title: HPr1AR_DHT_0hr_R4

data_processing:
Base-calling was performed using Illumina Real Time Analysis RTA.2.7.7.0 with default parameters
Alignment of raw sequence reads to the human transcriptome (hg19) via TopHat
Aligned reads translated to expression counts via featurecounts
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 for each gene accession number and sample

extract_protocol:
Total RNA was extracted from all samples using TRIzol
Sequencing was performed at the Roswell Park Genomics Shared Resource core facility, and sequencing libraries prepared with the TruSeq Stranded Total RNA kit (Illumina Inc), from 1ug total RNA

value: Prostate Epithelial Cell Line


title: blastoid 96h DN-155913

status: Public on Sep 15 2021

type: SRA

city: Vienna

first: Giovanni

last: Sestini

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

country: Austria

institute: IMBA - Institute of Molecular Biotechnology

library_source: transcriptomic

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

molecule: polyA RNA

organism: Homo sapiens

source_name: blastoid

extract_protocol:
Smart-Seq2 protocol
Smart-Seq2

tag: treatment


title: blastoid 96h DN-155917


title: HPr1AR_DHT_96hr_R3

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

country: USA

institute: Roswell Park Cancer Institute

molecule: total RNA

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.

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

tag: tissue

tag: cell line

tag: gender

value: male

value: 10nm DHT

tag: time


title: HPr1AR_DHT_24hr_R4


title: HPr1AR_DHT_0hr_R3

value: EtOH


title: HPr1AR_DHT_96hr_R2


title: blastoid 96h DN-155907


title: blastoid 96h DN-155905


title: HPr1AR_DHT_1hr_R4


title: blastoid 96h DN-155906


title: blastoid 96h DN-155910


title: blastoid 96h DN-155901


title: HPr1AR_DHT_96hr_R1


title: blastoid 96h DN-155902


title: blastoid 96h DN-155900


title: blastoid 96h DN-155908


title: HPr1AR_DHT_1hr_R3


title: HPr1AR_DHT_24hr_R3


title: blastoid 96h DN-155909


title: blastoid 96h TROP2 pl-155898


title: blastoid 96h TROP2 pl-155897


title: blastoid 96h TROP2 pl-155896


title: HPr1AR_DHT_96hr_R4


title: blastoid 96h DN-155904


title: HPr1AR_DHT_1hr_R2


title: HPr1AR_DHT_24hr_R2


title: NAFT18014_P5B6_D14_144_S10

city: Cambridge

first: Tomasz

last: Kostrzewski

address: 332 Cambridge Science Park

country: United Kingdom

institute: CN Bio Innovations

data_processing:
Demultiplexed using Illumina bcl2fastq2-v2.16
The quality of the reads was assessed using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc)
The reads were processed and mapped to the human genome using the Bcbio-nextgen framework version 1.1.2 (https://github.com/chapmanb/bcbio-nextgen)
Hisat2 v.2.1.0 (www.ncbi.nlm.nih.gov/pmc/articles/PMC4655817) was used to align reads and the alignment quality was assessed with QualiMap v.2.2.2 (http://qualimap.bioinfo.cipf.es).
Transcript-level abundances were imported and utilized for counts estimation using the TxImport package. Identification of differentially expressed genes at False Discovery Rate < 5% per comparison was performed using DESeq2 in R.
Genome_build: Human
Supplementary_files_format_and_content: tab-delimited text file include TPM values for each sample
Supplementary_files_format_and_content: tab-delimited text file include raw gene count for every gene and every sample

growth_protocol: Primary hepatocytes, kupffer and stellate cells were co-cultured in liver MPS plates (PhysioMimix - CN Bio Innovations) for fourteen days (co-cultures were performed at two ratios of NPCS)

extract_protocol:
Liver MPS scaffolds were removed, flash frozen, and RNA was harvested using Trizol reagent. 50 ng of total RNA was used as input to each mRNA-seq library. KAPA mRNA HyperPrep kit (Roche) was used for reverse transcription, generation of double stranded cDNA and subsequent library preparation
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Co-cultures were treated with either fat, fructose, cholesterol, TGF-B and LPS

value: Liver MPS co-culture tissue


title: blastoid 96h DN-155903


title: blastoid 96h TROP2 pl-155895


title: NAFT18014_P5A6_D14_138_S8


title: NAFT18014_P5A3_D14_135_S7


title: blastoid 96h TROP2 pl-155893


title: HPr1AR_DHT_0hr_R1


title: HPr1AR_DHT_0hr_R2


title: HPr1AR_DHT_24hr_R1


title: NAFT18014_P4B6_D14_132_S6


title: HPr1AR_DHT_1hr_R1


title: NAFT18014_P4A6_D14_126_S4


title: blastoid 96h TROP2 pl-155890


title: NAFT18014_P4A3_D14_123_S3


title: NAFT18015_P1B3_D14_153_S11


title: blastoid 96h TROP2 pl-155899


title: NAFT18014_P3B6_D14_120_S2


title: blastoid 96h TROP2 pl-155892


title: blastoid 96h TROP2 pl-155894


title: blastoid 96h TROP2 pl-155887


title: blastoid 96h TROP2 pl-155891


title: blastoid 96h TROP2 pl-155886


title: blastoid 96h TROP2 pl-155885


title: NAFT18014_P3A6_D14_114_S24


title: NAFT18013_P4A3_D14_39_rep_S13


title: NAFT18013_P1A1_D14_01_rep_S12

value: Lean


title: blastoid 96h TROP2 pl-155888


title: NAFT18014_P3B3_D14_117_S1


title: NAFT18014_P2A6_D14_102_S15


title: blastoid 96h TROP2 pl-155881


title: blastoid 96h TROP2 pl-155880


title: NAFT18014_P5B3_D14_141_S9


title: NAFT18014_P1B4_D14_94_S9


title: blastoid 96h TROP2 pl-155889


title: NAFT18014_P2B4_D14_106_S18


title: blastoid 96h TROP2 pl-155884


title: NAFT18014_P2A2_D14_98_S12


title: NAFT18014_P3A2_D14_110_S21


title: blastoid 96h TROP2 pl-155877


title: blastoid 96h TROP2 pl-155883


title: blastoid 96h TROP2 pl-155879


title: NAFT18014_P4B3_D14_129_S5


title: NAFT18013_P4A6_D14_42_S2


title: NAFT18013_P3A6_D14_30_S16


title: blastoid 96h TROP2 pl-155878


title: NAFT18013_P3A2_D14_26_S13


title: blastoid 96h TROP2 pl-155874


title: blastoid 96h TROP2 pl-155872


title: blastoid 96h TROP2 pl-155873


title: blastoid 96h TROP2 pl-155870


title: NAFT18013_P2A2_D14_14_S4


title: blastoid 96h TROP2 pl-155869


title: NAFT18013_P4B4_D14_46_S5


title: NAFT18013_P1B4_D14_10_S1


title: blastoid 96h TROP2 pl-155871


title: blastoid 96h TROP2 pl-155882


title: NAFT18013_P2B4_D14_22_S10


title: NAFT18013_P3B4_D14_34_S19


title: NAFT18013_P2A6_D14_18_S7


title: NAFT18012_P3B2_D14_80_S3


title: blastoid 96h TROP2 pl-155876


title: NAFT18013_P4A2_D14_38_S22


title: NAFT18012_P3A4_D14_76_S23


title: blastoid 96h TROP2 pl-155875


title: NAFT18012_P3B6_D14_84_S6


title: NAFT18012_P2B6_D14_72_S20


title: blastoid 96h TROP2 pl-155868


title: blastoid 96h TROP2 pl-155866


title: blastoid 96h TROP2 pl-155867


title: NAFT18012_P1B6_D14_60_S11


title: blastoid 96h TROP2 pl-155865


title: NAFT18012_P2B2_D14_68_S17


title: blastoid 96h TROP2 pl-155861


title: NAFT18015_P3B4_D14_177_S21


title: blastoid 96h TROP2 pl-155860


title: blastoid 96h TROP2 pl-155864


title: NAFT18015_P3B2_D14_175_S18


title: NAFT18015_P3A5_D14_173_S15


title: blastoid 96h TROP2 pl-155857


title: blastoid 96h TROP2 pl-155863


title: NAFT18012_P2A4_D14_64_S14


title: NAFT18015_P2B5_D14_167_S6


title: NAFT18015_P3B6_D14_179_S24


title: blastoid 96h TROP2 pl-155858


title: blastoid 96h TROP2 pl-155859


title: blastoid 96h TROP2 pl-155853


title: NAFT18012_P1B2_D14_56_S8


title: blastoid 96h TROP2 pl-155856


title: NAFT18015_P2A3_D14_159_S17


title: blastoid 96h TROP2 pl-155855


title: blastoid 96h TROP2 pl-155862


title: NAFT18015_P1B2_D14_152_S8


title: NAFT18015_P3A1_D14_169_S9


title: NAFT18015_P1B5_D14_155_S11


title: NAFT18015_P2B3_D14_165_S3


title: NAFT18014_P5B5_D14_143_S5


title: blastoid 96h TROP2 pl-155854


title: blastoid 96h TROP2 pl-155847


title: blastoid 96h TROP2 pl-155852


title: NAFT18015_P2B1_D14_163_S23


title: blastoid 96h TROP2 pl-155850


title: blastoid 96h TROP2 pl-155851


title: NAFT18015_P2A5_D14_161_S20


title: NAFT18015_P3A3_D14_171_S12


title: blastoid 96h TROP2 pl-155843


title: NAFT18014_P5A5_D14_137_S22


title: NAFT18014_P5A2_D14_134_S19


title: blastoid 96h TROP2 pl-155849


title: NAFT18015_P2A1_D14_157_S14


title: NAFT18014_P4B5_D14_131_S16


title: blastoid 96h TROP2 pl-155846


title: blastoid 96h TROP2 pl-155845


title: NAFT18014_P5B2_D14_140_S2


title: blastoid 96h TROP2 pl-155844


title: blastoid 96h TROP2 pl-155841


title: blastoid 96h TROP2 pl-155839


title: blastoid 96h TROP2 pl-155840


title: blastoid 96h TROP2 pl-155838


title: NAFT18014_P4B2_D14_128_S13


title: blastoid 96h TROP2 pl-155837


title: NAFT18014_P3B2_D14_116_S1


title: blastoid 96h TROP2 pl-155848


title: NAFT18014_P4A2_D14_122_S7


title: NAFT18014_P3A5_D14_113_S24


title: blastoid 96h TROP2 pl-155834


title: blastoid 96h TROP2 pl-155836


title: blastoid 96h TROP2 pl-155835


title: NAFT18014_P2A5_D14_101_S15


title: NAFT18014_P2B3_D14_105_S18


title: NAFT18013_P4B3_D14_45_S5


title: blastoid 96h TROP2 pl-155842


title: NAFT18014_P2A1_D14_97_S12


title: NAFT18014_P3B5_D14_119_S4


title: NAFT18014_P4A5_D14_125_S10


title: NAFT18013_P4A1_D14_37_S22


title: NAFT18014_P1B3_D14_93_S9


title: blastoid 96h TROP2 pl-155830


title: blastoid 96h TROP2 pl-155829


title: NAFT18013_P4A5_D14_41_S2


title: blastoid 96h TROP2 pl-155832


title: blastoid 96h TROP2 pl-155831


title: blastoid 96h TROP2 pl-155825


title: NAFT18014_P3A1_D14_109_S21


title: blastoid 96h TROP2 pl-155824


title: NAFT18013_P3B3_D14_33_S19


title: blastoid 96h TROP2 pl-155827


title: blastoid 96h TROP2 pl-155826


title: blastoid 96h TROP2 pl-155828


title: blastoid 96h TROP2 pl-155823


title: NAFT18013_P3A1_D14_25_S13


title: NAFT18013_P2B3_D14_21_S10


title: blastoid 96h TROP2 pl-155822


title: NAFT18013_P2A1_D14_13_S4


title: blastoid 96h TROP2 pl-155820


title: blastoid 96h TROP2 pl-155821


title: NAFT18013_P1B3_D14_09_S1


title: NAFT18012_P3B5_D14_83_S6


title: blastoid 96h TROP2 pl-155818


title: NAFT18012_P3B1_D14_79_S3


title: blastoid 96h TROP2 pl-155819


title: NAFT18012_P2B1_D14_67_S17


title: NAFT18012_P3A3_D14_75_S23


title: blastoid 96h TROP2 pl-155817


title: blastoid 96h TROP2 pl-155814


title: NAFT18012_P2B5_D14_71_S20


title: NAFT18013_P3A5_D14_29_S16


title: blastoid 96h TROP2 pl-155812


title: blastoid 96h TROP2 pl-155809


title: blastoid 96h TROP2 pl-155811


title: NAFT18012_P1B5_D14_59_S11


title: blastoid 96h TROP2 pl-155810


title: blastoid 96h TROP2 pl-155815


title: NAFT18012_P1B1_D14_55_S8


title: blastoid 96h TROP2 pl-155816


title: blastoid 96h TROP2 pl-155808


title: NAFT18013_P2A5_D14_17_S7


title: blastoid 96h TROP2 pl-155807


title: Input replicat.3

city: Montreal

first: Pierre

last: Bensidoun

state: Quebec

address: 4850 Avenue Hotel de ville

department: biochemistry

country: Canada

institute: ircm-universite de montreal

description: Poly(A) enriched

data_processing:
Data were analysed on galaxy platform  (Galaxy Version 0.38.0)
Adapter and other illumina-specific were removed using trimomatic  triming tool
Reads were mapped using the RNA seq aligner RNA-star on the yeast genome from  Ensemble Yeast Genome (R64-1-1 https://fungi.ensembl.org/Saccharomyces_cerevisiae/Info/Index?db=core)
The measure of gene expression  of the mapped reads  has been carried out with featurecounts read counting program
Differentially expressed genes across samples was determined using DESeq2

organism: Saccharomyces cerevisiae

source_name: Yeast

growth_protocol: asynchronous culture  grown in log phase in YPD

extract_protocol:
Affinity purification and trizol extraction follwed by isolation of the transcripts on Direct-zol column (Zymo research)
NEBNext Poly(A) mRNA Magnetic Isolation Module
Libraries were prepared according to Illumina's instructions accompanying the Illumina TRUSeq DNA UDI 96 Indexes , 96 samples.

treatment_protocol: Harvesting and Cryogrinding in liquid nitrogen of the cultures

tag: strain

tag: affinity purification

value: total extract/trizol extraction

tag: Stage

value: asynchronous culture  grown in log phase


title: Input replicat.1

description: Poly(A) enriched


title: background  Ctln GFP .replicat.3

description: Poly(A) enriched

value: GFP nanobody


title: Input replicat.2

description: Poly(A) enriched


title: NAFT18015_P3B5_D14_178_S24


title: NAFT18012_P2A3_D14_63_S14


title: blastoid 96h TROP2 pl-155813


title: NAFT18015_P3B3_D14_176_S21


title: NAFT18015_P3A4_D14_172_S15


title: blastoid 96h TROP2 pl-155804


title: NAFT18015_P3A6_D14_174_S18


title: background  Ctln GFP .replicat.2

description: Poly(A) enriched


title: NAFT18015_P3A2_D14_170_S12


title: background  Ctln GFP .replicat.1

description: Poly(A) enriched


title: blastoid 96h TROP2 pl-155799


title: blastoid 96h TROP2 pl-155802


title: blastoid 96h TROP2 pl-155803


title: NAFT18015_P2B6_D14_168_S9


title: blastoid 96h TROP2 pl-155798


title: background  Ctln PrA .replicat.3

description: Poly(A) enriched

value: IgG


title: blastoid 96h TROP2 pl-155797


title: blastoid 96h TROP2 pl-155796


title: NAFT18015_P2B4_D14_166_S6


title: blastoid 96h TROP2 pl-155806


title: background  Ctln PrA .replicat.2

description: Poly(A) enriched


title: blastoid 96h TROP2 pl-155794


title: background  Ctln PrA .replicat.1

description: Poly(A) enriched


title: blastoid 96h TROP2 pl-155795


title: NAFT18015_P2B2_D14_164_S3


title: blastoid 96h TROP2 pl-155805


title: blastoid 96h TROP2 pl-155792


title: NAFT18015_P2A6_D14_162_S23


title: blastoid 96h TROP2 pl-155790


title: all NPCs AP.replicat.2

description: Poly(A) enriched


title: blastoid 96h TROP2 pl-155791


title: all NPCs AP.replicat.3

description: Poly(A) enriched


title: blastoid 96h TROP2 pl-155793


title: blastoid 96h TROP2 pl-155800


title: NAFT18015_P2A4_D14_160_S20


title: blastoid 96h TROP2 pl-155789


title: NAFT18015_P1B6_D14_156_S14


title: all NPCs AP.replicat.1

description: Poly(A) enriched


title: NAFT18015_P2A2_D14_158_S17


title: blastoid 96h TROP2 pl-155786


title: NAFT18015_P1B4_D14_154_S11


title: blastoid 96h TROP2 pl-155784


title: blastoid 96h TROP2 pl-155788


title: Basket-less  pore AP.replicat.2

description: Poly(A) enriched


title: Basket-less  pore AP.replicat.3

description: Poly(A) enriched


title: blastoid 96h TROP2 pl-155781


title: Basket-less  pore AP.replicat.1

description: Poly(A) enriched


title: blastoid 96h TROP2 pl-155780


title: NAFT18015_P1B1_D14_151_S8


title: blastoid 96h TROP2 pl-155777


title: blastoid 96h TROP2 pl-155779


title: Basket-containing  pore AP.replicat.1

description: Poly(A) enriched


title: blastoid 96h TROP2 pl-155776


title: Basket-containing  pore AP.replicat.3

description: Poly(A) enriched


title: blastoid 96h TROP2 pl-155775


title: blastoid 96h TROP2 pl-155778


title: blastoid 96h TROP2 pl-155785


title: Basket-containing  pore AP.replicat.2

description: Poly(A) enriched


title: blastoid 96h TROP2 pl-155774


title: blastoid 96h TROP2 pl-155773


title: NAFT18014_P5A1_D14_133_S19


title: blastoid 60h TROP2 min-154973


title: blastoid 96h TROP2 pl-155783


title: blastoid 60h TROP2 min-154970


title: blastoid 60h TROP2 min-154972


title: blastoid 60h TROP2 min-154969


title: NAFT18014_P4B4_D14_130_S16


title: NAFT18014_P4B1_D14_127_S13


title: blastoid 60h TROP2 min-154967


title: NAFT18014_P5B4_D14_142_S5


title: blastoid 60h TROP2 min-154968


title: NAFT18014_P5B1_D14_139_S2


title: NAFT18014_P4A4_D14_124_S10


title: blastoid 60h TROP2 min-154965


title: NAFT18014_P4A1_D14_121_S7


title: blastoid 60h TROP2 min-154966


title: NAFT18014_P5A4_D14_136_S22


title: blastoid 60h TROP2 min-154964


title: blastoid 60h TROP2 min-154963


title: blastoid 96h TROP2 pl-155787


title: blastoid 60h TROP2 min-154962


title: Endometrium_RR_7

type: RNA

city: Valencia

first: Patricia

last: Sebastian-Leon

state: Valencia

address: EDIFICIO BIOPOLO - LA FE, Avenida Fernando Abril Martorell, 106 - Torre A, Planta 1ª

department: Genomics and Systems Reproductive Medicine

country: Spain

institute: IVI-RMA Foundation

hyb_protocol: Sample preparation and hybridization of the RNA, training set and pathological samples were adapted from the Agilent technical manual (one color) (Agilent Technologies, Madrid, Spain).

scan_protocol: Hybridized microarrays were scanned in an Axon 4100A scanner (Molecular Devices, Sunnyvale, CA), and the data were extracted with the GenePix Pro 6.0 software (Molecular Devices).

data_processing: Normalized signal was obtained using limma and preprocessCore R-packages. F532 Median and B532 Meadian are the columns used for estimate probeset expression. Background was corrected using normexp method and 8 replicates for each probe were averaged.

source_name: endometrial biopsy

label_protocol: Agilent one color

extract_protocol: Endometrial samples were snap-frozen in liquid nitrogen and stored at -80C. Total RNA was extracted using the TRIzol method according to the standard protocol (Life Technologies, Inc., Gaithersburg, MD). The RNA quality was assessed in the A2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany)

value: Endometrium

value: female

value: RR


title: Endometrium_RR_78


title: Endometrium_RR_9


title: Endometrium_RR_8


title: Endometrium_RR_77


title: blastoid 60h TROP2 min-154960


title: blastoid 60h TROP2 min-154961


title: NAFT18014_P3B4_D14_118_S4


title: blastoid 60h TROP2 min-154959


title: NAFT18014_P3B1_D14_115_S1


title: blastoid 60h TROP2 min-154956


title: NAFT18014_P2B6_D14_108_S21


title: blastoid 60h TROP2 min-154955


title: blastoid 60h TROP2 min-154954


title: Endometrium_RR_74


title: blastoid 60h TROP2 min-154953


title: Endometrium_RR_72


title: NAFT18014_P2B2_D14_104_S18


title: blastoid 60h TROP2 min-154951


title: NAFT18014_P2A4_D14_100_S15


title: blastoid 60h TROP2 min-154952


title: Endometrium_RR_75


title: Endometrium_RR_71


title: NAFT18014_P1B6_D14_96_S12


title: blastoid 60h TROP2 min-154948


title: blastoid 60h TROP2 min-154947


title: blastoid 60h TROP2 min-154950


title: NAFT18014_P3A4_D14_112_S24


title: blastoid 60h TROP2 min-154946


title: blastoid 60h TROP2 min-154945


title: Endometrium_RR_6


title: NAFT18013_P4B6_D14_48_S8


title: NAFT18014_P1B2_D14_92_S9


title: Endometrium_RR_70


title: Endometrium_RR_69


title: NAFT18013_P4B2_D14_44_S5


title: blastoid 60h TROP2 min-154942


title: blastoid 60h TROP2 min-154941


title: blastoid 60h TROP2 min-154944


title: blastoid 60h TROP2 min-154940


title: NAFT18013_P4A4_D14_40_S2


title: Endometrium_RR_73


title: Endometrium_RR_68


title: blastoid 60h TROP2 min-154949


title: Endometrium_RR_76


title: NAFT18013_P3B6_D14_36_S22


title: blastoid 60h TROP2 min-154939


title: blastoid 60h TROP2 min-154936


title: blastoid 60h TROP2 min-154937


title: NAFT18013_P3B2_D14_32_S19


title: Endometrium_RR_67


title: blastoid 60h TROP2 min-154938


title: Endometrium_RR_65


title: blastoid 60h TROP2 min-154935


title: blastoid 60h TROP2 min-154934


title: NAFT18013_P3A4_D14_28_S16


title: blastoid 60h TROP2 min-154933


title: NAFT18013_P2B6_D14_24_S13


title: Endometrium_RR_64


title: NAFT18013_P2B2_D14_20_S10


title: blastoid 60h TROP2 min-154930


title: blastoid 60h TROP2 min-154931


title: Endometrium_RR_63


title: blastoid 60h TROP2 min-154926


title: NAFT18013_P1B6_D14_12_S4


title: Endometrium_RR_66


title: blastoid 60h TROP2 min-154925


title: NAFT18013_P1B2_D14_08_S1


title: blastoid 60h TROP2 min-154929


title: Endometrium_RR_60


title: NAFT18012_P3B4_D14_82_S6


title: blastoid 60h TROP2 min-154922


title: blastoid 60h TROP2 min-154921


title: blastoid 60h TROP2 min-154924


title: Endometrium_RR_5


title: blastoid 60h TROP2 min-154920


title: blastoid 60h TROP2 min-154927


title: NAFT18013_P2A4_D14_16_S7


title: blastoid 60h TROP2 min-154919


title: Endometrium_RR_61


title: blastoid 60h TROP2 min-154928


title: blastoid 60h TROP2 min-154918


title: blastoid 60h TROP2 min-154932


title: blastoid 60h TROP2 min-154923


title: Endometrium_RR_58


title: blastoid 60h TROP2 min-154915


title: NAFT18012_P3A6_D14_78_S3


title: blastoid 60h TROP2 min-154917


title: Endometrium_RR_62


title: Endometrium_RR_56


title: NAFT18012_P2A6_D14_66_S17


title: Endometrium_RR_59


title: Endometrium_RR_57


title: NAFT18012_P2A2_D14_62_S14


title: blastoid 60h TROP2 min-154911


title: blastoid 60h TROP2 min-154914


title: blastoid 60h TROP2 min-154910


title: NAFT18012_P3A2_D14_74_S23


title: Endometrium_RR_54


title: NAFT18014_P3A3_D14_111_S23


title: blastoid 60h TROP2 min-154908


title: NAFT18012_P1B4_D14_58_S11


title: Endometrium_RR_55


title: Endometrium_RR_53


title: blastoid 60h TROP2 min-154909


title: blastoid 60h TROP2 min-154913


title: NAFT18012_P2B4_D14_70_S20


title: blastoid 60h TROP2 min-154916


title: blastoid 60h TROP2 min-154906


title: Endometrium_RR_52


title: NAFT18014_P2B1_D14_103_S17


title: blastoid 60h TROP2 min-154904


title: blastoid 60h TROP2 min-154912


title: NAFT18014_P2B5_D14_107_S20


title: blastoid 60h TROP2 min-154903


title: blastoid 60h TROP2 min-154905


title: NAFT18014_P1B5_D14_95_S11


title: blastoid 60h TROP2 min-154902


title: Endometrium_RR_51


title: NAFT18014_P2A3_D14_99_S14


title: blastoid 60h TROP2 min-154901


title: blastoid 60h TROP2 min-154898


title: blastoid 60h TROP2 min-154897


title: blastoid 60h TROP2 min-154899


title: blastoid 60h TROP2 min-154900


title: Endometrium_RR_50


title: NAFT18014_P1B1_D14_91_S8


title: Endometrium_RR_4


title: blastoid 60h TROP2 min-154896


title: NAFT18013_P4B1_D14_43_S4


title: Endometrium_RR_49


title: Endometrium_RR_48


title: blastoid 60h TROP2 min-154892


title: blastoid 60h TROP2 min-154891


title: blastoid 60h TROP2 min-154894


title: blastoid 60h TROP2 min-154890


title: NAFT18013_P4B5_D14_47_S7


title: Endometrium_RR_47


title: blastoid 60h TROP2 min-154893


title: Endometrium_RR_45


title: NAFT18013_P3B5_D14_35_S21


title: blastoid 60h TROP2 min-154889


title: blastoid 60h TROP2 min-154887


title: NAFT18013_P3B1_D14_31_S18


title: NAFT18013_P2B5_D14_23_S12


title: Endometrium_RR_43


title: blastoid 60h TROP2 min-154886


title: blastoid 60h TROP2 min-154888


title: NAFT18013_P3A3_D14_27_S15


title: blastoid 60h TROP2 min-154885


title: blastoid 60h TROP2 min-154883


title: Endometrium_RR_44


title: blastoid 60h TROP2 min-154882


title: Endometrium_RR_46


title: NAFT18013_P2B1_D14_19_S9


title: NAFT18013_P2A3_D14_15_S6


title: Endometrium_RR_42


title: blastoid 60h TROP2 min-154879


title: blastoid 60h TROP2 min-154878


title: blastoid 60h TROP2 min-154877


title: NAFT18013_P1B1_D14_07_S1


title: blastoid 60h TROP2 min-154876


title: Endometrium_RR_40


title: Endometrium_RR_3


title: NAFT18012_P3B3_D14_81_S5


title: Endometrium_RR_39


title: NAFT18012_P3A5_D14_77_S2


title: blastoid 60h TROP2 min-154881


title: blastoid 60h TROP2 min-154870


title: blastoid 60h TROP2 min-154873


title: blastoid 60h TROP2 min-154884


title: Endometrium_RR_38


title: blastoid 60h TROP2 min-154872


title: blastoid 60h TROP2 min-154871


title: Endometrium_RR_36


title: Endometrium_RR_37


title: NAFT18013_P1B5_D14_11_S3


title: Endometrium_RR_41


title: NAFT18012_P2B3_D14_69_S19


title: NAFT18012_P2A5_D14_65_S16


title: blastoid 60h TROP2 min-154867


title: blastoid 60h TROP2 min-154874


title: NAFT18012_P2A1_D14_61_S13


title: blastoid 60h TROP2 min-154863


title: blastoid 60h TROP2 min-154865


title: blastoid 60h TROP2 min-154866


title: Endometrium_RR_34


title: blastoid 60h TROP2 min-154875


title: blastoid 60h TROP2 min-154864


title: blastoid 60h TROP2 min-154861


title: Endometrium_RR_35


title: blastoid 60h TROP2 min-154862


title: Endometrium_RR_33


title: NAFT18012_P1B3_D14_57_S10


title: blastoid 60h TROP2 min-154868


title: blastoid 60h TROP2 min-154860


title: Endometrium_RR_32


title: blastoid 60h TROP2 min-154859


title: NAFT18015_P1A6_D14_150_S23

value: Fat


title: NAFT18015_P1A5_D14_149_S20


title: NAFT18015_P1A4_D14_148_S17


title: NAFT18015_P1A3_D14_147_S14


title: Endometrium_RR_31


title: NAFT18012_P3A1_D14_73_S22


title: blastoid 60h TROP2 min-154855


title: Endometrium_RR_30


title: blastoid 60h TROP2 min-154854


title: blastoid 60h TROP2 min-154853


title: blastoid 60h TROP2 min-154880


title: Endometrium_RR_2


title: blastoid 60h TROP2 min-154851


title: Endometrium_RR_29


title: blastoid 60h TROP2 min-154849


title: blastoid 60h TROP2 min-154850


title: blastoid 60h TROP2 min-154856


title: NAFT18015_P1A2_D14_146_S11


title: NAFT18015_P1A1_D14_145_S8


title: Endometrium_RR_27


title: blastoid 60h TROP2 min-154852


title: blastoid 60h TROP2 min-154858


title: Endometrium_RR_28


title: blastoid 60h TROP2 min-154848


title: blastoid 60h TROP2 min-154846


title: blastoid 60h TROP2 min-154847


title: NAFT18014_P1A6_D14_90_S5


title: Endometrium_RR_26


title: blastoid 60h TROP2 pl-154844


title: NAFT18014_P1A5_D14_89_S2


title: Endometrium_RR_25


title: blastoid 60h TROP2 pl-154842


title: NAFT18014_P1A4_D14_88_S22


title: blastoid 60h TROP2 pl-154839


title: blastoid 60h TROP2 pl-154841


title: blastoid 60h TROP2 pl-154840


title: blastoid 60h TROP2 pl-154838


title: Endometrium_RR_23


title: Endometrium_RR_24


title: blastoid 60h TROP2 pl-154836


title: NAFT18014_P1A2_D14_86_S16


title: blastoid 60h TROP2 pl-154837


title: blastoid 60h TROP2 pl-154835


title: NAFT18014_P1A1_D14_85_S13


title: blastoid 60h TROP2 pl-154834


title: blastoid 60h TROP2 pl-154833


title: NAFT18013_P1A5_D14_05_S12


title: blastoid 60h TROP2 pl-154845


title: blastoid 60h TROP2 pl-154832


title: Endometrium_RR_22


title: Endometrium_RR_20


title: Endometrium_RR_21


title: blastoid 60h TROP2 pl-154830


title: blastoid 60h TROP2 pl-154831


title: Endometrium_RR_1


title: NAFT18014_P1A3_D14_87_S19


title: blastoid 60h TROP2 pl-154843


title: NAFT18013_P1A4_D14_04_S9


title: NAFT18013_P1A3_D14_03_S6


title: NAFT18013_P1A2_D14_02_S3


title: blastoid 60h TROP2 pl-154826


title: blastoid 60h TROP2 pl-154825


title: blastoid 60h TROP2 pl-154827


title: blastoid 60h TROP2 pl-154829


title: NAFT18012_P1A6_D14_54_S10


title: Endometrium_RR_19


title: Endometrium_RR_17


title: blastoid 60h TROP2 pl-154824


title: blastoid 60h TROP2 pl-154821


title: NAFT18013_P1A6_D14_06_S15


title: blastoid 60h TROP2 pl-154823


title: Endometrium_RR_16


title: blastoid 60h TROP2 pl-154822


title: blastoid 60h TROP2 pl-154818


title: Endometrium_RR_14


title: NAFT18012_P1A5_D14_53_S7


title: Endometrium_RR_15


title: NAFT18012_P1A4_D14_52_S4


title: blastoid 60h TROP2 pl-154820


title: blastoid 60h TROP2 pl-154819


title: Endometrium_RR_12


title: blastoid 60h TROP2 pl-154817


title: Endometrium_RR_13


title: blastoid 60h TROP2 pl-154828


title: Endometrium_RR_18


title: Cal62 siADAR1 #2

city: Madrid

first: Julia

last: Ramirez-Moya

address: Arturo Duperier, 4

institute: Instituto de Investigaciones Biomédicas Alberto Sols

data_processing:
Raw reads were examined for quality issues using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Adapter sequences, other contaminant sequences were trimmed from reads using Atropos
Counts of reads aligning to known genes were generated by featureCounts
Transcripts Per Million (TPM) measurements per isoform were generated by quasialignment using Salmon
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: The tumor thyroid cell lines Cal62 was grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNA was isolated from siControl, siADAR1 #1 and siADAR1 #2 cells using the mirVana isolation kit
Library preparation was performed using the KAPA mRNA HyperPrep kit for poly(A+) RNA-seq and sequencing was performed on an Illumina NextSeq 500 using 75bp paired-end reads.

treatment_protocol: The siRNAs were purchased from Thermo Fisher: siControl (Silencer Select Negative Control #1 4390843), siADAR1 #1 (s1007), siADAR1 #2 (119581). All siRNAs were transfected using Lipofectamine RNAimax (Thermo Fisher).

tag: cell type

value: thyroid cancer cells

value: ADAR1 #2 siRNA


title: blastoid 60h TROP2 pl-154816


title: Endometrium_PS_9

value: PS


title: Cal62 siADAR1 #1

value: ADAR1 #1 siRNA


title: NAFT18012_P1A1_D14_49_S18


title: blastoid 60h TROP2 pl-154815


title: blastoid 60h TROP2 pl-154809


title: blastoid 60h TROP2 pl-154814


title: Endometrium_RR_11


title: Cal62 siControl

value: Control siRNA


title: blastoid 60h TROP2 pl-154813


title: Endometrium_PS_99


title: blastoid 60h TROP2 pl-154806


title: blastoid 60h TROP2 pl-154811


title: Endometrium_RR_10


title: NAFT18012_P1A3_D14_51_S1


title: blastoid 60h TROP2 pl-154808


title: blastoid 60h TROP2 pl-154807


title: NAFT18012_P1A2_D14_50_S21


title: blastoid 60h TROP2 pl-154810


title: Endometrium_PS_97


title: blastoid 60h TROP2 pl-154804


title: CML_cDC1.5

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

department: Department of Immunology

country: Japan

institute: Yokohama City University

data_processing:
The RNA-seq reads were aligned to a human reference genome (hg38/GRCh38) using TopHat software.
Duplicate reads were removed by using Picard tools (http://broadinstitute.github.io/picard).
FPKMs were calculated using Cufflinks.
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: TEXT file includes FPKM values for all samples

source_name: Peripheral blood cells

extract_protocol:
Total RNA was prepared using an RNeasy Micro Kit (QIAGEN) from approximately 3,000 to 10,000 cells according to the manufactures' instructions.
cDNA was synthesized and amplified using a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). Amplified cDNA was purified using Ampure XP beads (Beckman Coulter) to remove primer dimers. RNA-seq libraries were prepared using a Nextera XT Kit (Illumina). The prepared libraries were sequenced on a NextSeq 500 (Illumina) to generate single-end 75 nucleotide reads.

value: Type 1 conventional dendritic cells

tag: human state

value: CML patients

tag: cell isolation

value: Primary isolated cells

value: Peripheral blood

tag: sorting methods

value: MACS selection followed by FACS sorting

tag: surface markers

value: CD3e− CD19− CD303− CD1c− CD141+


title: blastoid 60h TROP2 pl-154805


title: blastoid 60h TROP2 pl-154812


title: CML_cDC1.2


title: blastoid 60h TROP2 pl-154799


title: CML_cDC1.1


title: blastoid 60h TROP2 pl-154796


title: blastoid 60h TROP2 pl-154801


title: blastoid 60h TROP2 pl-154803


title: Endometrium_PS_96


title: Endometrium_PS_95


title: Healthy_cDC1.5

value: Healthy donors


title: CML_cDC1.4


title: blastoid 60h TROP2 pl-154802


title: Endometrium_PS_98


title: CML_cDC1.3


title: blastoid 60h TROP2 pl-154800


title: blastoid 60h TROP2 pl-154798


title: blastoid 60h TROP2 pl-154797


title: Endometrium_PS_92


title: Healthy_cDC1.4


title: Endometrium_PS_94


title: Endometrium_PS_93


title: blastoid 60h TROP2 pl-154792


title: blastoid 60h TROP2 pl-154791


title: blastoid 60h TROP2 pl-154795


title: blastoid 60h TROP2 pl-154793


title: Healthy_cDC1.2


title: blastoid 60h TROP2 pl-154794


title: blastoid 60h TROP2 pl-154790


title: blastoid 60h TROP2 pl-154788


title: Healthy_cDC1.1


title: blastoid 60h TROP2 pl-154789


title: blastoid 60h TROP2 pl-154786


title: blastoid 60h TROP2 pl-154785


title: Endometrium_PS_91


title: CML_Baso.5

value: Basophils

value: FACS sorting


title: Endometrium_PS_90

value: Endometrium

value: female


title: Endometrium_PS_89


title: CML_Baso.4


title: blastoid 60h TROP2 pl-154784


title: blastoid 60h TROP2 pl-154787


title: blastoid 60h TROP2 pl-154783


title: Endometrium_PS_88


title: blastoid 60h TROP2 pl-154782


title: Healthy_cDC1.3


title: CML_Baso.3


title: blastoid 60h TROP2 pl-154781


title: CML_Baso.2


title: blastoid 60h TROP2 pl-154780


title: Endometrium_PS_8


title: blastoid 60h TROP2 pl-154779


title: blastoid 60h TROP2 pl-154778


title: blastoid 60h TROP2 pl-154777


title: CML_Baso.1


title: Endometrium_PS_85


title: Endometrium_PS_86


title: Endometrium_PS_87


title: blastoid 60h TROP2 pl-154776


title: blastoid 60h TROP2 pl-154774


title: Healthy_Baso.5


title: blastoid 60h TROP2 pl-154775


title: blastoid 60h TROP2 pl-154773


title: Healthy_Baso.3


title: blastoid 60h TROP2 pl-154771


title: Healthy_Baso.4


title: blastoid 60h TROP2 pl-154772


title: blastoid 60h TROP2 pl-154770


title: Endometrium_PS_83


title: Endometrium_PS_82


title: Endometrium_PS_84


title: blastoid 60h TROP2 pl-154769


title: Healthy_Baso.2


title: blastoid 60h TROP2 pl-154768


title: Healthy_Baso.1


title: CML_Mo.5

value: Monocytes


title: CML_Mo.4


title: Endometrium_PS_81


title: blastoid 60h TROP2 pl-154765


title: CML_Mo.3


title: blastoid 60h TROP2 pl-154762


title: blastoid 60h TROP2 pl-154764


title: blastoid 60h TROP2 pl-154763


title: Endometrium_PS_79


title: Endometrium_PS_7


title: CML_Mo.2


title: blastoid 60h TROP2 pl-154759


title: blastoid 60h TROP2 pl-154758


title: Endometrium_PS_76


title: blastoid 60h TROP2 pl-154760


title: blastoid 60h TROP2 pl-154755


title: blastoid 60h TROP2 pl-154754


title: blastoid 60h TROP2 pl-154766


title: Healthy_Mo.5


title: Endometrium_PS_80


title: blastoid 60h TROP2 pl-154761


title: Endometrium_PS_74


title: blastoid 60h TROP2 pl-154757


title: Endometrium_PS_78


title: blastoid 60h TROP2 pl-154767


title: blastoid 60h TROP2 pl-154752


title: Endometrium_PS_77


title: blastoid 60h TROP2 pl-154753


title: blastoid 60h TROP2 pl-154750


title: CML_Mo.1


title: Endometrium_PS_72


title: blastoid 60h TROP2 pl-154748


title: Healthy_Mo.3


title: blastoid 60h TROP2 pl-154756


title: Endometrium_PS_71


title: Endometrium_PS_75


title: Healthy_Mo.4


title: Endometrium_PS_73


title: blastoid 60h TROP2 pl-154751


title: Healthy_Mo.2


title: blastoid 60h TROP2 pl-154745


title: CML_Neu.4

value: Neutrophils


title: blastoid 60h TROP2 pl-154744


title: Endometrium_PS_6


title: blastoid 60h TROP2 pl-154747


title: blastoid 60h TROP2 pl-154749


title: Healthy_Mo.1


title: CML_Neu.5


title: CML_Neu.2


title: blastoid 60h TROP2 pl-154746


title: blastoid 60h TROP2 pl-154739


title: Endometrium_PS_68


title: blastoid 60h TROP2 pl-154740


title: blastoid 60h TROP2 pl-154737


title: Endometrium_PS_70


title: blastoid 60h TROP2 pl-154741


title: blastoid 60h TROP2 pl-154743


title: blastoid 60h TROP2 pl-154735


title: blastoid 60h TROP2 pl-154738


title: Endometrium_PS_66


title: blastoid 60h TROP2 pl-154742


title: blastoid 60h TROP2 pl-154732


title: Endometrium_PS_69


title: Healthy_Neu.3


title: blastoid 60h TROP2 pl-154736


title: Endometrium_PS_67


title: Healthy_Neu.5


title: Endometrium_PS_64


title: CML_Neu.1


title: blastoid 60h TROP2 pl-154734


title: blastoid 60h TROP2 pl-154733


title: blastoid 60h TROP2 pl-154728


title: Healthy_Neu.4


title: blastoid 60h TROP2 pl-154729


title: Endometrium_PS_63


title: CML_Neu.3


title: blastoid 60h TROP2 pl-154731


title: Healthy_Neu.2


title: Endometrium_PS_65


title: Healthy_Neu.1


title: blastoid 60h TROP2 pl-154724


title: Endometrium_PS_61


title: Kuramochi Input for CTCF

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

library_source: genomic

data_processing:
Sample(s) were aligned to the hg19 revision of the human reference genome using bowtie with configuration -p 4 --best -k 2 -m 2 --sam and -l set to the read length
Reads were counted in 50bp bins using MACS 1.4 with parameters -w -S --space=50 --nomodel --shiftsize=200
Genome_build: hg19
Supplementary_files_format_and_content: WIG files(s) represent counts of aligned reads within 50 bp bins with each read being extended 200 in the direction of alignment. Counts are in reads-per-million and floored at 0.1

molecule: genomic DNA

source_name: Ovarian cancer cell line

growth_protocol: Kuramochi, RPMI, 100 million cells per ChIP

extract_protocol:
CTCF ChIP-Seq was performed as previously described (Schmidt et al., Methods, 2009) using 25 μg chromatin sheared to 100-300 bp fragments using a Covaris E220 evolution Focused Ultrasonicator. ChIP libraries were constructed using the Kapa Hyper Library Preparation kit, quantified and sequenced on an Illumina NextSeq 500 sequencer.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.

value: Ovarian cancer cell line

value: Kuramochi

tag: chip antibody

tag: antibody manu.

tag: antibody catalog

tag: antibody lot


title: Kuramochi CTCF_2

extract_protocol:
CTCF ChIP-Seq was performed as previously described (Schmidt et al., Methods, 2009) using 25 μg chromatin and 5 μg anti-CTCF antibody (Active Motif, catalogue number 61311) and chromatin sheared to 100-300 bp fragments using a Covaris E220 evolution Focused Ultrasonicator. ChIP libraries were constructed using the Kapa Hyper Library Preparation kit, quantified and sequenced on an Illumina NextSeq 500 sequencer.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.

value: CTCF

value: Active Motif


title: Endometrium_PS_62

value: PS


title: blastoid 60h TROP2 pl-154723

tag: treatment


title: blastoid 60h TROP2 pl-154730


title: blastoid 60h TROP2 pl-154722


title: blastoid 60h TROP2 pl-154721


title: blastoid 60h TROP2 pl-154720


title: blastoid 60h TROP2 pl-154718


title: blastoid 60h TROP2 pl-154719


title: blastoid 60h TROP2 pl-154727


title: blastoid 60h TROP2 pl-154725


title: IK_OvCa_input_8

source_name: Ovary tissue

growth_protocol: Human tumor sample

extract_protocol:
Chromatin was extracted from human tumors. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies. Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 500 bp were immunoprecipitated using different antibodies.

value: Primary high-grade serous ovarian cancer


title: blastoid 24h-154717

value: PALLY


title: Endometrium_PS_60

tag: tissue


title: blastoid 24h-154716


title: blastoid 24h-154714


title: IK_OvCa_input_7


title: Kuramochi CTCF_1

tag: cell line


title: blastoid 60h TROP2 pl-154726


title: blastoid 24h-154713


title: IK_OvCa_input_6


title: Endometrium_PS_59

tag: gender


title: Endometrium_PS_5


title: Endometrium_PS_58


title: Endometrium_PS_57


title: Endometrium_PS_55


title: IK_OvCa_input_5


title: blastoid 24h-154712


title: blastoid 24h-154711


title: blastoid 24h-154710


title: blastoid 24h-154715


title: blastoid 24h-154707


title: blastoid 24h-154706


title: Endometrium_PS_54


title: Endometrium_PS_56


title: Endometrium_PS_53


title: blastoid 24h-154705


title: Endometrium_PS_52


title: blastoid 24h-154704


title: IK_OvCa_input_1


title: IK_OvCa_input_3


title: IK_OvCa_H3K27ac_8

growth_protocol: Human tumor sample.

value: Diagenode


title: Endometrium_PS_51


title: IK_OvCa_input_2


title: blastoid 24h-154702


title: IK_OvCa_input_4


title: blastoid 24h-154703


title: IK_OvCa_H3K27ac_7


title: Endometrium_PS_50


title: blastoid 24h-154709


title: blastoid 24h-154698


title: Endometrium_PS_4


title: blastoid 24h-154701


title: blastoid 24h-154697


title: blastoid 24h-154699


title: IK_OvCa_H3K27ac_6


title: blastoid 24h-154695


title: blastoid 24h-154696


title: Endometrium_PS_47


title: Endometrium_PS_49


title: IK_OvCa_H3K27ac_4


title: Endometrium_PS_48


title: blastoid 24h-154708


title: blastoid 24h-154694


title: blastoid 24h-154700


title: IK_OvCa_H3K27ac_2


title: blastoid 24h-154692


title: blastoid 24h-154689


title: IK_OvCa_H3K27ac_3


title: blastoid 24h-154690


title: Endometrium_PS_46


title: blastoid 24h-154691


title: blastoid 24h-154687


title: blastoid 24h-154693


title: blastoid 24h-154686


title: MCF7b (RJ4-5b) BR3

city: Nashville

first: Rachelle

last: Johnson

address: 2215B Garland Ave

institute: Vanderbilt University Medical Center

description:
15-RJ4-5b-PBS-1hr-BR3
biological replicate 3

data_processing:
Sequenced reads were mapped to hg38 genome by STAR (2.5.2a)
Mapped reads were assigned to Ensembl genes (v86) by HTSeq-Count with option -q -m intersection-nonempty -s no -i gene_id
Differential expression analaysis was performed by MultiRankSeq which was described in Guo Y, Zhao S, Ye F, Sheng Q, Shyr Y. MultiRankSeq: multiperspective approach for RNAseq differential expression analysis and quality control. Biomed Res Int. 2014;2014:248090. doi: 10.1155/2014/248090.
Genome_build: hg38
[MultiRankSeq_131415_vs_789.diff.txt]   Contains all of the analyses for these data. The processed data file provides relative gene expression values for DESeq, edgeR, and baySeq with adjusted p-values and Rank. The gene expression values provided indicate the fold change in gene expression in MCF7b cells relative to the MCF7NSC control cells.
[read_count_table_RJ45b_samples.txt]  Contains raw counts for all samples.

source_name: Human MCF7 breast cancer cells

extract_protocol:
Cells were harvested in TRIzol and extracted per the manufacturer's instructions using phenol/chloroform.
The library was generated for Illumina High Throughput Sequencing at the Stanford Functional Genomics Facility using their standard protocols and procedures.

treatment_protocol: The cells were grown in DMEM+10%FBS with no additional treatments. 16 hours prior to collection the cells were switched to DMEM+2%FBS and treated for 1hr prior to collection with 15-30ul PBS in DMEM+2%FBS.

tag: phenotype

value: bone-metastatic variant (MCF7b)


title: Endometrium_PS_45


title: blastoid 24h-154688


title: IK_OvCa_H3K27ac_5


title: blastoid 24h-154685


title: blastoid 24h-154684


title: Endometrium_PS_43


title: IK_OvCa_H3K27ac_1


title: Endometrium_PS_44


title: blastoid 24h-154683


title: MCF7b (RJ4-5b) BR1

description:
13-RJ4-5b-PBS-1hr-BR1
biological replicate 1


title: blastoid 24h-154682


title: MCF7NSC BR2

description:
8-MCF7NSC-PBS-1hr-BR2
biological replicate 2

value: control


title: MCF7b (RJ4-5b) BR2

description:
14-RJ4-5b-PBS-1hr-BR2
biological replicate 2


title: Endometrium_PS_41


title: MCF7NSC BR1

description:
7-MCF7NSC-PBS-1hr-BR1
biological replicate 1


title: blastoid 24h-154681


title: blastoid 24h-154679


title: Endometrium_PS_42


title: iPS microglia Hyb87_rep 3

city: FUJISAWA

first: Yuumi

last: Okuzono

state: KANAGAWA

address: 26-Muraoka-higashi 2-chome

institute: Takeda Pharmaceutical Company Limited

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.10.1).
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence, then mapped to hg19_AmpliSeq_Transcriptome_21K_v1 using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.10.1.2).
Count data were calculated using software provided with the Ion Torrent Proton sequencer (AmpliSeqRNA v5.10.1.2).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (read count) for each sample.

source_name: iPS microglia treated with Hyb87

growth_protocol: Human iPSCs were cultured on laminin-coated plates in StemFit containing penicillin and streptomycin. The cells were passaged every 6 to 7 days using 0.5 mM EDTA, seeded at the density of 2 × 104 cells/well on a 6-well plate, and maintained in the presence of 10 μM Y-27632. The culture media was replaced with StemFit containing penicillin and streptomycin in the absence of Y-27632 24 h after passaging.  iPSC-derived hematopoietic progenitors (iHPCs) were generated using defined conditions with several modifications to previously published protocols. Briefly, 0.5 to 1 × 105 cells were plated per well in a tissue culture-treated 6-well plate (day 0). The cells were cultured in 2 mL StemFit containing Y-27632 for 24 h under normoxic conditions.  Day 1: Media was changed to basal medium supplemented with 50 ng/mL FGF2, 50 ng/mL BMP4, 12.5 ng/mL activin-A, 10 μM Y-27632, and 2 mM LiCl. The cells were then placed under hypoxic cell culture conditions of 5% O2 and 5% CO2 for 2 days.  Day 3: The cells were further maintained in basal media supplemented with 50 ng/mL each of FGF2 and VEGF under hypoxic conditions.  Day 5: Media was changed to basal media containing 50 ng/mL FGF2, 50 ng/mL VEGF, 50 ng/mL TPO, 10 ng/mL SCF, 50 ng/mL IL-6, and 10 ng/mL IL-3. The cells were placed under normoxic conditions.  Day 7 and day 9: Medium was changed to that used on day 5.  iMGs were differentiated from iPSCs via embryoid bodies and HPCs using defined conditions with several modifications to a previously published protocol.   Day 11: iHPCs was washed using iMG basal differentiation medium. After centrifugation, the iHPCs were gently suspended in iMG complete differentiation medium containing 25 ng/mL M-CSF, 100 ng/mL IL-34, and 50 ng/mL TGF-β and seeded at the density of 2 × 105 cells per well on 6-well plates. One milliliter iMG complete differentiation medium was supplemented after every 2 days.  Day 23 and day 37: The cells were collected as iMGs and seeded in a 1:1 mixture of conditioned medium and iMG complete differentiation medium [34]. Cells were supplemented with 1 mL iMG complete differentiation medium after every two days.

extract_protocol:
Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy, QIAGEN)
10 ng of total RNA was reverse-transcribed using the SuperScript VILO cDNA Synthesis Kit (Thermo Fisher Scientific) followed by library generation using the Ion AmpliSeq Transcriptome Human Gene Expression Kit. Libraries were diluted to 45 pM and pooled equally, with 9-10 individual samples per pool.

treatment_protocol: iMGs were collected on day 39 and seeded on a 24-well non-tissue culture treated plate coated with 10 μg/mL Hyb87 or control mouse IgG

tag: sample type

value: iPS microglia


title: Endometrium_PS_40


title: blastoid 24h-154678


title: blastoid 24h-154673


title: Endometrium_PS_38


title: blastoid 24h-154672


title: blastoid 24h-154680


title: blastoid 24h-154676


title: blastoid 24h-154671


title: blastoid 24h-154670


title: blastoid 24h-154677


title: MCF7NSC BR3

description:
9-MCF7NSC-PBS-1hr-BR3
biological replicate 3


title: blastoid 24h-154668


title: Endometrium_PS_36


title: blastoid 24h-154674


title: iPS microglia control IgG_rep 2

source_name: iPS microglia treated with control IgG

value: Control IgG


title: iPS microglia Hyb87_rep 1


title: blastoid 24h-154675


title: Endometrium_PS_39


title: Endometrium_PS_37


title: iPS microglia Hyb87_rep 2


title: iPS microglia control IgG_rep 3


title: iPS microglia control IgG_rep 1


title: Endometrium_PS_3


title: blastoid 24h-154666


title: blastoid 24h-154667


title: iPS microglia PBS_rep 2

source_name: iPS microglia treated with PBS

value: PBS


title: blastoid 24h-154665


title: Endometrium_PS_34

value: Endometrium


title: Endometrium_PS_32

value: female


title: Endometrium_PS_33


title: blastoid 24h-154660


title: Endometrium_PS_35


title: iPS microglia PBS_rep 3


title: blastoid 24h-154664


title: blastoid 24h-154662


title: blastoid 24h-154658


title: Endometrium_PS_31


title: blastoid 24h-154656


title: blastoid 24h-154655


title: CM-4

city: Duarte

first: wei

last: chen

state: CA

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

data_processing:
Base calling was done using Illumina RTA and bcl2fastq v2.18.0.12
Sequences were aligned to mm10 using Tophat2 with default settings
Gene expression level of Ensembl GRCm38 coding genes were quantified using HTSeq v0.6.1p1
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text file gene expression counts

organism: Mus musculus

source_name: bone morrow

extract_protocol:
Library contruction was used KAPA RNA HyperPrep Kit with RiboErase (HMR) according to manufacturer's protocol.
Depletion of ribosomal RNA (rRNA) and the rapid construction of stranded RNA-Seq libraries

value: LSK from mice bone morrow cells

tag: genotype/variation

value: CM

value: poly(I;C)

value: pre-leukemic [6 weeks after poly(I;C) induction]

tag: molecule concentration


title: CM-5

tag: cell type

tag: Stage


title: Endometrium_PS_30


title: blastoid 24h-154657


title: blastoid 24h-154659


title: blastoid 24h-154669


title: blastoid 24h-154653


title: blastoid 24h-154654


title: blastoid 24h-154652


title: CM-3


title: Endometrium_PS_2


title: blastoid 24h-154663


title: Endometrium_PS_28


title: CM-1


title: Endometrium_PS_29


title: blastoid 24h-154661


title: CM-2


title: blastoid 24h-154649


title: Endometrium_PS_27


title: blastoid 24h-154648


title: CM/miR-126Δ/Δ-5


title: blastoid 24h-154647


title: blastoid 24h-154646


title: blastoid 24h-154645


title: blastoid 24h-154642


title: CM/miR-126Δ/Δ-3


title: blastoid 24h-154644


title: blastoid 24h-154651


title: blastoid 24h-154643


title: blastoid 24h-154650


title: Endometrium_PS_25


title: Endometrium_PS_24


title: Endometrium_PS_23


title: iPS microglia PBS_rep 1


title: blastoid 24h-154641


title: blastoid 24h-154640


title: blastoid 24h-154639


title: blastoid 24h-154637


title: Endometrium_PS_26


title: blastoid 24h-154636


title: CM/miR-126Δ/Δ-1


title: Endometrium_PS_22


title: TRIM28_Control_Input

city: Hangzhou

first: Hua

last: Yu

address: No.18 Shilongshan Road

country: China

institute: Westlake University

data_processing:
Basecalls performed using CASAVA version 1.8
All bulk RNA-seq reads were trimmed using Trimmomatic software with the following parameters “ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36” (Version 0.36). and were further quality-filtered using FASTX Toolkit’s fastq_quality_trimmer command (Version 0.0.13, http://hannonlab.cshl.edu/fastx_toolkit/) with the minimum quality score 20 and minimum percent of 80% bases that has a quality score larger than this cutoff value.
The ChIP-seq reads were aligned to mm10 with the options: -t -q -N 1 -L 25. All unmapped reads and PCR duplicates were removed.
The bamCoverage and bamCompare commands contained in deepTools (version 2.5.3) were adopted for downstream analysis. Using BamCoverage command with the parameters: -normalizeUsing BPM -of bigwig -binSize 100, we first normalized the raw reads signal to Bins Per Million mapped reads (BPM) signal and converted the alignment bam files to bigwig signal files. The bigwig files were imported into UCSC genome browser for visualization. To minimize the effect of chromatin structure and sequencing bias in our H3K9me3 ChIP-seq data, we corrected ChIP-seq signal using log2 ratio transformation between H3K9me3 signal and input signal by BamCompare command.
The “computeMatrix” and “plotProfile” commands of deepTools were used to produce the reads density distribution plot of ATAC-seq and ChIP-seq signal in the given genomic region.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using deepTools

source_name: ES cells

growth_protocol: Mouse ES cells were cultured on 0.1% gelatin-coated plates with MEF feeder cells in LIF/2i media for 2 days.

extract_protocol:
2x10^6 cells were cross-linked for 10 min with 1% final concentration fresh formaldehyde and quenched by 0.2M glycine for 5 min. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to VAHTS Universal DNA Library Prep Kit for Illumina V3 Kit (vazyme, ND607-01). Briefly, input DNA was phosphorylated at 5’ ends and dATP to yield a protruding 3-'A' base. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were purified by using DNA Clean Beads. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: ES cells


title: blastoid 24h-154635


title: CM/miR-126Δ/Δ-4


title: Endometrium_PS_21


title: Endometrium_PS_20


title: Endometrium_PS_1


title: blastoid 24h-154634


title: CM/miR-126Δ/Δ-2


title: blastoid 24h-154638


title: blastoid 24h-154633


title: TRIM28_CX-5461

value: TRIM28 (abcam, ab8899)


title: blastoid 24h-154632


title: Endometrium_PS_19

value: PS


title: blastoid 24h-154631


title: NCL_CX-5461

value: NCL (abcam, ab8899)


title: blastoid 24h-154630

value: PALLY


title: blastoid 24h-154629


title: Endometrium_PS_18


title: NCL_Control

value: NCL (abcam, ab8898)


title: blastoid 24h-154627


title: blastoid 24h-154626


title: blastoid 24h-154624


title: Mettl3 KO m6A enriched RNA: rep4

city: Columbus

first: Kalpana

last: Ghoshal

state: Ohio

address: 1645 Neil Ave

department: Pathology

institute: The Ohio State University

data_processing:
HISAT2 (version2.1)
Samtools (Version1.4)
Bedtools
Genome_build: mm10

source_name: liver

extract_protocol:
Trizol Reagent
Takara SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (634878; Takara)

tag: strain

tag: ip antibody

value: N6-Methyladenosine Antibody (NEB cat#:E1610S)

tag: genotype

value: Mettl3 -/-


title: Endometrium_PS_17


title: Mettl3 KO m6A enriched RNA: rep3


title: blastoid 24h-154625


title: blastoid 24h-154623


title: Endometrium_PS_170


title: blastoid 24h-154622


title: Mettl3 KO m6A enriched RNA: rep2


title: TRIM28_Control

tag: chip antibody

value: TRIM28 (abcam, ab8898)


title: blastoid 24h-154620


title: Mettl3 KO m6A enriched RNA: rep1


title: blastoid 24h-154619


title: Endometrium_PS_169


title: blastoid 24h-154618


title: blastoid 24h-154628


title: TRIM28_CX-5461_Input


title: Endometrium_PS_168


title: blastoid 24h-154616


title: Endometrium_PS_167


title: blastoid 24h-154617


title: WT liver m6A enriched RNA: rep4

value: WT


title: WT liver m6A enriched RNA: rep3


title: blastoid 24h-154615


title: blastoid 24h-154614


title: Endometrium_PS_165


title: Endometrium_PS_166


title: WT liver m6A enriched RNA: rep2


title: blastoid 24h-154621


title: Endometrium_PS_16


title: WT liver m6A enriched RNA: rep1


title: blastoid 24h-154613


title: blastoid 24h-154612


title: Endometrium_PS_164


title: blastoid 24h-154610


title: Endometrium_PS_163


title: Mettl3 KO  liver m6A iinput RNA: rep4


title: blastoid 24h-154607


title: blastoid 24h-154609


title: Mettl3 KO  liver m6A iinput RNA: rep3


title: Endometrium_PS_162


title: blastoid 24h-154608


title: blastoid 24h-154606


title: Mettl3 KO  liver m6A iinput RNA: rep2


title: blastoid 24h-154602


title: blastoid 24h-154604


title: blastoid 24h-154603


title: Endometrium_PS_161


title: blastoid 24h-154601


title: Endometrium_PS_160


title: blastoid 24h-154611


title: WT liver m6A input RNA: rep4


title: WT liver m6A input RNA: rep3


title: blastoid 24h-154600


title: blastoid 24h-154598


title: Endometrium_PS_15


title: blastoid 24h-154599


title: WT liver m6A input RNA: rep2


title: blastoid 24h-154594


title: WT liver m6A input RNA: rep1


title: Endometrium_PS_158


title: Brd4-CUT&Tag in naïve CD8+T cells_rep2

city: 广州

first: Peng

middle: zhi

last: lin

address: 74 Zhongshan 2 Rd

department: zhongshan school of medicine

institute: Sun-Yat sen university

description: BRD4Control_CD8_CutTag_BRD4_20210117_B1T2

data_processing:
library strategy:CUT&Tag-seq
Raw sequencing data were trimmed and filtered by using Trim Galore.
The paired-end reads with high quality (Q30) were aligned to the mouse reference genome mm10 using the Burrows Wheeler Aligner with default parameters and then sorted using the SAMtools software.
The “MarkDuplicates” function embedded in Picard was used to mark and discard PCR duplicates.
For comparison between different samples, mapped reads were down-sampled to equalize reads across samples by using Samtools. MACS2 was used to quantify the Brd4 CUT&Tag signal throughout the genome and within gene bodies
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Naïve CD8+T cells

extract_protocol: Fifty-thousand isolated CD8+ T cells were used to generate CUT&Tag library as a reference[31]. First, CD8+ T cell was incubated with primary antibody against Brd4 (1:50; Active motif AB_2615059) and then with guinea pig anti-rabbit secondary antibody (1:100; Antibodies Online ABIN101961). This was followed by adding the prepared pA-Tn5 complex. Next, DNA was fragmented by Mg2+ activator and the resulting DNA segments were extracted to amplify with PCR. Finally, PCR products were cleaned up and sequenced. Paired-end 150-bp sequencing was performed on an Illumina HiSeq 2500. Each DNA library for CUT&Tag was sequenced with HiSeq 2500 system (Illumina, USA) under the paired-end 150 bp mode. For data processing, raw sequencing data were trimmed and filtered by using Trim Galore. The paired-end reads with high quality (Q30) were aligned to the mouse reference genome mm10 using the Burrows Wheeler Aligner with default parameters and then sorted using the SAMtools software. The “MarkDuplicates” function embedded in Picard was used to mark and discard PCR duplicates. For comparison between different samples, mapped reads were down-sampled to equalize reads across samples by using Samtools. MACS2 was used to quantify the Brd4 CUT&Tag signal throughout the genome and within gene bodies.

value: Spleen-derived naive CD8+T cells

value: Brd4 (Active motif, AB_2615059, Catalog No 39910)

value: untreated


title: blastoid 24h-154595


title: Mettl3 KO  liver m6A iinput RNA: rep1


title: blastoid 24h-154592


title: blastoid 24h-154591


title: Endometrium_PS_156

value: Endometrium

value: female


title: blastoid 96h DN-154588


title: Endometrium_PS_157


title: blastoid 96h DN-154589


title: Endometrium_PS_155


title: Brd4-CUT&Tag in naïve CD8+T cells_rep1

description: BRD4Control_CD8_CutTag_BRD4_20210117_B1T1


title: blastoid 96h DN-154585


title: S3-1

city: Salt Lake City

first: Camille

last: Fung

state: UT

address: 295 Chipeta Way

department: Pediatric Neonatology

institute: University of Utah

description:
11441X10
11441X10_150409_D00550_0245_AC6V3CANXX_5

data_processing:
Fastq reads were aligned to the genome plus known transcript splices using Novocraft novoalign (version 2.8), allowing for up to 100 multiple hits. Transcript splices were generated using USeq MakeTranscriptome (version 8.8.8) with a radius of 46 bp, maximum number of splice junctions of 100K, and the UCSC mm10 EnsGene annotation.
Alignments to splice junctions were converted back to genomic coordinates with USeq SamTranscriptomeParser (version 8.8.8), allowing for one alignment per read, and saved as Bam files.
Coverage files were generated with USeq Sam2USeq and USeq2UCSC applications (version 8.8.8).
Alignment counts over annotation and differential expression was performed with USeq DefinedRegionDifferentialSeq application (version 8.8.8).
Genome_build: mm10
Supplementary_files_format_and_content: Raw alignment counts for genes are included as a tab-delimited text file. Genes with less than 10 counts and more than 50000 counts were excluded. Sequence coverage, normalized as Reads Per Million, are included as bigWig files.

source_name: e15.5 mouse hippocampus_sham

extract_protocol:
We dissected e15.5 sham and IUGR hippocampi from mouse brains. Total RNA was extracted, followed by verification of RNA quality and quantity by Agilent ScreenTape Assay at the University of Utah High-Throughput Genomics core facility. RNA samples with RIN values above 8 were used for library construction.
RNA sequencing library was made using Illumina TruSeq Stranded Total RNA Sample Prep K with Ribo-Zero Gold. RNA was chemically fragmented and random primed for reverse transcription to construct libraries. The average insert sizes of libraries was ~150bp with inserts ranging from 100-400bp.
Once libraries were made and validated, sequencing adapters were added and sequenced as single-reads using the HiSeq 2500 platform.

treatment_protocol: IUGR was induced by making pregnant mouse dams have hypertension via the implantation of a micro-osmotic pump containing U-46619 (thromboxane A2-analog) from e12.5. Sham surgery consisted of a vehicle-loaded micro-osmotic pump implantation at same gestational age.

tag: strain background

tag: developmental stage

value: Sham

value: hippocampus


title: blastoid 96h DN-154584


title: Endometrium_PS_159


title: blastoid 24h-154596


title: blastoid 24h-154597


title: blastoid 96h DN-154583


title: Endometrium_PS_154


title: blastoid 96h DN-154582


title: S3-4

description:
11441X14
11441X14_150409_D00550_0245_AC6V3CANXX_5


title: Endometrium_PS_152


title: blastoid 96h DN-154581


title: blastoid 24h-154593


title: S1-6

description:
11441X9
11441X9_150409_D00550_0245_AC6V3CANXX_5


title: blastoid 96h DN-154580


title: Endometrium_PS_151


title: blastoid 96h DN-154579


title: T1-4

description:
11441X6
11441X6_150409_D00550_0245_AC6V3CANXX_5

source_name: e15.5 mouse hippocampus_IUGR

value: IUGR


title: Endometrium_PS_150


title: blastoid 96h DN-154577

source_name: blastoid


title: S1-4

description:
11441X11
11441X11_150409_D00550_0245_AC6V3CANXX_5


title: blastoid 96h DN-154576


title: blastoid 96h DN-154575


title: T1-1

description:
11441X1
11441X1_150409_D00550_0245_AC6V3CANXX_5


title: Endometrium_PS_149


title: blastoid 96h DN-154572


title: Endometrium_PS_14


title: blastoid 96h DN-154571


title: blastoid 96h DN-154570


title: T1-3

description:
11441X3
11441X3_150409_D00550_0245_AC6V3CANXX_5


title: T1-5

description:
11441X4
11441X4_150409_D00550_0245_AC6V3CANXX_5


title: Endometrium_PS_153


title: blastoid 96h DN-154573


title: blastoid 96h DN-154569


title: blastoid 96h DN-154568


title: Naïve Rep 4

city: London

first: Jean

last: Langhorne

address: 1 Midland Road

institute: Francis Crick Institute

data_processing:
Fastq files QC using Multi QC (Babraham Institute).
Transcript were aligned and counted to the Mus musculus reference genome GRCm38 v86 using STAR v2.5.2 and RSEM v1.3.0.
Libraries normalised for size through DESeq2 v1.26 in R v3.6.3.
Genome_build: GRCm38 v86
Supplementary_files_format_and_content: EKD11.normalised_counts_with_controls.txt contains normalised count data of RMT, SBP and Naïve samples.
Supplementary_files_format_and_content: 2021_EKD11.vst_counts_with_controls.txt contains log transformed count data of RMT, SBP and Naïve samples.

source_name: Splenic

growth_protocol: SBP - 10^5 infected RBC taken from frozen stock of serially passaged parasites. RMT infections performed using 10^5 infected RBC taken from a mosquito transmitted infection.

extract_protocol:
Splenic Material was extracted using the RiboPure™ RNA extraction kit (Invitrogen, ThermoFisher) according to the manufacturer’s instructions. The quantity and quality of the RNA samples were verified using NanoDrop 1000 Spectrophotometer (Thermo Fisher Scientific) and Bioanalyser.
RNA was used for cDNA library preparation using the KAPA RNA Hyperprep with Riboerase kit.
100bp PE reads to depth of 25 million reads per sample.

value: Splenic

tag: infection

value: Naive

tag: time point

value: Day 1


title: Endometrium_PS_148

tag: tissue

value: PS


title: blastoid 96h DN-154578

extract_protocol:
Smart-Seq2 protocol
Smart-Seq2

tag: treatment


title: Naïve Rep 3

tag: gender


title: blastoid 96h DN-154567


title: Endometrium_PS_147


title: Endometrium_PS_146


title: blastoid 96h DN-154566


title: blastoid 96h DN-154563


title: blastoid 96h DN-154565


title: Endometrium_PS_144


title: Endometrium_PS_145


title: blastoid 96h DN-154564


title: blastoid 96h DN-154561


title: Naïve Rep 2


title: blastoid 96h DN-154562


title: Recently Mosquito Transmission Infection Day 6 Rep 4

value: P. c. chabaudi AS

tag: condition

value: RMT

value: Day 6


title: Naïve Rep 1


title: blastoid 96h DN-154559


title: Recently Mosquito Transmission Infection Day 6 Rep 2


title: blastoid 96h DN-154555


title: blastoid 96h DN-154560


title: Recently Mosquito Transmission Infection Day 6 Rep 3


title: Endometrium_PS_143


title: blastoid 96h DN-154554


title: blastoid 96h DN-154558


title: blastoid 96h DN-154553


title: Endometrium_PS_142


title: Endometrium_PS_140


title: Endometrium_PS_141


title: Endometrium_PS_13


title: blastoid 96h DN-154552


title: blastoid 96h DN-154550


title: blastoid 96h DN-154551


title: Endometrium_PS_139


title: blastoid 96h DN-154549


title: blastoid 96h DN-154546


title: Recently Mosquito Transmission Infection Day 4 Rep 2

value: Day 4


title: blastoid 96h DN-154545


title: Recently Mosquito Transmission Infection Day 3 Rep 4

value: Day 3


title: blastoid 96h DN-154544


title: blastoid 96h DN-154543


title: Endometrium_PS_138


title: blastoid 96h DN-154541


title: Recently Mosquito Transmission Infection Day 3 Rep 3


title: Recently Mosquito Transmission Infection Day 3 Rep 2


title: Recently Mosquito Transmission Infection Day 6 Rep 1


title: Recently Mosquito Transmission Infection Day 4 Rep 4


title: blastoid 96h DN-154542


title: blastoid 96h DN-154540


title: blastoid 96h DN-154539


title: Recently Mosquito Transmission Infection Day 4 Rep 3


title: Recently Mosquito Transmission Infection Day 3 Rep 1


title: blastoid 96h DN-154547


title: blastoid 96h DN-154548


title: blastoid 96h DN-154536


title: Endometrium_PS_134


title: Endometrium_PS_135


title: blastoid 96h DN-154538


title: Endometrium_PS_133


title: Endometrium_PS_137


title: blastoid 96h DN-154537


title: Recently Mosquito Transmission Infection Day 2 Rep 4

value: Day 2


title: blastoid 96h DN-154535


title: Endometrium_PS_131


title: blastoid 96h DN-154532


title: blastoid 96h DN-154530


title: blastoid 96h DN-154529


title: Endometrium_PS_132


title: Recently Mosquito Transmission Infection Day 2 Rep 2


title: blastoid 96h DN-154534


title: Recently Mosquito Transmission Infection Day 2 Rep 3


title: blastoid 96h DN-154528


title: blastoid 96h DN-154526


title: Recently Mosquito Transmission Infection Day 2 Rep 1


title: Recently Mosquito Transmission Infection Day 1 Rep 4


title: Recently Mosquito Transmission Infection Day 1 Rep 2


title: Endometrium_PS_130


title: Endometrium_PS_128


title: blastoid 96h DN-154533


title: Endometrium_PS_12


title: Endometrium_PS_136


title: blastoid 96h DN-154527


title: blastoid 96h DN-154531


title: Endometrium_PS_129


title: Recently Mosquito Transmission Infection Day 1 Rep 3


title: blastoid 96h DN-154522


title: Recently Mosquito Transmission Infection Day 1 Rep 1


title: Serially Blood Passaged Infection Day 6 Rep 4

value: SBP


title: blastoid 96h DN-154523


title: blastoid 96h DN-154521


title: blastoid 96h DN-154519


title: Endometrium_PS_127


title: blastoid 96h DN-154524


title: Serially Blood Passaged Infection Day 6 Rep 3


title: Endometrium_PS_126


title: blastoid 96h DN-154520


title: blastoid 96h DN-154518


title: Endometrium_PS_125


title: blastoid 96h DN-154517


title: Serially Blood Passaged Infection Day 6 Rep 2


title: Serially Blood Passaged Infection Day 6 Rep 1


title: blastoid 96h DN-154513


title: blastoid 96h DN-154516


title: Endometrium_PS_123


title: Endometrium_PS_124


title: blastoid 96h PDGFRa pl-154509


title: Endometrium_PS_121


title: blastoid 96h DN-154515


title: blastoid 96h DN-154514


title: blastoid 96h PDGFRa pl-154507


title: blastoid 96h DN-154512


title: blastoid 96h DN-154511


title: Serially Blood Passaged Infection Day 3 Rep 4


title: blastoid 96h PDGFRa pl-154505


title: Serially Blood Passaged Infection Day 4 Rep 1


title: Serially Blood Passaged Infection Day 4 Rep 4


title: Endometrium_PS_122


title: blastoid 96h PDGFRa pl-154504


title: Endometrium_PS_11


title: blastoid 96h PDGFRa pl-154508


title: blastoid 96h DN-154510


title: Serially Blood Passaged Infection Day 4 Rep 3


title: blastoid 96h PDGFRa pl-154500


title: Endometrium_PS_120


title: Endometrium_PS_119


title: blastoid 96h PDGFRa pl-154506


title: Serially Blood Passaged Infection Day 3 Rep 3


title: Serially Blood Passaged Infection Day 3 Rep 1


title: blastoid 96h PDGFRa pl-154502


title: blastoid 96h PDGFRa pl-154503


title: Serially Blood Passaged Infection Day 3 Rep 2


title: blastoid 96h PDGFRa pl-154501


title: blastoid 96h PDGFRa pl-154498


title: Endometrium_PS_117


title: blastoid 96h PDGFRa pl-154499


title: Serially Blood Passaged Infection Day 2 Rep 3


title: Serially Blood Passaged Infection Day 2 Rep 2


title: blastoid 96h PDGFRa pl-154496


title: Serially Blood Passaged Infection Day 2 Rep 4


title: blastoid 96h PDGFRa pl-154495


title: blastoid 96h PDGFRa pl-154497


title: Serially Blood Passaged Infection Day 2 Rep 1


title: blastoid 96h PDGFRa pl-154493


title: Endometrium_PS_118


title: blastoid 96h PDGFRa pl-154494


title: Endometrium_PS_113


title: Endometrium_PS_114


title: Serially Blood Passaged Infection Day 1 Rep 4


title: blastoid 96h PDGFRa pl-154492


title: blastoid 96h PDGFRa pl-154491


title: blastoid 96h PDGFRa pl-154490


title: Endometrium_PS_115


title: Endometrium_PS_112


title: Endometrium_PS_116


title: blastoid 96h PDGFRa pl-154486


title: Serially Blood Passaged Infection Day 1 Rep 3


title: blastoid 96h PDGFRa pl-154488


title: Serially Blood Passaged Infection Day 1 Rep 2


title: blastoid 96h PDGFRa pl-154487


title: Endometrium_PS_111


title: Endometrium_PS_110


title: blastoid 96h PDGFRa pl-154485


title: blastoid 96h PDGFRa pl-154484


title: blastoid 96h PDGFRa pl-154483


title: blastoid 96h PDGFRa pl-154489


title: blastoid 96h PDGFRa pl-154482


title: Serially Blood Passaged Infection Day 1 Rep 1


title: CX-5461 ES

data_processing:
Basecalls performed using CASAVA version 1.8
Short sequencing reads were first independently mapped to mouse mm10 reference genome using the bowtie2 aligner with end-to-end algorithm and ‘-very-sensitive’ option. To rescue the chimaeric fragments spanning the ligation junction, the ligation site was detected and the 5’ fraction of the reads was aligned back to the reference genome. Unmapped reads, multiple mapped reads and singletons were then discarded. Pairs of aligned reads were then assigned to MboI restriction fragments. Read pairs from uncut DNA, self-circle ligation and PCR artefacts were filtered out and the valid read pairs involving two different restriction fragments were used to build the contact matrix. Valid read pairs were then binned at a 40kb and 150kb resolution by dividing the genome into bins of equal size.
The binned interaction matrices were then corrected using Knight–Ruiz matrix balancing method using HiCExplorer (https://hicexplorer.readthedocs.io/en/latest/) (Version 3.3) hicCorrectMatrix command with --correctionMethod KR option. The Observed/Expected (O/E) Hi-C matrix and Pearson Hi-C matrix was obtained by HiCExplorer hicTransform command with --method obs_exp_norm and --method pearson option, respectively.
Aggregate analyses of OE matrices at MERVL were performed in 40kb matrices in a 2mb window around the central region. Visualization of Hi-C matrix was carried out by R software.
Genome_build: mm10
Supplementary_files_format_and_content: text generated using HiC-Pro

extract_protocol:
10^6 cells were cross-linked for 10 min with 1% final concentration fresh formaldehyde and quenched by 0.2M glycine for 5 min. The cross-linked cells were subsequently lysed in lysis buffer. Extracted nuclei were re-suspended with 150 μl 0.1% SDS and incubated at 65°C for 10 min, then SDS were quenched by 120 μl water and 30 μl 10% Triton X-100, and incubated at 37 °C for 15 min.
Purified DNA was sheared to a length of ~400 bp. Point ligation junctions were pulled down by Dynabeads MyOne Streptavidin C1(Thermofisher) according to manufacturers` instructions. The Hi-C library for Illumina sequencing was prepared by NEBNext Ultra II DNA library Prep Kit for Illumina (NEB) according to manufacturers` instructions. The final library was sequenced on the Illumina HiSeq X Ten platform (San Diego, CA, United States) with 150PEmode. Two replicates were generated for one group material.

value: CX-5461 treated ES cells


title: Endometrium_PS_10

value: Endometrium


title: blastoid 96h PDGFRa pl-154480


title: Control ES

value: Control ES cells


title: blastoid 96h PDGFRa pl-154478


title: CX-5461_ES 4

data_processing:
Single-cell gene expression matrix was further analyzed with Seurat v2.3.4 (https://satijalab.org/seurat/).
We excluded the genes with expressed cell number smaller than 3 and the cells with nUMIs smaller than 500 or the expression percentages of mitochondrial genes larger than 0.2 and used 16 Principle Components (PCs) for tSNE analysis.
Genome_build: mm10
Supplementary_files_format_and_content: txt, gene expression level (Counts)

extract_protocol: We used 10X Single Cell 3' Solution Reagents V2 following the manufacturer’s protocol (10x Genomics)

value: ICM-derived ES cells


title: blastoid 96h PDGFRa pl-154477

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


title: Endometrium_PS_108

extract_protocol: Endometrial samples were snap-frozen in liquid nitrogen and stored at -80C. Total RNA was extracted using the TRIzol method according to the standard protocol (Life Technologies, Inc., Gaithersburg, MD). The RNA quality was assessed in the A2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany)

value: female


title: blastoid 96h PDGFRa pl-154479


title: CX-5461_ES 3


title: blastoid 96h PDGFRa pl-154473


title: Endometrium_PS_107


title: CX-5461_ES 2


title: Endometrium_PS_106


title: blastoid 96h PDGFRa pl-154475


title: Endometrium_PS_105


title: blastoid 96h PDGFRa pl-154474


title: blastoid 96h PDGFRa pl-154472


title: blastoid 96h PDGFRa pl-154471


title: Endometrium_PS_109


title: Endometrium_PS_104


title: Endometrium_PS_103


title: blastoid 96h PDGFRa pl-154481


title: Control_ES 4

value: untreated


title: blastoid 96h PDGFRa pl-154468


title: CX-5461_ES 1


title: blastoid 96h PDGFRa pl-154469


title: blastoid 96h PDGFRa pl-154476


title: Control_ES 3


title: blastoid 96h PDGFRa pl-154467


title: blastoid 96h PDGFRa pl-154470


title: Control_ES 2


title: blastoid 96h PDGFRa pl-154464


title: blastoid 96h PDGFRa pl-154463


title: Control_ES 1


title: blastoid 96h PDGFRa pl-154465


title: Endometrium_PS_101


title: Endometrium_PS_102


title: blastoid 96h DN-154461


title: blastoid 96h PDGFRa pl-154462


title: blastoid 96h DN-154460


title: Embryo CX-5461_2

data_processing:
Basecalls performed using CASAVA version 1.8
All bulk RNA-seq reads were trimmed using Trimmomatic software with the following parameters “ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36” (Version 0.36). and were further quality-filtered using FASTX Toolkit’s fastq_quality_trimmer command (Version 0.0.13, http://hannonlab.cshl.edu/fastx_toolkit/) with the minimum quality score 20 and minimum percent of 80% bases that has a quality score larger than this cutoff value.
The high-quality reads were mapped to the mm10 genome by HISAT2, a fast and sensitive spliced alignment program for mapping RNA-seq reads, with -dta paramenter. PCR duplicate reads were removed using Picard tools and only uniquely mapped reads were kept for further analysis.
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm10
Supplementary_files_format_and_content: xlsx, gene expression level (TPM)

source_name: Embryo

growth_protocol: Mouse ES cells  and iPS cells were cultured on 0.1% gelatin-coated plates with MEF feeder cells in LIF/2i media for 2 days.

extract_protocol:
Cells were dissociated with Trypsin for 5 min, stopped with serum containing media, and depleted with MEF for at least half-an-hour, and total RNA was extracted by TRIzon
A total amount of 2 μg RNA per sample was used as input materials for the RNA sample preparation. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Purified mRNA was fragmentated at 94 °C for 15 min by using divalent cations under elevated temperature in NEBNext first strand synthesis reaction buffer (5X). First strand cDNA was synthesized using random primer and ProtoScript II reverse transcriptase in a preheated thermal cycler as follows: 10 min at 25 °C; 15 min at 42 °C; 15 min at 70 °C. Immediately finished, second strand synthesis reaction was performed by using second strand synthesis reaction buffer (10X) and enzyme mix at 16 °C for 1 hr. The library fragments were purified with QiaQuick PCR kits and elution with EB buffer, then terminal repair, A-tailing and adapter added were implemented. The products were retrieved and PCR was performed for library enrichment. The libraries were sequenced on an Illumina platform.

treatment_protocol: ES cells was  treated with CX-5461


title: Embryo CX-5461_1


title: Endometrium_PF_8

source_name: endometrial biopsy

value: PF


title: blastoid 96h DN-154457


title: blastoid 96h DN-154456


title: Endometrium_PF_7


title: blastoid 96h DN-154458


title: Endometrium_PF_9


title: blastoid 96h DN-154455


title: blastoid 96h DN-154454


title: Embryo Control_1


title: Endometrium_PF_6


title: Endometrium_PF_5


title: Endometrium_PS_100


title: blastoid 96h DN-154453


title: blastoid 96h DN-154459


title: blastoid 96h DN-154451


title: blastoid 96h DN-154452


title: ES Rotenone_1

value: Rotenone


title: ES Rapamycin_1

value: Rapamycin


title: Endometrium_PF_4


title: blastoid 96h DN-154449


title: blastoid 96h DN-154447


title: blastoid 96h DN-154450


title: ES Rapamycin_2


title: Endometrium_PF_33


title: Embryo Control_2


title: Endometrium_PF_3


title: blastoid 96h DN-154446


title: blastoid 96h DN-154445


title: Endometrium_PF_32


title: ES CX-5461_2


title: ES Rotenone_2


title: blastoid 96h DN-154444


title: ES CX-5461_1


title: Endometrium_PF_31


title: blastoid 96h DN-154443


title: blastoid 96h DN-154442


title: Endometrium_PF_30


title: blastoid 96h DN-154441


title: Endometrium_PF_2


title: blastoid 96h DN-154440


title: blastoid 96h DN-154438


title: ES Control_2


title: ES Control_1


title: Endometrium_PF_29


title: blastoid 96h DN-154435


title: blastoid 96h DN-154433


title: blastoid 96h DN-154434


title: Endometrium_PF_27


title: Endometrium_PF_28


title: H3K9me3_H3K27me3_CX-5461_Input

value: ES cells


title: blastoid 96h DN-154431


title: H3K4me3_H3K27ac_CX-5461_Input


title: blastoid 96h DN-154430


title: H3K4me3_H3K27ac_Control_Input


title: Endometrium_PF_25


title: blastoid 96h DN-154428


title: H3K27ac_Control

value: H3K27ac (abcam, ab8898)


title: H3K9me3_H3K27me3_Control_Input


title: blastoid 96h DN-154439


title: H3K27ac_CX-5461

value: H3K27ac (abcam, ab8899)


title: blastoid 96h DN-154427


title: blastoid 96h DN-154437


title: Endometrium_PF_24


title: Endometrium_PF_26


title: blastoid 96h DN-154425


title: blastoid 96h DN-154436


title: blastoid 96h DN-154422


title: blastoid 96h DN-154423


title: blastoid 96h DN-154421


title: H3K4me3_CX-5461

value: H3K4me3 (abcam, ab8899)


title: blastoid 96h DN-154420


title: H3K27me3_Control

value: H3K27me3 (abcam, ab8898)


title: blastoid 96h DN-154432


title: blastoid 96h DN-154419


title: Endometrium_PF_22


title: H3K4me3_Control

value: H3K4me3 (abcam, ab8898)


title: blastoid 96h DN-154417


title: Endometrium_PF_20


title: blastoid 96h DN-154415


title: Endometrium_PF_21


title: H3K9me3_CX-5461

value: H3K9me3 (abcam, ab8899)


title: blastoid 96h DN-154416


title: Endometrium_PF_23


title: blastoid 96h DN-154414


title: Endometrium_PF_19


title: blastoid 96h DN-154410


title: blastoid 96h DN-154411


title: blastoid 96h DN-154413


title: CX-5461

data_processing:
Basecalls performed using CASAVA version 1.8
All bulk RNA-seq reads were trimmed using Trimmomatic software with the following parameters “ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36” (Version 0.36). and were further quality-filtered using FASTX Toolkit’s fastq_quality_trimmer command (Version 0.0.13, http://hannonlab.cshl.edu/fastx_toolkit/) with the minimum quality score 20 and minimum percent of 80% bases that has a quality score larger than this cutoff value.
ATAC-seq reads were first aligned to mm10 genomes using Bowtie2 (version 2.3.4.1). The ATAC-seq reads were aligned with the parameters: -t -q -N 1 -L 25 -X 2000 no-mixed no-discordant.
The bamCoverage and bamCompare commands contained in deepTools (version 2.5.3) were adopted for downstream analysis. Using BamCoverage command with the parameters: -normalizeUsing BPM -of bigwig -binSize 100, we first normalized the raw reads signal to Bins Per Million mapped reads (BPM) signal and converted the alignment bam files to bigwig signal files. The bigwig files were imported into UCSC genome browser for visualization.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using deepTools

extract_protocol:
50,000 cells were harvested and lysed in 50 μl of cold lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA-630) for 10 min on ice to prepare the nuclei. Then, spin down immediately at 500 g for 5 min, 4 °C, to remove the supernatant. Nuclei were then incubated with TruePrep Tagment Enzyme (TD501, Vazyme) at 55 °C for 10 min. Immediately after the tag mentation, 1× VAHTS DNA Clean Beads (N411, Vazyme) was added into the reaction to purify DNA fragments.
Nuclei were then incubated with TruePrep Tagment Enzyme (TD501, Vazyme) at 55 °C for 10 min. Immediately after the tag mentation, 1× VAHTS DNA Clean Beads (N411, Vazyme) was added into the reaction to purify DNA fragments. PCR amplify the library with the following program: 72 °C for 3 min; 98 °C for 30 s; and thermocycling at 1 cycle of 98 °C for 15 s, 15 cycles of 60 °C for 30 s and 72 °C for 3 min; following by 72 °C for 5 min. Libraries were purified with the 0.6×/0.15× double sided size selection. Libraries were sequenced with the Illumina HiSeq 2500 System.

value: Lin28a knockout


title: H3K9me3_Control

value: H3K9me3 (abcam, ab8898)


title: Endometrium_PF_18

data_processing: Normalized signal was obtained using limma and preprocessCore R-packages. F532 Median and B532 Meadian are the columns used for estimate probeset expression. Background was corrected using normexp method and 8 replicates for each probe were averaged.

value: Endometrium


title: blastoid 96h PDGFRa pl-154466


title: H3K27me3_CX-5461

value: H3K27me3 (abcam, ab8899)


title: Endometrium_PF_17


title: blastoid 96h DN-154418


title: Control

value: wide-type


title: blastoid 96h DN-154409


title: blastoid 96h DN-154408


title: blastoid 96h DN-154407


title: blastoid 96h DN-154405


title: blastoid 96h DN-154406


title: blastoid 96h DN-154403


title: WT

treatment_protocol: ilet7 ES cells was  treated with Doxycycline for 3 days.

value: Lin28 knockdown


title: siLin28


title: DKO_rep3

source_name: iPS cells

value: MEF-reprogromed PS cells

value: Lin28a/b double knockout


title: Endometrium_PF_1

value: female

value: PF


title: blastoid 96h DN-154404


title: blastoid 96h DN-154402


title: blastoid 96h DN-154401


title: DKO_rep2


title: Endometrium_PF_15


title: Endometrium_PF_14


title: blastoid 96h DN-154400


title: blastoid 96h DN-154399


title: blastoid 96h DN-154398


title: Endometrium_PF_12


title: blastoid 96h DN-154448


title: DKO_rep1


title: Endometrium_PF_13


title: blastoid 96h DN-154396


title: blastoid 96h DN-154397


title: Endometrium_PF_16


title: WT_iPS_rep3

value: untreated


title: Endometrium_PF_11


title: WT_iPS_rep2


title: blastoid 96h DN-154393


title: blastoid 96h DN-154391


title: Endometrium_PF_10


title: blastoid 96h DN-154390


title: ilet7+Doxy_rep3

value: ICM-derived ES cells

value: Doxycycline


title: blastoid 96h DN-154388


title: blastoid 96h DN-154389


title: Endometrium_LR_8

value: LR


title: Endometrium_LR_9


title: Endometrium_LR_7


title: blastoid 96h DN-154386


title: blastoid 96h DN-154385


title: ilet7+Doxy_rep1


title: blastoid 96h DN-154383


title: ilet7-Ctrl_rep3


title: blastoid 96h DN-154382


title: Endometrium_LR_6


title: blastoid 96h DN-154381


title: blastoid 96h DN-154380


title: Endometrium_LR_4


title: Endometrium_LR_5


title: WT_iPS_rep1


title: ilet7-Ctrl_rep2


title: ilet7-Ctrl_rep1


title: blastoid 96h DN-154378


title: Endometrium_LR_3


title: ilet7+Doxy_rep2


title: blastoid 96h DN-154387


title: b null_rep3

value: Lin28b knockout


title: blastoid 96h DN-154377


title: blastoid 96h DN-154376


title: blastoid 96h DN-154384


title: Endometrium_LR_27


title: blastoid 96h DN-154374


title: Endometrium_LR_2


title: b null_rep2


title: b null_rep1


title: Endometrium_LR_26


title: blastoid 96h DN-154373


title: blastoid 96h DN-154424


title: blastoid 96h DN-154375


title: blastoid 96h DN-154379


title: a null_rep3


title: blastoid 96h DN-154370


title: blastoid 96h DN-154371


title: blastoid 96h DN-154368


title: Endometrium_LR_24


title: blastoid 96h DN-154366


title: Endometrium_LR_25


title: blastoid 96h DN-154365


title: Endometrium_LR_23


title: blastoid 96h DN-154364


title: Endometrium_LR_22


title: blastoid 96h DN-154361


title: blastoid 96h DN-154372


title: blastoid 96h DN-154369


title: WT_ES_rep3


title: Endometrium_LR_21


title: blastoid 96h DN-154363


title: blastoid 96h DN-154362


title: WT_ES_rep2


title: blastoid 96h DN-154359


title: blastoid 96h DN-154360


title: blastoid 96h DN-154358


title: blastoid 96h DN-154392


title: WT_ES_rep1


title: ES AKO Hi-C

value: Lin28a knockout ES cells


title: a null_rep2


title: Endometrium_LR_1


title: blastoid 96h DN-154355


title: blastoid 96h DN-154356


title: AKO_ES

data_processing:
Single-cell gene expression matrix was further analyzed with Seurat v2.3.4 (https://satijalab.org/seurat/).
We excluded the genes with expressed cell number smaller than 3 and the cells with nUMIs smaller than 500 or the expression percentages of mitochondrial genes larger than 0.2 and used 16 Principle Components (PCs) for tSNE analysis.
Genome_build: mm10
Supplementary_files_format_and_content: xlsx, gene expression level (Counts)

extract_protocol: We used InDrop system following the manufacturer’s protocol (OneCell)


title: a null_rep1


title: ES WT Hi-C

value: wide-type ES cells


title: blastoid 96h DN-154354


title: blastoid 96h DN-154357


title: Endometrium_LR_20


title: blastoid 96h DN-154353


title: Endometrium_LR_18


title: WT_ES


title: blastoid 96h DN-154351


title: Endometrium_LR_17


title: blastoid 96h DN-154352


title: blastoid 96h DN-154347


title: blastoid 96h DN-154348


title: ES rep-1

data_processing:
Basecalls performed using CASAVA version 1.4
We first trimmed 6bp random sequence of read’s 3’-terminal using fastx_trimmer command contained in FASTX Toolkit. Then, we clipped the adaptor sequence “AGATCGGAAGAGCACACGTCT” using FASTX Toolkit fastx_clipper.
CLIP-seq reads were aligned to mouse ribosomal DNA complete repeating unit (GenBank accession BK000964.1) by Bowtie with the parameters “-n 0 -norc --best -l 15”. Filtered reads that do not match to mouse ribosomal DNA complete repeating unit were mapped to mm10 genome by HISAT2 with -dta paramenter. The alignment results were filtered to remove PCR duplicate reads and leave only the uniquely mapped reads.
The CLIP tag density at the transcript level was qualified by TPM value of mapped CLIP-seq reads of a given region (defined by GENCODE M18 gene annotation or RepeatMasker repeat sequence annotation) produced from StringTie with -e -B -G parameters. The CLIP tag enrichment at the transcript level was estimated as log2 ratio between the TPM value from the CLIP library and the TPM value from the control RNA-seq library.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using deepTools

extract_protocol:
The cell pellets were resuspended in RIP buffer. Then treated the cell lysate with DNase I. The pre-equilibrated FLAG M2 resins were incubated with the lysate at 4°C overnight. The RNA/Protein complexes were eluted with 3 × FLAG elution buffer, then, incubated with pre-equilibrated streptavidin beads at 4°C overnight. Then the RNAs were partially digested with Micrococcal nuclease at 37°C for 10 min. The RNAs were purified by TRIzol™ Reagent and ligated with 5′ RNA adaptor.
the purified RNA fragments were reverse transcribed by Superscript III (Invitrogen) with RT primer and amplified for 20 cycles with 2× NEB HF PCR mix (NEB). Library index sequence was introduced by PCR with index primers for eight more cycles. Library was performed high-throughput sequencing by Illumina Hiseq 2500 sequencing platform.

treatment_protocol: About 3 × 107 cells were crosslinked at 254 nm UV light and harvested in pre-chilled PBS.

value: ES


title: Endometrium_LR_19


title: Endometrium_LR_16


title: ES rep-2


title: blastoid 96h DN-154345


title: blastoid 96h DN-154350


title: blastoid 96h DN-154342


title: Endometrium_LR_14


title: H3K9me3_WT

growth_protocol: Mouse  iPS cells were cultured on 0.1% gelatin-coated plates with MEF feeder cells in LIF/2i media for 2 days.

value: WT

value: H3K9me3 (abcam, ab8898)


title: Endometrium_LR_15

value: Endometrium


title: blastoid 96h DN-154343


title: blastoid 96h DN-154340


title: ES AKO

value: ES cells

value: Lin28a knockout


title: Endometrium_LR_13


title: blastoid 96h DN-154339


title: blastoid 96h DN-154338


title: blastoid 96h DN-154341


title: blastoid 96h DN-154337


title: ES WT

value: wide-type


title: Endometrium_LR_12


title: Endometrium_LR_11


title: blastoid 96h DN-154346


title: E_72h_R3

city: POZUELO DE ALARCON

first: M. ESTRELLA

last: SANTAMARIA

state: MADRID

address: Parque Científico y Tecnológico, UPM Campus de Montegancedo, Ctra, M-40, km 38

institute: CBGP (UPM-INIA)

data_processing:
Raw data obtained in FASTQ format was processed to remove adapters and poly-N sequences as well as low quality reads. DNA sequences were analysed and processed using Trimmomatic (Galaxy Version 0.38.0), dropping reads below Q15 with a sliding window of 4bp
Reads whose length was below 108bp were removed. Trimmed reads were aligned to the A. thaliana (TAIR10) genome
Kallisto was used to calculate the abundance of the transcripts as transcripts per million (TPM) by pseudo aligning the sample reads to the reference using the default k-mer length of 31 and 100 bootstrap repetitions.
Fold changes (FC) and adjusted p-values (q-value) for each gene were calculated using the Sleuth software. Each time point was compared to its corresponding control by means of a Wald test and the Lancaster aggregation method
Genome_build: A. thaliana (TAIR10) genome (https://www.arabidopsis.org)
Supplementary_files_format_and_content: abundance.tsv (results of the main quantification, i.e. the abundance estimate); run_info.json (summary of the run, including data on the number targets used for quantification, the number of bootstraps performed, the version of the program used and how it was called); abundance.h5 (contains the main quantification together with the boostraps in HDF5 format)

organism: Arabidopsis thaliana

growth_protocol: Sterilized seeds were planted in a mixture of peat moss and vermiculite (2:1 v/v) and incubated in the dark for 5 days at 4°C. Plants were then transferred to growth chambers (Sanyo MLR-350-H) under controlled conditions (23°C ± 1°C, >70% RH and a 16 h/8 h day/night photoperiod).

extract_protocol:
Frozen material was thoroughly grinded on liquid nitrogen and total RNA was extracted by means of the RNeasy plant mini kit (Qiagen), and a DNase treatment (Qiagen) following manufacturer´s instructions.
RNA libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina according to manufacturer’s instructions.

treatment_protocol: Three-week-old plants were treated by applying 2 μL of egg extract as described above. After 3, 24 and 72 hpt, whole rosettes were sampled, introduced in liquid nitrogen and stored at –80°C until used for RNA extraction.

tag: ecotype

value: Columbia (Col-0)

tag: treatment time (h)

value: Five whole rosettes pooled


title: blastoid 96h DN-154336

first: Giovanni

last: Sestini

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

institute: IMBA - Institute of Molecular Biotechnology


title: blastoid 96h DN-154335


title: E_72h_R2


title: blastoid 96h TROP2 pl-154332


title: Endometrium_LR_10

value: female


title: blastoid 96h DN-154334


title: Endometrium_LPR_9

value: LPR


title: E_72h_R1


title: blastoid 96h TROP2 pl-154330


title: blastoid 96h TROP2 pl-154329


title: E_3h_R3


title: Endometrium_LPR_99


title: blastoid 96h TROP2 pl-154328


title: Endometrium_LPR_98


title: blastoid 96h TROP2 pl-154326


title: blastoid 96h TROP2 pl-154327


title: E_3h_R2


title: Endometrium_LPR_96


title: blastoid 96h TROP2 pl-154324


title: E_24h_R3


title: blastoid 96h TROP2 pl-154323


title: E_3h_R1


title: blastoid 96h TROP2 pl-154333


title: E_24h_R2


title: blastoid 96h TROP2 pl-154325


title: blastoid 96h TROP2 pl-154331


title: Endometrium_LPR_94


title: blastoid 96h TROP2 pl-154319


title: Endometrium_LPR_95


title: blastoid 96h TROP2 pl-154322


title: C_72h_R2

value: water for 72h


title: Endometrium_LPR_92


title: blastoid 96h TROP2 pl-154313


title: blastoid 96h TROP2 pl-154321


title: blastoid 96h TROP2 pl-154315


title: Endometrium_LPR_97


title: H3K9me3_DKO

value: MEF-reprogromed PS cells

tag: genotype/variation

value: DKO


title: C_72h_R1


title: E_24h_R1


title: C_72h_R3


title: blastoid 96h TROP2 pl-154320


title: blastoid 96h TROP2 pl-154317


title: Endometrium_LPR_93


title: blastoid 96h TROP2 pl-154316


title: blastoid 96h TROP2 pl-154318


title: blastoid 96h TROP2 pl-154309


title: C_3h_R2

value: water for 3h


title: blastoid 96h TROP2 pl-154312


title: blastoid 96h TROP2 pl-154310


title: blastoid 96h TROP2 pl-154311


title: blastoid 96h TROP2 pl-154308


title: C_3h_R3


title: Endometrium_LPR_90


title: blastoid 96h TROP2 pl-154307


title: Endometrium_LPR_91


title: C_3h_R1


title: blastoid 96h TROP2 pl-154306


title: Endometrium_LPR_8


title: Endometrium_LPR_89


title: Endometrium_LPR_88


title: Endometrium_LPR_87


title: blastoid 96h TROP2 pl-154304


title: blastoid 96h TROP2 pl-154305


title: C_24h_R3

value: water for 24h