title: Replicate 3_24h_SAA

city: Ulm

first: Ann-Kathrin

last: Gaiser

address: Helmholtzstr. 20

institute: Ulm University

description: gene expression data from SAA-treated macrophages of biological replicate 3 at 24 h time point

hyb_protocol: according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Affymetrix® Expression Console™ Software for RMA normalization, BRB Array Tools for statistical analysis

label: biotin

source_name: peritoneal macrophages

growth_protocol: To obtain peritoneal macrophages, freshly isolated peritoneal cells were seeded in DMEM/F12 GlutaMAX, 10% heat-inactivated FCS, 10 mM L-glutamine, and penicillin/streptomycin in Falcon tissue-culture-treated 6-well plates (Corning) at a cell density of 5 Mio cells/well. After 4 h, non-adherent cells were removed by three intense wash steps with pre-warmed PBS. Peritoneal macrophages were further cultured for 2 days in above mentioned medium before treatment.

extract_protocol: Qiagen RNeasy Mini Kit

treatment_protocol: Treatment of peritoneal macrophages was started on day 2 post-isolation. Macrophages were treated with 50 µM mSAA1.1 (= 0.58 mg/ml) or 5.8% Ampuwa in culture medium for 6 or 24 h, respectively.

value: NMRI

tag: gender

value: female

tag: age (weeks)

value: 50 uM mSAA1.1 in medium for 24 h


title: Replicate 3_24h_Control

status: Public on Jul 20 2021

type: RNA

country: Germany

description: gene expression data from control macrophages of biological replicate 3 at 24 h time point

molecule: total RNA

organism: Mus musculus

label_protocol: Whole Transcript (WT) Sense Target Labeling Assay

tag: strain

tag: treatment

value: 5.8% Ampuwa in medium for 24 h


title: Lung_progenitors_mB2-3_3

type: SRA

city: Kyoto

first: Shimpei

last: Gotoh

address: 53 Kawaharacho, Shogoin, Sakyo-ku

department: Center for iPS cell Research and Application

country: Japan

institute: Kyoto University

library_source: transcriptomic

data_processing:
Sequenced reads from fasq files were mapped to GRCh37/hg19 whole genome using HISAT2.
Transcripts Per Kilobase Million (TPM) value of each gene was calculated using Stringtie.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample .

organism: Homo sapiens

source_name: 201B7 iPS cells

growth_protocol: Human iPS cell-derived lung progenitors were maintained under 5% CO2 at 37°C. Please refer to our manuscript about the medium in detail.

extract_protocol:
Total RNA was extracted using PureLink RNA mini kit (Thermo Fisher Scientific) or NucleoSpin RNA Plus XS (Takara Bio) according to manufacturer's protocol.
Library preparation was performed with Nextera XT DNA Library Prep Kit (Illumina) according to the manufacturer's instructions.

tag: cell line

value: Lung_progenitors_mB2-3 hiPSC line

tag: compound


title: spinal cord-culture-1 [AAATAC]

city: Neuherberg

first: Pawel

last: Smialowski

address: Ingolstädter Landstraße 1

institute: Helmholtz Zentrum Muenchen

data_processing:
Sixteen bases were sequenced within the first read to obtain cellular and molecular barcodes, and 50 bases were sequenced in the second read into the cDNA fragment
An additional eight bases were sequenced to obtain the i7 barcode
Gene-based transcripts counts were obtained by running the zUMI pipeline (Parekh et al., 2018) (version 0.0.2) using Ensembl annotation release 81
Genome_build: Ensembl annotation release 81
Supplementary_files_format_and_content: Gene-based transcripts counts

source_name: astrocytes

growth_protocol: Astrocytes were isolated via ACSA2-MACS-sorting and either immediately processed with PicoPure klt or seeded in grown for 7 days in astro medium (DMEM/F12, 10% FBS, 2% B27, P/S, Egf, Fgf, 10ng/ml). Cells were then trypsinized, seeded in 6-well plates and collected the subsequent day.

extract_protocol:
Cells were trypsinized, collected by centrifugation, and lyzed with lysis buffer from PicoPure kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: isolation

value: MACS-sorted

tag: cultured

value: culture

tag: age


title: HDX47_SLY_FRT_1: Tomato infected by S. sclerotiorum rep1 [re-analysis]

city: Castanet tolosan

first: Sylvain

last: Raffaele

address: 28 chemin de borde rouge

country: France

institute: INRAE

description: re-analysis of GSM2850651 in GSE106811

data_processing:
HiSeq control software 2.2.58, RTA 1.18.64.0, Illumina Casava1.8.2 software used for basecalling.
Trimmomatic v0.36 was employed to trim raw reads with settings for single- or paired-end sequencing and the following settings for paired-end: ILLUMINACLIP:TruSeq2-PE.fa:5:30:10 SLIDINGWINDOW:3:18 LEADING:6 TRAILING:6 MINLEN:90
FastQC v0.11.5 (Brabham bioinformatics) was used to perform quality control of the trimmed reads. Mapping was conducted with HISAT2 (Kim et al., 2015) with --max-intronlen 500 -k 1 against the S. sclerotiorum isolate 1980 reference genome
Sorted BAM files and indices were generated with samtools v1.7
FPKM (fragments per kilobase of transcript per million mapped reads) tables were generated using the Cufflinks function cuffnorm with --compatible-hits-norm --library-norm-method classic-fpkm
Genome_build: S. sclerotiorum 1980 version 2 (GCA_001857865.1); S. trifoliorum SwB9 v1 (PRJEB36746/ERZ1667436 at https://www.ebi.ac.uk/ena)
Supplementary_files_format_and_content: tab-delimited text files include total count of uniquely mapped reads per gene for each Sample

organism: Sclerotinia sclerotiorum 1980 UF-70

source_name: Periphery of ~20mm wide disease lesion on leaves

growth_protocol: Plants were  grown in Jiffy pots under controlled conditions at 23°C, with a 9 hour light period at intensity of 120 μmol/m²/s.

extract_protocol:
The edge and center of developed mycelial colonies (~20 mm diameter) was harvested and stored in liquid nitrogen. Samples were ground with metal beads (2.5 mm) in a Retschmill apparatus (24hertz for 2x1min) before solubilizing in 1mL Trizol reagent (ThermoFisher) and left for 5 min at RT. Chloroform (200 µL) was added and mixed thoroughly before incubating for 3 min at RT. After centrifugation at ~12,000g (4°C) for 15min, the upper aqueous phase was recovered and nucleic acids were precipitated by adding 2µL GlycoBlue (Ambion) and 500µL isopropanol (10 min at -20°C). After centrifugation at ~15,000g (4°C) for 15min, pellets were washed twice with 70% ethanol before drying and resuspended in RNAse-free water. To eliminate chloroform traces, water resuspended nucleic acids were further cleaned using an RNA extraction kit (Quiagen) following manufacturer’s instructions. Genomic DNA was removed by DNase treatment (TURBO DNase; Ambion) following manufacturer’s instructions. The quality and concentrations of RNAs preparations were assessed with an Agilent apparatus and chips (nano).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: S. sclerotiorum strain 1980 was subcultured on Potato Dextrose Agar plates at 22°C. For inoculations, a 5-mm wide agar plug containing actively growing S. sclerotiorum mycelium was placed at the center of a Petri dish or on the adaxial surface of leaves on 5-week old plants. The border (ring of ~5mm wide) and center of colonies were collected with a scalpel and frozen in liquid nitrogen.

tag: tissue

value: Mycelium from leaves of 5-week old plants

value: in planta (Sly)


title: HDX54_SLY_NEC_3: Tomato infected by S. sclerotiorum rep3

source_name: Center of ~20mm wide disease lesion on leaves


title: PD_1 decidual leukocytes-scRNA-seq

city: Beijing

first: Yan-Ling

last: Wang

state: Beijing

address: Beichen West Rd., Chaoyang, Beijing

department: State Key Laboratory of Stem Cell and Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
scRNA-Seq: We checked the quality of raw sequencing data by FastQC software.  We used 10x genomics cellranger count pipeline 2.0.0 to analyze the sequencing data and generated the single cell information, once for each individual sample. All the cells in different batches were merged together by cellranger aggr pipeline and normalized by equalizing the read depth among libraries. The final result was the matrix of all cells and their global gene expressions.
Genome_build: GRCh38
Supplementary_files_format_and_content: scRNA-Seq: UMI counts matrix with gene and barcode annotations

molecule: polyA RNA

source_name: CD45+ leukocytes

extract_protocol:
RNA were prepared for sequencing
Cell instrument to generate a single cell Gel bead in Emulsion(GEM). Single cell RNA libraries were prepared  for sequencing according to standard Illumina protocols accompanying the Single Cell 3’ Reagent Kits v2 (10X Genomics)

treatment_protocol: The fresh tissue samples were gently triturated with GentelMACS Dissociator (Miltenyi Biotec, Germany) in the RPMI-1640 medium (Invitrogen) and enzymatically digested twice for 30 minutes in 37℃ shaker with 1.6 mg/ml type IV collagenase (9001121, Gibco) and 10U/ml type I DNase (DN25, Sigma). the suspended cells were subsequently passed through 60 mesh and 200 mesh cell strainers, and centrifuged at 1000rpm for 10 min. After the supernatant was removed, the pelleted cells diluted 1:1 by PBS, followed by Ficoll-Paque Plus (17-1440-02, GE Healthcare,) separation, after washing with 1x PBS, then the lymphocytes were centrifuged at 1000rpm for 10 min. the cell pellets were resuspended in PBS, The lymphocytes were stained with eFluor 506-viability dye (65-0866-14, ebioscience) and FITC-labeled anti-CD45 antibody (11-0459-42, ebioscience), then subjected to FACS sorting to obtain CD45+ lymphocytes.

tag: ethnicity

value: Chinese

value: Uterus

tag: disease

value: recurrent spontaneous abortion (RSA) patient


title: ND_3 decidual leukocytes-scRNA-seq

value: normal pregnancy


title: Replicate 3_6h_Control

description: gene expression data from control macrophages of biological replicate 3 at 6 h time point

value: 5.8% Ampuwa in medium for 6 h


title: Replicate 2_6h_Control

description: gene expression data from control macrophages of biological replicate 2 at 6 h time point


title: Replicate 2_6h_SAA

description: gene expression data from SAA-treated macrophages of biological replicate 2 at 6 h time point

value: 50 uM mSAA1.1 in medium for 6 h


title: Replicate 3_6h_SAA

description: gene expression data from SAA-treated macrophages of biological replicate 3 at 6 h time point


title: Replicate 2_24h_SAA

description: gene expression data from SAA-treated macrophages of biological replicate 2 at 24 h time point


title: Replicate 2_24h_Control

description: gene expression data from control macrophages of biological replicate 2 at 24 h time point


title: HDX33_ATH_NEC_3: Arabidopsis infected by S. sclerotiorum rep3 [re-analysis]

description: re-analysis of GSM3212963 in GSE116194

value: in planta (Ath)


title: NK_input_RNA1

city: Hefei

first: Zhigang

last: Tian

state: Anhui

address: Huangshan Road，number 443

institute: Univerity of Science and Technology of China

data_processing:
Illumina Casava1.7 software used for basecalling.
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using fastp.
We used HISAT2 (Version 1.0) to map reads to the genome of Mus musculus (GRCm38) with default parameters.
Mapped reads of IP and input libraries were provided for R package exomePeak (Version 1.8), which identifies m6A peaks with bed or bam format that can be adapted for visualization on the UCSC genome browser or IGV software (http://www.igv.org/).
HOMER (Version 4.1) were used for de novo motif finding followed by localization of the motif with respect to peak summit by perl scripts in house. Called peaks were annotated by intersection with gene architecture using ChIPseeker (Version 1.0). Then StringTie (Version 1.0) was used to perform expression level for all mRNAs from input libraries by calculating FPKM (FPKM = [total_exon_fragments/mapped_reads(millions)×exon_length(kB)]). The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and p value < 0.05 by R package edgeR (Version 4.1).
Genome_build: GRCm38
Supplementary_files_format_and_content: peak text file

source_name: Spleen

extract_protocol:
The poly (A) mRNA fractions was fragmented into oligonucleotides of length ~100 nt using divalent cations under an increased temperature. Then, the cleaved RNA fragments were incubated with m6A-specific antibody, followed by construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
MeRIP-seq

tag: cell type

value: Splenic NK cell

tag: rip-antibody

value: Spleen


title: NK_m6A-MeRIP-rep2

value: m6A-specific antibody (Synaptic Systems, Goettingen, Germany)


title: NK_m6A-MeRIP-rep1


title: ND_1 decidual leukocytes-scRNA-seq


title: HDX32_ATH_NEC_2: Arabidopsis infected by S. sclerotiorum rep2 [re-analysis]

description: re-analysis of GSM3212962 in GSE116194


title: Replicate 1_24h_Control

description: gene expression data from control macrophages of biological replicate 1 at 24 h time point

value: NMRI

value: female


title: RCLG37_2

city: Wuxi

first: Nai-Xin

last: Lin

address: lihu avenue

institute: Jiangnan University

data_processing:
Illumina Casava software used for basecalling.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.  And then FPKM of each gene was calculated based on the length of the gene and  reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and  is currently the most commonly used method for estimating gene expression levels.
Supplementary_files_format_and_content: FPKM

organism: Komagataella pastoris

source_name: cell pellet

growth_protocol: samples were cultured in YPD medium

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

treatment_protocol: samples grew under normal and high temperature

tag: genotype

value: evolved

tag: culture temperature

value: high temperature


title: HDX31_ATH_NEC_1: Arabidopsis infected by S. sclerotiorum rep1 [re-analysis]

description: re-analysis of GSM3212961 in GSE116194


title: RCLG37_3


title: NK_RIP-input_RNA2

data_processing:
Illumina Casava1.7 software used for basecalling. Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adapter sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing.
Clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
The de-duplicated consensus sequences were used for protein binding site analysis. They were mapped to the reference genome of mus musculus GRCm38 using STAR software (version 2.5.3a) with default parameters. The RSeQC (version 2.6) was used for reads distribution analysis.
The exomePeak (Version 3.8) software was used for peak calling. Peaks were annotated using bedtools (Version 2.25.0). The deepTools (version 2.4.1) was used for peak distribution analysis. The differentially binding peaks were identified by a python script, using fisher test.
Sequence motifs enriched in peak regions were identified using Homer (version 4.10).
Genome_build: GRCm38
Supplementary_files_format_and_content: Mettl3-binding gene expression txt file

extract_protocol:
NK cells were treated with cell lysis buffer and Mettl3-mRNA complexes were isolated with antibody.
The stranded RNA sequencing library was constructed by using TruSeq Stranded mRNA Library Prep Kit for Illumina (cat. 20020594) following the manufacturer’s instruction. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.


title: NK_RIP-input_RNA3


title: HDX35_ATH_FRT_2: Arabidopsis infected by S. sclerotiorum rep2 [re-analysis]

description: re-analysis of GSM2850646 in GSE106811


title: NK_input_RNA2


title: Replicate 1_24h_SAA

description: gene expression data from SAA-treated macrophages of biological replicate 1 at 24 h time point

value: 50 uM mSAA1.1 in medium for 24 h


title: NK_RIP-input_RNA1


title: RCLG37_1


title: ND_2 decidual leukocytes-scRNA-seq


title: Replicate 1_6h_SAA

description: gene expression data from SAA-treated macrophages of biological replicate 1 at 6 h time point


title: NK_Mettl3-RIP-rep3

value: anti-Mettl3 antibody (CST, ab195352)


title: Replicate 1_6h_Control

description: gene expression data from control macrophages of biological replicate 1 at 6 h time point


title: HDX34_ATH_FRT_1: Arabidopsis infected by S. sclerotiorum rep1 [re-analysis]

description: re-analysis of GSM2850645 in GSE106811

value: Mycelium from leaves of 5-week old plants


title: RCLG30_3

value: normal temperature


title: NK_Mettl3-RIP-rep2


title: RCLG30_2


title: HDX60_PDA_NEC_3: PDA plate rep3 [re-analysis]

description: re-analysis of GSM3212960 in GSE116194

source_name: Center of ~20mm wide mycelium colony

value: Mycelium from in vitro culture

value: in vitro (PdaNec)


title: SHEP Cell Control replicate3

city: Houston

first: Eveline

last: Barbieri

state: Texas

address: 1102 Bates Street

department: Department of Pediatrics

country: USA

institute: Baylor College of Medicine

description: Gene expression from SHEP Cell Control replicate 3

hyb_protocol: cDNA was synthesized from 200 ng of total RNA by reverse transcription using T7 promoter-(N6) oligonucleotides as primers. cDNA was then fragmented and hybridized for 17 h at 45oC to GeneChip® Human Gene 2.0 ST Arrays (Affymetrix).

data_processing: Raw microarray CEL files were processed in R (3.4.1) using the biocLite Affy package (Gautier et al., 2004) function rma and the hugene.2.0st annotation.

source_name: SHEP Cells

growth_protocol: Human NB cell lines including SHEP, SK-N-AS, SH-SY5Y, LAN5, IMR32, SK-N-BE, NGP (all ATCC), and CHLA255 (Metelitsa Lab, BCM, Houston, TX) were maintained in RPMI 1640 medium (Lonza, Allendale, NJ) containing 10% FBS (Germini Bio-Products, West Sacramento, CA), 4 mM L-glutamine (Thermo Fisher Scientific, Waltham, MA), and 1% streptomycin/penicillin (Thermo Fisher Scientific).

extract_protocol: Total RNA was extracted and processed by the random primed RT-IVT-RT method using the GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix, Santa Clara CA).

treatment_protocol: To conditionally overexpress CHAF1A, a Tet-On inducible lentivector (pHAGE-ind-Lenti-CHAF1A-HA-neo) was used

value: SHEP

value: neuroblastoma

value: control

tag: timepoint


title: HDX59_PDA_NEC_2: PDA plate rep2 [re-analysis]

description: re-analysis of GSM3212958 in GSE116194


title: NK_Mettl3-RIP-rep1


title: HDX36_ATH_FRT_3: Arabidopsis infected by S. sclerotiorum rep3 [re-analysis]

description: re-analysis of GSM2850647 in GSE106811

value: in planta (Ath)


title: RCLG30_1


title: tRIP-seq_hnRNPK_siSrsf3_C2C12

city: Nagoya

first: Akio

last: Masuda

state: Aichi

address: 65 tsurumai-cho, Showa-ku

institute: Nagoya University Graduate School of Medicine

data_processing:
Library strategy: tRIP-seq
For paired-end read data, only P5 reads were used for analysis.
After standard HiSeq demultiplexing, reads were adapter-trimmed and reads less than 18 bp were discarded using cutadapt (v1.10).
Mapping was first performed against the mouse repetitive elements in RepBase with STAR (v2.5.2b).
Repeat-mapped reads were removed, and all others were then mapped against the mouse genome (mm10) with STAR (v 2.5.2b).
Multiply mapped reads were filtered out. Duplicates of reads uniquely mapped to the human or mouse genome were removed by Picard (v2.0.1).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage with a "--binsize 1" parameter.

source_name: Myoblast

growth_protocol: C2C12 cells were grown in DMEM with 10% fetal bovine serum at 37°C in 5% CO2.

extract_protocol:
C2C12 cells were UV-irradiated at 400 mJ, and whole cell lysates were harvested from the cells
tRIP was performed as previously described: Masuda et al. (2020):tRIP-seq reveals repression of premature polyadenylation by co-transcriptional FUS-U1 snRNP assembly.  EMBO Rep PMID: 32189459

value: Myoblast


title: HDX58_PDA_NEC_1: PDA plate rep1 [re-analysis]

description: re-analysis of GSM3212956 in GSE116194


title: SHEP Cell Control replicate1

description: Gene expression from SHEP Cell Control replicate 1

scan_protocol: GeneChip® Human Gene 2.0 ST Arrays (Affymetrix)

label_protocol: cDNA was synthesized from 200 ng of total RNA by reverse transcription using T7 promoter-(N6) oligonucleotides as primers.


title: tRIP-seq_hnRNPK_siControl_C2C12

value: siControl


title: RCLC37_3

value: wild type


description: Gene expression from SHEP Cells at 72 hr CHAF1A overexpression replicate 3

value: CHAF1A overexpression


title: tRIP-seq_hnRNPK_C2C12

value: no treatment


title: HDX57_PDA_FRT_3: PDA plate rep3 [re-analysis]

description: re-analysis of GSM3212959 in GSE116194

source_name: Periphery of ~20mm wide mycelium colony

value: in vitro (PdaFrt)


title: HDX56_PDA_FRT_2: PDA plate rep2 [re-analysis]

description: re-analysis of GSM3212957 in GSE116194


title: RCLC37_2

value: high temperature


description: Gene expression from SHEP Cells at 72 hr CHAF1A overexpression replicate 1


title: RNA-seq_siSrsf3+siHnrnpk_C2C12

data_processing:
Adaptor sequences were trimmed by Cutadapt (version 1.18). Reads were mapped to the mouse reference genome (mm10) using STAR version 2.5.2b.
PSIs of all internal exons in the RefSeq annotation were calculated by MISO.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Percent Spliced In (PSI) values and bays factors of control and siRNA-treated samples.

extract_protocol:
Total RNA was extracted from C2C12 cells transfected with the indicated siRNA using TRIZOL (Thermo Fisher Scientific), and was further purified with Quick-RNA Miniprep Kit (Zymo research) according to the manufacturer’s instructions.
The extracted RNA was subjected to RNA-seq at Macrogen, Japan. Sequencing libraries were prepared using the TruSeq Stranded mRNA kit (Illumina), and the libraries were read on Illumina NovaSeq 6000 (150 bp paired-end reads).

value: siSrsf3 and siHnrnpk


title: HDX55_PDA_FRT_1: PDA plate rep1 [re-analysis]

description: re-analysis of GSM3212955 in GSE116194


title: RCLC30_3


title: RCLC37_1


title: HDX15_PDB_3: PDB liquid culture rep3 [re-analysis]

description: re-analysis of GSM3212951 in GSE116194

source_name: ~20mm wide mycelium ball

value: in vitro (pdb)


title: RCLC30_2


title: RNA-seq_siSrsf3_C2C12


title: RCLC30_1


title: HDX14_PDB_2: PDB liquid culture rep2 [re-analysis]

description: re-analysis of GSM3212950 in GSE116194


title: RNA-seq_siHnrnpk_C2C12

value: siHnrnpk


title: HDX13_PDB_1: PDB liquid culture rep1 [re-analysis]

description: re-analysis of GSM3212949 in GSE116194


title: RNA-seq_siControl_C2C12


title: PA-8 cell RNA-seq rep3

status: Public on Jul 19 2021

city: Jingzhou

first: Liang

last: Hao

state: Hubei

address: JingMi road

institute: Yangtze University

data_processing:
Illumina Casava1.7 software used for basecalling.
Clean Data were mapped to the reference genome using HISAT2. HISAT2 is a specialized software for transcriptome sequencing reads mapping, can identify exon-exon junctions by splitting the mapped reads and mapping them to the reference genome again--rna-strandness RF --dta–t–p 4.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Sus_scrofa.Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Sus scrofa

source_name: Parthenogenetically activated (PA)

extract_protocol:
Pig oocytes were extracted and placed in liquid nitrogen,and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: sample type

value: PA8 cell

tag: obtained from

value: Parthenogenetically activated (PA)


title: PA-4 cell RNA-seq rep9

value: PA4 cell


description: Gene expression from SHEP Cells at 24 hr CHAF1A overexpression replicate 2

value: SHEP


title: PA-8 cell RNA-seq rep2


description: Gene expression from SHEP Cells at 72 hr CHAF1A overexpression replicate 2

value: neuroblastoma


description: Gene expression from SHEP Cells at 24 hr CHAF1A overexpression replicate 1


title: PA-4 cell RNA-seq rep6


description: Gene expression from SHEP Cells at 96 hr CHAF1A overexpression replicate 1


description: Gene expression from SHEP Cells at 24 hr CHAF1A overexpression replicate 3


title: PA-4 cell RNA-seq rep7


description: Gene expression from SHEP Cells at 96 hr CHAF1A overexpression replicate 3


description: Gene expression from SHEP Cells at 96 hr CHAF1A overexpression replicate 2


title: PA-8 cell RNA-seq rep1


title: PA-4 cell RNA-seq rep3


title: PA-4 cell RNA-seq rep2


title: PA-4 cell RNA-seq rep8


title: PA-4 cell RNA-seq rep1


title: PA-2 cell RNA-seq rep6

value: PA2 cell


title: PA-2 cell RNA-seq rep5


title: PA-2 cell RNA-seq rep3


title: PA-1 cell RNA-seq rep3

value: PA1 cell


title: PA-2 cell RNA-seq rep2


title: PA-2 cell RNA-seq rep1


title: PA-1 cell RNA-seq rep1


title: PA-1 cell RNA-seq rep2


title: IVF-8 cell RNA-seq rep1

source_name: In vitro fertilized (IVF)

value: IVF8 cell

value: In vitro fertilized (IVF)


title: PA-4 cell RNA-seq rep5


title: IVF-8 cell RNA-seq rep3


title: IVF-4 cell RNA-seq rep9

value: IVF4 cell


title: PA-4 cell RNA-seq rep4


title: IVF-4 cell RNA-seq rep7


title: IVF-4 cell RNA-seq rep6


title: IVF-4 cell RNA-seq rep8


title: PA-2 cell RNA-seq rep4


title: IVF-4 cell RNA-seq rep5


title: IVF-4 cell RNA-seq rep2


title: IVF-4 cell RNA-seq rep4


title: IVF-4 cell RNA-seq rep3


title: IVF-4 cell RNA-seq rep1


title: IVF-2 cell RNA-seq rep5

value: IVF2 cell


title: IVF-2 cell RNA-seq rep3


title: IVF-2 cell RNA-seq rep4


title: IVF-2 cell RNA-seq rep2


title: IVF-2 cell RNA-seq rep1


title: IVF-1 cell RNA-seq rep2

value: IVF1 cell


title: IVF-1 cell RNA-seq rep3


title: IVF-1 cell RNA-seq rep1


title: MII oocyte RNA-seq rep2

source_name: MII oocyte

value: MII oocyte


title: MII oocyte RNA-seq rep1


title: GV oocyte RNA-seq rep3

source_name: GV oocyte

value: GV oocyte


title: GV oocyte RNA-seq rep2


title: GV oocyte RNA-seq rep1


title: IVF-8 cell RNA-seq rep2


title: IVF-2 cell RNA-seq rep6


title: MII oocyte RNA-seq rep3


title: control diet, pre-hepatic and post-hepatic infusion with NaCL, biological rep 7

city: Braunschweig

first: Fabian

last: Billenkamp

address: Bundesallee 37

institute: Friedrich-Loeffler-Institute

description: Gene expression data from a non-perfused liver sample after feeding trial with deoxynivalenol and LPS challenge

hyb_protocol: Labelled DNA was hybridized on ChiGene-1_0-st Arrays. Chips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500 and BioConductor.

source_name: Liver samples taken at slaughter

label_protocol: Single stranded cDNA was synthesized, biotin-labelled and fragmented (WT Plus Expression kit) according to manufacturer’s instructions (Affymetrix, Santa Clara, CA)

growth_protocol: Pigs were fed restrictively with diets with or without deoxynivalenol contamination for 29 days. (C as first letter of group designation for control diet and D as first letter for deoxynivalenol contaminated diet)

extract_protocol: Deep frozen tissue was first homogenized in liquid nitrogen using a ball mill. The resulting powder was kept under liquid nitrogen until RNA purification using the NucleoSpin® RNA kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany).

treatment_protocol: LPS (L) or 0.9% NaCl (C) were infused post-hepatic via jugular vein (second letter of group designation) and pre-hepatic via portal vein (third letter of group designation), see Characteristics field. Samples were taken at slaughtering 195 minutes after infusion.

value: non-perfused liver

tag: diet

value: Control

tag: post-hepatic infusion

value: NaCl

tag: pre-hepatic infusion

tag: group

value: CCC


title: Deoxynivalenol contaminated diet, pre-hepatic infusion with LPS and post-hepatic infusion with NaCl, biological rep 6

value: Deoxynivalenol

value: LPS

value: DCL


title: control diet, pre-hepatic infusion with LPS and post-hepatic infusion with NaCl, biological rep 6

value: CCL


title: control diet, pre-hepatic and post-hepatic infusion with NaCL, biological rep 8


title: control diet, pre-hepatic infusion with LPS and post-hepatic infusion with NaCl, biological rep 7


title: control diet, pre-hepatic infusion with NaCl and post-hepatic infusion with LPS, biological rep 6

value: CLC


title: control diet, pre-hepatic infusion with NaCl and post-hepatic infusion with LPS, biological rep 5


title: Deoxynivalenol contaminated diet, pre-hepatic and post-hepatic infusion with NaCL, biological rep 7

value: DCC


title: control diet, pre-hepatic infusion with NaCl and post-hepatic infusion with LPS, biological rep 7


title: Deoxynivalenol contaminated diet, pre-hepatic infusion with NaCl and post-hepatic infusion with LPS, biological rep 6

value: DLC


title: control diet, pre-hepatic and post-hepatic infusion with NaCL, biological rep 6


title: control diet, pre-hepatic and post-hepatic infusion with NaCL, biological rep 4


title: control diet, pre-hepatic and post-hepatic infusion with NaCL, biological rep 5


title: Deoxynivalenol contaminated diet, pre-hepatic infusion with LPS and post-hepatic infusion with NaCl, biological rep 7


title: Deoxynivalenol contaminated diet, pre-hepatic and post-hepatic infusion with NaCL, biological rep 6


title: Deoxynivalenol contaminated diet, pre-hepatic infusion with NaCl and post-hepatic infusion with LPS, biological rep 5


title: control diet, pre-hepatic infusion with NaCl and post-hepatic infusion with LPS, biological rep 8


title: Deoxynivalenol contaminated diet, pre-hepatic infusion with NaCl and post-hepatic infusion with LPS, biological rep 4


title: Deoxynivalenol contaminated diet, pre-hepatic infusion with LPS and post-hepatic infusion with NaCl, biological rep 4


title: Deoxynivalenol contaminated diet, pre-hepatic infusion with LPS and post-hepatic infusion with NaCl, biological rep 3


title: Deoxynivalenol contaminated diet, pre-hepatic and post-hepatic infusion with NaCL, biological rep 4


title: Deoxynivalenol contaminated diet, pre-hepatic and post-hepatic infusion with NaCL, biological rep 5


title: control diet, pre-hepatic infusion with LPS and post-hepatic infusion with NaCl, biological rep 5


title: Deoxynivalenol contaminated diet, pre-hepatic infusion with LPS and post-hepatic infusion with NaCl, biological rep 5


title: control diet, pre-hepatic infusion with NaCl and post-hepatic infusion with LPS, biological rep 4


title: control diet, pre-hepatic infusion with NaCl and post-hepatic infusion with LPS, biological rep 3


title: Deoxynivalenol contaminated diet, pre-hepatic and post-hepatic infusion with NaCL, biological rep 3


title: control diet, pre-hepatic infusion with LPS and post-hepatic infusion with NaCl, biological rep 4


title: control diet, pre-hepatic infusion with LPS and post-hepatic infusion with NaCl, biological rep 3


title: control diet, pre-hepatic infusion with NaCl and post-hepatic infusion with LPS, biological rep 2


title: control diet, pre-hepatic infusion with LPS and post-hepatic infusion with NaCl, biological rep 2


title: SHEP Cell Control replicate2

description: Gene expression from SHEP Cell Control replicate 2

tag: cell line

value: SHEP

value: neuroblastoma

value: control


title: Deoxynivalenol contaminated diet, pre-hepatic infusion with LPS and post-hepatic infusion with NaCl, biological rep 2


title: Experiment5_A_Pool3_10xRNA [BS07702A]

city: New York

first: Matthew

middle: T

last: Maurano

state: New York

address: 435 East 30th Street

department: Institute for Systems Genetics

institute: NYU Grossman School of Medicine

data_processing:
Sequence reads were cleaned and processed using a custom pipeline (https://github.com/mauranolab/mapping/tree/master/transposon) to extract and clean Reporter BC and UMI sequences. iPCR libraries were additionally mapped to the hg38 human reference genome.
Read counts for DNA, RNA, and iPCR libraries were normalized per 1M sequenced reads and merged based on reporter BC. Missing RNA counts were imputed as 0, and only BCs with >10 DNA reads and an integration site were considered. Reporter activity was computed as log2(RNA/DNA + 1)
10x scRNA-seq 3’ libraries were analyzed using Cell Ranger v.4.0.0.
Genome_build: hg38
Supplementary_files_format_and_content: The `activity.bw` files indicate each reporter normalized activity as log2(FPKM+1) . For Experiment 5, the `barcodes.tsv.gz` and `features.tsv.gz` list the 3'scRNA cells and gene id, respectively. `matrix.mtx.gz` is the count 3'scRNA-seq count matrix

growth_protocol: K562 cells were obtained from ATCC (ATCC CCL-243) and cultured in RPMI 1640 medium with glutamine (Fisher cat# MT10040CV) supplemented with 10% FBS (Gemini Bio-Products cat# 100-106), 1 mM sodium pyruvate, and 10 U/mL penicillin-streptomycin. Cultures were maintained at 37 °C and 5% CO2, and were subcultured once cultures reached a density of 5x105 cells/mL.

extract_protocol:
For genomic DNA, frozen cell pellets were allowed to warm to room tem-perature, and then were resuspended in 385 µL DNA Quick Extract (Lucigen cat# QE09050) and transferred to a 1.5 mL tube. Cells were incubated at 65 °C for 15 min, followed by 98 °C for 5 min. After cooling briefly, 10 µL Proteinase K (Sigma-Aldrich cat# P4850-5ML) was added, and cell lysate was incubated at 55 °C overnight. The following day, 5 µL RNase A (Sigma-Aldrich cat# R4642-50MG) was added, and the cell lysate was incubated at 37 °C for 30 min. Genomic DNA was precipitated by adding 4 µL Glycoblue (Fisher cat# AM9515), 40 µL 3M Sodium Ace-tate, and 1 mL ice-cold 100% ethanol. After incubating at -80 °C for 1 h, DNA was pelleted by centrifugation at 20,000 g for 30 min at 4 °C. The DNA pellet was washed twice with 70% ethanol, and then resuspended in 200 µL Buffer EB (Qiagen cat# 19086).
For total RNA, cell pellets containing 1x106 cells each were resuspended in 350 µL Trizol solution (Fisher cat# 15596026) and stored at -80 °C until RNA extraction. Frozen samples were allowed to warm to room temperature, and then 350 µL cell solution was transferred to a Phase-Lock gel tube (Fisher cat# NC1093153). 70 µL chloroform was added to each Phase-lock tube and shaken vigorously, followed by a 2 min incubation at room temperature. Tubes were centrifuged at 12,000 x g for 10 min at 4 °C. Following centrifugation, the aqueous phase was decanted from each tube and transferred to a new tube. 350 µL 70% ethanol was added and mixed well, and the solution was transferred to a Qiagen RNeasy-mini spin column. Samples were centrifuged at 13,000 x g for 15 s, and the flow-through was discarded. 350 µL Buffer RW1 was added to each column, samples were centrifuged at 13,000 x g for 15 s, and the flow-through was discarded. This Buffer RW1 wash was repeated once more for a total of 2 washes. Next, 500 µL Buffer RPE was added to each column, samples were centrifuged at 13,000 x g for 15 s, and the flow-through was dis-carded. This Buffer RPE wash was repeated once more for a total of 2 washes. After the last RPE wash, the column was centrifuged for an additional 2 min at 13,000 x g to remove residual ethanol. Samples were eluted in 40 µL RNase-free H2O.
For DNA libraries, unique Molecular Identifiers (UMIs) and the inner portion of the P5 sequencing adapter were added. 20 µg of genomic DNA was digested with PstI (NEB cat# R3140L) for 1 h at 37 °C, and then purified using the Zymo Clean and Concentrate-25 (Zymo Research cat# D4034) protocol. One cycle of PCR was performed with the following conditions: 8 replicate 50 µL reactions were prepared, each containing 500 ng PstI digested DNA, 1x Phusion Hot Start Flex Mastermix (NEB cat# M0536L), and 200 nM of the primer P5_Plasmid_8N/9N/10N, and incubated at 98 °C for 5 min, 60 °C for 1 min, and 72 °C for 10 min. Replicate reactions were combined and then purified using the Zymo Clean and Concentrate-5 (Zymo Research cat# D4014) protocol, eluting the DNA in 20 µL.
For RNA libraries, cDNA was synthesized using the Superscript IV First Strand Synthesis kit (Invitrogen), with 5 µg RNA template and 2 µM primer P5_barcode_0N/1N/2N (containing a truncated sequencing adapter) in two replicate reactions per sample. RNA was first incubated with primers and dNTPs at 60 °C for 10 min, then placed on ice for 1 min. The remaining RT reagents were added, and samples were incubated at 55 °C for 10 min, 80 °C for 10 min, and then cooled to 4 °C. Next, 1 µL RNaseH was added to each reaction, and incubated at 37 °C for 20 min. Single-stranded cDNA was purified using the Zymo Clean and Concentrate-5 protocol (Zymo Research cat# D4014), using 7 volumes of DNA binding buffer and eluting in 10 µL Zymo DNA elution buffer. Unique Molecular Identifiers (UMIs) and the inner portion of the P7 sequencing adapter were added to each single-stranded cDNA molecule using 1 cycle of PCR with the following conditions: 2 replicate 50 µL reactions were prepared, each containing 5 µL cDNA, 1x Phusion Hot Start Flex Mastermix (NEB cat# M0536L), and 200 nM of the primer P7_Plasmid_8N/9N/10N, and incubated at 98 °C for 5 min, 64 °C for 5 min, and 72 °C for 5 min. Replicate reactions were combined and then purified using the Zymo Clean and Concentrate-5 (Zymo Research cat# D4014) protocol, eluting the DNA in 20 µL.
For inverse PCR (iPCR) libraries, 40 µg genomic DNA was digested with DpnII for 2 h at 37 °C. Digested DNA was purified using the Zymo Clean & Concentrate-25 column protocol, and digestion was verified by running 100 ng DpnII digested DNA out on a 1% agarose gel. Intramolecular DpnII ligation was performed using DpnII digested DNA at a concentration of 5 µg/mL, and T4 DNA ligase at a concentration of 10,000 U/mL. Ligation reactions were incubated overnight at 4 °C, and ligation products were purified using the Zymo Clean & Concentrate-25 column protocol.
scRNA-seq expression libraries were generated using the 10x Chromium NextGem Single Cell 3’ workflow (10X Genomics cat# 1000128). For experiment 4, an additional sort for GFP-positive cells was performed on day 4, and 5700 cells were collected for scRNA-seq (Supplemental Table S4) while the remaining cells were expanded in culture for an additional 7 d, at which point cell pellets were collected for RNA, DNA, and iPCR libraries.
Separate libraries enriched for reporter transcripts were generated from the cDNA produced in the Post GEM–RT Cleanup & cDNA Amplification step of the 10X Chromium Single Cell 3’ (v3.1) library protocol using PCR with the following conditions: 8 replicate 25 µL reactions were prepared, each containing 1 µL amplified 10X Chromium Single Cell cDNA, 1x Phusion Hot Start Flex Mastermix (NEB cat# M0536L), 500 nM of the primer P5_Halfsite, and 500 nM of the primer P7_10xSBbarcodeV2_0N, and incubated 1 cycle at 98 °C for 5 min; 8 cycles (sample dependent) at 98 °C for 15 s, 66 °C for 15 s, and 72 °C for 30 s; and 1 cycle of 72 °C for 10 min.

treatment_protocol: K562 cells were transfected using the ThermoFisher Neon Transfection System 100 μL Kit according to the manufacturer's instructions with varying amounts of transposon and transposase. Cells were transfected with 4 μL TE to use as a negative control for puromycin selection. Transfected cells were selected with puromycin (2.5 µg/mL). K562 media with puromycin was replaced every 2 days. Cell counts were performed either using PrestoBlue (Life Technologies cat# A13261) and fluorescence detection with the Synergy H1 Multi-Mode Microplate Reader, or were stained with trypan blue and counted on a hemocytometer.

tag: sample id

tag: lib strategy

value: enriched 10x scRNA

tag: r1 trim

tag: r2 trim

tag: experiment

tag: construct


title: Experiment5_Pool4_scRNA [BS07471]

tag: cell type

value: 10x scRNA


title: control diet, pre-hepatic infusion with LPS and post-hepatic infusion with NaCl, biological rep 1

tag: tissue


title: Experiment5_A_Pool3_10xRNA [BS07706A]


title: Experiment5_Pool3_scRNA [BS07470]


title: Experiment5_A_Pool2_10xRNA [BS07701A]


title: Experiment5_A_Pool4_10xRNA [BS07626A]


title: Deoxynivalenol contaminated diet, pre-hepatic infusion with NaCl and post-hepatic infusion with LPS, biological rep 3


title: Experiment5_A_Pool4_10xRNA [BS07703A]


title: Experiment5_A_Pool2_10xRNA [BS07705A]


title: Experiment5_Pool2_scRNA [BS07469]


title: Experiment5_A_Pool4_10xRNA [BS07512A]


title: Experiment5_A_Pool3_10xRNA [BS07511A]


title: control diet, pre-hepatic and post-hepatic infusion with NaCL, biological rep 2


title: Experiment5_A_Pool3_10xRNA [BS07625A]


title: Experiment5_Pool1_scRNA [BS07468]


title: control diet, pre-hepatic and post-hepatic infusion with NaCL, biological rep 3


title: Experiment5_A_Pool2_10xRNA [BS07624A]


title: Experiment5_A_Pool2_10xRNA [BS07510A]


title: Experiment5_A_Pool4_10xRNA [BS07707A]


title: Deoxynivalenol contaminated diet, pre-hepatic infusion with NaCl and post-hepatic infusion with LPS, biological rep 1


title: control diet, pre-hepatic infusion with NaCl and post-hepatic infusion with LPS, biological rep 1


title: Deoxynivalenol contaminated diet, pre-hepatic infusion with LPS and post-hepatic infusion with NaCl, biological rep 1


title: Deoxynivalenol contaminated diet, pre-hepatic and post-hepatic infusion with NaCL, biological rep 1


title: Deoxynivalenol contaminated diet, pre-hepatic and post-hepatic infusion with NaCL, biological rep 2


title: Experiment5_A_Pool1_10xRNA [BS07704A]


title: Experiment5_A_Pool1_10xRNA [BS07700A]


title: control diet, pre-hepatic and post-hepatic infusion with NaCL, biological rep 1


title: Experiment5_A_Pool1_10xRNA [BS07623A]


title: Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw2_RNA [BS07582A]

description: BS07582A-Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw2_RNA

value: Amplicon RNA

tag: transfection

value: D

tag: thaw


title: Experiment5_A_Pool1_10xRNA [BS07509A]


title: Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw2_RNA [BS07578A]

description: BS07578A-Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw2_RNA


title: Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_RNA [BS07577A]

description: BS07577A-Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_RNA

value: C


title: Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_RNA [BS07380A]

description: BS07380A-Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_RNA


title: Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_RNA [BS07221A]

description: BS07221A-Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_RNA


title: Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_RNA [BS07581A]

description: BS07581A-Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_RNA

value: B


title: Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_RNA [BS07220A]

description: BS07220A-Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_RNA


title: Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_RNA [BS07219A]

description: BS07219A-Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_RNA


title: Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw2_DNA [BS07570A]

description: BS07570A-Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw2_DNA

library_source: genomic

molecule: genomic DNA

value: Amplicon DNA


title: Experiment5_A_GGlo_HS2_Thaw2_RNA [BS07575A]

description: BS07575A-Experiment5_A_GGlo_HS2_Thaw2_RNA

value: A


title: Experiment5_A_GGlo_HS2_Thaw1_RNA [BS07215A]

description: BS07215A-Experiment5_A_GGlo_HS2_Thaw1_RNA


title: Experiment5_A_GGlo_HS2_Thaw1_RNA [BS07377A]

description: BS07377A-Experiment5_A_GGlo_HS2_Thaw1_RNA


title: Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_RNA [BS07378A]

description: BS07378A-Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_RNA


title: Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_RNA [BS07217A]

description: BS07217A-Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_RNA


title: Experiment5_A_GGlo_HS2_Thaw2_RNA [BS07579A]

description: BS07579A-Experiment5_A_GGlo_HS2_Thaw2_RNA


title: Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw2_DNA [BS07574A]

description: BS07574A-Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw2_DNA


title: Deoxynivalenol contaminated diet, pre-hepatic infusion with NaCl and post-hepatic infusion with LPS, biological rep 2

description: Gene expression data from a non-perfused liver sample after feeding trial with deoxynivalenol and LPS challenge

value: non-perfused liver

value: Deoxynivalenol

value: LPS

value: NaCl


title: Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_RNA [BS07216A]

description: BS07216A-Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_RNA


title: Experiment5_A_GGlo_HS2_Thaw1_RNA [BS07214A]

description: BS07214A-Experiment5_A_GGlo_HS2_Thaw1_RNA


title: Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_RNA [BS07218A]

description: BS07218A-Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_RNA


title: Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_DNA [BS07212A]

description: BS07212A-Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_DNA


title: Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_DNA [BS07376A]

description: BS07376A-Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_DNA


title: Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_RNA [BS07580A]

description: BS07580A-Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_RNA


title: Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_RNA [BS07576A]

description: BS07576A-Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_RNA


title: Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_DNA [BS07573A]

description: BS07573A-Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_DNA


title: Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_DNA [BS07569A]

description: BS07569A-Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_DNA


title: Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_DNA [BS07375A]

description: BS07375A-Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_DNA


title: Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_DNA [BS07213A]

description: BS07213A-Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_DNA


title: Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_DNA [BS07568A]

description: BS07568A-Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_DNA


title: Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_DNA [BS07572A]

description: BS07572A-Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_DNA


title: Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_DNA [BS07210A]

description: BS07210A-Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_DNA


title: Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_DNA [BS07374A]

description: BS07374A-Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_DNA


title: Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_DNA [BS07209A]

description: BS07209A-Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_DNA


title: Experiment5_A_GGlo_HS2_Thaw1_DNA [BS07206A]

description: BS07206A-Experiment5_A_GGlo_HS2_Thaw1_DNA


title: Experiment5_A_GGlo_HS2_Thaw1_DNA [BS07207A]

description: BS07207A-Experiment5_A_GGlo_HS2_Thaw1_DNA


title: Experiment5_A_GGlo_HS2_Thaw2_DNA [BS07567A]

description: BS07567A-Experiment5_A_GGlo_HS2_Thaw2_DNA


title: Experiment5_A_GGlo_HS2_Thaw1_DNA [BS07373A]

description: BS07373A-Experiment5_A_GGlo_HS2_Thaw1_DNA


title: Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw2_iPCR [BS07586A]

description: BS07586A-Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw2_iPCR

tag: molecule subtype

value: DpnII-digested ligated genomic DNA

value: Amplicon iPCR


title: Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_iPCR [BS07383A]

description: BS07383A-Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_iPCR


title: Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_iPCR [BS07384A]

description: BS07384A-Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_iPCR


title: Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw2_iPCR [BS07590A]

description: BS07590A-Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw2_iPCR


title: Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_iPCR [BS07227A]

description: BS07227A-Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_iPCR


title: Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_iPCR [BS07228A]

description: BS07228A-Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_iPCR


title: Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_iPCR [BS07585A]

description: BS07585A-Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_iPCR


title: Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_RNA [BS07379A]

description: BS07379A-Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_RNA


title: Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_iPCR [BS07224A]

description: BS07224A-Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_iPCR


title: Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_iPCR [BS07589A]

description: BS07589A-Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_iPCR


title: Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_DNA [BS07211A]

description: BS07211A-Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_DNA


title: Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_iPCR [BS07382A]

description: BS07382A-Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_iPCR


title: Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_iPCR [BS07584A]

description: BS07584A-Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_iPCR


title: Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_iPCR [BS07588A]

description: BS07588A-Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw2_iPCR


title: Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_iPCR [BS07229A]

description: BS07229A-Experiment5_D_C1CoreFw_GGlo_HS2_A1CoreFw_Thaw1_iPCR


title: Experiment5_A_GGlo_HS2_Thaw2_iPCR [BS07587A]

description: BS07587A-Experiment5_A_GGlo_HS2_Thaw2_iPCR


title: Experiment5_A_GGlo_HS2_Thaw2_iPCR [BS07583A]

description: BS07583A-Experiment5_A_GGlo_HS2_Thaw2_iPCR


title: Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_iPCR [BS07225A]

description: BS07225A-Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_iPCR


title: Experiment5_A_GGlo_HS2_Thaw2_DNA [BS07571A]

description: BS07571A-Experiment5_A_GGlo_HS2_Thaw2_DNA


title: Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_DNA [BS07208A]

description: BS07208A-Experiment5_B_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_DNA


title: Experiment5_A_GGlo_HS2_Thaw1_iPCR [BS07223A]

description: BS07223A-Experiment5_A_GGlo_HS2_Thaw1_iPCR


title: Experiment4_C1fw_GGlo_A1rv_HS2_10xRNA [BS03094A]

description: BS03094A-Experiment4_C1fw_GGlo_A1rv_HS2_10xRNA


title: Experiment5_A_GGlo_HS2_Thaw1_iPCR [BS07381A]

description: BS07381A-Experiment5_A_GGlo_HS2_Thaw1_iPCR


title: Experiment5_A_GGlo_HS2_Thaw1_iPCR [BS07222A]

description: BS07222A-Experiment5_A_GGlo_HS2_Thaw1_iPCR


title: Experiment4_C1fw_GGlo_A1rv_HS2_10xRNA [BS03095A]

description: BS03095A-Experiment4_C1fw_GGlo_A1rv_HS2_10xRNA


title: Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_iPCR [BS07226A]

description: BS07226A-Experiment5_C_C1CoreFw_GGlo_A1CoreFw_HS2_Thaw1_iPCR


title: Experiment4_C1fw_GGlo_A1rv_HS2_10xRNA [BS03093A]

description: BS03093A-Experiment4_C1fw_GGlo_A1rv_HS2_10xRNA


title: Experiment4_C1fw_GGlo_A1rv_HS2_10xRNA [BS03092A]

description: BS03092A-Experiment4_C1fw_GGlo_A1rv_HS2_10xRNA


title: Experiment4_C1fw_GGlo_A1rv_HS2_10xRNA [BS03091A]

description: BS03091A-Experiment4_C1fw_GGlo_A1rv_HS2_10xRNA


title: Experiment4_C1fw_GGlo_A1rv_HS2_10xRNA [BS03040B]

description: BS03040B-Experiment4_C1fw_GGlo_A1rv_HS2_10xRNA


title: Experiment4_C1fw_GGlo_A1rv_HS2_iPCR [BS03129A]

description: BS03129A-Experiment4_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment4_C1fw_GGlo_A1rv_HS2_iPCR [BS03129C]

description: BS03129C-Experiment4_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment4_C1fw_GGlo_A1rv_HS2_iPCR [BS03129B]

description: BS03129B-Experiment4_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment4_C1fw_GGlo_A1rv_HS2_RNA [BS03196A]

description: BS03196A-Experiment4_C1fw_GGlo_A1rv_HS2_RNA


title: Experiment4_C1fw_GGlo_A1rv_HS2_RNA [BS03079A]

description: BS03079A-Experiment4_C1fw_GGlo_A1rv_HS2_RNA


title: Experiment4_C1fw_GGlo_A1rv_HS2_DNA [BS03160A]

description: BS03160A-Experiment4_C1fw_GGlo_A1rv_HS2_DNA


title: Experiment4_C1fw_GGlo_A1rv_HS2_iPCR [BS03127A]

description: BS03127A-Experiment4_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment3_C1fw_GGlo_A1rv_HS2_RNA [BS03125C]

description: BS03125C-Experiment3_C1fw_GGlo_A1rv_HS2_RNA


title: Experiment3_C1fw_GGlo_A1rv_HS2_RNA [BS03125D]

description: BS03125D-Experiment3_C1fw_GGlo_A1rv_HS2_RNA


title: Experiment3_C1fw_GGlo_A1rv_HS2_iPCR [BS03097L]

description: BS03097L-Experiment3_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment3_C1fw_GGlo_A1rv_HS2_RNA [BS03125A]

description: BS03125A-Experiment3_C1fw_GGlo_A1rv_HS2_RNA


title: Experiment4_C1fw_GGlo_A1rv_HS2_DNA [BS03159A]

description: BS03159A-Experiment4_C1fw_GGlo_A1rv_HS2_DNA


title: Experiment3_C1fw_GGlo_A1rv_HS2_iPCR [BS03097K]

description: BS03097K-Experiment3_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment3_C1fw_GGlo_A1rv_HS2_iPCR [BS03097J]

description: BS03097J-Experiment3_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment3_C1fw_GGlo_A1rv_HS2_RNA [BS03125B]

description: BS03125B-Experiment3_C1fw_GGlo_A1rv_HS2_RNA


title: Experiment3_C1fw_GGlo_A1rv_HS2_iPCR [BS03097B]

description: BS03097B-Experiment3_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment3_C1fw_GGlo_A1rv_HS2_iPCR [BS03097I]

description: BS03097I-Experiment3_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment3_C1fw_GGlo_A1rv_HS2_iPCR [BS03097A]

description: BS03097A-Experiment3_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment4_C1fw_GGlo_A1rv_HS2_iPCR [BS03127B]

description: BS03127B-Experiment4_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment4_C1fw_GGlo_A1rv_HS2_iPCR [BS03127C]

description: BS03127C-Experiment4_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment3_GGlo_HS2_RNA [BS03124A]


title: Experiment3_GGlo_HS2_RNA [BS03124B]


title: Experiment3_GGlo_HS2_RNA [BS03124C]


title: Experiment3_GGlo_HS2_iPCR [BS03126C]


title: Experiment3_GGlo_HS2_RNA [BS03124D]


title: Experiment3_GGlo_HS2_iPCR [BS03126B]


title: Experiment3_GGlo_HS2_iPCR [BS03126A]


title: Experiment3_GGlo_RNA [BS03123C]

value: GGlo


title: Experiment3_GGlo_HS2_DNA [BS02953A]


title: Experiment3_GGlo_RNA [BS03123D]


title: Experiment3_GGlo_RNA [BS03123A]


title: Experiment3_GGlo_iPCR [BS03128B]


title: Experiment3_GGlo_DNA [BS03156A]


title: Experiment3_GGlo_DNA [BS02951A]


title: Experiment2_C1fw_GGlo_A1rv_HS2_RNA [BS02546A]

description: BS02546A-Experiment2_C1fw_GGlo_A1rv_HS2_RNA


title: Experiment2_C1fw_GGlo_A1rv_HS2_RNA [BS02545A]

description: BS02545A-Experiment2_C1fw_GGlo_A1rv_HS2_RNA


title: Experiment3_GGlo_iPCR [BS03128A]


title: Experiment2_C1fw_GGlo_A1rv_HS2_iPCR [BS02611A]

description: BS02611A-Experiment2_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment2_C1fw_GGlo_A1fw_HS2_RNA [BS02544A]

description: BS02544A-Experiment2_C1fw_GGlo_A1fw_HS2_RNA


title: Experiment3_C1fw_GGlo_A1rv_HS2_DNA [BS03158A]

description: BS03158A-Experiment3_C1fw_GGlo_A1rv_HS2_DNA


title: Experiment2_C1fw_GGlo_A1rv_HS2_iPCR [BS02612A]

description: BS02612A-Experiment2_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment2_C1fw_GGlo_A1rv_HS2_DNA [BS02567A]

description: BS02567A-Experiment2_C1fw_GGlo_A1rv_HS2_DNA


title: Experiment2_C1fw_GGlo_A1rv_HS2_iPCR [BS02611C]

description: BS02611C-Experiment2_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment3_C1fw_GGlo_A1rv_HS2_DNA [BS02955A]

description: BS02955A-Experiment3_C1fw_GGlo_A1rv_HS2_DNA


title: Experiment2_C1fw_GGlo_A1rv_HS2_DNA [BS02566A]

description: BS02566A-Experiment2_C1fw_GGlo_A1rv_HS2_DNA


title: Experiment2_C1fw_GGlo_A1fw_HS2_RNA [BS02543A]

description: BS02543A-Experiment2_C1fw_GGlo_A1fw_HS2_RNA


title: Experiment2_C1fw_GGlo_A1fw_HS2_RNA [BS02543B]

description: BS02543B-Experiment2_C1fw_GGlo_A1fw_HS2_RNA


title: Experiment2_C1fw_GGlo_A1fw_HS2_iPCR [BS02609B]

description: BS02609B-Experiment2_C1fw_GGlo_A1fw_HS2_iPCR


title: Experiment2_C1fw_GGlo_A1fw_HS2_iPCR [BS02610A]

description: BS02610A-Experiment2_C1fw_GGlo_A1fw_HS2_iPCR


title: Experiment2_C1fw_GGlo_A1fw_HS2_iPCR [BS02609A]

description: BS02609A-Experiment2_C1fw_GGlo_A1fw_HS2_iPCR


title: Experiment3_GGlo_RNA [BS03123B]


title: Experiment2_GGlo_HS2_RNA [BS02542A]


title: Experiment2_C1fw_GGlo_A1fw_HS2_DNA [BS02565A]

description: BS02565A-Experiment2_C1fw_GGlo_A1fw_HS2_DNA


title: Experiment2_GGlo_HS2_RNA [BS02541A]


title: Experiment2_GGlo_HS2_DNA [BS02563A]


title: Experiment2_GGlo_HS2_iPCR [BS02607C]


title: Experiment2_GGlo_HS2_iPCR [BS02607A]


title: Experiment2_GGlo_HS2_iPCR [BS02608A]


title: Experiment2_GGlo_RNA [BS02540A]


title: Experiment2_GGlo_RNA [BS02539B]


title: Experiment2_GGlo_iPCR [BS02606A]


title: Experiment2_GGlo_RNA [BS02539A]


title: Experiment2_GGlo_DNA [BS02560A]


title: Experiment2_GGlo_iPCR [BS02605B]


title: Experiment2_GGlo_DNA [BS02561A]


title: Experiment1_C1fw_GGlo_A1rv_HS2_RNA [BS02223A]

description: BS02223A-Experiment1_C1fw_GGlo_A1rv_HS2_RNA


title: Experiment1_C1fw_GGlo_A1rv_HS2_iPCR [BS02228B]

description: BS02228B-Experiment1_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment1_C1fw_GGlo_A1rv_HS2_RNA [BS02223B]

description: BS02223B-Experiment1_C1fw_GGlo_A1rv_HS2_RNA


title: Experiment1_C1fw_GGlo_A1rv_HS2_DNA [BS02215A]

description: BS02215A-Experiment1_C1fw_GGlo_A1rv_HS2_DNA


title: Experiment1_C1fw_GGlo_A1rv_HS2_iPCR [BS02228A]

description: BS02228A-Experiment1_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment2_C1fw_GGlo_A1fw_HS2_DNA [BS02564A]

description: BS02564A-Experiment2_C1fw_GGlo_A1fw_HS2_DNA


title: Experiment1_C1fw_GGlo_A1fw_HS2_iPCR [BS02227C]

description: BS02227C-Experiment1_C1fw_GGlo_A1fw_HS2_iPCR


title: Experiment1_C1fw_GGlo_A1fw_HS2_iPCR [BS02227B]

description: BS02227B-Experiment1_C1fw_GGlo_A1fw_HS2_iPCR


title: Experiment1_C1fw_GGlo_A1fw_HS2_RNA [BS02222A]

description: BS02222A-Experiment1_C1fw_GGlo_A1fw_HS2_RNA


title: Experiment1_C1fw_GGlo_A1rv_HS2_DNA [BS02219A]

description: BS02219A-Experiment1_C1fw_GGlo_A1rv_HS2_DNA


title: Experiment1_C1fw_GGlo_A1fw_HS2_RNA [BS02222B]

description: BS02222B-Experiment1_C1fw_GGlo_A1fw_HS2_RNA


title: Experiment2_GGlo_HS2_DNA [BS02562A]


title: Experiment1_C1fw_GGlo_A1fw_HS2_iPCR [BS02227A]

description: BS02227A-Experiment1_C1fw_GGlo_A1fw_HS2_iPCR


title: Experiment1_GGlo_HS2_RNA [BS02221B]


title: Experiment1_C1fw_GGlo_A1fw_HS2_DNA [BS02214A]

description: BS02214A-Experiment1_C1fw_GGlo_A1fw_HS2_DNA


title: Experiment1_C1fw_GGlo_A1fw_HS2_DNA [BS02218A]

description: BS02218A-Experiment1_C1fw_GGlo_A1fw_HS2_DNA


title: Experiment1_GGlo_HS2_RNA [BS02221A]


title: Experiment1_GGlo_HS2_iPCR [BS02226B]


title: Experiment1_GGlo_HS2_DNA [BS02217A]


title: Experiment1_GGlo_HS2_DNA [BS02213A]


title: Experiment2_GGlo_iPCR [BS02605A]


title: Experiment1_GGlo_RNA [BS02220B]


title: Experiment1_C1fw_GGlo_A1rv_HS2_iPCR [BS02228C]

description: BS02228C-Experiment1_C1fw_GGlo_A1rv_HS2_iPCR


title: Experiment1_GGlo_iPCR [BS02225C]


title: Experiment1_GGlo_iPCR [BS02225D]


title: Experiment1_GGlo_RNA [BS02220A]


title: DevTOX04-456_TBBA_10

city: Ottawa

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

data_processing:
none provided by the submitter
Supplementary_files_format_and_content: reads per gene

source_name: H9 hES

growth_protocol: H9 hES cells (WA09 ) were passaged and maintained on Corning Matrigel basement membrane matrix (growth factor reduced) in mTeSR medium as cell aggregates in 6-well dishes. Cultures were monitored microscopically for areas of differentiating cells which were removed by aspiration. Medium was changed daily and cultures were split when 90% confluent.

extract_protocol:
Twenty-four hours following the final treatment, spent media was removed and cells were lysed directly in the wells with TRIzol™ (Thermo Fisher Scientific) or QIAzol (Qiagen, Germantown, Maryland) reagent and stored at -80 degrees C. Total RNA was isolated by extracting with chloroform, mixing the aqueous phase with ethanol, and purification using the miRNeasy Mini Kit (Qiagen) including an on-column DNase I step to remove chromosomal DNA. The RNA was eluted in 100 microL of RNase-free water.
Ribodepletion and library preparation using the TruSeq® Stranded Total RNA HT Kit with RiboZero Gold.

treatment_protocol: For each experiment, cells were dissociated using TrypLE™ enzyme (Gibco, Thermo Fisher Scientific) into single cell suspensions, seeded onto Matrigel-coated 96-well plates at ~1X100,000 cells/well, and placed into a 37°C/5% CO2 incubator until exposure the following day. Cells were exposed daily, approximately 24 hours apart, with fresh medium containing test chemicals and vehicle control (0.1% DMSO) for 3 consecutive days. Five concentrations per chemical were tested in triplicate (6 wells/replicate) alongside concurrent vehicle controls.

tag: chemical

value: TBBA

tag: dose (um)


title: DevTOX04-451_BPS_10

value: BPS


title: DevTOX04-450_BPS_1


title: DevTOX04-4482_ctrl_0

value: ctrl


title: DevTOX04-445_TBBA_1


title: DevTOX04-448_ctrl_0


title: DevTOX04-441_BPS_10


title: Experiment1_GGlo_DNA [BS02216A]


title: Experiment1_GGlo_iPCR [BS02225A]


title: Experiment1_GGlo_DNA [BS02212A]


title: Experiment1_GGlo_HS2_iPCR [BS02226C]


title: Experiment1_GGlo_HS2_iPCR [BS02226A]


title: DevTOX04-4382_ctrl_0


title: DevTOX04-440_BPS_1


title: DevTOX04-446_TBBA_10


title: Experiment1_GGlo_iPCR [BS02225B]


title: DevTOX04-438_ctrl_0


title: DevTOX04-436_TBBA_10


title: DevTOX04-4282_ctrl_0


title: DevTOX04-430_BPS_1


title: DevTOX04-431_BPS_10


title: DevTOX04-435_TBBA_1


title: DevTOX04-428_ctrl_0


title: DevTOX04-426_BPF_10

value: BPF


title: DevTOX04-421_BPA_10

value: BPA


title: DevTOX04-425_BPF_1


title: DevTOX04-4182_ctrl_0


title: DevTOX04-418_ctrl_0


title: DevTOX04-455_TBBA_1


title: DevTOX04-416_BPF_10


title: DevTOX04-410_BPA_1


title: DevTOX04-400_BPA_1


title: DevTOX04-415_BPF_1


title: DevTOX04-406_BPF_10


title: DevTOX04-405_BPF_1


title: DevTOX04-401_BPA_10


title: DevTOX04-408_ctrl_0


title: DevTOX04-398_ctrl_0


title: devTOXB01_328_BPF_375


title: devTOXB01_331_BPF_250


title: devTOXB01_330_ctrl_0


title: devTOXB01_327_BPF_375


title: DevTOX04-4082_ctrl_0


title: devTOXB01_326_BPF_375


title: devTOXB01_325_ctrl_0


title: DevTOX04-411_BPA_10


title: DevTOX04-420_BPA_1


title: devTOXB01_320C_BPS_400


title: devTOXB01_333_BPF_250


title: devTOXB01_322C_BPS_500


title: DevTOX04-3982_ctrl_0


title: devTOXB01_319C_BPS_400


title: devTOXB01_318C_BPS_400


title: devTOXB01_317C_BPS_300


title: devTOXB01_332_BPF_250


title: devTOXB01_316C_BPS_300


title: devTOXB01_315C_BPS_300


title: devTOXB01_321C_BPS_500


title: devTOXB01_314C_ctrl_0


title: devTOXB01_312_BPF_400


title: devTOXB01_303_ctrl_0


title: devTOXB01_310_BPF_400


title: devTOXB01_311_BPF_400


title: devTOXB01_301C_BPA_250


title: devTOXB01_323C_BPS_500


title: devTOXB01_297C_BPA_225


title: devTOXB01_299C_BPA_250


title: devTOXB01_296C_BPA_225


title: devTOXB01_300C_BPA_250


title: devTOXB01_298C_BPA_225


title: devTOXB01_294C_BPA_200


title: devTOXB01_293C_BPA_200


title: devTOXB01_289C_TBBA_700


title: devTOXB01_286C_TBBA_650


title: devTOXB01_287C_TBBA_650


title: devTOXB01_295C_BPA_200


title: devTOXB01_284C_TBBA_500


title: devTOXB01_288C_TBBA_700


title: devTOXB01_283C_TBBA_500


title: devTOXB01_259C_CP_ctrl_0


title: devTOXB01_285C_TBBA_650


title: devTOXB01_281C_CP_ctrl_0


title: devTOXB01_282C_TBBA_500


title: devTOXB01_281C_BPA_ctrl_0


title: CIN_CRC_scRNAseq

city: Edmonton

first: Kristi

last: Baker

state: AB

address: 11560 University Ave NW, Room 2308

institute: University of Alberta

data_processing:
The data were first processed using the Cell Ranger v5.0 pipeline (10X Genomics) and then further analyzed using the Seurat package for R (v3.0) as described previously (Stuart et al., 2019; Wang et al., 2019; Mowat et al., 2021.).
Briefly, cells with either a unique gene count over 2,500 or less than 200 as well as genes found in fewer than 3 cells were filtered out. Principal component analysis (PCA) was used to visualize and explore these datasets and we used the default settings of the RunTSNE function to summarize the PCA with tSNE dimensionality. Cell clusters in the two-dimensional representations were annotated to known cell types using FindAllMarkers for all clusters. Differential expression analysis was performed using the DESeq2 package (Love et al., 2014).
Genome_build: mm10
Supplementary_files_format_and_content: Data matrices were generated in Seurat v3.0 using the barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz files generated by the Cell Ranger v5.0 pipeline.

source_name: Orthotopic colorectal cancer model

growth_protocol: 1.5x105 dMMR or CIN MC38 colorectal cancer cells (containing targeted mutations in Mlh1 or Kras, respectively) in 50 µl PBS into the wall of the descending colon using a flexible needle inserted through the working channel of an endoscope and visualized via the ColoView imaging system. Orthotopic tumour growth was monitored by endoscopy and tumours were harvested after 14-21 days.

extract_protocol:
Following enzymatic digestion, dead cells were removed using the EasySep Dead Cell Removal Kit (StemCell). CD45+ cells were purified using magnetic beads (StemCell) and then mixed at a 5:1 ratio of CD45+ cells to tumor cells.
Libraries were constructed using the Single Cell Immune Profiling kit (10X Genomics).

tag: strain

tag: genetic mutation

value: Kras mutation in MC38 cell line

value: chromosomally instable (CIN) colorectal cancer


title: dMMR_CRC_scRNAseq

value: Mlh1 deletion in MC38 cell line

value: orthotopic mismatch repair deficient (dMMR) colorectal cancer


title: Murine BAT cells_CPF rep 6

city: Hamilton

first: Gregory

middle: R

last: Steinberg

address: 1200 Main St W

department: Medicine

institute: McMaster University

data_processing:
Raw RNA-Sequencing (RNA-Seq) reads were obtained from an Illumina HiSeq as 50bp paired-end reads in FASTQ format with approximately 25 million reads per sample. Reads were analyzed for various quality control parameters including: per base sequence quality, per sequence GC content, sequence length distribution and sequence duplication levels and Kmer content using the FastQC tool.
Trimmomatic was used to trim/remove low quality reads or bases, plus Illumina adapters. Reads were then aligned to the Ensembl Mus musculus (GRCm38.92) reference genome using HiSAT2.
Read counts for each gene were then obtained for the aligned reads using the Htseq-counts tool. Raw counts data obtained from Htseq-counts were normalized using DESeq2 using size factors obtained from the total dataset and virtual reference sample based on the data.
Genome_build: Ensembl Mus musculus (GRCm38.92) genome
Supplementary_files_format_and_content: EXCEL DeSeq2 normalized counts

source_name: murine brown adipocyte cell culture

growth_protocol: Immortalized brown adipocytes were cultured in high glucose DMEM (GibcoTM) containing 10% fetal bovine serum and 1% antibiotic-antimycotic solution. For differentiation, confluent cells were placed in induction media (0.5 mM IBMX; 0.125 mM indomethacin; 0.2 μg ml-1 dexamethasone; 1 nM T3, 20 nM insulin) for 2 d and subsequently maintained on differentiation media (1 nM T3, 20 nM insulin) for 7 days.

extract_protocol:
Cell lysates were collected by administering 175µL per well of RNeasy Lysis Buffer (RLT) (Qiagen, Hilden, Germany) supplemented with 143mM beta-mercaptoethanol (Sigma-Aldrich) and vortexing until cells lifted from plates. Once cells were lifted from plates, 175µL of 70% ethanol was added to each well and lysates were transferred to a High Pure Filter tube from Roche RNA Isolation Kit (Roche Diagnostics, Mannheim, Germany). RNA isolation was done as outlined by manufacturers specifications.
Library preparations were conducted using the NEBNext Ultra II Directional RNA Library Prep Kit (NEB, Ipswich, MA, USA) and library fragment size distribution verified using Agilent 2100 Bioanalyser (Agilent, Santa Clara, CA, USA).

treatment_protocol: Cells were treated for 4 hours with either 1pM Chlorpyrifos or vehicle (DMSO) in Krebs-Ringer Bicarbonate Buffer (Sigma-Aldrich) supplemented with 10mM HEPES (Janssen Pharmaceuticals, 3a2440 Geel, Belgium), 1mM CaCl2, and 1% fatty-acid free Bovine Serum Albumin (BSA) (EquiTech Bio Inc., Texas, USA) at pH 7.4.

value: immortalized murine brown adipocyte cell culture

tag: cell state

value: fully differentiated

tag: treatment

value: Chlorpyrifos


title: Murine BAT cells_CPF rep 4


title: Murine BAT cells_CPF rep 5


title: devTOXB01_292C_ctrl_0


title: Murine BAT cells_CPF rep 3


title: Murine BAT cells_CPF rep 1


title: Murine BAT cells_CPF rep 2


title: Murine BAT cells_Vehicle rep 6

value: Vehicle


title: devTOXB01_290C_TBBA_700


title: Murine BAT cells_Vehicle rep 1


title: Murine BAT cells_Vehicle rep 4


title: iCount_d16_5_20180830_O20

city: Zürich

first: Baptiste

middle: N

last: Jaeger

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zürich

description: RawCount_Mouse_iCount_Embryonic_Cortex.txt

data_processing:
Single-end 126nt-long reads were adaptor removed and trimmed using cutadapt v1.16 and sickle v1.33 with default parameters.
Reads were mapped against the mouse GRCm38.90 primary assembly or the human GRCh38.p13 primary assembly using STAR v2.6.0c in `alignReads` mode.
Gene count matrices were quantified at the exon level ignoring multimappers using featurecounts from subread v1.6.2.
The following paramaters were used for QC filtering.In the human dataset, only cells with 3000-7000 genes detected, less than 10% of mitochondrial reads and more than 50’000 reads were kept. In each dataset (i.e. 384 well-plate), cells with more or less than 1.5-fold the median read content per cell were excluded.  In the mouse dataset, only nuclei with 1000-3000 genes detected, less than 5% of mitochondrial reads and more than 50’000 reads were kept. In each dataset (i.e. 384 well-plate), nuclei with more or less than 1.5-fold the median read content per cell were excluded
Seurat v3.1.1 was used to normalize read counts, regress out the library size and mitochondrial reads proportion per cell, find variable features with the `vst` method, integrate multiple plates, dimensionality reduce the data, cluster cells and test for differentially expressed genes.
For pseudotime calculation, independent component analysis was computed with fastICA package v1.2.2.
Genome_build: mouse GRCm38.90 and human GRCh38.p13
Supplementary_files_format_and_content: one single metadata file will both mouse and human data. One rawcout file for mouse single nucleus data. One rawcount file for human single cell data.

source_name: embryonic cortex

extract_protocol:
singe-cells and single-nulcei
illumina nextera

tag: mouse strain

value: H3.1-iCOUNT x ROSA26:CreERT2

tag: age of the mice/organoids at the time of the tamoxifen injection

tag: time of experiment

value: 38h post tamoxifen injection

tag: sorted material

value: individual iCount+ nuclei

tag: batch number

tag: icount color

value: Orange


title: iCount_d16_5_20180830_O23


title: iCount_d16_5_20180830_P05


title: iCount_d16_5_20180830_O18


title: iCount_d16_5_20180830_O06


title: iCount_d16_5_20180830_P10


title: iCount_d16_5_20180830_O21


title: iCount_d16_5_20180830_O13


title: iCount_d16_5_20180830_O05


title: iCount_d16_5_20180830_O16


title: iCount_d16_5_20180830_O19


title: iCount_d16_5_20180830_O17


title: iCount_d16_5_20180830_O09


title: iCount_d16_5_20180830_O03


title: Murine BAT cells_Vehicle rep 5

tag: cell type


title: iCount_d16_5_20180830_N20

value: Green


title: iCount_d16_5_20180830_O02


title: Murine BAT cells_Vehicle rep 3


title: iCount_d16_5_20180830_N19


title: iCount_d16_5_20180830_N18


title: iCount_d16_5_20180830_N15


title: iCount_d16_5_20180830_N16


title: iCount_d16_5_20180830_N14


title: Murine BAT cells_Vehicle rep 2


title: iCount_d16_5_20180830_N13


title: iCount_d16_5_20180830_O10


title: iCount_d16_5_20180830_O15


title: iCount_d16_5_20180830_N12


title: iCount_d16_5_20180830_N11


title: iCount_d16_5_20180830_N10


title: iCount_d16_5_20180830_N08


title: iCount_d16_5_20180830_N06


title: iCount_d16_5_20180830_N09


title: iCount_d16_5_20180830_N02


title: iCount_d16_5_20180830_N07


title: iCount_d16_5_20180830_M18


title: iCount_d16_5_20180830_M20


title: iCount_d16_5_20180830_M17


title: iCount_d16_5_20180830_M16


title: iCount_d16_5_20180830_N17


title: iCount_d16_5_20180830_M09


title: iCount_d16_5_20180830_M10


title: iCount_d16_5_20180830_M15


title: iCount_d16_5_20180830_M12


title: iCount_d16_5_20180830_M06


title: iCount_d16_5_20180830_M07


title: iCount_d16_5_20180830_M01


title: iCount_d16_5_20180830_M02


title: iCount_d16_5_20180830_M03


title: iCount_d16_5_20180830_L20


title: iCount_d16_5_20180830_L19


title: iCount_d16_5_20180830_M05


title: iCount_d16_5_20180830_L18


title: iCount_d16_5_20180830_L17


title: iCount_d16_5_20180830_L15


title: iCount_d16_5_20180830_L16


title: iCount_d16_5_20180830_N05


title: iCount_d16_5_20180830_M14


title: iCount_d16_5_20180830_L13


title: iCount_d16_5_20180830_L10


title: iCount_d16_5_20180830_L08


title: iCount_d16_5_20180830_L14


title: iCount_d16_5_20180830_L05


title: iCount_d16_5_20180830_L09


title: iCount_d16_5_20180830_M13


title: iCount_d16_5_20180830_L01


title: iCount_d16_5_20180830_L06


title: YTH1-16h_rep1

city: Indianapolis

first: Michael

middle: James

last: Holmes

state: IN

address: 635 Barnhill Drive

department: Pharmacology & Toxicology

institute: Indiana University School of Medicine

description:
YTH1_16h.gtf
YTH1_16h1

data_processing:
trim with TrimGalore!
map to Toxoplasma genome (v45 from toxodb) with HISAT2
get feature counts with htseq-count
differential expression with DESeq2
transcriptome assembly with StringTie
Genome_build: Toxoplasma gondii (ME49) v45 from toxodb.org
Supplementary_files_format_and_content: tab delimited file with gene counts

organism: Toxoplasma gondii

source_name: RH::TIR1::YTH1-AID strain Toxoplasma gondii

growth_protocol: parasites innoculated at MOI 10:1, grown in confluent human foreskin fibroblasts in DMEM+10%FBS (no antibiotic) for 36h prior to harvest

extract_protocol:
infected monolayer was scraped & syringe lysed. Parasites  washed 3x with PBS. Pellet resuspended in TRIzol
RNA libraries were prepared for sequencing using standard Illumina protocols
paired end 2x150bp RNAseq

treatment_protocol: treatment with 500 uM 3-indole acetic acid (IAA) for 0, 4 16h

value: 500uM IAA treatment, 16h


title: iCount_d16_5_20180830_L07


title: iCount_d16_5_20180830_K19


title: YTH1-16h_rep2

description:
YTH1_16h.gtf
YTH1_16h2


title: YTH1-16h_rep3

description:
YTH1_16h.gtf
YTH1_16h3


title: iCount_d16_5_20180830_K17


title: iCount_d16_5_20180830_K18


title: iCount_d16_5_20180830_K16


title: YTH1-0h_rep3

description:
YTH1_0h.gtf
YTH1_0h3

value: non treated


title: YTH1-4h_rep3

description:
YTH1_4h.gtf
YTH1_4h3

value: 500uM IAA treatment, 4h


title: iCount_d16_5_20180830_K14


title: YTH1-4h_rep2

description:
YTH1_4h.gtf
YTH1_4h2


title: iCount_d16_5_20180830_L03


title: iCount_d16_5_20180830_K15


title: YTH1-0h_rep2

description:
YTH1_0h.gtf
YTH1_0h2


title: iCount_d16_5_20180830_K13


title: YTH1-0h_rep1

description:
YTH1_0h.gtf
YTH1_0h1


title: iCount_d16_5_20180830_K12


title: WTAP-16h_rep3

description:
WTAP_16h.gtf
WTAP_16h3

source_name: RH::TIR1::WTAP-AID strain Toxoplasma gondii


title: iCount_d16_5_20180830_K11


title: WTAP-16h_rep2

description:
WTAP_16h.gtf
WTAP_16h2


title: iCount_d16_5_20180830_K07


title: WTAP-16h_rep1

description:
WTAP_16h.gtf
WTAP_16h1


title: WTAP-4h_rep3

description:
WTAP_4h.gtf
WTAP_4h3


title: WTAP-4h_rep2

description:
WTAP_4h.gtf
WTAP_4h2


title: iCount_d16_5_20180830_J21


title: iCount_d16_5_20180830_K05


title: YTH1-4h_rep1

description:
YTH1_4h.gtf
YTH1_4h1


title: WTAP-4h_rep1

description:
WTAP_4h.gtf
WTAP_4h1


title: WTAP-0h_rep3

description:
WTAP_0h.gtf
WTAP_0h3


title: iCount_d16_5_20180830_J17


title: iCount_d16_5_20180830_J20


title: WTAP-0h_rep1

description:
WTAP_0h.gtf
WTAP_0h1


title: iCount_d16_5_20180830_J19


title: METTL3-16h_rep3

description:
M3_16h.gtf
M3_16h3

source_name: RH::TIR1::METTL3-AID strain Toxoplasma gondii


title: iCount_d16_5_20180830_J16


title: METTL3-16h_rep2

description:
M3_16h.gtf
M3_16h2


title: METTL3-16h_rep1

description:
M3_16h.gtf
M3_16h1


title: iCount_d16_5_20180830_J14


title: iCount_d16_5_20180830_J15


title: iCount_d16_5_20180830_J13


title: iCount_d16_5_20180830_J12


title: iCount_d16_5_20180830_J11


title: METTL3-4h_rep3

description:
M3_4h.gtf
M3_4h3


title: METTL3-4h_rep1

description:
M3_4h.gtf
M3_4h1


title: METTL3-4h_rep2

description:
M3_4h.gtf
M3_4h2


title: METTL3-0h_rep3

description:
M3_0h.gtf
M3_0h3


title: iCount_d16_5_20180830_J10


title: iCount_d16_5_20180830_J09


title: METTL3-0h_rep2

description:
M3_0h.gtf
M3_0h2


title: METTL3-0h_rep1

description:
M3_0h.gtf
M3_0h1


title: WTAP-0h_rep2

description:
WTAP_0h.gtf
WTAP_0h2


title: iCount_d16_5_20180830_J18


title: iCount_d16_5_20180830_J07


title: iCount_d16_5_20180830_J05


title: iCount_d16_5_20180830_J06


title: iCount_d16_5_20180830_J01


title: iCount_d16_5_20180830_I19


title: iCount_d16_5_20180830_I17


title: iCount_d16_5_20180830_I21


title: iCount_hOrganoids_plateII_20190308BJ_P20

source_name: human forebrain organoids

value: 39 days in culture

value: 7 days post Cre electroporation

value: individual iCount+ cells

value: Red


title: iCount_hOrganoids_plateII_20190308BJ_P19


title: iCount_hOrganoids_plateII_20190308BJ_P17


title: iCount_hOrganoids_plateII_20190308BJ_P22


title: iCount_d16_5_20180830_J08


title: iCount_hOrganoids_plateII_20190308BJ_P16


title: iCount_hOrganoids_plateII_20190308BJ_P14


title: LMX1A- cells_biological rep 1

city: Seoul

first: Dong-Wook

last: Kim

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Dept. of Physiol.

country: South Korea

institute: Yonsei University College of Medicine

hyb_protocol: A 15μg labeled cRNA was fragmented by heat and ion-mediated hydrolysis at 94°C for 35 min. The fragmented cRNA was hybridized to the Affymetrix GeneChip Human U133 Plus 2.0 Array at 45°C for 16 hours.

scan_protocol: Arrays were scanned using the Affymetrix GCS3000 Scanner.

data_processing: The data were summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Expression Console™ Software (EC). We exported the result with gene level RMA analysis and performed the differentially expressed gene (DEG) analysis. Statistical significance of the expression data was determined using LPE test and fold change in which the null hypothesis was that no difference exists among groups. False discovery rate (FDR) was controlled by adjusting p value using Benjamini-Hochberg algorithm.

source_name: Isolated LMX1A- cells from hESC-derived vmDA precursors

label_protocol: Biotin-labeled, amplified RNA (aRNA) was synthesized from 100 ng total RNA using the GeneChip™ 3′IVT Plus reagent Kit.

growth_protocol: hESCs were grown in DMEM/F12 supplemented with 20% Knockout Serum Replacement including basic FGF. vmDA precursors were grown in DMEM/F12 N2 and B27 supplemented media without basic FGF.

extract_protocol: Total RNA was extracted using the Easy-Spin® Total RNA Extraction Kit (iNtRON) according to the manufacturer's instruction.

tag: source cell type

value: human embryonic stem cells (hESCs)

tag: marker expression

value: differentiated cells from hESCs


title: LMX1A- cells_biological rep 3

value: Isolated LMX1A- cells from hESC-derived vmDA precursors


title: iCount_d16_5_20180830_I15


title: iCount_d16_5_20180830_I13


title: iCount_d16_5_20180830_I14


title: iCount_hOrganoids_plateII_20190308BJ_P12


title: LMX1A+ cells_biological rep 1

source_name: Isolated LMX1A+ cells from hESC-derived vmDA precursors


title: iCount_d16_5_20180830_J03


title: LMX1A- cells_biological rep 2


title: iCount_hOrganoids_plateII_20190308BJ_P13


title: iCount_hOrganoids_plateII_20190308BJ_P10


title: iCount_hOrganoids_plateII_20190308BJ_P11


title: LMX1A+ cells_biological rep 3

value: Isolated LMX1A+ cells from hESC-derived vmDA precursors


title: LMX1A+ cells_biological rep 2


title: iCount_d16_5_20180830_I10


title: iCount_d16_5_20180830_I20


title: iCount_d16_5_20180830_I11


title: iCount_d16_5_20180830_I09


title: iCount_d16_5_20180830_I12


title: iCount_d16_5_20180830_I08


title: iCount_hOrganoids_plateII_20190308BJ_P09


title: iCount_hOrganoids_plateII_20190308BJ_P03


title: iCount_hOrganoids_plateII_20190308BJ_P05


title: iCount_d16_5_20180830_I16


title: iCount_d16_5_20180830_I07


title: iCount_hOrganoids_plateII_20190308BJ_P02


title: iCount_d16_5_20180830_I06


title: iCount_d16_5_20180830_I05


title: iCount_d16_5_20180830_I04


title: iCount_hOrganoids_plateII_20190308BJ_P01


title: iCount_d16_5_20180830_I03


title: iCount_hOrganoids_plateII_20190308BJ_O12


title: iCount_d16_5_20180830_H21


title: iCount_d16_5_20180830_H18


title: iCount_hOrganoids_plateII_20190308BJ_O18


title: iCount_d16_5_20180830_H20


title: iCount_d16_5_20180830_H19


title: iCount_hOrganoids_plateII_20190308BJ_P06


title: iCount_hOrganoids_plateII_20190308BJ_O07


title: iCount_hOrganoids_plateII_20190308BJ_O20


title: iCount_hOrganoids_plateII_20190308BJ_O11


title: iCount_hOrganoids_plateII_20190308BJ_O06


title: iCount_hOrganoids_plateII_20190308BJ_O01


title: iCount_d16_5_20180830_H15


title: iCount_hOrganoids_plateII_20190308BJ_O05


title: iCount_d16_5_20180830_H12


title: iCount_d16_5_20180830_H14


title: iCount_hOrganoids_plateII_20190308BJ_O09


title: iCount_d16_5_20180830_H11


title: iCount_hOrganoids_plateII_20190308BJ_N24


title: iCount_hOrganoids_plateII_20190308BJ_N22


title: iCount_d16_5_20180830_H09


title: iCount_d16_5_20180830_H16


title: iCount_d16_5_20180830_H08


title: iCount_hOrganoids_plateII_20190308BJ_N17


title: iCount_hOrganoids_plateII_20190308BJ_N21


title: iCount_d16_5_20180830_H13


title: iCount_d16_5_20180830_H22


title: iCount_d16_5_20180830_H07


title: iCount_hOrganoids_plateII_20190308BJ_N12


title: iCount_hOrganoids_plateII_20190308BJ_O02


title: iCount_hOrganoids_plateII_20190308BJ_N10


title: iCount_hOrganoids_plateII_20190308BJ_N11


title: iCount_d16_5_20180830_H05


title: iCount_d16_5_20180830_H06


title: iCount_hOrganoids_plateII_20190308BJ_N06


title: iCount_d16_5_20180830_H03


title: iCount_hOrganoids_plateII_20190308BJ_N05


title: iCount_hOrganoids_plateII_20190308BJ_N04


title: iCount_d16_5_20180830_H01


title: iCount_d16_5_20180830_H04


title: iCount_d16_5_20180830_G18


title: iCount_hOrganoids_plateII_20190308BJ_N03


title: iCount_hOrganoids_plateII_20190308BJ_N01


title: iCount_hOrganoids_plateII_20190308BJ_N02


title: iCount_hOrganoids_plateII_20190308BJ_M23


title: iCount_d16_5_20180830_G22


title: iCount_d16_5_20180830_G23


title: iCount_d16_5_20180830_H02


title: iCount_hOrganoids_plateII_20190308BJ_M22


title: iCount_d16_5_20180830_G20


title: iCount_d16_5_20180830_G16


title: iCount_hOrganoids_plateII_20190308BJ_M20


title: iCount_d16_5_20180830_G17


title: iCount_d16_5_20180830_G15


title: iCount_hOrganoids_plateII_20190308BJ_N09


title: iCount_hOrganoids_plateII_20190308BJ_M12


title: iCount_d16_5_20180830_G13


title: iCount_hOrganoids_plateII_20190308BJ_M11


title: iCount_d16_5_20180830_G12


title: iCount_d16_5_20180830_G21


title: iCount_hOrganoids_plateII_20190308BJ_M10


title: iCount_hOrganoids_plateII_20190308BJ_M09


title: iCount_d16_5_20180830_G11


title: iCount_hOrganoids_plateII_20190308BJ_M08


title: iCount_d16_5_20180830_G10


title: iCount_hOrganoids_plateII_20190308BJ_M07


title: iCount_hOrganoids_plateII_20190308BJ_M17


title: iCount_hOrganoids_plateII_20190308BJ_M03


title: iCount_hOrganoids_plateII_20190308BJ_M06


title: iCount_hOrganoids_plateII_20190308BJ_M02


title: iCount_hOrganoids_plateII_20190308BJ_M04


title: iCount_d16_5_20180830_G06


title: iCount_d16_5_20180830_G07


title: iCount_d16_5_20180830_G04


title: iCount_d16_5_20180830_G05


title: iCount_hOrganoids_plateII_20190308BJ_L16


title: iCount_d16_5_20180830_F20


title: iCount_d16_5_20180830_G02


title: iCount_hOrganoids_plateII_20190308BJ_L19


title: iCount_d16_5_20180830_G03


title: iCount_d16_5_20180830_G14


title: iCount_hOrganoids_plateII_20190308BJ_L12

value: Yellow


title: iCount_d16_5_20180830_F19

value: H3.1-iCOUNT x ROSA26:CreERT2


title: iCount_hOrganoids_plateII_20190308BJ_L09


title: iCount_d16_5_20180830_F17

value: 38h post tamoxifen injection


title: iCount_d16_5_20180830_F16

value: individual iCount+ nuclei


title: iCount_d16_5_20180830_F14


title: iCount_hOrganoids_plateII_20190308BJ_L08


title: iCount_hOrganoids_plateII_20190308BJ_L07


title: iCount_d16_5_20180830_G08


title: iCount_d16_5_20180830_F13


title: iCount_hOrganoids_plateII_20190308BJ_M01


title: iCount_hOrganoids_plateII_20190308BJ_L05


title: iCount_hOrganoids_plateII_20190308BJ_L06


title: iCount_d16_5_20180830_F12


title: iCount_d16_5_20180830_F11


title: iCount_hOrganoids_plateII_20190308BJ_L03


title: iCount_d16_5_20180830_F10


title: iCount_d16_5_20180830_F09


title: iCount_hOrganoids_plateII_20190308BJ_K22

value: Orange


title: iCount_hOrganoids_plateII_20190308BJ_L01


title: iCount_hOrganoids_plateII_20190308BJ_K21


title: iCount_hOrganoids_plateII_20190308BJ_L10


title: iCount_hOrganoids_plateII_20190308BJ_K19


title: iCount_hOrganoids_plateII_20190308BJ_K20


title: iCount_hOrganoids_plateII_20190308BJ_K18


title: iCount_d16_5_20180830_F06


title: iCount_d16_5_20180830_F05


title: iCount_d16_5_20180830_F07


title: iCount_d16_5_20180830_F08


title: iCount_d16_5_20180830_F04


title: iCount_d16_5_20180830_F03


title: iCount_hOrganoids_plateII_20190308BJ_K10


title: iCount_d16_5_20180830_F02


title: iCount_hOrganoids_plateII_20190308BJ_K09


title: iCount_d16_5_20180830_E22


title: iCount_d16_5_20180830_E21


title: iCount_hOrganoids_plateII_20190308BJ_K05


title: iCount_d16_5_20180830_E20


title: iCount_hOrganoids_plateII_20190308BJ_K04


title: iCount_hOrganoids_plateII_20190308BJ_K03


title: iCount_hOrganoids_plateII_20190308BJ_K06


title: iCount_d16_5_20180830_E18


title: iCount_hOrganoids_plateII_20190308BJ_K01


title: iCount_hOrganoids_plateII_20190308BJ_K02


title: iCount_d16_5_20180830_E17


title: iCount_hOrganoids_plateII_20190308BJ_L02


title: iCount_d16_5_20180830_E16


title: iCount_hOrganoids_plateII_20190308BJ_J24


title: iCount_d16_5_20180830_E15


title: iCount_d16_5_20180830_E14


title: iCount_hOrganoids_plateII_20190308BJ_J23


title: iCount_hOrganoids_plateII_20190308BJ_J18


title: iCount_hOrganoids_plateII_20190308BJ_J20


title: iCount_hOrganoids_plateII_20190308BJ_J19


title: iCount_hOrganoids_plateII_20190308BJ_J17


title: iCount_d16_5_20180830_E09


title: iCount_d16_5_20180830_E12


title: iCount_d16_5_20180830_E13


title: iCount_d16_5_20180830_E06


title: iCount_hOrganoids_plateII_20190308BJ_J16


title: iCount_hOrganoids_plateII_20190308BJ_J14


title: iCount_d16_5_20180830_E05


title: iCount_d16_5_20180830_E04


title: iCount_d16_5_20180830_D21


title: iCount_hOrganoids_plateII_20190308BJ_J11


title: iCount_d16_5_20180830_E01


title: iCount_hOrganoids_plateII_20190308BJ_J10


title: iCount_d16_5_20180830_D24


title: iCount_d16_5_20180830_D23


title: iCount_hOrganoids_plateII_20190308BJ_J13


title: iCount_d16_5_20180830_D16


title: iCount_hOrganoids_plateII_20190308BJ_J01


title: iCount_d16_5_20180830_E08


title: iCount_hOrganoids_plateII_20190308BJ_I22


title: iCount_d16_5_20180830_D22


title: iCount_hOrganoids_plateII_20190308BJ_I21


title: iCount_d16_5_20180830_D14


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