title: fetal cord tissue, S1150


title: fetal cord tissue, S1151

status: Public on Sep 15 2020

type: genomic

city: Singapore

first: Jonathan

middle: Yinhao

last: Huang

state: « choose one »

address: 30 Medical Drive

country: Singapore

institute: Singapore Institute for Clinical Sciences

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
GenomeStudio; R/Rstudio
green (RAW_ID_Grn.idat) and red (RAW_ID_Red.idat) channels provided
[value definition]  chip position, DNA extraction, and bisulfite conversion batch, and celltype-adjusted residuals provided

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: cord tissue

label_protocol: Standard Illumina Protocol

extract_protocol: Prior to purification, 250 mg crushed cord tissue was enzymatically digested with hyaluronidase (~2.7U in 250 µl PBS) for 30 minutes at 37 C, mixed with 250 µl TNES lysis buffer, transferred to gentleMACS M Tubes (Miltenyi 130-093-236) for 1-minute homogenization followed by overnight treatment with 200 µg Proteinase K at 55 C. QIASymphony SP was used for automated purification of (buffy coat/cord tissue) DNA in combination with QIASymphony DSP DNA Midi Kit (Qiagen #937255) and DNA was bisulfite converted using the EZ DNA Methylation Kit™ (Zymo Research).

tag: tissue

value: fetal cord tissue

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)

tag: child sex (male = 0; female = 1)

tag: pre-pregnancy bmi (kg/m^2)


title: fetal cord tissue, S1140


title: fetal cord tissue, S1138


title: fetal cord tissue, S1142


title: fetal cord tissue, S1136


title: fetal cord tissue, S1137


title: fetal cord tissue, S1139


title: fetal cord tissue, S1135


title: fetal cord tissue, S1134


title: fetal cord tissue, S1133


title: fetal cord tissue, S1132


title: fetal cord tissue, S1129


title: fetal cord tissue, S1128


title: fetal cord tissue, S1131


title: fetal cord tissue, S1122


title: fetal cord tissue, S1121


title: fetal cord tissue, S1130


title: fetal cord tissue, S1120


title: wild type, biological rep2

type: RNA

city: Freising

first: Tobias

last: Sieberer

address: Liesel-Beckmann-Strasse 1

department: Plant Sciences

country: Germany

institute: Technical University of Munich

description: Gene expression data from 10-day-old wild-type seedlings

hyb_protocol: Labeled samples were hybridized to the Genechip Arabidopsis ATH1 Genome Arrays (Affymetrix, Santa Clara, CA) according to the manufacturer's instructions (Affymetrix; www.affymetrix.com/)

scan_protocol: The GeneArrays were scanned using the Affymetrix GeneChip Scanner (Affymetrix) using standard NASC protocols.

data_processing: Microarray Suite 5.0

label: biotin

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Arabidopsis wild-type seedlings

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol (GeneChip® Expression Arrays Technical Manual, 2013, Affymetrix)

growth_protocol: Seeds were surface-sterilized with 70% ethanol + 0.05% SDS for 3 min, rinsed with 96% ethanol for 1 min, and subsequently dried in a laminar flow hood.  Sterile seeds were germinated and grown in 96-well plates (approximately 5 seeds per well) in 100mL liquid half-strength Murashige and Skoog medium containing 1% Sucrose and 1% DMSO. After stratification at 4°C in darkness for 2 days, seeds were placed in a growth incubator grown at 26°C grown under long d conditions (16 h, 80 mM m-2 s-1 cool-white light/8 h dark).

extract_protocol: Total RNA was extracted using the RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

value: whole seedlings

tag: genotype

value: wild type

tag: ecotype

tag: age

value: 10 days


title: fetal cord tissue, S1126


title: fetal cord tissue, S1117


title: fetal cord tissue, S1118


title: fetal cord tissue, S1115


title: fetal cord tissue, S1114


title: fetal cord tissue, S1116


title: fetal cord tissue, S1112


title: fetal cord tissue, S1119


title: fetal cord tissue, S1109


title: fetal cord tissue, S1111


title: fetal cord tissue, S1106


title: fetal cord tissue, S1108


title: fetal cord tissue, S1107


title: fetal cord tissue, S1103


title: fetal cord tissue, S1110


title: fetal cord tissue, S1124


title: fetal cord tissue, S1105


title: fetal cord tissue, S1099


title: fetal cord tissue, S1104


title: fetal cord tissue, S1102


title: fetal cord tissue, S1098


title: fetal cord tissue, S1125


title: fetal cord tissue, S1096


title: fetal cord tissue, S1095


title: fetal cord tissue, S1097


title: fetal cord tissue, S1113


title: fetal cord tissue, S1092


title: fetal cord tissue, S1094


title: fetal cord tissue, S1093


title: fetal cord tissue, S1090


title: fetal cord tissue, S1084


title: fetal cord tissue, S1091


title: fetal cord tissue, S1087


title: fetal cord tissue, S1081


title: fetal cord tissue, S1083


title: fetal cord tissue, S1075


title: fetal cord tissue, S1071


title: fetal cord tissue, S1101


title: fetal cord tissue, S1080


title: fetal cord tissue, S1076


title: fetal cord tissue, S1078


title: fetal cord tissue, S1077


title: fetal cord tissue, S1073


title: fetal cord tissue, S1068


title: fetal cord tissue, S1069


title: fetal cord tissue, S1070


title: fetal cord tissue, S1066


title: fetal cord tissue, S1067


title: fetal cord tissue, S1064


title: fetal cord tissue, S1057


title: fetal cord tissue, S1060


title: fetal cord tissue, S1086


title: fetal cord tissue, S1088


title: fetal cord tissue, S1059


title: fetal cord tissue, S1062


title: fetal cord tissue, S1058


title: fetal cord tissue, S1061


title: fetal cord tissue, S1079


title: fetal cord tissue, S1056


title: fetal cord tissue, S1053


title: fetal cord tissue, S1054


title: fetal cord tissue, S1050


title: fetal cord tissue, S1052


title: fetal cord tissue, S1047


title: fetal cord tissue, S1046


title: fetal cord tissue, S1048


title: fetal cord tissue, S1049


title: fetal cord tissue, S1043


title: fetal cord tissue, S1038


title: fetal cord tissue, S1044


title: fetal cord tissue, S1039


title: fetal cord tissue, S1036


title: fetal cord tissue, S1041


title: fetal cord tissue, S1040


title: 29SEt

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

hyb_protocol: Cy3-labeled cRNA (1.65 μg; specific activity of >9.0 pmol Cy3/μg of cRNA) was fragmented at 60 °C for 30 min in a reaction volume of 55 μl containing 1× Agilent fragmentation buffer and 2× Agilent blocking agent, following the manufacturer's instructions. On completion of the fragmentation reaction, 55 μl of 2× GEx Hybridization buffer HI-RPM was added to the fragmentation mixture, and mixtures were hybridized to Agilent Whole-Human Genome Oligo Microarrays (G4845A) for 17 h at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 min at 37 °C with GE Wash buffer 2 (Agilent Technologies) and then dried

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using the one-color scan setting for 1 × 44 k array slides (scan area of 61 × 21.6 mm; scan resolution of 5 μm; dye channel set to green; green PMT set to 100%).

data_processing: Scanned images were analyzed with Feature Extraction Software 12.0.0.7 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09 and Grid:  014868_D_20070820 ) to obtain background-subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Signal intensities were normalized using quantile normalization for GE .

organism: Mus musculus

label_protocol: Cy3-labeled cRNA was prepared from 1 μg of RNA using One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) (Agilent Technologies) according to the manufacturer's instructions, and RNeasy column purification was performed (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: RyR1 I4895T knock-in mice on a 129S2/SvPasCrl background were kindly provided by the S. Hamilton laboratory, Texas, USA. These founder mice were rederived using C57BL/6J for breeding. This resulted in a new sub-line with a mixed genetic background (approximately 50% 129S2/SvPasCrl and 50% C57BL/6J after rederivation). Since homozygotes have a perinatal lethal phenotype (Zvaritch et al. 2007), heterozygotes (HET) were crossed with wild type (WT) littermates or C57BL/6J mice (Charles River) to maintain the colony. At least five such crosses had occurred before the experiments. Ear snips from adult mice and tail snips from sacrificed neonates were retained for genotyping. DNA was extracted from tissue samples using the Extract-N-Amp kit (Sigma) and PCR was used to amplify the fragment covering the mutation site. Forward and reverse primers were 5’-GGTCTTCCTGTCTCAATAACCCGATCTAGAAAC-3’ and 5’-GATGGAGAAACCAAAGCTCAGAGAGACCAC-3’ respectively. Since the inserted mutation site also contains an Age I target sequence, only samples containing the mutated allele undergo Age I digestion.

extract_protocol: Total RNA was prepared from biopsies using TRIzol (Life Technologies) following the manufacturer's instructions.

treatment_protocol: no treatment

value: Soleo muscle

tag: gender

value: male

tag: mutation


title: fetal cord tissue, S1032


title: fetal cord tissue, S1030


title: fetal cord tissue, S1035


title: fetal cord tissue, S1029


title: fetal cord tissue, S1033


title: fetal cord tissue, S1023


title: fetal cord tissue, S1031


title: fetal cord tissue, S1037


title: fetal cord tissue, S1055


title: fetal cord tissue, S1027


title: fetal cord tissue, S1024


title: fetal cord tissue, S1021


title: fetal cord tissue, S1020


title: fetal cord tissue, S1018


title: fetal cord tissue, S1028


title: fetal cord tissue, S1042


title: fetal cord tissue, S1022


title: fetal cord tissue, S1017


title: fetal cord tissue, S1016


title: fetal cord tissue, S1015


title: fetal cord tissue, S1009


title: fetal cord tissue, S1010


title: fetal cord tissue, S1011


title: fetal cord tissue, S1008


title: fetal cord tissue, S1007


title: fetal cord tissue, S1005


title: fetal cord tissue, S1004


title: fetal cord tissue, S1006


title: fetal cord tissue, S1001


title: fetal cord tissue, S1003


title: fetal cord tissue, S0999


title: fetal cord tissue, S1002


title: fetal cord tissue, S1000


title: fetal cord tissue, S0998


title: fetal cord tissue, S1019


title: fetal cord tissue, S0995


title: fetal cord tissue, S0996


title: fetal cord tissue, S0993


title: fetal cord tissue, S0994


title: fetal cord tissue, S0987


title: fetal cord tissue, S0986


title: fetal cord tissue, S0988


title: fetal cord tissue, S0985


title: fetal cord tissue, S0984


title: fetal cord tissue, S0983


title: fetal cord tissue, S1012


title: fetal cord tissue, S1013


title: fetal cord tissue, S0979


title: fetal cord tissue, S0978


title: fetal cord tissue, S0976


title: fetal cord tissue, S0982


title: fetal cord tissue, S0973


title: fetal cord tissue, S0981


title: fetal cord tissue, S0980


title: fetal cord tissue, S0977


title: fetal cord tissue, S0974


title: fetal cord tissue, S0971


title: fetal cord tissue, S0972


title: fetal cord tissue, S0966


title: fetal cord tissue, S0967


title: fetal cord tissue, S0969


title: fetal cord tissue, S0991


title: fetal cord tissue, S0964


title: fetal cord tissue, S0965


title: fetal cord tissue, S0963


title: fetal cord tissue, S0970


title: fetal cord tissue, S0992


title: fetal cord tissue, S0989


title: fetal cord tissue, S0960


title: fetal cord tissue, S0959


title: fetal cord tissue, S0962


title: fetal cord tissue, S0958


title: fetal cord tissue, S0956


title: fetal cord tissue, S0961


title: fetal cord tissue, S0954


title: fetal cord tissue, S0953


title: fetal cord tissue, S0926


title: fetal cord tissue, S0942


title: fetal cord tissue, S0938


title: fetal cord tissue, S0923


title: fetal cord tissue, S0944


title: fetal cord tissue, S0952


title: fetal cord tissue, S0949


title: fetal cord tissue, S0920


title: fetal cord tissue, S0940


title: fetal cord tissue, S0939


title: fetal cord tissue, S0935


title: fetal cord tissue, S0922


title: fetal cord tissue, S0921


title: fetal cord tissue, S0936


title: fetal cord tissue, S0934


title: fetal cord tissue, S0941


title: fetal cord tissue, S0916


title: fetal cord tissue, S0915


title: fetal cord tissue, S0930


title: fetal cord tissue, S0918


title: fetal cord tissue, S0943


title: fetal cord tissue, S0975


title: fetal cord tissue, S0929


title: fetal cord tissue, S0917


title: fetal cord tissue, S0919


title: fetal cord tissue, S0911


title: fetal cord tissue, S0913


title: fetal cord tissue, S0906


title: fetal cord tissue, S0908


title: fetal cord tissue, S0904


title: fetal cord tissue, S0910


title: fetal cord tissue, A0894


title: fetal cord tissue, S0902


title: fetal cord tissue, S0896


title: fetal cord tissue, S0937


title: fetal cord tissue, S0948


title: fetal cord tissue, S0946


title: fetal cord tissue, S0933


title: fetal cord tissue, S0927


title: fetal cord tissue, S0899


title: fetal cord tissue, S0898


title: fetal cord tissue, S0897


title: fetal cord tissue, A0889


title: fetal cord tissue, A0888


title: fetal cord tissue, A0892


title: fetal cord tissue, A0891


title: fetal cord tissue, S0900


title: fetal cord tissue, S0895


title: fetal cord tissue, A0881


title: fetal cord tissue, A0890


title: fetal cord tissue, A0872


title: fetal cord tissue, A0875


title: fetal cord tissue, A0869


title: fetal cord tissue, A0867


title: fetal cord tissue, A0864


title: fetal cord tissue, A0863


title: fetal cord tissue, A0886


title: fetal cord tissue, A0885


title: fetal cord tissue, A0861


title: fetal cord tissue, S0903


title: fetal cord tissue, A0860


title: fetal cord tissue, A0859


title: fetal cord tissue, A0883


title: fetal cord tissue, A0880


title: fetal cord tissue, A0857


title: fetal cord tissue, A0856


title: fetal cord tissue, A0865


title: fetal cord tissue, A0879


title: fetal cord tissue, A0853


title: fetal cord tissue, A0854


title: fetal cord tissue, A0877


title: fetal cord tissue, A0871


title: fetal cord tissue, A0868


title: fetal cord tissue, A0862


title: fetal cord tissue, A0846


title: fetal cord tissue, A0844


title: fetal cord tissue, A0839


title: fetal cord tissue, A0837


title: fetal cord tissue, A0835


title: fetal cord tissue, A0833


title: fetal cord tissue, A0832


title: fetal cord tissue, A0876


title: fetal cord tissue, A0829


title: fetal cord tissue, A0830


title: fetal cord tissue, A0851


title: fetal cord tissue, A0884


title: fetal cord tissue, A0848


title: fetal cord tissue, A0845


title: fetal cord tissue, A0842


title: fetal cord tissue, A0847


title: fetal cord tissue, A0841


title: fetal cord tissue, A0840


title: fetal cord tissue, A0838


title: fetal cord tissue, A0858


title: fetal cord tissue, A0823


title: fetal cord tissue, A0852


title: fetal cord tissue, S0821


title: fetal cord tissue, A0831


title: fetal cord tissue, A0855


title: fetal cord tissue, S0819


title: fetal cord tissue, S0818


title: fetal cord tissue, A0827


title: fetal cord tissue, A0826


title: fetal cord tissue, A0825


title: fetal cord tissue, A0828


title: fetal cord tissue, S0816


title: fetal cord tissue, S0815


title: fetal cord tissue, S0812


title: fetal cord tissue, S0813


title: fetal cord tissue, S0811


title: fetal cord tissue, A0824


title: fetal cord tissue, A0822


title: fetal cord tissue, S0817


title: fetal cord tissue, S0807


title: fetal cord tissue, S0814


title: fetal cord tissue, S0809


title: fetal cord tissue, S0810


title: fetal cord tissue, S0808


title: fetal cord tissue, S0806


title: fetal cord tissue, S0804


title: fetal cord tissue, S0802


title: fetal cord tissue, S0801


title: fetal cord tissue, S0800


title: fetal cord tissue, S0798


title: fetal cord tissue, S0799


title: fetal cord tissue, S0796


title: fetal cord tissue, S0797


title: fetal cord tissue, S0792


title: fetal cord tissue, S0790


title: fetal cord tissue, S0794


title: fetal cord tissue, S0789


title: fetal cord tissue, S0787


title: fetal cord tissue, S0784


title: fetal cord tissue, S0788


title: fetal cord tissue, S0785


title: fetal cord tissue, S0782


title: fetal cord tissue, S0791


title: fetal cord tissue, S0803


title: fetal cord tissue, S0780


title: fetal cord tissue, S0778


title: fetal cord tissue, S0777


title: fetal cord tissue, S0776


title: fetal cord tissue, S0775


title: fetal cord tissue, S0774


title: fetal cord tissue, S0773


title: fetal cord tissue, S0772


title: fetal cord tissue, S0771


title: fetal cord tissue, S0793


title: fetal cord tissue, S0769


title: fetal cord tissue, S0767


title: fetal cord tissue, S0770


title: fetal cord tissue, S0768


title: fetal cord tissue, S0786


title: fetal cord tissue, S0765


title: fetal cord tissue, S0779


title: fetal cord tissue, S0766


title: fetal cord tissue, S0763


title: fetal cord tissue, S0764


title: fetal cord tissue, S0761


title: fetal cord tissue, S0758


title: fetal cord tissue, S0756


title: fetal cord tissue, S0752


title: fetal cord tissue, S0753


title: fetal cord tissue, S0748


title: fetal cord tissue, S0754


title: fetal cord tissue, S0757


title: fetal cord tissue, S0755


title: fetal cord tissue, S0746


title: fetal cord tissue, S0749


title: fetal cord tissue, S0751


title: fetal cord tissue, S0747


title: fetal cord tissue, S0740


title: fetal cord tissue, S0742


title: fetal cord tissue, S0741


title: fetal cord tissue, S0914


title: fetal cord tissue, S0905


title: fetal cord tissue, S0738


title: fetal cord tissue, S0736


title: fetal cord tissue, S0759


title: fetal cord tissue, S0734


title: fetal cord tissue, S0744


title: fetal cord tissue, S0743


title: fetal cord tissue, S0735


title: fetal cord tissue, S0739


title: fetal cord tissue, S0750


title: fetal cord tissue, S0730


title: fetal cord tissue, S0729


title: fetal cord tissue, S0727


title: fetal cord tissue, S0733


title: fetal cord tissue, S0728


title: fetal cord tissue, S0731


title: fetal cord tissue, S0726


title: fetal cord tissue, S0718


title: fetal cord tissue, S0745


title: fetal cord tissue, S0720


title: fetal cord tissue, S0721


title: fetal cord tissue, S0722


title: fetal cord tissue, S0719


title: fetal cord tissue, S0717


title: fetal cord tissue, S0712


title: fetal cord tissue, S0715


title: fetal cord tissue, S0716


title: fetal cord tissue, S0713


title: fetal cord tissue, S0714


title: fetal cord tissue, S0707


title: fetal cord tissue, S0709


title: fetal cord tissue, S0732


title: fetal cord tissue, S0704


title: fetal cord tissue, S0706


title: fetal cord tissue, S0708


title: fetal cord tissue, S0705


title: fetal cord tissue, S0711


title: fetal cord tissue, S0700


title: fetal cord tissue, S0702


title: fetal cord tissue, S0699


title: fetal cord tissue, S0696


title: fetal cord tissue, S0698


title: fetal cord tissue, S0697


title: fetal cord tissue, S0695


title: fetal cord tissue, S0694


title: fetal cord tissue, S0691


title: fetal cord tissue, S0692


title: fetal cord tissue, S0690


title: fetal cord tissue, S0693


title: fetal cord tissue, S0689


title: fetal cord tissue, S0688


title: fetal cord tissue, S0685


title: fetal cord tissue, S0681


title: fetal cord tissue, S0683


title: fetal cord tissue, S0682


title: fetal cord tissue, S0679


title: fetal cord tissue, S0674


title: fetal cord tissue, S0680


title: fetal cord tissue, S0678


title: fetal cord tissue, S0675


title: fetal cord tissue, S0677


title: fetal cord tissue, S0672


title: fetal cord tissue, S0673


title: fetal cord tissue, S0668


title: fetal cord tissue, S0667


title: fetal cord tissue, S0669


title: fetal cord tissue, S0666


title: fetal cord tissue, S0671


title: fetal cord tissue, S0664


title: fetal cord tissue, S0663


title: fetal cord tissue, S0665


title: fetal cord tissue, S0661


title: fetal cord tissue, S0662


title: fetal cord tissue, S0657


title: fetal cord tissue, S0659


title: fetal cord tissue, S0660


title: fetal cord tissue, S0658


title: fetal cord tissue, S0656


title: fetal cord tissue, S0653


title: fetal cord tissue, S0670


title: fetal cord tissue, S0652


title: fetal cord tissue, S0651


title: fetal cord tissue, S0650


title: fetal cord tissue, S0649


title: fetal cord tissue, S0648


title: fetal cord tissue, S0647


title: fetal cord tissue, S0646


title: fetal cord tissue, S0645


title: fetal cord tissue, S0644


title: fetal cord tissue, S0655


title: fetal cord tissue, S0901


title: fetal cord tissue, S0643


title: fetal cord tissue, S0640


title: fetal cord tissue, S0638


title: fetal cord tissue, S0637


title: fetal cord tissue, S0636


title: fetal cord tissue, S0635


title: Gata4-LSEC-KO liver biological rep10

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description:
gata4_lsec_ko_std_2256_18
Gene expression data of Gata4 EC-subtype specific KO liver biological rep10

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000.

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 8, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Clec4g-icre driver mice (C57BL/6N-Tg(Clec4g-icre)1.1Sgoe, MGI:6280453), were crossed to Gata4 floxed mice (STOCK Gata4tm1.1Sad/J, MGI:3778685, JAX:008194).

extract_protocol: Total RNA was extracted with innuPREP RNA Mini Kit (Analytik Jena), then treated with TURBO DNA-free Kit (Invitrogen).

treatment_protocol: Whole liver lysates were used for RNA extraction.

value: Whole liver

tag: diet

value: std


title: Gata4-LSEC-KO liver biological rep9

description:
gata4_lsec_ko_std_2255_18
Gene expression data of Gata4 EC-subtype specific KO liver biological rep9


title: fetal cord tissue, S0642


title: Gata4-LSEC-KO liver biological rep6

description:
gata4_lsec_ko_std_2252_18
Gene expression data of Gata4 EC-subtype specific KO liver biological rep6


title: Gata4-LSEC-KO liver biological rep8

description:
gata4_lsec_ko_std_2254_18
Gene expression data of Gata4 EC-subtype specific KO liver biological rep8


title: Gata4-LSEC-KO liver biological rep7

description:
gata4_lsec_ko_std_2253_18
Gene expression data of Gata4 EC-subtype specific KO liver biological rep7


title: Control liver biological rep10

description:
wt_std_2249_18
Gene expression data of control liver biological rep10

source_name: Control liver biological rep10

value: wt


title: Control liver biological rep11

description:
wt_std_2250_18
Gene expression data of control liver biological rep11

source_name: Control liver biological rep11


title: Gata4-LSEC-KO liver biological rep5

description:
gata4_lsec_ko_std_2251_18
Gene expression data of Gata4 EC-subtype specific KO liver biological rep5


title: fetal cord tissue, S0630


title: fetal cord tissue, S0631


title: fetal cord tissue, S0633


title: fetal cord tissue, S0634


title: Control liver biological rep9

description:
wt_std_2248_18
Gene expression data of control liver biological rep9

source_name: Control liver biological rep9


title: Gata4-LSEC-KO liver biological rep4

description:
gata4_lsec_ko_std_1684_18
Gene expression data of Gata4 EC-subtype specific KO liver biological rep4


title: Control liver biological rep7

description:
wt_std_2246_18
Gene expression data of control liver biological rep7

source_name: Control liver biological rep7


title: Gata4-LSEC-KO liver biological rep3

description:
gata4_lsec_ko_std_1683_18
Gene expression data of Gata4 EC-subtype specific KO liver biological rep3


title: Control liver biological rep8

description:
wt_std_2247_18
Gene expression data of control liver biological rep8

source_name: Control liver biological rep8


title: Control liver biological rep6

description:
wt_std_2245_18
Gene expression data of control liver biological rep6

source_name: Control liver biological rep6


title: Control liver biological rep5

description:
wt_std_1680_18
Gene expression data of control liver biological rep5

source_name: Control liver biological rep5


title: fetal cord tissue, S0629


title: fetal cord tissue, S0628


title: fetal cord tissue, S0632


title: Gata4-LSEC-KO liver biological rep2

description:
gata4_lsec_ko_std_1682_18
Gene expression data of Gata4 EC-subtype specific KO liver biological rep2


title: Control liver biological rep4

description:
wt_std_1679_18
Gene expression data of control liver biological rep4

source_name: Control liver biological rep4


title: Gata4-LSEC-KO liver biological rep1

description:
gata4_lsec_ko_std_1681_18
Gene expression data of Gata4 EC-subtype specific KO liver biological rep1


title: Control liver biological rep3

description:
wt_std_1678_18
Gene expression data of control liver biological rep3

source_name: Control liver biological rep3


title: fetal cord tissue, S0624


title: Control liver biological rep2

description:
wt_std_1677_18
Gene expression data of control liver biological rep2

source_name: Control liver biological rep2


title: fetal cord tissue, S0623


title: fetal cord tissue, S0622


title: fetal cord tissue, S0620


title: Control (WT) mLSEC biological rep5

description:
WT_4
Gene expression data of control primary murine liver sinusoidal endothelial cells, biological replicate no 5

source_name: Control primary murine liver sinusoidal endothelial cells, biological replicate no 5

treatment_protocol: Livers were perfused in situ through the portal vein with a collagenase/amino acid/saccharide solution (Sigma-Aldrich), dissected, mechanically disrupted, pooled from 3 mice, digested for 25 minutes at 38 °C in collagenase/Gey’s balanced salt solution (Sigma-Aldrich), and filtered through a mesh. Nonparynchymal cells were separated by a 19.3 % Nycodenz gradient. Afterward, liver sinusoidal endothelial cells (LSEC) were isolated by Magnetic-activated cell sorting (MACS) using CD146 MicroBeads (Miltenyi) according to manufacturers’ instructions.

tag: cell type

value: Primary liver sinusoidal endothelial cells

tag: genotype/variation

value: WT


title: fetal cord tissue, S0618


title: fetal cord tissue, S0619


title: fetal cord tissue, S0616


title: fetal cord tissue, S0617


title: fetal cord tissue, S0615


title: fetal cord tissue, S0613


title: fetal cord tissue, S0614


title: fetal cord tissue, S0626


title: fetal cord tissue, S0612


title: Control (WT) mLSEC biological rep2

description:
WT_1
Gene expression data of control primary murine liver sinusoidal endothelial cells, biological replicate no 2

source_name: Control primary murine liver sinusoidal endothelial cells, biological replicate no 2


title: Control (WT) mLSEC biological rep3

description:
WT_2
Gene expression data of control primary murine liver sinusoidal endothelial cells, biological replicate no 3

source_name: Control primary murine liver sinusoidal endothelial cells, biological replicate no 3


title: fetal cord tissue, S0611


title: Control (WT) mLSEC biological rep4

description:
WT_3
Gene expression data of control primary murine liver sinusoidal endothelial cells, biological replicate no 4

source_name: Control primary murine liver sinusoidal endothelial cells, biological replicate no 4


title: Control (WT) mLSEC biological rep1

description:
WT_0
Gene expression data of control primary murine liver sinusoidal endothelial cells, biological replicate no 1

source_name: Control primary murine liver sinusoidal endothelial cells, biological replicate no 1


title: fetal cord tissue, S0608

source_name: cord tissue


title: fetal cord tissue, S0609


title: Control liver biological rep1

description:
wt_std_1676_18
Gene expression data of control liver biological rep1

source_name: Control liver biological rep1


title: Gata4-LSEC-KO mLSEC biological rep5

description:
KO_4
Gene expression data of Gata4 EC-subtype specific KO primary murine liver sinusoidal endothelial cells, biological replicate no 5

value: KO


title: Gata4-LSEC-KO mLSEC biological rep3

description:
KO_2
Gene expression data of Gata4 EC-subtype specific KO primary murine liver sinusoidal endothelial cells, biological replicate no 3


title: Control mLSEC, biological rep4

description:
Std4
Gene expression data of control primary murine liver sinusoidal endothelial cells, biological replicate no 4

growth_protocol: Ten-week-old female C57BL/6N mice and control siblings were fed a CDAA diet containing 31% of fat per calorie and 1% cholesterol (E15666-94, Ssniff) or a control diet (V1534-000, Ssniff) for ten weeks.

treatment_protocol: Livers were perfused in situ through the portal vein with a collagenase/amino acid/saccharide solution (Sigma-Aldrich), dissected, mechanically disrupted, pooled from 3 mice, digested for 25 minutes at 38 °C in collagenase/Gey’s balanced salt solution (Sigma-Aldrich), and filtered through a mesh. Nonparynchymal cells were separated by a 19.3% Nycodenz gradient. Afterward, liver sinusoidal endothelial cells (LSEC) were isolated by Magnetic-activated cell sorting (MACS) using CD146 MicroBeads (Miltenyi) according to manufacturers’ instructions.

tag: treatment

value: Std diet

tag: treatment duration


title: fetal cord tissue, S0607


title: Control mLSEC, biological rep5

description:
Std5
Gene expression data of control primary murine liver sinusoidal endothelial cells, biological replicate no 5


title: fetal cord tissue, S0606


title: Control mLSEC, biological rep3

description:
Std3
Gene expression data of control primary murine liver sinusoidal endothelial cells, biological replicate no 3


title: fetal cord tissue, S0605


title: fetal cord tissue, S0604


title: fetal cord tissue, S0603


title: Gata4-LSEC-KO mLSEC biological rep4

description:
KO_3
Gene expression data of Gata4 EC-subtype specific KO primary murine liver sinusoidal endothelial cells, biological replicate no 4


title: Gata4-LSEC-KO mLSEC biological rep2

description:
KO_1
Gene expression data of Gata4 EC-subtype specific KO primary murine liver sinusoidal endothelial cells, biological replicate no 2


title: fetal cord tissue, S0610


title: Control mLSEC, biological rep2

description:
Std2
Gene expression data of control primary murine liver sinusoidal endothelial cells, biological replicate no 2


title: CDAA mLSEC, biological rep5

description:
CDAA5
Gene expression data of primary murine liver sinusoidal endothelial cells after 10 weeks of CDAA diet, biological replicate no 5

source_name: Primary murine liver sinusoidal endothelial cells after 10 weeks of CDAA diet, biological replicate no 5

value: CDAA diet


title: Gata4-LSEC-KO mLSEC biological rep1

description:
KO_0
Gene expression data of Gata4 EC-subtype specific KO primary murine liver sinusoidal endothelial cells, biological replicate no 1


title: CDAA mLSEC, biological rep3

description:
CDAA3
Gene expression data of primary murine liver sinusoidal endothelial cells after 10 weeks of CDAA diet, biological replicate no 3

source_name: Primary murine liver sinusoidal endothelial cells after 10 weeks of CDAA diet, biological replicate no 3


title: CDAA mLSEC, biological rep4

description:
CDAA4
Gene expression data of primary murine liver sinusoidal endothelial cells after 10 weeks of CDAA diet, biological replicate no 4

source_name: Primary murine liver sinusoidal endothelial cells after 10 weeks of CDAA diet, biological replicate no 4


title: fetal cord tissue, S0601


title: fetal cord tissue, S0602


title: miR-100_4

city: Freiburg

first: Christian

last: Smolka

state: Baden Württemberg

address: Breisacher Strasse 33

department: Department of Cardiology and Angiology I

institute: Heart Center Freiburg University

description: Gene expression data from male, 8 weeks old, untreated mice

hyb_protocol: Labeled fragments were hybridized to Affymetrix Mouse Clariom_S_Mouse arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645. Arrays were washed and stained using the Affymetrix wash and stain kit as described by the manufacturer.

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

data_processing:
CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software Version 4.0 and standard settings.
CEL-files were processed with Transcriptome Analysis Console 4.0 (TAC) using standard settings with Anova. Matrix data represent log2 transformed signal intensities from TAC.

source_name: heart left ventricle

label_protocol: We used the Affymetrix WT Plus kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

growth_protocol:
cardiac-specific miR-100 overexpression using Myh6-Cre (B6.FVB-Tg(Myh6-Cre)2182/J) crossed to miR-100flox/flox, both on C57/BL6J background, male Cre positive miR100flox/+ were selected
All mice were kept under a 12h/12h light/dark cycle in a specific pathogen-free animal facility with standard diet and water available ad libitum.

extract_protocol: TriPure extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Samples from male, 8 weeks old, untreated mice were used.

tag: strain

value: 8 weeks

value: heart left ventricle

value: untreated


title: fetal cord tissue, S0600

tag: tissue

value: fetal cord tissue


title: CDAA mLSEC, biological rep2

description:
CDAA2
Gene expression data of primary murine liver sinusoidal endothelial cells after 10 weeks of CDAA diet, biological replicate no 2

source_name: Primary murine liver sinusoidal endothelial cells after 10 weeks of CDAA diet, biological replicate no 2


title: Control mLSEC, biological rep1

description:
Std1
Gene expression data of control primary murine liver sinusoidal endothelial cells, biological replicate no 1


title: miR-100_3


title: fetal cord tissue, S0598

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)


title: CDAA mLSEC, biological rep1

description:
CDAA1
Gene expression data of primary murine liver sinusoidal endothelial cells after 10 weeks of CDAA diet, biological replicate no 1

source_name: Primary murine liver sinusoidal endothelial cells after 10 weeks of CDAA diet, biological replicate no 1


title: fetal cord tissue, S0599

tag: maternal age at delivery (years)


title: fetal cord tissue, S0597

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)


title: miR-100_1


title: X410B

type: SRA

city: College Station

first: Traver

last: Wright

state: TX

address: 675 John Kimbrough Blvd., TAMU 4253

department: Health and Kinesiology

country: USA

institute: Texas A&M University

library_source: transcriptomic

data_processing:
Base calling was using Illumina's bcl2fastq2-v2.20 converter
A genome index was built with STAR (v2.5.3amod) from the NCBI Hawaiian Monk Seal genome and corresponding annotation release 100.
Reads were aligned to the seal reference using the STAR software version 2.5.3amod with the parameters recommended for the ENCODE consortium.
Read counts per gene were produced with the --quantMode GeneCounts function of STAR
Differential gene expression was analyzed with the R (version 3.4.3) software DESeq2 (version 1.18.1)
Genome_build: GCF_002201575.1
Supplementary_files_format_and_content: Tab delimited table of raw read counts per gene

organism: Mirounga angustirostris

source_name: longissimus dorsi muscle, late molt

extract_protocol:
Samples were blotted free of RNAlater, flash-frozen in liquid nitrogen and pulverized using a mortar and pestle before mechanical homogenization with a rotary tissue grinder using an RNAqueous Total  RNA Isolation Kit.
Poly-A plus RNA was enriched from  ~0.1 ug of total RNA and used to generate libraries using the Illumina TruSeq RNA kit.

treatment_protocol: Skeletal muscle biopsies were taken from adult female northern elephant seals within 5 days of arrival on the beach for the annual molt. Muscle biopsies were taken again (not exclusively paired to the same animals) after an average of 34 days of molt before returning to sea. Samples were preserved in chilled RNAlater for 24 hours before freezing.

tag: Stage

value: late molt

value: skeletal muscle

tag: developmental stage

value: adult

tag: Sex

value: female


title: WT_4

growth_protocol: All mice were kept under a 12h/12h light/dark cycle in a specific pathogen-free animal facility with standard diet and water available ad libitum.

tag: genotype

value: wildtype

value: male


title: fetal cord tissue, S0595

tag: child sex (male = 0; female = 1)

tag: pre-pregnancy bmi (kg/m^2)


title: fetal cord tissue, S0596


title: fetal cord tissue, S0594


title: 9678B


title: WT_2

tag: gender

tag: age


title: 5572B


title: fetal cord tissue, S0593


title: miR-100_2


title: 4448B


title: fetal cord tissue, S0592


title: 6762A

source_name: longissimus dorsi muscle, early molt

value: early molt


title: fetal cord tissue, S0590


title: fetal cord tissue, S0591


title: 5842A


title: C497A


title: fetal cord tissue, S0588


title: fetal cord tissue, S0589


title: fetal cord tissue, S0587


title: 5572A


title: WT_3


title: fetal cord tissue, S0584


title: fetal cord tissue, S0586


title: fetal cord tissue, S0585


title: WT_1


title: emGFP-Rbm15 irCLIP_Rep1

city: Oxford

first: Guifeng

last: Wei

address: South Parks Road

department: Department of Biochemistry

country: United Kingdom

institute: University of Oxford

data_processing:
The irCLIP adaptors (sequence) from single-end sequencing reads were first cut by cutadapt (v1.12) (Martin 2011), and then collapsed by CTK toolkit to remove PCR duplication (Shah et al., 2017). The barcodes with UMI-containing 12 letters were moved to FASTQ header lines. The resulted single-end fastq reads, longer than 15nt, were mapped to mm10 genome by STAR (v2.5.2b) (Dobin et al., 2013) with key parameters (--outSAMattributes All --outFilterMultimapNmax 1 --outFilterMismatchNmax 2 --alignEndsType EndToEnd --seedSearchStartLmax 15 --outWigType bedGraph read1_5p). This setting is because RT stops were generated by reverse transcriptase around the UV crosslinked sites or crosslinking induced truncation sties (CITS), and RT-stops were main output when analysing the irCLIP-seq reads. The single nucleotide was considered as a CITS if there are no less than 3 stops (>=3) from independent strand-specific reads. In addition, crosslinking induced mutation sites (CIMS), particularly (deletion site) were also calculated. The single nucleotide was considered as a CIMS if this position has more than 2 deletions among total covered reads and the mutation rate is [0.01, 0.5], in order to avoid the potential contamination from the indels. Given that most of the RNA-binding proteins has 5-mer consensus motif, called CITSs or CIMSs from biological replicate 1 were kept if they were also called and within 5 nucleotides distance in biological replicate 2 (closestBed -a CITS_Rep1.bed -b CITS_Rep2.bed -s -d | awk ‘$13<=5’). The distribution of CITS and CIMS were analysed by the RNAmpp pipeline, described as above. Motifs around these CITSs or CIMSs were searched by Homer with key parameter (findMotifsGenome.pl CITS.bed mm10 MotifOutput -rna).
Genome_build: mm10
Supplementary_files_format_and_content: bw is the bigwig format which contains the strand-split normalized irCLIP-seq RT stops.

source_name: Rbm15 irCLIP

growth_protocol: mESCs were grown in feeder-dependent conditions on gelatinized plates at 37oC in a 5% CO2 incubator. Mitomycin C-inactivated mouse fibroblasts were used as feeders. mESCs medium consists of Dulbecco’s Modified Eagle Medium (DMEM, ThermoFisher) supplemented with 10% foetal calf serum (Seralab), 2 mM L-glutamine (ThermoFisher), 1X non-essential amino acids (ThermoFisher), 50 μM β-mercaptoethanol (ThermoFisher), 50 g/mL penicillin/streptomycin (ThermoFisher), and 1mL of Leukemia Inhibitory Factor (LIF)-conditioned medium made in-house.

extract_protocol: irCLIP-seq protocol (Zarnegar et al., 2016)

treatment_protocol: The emGFP-PreScission-RBM15 cell line was derived from mouse XY 3E ES cells, containing rtTA integrated into the Rosa26 locus and random integration of Dox-inducible Xist transgene into chr17 (Coker et al., 2020; Tang et al., 2010). In these cells, the puromycin resistance cassette at Rosa26 locus was replaced with hygromycin resistance (Moindrot et al., 2015). Then, cells were transfected and screened for stable integration of the pTRE-emGFP-PreScission-RBM15 plasmid. Cells treated with 1μg/mL Dox for 24hr simultaneously induce Xist RNA and emGFP-PreScission-RBM15 protein expression

value: Male

tag: cell line

value: Dox-inducible Xist transgene on chr17 and random integration of emGFP-Rbm15

tag: cell type

value: mESC

tag: agent

value: Dox

tag: time point

tag: molecule subtype

value: Rbm15 crosslinked RNA


title: fetal cord tissue, S0583

tag: tissue


title: H5_dTAG_input

data_processing:
rm6A-seq raw reads were mapped to mm10 + dm6 concatenated genome by STAR (v2.5.2b), input for conventional analysis were mapped to mm10 genome.
MeRIP-seq reads were split into positive and negative strands, and bigwig files were generated accordingly. Ten million mapped reads / library was used to perform normalization in conventional MeRIP-seq analysis, except calibrated MeRIP-seq analysis that was normalized to the sequenced Drosophila RNA reads.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files store the strand-split normalized m6A intensities in IP and input experiments.

extract_protocol: Total RNAs were isolated by Trizol, and were used for m6A-seq.

treatment_protocol: C3 and H5 are two clones in which Mettl3 C-terminus is dTAG inserted. Cells are either treated with dTAG-13 for 2 hours or not, then followed by the addition of doxycycline for another 24 hours. Xist expression driven by TetO promoter was induced by adding doxycycline (1.5μg/mL) to the culture medium

value: Female

tag: antibody


title: C3_m6AIP

value: anti-m6A antibody (Synaptic Systems, 202 003)


title: emGFP-Rbm15 irCLIP_Rep2


title: H5_input


title: fetal cord tissue, S0581

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)

tag: maternal age at delivery (years)


title: C3_dTAG_m6AIP


title: fetal cord tissue, S0582

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)


title: fetal cord tissue, S0580


title: fetal cord tissue, S0579


title: H5_dTAG_m6AIP


title: H5_m6AIP


title: fetal cord tissue, S0575


title: fetal cord tissue, S0574


title: Abcam_Input_Rep2

data_processing:
We performed peak calling on duplicate m6A IP and input bam files with MACS2 (2.1.1) tool (Zhang et al., 2008). SySy and Abcam ChrMeRIP-seq data were analyzed separately. Nascent transcriptome size was calculated from UCSC genome browser and used as genome size. The key parameters are (-q 0.05 --nomodel --extsize 100 --call-summits) in addition to the genome size (gsize) 2.4e8 for ChrMeRIP and 1.05e8 for standard MeRIP-seq (Dominissini et al., 2013). The strand-specific RNA-seq allows us to determine the peak strand by calculating the strand-specific fold change log2(IP/Input). Direction ambiguous peaks were removed from the analysis. The border of m6A peaks were further refined according to the summits output from MACS2. Given that RNAs were fragmented to a size slightly longer than 100nt for MeRIP-seq, we shrunk the peak size by only keeping the 125nt on both side of summits if the called m6A peak is larger than 250nt. For the subpeaks within broader peaks, we treated them as individual peak if they are 250nt further away. Otherwise, the border of these 2 subpeaks were determined as middle site between their summits. This analysis resulted in 10,749 and 11,726 peaks for SySy and Abcam antibody respectively. We further defined the high confidence m6A set (ConfGroup1, n=5277) if peak appears from 2 antibodies, medium confidence m6A set (ConfGroup2, n=5472) that were detected by SySy antibody and also has signal from Abcam antibody but below the cutoff to be called peaks by MACS2 (Zhang et al., 2008), and low confidence m6A set (ConfGroup3, n=6319) that were only detected by Abcam antibody and almost no signal from SySy antibody. Motifs for each group were searched and analysed by HOMER program (Heinz et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: bw is strand-split bigwig files for ChrMeRIP-seq. bed files are m6A modification peak files described in the study.

growth_protocol: E14 mouse embryonic stem cells were grown in Dulbecco’s Modified Eagle Medium (DMEM, from Life Technologies) supplemented with 10% foetal calf serum (FCS, from Seralab), 2 mM L-glutamine, 1X non-essential amino acids, 50 μM β-mercaptoethanol, 50 g/mL penicillin/streptomycin (all from invitrogen) and 1000 U/mL of LIF. Non-differentiating ES cells were grown on tissue culture dishes coated with PBS+1% gelatine. Cells were passaged using 0.05% trypsin-EDTA (Life Technologies) with 2% Chicken Serum (Life Technologies) and frozen in FCS +10% DMSO.

extract_protocol:
Chromatin-associated RNAs were isolated according to Nesterova et al. 2019. and then subject to standard MeRIP-seq
Illumina TruSeq Stranded Total RNA Library Prep Kit

tag: cell line/type

value: E14 mESC

value: input

value: ChrRNA


title: fetal cord tissue, S0576

value: fetal cord tissue


title: C3_dTAG_input


title: C3_input


title: Abcam_Input_Rep1


title: Abcam_ChrMeRIP_Rep2

value: anti-m6A antibody (Abcam ab151230)


title: Abcam_ChrMeRIP_Rep1


title: fetal cord tissue, S0573


title: fetal cord tissue, S0572


title: fetal cord tissue, S0571


title: SySy_Input_Rep2

description: HHMHYBGX2_GW_E14_M6A_17s000997-1-1_Gdula_lane1Input17


title: fetal cord tissue, S0570


title: SySy_ChrMeRIP_Rep2

description: HHMHYBGX2_GW_E14_M6A_17s000997-1-1_Gdula_lane1m6AIP17


title: fetal cord tissue, S0569


title: fetal cord tissue, S0567


title: H5_dTAG3h_4sU30min_Rep3

description:
Clone H5
Rep3-H5-dTAG-4sU30m_S19

data_processing:
library strategy: 4sU-RNA-seq
4sU-seq were mapped to mm10 genome by STAR (v2.5.2b) (Dobin et al., 2013) with following key parameters (--twopassMode Basic --outSAMstrandField intronMotif --outSAMattributes All --outFilterMultimapNmax 1 --outFilterMismatchNoverReadLmax 0.06 --alignEndsType EndToEnd).
For intron-centric differential splicing analysis, the leafcutter package (v0.2.7) (Li et al., 2018) was used to quantify intron usage and identify differentially spliced intron clusters between two conditions (dTAG13 treated and non-treated control, or wild-type versus Mettl3 knockout). Only splice junctions supported by uniquely mapped reads were used. The analysis followed the differential splicing documents from the package, except the split reads number for intron cluster. For dATG Mettl3 experiment, at least 30 split reads (6 replicates) are required. The splicing clusters were ranked and 3 different thresholds were set to generate differential splicing level (For dTAG Mettl3 experiment, q<0.05, q<0.2, p<0.05 were chosen. Here q is adjusted p-value). If the splicing cluster has one (or multiple) m6A peak(s) from any confident group overlap or within 500bp distance, it was considered as cis-m6A-regulated cluster, otherwise other cluster. Sashimi plots with deltaPSI were generated from leafcutter package (Li et al., 2018).
Genome_build: mm10
Supplementary_files_format_and_content: leafcutter_ds_effect_sizes.txt and leafcutter_ds_cluster_significance.txt are txt file format, that are direct output from Leafcutter software. The splicing clusters and their significance in the dTAG Mettl3 experiment.

extract_protocol:
Total RNAs were extracted according to TRIzol manuals, followed by DNaseI treatment.For each μg of total RNA, 2μL of Biotin-HPDP (Pierce, 50mg EZ-Link Biotin-HPDP), previously dissolved in DMF at a concentration of 1mg/mL, and 1μL of 10xBiotinylation buffer (100mM Tris HCl pH 7.4, 10mM EDTA), were added. The reaction was incubated with rotation for 15 min at 25ºC. Biotinylated 4sU-RNA was recovered using the μMacs Streptavidin Kit.
Illumina TruSeq Stranded Total RNA Library Prep Kit

treatment_protocol: Cells were either treated with dTAG-13 for 3hours or not, then 4sU was incorporated in the medium for another 30min.

tag: strain background

value: 129S x Cast

value: Mettl3 C-terminal FKBP12(F36V) and doxcycline-inducible Xist

value: mouse embryonic stem cells


title: fetal cord tissue, S0565


title: fetal cord tissue, S0577


title: C3_4sU30min_Rep3

description:
Clone C3
Rep3-C3-4sU30m_S16


title: C3_dTAG3h_4sU30min_Rep3

description:
Clone C3
Rep3-C3-dTAG-4sU30m_S13


title: fetal cord tissue, S0563


title: fetal cord tissue, S0564


title: H5_dTAG3h_4sU30min_Rep2

description:
Clone H5
Rep2-H5-dTAG3h-4sU30m_S18


title: fetal cord tissue, S0562


title: H5_4sU30min_Rep2

description:
Clone H5
Rep2-H5-4sU30m_S17


title: fetal cord tissue, S0561


title: fetal cord tissue, S0558


title: fetal cord tissue, S0557


title: H5_dTAG3h_4sU30min_Rep1

description:
Clone H5
D-H5-dTAG3h-4sU30m_S12


title: C3_4sU30min_Rep2

description:
Clone C3
Rep2-C3-4sU30m_S15


title: H5_4sU30min_Rep1

description:
Clone H5
C-H5-4sU30m_S11


title: C3_dTAG3h_4sU30min_Rep2

description:
Clone C3
Rep2-C3-dTAG3h-4sU30m_S12


title: SySy_Input_Rep1

description: HHMHYBGX2_GW_E14_M6A_17s000997-1-1_Gdula_lane1Input16


title: fetal cord tissue, S0556


title: fetal cord tissue, S0554


title: fetal cord tissue, S0555


title: C3_dTAG3h_4sU30min_Rep1

description:
Clone C3
B-C3-dTAG3h-4sU30m_S10


title: C3_4sU30min_Rep1

description:
Clone C3
A-C3-4sU30m_S9


title: fetal cord tissue, S0552


title: H5_4sU30min_Rep3

description:
Clone H5
GW_S16


title: fetal cord tissue, S0553


title: SySy_ChrMeRIP_Rep1

description: HHMHYBGX2_GW_E14_M6A_17s000997-1-1_Gdula_lane1m6AIP16


title: fetal cord tissue, S0550


title: fetal cord tissue, S0548


title: fetal cord tissue, S0549


title: fetal cord tissue, S0544


title: fetal cord tissue, S0543


title: fetal cord tissue, S0546


title: fetal cord tissue, S0542


title: fetal cord tissue, S0545


title: fetal cord tissue, S0560


title: fetal cord tissue, S0541


title: fetal cord tissue, S0539


title: fetal cord tissue, S0536


title: fetal cord tissue, S0538


title: fetal cord tissue, S0535


title: fetal cord tissue, S0532


title: fetal cord tissue, S0534


title: fetal cord tissue, S0533


title: fetal cord tissue, S0531


title: fetal cord tissue, S0530


title: fetal cord tissue, S0547


title: fetal cord tissue, S0529


title: fetal cord tissue, S0527


title: fetal cord tissue, S0526


title: fetal cord tissue, S0525


title: fetal cord tissue, S0524


title: fetal cord tissue, S0523


title: LSEC_wt_2

description: CD31+ CD146+ Lyve1+ Retinoid- ECs

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of mouse Mogene-2_0-type from Affymetrix. A Custom CDF Version 19 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: liver sinusoidal endothelial cell

growth_protocol: 3-4 mice were pooled to generate one LSEC/CEC sample. RNA was immediately extracted after the cell sorting procedure. Samples with a lower RNA integrity than 7 were excluded. All remaining samples were used for expression profiling analyis.

extract_protocol: PicoPure extraction kit (Life technologies) was used according to the manufacturer's recommendations.

tag: strain

value: liver sinusoidal endothelial cells (LSECs)


title: LSEC_wt_1

description: CD31+ CD146+ Lyve1+ Retinoid- ECs


title: CEC_wt_1

description: CD31+ CD146+ Lyve1- Retinoid- ECs

source_name: liver capillary endothelial cell

value: capillary endothelial cells (CECs)


title: CEC_wt_3

description: CD31+ CD146+ Lyve1- Retinoid- ECs


title: fetal cord tissue, S0537

tag: child sex (male = 0; female = 1)


title: fetal cord tissue, S0521

tag: pre-pregnancy bmi (kg/m^2)


title: fetal cord tissue, S0522


title: LSEC_wt_3

description: CD31+ CD146+ Lyve1+ Retinoid- ECs


title: SMLF30MBr.627

city: St Louis

first: Caryn

last: Carson

state: Missouri

address: 4515 McKinley Avenue

department: Genetics

institute: Washington University in St Louis

description:
processed data file: SMLFBAT.txt
*_SM_GTCGATA-GGCACGT

data_processing:
FASTQ files were filtered to remove low quality reads.
Reads were trimmed using the fastx toolkit (fastx_trimmer).
Trimmed reads were aligned against LG/J and SM/J custom genomes using STAR (version 2.6.0c).
Read counts were normalized via upper quartile normalization and a minimum normalized read depth of 10 was required.
Raw read counts for each strain x diet x tissue cohort (16 samples per cohort) were analyzed in edgeR. Expression of at least one count per million in at least half of the samples was required. Genes passing this expression threshold were TMM-normalized.
Genome_build: Custom LG/J and SM/J genomes based on the mm10 genome (doi.org/10.1101/579748).
Supplementary_files_format_and_content: processed data files include edgeR normalized read counts for genes expressed at 1cpm or higher in at least half of the samples. Rows are Ensembl IDs, Columns are samples.

source_name: SM/J_male_30 wks_lowfat_Interscapular Brown Adipose

extract_protocol:
Interscapular brown and reproductive white adipose tissue was removed and flash frozen in liquid nitrogen. RNA was harvested using the RNEasy Lipid Tissue Mini Kit from Qiagen (Catalog# 74804). 1 ug of total RNA was used for preparation of sequencing libraries
Libraries were constructed with the Illumina RiboZero kit from total RNA samples with RIN >7.5

value: SM/J

tag: Sex

value: male

value: 30 Weeks

tag: diet

value: lowfat

value: Interscapular Brown Adipose


title: SMLF30MBr.631

description:
processed data file: SMLFBAT.txt
*_SM_TGGTCTC-GGCGATT

tag: age


title: SMLF30MRep.552

description:
processed data file: SMLFWAT.txt
*_SM_CAGAGTC-CAGCCCA

source_name: SM/J_male_30 wks_lowfat_Reproductive White Adipose

value: Reproductive White Adipose


title: SMLF30MRep.631

description:
processed data file: SMLFWAT.txt
*_SM_AGCGCCG-CCGAATT


title: CEC_wt_2

description: CD31+ CD146+ Lyve1- Retinoid- ECs

tag: cell type


title: fetal cord tissue, S0519


title: SMLF30MBr.630

description:
processed data file: SMLFBAT.txt
*_SM_CATCGCG-AAATCCG


title: SMLF30MRep.630

description:
processed data file: SMLFWAT.txt
*_SM_TACAGAC-AAAGGGA


title: SMLF30MBr.552

description:
processed data file: SMLFBAT.txt
*_SM_GTATCCT-ACGACTT


title: SMLF30MRep.627

description:
processed data file: SMLFWAT.txt
*_SM_ACGTCTG-GAAGAAA


title: fetal cord tissue, S0514


title: fetal cord tissue, S0510


title: SMLF30FRep.662

description:
processed data file: SMLFWAT.txt
*_SM_AGACTGA-GTGCGAG

source_name: SM/J_female_30 wks_lowfat_Reproductive White Adipose

value: female


title: fetal cord tissue, S0512


title: fetal cord tissue, S0516


title: SMLF30FRep.661

description:
processed data file: SMLFWAT.txt
*_SM_ATCGAGC-ACTCCTA


title: fetal cord tissue, S0508


title: fetal cord tissue, S0507


title: fetal cord tissue, S0520


title: SMLF30FRep.490

description:
processed data file: SMLFWAT.txt
*_SM_ATGTTCT-CCATGCT


title: fetal cord tissue, S0505


title: fetal cord tissue, S0504


title: fetal cord tissue, S0506


title: fetal cord tissue, S0503


title: SMLF30FRep.489

description:
processed data file: SMLFWAT.txt
*_SM_GATAGTT-ATAGGAC


title: fetal cord tissue, S0501


title: SMLF30FBr.662

description:
processed data file: SMLFBAT.txt
*_SM_CTTGGAA-AGTAAGA

source_name: SM/J_female_30 wks_lowfat_Interscapular Brown Adipose


title: fetal cord tissue, S0502

source_name: cord tissue


title: fetal cord tissue, S0515


title: SMLF30FBr.490

description:
processed data file: SMLFBAT.txt
*_SM_GTAAAAA-GACAGCA


title: fetal cord tissue, S0496


title: SMLF30FBr.661

description:
processed data file: SMLFBAT.txt
*_SM_TACTCTA-GTGCTCT


title: SMLF30FBr.489

description:
processed data file: SMLFBAT.txt
*_SM_GGTGAAT-CGCTGGA


title: fetal cord tissue, S0495


title: fetal cord tissue, S0494


title: SMLF20MRep.731

description:
processed data file: SMLFWAT.txt
*_SM_CACATAT-TCGCGTT

source_name: SM/J_male_20 wks_lowfat_Reproductive White Adipose

value: 20 Weeks


title: fetal cord tissue, S0493


title: fetal cord tissue, S0509


title: fetal cord tissue, S0492


title: SMLF20MRep.650

description:
processed data file: SMLFWAT.txt
*_SM_CTCACCC-TGGTTCC


title: fetal cord tissue, S0491


title: fetal cord tissue, S0489


title: SMLF20MRep.542

description:
processed data file: SMLFWAT.txt
*_SM_AGGACCT-GGTAGTA


title: fetal cord tissue, S0488


title: fetal cord tissue, S0487


title: SMLF20MRep.336

description:
processed data file: SMLFWAT.txt
*_SM_ACGCGGG-GTTGCCG


title: fetal cord tissue, S0486


title: fetal cord tissue, S0485


title: fetal cord tissue, S0499


title: fetal cord tissue, S0500


title: SMLF20MBr.731

description:
processed data file: SMLFBAT.txt
*_SM_GTCCCTT-CTTCGGA

source_name: SM/J_male_20 wks_lowfat_Interscapular Brown Adipose


title: fetal cord tissue, S0484


title: SMLF20MBr.650

description:
processed data file: SMLFBAT.txt
*_SM_TCGTGCG-GTAACCT


title: fetal cord tissue, S0498


title: fetal cord tissue, S0483


title: SMLF20MBr.542

description:
processed data file: SMLFBAT.txt
*_SM_TTTTCGG-CCACAGG


title: fetal cord tissue, S0482


title: fetal cord tissue, S0480


title: fetal cord tissue, S0478


title: fetal cord tissue, S0474


title: fetal cord tissue, S0479


title: fetal cord tissue, S0477


title: fetal cord tissue, S0473


title: SMLF20FRep.761

description:
processed data file: SMLFWAT.txt
*_SM_TCTGCTT-AGCCCTG

source_name: SM/J_female_20 wks_lowfat_Reproductive White Adipose


title: fetal cord tissue, S0475


title: SMLF20MBr.336

description:
processed data file: SMLFBAT.txt
*_SM_GGAGTCC-GATGGCG


title: SMLF20FRep.730

description:
processed data file: SMLFWAT.txt
*_SM_CCTTGAC-ATACGAA


title: fetal cord tissue, S0472


title: SMLF20FRep.724

description:
processed data file: SMLFWAT.txt
*_SM_GTTTACC-TGGGCTC


title: fetal cord tissue, S0470


title: fetal cord tissue, S0469


title: fetal cord tissue, S0471


title: SMLF20FRep.699

description:
processed data file: SMLFWAT.txt
*_SM_ATTAGGA-TGTTACT


title: fetal cord tissue, S0468


title: fetal cord tissue, S0467


title: SMLF20FBr.761

description:
processed data file: SMLFBAT.txt
*_SM_AATGGTA-GTTACGT

source_name: SM/J_female_20 wks_lowfat_Interscapular Brown Adipose


title: fetal cord tissue, S0466


title: fetal cord tissue, S0465


title: fetal cord tissue, S0463


title: fetal cord tissue, S0464


title: SMLF20FBr.724

description:
processed data file: SMLFBAT.txt
*_SM_CAGTTGT-GGGATCG


title: SMLF20FBr.730

description:
processed data file: SMLFBAT.txt
*_SM_CCTCAAG-ACACAAT


title: fetal cord tissue, S0462


title: fetal cord tissue, S0460


title: fetal cord tissue, S0458


title: SMHF30MRep.700

description:
processed data file: SMHFWAT.txt
*_SM_ATACCCG-CGTGGAC

source_name: SM/J_male_30 wks_highfat_Reproductive White Adipose

value: highfat


title: SMLF20FBr.699

description:
processed data file: SMLFBAT.txt
*_SM_CGGATAC-GAACGCG


title: fetal cord tissue, S0457


title: SMHF30MRep.655

description:
processed data file: SMHFWAT.txt
*_SM_TGAGGTT-AACTGAG


title: fetal cord tissue, S0461


title: fetal cord tissue, S0453


title: fetal cord tissue, S0454


title: fetal cord tissue, S0451


title: fetal cord tissue, S0450


title: fetal cord tissue, S0455


title: fetal cord tissue, S0456


title: fetal cord tissue, S0449


title: fetal cord tissue, S0448


title: SMHF30MRep.656

description:
processed data file: SMHFWAT.txt
*_SM_ATGACAG-TTTGCCC


title: fetal cord tissue, S0447


title: fetal cord tissue, S0446


title: SMHF30MBr.700

description:
processed data file: SMHFBAT.txt
*_SM_CACTGTG-AATAGGA

source_name: SM/J_male_30 wks_highfat_Interscapular Brown Adipose


title: fetal cord tissue, S0445


title: SMHF30MRep.653

description:
processed data file: SMHFWAT.txt
*_SM_TGACTCT-GGCTGCT


title: SMHF30MBr.656

description:
processed data file: SMHFBAT.txt
*_SM_CACCTCC-CACTACG


title: SMHF30MBr.655

description:
processed data file: SMHFBAT.txt
*_SM_GCTTAGA-AGCAATG


title: fetal cord tissue, S0444


title: fetal cord tissue, S0441


title: fetal cord tissue, S0440


title: SMHF30MBr.653

description:
processed data file: SMHFBAT.txt
*_SM_TTTGGCG-CTGGATG


title: fetal cord tissue, S0442


title: fetal cord tissue, S0439


title: SMHF30FRep.786

description:
processed data file: SMHFWAT.txt
*_SM_CGTACAA-GGTGCTT

source_name: SM/J_female_30 wks_highfat_Reproductive White Adipose


title: fetal cord tissue, S0437


title: fetal cord tissue, S0436


title: fetal cord tissue, S0438


title: SMHF30FRep.740

description:
processed data file: SMHFWAT.txt
*_SM_AGCTCGC-CGGAAGG


title: fetal cord tissue, S0435


title: fetal cord tissue, S0434


title: SMHF30FRep.646

description:
processed data file: SMHFWAT.txt
*_SM_TTCGCTG-TAGTAGA


title: fetal cord tissue, S0430


title: SMHF30FBr.786

description:
processed data file: SMHFBAT.txt
*_SM_GATGTGA-CAGAGCC

source_name: SM/J_female_30 wks_highfat_Interscapular Brown Adipose


title: SMHF30FBr.740

description:
processed data file: SMHFBAT.txt
*_SM_TCAGCAC-ACACTGG


title: fetal cord tissue, S0431


title: fetal cord tissue, S0427


title: fetal cord tissue, S0426


title: fetal cord tissue, S0428


title: SMHF30FBr.729

description:
processed data file: SMHFBAT.txt
*_SM_AAACGAC-GGAATGT


title: fetal cord tissue, S0424


title: fetal cord tissue, S0425


title: fetal cord tissue, S0423


title: SMHF30FBr.646

description:
processed data file: SMHFBAT.txt
*_SM_TATCTTA-TGATACA


title: SMHF20MRep.734

description:
processed data file: SMHFWAT.txt
*_SM_CTAACTT-ATAGATC

source_name: SM/J_male_20 wks_highfat_Reproductive White Adipose


title: fetal cord tissue, S0421


title: fetal cord tissue, S0420


title: SMHF20MRep.704

description:
processed data file: SMHFWAT.txt
*_SM_GAATGGT-GTGCCAC


title: SMHF20MRep.703

description:
processed data file: SMHFWAT.txt
*_SM_GTGATTT-TACTACA


title: fetal cord tissue, S0415


title: fetal cord tissue, S0416


title: fetal cord tissue, S0418


title: SMHF30FRep.729

description:
processed data file: SMHFWAT.txt
*_SM_GTGTAGT-GTGGCTG


title: SMHF20MRep.290

description:
processed data file: SMHFWAT.txt
*_SM_ACTGTCG-TAGAGGT


title: fetal cord tissue, S0432


title: fetal cord tissue, S0414


title: fetal cord tissue, S0413


title: fetal cord tissue, S0411


title: SMHF20MBr.734

description:
processed data file: SMHFBAT.txt
*_SM_ATACTTC-CTCTTCG

source_name: SM/J_male_20 wks_highfat_Interscapular Brown Adipose


title: fetal cord tissue, S0410


title: SMHF20MBr.704

description:
processed data file: SMHFBAT.txt
*_SM_ATCGTCA-AACACAG


title: fetal cord tissue, S0408


title: fetal cord tissue, S0409


title: SMHF20MBr.703

description:
processed data file: SMHFBAT.txt
*_SM_TTGAGTG-GTACATT


title: fetal cord tissue, S0405


title: fetal cord tissue, S0422


title: fetal cord tissue, S0403


title: fetal cord tissue, S0406


title: SMHF20MBr.290

description:
processed data file: SMHFBAT.txt
*_SM_GTATTTG-AAGCCTT


title: fetal cord tissue, S0401


title: fetal cord tissue, S0407


title: fetal cord tissue, S0417


title: SMHF20FRep.862

description:
processed data file: SMHFWAT.txt
*_SM_GCTATAG-GTTAGAG

source_name: SM/J_female_20 wks_highfat_Reproductive White Adipose


title: fetal cord tissue, S0399


title: fetal cord tissue, S0397


title: fetal cord tissue, S0396


title: SMHF20FRep.292

description:
processed data file: SMHFWAT.txt
*_SM_GAGTACG-AAGATCC


title: C7_CAGE_seq_Rep2

data_processing:
The raw reads from our CAGE-seq data were mapped to the mm10 reference genome with STAR under the default parameters apart from (--outFilterMultimapNmax 1   --outFilterMismatchNmax 8   --alignEndsType EndToEnd).
For visualization of RNA-seq data in UCSC genome browser, the coverage was generated by Bedtools (v2.17.0) (Quinlan and Hall, 2010) and was normalized to 10 million mapped reads
Barcodes are extracted from pooled single-end RNA-seq reads and moved to the header line. The resulted fastq files were split according to the 3-letter barcode, and then mapped to mm10 genome by STAR (v2.4.2a) (Dobin et al., 2013) with default parameters expect (--outWigType bedGraph read1_5p --outFilterMultimapNmax 1 --outFilterMismatchNmax 4 --seedSearchStartLmax 15 --alignEndsType EndToEnd). Only uniquely mapped reads were kept for further analysis. The reads mapping summary for each sample were listed in Supplementary Table. CAGEr (1.28.0) (Haberle et al., 2015) were employed for CAGE-seq data analysis, including TSS detection, clustering, aggregation, promoter width, and quantification. The CAGE-seq libraries were normalized (powerLaw) and tpm (tags per million) scores were calculated as 10 million mapped reads. TSS clusters shorter than 100bp from same strand were further aggregated. GENCODE vM22 (comprehensive annotation) were used to annotate TSS cluster, resulted into promoter (Gencode), exonic, intronic, and intergenic TSS group. Two states (Up and down) were inferred for each TSS cluster in double knockout lines in relation to wild type E14 (Brocks et al., 2017). Intragenic TSSs overlapped with both ATAC-seq and H3K27ac peaks in mESC were removed. Then the “up” events in exonic and intronic regions were considered as “spurious” transcription initiation. Gene expression group were calculated from E14 RNA-seq and gene sets with high or low PWWP2A occupancy were obtained from previous ChIP-seq study (Zhang et al., 2018). CpG island annotation was retrieved from mm10 UCSC genome browser.
CAGE-seq mapped reads were split into positive and negative strands according to the flag filed in BAM file with samtools (1.3) (Li et al., 2009), and then visualized in UCSC or IGV genome browser.
Genome_build: mm10

source_name: E14 cells of double PWWP2A/B knockout clone C7

growth_protocol: E14 cells were grown in Dulbecco’s Modified Eagle Medium (DMEM, from Life Technologies) supplemented with 10% foetal calf serum (FCS, from Seralab), 2 mM L-glutamine, 1x non-essential amino acids, 50 μM β-mercaptoethanol, 50 g/mL penicillin/streptomycin (all from Invitrogen) and 1000 U/mL of LIF. Non-differentiating ES cells were grown on tissue culture dishes coated with PBS+1% gelatine. Cells were passaged using 0.05% trypsin-EDTA (Life Technologies) with 2% Chicken Serum (Life Technologies) and frozen in FCS + 10% DMSO. For cells stably expressing PWWP2A/B or PWWP2A truncations, ES cell medium were supplemented with 1.75 µg/ml Puromycin. SG4 Drosophila melanogaster cells were cultured at 27ºC with Schneider’s Drosophila Medium (ThermoFisher) supplemented with penicillin/streptomycin and 10% FCS.

extract_protocol:
For the extraction of nuclear RNA, cells were lysed for 5 minutes on ice in lysis buffer (20 mM Tris pH 7.5, 150 mM NaCl, 5% glycerol, 0.5% NP-40, 1x protease inhibitor) then centrifuged at 2000 rpm to pellet nuclei. The nuclei were washed once in cold PBS then directly lysed in Trizol followed by standard RNA extraction.
Libraries for all samples (E14 ´ 3, PWWP2A/B DKO C7 ´ 3, DKO A1 ´ 2) were prepared using the CAGE-seq kit purchased from cage-seq.com. Briefly, 5 mg of nuclear RNA for each sample was primed (random) and reverse transcribed to cDNA, followed by biotinylation of and capture of the 7-methylguanosine cap of all RNA Polymerase II transcripts. Adapters containing barcodes (3-letter) were ligated and samples were multiplexed. As this CAGE-seq protocol involves no PCR amplification step, the entire sample was denatured and loaded into the Illumina NextSeq500 for single end 80bp sequencing.

value: embryonic stem cell

tag: genotype/variation

value: double PWWP2A/B knockout


title: fetal cord tissue, S0394

value: fetal cord tissue


title: fetal cord tissue, S0393


title: SMHF20FBr.864

description:
processed data file: SMHFBAT.txt
*_SM_AGTCTAG-TTTGTCG

source_name: SM/J_female_20 wks_highfat_Interscapular Brown Adipose


title: SMHF20FBr.862

description:
processed data file: SMHFBAT.txt
*_SM_AAGAAGT-CCTATCC


title: fetal cord tissue, S0392


title: C7_CAGE_seq_Rep1


title: fetal cord tissue, S0391


title: fetal cord tissue, S0402


title: fetal cord tissue, S0390


title: SMHF20FRep.864

description:
processed data file: SMHFWAT.txt
*_SM_TGAAGGC-TCCATAG


title: fetal cord tissue, S0389


title: A1_CAGE_seq_Rep2

source_name: E14 cells of double PWWP2A/B knockout clone A1


title: SMHF20FBr.292

description:
processed data file: SMHFBAT.txt
*_SM_ACAGATA-ATGGCAT


title: fetal cord tissue, S0400


title: A1_CAGE_seq_Rep1


title: fetal cord tissue, S0388


title: fetal cord tissue, S0387


title: E14_CAGE_seq_Rep3

source_name: E14 cells wild-type

value: wild-type


title: LGLF30MRep.483

description:
processed data file: LGLFWAT.txt
*_LG_TGTGCCA-CTTCATT

source_name: LG/J_male_30 wks_lowfat_Reproductive White Adipose

value: LG/J


title: fetal cord tissue, S0384

source_name: cord tissue


title: E14_CAGE_seq_Rep2


title: SMHF20FRep.756

description:
processed data file: SMHFWAT.txt
*_SM_GACAACC-CCTTCGA


title: fetal cord tissue, S0398


title: C7_CAGE_seq_Rep3


title: fetal cord tissue, S0383


title: LGLF30MRep.482

description:
processed data file: LGLFWAT.txt
*_LG_TTGCCCC-CTCTCGT


title: fetal cord tissue, S0382


title: fetal cord tissue, S0380


title: E14_CAGE_seq_Rep1


title: fetal cord tissue, S0378


title: LGLF30MRep.481

description:
processed data file: LGLFWAT.txt
*_LG_CCGGACC-AACGTGC


title: SMHF20FBr.756

description:
processed data file: SMHFBAT.txt
*_SM_GATAAGG-AGTCCCA


title: fetal cord tissue, S0376


title: fetal cord tissue, S0377


title: fetal cord tissue, S0374


title: fetal cord tissue, S0375


title: LGLF30MRep.319

description:
processed data file: LGLFWAT.txt
*_LG_CTCAATG-TCGCAGA


title: LGLF30MBr.483

description:
processed data file: LGLFBAT.txt
*_LG_AACGGAG-AGTTCGG

source_name: LG/J_male_30 wks_lowfat_Interscapular Brown Adipose


title: fetal cord tissue, S0385


title: fetal cord tissue, S0372


title: ctl_atacseq_2

city: Waltham

first: Erin

middle: Amelia

last: Clark

state: MA

address: 415 South St

department: Biology

institute: Brandeis University

description: control

library_source: genomic

data_processing:
RNA-seq reads mapped by STAR quantified with featureCounts.
RNA-seq reads mapped by STAR. ATAC-seq reads were mapped using Bowtie2 and filtered to get none mitochondrial unique reads (noDupMT).
ATAC-seq peaks were identified using HOMER and IDR.
Differentially expressed genes were identified by Limma. Differential ATAC peaks were indentified using DiffBind.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts (RNA-seq) bw (ATAC-seq)

source_name: RORb-gfp heterozygous mice, P28-30

growth_protocol: In vivo

extract_protocol:
For RNA: Arcturus PicoPure RNA Isolation kit, for ATAC: lysis buffer and Zymo Clean and Concnetrator-5 kit
RNA libraries were prepared by using Ovation Trio RNA-Seq library preparation kit with mouse rRNA depletion. ATAC libraries were prepared as details in Clark, et al. BioProtocols

tag: genotype

value: one copy of GFP knocked into RORb locus

value: collected from L4


title: fetal cord tissue, S0369


title: LGLF30MBr.482

description:
processed data file: LGLFBAT.txt
*_LG_ACTCCAA-GTTTAGT


title: ko_atacseq_1

description: KO

source_name: RORb-gfp homozygous mice, P28-30

value: two copies of GFP knocked into RORb locus to create a full KO


title: fetal cord tissue, S0371


title: ko_atacseq_2

description: KO


title: fetal cord tissue, S0370


title: fetal cord tissue, S0367


title: fetal cord tissue, S0368


title: P30_ko_rnaseq_4

source_name: RORb-gfp homozygous mice, P30

value: collected from L4 S1


title: fetal cord tissue, S0366


title: LGLF30MBr.319

description:
processed data file: LGLFBAT.txt
*_LG_AAATGCA-GGAGAGT

value: male


title: P30_ko_rnaseq_3


title: fetal cord tissue, S0362


title: ctl_atacseq_1

description: control


title: fetal cord tissue, S0363


title: fetal cord tissue, S0361


title: LGLF30FRep.690

description:
processed data file: LGLFWAT.txt
*_LG_CCATCAT-CATCGGC

source_name: LG/J_female_30 wks_lowfat_Reproductive White Adipose

value: 30 Weeks


title: P30_ko_rnaseq_2


title: LGLF30FRep.524

description:
processed data file: LGLFWAT.txt
*_LG_CGAAAGT-TGAGTCC

value: lowfat


title: fetal cord tissue, S0360


title: fetal cord tissue, S0358


title: LGLF30FRep.342

description:
processed data file: LGLFWAT.txt
*_LG_TGTTTGT-AGCACCT


title: P30_ko_rnaseq_1


title: LGLF30MBr.481

description:
processed data file: LGLFBAT.txt
*_LG_GTACGGC-GCATCGC

value: Interscapular Brown Adipose


title: P7_ko_rnaseq_4

source_name: RORb-gfp homozygous mice, P7


title: fetal cord tissue, S0357


title: fetal cord tissue, S0356


title: LGLF30FBr.524

description:
processed data file: LGLFBAT.txt
*_LG_GCCTCCC-TTAAGGG

source_name: LG/J_female_30 wks_lowfat_Interscapular Brown Adipose


title: fetal cord tissue, S0352


title: LGLF30FBr.690

description:
processed data file: LGLFBAT.txt
*_LG_TAACAAG-TGGAGTG


title: P7_ko_rnaseq_2


title: fetal cord tissue, S0353


title: fetal cord tissue, S0351


title: P7_ko_rnaseq_3


title: fetal cord tissue, S0350


title: P7_ko_rnaseq_1


title: LGLF30FBr.342

description:
processed data file: LGLFBAT.txt
*_LG_TACATGG-CACGTTC


title: fetal cord tissue, S0348


title: fetal cord tissue, S0349


title: LGLF20MRep.613

description:
processed data file: LGLFWAT.txt
*_LG_TCAAACA-AGGTAGG

source_name: LG/J_male_20 wks_lowfat_Reproductive White Adipose

value: Reproductive White Adipose


title: fetal cord tissue, S0347


title: fetal cord tissue, S0346


title: P2_ko_rnaseq_4

source_name: RORb-gfp homozygous mice, P2


title: P2_ko_rnaseq_3


title: fetal cord tissue, S0345


title: LGLF20MRep.612

description:
processed data file: LGLFWAT.txt
*_LG_TCCCAGC-CGAAGGT


title: fetal cord tissue, S0359


title: fetal cord tissue, S0341


title: fetal cord tissue, S0344


title: P2_ko_rnaseq_2


title: fetal cord tissue, S0354


title: LGLF20MRep.535

description:
processed data file: LGLFWAT.txt
*_LG_GCAACGC-CCGGTTA


title: fetal cord tissue, S0343


title: P2_ko_rnaseq_1


title: LGLF20MRep.534

description:
processed data file: LGLFWAT.txt
*_LG_CAAGCCG-TAAATCC


title: fetal cord tissue, S0337


title: P30_ctl_rnaseq_4

source_name: RORb-gfp heterozygous mice, P30


title: LGLF30FBr.339

description:
processed data file: LGLFBAT.txt
*_LG_TCAACTG-CGATCCT

value: female


title: fetal cord tissue, S0336


title: fetal cord tissue, S0340


title: LGLF20MBr.612

description:
processed data file: LGLFBAT.txt
*_LG_CCTAATC-TCCCTAT

source_name: LG/J_male_20 wks_lowfat_Interscapular Brown Adipose

value: 20 Weeks


title: fetal cord tissue, S0335


title: fetal cord tissue, S0332


title: P30_ctl_rnaseq_2


title: LGLF30FRep.339

description:
processed data file: LGLFWAT.txt
*_LG_CGTCGCT-TAGTCTC


title: fetal cord tissue, S0331


title: P30_ctl_rnaseq_1


title: fetal cord tissue, S0330


title: P30_ctl_rnaseq_3


title: LGLF20MBr.534

description:
processed data file: LGLFBAT.txt
*_LG_GGGTCAA-ACCGTTA


title: fetal cord tissue, S0329


title: fetal cord tissue, S0328


title: P7_ctl_rnaseq_4

source_name: RORb-gfp heterozygous mice, P7


title: fetal cord tissue, S0327


title: LGLF20FRep.592

description:
processed data file: LGLFWAT.txt
*_LG_GCAGGGG-TACTGCC

source_name: LG/J_female_20 wks_lowfat_Reproductive White Adipose


title: P7_ctl_rnaseq_3


title: fetal cord tissue, S0326


title: fetal cord tissue, S0325


title: fetal cord tissue, S0338


title: P7_ctl_rnaseq_2


title: LGLF20FRep.587

description:
processed data file: LGLFWAT.txt
*_LG_CCGGCAG-CATGTGC


title: LGLF20MBr.613

description:
processed data file: LGLFBAT.txt
*_LG_ACCTGAA-GGACCGA


title: fetal cord tissue, S0339


title: P7_ctl_rnaseq_1


title: LGLF20FRep.350

description:
processed data file: LGLFWAT.txt
*_LG_ACCATAC-TTTCGCT


title: fetal cord tissue, S0320


title: fetal cord tissue, S0322


title: P2_ctl_rnaseq_4

source_name: RORb-gfp heterozygous mice, P2


title: fetal cord tissue, S0319


title: fetal cord tissue, S0321


title: P2_ctl_rnaseq_3


title: LGLF20FBr.592

description:
processed data file: LGLFBAT.txt
*_LG_AGATACT-GTGGACT

source_name: LG/J_female_20 wks_lowfat_Interscapular Brown Adipose


title: fetal cord tissue, S0317


title: LGLF20FBr.587

description:
processed data file: LGLFBAT.txt
*_LG_AATTCAT-CCATACA


title: LGLF20MBr.535

description:
processed data file: LGLFBAT.txt
*_LG_TGATTAC-ATCTTGC


title: fetal cord tissue, S0316


title: fetal cord tissue, S0318


title: fetal cord tissue, S0313


title: LGLF20FBr.350

description:
processed data file: LGLFBAT.txt
*_LG_AATACGC-GTGTAAG


title: fetal cord tissue, S0312


title: P2_ctl_rnaseq_1


title: LGLF20FBr.349

description:
processed data file: LGLFBAT.txt
*_LG_AAACCTT-AGTGCAA


title: fetal cord tissue, S0310


title: fetal cord tissue, S0308


title: fetal cord tissue, S0309


title: LGHF30MRep.625

description:
processed data file: LGHFWAT.txt
*_LG_GATGGCC-ATACTCA

source_name: LG/J_male_30 wks_highfat_Reproductive White Adipose

value: highfat


title: LGLF20FRep.349

description:
processed data file: LGLFWAT.txt
*_LG_TGCCCAT-CTGAGCG


title: fetal cord tissue, S0307

source_name: cord tissue


title: LGHF30MRep.619

description:
processed data file: LGHFWAT.txt
*_LG_CCAGGCA-ATGGAAC


title: fetal cord tissue, S0306


title: fetal cord tissue, S0305


title: fetal cord tissue, S0304


title: AM24Hr2

city: Chicago

first: Navdeep

last: Chandel

state: IL

address: 303 E Superior St, SQ5

department: Pulmonary and Critical Care

institute: Northwestern University

description: htseq.all.counts.txt

data_processing:
Raw BCL read files were demultiplexed and FASTQ files were generated using bcl2fastq and trimmed using Trimmomatic (Bolger et al., 2014).
Next, the reads were aligned to the hg38 reference genome using STAR to generate BAM files.
HTSeq was used to count reads in the exons of genes.
Genome_build: hg38
Supplementary_files_format_and_content: htseq.all.counts.txt is a tab delimited text file that contains counts data for all samples

source_name: Jurkat T-ALL cells

growth_protocol: Jurkat cells were cultured in RPMI 1640 media without L-glutamine with additions of 10% Nu-Serum IV Growth Medium Supplement, 1% GlutaMAX, and 1% Antibiotic-Antimycotic solution. Cells were kept at 37C 5%CO2 and 95% humidity

extract_protocol:
Cells were collected and resuspended in 350uL of RLT Plus buffer and 0.01% 2-mercaptoethanol. Cells suspensions were homogenized by 29-gauge needle and QIAShredder Spin Columns. RNA was extracted with the Rneasy Plus Mini Kit following manufacturer's protocol with an additional on-column DNase treatment with an RNase-Free DNase kit.
RNA was quantified and QC was checked using an Agilent 4200 TapeStation RNA ScreenTape. mRNA libraries were prepared using NEBNext Ultra RNA Library Prep Kit.

treatment_protocol: 1 hour or 24 hours with treatments, in growth media supplemented with vehicle (DMSO and alcohol), 400uM mitoTEMPO, 1uM Piericidin, 1uM Antimycin.

tag: treatment

value: Antimycin+MitoTEMPO

tag: time

value: 24 hour


title: AM24Hr3

description: htseq.all.counts.txt


title: AM24Hr1

description: htseq.all.counts.txt


title: AM24Hr4

description: htseq.all.counts.txt


title: fetal cord tissue, S0303

tag: tissue

value: fetal cord tissue


title: fetal cord tissue, S0302

tag: art treatment status (0 = spontaneous; 1 = assisted reproduction)


title: fetal cord tissue, S0315

tag: maternal age at delivery (years)


title: LGHF30MRep.533

description:
processed data file: LGHFWAT.txt
*_LG_AGTTATG-TCCAATG


title: Anti24Hr4

description: htseq.all.counts.txt

value: Antimycin


title: fetal cord tissue, S0300

tag: maternal ethnicity (0 = chinese; 1 = indian; 2 = malay)


title: fetal cord tissue, S0301


title: fetal cord tissue, S0324


title: P2_ctl_rnaseq_2


title: Anti24Hr3

description: htseq.all.counts.txt


title: fetal cord tissue, S0299


title: LGHF30MBr.619

description:
processed data file: LGHFBAT.txt
*_LG_TTTCAGA-CAAATGG

source_name: LG/J_male_30 wks_highfat_Interscapular Brown Adipose

value: LG/J


title: fetal cord tissue, S0298


title: LGHF30MBr.625

description:
processed data file: LGHFBAT.txt
*_LG_AGGCGAA-CCAGGAA


title: fetal cord tissue, S0297


title: Anti24Hr2

description: htseq.all.counts.txt


title: fetal cord tissue, S0296


title: LGHF30MBr.537

description:
processed data file: LGHFBAT.txt
*_LG_GACACAG-ATCCTGG


title: fetal cord tissue, S0295


title: fetal cord tissue, S0294


title: LGHF30MBr.533

description:
processed data file: LGHFBAT.txt
*_LG_CTGCAAT-GAATACT


title: PM24Hr4

description: htseq.all.counts.txt

value: Piericidin+MitoTEMPO


title: fetal cord tissue, S0293


title: LGHF30MRep.537

description:
processed data file: LGHFWAT.txt
*_LG_TGCTGGG-TGGTGAC


title: fetal cord tissue, S0291


title: PM24Hr3

description: htseq.all.counts.txt


title: fetal cord tissue, S0292


title: fetal cord tissue, S0289


title: fetal cord tissue, S0290


title: LGHF30FRep.510

description:
processed data file: LGHFWAT.txt
*_LG_CTCCCGA-TTGAGGC

source_name: LG/J_female_30 wks_highfat_Reproductive White Adipose


title: LGHF30FRep.509

description:
processed data file: LGHFWAT.txt
*_LG_GTCTGAT-CCGTCCT


title: fetal cord tissue, S0287


title: fetal cord tissue, S0286


title: LGHF30FRep.281

description:
processed data file: LGHFWAT.txt
*_LG_GGTCCTC-TCAGCTT


title: fetal cord tissue, S0288


title: Pier24Hr4

description: htseq.all.counts.txt

value: Piericidin


title: fetal cord tissue, S0285


title: fetal cord tissue, S0283


title: fetal cord tissue, S0284


title: Anti24Hr1

description: htseq.all.counts.txt


title: LGHF30FBr.688

description:
processed data file: LGHFBAT.txt
*_LG_GGCAGCG-CAACGTG

source_name: LG/J_female_30 wks_highfat_Interscapular Brown Adipose


title: fetal cord tissue, S0282


title: Pier24Hr2

description: htseq.all.counts.txt


title: PM24Hr1

description: htseq.all.counts.txt


title: fetal cord tissue, S0281


title: LGHF30FBr.509

description:
processed data file: LGHFBAT.txt
*_LG_CAATATC-TCACAAG


title: fetal cord tissue, S0280


title: LGHF30FRep.688

description:
processed data file: LGHFWAT.txt
*_LG_CCGATTA-TAGGTCG


title: Pier24Hr1

description: htseq.all.counts.txt


title: fetal cord tissue, S0279


title: LGHF30FBr.281

description:
processed data file: LGHFBAT.txt
*_LG_CGGTGGC-GGTCTTA


title: MT24Hr4

description: htseq.all.counts.txt

value: MitoTEMPO


title: PM24Hr2

description: htseq.all.counts.txt


title: fetal cord tissue, S0276


title: LGHF20MRep.403

description:
processed data file: LGHFWAT.txt
*_LG_TTTTGTC-CAAGGGT

source_name: LG/J_male_20 wks_highfat_Reproductive White Adipose


title: MT24Hr3

description: htseq.all.counts.txt


title: MT24Hr2

description: htseq.all.counts.txt


title: LGHF20MRep.351

description:
processed data file: LGHFWAT.txt
*_LG_CGCTACA-TTCACAA


title: fetal cord tissue, S0273


title: fetal cord tissue, S0277


title: fetal cord tissue, S0275


title: fetal cord tissue, S0272


title: fetal cord tissue, S0274


title: MT24Hr1

description: htseq.all.counts.txt


title: Ctrl24Hr4

description: htseq.all.counts.txt

value: Vehicle


title: Pier24Hr3

description: htseq.all.counts.txt


title: LGHF20MRep.344

description:
processed data file: LGHFWAT.txt
*_LG_GTTCTCA-TCTTTGG

value: male


title: LGHF30FBr.510

description:
processed data file: LGHFBAT.txt
*_LG_GCCGTTT-GTGGTTC

value: 30 Weeks


title: fetal cord tissue, S0264


title: fetal cord tissue, S0268


title: fetal cord tissue, S0269


title: fetal cord tissue, S0271


title: fetal cord tissue, S0265


title: Ctrl24Hr3

description: htseq.all.counts.txt


title: LGHF20MRep.276

description:
processed data file: LGHFWAT.txt
*_LG_GAGGCGT-TGTCTTT


title: fetal cord tissue, S0263


title: LGHF20MBr.403

description:
processed data file: LGHFBAT.txt
*_LG_ACCCACT-TACTGGA

source_name: LG/J_male_20 wks_highfat_Interscapular Brown Adipose


title: Ctrl24Hr2

description: htseq.all.counts.txt


title: fetal cord tissue, S0262


title: fetal cord tissue, S0261


title: fetal cord tissue, S0260


title: LGHF20MBr.344

description:
processed data file: LGHFBAT.txt
*_LG_CTGGTGG-GCTCCTC


title: Ctrl24Hr1

description: htseq.all.counts.txt


title: fetal cord tissue, S0259


title: LGHF20MBr.276

description:
processed data file: LGHFBAT.txt
*_LG_TTTAACT-GTGTTGG


title: fetal cord tissue, S0258


title: LGHF20FRep.709

description:
processed data file: LGHFWAT.txt
*_LG_CACCAGG-GATGCAC

source_name: LG/J_female_20 wks_highfat_Reproductive White Adipose


title: LGHF20MBr.351

description:
processed data file: LGHFBAT.txt
*_LG_TGGCATA-GTCTGGC


title: fetal cord tissue, S0257


title: AM1Hr4

description: htseq.all.counts.txt

value: 1 hour


title: fetal cord tissue, S0256


title: AM1Hr3

description: htseq.all.counts.txt


title: LGHF20FRep.623

description:
processed data file: LGHFWAT.txt
*_LG_ACTGGAT-CGTATTA


title: fetal cord tissue, S0254


title: fetal cord tissue, S0255


title: fetal cord tissue, S0253


title: AM1Hr1

description: htseq.all.counts.txt


title: Anti1Hr4

description: htseq.all.counts.txt


title: LGHF20FRep.520

description:
processed data file: LGHFWAT.txt
*_LG_CATTTAG-GCTTCCT


title: AM1Hr2

description: htseq.all.counts.txt


title: LGHF20FRep.517

description:
processed data file: LGHFWAT.txt
*_LG_TAGGTAA-GAACCGT


title: fetal cord tissue, S0251


title: Anti1Hr3

description: htseq.all.counts.txt


title: LGHF20FBr.709

description:
processed data file: LGHFBAT.txt
*_LG_CACAGCA-CCTTTAT

source_name: LG/J_female_20 wks_highfat_Interscapular Brown Adipose

value: Interscapular Brown Adipose


title: fetal cord tissue, S0250


title: Anti1Hr2

description: htseq.all.counts.txt


title: fetal cord tissue, S0249


title: fetal cord tissue, S0248


title: Anti1Hr1

description: htseq.all.counts.txt


title: fetal cord tissue, S0245


title: fetal cord tissue, S0243


title: fetal cord tissue, S0244


title: fetal cord tissue, S0267


title: fetal cord tissue, S0246


title: LGHF20FBr.623

description:
processed data file: LGHFBAT.txt
*_LG_GGCAAGA-TTTGCTT


title: PM1Hr4

description: htseq.all.counts.txt


title: LGHF20FBr.517

description:
processed data file: LGHFBAT.txt
*_LG_TCGAGAT-GCAATAT


title: LGHF20FBr.520

description:
processed data file: LGHFBAT.txt
*_LG_TCCGGGA-GGTCCAC


title: fetal cord tissue, S0240


title: fetal cord tissue, S0239


title: PM1Hr3

description: htseq.all.counts.txt


title: fetal cord tissue, S0238


title: PM1Hr2

description: htseq.all.counts.txt


title: fetal cord tissue, S0237


title: fetal cord tissue, S0236


title: PM1Hr1

description: htseq.all.counts.txt


title: HKO860-Knock-out bred rep2

city: san francisco

first: Tammy

middle: T

last: Chang

state: ca

address: 513 parnassus

department: surgery

institute: UCSF

data_processing:
" Real Time Analysis 3 " software was used for base calling.
Using ng_qc software, raw reads were filtered to remove reads that contain adapters or low quality data.  Reads with uncertain nucleotides that reflect more than 10% were filtered out.  In addition, low quality nucleotides (base quality < 20) that made up more than 50% of the reads were removed.
High-quality reads were imported into STAR2.5 for alignment into BAM files.
BAM files were imported into the RNA-Seq analysis pipeline at Novogene Inc. (Davis, CA).
FPKM counts were calculated by HTSeq v0.6.1. Then filtering the 5 types of counts:__no_feature,__ambiguous,__too_low_aQual,__not_aligned,__alignment_not_unique.
Genome_build: mm10
Supplementary_files_format_and_content: Excel table with raw gene counts and FPKM values for every gene in every sample.

source_name: Hepatocyte

growth_protocol: Liver epithelial-specific FAK-deficient mice (FAKfl/fl;Alb-Cre+) and littermate controls (FAKfl/fl;Alb-Cre-) were generated by breeding FVB FAKfl/fl mice (gift from Hilary E. Beggs), in which the FAK gene was flanked by loxP sites, with Alb-Cre mice (gift from Derek LeRoith) that carry the Cre recombinase under the albumin promoter. Hepatocyte-specific FAK deletion was induced by tail vein injection of FAKfl/fl mice with 2.5x1011 AAV8-TBG-Cre (gift from James M. Wilson; Addgene viral prep # 107787-AAV8; http://n2t.net/addgene:107787; RRID:Addgene_107787; Addgene, Watertown, MA).  Littermates controls were injected with 2.5x1011 viral particles/mouse of control viral vector that did not express Cre recombinase (AAV8-TBG-Null).

extract_protocol:
Livers were removed, preserved in RNALater for at least 24 hours, and then RNA was harvested using Qiagen RNeasy Plus mini kit.
Sequencing libraries were generated by NEBNext Ultra directional RNA library prep kit (Illumina, San Diego, CA) with 1 ug of total RNA using standard Illumina protocols.

treatment_protocol: Gradual cholestatic injury was induced by providing mice with 0.1% w/w DDC diet (TestDiet, St. Louis, MO) ad libitum for 4-8 weeks.

value: Liver

value: FVB

tag: genotype generation

value: FVB FAKfl/fl mice bred with Alb-Cre mice

value: FAKfl/fl;Alb-Cre+


title: fetal cord tissue, S0234


title: HKO894-Knock-out bred rep3


title: fetal cord tissue, S0232


title: fetal cord tissue, S0252


title: Pier1Hr4

description: htseq.all.counts.txt


title: fetal cord tissue, S0242


title: fetal cord tissue, S0231


title: HKO044-Knock-out bred rep1


title: HKO896-Knock-out bred rep4


title: fetal cord tissue, S0241


title: Pier1Hr3

description: htseq.all.counts.txt


title: HWT893-Wild-type bred rep4

value: FAKfl/fl;Alb-Cre-


title: fetal cord tissue, S0225


title: fetal cord tissue, S0228


title: fetal cord tissue, S0226


title: HWT861-Wild-type bred rep3


title: Pier1Hr2

description: htseq.all.counts.txt


title: Pier1Hr1

description: htseq.all.counts.txt


title: HWT798-Wild-type bred rep2


title: fetal cord tissue, S0229


title: fetal cord tissue, S0224


title: fetal cord tissue, S0235


title: fetal cord tissue, S0220


title: fetal cord tissue, S0221


title: fetal cord tissue, S0223


title: HWT045-Wild-type bred rep1


title: FAKKO284-Knock-out bred rep4

source_name: Liver


title: fetal cord tissue, S0219


title: MT1Hr4

description: htseq.all.counts.txt


title: FAKKO282-Knock-out bred rep3


title: FAKKO277-Knock-out bred rep2


title: MT1Hr1

description: htseq.all.counts.txt


title: fetal cord tissue, S0215


title: fetal cord tissue, S0216


title: fetal cord tissue, S0217


title: MT1Hr3

description: htseq.all.counts.txt


title: FAKWT285-Wild-type bred rep4


title: MT1Hr2

description: htseq.all.counts.txt


title: fetal cord tissue, S0212


title: fetal cord tissue, S0211


title: Ctrl1Hr3

description: htseq.all.counts.txt


title: fetal cord tissue, S0213


title: FAKWT283-Wild-type bred rep3


title: fetal cord tissue, S0208


title: Ctrl1Hr2

description: htseq.all.counts.txt


title: FAKWT280-Wild-type bred rep2


title: fetal cord tissue, S0205


title: fetal cord tissue, S0204


title: fetal cord tissue, S0203


title: fetal cord tissue, S0202


title: fetal cord tissue, S0214


title: fetal cord tissue, S0201


title: FAKKO276-Knock-out bred rep1


title: Ctrl1Hr1

description: htseq.all.counts.txt


title: fetal cord tissue, S0200


title: fetal cord tissue, S0209


title: Ctrl1Hr4

description: htseq.all.counts.txt


title: KO117M-Knock-out  virus rep2

source_name: Fibrotic Liver

value: AAV8-TBG-Cre virus injection


title: KO116M-Knock-out  virus rep1


title: fetal cord tissue, S0206

value: fetal cord tissue


title: WT114M-Wild-type virus rep3

value: AAV8-TBG-Null virus injection


title: input_ChIPseq_sonic_pSIN_EV

city: New York

first: Douglas

last: Barrows

state: NY

address: 1230 York Ave

institute: Rockefeller University

data_processing:
Low quality reads from each FASTQ file were filtered using the ShortRead R Bioconductor package, and filtered FASTQ files were aligned to the hg19 reference genome obtained from UCSC using the Rsubread R Bioconductor package. Bigwig files showing signal coverage over the genome were generated with the GenomicAlignments and rtracklayer R Bioconductor packages. Peak calling was done with macs2 using default settings, with the exception of using the ‘--broad’ flag for the histone H3K27ac, H3K27me3, and H3K4me1 ChIP sequencing experiments.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bigWig files normalized to read depth.
Supplementary_files_format_and_content: Peak files are macs2 output peak files.

source_name: UMUC1 bladder cancer cells

growth_protocol: Cells were maintained in Eagle’s Minimum Essential Medium (MEM, Corning, 10-009-CV), with 10% fetal bovine serum (Sigma-Aldrich) and then were harvested three days after being plated.

extract_protocol:
Three days after plating, UMUC1 cells were harvested from 15 cm tissue culture plates at ~75% confluency. For each histone ChIP, ~ 1x10e7 cells were harvested which yielded ~25 µg of chromatin DNA for immunoprecipitation after going through this protocol. For cell harvest, media was aspirated, cells were washed once in PBS, and then they were fixed directly on the plate with 1% paraformaldehyde in PBS for 5 minutes at room temperature with gentle shaking. Glycine, at a final concentration of 125 mM, was added directly to the plate, and the plate was incubated for 5 minutes at room temperature with gentle shaking. Cells were then put on ice, washed once with cold PBS, scraped off of the plate, and the fixed cells from each cell line (empty vector, wild-type UTX, and HEAA UTX) were pelleted. To get a soluble chromatin extract, cells were then washed in a series of buffers, LB1, LB2, and LB3 as specified below. Each cell line was resuspended in 1 mL LB1 buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1x protease inhibitor (Sigma, 11836170001)) and incubated while rotating at 4°C for 10 min. Samples were then centrifuged and resuspended in 1 mL LB2 buffer (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x protease inhibitor), and then were incubated while rotating at 4°C for 10 min. Samples were then centrifuged and resuspended in 1 mL LB3 buffer (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na deoxycholate, 0.5% N-lauroylsarcosine, 1% Triton X-100, 1x protease inhibitor). The lysates were then passed through a 27-gauge needle three times, sonicated for 14 minutes using a Covaris E220 ultra-sonicator at peak power 140 W, duty factor 5%, and cycles per burst 200, then centrifuged for 10 minutes at 20,000xG at 4°C and the supernatants were collected. 20 µL of each lysate was kept to measure DNA concentration, while the remainder was flash frozen and stored at -80°C. The 20 µL sample was added to 200 µL ChIP elution buffer (1% SDS, 50 mM Tris-HCl pH 8.0, 10 mM EDTA, 200 mM NaCl), incubated overnight at 65°C, treated with RNaseA for 1 hour at 37°C, then Proteinase K for 1 hour at 55°C, and the DNA was purified using the Qiagen PCR purification kit (28104) and lastly quantified with a Nanodrop. These quantifications were then used to dilute 25 µg of chromatin into 1 mL total of LB3, and 5% (50 µL) of each sample was set aside as an input sample. Then 75 µL of protein A Dynabeads that had been washed 3X with PBS + 0.01% Tween-20 and pre-bound with either 10 µL H3K27ac (Active Motif, 39133), 10 µL H3K4me1 (Abcam, ab8895), or 20 µL H3K27me3 (Cell Signaling Tech, 9733) antibody were added to each chromatin lysate and this mixture was incubated rotating overnight at 4°C. The beads were sequentially washed on a magnet two times each with low salt buffer (150 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl pH 8.0), high salt buffer (500 mM NaCl; 0.1% SDS; 1% Triton X-100; 1 mM EDTA; 50 mM Tris-HCl pH 8.0), LiCl buffer (150 mM LiCl; 0.5% Na deoxycholate; 0.1% SDS; 1% Nonidet P-40; 1 mM EDTA; 50 mM Tris-HCl pH 8.0) and once with TE buffer (1 mM EDTA; 10 mM Tris-HCl pH 8.0). After the TE wash the beads were spun down (not separated on the magnet), and 210 µL ChIP elution buffer was added to the beads and input samples. The samples were then incubated for 30 min at 65°C on a shaking heat block at 800 rpm. After centrifugation the eluate (supernatant) was reverse cross-linked by incubating overnight at 65°C. The eluate was then treated with RNaseA for 1 hr at 37°C then with Proteinase K for 1 hr at 55°C and DNA was recovered using the Qiagen PCR purification kit. Libraries were then prepared from this DNA using the Illumina TruSeq protocol and sequenced on a NextSeq500 sequencer.
Illumina TruSeq

tag: cell line

value: bladder cancer

value: stably expressing pSIN-puro empty vector

tag: chip antibody


title: input_ChIPseq_sonic_pSIN_WTUTX

value: stably expressing pSIN-puro wild type UTX


title: input_ChIPseq_sonic_pSIN_HEAAUTX

value: stably expressing pSIN-puro H1146A/E1148A-mutant UTX


title: fetal cord tissue, S0197

data_processing:
GenomeStudio; R/Rstudio
green (RAW_ID_Grn.idat) and red (RAW_ID_Red.idat) channels provided
[value definition]  chip position, DNA extraction, and bisulfite conversion batch, and celltype-adjusted residuals provided

extract_protocol: Prior to purification, 250 mg crushed cord tissue was enzymatically digested with hyaluronidase (~2.7U in 250 µl PBS) for 30 minutes at 37 C, mixed with 250 µl TNES lysis buffer, transferred to gentleMACS M Tubes (Miltenyi 130-093-236) for 1-minute homogenization followed by overnight treatment with 200 µg Proteinase K at 55 C. QIASymphony SP was used for automated purification of (buffy coat/cord tissue) DNA in combination with QIASymphony DSP DNA Midi Kit (Qiagen #937255) and DNA was bisulfite converted using the EZ DNA Methylation Kit™ (Zymo Research).

tag: child sex (male = 0; female = 1)