title: 11D_M_1282


title: 11D_M_1278

status: Public on Apr 24 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: 11D_M_1281


title: 11D_M_1280


title: 11D_M_1279


title: 11D_M_128


title: 11D_M_1276


title: 11D_M_1274


title: 11D_M_1275


title: 11D_M_1263


title: 11D_M_1268


title: 11D_M_127


title: 11D_M_1264


title: 11D_M_1272


title: 11D_M_1273


title: 11D_M_1266


title: 11D_M_1265


title: 11D_M_1262


title: 11D_M_1270


title: 11D_M_1267


title: 11D_M_1271


title: 11D_M_1269


title: 11D_M_1261


title: 11D_M_1260


title: 11D_M_126


title: 11D_M_1259


title: 11D_M_1258


title: 11D_M_1256


title: 11D_M_1257


title: 11D_M_1255


title: 11D_M_1252


title: 11D_M_1254


title: 11D_M_1253


title: 11D_M_1251


title: 11D_M_1277


title: 11D_M_1250


title: 11D_M_125


title: 11D_M_1248


title: 11D_M_1245


title: 11D_M_1240


title: 11D_M_1234


title: 11D_M_1243


title: 11D_M_1238


title: 11D_M_124


title: 11D_M_1235


title: 11D_M_1242


title: 11D_M_1239


title: 11D_M_1237


title: 11D_M_1246


title: 11D_M_1247


title: 11D_M_1236


title: 11D_M_1241


title: 11D_M_1232


title: 11D_M_1233


title: 11D_M_1231


title: 11D_M_1230


title: 11D_M_1249


title: 11D_M_1228


title: 11D_M_123


title: 11D_M_1229


title: 11D_M_1226


title: 11D_M_1223


title: 11D_M_1221


title: 11D_M_1222


title: 11D_M_1224


title: 11D_M_1225


title: 11D_M_1244


title: 11D_M_122


title: 11D_M_1220


title: 11D_M_1210


title: 11D_M_1216


title: 11D_M_1218


title: 11D_M_121


title: 11D_M_1217


title: 11D_M_1212


title: 11D_M_1219


title: 11D_M_1213


title: 11D_M_1211


title: 11D_M_1209


title: 11D_M_1208


title: 11D_M_1207


title: 11D_M_1227


title: 11D_M_1199


title: 11D_M_1198


title: 11D_M_1197


title: 11D_M_1204


title: 11D_M_1202


title: 11D_M_12


title: 11D_M_1200


title: 11D_M_1201


title: 11D_M_1203


title: 11D_M_1196


title: 11D_M_1195


title: 11D_M_1214


title: 11D_M_1215


title: 11D_M_1194


title: 11D_M_1189


title: 11D_M_1193


title: 11D_M_1190


title: 11D_M_1192


title: 11D_M_119


title: 11D_M_1205


title: 11D_M_1186


title: 11D_M_1184


title: 11D_M_1188


title: 11D_M_1181


title: 11D_M_1206


title: 11D_M_1185


title: 11D_M_120


title: 11D_M_1171


title: 11D_M_1173


title: 11D_M_1170


title: 11D_M_1177


title: 11D_M_1169


title: 11D_M_1178


title: 11D_M_117


title: 11D_M_1168


title: 11D_M_1176


title: 11D_M_118


title: 11D_M_1163


title: 11D_M_1165


title: 11D_M_1167


title: 11D_M_1166


title: 11D_M_1172


title: 11D_M_1183


title: 11D_M_1180


title: 11D_M_1179


title: 11D_M_1191


title: 11D_M_1187


title: 11D_M_1161


title: 11D_M_116


title: 11D_M_1159


title: 11D_M_1157


title: 11D_M_1156


title: 11D_M_1155


title: 11D_M_1175


title: 11D_M_1154


title: 11D_M_1151


title: 11D_M_1149


title: 11D_M_115


title: 11D_M_1152


title: 11D_M_1150


title: 11D_M_1148


title: 11D_M_1162


title: 11D_M_1160


title: 11D_M_1146


title: 11D_M_1145


title: 11D_M_1153


title: 11D_M_1147


title: 11D_M_1133


title: 11D_M_1140


title: 11D_M_1139


title: 11D_M_1134


title: 11D_M_114


title: 11D_M_1135


title: 11D_M_1144


title: 11D_M_1137


title: 11D_M_1132


title: 11D_M_1130


title: 11D_M_1131


title: 11D_M_1138


title: 11D_M_1158


title: 11D_M_113


title: 11D_M_1141


title: 11D_M_1143


title: 11D_M_1127


title: 11D_M_1142


title: 11D_M_1124


title: 11D_M_1125


title: 11D_M_1121


title: 11D_M_1126


title: 11D_M_1122


title: 11D_M_1128


title: 11D_M_1123


title: 11D_M_112


title: 11D_M_1119


title: 11D_M_1120


title: 11D_M_1118


title: 11D_M_1116


title: 11D_M_1117


title: 11D_M_111


title: 11D_M_1114


title: 11D_M_1115


title: 11D_M_1111


title: 11D_M_1107


title: 11D_M_1113


title: 11D_M_1108


title: 11D_M_1110


title: 11D_M_1105


title: 11D_M_1106


title: 11D_M_1112


title: 11D_M_1129


title: 11D_M_1104


title: 11D_M_1103


title: 11D_M_1102


title: 11D_M_11


title: 11D_M_1098


title: 11D_M_1101


title: 11D_M_1100


title: 11D_M_1097


title: 11D_M_1099


title: 11D_M_1093


title: 11D_M_1095


title: 11D_M_1094


title: 11D_M_1091


title: 11D_M_1090


title: 11D_M_109


title: 11D_M_1089


title: 11D_M_1086


title: 11D_M_1088


title: 11D_M_1087


title: 11D_M_1109


title: DAF-16 4KR rep-3

city: Taipei

first: Ao-Lin

last: Hsu

address: No.155, Sec.2, Linong Street

department: Institute of Biochemistry and Molecular Biology

country: Taiwan

institute: National Yang-Ming University

library_source: transcriptomic

data_processing:
Base calling and fastq files were generated by RTA version RTA1.18.64_bcl2fastq1.8.4
Raw reads were then trimmed for adapter and barcodes using the Trimmomatic software (v0.32)
Alignment of the reads was done using the Tophat2 software (v2.1.0) against the Wormbase genome (WS249)
DESeq2 (v1.14.1) was used to perform differential expression gene analysis on pairwise comparisons of the different samples
Genome_build: WS249
Supplementary_files_format_and_content: tab-delimited text files include read counts and fpm values for each sample.

molecule: total RNA

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Animals were cultured using the standard method at 20°C on nematode growth medium agar (NGM) plates seeded with E. coli strain OP50.

extract_protocol:
Total RNA was isolated from approximately 1000 day 1 adults using TRIzol reagent (Thermo Fisher Scientific) and Direct-zol RNA MiniPrep kit (Zymo Research).
RNA-seq libraries for multiple biological repeats were prepared with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).

tag: Stage

value: Day1 adult

tag: genotype


title: DAF-16 4KR rep-2


title: DAF-16 4KR rep-1


title: 11D_M_1085


title: 11D_M_1084


title: DAF-16 2KR rep-3


title: DAF-16 2KR rep-2


title: 11D_M_1083


title: 11D_M_1082


title: 11D_M_110


title: 11D_M_1096


title: 11D_M_1081


title: DAF-16 WT rep-3


title: DAF-16 WT rep-1


title: 11D_M_108


title: 11D_M_1080


title: DAF-16 WT rep-2


title: 11D_M_1092


title: 11D_M_1079


title: 11D_M_1078


title: N2 rep-2

value: wild type


title: N2 rep-1


title: 11D_M_1074


title: 11D_M_1072


title: 11D_M_1075


title: 11D_M_1076


title: 11D_M_1071


title: 11D_M_1070


title: NR [UM48]

first: Yungling

middle: Leo

last: Lee

address: Sec. 2, Academia Rd.

department: Institute of Biomedical Sciences

institute: Academia Sinica

description:
UM48
NEUseq_gene_count_matrix.csv

data_processing:
We use Trimmomatic for removing sequencing contaminants, adaptors and low-quality sequences.
HISAT2 and StringTie software were used to align and assemble RNA-seq reads for gene count quantification.
Assembly: human reference genome (GRCh38)
Supplementary files format and content: csv files include count values for samples from whole blood sequencing
Supplementary files format and content: csv files include count values for samples from peripheral neutrophil sequencing

organism: Homo sapiens

source_name: Peripheral neutrophils

extract_protocol:
RNA samples were isolated from whole blood and then extracted by Direct-zol™ RNA MiniPrep (Zymo Research). Neutrophil cells were isolated from peripheral blood by Histopaque gradient. Half of the neutrophils were used to RNA extraction by Direct-zol™ RNA MicroPrep (Zymo Research).
The sequencing library was prepared with the SMARTer Stranded total RNA-Seq Kit (Clontech).

tag: tissue

value: Peripheral neutrophils

tag: group

value: NR


title: R [UM46]

description:
UM46
NEUseq_gene_count_matrix.csv

value: R


title: NR [UM59]

description:
UM59
NEUseq_gene_count_matrix.csv


title: R [UM45]

description:
UM45
NEUseq_gene_count_matrix.csv


title: R [UM47]

description:
UM47
NEUseq_gene_count_matrix.csv


title: 11D_M_107


title: NR [UM49]

description:
UM49
NEUseq_gene_count_matrix.csv


title: NR [UM57]

description:
UM57
NEUseq_gene_count_matrix.csv


title: NR [UM44]

description:
UM44
NEUseq_gene_count_matrix.csv


title: NR [UM43]

description:
UM43
NEUseq_gene_count_matrix.csv


title: 11D_M_1069


title: DAF-16 2KR rep-1


title: NR [UM41]

description:
UM41
NEUseq_gene_count_matrix.csv


title: 11D_M_1066


title: 11D_M_1067


title: 11D_M_1068


title: 11D_M_1077


title: 11D_M_1063


title: R [UM50]

description:
UM50
NEUseq_gene_count_matrix.csv


title: R [UM40]

description:
UM40
NEUseq_gene_count_matrix.csv


title: 11D_M_1073


title: NR [UM39]

description:
UM39
NEUseq_gene_count_matrix.csv


title: 11D_M_1062


title: NR [UM35]

description:
UM35
NEUseq_gene_count_matrix.csv


title: R [UM36]

description:
UM36
NEUseq_gene_count_matrix.csv


title: NR [UM33]

description:
UM33
NEUseq_gene_count_matrix.csv


title: 11D_M_1060


title: 11D_M_106


title: NR [UM32]

description:
UM32
NEUseq_gene_count_matrix.csv


title: 11D_M_1059


title: 11D_M_1057


title: 11D_M_1058


title: NR [UM29]

description:
UM29
NEUseq_gene_count_matrix.csv


title: 11D_M_1056


title: R [UM30]

description:
UM30
NEUseq_gene_count_matrix.csv


title: R [UM28]

description:
UM28
NEUseq_gene_count_matrix.csv


title: 11D_M_1055


title: 11D_M_1054


title: NR [UM31]

description:
UM31
NEUseq_gene_count_matrix.csv


title: NR [UM27]

description:
UM27
NEUseq_gene_count_matrix.csv


title: NR [UM37]

description:
UM37
NEUseq_gene_count_matrix.csv


title: 11D_M_1064


title: 11D_M_1053


title: NR [UM24]

description:
UM24
NEUseq_gene_count_matrix.csv


title: R [UM25]

description:
UM25
NEUseq_gene_count_matrix.csv


title: 11D_M_1052


title: 11D_M_1051


title: R [UM23]

description:
UM23
NEUseq_gene_count_matrix.csv


title: R [UM22]

description:
UM22
NEUseq_gene_count_matrix.csv


title: 11D_M_1050


title: 11D_M_105


title: R [UM21]

description:
UM21
NEUseq_gene_count_matrix.csv


title: R [UM20]

description:
UM20
NEUseq_gene_count_matrix.csv


title: 11D_M_1048


title: 11D_M_1047


title: 11D_M_1045


title: 11D_M_1046


title: R [UM26]

description:
UM26
NEUseq_gene_count_matrix.csv


title: NR [UM17]

description:
UM17
NEUseq_gene_count_matrix.csv


title: 11D_M_1043


title: R [UM15]

description:
UM15
NEUseq_gene_count_matrix.csv


title: R [UM16]

description:
UM16
NEUseq_gene_count_matrix.csv


title: NR [UM18]

description:
UM18
NEUseq_gene_count_matrix.csv


title: R [UM09]

description:
UM09
NEUseq_gene_count_matrix.csv


title: NR [UM10]

description:
UM10
NEUseq_gene_count_matrix.csv


title: 11D_M_1041


title: 11D_M_1042


title: 11D_M_1040


title: NR [UM07]

description:
UM07
NEUseq_gene_count_matrix.csv


title: R [UM06]

description:
UM06
NEUseq_gene_count_matrix.csv


title: 11D_M_104


title: 11D_M_1039


title: 11D_M_1038


title: NR [UM05]

description:
UM05
NEUseq_gene_count_matrix.csv


title: R [QU67]

description:
QU67
Bloodseq_gene_count_matrix.csv

source_name: Whole blood

value: Whole blood


title: R [UM19]

description:
UM19
NEUseq_gene_count_matrix.csv


title: 11D_M_1037


title: R [UM01]

description:
UM01
NEUseq_gene_count_matrix.csv


title: 11D_M_1049


title: NR [QU66]

description:
QU66
Bloodseq_gene_count_matrix.csv


title: 11D_M_1036


title: 11D_M_1035


title: 11D_M_1044


title: 11D_M_1033


title: NR [QU64]

description:
QU64
Bloodseq_gene_count_matrix.csv


title: 11D_M_1034


title: NR [QU62]

description:
QU62
Bloodseq_gene_count_matrix.csv


title: R [QU63]

description:
QU63
Bloodseq_gene_count_matrix.csv


title: R [QU65]

description:
QU65
Bloodseq_gene_count_matrix.csv


title: 11D_M_1031


title: R [QU47]

description:
QU47
Bloodseq_gene_count_matrix.csv


title: NR [QU61]

description:
QU61
Bloodseq_gene_count_matrix.csv


title: NR [QU48]

description:
QU48
Bloodseq_gene_count_matrix.csv


title: NR [UM13]

description:
UM13
NEUseq_gene_count_matrix.csv


title: 11D_M_1028


title: 11D_M_103


title: 11D_M_1029


title: R [QU50]

description:
QU50
Bloodseq_gene_count_matrix.csv


title: NR [QU49]

description:
QU49
Bloodseq_gene_count_matrix.csv


title: 11D_M_1027


title: 11D_M_1032


title: 11D_M_1026


title: R [QU46]

description:
QU46
Bloodseq_gene_count_matrix.csv


title: R [QU44]

description:
QU44
Bloodseq_gene_count_matrix.csv


title: R [QU43]

description:
QU43
Bloodseq_gene_count_matrix.csv


title: 11D_M_1024


title: 11D_M_1030


title: 11D_M_1023


title: 11D_M_1022


title: NR [QU41]

description:
QU41
Bloodseq_gene_count_matrix.csv


title: 11D_M_1025


title: NR [QU40]

description:
QU40
Bloodseq_gene_count_matrix.csv


title: 11D_M_1021


title: 11D_M_1020


title: NR [QU39]

description:
QU39
Bloodseq_gene_count_matrix.csv


title: NR [QU38]

description:
QU38
Bloodseq_gene_count_matrix.csv


title: 11D_M_102


title: NR [QU37]

description:
QU37
Bloodseq_gene_count_matrix.csv


title: 11D_M_1019


title: R [QU31]

description:
QU31
Bloodseq_gene_count_matrix.csv


title: R [QU32]

description:
QU32
Bloodseq_gene_count_matrix.csv


title: 11D_M_1013


title: 11D_M_1017


title: 11D_M_1018


title: R [QU45]

description:
QU45
Bloodseq_gene_count_matrix.csv


title: R [QU34]

description:
QU34
Bloodseq_gene_count_matrix.csv


title: R [QU30]

description:
QU30
Bloodseq_gene_count_matrix.csv


title: 11D_M_1016


title: NR [QU35]

description:
QU35
Bloodseq_gene_count_matrix.csv


title: NR [QU33]

description:
QU33
Bloodseq_gene_count_matrix.csv


title: NR [QU29]

description:
QU29
Bloodseq_gene_count_matrix.csv


title: 11D_M_1015


title: NR [QU26]

description:
QU26
Bloodseq_gene_count_matrix.csv


title: R [QU23]

description:
QU23
Bloodseq_gene_count_matrix.csv


title: R [QU24]

description:
QU24
Bloodseq_gene_count_matrix.csv


title: 11D_M_1012


title: 11D_M_1009


title: 11D_M_1007


title: R [QU25]

description:
QU25
Bloodseq_gene_count_matrix.csv


title: 11D_M_1010


title: NR [QU22]

description:
QU22
Bloodseq_gene_count_matrix.csv


title: 11D_M_1011


title: NR [QU21]

description:
QU21
Bloodseq_gene_count_matrix.csv


title: 11D_M_101


title: R [QU20]

description:
QU20
Bloodseq_gene_count_matrix.csv


title: 11D_M_1008


title: 11D_M_1006


title: 11D_M_1014


title: R [QU19]

description:
QU19
Bloodseq_gene_count_matrix.csv


title: NR [QU17]

description:
QU17
Bloodseq_gene_count_matrix.csv


title: 11D_M_1004


title: NR [QU16]

description:
QU16
Bloodseq_gene_count_matrix.csv


title: R [QU13]

description:
QU13
Bloodseq_gene_count_matrix.csv


title: 11D_M_100


title: 11D_M_1001


title: R [QU15]

description:
QU15
Bloodseq_gene_count_matrix.csv


title: NR [QU14]

description:
QU14
Bloodseq_gene_count_matrix.csv


title: 11D_M_10


title: NR [QU08]

description:
QU08
Bloodseq_gene_count_matrix.csv


title: 11D_M_1


title: 11D_M_1003


title: R [QU10]

description:
QU10
Bloodseq_gene_count_matrix.csv


title: 11D_M_1002


title: R [QU03]

description:
QU03
Bloodseq_gene_count_matrix.csv


title: R [QU04]

description:
QU04
Bloodseq_gene_count_matrix.csv


title: activated CD4+ T cells, donor 73

city: Uppsala

first: Bryndis

last: Birnir

address: Husargatan 3

department: Department of Medical Cell Biology

country: Sweden

institute: Uppsala University

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Unique gene hit counts were calculated using feature Counts from the Subread package v.1.5.2.
Supplementary files format and content: tab-delimited text files include hit counts for each Sample

source_name: CD4+ T cells

growth_protocol: isolated CD4+ T cells were maintained in RPMI 1640 glucose-free medium supplemented with 2 mM glutamine, 10% heat-inactivated dialyzed fetal bovine serum, 100 U/ml penicillin, 10 mg/ml streptomycin, and 5 μM β-mercaptoethanol in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using RNA/Protein Purification Plus Kit (Norgen Biotek, Ontario, Canada). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Strand-specific RNAseq cDNA libraries with polyA selection were generated and sequenced using Illumina HiSeq sequencing platform (12 samples, 20.8-31.1 million reads, 150 bp paired end per sample).

treatment_protocol: CD4+ T cells were activated with 3 μg/ml plate-bound anti-CD3 in the presence of 5.6 mM glucose for 66_72 h.

tag: cell type

value: CD4+ T cells

value: female

tag: treatment

value: activated

tag: time

value: 66-72 hours


title: 11D_M_1005


title: activated CD4+ T cells, donor 74

value: male


title: NR [QU01]

description:
QU01
Bloodseq_gene_count_matrix.csv


title: 5xFAD; Bace1fl/fl

city: Farmington

first: John

last: Zhou

state: CT

address: 263 Farmington Avenue, E4030

institute: University of Connecticut Health Center

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: 3 Pooled brains

extract_protocol:
Mice were intercardially perfused with ice-cold HBss w/o Mg2+/Ca2+ before brain tissue was removed.  Tissue was digested and debris removed according to the Adult Brain Dissosciation Kit (Milltenyi).  Immunomagnetic beads for ACSA2+ were used to isolate astrocyte enriched fraction, which were resuspended in cold D-PBS with 0.05% w/v BSA.
Library was performed according to the manufacter’s instructions (single cell 3’ v protocol, 10x Genomics). Briefly, astroctyes were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Astrocytes

value: 3 Pooled brains

value: 5xFAD; Bace1fl/fl

value: 14 Months


title: Bace1+/+, replicate 2

description: 10x Genomics

source_name: Whole brain

value: Whole brain


title: Bace1+/+, replicate 3

description: 10x Genomics


title: activated CD4+ T cells, donor 69


title: Bace1+/+, replicate 1

description: 10x Genomics


title: Bace1-/-, replicate 3

description: 10x Genomics


title: activated CD4+ T cells, donor 65


title: R [QU05]

description:
QU05
Bloodseq_gene_count_matrix.csv


title: Bace1-/-, replicate 2

description: 10x Genomics


title: Bace1-/-, replicate 1

description: 10x Genomics


title: 11D_M_0


title: activated CD4+ T cells, donor 56


title: Melanoma tumor RNA-seq (TIL_9)

city: Ramat Gan

first: Ettai

last: Markovits

address: 2 Derech sheba st.

country: Israel

institute: Shaba Medical Center

data_processing:
Sequenced reads were aligned to the human genome (hg38) using STAR aligner
Gene expression counts were calculated using featureCounts based on Ensembl's human gene annotations.
Only genes with at least 10 counts in at least 10% of samples were included.
Ensembl gene annotations were converted to HGNC gene symbols.
Expression levels were normalized using TMM and then voom normalization as detailed in the LIMMA pipeline
Batch correction between the TIL ACT and PD-1 blockade cohorts was performed by the removebatcheffect funcion in LIMMA
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression data matrix (raw counts and counts normalized by TMM, voom and batch corrected according to the LIMMA pipeline).

source_name: melanoma

extract_protocol:
RNeasy FFPE kit
Illumina's Ribo Zero Gold and TruSeq stranded library prep kits

tag: disease state

value: advanced melanoma

value: of pre-immunotherapy tumor biopsy

value: TIL ACT


title: Melanoma tumor RNA-seq (TIL_5)


title: Melanoma tumor RNA-seq (TIL_7)


title: ATAC_L2C_mzKO_rep2

city: Beijing

first: Fengling

last: Chen

state: Beijing

address: 30 Shuangqing Rd.

country: China

institute: Tsinghua University

data_processing:
ATAC-Seq and Stacc-seq reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
RNA-seq reads were trimmed by Trim Galore v0.6.6 then mapped to mm9 genome by HISAT2 v2.2.1(Kim et al., 2019). StringTie v2.1.2(Pertea et al., 2016) was used to calculate the FPKM per gene based on mm9 refFlat from UCSC genome annotation database.
Assembly: mm9
Supplementary files format and content: Bigwig for Stacc-seq and ATAC-Seq signals
Supplementary files format and content: gene expression FPKM table for RNA-seq data

source_name: late 2-cell mouse embryos

growth_protocol: 2i ESCs were cultured on 0.1% gelatin pre-coated dishes in DMEM medium (Gibco, 11995-065) containing leukemia-inhibiting factor (LIF) (Millipore, ESG1107), 15% fetal bovine serum (FBS; Hyclone, SH30396.03), GlutaMAX (Gibco, 35050-061), penicillin/ streptomycin (Millipore, TMS-AB2-C), nucleosides (Millipore, ES-008-D), non-essential amino acids (Gibco, 25-025-CIR), and β-mercaptoethanol (Gibco, 21985- 023). Naïve mESCs (2i) mESCs were cultured on feeder-free dishes coated with 0.1% gelatin in the N2B27 medium supplemented with 1 μM PD035901, 3 μM Chir99021, and 1 × 103 units/mL LIF. The cells were passaged 1:10-1:20.

extract_protocol:
For embryos, the zona pellucida was gently removed by treatment with Tyrode’s solution (Sigma, T1844). Then the embryos were lysed in lysis buffer containing RNase inhibitor. 2i ESCs were lysed in lysis buffer containing RNase inhibitor. The following steps followed the Smart-seq2 protocol as previously described (Picelli et al., 2014). For whole genome sequence, the tail tip DNA were extracted with isopropanol precipitation method.
The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before being subjected to sequencing. For stacc-seq, the library was prepared following the protocol as descripted before (Liu et al., 2020). For ATAC-seq,  the library was prepared following the protocol as descripted before (Buenrostro et al., 2013; Wu ET AL., 2016).
The Smart-seq2, WGS (Picelli et al., 2014) and stacc-seq (Liu et al., 2020) library strategies were followed the protocols described.

treatment_protocol: siRNAs (25 uM for each) were injected into FGOs for maternal Obox KD and zygotes for zygotic Obox KD. For stacc-seq, Obox mRNA was injected into zygotes.

value: late 2-cell mouse embryos

value: Obox mzKO


title: Melanoma tumor RNA-seq (TIL_6)


title: Melanoma tumor RNA-seq (TIL_8)


title: ATAC_L2C_Ctrl_rep2

value: wild type


title: 5xFAD; Bace1fl/fl; UBC-creER

description: 10x Genomics

value: 5xFAD; Bace1fl/fl; UBC-creER


title: RNA_mESC_Nr5a2_WT_Obox3OE_rep1

source_name: mESC

value: mESC

value: Obox3 OE


title: RNA_mESC_Nr5a2_WT_Obox5OE_rep1

value: Obox5 OE


title: RNA_mESC_Nr5a2_WT_Obox3OE_rep2


title: Melanoma tumor RNA-seq (TIL_44)


title: RNA_mESC_Nr5a2_WT_GFP_rep2

value: GFP OE


title: activated CD4+ T cells, donor 62

value: CD4+ T cells

value: male

value: activated

value: 66-72 hours


title: Melanoma tumor RNA-seq (TIL_39)


title: RNA_mESC_Nr5a2_KO_Obox3OE_rep2

value: Nr5a2 KO


title: RNA_mESC_Nr5a2_KO_GFP_rep2


title: RNA_mESC_Nr5a2_KO_Obox5OE_rep1


title: Melanoma tumor RNA-seq (TIL_40)


title: RNA_mESC_Nr5a2_WT_GFP_rep1


title: Melanoma tumor RNA-seq (TIL_36)


title: Melanoma tumor RNA-seq (TIL_35)


title: Melanoma tumor RNA-seq (TIL_38)


title: RNA_mESC_Nr5a2_KO_Obox5OE_rep2


title: RNA_mESC_Nr5a2_WT_Obox5OE_rep2


title: RNA_mESC_Nr5a2_KO_GFP_rep1


title: Melanoma tumor RNA-seq (TIL_30)


title: Melanoma tumor RNA-seq (TIL_32)


title: Melanoma tumor RNA-seq (TIL_27)


title: Melanoma tumor RNA-seq (TIL_34)


title: Melanoma tumor RNA-seq (TIL_3)


title: Stacc_Flag_L2C_Obox5OE

data_processing:
ATAC-Seq and Stacc-seq reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
RNA-seq reads were trimmed by Trim Galore v0.6.6 then mapped to mm9 genome by HISAT2 v2.2.1(Kim et al., 2019). StringTie v2.1.2(Pertea et al., 2016) was used to calculate the FPKM per gene based on mm9 refFlat from UCSC genome annotation database.
Assembly: mm9
Supplementary files format and content: Bigwig for Stacc-seq and ATAC-Seq signals
Supplementary files format and content: gene expression FPKM table for RNA-seq data
Library strategy: Stacc-seq

extract_protocol:
For embryos, the zona pellucida was gently removed by treatment with Tyrode’s solution (Sigma, T1844). Then the embryos were lysed in lysis buffer containing RNase inhibitor. 2i ESCs were lysed in lysis buffer containing RNase inhibitor. The following steps followed the Smart-seq2 protocol as previously described (Picelli et al., 2014). For whole genome sequence, the tail tip DNA were extracted with isopropanol precipitation method.
The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before being subjected to sequencing. For stacc-seq, the library was prepared following the protocol as descripted before (Liu et al., 2020). For ATAC-seq, the library was prepared following the protocol as descripted before (Buenrostro et al., 2013; Wu ET AL., 2016).
The Smart-seq2, WGS (Picelli et al., 2014) and stacc-seq (Liu et al., 2020) library strategies were followed the protocols described.

tag: antibody

value: Flag (Sigma-Aldrich, F1804)


title: RNA_mESC_Nr5a2_KO_Obox3OE_rep1


title: Melanoma tumor RNA-seq (TIL_26)

value: advanced melanoma


title: Stacc_Flag_L2C_Obox2OE

value: Obox2 OE


title: Melanoma tumor RNA-seq (TIL_29)

value: of pre-immunotherapy tumor biopsy

value: TIL ACT


title: Melanoma tumor RNA-seq (TIL_42)


title: Melanoma tumor RNA-seq (TIL_28)


title: Melanoma tumor RNA-seq (TIL_4)


title: Stacc_Flag_E2C_Obox1OE

source_name: early 2-cell mouse embryos

value: early 2-cell mouse embryos

value: Obox1 OE


title: Stacc_Flag_E2C_Obox5OE

value: wild type


title: Pol2_E2C_mzKO_rep1

value: Pol II (Active Motif, 102660)

value: Obox mzKO


title: Stacc_Flag_L2C_Obox5R98EOE

value: late 2-cell mouse embryos

value: Obox5R98E OE


title: Melanoma tumor RNA-seq (TIL_21)


title: Pol2_E2C_Ctrl_rep2


title: Pol2_E2C_Ctrl_rep1


title: Melanoma tumor RNA-seq (TIL_23)


title: Melanoma tumor RNA-seq (TIL_22)


title: Stacc_Flag_L2C_Obox3OE

value: Obox3 OE


title: RNA_WT_L2C_Obox5oe

description:
RNA_WT_L2C_Obox5oe
Obox_RNASeq_FPKM.xlsx

value: Obox5 OE


title: Pol2_1C_mzKO_rep1

source_name: zygotes

value: zygotes


title: Melanoma tumor RNA-seq (TIL_20)


title: Pol2_1C_mzKO_rep2


title: RNA_WT_L2C_Obox3oe

description:
RNA_WT_L2C_Obox3oe
Obox_RNASeq_FPKM.xlsx


title: Melanoma tumor RNA-seq (TIL_15)


title: Melanoma tumor RNA-seq (TIL_17)


title: Melanoma tumor RNA-seq (TIL_14)


title: Melanoma tumor RNA-seq (TIL_2)


title: Pol2_1C_Ctrl_rep2


title: RNA_WT_L2C_Obox1oe

description:
RNA_WT_L2C_Obox1oe
Obox_RNASeq_FPKM.xlsx


title: Melanoma tumor RNA-seq (TIL_19)


title: Melanoma tumor RNA-seq (TIL_12)


title: Melanoma tumor RNA-seq (TIL_18)


title: Melanoma tumor RNA-seq (TIL_24)


title: RNA_WT_L2C_H2O

description:
RNA_WT_L2C_H2O
Obox_RNASeq_FPKM.xlsx


title: RNA_WT_L2C_Obox2oe

description:
RNA_WT_L2C_Obox2oe
Obox_RNASeq_FPKM.xlsx


title: Melanoma tumor RNA-seq (TIL_13)


title: RNA_WT_BL_Obox2oe

description:
RNA_WT_BL_Obox2oe
Obox_RNASeq_FPKM.xlsx

source_name: blastocyst mouse embryos

value: blastocyst mouse embryos


title: Melanoma tumor RNA-seq (TIL_10)


title: RNA_WT_BL_Obox3oe

description:
RNA_WT_BL_Obox3oe
Obox_RNASeq_FPKM.xlsx


title: RNA_WT_BL_Obox5oe

description:
RNA_WT_BL_Obox5oe
Obox_RNASeq_FPKM.xlsx


title: RNA_WT_BL_H2O

description:
RNA_WT_BL_H2O
Obox_RNASeq_FPKM.xlsx


title: Pol2_1C_Ctrl_rep1


title: Melanoma tumor RNA-seq (TIL_1)


title: RNA_WT_BL_Obox1oe

description:
RNA_WT_BL_Obox1oe
Obox_RNASeq_FPKM.xlsx


title: Melanoma tumor RNA-seq (PD1_9)

value: PD-1 blockade


title: Melanoma tumor RNA-seq (PD1_6)


title: Melanoma tumor RNA-seq (PD1_51)


title: Melanoma tumor RNA-seq (PD1_47)


title: Melanoma tumor RNA-seq (PD1_50)


title: Melanoma tumor RNA-seq (PD1_8)


title: Melanoma tumor RNA-seq (PD1_7)


title: Melanoma tumor RNA-seq (PD1_43)


title: Melanoma tumor RNA-seq (PD1_4)


title: Melanoma tumor RNA-seq (PD1_41)


title: Melanoma tumor RNA-seq (PD1_53)


title: Melanoma tumor RNA-seq (PD1_38)


title: Melanoma tumor RNA-seq (TIL_11)


title: Melanoma tumor RNA-seq (PD1_5)


title: KOFAD_7

city: New York

first: Insup

last: Choi

state: NY

address: 1 Gustave L. Levy Pl

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

description:
a bulk RNAseq / NEBNext Ultra II RNA library preparation kit
gene_count_ATG7WT_5xFAD_and_ATG7CKO_5xFAD.txt

data_processing:
Pre-processing (removing reads containing adapter, reads containing ploy-N and low quality reads from raw data)
paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Assembly: mm10
Supplementary files format and content: gene counting table

source_name: Brain

extract_protocol:
After removing the cerebellum, forebrains (hemispheres) were put into RNase-free RINOTM tubes (#PINKR1-RNA, Next Advance, NY) filled with 1ml of RLT lysis buffer (RNeasy® mini kit, Qiagen) and homogenized with Bullet Blender (Next Advance). After a brief centrifuge, 100µl of homogenates were diluted into 400µl of RLT buffer. After mixing with 500µl of 70% EtOH, total RNA was isolated according to the manufacturer’s protocol (RNeasy® mini kit, Qiagen).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. The library was prepared with NEBNext Ultra II RNA library preparation kit.

value: brain (forebrain)

value: 1.5mg of tamoxifen at 2-months-old


title: Melanoma tumor RNA-seq (PD1_45)

value: advanced melanoma


title: Melanoma tumor RNA-seq (PD1_36)

value: of pre-immunotherapy tumor biopsy


title: Melanoma tumor RNA-seq (PD1_32)


title: Melanoma tumor RNA-seq (PD1_44)


title: Melanoma tumor RNA-seq (PD1_33)


title: KOFAD_3


title: Melanoma tumor RNA-seq (PD1_46)


title: WTFAD_4

value: ATG7FF; 5xFAD


title: KOFAD_4


title: KOFAD_6


title: KOFAD_5


title: Melanoma tumor RNA-seq (PD1_29)


title: KOFAD_2


title: Melanoma tumor RNA-seq (PD1_27)


title: Melanoma tumor RNA-seq (PD1_20)


title: Melanoma tumor RNA-seq (PD1_26)


title: WTFAD_2


title: Melanoma tumor RNA-seq (PD1_25)


title: Melanoma tumor RNA-seq (PD1_24)


title: WTFAD_3


title: WTFAD_6


title: Melanoma tumor RNA-seq (PD1_49)


title: Melanoma tumor RNA-seq (PD1_19)


title: WTFAD_5


title: Melanoma tumor RNA-seq (PD1_17)


title: WTFAD_1


title: SCN,ZT23,biol rep 1

city: Didcot

first: Akanksha

last: Bafna

address: Harwell Campus

country: United Kingdom

institute: MRC HARWELL

data_processing:
GALAXY RNA-SEQ ANALYSIS PIPELINE
Paired-end FASTQ files were quality assessed (Phred<20 removed) with FastQC and Illumina adapters were trimmed with TrimGalore (v0.4.3)
The reads were aligned to mm10 genome assembly using STAR (v2.7.8a) with MAPQ value for unique mappers set to 60. Binary alignment map (BAM) files were used to generate read counts per gene by  FeatureCounts via Samtools (v1.11).
Read count extraction and normalization were performed using LIMMA-VOOM Method.
limma-voom method (Liu et al., 2015) from the Bioconductor package-limma (v3.48.0) was adopted to quantify differential gene expression .
Assembly: mm10
Supplementary files format and content: tab-delimited matrix file include log CPM values for each Sample

source_name: SCN

extract_protocol:
RNA was extracted, DNase treated and purified (RNeasy, Qiagen) for four biological replicates per time-point.
500ng-1ug of total RNA underwent quality control (Nanodrop) and libraries were prepared for directional Ribodepleted-RNA Sequencing using NEBNext reagents.

value: SCN

value: WT

tag: developmental stage

value: adult


title: Melanoma tumor RNA-seq (PD1_21)


title: SCN,ZT19,biol rep 4


title: SCN,ZT23,biol rep 4


title: SCN,ZT19,biol rep 3


title: Melanoma tumor RNA-seq (PD1_16)


title: SCN,ZT23,biol rep 3


title: SCN,ZT19,biol rep 2


title: Melanoma tumor RNA-seq (PD1_14)


title: SCN,ZT19,biol rep 1


title: SCN,ZT23,biol rep 2


title: SCN,ZT15,biol rep 4


title: Melanoma tumor RNA-seq (PD1_13)


title: Melanoma tumor RNA-seq (PD1_12)


title: KOFAD_1


title: TAMs from MYC-PyMT mouse # 4

first: Xian

last: Zhang

address: 417 E 68th St

institute: MSKCC

data_processing:
FASTQ files for bulk RNA-sequencing were first mapped to the mm10 genome using HiSat2 v2.0.542.
The genomic index along with the list of splice sites and exons were created by HiSat2 using the genome assembly GRCm38.p5 from ENSEMBL.
Gene-level counts were computed using Rsubread.
Counts were normalized with DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized log2 expression for all Samples

source_name: Mammary tumor

extract_protocol:
7-week-old Control-PyMT and MYC-PyMT mice were lethally irradiated and reconstituted with 3 million total bone marrow cells from WT B6 mice, and treated with low protein diet 2 weeks after. After 6 weeks of dietary switch, mice were sacrificed and tumors were collected for immune cell isolation. TAMs (DAPI-CD45+SiglecF-Ly6G-B220-Ly6C-F4/80+Vcam+) and MTMs (DAPI-CD45+SiglecF-Ly6G-B220-Ly6C-F4/80+Vcam-FOLR2+)14 were sorted based on their surface markers, directly into TRIZOL LS reagents. RNA was extracted using the RNeasy Mini Kit (QIAGEN catalog # 74104) according to instructions provided by the manufacturer. RNA was eluted in 30 µL nuclease-free water.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA with RIN values of 3.3-9.6 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102) with 8 cycles of PCR.

value: Mammary tumor

value: backcrossed to B6

value: TAMs

tag: Sex

value: female

value: S100a8-creRosa26-LSL-MYCPyMT reconstituted with WT BM

value: Low protein diet


title: MTMs from MYC-PyMT mouse # 2

value: MTMs


title: Melanoma tumor RNA-seq (PD1_11)


title: Melanoma tumor RNA-seq (PD1_10)


title: MTMs from MYC-PyMT mouse # 4


title: SCN,ZT15,biol rep 3


title: SCN,ZT11,biol rep 3


title: Melanoma tumor RNA-seq (PD1_1)


title: SCN,ZT15,biol rep 1


title: TAMs from MYC-PyMT mouse # 2


title: MTMs from control-PyMT mouse #3

value: PyMT reconstituted with WT BM


title: MTMs from control-PyMT mouse #5


title: TAMs from control-PyMT mouse #3


title: SCN,ZT11,biol rep 1


title: TAMs from MYC-PyMT mouse # 6


title: SCN,ZT11,biol rep 4


title: SCN,ZT7,biol rep 3


title: SCN,ZT7,biol rep 4


title: MTMs from control-PyMT mouse #1


title: MYC-PyMT replicate 1

data_processing:
FASTQ files for bulk RNA-sequencing were first mapped to the mm10 genome using HiSat2 v2.0.542.
The genomic index along with the list of splice sites and exons were created by HiSat2 using the genome assembly GRCm38.p5 from ENSEMBL.
Gene-level counts were computed using Rsubread.
Counts were normalized with DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized expression for all Samples

growth_protocol: Mouse mammary tumor

extract_protocol:
Tumor tissue was homogenized in liquid nitrogen and RNA isolated in TRIZOL. RNA was extracted using the RNeasy Mini Kit (QIAGEN catalog # 74104) according to instructions provided by the manufacturer.
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 500 ng of total RNA with RIN values of 3.3-9.6 underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA LT Kit, catalog # RS-122-2102) with 8 cycles of PCR.


title: Control-PyMT replicate 2

value: PyMT


title: TAMs from control-PyMT mouse #1


title: SCN,ZT15,biol rep 2


title: SCN,ZT3,biol rep 4


title: SCN,ZT7,biol rep 1


title: MYC-PyMT replicate 2


title: Control-PyMT replicate 1


title: SCN,ZT3,biol rep 2


title: TAMs from control-PyMT mouse #5


title: SCN,ZT3,biol rep 3


title: IMR32_B 2

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

data_processing:
RNASeq data was processed using kallisto (version 0.45.0) and human genome GRCh38 Ensembl version 94 annotation (Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.gtf). Gene-level TPM values and gene annotations were computed using tximport and biomaRt R package. A custom python script was used to organize the data and log reduced using log2(TPM) if TPM > 1 and TPM - 1 if TPM <= 1.
Assembly: Genome assembly: GRCh38.p12, Gene annotatiopn: Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.gtf
Supplementary files format and content: Tab-delimited text files report expression levels for each gene in each sample. Gene-expression levels are reported either as log2(TPM) values (when TPM>1), or as (TPM-1) values (when TPM=1 or TPM<1).

growth_protocol: Neuroblastoma cells were seeded at 60-70% confluence and allowed to attach for 24 hours, with four plates per cell line. Cells in two plates for each cell line were treated with 5μM 13-cis-retinoic acid for 48 hours, while other plates were left untreated.

extract_protocol:
Cells were lysed in the plates using Qiagen lysis buffer (Qiagen, Valencia, CA), and cell lysates from individual plates were homogenized separately using QIAshredder (Qiagen). Total cellular RNA was harvested from each lysate separately using the Qiagen mini RNeasy kit (Qiagen), following the manufacturer’s instructions. RNA sample quality was confirmed using a NanoDrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE) and Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA). A double-stranded DNA library was created using the Illumina TruSeq RNA library preparation protocol. 250ng of total RNA, quantitated by picogreen, was used for each sample. cDNA was created using the fragmented 3’ poly (A) selected portion of total RNA and random primers. Libraries were created from the cDNA by first blunt ending the fragments, attaching an adenosine to the 3’ end and finally ligating unique adapters to the ends. The ligated products were then amplified using 15 cycles of PCR. The resulting libraries were quantitated using the NanoDrop spectrophotometer and fragment size assessed with the Agilent 2100 Bioanalyzer. A qPCR assay was performed on the libraries to determine the concentration of adapter ligated fragments using the Applied Biosystems ViiA 7 Quantitative PCR instrument and a KAPA Library Quant Kit. All samples were pooled equimolar and re-quantitated by qPCR, and re-assessed on the Bioanalyzer.
Using the pooled concentration from the qPCR assay, the library pool was loaded onto each of two high output mode lanes at a concentration of 15pM, for cluster generation on the cBot and sequencing on the HiSeq 2500 (Illumina, San Diego, CA) at a read length of 100bp, using paired-end v3 chemistry.

value: C

tag: cell line


title: SCN,ZT3,biol rep 1


title: IMR32_B 1

treatment_protocol: Cells in two plates for each cell line were treated with 5μM 13-cis-retinoic acid for 48 hours, while other plates were left untreated.


title: SCN, INPUT, ZT23, biol rep 1

data_processing:
Paired-end FASTQ files were quality assessed by removing low quality bases (Phred<20) and trimmed using FastQc and Trimmomatic (v0.36), respectively.
FASTQ files containing trimmed sequences were then aligned to mm10 genome assembly to generate binary alignment map (BAM) files with Bowtie2 (v2.3.4.1).
Aligned files were filtered for minimum mapping quality (MAPQ)>20 by SAMtools (v1.8), and used for peak calling by MACS2(v 2.1.1.20160309) with the options –qvalue 0.05 –gsize mm:1.87e9 –format BAMPE.
bigWig files were generated using the bamCoverage (deepTools2). narrowPeak files were generated using MACS2  with above specified settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
Chromatin immunoprecipitation (ChIP) was conducted by Diagenode ChIP-seq/ChIP-qPCR Profiling service (Diagenode Cat# G02010000). Briefly, the chromatin was prepared using the True MicroChIP Kit (Diagenode Cat# C01010130). Samples were fixed with 1% FA for 8 min. Chromatin was sheared using Bioruptor® Pico sonication device (Diagenode Cat# B01060001) combined with the Bioruptor® Water cooler for 7 cycles using a 30’’ [ON] 30’’ [OFF] settings. Then, shearing was performed in 0.65 ml Bioruptor® Pico Microtubes (Diagenode Cat# C30010011).
500 ng of chromatin were immune-precipitated using 1 µg of each of the following Diagenode antibodies H3K4me3 (C15410003; Lot Nr. A1051D), H3K27ac (C15410196; Lot Nr. A1723-0041D) and Rabbit IgG (C15410206; Lot Nr. RIG001). Chromatin corresponding to 1% was set apart as Input.
H3K4me3 and H3K27ac immune-precipitated genomic DNA along with their corresponding input samples was sent to Oxford Genomics Centre, University of Oxford for library preparation and paired-end sequencing on NovaSeq6000 platform (Illumina).

tag: chip antibody


title: IMR32_A 2


title: IMR32_A 1


title: SCN, INPUT, ZT23, biol rep 2


title: IMR32+CRA_B 2

value: RA


title: SCN, INPUT, ZT19, biol rep 1


title: SCN, INPUT, ZT11, biol rep 1


title: SCN, INPUT, ZT11, biol rep 2


title: SCN,ZT7,biol rep 2


title: IMR32+CRA_A 1


title: IMR32+CRA_A 2


title: IMR32+CRA_B 1


title: SCN, INPUT, ZT7, biol rep 2


title: H3K27ac, SCN, ZT23, biol rep 1

value: H3K4me3(Diagenode #C15410196)


title: control pUC19, lambda phage, and T4-phage, no_TET_BS

city: Philadelphia

first: Rahul

middle: M.

last: Kohli

state: Pennsylvania

address: 3610 Hamilton Walk, 502B Johnson Pavilion

department: Department of Medicine

institute: University of Pennsylvania

data_processing:
For all workflows, reads were quality and length trimmed with Trim Galore! Reads were aligned with Bismark and deduplicated with Picard. All data was analyzed single-end. DM-Seq reads were filtered if 3 consecutive CpHs were non-converted using Bismark’s existing filter_non_conversion command. Only reads with MAPQ ≥ 30 were analyzed.
Assembly: pUC19, lambda phage ViralProj14204, T4 phage ViralProj14044
Supplementary files format and content: For control DNA samples where read level information for each control genome was analyzed, aligned files (.bam) are provided, not deduplicated and not filtered. The .bam format makes the number of reads mapping to each genome as well as data reporting percent modification accessible.

organism:
Cloning vector pUC19
Escherichia phage T4
Escherichia phage Lambda

extract_protocol:
In vitro derived controls for all other samples.
1 ng of sheared DNA input (consisting of fully unmodified C pUC19 DNA, fully 5mCpG modified Lambda control gDNA, and fully 5hmC-modified T4 phage gDNA) was used for each condition. DNA was added to a 20 μL reaction containing 1x NEB CutSmart buffer (50 mM Potassium Acetate 20 mM Tris-acetate, 10 mM Magnesium Acetate, and 100 μg/ml BSA), 0.04 nM UDP-glucose, and 10 U T4-βGT. The glucosylated DNA was then purified with SPRI magnetic beads (Beckman-Coulter) using a 1.2x left-sided selection. The purified DNA was then in a 50 μL reaction containing 1x NEB EM-Seq TET buffer (50 mM Tris pH 8.0, 1 mM DTT, 5 mM sodium-L-ascorbate, 20 mM αKG, 2 mM ATP, and 50 mM ammonium iron (II) sulfate hexahydrate) and 16 μg TET2 (NEB). The reaction was then incubated at 37°C for 80 min. Following oxidation, 0.8 U of Proteinase K (NEB) was added and the mixture was incubated for 30 min at 37°C. The oxidized DNA was then purified with SPRI magnetic beads (Beckman-Coulter) using a 1.2x left-sided selection. The no TET control was carried through mock oxidation reactions without TET enzyme. The DNA was then purified with SPRI magnetic beads (Beckman-Coulter) using a 1.2x left-sided selection. The purified oxidized sample was then end-prepped and ligated with the same protocol as above except for the adapters used, which was different for each method (no deamination, TAPS, TAPS-β: C adapters, BS-Seq: 5mC adapters, DM-Seq: 5pyC adapters). BS deamination, A3A deamination, pyridine borane deamination, or a no deamination control were then performed.

tag: sample type

value: no TET


title: control pUC19, lambda phage, and T4-phage, TET_BS

value: TET


title: H3K27ac, SCN, ZT19, biol rep 2

value: SCN


title: SKNAS_B 2

source_name: SKNAS

value: SKNAS


title: SCN, INPUT, ZT19, biol rep 2


title: H3K27ac, SCN, ZT19, biol rep 1


title: SCN, INPUT, ZT7, biol rep 1


title: SKNAS_B 1


title: SCN,ZT11,biol rep 2

value: WT

value: adult


title: H3K27ac, SCN, ZT23, biol rep 2


title: SKNAS_A 1


title: Pol2_E2C_mzKO_rep2

value: early 2-cell mouse embryos

value: Pol II (Active Motif, 102660)

value: Obox mzKO


title: control pUC19, lambda phage, and T4-phage, TET_A3A

data_processing:
For all workflows, reads were quality and length trimmed with Trim Galore! Reads were aligned with Bismark and deduplicated with Picard. All data was analyzed single-end. DM-Seq reads were filtered if 3 consecutive CpHs were non-converted using Bismark’s existing filter_non_conversion command. Only reads with MAPQ ≥ 30 were analyzed.
Assembly: pUC19, lambda phage ViralProj14204, T4 phage ViralProj14044
Supplementary files format and content: For control DNA samples where read level information for each control genome was analyzed, aligned files (.bam) are provided, not deduplicated and not filtered. The .bam format makes the number of reads mapping to each genome as well as data reporting percent modification accessible.
Library strategy: A3A


title: SKNAS+CRA_B 2


title: control pUC19, lambda phage, and T4-phage, TET_borane

data_processing:
For all workflows, reads were quality and length trimmed with Trim Galore! Reads were aligned with Bismark and deduplicated with Picard. All data was analyzed single-end. DM-Seq reads were filtered if 3 consecutive CpHs were non-converted using Bismark’s existing filter_non_conversion command. Only reads with MAPQ ≥ 30 were analyzed.
Assembly: pUC19, lambda phage ViralProj14204, T4 phage ViralProj14044
Supplementary files format and content: For control DNA samples where read level information for each control genome was analyzed, aligned files (.bam) are provided, not deduplicated and not filtered. The .bam format makes the number of reads mapping to each genome as well as data reporting percent modification accessible.
Library strategy: pyridine borane


title: H3K27ac, SCN, ZT7, biol rep 1


title: H3K27ac, SCN, ZT11, biol rep 2


title: H3K27ac, SCN, ZT11, biol rep 1


title: SKNAS_A 2


title: H3K4me3, SCN, ZT19, biol rep 2

value: H3K4me3(Diagenode #C15410003)


title: H3K4me3, SCN, ZT23, biol rep 1


title: SKNAS+CRA_A 2


title: H3K4me3, SCN, ZT19, biol rep 1


title: SKNSH_B 2

source_name: SKNSH

value: SKNSH


title: H3K4me3, SCN, ZT11, biol rep 2


title: H3K4me3, SCN, ZT11, biol rep 1


title: SKNAS+CRA_A 1


title: SKNAS+CRA_B 1


title: control pUC19, lambda phage, and T4-phage, no_TET_borane


title: control pUC19, lambda phage, and T4-phage, no_TET_no_deam

data_processing:
For all workflows, reads were quality and length trimmed with Trim Galore! Reads were aligned with Bismark and deduplicated with Picard. All data was analyzed single-end. DM-Seq reads were filtered if 3 consecutive CpHs were non-converted using Bismark’s existing filter_non_conversion command. Only reads with MAPQ ≥ 30 were analyzed.
Assembly: pUC19, lambda phage ViralProj14204, T4 phage ViralProj14044
Supplementary files format and content: For control DNA samples where read level information for each control genome was analyzed, aligned files (.bam) are provided, not deduplicated and not filtered. The .bam format makes the number of reads mapping to each genome as well as data reporting percent modification accessible.
Library strategy: no deamination


title: H3K27ac, CORTEX, ZT15, biol rep 2

source_name: CORTEX

value: CORTEX

value: H3K27ac (Diagenode #C15410196)


title: H3K4me3, SCN, ZT23, biol rep 2


title: control pUC19, lambda phage, and T4-phage, no_TET_A3A


title: H3K27ac, SCN, ZT7, biol rep 2


title: H3K4me3, SCN, ZT7, biol rep 1


title: SKNSH_B 1


title: control pUC19, lambda phage, and T4-phage, TET_no_deam


title: H3K27ac, CORTEX, ZT15, biol rep 1


title: SKNSH_A 2


title: control pUC19, lambda phage, and T4-phage, 100_mGpC_TAPSb

data_processing:
For all workflows, reads were quality and length trimmed with Trim Galore! Reads were aligned with Bismark and deduplicated with Picard. All data was analyzed single-end. DM-Seq reads were filtered if 3 consecutive CpHs were non-converted using Bismark’s existing filter_non_conversion command. Only reads with MAPQ ≥ 30 were analyzed.
Assembly: pUC19, lambda phage ViralProj14204, T4 phage ViralProj14044
Supplementary files format and content: For control DNA samples that were GpC methylated, tab-delimited text files (.txt) include genomic coordinates (chr, start, and end) and deamination (BS-Seq, DM-Seq, TAPS, TAPS-β) analysis (signal [C/(C+T)], sequencing coverage, and strand) of all annotated CpG sites in control genomes. They additionally have the +1 and +2 base identity.
Supplementary files format and content: For control DNA samples where read level information for each control genome was analyzed, aligned files (.bam) are provided, not deduplicated and not filtered. The .bam format makes the number of reads mapping to each genome as well as data reporting percent modification accessible.
Library strategy: TAPS-beta

extract_protocol:
In vitro derived controls for all other samples.
To compare 5 different sequencing workflows (no deamination, TAPS, TAPS-β, BS-Seq, DM-Seq), 1 ng of sheared DNA input (consisting of fully unmodified C pUC19 DNA, 5mCpG modified Lambda control gDNA, and fully 5hmC-modified T4 phage gDNA) was used for each condition. The 5mCpG modified lambda control gDNA was one of 4 possibilities: fully unmethylated, fully CpG-methylated, fully GpC-methylated, and ~50% CpG-methylated. The ~50% CpG methylated DNA was made by mixing equal amounts of unmethylated and fully CpG-methylated lambda DNA. DNA was end-prepped and ligated with the same protocol as above except for the adapters used, which was different for each method (no deamination, TAPS, and TAPS-β: C adapters, BS-Seq: 5mC adapters, DM-Seq: 5pyC adapters).
BS-Seq was performed using manufacturer instructions (Diagenode). Purified BS-Seq libraries were amplified using indexing primers (IDT) and HiFi HotStart Uracil+ Ready Mix (KAPA Biosystems) before purification over SPRI magnetic beads (0.8X) and ultimate characterization using a BioAnalyzer (High Sensitivity Kit, Agilent) and quantified (Qubit).
DM-Seq was performed with the optimized protocol. A methylated copy strand was created. 1 μM fully-methylated copy primer was annealed in a total volume of 10 μL in CutSmart Buffer and 1 mM final concentration (individually) of dATP/dGTP/dTTP (Promega) and dmCTP (NEB). 1 μl or 8 units Bst polymerase, large fragment (NEB) was added and incubated for 30 min at 65°C. The 5hmCs were then glucosylated with 40 μM UDP-Glucose and 1 μL or 10 units of T4 Phage β-glucosyltransferase (NEB) for 1 hour at 37°C in a final volume of 20 μL. Incompletely copied or uncopied fragments were degraded with 1 μL or 10 units Mung Bean Nuclease (NEB) for 30 min at 30°C. After SPRI magnetic bead purification (1.2x), libraries were mixed with 0.5 μM MBP-M.MpeI-N374K and 160 μM CxSAM in carboxymethylation buffer (50 mM NaCl, 10 mM Tris-HCl pH 7.9, 10 mM EDTA) and incubated overnight at 37°C followed by  denaturation for 5 min at 95°C. 1 μL or 0.8 units of Proteinase K (NEB) was subsequently added and incubated at 37°C for 15 min. The samples were purified using SPRI magnetic beads (1.2x) and eluted in 1 mM Tris-Cl, pH 8.0. DNA was then subjected to snap-cooling and A3A deamination in a final volume of 50 μL as previously described before SPRI magnetic beads purification (1.2x). DM-Seq libraries were amplified using indexing primers (IDT) and HiFi HotStart Uracil+ Ready Mix (KAPA Biosystems) before purification over SPRI magnetic beads (0.8X). Libraries were then characterized using a BioAnalyzer (High Sensitivity Kit, Agilent) and quantified (Qubit).
TAPS and TAPS-β were performed as previously described except for the source of TET enzyme (NEB, EM-Seq Conversion Module). 1 ng of sheared DNA input (consisting of fully unmodified C pUC19 DNA, 5mCpG-modified lambda phage gDNA, and fully 5hmC-modified T4 phage gDNA) was ligated to C-containing Y-shaped adaptors using the same protocol as described above (IDT). For TAPS-β, the ligated DNA was added to a 20 μL reaction containing 1x NEB CutSmart buffer (50 mM Potassium Acetate 20 mM Tris-acetate, 10 mM Magnesium Acetate, and 100 μg/ml BSA), 0.04 nM UDP glucose, and 10 U T4-βGT. The glucosylated DNA was then purified with SPRI magnetic beads (Beckman-Coulter) using a 1.2x left-sided selection. This glucosylation step was omitted for TAPS. The purified DNA was then incubated in a 50 μL reaction containing 1x NEB EM-Seq TET buffer (50 mM Tris pH 8.0, 1 mM DTT, 5 mM sodium-L-ascorbate, 20 mM αKG, 2 mM ATP, and 50 mM ammonium iron (II) sulfate hexahydrate) and 16 μg TET2 (NEB). The reaction was then incubated at 37°C for 80 min. Following oxidation, 0.8 U of Proteinase K (NEB) was added, and the mixture was incubated for 30 min at 37°C. The oxidized DNA was then purified with SPRI magnetic beads (Beckman-Coulter) using a 1.2x left-sided selection and input into a second round of TET oxidation. The oxidized DNA was added to a 5 μL reaction containing 600 mM sodium acetate (pH 4.3) and 1 M pyridine borane (Alfa Aesar). The reaction was incubated at 37 °C and 850 r.p.m. in a ThermoMixer (Eppendorf) placed in a chemical fume hood for 16 hrs and purified by Zymo-IC column (Zymo Research) with Oligo Binding Buffer (Zymo Research). The TAPS-β libraries were amplified using indexing primers (NEB) and HiFi Hotstart Uracil+ Ready Mix (KAPA Biosystems) before purification with SPRI magnetic beads (Beckman-Coulter) using a 1.2x left-sided selection. Libraries were ultimately characterized using a BioAnalyzer (High Sensitivity Kit, Agilent) and quantified (Qubit).

value: 100% GpC methylated


title: H3K27ac, SCN, ZT15, biol rep 2


title: H3K27ac, SCN, ZT15, biol rep 1


title: control pUC19, lambda phage, and T4-phage, 100_mGpC_TAPS

data_processing:
For all workflows, reads were quality and length trimmed with Trim Galore! Reads were aligned with Bismark and deduplicated with Picard. All data was analyzed single-end. DM-Seq reads were filtered if 3 consecutive CpHs were non-converted using Bismark’s existing filter_non_conversion command. Only reads with MAPQ ≥ 30 were analyzed.
Assembly: pUC19, lambda phage ViralProj14204, T4 phage ViralProj14044
Supplementary files format and content: For control DNA samples that were GpC methylated, tab-delimited text files (.txt) include genomic coordinates (chr, start, and end) and deamination (BS-Seq, DM-Seq, TAPS, TAPS-β) analysis (signal [C/(C+T)], sequencing coverage, and strand) of all annotated CpG sites in control genomes. They additionally have the +1 and +2 base identity.
Supplementary files format and content: For control DNA samples where read level information for each control genome was analyzed, aligned files (.bam) are provided, not deduplicated and not filtered. The .bam format makes the number of reads mapping to each genome as well as data reporting percent modification accessible.
Library strategy: TAPS


title: control pUC19, lambda phage, and T4-phage, 100_mGpC_DM

data_processing:
For all workflows, reads were quality and length trimmed with Trim Galore! Reads were aligned with Bismark and deduplicated with Picard. All data was analyzed single-end. DM-Seq reads were filtered if 3 consecutive CpHs were non-converted using Bismark’s existing filter_non_conversion command. Only reads with MAPQ ≥ 30 were analyzed.
Assembly: pUC19, lambda phage ViralProj14204, T4 phage ViralProj14044
Supplementary files format and content: For control DNA samples that were GpC methylated, tab-delimited text files (.txt) include genomic coordinates (chr, start, and end) and deamination (BS-Seq, DM-Seq, TAPS, TAPS-β) analysis (signal [C/(C+T)], sequencing coverage, and strand) of all annotated CpG sites in control genomes. They additionally have the +1 and +2 base identity.
Supplementary files format and content: For control DNA samples where read level information for each control genome was analyzed, aligned files (.bam) are provided, not deduplicated and not filtered. The .bam format makes the number of reads mapping to each genome as well as data reporting percent modification accessible.
Library strategy: DM-Seq


title: CORTEX, INPUT, ZT15, biol rep 2


title: SKNSH_A 1

value: C


title: CORTEX, INPUT, ZT15, biol rep 1


title: H3K4me3, SCN, ZT7, biol rep 2


title: control pUC19, lambda phage, and T4-phage, 100_mGpC_BS

data_processing:
For all workflows, reads were quality and length trimmed with Trim Galore! Reads were aligned with Bismark and deduplicated with Picard. All data was analyzed single-end. DM-Seq reads were filtered if 3 consecutive CpHs were non-converted using Bismark’s existing filter_non_conversion command. Only reads with MAPQ ≥ 30 were analyzed.
Assembly: pUC19, lambda phage ViralProj14204, T4 phage ViralProj14044
Supplementary files format and content: For control DNA samples that were GpC methylated, tab-delimited text files (.txt) include genomic coordinates (chr, start, and end) and deamination (BS-Seq, DM-Seq, TAPS, TAPS-β) analysis (signal [C/(C+T)], sequencing coverage, and strand) of all annotated CpG sites in control genomes. They additionally have the +1 and +2 base identity.
Supplementary files format and content: For control DNA samples where read level information for each control genome was analyzed, aligned files (.bam) are provided, not deduplicated and not filtered. The .bam format makes the number of reads mapping to each genome as well as data reporting percent modification accessible.


title: SCN, INPUT, ZT15, biol rep 2


title: SKNSH+CRA_B 2

value: RA


title: control pUC19, lambda phage, and T4-phage, 100_mCpG_TAPSb

value: 100% CpG methylated


title: H3K4me3, CORTEX, ZT15, biol rep 2


title: SKNSH+CRA_B 1


title: H3K4me3, CORTEX, ZT15, biol rep 1


title: SCN, INPUT, ZT15, biol rep 1


title: control pUC19, lambda phage, and T4-phage, 100_mCpG_TAPS


title: SKNSH+CRA_A 2


title: H3K4me3, SCN, ZT15, biol rep 2


title: H3K4me3, SCN, ZT15, biol rep 1


title: control pUC19, lambda phage, and T4-phage, 100_mCpG_DM


title: H3K27ac, CORTEX, ZT3, biol rep 1


title: H3K27ac, CORTEX, ZT3, biol rep 2


title: control pUC19, lambda phage, and T4-phage, 100_mCpG_BS


title: control pUC19, lambda phage, and T4-phage, 100_mCpG_no_deam

data_processing:
For all workflows, reads were quality and length trimmed with Trim Galore! Reads were aligned with Bismark and deduplicated with Picard. All data was analyzed single-end. DM-Seq reads were filtered if 3 consecutive CpHs were non-converted using Bismark’s existing filter_non_conversion command. Only reads with MAPQ ≥ 30 were analyzed.
Assembly: pUC19, lambda phage ViralProj14204, T4 phage ViralProj14044
Supplementary files format and content: For control DNA samples that were GpC methylated, tab-delimited text files (.txt) include genomic coordinates (chr, start, and end) and deamination (BS-Seq, DM-Seq, TAPS, TAPS-β) analysis (signal [C/(C+T)], sequencing coverage, and strand) of all annotated CpG sites in control genomes. They additionally have the +1 and +2 base identity.
Supplementary files format and content: For control DNA samples where read level information for each control genome was analyzed, aligned files (.bam) are provided, not deduplicated and not filtered. The .bam format makes the number of reads mapping to each genome as well as data reporting percent modification accessible.
Library strategy: no deamination


title: H3K27ac, SCN, ZT3, biol rep 2


title: SKNBE2_B 2


title: H3K27ac, SCN, ZT3, biol rep 1


title: CORTEX, INPUT, ZT3, biol rep 2


title: SKNBE2_B 1


title: CORTEX, INPUT, ZT3, biol rep 1


title: SCN, INPUT, ZT3, biol rep 2


title: control pUC19, lambda phage, and T4-phage, 50_mCpG_TAPSb

value: 50% CpG methylated


title: SCN, INPUT, ZT3, biol rep 1


title: SKNSH+CRA_A 1


title: SKNBE2_A 1


title: control pUC19, lambda phage, and T4-phage, 50_mCpG_TAPS


title: H3K4me3, CORTEX, ZT3, biol rep 2


title: SKNBE2_A 2


title: H3K4me3, CORTEX, ZT3, biol rep 1


title: control pUC19, lambda phage, and T4-phage, 50_mCpG_DM


title: H3K4me3, SCN, ZT3, biol rep 2


title: SKNBE2+CRA_B 2


title: control pUC19, lambda phage, and T4-phage, 50_mCpG_BS


title: WGS_homo_mouse3

data_processing:
ATAC-Seq and Stacc-seq reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
RNA-seq reads were trimmed by Trim Galore v0.6.6 then mapped to mm9 genome by HISAT2 v2.2.1(Kim et al., 2019). StringTie v2.1.2(Pertea et al., 2016) was used to calculate the FPKM per gene based on mm9 refFlat from UCSC genome annotation database.
Assembly: mm9
Supplementary files format and content: Bigwig for Stacc-seq and ATAC-Seq signals
Supplementary files format and content: gene expression FPKM table for RNA-seq data
Library strategy: WGS

source_name: mouse tail tip

value: mouse tail tip

value: Obox KO


title: WGS_homo_mouse2


title: control pUC19, lambda phage, and T4-phage, 50_mCpG_no_deam


title: SKNBE2+CRA_A 2


title: WGS_WT

value: wild type


title: WGS_homo_mouse1


title: control pUC19, lambda phage, and T4-phage, 0_TAPSb

value: unmethylated


title: Stacc_Flag_L2C_Obox1OE

data_processing:
ATAC-Seq and Stacc-seq reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
RNA-seq reads were trimmed by Trim Galore v0.6.6 then mapped to mm9 genome by HISAT2 v2.2.1(Kim et al., 2019). StringTie v2.1.2(Pertea et al., 2016) was used to calculate the FPKM per gene based on mm9 refFlat from UCSC genome annotation database.
Assembly: mm9
Supplementary files format and content: Bigwig for Stacc-seq and ATAC-Seq signals
Supplementary files format and content: gene expression FPKM table for RNA-seq data
Library strategy: Stacc-seq

value: late 2-cell mouse embryos

value: Flag (Sigma-Aldrich, F1804)

value: Obox1 OE


title: SKNBE2+CRA_A 1


title: P134_RA3


title: Pol2_L2C_mzKO_rep1

value: Pol II (Active Motif, 102660)

value: Obox mzKO


title: Pol2_L2C_mzKO_rep2


title: Stacc_Flag_L2C_NT


title: control pUC19, lambda phage, and T4-phage, 0_TAPS


title: control pUC19, lambda phage, and T4-phage, 0_DM


title: P134_RA2


title: Pol2_L2C_Ctrl_rep2


title: P134_RA1


title: Pol2_L2C_Ctrl_rep1


title: ATAC_L2C_Ctrl_rep1

data_processing:
ATAC-Seq and Stacc-seq reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
RNA-seq reads were trimmed by Trim Galore v0.6.6 then mapped to mm9 genome by HISAT2 v2.2.1(Kim et al., 2019). StringTie v2.1.2(Pertea et al., 2016) was used to calculate the FPKM per gene based on mm9 refFlat from UCSC genome annotation database.
Assembly: mm9
Supplementary files format and content: Bigwig for Stacc-seq and ATAC-Seq signals
Supplementary files format and content: gene expression FPKM table for RNA-seq data


title: control pUC19, lambda phage, and T4-phage, 0_no_deam


title: control pUC19, lambda phage, and T4-phage, 0_BS


title: H3K4me3, SCN, ZT3, biol rep 1

value: SCN

value: H3K4me3(Diagenode #C15410003)


title: SKNBE2+CRA_B 1


title: ATAC_L2C_mzKO_rep1


title: RNA_mESC_Obox5oe_rep4

description:
mESC_Obox5oe_rep4
Obox_RNASeq_FPKM.xlsx

value: mESC

value: Obox5 OE


title: P134_C3

value: C


title: RNA_mESC_Obox5oe_rep2

description:
mESC_Obox5oe_rep2
Obox_RNASeq_FPKM.xlsx


title: RNA_mESC_Obox5oe_rep3

description:
mESC_Obox5oe_rep3
Obox_RNASeq_FPKM.xlsx


title: RNA_mESC_Obox5oe_rep1

description:
mESC_Obox5oe_rep1
Obox_RNASeq_FPKM.xlsx


title: RNA_mESC_Obox3oe_rep4

description:
mESC_Obox3oe_rep4
Obox_RNASeq_FPKM.xlsx

value: Obox3 OE


title: control lambda phage, mGpC_DM

data_processing:
For all workflows, reads were quality and length trimmed with Trim Galore! Reads were aligned with Bismark and deduplicated with Picard. All data was analyzed single-end. DM-Seq reads were filtered if 3 consecutive CpHs were non-converted using Bismark’s existing filter_non_conversion command. Only reads with MAPQ ≥ 30 were analyzed.
Assembly: lambda phage ViralProj14204
Supplementary files format and content: Tab-delimited text files (.txt) include genomic coordinates (chr, start, and end) and deamination (BS-Seq, DM-Seq) analysis (signal [C/(C+T)], sequencing coverage, and strand) of all annotated CpG sites in control genomes. They additionally have the +1 and +2 base identity.
Library strategy: DM-Seq

organism: Escherichia phage Lambda

source_name: control lambda phage

extract_protocol:
In vitro derived controls for all other samples.
Lambda gDNA was either unmethylated, CpG methylated, or GpC methylated.
10 ng of sheared lambda gDNA ligated to 5pyC-containing adapters was used as input for DM-Seq when only comparing to BS-Seq. A methylated copy strand was created. 1 μM fully-methylated copy primer was annealed in a total volume of 10 μL in CutSmart Buffer and 1 mM final concentration (individually) of dATP/dGTP/dTTP (Promega) and dmCTP (NEB). 1 μl or 8 units Bst polymerase, large fragment (NEB) was added and incubated for 30 min at 65°C. The 5hmCs were then glucosylated with 40 μM UDP-Glucose and 1 μL or 10 units of T4 Phage β-glucosyltransferase (NEB) for 1 hour at 37°C in a final volume of 20 μL. Incompletely copied or uncopied fragments were degraded with 1 μL or 10 units Mung Bean Nuclease (NEB) for 30 min at 30°C. After SPRI magnetic bead purification (1.2x), libraries were mixed with 0.5 μM MBP-M.MpeI-N374K and 160 μM CxSAM in carboxymethylation buffer (50 mM NaCl, 10 mM Tris-HCl pH 7.9, 10 mM EDTA) and incubated overnight at 37°C followed by  denaturation for 5 min at 95°C. 1 μL or 0.8 units of Proteinase K (NEB) was subsequently added and incubated at 37°C for 15 min. The samples were purified using SPRI magnetic beads (1.2x) and eluted in 1 mM Tris-Cl, pH 8.0. DNA was then subjected to snap-cooling and A3A deamination in a final volume of 50 μL as previously described before SPRI magnetic beads purification (1.2x). DM-Seq libraries were amplified using indexing primers (IDT) and HiFi HotStart Uracil+ Ready Mix (KAPA Biosystems) before purification over SPRI magnetic beads (0.8X). Libraries were then characterized using a BioAnalyzer (High Sensitivity Kit, Agilent) and quantified (Qubit).
BS-Seq was performed on 10 ng of sheared lambda gDNA ligated to 5mC-containing adapters (xGen, IDT), when only comparing to DM-Seq, with no added copy or DM-Seq specific steps, using manufacturer instructions (Diagenode). Purified BS-Seq libraries were amplified using indexing primers (IDT) and HiFi HotStart Uracil+ Ready Mix (KAPA Biosystems) before purification over SPRI magnetic beads (0.8X) and ultimate characterization using a BioAnalyzer (High Sensitivity Kit, Agilent) and quantified (Qubit).

value: control lambda phage

value: GpC Methylated


title: P134_C2


title: control lambda phage, mCpG_DM

value: CpG Methylated


title: control lambda phage, mGpC_BS

data_processing:
For all workflows, reads were quality and length trimmed with Trim Galore! Reads were aligned with Bismark and deduplicated with Picard. All data was analyzed single-end. DM-Seq reads were filtered if 3 consecutive CpHs were non-converted using Bismark’s existing filter_non_conversion command. Only reads with MAPQ ≥ 30 were analyzed.
Assembly: lambda phage ViralProj14204
Supplementary files format and content: Tab-delimited text files (.txt) include genomic coordinates (chr, start, and end) and deamination (BS-Seq, DM-Seq) analysis (signal [C/(C+T)], sequencing coverage, and strand) of all annotated CpG sites in control genomes. They additionally have the +1 and +2 base identity.


title: P134_C1


title: RNA_mESC_Obox3oe_rep2

description:
mESC_Obox3oe_rep2
Obox_RNASeq_FPKM.xlsx


title: RNA_mESC_GFP_rep5

description:
mESC_GFP_rep5
Obox_RNASeq_FPKM.xlsx

value: GFP OE


title: NGP_RA3

source_name: NGP

value: RA

value: NGP


title: control lambda phage, mCpG_BS


title: NGP_RA2


title: RNA_mESC_GFP_rep4

description:
mESC_GFP_rep4
Obox_RNASeq_FPKM.xlsx

value: wild type


title: RNA_mESC_Obox3oe_rep1

description:
mESC_Obox3oe_rep1
Obox_RNASeq_FPKM.xlsx


title: control lambda phage, unmeth_DM

value: unmethylated


title: RNA_mESC_GFP_rep3

description:
mESC_GFP_rep3
Obox_RNASeq_FPKM.xlsx


title: control lambda phage, unmeth_BS


title: NGP_C3


title: RNA_mESC_Obox3oe_rep3

description:
mESC_Obox3oe_rep3
Obox_RNASeq_FPKM.xlsx


title: RNA_mESC_GFP_rep1

description:
mESC_GFP_rep1
Obox_RNASeq_FPKM.xlsx


title: NGP_C2


title: RNA_zKD_4C_siObox8_rep2

description:
zKD_4C_siObox8_rep2
Obox_RNASeq_FPKM.xlsx

source_name: 4-cell mouse embryos

value: 4-cell mouse embryos


title: RNA_zKD_4C_siObox8_rep1

description:
zKD_4C_siObox8_rep1
Obox_RNASeq_FPKM.xlsx


title: RNA_zKD_4C_siObox6_rep2

description:
zKD_4C_siObox6_rep2
Obox_RNASeq_FPKM.xlsx


title: inoculum 0h Giardia DMEM/F-12 cond biol rep 3

first: Staffan

middle: Gunnar

last: Svärd

department: Department of Cell and Molecular Biology

description:
matrix column name:
271

data_processing:
Illumina NovaSeq 6000 , Demultiplexing and conversion to FASTQ performed using the bclfastq2 (2.20.0.422) software
FASTQ files were mapped to combined Giardia WB genome and human GRCh38 using STAR v2.7.10a. ReadsPerGene.out.tab output from STAR with specifying --quantMode GeneCounts were used as the raw counts input for downstream analysis
Gene differential expression analysis was carried out in R v4.0.1 using edgeR v3.32.1 workflow. Quasi-likelihood F test was used to determine significant differential gene expression.
Assembly: Giardia intestinalis WB C6,  GCA_000002435.2 UU_WB_2.1
Assembly: GRCh38, release 106, GCA_000001405.28
Supplementary files format and content: Tab-delimited text file containing count matrix of human raw counts from STAR mapping of all samples (counts_human.txt).
Supplementary files format and content: Tab-delimited text file containing count matrix of Giardia intestinalis raw counts from STAR mapping of all samples (counts_giardia.txt).

organism: Giardia duodenalis assemblage A

source_name: trophozoites

growth_protocol:
Giardia intestinalis trophozoites were grown in TYDK at 37°C until 70% confluency. Trophozoites were washed twice in warm PBS and after incubated in either DMEM/F-12 supplemented with 10% FBS or with DMEM/F-12 for 1h at 37°C. After this preconditioning, trophozoites were detached, spun down, washed once in 1ml cold DMEM/F-12, spun down again and after resuspended in DMEM/F-12.
Human enteroids were maintained as 3D domes embedded in Matrigel in human Intesticult organoid growth media in humidified atmosphere with 5% CO2 at 37°C. For infections enteroids were grown as monolayers on PET-transwells and differentiated to an enterocyte phenotype by deprivation of WNT signaling for 4 to 5 days. 3h before the infection apical media was changed to DMEM/F-12 while the basal compartment was refreshed with differentiation media.

extract_protocol:
Total RNA extractions were performed using Trizol according to the manufactures instructions. RNA was then treated with DNaseI and extracted again by phenol chloroform extraction.
Sequencing libraries were prepared from 500ng total RNA using the TruSeq stranded mRNA library preparation kit (cat# 20020595, Illumina Inc.) including polyA selection. Unique dual indexes (cat# 20022371, Illumina Inc.) were used. The library preparation was performed according to the manufacturers’ protocol.

treatment_protocol:
Giardia intestinalis trophozoites were added apically to enterocytes for 1h and 3h. Uninfected enterocyte monolayers were collected after 1h and 3h as controls. Prior to infection preconditioned Giardia intestinalis trophozoites were collected as inoculum samples.
All samples were collected and lysed in Trizol reagent.

value: trophozoites

value: DMEM/F-12 preconditioned


title: RNA_zKD_4C_siObox6_rep1

description:
zKD_4C_siObox6_rep1
Obox_RNASeq_FPKM.xlsx


title: NGP_C1

data_processing:
RNASeq data was processed using kallisto (version 0.45.0) and human genome GRCh38 Ensembl version 94 annotation (Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.gtf). Gene-level TPM values and gene annotations were computed using tximport and biomaRt R package. A custom python script was used to organize the data and log reduced using log2(TPM) if TPM > 1 and TPM - 1 if TPM <= 1.
Assembly: Genome assembly: GRCh38.p12, Gene annotatiopn: Homo_sapiens.GRCh38.94.chr_patch_hapl_scaff.gtf
Supplementary files format and content: Tab-delimited text files report expression levels for each gene in each sample. Gene-expression levels are reported either as log2(TPM) values (when TPM>1), or as (TPM-1) values (when TPM=1 or TPM<1).


title: LAN1_RA3


title: RNA_zKD_4C_siCtrl_rep3

description:
zKD_4C_siCtrl_rep3
Obox_RNASeq_FPKM.xlsx

value: siCtrl


title: LAN1_RA2


title: LAN1_RA1


title: RNA_zKD_4C_siCtrl_rep1

description:
zKD_4C_siCtrl_rep1
Obox_RNASeq_FPKM.xlsx


title: RNA_zKD_L2C_siObox3_rep1

description:
zKD_L2C_siObox3_rep1
Obox_RNASeq_FPKM.xlsx

value: late 2-cell mouse embryos


title: inoculum 0h Giardia DMEM/F-12+FBS cond biol rep 2

description:
matrix column name:
261

value: DMEM/F-12+FBS preconditioned


title: RNA_mESC_GFP_rep2

description:
mESC_GFP_rep2
Obox_RNASeq_FPKM.xlsx

value: mESC


title: RNA_zKD_4C_siCtrl_rep2

description:
zKD_4C_siCtrl_rep2
Obox_RNASeq_FPKM.xlsx


title: inoculum 0h Giardia DMEM/F-12+FBS cond biol rep 1

description:
matrix column name:
260


title: RNA_zKD_E2C_siObox4_rep2

description:
zKD_E2C_siObox4_rep2
Obox_RNASeq_FPKM.xlsx

value: early 2-cell mouse embryos


title: NGP_RA1


title: RNA_zKD_L2C_siCtrl_rep1

description:
zKD_L2C_siCtrl_rep1
Obox_RNASeq_FPKM.xlsx


title: inoculum 0h Giardia DMEM/F-12+FBS cond biol rep 3

description:
matrix column name:
262


title: dsODN-rep4

city: Chicago

first: Tong

last: Wu

state: Illinois

address: 929 E 57th St. GCIS E335

institute: University of Chicago

description: GUIDE-seq

data_processing:
GUIDE-seq was analysed using an open-source guideseq software:  https://github.com/aryeelab/guideseq.
Assembly: hg19
Supplementary files format and content: read density that can be used for visualization on genome browsers.
Library strategy: GUIDE-seq

source_name: embryonic kidney

growth_protocol: HEK293T cells were purchased from (ATCC, CRL11268) were cultured in DMEM (Gibco 11995) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco, 15140).

extract_protocol:
Genomic DNA was isolated using Purelink Genomic DNA Mini Kit (Thermo Fisher, K1820)
1 µg gDNA was applied to fragmentation, end-repair, A-tailing, adapter ligation, and dsODN-specific amplification, following the published GUIDE-seq protocol.

value: embryonic kidney

value: Kidney epithelial

value: Wild type

value: Nucleofection

tag: ascas12f version


title: RNA_mKD_L2C_siObox7_rep2

description:
mKD_L2C_siObox7_rep2
Obox_RNASeq_FPKM.xlsx

source_name: late 2-cell mouse parthenotes

value: late 2-cell mouse parthenotes


title: dsODN-rep3

description: GUIDE-seq


title: LAN1_C2

value: C


title: RNA_mKD_L2C_siObox5_rep2

description:
mKD_L2C_siObox5_rep2
Obox_RNASeq_FPKM.xlsx


title: RNA_zKD_E2C_siCtrl_rep1

description:
zKD_E2C_siCtrl_rep1
Obox_RNASeq_FPKM.xlsx


title: RNA_mKD_L2C_siObox7_rep1

description:
mKD_L2C_siObox7_rep1
Obox_RNASeq_FPKM.xlsx


title: inoculum 0h Giardia DMEM/F-12 cond biol rep 1

description:
matrix column name:
269


title: RNA_zKD_E2C_siCtrl_rep2

description:
zKD_E2C_siCtrl_rep2
Obox_RNASeq_FPKM.xlsx


title: RNA_mKD_L2C_siObox5_rep1

description:
mKD_L2C_siObox5_rep1
Obox_RNASeq_FPKM.xlsx


title: LAN1_C3


title: RNA_mKD_L2C_siObox12mix_rep2

description:
mKD_L2C_siObox12mix_rep2
Obox_RNASeq_FPKM.xlsx


title: enAsCas12f-PDCD1-rep1

description: GUIDE-seq

tag: guide rna_target


title: inoculum 0h Giardia DMEM/F-12 cond biol rep 2

description:
matrix column name:
270


title: RNA_mKD_L2C_siCtrl_rep3

description:
mKD_L2C_siCtrl_rep3
Obox_RNASeq_FPKM.xlsx


title: RNA_mKD_L2C_siObox12mix_rep1

description:
mKD_L2C_siObox12mix_rep1
Obox_RNASeq_FPKM.xlsx


title: RNA_mKD_L2C_siCtrl_rep1

description:
mKD_L2C_siCtrl_rep1
Obox_RNASeq_FPKM.xlsx


title: RNA_mKD_L2C_siCtrl_rep2

description:
mKD_L2C_siCtrl_rep2
Obox_RNASeq_FPKM.xlsx


title: AsCas12f-v4.1-PDCD1-rep1

description: GUIDE-seq


title: RNA_Obox--_L2C_rep3

description:
Obox--_L2C_rep3
Obox_RNASeq_FPKM.xlsx

source_name: late 2-cell mouse embryos

value: Obox--


title: RNA_Obox--_L2C_rep2

description:
Obox--_L2C_rep2
Obox_RNASeq_FPKM.xlsx


title: RNA_Obox--_L2C_rep1

description:
Obox--_L2C_rep1
Obox_RNASeq_FPKM.xlsx


title: Kelly_C3

source_name: Kelly

value: Kelly


title: Kelly_RA1

value: RA


title: RNA_zKD_E2C_siObox4_rep1

description:
zKD_E2C_siObox4_rep1
Obox_RNASeq_FPKM.xlsx

source_name: early 2-cell mouse embryos

value: wild type


title: RNA_Obox--_L2C_rep4

description:
Obox--_L2C_rep4
Obox_RNASeq_FPKM.xlsx


title: Kelly_C2


title: AsCas12f-WT-PDCD1-rep2

description: GUIDE-seq

value: WT


title: RNA_Obox--_E2C_rep3

description:
Obox--_E2C_rep3
Obox_RNASeq_FPKM.xlsx


title: RNA_Obox--_E2C_rep1

description:
Obox--_E2C_rep1
Obox_RNASeq_FPKM.xlsx


title: LAN1_C1


title: AsCas12f-WT-PDCD1-rep1

description: GUIDE-seq


title: enAsCas12f-APOB-rep2

description: GUIDE-seq

value: APOB


title: RNA_Obox+-_L2C_rep3

description:
Obox+-_L2C_rep3
Obox_RNASeq_FPKM.xlsx

value: Obox+-


title: enAsCas12f-PDCD1-rep2

description: GUIDE-seq


title: AsCas12f-v4.1-PDCD1-rep2

description: GUIDE-seq


title: Kelly_RA2


title: Kelly_RA3


title: Kelly_C1


title: RNA_Obox+-_L2C_rep1

description:
Obox+-_L2C_rep1
Obox_RNASeq_FPKM.xlsx

value: late 2-cell mouse embryos


title: enAsCas12f-APOB-rep1

description: GUIDE-seq


title: RNA_Obox+-_E2C_rep2

description:
Obox+-_E2C_rep2
Obox_RNASeq_FPKM.xlsx


title: AsCas12f-v4.1-APOB-rep2

description: GUIDE-seq


title: HEK293, ICI-SNC80, 6h, n1

city: Geneva

first: Miriam

last: Stoeber

state: GE

address: Rue Michel Servet 1

department: PHYM

country: Switzerland

institute: University of Geneva

data_processing:
1.5h: Libraries generated for the 1.5 h treatment were sequenced using the Illumina NextSeq 500 or HiSeq 4000 devices with a single-end read length of 80-90 nucleotides yielding at least 3 millions mapped reads per sample. Sequences were mapped to the human genome GRC h38.12 using GENCODE v28 annotation with STAR v. 2.6.0c. Generated raw counts were normalized and genes with low expression were filtered out leaving 15,946 genes. Differential expression analyses and related statistics between control and treated conditions were conducted using the Limma-voom R package 3.38.2.
6h: libraries were sequenced using the Illumina HiSeq 4000 device with a single-end read length of 50 nucleotides yielding around 30 million mapped reads per sample. Fastq files were generated using Illumina bcl2fastq v. 2.20.0 and mapped to the human genome UCSC hg38 using STAR v. 2.7.0f. Aligned reads were quantified with the Python software htseq-count v. 0.9.1. Genes were filtered down to 14,467 after removal of low expressers and normalized using the R package EdgeR 3.28.1. Differential gene expression between control and DPDPE or ICI and ICI/SNC80 conditions was computed and statistics were performed using the General Linear Model, quasi-likelihood F-test (QL F-test) with FDR and Benjamini & Hochberg correction.
Assembly: GRC h38.12 (1.5h), UCSC hg38 (6h)
Supplementary files format and content: 1.5h: tab delimited text files including ensembl, hgnc, Log2FC, p-value, adj. p-value, description
Supplementary files format and content: 6h: tab delimited text file including hgnc, description, FC, p-value, adj. p-value, raw counts, normalized counts

source_name: HEK293 stably expressing DOR

growth_protocol: HEK293 cells were maintained in DMEM supplemented with 10%FBS and geneticin

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen), genomic DNA was removed using the RNase-free DNase kit (Qiagen) and samples analyzed using a bioanalyzer.
Multiplexed libraries for the 1.5 h samples were generated using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit and for the 6 h samples using TruSeqHT Stranded Total RNA Library Prep protocol (Illumina).

treatment_protocol: HEK293 cells stably expressing DOR were treated with vehicle control or DPDPE 100 nM or SNC80 100 nM or ICI 174, 864 100 uM + SNC80 100 nM for 1.5h or 6h (ICI preincubated for 5 min)

value: HEK293 stably expressing DOR

value: Human embryonic kidney

tag: time point


title: HEK293, ICI-SNC80, 6h, n2


title: HEK293, ICI-SNC80, 6h, n3


title: RNA_Obox+-_E2C_rep3

description:
Obox+-_E2C_rep3
Obox_RNASeq_FPKM.xlsx

value: early 2-cell mouse embryos


title: RNA_Obox+-_E2C_rep1

description:
Obox+-_E2C_rep1
Obox_RNASeq_FPKM.xlsx


title: HEK293, ICI, 6h, n3


title: RNA_Obox--_E2C_rep2

description:
Obox--_E2C_rep2
Obox_RNASeq_FPKM.xlsx


title: RNA_mKO_BL_rep1

description:
mKO_BL_rep1
Obox_RNASeq_FPKM.xlsx

source_name: blastocyst mouse embryos

value: blastocyst mouse embryos

value: Obox mKO


title: HEK293, ICI, 6h, n2


title: AsCas12f-WT-APOB-rep2

description: GUIDE-seq

value: embryonic kidney

value: Kidney epithelial

value: Wild type


title: RNA_mKO_L2C_rep2

description:
mKO_L2C_rep2
Obox_RNASeq_FPKM.xlsx


title: RNA_mKO_L2C_rep1

description:
mKO_L2C_rep1
Obox_RNASeq_FPKM.xlsx


title: AsCas12f-WT-APOB-rep1

description: GUIDE-seq

value: Nucleofection


title: HEK293, ICI, 6h, n1


title: enAsCas12f-MRPL39-rep2

description: GUIDE-seq


title: RNA_mKOCtrl_WT_L2C_rep2

description:
mKOCtrl_WT_L2C_rep2
Obox_RNASeq_FPKM.xlsx


title: RNA_Obox+-_L2C_rep2

description:
Obox+-_L2C_rep2
Obox_RNASeq_FPKM.xlsx


title: HEK293, DPDPE, 6h, n3

value: DPDPE 100 nM


title: RNA_mKOCtrl_WT_L2C_rep1

description:
mKOCtrl_WT_L2C_rep1
Obox_RNASeq_FPKM.xlsx


title: RNA_mzKO_BL_Obox4OE

description:
mzKO_BL_Obox4OE
Obox_RNASeq_FPKM.xlsx

source_name: arrested 2-cell mouse embryos

value: arrested 2-cell mouse embryos

value: Obox mzKO


title: enAsCas12f-MRPL39-rep1

description: GUIDE-seq


title: RNA_mzKO_BL_Obox157OE

description:
mzKO_BL_Obox157OE
Obox_RNASeq_FPKM.xlsx


title: RNA_mzKO_BL_Obox3OE

description:
mzKO_BL_Obox3OE
Obox_RNASeq_FPKM.xlsx


title: HEK293, DPDPE, 6h, n2


title: AsCas12f-v4.1-MRPL39-rep2

description: GUIDE-seq


title: AsCas12f-v4.1-APOB-rep1

description: GUIDE-seq


title: AsCas12f-v4.1-MRPL39-rep1

description: GUIDE-seq


title: HEK293, DPDPE, 6h, n1


title: RNA_mzKO_BL_rep2

description:
mzKO_BL_rep2
Obox_RNASeq_FPKM.xlsx


title: HEK293, CTRL, 6h, n3


title: RNA_mzKO_L2C_rep3

description:
mzKO_L2C_rep3
Obox_RNASeq_FPKM.xlsx


title: RNA_mKOCtrl_WT_BL_rep1

description:
mKOCtrl_WT_BL_rep1
Obox_RNASeq_FPKM.xlsx

value: wild type


title: drmy1_ap1cal_AP1-GR_rep2

city: Ithaca

first: Adrienne

last: Roeder

address: 239 Weill Hall, 526 Campus Road

department: Weill Institute of Cell and Molecular Biology and Plant Biology Section, School of Integrative Plant Science

institute: Cornell University

data_processing:
For quality-filtering of RNA-seq reads, we first used the Perl script quality_trim_fastq.pl (available at https:/  /github.com/SchwarzEM/ems_perl/blob/master/illumina/quality_trim_fastq.pl) to remove reads that failed CHASTITY and trim the last nucleotide off our raw reads; quality_trim_fastq.pl was run with the arguments '-q 33 -u 84'
We then used Trimmomatic 0.36 59 to remove adapter sequences and remove unreliable reads. Trimmomatic was run with the arguments 'SE -phred33 [...] ILLUMINACLIP:[...]/sepal_adapters_09dec2016.trimmomatic.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:[50 or 84]'.
We mapped RNA-seq reads to cDNA sequences of A. thaliana genes (i.e., coding sequences [CDSes] plus flanking 5' and 3' UTR sequences)
We used Salmon 0.14.161 to index the cDNA sequences and determine levels of gene expression for each RNA-seq replicate in transcripts per million (TPM). For indexing cDNA, we used the Salmon arguments '--no-version-check index -k 31 --perfectHash --type quasi --keepDuplicates'; for computing gene expression, we used the arguments '--no-version-check quant --seqBias --gcBias -- validateMappings --libType A --geneMap TAIR10_cdna_20101214_updated_w_GFP.tx2gene.tsv.txt --numBootstraps 200'.
To compare changes of gene expression between genotypes and identify which changes were statistically significant, we used DESeq2 version 1.18.1. We used a log2 fold change threshold of ±1 and a BH-adjusted p-value threshold of 0.05.
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file include read count and TPM for each sample

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: Inflorescence

growth_protocol: The ap1 cal AP1-GR and drmy1 ap1 cal AP1-GR plants were grown in soil under continuous light at 16°C to prevent premature floral induction.

extract_protocol:
RNA extraction was done using a commercial kit (RNeasy Plant Mini Kit, Qiagen, CAT NO. 74904) following the manual.
mRNA was isolated with Dynabeads oligo dT beads (Invitrogen Cat# 61006) and fragmented in first strand buffer at 94° C for 6 minutes. First strand cDNA was synthesized with random hexamers (Invitrogen Cat# 48190011) using Superscript II (Invitrogen Cat#18064014) and the second strand was synthesized with DNA Pol I (Fermentas Cat #EP0041) and RNAse H (Invitrogen Cat# 18021071). End repair was conducted with NEBNext End repair enzyme Mix (NEB Cat# E6050S) and Klenow DNA polymerase (NEB Cat# M0210S), A tailing with Klenow 3’ to 5’ exonuclease (Fermentas Cat# EP0421), and ligation of NEB NEXT adapters (NEB Cat# E7335L) with Mighty Mix Ligase (Clonetech TAK6023). The library was size-selected using Agencourt AmPure Beads (Beckman Coulter A63880). PCR enrichment and barcoding were conducted with NEBNext Multiplex Oligos for Illumina index primers (NEB Cat# E7335L) for 15 cycles using Phusion polymerase (NEB Cat# M0530L). The entire library was run on a 1.2% agarose gel and size-selected (about 200– 500 bp) to remove adapter dimers. RNA sequencing was done with the service HISEQ 2500 rapid run (run length 50 RR, single barcode) or NextSeq 500 (run length 75, single barcode) provided by Cornell Genomic facility.

treatment_protocol: Bolting ap1 cal AP1-GR and drmy1 ap1 cal AP1-GR plants were induced daily with an aqueous solution containing 10 µM dexamethasone (Sigma-Aldrich), 0.01% (v/v) ethanol, and 0.015% (v/v) Silwet L-77 (Rosecare.com). When sepals initiated from the floral meristems (on the fourth day after three daily inductions), 7 inflorescence samples per genotype (including inflorescence meristems and buds under stage 6) were collected.

value: Inflorescence

value: drmy1 ap1 cal AP1-GR

value: Dexamethasone for 3 days


title: drmy1_ap1cal_AP1-GR_rep1


title: AsCas12f-WT-MRPL39-rep1

description: GUIDE-seq

value: WT


title: drmy1_ap1cal_AP1-GR_rep3


title: RNA_mzKO_L2C_rep2

description:
mzKO_L2C_rep2
Obox_RNASeq_FPKM.xlsx

value: late 2-cell mouse embryos


title: AsCas12f-WT-MRPL39-rep2

description: GUIDE-seq


title: RNA_mzKO_BL_rep1

description:
mzKO_BL_rep1
Obox_RNASeq_FPKM.xlsx


title: ap1cal_AP1-GR_rep3

value: ap1 cal AP1-GR


title: RNA_mzKO_E2C_rep2

description:
mzKO_E2C_rep2
Obox_RNASeq_FPKM.xlsx

value: early 2-cell mouse embryos


title: ap1cal_AP1-GR_rep2


title: HEK293, ICI-SNC80, 1.5h, nE

value: HEK293 stably expressing DOR

value: Human embryonic kidney


title: ap1cal_AP1-GR_rep1


title: RNA_mzKO_L2C_rep1

description:
mzKO_L2C_rep1
Obox_RNASeq_FPKM.xlsx


title: HEK293, CTRL, 6h, n1


title: HEK293, CTRL, 6h, n2


title: HEK293, ICI-SNC80, 1.5h, nF


title: SR0030_03_b

city: Tochigi

first: Tsukasa

last: Ohmori

address: 3311-1 Yakushiji, Shimotsuke,

country: Japan

institute: Jichi Medical University

data_processing:
The isoseq3 tool was used to remove polyA tail sequences and concatemer reads, and high quality full-length reads were obtained after clustering.
The high-quality full-lengths were mapped to GRCh38.primary_assembly.genome using minimap2 software.
The cDNA_Cupcake was used to isolate isoforms by clustering and to qualify expression.
The annotation was attached to the isoforms using the SQANTI3 tool.
Assembly: GRCh38
Supplementary files format and content: The Excel file containing the count number and TPM value of each sample.

source_name: Gene-corrected patient derived iPSCs

growth_protocol: iPSCs were maintained in StemFitAK02N (Takara Bio) on plates coated with iMatrix-511 (Matrixome).

extract_protocol:
Total RNA was isolated using Rneasy Mini Kit (Qaigen) and purified using NucleoSpin RNA Kit (Takara Bio). The amount of total RNA was determined using Nanodrop, and the quality of RNA was checked using BioAnalyzer.
cDNA was synthesized using NEBNext Single Cell/Low cDNA Synthesis and Amplification Module (NEB) and Iso-Seq Express Oligo Kit. Libraries were then prepared using SMARTbell Express Template Prep Kit 2.0 and Barcoded Overhang Adapter Kit A/B according to the procedure and Checklist-Oso-Seq Express Template Preparation for Sequel and Sequel II Systems Version 02.
Iso-Seq

value: Gene-corrected patient derived iPSCs

value: iPSCs

value: Variant-corrected clone derived from Sample2

value: Undifferentiation state


title: SR0030_01_b

source_name: Hemophilia patient derived iPSCs

value: Hemophilia patient derived iPSCs

value: Healthy volunteer


title: RNA_mzKO_E2C_rep1

description:
mzKO_E2C_rep1
Obox_RNASeq_FPKM.xlsx

value: Obox mzKO


title: HEK293, ICI-SNC80, 1.5h, nD


title: RNA_OboxKO_MII_rep2

description:
OboxKO_MII_rep2
Obox_RNASeq_FPKM.xlsx

source_name: MII oocytes

value: MII oocytes

value: Obox KO


title: CW_S3

city: Zhengzhou

first: Liu

last: Xiaoting

address: 100 Science Avenue

institute: Zhengzhou University

data_processing:
Total RNA was isolated and purified using TRIzol reagent following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000. The RNA integrity was assessed by Bioanalyzer 2100.
The cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase. Then, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.
Cutadapt software was used to remove the reads that contained adaptor contamination. And After removed the low quality bases and undetermined bases ,we used HISAT2 software to map reads to the genome (http://www.wheatgenome.org/).
The mapped reads of each sample were assembled using StringTie with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software. After the final transcriptome was generated, StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM .
Assembly: International Whaet Genome Sequencing Consortium(http://www.wheatgenome.org/)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Triticum aestivum

source_name: purple grain wheat

growth_protocol: The white grain wheat and purple grain wheat were grown in pots containing a soil: vermiculite mixture (3:1) in a controlled artificial climatic chamber (16 h light/8 h dark photoperiod at 20°C/18 °C).

extract_protocol:
The stems and buds were collected,and RNA was harvested using Trizol reagent. 5–10 μg total RNA was used as the template for constructing RNA-seq libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: grain

tag: age

value: 30 days after flowering


title: HEK293, ICI-SNC80, 1.5h, nC


title: RNA_OboxKO_MII_rep1

description:
OboxKO_MII_rep1
Obox_RNASeq_FPKM.xlsx

extract_protocol:
For embryos, the zona pellucida was gently removed by treatment with Tyrode’s solution (Sigma, T1844). Then the embryos were lysed in lysis buffer containing RNase inhibitor. 2i ESCs were lysed in lysis buffer containing RNase inhibitor. The following steps followed the Smart-seq2 protocol as previously described (Picelli et al., 2014). For whole genome sequence, the tail tip DNA were extracted with isopropanol precipitation method.
The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before being subjected to sequencing. For stacc-seq, the library was prepared following the protocol as descripted before (Liu et al., 2020). For ATAC-seq,  the library was prepared following the protocol as descripted before (Buenrostro et al., 2013; Wu ET AL., 2016).
The Smart-seq2, WGS (Picelli et al., 2014) and stacc-seq (Liu et al., 2020) library strategies were followed the protocols described.

tag: genotype


title: CW_S2

tag: tissue


title: SR0030_02_b

source_name: Healthy volunteer derived iPSCs

value: Healthy volunteer derived iPSCs

value: Moderate Hemophilia A patient


title: HEK293, ICI-SNC80, 1.5h, nB


title: RNA_OboxKO_FGO_rep2

description:
OboxKO_FGO_rep2
Obox_RNASeq_FPKM.xlsx

source_name: FGO oocytes

value: FGO oocytes


title: Healthy control 5, week 0

city: Taichung

first: Kuo Tung

last: Tang

address: No. 1650, Sec. 4, Taiwan Blvd.

department: Division of Allergy, Immunology and Rheumatology

institute: Taichung Veterans General Hospital

data_processing:
Bases with low quality and sequences from adapters in raw data were removed using program Fastp (version 0.20.0).
Filtered reads were aligned to the reference genomes using the HISAT2 software (version 2.1.0).
The software FeatureCounts (v2.0.1) in Subread package was applied to quantify the gene abundance.
Assembly: GRCh38
Supplementary files format and content: *.xlsx: Excel spreadsheet files include counts and TPM values for each Sample.

source_name: blood

extract_protocol:
Total RNAs were extracted from isolated neutrophils using the TRIzol Reagent (Thermo Fisher Scientific) and purified using a GENEzol TriRNA Pure kit (Geneaid, Taiwan R.O.C.).
The purified RNA was used for the preparation of the sequencing library using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA).

treatment_protocol: Subcutaneous tocilizumab every 2-4 weeks.

value: healthy

value: blood

value: neutrophils

value: week 0

tag: donor

value: control 5


title: Healthy control 3, week 0

tag: cell type

value: control 3


title: CW_S1