title: PRV+DEX 3 (miRNA-seq)

city: Chongqing

first: Zhang

last: Chen

address: No. 160 Xueyuan Road, Changyuan Street

country: China

institute: Southwest University

data_processing:
Cutadapt-1.2.2 and mass fraction pretreatment method were used to obtain clean reads of raw reads.
The clean reads were screened against the GenBank non-coding RNA database (http://blast.ncbi.nlm.nih.gov/) and the Rfam database (http://pfam.janelia.org/) to remove non-coding RNA (such as rRNA, scRNA, tRNA, snRNA, snoRNA, and other ncRNA).
the remaining reads were aligned against the known rat miRNA precursors and mature miRNAs were deposited in the miRBase 21.0 to identify the rat known miRNAs.
all unique candidate sequences were re-queried against known animal mature miRNAs (from the miRBase database) by using BLASTn software to further identify of conserved rat miRNAs. Subsequently, sequences between 18 nt and 30 nt were aligned against raw sequence data by miRDeep2 software with the default parameter to confirm the novel miRNAs.
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include FPKM values for each sample .Matrix table with raw gene counts for every gene and every sample

growth_protocol: PC-12 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using the TRIzol method (Invitrogen, CA, USA) and treated with Nase-free DNase I (Takara, Kusatsu, Japan). Sequencing libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® and 1 ug of total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: WT

value: dexamethasone treatment after pseudorabies virus infection


title: HFS1_3

status: Public on Apr 30 2025

type: SRA

city: Cologne

first: Alvise

last: Schiavinato

address: Joseph-Stelzmann Str. 52

country: Germany

institute: Center for Biochemistry

description: Library name: Sample 15

library_source: transcriptomic

data_processing:
sequenced by Novogene with a Illumina NovaSeq X Plus at ~20 M paired-end reads. Reads were aligned to the reference genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: hg38
Supplementary files format and content: CSV file including raw counts for all the samples

molecule: total RNA

organism: Homo sapiens

source_name: Human dermal fibroblasts

growth_protocol: Primary human dermal fibroblasts were grown to confluency in 24 wells and then kept in culture for another 7 days in DMEM/F12 medium supplemented with 10% FCS,  1% P/S and 90umol ascorbate. The medium was refreshed every other day. For ANTXR2 knockdown, fibroblasts were reverse transfected using RNAiMAX.

extract_protocol:
RNA was extracted usingTrizol (Invitrogen)
Poly A enrichment

tag: cell type

value: Human dermal fibroblasts


title: HFS1_1

description: Library name: Sample 13


title: HFS1_2

description: Library name: Sample 14


title: CTRL1_3

description: Library name: Sample 12


title: CTRL1_2

description: Library name: Sample 11


title: PRV+DEX 1 (miRNA-seq)

organism: Rattus norvegicus

tag: cell line

tag: genotype

tag: treatment


title: PRV 3 (miRNA-seq)

value: pseudorabies virus treatment


title: PRV+DEX 2 (miRNA-seq)


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1148

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_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', 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'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:
Clustering was done by 'cBot' and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 1x51 setup using 'HiSeq SBS Kit v4' chemistry. The Bcl to FastQ conversion was performed using bcl2fastq_2.17 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

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: heterogenous protocol

tag: sequencing batch


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1147


title: CTRL1_1

description: Library name: Sample 10


title: PRV 1 (miRNA-seq)


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1146


title: Control 2 (miRNA-seq)


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1145


title: siANTXR2_b_3

description: Library name: Sample 9


title: PRV 2 (miRNA-seq)


title: Control 3 (miRNA-seq)


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1144


title: Control 1 (miRNA-seq)


title: siANTXR2_b_2

description: Library name: Sample 8


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1143


title: SKNBE2 cells, hiFBS15, rep3

city: Seattle

first: Research

middle: Scientific

last: Computing

state: WASHINGTON

address: 818 Stewart Street

department: Research Scientific Computing

country: USA

institute: Seattle Children's Research Institute

description: Library name: Sample 36

data_processing:
Raw sequencing reads were checked for quality using FastQC.
Raw sequencing reads were aligned to the hg38 assembly using gencode v39 and STAR.
Gene counting was performed against the UCSC database with HTSeq.
RSeQC was used to check for the quality of the alignments.
Differential expression analysis for RNASeq data was performed using R/Bioconductor package DESeq2 and edgeR
Assembly: hg38
Supplementary files format and content: tab delimited file including raw counts for each sample

source_name: Bone marrow

growth_protocol: Cultured DH-SY5Y in Eagle's Minimum Essential Medium with 15% heat-inactivated Fetal Bovine Serum and 10% Penicillin - Streptomycin.

extract_protocol:
Total RNA was extracted directly from culture wells with the Aurum total RNA mini kit (Biorad) following the manufacturer's protocol.
Reverse transcription (RT) was performed with the iScript cDNA synthesis kit (Biorad) to convert 500 ng of RNA into cDNA.

treatment_protocol: SY5Y cells were plated at 4 X 10 in 10 cm plates. The following day, added 100nM of either PBS, 231 or 237 was added and incubated for 72 hours.

tag: tissue

value: Bone marrow

value: epithelial

value: neuronal differentiation

tag: time

value: 72 hrs


title: genomic DNA from normal adipose tissues 7

type: genomic

city: Maebashi

first: Naoko

last: Hattori

state: Gunma

address: 3-39-15 Showa-mach

department: Institute for Molecular and Cellular Regulation

country: Japan

institute: Gunma University

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 (v1.9.0). Beta values were obtained after background correction and normalization to internal controls.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

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

value: normal adipose tissues


title: SKNBE2 cells, ag237, rep3

description:
Library name: Sample 35
Column name in raw_counts_all_samples.txt : S35


title: siANTXR2_b_1

description: Library name: Sample 7


title: SKNBE2 cells, ag231, rep3

description:
Library name: Sample 34
Column name in raw_counts_all_samples.txt : S34


title: SKNBE2 cells, PBS, rep3

description:
Library name: Sample 33
Column name in raw_counts_all_samples.txt : S33

value: PBS


title: siCTRL_3

description: Library name: Sample 6


title: SKNBE2 cells, hiFBS15, rep2

description: Library name: Sample 32


title: SKNBE2 cells, ag237, rep2

description:
Library name: Sample 31
Column name in raw_counts_all_samples.txt : S31


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1142


title: genomic DNA from WDLPS 16

value: well-differentiated liposarcomas


title: siCTRL_2

description: Library name: Sample 5


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1141


title: SKNBE2 cells, PBS, rep2

description:
Library name: Sample 29
Column name in raw_counts_all_samples.txt : S29


title: genomic DNA from DDLPS 20

value: dedifferentiated liposarcomas


title: siCTRL_1

description: Library name: Sample 4


title: SKNBE2 cells, ag231, rep2

description:
Library name: Sample 30
Column name in raw_counts_all_samples.txt : S30


title: genomic DNA from DDLPS 11


title: genomic DNA from normal adipose tissues 8


title: genomic DNA from WDLPS 14


title: genomic DNA from WDLPS 09


title: genomic DNA from DDLPS 08


title: siANTXR2_a_3

description: Library name: Sample 3


title: SKNBE2 cells, hiFBS15, rep1

description: Library name: Sample 28


title: genomic DNA from DDLPS 16


title: genomic DNA from DDLPS 40


title: genomic DNA from normal adipose tissues 4


title: SKNBE2 cells, PBS, rep1

description:
Library name: Sample 25
Column name in raw_counts_all_samples.txt : S25


title: IMR32 cells, hiFBS15, rep3

description: Library name: Sample 24


title: genomic DNA from normal adipose tissues 5


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1138


title: genomic DNA from WDLPS 11


title: SKNBE2 cells, ag237, rep1

description:
Library name: Sample 27
Column name in raw_counts_all_samples.txt : S27


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1140


title: genomic DNA from DDLPS 25


title: genomic DNA from normal adipose tissues 6


title: genomic DNA from DDLPS 01


title: SKNBE2 cells, ag231, rep1

description:
Library name: Sample 26
Column name in raw_counts_all_samples.txt : S26


title: IMR32 cells, ag231, rep3

description:
Library name: Sample 22
Column name in raw_counts_all_samples.txt : S22


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1139


title: IMR32 cells, PBS, rep3

description:
Library name: Sample 21
Column name in raw_counts_all_samples.txt : S21


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1137


title: genomic DNA from WDLPS 07


title: genomic DNA from DDLPS 06


title: siANTXR2_a_2

description: Library name: Sample 2


title: IMR32 cells, ag237, rep3

description:
Library name: Sample 23
Column name in raw_counts_all_samples.txt : S23


title: siANTXR2_a_1

description: Library name: Sample 1


title: IMR32 cells, hiFBS15, rep2

description: Library name: Sample 20


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1136


title: genomic DNA from normal adipose tissues 3


title: genomic DNA from DDLPS 19


title: MM1S-In_1

city: Shanghai

first: Hua

last: Yan

address: 197 Ruijin 2nd Road

institute: Ruijin Hospital

description: Library name: Sample 14

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismatch cost: 2 insertion cost: 3 deletion cost: 3 length fraction)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each samples

extract_protocol:
RNA was harvested using TRIzol regent. Total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were performed using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols.

value: plasma cell


title: IMR32 cells, PBS, rep2

description:
Library name: Sample 17
Column name in raw_counts_all_samples.txt : S17


title: IMR32 cells, ag231, rep2

description:
Library name: Sample 18
Column name in raw_counts_all_samples.txt : S18


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1135


title: genomic DNA from WDLPS 18


title: IMR32 cells, ag237, rep2

description:
Library name: Sample 19
Column name in raw_counts_all_samples.txt : S19


title: MM1S-In_3

description: Library name: Sample 16


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1134


title: MM1S-DMSO_3

description: Library name: Sample 13


title: MM1S-In_2

description: Library name: Sample 15


title: IMR32 cells, hiFBS15, rep1

description: Library name: Sample 16


title: IMR32 cells, ag237, rep1

description:
Library name: Sample 15
Column name in raw_counts_all_samples.txt : S15


title: IMR32 cells, PBS, rep1

description:
Library name: Sample 13
Column name in raw_counts_all_samples.txt : S13


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1132

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', 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'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', 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'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', 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'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: SY5Y cells, ag237, rep3

description:
Library name: Sample 11
Column name in raw_counts_all_samples.txt : S11


title: SY5Y cells, ag231, rep3

description:
Library name: Sample 10
Column name in raw_counts_all_samples.txt : S10


title: MM1S-DMSO_1

description: Library name: Sample 11


title: MM1S-DMSO_2

description: Library name: Sample 12


title: SY5Y cells, hiFBS15, rep3

description: Library name: Sample 12


title: SY5Y cells, PBS, rep3

description:
Library name: Sample 9
Column name in raw_counts_all_samples.txt : S9


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1131


title: MM1S shRBM39_2

description: Library name: Sample 10


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1130


title: SY5Y cells, hiFBS15, rep2

description: Library name: Sample 8


title: IMR32 cells, ag231, rep1

description:
Library name: Sample 14
Column name in raw_counts_all_samples.txt : S14


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1129


title: MM1S shRBM39_1

description: Library name: Sample 9


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1133


title: SY5Y cells, ag237, rep1

description:
Library name: Sample 3
Column name in raw_counts_all_samples.txt : S3


title: SY5Y cells, hiFBS15, rep1

description: Library name: Sample 4


title: SY5Y cells, ag231, rep2

description:
Library name: Sample 6
Column name in raw_counts_all_samples.txt : S6


title: MM1S SCR2

description: Library name: Sample 8


title: SY5Y cells, ag231, rep1

description:
Library name: Sample 2
Column name in raw_counts_all_samples.txt : S2


title: SY5Y cells, ag237, rep2

description:
Library name: Sample 7
Column name in raw_counts_all_samples.txt : S7


title: MM1S SCR1

description: Library name: Sample 7


title: SY5Y cells, PBS, rep1

description:
Library name: Sample 1
Column name in raw_counts_all_samples.txt : S1


title: HCT15_ov_RNF26 rep3

city: Beijing

first: Yalan

last: Lu

address: No. 5 Panjiayuan Nanli, Chaoyang District

department: Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Center

institute: Peking Union Medical College (PUMC)

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
The expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
Total RNA was extracted from the tissue using TRIzol Reagent according the manufacturer's instructions. Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies).
The RNA-seq transcriptome librariy was prepared following Illumina Stranded mRNA Prep, Ligation (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers. Then the synthesized cDNA was subjected to end-repair, phosphorylation and adapter addition according to library construction protocol. Libraries were size selected for cDNA target fragments of 300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles. After quantified by Qubit 4.0, the sequencing library was performed on NovaSeq X Plus platform(PE150) using NovaSeq Reagent Kit.

value: established cell line


title: SY5Y cells, PBS, rep2

description:
Library name: Sample 5
Column name in raw_counts_all_samples.txt : S5


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1128


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1126


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1127


title: HCT15_ov_RNF26 rep2


title: U87YTHDC1 KD+Ast-CTD-RNAPII_S2P-1

city: Hefei

first: Li

last: Wang

address: No. 443, Mount Huangshan Road, Shushan District

institute: University of Science and Technology of China

description:
Library name: Sample 19
libraries were generated from cells

library_source: genomic

data_processing:
For scRNA-seq data processing, raw reads were aligned to mouse reference genome GRCm39 using the Cell Ranger software (v8.0.0) to generate cell × gene matrices. Downstream analyses were conducted using the Seurat R package (v4.4.0). Cells with ≥ 200 detected genes and genes expressed in ≥ 3 cells were retained for further analyses. Cells were excluded based on the following criteria: (1) nFeature_RNA < 200, (2) nCount_RNA > 65,000 and (3) percent.mt > 10. Doublets were identified and removed using the DoubletFinder R package, resulting in a final data matrix of 23,282 genes cross 35,686 cells. Data normalization and scaling were processed using Seurat functions NormalizaData and ScaleData. The top 2,000 most variable genes were selected for downstream analysis. For CUT&Tag data processing, the genome browser tracks in bigwig format were produced from merged replicates using samtools and peaks were called using MACS2 using parameters ‘-f BAMPE--broad -nomodel’. The bigwig data were visualized using the IGV software (Broad Institute). Peak visualizations were prepared using Deeptools.
Assembly: hg18
Supplementary files format and content: BIGWIG
Library strategy: CUT&Tag

extract_protocol:
U87 cells from co-culture system of various groups were sorted using sorting flow cytometer
CUT&Tag libraries were generated following the manufacturer’s protocol (Vazyme, TD903-01). Library QC and sequencing were performed by Genewiz with sequencing and data analysis as follows. After trimming the adapters of reads and removing low-quality bases by Trim_Galore software in paired-end mode, clean reads were mapped to hg38 reference genome with Bowtie2 followed by removing PCR duplicates using Picard.

value: tumor cells

value: Cells were sorted from co culture system


title: U87YTHDC1 KD+Ast-CTD-RNAPII_S2P-2

description:
Library name: Sample 20
libraries were generated from cells


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1125


title: HCT15_ov_RNF26 rep1


title: U87WT+Ast-CTD-RNAPII_S2P-1

description:
Library name: Sample 17
libraries were generated from cells


title: U87YTHDC1 KD+Ast-CTD-RNAPII_S5P-2

description:
Library name: Sample 16
libraries were generated from cells


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1124


title: HCT15_con rep3


title: U87YTHDC1 KD+Ast-CTD-RNAPII_S5P-1

description:
Library name: Sample 15
libraries were generated from cells


title: HCT15_con rep2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1122


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1123


title: HCT15_con rep1


title: U87+Astshmt2 KO-CTD-RNAPII_S5P-1

description:
Library name: Sample 11
libraries were generated from cells


title: U87WT+Ast-CTD-RNAPII_S5P-2

description:
Library name: Sample 14
libraries were generated from cells


title: U87WT+Ast-CTD-RNAPII_S5P-1

description:
Library name: Sample 13
libraries were generated from cells


title: U87+AstWT-CTD-RNAPII_S5P-2

description:
Library name: Sample 10
libraries were generated from cells


title: HCT116_ov_RNF26 rep3


title: U87+AstWT-CTD-RNAPII_S5P-1

description:
Library name: Sample 9
libraries were generated from cells


title: HCT116_ov_RNF26 rep2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1120

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: U87+Astshmt2 KO-CTD-RNAPII_S2P-2

description:
Library name: Sample 6
libraries were generated from cells


title: U87-CTD-RNAPII_S5P-1

description:
Library name: Sample 7
libraries were generated from cells

value: Monocultured cells


title: U87-CTD-RNAPII_S5P-2

description:
Library name: Sample 8
libraries were generated from cells


title: U87+Astshmt2 KO-CTD-RNAPII_S2P-1

description:
Library name: Sample 5
libraries were generated from cells


title: U87WT+Ast-CTD-RNAPII_S2P-2

description:
Library name: Sample 18
libraries were generated from cells


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1121


title: HCT116_ov_RNF26 rep1


title: U87+AstWT-CTD-RNAPII_S2P-2

description:
Library name: Sample 4
libraries were generated from cells


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1119


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1118


title: HCT116_con rep3


title: U87-CTD-RNAPII_S2P-2

description:
Library name: Sample 2
libraries were generated from cells


title: U87+AstWT-CTD-RNAPII_S2P-1

description:
Library name: Sample 3
libraries were generated from cells


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1117


title: U87-CTD-RNAPII_S2P-1

description:
Library name: Sample 1
libraries were generated from cells


title: U87+Astshmt2 KO-CTD-RNAPII_S5P-2

description:
Library name: Sample 12
libraries were generated from cells


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1116


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1115


title: 5week_Aβ_MinusMicroglia

city: Vancouver

first: Haakon

middle: B.

last: Nygaard

state: BC

address: 2215 Wesbrook Mall

department: Division of Neurology

country: Canada

institute: University of British Columbia

description: 10X Genomics

data_processing:
FASTQ reads were processed and aligned to the wild-type human genome (hg38) using the relevant Cell Ranger software (cellranger count function) with settings as recommended by the manufacturer (10X Genomics).
The data packages contain the filtered digital gene expression for each sample obtained from the Cell Ranger Single Cell Pipeline.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Neurospheres

extract_protocol:
For single nuclear isolation, all samples were flash frozen in liquid nitrogen. Samples were dissociated as per protocol (Princess Margaret Genomics Centre).
Libraries were prepared according to the manufacturer's instructions (10X Genomics) using Nuc-seq NEXT Gem chemistry
snRNA-seq

value: Neurospheres

value: HN1 (In house control line, female, Apoe3/3)

value: iPSC derived astrocyte like and neuronal like cells

value: Aβ1-42 synthetic Aβ for 5 weeks


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1113

value: spinal neuron differentiation

value: heterogenous protocol


title: 3week_Aβ_PlusMicroglia

description: 10X Genomics

value: iPSC derived astrocyte like and neuronal like cells, with microglial like cells added

value: Aβ1-42 synthetic Aβ for 3 weeks


title: 3week_Aβ_MinusMicroglia

description: 10X Genomics


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1114


title: 5week_Aβ_PlusMicroglia

description: 10X Genomics


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1111


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1108


title: scrambledAβ_MinusMicroglia

description: 10X Genomics

value: scrambled Aβ1-42 for 3 weeks


title: NTM.6

city: beijing

first: xiaoyan

last: liu

address: Gongti South Road

institute: Capital Medical University

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn6 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Assembly: rn6(GCF_000001895.5_Rnor_6.0)
Supplementary files format and content: tab-delimited text files include counts for each Sample

source_name: lung

extract_protocol:
Total RNA was isolated from tissues using the Magzol Reagent (Magen, China)according to the manufacturer’s protocol.The quantity and integrity of RNA yield was assessed by using the K5500(Beijing Kaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately.
the mRNA was enriched by oligo dT according to instructions of NEB Next® Poly(A) mRNA Magnetic Isolation Module (NEB,USA). And then fragmented to approximately 200bp. Subsequently, the RNA fragments were subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycle according to instructions of  NEBNext® Ultra™ RNA Library Prep Kit for Illumina.

value: lung

tag: disease

value: PAH

value: FMT-treated rats (NTM)


title: NTM.5


title: NTM.3


title: NTM.4


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1105


title: NTM.2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1112


title: HCT116_con rep1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1104


title: NTM.1


title: HCT116_con rep2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1109


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1102


title: MCT.5

value: monocrotaline-induced PAH rats (MCT)


title: MCT.6


title: scrambledAβ_PlusMicroglia

description: 10X Genomics


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1110


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1101


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1100


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1103


title: MCT.3


title: MCT.4


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1107


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1098


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1099


title: MCT.2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_1106


title: Gαq 20 weeks 444767 RN

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

data_processing:
FASTQ files were aligned to mouse genome build mm10 using STAR (version 2.6.0c).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 1.6.2) and Ensembl annotation build 100 (uniquely aligned proper pairs, same strand).
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Variance-stabilizing transformation (VST) was accomplished using the varianceStabilizingTransformation function in the DESeq2 R package (version 1.23.10).
All analyses were performed using the R environment for statistical computing (version 3.6.0).
Assembly: mm10
Supplementary files format and content: counts.txt: 55450 x 16 matrix of counts produced by Subread featureCounts
Supplementary files format and content: varianceStabilizingTransformation.txt: 55450 x 16 matrix of variance-stabilizing-transformed (VST) expression values

organism: Mus musculus

source_name: left ventricle

growth_protocol: Wild type and cardiac-specific Gαq-overexpressing mice were group housed in the animal facility at Boston University Medical Center. Gαq mice as per Adams et al, PNAS 1998;95:10140-45, as previously described by us in Qin et al, Circ Heart Failure 2010;3:306-13.

extract_protocol: RNA was isolated from frozen powderized left ventricles and extracted with the Qiagen RNeasy Plus Universal mini kit with an on-column DNAse treatment. The Boston University Microarray and Sequencing Resource Core Facility performed RNA quantity and quality measurements, library preparation, and RNA sequencing. RNA integrity was confirmed via RNA Pico assay for total RNA Bioanalyzer QC analysis (Agilent).

value: left ventricle

tag: strain

value: FVB/N

value: Gnaq overexpressor (Galphaq)

tag: timepoint

value: 20 weeks

tag: cage

tag: notch

value: RN


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1096


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1094


title: Gαq 20 weeks 444767 NN

value: NN


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1092


title: Gαq 20 weeks 550660 BN

value: BN


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1095


title: Gαq 20 weeks 550660 LN

value: LN


title: WT 20 weeks 551636 BN

value: wild-type (WT)


title: WT 20 weeks 551636 RN


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1093

value: spinal neuron differentiation

value: heterogenous protocol


title: SF-9427-K27WT-PRC2KO_rep5

city: Austin

first: James

last: Robinson

state: MN

address: 801 16th Ave NE

department: The Hormel Institute

institute: University of Minnesota

description:
Library name: RNA-seq_Sample35
PE150

data_processing:
The analysis of RNA-seq data was conducted using a detailed in-house bioinformatics pipeline. Briefly, the quality of the raw sequencing data was initially assessed by FastQC (version 0.12.1) (42). Despite the common practice of bypassing trimming in favor of the STAR aligner's soft-clipping capabilities, we found that trimming adapters and poor-quality bases with fastp (version 0.23.2) (43) before alignment improved the unique read mapping percentage. Sequencing reads were aligned to the human reference genome (GRCh38.p14) using STAR (version 2.7.11a) (44). The Rsubread package (version 2.16.0), specifically through the featureCounts function (45), was then employed to assign aligned reads to genomic features, converting BAM format alignment files into raw gene read counts. Differential gene expression analysis was performed utilizing DESeq2 (version 1.40.2) (46). Differentially expressed genes (DEGs) were defined as genes with an absolute log2 fold change ≥ 1.5 and an adjusted p-value ≤ 0.05 (Benjamini-Hochberg correction).
Assembly: hg38
Supplementary files format and content: File Format: .csv
Supplementary files format and content: Processed file contains average transcript-per-million (TPM) values per gene, computed after normalization using edgeR. TPMs were calculated from raw gene-level counts and scaled across all samples to account for differences in sequencing depth and gene length. Each row represents a gene, and each column represents a sample.

source_name: cell line

growth_protocol: The pediatric glioma cell lines used in this study included SF9427 (RRID: CVCL_E5GC), SF8628 (RRID: CVCL_IT46), SF7761 (RRID: CVCL_IT45), and DIPGXVII/SU-DIPG-XVII (RRID: CVCL_C1MW). Cells were grown in DMEM-high glucose (Sigma Cat. No. D6546), 10% FBS, 2 mM L-Glutamine (EMD Millipore Cat. No. TMS-002-C), 1x Amphotericin, and 1x Penicillin-Streptomycin. Cell lines were cultured under adherent conditions at 37°C and 5% CO₂.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit (Qiagen, Cat# 74104) following the manufacturer’s instructions. RNA quality and quantity were assessed using a NanoDrop spectrophotometer and Agilent Bioanalyzer. Only samples with RIN > 8.0 were used for downstream processing.
RNA-seq libraries were prepared using standard Illumina protocols. Poly(A)+ RNA was isolated from total RNA, fragmented, and reverse transcribed to generate cDNA. Libraries were end-repaired, A-tailed, adapter-ligated, and PCR-amplified. Sequencing was performed on an Illumina platform with 150 bp paired-end reads.

treatment_protocol: To generate EZH1/2 KO (PRC2 loss); EZH1 and EZH2 CRISPR gRNAs were designed using GUIDES software (http://guides.sanjanalab.org/) (35). gRNAs were cloned into the BsmBI digested linear Lenti-Cas9-gRNA-GFP vector (Addgene #124770) as described earlier (Giuliano et al. 2019). Plasmids were propagated by transforming into Stbl3 E. coli. Further, HEK293T cells were transfected with Lenti-Cas9-gRNA-GFP along with packaging plasmids (pMD.2 and PAX) using the calcium phosphate method (36). 24 hrs of post transfection media was changed and virus containing supernatant was collected at 48 to 72 hours post-transfection. Lentivirus were filtered through a 0.45 μm syringe and transduced the target cells with 4-10 μg/mL polybrene. Culture media was changed after 24 hrs of transduction. GFP expressed target cells were sorted and single cell colonies were picked and expanded. The knockout clones were confirmed by western blot and sanger sequencing. We previously created of SF8628 H3.3 WT revertant clones (34) using CRISPR/HDR Cas9 editing to generate SF8628 H3.3 WT revertant cells. A custom gRNA targeted the K27M region of H3F3A. This complex, along with recombinant Cas9, H3F3A WT ssDNA, and a GFP-H3F3A WT HDR repair plasmid, was introduced into cells via electroporation. Colonies were screened for GFP expression using an IncuCyte S3 system and verified by Sanger sequencing and allele-specific PCR with agarose gel analysis.

value: Diffuse midline glioma

value: H3.3 K27WT; EZH 1/2 CRISPR knock out


title: SF-9427-K27WT-PRC2KO_rep4

description:
Library name: RNA-seq_Sample34
PE150


title: SF-9427-K27WT-PRC2KO_rep6

description:
Library name: RNA-seq_Sample36
PE150


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1091


title: SF-9427-K27WT-PRC2KO_rep3

description:
Library name: RNA-seq_Sample33
PE150


title: WT 20 weeks 444767 LN


title: SF-9427-K27WT-PRC2KO_rep2

description:
Library name: RNA-seq_Sample32
PE150


title: MCT.1

value: lung


title: SF-9427-K27WT-PRC2KO_rep1

description:
Library name: RNA-seq_Sample31
PE150


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1097


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1090


title: SF-9427-K27WT_rep4

description:
Library name: RNA-seq_Sample30
PE150

value: WT


title: SF-9427-K27WT_rep3

description:
Library name: RNA-seq_Sample29
PE150


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1089


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1088


title: SF-9427-K27WT_rep1

description:
Library name: RNA-seq_Sample27
PE150


title: SF-9427-K27WT_rep2

description:
Library name: RNA-seq_Sample28
PE150


title: SF-8628-K27WT-PRC2KO_rep6

description:
Library name: RNA-seq_Sample26
PE150


title: SF-8628-K27WT-PRC2KO_rep5

description:
Library name: RNA-seq_Sample25
PE150


title: SF-8628-K27WT-PRC2KO_rep4

description:
Library name: RNA-seq_Sample24
PE150


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1086


title: Gαq 4 weeks 559480 RN

value: 4 weeks


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1085


title: SF-8628-K27WT-PRC2KO_rep2

description:
Library name: RNA-seq_Sample22
PE150


title: SF-8628-K27WT-PRC2KO_rep3

description:
Library name: RNA-seq_Sample23
PE150


title: WT 4 weeks 554815 BN


title: SF-8628-K27WT-PRC2KO_rep1

description:
Library name: RNA-seq_Sample21
PE150


title: WT 20 weeks 550660 NN


title: SF-8628-K27WT_rep6

description:
Library name: RNA-seq_Sample20
PE150

value: WT (H3.3 K27M CRISPR reverted to H3.3 K27 WT)


title: WT 4 weeks 554815 NN

value: left ventricle


title: Gαq 4 weeks 554815 LN

value: FVB/N


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1084


title: SF-8628-K27WT_rep3

description:
Library name: RNA-seq_Sample17
PE150


title: SF-8628-K27WT_rep5

description:
Library name: RNA-seq_Sample19
PE150


title: SF-8628-K27WT_rep1

description:
Library name: RNA-seq_Sample15
PE150


title: Gαq 4 weeks 554815 RN

value: Gnaq overexpressor (Galphaq)


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1082


title: SF-8628-K27WT_rep4

description:
Library name: RNA-seq_Sample18
PE150


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1083


title: SF-8628-K27WT_rep2

description:
Library name: RNA-seq_Sample16
PE150


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1087


title: HR62_E16_replicate3

city: Madrid

first: Tirso

last: Pons

state: Madrid

address: C/ Darwin 3

department: Inmunology and Oncology

country: Spain

institute: Centro Nacional de Biotecnologia

data_processing:
Raw fastq reads were aligned to the UCSC mouse genome build mm10 (http://genome.ucsc.edu) using Burrows-Wheeler aligner BWA-MEM 0.7.15 (github.com/lh3/bwa.git) with standard settings, and converted to BAM files using Picard tools 2.9.0 (http://broadinstitute.github.io/picard).
BAM files were processed using MACS (github.com/taoliu/MACS/) version 3 3.0.0b3 for enrichment scoring and peak calling (MACS3 callpeak -B --extsize 147 -g mm -q 0.05 --broad --broad-cutoff 0.1 --nomodel --extsize 147).
Peaks overlap with ENCODE black list regions (mm10-blacklist.bed.gz) were removed from downstream analysis using Bedtools.
Differential binding between experimental conditions was performed using the bdgdiff function in MACS (MACS3 bdgdiff -g 73 -l 147).
BED files were annotated using the R/Bioconductor package ChIPseeker (github.com/YuLab-SMU/ChIPseeker). The promoter region was set to −1 kb to 200 bp of the TSS.
Assembly: mm10
Supplementary files format and content: tab-delimited text files (BED6+3 format) include the list of peak locations together with peak summit, fold enrichment, -log10(pvalue), and -log10(qvalue)  for each sample.

source_name: hematopoietic precursors (LSK cells)

extract_protocol:
LSK cells of WT and E16 mutant were isolated by sorting.
Libraries were prepared by the Genomics Unit of the Scientific Park Madrid

treatment_protocol: ChIP assays were performed with True MicroChIP-seq Kit (DIAGENODE Cat# C01010132) according to the manufacturer’s protocol.

value: hematopoietic precursors (LSK cells)

value: mouse hematopoietic precursors

value: DIDO3_E16 mutant

tag: chip antibody


title: SF-8628-K27M-PRC2KO_rep4

description:
Library name: RNA-seq_Sample12
PE150

value: H3.3 K27M; EZH 1/2 CRISPR knock out


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1081


title: WT 4 weeks 559480 NN

value: NN


title: WT 4 weeks 559480 LN

value: wild-type (WT)

value: LN


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1079

value: spinal neuron differentiation

value: heterogenous protocol


title: HR58_E16_replicate2


title: Gαq 4 weeks 559480 BN

value: BN


title: SF-8628-K27M-PRC2KO_rep2

description:
Library name: RNA-seq_Sample10
PE150

value: Diffuse midline glioma


title: SF-8628-K27M_rep4

description:
Library name: RNA-seq_Sample8
PE150


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1078


title: SF-8628-K27M_rep2

description:
Library name: RNA-seq_Sample6
PE150


title: HR56_E16_replicate1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1077


title: HR61_WT_replicate3

value: wild type


title: SF-8628-K27M-PRC2KO_rep6

description:
Library name: RNA-seq_Sample14
PE150


title: HR60_WT_replicate2


title: HR45_WT_replicate1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1075


title: SF-8628-K27M_rep1

description:
Library name: RNA-seq_Sample5
PE150


title: SF-8628-K27M-PRC2KO_rep5

description:
Library name: RNA-seq_Sample13
PE150


title: DIPG17-K27M_rep1

description:
Library name: RNA-seq_Sample1
PE150

value: SU-DIPG-XVII


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1076


title: DIPG17-K27M_rep2

description:
Library name: RNA-seq_Sample2
PE150


title: DIPG17-K27WT_rep2

description:
Library name: RNA-seq_Sample4
PE150

value: WT (H3.3 K27M CRISPR reverted to H3.3 K27 WT)


title: DIPG17-K27WT_rep1

description:
Library name: RNA-seq_Sample3
PE150


title: Ctrl_H3K4me3

value: H3K4me3, DIAGENODE (Cat# C15410003)


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1080


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1074


title: SF-8628-K27M-PRC2KO_rep3

description:
Library name: RNA-seq_Sample11
PE150


title: SF8628_K27WT_PRC2KO_rep2

description:
Library name: ATAC-seq_Sample6
PE42

data_processing:
Analysis of ATAC-seq data was very similar to the analysis of ChIP-Seq data. Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations. For differential analysis, reads were counted in all merged peak regions (using Subread), and the replicates for each condition were compared using DESeq2.
Assembly: hg38
Supplementary files format and content: File Format: .bed
Supplementary files format and content: peak files generated using MACS2

extract_protocol:
Cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay.
The cells were then thawed in a 37oC water bath, pelleted, washed with cold PBS, and tagmented as previously described (Buenrostro et al. 2013), with some modifications based on (Corces et al. 2017). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).  Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NovaSeq 6000 sequencer (Illumina).

value: H3.3 K27WT; EZH 1/2 CRISPR knock out


title: SF-8628-K27M-PRC2KO_rep1

description:
Library name: RNA-seq_Sample9
PE150


title: SF8628_K27WT_PRC2KO_rep1

description:
Library name: ATAC-seq_Sample5
PE42


title: SF8628_K27M_PRC2KO_rep2

description:
Library name: ATAC-seq_Sample4
PE42


title: Ctrl_IgG

value: IgG control, True MicroChIP-seq Kit (DIAGENODE Cat# C01010132)


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1073


title: SF-8628-K27M_rep3

description:
Library name: RNA-seq_Sample7
PE150


title: SF8628_K27M_PRC2KO_rep1

description:
Library name: ATAC-seq_Sample3
PE42