title: H3K36me3_heart_P5_EC_cell_1120


title: H3K36me3_heart_P5_EC_cell_1122

status: Public on Apr 30 2024

type: SRA

city: Beijing

first: Yaxi

last: Liu

address: 5 Yiheyuan Road

country: China

institute: Peking University

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were de-multiplexed to generate single cell profiles by custom scripts. For spliting single cell, we cut the first 21 bp of the read1 and the first 27 bp of the read2.
Reads were aligned to mouse genome mm10 by bowtie2 (v 2.3.1), with parameter of "--dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant -X 2000".
Reads whose MAPQ >= 30 were determined as uniquely mapping reads. Duplication reads were removed by Picard.
Cells with less than 1,000 non-duplicated were excluded.
Bed files were generated from bam files using bedtools (v2.25.0) bamToBed.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files were bed files. Each single cell bed file contain non-duplicated alignments as is in the bam file.  These files contain single cell genome-wide coverage files after  sorting and uniqing and removing duplicates. Since one cell only contains two copies of each genomic locus for assay, we usually use non-duplicated reads information to reflect peak information in one single cell (PMID: 31471188).

molecule: genomic DNA

organism: Mus musculus

source_name: P5 heart

extract_protocol:
Following CoBATCH protocol.
After PCR enrichment using 2X KAPA master mix, products were purified and selected by AMPure XP beads for 200-1000 bp.

treatment_protocol: Organs were digested with 0.06 Collagenase II at 37 °C. "Aged" animals are 17-19 months old.

tag: developmental stage

tag: tissue

value: heart

tag: strain

tag: tissue preparation

value: Fixed by methanol

tag: chip antibody

value: H3K36me3, Active motif, Cat. 61101


title: H3K36me3_heart_P5_EC_cell_1119


title: H3K36me3_heart_P5_EC_cell_1118


title: H3K36me3_heart_P5_EC_cell_1117


title: H3K36me3_heart_P5_EC_cell_1116


title: H3K36me3_heart_P5_EC_cell_1124


title: H3K36me3_heart_P5_EC_cell_1112


title: H3K36me3_heart_P5_EC_cell_1114


title: H3K36me3_heart_P5_EC_cell_1113


title: H3K36me3_heart_P5_EC_cell_1108


title: H3K36me3_heart_P5_EC_cell_1127


title: H3K36me3_heart_P5_EC_cell_1111


title: H3K36me3_heart_P5_EC_cell_1107


title: H3K36me3_heart_P5_EC_cell_1106


title: H3K36me3_heart_P5_EC_cell_1105


title: H3K36me3_heart_P5_EC_cell_1104


title: H3K36me3_heart_P5_EC_cell_1101


title: H3K36me3_heart_P5_EC_cell_1102


title: H3K36me3_heart_P5_EC_cell_1103


title: H3K36me3_heart_P5_EC_cell_1098


title: H3K36me3_heart_P5_EC_cell_1100


title: H3K36me3_heart_P5_EC_cell_1097


title: H3K36me3_heart_P5_EC_cell_1096


title: H3K36me3_heart_P5_EC_cell_1099


title: H3K36me3_heart_P5_EC_cell_1095


title: H3K36me3_heart_P5_EC_cell_1092


title: H3K36me3_heart_P5_EC_cell_1093


title: H3K36me3_heart_P5_EC_cell_1110


title: H3K36me3_heart_P5_EC_cell_1088


title: H3K36me3_heart_P5_EC_cell_1084


title: H3K36me3_heart_P5_EC_cell_1086


title: H3K36me3_heart_P5_EC_cell_1083


title: H3K36me3_heart_P5_EC_cell_1082


title: H3K36me3_heart_P5_EC_cell_1089


title: H3K36me3_heart_P5_EC_cell_1090


title: H3K36me3_heart_P5_EC_cell_1087


title: H3K36me3_heart_P5_EC_cell_1081


title: H3K36me3_heart_P5_EC_cell_1080


title: H3K36me3_heart_P5_EC_cell_1085


title: H3K36me3_heart_P5_EC_cell_1115


title: H3K36me3_heart_P5_EC_cell_1078


title: H3K36me3_heart_P5_EC_cell_1077


title: H3K36me3_heart_P5_EC_cell_1076


title: H3K36me3_heart_P5_EC_cell_1072


title: H3K36me3_heart_P5_EC_cell_1071


title: H3K36me3_heart_P5_EC_cell_1073


title: H3K36me3_heart_P5_EC_cell_1075


title: H3K36me3_heart_P5_EC_cell_1094


title: H3K36me3_heart_adult_EC_cell_29

source_name: adult heart

value: adult


title: H3K36me3_heart_P5_EC_cell_1091


title: H3K36me3_heart_P5_EC_cell_1070


title: H3K36me3_heart_P5_EC_cell_1067


title: H3K36me3_heart_P5_EC_cell_1074


title: H3K36me3_heart_P5_EC_cell_1079


title: H3K36me3_heart_P5_EC_cell_1064


title: H3K36me3_heart_P5_EC_cell_1065


title: H3K36me3_heart_P5_EC_cell_1066


title: H3K36me3_heart_P5_EC_cell_1061


title: H3K36me3_heart_P5_EC_cell_1056


title: H3K36me3_heart_P5_EC_cell_1055


title: H3K36me3_heart_P5_EC_cell_1059


title: H3K36me3_heart_P5_EC_cell_1054


title: H3K36me3_heart_P5_EC_cell_1109


title: H3K36me3_heart_P5_EC_cell_1053


title: H3K36me3_heart_P5_EC_cell_1068


title: H3K36me3_heart_P5_EC_cell_1069


title: H3K36me3_heart_P5_EC_cell_1051


title: H3K36me3_heart_P5_EC_cell_1049


title: H3K36me3_heart_P5_EC_cell_1063


title: H3K36me3_heart_adult_EC_cell_36


title: H3K36me3_heart_P5_EC_cell_1045


title: H3K36me3_heart_P5_EC_cell_1046


title: H3K36me3_heart_P5_EC_cell_1042


title: H3K36me3_heart_P5_EC_cell_1044


title: H3K36me3_heart_P5_EC_cell_1048


title: H3K36me3_heart_P5_EC_cell_1062


title: H3K36me3_heart_P5_EC_cell_1041


title: H3K36me3_heart_P5_EC_cell_1043


title: H3K36me3_heart_P5_EC_cell_1058


title: H3K36me3_heart_P5_EC_cell_1057


title: H3K36me3_heart_P5_EC_cell_1060


title: H3K36me3_heart_P5_EC_cell_1037


title: H3K36me3_heart_P5_EC_cell_1052


title: H3K36me3_heart_P5_EC_cell_1038


title: H3K36me3_heart_P5_EC_cell_1039


title: H3K36me3_heart_P5_EC_cell_1035


title: H3K36me3_heart_P5_EC_cell_1036


title: H3K36me3_heart_P5_EC_cell_1040


title: H3K36me3_heart_P5_EC_cell_1034


title: H3K36me3_heart_P5_EC_cell_1047


title: H3K36me3_heart_P5_EC_cell_1050


title: H3K36me3_heart_P5_EC_cell_1033


title: H3K36me3_heart_P5_EC_cell_1032


title: H3K36me3_heart_P5_EC_cell_1029


title: H3K36me3_heart_P5_EC_cell_1028


title: H3K36me3_heart_P5_EC_cell_1030


title: H3K36me3_heart_P5_EC_cell_1025


title: H3K36me3_heart_P5_EC_cell_1024


title: H3K36me3_heart_P5_EC_cell_1026


title: H3K36me3_heart_P5_EC_cell_1027


title: H3K36me3_heart_P5_EC_cell_1023


title: H3K36me3_heart_P5_EC_cell_1021


title: H3K36me3_heart_P5_EC_cell_1019


title: H3K36me3_heart_P5_EC_cell_1022


title: H3K36me3_heart_P5_EC_cell_1017


title: H3K36me3_heart_P5_EC_cell_1014


title: H3K36me3_heart_P5_EC_cell_1018


title: H3K36me3_heart_P5_EC_cell_1016


title: H3K36me3_heart_P5_EC_cell_1015


title: H3K36me3_heart_P5_EC_cell_1012


title: H3K36me3_heart_P5_EC_cell_1011


title: H3K36me3_heart_P5_EC_cell_1010


title: H3K36me3_heart_P5_EC_cell_1008


title: H3K36me3_heart_P5_EC_cell_1031


title: H3K36me3_heart_P5_EC_cell_1009


title: H3K36me3_heart_P5_EC_cell_1006


title: H3K36me3_heart_P5_EC_cell_1005


title: H3K36me3_heart_P5_EC_cell_1004


title: H3K36me3_heart_P5_EC_cell_1001


title: H3K36me3_heart_P5_EC_cell_1002


title: H3K36me3_heart_P5_EC_cell_1000


title: H3K36me3_heart_P5_EC_cell_999


title: H3K36me3_heart_P5_EC_cell_1020


title: H3K36me3_heart_P5_EC_cell_998


title: H3K36me3_heart_P5_EC_cell_995


title: H3K36me3_heart_P5_EC_cell_997


title: H3K36me3_heart_P5_EC_cell_994


title: H3K36me3_heart_P5_EC_cell_992


title: H3K36me3_heart_P5_EC_cell_996


title: H3K36me3_heart_P5_EC_cell_993


title: H3K36me3_heart_P5_EC_cell_990


title: H3K36me3_heart_P5_EC_cell_991


title: H3K36me3_heart_P5_EC_cell_989


title: H3K36me3_heart_P5_EC_cell_988


title: H3K36me3_heart_P5_EC_cell_987


title: H3K36me3_heart_P5_EC_cell_986


title: H3K36me3_heart_P5_EC_cell_1007


title: H3K36me3_heart_P5_EC_cell_1013


title: H3K36me3_heart_P5_EC_cell_985


title: H3K36me3_heart_P5_EC_cell_1003


title: H3K36me3_heart_P5_EC_cell_981


title: H3K36me3_heart_P5_EC_cell_983


title: H3K36me3_heart_P5_EC_cell_980


title: H3K36me3_heart_P5_EC_cell_977


title: H3K36me3_heart_P5_EC_cell_978


title: H3K36me3_heart_P5_EC_cell_975


title: H3K36me3_heart_P5_EC_cell_976


title: H3K36me3_heart_P5_EC_cell_973


title: H3K36me3_heart_P5_EC_cell_972


title: H3K36me3_heart_P5_EC_cell_974


title: H3K36me3_heart_P5_EC_cell_971


title: H3K36me3_heart_P5_EC_cell_969


title: H3K36me3_heart_P5_EC_cell_967


title: H3K36me3_heart_P5_EC_cell_966


title: H3K36me3_heart_P5_EC_cell_968


title: H3K36me3_heart_P5_EC_cell_964


title: H3K36me3_heart_P5_EC_cell_959


title: H3K36me3_heart_P5_EC_cell_963


title: H3K36me3_heart_P5_EC_cell_984


title: H3K36me3_heart_P5_EC_cell_960


title: H3K36me3_heart_P5_EC_cell_962


title: H3K36me3_heart_P5_EC_cell_961


title: H3K36me3_heart_P5_EC_cell_982


title: H3K36me3_heart_P5_EC_cell_958


title: H3K36me3_heart_P5_EC_cell_970


title: H3K36me3_heart_P5_EC_cell_979


title: H3K36me3_heart_P5_EC_cell_957


title: H3K36me3_heart_P5_EC_cell_955


title: H3K36me3_heart_P5_EC_cell_956


title: H3K36me3_heart_P5_EC_cell_952


title: H3K36me3_heart_P5_EC_cell_953


title: H3K36me3_heart_P5_EC_cell_954


title: H3K36me3_heart_P5_EC_cell_951


title: H3K36me3_heart_P5_EC_cell_950


title: H3K36me3_heart_P5_EC_cell_946


title: H3K36me3_heart_P5_EC_cell_947


title: H3K36me3_heart_P5_EC_cell_944


title: H3K36me3_heart_P5_EC_cell_965


title: H3K36me3_heart_P5_EC_cell_948


title: H3K36me3_heart_P5_EC_cell_942


title: H3K36me3_heart_P5_EC_cell_939


title: H3K36me3_heart_P5_EC_cell_938


title: H3K36me3_heart_P5_EC_cell_936


title: H3K36me3_heart_P5_EC_cell_935


title: H3K36me3_heart_P5_EC_cell_934


title: H3K36me3_heart_P5_EC_cell_937


title: H3K36me3_heart_P5_EC_cell_932


title: H3K36me3_heart_P5_EC_cell_933


title: H3K36me3_heart_P5_EC_cell_931


title: H3K36me3_heart_P5_EC_cell_929


title: H3K36me3_heart_P5_EC_cell_930


title: H3K36me3_heart_P5_EC_cell_928


title: H3K36me3_heart_P5_EC_cell_926


title: H3K36me3_heart_P5_EC_cell_923


title: H3K36me3_heart_P5_EC_cell_949


title: H3K36me3_heart_P5_EC_cell_924


title: H3K36me3_heart_P5_EC_cell_945


title: H3K36me3_heart_P5_EC_cell_922


title: H3K36me3_heart_P5_EC_cell_921


title: H3K36me3_heart_P5_EC_cell_919


title: H3K36me3_heart_P5_EC_cell_941


title: H3K36me3_heart_P5_EC_cell_920


title: H3K36me3_heart_P5_EC_cell_940


title: H3K36me3_heart_P5_EC_cell_918


title: H3K36me3_heart_P5_EC_cell_915


title: H3K36me3_heart_P5_EC_cell_916


title: H3K36me3_heart_P5_EC_cell_917


title: H3K36me3_heart_P5_EC_cell_913


title: H3K36me3_heart_P5_EC_cell_911


title: H3K36me3_heart_P5_EC_cell_907


title: H3K36me3_heart_P5_EC_cell_912


title: H3K36me3_heart_P5_EC_cell_910


title: H3K36me3_heart_P5_EC_cell_909


title: H3K36me3_heart_P5_EC_cell_925


title: H3K36me3_heart_P5_EC_cell_906


title: H3K36me3_heart_P5_EC_cell_908


title: H3K36me3_heart_P5_EC_cell_904


title: H3K36me3_heart_P5_EC_cell_905


title: H3K36me3_heart_P5_EC_cell_903


title: H3K36me3_heart_P5_EC_cell_900


title: H3K36me3_heart_P5_EC_cell_899


title: H3K36me3_heart_P5_EC_cell_901


title: H3K36me3_heart_P5_EC_cell_898


title: H3K36me3_heart_P5_EC_cell_896


title: H3K36me3_heart_P5_EC_cell_902


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title: H3K36me3_heart_P5_EC_cell_894


title: H3K36me3_heart_P5_EC_cell_895


title: H3K36me3_heart_P5_EC_cell_892


title: H3K36me3_heart_P5_EC_cell_893


title: H3K36me3_heart_P5_EC_cell_891


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title: H3K36me3_heart_P5_EC_cell_890


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title: H3K36me3_heart_P5_EC_cell_888


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title: H3K36me3_heart_P5_EC_cell_884


title: H3K36me3_heart_P5_EC_cell_885


title: H3K36me3_heart_P5_EC_cell_879


title: H3K36me3_heart_P5_EC_cell_881


title: H3K36me3_heart_P5_EC_cell_878


title: H3K36me3_heart_P5_EC_cell_880


title: H3K36me3_heart_P5_EC_cell_876


title: H3K36me3_heart_P5_EC_cell_875


title: H3K36me3_heart_P5_EC_cell_877


title: H3K36me3_heart_P5_EC_cell_874


title: H3K36me3_heart_P5_EC_cell_873


title: H3K36me3_heart_P5_EC_cell_872


title: H3K36me3_heart_P5_EC_cell_868


title: H3K36me3_heart_P5_EC_cell_864


title: H3K36me3_heart_P5_EC_cell_866


title: H3K36me3_heart_P5_EC_cell_869


title: H3K36me3_heart_P5_EC_cell_870


title: H3K36me3_heart_P5_EC_cell_871


title: H3K36me3_heart_P5_EC_cell_882


title: H3K36me3_heart_P5_EC_cell_861


title: H3K36me3_heart_P5_EC_cell_860


title: H3K36me3_heart_P5_EC_cell_863


title: H3K36me3_heart_P5_EC_cell_867


title: H3K36me3_heart_P5_EC_cell_858


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title: H3K36me3_heart_P5_EC_cell_943


title: H3K36me3_heart_P5_EC_cell_859


title: H3K36me3_heart_P5_EC_cell_851


title: H3K36me3_heart_P5_EC_cell_850


title: H3K36me3_heart_P5_EC_cell_865


title: H3K36me3_heart_P5_EC_cell_857


title: H3K36me3_heart_P5_EC_cell_855


title: H3K36me3_heart_P5_EC_cell_854


title: H3K36me3_heart_P5_EC_cell_845


title: H3K36me3_heart_P5_EC_cell_862


title: H3K36me3_heart_P5_EC_cell_849


title: H3K36me3_heart_P5_EC_cell_927


title: H3K36me3_heart_P5_EC_cell_914


title: H3K36me3_heart_P5_EC_cell_840


title: H3K36me3_heart_P5_EC_cell_839


title: H3K36me3_heart_P5_EC_cell_847


title: H3K36me3_heart_P5_EC_cell_856


title: H3K36me3_heart_P5_EC_cell_838


title: H3K36me3_heart_P5_EC_cell_848


title: H3K36me3_heart_P5_EC_cell_846


title: H3K36me3_heart_P5_EC_cell_837


title: H3K36me3_heart_P5_EC_cell_842


title: H3K36me3_heart_P5_EC_cell_843


title: H3K36me3_heart_P5_EC_cell_844


title: H3K36me3_heart_P5_EC_cell_841


title: H3K36me3_heart_P5_EC_cell_834


title: H3K36me3_heart_P5_EC_cell_827


title: H3K36me3_heart_P5_EC_cell_828


title: H3K36me3_heart_P5_EC_cell_823


title: H3K36me3_heart_P5_EC_cell_836


title: H3K36me3_heart_P5_EC_cell_832


title: H3K36me3_heart_P5_EC_cell_830


title: H3K36me3_heart_P5_EC_cell_835


title: H3K36me3_heart_P5_EC_cell_821


title: H3K36me3_heart_P5_EC_cell_816


title: H3K36me3_heart_P5_EC_cell_815


title: H3K36me3_heart_P5_EC_cell_811


title: H3K36me3_heart_P5_EC_cell_831


title: H3K36me3_heart_P5_EC_cell_829


title: H3K36me3_heart_P5_EC_cell_806


title: H3K36me3_heart_P5_EC_cell_826


title: H3K36me3_heart_P5_EC_cell_824


title: H3K36me3_heart_P5_EC_cell_825


title: H3K36me3_heart_P5_EC_cell_822


title: H3K36me3_heart_P5_EC_cell_820


title: H3K36me3_heart_P5_EC_cell_819


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title: H3K36me3_heart_P5_EC_cell_813


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title: H3K36me3_heart_P5_EC_cell_812


title: H3K36me3_heart_P5_EC_cell_807


title: H3K36me3_heart_P5_EC_cell_809


title: H3K36me3_heart_P5_EC_cell_798


title: H3K36me3_heart_P5_EC_cell_805


title: H3K36me3_heart_P5_EC_cell_795


title: H3K36me3_heart_P5_EC_cell_792


title: H3K36me3_heart_P5_EC_cell_808


title: H3K36me3_heart_P5_EC_cell_790


title: H3K36me3_heart_P5_EC_cell_789


title: H3K36me3_heart_P5_EC_cell_788


title: H3K36me3_heart_P5_EC_cell_804


title: H3K36me3_heart_P5_EC_cell_787


title: H3K36me3_heart_P5_EC_cell_786


title: H3K36me3_heart_P5_EC_cell_799


title: H3K36me3_heart_P5_EC_cell_797


title: H3K36me3_heart_P5_EC_cell_794


title: H3K36me3_heart_P5_EC_cell_796


title: H3K36me3_heart_P5_EC_cell_783


title: H3K36me3_heart_P5_EC_cell_793


title: H3K36me3_heart_P5_EC_cell_791


title: H3K36me3_heart_P5_EC_cell_780


title: H3K36me3_heart_P5_EC_cell_779


title: H3K36me3_heart_P5_EC_cell_778


title: H3K36me3_heart_P5_EC_cell_777


title: H3K36me3_heart_P5_EC_cell_775


title: H3K36me3_heart_P5_EC_cell_773


title: H3K36me3_heart_P5_EC_cell_784


title: H3K36me3_heart_P5_EC_cell_782


title: H3K36me3_heart_P5_EC_cell_781


title: H3K36me3_heart_P5_EC_cell_776


title: H3K36me3_heart_P5_EC_cell_785


title: H3K36me3_heart_P5_EC_cell_772


title: H3K36me3_heart_P5_EC_cell_771


title: H3K36me3_heart_P5_EC_cell_768


title: H3K36me3_heart_P5_EC_cell_762


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source_name: E16.5 heart


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title: H3K36me3_heart_P5_EC_cell_29


title: H3K36me3_heart_E16_EC_cell_691


title: H3K36me3_heart_P5_EC_cell_15


title: H3K36me3_heart_P5_EC_cell_2


title: H3K36me3_heart_E16_EC_cell_689


title: H3K36me3_heart_E16_EC_cell_708


title: H3K36me3_heart_E16_EC_cell_688


title: H3K36me3_heart_P5_EC_cell_1


title: H3K36me3_heart_E16_EC_cell_704


title: H3K36me3_heart_E16_EC_cell_686


title: H3K36me3_heart_E16_EC_cell_685


title: H3K36me3_heart_E16_EC_cell_684


title: H3K36me3_heart_E16_EC_cell_699


title: H3K36me3_heart_E16_EC_cell_690


title: H3K36me3_heart_E16_EC_cell_700


title: H3K36me3_heart_E16_EC_cell_701


title: H3K36me3_heart_E16_EC_cell_698


title: H3K36me3_heart_E16_EC_cell_682


title: H3K36me3_heart_E16_EC_cell_678


title: H3K36me3_heart_E16_EC_cell_695


title: H3K36me3_heart_E16_EC_cell_680


title: H3K36me3_heart_E16_EC_cell_703


title: H3K36me3_heart_E16_EC_cell_697


title: H3K36me3_heart_E16_EC_cell_692


title: H3K36me3_heart_E16_EC_cell_693


title: H3K36me3_heart_E16_EC_cell_694


title: H3K36me3_heart_E16_EC_cell_696


title: H3K36me3_heart_E16_EC_cell_676


title: H3K36me3_heart_E16_EC_cell_683


title: H3K36me3_heart_E16_EC_cell_675


title: H3K36me3_heart_E16_EC_cell_673


title: H3K36me3_heart_E16_EC_cell_674


title: H3K36me3_heart_E16_EC_cell_672


title: H3K36me3_heart_E16_EC_cell_671


title: H3K36me3_heart_E16_EC_cell_679


title: H3K36me3_heart_E16_EC_cell_677


title: H3K36me3_heart_E16_EC_cell_669


title: H3K36me3_heart_E16_EC_cell_681


title: H3K36me3_heart_E16_EC_cell_668


title: H3K36me3_heart_E16_EC_cell_670


title: H3K36me3_heart_E16_EC_cell_666


title: S1-seq_Spo11KO_14dpp_rep2

city: New York

first: Soonjoung

last: Kim

email: kims16@mskcc.org, soonjk@yuhs.ac

state: New York

address: 430 East 67th Street

department: Molecular Biology

country: USA

institute: Memorial Sloan Kettering Cancer C

data_processing:
After Qubit quantification and quality control by Agilent BioAnalyzer, libraries were pooled equimolar and run on an Illumina sequencer. A spike-in of PhiX was added to the run to increase diversity when necessary and for quality control purposes. Base calls were perfomed using bcl2fastq software v.2.20 or bcl-convert software v.3.9.3 to 3.10.5 for samples sequenced on Illumina NextSeq 500, NextSeq 2000, or NovaSeq 6000.  Reads were trimmed and filtered by Trim Galore version 0.6.6 with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>
Sequence reads were mapped onto the mouse reference genome (mm10) by bowtie2 version 2.3.5.1 (ref. 1) with the arguments -N 1 -X 1000. (ref. 1) Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). Duplicated reads were removed by Picard <https://broadinstitute.github.io/picard/>. Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools with the arguments -q 20 <http://www.htslib.org/>.
Reads for S1, Exo7/T, or ExoT-seq were counted at which a nucleotide next to biotinylated adaptor DNA was mapped (this corresponds to a position of ssDNA). Adaptors were swapped for some samples (indicated by sample names), and reads were counted at which a nucleotide next to the other (unbiotinylated) adaptor DNA was mapped. Maps were analyzed using R version 4.0.3 <http://www.r-project.org>.
Assembly: mm10
Supplementary files format and content: bigWig files contain read counts at positions of ssDNA. Reads were not normalized to RPM (reads per million mapped). Letter "F" or "R" in sample names indicates that reads were mapped on forward or reverse strand, respectively

source_name: testis

extract_protocol:
Testis cells from mice at indicated age were obtained as described previously (ref. 1). Cells were embedded in plugs of low-melting point agarose to protect DNA from shearing, and DNA was liberated by treatment with SDS and proteinase K as described previously (ref. 1). In-plug overhang removal with S1 endonuclease for S1-seq, exonuclease VII and exonuclease T for Exo7/T-seq, or exonuclease T for ExoT-seq, and adaptor ligation were performed as described previously (ref. 1, 2, 3) with minor modifications. In brief for S1-seq, plugs were washed in 0.5 ml of modified S1 buffer (50 mM sodium acetate, 280 mM NaCl, 4.5 mM ZnSO4, pH 4.7) for 30 min four times, treated with 9 units of S1 nulcease in 500 µl of modified S1 buffer at 37°C for 20 min and washed once with 1ml TE. For Exo7/T-seq, plugs were washed in 1 ml of exonuclease VII buffer for 15 min twice, treated with 50 units of exonuclease VII in 100 µl of exonuclease VII buffer at 37°C for 60 min and washed once with 1ml TE and followed by exonulcease T treamtment. For ExoT-seq, plugs were washed in 1 ml of NEBuffer 4 for 15 min 3 times, treated with 75 units of exonuclease T in 100 µl of NEBuffer 4 at 24°C for 90 min and washed 3 times with 8 ml of TE for 15 min. The nuclease treated ssDNA ends were further polished with T4 polymerase before the first adaptor ligation as previously described (ref. 1, 2, 3). After ligation to biotinylated adaptors, DNA was purified from the agarose, sheared by sonication, purified with streptavidin, ligated to second-end adaptors, amplified, and sequenced as described previously (ref. 1, 2, 3). (ref. 1) Yamada et al., Molecular structures and mechanisms of DNA break processing in mouse meiosis. Genes Dev 34, 806-818 (2020). (ref. 2) Mimitou et al., S. A global view of meiotic double-strand break end resection. Science 355, 40-45 (2017). (ref. 3) Mimitou et al., S1-seq Assay for Mapping Processed DNA Ends. Methods Enzymol 601, 309-330 (2018).
After Qubit quantification and quality control by Agilent BioAnalyzer, libraries were pooled equimolar and run on an Illumina sequencer. A spike-in of PhiX was added to the run to increase diversity when necessary and for quality control purposes. Base calls were perfomed using bcl2fastq software v.2.20 or bcl-convert software v.3.9.3 to 3.10.5 for samples sequenced on Illumina NextSeq 500, NextSeq 2000, or NovaSeq 6000.  Reads were trimmed and filtered by Trim Galore version 0.6.6 with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>. Sequence reads were mapped onto the mouse reference genome (mm10) by bowtie2 version 2.3.5.1 (ref. 1) with the arguments -N 1 -X 1000. (ref. 1) Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009). Duplicated reads were removed by Picard <https://broadinstitute.github.io/picard/>. Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools with the arguments -q 20 <http://www.htslib.org/>. Reads for S1, Exo7/T, or ExoT-seq were counted at which a nucleotide next to biotinylated adaptor DNA was mapped (this corresponds to a position of ssDNA). Maps were analyzed using R version 4.0.3 <http://www.r-project.org>.
S1-seq, Exo7/T-seq, ExoT-seq

value: testis

tag: cell type

value: Spermatocytes

tag: genotype

value: Spo11 knockout

tag: age

value: 14 days post partum

tag: group

value: S1 Spo11 knockout


title: H3K36me3_heart_E16_EC_cell_664


title: H3K36me3_heart_E16_EC_cell_667


title: H3K36me3_heart_E16_EC_cell_663


title: E7T-seq_wt_5wo_rep1

value: wild type

value: 5 weeks old

value: Exo7/T adult


title: E7T-seq_wt_5wo_rep2


title: H3K36me3_heart_E16_EC_cell_662


title: S1-seq_wt_11wo

value: 11 weeks old

value: S1 adult


title: ET-seq_wt_14dpp_rep2

value: ExoT juvenile


title: H3K36me3_heart_E16_EC_cell_660


title: H3K36me3_heart_E16_EC_cell_665


title: H3K36me3_heart_E16_EC_cell_659


title: S1-seq_wt_timecourse_16dpp_rep2

value: 16 days post partum

value: S1 timecourse


title: S1-seq_wt_timecourse_14dpp_rep2


title: H3K36me3_heart_E16_EC_cell_658

value: heart


title: H3K36me3_heart_E16_EC_cell_655

value: Fixed by methanol


title: S1-seq_wt_pH4.5

value: S1 nuclease buffer pH test


title: S1-seq_wt_pH4.1


title: S1-seq_wt_pH4.9


title: H3K36me3_heart_E16_EC_cell_654

value: H3K36me3, Active motif, Cat. 61101


title: S1-seq_wt_pH4.3

value: testis


title: H3K36me3_heart_E16_EC_cell_656


title: H3K36me3_heart_E16_EC_cell_651


title: H3K36me3_heart_E16_EC_cell_652


title: H3K36me3_heart_E16_EC_cell_653


title: H3K36me3_heart_E16_EC_cell_649


title: S3_CSA50mg

city: Seattle

first: Scott

middle: N

last: Furlan

address: 1100 Fairview Ave N

institute: CRD

description:
10x genomics 5p
RNA_counts_CD4.csv
RNA_counts_CD8csv

library_source: transcriptomic single cell

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression) was performed using the 10x genomics Cell Ranger pipeline  and aligning to the mm10 genome build and Ensembl 93 annotations.
Further processing was done with Seurat v3.0.0 (cell and gene filtering, clustering, differential gene expression analysis).
Supplementary files format and content: mm10
Supplementary files format and content: RNA  count matrices, cell metadata

molecule: polyA RNA

source_name: Spleen

extract_protocol:
Spleens were taken on day +7 after BMT and pooled from every 2 mice within the same group (n = 6 mice per group) leading to 3 samples per group. The samples were then stained with CD4-PE, CD8-FITC, CD90.2-Pacific Blue, 7-AAD and Hashtag (CD4, CD8, CD45.1 and Total Seq C)  and subsequently sort-puried to CD4+ and CD8+ T cells. The sort-purified CD4 and CD8 T cells were combined at 1:1 ratio within the same group leading to 3 specimens for 10X capture.
Samples were resuspended at 1000 cells/uL and libraries  were  generated  using  the Chromium Single Cell 5' Reagent Kits User Guide (v2 Chemistry Dual Index) following the manufacturer’s protocol (CG000331, Pleasanton, CA). Final library quality was assessed using the Tapestation 4200 (Agilent, Santa Clara, CA) and libraries were quantified by Qubit dsDNA kit .Pooled libraries were then subjected to paired-end Illumina sequencing according  to the  manufacturer’s  protocol

value: Spleen

value: T cells

tag: treatment

value: Mice are transplanted with allo-BMT and treated with CSA at 50mg/kg from day 0 to day 6


title: H3K36me3_heart_E16_EC_cell_650


title: S1_Saline

value: Mice are transplanted with allo-BMT and treated with saline from day 0 to day 6


title: Collagenase P14

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description: 10x Genomics

data_processing:
Sequencing was done on Nextseq2000 and raw reads were aligned against the zebrafish genome (mm10) and counted by StarSolo
Preprocessed counts were further analysed using Scanpy ollowed by secondary analysis in Annotated Data Format.
Preprocessed counts were further analyzed using Scanpy. Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration. We removed 168 cells in total that did not express more than 300 genes or had a mitochondrial content greater than 3.5%. Furthermore, we filtered 13018 genes if they were detected in less than 30 cells (<0.01%).
Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance. We initially reduced dimensionality of the dataset using PCA, retaining 50 principal components. Subsequent steps, like low-dimensional UMAP embedding (McInnes & Healy, https://arxiv.org/abs/1802.03426) and cell clustering via community detection, were based on the initial PCA.
Final data visualization was done by scanpy and cellxgene packages.
Assembly: mm10
Supplementary files format and content: starsolo outputs

molecule: total RNA

source_name: lung

extract_protocol:
FACS sorted cells were stained with DAPI for dead cell exclusion. The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 5000-10000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10xGenomics).
Library preparation was conducted according to the manufacturer indications.

value: lung

value: endothelial cells

value: wild type


title: Dispase P14

description: 10x Genomics


title: H3K36me3_heart_E16_EC_cell_648


title: S2_CSA5mg

value: Mice are transplanted with allo-BMT and treated with CSA at 5mg/kg from day 0 to day 6


title: S1-seq_wt_timecourse_15dpp_rep2

value: Spermatocytes

value: 15 days post partum


title: H3K36me3_heart_E16_EC_cell_646


title: Bulk ATAC-seq Yy1_KO/Ngn2+ rep2

city: Neuherberg

first: Boyan

last: Bonev

state: Deutschland

address: Ingolstädter Landstr. 1

institute: Helmholtz Zentrum München

description:
Yy1_KO_Ngn2+_ATAC_rep2.bw
Yy1_KO_Ngn2+_ATAC_merge.bw
Yy1_KO_Ngn2+_ATAC_peaks.bed.gz

data_processing:
Alignment of the raw reads to the mouse genome (mm10), post-alignment filtering and peak calling was performed by the ENCODE ATAC-seq pipeline. A high confidence reproducible peak set was generated by implementing a statistical procedure called irreproducible discovery rate (IDR) within the ENCODE ATAC-seq pipeline. Bigwig files were generated using Deeptools2 (version 3.1.3) with the following paramters: CPM normalization, bin size 10, MAPQ >=30
Processed data files represent Bigwig files for each replicate, merged replicate Bigwig file and bed file with coordinates of high confidence peak set
Assembly: mm10
Library strategy: OMNI ATAC-seq

source_name: Bulk ATAC-seq primary mouse astrocytes transduced transduced with doxycycline inducible lentivirus expressing Ngn2 in the context of Yy1 knock-out Bulk ATAC-seq Yy1_KO/Ngn2+ rep2

extract_protocol:
The cortex of post-natal mice aged P5/6 was isolated, mechanically dissociated to obtain a single cell suspension and cultured in medium containing 10% FBS, glucose, pen/strep, B27 supplement, epidermal growth factor and fibroblast growth factor. After culturing for 5 days, the astrocytes were infected with a lentivirus which constitutively expressed the Cre protein and tdTomato fluorescent protein. After culturing for 7 days, the astrocyte enriched culture was reseded on to poly-D-lysine coated 6 well plates and infected with a doxycycline-inducible lentiviral construct, which expressed Ngn2. The Ngn2 expressing lentiviral construct was induced by addition of doxycycline (2ug/ml) for 2 consecutive days in medium containing glucose, pen/strep, glutamine and B27 supplement. After 48 hours of doxycycline induction, the cells were harvested and FACS sorted based on the experimental conditions: Yy1_WT (RFP+), Yy1_KO (RFP+), Yy1_WT/Ngn2+ (GFP+), Yy1_KO/Ngn2+ (GFP+RFP+)
Directly after FACS isolation, the nuclei of 10,000 cells were transposed with a modified Tn5 transposase (Illumina Tagment DNA TDE1 Enzyme and Buffer kit, 20034198) according to the OMNI-ATAC-seq protocol (Corces et al., 2017), the trasposed DNA was isolated using the DNA clean and concentrator kit from Zymo Research (D4014) and the ATAC-seql ibraries were prepared using NEBNext Ultra II  Q5 Master mix  from NEB (M0544S) according to manufacturer's instructions. The size distribution of the ATAC-seq libraries was analysed using an Agilent 2100 Bioanalyser. The ATAC libraries were sequenced to a depth of 50 million reads (paired-end)

value: Brain

value: primary mouse cortical astrocytes

value: Doxycycline (2 microg/ml) was freshly added to the differentiation medium every 24 hours


title: S1-seq_wt_pH4.7

value: 14 days post partum


title: H3K36me3_heart_E16_EC_cell_657

value: heart

value: Fixed by methanol


title: H3K36me3_heart_E16_EC_cell_645

value: H3K36me3, Active motif, Cat. 61101


title: Bulk ATAC-seq Yy1_WT/Ngn2+ rep2

description:
Yy1_WT_Ngn2+_ATAC_rep2.bw
Yy1_WT_Ngn2+_ATAC_merge.bw
Yy1_WT_Ngn2+_ATAC_peaks.bed.gz

source_name: Bulk ATAC-seq primary mouse astrocytes transduced transduced with doxycycline inducible lentivirus expressing Ngn2 in the context of Yy1 knock-out Bulk ATAC-seq Yy1_WT/Ngn2+ rep2


title: Bulk ATAC-seq Yy1_WT/Ngn2+ rep1

description:
Yy1_WT_Ngn2+_ATAC_rep1.bw
Yy1_WT_Ngn2+_ATAC_merge.bw
Yy1_WT_Ngn2+_ATAC_peaks.bed.gz

source_name: Bulk ATAC-seq primary mouse astrocytes transduced transduced with doxycycline inducible lentivirus expressing Ngn2 in the context of Yy1 knock-out Bulk ATAC-seq Yy1_WT/Ngn2+ rep1


title: H3K36me3_heart_E16_EC_cell_644


title: Bulk ATAC-seq Yy1_KO rep2

description:
Yy1_KO_ATAC_rep2.bw
Yy1_KO_ATAC_merge.bw
Yy1_KO_ATAC_peaks.bed.gz

source_name: Bulk ATAC-seq primary mouse astrocytes transduced transduced with doxycycline inducible lentivirus expressing Ngn2 in the context of Yy1 knock-out Bulk ATAC-seq Yy1_KO rep2


title: H3K36me3_heart_E16_EC_cell_643


title: H3K36me3_heart_E16_EC_cell_642


title: Bulk ATAC-seq Yy1_KO rep1

description:
Yy1_KO_ATAC_rep1.bw
Yy1_KO_ATAC_merge.bw
Yy1_KO_ATAC_peaks.bed.gz

source_name: Bulk ATAC-seq primary mouse astrocytes transduced transduced with doxycycline inducible lentivirus expressing Ngn2 in the context of Yy1 knock-out Bulk ATAC-seq Yy1_KO rep1


title: H3K36me3_heart_E16_EC_cell_641


title: H3K36me3_heart_E16_EC_cell_661


title: Bulk ATAC-seq Yy1_WT rep2

description:
Yy1_WT_ATAC_rep2.bw
Yy1_WT_ATAC_merge.bw
Yy1_WT_ATAC_peaks.bed.gz

source_name: Bulk ATAC-seq primary mouse astrocytes transduced transduced with doxycycline inducible lentivirus expressing Ngn2 in the context of Yy1 knock-out Bulk ATAC-seq Yy1_WT rep2


title: H3K36me3_heart_E16_EC_cell_639


title: Bulk ATAC-seq Yy1_WT rep1

description:
Yy1_WT_ATAC_rep1.bw
Yy1_WT_ATAC_merge.bw
Yy1_WT_ATAC_peaks.bed.gz

source_name: Bulk ATAC-seq primary mouse astrocytes transduced transduced with doxycycline inducible lentivirus expressing Ngn2 in the context of Yy1 knock-out Bulk ATAC-seq Yy1_WT rep1


title: H3K36me3_heart_E16_EC_cell_638


title: H3K36me3_heart_E16_EC_cell_647


title: Sample 071, Fibulin-4 R/R aortic arch, female

city: Rotterdam

first: Sanne

last: Stefens

address: Dr. Molewaterplein 40

department: Molecular Genetics

country: Netherlands

institute: Erasmus MC

library_source: transcriptomic

data_processing:
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA v2.4.11 and Bcl2fastq v2.17.
Reads were mapped to the reference sequence Mus_Musculus_GRCm38.p3 using a short read aligner based on Burrows-Wheeler Transform with a default matching rate of 2%.
Read counts were generated using htseq-count.
Differential expression analysis was performed with DESeq2 v1.10.1, a statistical package within the R platform v2.15.3.
Assembly: Mus_Musculus_GRCm38.p3
Supplementary files format and content: CSV file including rlog transformed counts for each sample

source_name: Aortic arch

growth_protocol: Fibulin-4+/R mice were bred into a C57BL6 background to obtain Fibulin-4R/R and wildtype (Fibulin-4+/+) experimental animals. Mice were fed normal chow diet. Mice were sacrificed by CO2 inhalation at an age of 3 months (n = 7 per group, 3 male and 4 female).

extract_protocol:
Total RNA and µRNA was obtained from the aortic arch using the miRNeasy Mini Kit (Qiagen).
Library preparation, sequencing and primary data analysis were performed at GenomeScan B.V. (Genomescan B.V., Leiden, The Netherlands). The NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to process the samples. The sample preparation was performed according to the protocol "NEBNext Ultra Directional RNA Library Prep Kit for Illumina"(NEB #E7420S/L)

value: Aortic arch

tag: Sex

value: female

value: Fibulin-4 R/R


title: Sample 061, Fibulin-4 R/R aortic arch, female


title: H3K36me3_heart_E16_EC_cell_640


title: Sample 018, Fibulin-4 R/R aortic arch, female


title: Bulk ATAC-seq Yy1_KO/Ngn2+ rep1

description:
Yy1_KO_Ngn2+_ATAC_rep1.bw
Yy1_KO_Ngn2+_ATAC_merge.bw
Yy1_KO_Ngn2+_ATAC_peaks.bed.gz

source_name: Bulk ATAC-seq primary mouse astrocytes transduced transduced with doxycycline inducible lentivirus expressing Ngn2 in the context of Yy1 knock-out Bulk ATAC-seq Yy1_KO/Ngn2+ rep1


title: H3K36me3_heart_E16_EC_cell_635


title: Sample 083, Fibulin-4 +/+ aortic arch, female

value: Fibulin-4 +/+


title: H3K36me3_heart_E16_EC_cell_633


title: Sample 059, Fibulin-4 +/+ aortic arch, female


title: H3K36me3_heart_E16_EC_cell_632


title: Sample 069, Fibulin-4 +/+ aortic arch, female


title: H3K36me3_heart_E16_EC_cell_631


title: Sample 013, Fibulin-4 R/R aortic arch, male

value: male


title: Sample 021, Fibulin-4 R/R aortic arch, male


title: H3K36me3_heart_E16_EC_cell_630


title: H3K36me3_heart_E16_EC_cell_629


title: Sample 009, Fibulin-4 R/R aortic arch, male


title: H3K36me3_heart_E16_EC_cell_628


title: Sample 068, Fibulin-4 +/+ aortic arch, male


title: Sample 037, Fibulin-4 +/+ aortic arch, male


title: Sample 032, Fibulin-4 +/+ aortic arch, male


title: Sample 054, Fibulin-4 R/R aortic arch, female


title: H3K36me3_heart_E16_EC_cell_637


title: H3K36me3_heart_E16_EC_cell_626


title: H3K36me3_heart_E16_EC_cell_636


title: Sample 074, Fibulin-4 +/+ aortic arch, female


title: H3K36me3_heart_E16_EC_cell_625


title: H3K36me3_heart_E16_EC_cell_627


title: E7T-seq_wt_14dpp_onIce_1d

value: testis

value: Exo7/T cell storage condition test


title: E7T-seq_wt_14dpp_frozen

value: wild type


title: H3K36me3_heart_E16_EC_cell_634


title: H3K36me3_heart_E16_EC_cell_624


title: S1-seq_Spo11KO_14dpp_rep1

value: Spermatocytes

value: Spo11 knockout

value: S1 Spo11 knockout


title: H3K36me3_heart_E16_EC_cell_623


title: H3K36me3_heart_E16_EC_cell_622


title: ET-seq_wt_14dpp_rep1

value: ExoT juvenile


title: H3K36me3_heart_E16_EC_cell_621


title: E7T-seq_wt_14dpp_rep1

value: Exo7/T juvenile


title: E7T-seq_wt_14dpp_rep2

value: 14 days post partum


title: S1-seq_wt_14dpp_tech_rep

value: S1 juvenile (technical replicate of sample 6)


title: H3K36me3_heart_E16_EC_cell_618

value: heart

value: Fixed by methanol


title: H3K36me3_heart_E16_EC_cell_617

value: H3K36me3, Active motif, Cat. 61101


title: S1-seq_wt_14dpp

value: S1 juvenile


title: H3K36me3_heart_E16_EC_cell_619


title: H3K36me3_heart_E16_EC_cell_616


title: H3K36me3_heart_E16_EC_cell_614


title: H3K36me3_heart_E16_EC_cell_615


title: H3K36me3_heart_E16_EC_cell_612


title: H3K36me3_heart_E16_EC_cell_620


title: Female RISP wild type littermate_2

city: Chicago

first: Paul

middle: T

last: Schumacker

state: IL

address: 303 E. Superior SQBRC 4-526

department: Pediatrics

institute: Northwestern University Feinberg School of Medicine

description:
M8542
htseq.all.counts-RISP.txt

data_processing:
Sequencing data were processed using the modular pipeline Ceto using “Genomics Nodes” and “Analytics Nodes” on Quest, Northwestern University’s High-Performance Computing Cluster.
The data were demultiplexed using bcl2fastq (Illumina).  Following FastQC assessment and trimming with trimmomatic, the reads were mapped using TopHat2 to the mm10 reference genome and reads were quantified using htseq2.
Differential gene expression analysis was performed using the EdgeR statistical package.
Assembly: mm10
Supplementary files format and content: htseq.all.counts.txt are tab-delimited text files containing raw counts for each sample. htseq.normCounts.txt = tab-delimited text files with normalized counts for each sample.  htseq.fpkms.txt.  Note that these files contain data from other experiments not related to this project, so please ignore mouse numbers other than the ones specified above that pertain to the current study.
Supplementary files format and content: Tab-delimited text files include RPKM values for each sample.

source_name: Heart

extract_protocol:
Heart tissue was shredded to disrupt the cells (QIAshredder catalog no. 79656, QIAGEN) allowing total RNA to be isolated (RNeasy mini kit, catalog no. 74104, QIAGEN)
RNA-seq libraries were generated (NEB Next RNA Ultra library preparation kit with poly(A) enrichment module) from 500 ng of total RNA. RNA-seq- libraries were pooled and sequenced on a NextSeq 500 instrument (Illumina) using the High Output 75 cycles V2 kit to an average depth of 10M reads per sample.

treatment_protocol: Mice 5-8 weeks of age were administered tamoxifen (0.5 mg in corn oil) daily for 5 days.  At 60 days after completing the tamoxifen treatment, hearts were harvested for RNA extraction.  Littermate Cre-negative control mice received the same tamoxifen dosing.

value: Heart

value: Female

value: RISP wild type

value: Tamoxifen


title: Male RISP wild type littermate_4

description:
M8547
htseq.all.counts-RISP.txt

value: Male


title: Male RISP knockout_4

description:
M8546
htseq.all.counts-RISP.txt

value: RISP Knockout


title: H3K36me3_heart_E16_EC_cell_608


title: Male RISP wild type littermate_1

description:
M8483
htseq.all.counts-RISP.txt


title: H3K36me3_heart_E16_EC_cell_613


title: H3K36me3_heart_E16_EC_cell_687


title: Female RISP knockout_3

description:
M8541
htseq.all.counts-RISP.txt


title: H3K36me3_heart_E16_EC_cell_611


title: H3K36me3_heart_E16_EC_cell_609


title: H3K36me3_heart_E16_EC_cell_607


title: H3K36me3_heart_E16_EC_cell_603


title: Male RISP knockout_1

description:
M4021
htseq.all.counts-RISP.txt


title: OC+SM #3

city: Busan

first: Haeseung

last: Lee

address: 63 Beon-gil 2, Busandaehag-ro, Geumjeong-gu

department: College of Pharmacy

country: South Korea

institute: Pusan National University

description: Forty-week-old Balb/c female mice were orally administered SM at a dose of 2.5g/kg, five times a week for four weeks.

data_processing:
Initial evaluation of the quality of raw RNA-seq fastq file was conducted utilizing FASTQC (v1.9).
The BBduk module within the bbmap toolkit (v38.95) was conducted with specific parameters: k=13, ktrim=r, useshortkmers=t, mink=5, qtrim=t, trimq=10, and minlength=20 to eliminate adapter sequences and low-quality reads.
The cleaned reads were mapped to the mouse reference genome (build GRCm39) through the STAR aligner (v2.7.9a)
Transcript abundance per gene such as expected read count or Transcripts Per Million (TPM) was quantified by RSEM (v1.3.3) along with the gene structure file (GRCm39.104.gtf).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include Expected counts, FPKM, and TPM values for each Sample

source_name: Ovary

growth_protocol: Balb/c female mice were purchased from the Central Lab. Animal Inc.(Seoul, Korea). All mice were maintained on an ad libitum diet in a specific pathogen-free room under a 12-hour light-dark cycle. All mice handling and experimental procedures were approved by the Korea Institute of Oriental Medicine Institutional Animal Care and Use Committee (approval number 19-061).

extract_protocol:
Following SM administration for 4 weeks, to create a post-ovulatory state, mice were induced by intraperitoneal injection of 5 IU of pregnant mare serum gonadotropin (PMSG; HOR-272; Prospec, Rehovot, Israel), followed by an injection of 5 IU of human chorionic gonadotropin (hCG; HOR-250; Prospec) 48 hours later. Ovaries were removed from mice and weighed at 16h post-hCG administration. The ovary was immediately preserved in liquid nitrogen for RNA sequencing.  Total RNA of each ovary (n=6) was extracted using TRIzol (Invitrogen, Carlsbad, CA, USA), according to the manufacturers' protocol.
The quality of purity and integrity of the extracted RNA samples were analyzed using a NanoDrop ND-2000 Spectrophotometer (Thermo Inc., DE, USA) and Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands). RNA library was constructed using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions.

treatment_protocol: Mice were randomly divided into groups of n=6 each.  Aged mice(40-week-old) were orally administered either distilled water (OC group)  or SM at a dose of 2.5g/kg (OC+SM group), five times a week for four weeks. Young mice (8-week-old) received distilled water (YC group). Mice from the OC and OC+SM groups were separated within the same cage to synchronize their hormonal cycles.

value: Ovary

value: Balb/c

value: Wildtype

value: Forty-week-old

value: samul-tang


title: OC+SM #6


title: OC+SM #5


title: H3K36me3_heart_E16_EC_cell_610


title: YC #6

description: Eight-week-old Balb/c female mice were orally administered distilled water, five times a week for four weeks.

value: Eight-week-old

value: distilled water


title: H3K36me3_heart_E16_EC_cell_606

value: heart


title: OC+SM #2


title: H3K36me3_heart_E16_EC_cell_605

value: Fixed by methanol


title: OC+SM #1


title: Female RISP wild type littermate_3

description:
M8543
htseq.all.counts-RISP.txt


title: OC+SM #4


title: YC #3


title: Female RISP knockout_2

description:
M8540
htseq.all.counts-RISP.txt


title: H3K36me3_heart_E16_EC_cell_600

value: H3K36me3, Active motif, Cat. 61101


title: H3K36me3_heart_E16_EC_cell_602


title: H3K36me3_heart_E16_EC_cell_598


title: YC #1


title: YC #4


title: H3K36me3_heart_E16_EC_cell_595


title: YC #5


title: H3K36me3_heart_E16_EC_cell_604


title: H3K36me3_heart_E16_EC_cell_599


title: H3K36me3_heart_E16_EC_cell_594


title: OC #5

description: Forty-week-old Balb/c female mice were orally administered distilled water, five times a week for four weeks.


title: OC #4


title: H3K36me3_heart_E16_EC_cell_597


title: H3K36me3_heart_E16_EC_cell_592


title: YC #2


title: OC #6


title: H3K36me3_heart_E16_EC_cell_593


title: OC #2


title: H3K36me3_heart_E16_EC_cell_601


title: H3K36me3_heart_E16_EC_cell_596


title: H3K36me3_heart_E16_EC_cell_591


title: H3K36me3_heart_E16_EC_cell_589


title: H3K36me3_heart_E16_EC_cell_590


title: OC #3


title: H3K36me3_heart_E16_EC_cell_587


title: H3K36me3_heart_E16_EC_cell_586


title: OC + Paeoniflorigenone #1

description: Thirty-eight-week-old Balb/c female mice were orally administered single compound treatment at a dose of 5mg/kg, five times a week for four weeks.

growth_protocol: Thirty-eight-week-old Balb/c female mice were purchased from the Central Lab. Animal Inc.(Seoul, Korea). All mice were maintained on an ad libitum diet in a specific pathogen-free room under a 12-hour light-dark cycle. All mice handling and experimental procedures were approved by the Korea Institute of Oriental Medicine Institutional Animal Care and Use Committee (approval number 20-090).

extract_protocol:
Following compound administration for 4 weeks, to create a post-ovulatory state, mice were induced by intraperitoneal injection of 5 IU of pregnant mare serum gonadotropin (PMSG; HOR-272; Prospec, Rehovot, Israel), followed by an injection of 5 IU of human chorionic gonadotropin (hCG; HOR-250; Prospec) 48 hours later. Ovaries were removed from mice and weighed at 14h-16h post-hCG administration. The ovary was immediately preserved in liquid nitrogen for RNA sequencing.  Each left ovary (n=3) of a post-ovulation mouse was immersed in 300ul TRIzol (Invitrogen, Carlsbad, CA, USA) and homogenized using a disposable grinder (Biomasher II; 890863; LMS Co., Tokyo, Japan).
Total RNA was isolated using Trizol reagent (Invitrogen). The quality of purity and integrity of the extracted RNA samples were analyzed using a NanoDrop ND-2000 Spectrophotometer (Thermo Inc., DE, USA) and Agilent 2100 bioanalyzer (Agilent Technologies, Amstelveen, The Netherlands). RNA library was constructed using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions.

treatment_protocol: Mice were randomly divided into groups of n=3 each. Aged mice(38-week-old) were orally administered either vehicle (distilled water containing 0.5% Dimethyl sulfoxide) or each of the 39 single compounds at a dose of 5mg/kg, five times a week for four weeks.

value: Paeoniflorigenone


title: OC + Paeoniflorigenone #3


title: OC + Purpureaside C #3

value: Purpureaside C


title: OC + Purpureaside C #1

value: Female


title: OC + Purpureaside C #2


title: OC + Paeoniflorigenone #2


title: OC + Vitamin E #2

value: Vitamin E


title: H3K36me3_heart_E16_EC_cell_588


title: OC + Vitamin E #3


title: OC + Ursolic acid #3

value: Ursolic acid


title: H3K36me3_heart_E16_EC_cell_584


title: H3K36me3_heart_E16_EC_cell_583


title: H3K36me3_heart_E16_EC_cell_582


title: H3K36me3_heart_E16_EC_cell_585


title: H3K36me3_heart_E16_EC_cell_580


title: OC + Ursolic acid #2


title: H3K36me3_heart_E16_EC_cell_581


title: OC + Vitamin E #1


title: OC #1


title: H3K36me3_heart_E16_EC_cell_579


title: OC + Ursolic acid #1


title: OC + Picroside I #3

value: Picroside I


title: OC + Picroside I #1


title: H3K36me3_heart_E16_EC_cell_577


title: H3K36me3_heart_E16_EC_cell_578


title: H3K36me3_heart_E16_EC_cell_576


title: OC + Picroside I #2


title: OC + Levistilide A #3

value: Levistilide A


title: H3K36me3_heart_E16_EC_cell_573


title: OC + Levistilide A #1

value: Ovary


title: OC + Jionoside B1 #3

value: Balb/c

value: Jionoside B1


title: OC + Jionoside B1 #2

value: Wildtype


title: H3K36me3_heart_E16_EC_cell_574


title: H3K36me3_heart_E16_EC_cell_575


title: OC + Jionoside A1 #3

value: Jionoside A1


title: OC + Levistilide A #2


title: H3K36me3_heart_E16_EC_cell_570


title: H3K36me3_heart_E16_EC_cell_567


title: H3K36me3_heart_E16_EC_cell_569


title: OC + Hierochin D #3

value: Hierochin D


title: H3K36me3_heart_E16_EC_cell_571


title: OC + Hierochin D #2


title: OC + Jionoside A1 #1


title: H3K36me3_heart_E16_EC_cell_565


title: OC + Hierochin D #1


title: H3K36me3_heart_E16_EC_cell_564


title: H3K36me3_heart_E16_EC_cell_566


title: OC + Digoxin #2

value: Digoxin


title: H3K36me3_heart_E16_EC_cell_562

value: heart


title: H3K36me3_heart_E16_EC_cell_563

value: Fixed by methanol


title: OC + Jionoside B1 #1


title: H3K36me3_heart_E16_EC_cell_561

value: H3K36me3, Active motif, Cat. 61101


title: OC + Digoxin #1


title: OC + D-Arabinose #3

value: D-Arabinose


title: H3K36me3_heart_E16_EC_cell_568


title: H3K36me3_heart_E16_EC_cell_560


title: OC + D-Arabinose #2


title: H3K36me3_heart_E16_EC_cell_559


title: OC + D-Arabinose #1


title: OC + Apiopaeonoside #2

value: Apiopaeonoside


title: H3K36me3_heart_E16_EC_cell_557


title: OC + Apiopaeonoside #3

value: Female


title: OC + Apiopaeonoside #1


title: OC + Ajugol #2

value: Ajugol


title: OC + Digoxin #3


title: H3K36me3_heart_E16_EC_cell_553


title: H3K36me3_heart_E16_EC_cell_555


title: H3K36me3_heart_E16_EC_cell_552


title: OC + Oleanolic Acid #3

value: Oleanolic Acid


title: OC + Ajugol #3


title: H3K36me3_heart_E16_EC_cell_551


title: H3K36me3_heart_E16_EC_cell_572


title: OC + Ajugol #1


title: H3K36me3_heart_E16_EC_cell_554


title: OC + Oleanolic Acid #2


title: H3K36me3_heart_E16_EC_cell_550


title: OC + Oleanolic Acid #1


title: H3K36me3_heart_E16_EC_cell_558


title: OC + Marmesin #2

value: Marmesin


title: H3K36me3_heart_E16_EC_cell_549


title: OC + 7-Hydroxycoumarin #3


title: OC + Marmesin #1


title: OC + Marmesin #3


title: H3K36me3_heart_E16_EC_cell_547


title: H3K36me3_heart_E16_EC_cell_546


title: H3K36me3_heart_E16_EC_cell_545


title: OC + Ferulic Acid #3

value: Ferulic Acid


title: OC + 7-Hydroxycoumarin #1

value: Ovary


title: H3K36me3_heart_E16_EC_cell_543


title: H3K36me3_heart_E16_EC_cell_542


title: OC + Ferulic Acid #1

value: Balb/c


title: OC + 7-Hydroxycoumarin #2


title: H3K36me3_heart_E16_EC_cell_540


title: H3K36me3_heart_E16_EC_cell_538


title: H3K36me3_heart_E16_EC_cell_539


title: OC + Ferulic Acid #2


title: H3K36me3_heart_E16_EC_cell_541


title: H3K36me3_heart_E16_EC_cell_537


title: OC + Chlorogenic Acid #1

value: Chlorogenic Acid


title: H3K36me3_heart_E16_EC_cell_548


title: H3K36me3_heart_E16_EC_cell_536


title: OC + Chlorogenic Acid #2

value: Wildtype


title: H3K36me3_heart_E16_EC_cell_544


title: H3K36me3_heart_E16_EC_cell_534


title: OC + Rhmannioside D #3

value: Rhmannioside D


title: OC + Rhmannioside D #1


title: OC + Rhmannioside D #2


title: H3K36me3_heart_E16_EC_cell_535


title: OC + Chlorogenic Acid #3


title: OC + Paeonolide #2

value: Paeonolide


title: H3K36me3_heart_E16_EC_cell_532


title: OC + Paeonolide #1


title: H3K36me3_heart_E16_EC_cell_531


title: OC + Oxypaeoniflorin #2

value: Oxypaeoniflorin


title: OC + Oxypaeoniflorin #1


title: H3K36me3_heart_E16_EC_cell_529

value: heart


title: H3K36me3_heart_E16_EC_cell_527

value: Fixed by methanol


title: H3K36me3_heart_E16_EC_cell_526

value: H3K36me3, Active motif, Cat. 61101


title: OC + Mudanpioside C #2

value: Mudanpioside C


title: OC + Mudanpioside C #1


title: H3K36me3_heart_E16_EC_cell_525


title: OC + Mudanpioside C #3


title: OC + 6'-O-Galloyl paeoniflorin #3

value: 6'-O-Galloyl paeoniflorin


title: OC + Paeonolide #3

value: Female


title: H3K36me3_heart_E16_EC_cell_533


title: H3K36me3_heart_E16_EC_cell_523


title: H3K36me3_heart_E16_EC_cell_522


title: H3K36me3_heart_E16_EC_cell_524


title: OC + Jionoside A1 #2

value: Jionoside A1


title: H3K36me3_heart_E16_EC_cell_521


title: H3K36me3_heart_E16_EC_cell_530


title: OC + 6'-O-Galloyl paeoniflorin #1


title: OC + Catalpol #3

value: Catalpol


title: OC + Catalpol #1


title: H3K36me3_heart_E16_EC_cell_519


title: OC + Oxypaeoniflorin #3


title: H3K36me3_heart_E16_EC_cell_520


title: OC + Benzoyloxypeoniflorin #3

value: Benzoyloxypeoniflorin


title: H3K36me3_heart_E16_EC_cell_518


title: OC + Benzoyloxypeoniflorin #2


title: OC + Catalpol #2


title: H3K36me3_heart_E16_EC_cell_517


title: OC + Benzoyloxypeoniflorin #1


title: H3K36me3_heart_E16_EC_cell_516


title: OC + 6'-O-Galloyl paeoniflorin #2


title: H3K36me3_heart_E16_EC_cell_515


title: OC + Decursinol angelate #1

value: Decursinol angelate


title: H3K36me3_heart_E16_EC_cell_514


title: OC + Decursinol angelate #2

value: Ovary


title: OC + 1,2,3,4,6-O-Pentagalloylglucose #3

value: Balb/c


title: H3K36me3_heart_E16_EC_cell_513


title: H3K36me3_heart_E16_EC_cell_512


title: OC + 1,2,3,4,6-O-Pentagalloylglucose #2


title: H3K36me3_heart_E16_EC_cell_511


title: OC + 1,2,3,4,6-O-Pentagalloylglucose #1


title: OC + Nodakenin #3

value: Nodakenin


title: H3K36me3_heart_E16_EC_cell_509


title: H3K36me3_heart_E16_EC_cell_510


title: H3K36me3_heart_E16_EC_cell_508


title: OC + Nodakenin #1

value: Wildtype


title: OC + Nodakenin #2


title: H3K36me3_heart_E16_EC_cell_506


title: H3K36me3_heart_E16_EC_cell_507


title: OC + Ligustilide A #3

value: Ligustilide A


title: OC + Ligustilide A #1


title: OC + Decursinol angelate #3


title: OC + Ligustilide A #2


title: OC + 5-Hydroxymethyl-2-furaldehyde #3


title: H3K36me3_heart_E16_EC_cell_504


title: H3K36me3_heart_E16_EC_cell_502


title: H3K36me3_heart_E16_EC_cell_503


title: OC + 5-Hydroxymethyl-2-furaldehyde #1


title: OC + Decursin #3

value: Decursin


title: OC + Decursin #2


title: H3K36me3_heart_E16_EC_cell_501


title: H3K36me3_heart_E16_EC_cell_499


title: H3K36me3_heart_E16_EC_cell_505


title: H3K36me3_heart_E16_EC_cell_498


title: OC + Butylphthalide #3

value: Butylphthalide


title: H3K36me3_heart_E16_EC_cell_497

value: heart


title: OC + Butylphthalide #2


title: OC + Decursin #1


title: OC + Butylphthalide #1


title: H3K36me3_heart_E16_EC_cell_495

value: Fixed by methanol


title: H3K36me3_heart_E16_EC_cell_496

value: H3K36me3, Active motif, Cat. 61101


title: OC + Senkyunolide I #2

value: Senkyunolide I


title: OC + Senkyunolide I #1


title: H3K36me3_heart_E16_EC_cell_493


title: OC + Senkyunolide I #3


title: OC + Senkyunolide A #3

value: Senkyunolide A


title: OC + Senkyunolide A #2

value: Female


title: OC + 5-Hydroxymethyl-2-furaldehyde #2


title: H3K36me3_heart_E16_EC_cell_494


title: OC + Senkyunolide A #1


title: H3K36me3_heart_E16_EC_cell_500


title: H3K36me3_heart_E16_EC_cell_491


title: OC + Paeoniflorin #3

value: Paeoniflorin


title: OC + Paeoniflorin #2


title: OC + Isoacteoside #3

value: Isoacteoside


title: OC + Benzoylpaeoniflorin #3

value: Benzoylpaeoniflorin


title: H3K36me3_heart_E16_EC_cell_490


title: OC + Isoacteoside #2


title: MC-CONTROL_1

type: RNA

city: Jeddah

first: Sherin

last: Bakhashab

address: Abdullah Sulyman

department: Biochemistry

country: Saudi Arabia

institute: King Abdulaziz University

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were analyzed with TAC 4.0

label: biotin

organism: Homo sapiens

source_name: Human umbilical cord blood

label_protocol: 250 ng total RNA was used as input for amplification using Ambion WT expression sense kit (Life Technilogies, Grand Island, NY, USA), Poly A control was added as suggested by WT expression kit manual. cDNA amplification products were fragmented and labeled with biotin using Affymetrix GeneChip WT terminal labeling kit, hybridized to HG Gene 1.0 ST arrays (Affymetrix Inc., Santa Clara, CA, USA) using Affymetrix Hybridization Control Kit, and then washed and stained using Affymetrix Wash and Stain kit. All steps were processed following the manufactures suggestions.

growth_protocol: CD34+ cells were isolated from human umbilical cord blood and differentiated into mast cells using rhIL-6 and rh-SCF for 6-8 weeks.

extract_protocol: RNA samples were isolated from hCBMCs and  CD34- using the RNeasy Mini Kit (Qiagen) including the optional DNase treatment, according to the manufacturer's instructions. Total RNA was quantified using a Nanodrop Spectrophotometer 2000 (Thermo Scientific Inc., Waltham, MA, USA) and the quality confirmed (RIN > 7.0) on an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

tag: conddition

value: Normal


title: OC + Benzoylpaeoniflorin #2

value: Ovary


title: OC + Isoacteoside #1

value: Balb/c


title: CD34 Negative_2


title: H3K36me3_heart_E16_EC_cell_489


title: CD34 Negative_1


title: CD34 Negative_3


title: OC + Aucubin #3

value: Aucubin


title: H3K36me3_heart_E16_EC_cell_488


title: MC-CONTROL_2


title: H3K36me3_heart_E16_EC_cell_492


title: OC + Aucubin #2

value: Wildtype


title: OC + Aucubin #1


title: WT_Th2_K9me3_R1

city: Berlin

first: Ahmed

middle: Nabil

last: Hegazy

address: Hindenburgdamm 30

department: Department of Gastroenterology, Infectious Diseases and Rheumatology

institute: Charité - University Medicine Berlin

data_processing:
# Bowtie v1.2.1.1 bowtie -t -m 1 -S -q -p 8 <Genome Location > <FASTQ File > <SAM File Output >
# SICER v1.1 ( modified script )
SICER_modified.sh <Input file folder > <Input file name > <Control file name > <Output
folder > t mm10 1 200 150 0.8
# SICER params: ["InputDir"] ["bed file"] ["control file"] ["OutputDir"] ["Species"] ["redundancy threshold"] ["window sizes (bp) - submit multiple window sizes in quote"] ["fragment size"] ["effective genome fraction"] ["number of background islands for evalue (def: 1000)"]
Assembly: mm10
Supplementary files format and content: bed files: for K4me3 histone modifications the params are W200-G200-FDR0.01; for all others the params are W200-G600-FDR0.01

source_name: Spleen and lymph nodes

growth_protocol: Adoptively transferred WT, Tbx21+/-, Tbx21-/- LCMV‑TCRtg CD4+ Thy1.1+ cells from LCMV-challenged mice were isolated and MACS-sorted on day 10 of infection. Cells were cultured for two rounds under neutral (5 ng/ml IL-2 (Peprotech), 10 µg/ml anti–IL-4 (11B11), 10 µg/ml anti–IL-12 (C17.8), and 10 µg/ml anti–IFN-g (AN18.17.24)) or Th2 conditions (30 ng/ml IL-4 (Sigma-Aldrich), 5 ng/ml IL-2 (Peprotech), 10 µg/ml anti–IL-12 (C17.8), and 10 µg/ml anti–IFN-g (AN18.17.24)). On day 4 of the second round of stimulations the cells were harvested and processed for Chip-Seq.

extract_protocol:
Cells were incubated for 10min at room temperature with 1% formaldehyde. Cross-linking was terminated by addition of glycine to a final concentration of 125mM. ChIP was performed using iDeal ChIP-seq Kit (Diagenode) according to the manufacturer’s instructions. Antibodies against H3K4me3 (ab8580, Abcam), H3K4me1 (ab8895, Abcam), H3K27ac (ab4729, Abcam), H3K27me3 (ab6002, Abcam) and H3K9me3 (ab8898, Abcam) were used.
10ng of chromatin-immunoprecipitated DNA was end-repaired and dA-tailed. Subsequently, adaptor was ligated to the dA-tailed DNA. DNA was cleaned up using AMpure XP beads after each step. Adaptor-ligated DNA was size selected with AMpure XP beads using different DNA to beads ratio to an average fragment size of 200bp. At last step, size-selected and adaptor-ligated DNA was enriched by PCR with different index primers and cleaned up using AMpure XP beads. Purified library DNA was quantified with Qubit 2.0 and fragment size was assessed using Bioanalyzer (Agilent high sensitivity chip).

value: Spleen and lymph nodes

tag: cell line

value: Primary LCMV TCRtg CD4+ Thy1.1+ cells

value: CD4 T cells

value: Wild type

value: Th2 conditions


title: H3K36me3_heart_E16_EC_cell_486

source_name: E16.5 heart

value: heart

value: Fixed by methanol

value: H3K36me3, Active motif, Cat. 61101


title: WT_Th2_K4me3_R2

treatment_protocol: Cells were cultured for two rounds under neutral (5 ng/ml IL-2 (Peprotech), 10 µg/ml anti–IL-4 (11B11), 10 µg/ml anti–IL-12 (C17.8), and 10 µg/ml anti–IFN-g (AN18.17.24)) or Th2 conditions (30 ng/ml IL-4 (Sigma-Aldrich), 5 ng/ml IL-2 (Peprotech), 10 µg/ml anti–IL-12 (C17.8), and 10 µg/ml anti–IFN-g (AN18.17.24)).


title: WT_Th2_K4me3_R1


title: OC + Albiflorin #3

value: Female

value: Albiflorin


title: WT_Th2_K4me1_R2


title: OC + Albiflorin #2


title: WT_Th2_K9me3_R2


title: H3K36me3_heart_E16_EC_cell_485


title: OC + Albiflorin #1


title: OC #10

description: Thirty-eight-week-old Balb/c female mice were orally administered vehicle (distilled water containing 0.5% Dimethyl sulfoxide), five times a week for four weeks.

value: DMSO


title: OC #9


title: H3K36me3_heart_E16_EC_cell_484


title: WT_Th2_K27me3_R2


title: OC #8


title: WT_Th2_K27me3_R1


title: OC #6


title: OC + Benzoylpaeoniflorin #1

value: Benzoylpaeoniflorin


title: H3K36me3_heart_E16_EC_cell_487


title: H3K36me3_heart_E16_EC_cell_483


title: WT_Th2_K27ac_R2


title: OC #4


title: H3K36me3_heart_E16_EC_cell_481


title: H3K36me3_heart_E16_EC_cell_482


title: OC #5


title: OC #2


title: OC #3


title: WT_Th2_K27ac_R1


title: H3K36me3_heart_E16_EC_cell_480


title: DOT1LKO H3K4me3

city: Esch-sur-Alzette

first: Sebastian

last: Scheer

address: 29, rue Henri Koch

department: Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

data_processing:
Aligned bam files were then filtered to remove reads in black-listed regions, duplicate reads were marked using Picard MarkDuplicates
Bam files were filtered again to remove low quality reads (samtools view -q 10 -F 1800)
Bamcoverage was performed under standard parameters and visualised on IGV
Assembly: UCSC mm10
Supplementary files format and content: bigwig
Library strategy: CUT&TAG

source_name: splenic NK cells, cultured

extract_protocol:
input only contains secondary antibody (NBP1-72763), H3K4me3 was targeted using αH3K4me3  (Cell Signalling #9727), H3K27me3 was targeted using αH3K27me3 (Cell Signalling #9733)
Tn5-digested DNA underwent PCR witrh universal i5 primer and sample-specific, unique i7 primer, followed by SBS V2.5 chemistry

value: splenic NK cells

value: NK cells

value: NK cell enrichment followed by culturing for 5 days


title: H3K36me3_heart_E16_EC_cell_479


title: DOT1LKO H3K27me3


title: OC #1

value: Ovary

value: Balb/c


title: WT_Th2_K4me1_R1

value: Spleen and lymph nodes


title: WT_Th2_Input_R1

value: Primary LCMV TCRtg CD4+ Thy1.1+ cells


title: OC #7

value: Wildtype


title: H3K36me3_heart_E16_EC_cell_478


title: WT H3K27me3

value: WT


title: WT_Neutral_K9me3_R2

value: CD4 T cells

value: Wild type

value: Neutral conditions


title: WT input

value: none (input)


title: H3K36me3_heart_E16_EC_cell_476

value: heart

value: Fixed by methanol

value: H3K36me3, Active motif, Cat. 61101


title: H3K36me3_heart_E16_EC_cell_477


title: WT H3K4me3


title: WT_Neutral_K9me3_R1


title: WT_Neutral_K4me3_R2


title: H3K36me3_heart_E16_EC_cell_475


title: A172 cells, uc.110 siRNA-2, sample 4

city: Charlottesville

first: Roger

last: Abounader

email: ra6u@virginia.edu, mkg7x@virginia.edu

state: VA

address: 21 Hospital Drive

department: Microbiology

institute: University of Virginia

data_processing:
Fastq files were processed using Salmon from Combine Lab.
Assembly: hg38
Supplementary files format and content: BED format containing raw count outputs from Salmon for all samples.

source_name: brain

growth_protocol: Cells were seeded in 6-well culture plates with full serum media at 300k/well density at D0.

extract_protocol:
Cells were extracted using the Qiagen RNEasy Plus kit according to manufacturer instructions.
RNA Libraries were collected and transported to Azenta Life Sciences for sequencing via RNA-Seq on Day 2 (post transfection).

treatment_protocol: At D1, each well was transfected with 3 µL of siRNAs (20 µM) using 9 µL Lipofectamine 2000 in 300 µL OPTI-MEM and 700 µL antibiotic and empty media for 6 hours. At 6 hours, the media were replaced with fresh media containing antibiotics and FBS.

value: brain

value: adherent glioma cells

value: uc.110 siRNA-2


title: A172 cells, uc.110 siRNA-2, sample 2


title: A172 cells, uc.110 siRNA-2, sample 3


title: WT_Th2_Input_R2

value: Th2 conditions


title: H3K36me3_heart_E16_EC_cell_474


title: WT_Neutral_K4me3_R1


title: A172 cells, uc.110 siRNA-2, sample 1


title: A172 cells, uc.110 siRNA-1, sample 4

value: uc.110 siRNA-1


title: A172 cells, uc.110 siRNA-1, sample 2


title: DOT1LKO input

value: splenic NK cells

value: NK cells

value: NK cell enrichment followed by culturing for 5 days


title: A172 cells, uc.110 siRNA-1, sample 1


title: H3K36me3_heart_E16_EC_cell_473


title: WT_Neutral_K4me1_R2

value: Spleen and lymph nodes

value: Primary LCMV TCRtg CD4+ Thy1.1+ cells


title: A172 cells, scrambled control siRNA, sample 4

value: WT

value: scrambled control siRNA


title: WT_Neutral_K4me1_R1

value: CD4 T cells

value: Wild type

value: Neutral conditions


title: H3K36me3_heart_E16_EC_cell_472

value: heart

value: Fixed by methanol


title: A172 cells, scrambled control siRNA, sample 3

value: brain


title: WT_Neutral_K27me3_R2


title: A172 cells, scrambled control siRNA, sample 2

value: adherent glioma cells


title: H3K36me3_heart_E16_EC_cell_471

value: H3K36me3, Active motif, Cat. 61101


title: A172 cells, scrambled control siRNA, sample 1


title: WT_Neutral_K27me3_R1


title: H3K36me3_heart_E16_EC_cell_470


title: A172 cells, uc.110 siRNA-1, sample 3


title: WT_Neutral_K27ac_R2


title: H3K36me3_heart_E16_EC_cell_469


title: THP-1_p53-R282W

city: Shanghai

first: Yigang

last: Tang

address: No 197 RUIJIN ER RD

institute: Shanghai Jiaotong University

data_processing:
Raw sequence reads were initially processed using FastQC (Babraham Institute, Cambridge, UK) for quality control, then adapter sequences and poor-quality reads were removed using Cutadapt.
Quality-filtered reads were then mapped to the human genome using STAR software, and only uniquely mapped reads were kept. Read counts were calculated by using htseq count.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files includes FPKM value of each sample

source_name: Myeloid malignant cell line

growth_protocol: HCC1937 and THP-1 cells were cultured at 37 ℃ in medium suggested in the repository, supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 mg/mL streptomycin.

extract_protocol:
Total RNA was isolated using a Total RNA Purification Kit (B518651, Sangon Biotech)
Sequencing libraries was constructed from 1 μg of purified mRNA using an Illumina TruSeq RNA Sample Prep Kit (cat# FC-122-1001)

treatment_protocol: HCC1937 cells infected with  p53-R282W were treated with 0.3 μM DAC for 5 days. THP-1 cells infected with  p53-R282W were treated with 5 μM DAC for 2 days.

value: THP-1 (p53-/-) cells  infected with p53-R282W

tag: dac treatment

value: no


title: WT_Neutral_K27ac_R1


title: H3K36me3_heart_E16_EC_cell_468


title: WP-0614 untreated C

city: Santa Monica

first: Dave

last: Hoon

state: CA

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

data_processing:
Base calling and demultiplexing were processed using CASAVA version 1.8
Reads were mapped using the GENCODE release 19 reference using STAR version 2.4.2a
Read counts were generated using the quantMode GeneCounts option in STAR.

extract_protocol:
RNA was isolated using the ZR-Duet DNA/RNA MiniPrep kit (Zymo Research, Irvine CA.)
mRNA libraries were constructed using the Bioo Scientific NEXTflex Rapid Directional RNA-seq Library Prep Kit.

value: melanoma cancer cell line (MBM)

value: untreated


title: WP-0614 treated C

value: icaritin


title: WT_Neutral_Input_R2

value: Spleen and lymph nodes


title: H3K36me3_heart_E16_EC_cell_467


title: WP-0614 treated A


title: WP-0614 treated B


title: WP-0614 untreated B


title: WT_Neutral_Input_R1

value: Primary LCMV TCRtg CD4+ Thy1.1+ cells


title: DP-0574 treated C


title: H3K36me3_heart_E16_EC_cell_466


title: DP-0574 treated B


title: Naive_SM_Th2_K9me3_R2

value: Th2 conditions


title: DP-0574 treated A


title: THP-1_p53-R282W+DAC

value: yes


title: H3K36me3_heart_E16_EC_cell_465


title: DP-0574 untreated C


title: Naive_SM_Th2_K9me3_R1

value: CD4 T cells


title: DP-0574 untreated A


title: Naive_SM_Th2_K4me3_R2

value: Wild type


title: H3K36me3_heart_E16_EC_cell_463


title: WP-0614 untreated A


title: Naive_SM_Th2_K4me3_R1


title: H3K36me3_heart_E16_EC_cell_462


title: Naive_SM_Th2_K4me1_R2


title: Naive_SM_Th2_K4me1_R1


title: H3K36me3_heart_E16_EC_cell_460


title: Naive_SM_Th2_K27me3_R2


title: H3K36me3_heart_E16_EC_cell_461