng/mL


title: Sample 14_genomic DNA from stomach tissue 14

description: normal stomach tissue sample

value: normal

value: Normal stomach tissue


title: Developing mouse embryo sections E06G02_S342

value: E14 Mouse Embryo

value: Sagigital section


title: WT HEK293T LTM replicate 2

value: lactimidomycin


title: Developing mouse embryo sections E06G01_S246


title: Developing mouse embryo sections E05G06_S149


title: NFKB1-Null_IL-1B_rep2_P-4_G05


title: NFKB1-Null_TNFa_rep2_P-4_G11

value: TNFa

value: 0.5 ng/mL


title: hiPSC line_41


title: lpr

description: lpr

value: Joint


title: WT_IL-1B_rep2_P-4_G02


title: NFKB1-Null_IL-1B_rep3_P-4_G06


title: hiPSC line_39


title: Sample 2_genomic DNA from stomach tissue 2

description: normal stomach tissue sample


title: WT HEK293T LTM replicate 1

value: WT


title: WT HEK293T CHX replicate 1


title: WT HEK293T RNA-seq replicate 1

value: RNA-seq


title: WT HEK293T RNA-seq replicate 2


title: NFKB1-Null_Control_rep3_P-4_F10

value: Control


title: WT_IL-1B_rep1_P-4_G01

value: Wild type

value: HeLa


title: Developing mouse embryo sections E05G05_S53


title: hiPSC line_38

value: induced pluripotent stem cell (iPSC) line


title: hiPSC line_37


title: Developing mouse embryo sections E05G02_S341


title: hiPSC line_36


title: eIF3D KI HEK293T RNA-seq replicate 2

value: eIF3D-V5 KI


title: Developing mouse embryo sections E05G01_S245


title: NFKB1-Null_Control_rep2_P-4_F09


title: hiPSC line_35


title: NFKB1-Null_Control_rep1_P-4_F08


title: eIF3D KI HEK293T RNA-seq replicate 1


title: hiPSC line_34


title: Developing mouse embryo sections E04G06_S148


title: Developing mouse embryo sections E04G02_S340


title: Developing mouse embryo sections E04G05_S52


title: WT_Control_rep3_P-4_F07


title: Developing mouse embryo sections E04G01_S244


title: 40S eIF3B Sel-TCP-seq replicate 1

value: Sel-TCP-seq


title: WT_Control_rep1_P-4_F05


title: hiPSC line_32


title: 40S eIF3D-V5 Sel-TCP-seq replicate 1


title: RppH_plus

city: Nagoya

first: Kenji

last: Ichiyanagi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

institute: Nagoya University

data_processing:
The adaptor sequence was removed from the 3’ end of the reads by cutadapt (with an option -a AGATCGGAAGAGCACACGTCT), and reads that did not contain the adaptor sequence were discarded.
The retained reads were analyzed by using RepeatMasker.
Supplementary_files_format_and_content: normalized counts

source_name: brain

extract_protocol:
Total brain RNA was prepared by using isogene. Five hundred nanograms of RNAs were treated (or not treated as a control) with RNA 5' Pyrophosphohydrolase (RppH, New England Biolab) for 1 hour at 37 ºC in a 50-μl reaction mixture containing 1X Thermopol buffer (New England Biolab), and the reaction was stopped by phenol-chloroform extraction and ethanol precipitation.
NEBNExt small RNA library preparation kit (New England Biolab) was then used for constructing sequence libraries.  The libraries were run on a p% polyacrylamide gel and DNAs of 240 to 380 bp (corresponding to insert size of 113 to 253 bp) were purified from the gel.
The libraries were sequenced on MiSeq with MiSeq Reagent Kit v2 (300 cycles) in the 300-bp single-end mode

tag: strain

value: brain

tag: treatment of rna

value: RNA 5' Pyrophosphohydrolase (RppH)

tag: molecule subtype

value: medium length RNA (115-255 nt)


title: hiPSC line_31


title: hiPSC line_33


title: 40S eIF3D-V5 input replicate 1

tag: protocol


title: Developing mouse embryo sections E03G02_S339

value: E14 Mouse Embryo


title: Sample 3_genomic DNA from stomach tissue 3

description: Cancer stomach tissue sample

value: Stomach tissue

value: cancer

value: Signet Ring cell Adenocarcinoma


title: hiPSC line_29


title: Sample 1_genomic DNA from stomach tissue 1

description: Cancer stomach tissue sample

value: Adenocarcinoma


title: hiPSC line_28


title: Developing mouse embryo sections E03G05_S51

value: Sagigital section


title: 40S eIF3D-V5 input replicate 2


title: 40S eIF3B Sel-TCP-seq replicate 2

value: WT


title: Developing mouse embryo sections E03G01_S243


title: RppH_minus (Intact)


title: WT_Control_rep2_P-4_F06


title: UL79HF Pol II ChIP-seq

city: Iowa City

first: Jeffery

state: IA

address: SW34 GH, Department of Internal Medicine, University of Iowa. 200 Hawkins Drive

department: Departments of Internal Medicine and Epidemiology

institute: University of Iowa and Iowa City Veterans Affairs Health Care System

data_processing:
Adapter trimming using trim_galore 0.4.4.
Alignment of trimmed reads to concatenated hg38 (human), FJ616285.1 or KF297339.1 (Towne and TB40, respectively), and, for samples that included moth spike-in cells, JQCY02.1 (spodoptera) genome assemblies.
Deduplication of mapped reads according to unique molecular identifiers using dedup (https://github.com/P-TEFb/dedup).
Reads were parsed out based on the genome to which they aligned.
Bedgraphs were generated using bedTools genomecov 2.26 and Data were normalized by library size and spike-in reads accorind to Ball et. al. (2019, PMID: 30743000).
Bigwigs were generated using kentUtils.
Custom UCSC track hubs were set up for Towne and TB40/E data.
For analysis of host transcription effects upon depletion of UL87LTF or UL79LTF and annotation of gene 5' ends based on PRO-Seq data, we applied a new truQuant algorithm that utilizes our previously published tsrfinder tool. Our application of these tools is described in the manuscript. Source code is avaliable on GitHub at https://github.com/meierjl/truQuant.
Genome_build: hg38 (human), FJ616285.1 (HCMV Towne), KF297339.1 (HCMV TB40/E), JQCY02.1 (Spodoptera).
Supplementary_files_format_and_content: bigwigs contain PRO-Seq pileups, bigwigs for ChIP-Seq samples

source_name: HCMV-infected primary human foreskin fibroblast

growth_protocol: HFF were isolated and cultured as described in the manuscript. Cells were maintained in Minimum Essential Medium and grown to confluence for at least one week before infection. All HFF used for these studies were at passage number ≤ 6.

extract_protocol:
Nuclei isolation was carried out as described in Parida et. al. (2019, PMID: 30755505) and Li et. al. (2020, PMID: 32251483) .
PRO-Seq library preparation to extract and sequence nascent RNAs and ChIP-seq library preparation to extract and sequence is carefully detailed in the manuscript and was carried out as previously described by  Li et. al. (2020, PMID: 32251483), with noted modifications.

treatment_protocol:
Cells were treated with 16% paraformaldehyde to a final concentration of 1% for 10 min at room temperature. The crosslinking was stopped by adding Tris (pH 7.6) at final concentration 1.33 M. Cells were washed twice with ice-cold PBS and pelleted by centrifugation.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

value: HFF

tag: infection

value: HCMV strain TB40 BAC4

tag: infection duration

value: 72 hours

tag: ltf depletion

tag: chip antibody

value: Pol II antibody (Santa Cruz Biotechnology, catalog# sc-55492, lot# H2019)

tag: fraction

value: nascent RNA


title: hiPSC line_26

value: induced pluripotent stem cell (iPSC) line


title: Developing mouse embryo sections E03G06_S147


title: UL79HF HA ChIP-seq

value: anti-HA antibody (Cell Signaling, catalog# C29F4, lot# 9)


title: Developing mouse embryo sections E02G06_S146


title: hiPSC line_27


title: 40S eIF3D-V5 Sel-TCP-seq replicate 2

value: Sel-TCP-seq

value: eIF3D-V5 KI

tag: treatment


title: UL87H Pol II ChIP-seq

value: HCMV strain Towne BAC


title: Developing mouse embryo sections E02G05_S50

value: E14 Mouse Embryo


title: hiPSC line_30


title: not IRIS, 15924

city: Salvador

first: Artur

middle: Trancoso Lopo

last: Queiroz

address: Rua Waldemar Falcão, 121

country: Brazil

institute: Instituto Gonçalo Moniz

data_processing:
bcl2fastq software (Illumina inc.)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with trimmomatic, then mapped to transcriptome GRCh38 version using salmon
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample and Matrix table with raw mRNA counts for every mRNA and every sample

source_name: whole blood

extract_protocol:
RNA was isolated using the miRNeasy Serum/Plasma Advanced Kit (50) (cat# 217204) according to the manufacturers’ recommendation (QIAGEN).
The library preparation was done using the QIAseq RNA Library Kit (QIAGEN). A total of 5ul total RNA was converted into RNA NGS libraries. Adapters containing UMIs were ligated to the RNA. Then RNA was converted to cDNA. The cDNA was amplified using PCR (22 cycles) and during the PCR indices were added. After PCR, the samples were purified. Library preparation QC was performed using either Bioanalyzer 2100 (Agilent) or TapeStation 4200 (Agilent).

tag: disease state

value: not IRIS

tag: iris condition

value: not Mycobacterial

tag: gender

value: Male

tag: bmi

tag: age

value: whole blood


title: Exp2 48h WT PFA Flavo Pro-seq

treatment_protocol:
Cells were treated with Flavo 1h and PFA 48h during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

value: 48 hours

value: Flavo 1h and PFA 48h


title: UL87H HA ChIP-seq

value: HFF


title: hiPSC line_25


title: Developing mouse embryo sections E02G01_S242

tag: genotype

tag: tissue

tag: sample type

value: Sagigital section


title: not IRIS, 15922


title: hiPSC line_24

tag: cell type


title: not IRIS, 15923


title: hiPSC line_22


title: hiPSC line_21


title: hiPSC line_20


title: Exp2 12h WT Flavo Pro-seq

treatment_protocol:
Cells were treated with Flavo 1h and DMSO 12h during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

value: HCMV strain TB40 BAC4

value: 12 hours

value: WT

value: Flavo 1h and DMSO 12h


title: Sample 4_genomic DNA from stomach tissue 4

description: normal stomach tissue sample

value: Stomach tissue

tag: tissue type

value: normal

tag: histopathology

value: Normal stomach tissue


title: Developing mouse embryo sections E02G02_S338


title: IRIS, 15914

value: IRIS

value: Mycobacterial

value: Female


title: Exp2 48h WT Flavo Pro-seq

treatment_protocol:
Cells were treated with Flavo 1h and DMSO 48h during the final hours of infection before harvest.
HFF were infected with the indicated virus at an MOI of 1-3 for the indicated duration. Cells were treated with the indicated drugs (dTAG, Flavo, and/or PFA) or appropriate vehicle controls for the indicated times during the final hours of infection before harvest.

tag: infection

value: Flavo 1h and DMSO 48h

value: nascent RNA


title: Developing mouse embryo sections E01G05_S49

value: E14 Mouse Embryo