title: THP_MUT_VPX_2

city: Debrecen

first: József

last: Tőzsér

address: Egyetem tér 1., Life Science Building

department: Department of Biochemistry and Molecular Biology

country: Hungary

institute: University of Debrecen, Faculty of Medicine

data_processing:
We assessed the quality of Illumina NextSeq 500 reads using the FastQC software (v0.11.9) prior to and following trimming.
Reads were trimmed with Trimmomatic (v0.39).
From the RSEM (v1.3.3) workflow, we ran Bowtie 2 (v2.4.4) with the default 25 seed length parameter to align reads to the GRCh38.p13 human reference genome in order to produce BAM files.
After alignment, gene-level estimates were calculated by RSEM to generate the individual *genes.results files per sample. We used the EBSeq R package to prepare the count matrix table, and then to conduct the subsequent comparative gene expression profiling analysis.
Assembly: GRCh38.p13 human reference genome
Supplementary files format and content: VPX_raw counts.tsv: Tab-delimited counts matrix text file including raw counts for each sample.
Supplementary files format and content: Raw counts are provided as gene-level estimates. In RSEM this is an estimate of the number of fragments derived from a gene, as reads often map to more than a unique region. This count is frequently a non-integer value, which represents the number of alignable fragments from a gene based on its maximum likelihood (ML) abundances.
Supplementary files format and content: *.genes.results files: Data is also provided as individual files per sample, including other expression metrics such as TPM (Transcripts Per Million) and FPKM (Fragments Per Kilobase of transcript per Million mapped reads), along with their corresponding confidence intervals. These files represent the original output generated by RSEM.

growth_protocol: THP-1 monocyte cell-line (ATCC Number: TIB-202) were maintained in RPMI medium supplemented with 10% fetal bovine serum (FBS) (Thermo Fisher Scientific, MA, USA), without antibiotics.

extract_protocol:
Cells were incubated in 37°C, 5 % CO2 for 16 hours after transfection with 5 µg of pcDNA3.1-Vpx-NeGFP, pcDNA3.1-MutVpx-NeGFP or pcDNA3.1-NeGFP plasmids, then washed in 1 ml ice-cold PBS twice. Total RNA was extracted using TRIzol Reagent (Thermo Fisher Scientific, MA, USA) according to the manufacturer's instructions. Experiments were carried out as duplicates.
RNA-Seq libraries were prepared from total RNA using Ultra II RNA Sample Prep kit (New England Biolabs, Ipswich, MA, USA) according to the manufacturer’s protocol.

treatment_protocol: Cells were seeded into a 6-well plate (5×105cells/well) in 500 µl serum-and antibiotics-free OPTI-MEM (Thermo Fisher Scientific, MA, USA) and transfected with 5 µg of pcDNA3.1-Vpx-NeGFP, pcDNA3.1-MutVpx-NeGFP, or pcDNA3.1-NeGFP plasmids using Lipofectamine LTX reagent (Thermo Fisher Scientific, MA, USA), according to the manufacturer’s protocol.

value: monocyte cells

value: K68A and R70A mutant

value: Transfection


title: Control, 3

status: Public on Apr 30 2025

type: SRA

city: GAINESVILLE

first: Daniel

last: Kopinke

state: FL

address: 1200 Newell Dr.,

country: USA

institute: University of Florida

description: Library name: Ctrl_3

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. 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.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts[3] 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.
Assembly: GRCm38(mm10)
Supplementary files format and content: text document with gene fpkm for each sample
Supplementary files format and content: text document with gene counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: tibialis anterior

extract_protocol:
RNA was extracted used RNAeasy miniplus kit (Qiagen)
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

tag: tissue

value: tibialis anterior

tag: cell line

tag: cell type

value: whole muscle lysate

tag: genotype

value: Wildtype

tag: treatment

value: 5 days post glycerol injection


title: Control, 2

description: Library name: Ctrl_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_461

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

description: The rows in 'counts.txt' and 'rpkms.txt' are genes and the columns are the cell ids ('Cell_001', 'Cell_002', 'Cell_003', 'Cell_004', 'Cell_005', 'Cell_006', 'Cell_007', 'Cell_008', 'Cell_009', 'Cell_010', 'Cell_011', 'Cell_012', 'Cell_013', 'Cell_014', 'Cell_015', 'Cell_016', 'Cell_017', 'Cell_018', 'Cell_019', 'Cell_020', 'Cell_021', 'Cell_022', 'Cell_023', 'Cell_024', 'Cell_025', 'Cell_026', 'Cell_027', 'Cell_028', 'Cell_029', 'Cell_030', 'Cell_031', 'Cell_032', 'Cell_033', 'Cell_034', 'Cell_035', 'Cell_036', 'Cell_037', 'Cell_038', 'Cell_039', 'Cell_040', 'Cell_041', 'Cell_042', 'Cell_043', 'Cell_044', 'Cell_045', 'Cell_046', 'Cell_047', 'Cell_048', 'Cell_049', 'Cell_050', 'Cell_051', 'Cell_052', 'Cell_053', 'Cell_054', 'Cell_055', 'Cell_056', 'Cell_057', 'Cell_058', 'Cell_059', 'Cell_060', 'Cell_061', 'Cell_062', 'Cell_063', 'Cell_064', 'Cell_065', 'Cell_066', 'Cell_067', 'Cell_068', 'Cell_069', 'Cell_070', 'Cell_071', 'Cell_072', 'Cell_073', 'Cell_074', 'Cell_075', 'Cell_076', 'Cell_077', 'Cell_078', 'Cell_079', 'Cell_080', 'Cell_081', 'Cell_082', 'Cell_083', 'Cell_084', 'Cell_085', 'Cell_086', 'Cell_087', 'Cell_088', 'Cell_089', 'Cell_090', 'Cell_091', 'Cell_092', 'Cell_093', 'Cell_094', 'Cell_095', 'Cell_096', 'Cell_097', 'Cell_098', 'Cell_099', 'Cell_100', 'Cell_101', 'Cell_102', 'Cell_103', 'Cell_104', 'Cell_105', 'Cell_106', 'Cell_107', 'Cell_108', 'Cell_109', 'Cell_110', 'Cell_111', 'Cell_112', 'Cell_113', 'Cell_114', 'Cell_115', 'Cell_116', 'Cell_117', 'Cell_118', 'Cell_119', 'Cell_120', 'Cell_121', 'Cell_122', 'Cell_123', 'Cell_124', 'Cell_125', 'Cell_126', 'Cell_127', 'Cell_128', 'Cell_129', 'Cell_130', 'Cell_131', 'Cell_132', 'Cell_133', 'Cell_134', 'Cell_135', 'Cell_136', 'Cell_137', 'Cell_138', 'Cell_139', 'Cell_140', 'Cell_141', 'Cell_142', 'Cell_143', 'Cell_144', 'Cell_145', 'Cell_146', 'Cell_147', 'Cell_148', 'Cell_149', 'Cell_150', 'Cell_151', 'Cell_152', 'Cell_153', 'Cell_154', 'Cell_155', 'Cell_156', 'Cell_157', 'Cell_158', 'Cell_159', 'Cell_160', 'Cell_161', 'Cell_162', 'Cell_163', 'Cell_164', 'Cell_165', 'Cell_166', 'Cell_167', 'Cell_168', 'Cell_169', 'Cell_170', 'Cell_171', 'Cell_172', 'Cell_173', 'Cell_174', 'Cell_175', 'Cell_176', 'Cell_177', 'Cell_178', 'Cell_179', 'Cell_180', 'Cell_181', 'Cell_182', 'Cell_183', 'Cell_184', 'Cell_185', 'Cell_186', 'Cell_187', 'Cell_188', 'Cell_189', 'Cell_190', 'Cell_191', 'Cell_192', 'Cell_193', 'Cell_194', 'Cell_195', 'Cell_196', 'Cell_197', 'Cell_198', 'Cell_199', 'Cell_200', 'Cell_201', 'Cell_202', 'Cell_203', 'Cell_204', 'Cell_205', 'Cell_206', 'Cell_207', 'Cell_208', 'Cell_209', 'Cell_210', 'Cell_211', 'Cell_212', 'Cell_213', 'Cell_214', 'Cell_215', 'Cell_216', 'Cell_217', 'Cell_218', 'Cell_219', 'Cell_220', 'Cell_221', 'Cell_222', 'Cell_223', 'Cell_224', 'Cell_225', 'Cell_226', 'Cell_227', 'Cell_228', 'Cell_229', 'Cell_230', 'Cell_231', 'Cell_232', 'Cell_233', 'Cell_234', 'Cell_235', 'Cell_236', 'Cell_237', 'Cell_238', 'Cell_239', 'Cell_240', 'Cell_241', 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'Cell_1066', 'Cell_1067', 'Cell_1068', 'Cell_1069', 'Cell_1070', 'Cell_1071', 'Cell_1072', 'Cell_1073', 'Cell_1074', 'Cell_1075', 'Cell_1076', 'Cell_1077', 'Cell_1078', 'Cell_1079', 'Cell_1080', 'Cell_1081', 'Cell_1082', 'Cell_1083', 'Cell_1084', 'Cell_1085', 'Cell_1086', 'Cell_1087', 'Cell_1088', 'Cell_1089', 'Cell_1090', 'Cell_1091', 'Cell_1092', 'Cell_1093', 'Cell_1094', 'Cell_1095', 'Cell_1096', 'Cell_1097', 'Cell_1098', 'Cell_1099', 'Cell_1100', 'Cell_1101', 'Cell_1102', 'Cell_1103', 'Cell_1104', 'Cell_1105', 'Cell_1106', 'Cell_1107', 'Cell_1108', 'Cell_1109', 'Cell_1110', 'Cell_1111', 'Cell_1112', 'Cell_1113', 'Cell_1114', 'Cell_1115', 'Cell_1116', 'Cell_1117', 'Cell_1118', 'Cell_1119', 'Cell_1120', 'Cell_1121', 'Cell_1122', 'Cell_1123', 'Cell_1124', 'Cell_1125', 'Cell_1126', 'Cell_1127', 'Cell_1128', 'Cell_1129', 'Cell_1130', 'Cell_1131', 'Cell_1132', 'Cell_1133', 'Cell_1134', 'Cell_1135', 'Cell_1136', 'Cell_1137', 'Cell_1138', 'Cell_1139', 'Cell_1140', 'Cell_1141', 'Cell_1142', 'Cell_1143', 'Cell_1144', 'Cell_1145', 'Cell_1146', 'Cell_1147', 'Cell_1148', 'Cell_1149', 'Cell_1150', 'Cell_1151', 'Cell_1152', 'Cell_1153', 'Cell_1154', 'Cell_1155', 'Cell_1156', 'Cell_1157', 'Cell_1158', 'Cell_1159', 'Cell_1160', 'Cell_1161', 'Cell_1162', 'Cell_1163', 'Cell_1164', 'Cell_1165', 'Cell_1166', 'Cell_1167', 'Cell_1168', 'Cell_1169', 'Cell_1170', 'Cell_1171', 'Cell_1172', 'Cell_1173', 'Cell_1174', 'Cell_1175', 'Cell_1176', 'Cell_1177', 'Cell_1178', 'Cell_1179', 'Cell_1180', 'Cell_1181', 'Cell_1182', 'Cell_1183', 'Cell_1184', 'Cell_1185', 'Cell_1186', 'Cell_1187', 'Cell_1188', 'Cell_1189', 'Cell_1190', 'Cell_1191', 'Cell_1192', 'Cell_1193', 'Cell_1194', 'Cell_1195', 'Cell_1196', 'Cell_1197', 'Cell_1198', 'Cell_1199', 'Cell_1200', 'Cell_1201', 'Cell_1202', 'Cell_1203', 'Cell_1204', 'Cell_1205', 'Cell_1206', 'Cell_1207', 'Cell_1208', 'Cell_1209', 'Cell_1210', 'Cell_1211', 'Cell_1212', 'Cell_1213', 'Cell_1214', 'Cell_1215', 'Cell_1216', 'Cell_1217', 'Cell_1218', 'Cell_1219', 'Cell_1220', 'Cell_1221', 'Cell_1222', 'Cell_1223', 'Cell_1224', 'Cell_1225', 'Cell_1226', 'Cell_1227', 'Cell_1228', 'Cell_1229', 'Cell_1230', 'Cell_1231', 'Cell_1232', 'Cell_1233', 'Cell_1234', 'Cell_1235', 'Cell_1236', 'Cell_1237', 'Cell_1238', 'Cell_1239', 'Cell_1240', 'Cell_1241', 'Cell_1242', 'Cell_1243', 'Cell_1244', 'Cell_1245', 'Cell_1246', 'Cell_1247', 'Cell_1248', 'Cell_1249', 'Cell_1250', 'Cell_1251', 'Cell_1252', 'Cell_1253', 'Cell_1254', 'Cell_1255', 'Cell_1256', 'Cell_1257', 'Cell_1258', 'Cell_1259', 'Cell_1260', 'Cell_1261', 'Cell_1262', 'Cell_1263', 'Cell_1264', 'Cell_1265', 'Cell_1266', 'Cell_1267', 'Cell_1268', 'Cell_1269', 'Cell_1270', 'Cell_1271', 'Cell_1272', 'Cell_1273', 'Cell_1274', 'Cell_1275', 'Cell_1276', 'Cell_1277', 'Cell_1278', 'Cell_1279', 'Cell_1280', 'Cell_1281', 'Cell_1282', 'Cell_1283', 'Cell_1284', 'Cell_1285', 'Cell_1286', 'Cell_1287', 'Cell_1288', 'Cell_1289', 'Cell_1290', 'Cell_1291', 'Cell_1292', 'Cell_1293', 'Cell_1294', 'Cell_1295', 'Cell_1296', 'Cell_1297', 'Cell_1298', 'Cell_1299', 'Cell_1300', 'Cell_1301', 'Cell_1302', 'Cell_1303', 'Cell_1304', 'Cell_1305', 'Cell_1306', 'Cell_1307', 'Cell_1308', 'Cell_1309', 'Cell_1310', 'Cell_1311', 'Cell_1312', 'Cell_1313', 'Cell_1314', 'Cell_1315', 'Cell_1316', 'Cell_1317', 'Cell_1318', 'Cell_1319', 'Cell_1320', 'Cell_1321', 'Cell_1322', 'Cell_1323', 'Cell_1324', 'Cell_1325', 'Cell_1326', 'Cell_1327', 'Cell_1328', 'Cell_1329', 'Cell_1330', 'Cell_1331', 'Cell_1332', 'Cell_1333', 'Cell_1334', 'Cell_1335', 'Cell_1336', 'Cell_1337', 'Cell_1338', 'Cell_1339', 'Cell_1340', 'Cell_1341', 'Cell_1342', 'Cell_1343', 'Cell_1344', 'Cell_1345', 'Cell_1346', 'Cell_1347', 'Cell_1348', 'Cell_1349', 'Cell_1350', 'Cell_1351', 'Cell_1352', 'Cell_1353', 'Cell_1354', 'Cell_1355', 'Cell_1356', 'Cell_1357', 'Cell_1358', 'Cell_1359', 'Cell_1360', 'Cell_1361', 'Cell_1362', 'Cell_1363', 'Cell_1364', 'Cell_1365', 'Cell_1366', 'Cell_1367', 'Cell_1368', 'Cell_1369', 'Cell_1370', 'Cell_1371', 'Cell_1372', 'Cell_1373', 'Cell_1374', 'Cell_1375', 'Cell_1376', 'Cell_1377', 'Cell_1378', 'Cell_1379', 'Cell_1380', 'Cell_1381', 'Cell_1382', 'Cell_1383', 'Cell_1384', 'Cell_1385', 'Cell_1386', 'Cell_1387', 'Cell_1388', 'Cell_1389', 'Cell_1390', 'Cell_1391', 'Cell_1392', 'Cell_1393', 'Cell_1394', 'Cell_1395', 'Cell_1396', 'Cell_1397', 'Cell_1398', 'Cell_1399', 'Cell_1400', 'Cell_1401', 'Cell_1402', 'Cell_1403', 'Cell_1404', 'Cell_1405', 'Cell_1406', 'Cell_1407', 'Cell_1408', 'Cell_1409', 'Cell_1410', 'Cell_1411', 'Cell_1412', 'Cell_1413', 'Cell_1414', 'Cell_1415').

library_source: transcriptomic single cell

data_processing:
Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.7.0/RTA v3.4.4) with a 51nt(Read1)-8nt(Index1)-8nt(Index2)-51nt(Read2) setup using 'NovaSeqXp' workflow in 'S1' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Demultiplexing and quality control was performed at NGI Sweden (Stockholm node) as described for each fastq file. Each fastq file corresponds to a single cell.
Reads were mapped to the human reference genome hg38 using STAR version 2.7.0e (with parameter “-outSAMstrandField=intronMotif”) (Dobin A, et al. 2013. Bioinformatics, PMID: 23104886).
Aligned reads were assigned to genomic locations with the ‘rpkmforgenes.py’ script (Ramsköld  D, et al. 2009. PLoS Comput Biol, PMID: 20011106), using an annotation GTF file from Ensembl version 95 (GRCh38.95) (with parameters “-fulltranscript” and “-rmnameoverlap”).
Cells with less than 100,000 uniquely mapped reads and/or less than 5,000 detected genes were excluded.
Assembly: hg38
Supplementary files format and content: A counts table for all single cells named 'counts.txt'.
Supplementary files format and content: A data table with normalized abundance in reads per kilobase million (rpkm) for all single cells called 'rpkms.txt'.

molecule: polyA RNA

organism: Homo sapiens

extract_protocol:
Neuronal cultures were treated for 1 hour with 5 µM Y-27632 before dissociation with trypsin or accutase. The cells were resuspended in FACS buffer (HBSS with magnesium and calcium, 2% w/v bovine serum albumine, 2% v/v knockout serum replacement, 2% v/v B-27 supplement, 25 mM D-glucose, 5 µM Y-27632). Single live cells were isolated by fluorescence activated cell sorting (FACS) using Topro-3 iodide and were directly lysed in ice-cold single-cell lysis buffer (0.2% w/v Triton X-100, 0.5% v/v recombinant RNase inhibitor, 10 µM Smarter_oligo-dTVN, 25 mM dNTP, 100 mM DL-dithiothreitol, 4e-5 diluted ERCC spike-in RNAs, in ultrapure water). Protocol according to Schweingruber C, et al. 2023. Methods Mol Biol (PMID: 36264494).
Individual single cell libraries were prepared using the Smart-Seq2 protocol followed by tagmentation using components form the Nextera XT DNA library preparation kit (Illumina). Protocols with adaptations according to Schweingruber C, et al. 2023. Methods Mol Biol (PMID: 36264494).

treatment_protocol:
Heterogenous protocol: Differentiation of adherent cells for two days in medium 1 (200 nM LDN193189, 10 µM SB431542, 25 ng/mL SHH-C25II, 250 nM Purmorphamine, 1 µM retinoic acid), followed by seven days medium 2 (medium 1 with 3 µM CHIR99021), one day of medium d3 (Medium 2 with 200 µM ascorbic acid, 125 µM db-cAMP, 2.5 µM DAPT, 10 ng/mL each of BDNF, GDNF, NT-3, and CNTF), and three days of medium 4 (3 µM CHIR99021, 25 ng/mL SHH-C25II, 250 nM Purmorphamine, 1 µM retinoic acid, with 200 µM ascorbic acid, 125 µM db-cAMP, 2.5 µM DAPT, 10 ng/mL each of BDNF, GDNF, NT-3, and CNTF). From day 14 onwards, culture was kept in medium 5 (200 µM ascorbic acid, 125 µM db-cAMP, 2.5 µM DAPT, 10 ng/mL each of BDNF, GDNF, NT3, and CNTF).
Homogenous protocol according to Nijssen J, et al. 2019. Bioprotocol (PMID: 33654821). The neurons were cultured until day 28.

value: spinal neuron differentiation

value: homogenous protocol

tag: sequencing batch


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_462


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_467


title: THP_MUT_VPX_1


title: Control, 1

description: Library name: Ctrl_1


title: isolate vci_157, replicate 1

city: Boston

first: Peter

last: Culviner

state: MA

address: 677 Huntington Ave

department: IID

institute: Harvard School of Public Health

description: Library name: vci_157_1

data_processing:
See publication for complete details. Paired end reads were demultiplexed by their inline barcodes using cutadapt and a custom demultiplexer script.
Reads were mapped with bowtie2 to H37Rv reference.
Non-unique reads were removed with picard.
Reads were mapped to H37Rv regions with a custom script, removing low mapq reads. Reported values are log2 transformed and library depth normalized.
Assembly: NC_000962.3
Supplementary files format and content: 2D csvs with gene IDs and sample names

organism: Mycobacterium tuberculosis

source_name: bacterial

growth_protocol: Mtb was grown in a 1 mL volume in 24-well plates, covered with breathe-easy film, at 37°C x 100 RPM, in 7H9 media supplemented with 0.2% glycerol, 0.05% Tween-80, and 10% OADC. Strains were grown and back diluted as necessary over a 8 day period to achieve a final OD of ~0.4.

extract_protocol:
Crosslinks were reversed by incubating at 70°C. Cells were lysed in Trizol using bead beating tubes. RNA was extracted by adding chloroform and removing the aqueous upper layer. RNA was precipitated onto carboxylate-modified magnetic beads with isopropanol-GuHCl and beads were washed with ethanol. RNA was resuspended into tris-buffered water. See publication for full details.
RNA library preps were prepared for Illumina sequencing using a custom protocol, see publication for complete details. Briefly, cDNA was barcoded using random primers with inline barcodes and an Illumina sequencing adapter. Barcoded, single-stranded cDNA was pooled and a second adapter was added using a splint ligation. Reads corresponding to rRNA were depleted using Taq polymerase's endonuclease activity, combined with a library of guides. Libraries were amplified and sequenced on either a MiSeq or NovaSeq instrument.

treatment_protocol: To halt transcriptome dynamics and sterilize cultures, PFA was added to each 1 mL culture to a final concentration of 2% and allowed to incubate for 1 hour at room temperature.

value: bacterial

value: Clinical Isolate


title: THP_WT_VPX_2

value: WT


title: isolate vci_156, replicate 2

description: Library name: vci_156_2


title: isolate vci_157, replicate 2

description: Library name: vci_157_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_460


title: THP_WT_VPX_1


title: Nicotine, biol rep 3

city: Shanghai

first: Jiajun

last: Cui

address: No.131, Dong'an Road, Xuhui District, Shanghai, China

country: China

institute: Obstetrics and Gynecology Hospital of Fudan University

description:
Library name: Sample6
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.2.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: testis

extract_protocol:
Finishing exposure, fresh, intact, bilateral testes of each mouse were sterilely isolated and stored in 1 mL of tissue preservation solution (sCelLiVE®, Singleron) on ice. The specimens were washed with Hanks Balanced Salt Solution (HBSS) three times, the tunica albuginea was removed, and the specimens were minced into small pieces and then digested with Tissue Dissociation Solution (sCelLiVE®, Singleron) at 37°C for 15 min. The cell suspension was collected and filtered through a 40 μm sterile strainer, pelleted at 800xg for 2 mins, washed, and resuspended in cold PBS for sequencing. Before loading, the cell viability of each sample was evaluated by staining an aliquot with Trypan Blue, and the viability was typically determined to be greater than 80%.
Single-cell RNA sequencing library of testicular cells was prepared according to the manufacturer’s instructions. Briefly, freshly prepared cell suspension (10,000 cell for each sample) was loaded into Chromium microfluidic chips with 3’ (v3) chemistry and barcoded with a 10x Chromium Controller (10x Genomics). RNA from the barcoded cells was subsequently reverse-transcribed and sequencing libraries constructed with reagents from a Chromium Single Cell 3’ (v3) reagent kit (10x Genomics) according to the manufacturer’s instructions. Sequencing was performed with Illumina (NovaseqX Plus PE150) according to the manufacturer’s instructions (Illumina).

value: testis

tag: age

value: 11 weeks old

tag: strain

tag: Sex

value: male

value: nicotine-exposed mice


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_459


title: isolate vci_156, replicate 1

description: Library name: vci_156_1


title: THP_GFP_mock_control_2

value: mock


title: Nicotine, biol rep 2

description:
Library name: Sample5
10x Genomics


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_464


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_458


title: isolate vci_155, replicate 2

description: Library name: vci_155_2


title: Nicotine, biol rep 1

description:
Library name: Sample4
10x Genomics


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_457


title: isolate vci_155, replicate 1

description: Library name: vci_155_1


title: THP_GFP_mock_control_1

value: monocyte cells


title: Control, biol rep 3

description:
Library name: Sample3
10x Genomics

value: normal feeding mice


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_456


title: MDAMB231_3NEG

city: Torino

first: Ivan

last: Molineris

state: TO

address: Via Nizza 52

department: Life Science and System Biology

country: Italy

institute: University of Turin

data_processing:
STAR (version 2.5.4a)
For gene expression quantification read was assigned to exons using subread featureCounts v1.6.3, discarding multi mapping reads and ambiguous reads and summarizing over gene names
Passing filters reads were aligned to GRCh38 primary assembly genome, downloaded from GENCODE (version 29). As reference transcript annotation GENCODE basic annotation (version 29) was used, complemented with custom tracks of L1-MET transcripts described in Miglio et al, 2018
After low expressed genes filtration (1 count per million (CPM) in less than 9 samples), normalization factors were calculated using the trimmed-mean of M-values (TMM) method (implemented in the calcNormFactors function) and CPM were obtained using normalized library sizes.
Gene expression counts were next analysed using the edgeR package
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: breast

extract_protocol:
RNA was harvested using Maxwell Maxwell RSC miRNA tissue kit (Promega). 0.8 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq stranded mRNA kit (Illumina) following manufacturer's protocols.

value: breast

value: control


title: isolate vci_151, replicate 2

description: Library name: vci_151_2


title: MDAMB231_3L1MET1


title: isolate vci_151, replicate 1

description: Library name: vci_151_1


title: Control, biol rep 1

description:
Library name: Sample1
10x Genomics


title: MDAMB231_2NEG


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_454


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_455


title: isolate vci_150, replicate 2

description: Library name: vci_150_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_453


title: isolate vci_150, replicate 1

description: Library name: vci_150_1


title: MDAMB231_2L1MET1


title: MDAMB231_1NEG


title: isolate vci_149, replicate 2

description: Library name: vci_149_2


title: CD45+ cells, HCC

city: Minneapolis

first: Adam

last: Herman

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

institute: University of Minnesota

description:
10X Genomics
seurat.rds
feature_ref.csv

data_processing:
Cell inference  and  gene counting were perfomed with cellranger count (v7.1.0)
Secondary hashtag demultiplexing was done with cellhashR (v.1.0.4) (https://github.com/BimberLab/cellhashR)
Assembly: mm10
Supplementary files format and content: .rds file containing a Seurat object of the expression and hashtag count data prior to filtering. .csv containing the specific barcodes and read orientation necessary for running cellranger count

source_name: Liver

extract_protocol:
After euthanizing the mouse, the liver was perfused with 10 mL of PBS through the heart, collected, and disrupted using a gentleMACS tissue dissociator. The resulting tissue was resuspended in RPMI-1640 media containing 10% FBS and further digested with collagenase. The suspension was centrifuged at 60 g for 1 minute, and the supernatant containing hepatic immune cells was collected and centrifuged again at 480 g for 8 minutes. The pellet was resuspended in 10 mL of 37.5% Percoll (Sigma) in PBS and centrifuged at 850 g for 30 minutes. The resulting pellet was washed, followed by red blood cell lysis using ammonium-chloride-potassium (ACK) lysis buffer for 2 minutes at room temperature. Total CD45+ cells were then purified magnetically according to the manufacturer's protocol.
After labeling with hashtags, cells were pooled and loaded into the wells of a 10x Genomics chip using the single-cell 3’ kit. Gene expression and CMO libraries were sequenced on a NovaSeq S4 chip (2x150 bp PE).

treatment_protocol: At 8 weeks of age, MUP-uPA mice were fed a high-fat, high-carbohydrate (HFHC) diet consisting of 40% kcal from palm oil, 20% kcal from fructose, and 2% cholesterol, supplemented with 23.1 g/L d-fructose and 18.9 g/L d-glucose in the drinking water. Wild-type (Wt) mice of the same age were continued on a normal chow diet (NCD). Group-housed mice were maintained on either the HFHC or NCD diet for at least 48 weeks. MUP-uPA mice typically develop hepatocellular carcinoma (HCC) after 48 weeks of HFHC feeding, while Wt mice on NCD maintain a healthy liver phenotype.

value: Liver

value: CD45+ cells

value: MUP

tag: library type

value: mRNA

value: HFHC


title: CD45+ cells, NCD

description:
10X Genomics
seurat.rds
feature_ref.csv

value: Wt

value: HTO

value: NCD


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_451

value: spinal neuron differentiation

value: homogenous protocol


title: isolate vci_149, replicate 1

description: Library name: vci_149_1

value: bacterial

value: Clinical Isolate


title: MDAMB231_1L1MET1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_450


title: MDAMB231-3NEG


title: isolate vci_147, replicate 2

description: Library name: vci_147_2


title: MDAMB231-3L1MET2


title: V0303_oligo

city: shenzhen

first: CNSA

last: CNGB

address: BGI

institute: BGI

description: Library name: forager_V0303_20210220_Oligo

data_processing:
Cell Ranger v3.0.2 was used for processing raw sequencing data generated using the Chromium Single Cell 3’ v2 kit, while DNBelab C Series scRNA analysis software (MGI,https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_HT_scRNA-analysis-software) was used to process the other data.
Assembly: CNGB(CNP0003087,https://db.cngb.org/search/project/CNP0003087/)
Supplementary files format and content: CSV,TXT

organism: Apis mellifera

source_name: brain

extract_protocol:
Fieldwork was conducted in August 2020 at the apiary of China Agricultural University, Beijing, China. Single-cohort colonies were established to control worker bee age. Brood frames from a single hive were collected, and adult bees were removed. Frames were incubated at 35 °C and 50% relative humidity. After two days, ~1,000 newly emerged bees per frame were marked on the thorax with paint (Uni-Paint PX-20) and returned to their original hives. Ten-day-old marked bees observed placing their heads into honeycomb cells containing eggs or larvae were collected as nurse bees. Age-matched 21- to 23-day-old bees carrying pollen loads were collected as foragers. Bees were cared for daily with adequate food. For tissue collection, bees were gently collected, euthanized by CO₂ anesthesia, and dissected immediately. All bees were collected between 9:00 and 11:00 a.m. on August 20, 2020. Brains were dissected under a microscope (Canon), and hypopharyngeal glands, salivary glands, and eyes were removed. Dissected brains were stored at -80 °C until analysis. For each library, four frozen brains were homogenized in 2 ml ice-cold buffer (0.1 mM Tris-HCl, 0.1 mM NaCl, 0.03 mM MgCl₂, 0.1 mM DTT, protease inhibitor, 0.4 U/μl RNase inhibitor, 0.1% Nonidet P-40) using a Dounce homogenizer. After 20 min on ice, tissues were further homogenized (25 strokes, tight pestle), filtered (30-μm strainer), and centrifuged at 700 g for 10 min at 4 °C. The pellet was resuspended in PBS with 1.5% BSA and 0.2 U/μl RNase inhibitor, centrifuged again, and adjusted to 1,000 nuclei/μl in PBS with 0.04% BSA. snRNA-Seq libraries were prepared using the DNBelab C Series Single-Cell Library Prep Set (MGI). Single-nucleus suspensions were processed through droplet encapsulation, mRNA capture, reverse transcription, and cDNA amplification. Libraries were quantified (Qubit ssDNA Assay Kit, Thermo Fisher) and sequenced on the DIPSEQ T1 platform (China National GeneBank, Shenzhen) with a 41-bp Read 1 and 100-bp Read 2 strategy.
Briefly, single-cell suspensions were used for droplet generation, emulsion breakage, bead collection, reverse transcription, and cDNA amplification to generate barcoded libraries. Indexed libraries were constructed according to the manufacturer’s protocol. Libraries were constructed and the DNA nanoballs (DNBs) were loaded into the patterned nanoarrays and sequenced on a DNBSEQ-T1 sequencer at the China National GeneBank (Shenzhen, China) with the following sequencing strategy: 41-bp read length for read 1 and 100-bp read length for read 2.

value: brain

tag: group

value: forager


title: Control, biol rep 2

description:
Library name: Sample2
10x Genomics

value: testis

value: 11 weeks old

value: male

value: normal feeding mice


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_449


title: isolate vci_147, replicate 1

description: Library name: vci_147_1


title: V0302_oligo

description: Library name: forager_V0302_20210220_Oligo


title: V0305_oligo

description: Library name: forager_V0305_20210220_Oligo


title: V0304_oligo

description: Library name: forager_V0304_20210220_Oligo


title: MDAMB231-2NEG

value: breast

value: control


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_448


title: isolate vci_146, replicate 1

description: Library name: vci_146_1


title: MDAMB231-2L1MET2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_447


title: V0301_oligo

description: Library name: forager_V0301_20210220_Oligo


title: isolate vci_139, replicate 2

description: Library name: vci_139_2


title: V0305

description: Library name: forager_V0305_20210220_cDNA


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_452


title: MDAMB231-1NEG


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_446


title: isolate vci_139, replicate 1

description: Library name: vci_139_1


title: V0304

description: Library name: forager_V0304_20210220_cDNA


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_445


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_444


title: isolate vci_135, replicate 2

description: Library name: vci_135_2


title: MCF7_3NEG


title: isolate vci_135, replicate 1

description: Library name: vci_135_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_443


title: isolate vci_134, replicate 2

description: Library name: vci_134_2


title: V0301

description: Library name: forager_V0301_20210220_cDNA


title: MCF7_2NEG


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_442


title: isolate vci_134, replicate 1

description: Library name: vci_134_1


title: V0398

description: Library name: forager_V0398_20210414_cDNA


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_441


title: isolate vci_133, replicate 2

description: Library name: vci_133_2


title: V0405

description: Library name: forager_V0405_20210415_cDNA


title: MCF7_1NEG


title: isolate vci_133, replicate 1

description: Library name: vci_133_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_439


title: MDAMB231-1L1MET2


title: V0406

description: Library name: forager_V0406_20210415_cDNA


title: MCF7_1L1MET1


title: V04012

description: Library name: forager_V04012_20210415_cDNA


title: V0303

description: Library name: forager_V0303_20210220_cDNA


title: isolate vci_124, replicate 2

description: Library name: vci_124_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_438


title: MCF7-3NEG


title: MCF7-3L1MET2


title: V04011

description: Library name: forager_V04011_20210415_cDNA


title: isolate vci_109, replicate 2

description: Library name: vci_109_2


title: MCF7_3L1MET1


title: V0302

description: Library name: forager_V0302_20210220_cDNA


title: V04010

description: Library name: forager_V04010_20210415_cDNA


title: MCF7_2L1MET1


title: isolate vci_124, replicate 1

description: Library name: vci_124_1


title: MCF7-2NEG


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_436

description: The rows in 'counts.txt' and 'rpkms.txt' are genes and the columns are the cell ids ('Cell_001', 'Cell_002', 'Cell_003', 'Cell_004', 'Cell_005', 'Cell_006', 'Cell_007', 'Cell_008', 'Cell_009', 'Cell_010', 'Cell_011', 'Cell_012', 'Cell_013', 'Cell_014', 'Cell_015', 'Cell_016', 'Cell_017', 'Cell_018', 'Cell_019', 'Cell_020', 'Cell_021', 'Cell_022', 'Cell_023', 'Cell_024', 'Cell_025', 'Cell_026', 'Cell_027', 'Cell_028', 'Cell_029', 'Cell_030', 'Cell_031', 'Cell_032', 'Cell_033', 'Cell_034', 'Cell_035', 'Cell_036', 'Cell_037', 'Cell_038', 'Cell_039', 'Cell_040', 'Cell_041', 'Cell_042', 'Cell_043', 'Cell_044', 'Cell_045', 'Cell_046', 'Cell_047', 'Cell_048', 'Cell_049', 'Cell_050', 'Cell_051', 'Cell_052', 'Cell_053', 'Cell_054', 'Cell_055', 'Cell_056', 'Cell_057', 'Cell_058', 'Cell_059', 'Cell_060', 'Cell_061', 'Cell_062', 'Cell_063', 'Cell_064', 'Cell_065', 'Cell_066', 'Cell_067', 'Cell_068', 'Cell_069', 'Cell_070', 'Cell_071', 'Cell_072', 'Cell_073', 'Cell_074', 'Cell_075', 'Cell_076', 'Cell_077', 'Cell_078', 'Cell_079', 'Cell_080', 'Cell_081', 'Cell_082', 'Cell_083', 'Cell_084', 'Cell_085', 'Cell_086', 'Cell_087', 'Cell_088', 'Cell_089', 'Cell_090', 'Cell_091', 'Cell_092', 'Cell_093', 'Cell_094', 'Cell_095', 'Cell_096', 'Cell_097', 'Cell_098', 'Cell_099', 'Cell_100', 'Cell_101', 'Cell_102', 'Cell_103', 'Cell_104', 'Cell_105', 'Cell_106', 'Cell_107', 'Cell_108', 'Cell_109', 'Cell_110', 'Cell_111', 'Cell_112', 'Cell_113', 'Cell_114', 'Cell_115', 'Cell_116', 'Cell_117', 'Cell_118', 'Cell_119', 'Cell_120', 'Cell_121', 'Cell_122', 'Cell_123', 'Cell_124', 'Cell_125', 'Cell_126', 'Cell_127', 'Cell_128', 'Cell_129', 'Cell_130', 'Cell_131', 'Cell_132', 'Cell_133', 'Cell_134', 'Cell_135', 'Cell_136', 'Cell_137', 'Cell_138', 'Cell_139', 'Cell_140', 'Cell_141', 'Cell_142', 'Cell_143', 'Cell_144', 'Cell_145', 'Cell_146', 'Cell_147', 'Cell_148', 'Cell_149', 'Cell_150', 'Cell_151', 'Cell_152', 'Cell_153', 'Cell_154', 'Cell_155', 'Cell_156', 'Cell_157', 'Cell_158', 'Cell_159', 'Cell_160', 'Cell_161', 'Cell_162', 'Cell_163', 'Cell_164', 'Cell_165', 'Cell_166', 'Cell_167', 'Cell_168', 'Cell_169', 'Cell_170', 'Cell_171', 'Cell_172', 'Cell_173', 'Cell_174', 'Cell_175', 'Cell_176', 'Cell_177', 'Cell_178', 'Cell_179', 'Cell_180', 'Cell_181', 'Cell_182', 'Cell_183', 'Cell_184', 'Cell_185', 'Cell_186', 'Cell_187', 'Cell_188', 'Cell_189', 'Cell_190', 'Cell_191', 'Cell_192', 'Cell_193', 'Cell_194', 'Cell_195', 'Cell_196', 'Cell_197', 'Cell_198', 'Cell_199', 'Cell_200', 'Cell_201', 'Cell_202', 'Cell_203', 'Cell_204', 'Cell_205', 'Cell_206', 'Cell_207', 'Cell_208', 'Cell_209', 'Cell_210', 'Cell_211', 'Cell_212', 'Cell_213', 'Cell_214', 'Cell_215', 'Cell_216', 'Cell_217', 'Cell_218', 'Cell_219', 'Cell_220', 'Cell_221', 'Cell_222', 'Cell_223', 'Cell_224', 'Cell_225', 'Cell_226', 'Cell_227', 'Cell_228', 'Cell_229', 'Cell_230', 'Cell_231', 'Cell_232', 'Cell_233', 'Cell_234', 'Cell_235', 'Cell_236', 'Cell_237', 'Cell_238', 'Cell_239', 'Cell_240', 'Cell_241', 'Cell_242', 'Cell_243', 'Cell_244', 'Cell_245', 'Cell_246', 'Cell_247', 'Cell_248', 'Cell_249', 'Cell_250', 'Cell_251', 'Cell_252', 'Cell_253', 'Cell_254', 'Cell_255', 'Cell_256', 'Cell_257', 'Cell_258', 'Cell_259', 'Cell_260', 'Cell_261', 'Cell_262', 'Cell_263', 'Cell_264', 'Cell_265', 'Cell_266', 'Cell_267', 'Cell_268', 'Cell_269', 'Cell_270', 'Cell_271', 'Cell_272', 'Cell_273', 'Cell_274', 'Cell_275', 'Cell_276', 'Cell_277', 'Cell_278', 'Cell_279', 'Cell_280', 'Cell_281', 'Cell_282', 'Cell_283', 'Cell_284', 'Cell_285', 'Cell_286', 'Cell_287', 'Cell_288', 'Cell_289', 'Cell_290', 'Cell_291', 'Cell_292', 'Cell_293', 'Cell_294', 'Cell_295', 'Cell_296', 'Cell_297', 'Cell_298', 'Cell_299', 'Cell_300', 'Cell_301', 'Cell_302', 'Cell_303', 'Cell_304', 'Cell_305', 'Cell_306', 'Cell_307', 'Cell_308', 'Cell_309', 'Cell_310', 'Cell_311', 'Cell_312', 'Cell_313', 'Cell_314', 'Cell_315', 'Cell_316', 'Cell_317', 'Cell_318', 'Cell_319', 'Cell_320', 'Cell_321', 'Cell_322', 'Cell_323', 'Cell_324', 'Cell_325', 'Cell_326', 'Cell_327', 'Cell_328', 'Cell_329', 'Cell_330', 'Cell_331', 'Cell_332', 'Cell_333', 'Cell_334', 'Cell_335', 'Cell_336', 'Cell_337', 'Cell_338', 'Cell_339', 'Cell_340', 'Cell_341', 'Cell_342', 'Cell_343', 'Cell_344', 'Cell_345', 'Cell_346', 'Cell_347', 'Cell_348', 'Cell_349', 'Cell_350', 'Cell_351', 'Cell_352', 'Cell_353', 'Cell_354', 'Cell_355', 'Cell_356', 'Cell_357', 'Cell_358', 'Cell_359', 'Cell_360', 'Cell_361', 'Cell_362', 'Cell_363', 'Cell_364', 'Cell_365', 'Cell_366', 'Cell_367', 'Cell_368', 'Cell_369', 'Cell_370', 'Cell_371', 'Cell_372', 'Cell_373', 'Cell_374', 'Cell_375', 'Cell_376', 'Cell_377', 'Cell_378', 'Cell_379', 'Cell_380', 'Cell_381', 'Cell_382', 'Cell_383', 'Cell_384', 'Cell_385', 'Cell_386', 'Cell_387', 'Cell_388', 'Cell_389', 'Cell_390', 'Cell_391', 'Cell_392', 'Cell_393', 'Cell_394', 'Cell_395', 'Cell_396', 'Cell_397', 'Cell_398', 'Cell_399', 'Cell_400', 'Cell_401', 'Cell_402', 'Cell_403', 'Cell_404', 'Cell_405', 'Cell_406', 'Cell_407', 'Cell_408', 'Cell_409', 'Cell_410', 'Cell_411', 'Cell_412', 'Cell_413', 'Cell_414', 'Cell_415', 'Cell_416', 'Cell_417', 'Cell_418', 'Cell_419', 'Cell_420', 'Cell_421', 'Cell_422', 'Cell_423', 'Cell_424', 'Cell_425', 'Cell_426', 'Cell_427', 'Cell_428', 'Cell_429', 'Cell_430', 'Cell_431', 'Cell_432', 'Cell_433', 'Cell_434', 'Cell_435', 'Cell_436', 'Cell_437', 'Cell_438', 'Cell_439', 'Cell_440', 'Cell_441', 'Cell_442', 'Cell_443', 'Cell_444', 'Cell_445', 'Cell_446', 'Cell_447', 'Cell_448', 'Cell_449', 'Cell_450', 'Cell_451', 'Cell_452', 'Cell_453', 'Cell_454', 'Cell_455', 'Cell_456', 'Cell_457', 'Cell_458', 'Cell_459', 'Cell_460', 'Cell_461', 'Cell_462', 'Cell_463', 'Cell_464', 'Cell_465', 'Cell_466', 'Cell_467', 'Cell_468', 'Cell_469', 'Cell_470', 'Cell_471', 'Cell_472', 'Cell_473', 'Cell_474', 'Cell_475', 'Cell_476', 'Cell_477', 'Cell_478', 'Cell_479', 'Cell_480', 'Cell_481', 'Cell_482', 'Cell_483', 'Cell_484', 'Cell_485', 'Cell_486', 'Cell_487', 'Cell_488', 'Cell_489', 'Cell_490', 'Cell_491', 'Cell_492', 'Cell_493', 'Cell_494', 'Cell_495', 'Cell_496', 'Cell_497', 'Cell_498', 'Cell_499', 'Cell_500', 'Cell_501', 'Cell_502', 'Cell_503', 'Cell_504', 'Cell_505', 'Cell_506', 'Cell_507', 'Cell_508', 'Cell_509', 'Cell_510', 'Cell_511', 'Cell_512', 'Cell_513', 'Cell_514', 'Cell_515', 'Cell_516', 'Cell_517', 'Cell_518', 'Cell_519', 'Cell_520', 'Cell_521', 'Cell_522', 'Cell_523', 'Cell_524', 'Cell_525', 'Cell_526', 'Cell_527', 'Cell_528', 'Cell_529', 'Cell_530', 'Cell_531', 'Cell_532', 'Cell_533', 'Cell_534', 'Cell_535', 'Cell_536', 'Cell_537', 'Cell_538', 'Cell_539', 'Cell_540', 'Cell_541', 'Cell_542', 'Cell_543', 'Cell_544', 'Cell_545', 'Cell_546', 'Cell_547', 'Cell_548', 'Cell_549', 'Cell_550', 'Cell_551', 'Cell_552', 'Cell_553', 'Cell_554', 'Cell_555', 'Cell_556', 'Cell_557', 'Cell_558', 'Cell_559', 'Cell_560', 'Cell_561', 'Cell_562', 'Cell_563', 'Cell_564', 'Cell_565', 'Cell_566', 'Cell_567', 'Cell_568', 'Cell_569', 'Cell_570', 'Cell_571', 'Cell_572', 'Cell_573', 'Cell_574', 'Cell_575', 'Cell_576', 'Cell_577', 'Cell_578', 'Cell_579', 'Cell_580', 'Cell_581', 'Cell_582', 'Cell_583', 'Cell_584', 'Cell_585', 'Cell_586', 'Cell_587', 'Cell_588', 'Cell_589', 'Cell_590', 'Cell_591', 'Cell_592', 'Cell_593', 'Cell_594', 'Cell_595', 'Cell_596', 'Cell_597', 'Cell_598', 'Cell_599', 'Cell_600', 'Cell_601', 'Cell_602', 'Cell_603', 'Cell_604', 'Cell_605', 'Cell_606', 'Cell_607', 'Cell_608', 'Cell_609', 'Cell_610', 'Cell_611', 'Cell_612', 'Cell_613', 'Cell_614', 'Cell_615', 'Cell_616', 'Cell_617', 'Cell_618', 'Cell_619', 'Cell_620', 'Cell_621', 'Cell_622', 'Cell_623', 'Cell_624', 'Cell_625', 'Cell_626', 'Cell_627', 'Cell_628', 'Cell_629', 'Cell_630', 'Cell_631', 'Cell_632', 'Cell_633', 'Cell_634', 'Cell_635', 'Cell_636', 'Cell_637', 'Cell_638', 'Cell_639', 'Cell_640', 'Cell_641', 'Cell_642', 'Cell_643', 'Cell_644', 'Cell_645', 'Cell_646', 'Cell_647', 'Cell_648', 'Cell_649', 'Cell_650', 'Cell_651', 'Cell_652', 'Cell_653', 'Cell_654', 'Cell_655', 'Cell_656', 'Cell_657', 'Cell_658', 'Cell_659', 'Cell_660', 'Cell_661', 'Cell_662', 'Cell_663', 'Cell_664', 'Cell_665', 'Cell_666', 'Cell_667', 'Cell_668', 'Cell_669', 'Cell_670', 'Cell_671', 'Cell_672', 'Cell_673', 'Cell_674', 'Cell_675', 'Cell_676', 'Cell_677', 'Cell_678', 'Cell_679', 'Cell_680', 'Cell_681', 'Cell_682', 'Cell_683', 'Cell_684', 'Cell_685', 'Cell_686', 'Cell_687', 'Cell_688', 'Cell_689', 'Cell_690', 'Cell_691', 'Cell_692', 'Cell_693', 'Cell_694', 'Cell_695', 'Cell_696', 'Cell_697', 'Cell_698', 'Cell_699', 'Cell_700', 'Cell_701', 'Cell_702', 'Cell_703', 'Cell_704', 'Cell_705', 'Cell_706', 'Cell_707', 'Cell_708', 'Cell_709', 'Cell_710', 'Cell_711', 'Cell_712', 'Cell_713', 'Cell_714', 'Cell_715', 'Cell_716', 'Cell_717', 'Cell_718', 'Cell_719', 'Cell_720', 'Cell_721', 'Cell_722', 'Cell_723', 'Cell_724', 'Cell_725', 'Cell_726', 'Cell_727', 'Cell_728', 'Cell_729', 'Cell_730', 'Cell_731', 'Cell_732', 'Cell_733', 'Cell_734', 'Cell_735', 'Cell_736', 'Cell_737', 'Cell_738', 'Cell_739', 'Cell_740', 'Cell_741', 'Cell_742', 'Cell_743', 'Cell_744', 'Cell_745', 'Cell_746', 'Cell_747', 'Cell_748', 'Cell_749', 'Cell_750', 'Cell_751', 'Cell_752', 'Cell_753', 'Cell_754', 'Cell_755', 'Cell_756', 'Cell_757', 'Cell_758', 'Cell_759', 'Cell_760', 'Cell_761', 'Cell_762', 'Cell_763', 'Cell_764', 'Cell_765', 'Cell_766', 'Cell_767', 'Cell_768', 'Cell_769', 'Cell_770', 'Cell_771', 'Cell_772', 'Cell_773', 'Cell_774', 'Cell_775', 'Cell_776', 'Cell_777', 'Cell_778', 'Cell_779', 'Cell_780', 'Cell_781', 'Cell_782', 'Cell_783', 'Cell_784', 'Cell_785', 'Cell_786', 'Cell_787', 'Cell_788', 'Cell_789', 'Cell_790', 'Cell_791', 'Cell_792', 'Cell_793', 'Cell_794', 'Cell_795', 'Cell_796', 'Cell_797', 'Cell_798', 'Cell_799', 'Cell_800', 'Cell_801', 'Cell_802', 'Cell_803', 'Cell_804', 'Cell_805', 'Cell_806', 'Cell_807', 'Cell_808', 'Cell_809', 'Cell_810', 'Cell_811', 'Cell_812', 'Cell_813', 'Cell_814', 'Cell_815', 'Cell_816', 'Cell_817', 'Cell_818', 'Cell_819', 'Cell_820', 'Cell_821', 'Cell_822', 'Cell_823', 'Cell_824', 'Cell_825', 'Cell_826', 'Cell_827', 'Cell_828', 'Cell_829', 'Cell_830', 'Cell_831', 'Cell_832', 'Cell_833', 'Cell_834', 'Cell_835', 'Cell_836', 'Cell_837', 'Cell_838', 'Cell_839', 'Cell_840', 'Cell_841', 'Cell_842', 'Cell_843', 'Cell_844', 'Cell_845', 'Cell_846', 'Cell_847', 'Cell_848', 'Cell_849', 'Cell_850', 'Cell_851', 'Cell_852', 'Cell_853', 'Cell_854', 'Cell_855', 'Cell_856', 'Cell_857', 'Cell_858', 'Cell_859', 'Cell_860', 'Cell_861', 'Cell_862', 'Cell_863', 'Cell_864', 'Cell_865', 'Cell_866', 'Cell_867', 'Cell_868', 'Cell_869', 'Cell_870', 'Cell_871', 'Cell_872', 'Cell_873', 'Cell_874', 'Cell_875', 'Cell_876', 'Cell_877', 'Cell_878', 'Cell_879', 'Cell_880', 'Cell_881', 'Cell_882', 'Cell_883', 'Cell_884', 'Cell_885', 'Cell_886', 'Cell_887', 'Cell_888', 'Cell_889', 'Cell_890', 'Cell_891', 'Cell_892', 'Cell_893', 'Cell_894', 'Cell_895', 'Cell_896', 'Cell_897', 'Cell_898', 'Cell_899', 'Cell_900', 'Cell_901', 'Cell_902', 'Cell_903', 'Cell_904', 'Cell_905', 'Cell_906', 'Cell_907', 'Cell_908', 'Cell_909', 'Cell_910', 'Cell_911', 'Cell_912', 'Cell_913', 'Cell_914', 'Cell_915', 'Cell_916', 'Cell_917', 'Cell_918', 'Cell_919', 'Cell_920', 'Cell_921', 'Cell_922', 'Cell_923', 'Cell_924', 'Cell_925', 'Cell_926', 'Cell_927', 'Cell_928', 'Cell_929', 'Cell_930', 'Cell_931', 'Cell_932', 'Cell_933', 'Cell_934', 'Cell_935', 'Cell_936', 'Cell_937', 'Cell_938', 'Cell_939', 'Cell_940', 'Cell_941', 'Cell_942', 'Cell_943', 'Cell_944', 'Cell_945', 'Cell_946', 'Cell_947', 'Cell_948', 'Cell_949', 'Cell_950', 'Cell_951', 'Cell_952', 'Cell_953', 'Cell_954', 'Cell_955', 'Cell_956', 'Cell_957', 'Cell_958', 'Cell_959', 'Cell_960', 'Cell_961', 'Cell_962', 'Cell_963', 'Cell_964', 'Cell_965', 'Cell_966', 'Cell_967', 'Cell_968', 'Cell_969', 'Cell_970', 'Cell_971', 'Cell_972', 'Cell_973', 'Cell_974', 'Cell_975', 'Cell_976', 'Cell_977', 'Cell_978', 'Cell_979', 'Cell_980', 'Cell_981', 'Cell_982', 'Cell_983', 'Cell_984', 'Cell_985', 'Cell_986', 'Cell_987', 'Cell_988', 'Cell_989', 'Cell_990', 'Cell_991', 'Cell_992', 'Cell_993', 'Cell_994', 'Cell_995', 'Cell_996', 'Cell_997', 'Cell_998', 'Cell_999', 'Cell_1000', 'Cell_1001', 'Cell_1002', 'Cell_1003', 'Cell_1004', 'Cell_1005', 'Cell_1006', 'Cell_1007', 'Cell_1008', 'Cell_1009', 'Cell_1010', 'Cell_1011', 'Cell_1012', 'Cell_1013', 'Cell_1014', 'Cell_1015', 'Cell_1016', 'Cell_1017', 'Cell_1018', 'Cell_1019', 'Cell_1020', 'Cell_1021', 'Cell_1022', 'Cell_1023', 'Cell_1024', 'Cell_1025', 'Cell_1026', 'Cell_1027', 'Cell_1028', 'Cell_1029', 'Cell_1030', 'Cell_1031', 'Cell_1032', 'Cell_1033', 'Cell_1034', 'Cell_1035', 'Cell_1036', 'Cell_1037', 'Cell_1038', 'Cell_1039', 'Cell_1040', 'Cell_1041', 'Cell_1042', 'Cell_1043', 'Cell_1044', 'Cell_1045', 'Cell_1046', 'Cell_1047', 'Cell_1048', 'Cell_1049', 'Cell_1050', 'Cell_1051', 'Cell_1052', 'Cell_1053', 'Cell_1054', 'Cell_1055', 'Cell_1056', 'Cell_1057', 'Cell_1058', 'Cell_1059', 'Cell_1060', 'Cell_1061', 'Cell_1062', 'Cell_1063', 'Cell_1064', 'Cell_1065', 'Cell_1066', 'Cell_1067', 'Cell_1068', 'Cell_1069', 'Cell_1070', 'Cell_1071', 'Cell_1072', 'Cell_1073', 'Cell_1074', 'Cell_1075', 'Cell_1076', 'Cell_1077', 'Cell_1078', 'Cell_1079', 'Cell_1080', 'Cell_1081', 'Cell_1082', 'Cell_1083', 'Cell_1084', 'Cell_1085', 'Cell_1086', 'Cell_1087', 'Cell_1088', 'Cell_1089', 'Cell_1090', 'Cell_1091', 'Cell_1092', 'Cell_1093', 'Cell_1094', 'Cell_1095', 'Cell_1096', 'Cell_1097', 'Cell_1098', 'Cell_1099', 'Cell_1100', 'Cell_1101', 'Cell_1102', 'Cell_1103', 'Cell_1104', 'Cell_1105', 'Cell_1106', 'Cell_1107', 'Cell_1108', 'Cell_1109', 'Cell_1110', 'Cell_1111', 'Cell_1112', 'Cell_1113', 'Cell_1114', 'Cell_1115', 'Cell_1116', 'Cell_1117', 'Cell_1118', 'Cell_1119', 'Cell_1120', 'Cell_1121', 'Cell_1122', 'Cell_1123', 'Cell_1124', 'Cell_1125', 'Cell_1126', 'Cell_1127', 'Cell_1128', 'Cell_1129', 'Cell_1130', 'Cell_1131', 'Cell_1132', 'Cell_1133', 'Cell_1134', 'Cell_1135', 'Cell_1136', 'Cell_1137', 'Cell_1138', 'Cell_1139', 'Cell_1140', 'Cell_1141', 'Cell_1142', 'Cell_1143', 'Cell_1144', 'Cell_1145', 'Cell_1146', 'Cell_1147', 'Cell_1148', 'Cell_1149', 'Cell_1150', 'Cell_1151', 'Cell_1152', 'Cell_1153', 'Cell_1154', 'Cell_1155', 'Cell_1156', 'Cell_1157', 'Cell_1158', 'Cell_1159', 'Cell_1160', 'Cell_1161', 'Cell_1162', 'Cell_1163', 'Cell_1164', 'Cell_1165', 'Cell_1166', 'Cell_1167', 'Cell_1168', 'Cell_1169', 'Cell_1170', 'Cell_1171', 'Cell_1172', 'Cell_1173', 'Cell_1174', 'Cell_1175', 'Cell_1176', 'Cell_1177', 'Cell_1178', 'Cell_1179', 'Cell_1180', 'Cell_1181', 'Cell_1182', 'Cell_1183', 'Cell_1184', 'Cell_1185', 'Cell_1186', 'Cell_1187', 'Cell_1188', 'Cell_1189', 'Cell_1190', 'Cell_1191', 'Cell_1192', 'Cell_1193', 'Cell_1194', 'Cell_1195', 'Cell_1196', 'Cell_1197', 'Cell_1198', 'Cell_1199', 'Cell_1200', 'Cell_1201', 'Cell_1202', 'Cell_1203', 'Cell_1204', 'Cell_1205', 'Cell_1206', 'Cell_1207', 'Cell_1208', 'Cell_1209', 'Cell_1210', 'Cell_1211', 'Cell_1212', 'Cell_1213', 'Cell_1214', 'Cell_1215', 'Cell_1216', 'Cell_1217', 'Cell_1218', 'Cell_1219', 'Cell_1220', 'Cell_1221', 'Cell_1222', 'Cell_1223', 'Cell_1224', 'Cell_1225', 'Cell_1226', 'Cell_1227', 'Cell_1228', 'Cell_1229', 'Cell_1230', 'Cell_1231', 'Cell_1232', 'Cell_1233', 'Cell_1234', 'Cell_1235', 'Cell_1236', 'Cell_1237', 'Cell_1238', 'Cell_1239', 'Cell_1240', 'Cell_1241', 'Cell_1242', 'Cell_1243', 'Cell_1244', 'Cell_1245', 'Cell_1246', 'Cell_1247', 'Cell_1248', 'Cell_1249', 'Cell_1250', 'Cell_1251', 'Cell_1252', 'Cell_1253', 'Cell_1254', 'Cell_1255', 'Cell_1256', 'Cell_1257', 'Cell_1258', 'Cell_1259', 'Cell_1260', 'Cell_1261', 'Cell_1262', 'Cell_1263', 'Cell_1264', 'Cell_1265', 'Cell_1266', 'Cell_1267', 'Cell_1268', 'Cell_1269', 'Cell_1270', 'Cell_1271', 'Cell_1272', 'Cell_1273', 'Cell_1274', 'Cell_1275', 'Cell_1276', 'Cell_1277', 'Cell_1278', 'Cell_1279', 'Cell_1280', 'Cell_1281', 'Cell_1282', 'Cell_1283', 'Cell_1284', 'Cell_1285', 'Cell_1286', 'Cell_1287', 'Cell_1288', 'Cell_1289', 'Cell_1290', 'Cell_1291', 'Cell_1292', 'Cell_1293', 'Cell_1294', 'Cell_1295', 'Cell_1296', 'Cell_1297', 'Cell_1298', 'Cell_1299', 'Cell_1300', 'Cell_1301', 'Cell_1302', 'Cell_1303', 'Cell_1304', 'Cell_1305', 'Cell_1306', 'Cell_1307', 'Cell_1308', 'Cell_1309', 'Cell_1310', 'Cell_1311', 'Cell_1312', 'Cell_1313', 'Cell_1314', 'Cell_1315', 'Cell_1316', 'Cell_1317', 'Cell_1318', 'Cell_1319', 'Cell_1320', 'Cell_1321', 'Cell_1322', 'Cell_1323', 'Cell_1324', 'Cell_1325', 'Cell_1326', 'Cell_1327', 'Cell_1328', 'Cell_1329', 'Cell_1330', 'Cell_1331', 'Cell_1332', 'Cell_1333', 'Cell_1334', 'Cell_1335', 'Cell_1336', 'Cell_1337', 'Cell_1338', 'Cell_1339', 'Cell_1340', 'Cell_1341', 'Cell_1342', 'Cell_1343', 'Cell_1344', 'Cell_1345', 'Cell_1346', 'Cell_1347', 'Cell_1348', 'Cell_1349', 'Cell_1350', 'Cell_1351', 'Cell_1352', 'Cell_1353', 'Cell_1354', 'Cell_1355', 'Cell_1356', 'Cell_1357', 'Cell_1358', 'Cell_1359', 'Cell_1360', 'Cell_1361', 'Cell_1362', 'Cell_1363', 'Cell_1364', 'Cell_1365', 'Cell_1366', 'Cell_1367', 'Cell_1368', 'Cell_1369', 'Cell_1370', 'Cell_1371', 'Cell_1372', 'Cell_1373', 'Cell_1374', 'Cell_1375', 'Cell_1376', 'Cell_1377', 'Cell_1378', 'Cell_1379', 'Cell_1380', 'Cell_1381', 'Cell_1382', 'Cell_1383', 'Cell_1384', 'Cell_1385', 'Cell_1386', 'Cell_1387', 'Cell_1388', 'Cell_1389', 'Cell_1390', 'Cell_1391', 'Cell_1392', 'Cell_1393', 'Cell_1394', 'Cell_1395', 'Cell_1396', 'Cell_1397', 'Cell_1398', 'Cell_1399', 'Cell_1400', 'Cell_1401', 'Cell_1402', 'Cell_1403', 'Cell_1404', 'Cell_1405', 'Cell_1406', 'Cell_1407', 'Cell_1408', 'Cell_1409', 'Cell_1410', 'Cell_1411', 'Cell_1412', 'Cell_1413', 'Cell_1414', 'Cell_1415').


title: isolate vci_108, replicate 2

description: Library name: vci_108_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_434


title: isolate vci_108, replicate 1

description: Library name: vci_108_1


title: V0407

description: Library name: forager_V0407_20210415_cDNA


title: V0397

description: Library name: forager_V0397_20210414_cDNA


title: MCF7-1L1MET2


title: EBC1_3NEG

source_name: lung

value: lung


title: isolate vci_106, replicate 2

description: Library name: vci_106_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_432


title: isolate vci_106, replicate 1

description: Library name: vci_106_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_431


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_437


title: isolate vci_109, replicate 1

description: Library name: vci_109_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_430


title: isolate vci_104, replicate 2

description: Library name: vci_104_2


title: EBC1_2NEG


title: V0395

description: Library name: forager_V0395_20210414_cDNA


title: EBC1_2L1MET1


title: MCF7-2L1MET2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_435


title: V0257

description: Library name: nurse_V0257_20210115_cDNA

value: nurse


title: V0408

description: Library name: forager_V0408_20210415_cDNA


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_429


title: isolate vci_104, replicate 1

description: Library name: vci_104_1


title: MCF7-1NEG


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_433


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_428


title: isolate vci_102, replicate 2

description: Library name: vci_102_2


title: V0253

description: Library name: nurse_V0253_20210115_cDNA


title: V0396

description: Library name: forager_V0396_20210414_cDNA


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_427


title: isolate vci_102, replicate 1

description: Library name: vci_102_1


title: EBC1_1L1MET1


title: EBC1_3L1MET1


title: V0247

description: Library name: nurse_V0247_20210115_cDNA


title: isolate vci_105, replicate 2

description: Library name: vci_105_2


title: EBC1-3NEG


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_426


title: V0244

description: Library name: nurse_V0244_20210115_cDNA


title: isolate vci_101, replicate 2

description: Library name: vci_101_2


title: isolate vci_101, replicate 1

description: Library name: vci_101_1


title: V0243

description: Library name: nurse_V0243_20210115_cDNA


title: V0242

description: Library name: nurse_V0242_20210115_cDNA


title: EBC1-2NEG


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_424


title: isolate vci_100, replicate 2

description: Library name: vci_100_2


title: EBC1-3L1MET2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_425


title: EBC1_1NEG


title: EBC1-2L1MET2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_423


title: isolate vci_100, replicate 1

description: Library name: vci_100_1


title: V0254

description: Library name: nurse_V0254_20210115_cDNA


title: V0241

description: Library name: nurse_V0241_20210115_cDNA


title: EBC1-1NEG


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_422


title: isolate vci_099, replicate 2

description: Library name: vci_099_2


title: V0152

description: Library name: nurse_V0152_20210107_cDNA


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_421


title: EBC1-1L1MET2


title: V0151

description: Library name: nurse_V0151_20210107_cDNA


title: isolate vci_099, replicate 1

description: Library name: vci_099_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_420


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_440


title: V0148

description: Library name: nurse_V0148_20210107_cDNA


title: isolate vci_098, replicate 1

description: Library name: vci_098_1


title: A549_3L1MET1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_419


title: isolate vci_096, replicate 2

description: Library name: vci_096_2


title: A549_2NEG


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_417


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_418


title: isolate vci_093, replicate 1

description: Library name: vci_093_1


title: A549_1NEG


title: isolate vci_096, replicate 1

description: Library name: vci_096_1


title: V0142

description: Library name: nurse_V0142_20210107_cDNA


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_416


title: V0256

description: Library name: nurse_V0256_20210115_cDNA


title: A549_2L1MET1


title: isolate vci_092, replicate 2

description: Library name: vci_092_2


title: V0409

description: Library name: forager_V0409_20210415_cDNA


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_415


title: isolate vci_092, replicate 1

description: Library name: vci_092_1


title: A549_1L1MET1


title: isolate vci_091, replicate 1

description: Library name: vci_091_1


title: A549_3NEG


title: A549-3NEG


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_414


title: V0248

description: Library name: nurse_V0248_20210115_cDNA


title: A549-3L1MET2


title: V0246

description: Library name: nurse_V0246_20210115_cDNA


title: isolate vci_090, replicate 2

description: Library name: vci_090_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_413


title: V0144

description: Library name: nurse_V0144_20210107_cDNA


title: A549-2NEG


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_412


title: V0143

description: Library name: nurse_V0143_20210107_cDNA


title: V0062

description: Library name: nurse_V0062_20201229_cDNA


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_411


title: isolate vci_090, replicate 1

description: Library name: vci_090_1


title: isolate vci_089, replicate 2

description: Library name: vci_089_2


title: A549-2L1MET2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_410


title: A549-1NEG


title: V0255

description: Library name: nurse_V0255_20210115_cDNA


title: isolate vci_088, replicate 2

description: Library name: vci_088_2


title: V0252

description: Library name: nurse_V0252_20210115_cDNA


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_409


title: V0251

description: Library name: nurse_V0251_20210115_cDNA


title: eCLIP-Seq of FLAG-MYC-ΔHLHLZ , IP Rep2

city: Pittsburgh

first: Da

last: Yang

state: PA

address: 3501 Terrace

department: School of Pharmacy

institute: University of Pittsburgh

data_processing:
These fastq files were generated after demultiplexing. Following steps were performed based CTK.
Peak calling was done using endogenous MYC by MACS2.
bedgraph files were generated by CTK and the difference between IP and Input were calculated using an ad-hoc script. Then they were converted to bw files.
IDR analysis was done to identify a list of reproducible peaks between the two replicates.
Assembly: hg38
Supplementary files format and content: eCLIP_endogenous_MYC.R2.peaks_w_annotation.txt, tab-delimited text files include peak information called by the endogenous MYC eCLIP-Seq IP and Input.
Supplementary files format and content: bw files showing the difference between merged IP and Input contains the read distribution across the genome.

source_name: Mammary gland/Breast

growth_protocol: Parental MCF-7 cells and MCF-7 stably expressing shMYC RNA with an shRNA-resistant FLAG-MYC-FL, FLAG-MYC-ΔTAD, and FLAG-MYC-ΔHLHLZ, were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Protein-associated RNAs by eCLIP and input RNA were extracted using acid phenol:chloroform:isoamyl alcohol (25:24:1, pH 6.6) (Invitrogen) and RNA cleanup was performed with RNA Clean & Concentrator-5 columns (Zymo). After reverse transcription, qPCR was performed to the Ct value of the cDNA with Power SYBR Green Master Mix (Applied Biosystems).
eCLIP-seq libraries were prepared with primers containing Illumina adapter sequences using Q5 High-Fidelity 2× Master Mix (NEB) for 9 to 18 cycles and PCR products were purified with Agencourt AMPureXP beads (Beckman Coulter). After separating on a 3% Nusieve GTG agarose gel (Lonza), DNA ranging from 175-300 bp gel fragments was excised and extracted using the MinElute Gel Extraction Kit (Qiagen) and libraries were validated using the Agilent High Sensitivity DNA Kit (Invitrogen).

treatment_protocol: Cells at exponential phase were washed twice with ice-cold PBS, UV-crosslinked on ice with 254 nm at 400 mJ/cm2 with a UV crosslinker (XL-1000, Spectrolinker). For each reaction, 20 million cells were lysed in eCLIP lysis buffer for 15 minutes on ice and incubated at 37 °C for 5 min with RNase I (Ambion) and Turbo DNase (Ambion) on a ThermoMixer C (Eppendorf).

value: Mammary gland/Breast

tag: disease

value: Adenocarcinoma

value: Human epithelial cell

tag: antibody for_eclip

value: FLAG (Sigma, #F3165)


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_408

value: spinal neuron differentiation

value: homogenous protocol


title: isolate vci_088, replicate 1

description: Library name: vci_088_1

value: bacterial

value: Clinical Isolate


title: isolate vci_086, replicate 2

description: Library name: vci_086_2


title: V0245

description: Library name: nurse_V0245_20210115_cDNA

value: brain


title: V0155

description: Library name: nurse_V0155_20210107_cDNA


title: V0156

description: Library name: nurse_V0156_20210107_cDNA


title: eCLIP-Seq of FLAG-MYC-ΔHLHLZ, Input


title: isolate vci_089, replicate 1

description: Library name: vci_089_1


title: isolate vci_086, replicate 1

description: Library name: vci_086_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_406


title: A549-1L1MET2


title: isolate vci_085, replicate 2

description: Library name: vci_085_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_405

value: Control


title: V0154

description: Library name: nurse_V0154_20210107_cDNA


title: eCLIP-Seq of FLAG-MYC-ΔTAD, IP Rep2


title: V0153

description: Library name: nurse_V0153_20210107_cDNA


title: eCLIP-Seq of FLAG-MYC-ΔTAD, IP Rep1


title: isolate vci_085, replicate 1

description: Library name: vci_085_1


title: V0149

description: Library name: nurse_V0149_20210107_cDNA


title: eCLIP-Seq of FLAG-MYC-ΔTAD, Input


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_404


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_403


title: eCLIP-Seq of FLAG-MYC-FL, IP Rep2


title: eCLIP-Seq of FLAG-MYC-ΔHLHLZ , IP Rep1


title: V0147

description: Library name: nurse_V0147_20210107_cDNA


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_402


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_407


title: V0146

description: Library name: nurse_V0146_20210107_cDNA


title: eCLIP-Seq of FLAG-MYC-FL, IP Rep1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_401


title: isolate vci_083, replicate 2

description: Library name: vci_083_2


title: V0145

description: Library name: nurse_V0145_20210107_cDNA


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_400


title: isolate vci_083, replicate 1

description: Library name: vci_083_1


title: eCLIP-Seq of FLAG-MYC-FL, Input


title: eCLIP-Seq of endenous MYC, IP Rep2

value: WT


title: V0141

description: Library name: nurse_V0141_20210107_cDNA


title: isolate vci_082, replicate 2

description: Library name: vci_082_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_398


title: V0064

description: Library name: nurse_V0064_20201229_cDNA


title: isolate vci_084, replicate 2

description: Library name: vci_084_2


title: eCLIP-Seq of endenous MYC, IP Rep1


title: V0063

description: Library name: nurse_V0063_20201229_cDNA


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_399


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_396


title: ChIP-Seq of MYC, AM treated, IP Rep2

description:
ChIP_MYC_DMSO.peaks_w_annotation.txt
ChIP_MYC_AM_Rep2.IP_Input_diff.bw

library_source: genomic

data_processing:
Reads were aligned using bowtie2 and duplicates were removed using sambamba.
MACS2 was used to do peak calling.
IDR analysis was done to identify a list of reproducible peaks between the two replicates.
bedgraph files were generated by bedtools and the difference between IP and Input were calculated using an ad-hoc script. Then they were converted to bw files.
Assembly: hg38
Supplementary files format and content: ChIP_MYC_DMSO.peaks_w_annotation.txt, tab-delimited text files include peak information called by the MYC ChIP-Seq IP and Input treated with DMSO.
Supplementary files format and content: bw files showing the difference between IP and Input contains the read distribution across the genome.

molecule: genomic DNA

growth_protocol: MCF-7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Pico (Diagenode).
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB). 5 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 9 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 (Invitrogen).

treatment_protocol: Cells at exponential phase were treated for 2 h with DMSO and a combination of 1 µM of Actinomycin D (ActD)/10 µM MG132.

tag: chip antibody

value: co-treatment Actinomycin D and MG132 for 2 h


title: isolate vci_084, replicate 1

description: Library name: vci_084_1


title: V0061

description: Library name: nurse_V0061_20201229_cDNA


title: eCLIP-Seq of endenous MYC, Input


title: V0074

description: Library name: forager_V0074_20201229_cDNA

value: forager


title: isolate vci_080, replicate 2

description: Library name: vci_080_2


title: ChIP-Seq of MYC, AM treated, IP Rep1

description:
ChIP_MYC_DMSO.peaks_w_annotation.txt
ChIP_MYC_AM_Rep1.IP_Input_diff.bw


title: V0073

description: Library name: forager_V0073_20201229_cDNA


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_395


title: isolate vci_078, replicate 2

description: Library name: vci_078_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_397


title: ChIP-Seq of MYC, DMSO, IP Rep2

description:
ChIP_MYC_DMSO.peaks_w_annotation.txt
ChIP_MYC_DMSO_Rep2.IP_Input_diff.bw

value: DMSO


title: isolate vci_078, replicate 1

description: Library name: vci_078_1


title: ChIP-Seq of MYC, DMSO, IP Rep1

description:
ChIP_MYC_DMSO.peaks_w_annotation.txt
ChIP_MYC_DMSO_Rep1.IP_Input_diff.bw


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_393


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_394


title: isolate vci_077, replicate 2

description: Library name: vci_077_2


title: isolate vci_082, replicate 1

description: Library name: vci_082_1


title: ChIP-Seq of MYC, AM treated, Input Rep2


title: V0072

description: Library name: forager_V0072_20201229_cDNA


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_392


title: ChIP-Seq of MYC, AM treated, Input Rep1


title: isolate vci_077, replicate 1

description: Library name: vci_077_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_391


title: isolate vci_076, replicate 2

description: Library name: vci_076_2


title: isolate vci_080, replicate 1

description: Library name: vci_080_1


title: ChIP-Seq of MYC, DMSO, Input Rep2


title: ChIP-Seq of MYC, DMSO, Input Rep1


title: isolate vci_076, replicate 1

description: Library name: vci_076_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_390


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_389


title: isolate vci_075, replicate 1

description: Library name: vci_075_1


title: isolate vci_075, replicate 2

description: Library name: vci_075_2


title: Nude mice, glioma-associated CD11b+ cells, tumour bearing mouse, RGD+Anti-PD-1+RGD 4

city: Barcelona

first: Adria-Jaume

last: Roura

address: Carrer de Baldiri Reixac, 10

country: Spain

institute: IRB Barcelona

data_processing:
Illumina-specific adapters, short reads, and low quality 5′ and 3′ bases were filtered out in the FASTQ format files using Trimmomatic.
The resulting RNA sequencing reads were aligned to a reference mouse genome sequence (mm10) with STAR aligner.
Quantification of mapped reads and summarization by gene was performed using HTSeq-count (version 0.11.1), with paired mode (-p) and reverse stranded mode (-s reverse) enabled, and only reads with MapQ values of 10 or higher were considered.
Low-expressed features were filtered out and an analysis of differentially expressed genes was performed using NOIseq. Only mRNAs encoding protein-coding genes were retained for downstream analysis.
Differential expression analysis was performed using NOIseq methods, with the control state (Vehicle) as the reference group and compared with the RGD, RAE or RGD, anti-PD-1 and combination of RGD+anti-PD-1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes RPKM values for each sample

source_name: Glioma-associated CD11b+ cells

extract_protocol:
CD11b+ cells were FACS sorted from naive or tumor-bearing hemispheres (pooled from 2 animals per sample at day 21 and from individual mice at day 28) using Cell Sorter BD FACSAriaII. Immediately after sorting, cells were centrifuged and lysed for further isolation of RNA using the RNeasy Plus Mini Kit (Qiagen, Germany) according to manufacturer’s protocol. The integrity and quality of RNA were assessed on an Agilent 2100 Bioanalyzer with an RNA 6000 Pico Kit (Agilent Technologies, CA, USA).
Strand-specific RNA libraries were prepared for sequencing (3 - 4 biological replicates/treatment) using a KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, MA, USA). Poly-A mRNAs were purified from 100 ng of total RNA using poly-T-oligo-magnetic beads (Kapa Biosystems, MA, USA). mRNAs were fragmented and a first-strand cDNA was synthesized using reverse transcriptase and random hexamers. A second-strand cDNA synthesis was performed by removing RNA templates and synthesizing replacement strands, incorporating dUTP in place of dTTP to generate double-stranded (ds) cDNA. dsDNA was then subjected to addition of “A” bases to the 3′ ends and ligation of adapters from NEB, followed by uracil digestion by USER enzyme (NEB, MA, USA). Amplification of fragments with adapters ligated on both ends was performed by PCR using primers containing TruSeq barcodes (NEB, Ipswich, MA, USA). Final libraries were analyzed using Bioanalyzer and Agilent DNA High Sensitivity chips (Agilent Technologies, Santa Clara, CA, USA) to confirm fragment sizes (~300bp). Quantification was performed using a Quantus fluorometer and the QuantiFluor dsDNA System (Promega, Madison, Wisconsin, US).

value: Glioma-associated CD11b+ cells


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_388


title: Nude mice, glioma-associated CD11b+ cells, tumour bearing mouse, RGD+Anti-PD-1+RGD 2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_387


title: Nude mice, glioma-associated CD11b+ cells, tumour bearing mouse, RGD+Anti-PD-1+RGD 1


title: isolate vci_074, replicate 2

description: Library name: vci_074_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_386


title: isolate vci_074, replicate 1

description: Library name: vci_074_1


title: Nude mice, glioma-associated CD11b+ cells, tumour bearing mouse, Anti-PD-1 4


title: isolate vci_073, replicate 2

description: Library name: vci_073_2


title: Nude mice, glioma-associated CD11b+ cells, tumour bearing mouse, Anti-PD-1 3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_385


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_384


title: Nude mice, glioma-associated CD11b+ cells, tumour bearing mouse, RGD+Anti-PD-1+RGD 3


title: Nude mice, glioma-associated CD11b+ cells, tumour bearing mouse, Anti-PD-1 1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_383


title: isolate vci_070, replicate 2

description: Library name: vci_070_2


title: Nude mice, glioma-associated CD11b+ cells, tumour bearing mouse, Anti-PD-1 2


title: isolate vci_073, replicate 1

description: Library name: vci_073_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_382


title: isolate vci_070, replicate 1

description: Library name: vci_070_1


title: Nude mice, glioma-associated CD11b+ cells, tumour bearing mouse, RGD 4

value: RGD peptide


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_381


title: isolate vci_068, replicate 2

description: Library name: vci_068_2


title: Nude mice, glioma-associated CD11b+ cells, tumour bearing mouse, RGD 3


title: Ndrg2-/- vs wild type_rep4

type: RNA

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa University

description: Differential gene expresion: Ndrg2-/- vs wild type_rep4

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) containing fragmented Cydye-labeled cRNA labeled were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially by Wash Buffer 1 (6× SSPE, 0.005% N-lauroylsarcosine) and Wash Buffer 2 (0.06× SSPE, 0.005% N-lauroylsarcosine) for 1 min at room temperture.

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: wild type_rep4

label_protocol: Total RNA samples (200 ng) from untreated and treated shoots were used to prepare Cy3- or Cy5-labeled cRNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) following manufacturer's instructions

growth_protocol: Three months old adult male mice of Ndrg2-/- or wild type (C57BL/6N background) were used. All mice were housed in a 12h light/dark cycle with free access to water and food in a temperature- and humidity-controlled room.

extract_protocol: Total RNA extracted using RNeasy following manufacturer's instructions. The quality of total RNA was checked by Agilent tapestation 2200.

treatment_protocol: Total RNA were prepared from the cerebral cortex of mice brain


title: Multiome, Sun1sfGFP; ChAT-Cre; Mettl14floxed-ATAC

city: Taipei

first: Ya-Ping

last: Yen

address: 128 Academia Road, Section 2, Nankang

department: Institute of molecular biology

country: Taiwan

institute: Academia Sinica

description: Library name: KO-ATAC

library_source: genomic single cell

data_processing:
Raw sequencing data were processed using the standard Cell Ranger ARC pipeline (version 7.0.0, 10X Genomics) for demultiplexing, mapping to the mm10 reference genome, barcode, and UMI (unique molecular identifier) counting, and generating the gene count matrix.
Assembly: mm10
Supplementary files format and content: h5 files for filtered and bigwin/tsv.gz file for ATAC fragment regions, sequenced in Illumina Next-seq 500 plateform

source_name: lumbar spinal cord

extract_protocol:
Lumbar segments from the P100~P120 Sun1sfGFP; ChAT-Cre; Mettl14floxed (cKO) and Sun1sfGFP; ChAT-Cre (control) spinal cord were dissected based on morphology and dissociated two at a time in 2 mL pre-chilled lysis buffer with a 7 mL Dounce Homogenizer (pestle A: eight strokes; pestle B: 5 strokes). An additional 3 mL lysis buffer was added, and the entire homogenate was filtered through a 100 µm strainer. Then, 5 mL of 50 % iodixanol was added to create a 10 mL suspension of 25 % iodixanol. The suspension was inverted to mix well before equally splitting into two 15 mL tubes. Iodixanol (40 %, 2 mL) was layered gently at the bottom of the homogenate and centrifuged at 1,000 g for 12 minutes at 4 oC, with a swing bucket centrifuge (brand). The interphase nuclei were transferred to a new 15 mL tube and resuspended with 1:1 volume of 10 X wash buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 1 % BSA, 0.1 % Tween 20, 1 mM DTT, and 1 U/µL RNase inhibitor), followed by centrifuging at 500 g for 10 minutes at 4 oC. The supernatant was discarded and the pellet was resuspended in 800 µL diluted nuclei buffer (20X Nuclei Buffer from Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit supplemented with 1 mM DTT, and 1 U/µL RNase inhibitor), before conducting FANS (fluorescence-activated nuclei sorting) using a BD FACS Aria III cell sorter (BD BioSciences, USA). GFPon nuclei were collected in diluted nuclei buffer and centrifuged at 500 g for 7 minutes at 4 oC. Nuclei were adjusted to an appropriate concentration following the manufacturer’s protocol (10x Genomics, 1000285) with diluted nuclei buffer. Then the sorted nuclei from Sun1sfGFP; ChAT-Cre; Mettl14floxed (cKO) and Sun1sfGFP; ChAT-Cre (control) were procced for 10x Genomics Chromium Next GEM single Cell Multiome ATAC+Gene expression experiment.
single-nucleus multiome libraries were prepared following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol CG000338 Rev F (10X Genomics, Pleasanton, CA).

value: lumbar spinal cord

value: Cholinergic neurons


title: Ndrg2-/- vs wild type_rep2

description: Differential gene expresion: Ndrg2-/- vs wild type_rep2

source_name: wild type_rep2


title: isolate vci_068, replicate 1

description: Library name: vci_068_1


title: WT vs Ndrg2KO_ipsilateral coretex 24h after pMCAO_rep3

description: WT vs Ndrg2KO_pMCAO

growth_protocol: Mice were housed in a temparature and humidity controlled room under a 12hours light/dark cycles, with free access to food and water.

treatment_protocol: Mice were deeply anesthetized under isoflurane inhalation. Permanent focal cerebral ischemia was induced by permanent occulusion of the left middle cerebral artery (pMCAO) by electrocoagulation and subsequent disconnection just distal to its crossing of the olfactry tract. Ipsilateral cortices were isolated from WT mice and Ndrg2KO mice 24h after pMCAO.

value: ipsilateral cortex

value: 8 weeks

value: permanent MCAO

tag: time after treatment

value: wildtype


title: Appendix 2

type: genomic

city: Jerusalem

first: Ilana

last: Fox-Fisher

address: Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University of Jerusalem

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner setting

data_processing: Methylation array data were processed with the minfi package in R. For each sample analyzed on the Illumina Methylation array, CpG sites were filtered out if they were represented by less than 3 beads on the array, if the detection p-value (representing total fluorescence of the relevant probes) was greater than 0.01, or if they mapped to a sex chromosome. Background correction and normalization were performed with the preprocessIllumina function, which removes background calculated based on internal control probes and normalizes all samples to a predetermined control sample.

label: Cy3 and Cy5

source_name: appendix

label_protocol: Standard Illumina Protocol

extract_protocol: A fresh surgical appendix specimen was obtained from a right hemicolectomy surgery due to carcinoma of the colon. The appendix tissue was verified by a pathologist that it was not cancerous. The appendix was placed in 10 mL of ice-cold HBSS. Mucosal and muscle layers were separated with fine curved iris scissors. Mucosal strips were thoroughly rinsed in a petri dish containing fresh HBSS and then transferred to a 50ml tube containing 50 mL of HBSS, 0.15% dithiothreitol (75mg/50ml). Tubes were placed on an orbital plate at room temperature and were stirred at 0.3g for 30 minutes until residual mucus and free additional debris were dissolved. The solution was moved to a new 50 ml tube, 10 ml of pre-warmed (37ᵒC) PBS 20mM ph7.2 EDTA was added and warmed for 10 min at 37ᵒC and mixed every 2 minutes, PBS/EDTA removed. 10 ml of cold PBS was added and then shaken vigorously. For at least 10 minutes until crypts structures are seen. Centrifuge the crypts:  1000 rpm 7 min at 4ᵒC. supernatant is removed and resuspended with 5ml cold PBS and transferred to a new 15ml tube and centrifuged for 2 minutes in 200g at 4ᵒC. the supernatant was removed and re-suspended in 1ml Tryp LE + 0.5mg/ml DNaseI and incubated at 37°C for 10-30 minutes until single cells were seen under a microscope. Tryp LE was stopped by adding PBS 0.5% BSA (up to 10-15ml). centrifuge:300g 5 minutes at 4ᵒC. cells were then stained with CD326+, CD45-, CD31-, CD235- for flow cytometry sorting

value: appendix

value: Healthy appendix epithelial cells


title: Ndrg2-/- vs wild type_rep3

description: Differential gene expresion: Ndrg2-/- vs wild type_rep3

source_name: wild type_rep3


title: Multiome, Sun1sfGFP; ChAT-Cre; Mettl14floxed-GEX

description: Library name: KO-GE

value: Sun1sfGFP; ChAT-Cre; Mettl14floxed (cKO)


title: Ndrg2-/- vs wild type_rep1

description: Differential gene expresion: Ndrg2-/- vs wild type_rep1

source_name: wild type_rep1

value: brain


title: WT vs Ndrg2KO_ipsilateral coretex 24h after pMCAO_rep1

description: WT vs Ndrg2KO_pMCAO


title: WT vs Ndrg2KO_ipsilateral coretex 24h after pMCAO_rep4

description: WT vs Ndrg2KO_pMCAO


title: Appendix 1


title: Nude mice, glioma-associated CD11b+ cells, tumour bearing mouse, RGD 1


title: isolate vci_067, replicate 2

description: Library name: vci_067_2

value: bacterial

value: Clinical Isolate


title: Nude mice, glioma-associated CD11b+ cells, tumour bearing mouse, solvent control 4

value: solvent control


title: Multiome, Ctrl-GEX

description: Library name: WT-GE

value: Ctrl