title: Bartolomei_RNA_Liver_Ctrl_5month_Male_biorep4

description: UUID:5b57531b240ce376aa97411f,QC_score:3,QC_stats:Pass


title: Dolinoy_ATAC_Blood_Pb_5month_Male_biorep1

status: Public on May 20 2020

type: SRA

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

country: USA

institute: Washington University in St. Louis

description: UUID:5cacdddeb585665ad314d05c,QC_score:9,QC_stats:Pass

library_source: genomic

data_processing:
RNA-seq and ATAC-seq were sequenced by data production centers and processed by the TaRGET II DCC with standardized data processing pipelines. Library QC was assayed based on key QC parameters. Please refer to the TaRGET II data portal for detailed pipeline description and QC standard (https://data.targetepigenomics.org).
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak output for ATAC-seq and gene count table for RNA-seq

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Sample collection was performed by Dana Dolinoy lab at University of Michigan. 5 month mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by Dana Dolinoy lab at University of Michigan. mRNA and nuclei from 5 month mice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.

tag: strain

value: Avy

tag: age

value: 5 month

tag: gender

value: Male

tag: tissue

value: Blood

tag: treatment

value: Pb 16ppm lead acetate


title: Dolinoy_ATAC_Liver_Pb_5month_Female_biorep1

description: UUID:5b75b36e0331b90c8eafd282,QC_score:10,QC_stats:Pass

value: Female

value: Liver


title: Bartolomei_RNA_Liver_Ctrl_5month_Male_biorep3

description: UUID:5b575265240ce3fead974118,QC_score:3,QC_stats:Pass

library_source: transcriptomic

molecule: polyA RNA

extract_protocol:
Sample collection was performed by Marisa Bartolomei lab at University of Pennsylvania. 5 month mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by Marisa Bartolomei lab at University of Pennsylvania. mRNA and nuclei from 5 month mice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.

value: Control Diet NA


title: Dolinoy_ATAC_Liver_DEHP_5month_Male_biorep3

description: UUID:5b75b331dbb5040a2db01761,QC_score:6,QC_stats:Pass

value: DEHP (bis (2-ethylhexyl) phthalate) 25mg DEHP/kg


title: Dolinoy_ATAC_Blood_Pb_5month_Female_biorep6

description: UUID:5cace52190c5f626223e5150,QC_score:9,QC_stats:Pass


title: Mutlu_ATAC_Blood_Ctrl_5month_Female_biorep4

description: UUID:5d1d3d8f1657b23a5e6f04d9,QC_score:5,QC_stats:Pass

extract_protocol:
Sample collection was performed by Gokhan Mutlu lab at University of Chicago. 5 month mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by Gokhan Mutlu lab at University of Chicago. mRNA and nuclei from 5 month mice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.

value: Filtered Air 0 particles/cm3/8hours/day


title: Dolinoy_ATAC_Blood_Pb_5month_Female_biorep4

description: UUID:5cace1628ad8b274405d12dc,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Liver_DEHP_5month_Male_biorep6

description: UUID:5b75bba10331b962f6afd29b,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Blood_Pb_5month_Female_biorep2

description: UUID:5cacdeceb585664c6514d061,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Blood_Pb_5month_Female_biorep3

description: UUID:5cace036b6036dfc4e68c0eb,QC_score:5,QC_stats:Pass


title: Dolinoy_ATAC_Blood_Pb_5month_Female_biorep1

description: UUID:5cacdd29b5856669ca14d05b,QC_score:10,QC_stats:Pass


title: Bartolomei_RNA_Liver_Ctrl_5month_Male_biorep1

description: UUID:5b1b46357577de29e43f2067,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Liver_Ctrl_5month_Female_biorep6

description: UUID:5d37229e749ee812013260fa,QC_score:3,QC_stats:Pass


title: Dolinoy_ATAC_Liver_DEHP_5month_Female_biorep5

description: UUID:5b75bb66dbb504f96ab01787,QC_score:8,QC_stats:Pass


title: Bartolomei_RNA_Liver_Ctrl_5month_Female_biorep5

description: UUID:5d37229c4b679d8fdb0240ee,QC_score:3,QC_stats:Pass


title: Dolinoy_ATAC_Blood_DEHP_5month_Male_biorep5

description: UUID:5cace305aa1d5f45c25840e5,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Liver_DEHP_5month_Female_biorep4

description: UUID:5b75bb29dbb5047565b01786,QC_score:6,QC_stats:Pass


title: Dolinoy_ATAC_Blood_DEHP_5month_Male_biorep7

description: UUID:5cace4e590c5f672403e514f,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Liver_DEHP_5month_Male_biorep4

description: UUID:5b75b67adbb5042d23b0176d,QC_score:9,QC_stats:Pass


title: Bartolomei_RNA_Liver_Ctrl_5month_Female_biorep2

description: UUID:5bd8d5cb06a950130ea53c2e,QC_score:3,QC_stats:Pass


title: Dolinoy_ATAC_Blood_DEHP_5month_Male_biorep6

description: UUID:5cace342e8e823fb57fb23bc,QC_score:10,QC_stats:Pass


title: Dolinoy_ATAC_Blood_DEHP_5month_Male_biorep4

description: UUID:5cace1258ad8b2623a5d12d9,QC_score:9,QC_stats:Pass


title: Bartolomei_RNA_Liver_Ctrl_5month_Female_biorep1

description: UUID:5b575266240ce33b09974119,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Liver_Ctrl_5month_Male_biorep2

description: UUID:5b1b46727577de651b3f2068,QC_score:3,QC_stats:Pass


title: Control Sample 4

city: Haifa

first: Thomas

last: Schultheiss

address: Efron 1

department: Faculty of Medicine

country: Israel

institute: Technion-Israel Institute of Technology

data_processing:
Data filtering steps: Raw reads were pre-processed by trimming Illumina adapters, polyA and poly T tails and also by trimming edges of reads with quality below 10 using Cutadapt v1.8.3(Martin, 2011). Reads with length below 30 were discarded.
Read alignment software: The processed reads were mapped to the Gallus gallus genome, Galgal4, using STAR v2.4 (Dobin et al., 2013) and then the number of reads that were mapped to each gene was calculated using HTSeq-count, v0.6.1p1 (Anders et al., 2015).
Gene annotation: The gene annotation used for the counting was Ensemble annotation for Galgal4, release 85.
Differential expression was carried out using Deseq2 (Love et al., 2014). Genes that obtained absolute fold change greater than 1.5 and also had adjusted p-value lower than 0.1 Differentiatal Expression evaluation: were considered as differentially expressed. Adjusted p-values were taken from Deseq correction for multiple testing, which is based on Benjamin-Hochberg FDR (Benjamini and Hochberg, 1995).
Genome_build: Gallus gallus genome, Galgal4
Supplementary_files_format_and_content: Matrix Table is the Table of normalized counts for all samples
Supplementary_files_format_and_content: de_stats is an Excel file containing a complete list of genes with their relative expression between the experimental and control group.

molecule: total RNA

organism: Gallus gallus

source_name: coelomic epithelium

extract_protocol:
HH Stage 12-13 chick embryos were electroporated with either pCIG-PtcDLoop2, which also expresses GFP, or with pMES, which expresses GFP alone. Embryos were incubated for 14 hours (until approximately HH St. 16), harvested and transferred into culture dishes containing chilled 1xPBS. Each embryo was dissected on a silicone plate using a microscalpel (Feather) to cut out the desired area (from just posterior to the heart to the posterior end of the embryo, including both sides of the embryo). The dissected tissue was transferred into chilled DMEM in a small tissue culture plate. Each sample was roughly chopped into several small pieces (4-5) and transferred, with minimal DMEM, into a 50 ml tube, containing 5ml Trypsin (0.25%, Biological Industries), on ice. Trypsin treatment was performed at 370C first in a water bath for 10 minutes and then 20 minutes in a rotary shaker (80 RPM). The reaction was stopped by adding 1ml chilled FBS. A 5ml tip was used to triturate the sample; when no visible tissue chunks were seen the sample was filtered first through a 70 μM cell strainer and then through a 40μM strainer into a 50ml tube, and then pelleted in a swinging bucket rotor, at 500G for 7 minutes. The supernatant was carefully aspirated and each sample was resuspended in 750 μl of FACS solution (1xPBS, 2% FBS, 2mM EDTA pH8) and held on ice until the FACS procedure was started.  Each embryo sample was sorted independently on a FACSAria™ IIIu (BD Biosciences) operating with BD FACSDiva 7.0 (build 2012.09.24.19.43) software, using a 561nm laser, nozzle size 100mm and pressure 4.4. Five PtcDLoop2 and five pMES electroporated embryos were sorted. Cells were determined based on FSC/SSC plot with default threshold settings. Two sequential hierarchical doublet discriminating schemes based on FSC-W/FSC-H and SSC-W/SSC-H were followed. A non electroporated eGFP negative control sample was used to determined the boundaries of positive and negative eGFP global gates. Positive cells represented approximately 0.5% of the pre-sort population for each sample. Sorted cells were collected into a 1.5ml Eppendorf tube containing 500 ml 1xPBS and 2% FBS. Tubes were centrifuged at 500g for 5 min at 40C, supernatant was removed carefully, and the pellet (containing about 500-3000 cells) was suspended in 10.5 ml of Single Cell Lysis Buffer (Clontech), incubated for 5 min at RT, pipetted to resuspend, and kept at -800C.
10 samples of 322-3100 lysed cells each were amplified separately using SMARTSeq Ultra Low Input RNA V4 kit from Clontech (cat# 634890). After the amplification step (15 cycles), the amplicons were fragmented to fragment sizes of about 300bp using Covaris E220 (Covaris,Inc.,Woburn, MA, USA). The amplified fragments were processed to libraries according to the Chip-seq protocol previously described (Blecher-Gonen et al., 2013). Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing of 10 samples in one lane. Between 19-24 million single-end 60-bp reads were sequenced per sample on an Illumina HiSeq 2500 V4 instrument.

tag: Stage

value: HH Stage 12-13

value: coelomic epithelium

tag: electroporated with

value: GFP


title: Control Sample 3


title: Dolinoy_ATAC_Liver_DEHP_5month_Male_biorep2

description: UUID:5b75b2f6dbb504086bb01760,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Liver_DEHP_5month_Female_biorep3

description: UUID:5b75ba76dbb504640fb0177f,QC_score:10,QC_stats:Pass


title: Dolinoy_ATAC_Liver_DEHP_5month_Female_biorep2

description: UUID:5b75b6b60331b93449afd295,QC_score:10,QC_stats:Pass


title: Dolinoy_ATAC_Blood_DEHP_5month_Male_biorep3

description: UUID:5cacdff950bb2f8f68743e66,QC_score:10,QC_stats:Pass


title: Bartolomei_RNA_Liver_BPA_10ug_5month_Male_biorep6

description: UUID:5d3722a24b679d70750240f3,QC_score:3,QC_stats:Pass

value: BPA (Bisphenol A) 10 UG/KGBW/DAY


title: Dolinoy_ATAC_Blood_DEHP_5month_Male_biorep2

description: UUID:5cacde91b5856655f814d060,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Liver_DEHP_5month_Female_biorep1

description: UUID:5b75b205dbb5049bfbb0175b,QC_score:6,QC_stats:Pass


title: Bartolomei_RNA_Liver_BPA_10ug_5month_Male_biorep5

description: UUID:5d37229c4b679d1b020240f0,QC_score:3,QC_stats:Pass


title: Dolinoy_ATAC_Liver_DEHP_5month_Male_biorep1

description: UUID:5b75b27edbb5046176b0175d,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Blood_DEHP_5month_Male_biorep1

description: UUID:5cacdcedaa1d5f9bb95840d2,QC_score:10,QC_stats:Pass


title: Control Sample 1


title: Dolinoy_ATAC_Blood_DEHP_5month_Female_biorep5

description: UUID:5cace4a990c5f636c33e514c,QC_score:9,QC_stats:Pass


title: Bartolomei_RNA_Liver_BPA_10ug_5month_Male_biorep2

description: UUID:5bd8d11a345ff02db1b53798,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Liver_BPA_10ug_5month_Male_biorep4

description: UUID:5d37229a4b679d7ef70240e8,QC_score:3,QC_stats:Pass


title: Dolinoy_ATAC_Blood_DEHP_5month_Female_biorep4

description: UUID:5cace0e970a714584857decd,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Ctrl_5month_Male_biorep4

description: UUID:5b75b5890331b97c0dafd28d,QC_score:8,QC_stats:Pass

value: Control Diet Control


title: Experimental Sample 5

value: PatchedDLoop2 - GFP


title: Dolinoy_ATAC_Liver_Ctrl_5month_Male_biorep6

description: UUID:5b75b9fedbb5046d44b0177e,QC_score:9,QC_stats:Pass


title: Experimental Sample 4


title: Dolinoy_ATAC_Blood_DEHP_5month_Female_biorep3

description: UUID:5cacdfbd9b7fcc0859efb0d8,QC_score:10,QC_stats:Pass


title: Bartolomei_RNA_Liver_BPA_10ug_5month_Male_biorep1

description: UUID:5b5754453e4876820a84212e,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Liver_BPA_10ug_5month_Female_biorep6

description: UUID:5d3722a1749ee8922b326102,QC_score:3,QC_stats:Pass


title: Experimental Sample 2


title: Dolinoy_ATAC_Liver_Ctrl_5month_Male_biorep3

description: UUID:5b75b4d5dbb504d0a1b01768,QC_score:10,QC_stats:Pass


title: Dolinoy_ATAC_Blood_DEHP_5month_Female_biorep2

description: UUID:5cacde56b58566f9ac14d05e,QC_score:9,QC_stats:Pass


title: Control Sample 2


title: Dolinoy_ATAC_Blood_DEHP_5month_Female_biorep1

description: UUID:5cacdcedaa1d5f74775840d4,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Ctrl_5month_Male_biorep2

description: UUID:5b75b1cb9e0913187bf625c3,QC_score:10,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Ctrl_5month_Male_biorep1

description: UUID:5b75b152dbb50417c7b01759,QC_score:9,QC_stats:Pass


title: Experimental Sample 1


title: Bartolomei_RNA_Liver_BPA_10ug_5month_Female_biorep4

description: UUID:5d3722624b679dd1460240d7,QC_score:3,QC_stats:Pass


title: Dolinoy_ATAC_Blood_Ctrl_5month_Male_biorep6

description: UUID:5cace55e90c5f6e7303e5155,QC_score:10,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Ctrl_5month_Female_biorep5

description: UUID:5b75b986dbb5046396b01779,QC_score:10,QC_stats:Pass


title: Bartolomei_RNA_Liver_BPA_10ug_5month_Female_biorep2

description: UUID:5b575356240ce3a183974120,QC_score:3,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Ctrl_5month_Male_biorep5

description: UUID:5b75b6020331b9e2b3afd290,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Blood_Ctrl_5month_Male_biorep5

description: UUID:5cace28eaa1d5f19865840e0,QC_score:10,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Ctrl_5month_Female_biorep4

description: UUID:5b75b94adbb5043fd0b01777,QC_score:9,QC_stats:Pass


title: Bartolomei_RNA_Liver_BPA_10ug_5month_Female_biorep1

description: UUID:5b5751ed3e48762324842126,QC_score:3,QC_stats:Pass


title: Dolinoy_ATAC_Blood_Ctrl_5month_Male_biorep4

description: UUID:5cace0ad90c5f649b23e514b,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Ctrl_5month_Female_biorep3

description: UUID:5b75b54ddbb504ea0fb01769,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Blood_Ctrl_5month_Male_biorep3

description: UUID:5cacdf8150bb2f7f4e743e63,QC_score:9,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Ctrl_5month_Female_biorep2

description: UUID:5b75b1169e09138f07f625c1,QC_score:8,QC_stats:Pass


title: Dolinoy_ATAC_Blood_Pb_5month_Female_biorep5

description: UUID:5cace3b9b6036d3f4d68c0f1,QC_score:9,QC_stats:Pass


title: Bartolomei_RNA_Liver_BPA_10mg_5month_Male_biorep6

description: UUID:5d3722a24b679d05290240f4,QC_score:3,QC_stats:Pass

value: BPA (Bisphenol A) 10 MG/KGBW/DAY


title: Bartolomei_RNA_Liver_BPA_10ug_5month_Female_biorep5

description: UUID:5d37229f749ee869f83260fb,QC_score:3,QC_stats:Pass


title: Dolinoy_ATAC_Blood_Ctrl_5month_Male_biorep2

description: UUID:5cacde1ab58566fc2e14d05d,QC_score:10,QC_stats:Pass

value: Avy


title: Dolinoy_ATAC_Blood_Ctrl_5month_Male_biorep1

description: UUID:5cacdc76aa1d5f897c5840d0,QC_score:10,QC_stats:Pass

value: 5 month


title: Biswal_RNA_Blood_PM2.5_5month_Female_biorep4

description: UUID:5c83d8b25c755ce2c0af4fbd,QC_score:3,QC_stats:Pass

extract_protocol:
Sample collection was performed by Shyam Biswal Lab at Johns Hopkins University. 5 month mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by Shyam Biswal Lab at Johns Hopkins University. mRNA and nuclei from 5 month mice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.


title: Bartolomei_RNA_Liver_BPA_10mg_5month_Male_biorep3

description: UUID:5d37225e749ee888aa3260ee,QC_score:3,QC_stats:Pass

value: Male


title: Bartolomei_RNA_Liver_BPA_10mg_5month_Male_biorep4

description: UUID:5d3722964b679d11ce0240e0,QC_score:3,QC_stats:Pass


title: Mutlu_ATAC_Blood_Ctrl_5month_Female_biorep8

description: UUID:5d9e0009b529a9304de74b38,QC_score:9,QC_stats:Pass

value: Blood


title: Dolinoy_ATAC_Blood_Ctrl_5month_Female_biorep6

description: UUID:5cace46db6036dacbb68c0f5,QC_score:9,QC_stats:Pass


title: Bartolomei_RNA_Liver_BPA_10mg_5month_Male_biorep5

description: UUID:5d37229d749ee8beb73260f6,QC_score:3,QC_stats:Pass


title: Dolinoy_ATAC_Blood_Ctrl_5month_Female_biorep5

description: UUID:5cace21570a71493a857ded3,QC_score:9,QC_stats:Pass


title: Biswal_RNA_Blood_PM2.5_5month_Female_biorep2

description: UUID:5c83d7c28a0bc40c9e5664aa,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Liver_BPA_10mg_5month_Male_biorep2

description: UUID:5bd8d552345ff0d267b537bf,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Liver_BPA_10mg_5month_Male_biorep1

description: UUID:5b57522a3e4876c9aa842129,QC_score:3,QC_stats:Pass


title: Dolinoy_ATAC_Blood_Ctrl_5month_Female_biorep4

description: UUID:5cace072b6036d069868c0ed,QC_score:9,QC_stats:Pass


title: Biswal_RNA_Blood_PM2.5_5month_Female_biorep3

description: UUID:5c83d8395c755c2709af4fbc,QC_score:3,QC_stats:Pass


title: Biswal_RNA_Blood_PM2.5_5month_Female_biorep1

description: UUID:5c83d7495c755c748caf4fb8,QC_score:3,QC_stats:Pass


title: Dolinoy_ATAC_Liver_Ctrl_5month_Female_biorep1

description: UUID:5b75b0a0dbb5042334b01756,QC_score:6,QC_stats:Pass


title: Dolinoy_ATAC_Blood_Ctrl_5month_Female_biorep3

description: UUID:5cacdf4550bb2f2cae743e62,QC_score:9,QC_stats:Pass


title: Bartolomei_RNA_Liver_BPA_10mg_5month_Female_biorep5

description: UUID:5d37229d4b679d56b20240f1,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Liver_BPA_10mg_5month_Female_biorep6

description: UUID:5d37229e749ee8c0193260f9,QC_score:3,QC_stats:Pass


title: Biswal_RNA_Blood_Ctrl_5month_Male_biorep3

description: UUID:5c83d6d28a0bc48a145664a8,QC_score:3,QC_stats:Pass

value: Filtered Air NA


title: Biswal_RNA_Blood_Ctrl_5month_Male_biorep2

description: UUID:5c83d65a5c755c1540af4fb4,QC_score:3,QC_stats:Pass


title: Dolinoy_ATAC_Blood_Ctrl_5month_Female_biorep2

description: UUID:5cacde19aa1d5f5a135840da,QC_score:9,QC_stats:Pass

value: Female


title: Bartolomei_RNA_Liver_BPA_10mg_5month_Female_biorep4

description: UUID:5d372297749ee86f233260f5,QC_score:3,QC_stats:Pass

value: Liver


title: Dolinoy_ATAC_Blood_Ctrl_5month_Female_biorep1

description: UUID:5cacdc39aa1d5f2fc55840cf,QC_score:9,QC_stats:Pass


title: Biswal_RNA_Blood_Ctrl_5month_Male_biorep1

description: UUID:5c83d5e28a0bc47beb5664a5,QC_score:3,QC_stats:Pass


title: MATN3 T120M isogenic control, biological replicate 1

type: RNA

city: Kyoto

first: Junya

last: Toguchida

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Center for iPS Cell Research and Application

description: gene-corrected rescue

hyb_protocol: Samples were hybridized to the arrays with the GeneChip Hybridization Wash and Stain Kit. The arrays were washed and stained on the GeneChip Fluidics Station 450.

scan_protocol: The arrays were scanned with the GeneChip Scanner 3000 7G.

data_processing:
The GeneSpring GX 14.9 software was used for analysis. Data were normalized using the RMA-16 algorithm and the baseline was adjusted to the median of all samples.
Gene expression values normalized by the RMA-16 algorithm in GeneSpring GX 14.9, with the baseline adjusted to the median of all samples.

label: biotin

organism: Homo sapiens

source_name: MATN3 T120M isogenic control iPSC-derived cartilage pellet

label_protocol: Samples were fragmented and labeled with the GeneChip WT Terminal Labeling and Controls kit.

growth_protocol: iPSCs were differentiated into hypertrophic chondrocytes in 3D culture

extract_protocol: Cartilage pellets were frozen in liquid nitrogen and powderized before RNA extraction with the QIAGEN RNeasy Micro Kit. 50-100 ng of total RNA was used for reverse transcription and amplification with the Ambion WT Expression Kit.

treatment_protocol: not applicable

value: cartilage (iPSC-derived)

tag: genotype

value: wild type


title: MATN3 T120M isogenic control, biological replicate 3

description: gene-corrected rescue


title: Biswal_RNA_Blood_Ctrl_5month_Female_biorep4

description: UUID:5c83d4f25c755c6a4faf4faf,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Liver_BPA_10mg_5month_Female_biorep3

description: UUID:5d37225f4b679d25410240d2,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Blood_Ctrl_5month_Male_biorep5

description: UUID:5d3b6bb6bd3a5840ba13ed1d,QC_score:3,QC_stats:Pass

value: Control Diet NA


title: COL10A1 L614RfsX8 isogenic control, biological replicate 3

description: gene-corrected rescue

source_name: COL10A1 L614RfsX8 isogenic control iPSC-derived cartilage pellet


title: Biswal_RNA_Blood_Ctrl_5month_Female_biorep3

description: UUID:5c83d4b55c755c1dddaf4fae,QC_score:3,QC_stats:Pass


title: Biswal_RNA_Blood_Ctrl_5month_Female_biorep6

description: UUID:5cddc1075695d90a97020b0b,QC_score:3,QC_stats:Pass


title: Biswal_RNA_Blood_Ctrl_5month_Female_biorep2

description: UUID:5c83d43d5c755cdcf1af4fad,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Liver_BPA_10mg_5month_Female_biorep2

description: UUID:5b57540a3e4876d8c584212d,QC_score:3,QC_stats:Pass


title: Biswal_RNA_Liver_PM2.5_5month_Male_biorep6

description: UUID:5bc8dd5a83168fc632cc3842,QC_score:3,QC_stats:Pass


title: MATN3 T120M isogenic control, biological replicate 2

description: gene-corrected rescue


title: Biswal_RNA_Liver_PM2.5_5month_Male_biorep4

description: UUID:5bc8dc6983168f8169cc383e,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Liver_BPA_10mg_5month_Female_biorep1

description: UUID:5b5752dd3e4876241984212b,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Blood_Ctrl_5month_Male_biorep6

description: UUID:5dd2e97fc7daab3152a2ffa1,QC_score:3,QC_stats:Pass


title: Biswal_RNA_Liver_PM2.5_5month_Male_biorep3

description: UUID:5bc8dbf13c228d7e906eb7b9,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Blood_Ctrl_5month_Male_biorep4

description: UUID:5d3b6bb5b2e2697f97346ccb,QC_score:3,QC_stats:Pass


title: COL10A1 L614RfsX8 isogenic control, biological replicate 2

description: gene-corrected rescue


title: Biswal_RNA_Blood_Ctrl_5month_Female_biorep1

description: UUID:5c83d3c75c755c62fbaf4fac,QC_score:3,QC_stats:Pass


title: COL10A1 G18E isogenic control, biological replicate 2

description: gene-corrected rescue

source_name: COL10A1 G18E isogenic control iPSC-derived cartilage pellet


title: COL10A1 G18E isogenic control, biological replicate 1

description: gene-corrected rescue


title: COL10A1 G18E isogenic control, biological replicate 3

description: gene-corrected rescue


title: Biswal_ATAC_Liver_PM2.5_5month_Male_biorep6

description: UUID:5bce99b656149c6533eec76a,QC_score:8,QC_stats:Pass


title: COL10A1 L614RfsX8 isogenic control, biological replicate 1

description: gene-corrected rescue


title: Biswal_RNA_Liver_PM2.5_5month_Male_biorep5

description: UUID:5bc8dce183168f5db1cc383f,QC_score:3,QC_stats:Pass


title: MATN3 R209P mutant, biological replicate 3

description: mutant created from 414C2 iPSC line

source_name: MATN3 R209P mutant iPSC-derived cartilage pellet

value: MATN3 R209P


title: Biswal_ATAC_Liver_PM2.5_5month_Male_biorep4

description: UUID:5bce990256149cc5c3eec766,QC_score:4,QC_stats:Fail


title: Biswal_RNA_Liver_PM2.5_5month_Male_biorep2

description: UUID:5bc8db799992464ada0f3581,QC_score:3,QC_stats:Pass


title: Experimental Sample 3

value: HH Stage 12-13

value: coelomic epithelium


title: Biswal_RNA_Liver_PM2.5_5month_Male_biorep1

description: UUID:5bc8db023c228d03d06eb7b8,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Blood_Ctrl_5month_Male_biorep1

description: UUID:5c63403e5ffef260cf536746,QC_score:0,QC_stats:Fail


title: Biswal_RNA_Liver_PM2.5_5month_Female_biorep4

description: UUID:5bc8ff19600a6402eb382c0e,QC_score:3,QC_stats:Pass


title: MATN3 T120M mutant, biological replicate 3

description: patient-derived mutant

source_name: MATN3 T120M mutant iPSC-derived cartilage pellet

value: MATN3 T120M


title: Biswal_RNA_Liver_PM2.5_5month_Female_biorep3

description: UUID:5bc8fd768f4d35b1b84e2b8a,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Liver_PM2.5_5month_Male_biorep2

description: UUID:5bce988a56149cf3feeec760,QC_score:5,QC_stats:Pass


title: Bartolomei_RNA_Blood_Ctrl_5month_Male_biorep3

description: UUID:5c6348eaadb967128ead380b,QC_score:3,QC_stats:Pass


title: Biswal_RNA_Liver_PM2.5_5month_Female_biorep6

description: UUID:5bc900bd1e17017045b502b7,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Liver_PM2.5_5month_Male_biorep5

description: UUID:5bce993e8fc24533d25e98c5,QC_score:8,QC_stats:Pass


title: Bartolomei_RNA_Blood_Ctrl_5month_Female_biorep8

description: UUID:5dea988e0322ccca7879999a,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Liver_PM2.5_5month_Male_biorep1

description: UUID:5bce981256149c6cbfeec75e,QC_score:5,QC_stats:Pass


title: Biswal_RNA_Liver_PM2.5_5month_Female_biorep2

description: UUID:5bc8fcc28f4d3581bd4e2b87,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Liver_PM2.5_5month_Male_biorep3

description: UUID:5bce98c556149c4220eec761,QC_score:8,QC_stats:Pass


title: Bartolomei_RNA_Blood_Ctrl_5month_Female_biorep6

description: UUID:5d3b6bb6b2e2690d0e346ccc,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Blood_Ctrl_5month_Female_biorep7

description: UUID:5dd2e987c7daab8e09a2ffb6,QC_score:3,QC_stats:Pass


title: Biswal_RNA_Liver_PM2.5_5month_Female_biorep1

description: UUID:5bc8fb5af5df5f946bdcd0b0,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Liver_PM2.5_5month_Female_biorep6

description: UUID:5bce9e2a68e6ef533ef24f11,QC_score:5,QC_stats:Pass


title: Biswal_ATAC_Liver_PM2.5_5month_Female_biorep5

description: UUID:5bce9db27752c708fa796771,QC_score:6,QC_stats:Pass


title: Biswal_RNA_Liver_Ctrl_5month_Male_biorep6

description: UUID:5bc8da89cedf35cca371c44f,QC_score:3,QC_stats:Pass


title: Biswal_RNA_Liver_Ctrl_5month_Male_biorep5

description: UUID:5bc8d9d6eb46a34efa159102,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Blood_Ctrl_5month_Male_biorep2

description: UUID:5c634691adb9675099ad37f8,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Liver_PM2.5_5month_Female_biorep4

description: UUID:5bce9cfe5ffaa66cf92143ee,QC_score:6,QC_stats:Pass


title: Bartolomei_RNA_Blood_Ctrl_5month_Female_biorep5

description: UUID:5d37225c4b679d699d0240cd,QC_score:2,QC_stats:Fail


title: Bartolomei_RNA_Blood_Ctrl_5month_Female_biorep3

description: UUID:5c6347beadb9674801ad37ff,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Blood_Ctrl_5month_Female_biorep4

description: UUID:5c635a06adb9675f44ad38c3,QC_score:3,QC_stats:Pass


title: MATN3 R209P mutant, biological replicate 1

description: mutant created from 414C2 iPSC line


title: COL10A1 L614RfsX8 mutant, biological replicate 3

description: patient-derived mutant

source_name: COL10A1 L614RfsX8 mutant iPSC-derived cartilage pellet

value: COL10A1 L614RfsX8


title: MATN3 T120M mutant, biological replicate 1

description: patient-derived mutant


title: COL10A1 L614RfsX8 mutant, biological replicate 2

description: patient-derived mutant


title: MATN3 T120M mutant, biological replicate 2

description: patient-derived mutant


title: MATN3 R209P mutant, biological replicate 2

description: mutant created from 414C2 iPSC line


title: COL10A1 L614RfsX8 mutant, biological replicate 1

description: patient-derived mutant


title: Biswal_ATAC_Liver_PM2.5_5month_Female_biorep3

description: UUID:5bce9cc25ffaa67a142143ed,QC_score:1,QC_stats:Fail


title: Bartolomei_RNA_Blood_Ctrl_5month_Female_biorep2

description: UUID:5c6345a1fc74d32c2511ee91,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Liver_PM2.5_5month_Female_biorep2

description: UUID:5bce9c868fc245ec285e98d2,QC_score:-3,QC_stats:Fail


title: Biswal_RNA_Liver_Ctrl_5month_Male_biorep4

description: UUID:5bc8d921829d843d57fbc42a,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Liver_PM2.5_5month_Female_biorep1

description: UUID:5bce9c4956149c5a26eec778,QC_score:6,QC_stats:Pass


title: Biswal_RNA_Liver_Ctrl_5month_Male_biorep2

description: UUID:5bc8d7f546ce843859d2eb54,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Blood_Ctrl_5month_Female_biorep1

description: UUID:5c634439306a39c3f274937e,QC_score:1,QC_stats:Fail


title: Biswal_ATAC_Liver_Ctrl_5month_Male_biorep6

description: UUID:5bce97d68fc2452e895e98c2,QC_score:0,QC_stats:Fail


title: Biswal_RNA_Liver_Ctrl_5month_Male_biorep1

description: UUID:5bc8d77de59b4b70226c2c58,QC_score:3,QC_stats:Pass


title: Biswal_RNA_Liver_Ctrl_5month_Male_biorep3

description: UUID:5bc8d8aa83168f985ecc383b,QC_score:3,QC_stats:Pass


title: COL10A1 S600P mutant, biological replicate 3

description: mutant created from 414C2 iPSC line

source_name: COL10A1 S600P mutant iPSC-derived cartilage pellet

value: COL10A1 S600P


title: Bartolomei_RNA_Blood_BPA_10ug_5month_Male_biorep6

description: UUID:5dd2e98a92d6a0c44aa85fb7,QC_score:3,QC_stats:Pass

value: BPA (Bisphenol A) 10 UG/KGBW/DAY


title: Biswal_ATAC_Liver_Ctrl_5month_Male_biorep5

description: UUID:5bce979a56149c6d91eec75d,QC_score:2,QC_stats:Fail


title: Biswal_RNA_Liver_Ctrl_5month_Female_biorep6

description: UUID:5bc8faa5f5df5f08d7dcd0ab,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Blood_BPA_10ug_5month_Male_biorep5

description: UUID:5dd2e983c7daaba3f4a2ffad,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Liver_Ctrl_5month_Male_biorep4

description: UUID:5bce97228fc245e4a65e98bf,QC_score:8,QC_stats:Pass


title: Biswal_RNA_Liver_Ctrl_5month_Female_biorep5

description: UUID:5bc8fa2d8aaf32ef8146f19c,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Blood_BPA_10ug_5month_Male_biorep4

description: UUID:5dd2e983c7daab23eba2ffae,QC_score:3,QC_stats:Pass


title: huC3 + C5 mAb 4

city: Tarrytown

first: Gabor

last: Halasz

state: New York

address: 777 old saw mill river road

institute: Regeneron Pharmaceuticals

description:
906072
PolyA RNA
processed data file: experiment3.counts.tsv
processed data file: experiment3.TPM.tsv

data_processing:
Raw sequence data (BCL files) were converted to FASTQ format via Illumina Casava 1.8.2. Reads were decoded based on their barcodes, and read quality was evaluated with FastQC. Reads were mapped to the mouse genome (NCBI GRCm38) and mouse transcriptome (NCBI RefSeq) using ArrayStudio® software (OmicSoft®, Cary, NC) allowing two mismatches. Reads mapped to the sense-strand exons of a gene were summed at the gene level.
Genome_build: GRCm38
Supplementary_files_format_and_content: *.counts.tsv: Tab-delimited text files include counts.
Supplementary_files_format_and_content: *.TPM.tsv: Tab-delimited text files include TPMs.

source_name: kidney

extract_protocol:
Total RNA was extracted from the mouse tissue samples using the MagMAX kit (Life Tech, Carlsbad, CA).
Strand-specific RNA-seq libraries were prepared from 500 ng RNA using KAPA stranded mRNA-Seq Kit (KAPA Biosystems). Twelve-cycle PCR was performed to amplify libraries.

value: 75% C57BL/6NTac 25% 129S6/SvEvTac

value: humanized C3

tag: Sex

tag: date of birth

value: kidney

value: C5 mAb

tag: experiment

value: experiment 3


title: Biswal_ATAC_Liver_Ctrl_5month_Male_biorep3

description: UUID:5bce96e58fc245efa15e98bd,QC_score:5,QC_stats:Pass

value: 5 month

value: Male

value: Filtered Air NA


title: Bartolomei_RNA_Blood_BPA_10ug_5month_Male_biorep3

description: UUID:5dd2e980c7daaba8f4a2ffa2,QC_score:3,QC_stats:Pass

value: Blood


title: COL10A1 G18E mutant, biological replicate 3

description: patient-derived mutant

source_name: COL10A1 G18E mutant iPSC-derived cartilage pellet

value: cartilage (iPSC-derived)

value: COL10A1 G18E


title: Biswal_RNA_Liver_Ctrl_5month_Female_biorep3

description: UUID:5bc8f7218aaf32271e46f192,QC_score:3,QC_stats:Pass

value: Female

value: Liver


title: COL10A1 S600P mutant, biological replicate 1

description: mutant created from 414C2 iPSC line


title: COL10A1 G18E mutant, biological replicate 2

description: patient-derived mutant


title: COL10A1 G18E mutant, biological replicate 1

description: patient-derived mutant


title: COL10A1 S600P mutant, biological replicate 2

description: mutant created from 414C2 iPSC line


title: Biswal_RNA_Liver_Ctrl_5month_Female_biorep2

description: UUID:5bc8f6328aaf327f7c46f18d,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Blood_BPA_10ug_5month_Male_biorep1

description: UUID:5c633c05e905db5546a4e06d,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Blood_BPA_10ug_5month_Female_biorep5

description: UUID:5dd2e98992d6a07935a85fb2,QC_score:3,QC_stats:Pass


title: Biswal_RNA_Liver_Ctrl_5month_Female_biorep1

description: UUID:5bc8eb2d6f9bf44ad8fc6e50,QC_score:3,QC_stats:Pass


title: huC3 + C5 mAb 1

description:
891050
PolyA RNA
processed data file: experiment3.counts.tsv
processed data file: experiment3.TPM.tsv


title: Normal_control_2

type: genomic

city: Lublin

first: Monika

last: Szelest

address: ul. Antoniego Gębali 6

department: Laboratory of Genetic Diagnostics

country: Poland

institute: Medical University of Lublin

hyb_protocol: The 250 ng of genomic DNA from the leukemic cells was subjected to microarray examination according to the manufacturer's protocols as follows: i) Digestion with the restriction enzyme NspI; ii) adapter ligation, polymerase chain reaction (PCR) amplification and magnetic bead purification; iii) fragmentation and end-labeling with biotin; iv) washing and staining using a GeneChip ® Fluidics Station 450; and v) scanning using an Affymetrix GeneChip Scanner 3000 7G (Affymetrix). Scanned data files were generated using Affymetrix GeneChip Command Console Software, and analyzed with Affymetrix Chromosome Analysis Suite v 3.3 (Affymetrix).

data_processing: To calculate the copy number of altered regions, the data were normalized to baseline reference intensities using NA 32.3 FFPE v.2 reference model (Affymetrix). The hidden Markov model available within the software package was used to determine the copy number states (CN) and their breakpoints. Thresholds of log 2 ratio ≥0.58 and ≤1 were used to categorize altered regions as CN variation (CNV) gains (amplifications) and copy number losses (deletions), respectively. To prevent the detection of false-positive CNVs arising due to microarray unspecific signals, only regions that involved at least 50 consecutive probes were considered in the analysis of gains or losses in this study. Amplificationsand deletions were analyzed separately. To exclude aberrations representing common normal CNVs, all the identified CNVs were compared with those reported in the Database of Genomic Variants ( http://projects.tcag.ca/variation/ ). To identify the genes involved in the CNVs further, the UCSC database ( http://genome.ucsc.edu) and Ensemble (http://www.ensembl.org) were used.

source_name: blast cells, bone marrow

growth_protocol: Karyotypes are prepared from mitotic cells that have been arrested in the metaphase or prometaphase portion of the cell cycle, when chromosomes assume their most condensed conformations. For cancer diagnoses, typical specimens include bone marrow samples. The process of generating a karyotype begins with the short-term culture of cells derived from a specimen. After a period of cell growth and multiplication, dividing cells are arrested in metaphase by addition of colchicine, which poisons the mitotic spindle. The cells are next treated with a hypotonic solution that causes their nuclei to swell and the cells to burst. The nuclei are then treated with a chemical fixative, dropped on a glass slide, and treated with various stains that reveal structural features of the chromosomes.

extract_protocol: The researched material was the genomic DNA extracted from bone marrow samples using the QIAamp DNA Blood Mini Kit (Qiagen, Hilden, Germany).

tag: disease state

value: healthy

value: bone marrow

tag: cell type

value: blast cells


title: Normal_control_4

scan_protocol: The 250 ng of genomic DNA from the leukemic cells was subjected to microarray examination according to the manufacturer's protocols as follows: i) Digestion with the restriction enzyme NspI; ii) adapter ligation, polymerase chain reaction (PCR) amplification and magnetic bead purification; iii) fragmentation and end-labeling with biotin; iv) washing and staining using a GeneChip ® Fluidics Station 450; and v) scanning using an Affymetrix GeneChip Scanner 3000 7G (Affymetrix). Scanned data files were generated using Affymetrix GeneChip Command Console Software, and analyzed with Affymetrix Chromosome Analysis Suite v 3.3 (Affymetrix).

treatment_protocol: After a period of cell growth and multiplication, dividing cells are arrested in metaphase by addition of colchicine, which poisons the mitotic spindle. The cells are next treated with a hypotonic solution that causes their nuclei to swell and the cells to burst. The nuclei are then treated with a chemical fixative, dropped on a glass slide, and treated with various stains that reveal structural features of the chromosomes.


title: Bartolomei_RNA_Blood_BPA_10ug_5month_Female_biorep4

description: UUID:5dd2e98892d6a0d415a85fb0,QC_score:3,QC_stats:Pass

value: BPA (Bisphenol A) 10 UG/KGBW/DAY


title: huC3 control 3

description:
906070
PolyA RNA
processed data file: experiment3.counts.tsv
processed data file: experiment3.TPM.tsv

value: 75% C57BL/6NTac 25% 129S6/SvEvTac

value: control antibody


title: Normal_control_1

label_protocol: The 250 ng of genomic DNA from the leukemic cells was subjected to microarray examination according to the manufacturer's protocols as follows: i) Digestion with the restriction enzyme NspI; ii) adapter ligation, polymerase chain reaction (PCR) amplification and magnetic bead purification; iii) fragmentation and end-labeling with biotin; iv) washing and staining using a GeneChip ® Fluidics Station 450; and v) scanning using an Affymetrix GeneChip Scanner 3000 7G (Affymetrix). Scanned data files were generated using Affymetrix GeneChip Command Console Software, and analyzed with Affymetrix Chromosome Analysis Suite v 3.3 (Affymetrix).


title: Bartolomei_RNA_Blood_BPA_10ug_5month_Male_biorep2

description: UUID:5d37229f749ee8a9ae3260fd,QC_score:2,QC_stats:Fail


title: Biswal_ATAC_Liver_Ctrl_5month_Male_biorep2

description: UUID:5bce96aa8fc24514025e98bc,QC_score:0,QC_stats:Fail


title: huC3 + C5 mAb 3

description:
906071
PolyA RNA
processed data file: experiment3.counts.tsv
processed data file: experiment3.TPM.tsv

value: humanized C3

value: kidney


title: huC3 + C5 mAb 2

description:
891051
PolyA RNA
processed data file: experiment3.counts.tsv
processed data file: experiment3.TPM.tsv

value: C5 mAb

value: experiment 3


title: Biswal_ATAC_Liver_Ctrl_5month_Female_biorep6

description: UUID:5bce9bd256149caa6aeec775,QC_score:5,QC_stats:Pass

value: 5 month


title: Biswal_ATAC_Liver_Ctrl_5month_Female_biorep5

description: UUID:5bce9b9556149c0073eec774,QC_score:4,QC_stats:Fail

value: Filtered Air NA


title: Bartolomei_RNA_Blood_BPA_10ug_5month_Female_biorep3

description: UUID:5dd2e981c7daab2990a2ffa7,QC_score:3,QC_stats:Pass

value: Blood


title: Biswal_RNA_Blood_PM2.5_5month_Male_biorep5

description: UUID:5c86a1e54a997af5ec76bb0f,QC_score:3,QC_stats:Pass

value: Male


title: Biswal_ATAC_Liver_Ctrl_5month_Male_biorep1

description: UUID:5bce966f8fc2451acc5e98bb,QC_score:5,QC_stats:Pass


title: Biswal_ATAC_Liver_Ctrl_5month_Female_biorep4

description: UUID:5bce9b598fc245abfa5e98cc,QC_score:3,QC_stats:Fail


title: huC3 control 1

description:
891046
PolyA RNA
processed data file: experiment3.counts.tsv
processed data file: experiment3.TPM.tsv


title: Bartolomei_RNA_Blood_BPA_10ug_5month_Female_biorep2

description: UUID:5d3b6bb8b2e2695228346cd4,QC_score:3,QC_stats:Pass


title: Biswal_RNA_Blood_PM2.5_5month_Male_biorep4

description: UUID:5c869fc94a997a707876bb09,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Liver_Ctrl_5month_Female_biorep3

description: UUID:5bce9ae256149c2fcceec76f,QC_score:5,QC_stats:Pass


title: Biswal_RNA_Blood_PM2.5_5month_Male_biorep6

description: UUID:5c86a3c5e1ad3605f4d7f821,QC_score:3,QC_stats:Pass


title: Biswal_RNA_Blood_PM2.5_5month_Male_biorep3

description: UUID:5c869dad4a997a1d5576bb05,QC_score:3,QC_stats:Pass


title: Biswal_ATAC_Liver_Ctrl_5month_Female_biorep1

description: UUID:5bce9a2d8fc24565645e98c9,QC_score:3,QC_stats:Fail


title: Bartolomei_RNA_Blood_BPA_10ug_5month_Female_biorep1

description: UUID:5d3b6bb7b2e2695e3d346ccf,QC_score:3,QC_stats:Pass


title: WT control 5

description:
891043
PolyA RNA
processed data file: experiment3.counts.tsv
processed data file: experiment3.TPM.tsv

value: WT

value: control


title: Bartolomei_RNA_Blood_BPA_10mg_5month_Male_biorep6

description: UUID:5dd2e98b92d6a0798ca85fbb,QC_score:3,QC_stats:Pass

value: BPA (Bisphenol A) 10 MG/KGBW/DAY


title: WT control 3

description:
891041
PolyA RNA
processed data file: experiment3.counts.tsv
processed data file: experiment3.TPM.tsv


title: Biswal_RNA_Blood_PM2.5_5month_Male_biorep2

description: UUID:5c869b554a997aaa4f76bb01,QC_score:3,QC_stats:Pass


title: WT control 4

description:
891042
PolyA RNA
processed data file: experiment3.counts.tsv
processed data file: experiment3.TPM.tsv


title: Biswal_ATAC_Liver_Ctrl_5month_Female_biorep2

description: UUID:5bce9aa556149ccc66eec76d,QC_score:5,QC_stats:Pass

value: Female

value: Liver


title: Bartolomei_RNA_Blood_BPA_10mg_5month_Male_biorep5

description: UUID:5dd2e97dc7daab7c92a2ff9c,QC_score:3,QC_stats:Pass


title: Biswal_RNA_Blood_PM2.5_5month_Female_biorep6

description: UUID:5c86957b2cc8ec63b57e2262,QC_score:3,QC_stats:Pass


title: Ctr_190-7

city: Freiburg im Breisgau

first: Angelica

last: Gray de Cristoforis

address: Albertstr. 19

department: Department of Molecular Embryology

country: Germany

institute: Albert-Ludwigs University Freiburg, Institute of Anatomy and Cell Biology

data_processing:
Raw fastq files were processed via the RNA-seq pipiline of  snakePipes (v1.2.2). QC matrices, mapping, counting and bigWig generation were all performed within the snakePipes workflow (Bhardwaj at al, 2018).
We use gencode M18 as reference gene model annotation
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig, normalized coverage

source_name: Lumbar spinal cord and dorsal root ganglia

extract_protocol:
Lumbar spinal cords were removed, flash frozen on dry ice, and RNA was harvested using RNAeasy Mini kit (#74106, Qiagen).
Libraries for each sample were prepared according to the manual instructions of the NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530S/L, NEB), performing 12 cycles.

value: Embryonic lumbar spinal cord without removing dorsal root ganglia

value: E12.5 embryo


title: huC3 control 2

description:
906069
PolyA RNA
processed data file: experiment3.counts.tsv
processed data file: experiment3.TPM.tsv

value: 75% C57BL/6NTac 25% 129S6/SvEvTac


title: WT control 2

description:
891040
PolyA RNA
processed data file: experiment3.counts.tsv
processed data file: experiment3.TPM.tsv


title: WT control 1

description:
891039
PolyA RNA
processed data file: experiment3.counts.tsv
processed data file: experiment3.TPM.tsv


title: Biswal_RNA_Blood_PM2.5_5month_Female_biorep5

description: UUID:5c868fd94a997a047176bafa,QC_score:3,QC_stats:Pass


title: Mut_190-6


title: Normal_control_5

value: healthy

value: bone marrow

value: blast cells


title: Biswal_RNA_Blood_Ctrl_5month_Male_biorep6

description: UUID:5c868c195834876687b01d39,QC_score:3,QC_stats:Pass


title: Normal_control_3


title: Bartolomei_RNA_Blood_BPA_10mg_5month_Male_biorep4

description: UUID:5dd2e94a92d6a04784a85f98,QC_score:1,QC_stats:Fail


title: Bartolomei_RNA_Blood_BPA_10mg_5month_Male_biorep1

description: UUID:5c634872fc74d37d1111eea3,QC_score:3,QC_stats:Pass


title: huC3 sample 6

description:
822591
PolyA RNA
processed data file: experiment2.counts.tsv
processed data file: experiment2.TPM.tsv

value: humanized C3

value: kidney

value: experiment 2


title: Biswal_RNA_Liver_Ctrl_5month_Female_biorep4

description: UUID:5bc8f8898aaf32297446f193,QC_score:3,QC_stats:Pass

value: 5 month

value: Filtered Air NA


title: huC3 sample 5

description:
822589
PolyA RNA
processed data file: experiment2.counts.tsv
processed data file: experiment2.TPM.tsv

value: Male


title: Bartolomei_RNA_Blood_BPA_10mg_5month_Male_biorep2

description: UUID:5d3b6bb7b2e2691496346cd0,QC_score:3,QC_stats:Pass

value: Blood


title: huC3 sample 4

description:
822588
PolyA RNA
processed data file: experiment2.counts.tsv
processed data file: experiment2.TPM.tsv


title: Mut_181-7


title: Ctr_181-5


title: Ctr_190-5


title: Biswal_RNA_Blood_PM2.5_5month_Male_biorep1

description: UUID:5c8698fd4a997a892676bafd,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Blood_BPA_10mg_5month_Female_biorep7

description: UUID:5dd2e98b92d6a01bcca85fba,QC_score:3,QC_stats:Pass


title: huC3 sample 2

description:
822586
PolyA RNA
processed data file: experiment2.counts.tsv
processed data file: experiment2.TPM.tsv


title: Ctr_181-9


title: Biswal_RNA_Liver_PM2.5_5month_Female_biorep5

description: UUID:5bc8ffcd5195884ed3982635,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Blood_BPA_10mg_5month_Female_biorep4

description: UUID:5d3b6bb4bd3a58113b13ed1b,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Liver_Ctrl_5month_Female_biorep4

description: UUID:5c8939a589ec40ca7f2c4e99,QC_score:3,QC_stats:Pass

value: Control Diet NA


title: Ctr_181-4


title: Biswal_RNA_Blood_Ctrl_5month_Female_biorep5

description: UUID:5c85d0232795848a29fa2cbf,QC_score:3,QC_stats:Pass


title: Biswal_RNA_Blood_Ctrl_5month_Male_biorep4

description: UUID:5c8686b5583487faf8b01d30,QC_score:3,QC_stats:Pass


title: Bartolomei_RNA_Blood_BPA_10mg_5month_Female_biorep5

description: UUID:5d3b6bb5b2e2697093346cca,QC_score:3,QC_stats:Pass

value: BPA (Bisphenol A) 10 MG/KGBW/DAY


title: WT sample 3

description:
822584
PolyA RNA
processed data file: experiment2.counts.tsv
processed data file: experiment2.TPM.tsv

value: WT


title: Mut_181-3


title: Mut_190-4


title: Bartolomei_RNA_Blood_BPA_10mg_5month_Female_biorep3

description: UUID:5c6358daadb96783d4ad38a8,QC_score:3,QC_stats:Pass

value: Female


title: Bartolomei_RNA_Liver_BPA_10ug_5month_Male_biorep3

description: UUID:5c89383e9a1c3c11380a84e1,QC_score:3,QC_stats:Pass

value: Liver

value: BPA (Bisphenol A) 10 UG/KGBW/DAY


title: WT sample 2

description:
822583
PolyA RNA
processed data file: experiment2.counts.tsv
processed data file: experiment2.TPM.tsv

value: 75% C57BL/6NTac 25% 129S6/SvEvTac


title: RNA-seq_DKO_Rep6

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

country: France

institute: CNRS

data_processing:
Reads were aligned to the mouse mm10 genome with TopHat2 v2.0.13 using default parameters and a RefSeq transcriptome index.
For data visualization, bigwig files were generated using bam2wig.py from the RSeQC package v2.6.4 using the parameters -u -t 5000000000.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files for RNA-seq visualization.

source_name: RNA-seq_DKO_E8.5 whole embryos

extract_protocol:
Total RNA was extracted with the AllPrep DNA/RNA Mini Kit (Qiagen).
RNA-Seq libraries were prepared with the TruSeq Stranded Total RNA Sample Prep Kit (Illumina) with Ribo-Zero depletion according to the manufacturer’s instructions.

tag: strain background

tag: genotype/variation

value: Dnmt3a-/- Dnmt3b-/-

tag: developmental stage

tag: tissue/cell type

value: whole embryos


title: Bartolomei_RNA_Blood_BPA_10mg_5month_Female_biorep6

description: UUID:5dd2e98692d6a024c1a85fad,QC_score:2,QC_stats:Fail

tag: strain


title: Bartolomei_RNA_Blood_BPA_10mg_5month_Female_biorep2

description: UUID:5c6343495ffef25f3b53674a,QC_score:3,QC_stats:Pass

tag: age


title: huC3 sample 3

description:
822587
PolyA RNA
processed data file: experiment2.counts.tsv
processed data file: experiment2.TPM.tsv


title: Bartolomei_RNA_Liver_BPA_10ug_5month_Female_biorep3

description: UUID:5c893a5989ec40b8392c4ea0,QC_score:3,QC_stats:Pass

tag: gender


title: WT sample 1

description:
822552
PolyA RNA
processed data file: experiment2.counts.tsv
processed data file: experiment2.TPM.tsv

tag: tissue


title: liver huC3 sample 1-3

description:
743688
PolyA RNA

source_name: liver

value: liver

tag: treatment

value: experiment 1


title: Bartolomei_RNA_Blood_BPA_10mg_5month_Male_biorep3

description: UUID:5d3b6bb8b2e2691783346cd3,QC_score:3,QC_stats:Pass


title: Mut_181-2

value: Embryonic lumbar spinal cord without removing dorsal root ganglia

value: E12.5 embryo


title: RNA-seq_DKO_Rep5


title: Bartolomei_RNA_Blood_BPA_10mg_5month_Female_biorep1

description: UUID:5c6341e1e905db94baa4e07c,QC_score:3,QC_stats:Pass

value: 5 month


title: liver huC3 sample 1-2

description:
743687
PolyA RNA

value: humanized C3


title: Bartolomei_ATAC_Liver_Ctrl_5month_Male_biorep6

description: UUID:5bd8d461345ff021bdb537b3,QC_score:10,QC_stats:Pass

value: Male


title: RNA-seq_DKO_Rep4


title: Aylor_RNA_Liver_TCDD_5month_Male_biorep6

description: UUID:5ce2e89e22037f8571336cf6,QC_score:3,QC_stats:Pass

extract_protocol:
Sample collection was performed by David Aylor lab at North Carolina State University. 5 month mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by David Aylor lab at North Carolina State University. mRNA and nuclei from 5 month mice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.

value: TCDD (2,3,7,8-tetrachlorodibenzo-p-dixoin) 1 microgram per kilogram


title: huC3 sample 1

description:
822585
PolyA RNA
processed data file: experiment2.counts.tsv
processed data file: experiment2.TPM.tsv

value: kidney

value: experiment 2


title: Bartolomei_ATAC_Liver_Ctrl_5month_Male_biorep5

description: UUID:5bd8d2bd06a9505d7da53c0f,QC_score:9,QC_stats:Pass

value: Control Diet NA


title: liver huC3 sample 1-1

description:
743686
PolyA RNA


title: RNA-seq_DKO_Rep3

value: Female


title: Aylor_RNA_Liver_TCDD_5month_Male_biorep3

description: UUID:5ce2e895f3c810a518472789,QC_score:3,QC_stats:Pass

value: Liver


title: RNA-seq_DKO_Rep2


title: Bartolomei_ATAC_Liver_Ctrl_5month_Male_biorep4

description: UUID:5bd8d1ce06a950e6b8a53c04,QC_score:9,QC_stats:Pass


title: Biswal_RNA_Blood_Ctrl_5month_Male_biorep5

description: UUID:5c8688d158348767d6b01d34,QC_score:3,QC_stats:Pass

value: Blood

value: Filtered Air NA


title: liver WT sample 1-3

description:
743685
PolyA RNA

value: 75% C57BL/6NTac 25% 129S6/SvEvTac

value: WT


title: Bartolomei_RNA_Liver_Ctrl_5month_Female_biorep3

description: UUID:5c8938f29a1c3c36440a84e6,QC_score:3,QC_stats:Pass


title: Aylor_RNA_Liver_TCDD_5month_Male_biorep2

description: UUID:5ce2e88ff3c8100cbd47277f,QC_score:3,QC_stats:Pass


title: RNA-seq_DKO_Rep1

value: Dnmt3a-/- Dnmt3b-/-

value: whole embryos


title: Aylor_RNA_Liver_TCDD_5month_Male_biorep1

description: UUID:5ce2e88e22037f6364336cdd,QC_score:3,QC_stats:Pass


title: RNA-seq_D3aHet_Rep4

source_name: RNA-seq_D3aHet_E8.5 whole embryos


title: Bartolomei_ATAC_Liver_Ctrl_5month_Male_biorep2

description: UUID:5b1e9d364bdc284ce9f48b2b,QC_score:10,QC_stats:Pass


title: liver WT sample 1-1

description:
743683
PolyA RNA

value: liver

value: experiment 1


title: Aylor_RNA_Liver_TCDD_5month_Male_biorep5

description: UUID:5ce2e89c22037fefd0336cf3,QC_score:3,QC_stats:Pass

value: 5 month


title: Aylor_RNA_Liver_TCDD_5month_Female_biorep6

description: UUID:5ce2e898f3c810b98047278e,QC_score:3,QC_stats:Pass


title: Aylor_RNA_Liver_TCDD_5month_Male_biorep4

description: UUID:5ce2e896f3c810365e47278b,QC_score:3,QC_stats:Pass


title: RNA-seq_D3aHet_Rep3


title: Walker_RNA_Liver_TBT_5month_Male_biorep5

description: UUID:5aa7e861f3b7070f31a2c2cc,QC_score:3,QC_stats:Pass

extract_protocol:
Sample collection was performed by Cheryl Walker lab at Baylor College of Medicine. 5 month mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by Cheryl Walker lab at Baylor College of Medicine. mRNA and nuclei from 5 month mice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.

value: TBT (Tributyltin chloride) 0.5 mg/kg bw/d


title: Bartolomei_ATAC_Liver_Ctrl_5month_Female_biorep6

description: UUID:5bd8d33506a9507dfaa53c13,QC_score:10,QC_stats:Pass


title: Bartolomei_ATAC_Liver_Ctrl_5month_Female_biorep5

description: UUID:5bd8d20a06a95044fea53c07,QC_score:9,QC_stats:Pass


title: RNA-seq_D3aHet_Rep2


title: RNA-seq_D3aHet_Rep1


title: Walker_RNA_Liver_TBT_5month_Male_biorep3

description: UUID:5aa7e55840b1dc61db6b6454,QC_score:2,QC_stats:Fail

value: Male


title: Aylor_RNA_Liver_TCDD_5month_Female_biorep4

description: UUID:5ce2e89722037f85aa336ce7,QC_score:3,QC_stats:Pass

value: TCDD (2,3,7,8-tetrachlorodibenzo-p-dixoin) 1 microgram per kilogram


title: RNA-seq_D1KO_Rep3

source_name: RNA-seq_D1KO_E8.5 whole embryos


title: Bartolomei_ATAC_Liver_Ctrl_5month_Female_biorep3

description: UUID:5b1ea0414bdc28998df48b3c,QC_score:8,QC_stats:Pass


title: Walker_RNA_Liver_TBT_5month_Male_biorep4

description: UUID:5aa7e6faf3b707001ca2c2b5,QC_score:1,QC_stats:Fail


title: RNA-seq_D1KO_Rep2


title: Walker_RNA_Liver_TBT_5month_Male_biorep2

description: UUID:5aa7e37740b1dcce666b6446,QC_score:3,QC_stats:Pass


title: liver WT sample 1-2

description:
743684
PolyA RNA


title: Bartolomei_ATAC_Liver_Ctrl_5month_Female_biorep2

description: UUID:5b1ea0054bdc28c060f48b39,QC_score:10,QC_stats:Pass


title: Walker_RNA_Liver_TBT_5month_Male_biorep1

description: UUID:5aa7e285bba1a51a134cbfdb,QC_score:3,QC_stats:Pass


title: Bartolomei_ATAC_Liver_Ctrl_5month_Male_biorep1

description: UUID:5b1e9c467ed6a37aa691e309,QC_score:10,QC_stats:Pass


title: Aylor_RNA_Liver_Ctrl_5month_Male_biorep5

description: UUID:5ce2e89af3c81031f4472790,QC_score:3,QC_stats:Pass

value: Control Oral Gavage 10 microliter per kilogram


title: Bartolomei_ATAC_Liver_Ctrl_5month_Female_biorep1

description: UUID:5b1e9f157ed6a34c4191e317,QC_score:10,QC_stats:Pass


title: RNA-seq_D1KO_Rep1


title: Walker_RNA_Liver_Ctrl_5month_Male_biorep1

description: UUID:5aa7e89fe80facce0c5b7d14,QC_score:3,QC_stats:Pass

value: Control Drinking Water 0 mg/kg


title: Aylor_RNA_Liver_TCDD_5month_Female_biorep5

description: UUID:5ce2e89722037fe762336ce8,QC_score:3,QC_stats:Pass


title: Aylor_RNA_Liver_TCDD_5month_Female_biorep3

description: UUID:5ce2e896f3c8107e6d47278c,QC_score:3,QC_stats:Pass


title: Walker_RNA_Liver_Ctrl_5month_Female_biorep1

description: UUID:5aa7e11ef3b707fa93a2c2a9,QC_score:3,QC_stats:Pass


title: Aylor_RNA_Liver_TCDD_5month_Female_biorep2

description: UUID:5ce2e89122037f9330336ce2,QC_score:3,QC_stats:Pass


title: RNA-seq_D3abWT_Rep2

source_name: RNA-seq_D3abWT_E8.5 whole embryos

value: wild type


title: Bartolomei_ATAC_Liver_BPA_10ug_5month_Male_biorep3

description: UUID:5b1e9ed97ed6a375c891e315,QC_score:10,QC_stats:Pass

value: BPA (Bisphenol A) 10 UG/KGBW/DAY


title: Aylor_RNA_Liver_Ctrl_5month_Male_biorep2

description: UUID:5ce2e88ff3c810377747277e,QC_score:3,QC_stats:Pass

value: Liver


title: Walker_RNA_Liver_Ctrl_5month_Female_biorep2

description: UUID:5aa7e20f40b1dc4f5d6b643a,QC_score:3,QC_stats:Pass

value: Female


title: Aylor_RNA_Liver_TCDD_5month_Female_biorep1

description: UUID:5ce2e89022037f266b336cdf,QC_score:3,QC_stats:Pass


title: Walker_RNA_Blood_TBT_5month_Male_biorep4

description: UUID:5d138845c097441c3d762398,QC_score:2,QC_stats:Fail

value: Blood


title: Aylor_RNA_Liver_Ctrl_5month_Male_biorep4

description: UUID:5ce2e89722037f53db336ce6,QC_score:3,QC_stats:Pass


title: RNA-seq_D3abWT_Rep1


title: Bartolomei_ATAC_Liver_BPA_10ug_5month_Male_biorep5

description: UUID:5bd8d55106a9500192a53c25,QC_score:9,QC_stats:Pass


title: RNA-seq_D1WT_Rep3

source_name: RNA-seq_D1WT_E8.5 whole embryos


title: Bartolomei_ATAC_Liver_BPA_10ug_5month_Male_biorep6

description: UUID:5bd8d7aa06a95070c0a53c37,QC_score:8,QC_stats:Pass


title: Aylor_RNA_Liver_Ctrl_5month_Male_biorep3

description: UUID:5ce2e892f3c810710d472782,QC_score:3,QC_stats:Pass


title: Bartolomei_ATAC_Liver_BPA_10ug_5month_Male_biorep4

description: UUID:5bd8d0de06a950564da53bfc,QC_score:8,QC_stats:Pass


title: Walker_RNA_Blood_TBT_5month_Male_biorep6

description: UUID:5d138853c0974464487623c1,QC_score:2,QC_stats:Fail


title: RNA-seq_D1WT_Rep2


title: Aylor_RNA_Liver_Ctrl_5month_Female_biorep6

description: UUID:5ce2e89922037f2b2e336cec,QC_score:3,QC_stats:Pass


title: Bartolomei_ATAC_Liver_BPA_10ug_5month_Male_biorep1

description: UUID:5b1e9c094bdc28d019f48b27,QC_score:8,QC_stats:Pass


title: RRBS_MEF_cDKO_d69_Tam_Rep2

data_processing:
Reads were cleaned with Trim Galore v0.4.2 using the parameters --rrbs --paired -r1 30 -r2 30 -q 20 --length 20 --stringency 5 --retain_unpaired. Reads were aligned to the mouse mm10 genome with BSMAP v2.74 using the parameters -v 2 -w 100 -r 1 -x 400 -m 30 -D C-CGG -n 1. Methylation percent values were extracted with methratio.py from BSMAP v2.74 using the parameters -z -u -g. CGs were filtered to have a minimum sequencing depth of 8X using custom developped scripts in R.
Genome_build: mm10
Supplementary_files_format_and_content: IGV files containing methylation scores for all CGs with at least 8X sequencing depth.

extract_protocol:
Genomic DNA was extracted with the AllPrep DNA/RNA Mini Kit (Qiagen).
RRBS libraries were prepared as described in Auclair et al., Genome Biol 15:545 (2014). Briefly, we digested genomic DNA 5 hours with MspI (ThermoFisher Scientific), followed by end-repair and A-tailing with 5 U Klenow-fragment exo- (ThermoFisher Scientific) and ligation to methylated adapters overnight at 16°C with 30 U T4 DNA ligase (ThermoFisher Scientific) in Tango 1X buffer. Fragments between 150 and 400 bp were excised from a 3% agarose 0.5X TBE gel with the MinElute kit (Qiagen) and bisulfite-converted with the EpiTect Bisulfite kit (Qiagen) using two consecutive rounds of conversion. Final RRBS libraries were amplified with 14-16 cycles of PCR. The libraries were purified using Ampure XP beads (Beckman Coulter).

value: Dnmt3a L1/L1 Dnmt3b L1/L1

value: Mouse Embryonic Fibroblasts


title: RRBS_MEF_cDKO_d69_Tam_Rep1


title: Walker_RNA_Blood_TBT_5month_Male_biorep5

description: UUID:5d138851c0974425287623bc,QC_score:2,QC_stats:Fail


title: Bartolomei_ATAC_Liver_Ctrl_5month_Female_biorep4

description: UUID:5bd8d155345ff00badb5379a,QC_score:8,QC_stats:Pass

value: Control Diet NA


title: Aylor_RNA_Liver_Ctrl_5month_Male_biorep6

description: UUID:5ce2e89c22037f8cca336cf4,QC_score:3,QC_stats:Pass


title: Bartolomei_ATAC_Liver_BPA_10ug_5month_Female_biorep5

description: UUID:5bd8d20a345ff0b25eb5379e,QC_score:9,QC_stats:Pass


title: RNA-seq_D1WT_Rep1

value: whole embryos


title: Bartolomei_ATAC_Liver_BPA_10ug_5month_Male_biorep2

description: UUID:5b1e9cbd7ed6a349c691e30a,QC_score:10,QC_stats:Pass


title: RRBS_MEF_cDKO_d69_noTam_Rep2

value: Dnmt3a L2/L2 Dnmt3b L2/L2


title: Aylor_RNA_Liver_Ctrl_5month_Female_biorep5

description: UUID:5ce2e89822037f0508336ce9,QC_score:3,QC_stats:Pass


title: Walker_RNA_Blood_TBT_5month_Female_biorep4

description: UUID:5d13883fc0974439ea762388,QC_score:2,QC_stats:Fail


title: Aylor_RNA_Liver_Ctrl_5month_Male_biorep1

description: UUID:5ce2e88ef3c810170847277c,QC_score:3,QC_stats:Pass


title: RRBS_MEF_cDKO_d69_noTam_Rep1


title: Walker_RNA_Blood_TBT_5month_Male_biorep3

description: UUID:5d138840c09744fcd3762389,QC_score:2,QC_stats:Fail


title: RRBS_MEF_cDKO_d69_Tam_Rep3


title: Aylor_RNA_Liver_Ctrl_5month_Female_biorep1

description: UUID:5ce2e88ef3c810f0a247277d,QC_score:3,QC_stats:Pass


title: RRBS_MEF_cDKO_d23_Tam_Rep3


title: RRBS_MEF_cDKO_d69_noTam_Rep3


title: Walker_RNA_Blood_TBT_5month_Female_biorep3

description: UUID:5d13883ec097440dba762383,QC_score:1,QC_stats:Fail


title: Walker_RNA_Blood_TBT_5month_Male_biorep1

description: UUID:5aa7e6fbf3b7070196a2c2b7,QC_score:0,QC_stats:Fail


title: Walker_RNA_Blood_TBT_5month_Male_biorep2

description: UUID:5d13883ec097445130762385,QC_score:2,QC_stats:Fail


title: Bartolomei_ATAC_Liver_BPA_10ug_5month_Female_biorep2

description: UUID:5b1e9e617ed6a316c391e312,QC_score:10,QC_stats:Pass


title: Aylor_RNA_Liver_Ctrl_5month_Female_biorep3

description: UUID:5ce2e89222037f5e58336ce4,QC_score:3,QC_stats:Pass


title: Aylor_RNA_Liver_Ctrl_5month_Female_biorep4

description: UUID:5ce2e893f3c8109b64472784,QC_score:3,QC_stats:Pass


title: Walker_RNA_Blood_TBT_5month_Female_biorep6

description: UUID:5d138848c097449c9a7623a1,QC_score:2,QC_stats:Fail


title: Walker_RNA_Blood_TBT_5month_Female_biorep5

description: UUID:5d138842c09744a9ca76238e,QC_score:1,QC_stats:Fail


title: Aylor_RNA_Blood_TCDD_5month_Male_biorep6

description: UUID:5d2cd31a963fdf63910fe883,QC_score:3,QC_stats:Pass


title: Bartolomei_ATAC_Liver_BPA_10mg_5month_Male_biorep5

description: UUID:5bd8d19206a9502666a53c01,QC_score:10,QC_stats:Pass

value: BPA (Bisphenol A) 10 MG/KGBW/DAY


title: Bartolomei_ATAC_Liver_BPA_10ug_5month_Female_biorep1

description: UUID:5b1e9b927ed6a3586191e307,QC_score:8,QC_stats:Pass

value: 5 month


title: Walker_RNA_Blood_TBT_5month_Female_biorep2

description: UUID:5d13883bc09744faf176237d,QC_score:1,QC_stats:Fail

value: TBT (Tributyltin chloride) 0.5 mg/kg bw/d


title: RRBS_MEF_cDKO_d23_Tam_Rep1


title: Walker_RNA_Blood_TBT_5month_Female_biorep1

description: UUID:5aa7e7aff3b70770a9a2c2c0,QC_score:0,QC_stats:Fail


title: Bartolomei_ATAC_Liver_BPA_10ug_5month_Female_biorep3

description: UUID:5bd8d0a2345ff02975b53795,QC_score:5,QC_stats:Pass


title: Bartolomei_ATAC_Liver_BPA_10mg_5month_Male_biorep6

description: UUID:5bd8d67e345ff0bdcbb537c7,QC_score:9,QC_stats:Pass

value: Male


title: Bartolomei_ATAC_Liver_BPA_10mg_5month_Male_biorep4

description: UUID:5b1e9fca4bdc28aa0bf48b37,QC_score:10,QC_stats:Pass


title: Walker_RNA_Blood_Ctrl_5month_Male_biorep6

description: UUID:5d13884dc097440f1c7623b1,QC_score:1,QC_stats:Fail


title: Aylor_RNA_Blood_TCDD_5month_Male_biorep3

description: UUID:5d2cd317398e61158ceb8d18,QC_score:3,QC_stats:Pass

value: TCDD (2,3,7,8-tetrachlorodibenzo-p-dixoin) 1 microgram per kilogram


title: Aylor_RNA_Blood_TCDD_5month_Male_biorep5

description: UUID:5d2cd319963fdf1a530fe880,QC_score:3,QC_stats:Pass


title: RRBS_MEF_cDKO_d23_Tam_Rep2


title: Bartolomei_ATAC_Liver_BPA_10mg_5month_Male_biorep3

description: UUID:5b1e9e267ed6a3338a91e310,QC_score:10,QC_stats:Pass


title: RRBS_MEF_cDKO_d23_noTam_Rep2


title: Walker_RNA_Blood_Ctrl_5month_Male_biorep5

description: UUID:5d13884bc0974402b17623a9,QC_score:2,QC_stats:Fail


title: Walker_RNA_Blood_Ctrl_5month_Male_biorep4

description: UUID:5d13883dc097442dcb762381,QC_score:2,QC_stats:Fail


title: RRBS_MEF_cDKO_d23_noTam_Rep1


title: Aylor_RNA_Liver_Ctrl_5month_Female_biorep2

description: UUID:5ce2e88f22037f132f336cde,QC_score:3,QC_stats:Pass

value: Control Oral Gavage 10 microliter per kilogram


title: Bartolomei_ATAC_Liver_BPA_10mg_5month_Male_biorep2

description: UUID:5b1e9de97ed6a3018791e30f,QC_score:10,QC_stats:Pass


title: Aylor_RNA_Blood_TCDD_5month_Male_biorep2

description: UUID:5d2cd315398e6186eceb8d12,QC_score:3,QC_stats:Pass


title: Bartolomei_ATAC_Liver_BPA_10mg_5month_Male_biorep1

description: UUID:5b1e9cf94bdc282b37f48b2a,QC_score:0,QC_stats:Fail


title: Bartolomei_ATAC_Liver_Ctrl_5month_Male_biorep3

description: UUID:5b1e9f517ed6a31ea991e31a,QC_score:10,QC_stats:Pass


title: RRBS_DKO_Rep3

source_name: RRBS_DKO_E8.5 whole embryos

value: Dnmt3a-/- Dnmt3b-/-


title: RRBS_DKO_Rep2


title: Walker_RNA_Blood_Ctrl_5month_Male_biorep1

description: UUID:5aa7e736e80fac678b5b7d03,QC_score:3,QC_stats:Pass

value: Control Drinking Water 0 mg/kg


title: Bartolomei_ATAC_Liver_BPA_10mg_5month_Female_biorep6

description: UUID:5bd8d7aa06a9505c85a53c36,QC_score:9,QC_stats:Pass


title: Aylor_RNA_Blood_TCDD_5month_Female_biorep6

description: UUID:5d2cd31c963fdf5e410fe888,QC_score:3,QC_stats:Pass


title: Aylor_RNA_Blood_TCDD_5month_Male_biorep1

description: UUID:5d2cd313398e612f2aeb8d09,QC_score:3,QC_stats:Pass


title: Bartolomei_ATAC_Liver_BPA_10mg_5month_Female_biorep5

description: UUID:5bd8d76e345ff08ba7b537cb,QC_score:10,QC_stats:Pass


title: Aylor_RNA_Blood_TCDD_5month_Female_biorep5

description: UUID:5d2cd31b963fdf151f0fe885,QC_score:3,QC_stats:Pass


title: RRBS_DKO_Rep1


title: Walker_RNA_Blood_Ctrl_5month_Female_biorep6

description: UUID:5d13884fc097445d2b7623b6,QC_score:2,QC_stats:Fail


title: RRBS_MEF_cDKO_d23_noTam_Rep3


title: Bartolomei_ATAC_Liver_BPA_10mg_5month_Female_biorep4

description: UUID:5bd8d6f506a9508f70a53c33,QC_score:10,QC_stats:Pass


title: Aylor_RNA_Blood_TCDD_5month_Male_biorep4

description: UUID:5d2cd319398e61a66aeb8d1a,QC_score:3,QC_stats:Pass


title: RRBS_D3abHet_Rep3

source_name: RRBS_D3abHet_E8.5 whole embryos

value: Dnmt3a-/+ Dnmt3b-/+


title: Walker_RNA_Blood_Ctrl_5month_Female_biorep5

description: UUID:5d138847c0974433ee76239d,QC_score:2,QC_stats:Fail


title: Bartolomei_ATAC_Liver_BPA_10mg_5month_Female_biorep3

description: UUID:5bd8d64206a950e427a53c2f,QC_score:10,QC_stats:Pass

value: Liver


title: Aylor_RNA_Blood_TCDD_5month_Female_biorep3

description: UUID:5d2cd315398e612630eb8d10,QC_score:3,QC_stats:Pass

value: Female


title: Walker_RNA_Blood_Ctrl_5month_Female_biorep4

description: UUID:5d138846c09744100776239a,QC_score:2,QC_stats:Fail

value: Blood


title: Walker_RNA_Blood_Ctrl_5month_Male_biorep2

description: UUID:5d138838c097448c51762375,QC_score:3,QC_stats:Pass


title: Bartolomei_ATAC_Liver_BPA_10mg_5month_Female_biorep2

description: UUID:5bd8d282345ff00842b537a2,QC_score:10,QC_stats:Pass


title: RRBS_D3abHet_Rep2


title: Aylor_RNA_Blood_TCDD_5month_Female_biorep2

description: UUID:5d2cd314398e61de73eb8d0d,QC_score:3,QC_stats:Pass


title: RRBS_D3abHet_Rep1


title: Bartolomei_ATAC_Liver_BPA_10mg_5month_Female_biorep1

description: UUID:5b1e9dad4bdc28b6fef48b2e,QC_score:9,QC_stats:Pass


title: Aylor_RNA_Blood_Ctrl_5month_Male_biorep6

description: UUID:5d2cd317398e61022beb8d16,QC_score:3,QC_stats:Pass


title: Walker_RNA_Blood_Ctrl_5month_Female_biorep2

description: UUID:5d138840c09744084a76238a,QC_score:3,QC_stats:Pass


title: Bartolomei_ATAC_Blood_Ctrl_5month_Male_biorep9

description: UUID:5de967e0a0134f145ed8fec6,QC_score:7,QC_stats:Pass


title: Walker_RNA_Blood_Ctrl_5month_Female_biorep1

description: UUID:5aa7e0e2e80fac06e45b7cec,QC_score:0,QC_stats:Fail


title: Aylor_RNA_Blood_TCDD_5month_Female_biorep1

description: UUID:5d2cd310963fdf376c0fe876,QC_score:3,QC_stats:Pass


title: Aylor_RNA_Blood_Ctrl_5month_Male_biorep5

description: UUID:5d2cd315398e6162bbeb8d0f,QC_score:3,QC_stats:Pass


title: Aylor_RNA_Blood_TCDD_5month_Female_biorep4

description: UUID:5d2cd317398e61fb96eb8d19,QC_score:3,QC_stats:Pass


title: Aylor_RNA_Blood_Ctrl_5month_Male_biorep4

description: UUID:5d2cd314398e61d720eb8d0e,QC_score:3,QC_stats:Pass


title: Skeletal Muscle, M-M-41

city: New York

first: Yongchao

last: Ge

state: NY

address: One Gustave L Levy Place #1137

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The RNA-seq fastq files were aligned with STAR v2.5.1b with the human GENCODE annotation.
featureCounts v1.5.0-p1 is used to summarize the reads for all genes and samples.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited file including the counts of reads for all genes and for all samples

extract_protocol:
Skeletal muscle samples were homogenized in a Bead Ruptor Elite bead mill homogenizer cooled by liquid nitrogen to 10°C for 2 x 20 seconds at 4.2 m/s. Muscle homogenates were processed using the Agencourt RNAdvance Tissue Kit on a BioMek FXP Laboratory Automation Workstation
cDNA libraries were constructed from 250 ng of total RNA using the Universal Plus mRNA-Seq kit from NuGEN

value: control

value: Skeletal Muscle (vastus lateralis muscle)


title: RRBS_D1KO_Rep3

source_name: RRBS_D1KO_E8.5 whole embryos


title: RRBS_D3aHet_Rep1

source_name: RRBS_D3aHet_E8.5 whole embryos


title: Skeletal Muscle, M-M-40


title: RRBS_D3aHet_Rep2


title: Bartolomei_ATAC_Blood_Ctrl_5month_Male_biorep6

description: UUID:5c636366adb967062bad395d,QC_score:3,QC_stats:Fail

value: Control Diet NA


title: Bartolomei_ATAC_Liver_BPA_10ug_5month_Female_biorep4

description: UUID:5bd8d11a345ff0406eb53797,QC_score:10,QC_stats:Pass

value: BPA (Bisphenol A) 10 UG/KGBW/DAY


title: Aylor_RNA_Blood_Ctrl_5month_Male_biorep3

description: UUID:5d2cd311963fdfb63b0fe877,QC_score:3,QC_stats:Pass


title: Skeletal Muscle, M-M-39

value: Parkinson's Disease


title: Walker_RNA_Blood_Ctrl_5month_Female_biorep3

description: UUID:5d138844c0974454ec762394,QC_score:1,QC_stats:Fail


title: RRBS_D1KO_Rep1

value: whole embryos


title: Aylor_RNA_Blood_Ctrl_5month_Male_biorep2

description: UUID:5d2cd311963fdf7c0f0fe879,QC_score:3,QC_stats:Pass

value: 5 month


title: Bartolomei_ATAC_Blood_Ctrl_5month_Male_biorep4

description: UUID:5c6354295ffef2655b53679f,QC_score:6,QC_stats:Pass


title: Bartolomei_ATAC_Blood_Ctrl_5month_Male_biorep8

description: UUID:5c6366725ffef254cc53687a,QC_score:-3,QC_stats:Fail


title: Bartolomei_ATAC_Blood_Ctrl_5month_Male_biorep5

description: UUID:5c6358255ffef26dca5367ba,QC_score:9,QC_stats:Pass


title: Aylor_RNA_Blood_Ctrl_5month_Male_biorep1

description: UUID:5d2cd30e398e612d70eb8d06,QC_score:3,QC_stats:Pass


title: RRBS_D3abWT_Rep2

source_name: RRBS_D3abWT_E8.5 whole embryos

value: wild type


title: Bartolomei_ATAC_Blood_Ctrl_5month_Male_biorep3

description: UUID:5c634871adb967b562ad3804,QC_score:6,QC_stats:Pass

value: Male


title: Skeletal Muscle, M-M-36


title: Aylor_RNA_Blood_Ctrl_5month_Female_biorep6

description: UUID:5d2cd31b963fdfacfc0fe886,QC_score:3,QC_stats:Pass


title: RRBS_D3abWT_Rep1


title: Bartolomei_ATAC_Blood_Ctrl_5month_Male_biorep7

description: UUID:5c636671adb9678b37ad39ad,QC_score:4,QC_stats:Fail


title: Skeletal Muscle, M-M-37


title: Bartolomei_ATAC_Blood_Ctrl_5month_Male_biorep2

description: UUID:5c63470afc74d37a9911ee99,QC_score:5,QC_stats:Pass


title: Aylor_RNA_Blood_Ctrl_5month_Female_biorep5

description: UUID:5d2cd317398e618273eb8d17,QC_score:3,QC_stats:Pass


title: RRBS_D1WT_Rep3

source_name: RRBS_D1WT_E8.5 whole embryos


title: Bartolomei_ATAC_Blood_Ctrl_5month_Male_biorep1

description: UUID:5bd8d516345ff0d4cfb537bd,QC_score:3,QC_stats:Fail


title: Skeletal Muscle, M-M-35


title: RRBS_D3aHet_Rep3


title: Aylor_RNA_Blood_Ctrl_5month_Female_biorep4

description: UUID:5d2cd316398e612018eb8d13,QC_score:3,QC_stats:Pass


title: Skeletal Muscle, M-M-38


title: Bartolomei_ATAC_Blood_Ctrl_5month_Female_biorep9

description: UUID:5de967dfb4697acf6dd96f9e,QC_score:9,QC_stats:Pass


title: RRBS_D1WT_Rep2


title: Aylor_RNA_Blood_Ctrl_5month_Female_biorep3

description: UUID:5d2cd314398e61f7eceb8d0c,QC_score:3,QC_stats:Pass


title: Skeletal Muscle, M-M-34


title: RRBS_D1WT_Rep1


title: Bartolomei_ATAC_Blood_Ctrl_5month_Female_biorep8

description: UUID:5de967deb4697a0912d96f9d,QC_score:9,QC_stats:Pass


title: Aylor_RNA_Blood_Ctrl_5month_Female_biorep2

description: UUID:5d2cd310963fdf17930fe874,QC_score:3,QC_stats:Pass


title: RRBS_D1KO_Rep2


title: Skeletal Muscle, M-M-33


title: WGBS_DKO_Rep1

data_processing:
Reads were cleaned to remove low quality bases as well as the first five bases of reads R1 and ten bases of reads R2 with Trim Galore v0.4.2 using the parameters --paired -q 20 --stringency 2 --clip_R1 5 --clip_R2 10. The reads were aligned to the mm10 genome and cleaned for duplicates using Bismark v0.22.1 with default parameters. Reads with signs of incomplete conversion were removed using the filter_non_conversion option in Bismark with the parameters --minimum_count 5 and --percentage_cutoff 50. Methylation calls were extracted using the Bismark methylation extractor. CGs were filtered to have a minimum sequencing depth of 5X using custom developped scripts in R.
Genome_build: mm10
Supplementary_files_format_and_content: IGV files containing methylation scores for all CGs with at least 5X sequencing depth.

source_name: WGBS_DKO_Rep1_E8.5 whole embryos

extract_protocol:
Genomic DNA was extracted with the AllPrep DNA/RNA Mini Kit (Qiagen).
50 ng of genomic DNA were fragmented to 350 bp using a Covaris E220 sonicator. DNA was bisulfite-converted with the EZ DNA Methylation-Gold kit (Zymo Research) and WGBS libraries were prepared using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences) according to the manufacturer's instructions with 7 PCR cycles for the final amplification. The libraries were purified using Ampure XP beads (Beckman Coulter).


title: Aylor_RNA_Blood_Ctrl_5month_Female_biorep1

description: UUID:5d2cd30f963fdf5b080fe871,QC_score:3,QC_stats:Pass


title: Skeletal Muscle, M-M-32


title: Bartolomei_ATAC_Blood_Ctrl_5month_Female_biorep7

description: UUID:5c6365f95ffef2bae353686e,QC_score:10,QC_stats:Pass


title: WGBS_D1KO_Rep1

source_name: WGBS_D1KO_Rep1_E8.5 whole embryos


title: Bartolomei_ATAC_Blood_Ctrl_5month_Female_biorep6

description: UUID:5c6365beadb9679e46ad39a4,QC_score:-3,QC_stats:Fail


title: Skeletal Muscle, M-M-30


title: Skeletal Muscle, M-M-31


title: WGBS_WT_Rep1

source_name: WGBS_WT_Rep1_E8.5 whole embryos


title: Aylor_ATAC_Liver_TCDD_5month_Male_biorep6

description: UUID:5d39fbf779452c100a795229,QC_score:10,QC_stats:Pass

value: TCDD (2,3,7,8-tetrachlorodibenzo-p-dixoin) 1 microgram per kilogram


title: Aylor_ATAC_Liver_TCDD_5month_Male_biorep5

description: UUID:5d39fbf679452cf94d795227,QC_score:10,QC_stats:Pass


title: N12

city: Nanjing

first: Sisi

last: Mo

state: Jiangsu

address: 87 Dingjia Qiao, Gulou District

country: China

institute: Zhongda Hospital, Southeast University

description:
MRI
S-100

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.0.5)software
The transcript abundances for each sample was estimated with StringTie（1.3.1c）
the FPKM value for gene and transcript level were calculated with R package Ballgown (v2.6.0)
The circRNA reads were aligned to reference genome using STAR(2.5.2b)detecting backesplicec junction reads with CIRCexplore2 (2.2.6)
Genome_build: hg19

source_name: Peripheral venous blood

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer
Total RNA of each sample was used to prepare the RNA sequencing library

value: Peripheral venous blood

tag: diagnosis

value: with PWMD


title: Bartolomei_ATAC_Blood_Ctrl_5month_Female_biorep5

description: UUID:5c63614a5ffef22e7c53682a,QC_score:2,QC_stats:Fail


title: Skeletal Muscle, M-M-29


title: Aylor_ATAC_Liver_TCDD_5month_Male_biorep4

description: UUID:5d39fbc1c310a93dcaf3444d,QC_score:10,QC_stats:Pass


title: Bartolomei_ATAC_Blood_Ctrl_5month_Female_biorep4

description: UUID:5c6352855ffef29268536789,QC_score:-1,QC_stats:Fail


title: N15

description:
MRI
S-100


title: Bartolomei_ATAC_Blood_Ctrl_5month_Female_biorep3

description: UUID:5c63515a5ffef22ff5536781,QC_score:0,QC_stats:Fail


title: Skeletal Muscle, M-M-27


title: N13

description:
MRI
S-100

value: no brain injury


title: N27

description:
MRI
S-100


title: Aylor_ATAC_Liver_TCDD_5month_Male_biorep2

description: UUID:5d39fbbf79452c3fa7795221,QC_score:10,QC_stats:Pass


title: Skeletal Muscle, M-M-28


title: Skeletal Muscle, M-M-26


title: Bartolomei_ATAC_Blood_Ctrl_5month_Female_biorep10

description: UUID:5de967e2a0134fb454d8fece,QC_score:7,QC_stats:Pass


title: Bartolomei_ATAC_Blood_Ctrl_5month_Female_biorep2

description: UUID:5c6348e9adb96758dbad380a,QC_score:1,QC_stats:Fail


title: Aylor_ATAC_Liver_TCDD_5month_Male_biorep1

description: UUID:5d39fbbcc310a91e02f34447,QC_score:10,QC_stats:Pass


title: N55

description:
MRI
S-100


title: Skeletal Muscle, M-M-25


title: Aylor_ATAC_Liver_TCDD_5month_Male_biorep3

description: UUID:5d39fbc079452c20a7795224,QC_score:10,QC_stats:Pass


title: Aylor_ATAC_Liver_TCDD_5month_Female_biorep6

description: UUID:5d39fbf979452c22d679522f,QC_score:10,QC_stats:Pass


title: Bartolomei_ATAC_Blood_Ctrl_5month_Female_biorep1

description: UUID:5c6347befc74d36d8e11ee9e,QC_score:4,QC_stats:Fail


title: N78

description:
MRI
S-100


title: Skeletal Muscle, M-M-24


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Male_biorep8

description: UUID:5c63610d5ffef27027536828,QC_score:2,QC_stats:Fail


title: cow Oocyte Bsseq

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

data_processing:
Libraries were sequenced on the Illumina HiSeq platform using the default RTA analysis software.
Raw sequence reads had the first 9 base pairs clipped off the 5' end to remove the 9N random priming portion of the reads, and were also trimmed to remove both poor quality calls and adapters using Trim Galore (v0.6.4, www.bioinformatics.babraham.ac.uk/projects/trim_galore/, parameters: --clip_r1 9). The remaining sequences were then aligned to the respective genomes in single-end mode using Bismark (v0.19.1; parameters: --pbat). The cow Oocyte data was processed as single-cell data: it was trimmed and aligned in the same manner but with the following parameters (v0.19.1; --non_directional). Methylation calls were extracted after duplicate sequences had been excluded.
Genome_build: Pig: Sscrofa11.1
Genome_build: Cow: UMD3.1
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>

organism: Bos taurus

source_name: Oocyte

extract_protocol:
For pig, in vitro maturation (IVM) of oocytes was performed as previously described (Coy et al., 2010). Semen samples were collected by the gloved hand method from fertility-tested boars. Spermatozoa and oocytes were cocultured at 38.5°C under 5% CO2 in air saturated of humidity and 18 hours post insemination (hpi) the putative zygotes were washed and transferred to embryo culture medium. At 48, 72, 120 and 168 hpi, pools of forty 2-4 cell embryos, twenty 8-16 cell embryos, ten morula and single expanded blastocyst were selected, washed in PBS and ZP digested by 0.5% w/v pronase in PBS. Finally, embryos were washed three times in PBS and snap frozen in liquid nitrogen until further processing. For cow, non-lactating and non-pregnant cows  were used as oocyte donors. Ultrasound evaluation was performed in order to assess the size of follicle(s) or to count the number of puncturable follicles. Ovum pick up was performed on ≥ 15mm of diameter follicles. For single cell oocyte collection affter aspiration oocytes were collected under a stereomicroscope, washed in Dulbecco’s Phosphate buffered (without calcium nor magnesium, PBS) supplemented with 0.5% polyvinyl alcohol (wt/v). Cumulus cells were removed with gentle pipetting and treatment with hyaluronidase. Zona pellucida was removed using pronase. Oocytes were put in 5µl of RLT buffer, immediately frozen in liquid nitrogen and stored at -80ºC until processing for sc-BS seq. For embryo production, immature cumulus-oocyte complexes (COCs) were obtained by aspirating follicles (2-8 mm) from the ovaries of matured heifers and cows collected at slaughter house from local abattoirs. COCs were matured in four-well dishes in TCM-199 maturation medium, supplemented with 10% (v/v) fetal calf serum (FCS) and 10 ng/ml epidermal growth factor (EGF) in 4 well dishes in groups of 50 COCs per well at 38.5°C under an atmosphere of 5% CO2 in air with maximum humidity (Rizos et al., 2002).  After 24h of maturation, a representative number of the in vitro matured COCs were suspended in 100 μL of PBS without calcium nor magnesium supplemented with 1% BSA and their cumulus cells (CCs) completely removed by pipetting. Matured oocytes were in vitro fertilized (IVF). IVF was performed as described previously (Lopera-Vasquez et al., 2015)  The remaining matured oocytes were in vitro fertilized (IVF) for embryo production. IVF was performed as described previously (Lopera-Vasquez et al., 2015).
sample lysis: an individual sample (oocyte, 2-4, 8-16 cell, morula pools or individual blastocyst) was lysed for 1 hr in 1% SDS with proteinase K (1ul, 20 mg/mL) at 37C. Alternatively, either bull and boar sperm DNA was extracted from ejaculates of two biological individuals. Cells were lysed in the lysis buffer containing 10% SDS with proteinase K, 20 mM Tris, 10 mM DTT, 10 mM EDTA, 150 mM NaCl, 10 mM KCl for 2 hours at 50C. Further, DNA was purified with phenol:chloroform at 1:1 ratio and precipitated with equal volume of isopropanol. DNA pellet was washed with 70% ethanol, air dried and dissolved in EB buffer. DNA concentration was measured using Nanodrop and 10 ng was used for bisulfite conversion and PBAT library preparation as described below
Post bisulfite adapter tagging (PBAT) as  described in Muira et al (2012, PMID: 22649061) with few modifications (Canovas et al, 2017) (PMID: 28134613). Alternatively, for sc-BS-seq (single cow oocytes) protocol described by Smallwood et al, 2014 was used.

value: Oocyte


title: Aylor_ATAC_Liver_TCDD_5month_Female_biorep4

description: UUID:5d39fbc3c310a917dbf34455,QC_score:10,QC_stats:Pass

value: Liver


title: Aylor_ATAC_Liver_TCDD_5month_Female_biorep5

description: UUID:5d39fbf879452c1cb579522c,QC_score:10,QC_stats:Pass

value: Female


title: Aylor_ATAC_Liver_TCDD_5month_Female_biorep3

description: UUID:5d39fbc2c310a9e2c8f34452,QC_score:10,QC_stats:Pass


title: cow Sperm BSseq

source_name: Sperm

value: Sperm


title: cow Morula BSseq

source_name: Morula

value: Morula


title: Skeletal Muscle, M-M-23

value: control

value: Skeletal Muscle (vastus lateralis muscle)


title: Skeletal Muscle, M-M-21

value: 16-wk high intensity resistance training


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Male_biorep7

description: UUID:5c635eb5adb96749b7ad3911,QC_score:2,QC_stats:Fail

value: Blood

value: BPA (Bisphenol A) 10 UG/KGBW/DAY


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Male_biorep6

description: UUID:5c635d8a5ffef2608d5367f6,QC_score:8,QC_stats:Pass

value: 5 month


title: cow Blastocyst BSseq

source_name: Blastocyst

value: Blastocyst


title: Aylor_ATAC_Liver_TCDD_5month_Female_biorep2

description: UUID:5d39fbc079452c769d795225,QC_score:10,QC_stats:Pass


title: Skeletal Muscle, M-M-20

value: Parkinson's Disease

value: Male


title: cow 8-16 cells BSseq

source_name: 8-16 cell embryo

value: 8-16 cell embryo


title: Skeletal Muscle, M-M-19


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Male_biorep4

description: UUID:5c6350695ffef241c5536772,QC_score:7,QC_stats:Pass


title: Skeletal Muscle, M-M-18


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Male_biorep3

description: UUID:5c634619fc74d36aef11ee93,QC_score:-1,QC_stats:Fail


title: Aylor_ATAC_Liver_Ctrl_5month_Male_biorep5

description: UUID:5d39fbf979452c4bcd795230,QC_score:10,QC_stats:Pass

value: Control Oral Gavage 10 microliter per kilogram


title: cow Oocyte

data_processing:
Raw sequence reads were trimmed using Trim Galore (v0.6.4) to remove adapter contamination and reads with poor quality (Phred score cutoff 20); HISAT2 (v2.1.0) was used to align the reads in a splice aware manner. Data were passed through an additional filter of having a MAPQ score of 20 or more before quantitation.
The RNA-Seq pipeline of  Seqmonk was used to quantify mRNA features. Similar transcripts were merged. Log transformed (log2FPM)
Genome_build: Pig: Sscrofa11.1
Genome_build: Cow: UMD3.1
Supplementary_files_format_and_content: The RNA-Seq reports are tab-delimited and show annotated gene coordinates and their log2(FPM) values as follows: col 1: <gene name>, col2: <Chromosome>, col 3:  <Start>, col 4: <End>, col 5: <Probe strand> and then listed samples <columns 12-end>.

source_name: oocyte

extract_protocol:
ARCTURUS® PicoPure® RNA Isolation Kit (KIT0204, Life Technologies) was used to extract the RNA
Libraries were generated using Ovation RNA-Seq System V2 (NuGEN, Cat. 7102-08) for low amount of starting material and further amplified with NEB Next DNA Library Prep Master Mix for Illumina for 8 PCR cycles (NEB, Cat. E6040S)

value: oocyte


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Male_biorep2

description: UUID:5c634529306a395a58749383,QC_score:3,QC_stats:Fail

extract_protocol:
Sample collection was performed by Marisa Bartolomei lab at University of Pennsylvania. 5 month mice were CO2 euthanized. Liver and blood cells from individual mouse were isolated for subsequent DNA and RNA extractions according to the standard operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.
ATAC-seq and mRNA-seq experiments were performed by Marisa Bartolomei lab at University of Pennsylvania. mRNA and nuclei from 5 month mice liver and blood were isolated for subsequent ATAC-seq and mRNA-seq library preparations according to the operation procedure described by the TaRGET II consortium. Please refer to TaRGET II data portal (https://data.targetepigenomics.org) for details.


title: Aylor_ATAC_Liver_Ctrl_5month_Male_biorep4

description: UUID:5d39fbf679452c22af795226,QC_score:10,QC_stats:Pass


title: Skeletal Muscle, M-M-17


title: cow 2-4 cells BSseq

source_name: 2-4 cell embryo

value: 2-4 cell embryo


title: Skeletal Muscle, M-M-16


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Male_biorep1

description: UUID:5bd8d58e06a9509d66a53c28,QC_score:5,QC_stats:Pass


title: cow 8-16 cells


title: Skeletal Muscle, M-M-15


title: Aylor_ATAC_Liver_Ctrl_5month_Male_biorep3

description: UUID:5d39fbc4c310a9ee72f34458,QC_score:10,QC_stats:Pass

value: Liver


title: cow Blastocyst


title: Aylor_ATAC_Liver_TCDD_5month_Female_biorep1

description: UUID:5d39fbbd79452c23ac79521d,QC_score:10,QC_stats:Pass

value: Female

value: TCDD (2,3,7,8-tetrachlorodibenzo-p-dixoin) 1 microgram per kilogram


title: Skeletal Muscle, M-M-14


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Male_biorep5

description: UUID:5c635519adb9675a7bad3873,QC_score:-2,QC_stats:Fail


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Male_biorep9

description: UUID:5c636581adb9676eedad399d,QC_score:5,QC_stats:Pass


title: Skeletal Muscle, M-M-13


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Female_biorep9

description: UUID:5d3b6beebd3a5820ae13ed1f,QC_score:7,QC_stats:Pass


title: Skeletal Muscle, M-M-22


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Female_biorep8

description: UUID:5c636545adb96742a3ad3990,QC_score:3,QC_stats:Fail


title: cow 2-4 cells


title: xrn1_KO_selection_RNAseq

first: David

middle: P.

last: Bartel

state: MA

address: 455 Main St.

institute: Whitehead Institute

data_processing:
Illumina 1.5; Conventional base calls
The N. castellii genome used for analysis of small-RNA and RNA sequencing from wild-type (WT_non-selection), AGO1 slicing-impaired (ago1_mut_non-selection), and Δxrn1 (xrn1_KO_non-selection) strains was downloaded from NCBI (ASM23734v1), and the sequences of the Y′-consensus ORF (Drinnenberg et al., 2009) as well as the chloramphenicol and firefly luciferase internal-standard mRNA sequences were added to the FASTA file (Ncastellii_non-selection_genome.fsa).  The N. castellii genome used for analysis of RNA sequencing from wild-type (WT_selection) and Δxrn1 (xrn1_KO_selection) genetic-selection strains was downloaded from NCBI (ASM23734v1) and supplemented with the Y′-consensus ORF as well as the chloramphenicol and luciferase internal-standard mRNA sequences.  Sequences of the integrating plasmids containing GFP, URA3 and HIS3-PEST along with their silencing constructs, as well as the integrating plasmids containing extra copies of AGO1 and DCR1 were inserted into the FASTA file (Ncastellii_selection_genome.fsa).  STAR (v.2.4) was used to generate indexed genomes.  The coordinates of annotated small-RNA clusters (Drinnenberg et al., 2009) were converted from scaffolds of the unfinished N. castellii genome to the genomic coordinates of the finished N. castellii genome using the liftOver command line tool from UCSC (https://genome.ucsc.edu/).  The sequence of one annotated small-RNA cluster did not match the finished genome, and thus this cluster was omitted.  For some small-RNA clusters, the former scaffold coordinates overlapped in the finished genome; these were combined to generate larger clusters in the updated set of small-RNA clusters.  In instances in which a region of a previously annotated small-RNA cluster was partially deleted in the new genome, the remainder was retained as a smaller cluster.  In cases in which the scaffold sequence of a small-RNA cluster mapped to multiple sequences in the finished genome, only one set of coordinates for the cluster was retained.  Several new clusters were also identified as genomic regions for which 22–23-nt reads mapped but were not previously annotated as small-RNA clusters and did not overlap known rRNA or tRNA loci.  GTFs of the genomic coordinates of the small-RNA clusters is provided (Ncastellii_sRNA_cluster_non-selection strain, Ncastellii_sRNA_cluster_non-selection strain).
For the small RNA sequencing libraries, the first four nucleotides of each sequencing read were removed using fastx_trimmer from the FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html).  The 3′ adapter was then trimmed using cutadapt (v1.8) (Martin 2011) with parameters ‘-a NNNNTCGTATGCCGTCTTCTGCTTG -m 9’.  High-quality reads were then selected using fastq_quality_filter from the FASTX-toolkit with parameters ‘-v -q 30 -p 100 -Q 64 -z’.  9–26-nt, and 10–12-nt or 22–23-nt high-quality reads were selected using cutadapt (displayed in custom read counts tables).  Reads were aligned to their appropriate N. castellii genomes using STAR (v.2.4) allowing no mismatches or gaps with the parameters ‘--runThreadN 30 --alignIntronMax 1 --alignIntronMin 2 --scoreDelOpen -10000 --scoreInsOpen -10000 --outFilterMismatchNmax 0 --seedSplitMin 9 --outFilterType BySJout --outFilterMultimapNmax 1000 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignEndsType EndToEnd’.  To remove rRNA and tRNA reads, featureCounts (Liao et al., 2014) was used to fractionally count the number of times each read mapped to annotated rRNA loci and their intergenic regions (Ncas_Chr3: 572204–588441) and to annotated tRNA loci in the N. castellii genome (Ncastellii_rrna_w_intergenic_trna_no_intergenic.gtf) using the parameters ‘-s 1 -f -O -M --fraction --donotsort’.  Additionally, featureCounts was used to produce a SAM file of these rRNA and tRNA reads which were then removed from the original files of 9–26-nt, 10–12-nt or 22–23-nt high quality reads using custom Python scripts.  The high-quality reads that were depleted of rRNA and tRNA reads were then aligned to the appropriate N. castellii genomes using STAR (v.2.4) with the same parameters as before.  To fractionally count the number of times each read mapped to specific features in the N. castellii genome, featureCounts was utilized using the parameters ‘-s 1 -f -O -M --fraction --donotsort’.  For the small-RNA sequencing analysis with wild-type (WT_non-selection), AGO1 slicing-impaired (ago1_mut_non-selection), and Δxrn1 (xrn1_KO_non-selection) strains, this fractional counting was performed using a GTF file of the previously annotated small-RNA clusters, which included the Y′-consensus ORF (Ncastellii_sRNA_cluster_non-selection_strain.gtf).  For the small-RNA sequencing analysis with wild-type (WT_selection) and Δxrn1 (xrn1_KO_selection) genetic-selection strains, this fractional counting was performed using a GTF file of the previously annotated small-RNA clusters, including the Y′-consensus ORF as well as the synthetic hairpins used in the genetic selection (Ncastellii_sRNA_cluster_selection_strain.gtf).
For the RNA sequencing libraries, RNA-seq reads were aligned to the genome using STAR (v.2.4) with the parameters ‘--outFilterType BySJout --outFilterMultimapNmax 1000 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMax 1100 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outFilterIntronMotifs RemoveNoncanonicalUnannotated’.  As with the small-RNA sequencing, featureCounts were used to fractionally count the number of times each read mapped to the genome using the parameters ‘-s 2 -f -O -M --fraction --donotsort’.  This fractional counting was performed using GTF files of the previously annotated small-RNA clusters (Ncastellii_sRNA_cluster_non-selection_strain.gtf and .  The fractional counts were converted to transcripts per million and normalized in the same manner as the small-RNA sequencing libraries (Ncastellii_sRNA_cluster_selection_strain.gtf).
Genome_build: ASM23734v1 - N. castellii CBS4309; Additional sequences were added to this genome build as described above and the FASTA files are included.
Supplementary_files_format_and_content: FASTA files of the genome sequences of the N. castellii non-selection and genome-selection strains, as well as the GTF files annotating the small RNA (sRNA) clusters in each genome. A GTF file of the annotated rRNA and tRNA loci that were used to perform the removal of rRNA and tRNA reads as described above. Custom gene expression tables are tab-delimited text files that include fractional read counts for each sRNA cluster for each sample. Custom read counts tables are tab-delimited text files that include 9–26-nt, 10–12-nt or 22–23-nt read counts.

organism: Naumovozyma castellii

source_name: N. castellii CBS4310

growth_protocol: Each N. castellii strain was grown at 30C until mid-log phase (OD 600 nm: ~0.8) in synthetic complete (+ 2% galactose) media.

extract_protocol:
Total RNA was isolated from the cultures using the hot-phenol method.
For small-RNA sequencing, 0.5 nM of four small RNA oligonucleotides (xtr miR-427, 5′-GAAAGUGCUUUCUGUUUUGGGCG;   dme miR-14, 5′-GGGAGCGAGACGGGGACTCACT; Synthetic_siRNA_1_Guide, 5′-UAGUGCAGGUAGGUAUUUUUGUU; Synthetic_siRNA_1_Passenger, 5′-CAAAAAUACCUACCUGCACUAUA) were added to 10 ug of total RNA for use as internal standards.  Small-RNA cDNA libraries were prepared as described (Fang and Bartel, 2015), except 9–26-nt RNAs were isolated and sequenced, using 9-nt and 26-nt RNA radiolabeled standards (5′-AAACCAGUC and 5′ -AGCGUGUACUCCGAAGAGGAUCCAAA) to follow ligations and purifications. For RNA-seq, 0.5 ng of two mRNAs (chloramphenicol and firefly luciferase) were added to 5 ug of total RNA for use as internal standards.  Ribosomal RNA was depleted from the samples using Ribo-Zero Gold rRNA Removal Kit (Yeast) (Illumina, MRZY1324).  RNA cDNA libraries were prepared using NEXTflex rapid directional mRNA-seq kit (Bioo Scientific, NOVA-5138-10).

value: xrn1 knockout (KO)

value: Selection


title: Aylor_ATAC_Liver_Ctrl_5month_Female_biorep6

description: UUID:5d39fbf879452c329079522d,QC_score:10,QC_stats:Pass


title: Aylor_ATAC_Liver_Ctrl_5month_Female_biorep5

description: UUID:5d39fbc3c310a9e265f34454,QC_score:10,QC_stats:Pass


title: cow Morula

value: Morula


title: Skeletal Muscle, M-M-12

value: Skeletal Muscle (vastus lateralis muscle)


title: WT_selection_RNAseq

value: WT (wild-type)


title: Aylor_ATAC_Liver_Ctrl_5month_Male_biorep2

description: UUID:5d39fbc4c310a98e48f34457,QC_score:10,QC_stats:Pass


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Male_biorep10

description: UUID:5de967e1a0134f1f75d8fecb,QC_score:9,QC_stats:Pass

value: Blood

value: BPA (Bisphenol A) 10 UG/KGBW/DAY


title: Aylor_ATAC_Liver_Ctrl_5month_Female_biorep4

description: UUID:5d39fbc3c310a957b0f34453,QC_score:10,QC_stats:Pass

value: 5 month


title: Skeletal Muscle, M-M-10

value: control


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Female_biorep5

description: UUID:5c63533aadb9675afdad3868,QC_score:6,QC_stats:Pass


title: Aylor_ATAC_Liver_Ctrl_5month_Female_biorep3

description: UUID:5d39fbbfc310a96ecdf3444c,QC_score:10,QC_stats:Pass


title: xrn1_KO_non-selection_RNAseq

value: Non-selection


title: Bartolomei_ATAC_Blood_BPA_10ug_5month_Female_biorep4

description: UUID:5c63499dfc74d3288e11eea7,QC_score:5,QC_stats:Pass


title: Aylor_ATAC_Liver_Ctrl_5month_Female_biorep2

description: UUID:5d39fbbe79452c05ee79521f,QC_score:10,QC_stats:Pass


title: Skeletal Muscle, M-M-08

value: Parkinson's Disease


title: xrn1_KO_selection_sRNA