title: Blimp-1 positive biol rep 2

city: Irvine

first: Yoseop

last: Yoon

state: CA

address: 1002 Health Sciences Rd

institute: University of California Irvine

data_processing:
Adapters and low-quality reads were removed from the raw fastq files using Cutadapt (Martin, 2011)
The paired-end reads were aligned to the mouse genome (mm9) using STAR (Dobin et al., 2013)
Differential expression analysis was performed using edgeR (Robinson et al., 2010).
Assembly: mm9
Supplementary files format and content: bw

source_name: B cell

growth_protocol: Primary B cells stimulated with LPS+cytokines for 4 days in IMDM contianing supplements HEPES, Glutamax, NEAA, 2-ME, Na-Pyruvate, Penicillin/Streptomycin, 10%FCS

extract_protocol:
TRIZOL
Complementary DNA (cDNA) libraries for Illumina sequencing were generated using the TruSeq Stranded mRNA Library Prep kit (Illumina, cat: 20020595), following the manufacturer’s instructions

treatment_protocol: Spleens were harvested from µR x Blimp-1 reporter mice and B cells were immunomagnetically enriched via negative selection. B cells were stimulated with LPS+IL2+IL5 at low density cultured for 4 days. At day 4 live cells were sorted based on fluorescent protein reporter expression and cells were pelleted and flash frozen.

value: B cell

value: Blimp-1 positive

value: stimulated B cells sorted on day4 based on reporter expression


title: isolate vci_332, replicate 2

status: Public on Apr 30 2025

type: SRA

city: Boston

first: Peter

last: Culviner

state: MA

address: 677 Huntington Ave

department: IID

country: USA

institute: Harvard School of Public Health

description: Library name: vci_332_2

library_source: transcriptomic

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

molecule: total RNA

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.

tag: cell type

value: bacterial

tag: genotype

value: Clinical Isolate


title: isolate vci_332, replicate 1

description: Library name: vci_332_1


title: Blimp-1 positive biol rep 1

organism: Mus musculus

tag: treatment


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_595

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

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'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.

tag: cell line

value: spinal neuron differentiation

value: homogenous protocol

tag: sequencing batch


title: isolate vci_329, replicate 2

description: Library name: vci_329_2


title: isolate vci_331, replicate 2

description: Library name: vci_331_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_603


title: oocyte-2, rep1

city: Hefei

first: Tie

last: Chang

address: Huangshan Road

country: China

institute: University of Science and Technology of China

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the mus musculus（ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: oocyte

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: oocyte


title: oocyte-1, rep3

value: fresh


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_594


title: isolate vci_327, replicate 2

description: Library name: vci_327_2


title: uS HI Blimp-1 positive biol rep 3

value: uS HI Blimp-1 positive


title: Blimp-1 negative biol rep 1

value: Blimp-1 negative


title: isolate vci_325, replicate 2

description: Library name: vci_325_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_591


title: isolate vci_325, replicate 1

description: Library name: vci_325_1


title: uS HI Blimp-1 positive biol rep 1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_590


title: uS HI Blimp-1 positive biol rep 2


title: isolate vci_324, replicate 2

description: Library name: vci_324_2


title: uS INT Blimp-1 positive biol rep 3

value: uS INT Blimp-1 positive


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_589


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_588


title: isolate vci_323, replicate 2

description: Library name: vci_323_2


title: uS INT Blimp-1 positive biol rep 2


title: uS INT Blimp-1 positive biol rep 1


title: Blimp-1 negative biol rep 2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_587


title: isolate vci_324, replicate 1

description: Library name: vci_324_1


title: isolate vci_317, replicate 2

description: Library name: vci_317_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_593


title: uS HI Blimp-1 negative biol rep 2

value: uS HI Blimp-1 negative


title: isolate vci_329, replicate 1

description: Library name: vci_329_1


title: isolate vci_311, replicate 1

description: Library name: vci_311_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_592


title: uS INT Blimp-1 negative biol rep 2

value: uS INT Blimp-1 negative


title: uS HI Blimp-1 negative biol rep 1


title: isolate vci_316, replicate 1

description: Library name: vci_316_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_585


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_584


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_586


title: uS INT Blimp-1 negative biol rep 1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_583


title: isolate vci_295, replicate 2

description: Library name: vci_295_2


title: isolate vci_310, replicate 2

description: Library name: vci_310_2


title: Lung, replicate 1, scRNAseq

city: Suita

first: Kei

last: Higaki

state: Osaka

address: Nanobiotechnology building 3F, 1-3 Yamadaoka

department: Graduate School of Frontier Biosciences, Graduate School of Medicine, Immunology Frontier Research Center, World Premier International Research Center (WPI)

country: Japan

institute: Osaka University

description: 10x Genomics

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of eGFP and to the mouse genome (mm10).
Filtering was applied to remove low‐quality cells by excluding cells expressing <500 or >6,000 unique genes, as well as cells with >15% mitochondrial gene expression.
We removed cells expressing one of the markers Ptprc (Cd45), Pecam (Cd31), Myh11, or Msln. Next, individual Seurat objects obtained from the lung and the ectopic bones were merged and used for batch effect correction and integration using Harmony (v0.1.1).
Single-cell trajectories was computed using the algorithm slingshot (v1.8.0), which enables computation of lineage structures in a low-dimensional space.
Assembly: mm10_EGFP
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
To isolate cells from ectopic bones, tissues were minced and digested with collagenase type I and DNase I at 37°C for 30 min. To isolate lung non-hematopoietic cells, the minced lung was placed in digestion solution containing collagenase Type I and DNase. The suspension was incubated at 37°C for 60 min under constant agitation. Cells were then incubated with red blood cell lysis buffer for 5 min. Preparations from all tissues were passed through a 100-μm cell strainer (Falcon) to remove debris.
Libraries were constructed following the recommended protocol for the Chromium Next GEM Single Cell 3’Reagent Kits (v3)

tag: tissue

value: lung

value: Naive


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_582


title: isolate vci_292, replicate 1

description: Library name: vci_292_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_581


title: HO, replicate 2, scRNAseq

description: 10x Genomics

source_name: ectopic bone

value: ectopic bone

value: FACS-sorted populations from the lung of Ubc-GFP;CXCL12-tdTomato mice were intramuscularly injected into the mid-belly of the tibialis anterior muscle with growth factor-reduced Matrigel (BD Biosciences, Bedford, MA, USA)  and human recombinant BMP2 (PeproTech, 120-02) at a concentration of 2.5 ug/50 μl.


title: HO, replicate 1, scRNAseq

description: 10x Genomics

value: FACS-sorted populations from the lung of Ubc-GFP mice were intramuscularly injected into the mid-belly of the tibialis anterior muscle with growth factor-reduced Matrigel (BD Biosciences, Bedford, MA, USA)  and human recombinant BMP2 (PeproTech, 120-02) at a concentration of 2.5 ug/50 μl.


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_580


title: cHET_F

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

description:
10x Genomics
7166-MR-75

data_processing:
Raw sequencing data were processed with Cell Ranger (v6.1.2). Cellranger mkfastq command was used to demultiplex the different samples and cellranger count command was used to generate gene – cell expression matrices. Ambient RNA contamination was inferred and removed using CellBender (v0.232) with standard parameters. Mouse genome mm10 was used for the alignment and genecode vM25 was used for gene annotation and coordinates. We used the R package Seurat (v4.1.0) and customized R scripts for data analyses Data from different samples (control vs. cHet) were merged into a unique single cell object. Nuclei with > 250 genes, < 10000 UMIs, and < 5% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) for a resultant expression matrix with 21,516 genes and 52,743 cells. The SCTransform workflow was used for count normalization and data integration using 30 principal components and resolution of 0.5 for Louvain clustering and UMAP. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. After removing 4 clusters showing high expression of glutamatergic neuronal markers and subsequent re-clustering, we identified 20 final distinct clusters. Cell annotation was performed using two different approaches: 1) markers enrichment using a Nucleus Accumbens independent data by Fisher’s exact test and 2) a predictive machine learning model based on a Nucleus Accumbens atlas reference data using the R package scPred. Cell annotation then was manually curated to reflect both analyses. To identify differentially expressed genes between conditions (control vs. cHet) in each defined cell types, the R package LIBRA with option MAST was used to perform zero-inflated regression analysis. Genes were defined as significantly differentially expressed at Benjamini–Hochberg correction FDR < 0.05 and abs(log2(Fold Change)) > 0.2. We further confirmed these results using a Wilcoxon’s rank sum test.
Assembly: Mus musculus mm10
Supplementary files format and content: HDF5 Feature-Barcode Matrix

source_name: PFC

extract_protocol:
8-week old Mef2c cHetVgat and littermate control mice (Vgat-cre positive) were live-decapitated, and brains were rapidly extracted into ice-cold 4˚C Hibernate A medium, with GlutaMAX (Fisher), B27 (Fisher), and NxGen RNase inhibitor (0.2U/µL, Lucigen), and incubated for approximately 30 seconds. The brain was sectioned into 1 mm sections using a brain matrix and cold razor blades. The PFC was isolated with fine forceps and collected, flash frozen on dry ice, and stored at -80oC until the day of nuclear isolation. Bilateral prefrontal cortices were collected separately from three mice per group. We modified the nuclear isolation protocol described in Savell et al., 2020. On the day of nuclear isolation, the frozen tissue was thawed on ice and chopped with a scalpel blade 200 times in two orthogonal directions on a glass petri dish atop ice. The chopped tissue were then pooled per group and transferred into a lysis buffer (10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL (Sigma) in Nuclease-Free Water). Supplemented Hibernate A medium was added to the lysis buffer to quench the reaction, and the tissue was triturated ~30 times/sample using three glass pipettes of decreasing diameter. This trituration cycle was repeated two more times. The mixture was filtered using a 40 micron filter (Fisher). The nuclei were isolated using 500xg centrifugation and washed with 1x PBS+1.0% BSA and 0.2U/µL RNase inhibitor. Nuclei were incubated with 7-aminoactinomycin D (7-AAD) (Invitrogen) for five minutes and sorted for 7-AAD-positive single nuclei using fluorescence-activated nuclear sorting on the BD FACS Aria II. Samples were counted and diluted to 1500 nuclei/µL before processing on the 10x Genomics Single-Cell Protocol by the MUSC Translation Science Lab. Libraries were constructed using the Chromium Single Cell 3’ Library Construction Kit (10x Genomics, v3.1) and sequenced at Vanderbilt’s Next Gen Sequencing Core (Illumina NovaSeq 6000).
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3’ v3.1 according to the manufacturer’s protocol. Libraries and sequencing were performed at the Translational Science Lab at MUSC.

value: PFC

tag: library type

value: 10X single-nuclei RNA-seq

tag: strain

tag: age

value: 8 weeks old

tag: protocol

value: Protocol 1


title: isolate vci_291, replicate 1

description: Library name: vci_291_1

value: bacterial

value: Clinical Isolate


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_579

value: spinal neuron differentiation

value: Control

value: homogenous protocol


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_578


title: isolate vci_289, replicate 1

description: Library name: vci_289_1


title: isolate vci_289, replicate 2

description: Library name: vci_289_2


title: CONTROL_F

description:
10x Genomics
7166-MR-74


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_577


title: D_2: CKO-MI-D42

city: Hangzhou

first: Sheng-an

last: Su

state: Zhejiang

address: No. 88 Jiefang Road

institute: Zhejiang University

data_processing:
we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing polyA and polyG; 3) removing reads containing more than 5% of unknown nucleotides (N); 4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data. After that, a total of G bp of cleaned, paired-end reads were produced.

source_name: myocardium

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: myocardium

value: Piezo1 knockout

value: myocardial infarction


title: D_1: CKO-MI-D42


title: isolate vci_283, replicate 2

description: Library name: vci_283_2


title: isolate vci_287, replicate 1

description: Library name: vci_287_1


title: C_1: fl/fl-MI-D42

value: WT


title: isolate vci_287, replicate 2

description: Library name: vci_287_2


title: isolate vci_283, replicate 1

description: Library name: vci_283_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_576


title: C_2: fl/fl-MI-D42


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_575


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_573


title: B_1: CKO-Sham

value: sham


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_574


title: isolate vci_295, replicate 1

description: Library name: vci_295_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_572


title: isolate vci_280, replicate 1

description: Library name: vci_280_1


title: A_2: fl/fl-Sham


title: isolate vci_276, replicate 2

description: Library name: vci_276_2


title: isolate vci_276, replicate 1

description: Library name: vci_276_1


title: A_1: fl/fl-Sham


title: isolate vci_271, replicate 2

description: Library name: vci_271_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_570


title: Kupffer cells, induced with MC38-VT exosomes, induced for 48h, biol rep2

city: Guangzhou

first: Zhonghua

last: Chu

state: Guangdong

address: 107 Yan Jiang West Road

institute: Sun Yat-sen Memorial Hospital,Sun Yat-sen University

data_processing:
Clean reads was compared with the reference genome sequence.
According to the annotation file and reads of the genome, the number of reads contained in each gene, namely the expression level, was calculated.
Then, differentially expressed genes were obtained by statistical test.
Finally, functional annotation of differentially expressed genes and GO and KEGG enrichment tests were performed to obtain the GO and KEGG collections enriched by differentially expressed genes
In the RNA-Seq technique, FPKM (Fragments Per Kilo bases per Million mapped Reads) is a general method to represent the level of gene. With RSEM (http://deweylab.github.io/RSEM/) software respectively to the level of gene transcription level/the whole expression for quantitative analysis expression, representing the number of reads per million from a gene per thousand base length.
DESeq2 was used for differential expression analysis.For statistical significance, the level of significance was determined by p value or corrected p value (padj).Padj is the value obtained when the false positive rate is high by using BH method for multiple test correction of p-value.Use the default pvalue < 0.05, | log2FoldChange | > 1 as the standard significance of difference. In final sample 1, up-regulated gene 357 and down-regulated gene 220 were detected.Sample 2 up-regulated gene 354 and down-regulated gene 131
Assembly: mm10

source_name: Kupffer cell in liver

growth_protocol: We carefully selected Kupffer cells with robust viability and exposed them to MC38-PRL-3 Exo and MC38-VT 10ug Exo for 48 hours, and then extracted RNA of Kupffer cells

extract_protocol:
48 h after induction of Kupffer cells by exosomes, total RNA was extracted by TRIzol reagent, and commissioned by IGE Biotechnology for RNA-SEQ
mRNA Capture Beads are used to enrich eukaryotes mRNA (in the case of prokaryotes, rRNA is removed by the kit to enrich mRNA). Then, high temperature and metal ion action are used to achieve mRNA fragmentation.Using mRNA as template, a cDNA strand was synthesized with six-base random hexamers, then the synthesis reaction of two-strand cDNA was carried out, and then the DNA Clean Beads were used to purify the double-strand cDNA.The purified double-stranded cDNA was first end-repaired, A tail was added and sequencing joints were connected, and then DNA Clean Beads were used for fragment size sorting.Finally, PCR amplification was carried out and DNA Clean Beads were used to purify PCR products to get the final library.After the completion of the library construction, the concentration was preliminarily measured using Qubit 3.0, and then the library insertion fragment was detected using Agilent 2100 Bioanalyzer.The effective concentration of the library was accurately quantified by ABI Step One Plus Real-Time PCR system

treatment_protocol: Kupffer cells were induced by MC38-PRL-3 and MC38-VT exosomes, MC38-VT exosomes as control group and MC38-PRL-3 exosomes as experimental group

value: Kupffer cell in liver

value: macrophage

tag: cell population

value: Kupffer cell

tag: exosome

value: MC38-VT Exo

value: treated with colon cancer cells's exosomes


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_571


title: isolate vci_271, replicate 1

description: Library name: vci_271_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_568


title: Kupffer cells, induced with MC38-PRL-3 exosomes, induced for 48h, biol rep2

value: MC38-PRL-3 Exo


title: B_2: CKO-Sham


title: isolate vci_269, replicate 2

description: Library name: vci_269_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_566


title: isolate vci_269, replicate 1

description: Library name: vci_269_1


title: isolate vci_266, replicate 1

description: Library name: vci_266_1


title: Kupffer cells, induced with MC38-PRL-3 exosomes, induced for 48h, biol rep1


title: MK801,Input,replicate 1

city: Beijing

first: Liting

last: Xue

address: 10 Xitoutiao Road, You'anmenwai, Fengtai District

department: Department of Medical Genetics and Developmental Biology School of Basic Medical Sciences

institute: Capital Medical University

data_processing:
ac4C-RIP-seq reads were trimmed using Trimmomatic v0.39.
ac4C-RIP-seq reads were aligned to the UCSC mm10 genome using STAR version  2.7.5c.
Peaks were called uing exomePeak version 2.17.0.
Assembly: mm10
Supplementary files format and content: bed

source_name: brain,the prefrontal cortex

extract_protocol:
Total RNA was extracted from the prefrontal cortex of MK-801-exposed male C57/BL6 mice and saline controls using TRIzol reagent (Invitrogen), rRNA was depleted using RiboMinus Eukaryote Kit v2 (Invitrogen), RiboMinus-treated RNA samples were fragmented using a NEBNext Magnesium RNA Fragmentation Kit (NEB).
ac4C-RIP-seq libraries were prepared using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®. 10 ng of RNA was used as starting material for input and ip samples.
ac4C-RIP-seq

treatment_protocol: C57BL/6J male mice were injected intraperitoneally with either MK-801 (0.5 mg/kg), or solvent (0.9% physiological saline, 10 ml/kg).

value: brain,the prefrontal cortex

tag: Sex

value: male

value: 7-9 weeks old


title: isolate vci_266, replicate 2

description: Library name: vci_266_2

value: bacterial

value: Clinical Isolate


title: MK801,Input,replicate 2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_563

value: spinal neuron differentiation

value: Control

value: homogenous protocol


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_567


title: isolate vci_265, replicate 2

description: Library name: vci_265_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_565


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_564


title: WT,Input,replicate 2

value: i.p.  0.9% physiological saline,10 ml/kg


title: isolate vci_265, replicate 1

description: Library name: vci_265_1


title: WT,Input,replicate 1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_562


title: isolate vci_264, replicate 2

description: Library name: vci_264_2


title: MK801,IP,replicate 2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_561


title: MK801,IP,replicate 1


title: isolate vci_264, replicate 1

description: Library name: vci_264_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_569


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_560


title: isolate vci_262, replicate 2

description: Library name: vci_262_2


title: WT,IP,replicate 2


title: isolate vci_262, replicate 1

description: Library name: vci_262_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_559


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_558


title: WT,IP,replicate 1


title: isolate vci_261, replicate 2

description: Library name: vci_261_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_557


title: isolate vci_261, replicate 1

description: Library name: vci_261_1


title: isolate vci_259, replicate 2

description: Library name: vci_259_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_555


title: Kupffer cells, induced with MC38-VT exosomes, induced for 48h, biol rep1


title: isolate vci_259, replicate 1

description: Library name: vci_259_1


title: Retina, T2Isl1 1

city: Houston

first: Chai-An

last: Mao

state: Texas

address: 6431 Fannin Street, MSB7.242

department: Ophthalmology And Visual Scien

institute: University of Texas McGovern Medical School

description: pool of 8 retinas

data_processing:
Illumina Casava software used for basecalling.
Read alignment by Tophat program (version 2.1.1)
Transcript assemble, transcript abundance, and differential expression tests were processed by Cufflinks program (version 2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample, pvalue and adjusted pvalue for each group.

source_name: Retina

extract_protocol:
Retinas were extracted, stored in RNAlater solution(QIAGEN). RNA was harvested using RNAeasy mini kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: retina

value: embryonic E15.5


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_554


title: isolate vci_255, replicate 2

description: Library name: vci_255_2


title: Retina, T2Isl1 3

description: pool of 8 retinas


title: Retina, T2Isl1 2

description: pool of 8 retinas


title: Retina, T2fx 2

description: pool of 8 retinas


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_556


title: Retina, T2fx 3

description: pool of 8 retinas


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_553


title: isolate vci_255, replicate 1

description: Library name: vci_255_1


title: Retina, T2fx 1

description: pool of 8 retinas


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_552


title: isolate vci_254, replicate 1

description: Library name: vci_254_1


title: isolate vci_254, replicate 2

description: Library name: vci_254_2


title: OVC-68  [Serum]

type: RNA

city: Bologna

first: Gloria

last: Ravegnini

state: BO

address: via irnerio 48

department: PHARMACY AND BIOTECHNOLOGY

country: Italy

institute: UNIVERSITY OF BOLOGNA

description:
Test
SAMPLE 29

data_processing:
miRNAs with Ct>35 were considered as not expressed and excluded from further analysis.
Matrix normalized worksheet reports normalized signals. The normalization was performed according to the manufacturers instructions and array data were normalized using the average of hsa-miR-16-5p (Assay ID: 477860_mir) as endogenous control and after the review of the Literature and the assessment of its stability in our study cohort.
Fold Change worksheet reports the fold change of each single miRNA. Fold change is expressed as log22-DDCt where -DDCt was calculated as - [(DCt miRNA ascitic fluid) - (DCt miRNA serum)]

label: FAM

source_name: Serum

label_protocol: The cDNAs were then amplified using the Universal miR-Amp Primers and Master Mix, contained in the kit and following the manufacturer’s protocol, to uniformly increase the amount of cDNA for each target, maintaining the relative differential expression levels.

extract_protocol: 2 μl of RNA eluate was reverse transcribed to cDNA, using TaqMan Advanced miRNA cDNA synthesis kit (Applied Biosystems Cat No. A28007) in the Thermal Cycler T100 (Biorad).

value: Female


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_551


title: OVC-72  [Serum]

description:
Test
SAMPLE 30


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_550


title: isolate vci_252, replicate 2

description: Library name: vci_252_2


title: OVC-28  [Serum]

description:
Test
SAMPLE 28


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_549


title: OVC-27  [Serum]

description:
Test
SAMPLE 27


title: isolate vci_252, replicate 1

description: Library name: vci_252_1


title: OVC-24 [Serum]

description:
Test
SAMPLE 26


title: isolate vci_251, replicate 2

description: Library name: vci_251_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_547


title: OVC-21  [Serum]

description:
Test
SAMPLE 25


title: OVC-15  [Serum]

description:
Test
SAMPLE 23


title: OVC-16 [Serum]

description:
Test
SAMPLE 24


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_546


title: isolate vci_246, replicate 2

description: Library name: vci_246_2


title: isolate vci_251, replicate 1

description: Library name: vci_251_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_545


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_544


title: isolate vci_245, replicate 2

description: Library name: vci_245_2


title: isolate vci_246, replicate 1

description: Library name: vci_246_1


title: OVC-14  [Serum]

description:
Test
SAMPLE 22


title: isolate vci_245, replicate 1

description: Library name: vci_245_1


title: OVC-11  [Serum]

description:
Test
SAMPLE 21


title: OVC-10  [Serum]

description:
Test
SAMPLE 20


title: isolate vci_241, replicate 2

description: Library name: vci_241_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_543


title: isolate vci_241, replicate 1

description: Library name: vci_241_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_541


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_542


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_540


title: OVC-8  [Serum]

description:
Test
SAMPLE 18


title: isolate vci_240, replicate 2

description: Library name: vci_240_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_548


title: OVC-6  [Serum]

description:
Test
SAMPLE 17


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_539


title: isolate vci_238, replicate 1

description: Library name: vci_238_1


title: isolate vci_240, replicate 1

description: Library name: vci_240_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_538


title: OVC-1  [Serum]

description:
Test
SAMPLE 16


title: OVC-72  [Ascitic fluid]

description:
Test
SAMPLE 15

source_name: Ascitic fluid


title: OVC-68  [Ascitic fluid]

description:
Test
SAMPLE 14


title: isolate vci_237, replicate 1

description: Library name: vci_237_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_537


title: OVC-28  [Ascitic fluid]

description:
Test
SAMPLE 13


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_534


title: isolate vci_235, replicate 1

description: Library name: vci_235_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_536


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_535


title: isolate vci_234, replicate 1

description: Library name: vci_234_1


title: OVC-27  [Ascitic fluid]

description:
Test
SAMPLE 12


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_533


title: OVC-9 [Serum]

description:
Test
SAMPLE 19


title: OVC-21  [Ascitic fluid]

description:
Test
SAMPLE 10


title: OVC-24 [Ascitic fluid]

description:
Test
SAMPLE 11


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_532


title: isolate vci_229, replicate 2

description: Library name: vci_229_2


title: isolate vci_230, replicate 1

description: Library name: vci_230_1


title: isolate vci_233, replicate 1

description: Library name: vci_233_1


title: OVC-16 [Ascitic fluid]

description:
Test
SAMPLE 9


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_530


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_531


title: isolate vci_229, replicate 1

description: Library name: vci_229_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_529


title: OVC-14  [Ascitic fluid]

description:
Test
SAMPLE 7


title: OVC-15  [Ascitic fluid]

description:
Test
SAMPLE 8


title: isolate vci_228, replicate 2

description: Library name: vci_228_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_528


title: Donor_3_d6_BCG_H3K18lac

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa. For peak calling the BAM files were first filtered to remove the reads with mapping quality less than 15. The peak calling algorithm MACS2 http://github.com/taoliu/MACS/) was used to detect the genomic regions enriched for H3K18lac at p-value of 10-5, using the default (narrow) setting.
Assembly: hg19
Supplementary files format and content: BigWig files for visualization

molecule: genomic DNA

source_name: Adult Human Peripheral Blood

growth_protocol: Monocytes were isolated with negative selection with beads and differentiated into resting or trained  macrophages by ex vivo culture in Dutch modified RPMI 1640 culture medium supplemented with gentamicin (50 µg/mL; Centrafarm), glutamax (2 mM; GIBCO), pyruvate (1mM; GIBCO) and 10% (v/v) human pooled serum.Medium was excahenged in days 1, 3 and 6.

extract_protocol:
Purified cells were fixed with 1% methanol-free formaldehyde and quenched with glycine. Fixed cell preparations were lysed, and equal amounts of chromatin were incubated with 1µg of H3K18la antibody (PTM-1406; PTM Biolabs), and incubated overnight at 4ºC with rotation. Dynabeads protein A/G magnetic beads , were washed, centrifuged, mixed with the samples (20 µL/sample) and rotated for 1 hour at 4°C. The bead-bound chromatin complexes  were washed with 400µl buffer for 10 minutes at 4°C with five rounds of washes. After washing chromatin was eluted in 200µl of 0.1 M NaHCO3, 1% SDS elution buffer for 20 minutes in RT. Supernatant was collected, and incubated with proteinase K  for 4 hours at 65°C to disrupt cross‐links between proteins and DNA. Finally samples were purified using Qiaquick MinElute PCR purification Kit (Qiagen)  and eluted in 20µl EB.
ChIP-seq libraries were prepared using the Kapa Hyper Prep Kit according to manufacturer’s protocol, with the following modifications. 2.5 mL of the NEXTflex adaptor stock (600 nM, Bio Scientific) was used for adaptor ligation of each sample. Libraries were amplified with 12-15 PCR cycles followed by a double post-amplification clean-up was used to ensure proper removal of adapters. Libraries were paired-end sequenced to a read length of 50 bp on an Illumina NextSeq500.

treatment_protocol: Cells were cultured  to medium  for 6 days or treated with BCG vaccine for 24 hours, followed by 5 days culture.

value: Adult Human Peripheral Blood

tag: donor

value: Monocyte

tag: chip antibody

value: Rabbit anti-H3K18lac Antibody (PTM-1406; PTM Biolabs)

value: BCG exposed for 24 hours, culture for 5 days to macrophage


title: isolate vci_228, replicate 1

description: Library name: vci_228_1


title: OVC-11  [Ascitic fluid]

description:
Test
SAMPLE 6


title: OVC-10  [Ascitic fluid]

description:
Test
SAMPLE 5


title: isolate vci_230, replicate 2

description: Library name: vci_230_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_527


title: Donor_3_d6_RPMI_H3K18lac

value: RPMI media only for 6 days to macrophage


title: isolate vci_227, replicate 2

description: Library name: vci_227_2


title: OVC-9 [Ascitic fluid]

description:
Test
SAMPLE 4


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_526


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_525


title: Donor_3_d0_H3K18lac

value: Baseline monocytes isolated with beads


title: Donor_3_d1_BCG_H3K18lac

value: BCG exposed, collected at 24 hours post exposure


title: isolate vci_225, replicate 2

description: Library name: vci_225_2


title: OVC-6  [Ascitic fluid]

description:
Test
SAMPLE 2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_523


title: isolate vci_224, replicate 2

description: Library name: vci_224_2


title: OVC-1  [Ascitic fluid]

description:
Test
SAMPLE 1


title: Donor_2_d6_BCG_H3K18lac


title: Donor_2_d6_RPMI_H3K18lac


title: isolate vci_221, replicate 2

description: Library name: vci_221_2


title: Donor_2_d1_BCG_H3K18lac


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_521


title: Donor_2_d1_RPMI_H3K18lac

value: RPMI media only, collected at 24 hours post culture


title: isolate vci_227, replicate 1

description: Library name: vci_227_1

value: bacterial


title: 36_sig54_rep2

first: Syed

middle: Meraj Azhar

last: Rizvi

address: University of California Irvine

department: Microbiology and Molecular Genetics

country: India

description: Library name: sig54_ChIP16

data_processing:
The intensities of the spots on the images and the base calls are computed directly during the run using Illumina’s Real Time Analysis (RTA) software installed on a computer located in the GHTF.
Data analysis was done using Qiagen CLC genomics workbench version 21.0.5. DIP-peaks were called and annotated using Transcription Factor ChIP-seq function of the CLC Genomics Workbench software with p-value<0.1
Assembly: GCA_000068585.1
Supplementary files format and content: bedgraph

organism: Chlamydia trachomatis

source_name: HeLa

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

extract_protocol:
C. trachomatis infected HeLa cells collected washed and collected in sonication buffer (1mMEDTA, 10mMTris-HCl (pH7.5), 0.1%SDS) and sonicated in Covaris M220 sonicatior
Library constructed with NextFlexChIP-seq Kit with NextFlex barcodes from Bioo Scientific. binding reaction was carried in 30 µl with recombinant Euo (50ng), sheared DNA (1µg), 1 µg salmon sperm DNA, 9 µg bovine serum albumin in buffer B [20 mM Tris, pH 7.5, 100 mM NaCl, 10%(v/v) glycerol] for 30 min at 37˚C

value: HeLa

value: Human epithelial


title: 36_sig54_rep1

description: Library name: sig54_ChIP15


title: Donor_3_d1_RPMI_H3K18lac


title: isolate vci_219, replicate 2

description: Library name: vci_219_2

value: Clinical Isolate


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_520

value: spinal neuron differentiation

value: homogenous protocol


title: Donor_2_d0_H3K18lac


title: 36_NoAb_rep2

description: Library name: sig54_ChIP14


title: OVC-8  [Ascitic fluid]

description:
Test
SAMPLE 3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_524


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_518


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_519


title: isolate vci_216, replicate 2

description: Library name: vci_216_2


title: isolate vci_224, replicate 1

description: Library name: vci_224_1


title: 36_NoAb_rep1

description: Library name: sig54_ChIP13


title: isolate vci_219, replicate 1

description: Library name: vci_219_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_522


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_516


title: Donor_1_d1_BCG_H3K18lac


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_517


title: 32_sig54_rep2

description: Library name: sig54_ChIP12


title: isolate vci_215, replicate 2

description: Library name: vci_215_2


title: isolate vci_215, replicate 1

description: Library name: vci_215_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_515


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_513


title: isolate vci_214, replicate 2

description: Library name: vci_214_2


title: isolate vci_221, replicate 1

description: Library name: vci_221_1


title: Donor_1_d1_RPMI_H3K18lac


title: isolate vci_214, replicate 1

description: Library name: vci_214_1


title: isolate vci_212, replicate 2

description: Library name: vci_212_2


title: 28_sig54_rep2

description: Library name: sig54_ChIP8


title: 32_NoAb_rep2

description: Library name: sig54_ChIP10


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_514


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_512


title: 28_NoAb_rep2

description: Library name: sig54_ChIP6


title: 28_sig54_rep1

description: Library name: sig54_ChIP7


title: Donor_4_H3K4me1_week_2

data_processing:
ChIP-seq reads were aligned to the genome using bwa. For peak calling the BAM files were first filtered to remove the reads with mapping quality less than 15. The peak calling algorithm MACS2 http://github.com/taoliu/MACS/) was used to detect the genomic regions enriched for histone marks at p-value of 10-5. H3K4me1 peaks were called using the broad setting of MACS2 while H3K27ac and H3K18lac peaks were called using the default (narrow) setting.
Assembly: hg19
Supplementary files format and content: BigWig files for visualization

growth_protocol: We performed a prospective cohort study (300 BCG) and isolated PBMCs collected before BCG vaccination and at 2 time points post BCG. Following PBMC isolation we further purified the monocytes using a Pan monocyte isolation by following manufacturer’s instructions (MACS, human; Miltenyi Biotec).

extract_protocol:
Monocytes were counted, fixed with 1% methanol-free formaldehyde and quenched with glycine. Fixed cells preparations were lysed, and equal amounts of chromatin were incubated with 1µg of H3K18la antibody (PTM-1406; PTM Biolabs), and incubated overnight at 4ºC with rotation. Dynabeads protein A/G magnetic beads , were washed, centrifuged, mixed with the samples (20 µL/sample) and rotated for 1 hour at 4°C. The bead-bound chromatin complexes  were washed with 400µl buffer for 10 minutes at 4°C with five rounds of washes. After washing chromatin was eluted in 200µl of 0.1 M NaHCO3, 1% SDS elution buffer for 20 minutes in RT. Supernatant was collected, and incubated with proteinase K  for 4 hours at 65°C to disrupt cross‐links between proteins and DNA. Finally samples were purified using Qiaquick MinElute PCR purification Kit (Qiagen)  and eluted in 20µl EB.
Library preparation was performed using the Ovation Ultralow DNA-seq library preparation kit and libraries were sequenced on the IlluminaNovaSeq 6000 instrument generating an average of 30 million reads per sample.

treatment_protocol: Subjects were intradermally vaccinated in the left upper arm with a standard dose of 0.1 mL BCG vaccine (BCG-Bulgaria, Intervax). Blood samples were obtained immediately before BCG vaccination (day 0) and subsequently on day 14 and day 90 post-vaccination

value: Rabbit anti-H3K4me1 Antibody (C15410194 [pAb-194-059]; Diagenode)

value: Exposed Monocytes. Blood collected 2 weeks post BCG vaccination


title: isolate vci_212, replicate 1

description: Library name: vci_212_1


title: Donor_1_d6_BCG_H3K18lac


title: isolate vci_216, replicate 1

description: Library name: vci_216_1


title: 28_NoAb_rep1

description: Library name: sig54_ChIP5


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_510


title: Donor_1_d6_RPMI_H3K18lac


title: 24_sig54_rep2

description: Library name: sig54_ChIP4


title: Donor_2_H3K4me1_month_3

value: Exposed Monocytes. Blood collected 3 month post BCG vaccination


title: isolate vci_210, replicate 2

description: Library name: vci_210_2


title: 32_sig54_rep1

description: Library name: sig54_ChIP11


title: Donor_4_H3K4me1_month_3

value: Adult Human Peripheral Blood


title: 32_NoAb_rep1

description: Library name: sig54_ChIP9


title: Donor_1_d0_H3K18lac

value: Monocyte


title: isolate vci_210, replicate 1

description: Library name: vci_210_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_509


title: Donor_2_H3K4me1_week_2


title: Donor_2_H3K4me1_baseline

value: Baseline monocytes. Blood collected before BCG vaccination


title: 24_sig54_rep1

description: Library name: sig54_ChIP3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_511


title: 24_NoAb_rep2

description: Library name: sig54_ChIP2


title: Donor_1_H3K4me1_month_3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_507


title: isolate vci_206, replicate 2

description: Library name: vci_206_2


title: 24_NoAb_rep1

description: Library name: sig54_ChIP1


title: isolate vci_204, replicate 2

description: Library name: vci_204_2


title: Donor_1_H3K4me1_week_2


title: Donor_1_H3K4me1_baseline


title: isolate vci_203, replicate 2

description: Library name: vci_203_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_505


title: Donor_4_H3K4me1_baseline


title: 36_sig28_2

description: Library name: sig28_ChIP_16

data_processing:
The intensities of the spots on the images and the base calls are computed directly during the run using Illumina’s Real Time Analysis (RTA) software installed on a computer located in the GHTF.
Data analysis was done using Qiagen CLC genomics workbench version 21.0.5. DIP-peaks were called and annotated using Transcription Factor ChIP-seq function of the CLC Genomics Workbench software with p-value<0.1
Assembly: GCA_000068585.1
Supplementary files format and content:  bedgraph


title: Donor_4_H3K27ac_month_3

value: Rabbit anti-H3K27ac Antibody (C15410196 [pAb-196-050]; Diagenode)


title: 36_sig28_1

description: Library name: sig28_ChIP_15


title: isolate vci_203, replicate 1

description: Library name: vci_203_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_506


title: Donor_4_H3K27ac_week_2


title: isolate vci_209, replicate 2

description: Library name: vci_209_2


title: 36_NoAb_2

description: Library name: sig28_ChIP_14


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_504


title: isolate vci_202, replicate 2

description: Library name: vci_202_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_503


title: 36_NoAb_1

description: Library name: sig28_ChIP_13


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_508


title: Donor_4_H3K27ac_baseline


title: 32_sig28_2

description: Library name: sig28_ChIP_12


title: isolate vci_202, replicate 1

description: Library name: vci_202_1


title: Donor_2_H3K27ac_month_3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_501


title: isolate vci_198, replicate 2

description: Library name: vci_198_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_500


title: isolate vci_198, replicate 1

description: Library name: vci_198_1


title: Donor_2_H3K27ac_baseline


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_499


title: isolate vci_194, replicate 2

description: Library name: vci_194_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_498


title: Donor_1_H3K27ac_month_3


title: 32_NoAb_1

description: Library name: sig28_ChIP_9


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_497


title: 32_NoAb_2

description: Library name: sig28_ChIP_10


title: isolate vci_194, replicate 1

description: Library name: vci_194_1


title: 28_sig28_1

description: Library name: sig28_ChIP_7


title: Donor_1_H3K27ac_week_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_496


title: isolate vci_192, replicate 1

description: Library name: vci_192_1


title: Donor_1_H3K27ac_baseline


title: Donor_5_H3K18lac_month_3

value: Rabbit anti-H3K18lac Antibody (PTM-1406]; PTM Biolabs)


title: isolate vci_192, replicate 2

description: Library name: vci_192_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_495


title: 28_NoAb_2

description: Library name: sig28_ChIP_6


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_502


title: 32_sig28_1

description: Library name: sig28_ChIP_11


title: isolate vci_189, replicate 2

description: Library name: vci_189_2


title: Donor_5_H3K18lac_week_2


title: 28_NoAb_1

description: Library name: sig28_ChIP_5


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_494


title: isolate vci_188, replicate 2

description: Library name: vci_188_2


title: Donor_5_H3K18lac_baseline


title: 28_sig28_2

description: Library name: sig28_ChIP_8


title: 24_sig28_2

description: Library name: sig28_ChIP_4


title: isolate vci_188, replicate 1

description: Library name: vci_188_1


title: Donor_4_H3K18lac_month_3


title: isolate vci_187, replicate 2

description: Library name: vci_187_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_492


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_491


title: 24_sig28_1

description: Library name: sig28_ChIP_3


title: Donor_4_H3K18lac_week_2


title: isolate vci_185, replicate 2

description: Library name: vci_185_2


title: 24_NoAb_2

description: Library name: sig28_ChIP_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_490

value: Control


type: genomic

city: Maebashi

first: Naoko

last: Hattori

state: Gunma

address: 3-39-15 Showa-mach

department: Institute for Molecular and Cellular Regulation

institute: Gunma University

description:
207080920043_R06C01
genomic DNA from LPS12 treated with 5-aza-dC and rosiglitazon

hyb_protocol: Standard Illumina Protocol

scan_protocol: Arrays were imaged using Illumina iScan according to manufacturer's specifications (Illumina Inc.).

data_processing:
The data were analyzed using GenomeStudio Methylation Module Software. Beta values were obtained after background correction and normalization to internal controls.
Average Beta, intensity, Detection P-value

label: Cy5 and Cy3

source_name: Cell line of dedifferentiated liposarcoma

label_protocol: Standard Illumina Protocol

growth_protocol: TGW cell line was maintained in MEM medium with 10% FBS.

extract_protocol: High-quality DNA was extracted by the phenol/chloroform method.

treatment_protocol: Cells were seeded on Day 0. On Days 1, 2, and 3, the medium was replaced with a medium containing 0.3 µM of 5-aza-dC. On Day 4, the cells were collected for genomic DNA extraction.

value: 5-aza-dC and rosiglitazon


title: Donor_3_H3K18lac_month_3


description:
207080920043_R05C01
genomic DNA from LPS12 treated with 5-aza-dC

value: Cell line of dedifferentiated liposarcoma


title: isolate vci_181, replicate 2

description: Library name: vci_181_2

value: bacterial


title: 24_NoAb_1

description: Library name: sig28_ChIP_1

value: HeLa


title: Donor_3_H3K18lac_week_2


title: isolate vci_185, replicate 1

description: Library name: vci_185_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_489


title: Donor_3_H3K18lac_baseline


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_488


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_487


title: isolate vci_179, replicate 2

description: Library name: vci_179_2


description:
207080920043_R04C01
genomic DNA from LPS12 treated with mockline

value: Mock (DMSO)


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_493


description:
207080920043_R03C01
genomic DNA from LP6 treated with 5-aza-dC and rosiglitazon


title: isolate vci_179, replicate 1

description: Library name: vci_179_1

value: Clinical Isolate


description:
207080920043_R02C01
genomic DNA from LP6 treated with 5-aza-dC


title: Donor_2_H3K18lac_week_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_485

value: spinal neuron differentiation


description:
207080920043_R01C01
genomic DNA from LP6 treated with mockline


title: Donor_2_H3K18lac_baseline


title: Donor_4_H3K18lac_baseline


title: Donor_2_H3K18lac_month_3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_484

value: homogenous protocol


title: isolate vci_178, replicate 1

description: Library name: vci_178_1


title: isolate vci_178, replicate 2

description: Library name: vci_178_2


title: isolate vci_177, replicate 2

description: Library name: vci_177_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_483


title: Donor_1_H3K18lac_month_3


title: Intramuscular adipocytes, Ad_ circPPARG1 transduction, Day4, rep2

city: Nanning

first: Huang

last: JiePing

address: Xixiangtang District

institute: Guangxi University

data_processing:
To obtain clean reads, Low-quality reads, adapter reads, and those reads with more than 3% N were removed by SOAPnuke software (Chen et al. 2018).
The buffalo reference genome (GVM000043) and gene model annotation files were downloaded from the Genome Variation Map database (https://ngdc.cncb.ac.cn/gvm).
Clean reads were aligned to the reference genome by HISAT2 (Kim et al. 2019).
Mapped reads were assembled using StringTie (Pertea et al. 2015).
Expression of transcript was analyzed by StringTie (Pertea et al. 2015) and presented as fragments per kilobase of transcript per million mapped reads (FPKM).
Assembly: The river buffalo genome was assembled by our team (not published) and can be provided from corresponding authors by e-mail.
Assembly: FASTA of transcript sequences is available on the series record.
Supplementary files format and content: Excel file (.xlsx) include all the identified mRNA with FPKM values for all samples

organism: Bubalus bubalis

source_name: Intramuscular adipocytes

growth_protocol: Cells were cultured with complete culture medium containing 10% fetal bovine serum and 1% penicillin–streptomycin (Gibco, Grand Island, NY) at 37℃ with 5% CO2.

extract_protocol:
Total RNAs were isolated using a TRIzol regent according to a manufacturer’s protocol (Invitrogen, Carlsbad, CA, USA).
Take a certain amount of total RNA samples, and use oligo dT beads to enrich mRNA with poly A tail; mRNA molecules were fragmented into small pieces; The fragmented mRNA was synthesized into first strand cDNA using random primers; The second strand cDNA was synthesized; The synthesized cDNA was subjected to end-repair and 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; PCR amplification and purification; Library quality control; Library circularization; The library was amplified to make DNA nanoball (DNB); Sequencing on DNBSEQ (DNBSEQ Technology) platform.

treatment_protocol: Intramuscular adipocytes were planted in six-well plates in triplicate. When the cells reach 80% confluence, transduction was performed. Adenovirus were added to cells at the indicated MOI. The culture media was exchanged three hours later. When transduction occurs for 48 hours, cells were treated with an inducing medium. Cells were collected for RNA sequencing after 48 hours of induction.

value: Intramuscular adipocytes

value: circPPARG1 overexpress

value: adipogenic differentiation, Ad_EGFP transduction


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_482


title: Donor_1_H3K18lac_week_2

value: Adult Human Peripheral Blood

value: Exposed Monocytes. Blood collected 2 weeks post BCG vaccination


title: isolate vci_181, replicate 1

description: Library name: vci_181_1


title: isolate vci_177, replicate 1

description: Library name: vci_177_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_481


title: isolate vci_176, replicate 2

description: Library name: vci_176_2


title: Intramuscular adipocytes, Ad_ circPPARG1 transduction, Day4, rep1


title: Intramuscular adipocytes,  Ad_EGFP transduction,  Day4, rep3

value: WT


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_486


title: Donor_1_H3K18lac_baseline

value: Monocyte

value: Baseline monocytes. Blood collected before BCG vaccination


title: Exosomes purified from peripheral blood - TCF3-PBX1+ patient 005

city: Montreal

first: Sinnett

last: Daniel

address: 3175 Chem. de la Cote-Sainte-Catherine

country: Canada

institute: CHU Ste-Justine Research Center

data_processing:
Sequence reads were trimmed for adapter sequence/low-quality sequence using TrimGalore
Sequence reads were mapped to the transciptome using Salmon 1,9,0 with the following parameters : -l ISR – minScoreFraction 0.55 –seqBias –gcBias –dumpEq
The transcriptome reference used for alignment is a non-redundant merge of : Gencode V29, LNCipedia 5.2 and circRNAs discovered in all samples using both CIRI2 and circexplorer2
Raw read counts and TPM values at the gene level are exported from the salmon quant files using the tximport R package
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes gene level raw counts for all samples
Supplementary files format and content: tab-delimited text file includes gene level TPM values for all samples

source_name: exosomes (from peripheral blood)

extract_protocol:
RNA was harvested using Total RNA Purification Micro Kit (Norgen). 1 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) following the manufacturer's protocol

value: F

tag: age at_diagnosis

value: exosomes (from peripheral blood)


title: isolate vci_176, replicate 1

description: Library name: vci_176_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


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_480

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'.

value: Control


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_479


title: Exosomes purified from peripheral blood - TCF3-PBX1+ patient 004


title: Intramuscular adipocytes,  Ad_EGFP transduction,  Day4, rep2


title: Exosomes purified from peripheral blood - TCF3-PBX1+ patient 003


title: Intramuscular adipocytes,  Ad_EGFP transduction,  Day4, rep1


title: isolate vci_174, replicate 2

description: Library name: vci_174_2

value: bacterial


title: Exosomes purified from peripheral blood - TCF3-PBX1+ patient 002

value: M


title: isolate vci_172, replicate 2

description: Library name: vci_172_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_478


title: Intramuscular adipocytes, Ad_ circPPARG1 transduction, Day4, rep3


title: Tnni3R193H/R193H mice heart tissue, AAV treated, biol rep2

city: Xihu District, Hangzhou

first: Xing

address: No.18 Shilongshan Road Cloud Town

department: School of Life Sciences

institute: Westlake University

description:
Library name: Sample 5
Column name in raw_counts_All_Samples.txt: Treated-rep2

data_processing:
Adapter sequences were removed from reads using Trim Galore (v.0.6.10).
Reads were aligned to mm39 by STAR (v.2.7.10b).
Aligned BAMs were tag added and sorted by SAMtools (v.1.18). Duplication was removed by the Picard MarkDuplicates module (v.3.11) and unmapped reads were filtered with SAMtools. BAMs were converted to mpileup format using SAM- tools.
Assembly: mm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Heart

growth_protocol: Both male and female homozygous Tnni3R193H/R193H mice, along with heterozygous and wild-type controls, were maintained under standardized environmental conditions (21–23°C, 45–55% humidity, 12-hour light-dark cycle).

extract_protocol:
RNA was harvested using Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)
Total RNA was processed using the Illumina TruSeq RNA Sample Preparation Kit (Cat# FC-122-1001) according to the manufacturer's protocol. Briefly, polyadenylated mRNA was enriched from 1 µg of total RNA using poly-T oligo-attached magnetic beads, followed by thermal fragmentation to generate appropriate fragment sizes. First-strand cDNA synthesis was carried out using random hexamer primers and reverse transcriptase, followed by second-strand synthesis to obtain double-stranded cDNA. The resulting fragments were end-repaired, A-tailed, and ligated to indexed Illumina adapters. After PCR amplification, the libraries were purified, assessed for quality and fragment size distribution using an Agilent Bioanalyzer, and quantified by Qubit fluorometry prior to sequencing.

treatment_protocol: Six-week-old Tnni3R193H/R193H mice were administered 1.5×10¹² genomic copies of AAV particles at a 1:1 ratio via intrathoracic injection (I.T.). The treatment was followed by a monitoring period of 24-48 hours to ensure recovery from the injection procedure, with the animals housed under standard conditions with ad libitum access to food and water. After the designated treatment period, tissues were harvested from the treated mice for RNA extraction. Untreated wild-type mice were included as control animals for comparative purposes.

value: Heart

value: heart tissue

value: Tnni3R193H/R193H mice

value: dual AAV vector contains SpRY-based ABE8e and sgRNA


title: Exosomes purified from peripheral blood - TCF3-PBX1+ patient 001


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_476

value: spinal neuron differentiation

value: homogenous protocol


title: Tnni3R193H/R193H mice heart tissue, AAV treated, biol rep3

description:
Library name: Sample 6
Column name in raw_counts_All_Samples.txt: Treated-rep3


title: Tnni3R193H/R193H mice heart tissue, AAV treated, biol rep1

description:
Library name: Sample 4
Column name in raw_counts_All_Samples.txt: Treated-rep1


title: Donor_2_H3K27ac_week_2

value: Rabbit anti-H3K27ac Antibody (C15410196 [pAb-196-050]; Diagenode)


title: isolate vci_172, replicate 1

description: Library name: vci_172_1

source_name: bacterial

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.

value: Clinical Isolate


title: isolate vci_171, replicate 2

description: Library name: vci_171_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_475

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).


title: Exosomes purified from peripheral blood - ETV6-RUNX1+ patient 005


title: Exosomes purified from peripheral blood - ETV6-RUNX1+ patient 004


title: Tnni3R193H/R193H mice heart tissue, mock, biol rep3

description:
Library name: Sample 3
Column name in raw_counts_All_Samples.txt: Mock-rep3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_474


title: isolate vci_170, replicate 2

description: Library name: vci_170_2


title: isolate vci_171, replicate 1

description: Library name: vci_171_1


title: Tnni3R193H/R193H mice heart tissue, mock, biol rep2

description:
Library name: Sample 2
Column name in raw_counts_All_Samples.txt: Mock-rep2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_473


title: isolate vci_170, replicate 1

description: Library name: vci_170_1


title: Exosomes purified from peripheral blood - ETV6-RUNX1+ patient 003


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_477


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_472


title: Tnni3R193H/R193H mice heart tissue, mock, biol rep1

description:
Library name: Sample 1
Column name in raw_counts_All_Samples.txt: Mock-rep1


title: isolate vci_169, replicate 2

description: Library name: vci_169_2


title: Exosomes purified from peripheral blood - ETV6-RUNX1+ patient 001


title: Exosomes purified from peripheral blood - ETV6-RUNX1+ patient 002


title: FAP no ppary WM, KO, 6

city: GAINESVILLE

first: Daniel

last: Kopinke

state: FL

address: 1200 Newell Dr.,

institute: University of Florida

description: Library name: KO_6

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

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.

value: tibialis anterior

value: whole muscle lysate

value: FAP no ppary

value: 5 days post glycerol injection


title: isolate vci_169, replicate 1

first: Peter

address: 677 Huntington Ave

description: Library name: vci_169_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_471

first: Eva

address: Svante Arrhenius v. 16C


title: REH CCM derived exosomes

source_name: exosomes

growth_protocol: REH cells were maintained in X-Vivo 15 serum free medium in humidified atmosphere with 5% CO2 at 37C

value: exosomes

value: REH

value: B cell precursor leukemia

value: WT


title: FAP no ppary WM, KO, 5

description: Library name: KO_5


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_470

value: Control


title: isolate vci_167, replicate 2

description: Library name: vci_167_2

value: bacterial


title: FAP no ppary WM, KO, 4

description: Library name: KO_4


title: isolate vci_167, replicate 1

description: Library name: vci_167_1


title: REH CCM derived small extracellular vesicles

source_name: small extracellular vesicles

value: small extracellular vesicles


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_469


title: FAP no ppary WM, KO, 3

description: Library name: KO_3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_468


title: isolate vci_163, replicate 2

description: Library name: vci_163_2


title: FAP no ppary WM, KO, 2

description: Library name: KO_2


title: REH CCM derived microvesicles

source_name: microvesicles

value: microvesicles


title: isolate vci_163, replicate 1

description: Library name: vci_163_1


title: REH whole cells extract

source_name: whole cells

value: whole cells


title: FAP no ppary WM, KO, 1

description: Library name: KO_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_466

value: spinal neuron differentiation


title: 697 CCM derived exosomes

growth_protocol: 697 cells were maintained in X-Vivo 15 serum free medium in humidified atmosphere with 5% CO2 at 37C


title: Control, 6

description: Library name: Ctrl_6

value: Wildtype


title: isolate vci_160, replicate 2

description: Library name: vci_160_2


title: 697 CCM derived microvesicles


title: Control, 5

description: Library name: Ctrl_5


title: isolate vci_160, replicate 1

description: Library name: vci_160_1


title: 697 CCM derived small extracellular vesicles


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_465

value: homogenous protocol


title: Control, 4

description: Library name: Ctrl_4


title: 697 whole cells extract


title: isolate vci_158, replicate 2

description: Library name: vci_158_2

value: Clinical Isolate


title: isolate vci_158, replicate 1

description: Library name: vci_158_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_463