title: 8F_M_2892


title: 8F_M_2893

status: Public on Jul 15 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


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title: 8F_M_173


title: 8F_M_167


title: 8F_M_164


title: 8F_M_176


title: 8F_M_155


title: 8F_M_1517


title: 8F_M_183


title: 8F_M_163


title: 8F_M_162


title: 8F_M_160


title: 8F_M_16


title: 8F_M_1510


title: 8F_M_151


title: 8F_M_159


title: 8F_M_1509


title: 8F_M_158


title: 8F_M_156


title: 8F_M_157


title: 8F_M_1507


title: 8F_M_1506


title: 8F_M_1505


title: 8F_M_154


title: 8F_M_1502


title: 8F_M_153


title: 8F_M_1516


title: 8F_M_1501


title: 8F_M_1515


title: 8F_M_1514


title: 8F_M_1512


title: 8F_M_1513


title: 8F_M_1511


title: 8F_M_1499


title: 8F_M_1496


title: 8F_M_1508


title: 8F_M_149


title: 8F_M_1504


title: 8F_M_152


title: 8F_M_1495


title: 8F_M_1494


title: 8F_M_1500


title: 8F_M_150


title: 8F_M_15


title: 8F_M_1491


title: 8F_M_1503


title: 8F_M_1493


title: 8F_M_1497


title: 8F_M_1488


title: 8F_M_1490


title: 8F_M_1492


title: 8F_M_1489


title: 8F_M_1485


title: 8F_M_1480


title: 8F_M_1487


title: 8F_M_1486


title: 8F_M_1479


title: 8F_M_1484


title: 8F_M_1498


title: 8F_M_1483


title: 8F_M_1481


title: 8F_M_148


title: 8F_M_1477


title: 8F_M_1476


title: 8F_M_1474


title: 8F_M_1473


title: 8F_M_1475


title: 8F_M_1472


title: 8F_M_1470


title: 8F_M_147


title: 8F_M_1471


title: 8F_M_1465


title: 8F_M_1468


title: 8F_M_1463


title: 8F_M_1462


title: 8F_M_1464


title: 8F_M_1460


title: 8F_M_1466


title: 8F_M_1467


title: 8F_M_1469


title: 8F_M_1461


title: 8F_M_1482


title: 8F_M_1454


title: 8F_M_1457


title: 8F_M_1456


title: 8F_M_1455


title: 8F_M_1453


title: 8F_M_1478


title: 8F_M_1458


title: 8F_M_1452


title: 8F_M_1459


title: 8F_M_1451


title: 8F_M_1450


title: 8F_M_145


title: 8F_M_1449


title: 8F_M_1448


title: 8F_M_1447


title: 8F_M_146


title: 8F_M_1445


title: 8F_M_1446


title: 8F_M_1443


title: 8F_M_1444


title: 8F_M_1441


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title: 8F_M_1437


title: 8F_M_1439


title: 8F_M_1435


title: 8F_M_1436


title: 8F_M_1434


title: 8F_M_1431


title: 8F_M_1428


title: 8F_M_1433


title: 8F_M_1429


title: 8F_M_143


title: 8F_M_1430


title: 8F_M_1432


title: 8F_M_1427


title: 8F_M_1425


title: 8F_M_1424


title: 8F_M_1422


title: 8F_M_1423


title: 8F_M_1421


title: 8F_M_1442


title: 8F_M_1420


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title: 8F_M_1438


title: 8F_M_1419


title: 8F_M_1415


title: 8F_M_1418


title: 8F_M_1416


title: 8F_M_1417


title: 8F_M_1414


title: 8F_M_1426


title: 8F_M_1412


title: 8F_M_1410


title: 8F_M_1411


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title: 8F_M_1409


title: 8F_M_1407


title: 8F_M_1408


title: 8F_M_1404


title: 8F_M_1403


title: 8F_M_1402


title: 8F_M_1401


title: 8F_M_1406


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title: 8F_M_1400


title: 8F_M_1397


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title: 8F_M_1389


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title: 8F_M_1391


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title: 8F_M_1387


title: 8F_M_1405


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title: 8F_M_1368


title: 8F_M_1367


title: 8F_M_1363


title: 8F_M_1381


title: 8F_M_1386


title: 8F_M_1366


title: 8F_M_1379


title: 8F_M_1365


title: 8F_M_1383


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title: 8F_M_1356


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title: 8F_M_1358


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title: 8F_M_1322


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title: 8F_M_1316


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title: 8F_M_1315


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title: 8F_M_1329


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title: 8F_M_1311


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title: 8F_M_1332


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title: 8F_M_1308


title: 8F_M_1306


title: 8F_M_1303


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title: 8F_M_1317


title: 8F_M_130


title: 8F_M_13


title: 8F_M_1301


title: 8F_M_1298


title: 8F_M_1297


title: 8F_M_1294


title: 8F_M_1290


title: 8F_M_1292


title: 8F_M_1291


title: 8F_M_1296


title: 8F_M_1299


title: 8F_M_1286


title: 8F_M_1293


title: 8F_M_1289


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title: 8F_M_1285


title: 8F_M_1281


title: 8F_M_1307


title: 8F_M_1284


title: 8F_M_1287


title: 8F_M_1295


title: 8F_M_1283


title: 8F_M_1300


title: 8F_M_1282


title: 8F_M_1280


title: 8F_M_1279


title: 8F_M_1278


title: 8F_M_1277


title: 8F_M_1276


title: 8F_M_1275


title: 8F_M_1274


title: 8F_M_128


title: 8F_M_1271


title: 8F_M_1272


title: 8F_M_1273


title: 8F_M_1288


title: 8F_M_1270


title: 8F_M_127


title: 8F_M_1269


title: 8F_M_1267


title: 8F_M_1264


title: 8F_M_1266


title: 8F_M_1265


title: 8F_M_1263


title: 8F_M_1262


title: 8F_M_1261


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title: 8F_M_1259


title: 8F_M_1256


title: 8F_M_1260


title: 8F_M_1257


title: 8F_M_1255


title: 8F_M_1250


title: 8F_M_1253


title: 8F_M_1252


title: 8F_M_1254


title: 8F_M_1251


title: 8F_M_1268


title: 8F_M_125


title: 8F_M_1249


title: 8F_M_1243


title: 8F_M_1245


title: 8F_M_124


title: 8F_M_1240


title: 8F_M_126


title: 8F_M_1248


title: 8F_M_1246


title: 8F_M_1234


title: 8F_M_1237


title: 8F_M_1239


title: 8F_M_1233


title: 8F_M_1232


title: 8F_M_1238


title: 8F_M_1244


title: 8F_M_1231


title: 8F_M_133


title: 8F_M_1228


title: 8F_M_1229


title: 8F_M_1226


title: 8F_M_1242


title: 8F_M_1241


title: 8F_M_1236


title: 8F_M_1235


title: 8F_M_123


title: 8F_M_1225


title: 8F_M_1227


title: 8F_M_1230


title: 8F_M_122


title: 8F_M_1223


title: 8F_M_1224


title: 8F_M_1218


title: 8F_M_1212


title: 8F_M_1215


title: 8F_M_1217


title: 8F_M_1247


title: 8F_M_1221


title: 8F_M_1220


title: 8F_M_121


title: 8F_M_1214


title: 8F_M_1219


title: 8F_M_1209


title: 8F_M_1208


title: 8F_M_1222


title: 8F_M_1213


title: 8F_M_1211


title: 8F_M_1210


title: 8F_M_1207


title: 8F_M_1203


title: 8F_M_120


title: 8F_M_1206


title: 8F_M_1201


title: 8F_M_12


title: 8F_M_1196


title: 8F_M_1198


title: 8F_M_1199


title: 8F_M_1195


title: 8F_M_1197


title: 8F_M_1194


title: 8F_M_1190


title: 8F_M_1205


title: 8F_M_119


title: 8F_M_1189


title: 8F_M_1186


title: 8F_M_1202


title: 8F_M_1188


title: 8F_M_1204


title: 8F_M_1200


title: 8F_M_1185


title: 8F_M_1183


title: 8F_M_1184


title: 8F_M_1178


title: 8F_M_1192


title: 8F_M_1182


title: 8F_M_1181


title: 8F_M_1180


title: 8F_M_118


title: 8F_M_1179


title: 8F_M_1177


title: 8F_M_1216


title: 8F_M_1172


title: 8F_M_1171


title: 8F_M_1176


title: 8F_M_1169


title: 8F_M_1175


title: 8F_M_1173


title: 8F_M_1168


title: 8F_M_1174


title: 8F_M_117


title: 8F_M_1167


title: 8F_M_1166


title: 8F_M_1170


title: 8F_M_1164


title: 8F_M_1165


title: 8F_M_1163


title: 8F_M_1162


title: 8F_M_1160


title: 8F_M_1161


title: 8F_M_1155


title: 8F_M_1156


title: 8F_M_1157


title: 8F_M_116


title: 8F_M_1158


title: 8F_M_1159


title: 8F_M_1153


title: 8F_M_1193


title: 8F_M_1152


title: 8F_M_1148


title: 8F_M_1151


title: 8F_M_115


title: 8F_M_1141


title: 8F_M_1149


title: 8F_M_1142


title: 8F_M_1145


title: 8F_M_1140


title: 8F_M_1144


title: 8F_M_114


title: 8F_M_1143


title: 8F_M_1146


title: 8F_M_1138


title: 8F_M_1139


title: 8F_M_1137


title: 8F_M_1136


title: 8F_M_1154


title: 8F_M_1135


title: 8F_M_1134


title: 8F_M_1130


title: 8F_M_1132


title: 8F_M_1131


title: 8F_M_113


title: 8F_M_1133


title: 8F_M_1147


title: 8F_M_1150


title: 8F_M_1129


title: 8F_M_112


title: 8F_M_1117


title: 8F_M_1116


title: 8F_M_1125


title: 8F_M_1123


title: 8F_M_1124


title: 8F_M_1122


title: 8F_M_1118


title: 8F_M_1128


title: 8F_M_1120


title: 8F_M_1121


title: 8F_M_1119


title: 8F_M_1112


title: 8F_M_1126


title: 8F_M_1127


title: 8F_M_1108


title: 8F_M_1111


title: 8F_M_1107


title: 8F_M_1105


title: 8F_M_1109


title: 8F_M_1110


title: 8F_M_1100


title: 8F_M_11


title: 8F_M_1106


title: 8F_M_1103


title: 8F_M_1102


title: 8F_M_1104


title: 8F_M_111


title: 8F_M_1095


title: 8F_M_1115


title: 8F_M_1114


title: 8F_M_1098


title: 8F_M_1093


title: 8F_M_1094


title: 8F_M_1113


title: 8F_M_1091


title: 8F_M_1101


title: 8F_M_1089


title: 8F_M_1087


title: 8F_M_1088


title: 8F_M_1092


title: 8F_M_1090


title: 8F_M_110


title: 8F_M_1099


title: 8F_M_1085


title: 8F_M_1096


title: 8F_M_1097


title: 8F_M_1080


title: 8F_M_1081


title: 8F_M_1083


title: 8F_M_1082


title: 8F_M_1078


title: 8F_M_108


title: 8F_M_1079


title: 8F_M_1077


title: 8F_M_1076


title: 8F_M_1073


title: 8F_M_1072


title: 8F_M_109


title: 8F_M_1075


title: 8F_M_1074


title: 8F_M_1070


title: 8F_M_1071


title: 8F_M_1069


title: 8F_M_1068


title: 8F_M_1086


title: 8F_M_1067


title: 8F_M_107


title: 8F_M_1084


title: 8F_M_1065


title: 8F_M_1063


title: 8F_M_1066


title: 8F_M_1060


title: 8F_M_1064


title: 8F_M_1062


title: 8F_M_1058


title: 8F_M_1059


title: 8F_M_1057


title: 8F_M_1055


title: 8F_M_1054


title: 8F_M_1191


title: 8F_M_1056


title: 8F_M_1053


title: 8F_M_1187


title: Experiment 2 IL6R KO IL-27R KO TFH

type: RNA

city: London

first: James

last: Harker

address: SAF Building, South Kensington

department: NHLI

country: United Kingdom

institute: Imperial College London

hyb_protocol: amples were hybridized with the Affymetrix Mouse Transcriptome Array 1.0 (MTA-1.0) and scanned at the UCSD genomics facility

scan_protocol: Array scanning was performed according to manufacturer (Affymetrix) instructions

data_processing: Bioconductor Oligo package (Carvalho & Irizarry et al 2010) was used for preprocessing data (RMA normalization). Expression sets were then filtered using genefilter (Gentleman et al 2018) to exclude values with low expression or variance, as well as probes that did not correspond to an ENTREZ entry. Data was then subjected to paired analysis with Limma (Linear Models for Microarray Analysis) to determine differential gene expression (Ritche et al 2010, Phipson et al 2016). A false discovery rate cutoff of 0.1 was used to define differentially expressed genes between the conditions analyzed.

label: biotin

molecule: total RNA

source_name: Splenic T follicular helper cells 30 days post infection

label_protocol: Extracted RNA was labeled and hybridized to Affymetrix Mouse Transcriptome Array 1.0 (MTA-1.0; one array per subject) according to the manufacturer’s instructions. WT cDNA Synthesis and Amplification kit and WT Sense Target Labelling and Control Reagents (Affymetrix) were used

growth_protocol: Mixed bone marrow mouse chimeras of WT (CD45.1+) and receptor deficient (CD45.2+) bone marrow were allowed to engraft for 8 weeks in adult (8 week old) CD45.2 C57BL6 mice.

extract_protocol: At day 30 post infection mice were euthanized by cervical dislocation plus exanguination. Spleen was extracted and collagenase disgested, and stained with fluorescent antibodies for T cell specific markers and CD45.1 and CD45.2. Cells from at least 5 mice per experiment were equally pooled and FACS isolated based on CD45.1 (Wildtype) and CD45.2 (receptor deficient). RNA was then extracted using RNAeasy micro columns.

treatment_protocol: Mixed bone marrow chimeras were challenged with 2 x 10e6 LCMV Cl13 intravenously and left for 30 days.

tag: tissue

value: Spleen

tag: cell type

value: TFH cells

tag: infection

value: day 30 LCMV Clone13 infection

tag: genotype

value: IL-6RKO IL-27RKO CD45.2+


title: Experiment 2 WT TFH


title: Experiment 1 IL6R KO IL-27R KO TFH


title: 8F_M_1051


title: 8F_M_1052


title: Experiment 1 WT TFH


title: Experiment 3 Gp130 KO PD1+ CD4+ T cells

source_name: Splenic PD1+ CD4+ T cells 30 days post infection

value: PD1+ CD4+ T cells


title: Experiment 2 Gp130 KO PD1+ CD4+ T cells


title: 8F_M_1049


title: 8F_M_105


title: Experiment 1 Gp130 KO PD1+ CD4+ T cells


title: 8F_M_1047


title: 8F_M_106


title: 8F_M_1061


title: Experiment 3 WT PD1+ CD4+ T cells

value: wildtype CD45.1+


title: Experiment 2 WT PD1+ CD4+ T cells


title: Experiment 1 WT PD1+ CD4+ T cells


title: 8F_M_1046


title: 8F_M_1045


title: 8F_M_1042


title: 8F_M_1041


title: TAZG197V 2

city: Göttingen

first: André

last: Fischer

state: Niedersachsen

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

country: Germany

institute: Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE)

library_source: transcriptomic

data_processing:
Illumina’s bcl2fastq (v2.20.0) was used for base calling, adaptor trimming and demultiplexing to generate FASTQ files.
Quality control of raw sequencing data was performed using FastQC (v 0.11.9)
Reads were  mapped to the genome using STAR (v2.7.3a), with a maximum number of two mismatches allowed per pair, and other default parameters.
The number of aligned reads overlapping with exons for each gene was counted with the featureCounts program from the Subread package (v2.0.0) .
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each sample

source_name: heart

growth_protocol: Mice generation: Mice were maintained and the experiments on them were performed according to the guidelines from the German Animal Welfare Act and approved by the Landesamt für Verbraucherschutz und Lebensmittelsicherheit, Niedersachsen, Germany (AZ: 33.9-42502-04-15/1991). TAZG197V mice were generated through CRISPR/Cas9 based genome engineering. C57BL/6N donor female mice were super ovulated to obtain zygotes for microinjection. Pronuclear injection with a mix containing the CAs9 enzyme, sgRNA targeting the TAZ locus and a single stranded oligonucleotide DNA repair template was carried out using micro manipulators. Embryos were then surgically transferred into C57BL/6N pseudo pregnant female mice. Edited founders were identified by Sanger sequencing from ear biopsies. Mice carrying the desired modification events were crossed with C57BL6/J for two generations to ensure germline transmission and eliminate any possible mosaicism. Heterozygous animals with the same modification were then mated to generate homozygous offspring. Subsequent genotypings were carried out by PACE (PCR Allele Competitive Extension) fluorescent endpoint genotyping.

extract_protocol:
1. For heart tissue samples a small piece was minced in 500 ul TRIZOL with a hand held homogeniser.   2. Frozen tissue samples containing TRIZOL are moved to a 1.5 mL tube and incubated at 24oC for 5 minutes (no shaking).  3. Add 100 ul of chloroform and vortex the samples for 15 seconds vigorously.  4. Incubate samples for 3 minutes in a thermal heater at 24oC.   5. Centrifuge for 15 minutes at 12000g at 4oC.  6. Remove the upper phase very carefully into an Eppendorf and throw away the rest (do not touch the middle phase. You can leave a little bit behind.)  7. To this upper phase add 250 ul of isopropanol.  8. Shake the samples gently and incubate for 10 minutes at 24oC.  9. Centrifuge the samples for 10 minutes at 12000g at 4oC.  10. Decant the supernatant  11. Add 500 mL of 75% Ethanol to each sample and mix the samples briefly.   12. Centrifuge for 5 minutes at 7500g at 40C.  13. Decant the supernatant using a pipette since it is loose.   14. Keep the samples in a thermal heater at 24oC for 10 to 15 minutes until the pellet is dry. (Pellet will become translucent from white).  15. Resuspend pellet in DNase, RNase free water 25 ul (10-50 ul).  16. Incubate for 10 minutes at 60oC in thermal heater.   17. Measure concentration immediately or store at -80C until usage.
cDNA libraries were prepared with 500 ng of total RNA using the TrueSeq® Library preparation kit (Illumina, USA).

value: heart


title: TAZG197V 3


title: 8F_M_1040


title: 8F_M_1050


title: TAZG197V 1


title: WT 3

value: WT


title: 8F_M_104


title: 8F_M_1038


title: 8F_M_1048


title: 8F_M_1039


title: WT 2


title: A2780-295D

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto St

department: Environmental and Occupational Health

institute: University of Pittsburgh

data_processing:
Space Ranger v1.3.1
Seurat v4.1.0
Assembly: mm10
Supplementary files format and content: The processed data file is a big matrix of SCT normalized gene expression features for high-quality spots. Each row is a gene and each column represents a barcode (spot). All samples are combined in one matrix.
Library strategy: Spatial Transcriptomics

source_name: brain

extract_protocol:
One hemisphere of mouse brain used for Visium was embedded in optimal cutting temperature (OCT) in a cryomold and lowered into isopentane cooled with liquid nitrogen until the OCT was completely frozen. The OCT embedded tissue block were stored in a sealed container at –80°C until cryosectioning. Mouse brains were cryosectioned (Center for Biologic Imaging, University of Pittsburgh) at 10 μm and placed directly onto the Visium slides ensuring placement within the capture area. To ensure sampling of different brain regions, two sections were used from each mouse with the first section 500µm caudal to the first appearance of the dente gryus, and each 10-μm section was 500 μm apart.
Visium tissue optimization and spatial gene expression protocols were followed exactly as described by 10x Genomics (https://10xgenomics.com/) using immunofluorescence as the counterstain.

value: brain

value: APP/PS +

tag: treatment

value: S. aureus


title: A2780-294D


title: 8F_M_1037


title: A2788-295B


title: WT 1


title: A2788-294B


title: Case 26 Recurrence

type: genomic

city: Hamburg

first: Lea

last: Altendorf

address: Martinistraße 52

institute: Universitätsklinikum Hamburg-Eppendorf

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium "HumanMethylation450" or "MethylationEPIC" Beadchip array using standard Illumina protocol.

scan_protocol: Arrays were imaged using “iScan device” (Illumina) using standard recommended Illumina scanner setting.

data_processing: Mset: Noob-normalization; beta values; all probes of sex chromosomes and probes with SNPs within 2 nucleotides distant from CpG were removed; sorted by decreasing standard deviations; batch correction for array and conservation type

label: Cy5, Cy3

organism: Homo sapiens

source_name: tumor tissue

label_protocol: Bisulfite conversion was performed with the “EZ DNA Methylation Kit” (Zymo Research) using 100-500 ng DNA. FFPE DNA was cleaned and converted using the “DNA Clean & Concentrator-5 Kit” (Zymo Research) and the “Infinium HD FFPE DNA Restore Kit” (Illumina).

extract_protocol: Genomic DNA was extracted and purified from FFPE tissue using “Maxwell® FFPE DNA Kit” (Promega) and from KRYO tissue using “High Pure PCR Template Preparation Kit” (Roche) according to standard instructions.

tag: case-id

value: TYR

tag: classifier_ atrt_score_ v11b4

tag: classifier_ subgroup_ score_v11b4

tag: conservation_ type

value: FFPE

tag: disease_ status

value: Recurrence

value: Hamburg

tag: Sex

value: Male

tag: age_ onset_ years

tag: time_to_ relapse_ months

tag: localization

value: CNS, infratentorial

tag: life_ status

value: alive

tag: follow_up_ months

tag: smarcb1_ germline_ mutation

value: yes


title: A2779-294C

tag: tissue

value: PBS


title: 8F_M_1036

tag: brain region

tag: age

tag: strain


title: Case 26 Primary

value: Primary


title: 8F_M_1043


title: 8F_M_1044


title: TAZG197V 4

tag: genotype


title: A2776-295A

tag: treatment


title: 8F_M_1035


title: Case 25 Recurrence

tag: case-id

tag: classifier_ atrt_score_ v11b4

value: Regensburg

value: Female

value: CNS, supratentorial

tag: therapy_ protocol

value: EU-RHAB


title: WT 4

value: heart

value: WT


title: A2776-294A

value: brain

value: APP/PS +


title: 8F_M_1034


title: Case 25 Primary

tag: classifier_ subgroup_ score_v11b4

tag: conservation_ type

value: FFPE

tag: disease_ status


title: Case 24 Primary

value: N627/II P

value: Münster

tag: Sex

tag: age_ onset_ years

value: dead

value: wild type

tag: smarcb1_ somatic_ mutation

tag: smarca4_ germline_ mutation

tag: smarca4_ somatic_ mutation


title: 8F_M_1033


title: Case 23 Recurrence

value: KRYO

value: Recurrence

value: Würzburg

value: Hamburg

value: Male

tag: time_to_ relapse_ months

tag: localization

tag: life_ status

tag: follow_up_ months

tag: smarcb1_ germline_ mutation


title: 8F_M_1031

tag: brain region

tag: age

tag: strain


title: Case 24 Recurrence

tag: case-id

tag: classifier_ atrt_score_ v11b4

value: CNS, infratentorial

value: yes


title: 8F_M_1030


title: Case 23 Primary

tag: classifier_ subgroup_ score_v11b4

tag: conservation_ type

value: Primary

value: CNS, supratentorial

tag: therapy_ protocol

value: EU-RHAB


title: Case 22 Recurrence

value: MYC

tag: disease_ status

value: Denver

tag: Sex

tag: age_ onset_ years

value: individual


title: A2779-295C

tag: tissue

value: brain

tag: genotype

value: APP/PS +

tag: treatment

value: PBS


title: Case 22 Primary

tag: time_to_ relapse_ months

tag: localization

tag: life_ status

value: dead


title: 8F_M_1029

tag: brain region


title: 8F_M_1028

tag: age


title: Case 21 Recurrence

value: 0.89 for control tissue, hemispheric cortex

value: KRYO

value: Female

tag: follow_up_ months

tag: smarcb1_ germline_ mutation

tag: smarcb1_ somatic_ mutation


title: mouse, bulk, Cd11b+, Skull, WT, donor253, rep9

city: Munich

first: Louis

last: Kuemmerle

address: Ingolstädter Landstraße 1

institute: Helmholtz Centre Munich

description:
P6F6
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6F6

data_processing:
BCL files were demultiplexed with the bcl2fastq software from Illumina. After quality control with FastQC, reads were aligned using rnaSTAR65 to the GRCm38 (mm10) genome with ERCC synthetic RNA added. Read counts were collected using the parameter “quantMode GeneCounts” of rnaSTAR and using the unstranded values.
Data points with less than 6000 genes or a mitochondrial fraction above 0.0015 were filtered out.
Assembly: mm10
Supplementary files format and content: hf5 files with raw counts and meta data of all samples (5xFAD_adata_raw.h5ad) and after QC (5xFAD_adata.h5ad)

molecule: polyA RNA

source_name: Skull, bone marrow

extract_protocol:
The bones were dissected from the body and the muscles and connective tissue were meticulously cleared off. The bone marrow inside was flushed out to the collection tube with the help of a syringe and further dissection of the bone was performed by fine pincers. The remaining bone was cut in to small pieces and added to the cell mix. This mixture was shortly vortexed with 37C warmed DMEM with 10% heat inactivated FBS and filtered with 70 μm. Staining for sorting was performed for 15 min using 7AAD (Thermo Fisher, A1310, 25 ug/ml) and the antibodies against CD45 (eFluor 450,30-F11, eBioscience,Cat.:48-0451-82, 1:200) and CD11b (PE/Cy7,M1/70, eBioscience, Cat:25-0112-82,1:200). Cells were then washed with PBS (Sigma, D8537). Viable (7AAD negative) immune cells (CD45 and CD11b positive cells) were sorted by flow cytometry (SH800; Sony) into the 96-well plates by groups of 50 cells per well. The 96-well plates were filled with 4 µl lysis buffer containing 0.05% Triton X-100 (Sigma), ERCC (External RNA Controls Consortium) RNA spike-in Mix (Ambion,Life Technologies) (1:24000000 dilution), 2.5 µM oligo-dT, 2.5 mM dNTP and 2 U/µl of recombinant RNase inhibitor (Clontech). The plate was spun down and frozen at -80 C.
cDNA libraries were generated using an improved version of the Smart-seq2 protocol. The plates with the sorted pools were first thawed and then incubated for 3 min at 72°C and immediately placed on ice. To perform reverse transcription (RT), we added to each well a mix of 0.59 μl H2O, 0.5 μL SMARTScribe™ Reverse Transcriptase (Clontech), 2 μL 5x First Strand buffer, 0.25 μl Recombinant RNase Inhibitor (Clontech), 2 μl Betaine (5 M Sigma), 0.5 μl DTT (100 mM), 0.06 μl MgCl2 (1 M Sigma), and 0.1 μl Template-switching oligos (TSO) (100 μM AAGCAGTGGTATCAACGCAGAGTACrGrG+G). Next, RT reaction mixes were incubated at 42°C for 90 min followed by 70°C for 5 min and 10 cycles of 50°C 2 min, 42°C 2 min; finally ending with 70°C for 5 min for enzyme inactivation. Pre-amplification of cDNA was performed by adding 12.5 μl KAPA HiFi Hotstart 2x (KAPA Biosystems), 2.138 μl H2O, 0.25 μl ISPCR primers (10 μM, 5′ AAGCAGTGGTATCAACGCAGAGT-3), 0.1125 μl Lambda Exonuclease under the following conditions: 37°C for 30 min, 95°C for 3 min, 20 cycles of (98°C for 20 sec, 67°C for 15 sec, 72°C for 4 min), and a final extension at 72°C for 5 min. Libraries were then cleaned using AMPure bead (Beckman-Coulter) cleanup at a 0.7:1 ratio of beads to PCR product. Library was assessed by Bioanalyzer (Agilent 2100), using the High Sensitivity DNA analysis kit, and also fluorometrically using Qubit’s DNA HS assay kits and a Qubit 4.0 Fluorometer (Invitrogen, LifeTechnologies) to measure the concentrations. Samples were normalized to 160 pg/µL. Sequencing libraries were constructed by using an in-house produced Tn5 transposase101. Libraries were barcoded with the Illumina Nextera XT (FC-131-1096, Illumina) and pooled, then went through three rounds of AMPure bead (Beckman-Coulter) cleanup at a 0.8:1 ratio of beads to library.

value: Skull, bone marrow

tag: cell type

value: Cd45+/Cd11b+ cells

value: wildtype

tag: disease state

value: healthy


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor219, rep10

description:
P6E7
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6E7

value: 5xFAD (B6SJL)

value: AD


title: mouse, bulk, Cd11b+, Skull, WT, donor253, rep8

description:
P6F5
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6F5


title: mouse, bulk, Cd11b+, Skull, WT, donor253, rep12

description:
P6F9
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6F9


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor219, rep9

description:
P6E6
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6E6


title: mouse, bulk, Cd11b+, Skull, WT, donor253, rep4

description:
P6F1
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6F1


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor219, rep8

description:
P6E5
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6E5


title: mouse, bulk, Cd11b+, Skull, WT, donor253, rep5

description:
P6F2
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6F2


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor219, rep12

description:
P6E9
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6E9


title: mouse, bulk, Cd11b+, Skull, WT, donor253, rep11

description:
P6F8
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6F8


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor219, rep7

description:
P6E4
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6E4


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor219, rep11

description:
P6E8
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6E8


title: mouse, bulk, Cd11b+, Skull, WT, donor253, rep10

description:
P6F7
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6F7


title: mouse, bulk, Cd11b+, Skull, WT, donor253, rep6

description:
P6F3
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6F3


title: mouse, bulk, Cd11b+, Skull, WT, donor253, rep7

description:
P6F4
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6F4


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor219, rep6

description:
P6E3
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6E3


title: Case 21 Primary

tag: case-id

tag: classifier_ atrt_score_ v11b4

tag: classifier_ subgroup_ score_v11b4

tag: conservation_ type

value: Primary

value: CNS, supratentorial

tag: therapy_ protocol


title: 8F_M_1027

tag: strain


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor219, rep5

description:
P6E2
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6E2

tag: tissue

tag: genotype


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor219, rep4

description:
P6E12
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6E12


title: Case 20 Primary

tag: disease_ status

value: Denver

tag: Sex

value: Male

tag: age_ onset_ years

tag: time_to_ relapse_ months

tag: localization

value: DFCI protocol


title: Case 20 Recurrence

value: Recurrence

tag: life_ status

tag: follow_up_ months


title: 8F_M_1026

tag: brain region

tag: age


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor219, rep2

description:
P6E10
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6E10

tag: cell type

tag: disease state


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor219, rep1

description:
P6E1
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6E1


title: mouse, bulk, Cd11b+, Skull, 5xFAD, donor219, rep3

description:
P6E11
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6E11


title: 8F_M_1032


title: 8F_M_1025


title: 8F_M_103


title: 8F_M_1024


title: mouse, bulk, Cd11b+, Femur, WT, donor352, rep10

description:
P6D7
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6D7

source_name: Femur, bone marrow

value: Femur, bone marrow


title: Case 19 Primary

tag: case-id

tag: classifier_ atrt_score_ v11b4

tag: classifier_ subgroup_ score_v11b4

value: dead


title: Case 19 Recurrence

tag: conservation_ type

tag: therapy_ protocol


title: mouse, bulk, Cd11b+, Femur, WT, donor352, rep9

description:
P6D6
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6D6

tag: tissue

tag: genotype


title: mouse, bulk, Cd11b+, Femur, WT, donor352, rep11

description:
P6D8
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6D8


title: 8F_M_1023

tag: strain


title: mouse, bulk, Cd11b+, Femur, WT, donor352, rep7

description:
P6D4
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6D4


title: 8F_M_1021


title: 8F_M_1022


title: Case 18 Recurrence

value: MYC

value: FFPE

tag: disease_ status

value: Budapest

value: Hamburg

tag: Sex

tag: age_ onset_ years

value: individual

tag: smarcb1_ germline_ mutation

value: yes

tag: smarcb1_ somatic_ mutation


title: Case 17 Recurrence

value: TYR

value: Tübingen

value: Female

tag: time_to_ relapse_ months

tag: localization

value: CNS, infratentorial


title: mouse, bulk, Cd11b+, Femur, WT, donor352, rep8

description:
P6D5
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6D5

tag: cell type

value: Cd45+/Cd11b+ cells

value: wildtype

value: healthy


title: mouse, bulk, Cd11b+, Femur, WT, donor352, rep5

description:
P6D2
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6D2

tag: disease state


title: mouse, bulk, Cd11b+, Femur, WT, donor352, rep6

description:
P6D3
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6D3


title: mouse, bulk, Cd11b+, Femur, WT, donor352, rep12

description:
P6D9
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6D9


title: mouse, bulk, Cd11b+, Femur, WT, donor352, rep4

description:
P6D12
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6D12


title: mouse, bulk, Cd11b+, Femur, WT, donor352, rep3

description:
P6D11
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6D11


title: mouse, bulk, Cd11b+, Femur, WT, donor352, rep2

description:
P6D10
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6D10


title: mouse, bulk, Cd11b+, Femur, WT, donor352, rep1

description:
P6D1
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6D1


title: Case 18 Primary

tag: case-id

value: Primary

value: Male

value: CNS, supratentorial

tag: life_ status

tag: follow_up_ months


title: Case 16 Recurrence

tag: classifier_ atrt_score_ v11b4

tag: classifier_ subgroup_ score_v11b4

tag: conservation_ type

value: KRYO

value: Recurrence

value: Berlin

value: Heidelberg

value: EU-RHAB

value: dead

value: wild type


title: mouse, bulk, Cd11b+, Femur, WT, donor353, rep9

description:
P6C7
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6C7

tag: tissue

value: Femur, bone marrow

tag: genotype


title: Case 16 Primary

value: FFPE

tag: disease_ status

value: Hamburg

tag: therapy_ protocol


title: mouse, bulk, Cd11b+, Femur, WT, donor353, rep8

description:
P6C6
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6C6


title: Case 15 Recurrence

value: 0.131 for plexus tumor, subclass pediatric B

value: Amsterdam

tag: Sex

tag: age_ onset_ years


title: 8F_M_1020

tag: brain region

tag: age

tag: strain


title: 8F_M_102


title: 8F_M_1019


title: 8F_M_1018


title: Case 15 Primary

tag: time_to_ relapse_ months

tag: localization


title: mouse, bulk, Cd11b+, Femur, WT, donor353, rep7

description:
P6C5
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6C5

tag: cell type

value: Cd45+/Cd11b+ cells

value: wildtype

tag: disease state


title: 8F_M_1017


title: mouse, bulk, Cd11b+, Femur, WT, donor353, rep6

description:
P6C4
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6C4

value: healthy


title: mouse, bulk, Cd11b+, Femur, WT, donor353, rep4

description:
P6C2
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6C2


title: Case 17 Primary

tag: case-id

value: TYR

value: Primary

value: Tübingen

value: Female

value: CNS, infratentorial


title: mouse, bulk, Cd11b+, Femur, WT, donor353, rep5

description:
P6C3
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6C3


title: mouse, bulk, Cd11b+, Femur, WT, donor353, rep10

description:
P6C8
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6C8


title: 8F_M_1016


title: Case 14 Recurrence

tag: classifier_ atrt_score_ v11b4

value: Recurrence

value: Male

tag: life_ status

tag: follow_up_ months

tag: smarcb1_ germline_ mutation


title: mouse, bulk, Cd11b+, Femur, WT, donor353, rep3

description:
P6C12
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6C12

tag: tissue

tag: genotype


title: mouse, bulk, Cd11b+, Femur, WT, donor353, rep11

description:
P6C9
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6C9


title: 8F_M_1015


title: mouse, bulk, Cd11b+, Femur, WT, donor353, rep2

description:
P6C11
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6C11


title: 8F_M_1014


title: Case 14 Primary

tag: classifier_ subgroup_ score_v11b4

tag: conservation_ type

tag: disease_ status

tag: therapy_ protocol

value: EU-RHAB

value: dead


title: mouse, bulk, Cd11b+, Skull, WT, donor253, rep3

description:
P6C10
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6C10

value: Skull, bone marrow


title: mouse, bulk, Cd11b+, Femur, WT, donor353, rep1

description:
P6C1
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6C1

value: Femur, bone marrow


title: mouse, bulk, Cd11b+, Skull, WT, donor352, rep10

description:
P6B9
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6B9


title: mouse, bulk, Cd11b+, Skull, WT, donor352, rep9

description:
P6B8
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6B8


title: 8F_M_1013

tag: brain region

tag: age


title: Case 3 Recurrence

value: FFPE

value: München

value: Hamburg

tag: Sex

tag: age_ onset_ years

tag: time_to_ relapse_ months

value: CNS, supratentorial

value: Rhabdoid 07

value: wild type


title: mouse, bulk, Cd11b+, Skull, WT, donor352, rep8

description:
P6B7
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6B7

tag: cell type

value: Cd45+/Cd11b+ cells

value: wildtype

tag: disease state

value: healthy


title: Case 3 Primary

tag: case-id

value: TYR

tag: classifier_ atrt_score_ v11b4

value: Primary

tag: localization


title: 8F_M_1011

tag: strain


title: Case 2 Primary

value: KRYO

value: Heidelberg

tag: life_ status

value: alive

tag: follow_up_ months

tag: smarcb1_ germline_ mutation


title: 8F_M_1010


title: mouse, bulk, Cd11b+, Femur, WT, donor253, rep3

description:
P6B3
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6B3

tag: tissue

tag: genotype


title: mouse, bulk, Cd11b+, Femur, WT, donor253, rep5

description:
P6B5
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6B5


title: 8F_M_1009


title: 8F_M_101


title: mouse, bulk, Cd11b+, Skull, WT, donor352, rep7

description:
P6B12
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6B12


title: mouse, bulk, Cd11b+, Femur, WT, donor253, rep1

description:
P6B1
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6B1


title: mouse, bulk, Cd11b+, Skull, WT, donor352, rep6

description:
P6B11
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6B11


title: mouse, bulk, Cd11b+, Skull, WT, donor352, rep5

description:
P6B10
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6B10


title: 8F_M_1008


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor219, rep7

description:
P6A8
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6A8

value: 5xFAD (B6SJL)

value: AD


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor219, rep6

description:
P6A7
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6A7

value: Femur, bone marrow


title: 8F_M_1007


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor219, rep5

description:
P6A6
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6A6


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor219, rep4

description:
P6A5
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6A5


title: mouse, bulk, Cd11b+, Femur, WT, donor253, rep4

description:
P6B4
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6B4


title: 8F_M_1012


title: mouse, bulk, Cd11b+, Femur, WT, donor253, rep6

description:
P6B6
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6B6


title: Case 2 Recurrence

tag: classifier_ subgroup_ score_v11b4

tag: conservation_ type

tag: disease_ status

value: Recurrence

value: Male

tag: therapy_ protocol

value: EU-RHAB


title: 8F_M_1006

tag: brain region

tag: age


title: mouse, bulk, Cd11b+, Femur, WT, donor253, rep2

description:
P6B2
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6B2

tag: cell type


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor219, rep3

description:
P6A4
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6A4

tag: disease state


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor219, rep2

description:
P6A3
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6A3


title: 8F_M_1005


title: mouse, bulk, Cd11b+, Skull, WT, donor253, rep2

description:
P6A2
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6A2

value: Skull, bone marrow


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor219, rep8

description:
P6A9
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6A9


title: 8F_M_1004


title: mouse, bulk, Cd11b+, Femur, 5xFAD, donor219, rep1

description:
P6A12
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6A12


title: mouse, bulk, Cd11b+, Skull, WT, donor352, rep3

description:
P6A10
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6A10


title: mouse, bulk, Cd11b+, Skull, WT, donor253, rep1

description:
P6A1
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6A1


title: mouse, bulk, Cd11b+, Skull, WT, donor352, rep4

description:
P6A11
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P6A11


title: 8F_M_1003


title: TSS  tur1delta 30S rep 3

city: Paris

first: Guilhem

last: Janbon

address: 25 rue du Dr Roux

country: France

institute: Institut Pasteur

data_processing:
Single 50 bases single end reads were obtained using an an Illumina Nextses500 instrument according to the manufacturer’s instructions
For TSS analysis we kept only the reads containing both the oligo 3665 (AGATCGGAAGAGCACACGTCTGAAC) and the 11NCGCCGCGNNN tag. These sequenced were removed using cutadapt/1.18 and the trimmed reads were mapped to the Cryptococcus neoformans H99 genome using Tophat2 using previously published setting (Gonzalez-Hilarion et al Sci Rep 2016). Wig files were constructed using the 5’ extremities of each reads. Their coverage was normalized using the normalization factor used for spiked in RNA-Seq.

organism: Cryptococcus neoformans

growth_protocol: Cells were grown on YPD at 30°C in early stationnary phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in expontial  phase.

extract_protocol: none provided

tag: cell line


title: mouse, bulk, Cd11b+, Skull, WT, donor373, rep9

description:
P5H9
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5H9


title: RNA whole body tur1delta 30S rep 3

data_processing:
150 bases were sequenced from both ends using an Illumina NextSeq500 instrument according to the manufacturer’s instructions (Illumina).
The reads were then cleaned using cutadapt/1.18. Trimmed reads were mapped to the C. neoformans H99 and to the S. cerevisiae S288C genomes with Tophat2 using previously published setting (Gonzalez-Hilarion et al Sci Rep 2016). RNA Reads count were evaluated using HTSeq/0.6.1 (intersection-nonempty) normalized using the S. cerevisiae DNA/RNA spike in alpha factor and used to calculate FPKM values.


title: 8F_M_1002


title: mouse, bulk, Cd11b+, Skull, WT, donor373, rep8

description:
P5H8
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5H8


title: DNA tur1delta 30S rep 3

data_processing:
150 bases were sequenced from both ends using an Illumina NextSeq500 instrument according to the manufacturer’s instructions (Illumina).
The reads were then cleaned using cutadapt/1.18. Trimmed reads were mapped to the C. neoformans H99 and to the S. cerevisiae S288C  genomes with Bowtie2 using default settings. For each sample, total DNA and RNA reads counts aligned to each organism were used to calculate an alpha normalization factor.


title: 8F_M_1001


title: TSS tur1delta 30S rep 2


title: mouse, bulk, Cd11b+, Skull, WT, donor373, rep7

description:
P5H7
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5H7


title: mouse, bulk, Cd11b+, Skull, WT, donor373, rep6

description:
P5H6
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5H6


title: 8F_M_1000


title: mouse, bulk, Cd11b+, Skull, WT, donor373, rep5

description:
P5H5
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5H5


title: metformin group,   biological rep3

city: Kueishan

first: Ming-Yang

last: Chang

state: Taoyuan

address: 5 Fu-Shing Street

department: Kidney Research Center

country: Taiwan

institute: Chang Gung Memorial Hospital

hyb_protocol: Standard Applied Biosystems GeneChip WT PLUS Reagent Kit protocol

scan_protocol: Standard Applied Biosystems protocol

data_processing: Normalize with SST-RMA by Applied Biosystems Transcriptome Analysis Console Ver 4.0

source_name: Mouse kidney in metformin group

growth_protocol: Pkd1 miR transgenic mice received treatment from postnatal day 35 to day 63. Mice were sacrificed at day 63 and kidneys were harvested for RNA extraction.

extract_protocol: Total RNA was extracted from snap-frozen kidney tissues using TRIzol reagent according to the manufacturer’s protocol

treatment_protocol: Metformin treatment group received intraperitoneal injection of metformin (150 mg/kg/day) and control group received saline injection.

value: kidney

tag: treatment

value: metformin

tag: gender

value: female


title: RNA whole body tur1delta 30S rep 2


title: mouse, bulk, Cd11b+, Skull, WT, donor373, rep4

description:
P5H4
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5H4

value: Cd45+/Cd11b+ cells

value: wildtype


title: metformin group,  biological rep2

label_protocol: Standard Applied Biosystems GeneChip WT PLUS Reagent Kit protocol


title: metformin group,  biological rep1


title: saline group,   biological rep2

source_name: Mouse kidney in control group

value: saline


title: saline group,  biological rep3


title: saline group,  biological rep1


title: 8F_M_100

tag: strain


title: mouse, bulk, Cd11b+, Skull, WT, donor352, rep2

description:
P5H2
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5H2

value: healthy


title: DNA tur1delta 30S rep 2


title: TSS tur1delta 30S rep 1


title: RNA whole body tur1delta 30S rep 1


title: 8F_M_1


title: mouse, bulk, Cd11b+, Skull, WT, donor352, rep1

description:
P5H1
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5H1


title: mouse, bulk, Cd11b+, Skull, WT, donor373, rep1

description:
P5H10
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5H10


title: 8F_M_10


title: 8F_M_0


title: DNA tur1delta 30S rep 1


title: mouse, bulk, Cd11b+, Skull, WT, donor294, rep7

description:
P5G8
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5G8


title: TSS  tur1delta 30E rep 3

growth_protocol: Cells were grown on YPD at 30°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in expontial  phase.


title: mouse, bulk, Cd11b+, Skull, WT, donor353, rep10

description:
P5G7
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5G7


title: RNA whole body  tur1delta 30E rep 3


title: mouse, bulk, Cd11b+, Skull, WT, donor373, rep3

description:
P5H3
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5H3


title: mouse, bulk, Cd11b+, Skull, WT, donor294, rep6

description:
P5G6
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5G6


title: mouse, bulk, Cd11b+, Skull, WT, donor373, rep2

description:
P5H11
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5H11


title: mouse, bulk, Cd11b+, Skull, WT, donor353, rep11

description:
P5H12
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5H12


title: Syngeneic_mouse_lung, 2hrs_post_reperfusion, Vehicle_recipient, scRNAseq

city: Saint Louis

first: Daniel

last: Kreisel

state: Missouri

address: 660 S Euclid Ave

department: Surgery

institute: Washington University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Analysis was performed using the R Seurat v4.0.0 package. The following quality control steps were performed to filter the count matrices: 1) Cells expressing fewer than 500 genes were removed; 2) cells expressing over 6,000 genes were discarded as these could be potential multiplet events where more than a single cell was encapsulated within the same barcoded GEM; 3) cells with >5% mitochondrial content were filtered out as these were deemed to be of low-quality. Normalization and variance-stabilization of raw counts was performed using  SCTransform, and cell cycle scores were computed and regressed out in combination with percentage mitochondrial reads. The normalized R object was then used for subsequent clustering and differential expression testing. Briefly, clusters were annotated into major cell populations, each major cell type was subsetted, and renormalized, PCA, Uniform Manifold Approximation and Projection (UMAP) embedding, clustering, and DE analysis performed. Clusters which resembled low-quality cells or doublets were removed from subsequent analysis. We then computed the principal components and used these to integrate all samples with harmony. Informed by the ElbowPlot, we used 50 components to construct the UMAP embedding, find nearest neighbors, and clustered the data at multiple resolutions. We then used the FindAllMarkers function in Seurat to perform differential expression testing and annotated clusters into distinct cell types based on canonical gene markers. We identified a single population that represented a stromal contaminant consistent with vascular endothelium, which was excluded from further analysis. To identify genetic changes induced by treatment, major cell populations were subsetted, renormalized, reclustered, recomputed the UMAP, and differential gene expression analyzed. All differential gene expression used to identify cell types was performed using the normalized assay with the FindAllMarkers function and the Wilcoxon rank sum test with a min.pct = 0.1 and logfc.threshold = 0.25. Differential gene expression of violin plots for individual genes between treatment groups was performed using pairwise comparisons using Wilcox test through the ggpubr package. For pathway analysis, differentially down-regulated genes in RvD1-treated compared to vehicle-treated lungs were used if P < 0.05 and Log2FC > 0.58 and analyzed by MSigDB Hallmark 2020 Pathway analysis (https://maayanlab.cloud/Enrichr).
Assembly: mm10-2020-A
Supplementary files format and content: CellRanger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: B6 left lung 2 hours after syngeneic transplantation

extract_protocol:
Two hours after lung transplantation, left lung grafts from two mice were collected and pooled for submission of each sample. Lung tissue was digested and single cell suspensions were prepared as previously described [PMID 28615357].
Single-cell suspensions were submitted to the Genome Technology Access Center core facility (Washington University in St. Louis) for single-cell GEM construction and cDNA synthesis and library construction. Samples were processed using the Chromium Single Cell 3' Library & Gel Bead Kit (10X Genomics, v3) following the manufacterer's protocol. The libraries were sequenced on NovaSeq S4 (Illumina) targeting 50,000 reads per cell and 500 million read pairs per library.

treatment_protocol: Recipient mice were treated with intravenous Resolvin D1 (200 ng per mouse in 200 uL 1% ethanol) or vehicle immediately prior to transplantation. Left lung grafts were stored in low-potassium dextran glucose solution for 60 minutes at 4 degrees Celsius with an additional 45 minutes at 28 degrees Celcius priuor to orthotopic vascularized transplantation into syngeneic recipients.

value: CD45+ recipient leukocytes

value: vehicle


title: DNA tur1delta 30E rep 3


title: mouse, bulk, Cd11b+, Skull, WT, donor294, rep8

description:
P5G9
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5G9


title: mouse, bulk, Cd11b+, Skull, WT, donor294, rep5

description:
P5G5
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5G5


title: Syngeneic_mouse_lung, 2hrs_post_reperfusion, RvD1_donor, scRNAseq

description: 10x Genomics

value: B6 left lung 2 hours after syngeneic transplantation

value: CD45+ donor leukocytes


title: Syngeneic_mouse_lung, 2hrs_post_reperfusion, RvD1_recipient, scRNAseq

description: 10x Genomics


title: mouse, bulk, Cd11b+, Skull, WT, donor294, rep4

description:
P5G4
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5G4


title: TSS tur1delta 30E rep 2


title: mouse, bulk, Femur, MCAo, donorM6

description:
X23L000469
bulk_rna_raw_counts.tsv

data_processing:
For count matrix generation reads were aligned to the GRCm39 genome with Salmon using the nf-core/rnaseq pipeline (v. 3.9)
Assembly: GRCm39
Supplementary files format and content: The raw count matrix with sample ids and gene ids/symbols is given as a tab-delimited text file

extract_protocol:
The bones were dissected from the body and the muscles and connective tissue were meticulously cleared off. The bone marrow inside was flushed out to the collection tube with the help of a syringe and further dissection of the bone was performed by fine pincers. The remaining bone was cut in to small pieces and added to the cell mix. This mixture was shortly vortexed with 37C warmed DMEM with 10% heat inactivated FBS and filtered with 70 μm. The sample was placed in 5 ml of trypsin enzyme with 0.05% concentration and incubated in a pre-heated 37 °C water bath for 2 minutes. Following this, the reaction was stopped with 10 ml of 37°C pre-warmed DMEM with 10% heat inactivated FBS, the cells were dissociated by gentle trituration with a 1000μl and 200μl pipette and filtered through 70 μm Falcon™ Cell Strainers. Samples were centrifuged at 4 °C, with 1000 rpm, for 5 minutes.The supernatant of all samples was then discarded and remaining precipitate was put into small 1.5 ml Eppendorf tubes after resuspension with DMEM.
Illumina ligation stranded mRNA prep kit

value: MCAo


title: mouse, bulk, Femur, MCAo, donorM5

description:
X23L000468
bulk_rna_raw_counts.tsv

value: Femur, bone marrow


title: DNA tur1delta 30E rep 2


title: mouse, bulk, Cd11b+, Skull, WT, donor294, rep3

description:
P5G3
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5G3


title: mouse, bulk, Cd11b+, Skull, WT, donor294, rep2

description:
P5G2
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5G2


title: mouse, bulk, Femur, MCAo, donorM3

description:
X23L000466
bulk_rna_raw_counts.tsv


title: TSS  tur1delta 30E rep 1

growth_protocol: Cells were grown on YPD at 30°C in exponential phase. The Cryptococcus cell preparation was spiked in with one tenth (OD/OD) of S. cerevisiae strain FY834 cells grown in YPD at 30°C in exponential  phase.


title: RNA whole body  tur1delta 30E rep 1


title: mouse, bulk, Cd11b+, Skull, WT, donor353, rep9

description:
P5G12
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5G12


title: mouse, bulk, Cd11b+, Skull, WT, donor294, rep1

description:
P5G11
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5G11


title: mouse, bulk, Femur, MCAo, donorM2

description:
X23L000465
bulk_rna_raw_counts.tsv


title: mouse, bulk, Femur, MCAo, donorM4

description:
X23L000467
bulk_rna_raw_counts.tsv


title: DNA tur1delta 30E rep 1

source_name: yeast

value: yeast


title: NRAS-/- CCl4  N30

city: Madrid

first: Francisco

middle: Javier

last: Cubero

address: c/Doctor Severo Ochoa, 9

department: Department of Immunology, Ophthalmology & ENT

country: Spain

institute: Complutense University School of Medicine

description: Gene expression data from livers of NRAS-/- mouse underwent CCl4

hyb_protocol: The labeled and fragmented ss cDNA was spiked with cDNA hybridization controls. The spiked cDNA samples were hybridized in a GeneChip Hybridization Oven at 45°C for 16 h with rotation (60 rpm). After hybridization, microarrays were stained in two binding cycles using anti-Biotin antibodies and a Streptavidin-phycoerythrin conjugate

scan_protocol: Subsequently, the microarrays were washed with increasing stringency and conserved in holding buffer using the Affymetrix GeneChip® 3000 7 G Fluidics Station in combination with the Affymetrix GeneChip® Command Console (AGCC) software.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: NRAS-/- mouse CCl4

label_protocol: 200 ng of each RNA was used as template to produce Cy3- labeled cRNA. The RNA samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer’s protocol. The quality of second cycle cDNA and fragmented single-stranded (ss) cDNA were analyzed on the 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: Wildtype or NRAS-/- male mouse was included at the age of 8-10 weeks, then they were randomly assigned in to one of the eight groups.

extract_protocol: The RNA was isolated by using the Trizol total RNA extraction method according to the manufacturer's instructions including on-column DNase digestion. Total RNA was eluted in 30 µl RNase-free water. RNA concentration and purity were measuered on the NanoDrop One spectral photometer (peqlab) and on the 2100 Bioanalyzer (Agilent Technologies) using the RNA 6000 Nano LabChip Kit (Agilent Technologies).

treatment_protocol: In BDL experiment, wildtype and NRAS-/- mice received either sham operation or bile duct ligation operation, the operated mice were sacrified on day 28 after operations. In CCl4 treatment experimetnt,  wildtype and NRAS-/- mice received either corn oil or CCl4 injection twice a week, the mice were sacrified after 4 weeks treatments.

value: liver

value: NRAS-/-


title: RNA whole body  tur1delta 30E rep 2


title: NRAS-/- corn oil  N28

description: Gene expression data from livers of NRAS-/- mouse underwent corn oil

source_name: NRAS-/- mouse corn oil

value: corn oil


title: NRAS-/- CCl4  N31


title: mouse, bulk, Cd11b+, Skull, WT, donor353, rep8

description:
P5G1
5xFAD_adata_raw.h5ad
5xFAD_adata.h5ad
P5G1

value: Skull, bone marrow