title: t2: cpt-cef treated cells, replicate 2

status: Public on Sep 15 2021

city: Chennai

first: Suresh

middle: Kumar

last: Subbiah

address: 173, Agaram Main Rd, Selaiyur, Chennai, Tamil Nadu 600073, India

country: India

institute: Bharath university

description:
Sample 4
Total RNA, mRNA-enriched

data_processing:
The protocol was adapted from Love et al., F1000Res, 2018. In brief, sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the GRCh38 transcriptome using Salmon with example parameters: salmon quant -i CRCh38_index -l A -1 Example_R1.fastq -2 Example_R2.fastq -p 8 --validateMappings -o Example_quant. k-mer was designated as 31
Transcript abundance obtained with Salmon (v1.1.0) were converted to the gene level with Tximport and used as an input for DESeq2 (v3.2) for normalization and quantification.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include normalized expression values for each sample

source_name: colorectal adenocarcinoma

growth_protocol: The final stock solution of each compound was made by dissolving them in 10% DMSO and cell culture media. Multiple concentrations were made by serial dilutions, using cell culture medium. DMSO concentration was kept below 1% (v/v) in all analyses. As vehicle control, complete cell culture medium was added to the cells without imposing any treatment.

extract_protocol:
The HT29 colon cancer cell line were incubated with CPT-CEF as mentioned in our previous study(Krishnan et al., 2017). Then, the total RNA was extracted from the cells using RNeasy mini kit according to recommendation from the manufacturer (Qiagen; Hilden Germany). Samples with RNA integrity (RIN) value more than 7 and high purity (A260/A280 ratio = 2) would be used for downstream experiment. The Bioanalyzer 2100 system (Agilent Technologies; CA, USA) was used to measure RNA integrity whereas the NanoDrop 2000 Spectrophotometer (Thermo Scientific; MA, USA) was used to measure the A260/A280 ratio.
Library preparation was performed using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs, MA, USA) according to the manufacturer’s protocol. The isolated RNA was further enriched to obtain mRNA. To do this, total RNA was incubated with 50 µL of oligo dT beads and binding buffer at 65°C for 5 mins in a PCR tube. The tubes were then placed onto a magnetic stand to capture the beads. The contents of the tubes were washed several times to remove residual rRNA and other RNA types. Then, the beads were mixed with 50 µL of Tris-buffer and incubated in a thermal cycler at 80°C for 2 mins, followed by a cooling step to a temperature of 25°C before elution.

treatment_protocol: Cells were procured from the Laboratory of Vaccine and Immunotherapy (LIVES) Institute of Biosciences (IBS), UPM. The cell lines were grown adherently using RPMI media supplemented with 10% foetal calf serum, 100 U/mL penicillin, and 100 μg/mL streptomycin at 5% CO2 at 37 °C. The cells were seeded in 96-well plates at a concentration of 1 × 10e4 in 100 µl of cell culture medium. Cells were allowed to grow for 24 h to reach approximately 90% confluency.

value: colon adenocarcinoma cell line HT29

value: colon

tag: cell source

value: 44 years adult--cell strain

value: β-cyclodextrin-EDTA-Fe3O4 nanoparticles

value: Wild type


title: u2:  untreated cells, replicate 2

type: SRA

description:
Sample 2
Total RNA, mRNA-enriched

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: tissue

tag: treatment

value: control

tag: genotype


title: t1: cpt-cef treated cells, replicate 1

description:
Sample 3
Total RNA, mRNA-enriched


title: u1: untreated cells, replicate 1

description:
Sample 1
Total RNA, mRNA-enriched


title: Human Donor Lung 6

status: Public on Sep 16 2021

city: San Francisco

first: Seoyeon

last: Lee

state: CA

address: 513 Parnassus Ave HSE 1355B

department: Pulmonary and Critical Care Medicine

country: USA

institute: University of California, San Francisco

data_processing:
Raw reads were aligned and gene counts generated with STAR v2.7.1a to the HG38 human genome and the Ensembl gene build v95 with the following parameters: --outSAMtype BAM   Unsorted      --outFilterType BySJout   --outFilterMultimapNmax 1   --outFilterMismatchNmax 999   --outFilterMismatchNoverLmax 0.04   --clip3pAdapterSeq GATCGGAAGAGCACACGTCTGAACTCCAGTCAC      --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000   --alignSJDBoverhangMin 1   --quantMode GeneCounts
Individual sample counts matrix were merged using custom python scripts and used as input to DESeq2 1.24.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with DESeq2 normalized gene counts for every gene and every sample

source_name: Lung

extract_protocol:
Snap-frozen lungs were homogenized in Qiazol reagent. RNA was extracted using the miRNeasy Mini Kit (Qiagen).
First the mRNA was randomly fragmented; after cDNA first strand synthesis, second strand was generated by nick-translation, followed by purification, terminal repair, Atailing, ligation of sequencing adapters, size selection and PCR enrichment.

tag: age

value: distal lung


title: X158_D13_3

city: Munich

first: Irmela

last: Jeremias

address: Feodor-Lynenstr. 21

department: Research Unit Apoptosis in Hematopoietic Stem Cells

country: Germany

institute: Helmholtz Zentrum München, German Center for Environmental Health (HMGU), Munich, Germany

description: SFFV/sh-XIAP 13 days post-transduction

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned to a combined Human Genome (hg38) and Mouse Genome (mm10) with STAR 2.6.0a
Quantification was done with ENSEMBL gene models (Homo_sapiens:GRCh38.84, Mus_musculus:GRCm38.85)
Mouse reads were excluded for further analysis
5 outlier samples were excluded for further analysis
Genome_build: hg38
Supplementary_files_format_and_content: cell (columns) and gene (rows) -wise UMI expression table

growth_protocol: NALM6 cells have been transduced and followed up in vitro

extract_protocol:
prime-seq
Library was constructed using the prime-seq protocol

treatment_protocol: NALM6 cells have been transduced with different constructs (144 or 146 or 153 or 158) and followed up in vitro

tag: cell type

value: preB-ALL cell

tag: transduction

value: SFFV/sh-XIAP

tag: time point

value: 13 days post-transduction


title: X158_D13_1

description: SFFV/sh-XIAP 13 days post-transduction


title: X153_D13_2

description: EF1a/sh-XIAP 13 days post-transduction


title: X153_D13_3

description: EF1a/sh-XIAP 13 days post-transduction


title: X158_D13_2

description: SFFV/sh-XIAP 13 days post-transduction


title: Human Donor Lung 1


title: X153_D13_1

description: EF1a/sh-XIAP 13 days post-transduction


title: X146_D13_2

description: SFFV/sh-CTRL 13 days post-transduction

value: SFFV/sh-CTRL


title: X146_D13_1

description: SFFV/sh-CTRL 13 days post-transduction


title: sgMyc_RNA-seq_rep2

city: Hong Kong

first: Yingzhe

last: Ding

state: Shatin NT.

address: Rm503,Li Ka Shing Medical Science Build.,Prince of Wales Hosp.,30-32 Ngan SHing St.

department: Chemical Pathology

country: Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using trimmomatic v0.36 with parameter SLIDINGWINDOW:4:15 MINLEN:50, and low-quality or duplication sequence are removed by a in-house scripts, then mapped to mm9 whole genome using tophat2 with parameters -a 8 -m 0 -I 500000 -p 20 -g 20 --library-type fr-firststrand --segment-mismatches 2 --no-coverage-search -r 50 --mate-std-dev 60
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v2.2.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

molecule: polyA RNA

organism: Mus musculus

source_name: Skeletal muscle

growth_protocol: Isolated muscle stem cells were cultured in growth medium containing F10, 20% FBS, 5 ng/mL basic fibroblast growth factor (bFGF) and 1% pen/strep for 24h.

extract_protocol:
RNA from freshly isolated or culture muscle stem cells was harvested using Trizol reagent.
Purified mRNAs were fragmented and the cDNA were synthesized by reverse transcription. The resulting double-stranded DNA fragments were end-repaired and A-nucleotide overhangs were added. RNA-seq libraries were constructed according to the standard illumina pair-end sequencing procedure.

tag: strain

value: muscle stem cells

value: post natal day 38


title: X144_D13_3

description: EF1a/sh-CTRL 13 days post-transduction


title: X158_D10_3

description: SFFV/sh-XIAP 10 days post-transduction

value: 10 days post-transduction


title: X158_D10_1

description: SFFV/sh-XIAP 10 days post-transduction


title: X153_D10_1

description: EF1a/sh-XIAP 10 days post-transduction


title: X144_D13_1

description: EF1a/sh-CTRL 13 days post-transduction


title: X153_D10_2

description: EF1a/sh-XIAP 10 days post-transduction


title: X158_D10_2

description: SFFV/sh-XIAP 10 days post-transduction


title: X146_D10_1

description: SFFV/sh-CTRL 10 days post-transduction


title: X144_D10_3

description: EF1a/sh-CTRL 10 days post-transduction


title: MEL624_mockB

type: RNA

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

description: MEL624 transfected with empty pQCXIP plasmid, biological replicate B

data_processing: Gene-level analyses was performed. RMA normalization, summarization by mean and batch effect removal, all were done by Partek Genomics suite (version 6.4) Copyright ©

label: biotin

label_protocol: Biotinylated cRNA were prepared  using WT expression kit according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

growth_protocol: cell line WM266-4 was obtained from the ATCC and was cultured in DMEM medium supplemented with 10% fetal bovine serum, 1%NaP, 1%L-glu, 1%pen/strep and 1%non-essential amino acids. Human melanoma cell line MEL624 (obtained from Dr. SA Rosenberg, Surgery Branch, NCI, Bethesda, MD, USA) was cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 1%NaP, 1%L-glu, 1%pen/strep and 2.5%HEPES.

extract_protocol: Total RNA was isolated using Trizol reagent (Sigma-Aldrich), according to manufacturer’s instructions

treatment_protocol: naïve cell lines (WM266-4 and MEL624) were transfected with empty pQCXIP vector (mock) or with SNX18-V1 consrtuct. Two biological replicates were done for each cell line.

value: metastatic melanoma cell line

tag: tansfection of

value: empty pQCXIP plasmid


title: MEL624_SNX18B

description: MEL624  transfected with SNX18-V1 pQCXIP plasmid, biological replicate B

hyb_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)

value: SNX18-V1 pQCXIP plasmid


title: WM266-4_mockB

description: WM266-4 transfected with empty pQCXIP plasmid, biological replicate B

scan_protocol: according to the manufacturer's protocol (Affymetrix, Santa Clara, CA, USA)


title: WM266-4_mockA

description: WM266-4 transfected with empty pQCXIP plasmid, biological replicate A


title: MEL624_mockA

description: MEL624 transfected with empty pQCXIP plasmid, biological replicate A


title: WM266-4_SNX18A

description: WM266-4  transfected with SNX18-V1 pQCXIP plasmid, biological replicate A


title: WM266-4_SNX18B

description: WM266-4 transfected with SNX18-V1 pQCXIP plasmid, biological replicate B


title: MEL624_SNX18A

description: MEL624  transfected with SNX18-V1 pQCXIP plasmid, biological replicate A


title: X144_D10_2

description: EF1a/sh-CTRL 10 days post-transduction


title: X144_D10_1

description: EF1a/sh-CTRL 10 days post-transduction


title: X153_D4_1

description: EF1a/sh-XIAP 4 days post-transduction

value: 4 days post-transduction


title: X153_D4_2

description: EF1a/sh-XIAP 4 days post-transduction


title: X158_D4_3

description: SFFV/sh-XIAP 4 days post-transduction


title: X158_D4_1

description: SFFV/sh-XIAP 4 days post-transduction


title: X146_D4_2

description: SFFV/sh-CTRL 4 days post-transduction


title: X146_D4_3

description: SFFV/sh-CTRL 4 days post-transduction


title: X144_D4_3

description: EF1a/sh-CTRL 4 days post-transduction


title: X146_D4_1

description: SFFV/sh-CTRL 4 days post-transduction


title: CONT_1

city: Chicago

first: Raghavendra

middle: G

last: Mirmira

state: IL

address: 900 E. 57th Street

department: Medicine

institute: University of Chicago

data_processing:
Sequence reads were aligned to the mouse reference genome mm10 with STAR-2.4.2a.
featureCounts (subread-1.5.0) was used to quantify gene expression (parameters applied: "“-s 1 –Q 10")
Differential expression analysis was performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw count for each sample.

source_name: Bone marrow macrophages

extract_protocol:
RNeasy MiniPlus kit (Qiagen)
Purified total RNA was first evaluated for its quantity, and quality, using Agilent Bioanalyzer 2100. All RNA samples had a RIN (RNA Integrity Number) of eight or higher. Each library was quantified, and its quality accessed by Qubit and Agilent Bioanalyzer, and multiple libraries were pooled in equal molarity. Average size of library insert was approximately 110b. Pooled libraries were applied to Ion Sphere Particles (ISP) with template preparation and amplification using Ion OneTouch 2, followed by ISP loading onto a PI chip and sequencing on Ion Proton semiconductor (Life Technologies). A Phred quality score (Q score) was used to measure the quality of sequencing. More than 90% of the sequencing reads reached Q30 (99.9% base call accuracy).

value: Bone marrow-derived macrophages


title: CONT_3


title: CONT_2


title: X144_D4_2

description: EF1a/sh-CTRL 4 days post-transduction


title: Liver_IgG_2_RIPseq

city: ATHENS

first: Gargani

last: Sofia

state: Please Select

address: 34, Alexander Fleming Street

country: Greece

institute: BSRC Fleming

data_processing:
Basecalls performed using Ion Proton™ system
The sequencing data were mapped to the mm10 genome using Bowtie2  with the settings --local --very-sensitive according to the manufacturer’s recommendations. (Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat Methods 9, 357-359, doi:10.1038/nmeth.1923 (2012).
The reads were assigned to exons calculating RPKM values using the featureCounts package and exon annotations were obtained from ftp://ftp.ensembl.org/pub/release-93/gtf/mus_musculus (Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923-930, doi:10.1093/bioinformatics/btt656 (2014)
Genome_build: mm10 genome
Supplementary_files_format_and_content: all data exonGencode.groups.rpkm .csv

source_name: Liver

extract_protocol:
RIP was performed in native conditions using the lysate from one mouse liver per IP. The dissected mouse liver was rapidly homogenized in ice cold PBS and cells were lysed in low salt lysis buffer.
Libraries were prepared using the Ion Total RNA-Seq Kit v2 protocol and reagents (ThermoFisher Scientific) according to the manufacturer’s instructions.

value: C57BL/6 WT

tag: tissuue

value: Whole Healthy Liver

value: 8 weeks old


title: KO_3

value: Macrophage specific knockout (Dhps_delta_Myel)


title: X146_D10_2

description: SFFV/sh-CTRL 10 days post-transduction


title: Liver_IgG_1_RIPseq


title: Liver_HuR_2_RIPseq


title: Liver_Input_3


title: Liver_Input_1


title: Liver_IgG_3_RIPseq


title: X144_D4_1

description: EF1a/sh-CTRL 4 days post-transduction


title: Liver_HuR_1_RIPseq


title: KO_2


title: KO_1


title: Liver_Input_2


title: Liver_HuR_3_RIPseq


title: 18hr KO CD8+T cells rep1

city: 广州

first: Peng

middle: zhi

last: lin

address: 74 Zhongshan 2 Rd

department: zhongshan school of medicine

country: China

institute: Sun-Yat sen university

data_processing:
Seqtk was used to remove rRNA reads, adaptors and poor quality reads (length < 25 or Q20>0.01).
Clean reads were mapped to mm10 genome by Hisat2 v2.0.4 (Pertea M et al., 2016) with default parameters.
Fragments Per Kilobase of exon model per Million mapped reads (FPKM) of gene expression was calculated by Stringtie v1.3.0 (Pertea M et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: counts and FPKM value of gene expression for each sample

source_name: CD8+T cells

extract_protocol:
Naïve CD8+T cells were isolated by FACS, followed by activation with anti-CD3 and CD28 antibody for 18hr in vitro. RNA was extracted using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: 8-week old

value: CD8+T cells


title: Naïve WT CD8+T cells rep1

description: BRD4Control_NaiveCD8_RNAseq_0h_20210309_B1

value: wild type


title: 18hr WT CD8+T cells rep1


title: Naïve KO CD8+T cells rep1


title: X144_D13_2

description: EF1a/sh-CTRL 13 days post-transduction

value: preB-ALL cell

value: 13 days post-transduction


title: Liver_Mettl3_KO6

city: Columbus

first: Kalpana

last: Ghoshal

state: OH

address: 420 W 12th Ave

institute: The Ohio State University

data_processing:
Libraries were pooled to 3nM and ran on Illumina Hi-Seq machine with the following settings (Single-Read 50bp and pooled on two lanes).
Analysis of RNA-seq was performed with a combination of kallisto (Bray et al., 2016) and sleuth (Pimentel et al., 2017)
Transcript annotation indices for mouse kallisto were created from FASTA files from the mouse Ensembl release 96 with a k-mer length of 19 (-k 19)
Kallisto quantification was done on single-end RNA-seq (--single -l 50 -s 1) data with the respective transcript index and 100 bootstraps (-b 100)
The kallisto output was next analyzed with sleuth (Pimentel et al., 2017) for differential expression at gene-level annotation
Genome_build: mm10
Supplementary_files_format_and_content: Our model matrix was performed as follows (∼genotype). Gene names and attributes were queried from Ensembl using biomaRt.

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. NGS Illumina Sequencing Library was prepared using Takara SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (634878; Takara) per manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mettl3 floxed, Alb-Cre

value: Liver


title: Liver_Mettl3_KO7


title: Liver_Mettl3_KO8


title: Liver_Mettl3_KO5


title: Liver_Mettl3_KO4


title: R26: HBE-PM2.5 high

city: Beijing

first: Rui

last: Chen

address: No.10 Xitoutiao, You An Men

institute: Capital medical university

description: The HBE cells were available from American Type Culture Collection

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

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner

data_processing: Extract data using Agilent Feature Extraction Software

label_protocol: Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: The HBE cells (American Type Culture Collection) were maintained in Dulbecco′s modified Eagle′s medium (DMEM). The culture medium was supplemented with 10 % (v/v) fetal bovine serum (FBS), 100 U/ml penicillin, and 100 μg/ml streptomycin at 37 °C with 5% CO2.

extract_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

treatment_protocol: Cells were exposed to 100 μg/ml Al2O3 NPs，100/500 μg/ml PM2.5, 50 μg/mlDEP.

value: HBE


title: Liver_Mettl3_KO3


title: Liver_Mettl3_KO2


title: R27: HBE-PM2.5 high


title: R23: HBE-PM2.5 low


title: R21: HBE-Al2O3 NPs

source_name: HBE,100 μg/ml Al2O3,24h

value: Al2O3 NPs


title: R20: HBE-Al2O3 NPs


title: R29: HBE-DEP

source_name: HBE,50 μg/ml DEP,24h

value: DEP


title: R22: HBE-PM2.5 low


title: R24: HBE-PM2.5 low


title: R19: HBE-Al2O3 NPs


title: R16: HBE-PBS

source_name: HBE,100 μg/ml PBS,24h

value: PBS


title: R25: HBE-PM2.5 high


title: R17: HBE-PBS


title: R30: HBE-DEP


title: R28: HBE-DEP


title: Liver_WT6

value: Mettl3 floxed


title: Liver_WT3


title: Liver_WT2


title: R18: HBE-PBS


title: Liver_WT4


title: Liver_Mettl3_KO1


title: Liver_WT5


title: Liver_WT1


title: infanticide  replicate 3 Input fraction

city: Cambridge

first: Catherine

last: Dulac

state: MA

address: 16 Divinity Avenue, BL4000

department: Molecular and Cellular Biology

institute: Harvard University

description: Dulac_ps6_Infantx_PAG_PeFA_1_4_16_68_GAGATTCC-AGGCGAAG

data_processing:
Basecalling performed with blc2fastq version 1.8.3
Read alignment performed with the STAR aligner (Dobin et al., 2013) version 2.5.3a to the mm10 reference mouse genome and the Gencode vM12 primary assembly annotation to which non-redundant UCSC transcripts were added, using the two-round mapping approach. STAR parameters used are: outSAMprimaryFlag =”AllBestScore”; outFilterMultimapNmax=”10”; outFilterMismatchNoverLmax=”0.05”, outFilterIntronMotifs=”RemoveNoncanonical”
Transcript expression estimation using MMSEQ (Turro et al., 2011)
Collapsing indistinguishable transcript using MMCOLLAPSE (Turro et al., 2014) and converting MMSEQ's (Turro et al., 2011) posterion FPKM estimates to TPM
Per each animal, subtract the posterior mean ln(TPM) of the input sample from that of the IP sample, per each transcript thereby giving a posterior mean of IP/input fold-change
Per each animal, sum the posterior variance ln(TPM)s of the input and IP samples and divide its square root by the number of posterior samples (1000), per each transcript thereby giving a posterior standard deviation of IP/input fold-change
Fit a Bayesian regression model (Perez et al., 2015) to the posterior mean and of IP/input fold-change , treated as the response with the corresponding posterior standard deviation treated as the uncertainty of the response, to all samples per each transcript, where the only covariate was defined as the animal's behavior, infanticidal or naive, setting navie as baseline
Genome_build: mm10
Supplementary_files_format_and_content: An excel file where for each transcript provided are its: gene symbol; Ensembl and/or UCSC gene ID; Ensembl and/or UCSC transcript ID; a label indicating whether it is a neuropeptide/neuropeptide receptor/Immediate Early Gene (ieg)/NA (none of the previous); genomic locus; encoding strand; posterior probability of the behavior (infanticidal IP/input ln(TPM) being significantly different from the navie IP/input ln(TPM)); infanticial IP/input mean ln(TPM) across all samples; naive IP/input mean ln(TPM) across all samples
Supplementary_files_format_and_content: A CSV file where for transcript provided are the posterior mean TPMs or var TPMs of each sample

source_name: infanticide _Input fraction

growth_protocol: Mice were maintained on a 12hr loght dark cycle and given ab libitum access to chow and water. Mice were individually housed ~1 week before behavior and sample extraction.

extract_protocol:
The tissue was processed for pS6 immunoprecipitation as described previously (Knight et al, 2012).  RNA was isolated using the RNAeasy Micro kit (Qiagen) according to manufacturer’s instructions. RNA was checked for quality and quantity on an Agilent tape station.
High quality samples from matched input and IP fractions were prepared using the (Low-input Library Prep kit (Clontech).

treatment_protocol: Adult male mice were habituated in their home cages to a testing room for 4 hours. Males were then either presented with a 1-4 day old C57BL/6J pup or no stimulus and allowed to interact for 10 minutes, after which time behavior was recorded and the pup was removed. Sixty minutes after stimulus presentation, males were sacrificied and a punch (1 mm diameter) was collected from a 2mm thick brain slice containing the perifornical area, the paraventricular nucleus, and part of the anterior hypothalamus

tag: strain background

tag: Sex

value: Male

value: 8 weeks

value: hypothalamic perifornical area

tag: antibody

value: none (input)


title: naïve replicate 4 Input fraction

description: 3_3_MALE_NAIVE_PEFA_REP2_CGGCTATG-GTACTGAC

source_name: naïve_Input fraction

value: none; naïve


title: naïve replicate 2 Input fraction

description: Dulac_ps6_Infantx_PAG_PeFA_1_4_16_22_TCCGCGAA-CCTATCCT


title: naïve replicate 3 IP fraction

description: Dulac_ps6_Infantx_PAG_PeFA_1_4_16_65_ATTACTCG-AGGCGAAG

source_name: naïve_IP fraction

value: Phospho-S6 (Ser244, Ser247) Antibody (44-923G)

tag: antibody info

value: Cell Signaling (Invitrogen) 44923G, batch RF228700


title: naïve replicate 3 Input fraction

description: Dulac_ps6_Infantx_PAG_PeFA_1_4_16_66_TCCGGAGA-AGGCGAAG


title: naïve replicate 1 Input fraction

description: Dulac_ps6_Infantx_PAG_PeFA_1_4_16_6_TCCGGAGA-CCTATCCT


title: infanticide replicate 3 IP fraction

description: Dulac_ps6_Infantx_PAG_PeFA_1_4_16_67_CGCTCATT-AGGCGAAG

source_name: infanticide_IP fraction

value: presented with a 1-4 day old C57BL/6J pup


title: infanticide  replicate 1 Input fraction

description: Dulac_ps6_Infantx_PAG_PeFA_1_4_16_8_GAGATTCC-CCTATCCT


title: naïve replicate 2 IP fraction

description: Dulac_ps6_Infantx_PAG_PeFA_1_4_16_21_CGGCTATG-CCTATCCT


title: infanticide replicate 1 IP fraction

description: Dulac_ps6_Infantx_PAG_PeFA_1_4_16_7_CGCTCATT-CCTATCCT


title: PBMC31_DLB

first: David

last: Gate

address: 303 E Chicago Ave

institute: Northwestern University

description: PBMCs matching CSF31

data_processing:
Raw sequencing reads from DIPSEQ T1 sequencer were filtered and demultiplexed using PISA (version 0.2) (https://github.com/shiquan/PISA).
Reads were aligned to hg38 genome using STAR (version 2.7.4a) (Dobin et al., 2013), and sorted by sambamba (version 0.7.0) (Tarasov et al., 2015).
Genes were annotated according to GENCODE 32. Cell versus gene UMI count matrix was generated with PISA.
Genome_build: hg38

source_name: PBMCs matching CSF31

extract_protocol:
Frozen PBMCs vials were rapidly thawed in a 37°C water bath for ~2 minutes, and the vials were removed when a tiny ice crystal was left. Thawed PBMCs were quenched with 13 ml 37°C pre-warmed 1X phosphate-buffered saline (PBS, Thermo Fisher Scientific, #10010031) supplemented with 10% fetal bovine serum (FBS, Thermo Fisher Scientific, #A3160601). Cells were centrifuged at 300 x g for 10 minutes at room temperature. The supernatant was removed, and cell pellet was resuspended in 3 ml 1X PBS containing 10% FBS, passed through a 40μm cell strainer (Falcon, #352340), then centrifuged at 300 x g for 10 minutes at room temperature. Dead cells were removed by magnetic beads purification (Miltenyi Biotech, #130-090-101) according to the manufacturer’s protocol. Cells were resuspended with cell resuspension buffer at a concentration of 1,000 viable cells/μl.
The DNBelab C Series Single-Cell Library Prep Set (MGI, #1000021082) was utilized as previously described (Liu et al., 2019). In brief, single-cell suspensions were used for droplet generation, emulsion breakage, beads collection, reverse transcription, and cDNA amplification to generate barcoded libraries. Indexed scRNA-seq libraries were constructed according to the manufacturer’s protocol. The DNA nanoballs (DNBs)-based libraries were sequenced by the ultra-high-throughput DIPSEQ T1 sequencer at China National GeneBank (CNGB). The read structure was paired-end with Read 1, covering 30 bases inclusive of 10-bp cell barcode 1, 10-bp cell barcode 2 and 10-bp unique molecular identifier (UMI), and Read 2 containing 100 bases of transcript sequence, 10-bp sample index.

value: PBMCs

tag: diagnosis

value: Dementia with Lewy Bodies


title: infanticide  replicate 2 Input fraction

description: Dulac_ps6_Infantx_PAG_PeFA_1_4_16_24_AGCGATAG-CCTATCCT


title: ZNF333-FLAG Rep 2

city: Singapore

first: Roger

last: Foo

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

description: ChIP-seq

library_source: genomic

data_processing:
Raw sequencing from ChIP-seq experiments were mapped using BWA. The mapped sequences were PCR-duplicate removed. The peak-calling tool Dfilter was used to identify significant peaks with the parameters of ks = 60, bs = 100, lpval = 6.
Genome_build: hg19
Supplementary_files_format_and_content: bed

molecule: genomic DNA

extract_protocol:
Experiments were performed in two biological replicates for each tag (FLAG and Myc). In addition one GFP transfection was incubated with antibodies against each tag separately as control for IP specificity. Moreover, two input control experiments (ZNF333 transfected and GFP transfected) were performed. ZNF333 or GFP transfected HCT116 cells were cross-linked with 1% formaldehyde for 10 min at room temperature and quenched with 0.125 M glycine for 5 mins. Cells were then washed in ice-cold PBS, scraped and pelleted down at 800g for 5 min at 4°C. The pellet was resuspended in FA lysis buffer to facilitate cell lysis. Nuclei were pelleted by centrifugation at 3,000 rpm for 5 min at 4°C and resuspended in 1% SDS lysis buffer (1% SDS, 1% Triton X-100, 2 mM EDTA, 50 mM HEPES-KOH (pH 7.5), 0.1% sodium dodecyl sulfate, Roche 1X Complete protease inhibitor) to lyse nuclei. Chromatin was then isolated using ultracentrifugation at 20,000 rpm for 30 mins at 4°C, resuspended in 300 µl 0.1% SDS lysis buffer and fragmented via sonication to an average size of 200–500 bp (Bioruptor Next gen, Diagenode). Solubilised chromatin was immunoprecipitated using anti-Flag antibody (Sigma, #F3165) or anti-Myc (Abcam, #ab9106) overnight. Antibody-chromatin complexes were pulled-down using Protein G Dynabeads (Invitrogen), washed and eluted with elution buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl (pH 8)). After cross-link reversal and Proteinase K treatment, immunoprecipitated DNA was extracted with phenol-chloroform, ethanol precipitated, and treated with RNase. ChIP DNA was quantified using Qubit fluorometric quantification (Thermo Fisher Scientific).
Library Prep was performed using New England Biolabs Ultra II Kit according to the manufacturer’s specifications and sequenced on the Illumina NextSeq High platform with 76bp single end reads.

value: ZNF333 FLAG


title: PBMC25_DLB

description: PBMCs matching CSF25

source_name: PBMCs matching CSF25


title: PBMC28_HC

description: PBMCs matching CSF28

source_name: PBMCs matching CSF28

value: healthy control


title: PBMC27_PD

description: PBMCs matching CSF27

source_name: PBMCs matching CSF27

value: Parkinson's Disease


title: PBMC24_PD

description: PBMCs matching CSF24

source_name: PBMCs matching CSF24


title: PBMC14_PD

description: PBMCs matching CSF14

source_name: PBMCs matching CSF14


title: naïve replicate 4 IP fraction

description: 3_3_MALE_NAIVE_PEFA_INPUT_REP2_TCCGCGAA-GTACTGAC


title: naïve replicate 1 IP fraction

description: Dulac_ps6_Infantx_PAG_PeFA_1_4_16_5_ATTACTCG-CCTATCCT


title: PBMC30_PD

description: PBMCs matching CSF30

source_name: PBMCs matching CSF30


title: PBMC20_HC

description: PBMCs matching CSF20

source_name: PBMCs matching CSF20


title: PBMC21_PD

description: PBMCs matching CSF21

source_name: PBMCs matching CSF21


title: PBMC8_HC

description: PBMCs matching CSF8

source_name: PBMCs matching CSF8


title: PBMC23_HC

description: PBMCs matching CSF23

source_name: PBMCs matching CSF23


title: PBMC10_PD

description: PBMCs matching CSF10

source_name: PBMCs matching CSF10


title: infanticide replicate 2 IP fraction

description: Dulac_ps6_Infantx_PAG_PeFA_1_4_16_23_TCTCGCGC-CCTATCCT


title: HCC1806-Zeb1 rep1

first: Anushka

last: Dongre

address: 455 Main St

institute: Whitehead Institute

scan_protocol: Transcriptomic analysis was performed using the nCounter PanCancer Immune Profiling Panel (Nanostring Technologies) to digitally count transcripts

data_processing: Normalization was performed using DESeq2 from the BioConductor package

source_name: Breast cancer cell line expressing EMT-TFs

extract_protocol: RNA was extracted from the indicated cell lines cultured in vitro or from sorted GFP+ tumor cells using the RNeasy Mini Kit (Qiagen)

treatment_protocol: E cell lines expressing doxycylin-induced EMT-transcription factors  were treated with 1 μg/ml doxycycline hyclate every two days for a total period of 6 days

tag: phenotype

value: Epithelial cell line induced to undergo an EMT in vitro by over-expression of Zeb1


title: HCC1806-Zeb1 rep2

tag: cell line


title: PBMC32_HC

description: PBMCs matching CSF32

source_name: PBMCs matching CSF32

tag: tissue


title: HCC1806-Snail rep1

value: Epithelial cell line induced to undergo an EMT in vitro by over-expression of Snail


title: HCC1806-Snail rep2


title: HMLERas-Zeb1

value: HMLER

value: Epithelial cell line induced to undergo an EMT in vitro by doxycyline-induced expression of Zeb1


title: MCF7Ras-Slug Sox9 rep2

value: Epithelial cell line induced to undergo an EMT in vitro by doxycyline-induced co-expression of Slug and Sox9


title: CbP9 input_rep1

city: Vancouver

first: Miguel

last: Ramirez

state: BC

address: 950 W 28th Ave

department: Centre for Molecular Medicine and Therapeutics

country: Canada

institute: BC Children's Hospital Research Institute

data_processing:
50-bp single-end ChIP-seq reads were aligned to the NCBI37/mm9 reference genome and converted to binary alignment/map (BAM) format by Bowtie2 v.2.3.4
Duplicate reads were marked using Picard v.1.52. Putative PCR artifacts filtered from mapped DNase-seq and ChIP-seq prior to peak calls
Peak enrichment was computed using MACS v.2.1.122 with a false discovery rate (FDR) cutoff of 0.01 (P-value < 1E-5) using input samples as a control for each replicate.
Bigwigs were generated using BamCompare command from the Deeptools v3.3 software calculating average coverage in 50 bp bins and normalized by input samples
Genome_build: mm9
Supplementary_files_format_and_content: .bed files contain all MACS peak calls and scores, .bigwig files for visualization

source_name: P9 Mouse Cerebellum

growth_protocol: C57BL/6 J mice were originally purchased from JAX laboratory and maintained and bred in a pathogen-free animal facility with 12/12 hour light/dark cycle and a controlled environment. Embryonic ages utilized in these experiments were confirmed based upon the appearance of a vaginal plug. The morning that a vaginal plug was detected was designated as E0.5. Pregnant females were cervically dislocated and embryos were harvested from the uterus. Postnatal ages were determined based upon the date of birth with the morning of the observation of newborn pups considered as P0.5. All studies were conducted according to the protocols approved by the Institutional Animal Care and Use Committee and the Canadian Council on Animal Care at the University of British Columbia.

extract_protocol:
C57BL/6 J mice (male and female) at E12.5, P0.5 and P9.5 (henceforth referred to as E12, P0, and P9) were decapitated for dissection of cerebella. Cerebella were dissected and collected in ice cold Dulbecco’s PBS (DPBS) without magnesium or calcium and subsequently washed 2x for 5 minutes. Samples from each litter were pooled and trypsinized in DPBS containing 0.25% trypsin for 10, 15 and 30 min at room temperature for E12, P0 and P9, respectively. Following 3 washes with fresh DPBS, the tissue was triturated with 3 progressively smaller (1, 0.5, 0.1mm) bore polished and sterile pipettes in DPBS containing 250U/ml DNase, 0.25% glucose, and 8mg/ml BSA. The triturated cells were diluted 1:4 with cold DPBS and passed through a cell strainer (40μm mesh) to remove large cellular debris. The cells were collected by mild centrifugation, washed in fresh DPBS and counted. The cells were split into 100,000 cell aliquots, pelleted and snap frozen using liquid nitrogen. Cell pellets were stored at -80°C. We performed native chromatin immunoprecipitation (ChIP) using validated antibodies against H3K4me1 and H3K27ac according to previously established protocols by the International Human Epigenomics Consortium (IHEC). Briefly, cells were lysed in mild non-ionic detergents (0.1% Triton X-100 and Deoxycholate) and protease inhibitor cocktail (Calbiochem) to preserve the integrity of histones harbouring epitopes of interest during cell lysis. Cells were digested by Microccocal nuclease (MNase) at room temperature for 5 minutes and 0.25mM EDTA was used to stop the reaction. Antibodies to H3K4me1 (Diagenode: Catalogue #C15410037, lot A1657D) and H3K27ac (Hiroshi Kimura, Cell Biology Unit, Tokyo Institute of Technology) were incubated with anti-IgA magnetic beads (Dynabeads from Invitrogen) for 2  hours. Digested chromatin was incubated with magnetic beads alone for 1.5 hours. Digested chromatin was separated from the beads and incubated with antibody-bead complex overnight in immunoprecipitation buffer (20mM Tris-HCl pH 7.5, 2mM EDTA, 150mM NaCl, 0.1% Triton X-100, 0.1% Deoxycholate). The resulting immunoprecipitations were washed 2 times by low salt (20mM Tris-HCl pH 8.0, 2mM EDTA, 150mM NaCl, 1% Triton X-100, 0.1% SDS) and then high salt (20mM Tris-HCl pH 8.0, 2mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% SDS) wash buffers. Immunoprecipitations were eluted in an elution buffer (1% SDS, 100 mM Sodium Bicarbonate) for 1.5 hours at 65°C. Remaining histones were digested by Protease (Invitrogen) for 30 minutes at 50°C and DNA fragments were purified using Ampure XP beads (Beckman Coulter).
The library preparation was conducted by Diagenode ChIP-seq/ChIP-qPCR Profiling service (Diagenode Cat# G02010000) using the MicroPlex Library Preparation Kit v2 (Diagenode Cat. C05010013).

value: Cerebellum

tag: developmental stage

tag: chip antibody


title: HCC1806-Luciferase rep2

source_name: Breast cancer cell line

value: Epithelial cell line cultured in vitro


title: HMLERas-Luciferase


title: CbP0 input_rep1

source_name: P0 Mouse Cerebellum


title: CbP0 input_rep2


title: CbP9 input_rep2


title: CbP9 H3K27ac_rep1

value: H3K27ac (Hiroshi Kimura, Cell Biology Unit, Tokyo Institute of Technology)


title: CbE12 input_rep1

source_name: E12 Mouse Cerebellum


title: CbP9 H3K27ac_rep2


title: MCF7Ras-Slug Sox9 rep1


title: MCF7Ras -Luciferase rep1


title: CbE12 H3K27ac_rep2


title: CbP0 H3K27ac_rep1


title: CbE12 input_rep2


title: CbP0 H3K27ac_rep2


title: HCC1806-Luciferase rep1


title: CbE12 H3K27ac_rep1


title: CbP0 H3K4me1_rep2

value: H3K4me1 (Diagenode:Catalogue #C15410037, lot A1657D)


title: CbP9 H3K4me1_rep1


title: CbP9 H3K4me1_rep2


title: CbP0 H3K4me1_rep1


title: KI-V5

city: Rochester

first: Sanjay

last: Misra

state: MN

address: 200 First Street SW

department: Radiology

institute: Mayo Clinic

description: Vehicle

data_processing:
Libraries were sequenced at four samples per lane following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cell was sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 using HiSeq 3000/4000 sequencing kit and HD 3.4.0.38 collection software. Base-calling was performed using Illumina’s RTA version 2.7.7.
BAM files were imported into the RNA-Seq pipeline of mm10. Exclusions included a minimum RPKM value of 0.01.
Genome_build: mm10
Supplementary_files_format_and_content: The average RPKMs of each group (KI-A or KI-V) were calculated and KI-A/KI-V was considered as fold change.  The genes that were >1.5 or <0.75 were considered as differentially expressed genes and the genes that were <1.5 or > 0. 75 were excluded. A simple t-test was performed to determine the P value and P<0.05 was considered as significant different compared to KI-V and the genes that were >0.05 were excluded.

source_name: Vein

extract_protocol:
Extraction protocol 0.5 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.
0.5 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit.

treatment_protocol: Chronic Kidney disease created to a human CX3CR1 knock-in mouse as described in methods. 28days later an arteriovenous fistula was clreated by ligation of carotid artery and jugular vein. Mice were injected human CX3CR1 (30 mg/kg) antibody (KI+AB) or equal volume of vehicle control (KI-V) intraperitonially for two times per week. 7 days after AVF creation, animals were euthanized and the outflow veins of AVFs were harvested.

tag: model

value: hCX3CR1 knock in


title: KI-V3

description: Vehicle


title: KI-V4

description: Vehicle


title: CbE12 H3K4me1_rep2


title: KI-AB4

description: Antibody


title: KI-V1

description: Vehicle


title: KI-AB5

description: Antibody


title: KI-AB1

description: Antibody


title: KI-AB2

description: Antibody


title: KI-AB3

description: Antibody


title: UNC1999_3_NK92MI

city: Tianjin

first: Yang

last: Li

address: Anshan Road No.154

institute: Tianjin Medical University General Hospital

data_processing:
Raw sequencing data was preprocessed by fastp software
Clean data was mapped to hg19 reference genome by using STAR software version 2.7.9
Expression quantification of genome-wide genes was performed by using htseq-count version 0.13.5
Differential expression analysis was performed by using edgeR R package version 3.34.0
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: NK92MI cell line

growth_protocol: NK92MI cells were maintained in α-MEM (GIBCO) supplemented with 2 mM L-glutamine (GIBCO), 0.2 mM I-inositol (Sigma-Aldrich), 0.02 mM folic acid (Sigma-Aldrich), 0.1 mM 2-mercaptoethanol (Invitrogen), 12.5% FB (GIBCO), and 12.5% horse serum (GIBCO).

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen) and assessed with Agilent 2100 BioAnalyzer (Agilent Technologies) and Qubit Fluorometer (Invitrogen).
The NEB Next  Ultra RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries for sequencing.

treatment_protocol: NK92MI cells were cultured in the presence of DMSO or 10μM UNC1999.

value: Lymphoid

tag: treatment

value: 10uM UNC1999 for 48h


title: UNC1999_2_NK92MI


title: UNC1999_1_NK92MI


title: control_2_NK92MI

value: DMSO


title: control_1_NK92MI


title: Endo_PLIN2KD_3

city: Nashville

first: Xin

last: Tong

state: TN

address: 2213 Garland Ave

institute: Vanderbilt University

data_processing:
Genialis Expression software
reads are preprocessed by BBDuk which removes adapters, trims reads for quality from the 3'-end, and discards reads that are too short after trimming
preprocessed reads are aligned by STAR aligner
quantification of reads is done using featureCounts
FastQC reports, alignment statistics and rRNA/globin depletion rate QC information is automatically summarized by the MultiQC tool
differential gene expression analyses performed with DESeq2 (Love et al., 2014) with a log2(fold change) threshold of 1 and FDR<0.05.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: EndoCbH2-Cre cells

growth_protocol: regular EndoC cell media

extract_protocol:
Total RNA was isolated from EndoCβH2-Cre cells using the RNeasy mini plus kit (QIAGEN), and then analyzed on an Agilent 2100 Bioanalyzer. Only samples with an RNA Integrity Number >8.0 were used for library preparation
cDNA libraries were constructed and paired-end sequencing of 3 replicates was performed on an Illumina NovaSeq6000 (150 nucleotide reads).

treatment_protocol: Lentivirus mediated scramble control (Sham), shRNA knockdown (PLIN2KD) or overexpression (PLIN2OE), followed by Cre expressing lentivirus treatment

tag: cell type

tag: age

value: passage 75

tag: genotype/variation


title: Endo_PLIN2KD_1


title: Endo_PLIN2KD_2


title: Endo_Sham_1

value: Sham


title: Endo_Sham_3


title: Endo_PLIN2OE_1


title: Endo_PLIN2OE_2


title: Endo_Sham_2


title: KI-V2

description: Vehicle

tag: strain


title: CbE12 H3K4me1_rep1


title: Endo_PLIN2OE_3


title: 501YT17

city: Ann Arbor

first: Adam

last: Helms

state: MI

address: 7220 MSRB3, 1150 W. Medical Center Dr., SPC 5644

department: Internal Medicine

institute: University of Michigan

data_processing:
Reads aligned to genome using STAR (gene level)
Read counts per gene exported from STAR
Reads normalized to library size for each sample using DESeq2
Differential expression quantified using DESeq2
For comparisons of RNA read counts to other datasets, RNA read counts were normalized to TNNT2 reads.

growth_protocol: iPSCs were differentiated and purified by metabolic selection to >95% pure cardiomyocytes then re-plated in treatment conditions

extract_protocol:
Qiagen Rneasy
RNA libraries were prepared for sequencing using standard Illumina protocols (stranded, polyA library).

value: iPSC-derived cardiomyocytes

tag: growth

tag: media

value: Regular media


title: 501YT18


title: 501YT19

value: OxPhos media


title: 501YT20


title: 501YT15

value: monolayer


title: 501YT16


title: 501YT13


title: 501YT7


title: 501YT12

value: T3, dexamethasone


title: 501YT11


title: 501YT8


title: 501YT6


title: 501YT14


title: 501YT9


title: 501YT10


title: 501YT5


title: 501YT4


title: 501YT21


title: 501YT2


title: MCF7Ras -Luciferase rep2


title: 501YT1


title: 501YT3


title: 160585-Rao_TESC.R.B2_from_MIPS_220_B7_p8

city: Vienna

first: Giovanni

last: Sestini

address: Dr.-Bohr-Gasse 3, 1030 Wien

country: Austria

institute: IMBA - Institute of Molecular Biotechnology

description: TSC converted from primed PSC by TM4 treatment

data_processing:
RNA-seq reads were first trimmed using trimgalore v0.5.0 and reads mapping to abundant sequences included in the iGenomes Ensembl GRCh38 bundle  (rDNA, mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment.
Remaining reads were analyzed using genome and gene annotation for the GRCh38/hg38 assembly obtained from Ensembl release 94. Reads were aligned to the genome using star v2.6.0c and reads in genes were counted with featureCounts (subread v1.6.2) and parameter -s 0. Differential gene expression analysis on raw counts and variance-stabilized transformation of count data for heatmap visualization were performed using DESeq2 v1.18.1.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files with per gene read counts

extract_protocol: none provided by the submitter

tag: genetic background


title: 160584-Rao_TESC.R.B2_from_MIPS_220_B7_p5

source_name: TSC converted from primed PSC by TM4 treatment


title: 160586-Rao_TESC.R.B2_from_MIPS_220_B7_p8


title: 160580-H9_bap_mefs_d6

description: TSC converted from primed PSC by BAP treatment


title: 160579-H9_bap_mefs_d0

source_name: TSC converted from primed PSC by BAP treatment


title: 160581-Primed_MIPS_220.B7_

description: Primed PSC cltured in Essential 8

source_name: Primed PSC cltured in Essential 8


title: 160574-Shef6_NK2_PrE_differentiation

description: PrE differentiated cell in RACL

source_name: PrE differentiated cell in RACL


title: 160575-Shef6_NK2_PrE_differentiation

description: PrE differentiated cell in RACL


title: 160570-HNES1_PrE_differentiation

description: PrE differentiated cell in RACL


title: 160576-Shef6_NK2_PrE_differentiation

description: PrE differentiated cell in RACL


title: 160567-H9_nEnd

description: nEND cell in NACL

source_name: nEND cell in NACL


title: 160565-H9_nEnd

description: nEND cell in NACL


title: 160568-HNES1_PrE_differentiation

description: PrE differentiated cell in RACL


title: 160573-HNES1_nEnd

description: nEND cell in NACL


title: 160571-HNES1_nEnd

description: nEND cell in NACL


title: 160564-H9_PrE_differentiation

description: PrE differentiated cell in RACL


title: 160560-Primed_H9

description: Primed PSC cltured in Essential 8


title: 160566-H9_nEnd

description: nEND cell in NACL


title: 160561-Primed_H9

description: Primed PSC cltured in Essential 8


title: 160558-Blastoid_96h_DN

description: TROP2-/PDGFRa- cells isolated from blastoid at 96hour


title: 160559-Primed_H9

description: Primed PSC cltured in Essential 8


title: 160557-Blastoid_96h_DN

source_name: TROP2-/PDGFRa- cells isolated from blastoid at 96hour


title: 160556-Blastoid_96h_DN


title: 160562-H9_PrE_differentiation

description: PrE differentiated cell in RACL


title: 160552-Blastoid_96h_TROP2+

description: TROP2+ cells isolated from blastoid at 96hour


title: 160551-Blastoid_96h_TROP2+

source_name: TROP2+ cells isolated from blastoid at 96hour


title: 160554-Blastoid_96h_PDGFRa+

description: PDGFRa+ cells isolated from blastoid at 96hour


title: 160553-Blastoid_96h_PDGFRa+

source_name: PDGFRa+ cells isolated from blastoid at 96hour


title: 160550-Blastoid_96h_TROP2+


title: 160546-OKAE_re_derived_C2

description: hTSCs derived from blastoid

source_name: hTSCs derived from blastoid


title: 160572-HNES1_nEnd

description: nEND cell in NACL


title: 160582-Primed_MIPS_220_B7_iPSC

description: Primed PSC cltured in Essential 8


title: 160547-OKAE_re_derived_C6

description: hTSCs derived from blastoid


title: 160569-HNES1_PrE_differentiation

description: PrE differentiated cell in RACL


title: 160563-H9_PrE_differentiation

description: PrE differentiated cell in RACL


title: 160541-OKAE_re_derived_C1

description: hTSCs derived from blastoid


title: 160548-OKAE_re_derived_C6

description: hTSCs derived from blastoid


title: 160542-OKAE_re_derived_C1

description: hTSCs derived from blastoid


title: 160544-OKAE_re_derived_C2

description: hTSCs derived from blastoid


title: 160539-OKAE_bTS5

description: hTSCs clutred in 2D

source_name: hTSCs clutred in 2D


title: 160524-XMU

description: XMU-MP-1 treated trophosphere

source_name: XMU-MP-1 treated trophosphere


title: 160521-OKAE_aggregate

description: hTSCs clutred in 3D

source_name: hTSCs clutred in 3D


title: 160525-XMU

description: XMU-MP-1 treated trophosphere


title: 160543-OKAE_re_derived_C1

description: hTSCs derived from blastoid


title: 160522-OKAE_aggregate

description: hTSCs clutred in 3D


title: 160519-SC144

description: SC144 treated trophosphere

source_name: SC144 treated trophosphere


title: 160518-SC144

description: SC144 treated trophosphere


title: 160538-OKAE_bTS5

description: hTSCs clutred in 2D


title: 160517-SC144

description: SC144 treated trophosphere


title: 160516-Naive_re_derived_C4

description: Naive PSC cultured in PXGL derived from blastoid


title: 160507-Naive_re_derived_C1

source_name: Naive PSC cultured in PXGL derived from blastoid


title: 160513-Naive_re_derived_C2


title: 160514-Naive_re_derived_C2


title: 160508-Naive_H9_WT

description: Naive PSC cultured in PXGL

source_name: Naive PSC cultured in PXGL


title: 160506-Naive_re_derived_C1


title: blastoid 60h PDGFRa pl-161998

data_processing:
Smart-Seq transcriptome sequencing experiments were analyzed using genome sequence and gene annotation from Ensembl GRCh38 release 103 as reference. For gene expression quantification RNA-seq reads were first trimmed using trim-galore v0.6.6 and thereafter aligned to the genome using hisat2 v2.2.1. Uniquely mapping reads in genes were quantified using htseq-count v0.13.5 with parameter -s no. TPM estimates were obtained using RSEM v1.3.3 with parameter --single-cell-prior. Further analysis was performed in R v4.0.3 with Seurat v4.0.1. Based on initial evaluation of per-cell quality control metrices and outlier identification using the median absolute deviation algorithm, cells with <= 2000 detected genes or >= 12.5% mitochondrial gene percentage were filtered out.
Genome_build: hg38
Supplementary_files_format_and_content: tsv of read counts per gene

source_name: blastoid

extract_protocol:
Smart-Seq2 protocol
Smart-Seq2


title: blastoid 60h PDGFRa pl-161994


title: blastoid 60h PDGFRa pl-161992


title: 160509-Naive_H9_WT

description: Naive PSC cultured in PXGL


title: blastoid 60h PDGFRa pl-161997


title: 160505-Naive_re_derived_C1


title: 160540-OKAE_bTS5

description: hTSCs clutred in 2D


title: 160523-XMU

description: XMU-MP-1 treated trophosphere


title: 160520-OKAE_aggregate

description: hTSCs clutred in 3D


title: blastoid 60h PDGFRa pl-161990


title: blastoid 60h PDGFRa pl-161991


title: blastoid 60h PDGFRa pl-161985


title: blastoid 60h TROP2 pl-161981


title: blastoid 60h PDGFRa pl-161988


title: blastoid 60h TROP2 pl-161977


title: 160515-Naive_re_derived_C2


title: blastoid 60h TROP2 pl-161978


title: blastoid 60h TROP2 pl-161980


title: blastoid 60h TROP2 pl-161975


title: blastoid 60h TROP2 pl-161976


title: blastoid 60h TROP2 pl-161974


title: blastoid 60h TROP2 pl-161972


title: blastoid 60h TROP2 pl-161979


title: blastoid 60h TROP2 pl-161969


title: blastoid 60h TROP2 min-161965


title: blastoid 60h TROP2 min-161960


title: blastoid 60h TROP2 pl-161968


title: blastoid 60h TROP2 min-161964


title: blastoid 60h TROP2 pl-161971


title: blastoid 60h TROP2 min-161962


title: blastoid 60h TROP2 pl-161967


title: blastoid 60h TROP2 min-161959


title: blastoid 60h TROP2 min-161955


title: blastoid 60h TROP2 min-161954


title: blastoid 60h TROP2 min-161953


title: blastoid 60h TROP2 min-161952


title: blastoid 60h TROP2 min-161957


title: blastoid 60h TROP2 min-161956


title: blastoid 60h TROP2 min-161951


title: blastoid 60h TROP2 min-161947


title: blastoid 60h TROP2 pl-161973


title: blastoid 60h TROP2 min-161945


title: blastoid 60h TROP2 min-161934


title: blastoid 60h TROP2 min-161937


title: blastoid 60h TROP2 min-161936


title: blastoid 60h TROP2 min-161939


title: blastoid 60h TROP2 min-161933


title: blastoid 60h TROP2 min-161940


title: blastoid 60h TROP2 min-161932


title: blastoid 60h TROP2 min-161931


title: blastoid 60h TROP2 min-161935


title: blastoid 60h TROP2 min-161958


title: blastoid 60h TROP2 min-161929


title: blastoid 60h TROP2 min-161927


title: blastoid 60h TROP2 min-161920


title: blastoid 60h TROP2 min-161923


title: blastoid 60h TROP2 min-161918


title: blastoid 60h TROP2 min-161919


title: blastoid 60h TROP2 min-161925


title: blastoid 60h TROP2 min-161950


title: blastoid 60h TROP2 min-161914


title: blastoid 60h TROP2 min-161913


title: blastoid 60h TROP2 min-161917


title: blastoid 60h TROP2 min-161915


title: blastoid 60h TROP2 min-161916


title: blastoid 60h TROP2 min-161910


title: blastoid 60h TROP2 min-161909


title: blastoid 60h TROP2 min-161907


title: blastoid 60h TROP2 min-161902


title: blastoid 60h TROP2 min-161906


title: blastoid 60h TROP2 min-161900


title: blastoid 60h TROP2 min-161901


title: blastoid 60h TROP2 min-161898


title: blastoid 60h TROP2 min-161903


title: blastoid 60h TROP2 min-161897


title: blastoid 60h TROP2 min-161899


title: blastoid 60h TROP2 min-161895


title: blastoid 60h TROP2 min-161922


title: blastoid 60h TROP2 min-161893


title: blastoid 60h TROP2 min-161890


title: blastoid 60h TROP2 min-161892


title: blastoid 60h TROP2 min-161911


title: blastoid 60h TROP2 min-161886


title: blastoid 60h TROP2 min-161885


title: blastoid 60h TROP2 min-161881


title: blastoid 60h TROP2 min-161880


title: blastoid 60h TROP2 min-161884


title: blastoid 60h TROP2 min-161887


title: blastoid 60h TROP2 min-161883


title: blastoid 60h TROP2 min-161908


title: blastoid 60h TROP2 min-161879


title: blastoid 60h TROP2 min-161882


title: blastoid 60h TROP2 min-161877


title: blastoid 60h TROP2 min-161878


title: blastoid 60h TROP2 min-161876


title: blastoid 60h TROP2 min-161905


title: blastoid 60h TROP2 min-161875


title: blastoid 60h TROP2 min-161874


title: blastoid 60h TROP2 min-161869


title: blastoid 60h TROP2 min-161867


title: blastoid 60h TROP2 min-161891


title: blastoid 60h TROP2 min-161870


title: blastoid 60h TROP2 min-161866


title: blastoid 60h TROP2 min-161872


title: blastoid 60h TROP2 min-161868


title: blastoid 60h TROP2 min-161865


title: blastoid 60h TROP2 min-161861


title: blastoid 60h TROP2 min-161889


title: blastoid 60h TROP2 min-161856


title: blastoid 60h TROP2 min-161860


title: blastoid 60h TROP2 min-161854


title: blastoid 60h TROP2 min-161855


title: blastoid 60h TROP2 min-161853


title: blastoid 60h TROP2 min-161848


title: blastoid 60h TROP2 min-161851


title: blastoid 60h TROP2 min-161850


title: blastoid 60h TROP2 min-161846


title: blastoid 60h TROP2 min-161852


title: blastoid 60h TROP2 min-161847


title: blastoid 60h TROP2 min-161873


title: blastoid 60h TROP2 min-161845


title: blastoid 60h TROP2 min-161841


title: blastoid 60h TROP2 min-161840


title: blastoid 60h TROP2 min-161843


title: blastoid 60h TROP2 min-161844


title: blastoid 60h TROP2 min-161842


title: blastoid 60h TROP2 min-161857


title: blastoid 60h TROP2 min-161828


title: blastoid 60h TROP2 min-161830


title: blastoid 60h TROP2 min-161833


title: blastoid 60h TROP2 min-161837


title: blastoid 60h TROP2 min-161825


title: blastoid 60h TROP2 min-161826


title: blastoid 60h TROP2 min-161832


title: blastoid 60h TROP2 min-161822


title: blastoid 60h TROP2 min-161839


title: blastoid 60h TROP2 min-161824


title: blastoid 60h TROP2 min-161821


title: blastoid 60h TROP2 min-161820


title: blastoid 60h TROP2 min-161819


title: blastoid 60h TROP2 min-161818


title: blastoid 60h TROP2 min-161816


title: blastoid 60h TROP2 min-161817


title: blastoid 60h TROP2 min-161814


title: blastoid 60h TROP2 min-161815


title: blastoid 60h TROP2 min-161809


title: blastoid 60h TROP2 min-161813


title: blastoid 60h TROP2 min-161812


title: blastoid 60h TROP2 min-161807


title: blastoid 60h TROP2 min-161811


title: blastoid 60h TROP2 pl-161805


title: blastoid 60h TROP2 min-161810


title: blastoid 60h TROP2 pl-161804


title: blastoid 60h TROP2 min-161827


title: blastoid 60h TROP2 min-161836


title: blastoid 60h TROP2 pl-161806


title: blastoid 60h TROP2 pl-161803


title: blastoid 60h TROP2 pl-161801


title: blastoid 60h TROP2 pl-161800


title: blastoid 60h TROP2 pl-161797


title: blastoid 60h TROP2 pl-161798


title: blastoid 60h TROP2 pl-161802


title: blastoid 60h TROP2 pl-161790


title: blastoid 60h TROP2 pl-161792


title: blastoid 60h TROP2 pl-161794


title: blastoid 60h TROP2 pl-161793


title: blastoid 60h TROP2 pl-161788


title: blastoid 60h TROP2 pl-161786


title: blastoid 60h TROP2 pl-161789


title: blastoid 60h TROP2 pl-161785


title: blastoid 60h TROP2 pl-161787


title: blastoid 60h TROP2 pl-161775


title: blastoid 60h TROP2 pl-161782


title: blastoid 60h TROP2 pl-161781


title: blastoid 60h TROP2 pl-161780


title: blastoid 60h TROP2 pl-161778


title: blastoid 60h TROP2 pl-161774


title: blastoid 60h TROP2 pl-161770


title: blastoid 60h TROP2 pl-161771


title: blastoid 60h TROP2 pl-161799


title: blastoid 60h TROP2 pl-161768


title: blastoid 60h TROP2 pl-161796


title: blastoid 60h TROP2 pl-161773


title: blastoid 60h TROP2 pl-161784


title: blastoid 60h TROP2 pl-161764


title: blastoid 60h TROP2 pl-161760


title: blastoid 60h TROP2 pl-161762


title: blastoid 60h TROP2 pl-161761


title: blastoid 60h TROP2 pl-161769


title: blastoid 60h TROP2 pl-161759


title: blastoid 60h TROP2 pl-161766


title: blastoid 60h TROP2 pl-161767


title: blastoid 60h TROP2 pl-161765


title: blastoid 60h TROP2 pl-161757


title: blastoid 60h TROP2 pl-161756


title: blastoid 60h TROP2 pl-161763


title: blastoid 60h TROP2 pl-161753


title: blastoid 60h TROP2 pl-161755


title: blastoid 60h TROP2 pl-161776


title: blastoid 60h TROP2 pl-161742


title: blastoid 60h TROP2 pl-161748


title: blastoid 60h TROP2 pl-161743


title: blastoid 60h TROP2 pl-161750


title: blastoid 60h TROP2 pl-161744


title: blastoid 60h TROP2 pl-161741


title: blastoid 60h TROP2 pl-161745


title: blastoid 60h TROP2 pl-161734


title: blastoid 60h TROP2 pl-161740


title: blastoid 60h TROP2 pl-161731


title: blastoid 60h TROP2 pl-161736


title: blastoid 60h TROP2 pl-161733


title: blastoid 60h TROP2 pl-161758


title: blastoid 60h TROP2 pl-161737


title: blastoid 60h TROP2 pl-161728


title: blastoid 60h TROP2 pl-161727


title: blastoid 60h TROP2 pl-161738


title: blastoid 60h TROP2 pl-161730


title: blastoid 60h TROP2 pl-161726


title: blastoid 60h TROP2 pl-161725


title: blastoid 60h TROP2 pl-161732


title: blastoid 60h TROP2 pl-161729


title: blastoid 60h TROP2 pl-161746


title: blastoid 60h TROP2 pl-161720


title: blastoid 60h TROP2 pl-161723


title: blastoid 60h TROP2 pl-161722


title: blastoid 60h TROP2 pl-161724


title: blastoid 60h TROP2 pl-161719


title: blastoid 60h TROP2 pl-161717


title: blastoid 60h TROP2 pl-161718


title: blastoid 60h TROP2 pl-161713


title: blastoid 60h TROP2 pl-161712


title: blastoid 60h TROP2 pl-161715


title: blastoid 60h TROP2 pl-161714


title: blastoid 60h TROP2 pl-161710


title: blastoid 60h TROP2 pl-161709


title: blastoid 60h TROP2 pl-161706


title: blastoid 60h TROP2 pl-161698


title: blastoid 60h TROP2 pl-161700


title: blastoid 60h TROP2 pl-161702


title: blastoid 60h TROP2 pl-161704


title: blastoid 60h TROP2 pl-161692


title: blastoid 60h TROP2 pl-161699


title: blastoid 60h TROP2 pl-161691


title: blastoid 60h TROP2 pl-161688


title: blastoid 60h TROP2 pl-161687


title: blastoid 60h TROP2 pl-161689


title: blastoid 60h TROP2 pl-161684


title: blastoid 60h TROP2 pl-161716


title: blastoid 60h TROP2 pl-161683


title: blastoid 60h TROP2 pl-161697


title: blastoid 60h TROP2 pl-161694


title: blastoid 60h TROP2 pl-161686


title: blastoid 60h TROP2 pl-161695


title: blastoid 60h TROP2 pl-161696


title: blastoid 60h TROP2 pl-161682


title: blastoid 60h TROP2 pl-161681


title: blastoid 60h TROP2 pl-161679


title: blastoid 60h TROP2 pl-161678


title: blastoid 60h TROP2 pl-161674


title: blastoid 60h TROP2 pl-161671


title: blastoid 60h TROP2 pl-161690


title: blastoid 60h TROP2 pl-161677


title: blastoid 60h TROP2 pl-161672


title: blastoid 60h TROP2 pl-161670


title: blastoid 60h TROP2 pl-161693


title: blastoid 60h TROP2 pl-161708


title: blastoid 60h TROP2 pl-161680


title: blastoid 60h TROP2 pl-161667


title: blastoid 60h TROP2 pl-161675


title: blastoid 60h TROP2 pl-161669


title: blastoid 60h TROP2 pl-161668


title: blastoid 60h TROP2 pl-161666


title: blastoid 60h TROP2 pl-161657


title: blastoid 60h TROP2 pl-161660


title: blastoid 60h TROP2 pl-161652


title: blastoid 60h TROP2 pl-161655


title: blastoid 60h TROP2 pl-161664


title: blastoid 60h TROP2 pl-161653


title: blastoid 60h TROP2 pl-161662


title: blastoid 60h TROP2 pl-161661


title: blastoid 60h TROP2 pl-161654


title: blastoid 60h TROP2 pl-161656


title: blastoid 60h TROP2 pl-161649


title: blastoid 60h TROP2 pl-161658


title: blastoid 60h TROP2 pl-161650


title: blastoid 60h TROP2 pl-161648


title: blastoid 60h TROP2 pl-161647


title: naive H9-161645

source_name: stem cells

value: PXGL


title: naive H9-161646


title: blastoid 60h TROP2 pl-161663


title: naive H9-161643


title: naive H9-161642


title: naive H9-161641


title: naive H9-161639


title: naive H9-161638


title: blastoid 60h TROP2 pl-161651


title: naive H9-161637


title: naive H9-161634


title: naive H9-161635


title: naive H9-161636


title: naive H9-161633


title: naive H9-161627


title: naive H9-161632


title: naive H9-161631


title: naive H9-161624


title: naive H9-161625


title: naive H9-161626


title: naive H9-161628


title: naive H9-161619


title: naive H9-161617


title: naive H9-161622


title: naive H9-161629


title: naive H9-161644


title: naive H9-161640


title: naive H9-161616


title: blastoid 60h TROP2 pl-161676


title: naive H9-161615


title: blastoid 96h PDGFRa pl-159860


title: blastoid 96h PDGFRa pl-159866


title: blastoid 96h PDGFRa pl-159862


title: blastoid 96h PDGFRa pl-159863


title: blastoid 96h PDGFRa pl-159859


title: blastoid 96h PDGFRa pl-159867


title: blastoid 96h PDGFRa pl-159868


title: blastoid 96h PDGFRa pl-159861


title: blastoid 96h PDGFRa pl-159852


title: blastoid 96h PDGFRa pl-159856


title: blastoid 96h PDGFRa pl-159854


title: naive H9-161620


title: naive H9-161621


title: naive H9-161618


title: blastoid 96h PDGFRa pl-159850


title: blastoid 96h PDGFRa pl-159844


title: blastoid 96h PDGFRa pl-159849


title: blastoid 96h PDGFRa pl-159851


title: blastoid 96h PDGFRa pl-159843


title: blastoid 96h PDGFRa pl-159845


title: blastoid 96h PDGFRa pl-159839


title: blastoid 96h PDGFRa pl-159841


title: blastoid 96h PDGFRa pl-159840


title: blastoid 96h PDGFRa pl-159834


title: blastoid 96h PDGFRa pl-159833


title: blastoid 96h PDGFRa pl-159835


title: blastoid 96h PDGFRa pl-159831


title: blastoid 96h PDGFRa pl-159838


title: blastoid 96h PDGFRa pl-159830


title: blastoid 96h PDGFRa pl-159829


title: blastoid 96h PDGFRa pl-159822


title: blastoid 96h PDGFRa pl-159817


title: blastoid 96h PDGFRa pl-159824


title: blastoid 96h PDGFRa pl-159825


title: blastoid 96h PDGFRa pl-159818


title: blastoid 96h PDGFRa pl-159827


title: blastoid 96h PDGFRa pl-159820


title: blastoid 96h PDGFRa pl-159826


title: blastoid 96h PDGFRa pl-159846


title: blastoid 96h PDGFRa pl-159819


title: blastoid 96h PDGFRa pl-159816


title: blastoid 96h PDGFRa pl-159811


title: blastoid 96h PDGFRa pl-159815


title: blastoid 96h PDGFRa pl-159814


title: blastoid 96h PDGFRa pl-159813


title: blastoid 96h PDGFRa pl-159842


title: blastoid 96h PDGFRa pl-159806


title: blastoid 96h PDGFRa pl-159807


title: blastoid 96h PDGFRa pl-159808


title: blastoid 96h PDGFRa pl-159804


title: blastoid 96h PDGFRa pl-159802


title: blastoid 96h PDGFRa pl-159800


title: blastoid 96h PDGFRa pl-159799


title: blastoid 96h PDGFRa pl-159797


title: blastoid 96h PDGFRa pl-159803


title: blastoid 96h PDGFRa pl-159798


title: blastoid 96h PDGFRa pl-159792


title: blastoid 96h PDGFRa pl-159796


title: blastoid 96h PDGFRa pl-159791


title: blastoid 96h PDGFRa pl-159794


title: blastoid 96h PDGFRa pl-159790


title: blastoid 96h PDGFRa pl-159789


title: blastoid 96h PDGFRa pl-159785


title: blastoid 96h PDGFRa pl-159810


title: blastoid 96h PDGFRa pl-159787


title: blastoid 96h PDGFRa pl-159781


title: blastoid 96h PDGFRa pl-159805


title: blastoid 96h PDGFRa pl-159779


title: blastoid 96h PDGFRa pl-159777


title: blastoid 96h PDGFRa pl-159783


title: blastoid 96h PDGFRa pl-159773


title: blastoid 96h PDGFRa pl-159771


title: blastoid 96h PDGFRa pl-159782


title: blastoid 96h PDGFRa pl-159786


title: blastoid 96h PDGFRa pl-159774


title: blastoid 96h PDGFRa pl-159775


title: blastoid 96h PDGFRa pl-159765


title: blastoid 96h PDGFRa pl-159788


title: blastoid 96h PDGFRa pl-159756


title: blastoid 96h PDGFRa pl-159763


title: blastoid 96h PDGFRa pl-159776


title: blastoid 96h PDGFRa pl-159764


title: blastoid 96h PDGFRa pl-159759


title: blastoid 96h PDGFRa pl-159754


title: blastoid 96h PDGFRa pl-159769


title: blastoid 96h PDGFRa pl-159768


title: blastoid 96h PDGFRa pl-159766


title: blastoid 96h PDGFRa pl-159753


title: blastoid 96h PDGFRa pl-159772


title: blastoid 96h PDGFRa pl-159767


title: blastoid 96h PDGFRa pl-159757


title: blastoid 96h PDGFRa pl-159755


title: blastoid 96h PDGFRa pl-159750


title: blastoid 96h PDGFRa pl-159743


title: blastoid 96h PDGFRa pl-159747


title: blastoid 96h PDGFRa pl-159744


title: blastoid 96h PDGFRa pl-159749


title: blastoid 96h PDGFRa pl-159770


title: blastoid 96h DN-159740


title: blastoid 96h PDGFRa pl-159745


title: blastoid 96h PDGFRa pl-159742


title: blastoid 96h PDGFRa pl-159761


title: blastoid 96h PDGFRa pl-159741


title: blastoid 96h DN-159736


title: blastoid 96h DN-159732


title: blastoid 96h DN-159739


title: blastoid 96h PDGFRa pl-159751


title: blastoid 96h DN-159727


title: blastoid 96h DN-159729


title: blastoid 96h DN-159735


title: blastoid 96h DN-159734


title: blastoid 96h DN-159733


title: blastoid 96h DN-159718


title: blastoid 96h DN-159725


title: blastoid 96h DN-159719


title: blastoid 96h PDGFRa pl-159748


title: blastoid 96h DN-159717


title: blastoid 96h DN-159720


title: blastoid 96h DN-159723


title: blastoid 96h DN-159721


title: blastoid 96h DN-159726


title: blastoid 96h DN-159722


title: blastoid 96h DN-159724


title: blastoid 96h DN-159716


title: blastoid 96h DN-159714


title: blastoid 96h DN-159712


title: blastoid 96h DN-159709


title: blastoid 96h DN-159713


title: blastoid 96h DN-159711


title: blastoid 96h DN-159715


title: blastoid 96h DN-159738


title: blastoid 96h DN-159707


title: blastoid 96h DN-159708


title: blastoid 96h DN-159730


title: blastoid 96h DN-159703


title: blastoid 96h DN-159702


title: blastoid 96h DN-159706


title: blastoid 96h DN-159704


title: blastoid 96h DN-159705


title: blastoid 96h DN-159701


title: blastoid 96h DN-159700


title: blastoid 96h DN-159697


title: blastoid 96h DN-159692


title: blastoid 96h DN-159691


title: blastoid 96h DN-159689


title: blastoid 96h DN-159687


title: blastoid 96h DN-159696


title: blastoid 96h DN-159698


title: blastoid 96h DN-159699


title: blastoid 96h DN-159688


title: blastoid 96h DN-159686


title: blastoid 96h DN-159684


title: blastoid 96h DN-159685


title: blastoid 96h DN-159680


title: blastoid 96h DN-159681


title: blastoid 96h DN-159683


title: blastoid 96h DN-159682


title: blastoid 96h DN-159678


title: blastoid 96h DN-159673


title: blastoid 96h DN-159667


title: blastoid 96h DN-159676


title: blastoid 96h DN-159671


title: blastoid 96h DN-159677


title: blastoid 96h DN-159672


title: blastoid 96h DN-159679


title: blastoid 96h DN-159690


title: blastoid 96h DN-159670


title: blastoid 96h DN-159675


title: blastoid 96h DN-159669


title: blastoid 96h DN-159665


title: blastoid 96h DN-159668


title: blastoid 96h DN-159664


title: blastoid 96h DN-159662


title: blastoid 96h DN-159657


title: blastoid 96h DN-159663


title: blastoid 96h DN-159660


title: blastoid 96h DN-159661


title: blastoid 96h DN-159659


title: blastoid 96h DN-159656


title: blastoid 96h DN-159655


title: blastoid 96h DN-159653


title: blastoid 96h DN-159652


title: blastoid 96h DN-159651


title: blastoid 96h DN-159650


title: blastoid 96h DN-159649


title: blastoid 96h DN-159666


title: blastoid 96h DN-159648


title: blastoid 96h DN-159641


title: blastoid 96h DN-159639


title: blastoid 96h DN-159645


title: blastoid 96h DN-159640


title: blastoid 96h DN-159642


title: blastoid 96h DN-159643


title: blastoid 96h DN-159647


title: blastoid 96h DN-159646


title: blastoid 96h DN-159638


title: blastoid 96h DN-159637


title: blastoid 96h DN-159636


title: blastoid 96h DN-159654


title: blastoid 96h DN-159634


title: blastoid 96h DN-159632


title: blastoid 96h DN-159631


title: blastoid 96h DN-159633


title: blastoid 96h DN-159629


title: blastoid 96h DN-159625


title: blastoid 96h DN-159626


title: blastoid 96h DN-159623


title: blastoid 96h DN-159624


title: blastoid 96h DN-159621


title: blastoid 96h DN-159620


title: blastoid 96h DN-159619


title: blastoid 96h DN-159617


title: blastoid 96h DN-159618


title: blastoid 96h DN-159644


title: blastoid 96h DN-159616


title: blastoid 96h DN-159614


title: blastoid 96h DN-159635


title: blastoid 96h DN-159615


title: blastoid 96h DN-159613


title: blastoid 96h TROP2 pl-159610


title: blastoid 96h DN-159628


title: blastoid 96h TROP2 pl-159612


title: blastoid 96h TROP2 pl-159609


title: blastoid 96h DN-159627


title: blastoid 96h TROP2 pl-159605


title: blastoid 96h TROP2 pl-159611


title: blastoid 96h TROP2 pl-159608


title: blastoid 96h TROP2 pl-159607


title: blastoid 96h TROP2 pl-159606


title: blastoid 96h TROP2 pl-159600


title: blastoid 96h TROP2 pl-159599


title: blastoid 96h TROP2 pl-159598


title: blastoid 96h TROP2 pl-159603


title: blastoid 96h TROP2 pl-159602


title: blastoid 96h TROP2 pl-159604


title: blastoid 96h TROP2 pl-159597


title: blastoid 96h TROP2 pl-159596


title: blastoid 96h TROP2 pl-159595


title: blastoid 96h TROP2 pl-159594


title: blastoid 96h TROP2 pl-159593


title: blastoid 96h TROP2 pl-159591


title: blastoid 96h TROP2 pl-159592


title: blastoid 96h TROP2 pl-159590


title: blastoid 96h TROP2 pl-159589


title: blastoid 96h TROP2 pl-159587


title: blastoid 96h TROP2 pl-159581


title: blastoid 96h TROP2 pl-159583


title: blastoid 96h TROP2 pl-159585


title: blastoid 96h TROP2 pl-159580


title: blastoid 96h TROP2 pl-159586


title: blastoid 96h TROP2 pl-159577


title: blastoid 96h TROP2 pl-159576


title: blastoid 96h TROP2 pl-159575


title: blastoid 96h TROP2 pl-159574


title: blastoid 96h TROP2 pl-159572


title: blastoid 96h TROP2 pl-159569


title: blastoid 96h TROP2 pl-159571


title: blastoid 96h TROP2 pl-159568


title: blastoid 96h TROP2 pl-159570


title: blastoid 96h TROP2 pl-159573


title: blastoid 96h TROP2 pl-159567


title: blastoid 96h TROP2 pl-159566


title: blastoid 96h TROP2 pl-159563


title: blastoid 96h TROP2 pl-159562


title: blastoid 96h TROP2 pl-159588


title: blastoid 96h TROP2 pl-159558


title: blastoid 96h TROP2 pl-159557


title: blastoid 96h TROP2 pl-159561


title: blastoid 96h TROP2 pl-159555


title: blastoid 96h TROP2 pl-159551


title: blastoid 96h TROP2 pl-159559


title: blastoid 96h TROP2 pl-159579


title: blastoid 96h TROP2 pl-159578


title: blastoid 96h TROP2 pl-159550


title: blastoid 96h TROP2 pl-159549


title: blastoid 96h TROP2 pl-159554


title: blastoid 96h TROP2 pl-159565


title: blastoid 96h TROP2 pl-159540


title: blastoid 96h TROP2 pl-159545


title: blastoid 96h TROP2 pl-159538


title: blastoid 96h TROP2 pl-159531


title: blastoid 96h TROP2 pl-159539


title: blastoid 96h TROP2 pl-159527


title: blastoid 96h TROP2 pl-159543


title: blastoid 96h TROP2 pl-159535


title: blastoid 96h TROP2 pl-159533


title: blastoid 96h TROP2 pl-159530


title: blastoid 96h TROP2 pl-159524


title: blastoid 96h TROP2 pl-159536


title: blastoid 96h TROP2 pl-159537


title: blastoid 96h TROP2 pl-159528


title: blastoid 96h TROP2 pl-159526


title: blastoid 96h TROP2 pl-159548


title: blastoid 96h TROP2 pl-159523


title: blastoid 96h TROP2 pl-159522


title: blastoid 96h TROP2 pl-159520


title: blastoid 96h TROP2 pl-159514


title: blastoid 96h TROP2 pl-159521


title: blastoid 96h TROP2 pl-159516


title: blastoid 96h TROP2 pl-159518


title: blastoid 96h TROP2 pl-159511


title: blastoid 96h TROP2 pl-159515


title: blastoid 96h TROP2 pl-159507


title: blastoid 96h TROP2 pl-159512


title: blastoid 96h TROP2 pl-159506


title: blastoid 96h TROP2 pl-159510


title: blastoid 96h TROP2 pl-159505


title: blastoid 96h TROP2 pl-159504


title: blastoid 96h TROP2 pl-159496


title: blastoid 96h TROP2 pl-159495


title: blastoid 96h TROP2 pl-159494


title: blastoid 96h TROP2 pl-159498


title: blastoid 96h TROP2 pl-159499


title: blastoid 96h TROP2 pl-159493


title: blastoid 96h TROP2 pl-159492


title: blastoid 96h TROP2 pl-157637


title: blastoid 96h DN-157633


title: blastoid 96h DN-157632


title: blastoid 96h TROP2 pl-157636


title: blastoid 96h DN-157634


title: blastoid 96h DN-157639


title: blastoid 96h DN-157642


title: blastoid 96h DN-157631


title: blastoid 96h TROP2 pl-157630


title: blastoid 96h TROP2 pl-157638


title: blastoid 96h TROP2 pl-157627


title: blastoid 96h TROP2 pl-157628


title: blastoid 96h DN-157625


title: blastoid 96h TROP2 pl-159502


title: blastoid 96h TROP2 pl-157629


title: blastoid 96h DN-157626


title: blastoid 96h TROP2 pl-159541


title: blastoid 96h DN-157624


title: blastoid 96h TROP2 pl-159501


title: blastoid 96h DN-157623


title: blastoid 96h TROP2 pl-157622


title: blastoid 96h TROP2 pl-159490


title: blastoid 96h TROP2 pl-157621


title: blastoid 96h TROP2 pl-157619


title: blastoid 96h TROP2 pl-159486


title: blastoid 96h TROP2 pl-159489


title: blastoid 96h DN-157617


title: blastoid 96h DN-157616


title: blastoid 96h DN-157615


title: blastoid 96h TROP2 pl-157614


title: blastoid 96h TROP2 pl-157612


title: blastoid 96h DN-157610


title: blastoid 96h DN-157609


title: blastoid 96h DN-157607


title: blastoid 96h TROP2 pl-157606


title: blastoid 96h TROP2 pl-157603


title: blastoid 96h TROP2 pl-157611


title: blastoid 96h TROP2 pl-157604


title: blastoid 96h TROP2 pl-157605


title: blastoid 96h DN-157600


title: blastoid 96h DN-157602


title: blastoid 96h DN-157599


title: blastoid 96h TROP2 pl-157597


title: blastoid 96h TROP2 pl-157598


title: blastoid 96h DN-157601


title: blastoid 96h DN-157591


title: blastoid 96h DN-157594


title: blastoid 96h TROP2 pl-157596


title: blastoid 96h DN-157593


title: blastoid 96h DN-157592


title: blastoid 96h TROP2 pl-157620


title: blastoid 96h TROP2 pl-157595


title: blastoid 96h TROP2 pl-157589


title: blastoid 96h TROP2 pl-157588


title: blastoid 96h DN-157608


title: blastoid 96h TROP2 pl-157590


title: blastoid 96h TROP2 pl-157613


title: blastoid 96h DN-157583


title: blastoid 96h TROP2 pl-157582


title: blastoid 96h TROP2 pl-157581


title: blastoid 96h TROP2 pl-157579


title: blastoid 96h DN-157577


title: blastoid 96h DN-157578


title: blastoid 96h DN-157576


title: blastoid 96h TROP2 pl-157587


title: blastoid 96h TROP2 pl-157573


title: blastoid 96h TROP2 pl-157580


title: blastoid 96h DN-157575


title: blastoid 96h TROP2 pl-157571


title: blastoid 96h TROP2 pl-157566


title: blastoid 96h DN-157567


title: blastoid 96h TROP2 pl-157574


title: blastoid 96h DN-157586


title: blastoid 96h DN-157568


title: blastoid 96h DN-157570


title: blastoid 96h DN-157569


title: blastoid 96h TROP2 pl-157572


title: blastoid 96h DN-157560


title: blastoid 96h DN-157561


title: blastoid 96h DN-157562


title: blastoid 96h DN-157584


title: blastoid 96h TROP2 pl-157558


title: blastoid 96h DN-157585


title: blastoid 96h TROP2 pl-157564


title: blastoid 96h TROP2 pl-157563


title: blastoid 96h TROP2 pl-157557


title: blastoid 96h DN-157559


title: blastoid 96h TROP2 pl-157556


title: blastoid 96h TROP2 pl-157555


title: blastoid 96h DN-157554


title: blastoid 96h DN-157553


title: blastoid 96h DN-157551


title: blastoid 96h TROP2 pl-157549


title: blastoid 96h TROP2 pl-157550


title: blastoid 96h TROP2 pl-157548


title: blastoid 96h TROP2 pl-157565


title: blastoid 96h DN-157546


title: blastoid 96h DN-157544


title: blastoid 96h TROP2 pl-157540


title: blastoid 96h DN-157543


title: blastoid 96h TROP2 pl-157542


title: blastoid 96h TROP2 pl-157539


title: blastoid 96h TROP2 pl-157541


title: blastoid 96h DN-157537


title: blastoid 96h DN-157535


title: blastoid 96h TROP2 pl-157532


title: blastoid 96h DN-157530


title: blastoid 96h TROP2 pl-157534


title: blastoid 96h TROP2 pl-157533


title: blastoid 96h DN-157529


title: blastoid 96h DN-157536


title: blastoid 96h DN-157528


title: blastoid 96h DN-157552


title: blastoid 96h TROP2 pl-157526


title: blastoid 96h TROP2 pl-157524


title: blastoid 96h DN-157527


title: blastoid 96h TROP2 pl-157525


title: blastoid 96h TROP2 pl-157523


title: blastoid 96h TROP2 pl-157547


title: blastoid 96h DN-157522


title: blastoid 96h DN-157521


title: blastoid 96h DN-157520


title: blastoid 96h TROP2 pl-157517


title: blastoid 96h TROP2 pl-157516


title: blastoid 96h TROP2 pl-157515


title: blastoid 96h DN-157514


title: blastoid 96h DN-157511


title: blastoid 96h DN-157513


title: blastoid 96h DN-157538


title: blastoid 96h TROP2 pl-157510


title: blastoid 96h DN-157512


title: blastoid 96h TROP2 pl-157509


title: blastoid 96h DN-157504


title: blastoid 96h TROP2 pl-157500


title: blastoid 96h DN-157505


title: blastoid 96h TROP2 pl-157507


title: blastoid 96h TROP2 pl-157502


title: blastoid 96h DN-157506


title: blastoid 96h DN-157503


title: blastoid 96h TROP2 pl-157518


title: blastoid 96h TROP2 pl-157501


title: blastoid 96h TROP2 pl-157499


title: blastoid 96h TROP2 pl-157493


title: blastoid 96h DN-157496


title: blastoid 96h DN-157497


title: blastoid 96h TROP2 pl-157492


title: blastoid 96h DN-157519


title: blastoid 96h TROP2 pl-157494


title: blastoid 96h DN-157495


title: blastoid 96h DN-157490


title: blastoid 96h TROP2 pl-157491


title: blastoid 96h DN-157498


title: blastoid 96h DN-157489


title: blastoid 96h TROP2 pl-157508


title: blastoid 96h DN-157487


title: blastoid 96h DN-157488


title: blastoid 96h TROP2 pl-157484


title: blastoid 96h DN-157482


title: blastoid 96h TROP2 pl-157486


title: blastoid 96h TROP2 pl-157485


title: blastoid 96h DN-157480


title: blastoid 96h TROP2 pl-157475


title: blastoid 96h DN-157479


title: blastoid 96h TROP2 pl-157477


title: blastoid 96h TROP2 pl-157476


title: blastoid 96h DN-157474


title: blastoid 96h TROP2 pl-157478


title: blastoid 96h DN-157472


title: blastoid 96h DN-157473


title: blastoid 96h DN-157471


title: blastoid 96h DN-157464


title: blastoid 96h DN-157465


title: blastoid 96h TROP2 pl-157469


title: blastoid 96h DN-157463


title: blastoid 96h DN-157466


title: blastoid 96h TROP2 pl-157470


title: blastoid 96h TROP2 pl-157467


title: blastoid 96h TROP2 pl-157468


title: blastoid 96h TROP2 pl-157462


title: blastoid 96h TROP2 pl-157459


title: blastoid 96h DN-157481


title: blastoid 96h TROP2 pl-157461


title: blastoid 96h DN-157456


title: blastoid 96h DN-157457


title: blastoid 96h TROP2 pl-157454


title: blastoid 96h TROP2 pl-157453


title: blastoid 96h TROP2 pl-157452


title: blastoid 96h TROP2 pl-157451


title: blastoid 96h DN-157352


title: blastoid 96h DN-157347


title: blastoid 96h DN-157349


title: blastoid 96h DN-157351


title: blastoid 96h TROP2 pl-157460


title: blastoid 96h DN-157348


title: blastoid 96h DN-157346


title: blastoid 96h DN-157345


title: blastoid 96h DN-157344


title: blastoid 96h DN-157350


title: blastoid 96h DN-157343


title: blastoid 96h DN-157341


title: blastoid 96h DN-157455


title: blastoid 96h DN-157338


title: blastoid 96h DN-157333


title: blastoid 96h DN-157335


title: blastoid 96h DN-157342


title: blastoid 96h DN-157337


title: blastoid 96h DN-157334


title: blastoid 96h DN-157336


title: blastoid 96h DN-157332


title: blastoid 96h DN-157326


title: blastoid 96h DN-157354


title: blastoid 96h DN-157329


title: blastoid 96h DN-157325


title: blastoid 96h DN-157330


title: blastoid 96h DN-157328


title: blastoid 96h DN-157324


title: blastoid 96h DN-157321


title: blastoid 96h DN-157318


title: blastoid 96h DN-157319


title: blastoid 96h DN-157317


title: blastoid 96h DN-157322


title: blastoid 96h DN-157320


title: blastoid 96h DN-157323


title: blastoid 96h DN-157339


title: blastoid 96h DN-157340


title: blastoid 96h DN-157314


title: blastoid 96h DN-157331


title: blastoid 96h DN-157315


title: blastoid 96h DN-157311


title: blastoid 96h DN-157307


title: blastoid 96h DN-157312


title: blastoid 96h DN-157313


title: blastoid 96h DN-157306


title: blastoid 96h DN-157304


title: blastoid 96h DN-157303


title: blastoid 96h DN-157310


title: blastoid 96h DN-157309


title: blastoid 96h DN-157300


title: blastoid 96h DN-157302


title: blastoid 96h DN-157305


title: blastoid 96h DN-157301


title: blastoid 96h DN-157308


title: blastoid 96h DN-157299


title: blastoid 96h DN-157316


title: blastoid 96h DN-157294


title: blastoid 96h DN-157295


title: blastoid 96h DN-157296


title: blastoid 96h DN-157297


title: blastoid 96h DN-157293


title: blastoid 96h DN-157286


title: blastoid 96h DN-157285


title: blastoid 96h DN-157292


title: blastoid 96h DN-157291


title: blastoid 96h DN-157288


title: blastoid 96h DN-157289


title: blastoid 96h DN-157290


title: blastoid 96h DN-157287


title: blastoid 96h DN-157284


title: blastoid 96h DN-157283


title: blastoid 96h DN-157281


title: blastoid 96h DN-157276


title: blastoid 96h DN-157275


title: blastoid 96h DN-157277


title: blastoid 96h DN-157274


title: blastoid 96h DN-157272


title: blastoid 96h DN-157271


title: blastoid 96h DN-157270


title: blastoid 96h DN-157273


title: blastoid 96h DN-157269


title: blastoid 96h DN-157263


title: blastoid 96h DN-157267


title: blastoid 96h DN-157268


title: blastoid 96h DN-157266


title: blastoid 96h DN-157259


title: blastoid 96h DN-157280


title: blastoid 96h DN-157261


title: blastoid 96h DN-157282


title: blastoid 96h PDGFRa pl-156146


title: blastoid 96h DN-157278


title: blastoid 96h DN-156155


title: blastoid 96h PDGFRa pl-156144


title: blastoid 96h PDGFRa pl-156145


title: blastoid 96h PDGFRa pl-156149


title: blastoid 96h DN-157262


title: blastoid 96h DN-157264


title: blastoid 96h PDGFRa pl-156147


title: blastoid 96h DN-156139


title: blastoid 96h PDGFRa pl-156143


title: blastoid 96h DN-157279


title: blastoid 96h PDGFRa pl-156142


title: blastoid 96h DN-156137


title: blastoid 96h DN-156136


title: blastoid 96h DN-156134


title: blastoid 96h PDGFRa pl-156132


title: blastoid 96h PDGFRa pl-156129


title: blastoid 96h PDGFRa pl-156131


title: blastoid 96h PDGFRa pl-156133


title: blastoid 96h PDGFRa pl-156128


title: blastoid 96h DN-156150


title: blastoid 96h PDGFRa pl-156127


title: blastoid 96h PDGFRa pl-156130


title: blastoid 96h DN-156122


title: blastoid 96h PDGFRa pl-156125


title: blastoid 96h DN-156120


title: blastoid 96h PDGFRa pl-156126


title: blastoid 96h DN-157260


title: blastoid 96h DN-156118


title: blastoid 96h DN-156119


title: blastoid 96h PDGFRa pl-156114


title: blastoid 96h PDGFRa pl-156117


title: blastoid 96h PDGFRa pl-156113


title: blastoid 96h PDGFRa pl-156115


title: blastoid 96h PDGFRa pl-156112


title: blastoid 96h PDGFRa pl-156111


title: blastoid 96h PDGFRa pl-156116


title: blastoid 96h PDGFRa pl-156109


title: blastoid 96h PDGFRa pl-156108


title: blastoid 96h PDGFRa pl-156110


title: blastoid 96h DN-156104


title: blastoid 96h DN-156103


title: blastoid 96h DN-156101


title: blastoid 96h DN-156102


title: blastoid 96h PDGFRa pl-156100


title: blastoid 96h PDGFRa pl-156096


title: blastoid 96h PDGFRa pl-156099


title: blastoid 96h DN-156105


title: blastoid 96h PDGFRa pl-156098


title: blastoid 96h PDGFRa pl-156097


title: blastoid 96h PDGFRa pl-156092


title: blastoid 96h PDGFRa pl-156094


title: blastoid 96h PDGFRa pl-156095


title: blastoid 96h PDGFRa pl-156093


title: blastoid 96h DN-156091


title: blastoid 96h DN-156089


title: blastoid 96h DN-156121


title: blastoid 96h PDGFRa pl-156084


title: blastoid 96h DN-156106


title: blastoid 96h DN-156088


title: blastoid 96h DN-156107


title: blastoid 96h DN-156086


title: blastoid 96h DN-156085


title: blastoid 96h PDGFRa pl-156081


title: blastoid 96h PDGFRa pl-156083


title: blastoid 96h DN-156135


title: blastoid 96h PDGFRa pl-156080


title: blastoid 96h PDGFRa pl-156076


title: blastoid 96h DN-156075


title: blastoid 96h PDGFRa pl-156077


title: blastoid 96h PDGFRa pl-156078


title: blastoid 96h DN-156074


title: blastoid 96h DN-156071


title: blastoid 96h DN-156070


title: blastoid 96h PDGFRa pl-156082


title: blastoid 96h DN-156072


title: blastoid 96h DN-156087


title: blastoid 96h PDGFRa pl-156068


title: blastoid 96h PDGFRa pl-156065


title: blastoid 96h PDGFRa pl-156062


title: blastoid 96h DN-156069


title: blastoid 96h PDGFRa pl-156060


title: blastoid 96h PDGFRa pl-156079


title: blastoid 96h DN-156057


title: blastoid 96h PDGFRa pl-156066


title: blastoid 96h PDGFRa pl-156067


title: blastoid 96h DN-156059


title: blastoid 96h DN-156058


title: blastoid 96h PDGFRa pl-156050


title: blastoid 96h DN-156053


title: blastoid 96h PDGFRa pl-156052


title: blastoid 96h PDGFRa pl-156051


title: blastoid 96h DN-156056


title: blastoid 96h DN-156054


title: blastoid 96h PDGFRa pl-156046


title: blastoid 96h PDGFRa pl-156047


title: blastoid 96h PDGFRa pl-156049


title: blastoid 96h PDGFRa pl-156048


title: blastoid 96h PDGFRa pl-156045


title: blastoid 96h PDGFRa pl-156064


title: blastoid 96h PDGFRa pl-156063


title: blastoid 96h PDGFRa pl-156044


title: blastoid 96h DN-156042


title: blastoid 96h DN-156043


title: blastoid 96h DN-156039


title: blastoid 96h DN-156055


title: blastoid 96h DN-156036


title: blastoid 96h DN-156037


title: blastoid 96h DN-156040


title: blastoid 96h DN-156033


title: blastoid 96h DN-156031


title: blastoid 96h DN-156029


title: blastoid 96h DN-156034


title: blastoid 96h DN-156028


title: blastoid 96h DN-156030


title: blastoid 96h DN-156024


title: blastoid 96h DN-156026


title: blastoid 96h DN-156027


title: blastoid 96h DN-156023


title: blastoid 96h DN-156022


title: blastoid 96h DN-156015


title: blastoid 96h DN-156019


title: blastoid 96h DN-156021


title: blastoid 96h DN-156016


title: blastoid 96h DN-156020


title: blastoid 96h DN-156038


title: blastoid 96h DN-156014


title: blastoid 96h DN-156013


title: blastoid 96h DN-156035


title: blastoid 96h DN-156012


title: blastoid 96h DN-156017


title: blastoid 96h DN-156018


title: blastoid 96h DN-156032


title: blastoid 96h DN-156011


title: blastoid 96h DN-156009


title: blastoid 96h DN-156010


title: blastoid 96h DN-156004


title: blastoid 96h DN-156008


title: blastoid 96h DN-156025


title: blastoid 96h DN-156002


title: blastoid 96h DN-156003


title: blastoid 96h DN-156006


title: blastoid 96h DN-156005


title: blastoid 96h DN-156000


title: blastoid 96h DN-155998


title: blastoid 96h DN-155997


title: blastoid 96h DN-155999


title: blastoid 96h DN-156001


title: blastoid 96h DN-155995


title: blastoid 96h DN-155992


title: blastoid 96h DN-155994


title: blastoid 96h DN-155993


title: blastoid 96h DN-156007


title: blastoid 96h DN-155988


title: blastoid 96h DN-155980


title: blastoid 96h DN-155983


title: blastoid 96h DN-155978


title: blastoid 96h DN-155981


title: blastoid 96h DN-155987


title: blastoid 96h DN-155986


title: blastoid 96h DN-155971


title: blastoid 96h DN-155974


title: blastoid 96h DN-155969


title: blastoid 96h DN-155970


title: blastoid 96h DN-155967


title: blastoid 96h DN-155968


title: blastoid 96h DN-155972


title: blastoid 96h DN-155989


title: blastoid 96h DN-155973


title: blastoid 96h DN-155976


title: blastoid 96h DN-155996


title: blastoid 96h DN-155966


title: blastoid 96h DN-155961


title: blastoid 96h DN-155965


title: blastoid 96h DN-155962


title: blastoid 96h DN-155964


title: blastoid 96h DN-155990


title: blastoid 96h DN-155960


title: blastoid 96h DN-155957


title: blastoid 96h DN-155984


title: blastoid 96h DN-155954


title: blastoid 96h DN-155955


title: blastoid 96h DN-155953


title: blastoid 96h DN-155979


title: blastoid 96h DN-155951


title: blastoid 96h DN-155946


title: blastoid 96h DN-155944


title: blastoid 96h DN-155958


title: blastoid 96h DN-155949


title: blastoid 96h DN-155945


title: blastoid 96h DN-155956


title: blastoid 96h DN-155959


title: blastoid 96h DN-155948


title: blastoid 96h DN-155943


title: blastoid 96h DN-155947


title: V16D-H19-Rep1-H3K27me3

city: Tucson

first: Ritu

last: Pandey

state: Arizona

address: 1515 N Campbell Ave.,

department: Cellular and Molecular Medicine, Arizona Cancer Center

institute: University of Arizona

data_processing:
Peaks for each replicate (n=3) from each cell line, were called from BAM alignment files using MACS2 with default parameters. Narrow peaks were called for the H3K4me3 mark and broad peaks were called for the H3K27me3 mark using the same input for each sample.
The peaks were then assessed for coverage and signal distribution using the ChIPQC Bioconductor package and interrogated for peak occupancy and differential binding using the DiffBind R Bioconductor package.
For occupancy analysis, Consensus peaks were generated (using the replicates for each mark and cell line) with an overlap rate of 0.66 and bivalent/biphasic regions were defined as regions of overlap between H3K4me3 and H3K27me3 marks for each cell line. Consensus peaks and bivalent/biphasic regions were annotated for proximity to genes using the ChIPseeker R Bioconductor package.
Differential binding analysis for V16D/H19 vs V16D/CTL was performed for the H3K4me3 and H3K27me3 marks. Significantly differentially bound sites for each comparison were then annotated for proximity to genes using the ChIPseeker R Bioconductor package.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig, peak text, diffbing text files

source_name: derived from castration sensitive and androgen sensitive LNCaP cells

growth_protocol: V16D CRPC cells were cultured in 15cm dishes in 20ml RPMI1640 with 10% fetal bovine serum

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP and input DNA libraries were prepared with 5ng of DNA using KAPA Hyper Prep kits (Kapa Biosystems, KK8502) per manufacturer’s instructions and included post-adapter ligation size selection step (0.6X-0.9X) using Ampure XP SPRI magnetic beads (Beckman Coutler, A63881). PCR amplified (11 cycles) libraries were quantitated by Qubit, assessed with a Bioanalyzer (Agilent), and sequenced using 75bp single-end reads on an Illumina NextSeq 500.

treatment_protocol: V16D CRPC cells were transduced (in biological triplicates; n=3) with control lentivector (V16D cells) and lentivector overexpressing lncRNA H19 (V16D/H19 cells)

value: castration resistant prostate cancer cells

value: H3K27me3 (Cell Signaling Technologies, 9733)

value: Vector overexpressing lncRNA H19

tag: cell line source

value: Derived from LNCaP cells developed to be castration resistant


title: blastoid 96h DN-155936


title: blastoid 96h DN-155950


title: V16D-H19-Rep3-Input


title: blastoid 96h DN-155942


title: blastoid 96h DN-155934


title: blastoid 96h DN-155937


title: V16D-H19-Rep3-H3K27me3


title: blastoid 96h DN-155939


title: V16D-H19-Rep2-H3K27me3


title: V16D-Rep3-H3K27me3

value: Control vector


title: V16D-H19-Rep1-Input


title: blastoid 96h DN-155952


title: blastoid 96h DN-155940


title: V16D-Rep1-H3K27me3


title: V16D-H19-Rep3-H3K4me3

value: H3K4me3 (Diagenode, Cat # C15410003)


title: blastoid 96h DN-155929


title: blastoid 96h DN-155938


title: blastoid 96h DN-155928


title: V16D-H19-Rep1-H3K4me3


title: V16D-H19-Rep2-H3K4me3


title: blastoid 96h DN-155935


title: blastoid 96h DN-155932


title: V16D-H19-Rep2-Input


title: blastoid 96h DN-155930


title: blastoid 96h DN-155931


title: blastoid 96h DN-155926


title: V16D-Rep2-Input


title: V16D-Rep2-H3K27me3


title: blastoid 96h DN-155925


title: V16D-Rep1-Input


title: blastoid 96h DN-155927


title: blastoid 96h DN-155923


title: V16D-Rep2-H3K4me3


title: HPr1AR_DHT_24hr

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

data_processing:
Base-calling was performed using Illumina Real Time Analysis RTA.2.7.7.0 with default parameters
Raw sequencing reads were aligned to the human genome (hg19) and methylation levels called using bismark.
Genome_build: hg19
Supplementary_files_format_and_content: processed data is in supplementary file, which is a comma-separated text file containing a matrix of methylation levels determined for CpG positions covered by WGBS at 20x across all samples

source_name: Prostate Epithelial Cell Line

growth_protocol: Cells were maintained at 37oC and 5.0% CO2 using a cell culture incubator with UV contamination control. HPr1-AR cells were maintained in Keratinocyte-Serum Free Medium (KSF) containing human recombinant Epidermal Growth Factor 1-53 (EGF 1-53) and Bovine Pituitary Extract (BPE). Media was supplemented with 100 U/mL Penicillin-Streptomycin.

extract_protocol:
Total DNA was extracted from all samples using Qiagen DNeasy Blood & Tissue Kits
Sequencing was performed at the Roswell Park Genomics Shared Resource core facility, and sequencing libraries prepared with the TruSeq DNA Methylation Library Prep Kit, from 1ug total DNA

treatment_protocol: Cells were treated with indicated concentration of DHT or EtOH for 1, 24 or 96 hours.

tag: gender

value: male

value: 10nm DHT

tag: time


title: V16D-Rep3-Input


title: blastoid 96h DN-155924


title: blastoid 96h DN-155918


title: blastoid 96h DN-155920


title: V16D-Rep1-H3K4me3


title: HPr1AR_DHT_96hr


title: HPr1AR_DHT_0hr

value: EtOH


title: V16D-Rep3-H3K4me3


title: blastoid 96h DN-155916


title: blastoid 96h DN-155921


title: HPr1AR_DHT_1hr


title: MC HPr1AR_DHT_0hr_R1

data_processing:
Library strategy: Methyl Capture
Base-calling was performed using Illumina Real Time Analysis RTA.2.7.7.0 with default parameters
Raw sequencing reads were aligned to the human genome (hg19) and methylation levels called using bismark.
Genome_build: hg19
Supplementary_files_format_and_content: processed data is in supplementary file, which is a comma-separated text file containing a matrix of read counts mapping to each captured CpG position and determined methylation level

extract_protocol:
Total DNA was extracted from all samples using Qiagen DNeasy Blood & Tissue Kits
Sequencing was performed at the Roswell Park Genomics Shared Resource core facility, and sequencing libraries prepared with the TruSeq Methyl Capture EPIC Library Prep Kit, from 1ug total DNA


title: blastoid 96h DN-155933


title: blastoid 96h DN-155912


title: MC HPr1AR_DHT_96hr_R1


title: blastoid 96h DN-155911


title: blastoid 96h DN-155922


title: MC HPr1AR_DHT_24hr_R1


title: MC HPr1AR_DHT_1hr_R1


title: blastoid 96h DN-155914