title: 6H2_M_1230


title: 6H2_M_1236

status: Public on Jul 08 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-seq3

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


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title: 6H_M_1248


title: 6H_M_1247


title: 6H_M_1246


title: 6H_M_1245


title: 6H_M_1244


title: 6H_M_1243


title: 6H_M_1264


title: 6H_M_1241


title: 6H_M_1242


title: 6H_M_1252


title: 6H_M_1237


title: 6H_M_1236


title: 6H_M_1240


title: 6H_M_1238


title: 6H_M_1235


title: 6H_M_1230


title: 6H_M_1234


title: 6H_M_124


title: 6H_M_123


title: 6H_M_1239


title: 6H_M_1229


title: 6H_M_1231


title: 6H_M_1232


title: 6H_M_1226


title: 6H_M_1228


title: 6H_M_1225


title: 6H_M_1224


title: 6H_M_1227


title: 6H_M_1222


title: 6H_M_1221


title: 6H_M_1223


title: 6H_M_122


title: 6H_M_1366


title: 6H_M_1220


title: 6H_M_1219


title: 6H_M_1218


title: 6H_M_1217


title: 6H_M_1216


title: 6H_M_1233


title: 6H_M_1215


title: 6H_M_1214


title: 6H_M_1211


title: 6H_M_1210


title: 6H_M_1212


title: 6H_M_1209


title: 6H_M_1208


title: 6H_M_1207


title: 6H_M_1206


title: 6H_M_1203


title: 6H_M_1205


title: 6H_M_1204


title: 6H_M_1198


title: 6H_M_1197


title: 6H_M_1199


title: 6H_M_1202


title: 6H_M_12


title: 6H_M_1201


title: 6H_M_1193


title: 6H_M_1195


title: 6H_M_1194


title: 6H_M_1200


title: 6H_M_1192


title: 6H_M_1196


title: 6H_M_1191


title: 6H_M_1190


title: 6H_M_119


title: 6H_M_1213


title: 6H_M_121


title: 6H_M_1189


title: 6H_M_1188


title: 6H_M_1184


title: 6H_M_1186


title: 6H_M_1185


title: 6H_M_1187


title: 6H_M_1180


title: 6H_M_1181


title: 6H_M_118


title: 6H_M_1179


title: 6H_M_1182


title: 6H_M_1178


title: 6H_M_1176


title: 6H_M_1170


title: 6H_M_1171


title: 6H_M_1175


title: 6H_M_1174


title: 6H_M_1173


title: 6H_M_1167


title: 6H_M_1177


title: 6H_M_1169


title: 6H_M_1164


title: 6H_M_1166


title: 6H_M_117


title: 6H_M_1163


title: 6H_M_1161


title: 6H_M_1162


title: 6H_M_1159


title: 6H_M_1160


title: 6H_M_1183


title: 6H_M_116


title: 6H_M_1158


title: 6H_M_1157


title: 6H_M_1156


title: 6H_M_1155


title: 6H_M_1152


title: 6H_M_1153


title: 6H_M_1151


title: 6H_M_115


title: 6H_M_1150


title: 6H_M_1168


title: 6H_M_1148


title: 6H_M_1142


title: 6H_M_1147


title: 6H_M_1144


title: 6H_M_1149


title: 6H_M_1145


title: 6H_M_1141


title: 6H_M_1136


title: 6H_M_1138


title: 6H_M_114


title: 6H_M_1133


title: 6H_M_1140


title: 6H_M_1143


title: 6H_M_1135


title: 6H_M_1134


title: 6H_M_1130


title: 6H_M_1137


title: 6H_M_1154


title: 6H_M_113


title: 6H_M_1129


title: 6H_M_1132


title: 6H_M_1128


title: 6H_M_1126


title: 6H_M_1127


title: 6H_M_1123


title: 6H_M_1120


title: 6H_M_1121


title: 6H_M_112


title: 6H_M_1122


title: 6H_M_1119


title: 6H_M_1118


title: 6H_M_1146


title: 6H_M_1117


title: 6H_M_1131


title: 6H_M_1116


title: 6H_M_1113


title: 6H_M_1114


title: 6H_M_1111


title: 6H_M_111


title: 6H_M_1125


title: 6H_M_1112


title: 6H_M_1124


title: 6H_M_1106


title: 6H_M_1108


title: 6H_M_1105


title: 6H_M_1110


title: 6H_M_1107


title: 6H_M_1102


title: 6H_M_1104


title: 6H_M_1101


title: 6H_M_1100


title: 6H_M_110


title: 6H_M_11


title: 6H_M_1097


title: 6H_M_1096


title: 6H_M_1115


title: 6H_M_1095


title: 6H_M_1094


title: 6H_M_1093


title: 6H_M_1109


title: 6H_M_1139


title: 6H_M_1092


title: 6H_M_1103


title: 6H_M_109


title: 6H_M_1091


title: 6H_M_1088


title: 6H_M_1089


title: 6H_M_1082


title: 6H_M_1085


title: 6H_M_1084


title: 6H_M_1086


title: 6H_M_1087


title: 6H_M_1083


title: 6H_M_1080


title: 6H_M_108


title: 6H_M_1081


title: 6H_M_1099


title: 6H_M_1098


title: 6H_M_1079


title: 6H_M_1078


title: 6H_M_1076


title: 6H_M_1073


title: 6H_M_1090


title: 6H_M_1070


title: 6H_M_1069


title: 6H_M_1068


title: 6H_M_107


title: 6H_M_1067


title: 6H_M_1061


title: 6H_M_1065


title: 6H_M_1060


title: 6H_M_1063


title: 6H_M_106


title: 6H_M_1062


title: 6H_M_1066


title: 6H_M_1059


title: 6H_M_1064


title: 6H_M_1058


title: 6H_M_1057


title: 6H_M_1056


title: 6H_M_1055


title: 6H_M_1054


title: 6H_M_1077


title: 6H_M_1051


title: 6H_M_1075


title: 6H_M_1053


title: 6H_M_1052


title: 6H_M_1074


title: 6H_M_1072


title: 6H_M_105


title: 6H_M_1071


title: 6H_M_1049


title: 6H_M_1048


title: 6H_M_1047


title: 6H_M_1046


title: 6H_M_1044


title: 6H_M_1045


title: 6H_M_1043


title: 6H_M_1042


title: 6H_M_1038


title: 6H_M_1039


title: 6H_M_1040


title: 6H_M_1030


title: 6H_M_1036


title: 6H_M_1041


title: 6H_M_103


title: 6H_M_1029


title: 6H_M_1032


title: 6H_M_104


title: 6H_M_1027


title: 6H_M_1025


title: 6H_M_1050


title: 6H_M_1024


title: 6H_M_1028


title: 6H_M_1021


title: 6H_M_1037


title: 6H_M_1022


title: 6H_M_1026


title: 6H_M_1020


title: 6H_M_1023


title: 6H_M_1019


title: 6H_M_102


title: 6H_M_1016


title: 6H_M_1017


title: 6H_M_1035


title: 6H_M_1034


title: 6H_M_1012


title: 6H_M_1014


title: 6H_M_1013


title: 6H_M_1008


title: 6H_M_1011


title: 6H_M_1009


title: 6H_M_1007


title: 6H_M_101


title: 6H_M_1006


title: 6H_M_1010


title: 6H_M_1


title: 6H_M_10


title: 6H_M_1001


title: 6H_M_0


title: 6H_M_1018


title: 6H_M_1005


title: 6H_M_1004


title: 6H_M_1002


title: 6H_M_1000


title: 6H_M_100


title: 6H_M_1015


title: AAV8 transduced liver 2

city: Ultimo

first: Alexandra

last: Mahoney

state: NSW

address: Thomas St

country: Australia

institute: University of Technology Sydney

library_source: transcriptomic

data_processing:
CLC Genomics Workbench v20
CLC Genomics Workbench was utilised to process and analyse the RNA-Seq data of the biological replicates in each group (normal, Diabetic, AAV, and AAV8/piggyBac). Raw RNA-Seq data was imported into CLC and were mapped to mus-musculus reference genome.
After mapping the reads, each read was assigned to specific genes or features based on their mapping positions, generating read counts, representing the number of reads that align to each gene or feature.
Read counts were normalised, including trimming and upper-quartile normalisation
Gene expression analysis was undergone on each treatment compared to normal
Assembly: mm10
Supplementary files format and content: Raw data files include all reads as a fastq file
Supplementary files format and content: Processed data file is one file with the tabs containing each separate gene expression analysis

molecule: total RNA

source_name: Liver of female non-obese diabetic mouse

extract_protocol: RNA was extracted from liver tissue using

tag: tissue

tag: treatment

value: AAV8-INS-FUR vector


title: AAV8/piggyBac transduced liver 3

value: Liver of female non-obese diabetic mouse

value: AAV8/piggyBac-INS-FUR vector


title: AAV8/piggyBac transduced liver 2


title: AAV8 transduced liver 3


title: AAV8 transduced liver 1


title: AAV8/piggyBac transduced liver 1


title: Diabetic, untreated liver 3

value: No treatment


title: Diabetic, untreated liver 2


title: 6H_M_1003


title: Non-diabetic, untreated liver 2


title: Diabetic, untreated liver 1


title: serum_R_190

city: Guangzhou

first: Jiale

last: Qu

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-Sen Street, Yuexiu District

department: Zhongshan School of Medicine

country: China

institute: Sun Yat-sen University

data_processing:
Trimming the adaptor sequence: Adaptors and low-quality reads of Hi-C and RNA information were trimmed with Trim Galore (version 0.6.6, https://github.com/FelixKrueger/TrimGalore)
Alignment: Reads were aligned to mm10. For Hi-C data, HiC-Pro (PMID: 26619908) was used (version 3.0.0). For RNA-seq data, STAR (PMID: 23104886) was used with default parameters.
Quantification of gene expression: uniquely mapped reads of RNA-seq data were counted by scRNA-seq pipeline of sci-CAR analysis (https://github.com/JunyueC/sci-CAR_analysis).
Generation of hic files: All valid pairs were generated by HiC-Pro (PMID: 26619908) (version 3.0.0).
Assembly: mm10
Supplementary files format and content: *_raw_gene_counts.txt: raw read counts of each genes from RNA-seq data for expression analysis
Supplementary files format and content: *_allValidPairs: valid read pairs from Hi-C data for domain analysis or differential contact analysis
Library strategy: scCARE-seq

molecule: polyA RNA

growth_protocol: The mESCs were derived from a mixed (129X1 x 129S1) mouse. For serum medium, it consists of high-glucose DMEM (Hyclone, SH30022.01), 15% (v/v) fetal bovine serum (LONSERA, S711-001S), 1X GlutaMAX (Thermo Fisher, 30050-061), 1X MEM non-essential amino acids (Thermo Fisher, 11140-050), 0.1mM β-mercaptoethanol (Sigma, M6250), 1X penicillin/streptomycin (Thermo Fisher, 15140-122), 1% (v/v) nucleoside mix (Sigma), 1000 U/mL recombinant leukemia inhibitory factor (Millipore, ESG1107). The serum-to-2i transition was accomplished with washing mESCs twice in PBS (Hyclone, SH30256.01) and then switching to 2i medium. For 2i medium, cells were grown in the culturing conditions which contained 50% Neurobasal (Thermo Fisher, 21103-049), 50% DMEM/F12 (Thermo Fisher, 11330-032), 1X N-2 Supplement (Thermo Fisher, 17502-048), 1X B-27 supplement (Thermo Fisher, 12587-010), 1X GlutaMAX (Thermo Fisher, 30050-061), 1X MEM non-essential amino acids (Thermo Fisher, 11140-050), 0.1mM β-mercaptoethanol (Sigma, M6250), 1X penicillin/streptomycin (Thermo Fisher, 15140-122), 1,000 U/mL recombinant leukemia inhibitory factor (Millipore, ESG1107), 1 μM MEK inhibitor PD0325901 (Selleck, S1036) and 3 μM GSK3 inhibitor CHIR-99021 (Selleck, S1263). All cells were cultured at 37°C with 5% CO2 and in feeder free conditions on 0.1% gelatin-coated dishes.

extract_protocol:
We developed a single-cell multimodal omics method for simultaneously detecting chromatin architecture and mRNA expression by sequencing (scCARE-seq). Cells were fixed with 1% formaldehyde for 10 minutes. Cells were flow sorted into individual cells before cell lysis, and chromatin was tagmentation with Tn5. scCARE-seq_DNA and scCARE-seq _RNA respectively represents the information of 3D chromatin structure and transcription in the same single cell, separated by barcode.
Briefly, mRNA reverse transcription, genome digestion (MboI) and ligation were performed in intact nuclei, and the individual cells were sorted by flow cytometry into separate wells and lysed. After adding Tn5 transposase to each well for tagmentation, each cell library was pre-amplified, and divided into two halves for DNA and RNA library amplification using respective primer pairs.

tag: cell line

tag: cell type

value: cultured mouse embryonic stem cells

value: serum condition


title: serum_R_189


title: serum_R_184


title: serum_R_186


title: serum_R_191


title: serum_R_188


title: serum_R_187


title: serum_R_178


title: serum_R_183


title: serum_R_182


title: serum_R_179


title: serum_R_180


title: serum_R_175


title: serum_R_185


title: serum_R_181


title: serum_R_176


title: serum_R_177


title: serum_R_174


title: serum_R_168


title: serum_R_169


title: serum_R_171


title: serum_R_170


title: serum_R_173


title: serum_R_172


title: serum_R_166


title: serum_R_167


title: serum_R_192


title: serum_R_165


title: serum_R_164


title: serum_R_162


title: serum_R_161


title: serum_R_158


title: serum_R_160


title: serum_R_157


title: serum_R_155


title: serum_R_153


title: serum_R_148


title: serum_R_152


title: serum_R_156


title: serum_R_147


title: serum_R_159


title: serum_R_145


title: serum_R_150


title: serum_R_146


title: serum_R_151


title: serum_R_143


title: serum_R_138


title: serum_R_149


title: serum_R_142


title: serum_R_141


title: serum_R_140


title: serum_R_137


title: serum_R_136


title: serum_R_135


title: serum_R_163


title: serum_R_134


title: serum_R_133


title: serum_R_154


title: serum_R_132


title: serum_R_144


title: serum_R_131


title: serum_R_127


title: serum_R_126


title: serum_R_128


title: serum_R_125


title: serum_R_124


title: serum_R_116


title: serum_R_113


title: serum_R_112


title: serum_R_115


title: serum_R_130


title: serum_R_123


title: serum_R_119


title: serum_R_110


title: serum_R_121


title: serum_R_117


title: serum_R_108


title: serum_R_114


title: serum_R_118


title: serum_R_107


title: serum_R_120


title: serum_R_111


title: serum_R_129


title: serum_R_109


title: serum_R_105


title: serum_R_122


title: serum_R_101


title: serum_R_102


title: serum_R_103


title: serum_R_97


title: serum_R_98


title: serum_R_99


title: serum_R_100


title: serum_R_93


title: serum_R_94


title: serum_R_96


title: serum_R_95


title: serum_R_92


title: serum_R_90


title: serum_R_91


title: serum_R_88


title: serum_R_87


title: serum_R_89


title: serum_R_85


title: serum_R_139


title: serum_R_86


title: serum_R_84


title: serum_R_106


title: serum_R_79


title: serum_R_80


title: serum_R_82


title: serum_R_81


title: serum_R_78


title: serum_R_104


title: serum_R_77


title: serum_R_76


title: serum_R_75


title: serum_R_74


title: serum_R_72


title: serum_R_70


title: serum_R_71


title: serum_R_73


title: serum_R_69


title: serum_R_67


title: serum_R_65


title: serum_R_83


title: serum_R_64


title: serum_R_66


title: serum_R_62


title: serum_R_68


title: serum_R_59


title: serum_R_56


title: serum_R_58


title: serum_R_60


title: serum_R_57


title: serum_R_55


title: serum_R_61


title: serum_R_54


title: serum_R_52


title: serum_R_51


title: serum_R_53


title: serum_R_50


title: serum_R_49


title: serum_R_48


title: serum_R_46


title: serum_R_47


title: serum_R_45


title: serum_R_43


title: serum_R_44


title: serum_R_42


title: serum_R_41


title: serum_R_63


title: serum_R_38


title: serum_R_37


title: serum_R_39


title: serum_R_33


title: serum_R_34


title: serum_R_36


title: serum_R_32


title: serum_R_31


title: serum_R_30


title: serum_R_24


title: serum_R_26


title: serum_R_27


title: serum_R_25


title: serum_R_29


title: serum_R_28


title: serum_R_21


title: serum_R_22


title: serum_R_23


title: serum_R_20


title: serum_R_19


title: serum_R_17


title: serum_R_18


title: serum_R_40


title: serum_R_16


title: serum_R_13


title: serum_R_11


title: serum_R_15


title: serum_R_35


title: serum_R_8


title: serum_R_9


title: serum_R_6


title: serum_R_5


title: serum_R_3


title: serum_R_4


title: serum_R_2


title: serum_R_1


title: 2i_R_191

value: 2i condition


title: 2i_R_190


title: 2i_R_188


title: 2i_R_189


title: 2i_R_187


title: 2i_R_185


title: 2i_R_186


title: serum_R_14


title: 2i_R_183


title: 2i_R_184


title: 2i_R_182


title: serum_R_10


title: 2i_R_180


title: 2i_R_179


title: 2i_R_178


title: serum_R_7


title: serum_R_12


title: 2i_R_175


title: 2i_R_174


title: 2i_R_173


title: 2i_R_172


title: 2i_R_192


title: 2i_R_171


title: 2i_R_169


title: 2i_R_177


title: 2i_R_170


title: 2i_R_168


title: 2i_R_167


title: 2i_R_166


title: 2i_R_162


title: 2i_R_164


title: 2i_R_165


title: 2i_R_161


title: 2i_R_181


title: 2i_R_159


title: 2i_R_176


title: 2i_R_158


title: 2i_R_157


title: 2i_R_155


title: 2i_R_154


title: 2i_R_153


title: 2i_R_160


title: 2i_R_150


title: 2i_R_151


title: 2i_R_147


title: 2i_R_145


title: 2i_R_148


title: 2i_R_149


title: 2i_R_146


title: 2i_R_142


title: 2i_R_140


title: 2i_R_144


title: 2i_R_141


title: 2i_R_138


title: 2i_R_136


title: 2i_R_137


title: 2i_R_152


title: 2i_R_156


title: 2i_R_135


title: 2i_R_132


title: 2i_R_130


title: 2i_R_128


title: 2i_R_133


title: 2i_R_127


title: 2i_R_126


title: 2i_R_131


title: 2i_R_123


title: 2i_R_134


title: 2i_R_163


title: 2i_R_121


title: 2i_R_124


title: 2i_R_129


title: 2i_R_119


title: 2i_R_117


title: 2i_R_122


title: 2i_R_118


title: 2i_R_114


title: 2i_R_139


title: 2i_R_143


title: 2i_R_113


title: 2i_R_111


title: 2i_R_112


title: 2i_R_125


title: 2i_R_110


title: 2i_R_109


title: 2i_R_107


title: 2i_R_106


title: 2i_R_120


title: 2i_R_108


title: 2i_R_105


title: 2i_R_104


title: 2i_R_100


title: 2i_R_102


title: 2i_R_97


title: 2i_R_96


title: 2i_R_103


title: 2i_R_116


title: 2i_R_95


title: 2i_R_115


title: 2i_R_101


title: 2i_R_94


title: 2i_R_98


title: 2i_R_93


title: 2i_R_92


title: 2i_R_89


title: 2i_R_88


title: 2i_R_85


title: 2i_R_87


title: 2i_R_86


title: 2i_R_84


title: 2i_R_83


title: 2i_R_82


title: 2i_R_80


title: 2i_R_79


title: 2i_R_99


title: 2i_R_81


title: 2i_R_77


title: 2i_R_75


title: 2i_R_73


title: 2i_R_67


title: 2i_R_71


title: 2i_R_70


title: 2i_R_65


title: 2i_R_66


title: 2i_R_76


title: 2i_R_68


title: 2i_R_91


title: 2i_R_63


title: 2i_R_74


title: 2i_R_64


title: 2i_R_90


title: 2i_R_72


title: 2i_R_69


title: 2i_R_61


title: 2i_R_62


title: 2i_R_59


title: 2i_R_58


title: 2i_R_60


title: 2i_R_57


title: 2i_R_78


title: 2i_R_56


title: 2i_R_55


title: 2i_R_54


title: 2i_R_53


title: 2i_R_52


title: 2i_R_51


title: 2i_R_49


title: 2i_R_50


title: 2i_R_48


title: 2i_R_47


title: 2i_R_46


title: 2i_R_42


title: 2i_R_45


title: 2i_R_39


title: 2i_R_37


title: 2i_R_36


title: 2i_R_32


title: 2i_R_33


title: 2i_R_31


title: 2i_R_44


title: 2i_R_43


title: 2i_R_41


title: 2i_R_38


title: 2i_R_40


title: 2i_R_35


title: 2i_R_25


title: 2i_R_27


title: 2i_R_22


title: 2i_R_23


title: 2i_R_24


title: 2i_R_28


title: 2i_R_20


title: 2i_R_26


title: 2i_R_18


title: 2i_R_19


title: 2i_R_34


title: 2i_R_21


title: 2i_R_15


title: 2i_R_14


title: 2i_R_13


title: 2i_R_17


title: 2i_R_12


title: 2i_R_11


title: 2i_R_16


title: 2i_R_30


title: 2i_R_9


title: 2i_R_8


title: 2i_R_29


title: 2i_R_10


title: 2i_R_6


title: 2i_R_5


title: 2i_R_3


title: 2i_R_2


title: serum_H_192


title: 2i_R_1


title: serum_H_185


title: serum_H_182


title: serum_H_181


title: serum_H_191


title: serum_H_190


title: serum_H_186


title: serum_H_178


title: serum_H_175


title: serum_H_177


title: serum_H_188


title: serum_H_183


title: serum_H_174


title: serum_H_180


title: serum_H_176


title: serum_H_170


title: serum_H_179


title: serum_H_173


title: 2i_R_7


title: serum_H_171


title: serum_H_169


title: 2i_R_4


title: serum_H_184


title: serum_H_168


title: serum_H_167


title: serum_H_166


title: serum_H_164


title: serum_H_165


title: serum_H_189


title: serum_H_163


title: serum_H_162


title: serum_H_161


title: serum_H_160


title: serum_H_159


title: serum_H_158


title: serum_H_156


title: serum_H_157


title: serum_H_154


title: serum_H_172


title: serum_H_152


title: serum_H_153


title: serum_H_155


title: serum_H_147


title: serum_H_150


title: serum_H_141


title: serum_H_146


title: serum_H_145


title: serum_H_139


title: serum_H_137


title: serum_H_149


title: serum_H_144


title: serum_H_135


title: serum_H_136


title: serum_H_142


title: serum_H_187


title: serum_H_143


title: serum_H_132


title: serum_H_131


title: serum_H_130


title: serum_H_138


title: serum_H_128


title: serum_H_126


title: serum_H_133


title: serum_H_148


title: serum_H_134


title: serum_H_129


title: serum_H_127


title: serum_H_125


title: serum_H_121


title: serum_H_122


title: serum_H_117


title: serum_H_120


title: serum_H_118


title: serum_H_112


title: serum_H_116


title: serum_H_151


title: serum_H_109


title: serum_H_115


title: serum_H_108


title: serum_H_113


title: serum_H_114


title: serum_H_111


title: serum_H_103


title: serum_H_124


title: serum_H_123


title: serum_H_104


title: serum_H_110


title: serum_H_107


title: serum_H_105


title: serum_H_102


title: serum_H_95


title: serum_H_100


title: serum_H_101


title: serum_H_97


title: serum_H_90


title: serum_H_96


title: serum_H_94


title: serum_H_98


title: serum_H_99


title: serum_H_119


title: serum_H_92


title: serum_H_91


title: serum_H_81


title: serum_H_79


title: serum_H_88


title: serum_H_87


title: serum_H_89


title: serum_H_86


title: serum_H_74


title: serum_H_82


title: serum_H_83


title: serum_H_78


title: serum_H_80


title: serum_H_140


title: serum_H_93


title: serum_H_77


title: serum_H_72


title: serum_H_75


title: serum_H_76


title: serum_H_85


title: serum_H_84


title: serum_H_70


title: serum_H_69


title: serum_H_67


title: serum_H_71


title: serum_H_62


title: serum_H_63


title: serum_H_65


title: serum_H_64


title: serum_H_58


title: serum_H_73


title: serum_H_60


title: serum_H_59


title: serum_H_66


title: serum_H_55


title: serum_H_56


title: serum_H_57


title: serum_H_53


title: serum_H_49


title: serum_H_48


title: serum_H_51


title: serum_H_50


title: serum_H_45


title: serum_H_44


title: serum_H_46


title: serum_H_52


title: serum_H_42


title: serum_H_40


title: serum_H_39


title: serum_H_68


title: serum_H_106


title: serum_H_61


title: serum_H_37


title: serum_H_41


title: serum_H_35


title: serum_H_36


title: serum_H_34


title: serum_H_54


title: serum_H_28


title: serum_H_32


title: serum_H_30


title: serum_H_33


title: serum_H_47


title: serum_H_38


title: serum_H_25


title: serum_H_24


title: serum_H_23


title: serum_H_22


title: serum_H_26


title: serum_H_21


title: serum_H_19


title: serum_H_18


title: serum_H_17


title: serum_H_16


title: serum_H_43


title: serum_H_15


title: serum_H_13


title: serum_H_11


title: serum_H_12


title: serum_H_14


title: serum_H_10


title: serum_H_29


title: serum_H_8


title: serum_H_9


title: serum_H_7


title: serum_H_27


title: serum_H_6


title: serum_H_4


title: serum_H_1


title: serum_H_3


title: 2i_H_192


title: serum_H_2


title: 2i_H_189


title: 2i_H_191


title: serum_H_20


title: 2i_H_190


title: 2i_H_185


title: 2i_H_184


title: 2i_H_187


title: 2i_H_186


title: 2i_H_182


title: 2i_H_183


title: 2i_H_178


title: 2i_H_180


title: 2i_H_176


title: 2i_H_181


title: serum_H_5


title: 2i_H_174


title: 2i_H_175


title: 2i_H_173


title: 2i_H_177


title: serum_H_31


title: 2i_H_172


title: 2i_H_171


title: 2i_H_168


title: 2i_H_167


title: 2i_H_169


title: 2i_H_188


title: 2i_H_166


title: 2i_H_164


title: 2i_H_163


title: 2i_H_165


title: 2i_H_162


title: 2i_H_179


title: 2i_H_158


title: 2i_H_159


title: 2i_H_156


title: 2i_H_155


title: 2i_H_153


title: 2i_H_154


title: 2i_H_147


title: 2i_H_151


title: 2i_H_143


title: 2i_H_170


title: 2i_H_144


title: 2i_H_149


title: 2i_H_150


title: 2i_H_148


title: 2i_H_145


title: 2i_H_138


title: 2i_H_161


title: 2i_H_139


title: 2i_H_136


title: 2i_H_135


title: 2i_H_132


title: 2i_H_133


title: 2i_H_134


title: 2i_H_142


title: 2i_H_141


title: 2i_H_140


title: 2i_H_131


title: 2i_H_152


title: 2i_H_146


title: 2i_H_137


title: 2i_H_125


title: 2i_H_126


title: 2i_H_124


title: 2i_H_123


title: 2i_H_122


title: 2i_H_119


title: 2i_H_160


title: 2i_H_118


title: 2i_H_113


title: 2i_H_115


title: 2i_H_130


title: 2i_H_157


title: 2i_H_110


title: 2i_H_108


title: 2i_H_109


title: 2i_H_105


title: 2i_H_100


title: 2i_H_99


title: 2i_H_96


title: 2i_H_95


title: 2i_H_128


title: 2i_H_129


title: 2i_H_93


title: 2i_H_127


title: RELA_KO2_Fulvestrant rep1

city: Boston

first: Yingtian

last: Xie

state: MA

address: 450 BROOKLINE AVE

institute: DANA FARBER CANCER INSTITUTE INC

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to hg19 using Bowtie
For peak calling STAR was used.
Assembly: hg19
Supplementary files format and content: bw files were generated using STAR using the VIPER pipeline

organism: Homo sapiens

source_name: Breast

growth_protocol: MCF7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA isolation was performed using the RNeasy Mini Kit (Qiagen). DNA was degraded on columns with DNase I (Qiagen).
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit (Illumina) adapted for use on the Sciclone (Perkin-Elmer) liquid handler.

treatment_protocol: MCF7 control, MCF7_RELA_KO1 and MCF7_RELA_KO2 cells were grown in phenol-red free medium supplemented with 10% heat-inactivated charcoal-stripped (CS)-FBS (HD) or HD in the presence of E2 (estradiol 10nM) for 72h (E2). Or treated with DMSO or Fulvestrant 10nM for 72h with and without stimulation with IFNg (10ng/mL) for 6h.

value: Breast

value: ER+ breast cancer cell line

tag: genotype

value: RELA KO2


title: 2i_H_91


title: 2i_H_121


title: 2i_H_120


title: 2i_H_114


title: 2i_H_117


title: 2i_H_90


title: 2i_H_116


title: 2i_H_106


title: 2i_H_112


title: RELA_KO2_6h_E2 rep3


title: 2i_H_111


title: 2i_H_88


title: 2i_H_107


title: 2i_H_102


title: 2i_H_104


title: 2i_H_98


title: 2i_H_103


title: RELA_KO2_Fulvestrant rep3


title: 2i_H_94


title: 2i_H_97


title: RELA_KO2_ED_6h rep3


title: RELA_KO2_Fulvestrant rep2


title: 2i_H_92


title: RELA_KO2_DMSO rep3


title: 2i_H_101


title: RELA_KO2_E2 rep2


title: RELA_KO2_DMSO rep2


title: RELA_KO2_ED rep2


title: 2i_H_89


title: RELA_KO2_DMSO rep1


title: 2i_H_87


title: 2i_H_86


title: RELA_KO2_E2_6h rep2


title: RELA_KO2_ED_6h rep1


title: 2i_H_85


title: RELA_KO1_Fulvestrant_6h rep3

value: RELA KO1


title: Triticonazole_GD21_M57c

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

data_processing:
library strategy: 3'DGE-Seq
Samples demultiplexing transforms the raw paired-end fastq files into a single-end fastq file for each sample.
All sixteen bases of the first read (from the read pairs) must have quality scores of at least 10 and the first six bases must correspond exactly to a designed well-specific barcode.
The second reads were aligned to the rat reference transcriptome from the UCSC website (release rn6, downloaded in December 2019 ) using bwa version 0.7.4 4.
Genome_build: rn6
Supplementary_files_format_and_content: Expression file in dat format. Contains for each sample, the number of unique umis (unique molecular identifier) associated with the 17,349 genes detected.

organism: Rattus norvegicus

growth_protocol: The animals were housed in a room with controlled environmental conditions with reversed light/dark cycles of 12 hours. All animals had ad libitum access to standard diet based on altromin 1314 (soy- and alfalfa-free) and tap water in Bisphenol A-free bottles.

extract_protocol:
Fetal testes were removed at gestational day 17 or 21 and stored in RNA-later at -80°C. RNA was harvested using RNeasy Micro Kit (Qiagen, Germany) including on-column DNase I treatment according to manufacturer’s instructions.
Libraries were prepared from 10 ng of total RNA. Poly(A) tailed mRNAs were tagged with universal adapters, well-specific barcodes and unique molecular identifiers (UMIs) during reverse transcription. Barcoded cDNAs from multiple samples were then pooled, amplified, and tagmented using a transposon-fragmentation approach that enriches for 3′ ends of cDNA. The resulting library of 350-800 bp was sequenced on anIllumina HiSeq 2500 using a TruSeq Rapid SBS kit (Illumina, San Diego, CA, USA).

treatment_protocol: Pregnant rat dams were exposed orally for two weeks during gestation (day 7-21) to 45 mg/kg bw/day flusilazole, 450 mg/kg bw/day triticonazole or corn oil (vehicle control).

value: wild type

value: Gestational Day 21

value: exposed to triticonazole during gestation (from day 7-21)

value: Testis


title: Triticonazole_GD21_M60c


title: Triticonazole_GD21_M59c


title: Triticonazole_GD21_M60a


title: RELA_KO1_Fulvestrant_6h rep2


title: RELA_KO2_ED rep1


title: RELA_KO2_E2 rep1


title: RELA_KO2_ED_6h rep2


title: Triticonazole_GD21_M58c


title: Triticonazole_GD21_M20c


title: 2i_H_83


title: 2i_H_84


title: RELA_KO1_DMSO_6h rep1


title: 2i_H_80


title: RELA_KO1_DMSO_6h rep3


title: RELA_KO1_Fulvestrant_6h rep1


title: Triticonazole_GD21_M19c


title: 2i_H_82


title: RELA_KO1_E2_6h rep2


title: RELA_KO1_E2_6h rep3


title: RELA_KO1_E2_6h rep1


title: Triticonazole_GD21_M18a


title: Triticonazole_GD21_M18c


title: RELA_KO1_ED_6h rep3


title: 2i_H_78


title: 2i_H_79


title: 2i_H_81


title: Triticonazole_GD21_M17c


title: RELA_KO1_DMSO_6h rep2


title: RELA_KO1_E2 rep1


title: RELA_KO1_E2 rep2


title: RELA_KO1_ED_6h rep1


title: RELA_KO1_ED_6h rep2


title: Triticonazole_GD21_M17a


title: RELA_KO2_E2_6h rep3


title: 2i_H_77


title: RELA_KO1_ED rep2


title: 2i_H_76


title: 2i_H_75


title: RELA_KO1_ED rep1


title: Flusilazole_GD21_M43c

value: exposed to flusilazole during gestation (from day 7-21)


title: 2i_H_73


title: RELA_Control_DMSO_6h rep3

value: RELA wildtype


title: RELA_Control_Fulvestrant_6h rep2


title: 2i_H_74


title: Flusilazole_GD21_M44a


title: RELA_Control_Fulvestrant_6h rep1


title: 2i_H_72


title: RELA_Control_DMSO_6h rep1


title: RELA_Control_E2_6h rep3


title: RELA_Control_Fulvestrant_6h rep3


title: Flusilazole_GD21_M44c


title: Flusilazole_GD21_M41c


title: RELA_Control_E2_6h rep1


title: 2i_H_71


title: Flusilazole_GD21_M12c


title: RELA_Control_ED_6h rep2


title: 2i_H_69


title: Flusilazole_GD21_M11d


title: RELA_Control_E2 rep2


title: RELA_Control_ED_6h rep1


title: Flusilazole_GD21_M42c


title: RELA_Control_E2 rep1


title: RELA_Control_DMSO_6h rep2


title: 2i_H_68


title: RELA_Control_ED rep2


title: RELA_Control_ED rep1


title: RELA_Control_E2_6h rep2


title: 2i_H_66


title: Flusilazole_GD21_M9c


title: ATAC_MCF7_E2_IFN_1

data_processing:
Burrows-Wheeler Aligner (BWA) to map sequencing reads to the reference genome
MACS2 for peakcalling
DESeq2 was applied to identify the differentially accessible regions with or without IFNg treatment
Assembly: hg19

source_name: breast

growth_protocol: Cells were grown in phenol-red free medium supplemented with 10% heat-inactivated charcoal-stripped (CS)-FBS (HD) or HD in the presence of E2 (estradiol 10nM) for 72h. Then stimulated or nort with IFNg (10ng/mL) for 24h.

extract_protocol:
Cells was fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep kit (Rubicon Genomics). Libraries were sequenced using 75-bp reads on the Illumina platform at the Dana-Farber Cancer Institute.

value: breast

value: E2 + IFNg 10ng/mL


title: ATAC_MCF7_E2_IFN_2


title: 2i_H_67


title: Flusilazole_GD21_M10a


title: 2i_H_70


title: ATAC_MCF7_WM_IFN_1

value: HD + IFNg 10ng/mL


title: 2i_H_65


title: ATAC_MCF7_E2_2


title: 2i_H_64


title: ATAC_MCF7_E2_1


title: Ctrl_GD21_M28c

value: exposed to vehicle during gestation (from day 7-21)


title: ATAC_MCF7_WM_IFN_2


title: ATAC_MCF7_WM_2

value: HD


title: Flusilazole_GD21_M10c


title: ATAC_MCF7_WM_1


title: 2i_H_63

value: cultured mouse embryonic stem cells


title: Ctrl_GD21_M27c


title: 2i_H_62

value: 2i condition


title: Ctrl_GD21_M27a


title: Ctrl_GD21_M26c


title: MCF7 cells, Combination, IFNg_rep2

treatment_protocol: Cells were treated with vehicle DMSO, Fulvestrant (10nM), Birinapant (100nM) and the combination for 72h with or without the stimulation of IFNg (10ng/mL) for the last 24 hours.

value: Breast

value: Combination + IFNg


title: Flusilazole_GD21_M9a


title: Content-24: Content-Probiotic20-5(PND36)

type: RNA

city: Toronto

first: Elena

last: Comelli

state: Ontario

address: 1 king's college circle, MSB5354

department: Nutritional Sciences

country: Canada

institute: University of Toronto

hyb_protocol: 100 ng of total RNA per sample, was first hybridized with capture and reporter probes which then hybridize to the target molecules, using Nanostring miRNA assay kit and following the manufacturer’s instructions (NanoString Technologies, Inc., Seattle, WA, U.S.).

scan_protocol: Following the manufacturer’s instructions (NanoString Technologies, Inc., Seattle, WA, U.S.)

data_processing: MiRNA expression data were processed using the Bioconductor package NanoStringNorm (Waggott et al., 2012) v1.2.0; 2). Briefly, data were normalized by adjusting for a technical assay variation by using the geometric mean calculated across all the samples as a normalizing factor. The data were background-corrected by subtracting the mean of negative controls, adjusted for sample content variation using the total sum of all the endogenous probes, and finally, log2 transformed. Please note that RCC files are raw data collected using the Nanostring digital analyzer, while, the txt files correspond to the raw data extracted from the RCC files.

label: Fluorescent barcode and biotin moiety

source_name: Mouse cecum

label_protocol: Not supplied

extract_protocol: Total RNA was extracted from cecal tissue and cecal content using the mirVana™ miRNA Isolation Kit (catalog no. AM1561, Invitrogen™, Thermo Fisher Scientific, Vilnius, Lithuania), following the manufacturer’s protocol

tag: sample

value: Cecal Content

tag: treatment group

value: Probiotics

tag: dam no.

tag: pup no.

tag: postnatal day (pnd)

value: Mouse cecum


title: 2i_H_61


title: MCF7 cells, Combination, IFNg_rep1

value: ER+ breast cancer cell line


title: Ctrl_GD21_M26a

value: wild type

value: Gestational Day 21


title: MCF7 cells, Birinapant, IFNg_rep3

value: Birinapant + IFNg


title: 2i_H_60


title: 2i_H_59


title: Content-22: Content-Probiotic17-1(PND36)


title: Content-23: Content-Probiotic20-1(PND21)


title: Content-21: Content-Probiotic17-3(PND21)


title: 2i_H_58


title: Ctrl_GD21_M4c

value: Testis


title: Ctrl_GD21_M25a


title: MCF7 cells, Birinapant, IFNg_rep2


title: Ctrl_GD21_M3c


title: 2i_H_57


title: Ctrl_GD21_M25c


title: MCF7 cells, Birinapant, IFNg_rep1


title: MCF7 cells, Fulvestrant, IFNg_rep3

value: Fulvestrant + IFNg


title: 2i_H_56


title: Content-20: Content-Probiotic10-5(PND21)


title: MCF7 cells, Fulvestrant, IFNg_rep2


title: Ctrl_GD21_M2c


title: MCF7 cells, Combination, IFNg_rep3


title: Content-18: Content-Control20-4(PND36)

value: Control


title: Content-17: Content-Control20-3(PND21)


title: MCF7 cells, Fulvestrant, IFNg_rep1


title: Content-16: Content-Control20-1(PND14)


title: 2i_H_54


title: 2i_H_53


title: Ctrl_GD21_M1c


title: Content-15: Content-Control19-6(PND36)


title: MCF7 cells, DMSO, IFNg_rep2

value: Control DMSO + IFNg


title: Ctrl_GD21_M1a

value: exposed to vehicle during gestation (from day 7-21)


title: MCF7 cells, DMSO, IFNg_rep1


title: 2i_H_52


title: Content-14: Content-Control19-3(PND21)


title: Content-19: Content-Probiotic10-3(PND14)


title: Triticonazole_GD17_M56e

value: Gestational Day 17

value: exposed to triticonazole during gestation (from day 7-21)


title: 2i_H_55

value: cultured mouse embryonic stem cells

value: 2i condition


title: Content-13: Content-Control19-1(PND14)


title: Triticonazole_GD17_M56c


title: Triticonazole_GD17_M56a


title: Content-12: Content-Probiotic21-3(PND36)


title: MCF7 cells, Combination, No IFNg_rep2

value: Breast

value: Combination


title: Content-11: Content-Probiotic16-3(PND36)

value: Cecal Content

value: Probiotics


title: Triticonazole_GD17_M55c


title: Content-10: Content-Probiotic16-1(PND21)

value: Mouse cecum


title: Triticonazole_GD17_M55a

value: wild type


title: MCF7 cells, Birinapant, No IFNg_rep3

value: ER+ breast cancer cell line

value: Birinapant


title: MCF7 cells, DMSO, IFNg_rep3


title: 2i_H_48


title: Ctrl_GD21_M2a

value: Gestational Day 21

value: Testis


title: 2i_H_47


title: MCF7 cells, Combination, No IFNg_rep3


title: 2i_H_51


title: Content-09: Content-Probiotic16-7(PND14)


title: RELA_Control_ED_6h rep3

value: RELA wildtype


title: Content-08: Content-Probiotic11-3(PND21)


title: MCF7 cells, Birinapant, No IFNg_rep2


title: 2i_H_45


title: 2i_H_50


title: MCF7 cells, Fulvestrant, No IFNg_rep3

value: Fulvestrant


title: 2i_H_46


title: MCF7 cells, Combination, No IFNg_rep1


title: Triticonazole_GD17_M54a


title: 2i_H_44


title: 2i_H_49


title: Content-06: Content-Control11-5(PND36)

value: Control


title: Triticonazole_GD17_M53e

value: Gestational Day 17


title: Triticonazole_GD17_M54c

value: exposed to triticonazole during gestation (from day 7-21)


title: MCF7 cells, Birinapant, No IFNg_rep1


title: Content-05: Content-Control11-1(PND21)


title: Content-07: Content-Probiotic11-5(PND14)


title: 2i_H_42

value: cultured mouse embryonic stem cells


title: MCF7 cells, Fulvestrant, No IFNg_rep2


title: 2i_H_43

value: 2i condition


title: MCF7 cells, DMSO, No IFNg_rep3

value: Breast

value: Control DMSO


title: Triticonazole_GD17_M54e


title: Triticonazole_GD17_M53c


title: MCF7 cells, Fulvestrant, No IFNg_rep1


title: 2i_H_39


title: Flusilazole_GD17_M40c

value: exposed to flusilazole during gestation (from day 7-21)


title: MCF7 cells, DMSO, No IFNg_rep2


title: Triticonazole_GD17_M53a


title: Flusilazole_GD17_M40a


title: 2i_H_41


title: Content-04: Content-Control11-7(PND14)

value: Cecal Content


title: Content-02: Content-Control10-1(PND21)

value: Mouse cecum


title: Content-03: Content-Control10-5(PND36)


title: MCF7 cells, DMSO, No IFNg_rep1


title: MCF7_Talen_E2_INF_1

growth_protocol: MCF7 cells ER wildtype or (Talen)Y537S Knock-in were grown in phenol-red free medium supplemented with 10% heat-inactivated charcoal-stripped (CS)-FBS (HD) or HD in the presence of E2 (estradiol 10nM) for 72h. Then stimulated with IFNg (10ng/mL) for 24h.

value: breast

value: ER Y537S Knock-in

value: E2 + IFNg 10ng/mL 24h


title: Content-01: Content-Control10-6(PND14)


title: MCF7_Talen_WM_INF_2

value: ER+ breast cancer cell line

value: HD + IFNg 10ng/mL 24h


title: 2i_H_36


title: Flusilazole_GD17_M39a

value: wild type

value: Testis


title: 2i_H_37


title: Flusilazole_GD17_M40e


title: MCF7_Talen_E2_INF_2

value: E2+ IFNg 10ng/mL 24h


title: MCF7_Talen_WM_INF_1


title: Tissue-24: Tissue-Probiotic20-5(PND36)

value: Cecal Tissue

value: Probiotics


title: Flusilazole_GD17_M38e

value: Gestational Day 17


title: 2i_H_40

value: cultured mouse embryonic stem cells

value: 2i condition


title: 2i_H_38


title: Flusilazole_GD17_M39c


title: Tissue-22: Tissue-Probiotic17-1(PND36)


title: Tissue-23: Tissue-Probiotic20-1(PND21)


title: 2i_H_35


title: Tissue-21: Tissue-Probiotic17-3(PND21)


title: 2i_H_34


title: Flusilazole_GD17_M38a


title: Flusilazole_GD17_M38c


title: MCF7_Talen_E2_1


title: 2i_H_33


title: Flusilazole_GD17_M37e


title: Tissue-20: Tissue-Probiotic10-5(PND21)


title: 2i_H_32


title: MCF7_Talen_WM_2

value: HD


title: Flusilazole_GD17_M37c

value: exposed to flusilazole during gestation (from day 7-21)


title: MCF7_Talen_WM_1


title: Tissue-18: Tissue-Control20-4(PND36)

value: Control


title: Tissue-19: Tissue-Probiotic10-3(PND14)

value: Mouse cecum


title: 2i_H_30


title: Tissue-17: Tissue-Control20-3(PND21)


title: Flusilazole_GD17_M37a


title: 2i_H_31


title: MCF7_E2_INF_2

value: breast

value: ER wildtype


title: MCF7_E2_INF_1

value: E2 + IFNg 10ng/mL 24h


title: Ctrl_GD17_M24e

value: exposed to vehicle during gestation (from day 7-21)


title: MCF7_Talen_E2_2

value: ER+ breast cancer cell line

value: ER Y537S Knock-in


title: 2i_H_29


title: Ctrl_GD17_M24c

value: wild type

value: Testis


title: 2i_H_28


title: MCF7_WM_INF_2

value: HD + IFNg 10ng/mL 24h


title: Tissue-15: Tissue-Control19-6(PND36)

value: Cecal Tissue


title: Tissue-16: Tissue-Control20-1(PND14)


title: 2i_H_26


title: Ctrl_GD17_M23e

value: Gestational Day 17


title: MCF7_E2_2


title: Ctrl_GD17_M23c


title: Tissue-14: Tissue-Control19-3(PND21)


title: Tissue-13: Tissue-Control19-1(PND14)


title: 2i_H_27

value: cultured mouse embryonic stem cells


title: Tissue-12: Tissue-Probiotic21-3(PND36)

value: Probiotics


title: Tissue-11: Tissue-Probiotic16-3(PND36)


title: Ctrl_GD17_M23a


title: Ctrl_GD17_M22c


title: 2i_H_23

value: 2i condition


title: Tissue-10: Tissue-Probiotic16-1(PND21)


title: MCF7_WM_1

value: HD


title: 2i_H_25


title: Ctrl_GD17_M22a


title: MCF7_WM_INF_1


title: 2i_H_22


title: MCF7 cells,  E2, IFNg 48h rep3

treatment_protocol: Cells were grown in phenol-red free medium supplemented with 10% heat-inactivated charcoal-stripped (CS)-FBS (HD) or HD in the presence of E2 (estradiol 10nM) for 72h. Then stimulated with IFNg (10ng/mL) for 6, 12, 24 and 48h.

value: Breast

value: E2 + IFNg 48h


title: MCF7 cells,  E2, IFNg 48h rep2


title: Ctrl_GD17_M21e


title: 2i_H_21


title: Tissue-08: Tissue-Probiotic11-3(PND21)

value: Mouse cecum


title: Ctrl_GD17_M24a


title: MCF7_E2_1

value: breast

value: ER wildtype


title: Tissue-07: Tissue-Probiotic11-5(PND14)


title: Ctrl_GD17_M21a

value: exposed to vehicle during gestation (from day 7-21)


title: 2i_H_20


title: MCF7 cells,  E2, IFNg 48h rep1

value: ER+ breast cancer cell line


title: MCF7_WM_2


title: HepG2,TRIM8_KO-3

city: Shanghai

first: xin

last: zhang

address: 415 Fengyang Road

institute: Changzheng hospital

data_processing:
Raw reads in fastq format were processed to remove contaminating adapter sequences using Trimmomatics
Quality distribution plot and base content distribution were generated by FASTQC
RNAseq reads were aligned to the hg38 genome using STAR.
Read counts for individual gene of each sample were produced with HTSeq-count
Assembly: hg38
Supplementary files format and content: txt(gene expression of all sample)

growth_protocol: HepG2 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS)  with 5% CO2 at 37C

extract_protocol:
RNA was extracted using Trizol following the manufacturer's protocol.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: hepatocllular

value: TRIM8 knockout


title: Tissue-06: Tissue-Control11-5(PND36)

value: Control


title: 2i_H_19


title: 2i_H_24


title: Tissue-05: Tissue-Control11-1(PND21)


title: 2i_H_18


title: HepG2,TRIM8_KO-1


title: Tissue-04: Tissue-Control11-7(PND14)


title: 2i_H_17


title: Tissue-09: Tissue-Probiotic16-7(PND14)


title: HepG2,G2_WT-3

value: WT


title: 2i_H_16


title: MCF7 cells,  E2, IFNg 12h rep3

value: E2 + IFNg 12h


title: HepG2,G2_WT-2


title: Tissue-03: Tissue-Control10-5(PND36)

value: Cecal Tissue


title: 2i_H_15

value: cultured mouse embryonic stem cells


title: sample22

city: Blacksburg

first: Fernando

middle: H

last: Biase

state: VA

address: 175 West Campus Drive

department: School of Animal Sciences

institute: Virginia Tech

data_processing:
We aligned the RNA-sequencing data to the cattle reference genome (ARS-UCD1.2/bosTau9) obtained from the Ensembl database  using HISAT2 (v2.2.1), followed by filtering with samtools (v1.17)  and removal of duplicates with biobambam2 (v2.0.95). Next, we counted the sequences matching the reference annotation (Bos_taurus.ARS-UCD1.2.105.gtf) using featureCounts (v2.0.1) .
Assembly: ARS-UCD1.2/bosTau9
Supplementary files format and content: raw counts

organism: Bos taurus

source_name: blastocyst

extract_protocol:
We lysed the embryos by adding 10 µL of lysis solution, consisting of: 8.3 µL Luna Cell Ready Lysis Buffer 2X (New England Biolabs, Ipswich, MA), 0.66 µL Luna Cell Ready RNA Protection Reagent 25X (New England Biolabs, Ipswich, MA), 0.66 µL Luna Cell Ready Protease 25X, (New England Biolabs, Ipswich, MA), and 0.33µL RNasin® Plus Ribonuclease Inhibitor (40U/ µL) (Promega, Madison, WI).  We incubated the solution on ice for 10 minutes, mixed by pipetting, then split the solution into two tubes. We extracted total RNA and from each ½ blastocyst using TRIzol reagent with Phasemaker Tubes for enhanced RNA purity and yield.
First we amplified the cDNA using a modified mcSCRB-seq protocol. Next we used 1ng of amplified cDNA as an input for the Illumina DNA flex library preparation, using two index strategy to distinguish libraries.

value: blastocyst

value: wild type


title: Tissue-02: Tissue-Control10-1(PND21)


title: MCF7 cells,  E2, IFNg 24h rep3

value: E2 + IFNg 24h


title: 2i_H_14

value: 2i condition


title: MCF7 cells,  E2, IFNg 12h rep1

value: Breast


title: sample21


title: HepG2,G2_WT-1


title: MCF7 cells,  E2, IFNg 24h rep2


title: HepG2,TRIM8_KO-2


title: MCF7_RELA_E2_IFNG_1h rep1

data_processing:
ChIP-seq analysis was performed as previously reported in ref 56
ChIP reads were aligned to the hg19 genome assembly using BWA
ChIP-seq peaks were called using MACS 2.0
DEseq2 was used to assign differential intensities and statistics
Differential binding sites was determined by filtering out insignificant peaks (adjusted p-value<0.05) and then determining log2FC values between samples for each region using a log2 FC >0 or <0
Assembly: hg19
Supplementary files format and content: Analysis was done using the CoBRA workflow

growth_protocol: Cells were grown in phenol-red free medium supplemented with 10% heat-inactivated charcoal-stripped (CS)-FBS (HD) or HD in the presence of E2 (estradiol 10nM) for 72h

treatment_protocol: MCF7 cells were grown in HD or E2 and stimulated or not with IFNg 10 ng/mL for 1h.

tag: chip antibody


title: MCF7 cells,  E2, IFNg 6h rep3

value: E2 + IFNg 6h


title: 2i_H_12


title: MCF7 cells,  E2, IFNg 24h rep1


title: 2i_H_13


title: MCF7 cells,  E2, IFNg 6h rep2


title: MCF7_RELA_E2_IFNG_1h rep2


title: sample19


title: sample20


title: MCF7 cells,  E2, IFNg 6h rep1


title: sample18


title: MCF7_RELA_E2 rep2


title: MCF7 cells,  E2, No IFNg rep3


title: 2i_H_11


title: MCF7 cells,  E2, IFNg 12h rep2


title: sample16


title: 2i_H_10


title: MCF7 cells,  E2, No IFNg rep2


title: MCF7_RELA_HD_IFNG_1h rep2


title: 2i_H_9


title: sample15


title: MCF7_RELA_HD_IFNG_1h rep1


title: MCF7 cells,  E2, No IFNg rep1


title: sample12

value: lacking exon 1 OCT4


title: 2i_H_8


title: MCF7_RELA_HD rep2


title: 2i_H_7


title: sample11


title: 2i_H_6


title: MCF7_RELA_HD rep1


title: MCF7 cells, HD, IFNg 48h rep3

value: HD + IFNg 48h


title: sample10


title: MCF7 cells, HD, IFNg 48h rep1


title: MCF7_RELA_E2 rep1


title: 2i_H_5


title: Prurigo nodularis, patient 5

city: Paris

first: Jean-David

last: Bouaziz

state: Ile-de-France

address: 1 Avenue Claude Vellefaux

department: Dermatology

institute: Hôpital Saint-Louis

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Drop-Seq core computational protocol 1.2
Cell Ranger 3.0.2
Assembly: GrCh38
Supplementary files format and content: barcode.tsv.gz; 1-column gzip compressed tsv file with list of barcodes used
Supplementary files format and content: features.tsv.gz; 3-columns gzip compressed tsv file with ENSEMBL ID, Gene SYMBOL, Feature type (Gene Expression)
Supplementary files format and content: matrix.mtx.gz; 3-column gzip compressed Market Exchange Format (MEX) file with gene count data per cell

source_name: Skin

extract_protocol:
Lymphocyte's concentrations were adjusted to load 2000 cells and enable the capture of 1000 cells per tissue sample. Cell suspensions were loaded onto separate chip inlet to perform cell encapsulation into droplets. Reverse transcription, cDNA generation and library preparation were achieve using the standard 10X Genomics single cell protocol (Chromium Single Cell 3  Reagent Kit V3.1.). The library was sequenced on the Illumina NovaSeq6000 platform following manufacturer s recommendations to obtain approximately 50 million reads per sample.
Single cells were captured using the droplet-based microfluidic system Chromium (10x Genomics) according to the manufacturer’s instructions. Lymphocyte’s concentrations were adjusted to enable the capture of ~2 000 cells per tissue sample.  The standard protocol for the 10x single cell Chromium Single Cell 3’ Reagent Kit V2 was followed and cells were loaded onto a separate chip inlet. The library was sequenced on the Illumina HiSeq 4000 platform following manufacturer’s recommendations to obtain approximately 50 million reads per sample

treatment_protocol: Wash-out period of topical treatments (2 weeks) and systemic treatments (3 months)

value: Skin

value: CD3+ T lymphocytes

tag: disease state

value: Prurigo nodularis


title: Prurigo nodularis, patient 6

description: 10X Genomics

value: Wash-out period of topical treatments (2 weeks) and systemic treatments (3 months)


title: sample07


title: MCF7 cells, HD, IFNg 24h rep3

value: ER+ breast cancer cell line

value: HD + IFNg 24h


title: sample04


title: Prurigo nodularis, patient 4

description: 10X Genomics


title: MCF7 cells, HD, IFNg 24h rep2


title: 2i_H_3


title: Ischemic stroke patient-Replicate 3

city: Beijing

first: JUNFEN

last: FAN

address: 45 Changchun St, Beijing 100053, China

institute: Xuanwu hospital of Capital Medical University

hyb_protocol: The Cy5 and Cy3 labeled  cRNAs were combined together and hybridized onto Arraystar Human mRNA&lncRNA Epitranscriptomic Microarray (8x60K, Arraystar).

scan_protocol: After washing the slides, the arrays were scanned in two-color channels by an Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 6 samples were retained as “All Targets Value” in the Excel sheet for further “m6A methylation level”, “m6A quantity” and “expression level” analyses. “m6A methylation level” was calculated for the percentage of modification based on the IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities. “expression level” was calculated based on the total of IP (Cy5-labelled) and Sup (Cy3-labelled) normalized intensities of RNA.
Differentially m6A-methylated RNAs or differentially expressed RNAs between two comparison groups were identified by filtering with the fold change and statistical significance (p-value) thresholds.

source_name: IP

label_protocol: The total RNAs were immunoprecipitated with anti-N6-methyadenosine (m6A) antibody. The modified RNAs were eluted from the immunoprecipitated magnetic beads as the “IP”. The unmodified RNAs were recovered from the supernatant as “Sup”. The “IP” and “Sup” RNAs were labeled with Cy5 and Cy3 respectively as cRNAs in separate reactions using Arraystar Super RNA Labeling Kit.

growth_protocol: Venous blood samples of ischemic stroke patients and healthy controls were collected into an EDTA anticoagulant vacuum tube.

extract_protocol: Total RNA was isolated from the neutrophils with the TRIzol reagent per the manufacturer’s instructions.

treatment_protocol: Neutrophils were separated by a standard Ficoll-Paque Plus gradient method, preserved in TRIzol Reagent and stored in the −80 °C refrigerator.

tag: gender

value: Male

value: Peripheral blood neutrophils

value: ischemic stroke

source_name: supernant


title: MCF7 cells, HD, IFNg 48h rep2


title: MCF7 cells, HD, IFNg 24h rep1


title: 2i_H_2

value: cultured mouse embryonic stem cells


title: Ischemic stroke patient-Replicate 2

value: Female


title: Prurigo nodularis, patient 2

description: 10X Genomics


title: MCF7 cells, HD, IFNg 12h rep3

value: HD + IFNg 12h


title: 2i_H_1

value: 2i condition


title: Prurigo nodularis, patient 1

description: 10X Genomics


title: Ischemic stroke patient-Replicate 1


title: CARE_rep2_RNA

data_processing:
Trimming the adaptor sequence: Adaptors and low-quality reads of Hi-C and RNA information were trimmed with Trim Galore (version 0.6.6, https://github.com/FelixKrueger/TrimGalore)
Alignment: Reads were aligned to mm10. For Hi-C data, HiC-Pro (PMID: 26619908) was used (version 3.0.0). For RNA-seq data, STAR (PMID: 23104886) was used with default parameters.
Quantification of gene expression: uniquely mapped reads of RNA-seq data were counted by scRNA-seq pipeline of sci-CAR analysis (https://github.com/JunyueC/sci-CAR_analysis).
Generation of hic files: All valid pairs were generated by HiC-Pro (PMID: 26619908) (version 3.0.0).
Assembly: mm10
Supplementary files format and content: *_raw_gene_counts.txt: raw read counts of each genes from RNA-seq data for expression analysis
Supplementary files format and content: *_allValidPairs: valid read pairs from Hi-C data for domain analysis or differential contact analysis
Library strategy: CARE-seq

extract_protocol:
For bulk cells (CARE-seq), the same as scCARE-seq, but the procedure does not require flow sorting. CARE-seq_DNA and CARE-seq _RNA respectively represents the information of 3D chromatin structure and transcription in the same cell population, separated by barcode.
For bulk cells (CARE-seq), oligo-biotin-dT was used for reverse transcription, and Tn5 tagmentation was performed after cell lysis without single cell sorting. The libraries were constructed after biotin enrichment.


title: Healthy control-Replicate 3

value: healthy


title: CARE_rep1_RNA


title: MCF7 cells, HD, IFNg 12h rep1

value: Breast


title: MCF7 cells, HD, IFNg 12h rep2


title: Atopic dermatitis, patient 4

description: 10X Genomics

value: Atopic dermatitis


title: 2i_H_4


title: MCF7 cells, HD, IFNg 6h rep3

value: HD + IFNg 6h


title: Tissue-01: Tissue-Control10-6(PND14)

value: Cecal Tissue

value: Control

value: Mouse cecum


title: MCF7 cells, HD, IFNg 6h rep2


title: Healthy control-Replicate 2


title: CARE_rep1


title: Atopic dermatitis, patient 5

description: 10X Genomics

value: Skin

value: CD3+ T lymphocytes

value: Wash-out period of topical treatments (2 weeks) and systemic treatments (3 months)


title: MCF7 cells, HD, IFNg 6h rep1

value: ER+ breast cancer cell line


title: Atopic dermatitis, patient 2

description: 10X Genomics


title: Prurigo nodularis, patient 3

description: 10X Genomics

value: Prurigo nodularis


title: Healthy control-Replicate 1

value: Male

value: Peripheral blood neutrophils


title: total_rep2_RNA

data_processing:
Trimming the adaptor sequence: Adaptors and low-quality reads of Hi-C and RNA information were trimmed with Trim Galore (version 0.6.6, https://github.com/FelixKrueger/TrimGalore)
Alignment: Reads were aligned to mm10. For Hi-C data, HiC-Pro (PMID: 26619908) was used (version 3.0.0). For RNA-seq data, STAR (PMID: 23104886) was used with default parameters.
Quantification of gene expression: uniquely mapped reads of RNA-seq data were counted by scRNA-seq pipeline of sci-CAR analysis (https://github.com/JunyueC/sci-CAR_analysis).
Generation of hic files: All valid pairs were generated by HiC-Pro (PMID: 26619908) (version 3.0.0).
Assembly: mm10
Supplementary files format and content: *_raw_gene_counts.txt: raw read counts of each genes from RNA-seq data for expression analysis
Supplementary files format and content: *_allValidPairs: valid read pairs from Hi-C data for domain analysis or differential contact analysis

extract_protocol:
RNA was harvested using Trizol (Invitrogen). 3 ug of total RNA was used for the construction of sequencing libraries. Or RNA was reversed in cell before cell lysis to harvest.
RNA libraries for RNA-seq were prepared using previous published protocols (PMID: 28818938; PMID: 22128135).

value: cultured mouse embryonic stem cells


title: Atopic dermatitis, patient 1

description: 10X Genomics


title: CARE_rep2


title: MCF7 cells, HD, No IFNg rep3

value: HD


title: WT_CDM_HA_Brg1_rep2

city: Houston

first: Junwoo

last: Lee

state: Texas

address: 2120 El Paseo Street, Apt.603

department: Epigenetics and Molecular Carcinogenesis

institute: MD Anderson Cancer Center

description:
WT_CDM_HA_Brg1_neg.bw
WT_CDM_HA_Brg1_pos.bw

data_processing:
All RIP-seq data were sequenced in single-end 75 bp length and reads were aligned to mm10 using Bowtie2 alignment tool using --very-sensitive-local  preset parameter. The mapped reads were compressed as binary form using samtools.
Data from two biological replicates were first merged into a single read file for each cell type for further downstream analysis.
RIP peaks were called using MACS2 with the following parameters:  --broad -q 0.01 --nomodel --keepdup all --max-gap 76. No-HA tag line was used as control for peak calling.
Peaks were annotated using the ‘annotatePeaks’ module of HOMER package.
Assembly: mm10, M22
Supplementary files format and content: bw files normalized by spike-in and No-HA tag controls. Spike-in normalized bedgraph files for No-HA tag control samples.

molecule: nuclear RNA

growth_protocol: Mouse embryonic stem cells (E14Tg2a, ATCC) were maintained in primed stage.

extract_protocol:
Mouse ESCs were fixed in 0.3% methanol-free formaldehyde for 30 min at 4 °C. Formaldehyde was quenched with 125 mM glycine for 5 min at room temperature (RT). Cells were washed three times in PBS at RT and resuspended at a final concentration of 10 million cells/mL. Cells were resuspended in 0.5 ml radioimmunoprecipitation assay (RIPA) buffer (50 mM Tris-HCl pH 8, 1% Triton X-100, 0.5% sodium deoxycholate, 0.1% SDS, 5 mM EDTA, 150 mM KCl) plus 0.5 mM DTT with 1× protease inhibitors (Sigma) and 2.5 μl RNAsin, and incubated on ice for 10 min prior to lysing using a Bioruptor (Diagenode) for two cycles of 30 s on and 1 min off, followed by centrifugation at 4 °C for 10 min at maximum speed. Protein A magnetic beads (Biorad) were pre-conjugated with antibody for 2 hr at 4 °C. Cells were then incubated overnight at 4 °C with antibody-conjugated beads. Beads were washed consecutively with fRIP buffer (25 mM Trix-HCl pH 7.5, 5 mM EDTA, 0.5% Ipegal CA-630, 150 mM KCl), three times in ChIP buffer (50 mM Tris-HCl pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), 1× in high salt buffer (ChIP buffer, but with 500 mM NaCl) and 1× in fRIP buffer. All washes were performed for 5 min at 4 °C. After the final wash, beads were resuspended in 100 μl of 1× reverse crosslinking buffer (3× PBS, 6% N-lauroyl sarcosine, 30 mM EDTA) supplemented with 5 mM DTT, 20 μl proteinase K and 1 μl SUPERaseIN and incubated 1 h at 42 °C, 1 h at 55 °C, and 30 min at 65 °C. Following elution and crosslink reversal, Trizol was used to extract RNA. Finally, RNA in the aqueous phase was supplemented with 1 volume of ethanol and purified using a Zymo-spin IC column, including the on-column DNase digestion, as per the manufacturer’s instruction. RNA was eluted in 15 μl double distilled water (ddH20).
RNA-seq libraries were prepared by using equal volume of the immunoprecipitate and included 1 μl of 1:250 μl dilution of ERCC spike-in mix 1 (Life Technologies). Libraries were then prepared using the Kapa Ribo-zero kit following the manufacturer’s instructions, pooled, and sequenced using single-end 75-bp reads on an Illumina Nextseq 500.

value: embryonic stem cells

tag: medium

value: CDM

value: WT

tag: rip antibody

value: Anti-HA (Invitrogen, cat# 26183; RRID:AB_10978021)


title: WT_CDM_No-HA_rep2

description:
WT_CDM_No_HA_rep1.neg.bedgraph
WT_CDM_No_HA_rep1.pos.bedgraph

value: No-HA


title: WT_CDM_No-HA_rep1


title: MCF7 cells, HD, No IFNg rep2

value: Breast


title: nuclei_rep2_RNA


title: Heathy control, patient 5

description: 10X Genomics

value: Plastic surgery (discarded skin)

value: Healthy control


title: MCF7 cells, HD, No IFNg rep1


title: nuclei_rep1_RNA


title: Heathy control, patient 4

description: 10X Genomics

value: Skin


title: Atopic dermatitis, patient 3

description: 10X Genomics

value: CD3+ T lymphocytes

value: Atopic dermatitis


title: Heathy control, patient 3

description: 10X Genomics


title: dAT2_CDM_HA_Brg1_rep2

description:
dAT2_CDM_HA_Brg1_neg.bw
dAT2_CDM_HA_Brg1_pos.bw

value: dAT


title: WT_CDM_HA_Brg1_rep1


title: HiC_rep2

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was tagmentation by Tn5 and enriched by Dynabeads MyOne Streptavidin T1 (Invitrogen).
In situ Hi-C was performed according to a published protocol (PMID: 25497547; PMID: 31442560). But the library preparation was optimized. Briefly, chromatin was digested by AluI, and after sonication, the purified DNA per 0.5 million cells was add Tagmentation Buffer (27   L ddH2O, 10   L 5x TAPS-DMF, 3   L 12.5   M in-house Tn5). And then the sample was enriched by Streptavidin T1 Beads (Invitrogen, 65602). Libraries were amplified using 10-14 cycles on the thermocycler. Post amplification libraries were size selected using 0.8X Agencourt AMPure XP beads from Beckman Coulter.


title: LN229 ARNT2 KO C4 sample 3

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

data_processing:
Raw reads were aligned to hg38 using STAR 2.7.3a
Gene expression was quantified using Subread 1.6.3
Gene expression was normalized using R package DESeq2

growth_protocol: All cells were maintained in DMEM supplemented with 5% FBS in humidified incubator with 5% CO2 at 37C.

extract_protocol:
RNA samples were extracted by Genewiz (now Azenta)
Library was constructed by Genewiz (now Azenta)

value: Glioblastoma

value: ARNT2 KO


title: Heathy control, patient 2

description: 10X Genomics


title: LN229 ARNT2 KO C4 sample 2


title: HiC_rep1


title: dAT1_CDM_HA_Brg1_rep2

description:
dAT1_CDM_HA_Brg1_neg.bw
dAT1_CDM_HA_Brg1_pos.bw


title: Heathy control, patient 1

description: 10X Genomics


title: LN229 ARNT2 KO C4 sample 1


title: HuR_3

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house  perl scripts. In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database  of splice junctions based on the gene model annotation file and thus a better mapping  result than other non-splice mapping tools
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and is  currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using the  DESeq2 R package (1.16.1). DESeq2 provide statistical routines for determining  differential expression in digital gene expression data using a model based on the  negative binomial distribution. The resulting P-values were adjusted using the  Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes  with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially  expressed
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: abundance measurements

source_name: HuR-overexpressing primary hepatocytes

growth_protocol: Primary hepatocytes were isolated from C57BL/6 mice by liver-perfusion with type II collagenase (Worthington Biochem, Lakewood, NJ) and cultured at 37°C and 5% CO2 in RPMI 1640 medium supplemented with 2% FBS.

extract_protocol:
Total RNAs were extracted using TriPure Isolation Reagent (Roche, Mannheim, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Primary hepatocytes were infected with βGal and HuR adenoviruses overnight.

tag: tag

tag: genotype/variation

value: primary hepatocytes

value: HuR


title: total_rep1_RNA

value: cultured mouse embryonic stem cells


title: LN229 ARNT2 KO B3 sample 3


title: SiHa-1

city: Shenzhen

first: sheng

last: zhong

address: The Xinhu Road 1333

institute: The Sourthern Medical University

data_processing:
Trimmomatic software were used to remove adapter and low quality reads.
Mapping of pair-end reads. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the bwa program.
We calculate the fragment sizes for read pairs given a BAM file from paired-end sequencing. Several regions are sampled depending on the size of the genome and number of processors to estimate the summary statistics on the fragment lengths. Properly paired reads are used for computation.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
The HOMER's findMotifsGenome.pl tool was used for Motif analysis. The input file is the peak file and the genome fasta file. The DNA sequence is extracted according to the peak file, and the sequence is compared with the Motif database to obtain the Motif.Peaks were annotated by the function of annotatePeak of ChIPseeker.
Assembly: hg38
Supplementary files format and content: bw
Library strategy: CUT&Tag

source_name: SiHa

extract_protocol:
The procedure includes Tn5-adapter complex formation,binding cells to Concanavalin A-coated beads,binding primary antibody,binding secondary antibody,binding pA-Tn5, adapter complex,tagmentation and DNA extraction.
Determine the size distribution and concentration of libraries by capillary electrophoresis using an Agilent 4200 TapeStation or equivalent.

value: SiHa

value: cervical cancer cells

value: wildtype


title: HuR_2


title: SiHa-1_IgG


title: LN229 ARNT2 KO B3 sample 2


title: dAT1_CDM_HA_Brg1_rep1

value: embryonic stem cells

value: CDM

value: Anti-HA (Invitrogen, cat# 26183; RRID:AB_10978021)


title: 22Rv1 clip_rep2

city: Chicago

first: Chuan

last: He

state: Illinois

address: 929 E 57th St, Room E319B

institute: University of Chicago

data_processing:
Adapter trimming by Cutadapt
Reads mapping by STAR to hg19 transcriptome
Peak calling by omniCLIP
Assembly: hg19
Supplementary files format and content: For [Dataset 1], excel files with peaks annotated by omniCLIP

source_name: 22Rv1 cells

growth_protocol: Wild-type 22Rv1 cells are maintained in RPMI1640 + 10% FBS.

extract_protocol:
For [Dataset 1], cell lysates were treated with Rnase T1 to fragment, and RBM15-bound RNAs were extracted by immunoprecipitation. Both input and CLIP RNA were subjected to end-repair with T4 PNK.
For [Dataset 1], Rna libraries were constructed with NEBNext® Small RNA Library Prep Set for Illumina®(NEB, E7330S)

value: wild-type (ATCC, CRL-2505)

tag: ip antibody

value: Proteintech 10587-1-AP


title: Vcap,H3K4me1,ABCAM_2

city: Rochester

first: LIGUO

last: WANG

state: MN

address: 200 1st St SW

department: Division of Computational Biology

institute: Mayo Clinic

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg19 genome (GRCh37) using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg19/GRCh37
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: Vcap

growth_protocol: DMEM, 10% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Vcap

value: prostate cancer cell line


title: LN229 ARNT2 KO B3 sample 1


title: Gal_3

value: beta-Gal


title: 22Rv1 clip_rep1


title: dAT2_CDM_HA_Brg1_rep1

value: dAT


title: LN229 WT sample 3

value: Glioblastoma

value: WT