title: P60_14d_WT_96, scRNA-seq


title: P18_181, scRNA-seq

status: Public on Jun 26 2023

type: SRA

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

description:
mSTRT-seq
readcount.mSTRT-seq.csv

library_source: transcriptomic

data_processing:
For mSTRT-seq, libraries were sequenced as 150-bp paired-end reads on an Illumina HiSeq 4000 platform. Raw files (fastq format) were separated based on cell-specific barcode sequences. PolyA sequences were trimmed from R1 reads (3’ end of cDNA). Preprocessed R1 reads from each cell were then aligned to the Mus musculus reference genome GRCm38/mm10 with TopHat V2.1.0. Bam files were annotated to genes with featureCounts (v1.5.3). We used samtools (v1.3.1) to sort and index the output bam files. UMIs of each gene were counted with umi-tools (v0.5.0) with the “unique” method.
For Smart-seq 3, libraries were sequenced as 100-bp paired-end reads on an MGI-seq 2000 platform. We trimmed the index, primer and adaptor sequences from the paired-end reads using Trimmomatic v0.39. The trimmed reads were aligned to the M. musculus reference genome GRCm38/mm10 with HISAT v2.1.0. Bam files were annotated to genes with featureCounts (v2.0.0). Either 5’ fragments or internal fragments were used during alignment.
For snRNA-seq, libraries were sequenced as 150-bp paired-end reads on an Illumina HiSeq 4000 platform. The alignment processes of snRNA-seq were similar to those of mSTRT-seq. The specific parameter of featureCounts (v1.5.3) during snRNA-seq alignment was “-t transcript” to ensure that the intron of mRNA could be detected.
For RNA-seq, libraries were sequenced as 150-bp paired-end reads on an Illumina HiSeq 2500 platform. the sequencing reads were aligned to the M. musculus genome (mm10) using TopHat (v2.1.0; https://ccb.jhu.edu/software/tophat/index.shtml) with the parameters ‘-o out_dir -G gtf –transcriptome-index trans_index bowtie2_index input_fastq1 input_fastq2’. Reads aligned to genes were counted using HTSeq (v0.6.0; https://htseq.readthedocs.io/) with the parameters ‘htseq-count -f bam -r pos -s reverse -a 30 input_bam gtf’.
Assembly: mm10
Supplementary files format and content: Comma-Separated Values files (.csv)

molecule: total RNA

organism: Mus musculus

source_name: liver

extract_protocol:
For scRNA-seq, single cells were picked up into cell lysis buffer, and mRNA was reverse transcribed and amplified. For snRNA-seq, nucleus extraction was performed as previously reported(Krishnaswami et al., 2016). In brief, hepatocytes were collected through FACS sorting. Cell membranes were broken down with a homogenizer in homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 10 mM Tris buffer (pH 8.0), 1 µM DTT, protease inhibitor, RNase inhibitor and 0.1% Triton X-100). After centrifugation (5 min, 500 g, 4° C), the nucleus was washed with PBS containing RNase inhibitor and stained with 0.5 ug/ml DAPI. The single nucleus was sorted into cell lysis. SnRNA-seq was performed using well-based mSTRT-seq just as scRNA-seq, but the cycles of cDNA amplification was 4 + 16. For bulk RNA-seq, total RNA was extracted using the RNAprep Pure Micro Kit. Poly(A) RNA was purified with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, #E7490).
For well-based mSTRT-seq(Li et al., 2017), barcoded DNA products were pooled and libraries were constructed with a Kapa Hyper Prep Kit (Kapa Biosystems, KK8505). For Smart-seq3(Hagemann-Jensen et al., 2022), the library of each cell was constructed separately with TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501).  For bulk RNA-seq, libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep with Sample Purification Beads (NEB, #E7765) according to the manufacturer’s instructions.

tag: tissue

value: liver

tag: cell type

value: hepatocyte

tag: genotype

value: Alb-Cre; Rosa-tdTomato

tag: age

tag: ploidy

tag: treatment

tag: zonation


title: P60_14d_WT_94, scRNA-seq

description:
MGI-seq 2000
Smart-seq3
readcount.Smartseq3.csv

value: WT


title: P60_14d_WT_89, scRNA-seq


title: P60_14d_WT_93, scRNA-seq


title: P18_184, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_180, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_92, scRNA-seq


title: P60_14d_WT_98, scRNA-seq


title: P60_14d_WT_88, scRNA-seq


title: P18_178, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_179, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_87, scRNA-seq


title: P18_176, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_86, scRNA-seq


title: P18_177, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_85, scRNA-seq


title: P60_14d_WT_84, scRNA-seq


title: P18_174, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_172, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_175, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_173, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_80, scRNA-seq


title: P60_14d_WT_83, scRNA-seq


title: P60_14d_WT_82, scRNA-seq


title: P60_14d_WT_81, scRNA-seq


title: P18_170, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_78, scRNA-seq


title: P60_14d_WT_79, scRNA-seq


title: P18_168, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_169, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_76, scRNA-seq


title: P60_14d_WT_77, scRNA-seq


title: P18_167, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_75, scRNA-seq


title: P18_165, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_166, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_74, scRNA-seq


title: P18_164, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_73, scRNA-seq


title: P60_14d_WT_71, scRNA-seq


title: P18_162, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_161, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_163, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_70, scRNA-seq


title: P18_160, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_69, scRNA-seq


title: P60_14d_WT_72, scRNA-seq


title: P60_14d_WT_68, scRNA-seq


title: P18_158, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_157, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_63, scRNA-seq


title: P60_14d_WT_67, scRNA-seq


title: P60_14d_WT_65, scRNA-seq


title: P60_14d_WT_66, scRNA-seq


title: P18_159, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_64, scRNA-seq


title: P60_14d_WT_62, scRNA-seq


title: P60_14d_WT_61, scRNA-seq


title: P60_14d_WT_60, scRNA-seq


title: P60_14d_WT_59, scRNA-seq


title: P18_171, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_58, scRNA-seq


title: P60_14d_WT_55, scRNA-seq


title: P60_14d_WT_57, scRNA-seq


title: P60_14d_WT_56, scRNA-seq


title: P18_156, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_148, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_153, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_155, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_150, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_149, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_152, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_154, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_147, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_145, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_146, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_54, scRNA-seq


title: P18_144, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_143, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_142, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_151, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_141, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_53, scRNA-seq


title: P60_14d_WT_51, scRNA-seq


title: P60_14d_WT_50, scRNA-seq


title: P18_139, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_140, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_49, scRNA-seq


title: P60_14d_WT_48, scRNA-seq


title: P18_138, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_137, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_136, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_46, scRNA-seq


title: P60_14d_WT_45, scRNA-seq


title: P60_14d_WT_52, scRNA-seq


title: P18_134, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_135, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_131, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_44, scRNA-seq


title: P60_14d_WT_43, scRNA-seq


title: P18_133, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_41, scRNA-seq


title: P60_14d_WT_42, scRNA-seq


title: P18_132, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_128, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_38, scRNA-seq


title: P60_14d_WT_37, scRNA-seq


title: P18_127, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_130, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_36, scRNA-seq


title: P60_14d_WT_39, scRNA-seq


title: P18_125, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_126, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_35, scRNA-seq


title: P18_124, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_34, scRNA-seq


title: P60_14d_WT_47, scRNA-seq


title: P60_14d_WT_33, scRNA-seq


title: P18_123, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_122, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_129, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_40, scRNA-seq


title: P18_121, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_32, scRNA-seq


title: P60_14d_WT_31, scRNA-seq


title: P60_14d_WT_30, scRNA-seq


title: P18_119, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_28, scRNA-seq


title: P60_14d_WT_29, scRNA-seq


title: P60_14d_WT_25, scRNA-seq


title: P18_116, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_117, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_114, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_120, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_27, scRNA-seq


title: P60_14d_WT_24, scRNA-seq


title: P18_112, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_113, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_22, scRNA-seq


title: P18_111, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_20, scRNA-seq


title: P18_110, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_19, scRNA-seq


title: P18_108, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_118, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_107, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_115, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_26, scRNA-seq


title: P60_14d_WT_17, scRNA-seq


title: P60_14d_WT_15, scRNA-seq


title: P18_106, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_23, scRNA-seq


title: P18_104, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_14, scRNA-seq


title: P60_14d_WT_13, scRNA-seq


title: P18_103, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_101, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_10, scRNA-seq


title: P60_14d_WT_21, scRNA-seq


title: P60_14d_WT_12, scRNA-seq


title: P18_100, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_7, scRNA-seq


title: P18_99, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_97, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_109, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_18, scRNA-seq


title: P60_14d_WT_16, scRNA-seq


title: P60_14d_WT_6, scRNA-seq


title: P60_14d_WT_5, scRNA-seq


title: P18_105, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_4, scRNA-seq


title: P60_14d_WT_2, scRNA-seq


title: P18_94, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_11, scRNA-seq


title: P18_93, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_95, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_102, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_WT_9, scRNA-seq


title: P60_14d_WT_1, scRNA-seq


title: P60_14d_WT_8, scRNA-seq


title: P18_89, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_92, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_90, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_156, scRNA-seq


title: P60_14d_Usf1-KO_154, scRNA-seq


title: P18_98, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_91, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_88, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_152, scRNA-seq


title: P60_14d_Usf1-KO_151, scRNA-seq


title: P60_14d_Usf1-KO_153, scRNA-seq


title: P18_86, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_96, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_85, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_150, scRNA-seq


title: P60_14d_WT_3, scRNA-seq


title: P60_14d_Usf1-KO_149, scRNA-seq


title: P18_84, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_145, scRNA-seq


title: P18_83, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_80, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_81, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_82, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_148, scRNA-seq


title: P60_14d_Usf1-KO_147, scRNA-seq


title: P60_14d_Usf1-KO_146, scRNA-seq


title: P60_14d_Usf1-KO_155, scRNA-seq


title: P18_87, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_78, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_79, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_142, scRNA-seq


title: P60_14d_Usf1-KO_143, scRNA-seq


title: P60_14d_Usf1-KO_141, scRNA-seq


title: P60_14d_Usf1-KO_144, scRNA-seq


title: P18_76, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_140, scRNA-seq


title: P18_74, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_139, scRNA-seq


title: P18_73, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_72, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_138, scRNA-seq


title: P60_14d_Usf1-KO_137, scRNA-seq


title: P18_71, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_136, scRNA-seq


title: P18_70, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_135, scRNA-seq


title: P18_69, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_68, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_133, scRNA-seq


title: P60_14d_Usf1-KO_134, scRNA-seq


title: P60_14d_Usf1-KO_132, scRNA-seq


title: P18_77, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_75, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_131, scRNA-seq


title: P60_14d_Usf1-KO_130, scRNA-seq


title: P60_14d_Usf1-KO_129, scRNA-seq


title: P18_65, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_66, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_63, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_67, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_64, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_127, scRNA-seq


title: P18_62, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_60, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_126, scRNA-seq


title: P60_14d_Usf1-KO_125, scRNA-seq


title: P18_61, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_59, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_124, scRNA-seq


title: P60_14d_Usf1-KO_123, scRNA-seq


title: P18_58, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_122, scRNA-seq


title: P18_56, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_57, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_121, scRNA-seq


title: P60_14d_Usf1-KO_119, scRNA-seq


title: P18_54, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_53, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_118, scRNA-seq


title: P18_52, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_120, scRNA-seq


title: P18_55, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_117, scRNA-seq


title: P60_14d_Usf1-KO_128, scRNA-seq


title: P18_49, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_50, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_116, scRNA-seq


title: P60_14d_Usf1-KO_115, scRNA-seq


title: P60_14d_Usf1-KO_114, scRNA-seq


title: P18_47, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_112, scRNA-seq


title: P60_14d_Usf1-KO_111, scRNA-seq


title: P18_46, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_113, scRNA-seq


title: P60_14d_Usf1-KO_110, scRNA-seq


title: P18_51, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_44, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_48, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_109, scRNA-seq


title: P60_14d_Usf1-KO_108, scRNA-seq


title: P60_14d_Usf1-KO_107, scRNA-seq


title: P18_43, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_42, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_41, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_105, scRNA-seq


title: P18_38, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_40, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_103, scRNA-seq


title: P60_14d_Usf1-KO_106, scRNA-seq


title: P60_14d_Usf1-KO_104, scRNA-seq


title: P18_39, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_37, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_45, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_99, scRNA-seq


title: P18_34, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_36, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_35, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_101, scRNA-seq


title: P60_14d_Usf1-KO_97, scRNA-seq


title: P18_31, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_100, scRNA-seq


title: P60_14d_Usf1-KO_102, scRNA-seq


title: P18_30, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_96, scRNA-seq


title: P60_14d_Usf1-KO_98, scRNA-seq


title: P60_14d_Usf1-KO_95, scRNA-seq


title: P18_29, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_94, scRNA-seq


title: P18_27, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_93, scRNA-seq


title: P18_28, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_92, scRNA-seq


title: P18_26, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_24, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_23, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_91, scRNA-seq


title: P60_14d_Usf1-KO_90, scRNA-seq


title: P18_25, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_89, scRNA-seq


title: P18_33, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_88, scRNA-seq


title: P60_14d_Usf1-KO_87, scRNA-seq


title: P60_14d_Usf1-KO_86, scRNA-seq


title: P18_22, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_32, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_21, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_85, scRNA-seq


title: P60_14d_Usf1-KO_84, scRNA-seq


title: P60_14d_Usf1-KO_83, scRNA-seq


title: P18_16, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_19, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_17, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_82, scRNA-seq


title: P60_14d_Usf1-KO_81, scRNA-seq


title: P18_18, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_15, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_80, scRNA-seq


title: P18_13, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_79, scRNA-seq


title: P18_14, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_78, scRNA-seq


title: P18_12, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_11, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_76, scRNA-seq


title: P60_14d_Usf1-KO_77, scRNA-seq


title: P18_10, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_20, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_9, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_75, scRNA-seq


title: P60_14d_Usf1-KO_74, scRNA-seq


title: P18_7, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_73, scRNA-seq


title: P60_14d_Usf1-KO_71, scRNA-seq


title: P18_5, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_6, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_8, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_72, scRNA-seq


title: P60_14d_Usf1-KO_69, scRNA-seq


title: P60_14d_Usf1-KO_67, scRNA-seq


title: P60_14d_Usf1-KO_68, scRNA-seq


title: P18_1, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_70, scRNA-seq


title: P18_4, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_3, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_153, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_66, scRNA-seq


title: P15_152, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_64, scRNA-seq


title: P60_14d_Usf1-KO_65, scRNA-seq


title: P15_151, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P18_2, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_63, scRNA-seq


title: P15_150, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_149, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_62, scRNA-seq


title: P60_14d_Usf1-KO_61, scRNA-seq


title: P60_14d_Usf1-KO_60, scRNA-seq


title: P15_148, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_59, scRNA-seq


title: P60_14d_Usf1-KO_58, scRNA-seq


title: P15_144, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_145, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_56, scRNA-seq


title: P60_14d_Usf1-KO_57, scRNA-seq


title: P15_143, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_141, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_142, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_140, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_54, scRNA-seq


title: P60_14d_Usf1-KO_53, scRNA-seq


title: P60_14d_Usf1-KO_55, scRNA-seq


title: P60_14d_Usf1-KO_52, scRNA-seq


title: P15_139, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_138, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_137, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_147, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_50, scRNA-seq


title: P15_136, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_51, scRNA-seq


title: P15_135, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_134, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_46, scRNA-seq


title: P60_14d_Usf1-KO_47, scRNA-seq


title: P60_14d_Usf1-KO_48, scRNA-seq


title: P15_133, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_132, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_45, scRNA-seq


title: P15_146, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_44, scRNA-seq


title: P60_14d_Usf1-KO_43, scRNA-seq


title: P15_130, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_131, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_129, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_42, scRNA-seq


title: P60_14d_Usf1-KO_41, scRNA-seq


title: P60_14d_Usf1-KO_49, scRNA-seq


title: P60_14d_Usf1-KO_40, scRNA-seq


title: P15_128, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_127, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_38, scRNA-seq


title: P15_126, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_125, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_36, scRNA-seq


title: P15_123, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_37, scRNA-seq


title: P60_14d_Usf1-KO_35, scRNA-seq


title: P15_122, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_121, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_33, scRNA-seq


title: P15_119, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_32, scRNA-seq


title: P60_14d_Usf1-KO_31, scRNA-seq


title: P60_14d_Usf1-KO_30, scRNA-seq


title: P15_120, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_118, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_117, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_28, scRNA-seq


title: P60_14d_Usf1-KO_34, scRNA-seq


title: P15_116, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_39, scRNA-seq


title: P15_114, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_26, scRNA-seq


title: P15_113, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_25, scRNA-seq


title: P15_112, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_115, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_124, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_27, scRNA-seq


title: P60_14d_Usf1-KO_23, scRNA-seq


title: P60_14d_Usf1-KO_24, scRNA-seq


title: P15_110, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_111, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_22, scRNA-seq


title: P15_109, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_21, scRNA-seq


title: P15_108, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_19, scRNA-seq


title: P15_105, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_18, scRNA-seq


title: P15_107, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_20, scRNA-seq


title: P60_14d_Usf1-KO_29, scRNA-seq


title: P15_104, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_16, scRNA-seq


title: P15_103, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_15, scRNA-seq


title: P15_101, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_100, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_14, scRNA-seq


title: P60_14d_Usf1-KO_13, scRNA-seq


title: P15_98, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_97, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_11, scRNA-seq


title: P15_96, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_9, scRNA-seq


title: P60_14d_Usf1-KO_10, scRNA-seq


title: P15_106, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_94, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_17, scRNA-seq


title: P15_93, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_5, scRNA-seq


title: P15_92, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_3, scRNA-seq


title: P15_102, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_90, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_89, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Usf1-KO_12, scRNA-seq


title: P60_14d_Usf1-KO_1, scRNA-seq


title: P15_99, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_161, scRNA-seq


title: P15_87, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_160, scRNA-seq


title: P60_14d_Usf1-KO_8, scRNA-seq


title: P15_86, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_95, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_85, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_158, scRNA-seq


title: P60_14d_Nr2f2-KO_157, scRNA-seq


title: P60_14d_Usf1-KO_7, scRNA-seq


title: P60_14d_Usf1-KO_6, scRNA-seq


title: P60_14d_Usf1-KO_4, scRNA-seq


title: P60_14d_Nr2f2-KO_156, scRNA-seq


title: P15_83, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_155, scRNA-seq


title: P15_91, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_81, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_82, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_80, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_154, scRNA-seq


title: P60_14d_Usf1-KO_2, scRNA-seq


title: P60_14d_Nr2f2-KO_153, scRNA-seq


title: P15_79, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_78, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_151, scRNA-seq


title: P60_14d_Nr2f2-KO_152, scRNA-seq


title: P15_88, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_76, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_84, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_159, scRNA-seq


title: P15_77, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_150, scRNA-seq


title: P60_14d_Nr2f2-KO_149, scRNA-seq


title: P15_72, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_145, scRNA-seq


title: P15_75, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_74, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_147, scRNA-seq


title: P60_14d_Nr2f2-KO_148, scRNA-seq


title: P15_71, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_68, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_70, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_69, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_66, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_141, scRNA-seq


title: P15_65, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_142, scRNA-seq


title: P60_14d_Nr2f2-KO_140, scRNA-seq


title: P15_67, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_139, scRNA-seq


title: P60_14d_Nr2f2-KO_146, scRNA-seq


title: P15_63, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_138, scRNA-seq


title: P15_62, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_59, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_61, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_60, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_136, scRNA-seq


title: P15_73, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_58, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_144, scRNA-seq


title: P15_57, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_135, scRNA-seq


title: P15_55, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_54, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_53, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_51, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_48, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_46, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_130, scRNA-seq


title: P15_45, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_128, scRNA-seq


title: P60_14d_Nr2f2-KO_129, scRNA-seq


title: P15_41, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_127, scRNA-seq


title: P60_14d_Nr2f2-KO_126, scRNA-seq


title: P60_14d_Nr2f2-KO_143, scRNA-seq


title: P15_38, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_125, scRNA-seq


title: P15_37, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_36, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_56, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_134, scRNA-seq


title: P15_33, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_35, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_123, scRNA-seq


title: P15_32, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_133, scRNA-seq


title: P60_14d_Nr2f2-KO_122, scRNA-seq


title: P15_52, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_64, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_50, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_132, scRNA-seq


title: P15_28, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_49, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_131, scRNA-seq


title: P15_47, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_44, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_43, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_40, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_39, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_42, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_124, scRNA-seq


title: P15_34, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_31, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_30, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_121, scRNA-seq


title: P15_29, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_120, scRNA-seq


title: P60_14d_Nr2f2-KO_137, scRNA-seq


title: P15_27, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_24, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_118, scRNA-seq


title: P15_22, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_117, scRNA-seq


title: P15_21, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_116, scRNA-seq


title: P15_16, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_114, scRNA-seq


title: P60_14d_Nr2f2-KO_113, scRNA-seq


title: P15_11, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_10, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_111, scRNA-seq


title: P15_9, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_7, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_26, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_6, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_5, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_108, scRNA-seq


title: P15_3, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_119, scRNA-seq


title: P15_2, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_1, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_25, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_20, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_150, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_106, scRNA-seq


title: P15_19, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_115, scRNA-seq


title: P15_18, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_17, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_23, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_15, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_14, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_13, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_112, scRNA-seq


title: P15_12, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P15_8, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_110, scRNA-seq


title: P60_14d_Nr2f2-KO_109, scRNA-seq


title: P15_4, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_107, scRNA-seq


title: P60_14d_Nr2f2-KO_105, scRNA-seq


title: P12_147, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_146, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_145, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_144, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_102, scRNA-seq


title: P60_14d_Nr2f2-KO_103, scRNA-seq


title: P12_141, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_140, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_139, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_100, scRNA-seq


title: P12_138, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_136, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_135, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_134, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_132, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_133, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_97, scRNA-seq


title: P60_14d_Nr2f2-KO_98, scRNA-seq


title: P12_131, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_149, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_130, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_129, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_148, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_128, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_95, scRNA-seq


title: P60_14d_Nr2f2-KO_94, scRNA-seq


title: P12_125, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_123, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_104, scRNA-seq


title: P12_122, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_92, scRNA-seq


title: P12_143, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_142, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_120, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_93, scRNA-seq


title: P60_14d_Nr2f2-KO_90, scRNA-seq


title: P12_117, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_137, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_101, scRNA-seq


title: P60_14d_Nr2f2-KO_88, scRNA-seq


title: P60_14d_Nr2f2-KO_87, scRNA-seq


title: P60_14d_Nr2f2-KO_99, scRNA-seq


title: P60_14d_Nr2f2-KO_86, scRNA-seq


title: P12_110, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_108, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_85, scRNA-seq


title: P12_109, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_106, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_104, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_103, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_101, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_83, scRNA-seq


title: P12_99, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_80, scRNA-seq


title: P12_98, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_96, scRNA-seq


title: P12_97, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_79, scRNA-seq


title: P12_94, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_93, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_92, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_127, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_126, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_88, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_124, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_121, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_91, scRNA-seq


title: P12_119, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_118, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_116, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_89, scRNA-seq


title: P12_115, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_114, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_84, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_73, scRNA-seq


title: P12_83, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_113, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_112, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_111, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_107, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_105, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_84, scRNA-seq


title: P60_14d_Nr2f2-KO_71, scRNA-seq


title: P12_102, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_79, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_70, scRNA-seq


title: P12_78, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_81, scRNA-seq


title: P60_14d_Nr2f2-KO_82, scRNA-seq


title: P12_100, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_95, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_78, scRNA-seq


title: P12_96, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_80, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_77, scRNA-seq


title: P12_91, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_69, scRNA-seq


title: P60_14d_Nr2f2-KO_75, scRNA-seq


title: P12_74, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_76, scRNA-seq


title: P60_14d_Nr2f2-KO_74, scRNA-seq


title: P12_70, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_86, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_68, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_90, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_67, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_65, scRNA-seq


title: P12_87, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_85, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_72, scRNA-seq


title: P12_89, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_81, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_77, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_63, scRNA-seq


title: P60_14d_Nr2f2-KO_62, scRNA-seq


title: P12_76, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_64, scRNA-seq


title: P12_60, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_67, scRNA-seq


title: P12_82, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_58, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_68, scRNA-seq


title: P12_72, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_75, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_59, scRNA-seq


title: P12_73, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_54, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_66, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_65, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_61, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_62, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_66, scRNA-seq


title: P12_63, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_69, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_53, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_52, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_61, scRNA-seq


title: P12_64, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_57, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_56, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_49, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_58, scRNA-seq


title: P60_14d_Nr2f2-KO_57, scRNA-seq


title: P60_14d_Nr2f2-KO_60, scRNA-seq


title: P12_48, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_43, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_51, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_47, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_56, scRNA-seq


title: P12_55, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_39, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_54, scRNA-seq


title: P12_50, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_53, scRNA-seq


title: P12_59, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_51, scRNA-seq


title: P12_40, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_52, scRNA-seq


title: P60_14d_Nr2f2-KO_55, scRNA-seq


title: P12_41, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_46, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_50, scRNA-seq


title: P12_37, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_45, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_36, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_38, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_49, scRNA-seq


title: P12_44, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_35, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_42, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_32, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_48, scRNA-seq


title: P12_30, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_29, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_31, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_47, scRNA-seq


title: P60_14d_Nr2f2-KO_46, scRNA-seq


title: P12_26, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_44, scRNA-seq


title: P12_27, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_45, scRNA-seq


title: P12_24, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_23, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_42, scRNA-seq


title: P60_14d_Nr2f2-KO_43, scRNA-seq


title: P60_14d_Nr2f2-KO_41, scRNA-seq


title: P60_14d_Nr2f2-KO_40, scRNA-seq


title: P12_17, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_33, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_34, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_16, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_18, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_39, scRNA-seq


title: P12_15, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_28, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_25, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_14, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_38, scRNA-seq


title: P12_12, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_22, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_20, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_36, scRNA-seq


title: P12_13, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_19, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_21, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_35, scRNA-seq


title: P12_9, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_10, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_8, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_7, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_34, scRNA-seq


title: P12_6, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_5, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_4, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_33, scRNA-seq


title: P12_3, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_32, scRNA-seq


title: P12_2, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_11, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_148, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_1, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_37, scRNA-seq


title: P60_14d_Nr2f2-KO_31, scRNA-seq


title: P9_146, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_145, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_147, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_29, scRNA-seq


title: P9_142, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_30, scRNA-seq


title: P9_143, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_140, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_139, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_27, scRNA-seq


title: P60_14d_Nr2f2-KO_26, scRNA-seq


title: P60_14d_Nr2f2-KO_28, scRNA-seq


title: P9_141, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_144, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_25, scRNA-seq


title: P60_14d_Nr2f2-KO_24, scRNA-seq


title: P60_14d_Nr2f2-KO_23, scRNA-seq


title: P60_14d_Nr2f2-KO_22, scRNA-seq


title: P9_133, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_136, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_138, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_134, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_135, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_130, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_132, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_131, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_137, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_129, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_21, scRNA-seq


title: P60_14d_Nr2f2-KO_20, scRNA-seq


title: P9_128, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_71, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_19, scRNA-seq


title: P9_127, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_125, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_17, scRNA-seq


title: P9_126, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_18, scRNA-seq


title: P60_14d_Nr2f2-KO_16, scRNA-seq


title: P60_14d_Nr2f2-KO_15, scRNA-seq


title: P60_14d_Nr2f2-KO_14, scRNA-seq


title: P9_122, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: Mmut_hemizygous_KOKI_rep9

type: RNA

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 9

hyb_protocol: According to the Thermo Fisher Scientific expression protocol (HWS kit)

scan_protocol: According to the Thermo Fisher Scientific expression protocol, Scanner 3000 7G

data_processing: SST-RMA gene-level probeset summary with standard settings of theTranscriptome Analysis Console (TAC; version 4.0.0.25; Thermo Fisher Scientific)

label: biotin

source_name: Liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 9

label_protocol: Total RNA was amplified using the WT PLUS Reagent Kit (Thermo Fisher Scientific Inc., Waltham, USA).

growth_protocol: Mice were housed according to the German Mouse Clinic housing conditions and German laws, and in strict accordance with directive 2010/63/EU. They were housed in individually ventilated caging systems operating with positive pressure (Sealsafe plus, GM 500, Tecniplast, Buggugiate, Italy) under specific pathogen-free conditions. All mice received autoclaved wood chips (Lignocel select fine, J. Rettenmaier & Soehne GmbH, Rosenberg, Germany) and paper stripes (Arbocel crinclets natural Rettenmaier & Soehne GmbH) as bedding and nesting material, and sterile-filtered tap water ad libitum. Light was adjusted to a 12:12 hour light/dark cycle with a 10 min period of dimmed light to simulate sunrise/sunset.

extract_protocol: Total RNA was isolated employing the RNeasy Mini kit (Qiagen, Hilden, Germany) including Trizol treatment

treatment_protocol: No treatment

tag: strain

value: 20 weeks

tag: gender

value: male

tag: genotype/variation


title: P9_121, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: Mmut_hemizygous_KOKI_rep8

description: Gene expression data from liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 8

source_name: Liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 8


title: P60_14d_Nr2f2-KO_13, scRNA-seq


title: Mmut_hemizygous_KOKI_rep10

description: Gene expression data from liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 10

source_name: Liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 10


title: P9_124, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_119, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_11, scRNA-seq


title: P9_118, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: Mmut_hemizygous_KOKI_rep5

description: Gene expression data from liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 5

source_name: Liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 5


title: Mmut_hemizygous_KOKI_rep4

description: Gene expression data from liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 4

source_name: Liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 4


title: Mmut_hemizygous_KOKI_rep2

description: Gene expression data from liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 2

source_name: Liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 2


title: P60_14d_Nr2f2-KO_9, scRNA-seq


title: P60_14d_Nr2f2-KO_10, scRNA-seq


title: Mmut_hemizygous_KOKI_rep6

description: Gene expression data from liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 6

source_name: Liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 6


title: Mmut_hemizygous_KOKI_rep3

description: Gene expression data from liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 3

source_name: Liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 3


title: P9_117, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_123, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: Mmut_control_KIWT_rep8

description: Gene expression data from liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 8

source_name: Liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 8


title: P9_116, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: Mmut_control_KIWT_rep9

description: Gene expression data from liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 9

source_name: Liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 9


title: Mmut_hemizygous_KOKI_rep7

description: Gene expression data from liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 7

source_name: Liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 7


title: P9_120, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_12, scRNA-seq


title: P9_115, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_8, scRNA-seq


title: P60_14d_Nr2f2-KO_7, scRNA-seq


title: P9_114, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: Mmut_hemizygous_KOKI_rep1

description: Gene expression data from liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 1

source_name: Liver of hemizygous mice with knock-out allele and knock-in (ki, MMUT-p.Met700Lys) allele, biological replicate 1


title: Mmut_control_KIWT_rep7

description: Gene expression data from liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 7

source_name: Liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 7


title: P9_113, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_4, scRNA-seq


title: P9_112, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_111, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P60_14d_Nr2f2-KO_6, scRNA-seq


title: Mmut_control_KIWT_rep3

description: Gene expression data from liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 3

source_name: Liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 3


title: Mmut_control_KIWT_rep4

description: Gene expression data from liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 4

source_name: Liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 4


title: P60_14d_Nr2f2-KO_2, scRNA-seq


title: P9_109, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: Mmut_control_KIWT_rep5

description: Gene expression data from liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 5

source_name: Liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 5


title: P9_110, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

source_name: liver


title: Mmut_control_KIWT_rep2

description: Gene expression data from liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 2

source_name: Liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 2


title: P60_14d_Nr2f2-KO_3, scRNA-seq

description:
MGI-seq 2000
Smart-seq3
readcount.Smartseq3.csv


title: E14_PhenDC3_ActinD_CTCF_Rep1

city: Philadelphia

first: Phillip

last: Wulfridge

state: Pennsylvania

address: 3601 Spruce St

country: USA

institute: The Wistar Institute

library_source: genomic

data_processing:
Alignment (CUT&RUN, MapR, ChIP, HiC): Bowtie2
Alignment (RNA-Seq): STAR
RNA expected counts were generated with RSEM.
Bigwig files were made from .bam files using "deepTools bamCoverage --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and RPM or spike-in normalization. PCR duplicate reads were removed for ChIP samples. HiC contact maps were generated using HiC-Pro and are usable in Juicebox.
Assembly: mm10
Supplementary files format and content: bigwig files compatible with UCSC genome browser and IGV, TPM output in .counts tab-delimited for RNA-Seq alignment, contact maps in .hic for HiC

molecule: genomic DNA

growth_protocol: Mouse embryonic stem cells were grown in DMEM medium with 15% FBS, 25mM HEPES, 1x GlutaMAX, 1x non-essential amino acids, 100 U/mL penicillin-steptomycin, LIF, 3µM GSK inhibitor, 1µM MEK1/2 inhibitor at 37 ˚C.

extract_protocol:
CUT&RUN for CTCF, ADNP, EZH2, and H3K4me3 was performed on cells as previously described (Skene and Henikoff, eLife 2017).
R-loop containing DNA was collected using MapR protocol as previously described (Yan et al., Cell Reports 2019).
Total RNA was collected using Trizol (Invitrogen) and digested with Turbo Dnase (Ambion). rRNA was selectively depleted using FastSelect (Qiagen).
ChIP for CTCF was performed on cells as previously described (Trizzino et al., Cell Rep. 2018).
HiC was performed using the Arima Genomics Hi-C+ for High Coverage kit.
rRNA-depleted RNA was converted to cDNA using the Ultra II Directional RNA kit for Illumina (NEB #E7760).
CUT&RUN, MapR, RNA-Seq, and ChIP samples were end-repaired using End-Repair Mix (Enzymatics), A-tailed using Klenow exonuclease minus (Enzymatics), purified with MinElute columns (Qiagen), and ligated to Illumina adapters (NEB E7600) with T4 DNA ligase (Enzymatics).  Size selection for fragments >150 bp was performed with AMPure XP (Beckman Coulter).  Libraries were PCR amplified with dual index barcode primers for Illumina sequencing (NEB E7600) using Q5 DNA polymerase (NEB M0491) and purified with MinElute.
HiC samples were prepared using the NEBNext Ultra II DNA Library Prep Kit with modifications according to the Arima Genomics Hi-C kit.

value: Wildtype

tag: protocol

value: ChIP-Seq

tag: antibody

value: CTCF

value: PhenDC3 + Actinomycin D

tag: cell line


title: E14_PhenDC3_ActinD_CTCF_Rep2

description: processed data linked to Rep1


title: P12_40d_Xbp1-KO_207, scRNA-seq


title: P60_14d_Nr2f2-KO_1, scRNA-seq


title: P9_107, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_108, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: E14_PhenDC3_CTCF_Rep2

description: processed data linked to Rep1


title: P12_40d_Xbp1-KO_206, scRNA-seq


title: E14_PDS_ActinD_CTCF_Rep1

value: Pyridostatin + Actinomycin D


title: P9_106, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: E14_PDS_ActinD_CTCF_Rep2

description: processed data linked to Rep1


title: P12_40d_Xbp1-KO_204, scRNA-seq


title: P9_105, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_205, scRNA-seq


title: P9_104, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_203, scRNA-seq


title: E14_PDS_CTCF_Rep2

description: processed data linked to Rep1

value: Pyridostatin


title: E14_PhenDC3_CTCF_Rep1


title: Mmut_control_KIWT_rep6

description: Gene expression data from liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 6

source_name: Liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 6


title: Mmut_control_KIWT_rep1

description: Gene expression data from liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 1

source_name: Liver of control mice with WT allele and knock-in allele (ki, MMUT-p.Met700Lys), biological replicate 1


title: E14_Mock_CTCF_Rep2

description: processed data linked to Rep1

value: Untreated


title: E14_PDS_CTCF_Rep1


title: P9_103, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_102, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_202, scRNA-seq


title: E14_Mock_CTCF_Rep1


title: P9_101, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_200, scRNA-seq


title: E14_PhenDC3_G4

data_processing:
Alignment (CUT&RUN, MapR, ChIP, HiC): Bowtie2
Alignment (RNA-Seq): STAR
RNA expected counts were generated with RSEM.
Bigwig files were made from .bam files using "deepTools bamCoverage --extendReads --binSize 5", an ENCODE blacklist file for biased regions (Amemiya et al. Nature 2019), and RPM or spike-in normalization. PCR duplicate reads were removed for ChIP samples. HiC contact maps were generated using HiC-Pro and are usable in Juicebox.
Assembly: mm10
Supplementary files format and content: bigwig files compatible with UCSC genome browser and IGV, TPM output in .counts tab-delimited for RNA-Seq alignment, contact maps in .hic for HiC
Library strategy: CUT&RUN

value: CUT&RUN


title: E14_PhenDC3_Mock_G4


title: P12_40d_Xbp1-KO_198, scRNA-seq


title: P12_40d_Xbp1-KO_197, scRNA-seq


title: P9_99, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_98, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_195, scRNA-seq


title: P9_97, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_196, scRNA-seq


title: P9_96, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_95, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: E14_Mock_HiC_Rep2

value: Hi-C


title: E14_PDS_HiC_Rep1


title: P12_40d_Xbp1-KO_194, scRNA-seq


title: P12_40d_Xbp1-KO_201, scRNA-seq


title: P9_94, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_199, scRNA-seq


title: E14_Praf2_WT_G4


title: P9_93, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: E14_Mock_HiC_Rep1


title: E14_PDS_HiC_Rep2


title: HCT_ChIPseq_Input_control

city: Solna

first: Federico

last: Agostini

state: Stockholm

address: Tomtebodavägen 23a

country: Sweden

institute: Science for Life Laboratories

data_processing:
Sequencing quality checks were performed on all experiments using FastQC (v0.11.9). X
Adapter sequences were removed using TrimGalore (v0.6.4_dev) and reads shorter than 20 nt were discarded.
Reads were aligned to the human reference genome (GRCh38/hg38) using bwa-mem (v0.7.17-r1188) with default options.
Reads that failed to align and those with MAPQ ≤ 30 were filtered out, and PCR duplicates were discarded using the Picard MarkDuplicates (v2.18.11) module.
Genome coverage tracks in bigWig format were generated using the bamCoverage module from deeptools (v3.2.1) with --binSize 50 --normalizeUsing CPM options.
Assembly: GRCh38/hg38
Supplementary files format and content: bigWig, genomic coverage CPM-normalized

organism: Homo sapiens

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

extract_protocol:
6 to 10 million cells were crosslinked for 5 minutes at room temperature with 16% methanol-free formaldehyde (Thermo Fisher Scientific) used at a final concentration of 1%. After quenching the reaction with 125 mM glycine final concentration, cells were washed twice in ice-cold PBS and collected by scraping. Pellets were resuspended in buffer A (5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP-40 substitute) and incubated on ice for 10 minutes. After centrifugation (5000 rpm for 5 minutes at 4°C), the supernatants containing the cytoplasm were removed and the nuclei-containing pellets were washed in buffer A without detergent. Pellets were then resuspended in shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 0.1% SDS) and sonicated with a ME220 focused-ultrasonicator (Covaris). After clarification by centrifugation (13000 rpm for 10 minutes at 4°C), the supernatant was adjusted in composition to RIPA buffer and transferred to a new tube to be used for immunoprecipitation. Equal amounts of chromatin (as measured by DNA concentration) were incubated rotating overnight at 4°C with pre-conjugated beads (20 μl of Dynabeads and 3 μg antibody, dyskerin (Abnova, H00001736-m04) or RNAPII (MBL, MAB0601)) in RIPA buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 200 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS). Immunoprecipitates were washed once with each of the following: RIPA buffer, RIPA buffer high salt (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 500 mM NaCl, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS), LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, 250 mM LCiCl, 0.5% NP-40 substitute, 0.5% sodium deoxycholate), and twice with TE buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The beads were then resuspended in TE buffer with 0.5% SDS supplemented with proteinase K (New England Biolabs) and RNase A (Thermo Fisher Scientific) and incubated with shaking at 65°C for 4 hours. The DNA was recovered by phenol:chloroform:isoamyl alcohol extraction followed by ethanol precipitation using standard procedures, and resuspended in TE buffer.
Libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer’s instructions.

treatment_protocol: 250nM flavopiridol for 2 hours prior to cell harvest, added directly to culture medium.

value: Human colorectal carcinoma

value: Vehicle


title: P12_40d_Xbp1-KO_192, scRNA-seq

value: liver


title: P9_100, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

value: hepatocyte


title: P12_40d_Xbp1-KO_191, scRNA-seq


title: P9_92, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

value: Alb-Cre; Rosa-tdTomato


title: HCT116_ChIPseq_Dyskerin_control_rep1

tag: chip antibody

value: dyskerin (Abnova, H00001736-m04)


title: P9_91, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_90, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_193, scRNA-seq


title: P12_40d_Xbp1-KO_189, scRNA-seq


title: Tumour 6 (T6)

city: Illkirch-Graffenstaden

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

country: France

institute: I.G.B.M.C. - Institut de génétique et de biologie moléculaire et cellulaire

library_source: transcriptomic single cell

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment to reference genome hg19 and gene quantification for each cell was done using CellRanger v3.1.
Data are imported into R and analyzed using the Seurat package v3.1.4.
Assembly: hg19
Supplementary files format and content: TSV files containing raw UMI counts for cells used in Seurat analysis.

source_name: Captured single cell RNA

extract_protocol:
Tumor dissociation kit (Miltenyi, 130-095-929); Dead cell removal kit (Miltenyi, 130-090-101)
Single Cell 3ʹ Gene Expression libraries comprise standard Illumina paired-end constructs which begin with P5 and end with P7. 16 bp 10x Barcodes are encoded at the start of TruSeq Read 1, while 8 bp sample index sequences are incorporated as the i7 index read. TruSeq Read 1 and Read 2 are standard Illumina sequencing primer sites used in paired-end sequencing. TruSeq Read 1 is used to sequence 16 bp 10x Barcodes and 12 bp UMI.

tag: disease state

value: clear-cell renal cell carcinoma

value: Kidney

tag: sample type

value: Tumour

tag: patient

value: Patient 6

tag: disease stage

value: Stage I

tag: tumour grade

tag: prior treatment

value: Naive


title: P12_40d_Xbp1-KO_188, scRNA-seq

tag: tissue

tag: cell type

tag: genotype

tag: age


title: P9_88, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

tag: ploidy

tag: treatment

tag: zonation


title: P12_40d_Xbp1-KO_187, scRNA-seq


title: Tumour 7 (T7)

value: Patient 7

value: Stage III


title: Tumour 5 (T5)

value: Patient 5

value: Stage II


title: P9_89, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_87, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_86, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: Tumour 4 (T4)

value: Patient 4


title: P9_85, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_190, scRNA-seq


title: P12_40d_Xbp1-KO_186, scRNA-seq


title: P9_84, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_183, scRNA-seq


title: P9_83, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_182, scRNA-seq


title: P12_40d_Xbp1-KO_185, scRNA-seq


title: S4_SiNREP

type: protein

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

description: hepatocytes transduced with NREP siRNA

hyb_protocol: After blocking non-specific binding sites on the array, an incubation chamber is mounted onto the microarray to permit the loading of 2 samples side by side on the same chip and prevent mixing of the samples. Following sample incubation, unbound proteins are washed away and the array is then probed with anti-biotin antibody that is labelled with a proprietary fluorescent dye combination.

scan_protocol: Each array produces a pair of 16-bit images, which are captured with a Perkin-Elmer ScanArray Reader laser array scanner (Waltham, MA).

data_processing: Signal quantification is performed with ImaGene 9.0 from BioDiscovery (El Segundo, CA) with predetermined settings for spot segmentation and background correction. The background-corrected raw intensity data are logarithmically transformed with base 2.

molecule: protein

source_name: hepatocytes

label_protocol: Proteins were covalently labeled with biotin. Free biotin molecules are then removed at the completion of labeling reactions by gel filtration.

growth_protocol: We used pure, highly viable, and plateable primary human hepatocytes from 5 pooled donors (ThermoFisher, #HMCPP5). Briefly, hepatocytes were seeded on 6-well collagen-treated plates containing William E media supplemented with primary hepatocyte supplements (ThermoFisher) and HepExtend supplement (ThermoFisher).

extract_protocol: Total proteins were harvested from cell  lysates using extraction buffer supplemented with proteinase and phosphatase inhibitors according to standard protocol.

treatment_protocol: Hepatocytes were allowed to attach for 6h. Media was exchanged to eliminate non-viable/attached cells that were forward transfected with Lipofectamine RNAiMAX (ThermoFisher) and 100nM of siGENOME Non-Targeting siRNA Pool (Dharmacon, # D-001206-13-05), or siGENOME human NREP siRNA (Dharmacon, # M-019848-00-0005) in complete media. Media was then changed at 6h post-transfection with complete media.

value: SiNREP

tag: array


title: S6_SiNREP

description: hepatocytes transduced with NREP siRNA


title: P9_82, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_181, scRNA-seq


title: S3_SiScramble

description: hepatocytes transduced with non-targeting siRNA

value: SiScramble


title: S5_SiNREP

description: hepatocytes transduced with NREP siRNA


title: P12_40d_Xbp1-KO_180, scRNA-seq

value: liver


title: P9_81, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

value: hepatocyte


title: P9_80, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

value: Alb-Cre; Rosa-tdTomato


title: P12_40d_Xbp1-KO_179, scRNA-seq


title: P12_40d_Xbp1-KO_184, scRNA-seq


title: S2_SiScramble


title: P9_79, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: Mm-prostate-06

first: Christina

last: Sharkey

state: MA

address: 99 Brookline Ave Rm 389

department: Urology

institute: Beth Israel Deaconess Medical Center

description: 10X Genomics

data_processing:
To align the sequencing reads with the mouse mm10 genome, we employed CellRanger V 3.1.0, provided by 10× Genomics.
Assembly: mm10
Supplementary files format and content: tsv files and matrix files

source_name: Prostate tissue

extract_protocol: To obtain single cells, intact prostate tissues were collected from 12-week-old Srd5a2-/- and Srd5a2+/- mice. Whole fresh prostate tissues were subjected to a digestion process using collagenase type I supplemented with 10 μM rock inhibitor, 1 nmol Dihydrotestosterone, and DNase I in Hank's Balanced Salt Solution (HBSS) for 2 hours at 37°C. The cells were further treated with TrypLE Express supplemented with 10 μM rock inhibitor for 10 mins at 37°C. The resulting cell solution was neutralized in HBSS supplemented with 5% fetal bovine serum and 1% penicillin-streptomycin solution. Subsequently, the cells were resuspended in Red Blood Cell lysis buffer and incubated for 3 min on ice to remove red blood cells. The single cell suspension was washed with a 0.02% PBS-BSA solution and counted. The viability of cells was between 80%~90%, assessed by Trypan Blue.

value: Prostate tissue

tag: strain

value: 12-15 Weeks

value: Srd5a2 Heterozygous


title: Mm-prostate-04

description: 10X Genomics


title: S1_SiScramble


title: P12_40d_Xbp1-KO_177, scRNA-seq


title: P12_40d_Xbp1-KO_178, scRNA-seq


title: Mm-prostate-02

description: 10X Genomics

value: Srd5a2 knockout


title: P9_77, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_176, scRNA-seq


title: HCT116_ChIPseq_Dyskerin_control_rep2

tag: cell line

value: Human colorectal carcinoma

value: Vehicle

value: dyskerin (Abnova, H00001736-m04)


title: P12_40d_Xbp1-KO_175, scRNA-seq


title: P9_75, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: Normal Adjacent Tissue 2 (N2)

value: clear-cell renal cell carcinoma

value: Kidney

value: Normal Adjacent Tissue

value: Naive


title: P9_78, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: 4aKO.4gKO.mTEChi.Thy#3

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: mTEChi

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Assembly: mm10
Supplementary files format and content: raw read counts

source_name: Thymus

extract_protocol:
1000 cells were cytofluorometrically sorted into 5ul TCL buffer (Qiagen) with 1% 2-mercaptoethanol (Sigma). Cells were double-sorted when cell numbers permitted. Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter).
Total RNA was captured and purified on RNAClean XP beads (Beckman Coulter). Polyadenylated mRNA was then selected using an anchored oligo(dT) primer (5′–AAGCAGTGGTATCAACGCAGAGTACT30VN-3) and converted to cDNA via reverse transcription. First-strand cDNA was subjected to limited PCR amplification followed by Tn5 transposon-based fragmentation using the Nextera XT DNA Library Preparation Kit (Illumina). Samples were then PCR amplified for 18 cycles using barcoded primers such that each sample carried a specific combination of eight-base Illumina P5 and P7 barcodes and were pooled together prior to Smart sequencing. Smart-seq paired-end sequencing was performed on an Illumina NextSeq500 using 2 x 38bp reads with no further trimming.

treatment_protocol: mTEC subsets were prepared by digesting thymi with collagenase and dispase, magnetically depleting CD45+ cells, staining with fluorescent antibodies and flow sorting subsets of interest into 5ul TCL buffer plus 1% 2-mercaptoethanol.

value: mTEChi


title: 4aKO.4gKO.mTEChi.Thy#2

description: mTEChi


title: P9_74, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: 4aKO.4gKO.mTEChi.Thy#4

description: mTEChi


title: P12_40d_Xbp1-KO_173, scRNA-seq


title: Megakaryocytes dexamethasone, biological rep 6

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
21910_1247_6_hr_DEX_8_Rep_6
Gene expression from in vitro differentiated megakaryocytes treated 6hr with 100nM dexamethasone.

hyb_protocol: Five micrograms (5 μg) of amplified biotin-cDNAs were fragmented and hybridized to each array for 18 hours at 45°C in a rotating hybridization oven. Array slides were stained with streptavidin/phycoerythrin utilizing a double-antibody staining procedure and then washed for antibody amplification per the GeneChip Hybridization, Wash and Stain Kit and user manual following protocol FS450-0004.

scan_protocol: Arrays were scanned in an Affymetrix Scanner 3000.

data_processing: Data was obtained using TAC Software, Version 4.0.

source_name: In vitro differentiated megakaryocytes treated 6hr with 100nM dexamethasone

label_protocol: Fifty nanograms (50 ng) of total RNA was amplified as directed in the Nugen WT-Ovation Pico RNA Amplification System protocol and labeling with biotin following the Nugen Encore Biotin Module protocol.

growth_protocol: Megakaryocytes were differentiated from hematopoietic stem cells by culturing the progenitors for 3 days at 37⁰C 5%CO2 with 100 ng/ml thrombopoiestin. Then, cells were washed, resuspended and cultured overnight in fresh complete DMEM supplemented with 10% charcoal stripped heat-inactivated fetal bovine serum. Day 4-megakaryocytes were purified on a 0/1.5/3% bovine serum albumin glucocorticoid gradient.

extract_protocol: Total RNA was isolated using the RNeasy mini kit and DNase digested using the RNase-Free DNase I Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol.

treatment_protocol: Megakaryocytes from the same culture were split in two treatments for 6 hr: 100nM dexamethasone or its vehicle.

tag: originating cell type

value: Bone marrow hematopoietic stem cells

value: in vitro differentiated megakaryocytes

tag: gender

value: male

value: dexamethasone


title: Megakaryocytes dexamethasone, biological rep 5

description:
21909_1247_6_hr_DEX_7_Rep_5
Gene expression from in vitro differentiated megakaryocytes treated 6hr with 100nM dexamethasone.


title: Megakaryocytes dexamethasone, biological rep 3

description:
21907_1247_6_hr_DEX_5_Rep_3
Gene expression from in vitro differentiated megakaryocytes treated 6hr with 100nM dexamethasone.


title: P12_40d_Xbp1-KO_172, scRNA-seq

value: liver

value: hepatocyte


title: Megakaryocytes dexamethasone, biological rep 2

description:
21906_1247_6_hr_DEX_4_Rep_2
Gene expression from in vitro differentiated megakaryocytes treated 6hr with 100nM dexamethasone.


title: 4aHet.4gHet.mTEChi.Thy#4

description: mTEChi


title: P9_72, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

value: Alb-Cre; Rosa-tdTomato


title: Megakaryocytes dexamethasone, biological rep 4

description:
21908_1247_6_hr_DEX_6_Rep_4
Gene expression from in vitro differentiated megakaryocytes treated 6hr with 100nM dexamethasone.


title: Megakaryocytes dexamethasone, biological rep 1

description:
21904_1247_6_hr_DEX_1_Rep_1
Gene expression from in vitro differentiated megakaryocytes treated 6hr with 100nM dexamethasone.


title: Megakaryocytes vehicle, biological rep 6

description:
21896_1247_Vehicle_8_Rep_6
Gene expression from in vitro differentiated megakaryocytes treated 6hr with the vehicle for dexamethasone.

source_name: In vitro differentiated megakaryocytes treated 6hr with the vehicle for dexamethasone

value: vehicle


title: P60_14d_Nr2f2-KO_5, scRNA-seq


title: P9_76, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_174, scRNA-seq


title: 4aKO.4gKO.mTEChi.Thy#1

description: mTEChi


title: P12_40d_Xbp1-KO_170, scRNA-seq


title: 4aHet.4gHet.mTEChi.Thy#1

description: mTEChi


title: P9_73, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: 4aHet.4gHet.mTEChi.Thy#3

description: mTEChi


title: 4aHet.4gHet.mTEChi.Thy#2

description: mTEChi


title: P9_70, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_69, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_168, scRNA-seq


title: Megakaryocytes vehicle, biological rep 4

description:
21894_1247_Vehicle_6_Rep_4
Gene expression from in vitro differentiated megakaryocytes treated 6hr with the vehicle for dexamethasone.


title: Megakaryocytes vehicle, biological rep 2

description:
21892_1247_Vehicle_4_Rep_2
Gene expression from in vitro differentiated megakaryocytes treated 6hr with the vehicle for dexamethasone.


title: C.elegans, Vehicle-treated, batch3 [DMSO-21_S10]

city: Clayton

first: Stuart

middle: Kenneth

last: Archer

state: VIC

address: 15 Innovation Walk, Monash University

department: Monash Bioinformatics Platform

country: Australia

institute: Monash University

data_processing:
Fastq files generated by bcl2fastq with adapter trimming
Mapped R1 to WBcel235 as single-end using STAR v2.5.2b
Assign uniquely-mapping reads to transcript exons and splice-junctions using Featurecounts v1.5.2
Assembly: WBcel235
Supplementary files format and content: UrsolateExpCounts.tsv: Matrix of read counts per-gene (rows) and per sample (columns); tab-separated

organism: Caenorhabditis elegans

source_name: Whole animal

growth_protocol: N2 gravid hermaphrodites were bleached with hypochlorite solution and eggs hatched overnight in M9 buffer. Resultant synchronized L1 larvae were fed with OP50 and incubated for 34 h until they reached the L3 stage.

extract_protocol:
After treatment, worms (now L4 larvae) were harvested and washed with M9 buffer three times to remove bacteria, before being resuspended in Trizol and flash frozen in liquid nitrogen. Total RNA was extracted by phase separation with chloroform, followed by the RNeasy Mini Kit (Qiagen) protocol. RNAse-free DNase was applied to RNA samples to remove DNA contamination.
RNA was poly-A selected using oligo dT magnetic beads, fragmented and library prepared using TruSeq stranded kit (Illumina)

treatment_protocol: L3 larvae were washed from the plates with M9 buffer and exposed to UA (50 µM), DMSO (vehicle) or no treatment for 12 h.

value: Whole animal

value: DMSO


title: P9_68, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_67, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_167, scRNA-seq


title: P12_40d_Xbp1-KO_171, scRNA-seq


title: C.elegans, Vehicle-treated, batch1 [DMSO-06_S19]


title: KPC689 vehicle in vitro

city: Houston

first: Kalluri

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Pancreata were digested with 4 mg/mL collagenase IV and dispase at 37C for 30 minutes. Cells were filtered once with a 70 um filter and once more with a 40 um filter. To stop the digestion, 25 mL of DMEM containing 10% FBS was added. Cells were then centrifuged at 500 g for 5 minutes, and the supernatant was removed, washed with 10 mL of FACS buffer (2% FBS in PBS), and centrifuged at 500 g for 5 minutes at 4°C. Cells were resuspended in 1 mL of FACS buffer and stained with 1 uL of Fixable Viability Dye eFluor™ 780 (eBioscience, dilution of 1:1,000) on ice for 10 minutes. Cells were washed with 3.5 mL of FACS buffer, centrifuged at 300 g for 5 minutes at 4°C, washed again, and resuspended in 1 mL of FACS buffer. For in vitro samples, cells were trypsinized, washed with PBS and prepared with  Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1. Live cells were sorted and samples prepared with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1.
Constructed according to Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol

value: Vehicle (DMSO)


title: KPC689 MRTX1133 in vitro


title: P9_66, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: Megakaryocytes vehicle, biological rep 5

description:
21895_1247_Vehicle_7_Rep_5
Gene expression from in vitro differentiated megakaryocytes treated 6hr with the vehicle for dexamethasone.


title: P12_40d_Xbp1-KO_165, scRNA-seq


title: P12_40d_Xbp1-KO_166, scRNA-seq


title: KPC689 untreated in vitro

value: Untreated


title: C.elegans, Vehicle-treated, batch5 [DMSO-26_S16]


title: C.elegans, Vehicle-treated, batch2 [DMSO-14_S7]


title: KPPC MRTX1133

source_name: Pancreas

value: Pancreas

value: Mixed

value: Pdx1-Cre; LSL-KrasG12D/+; LSL-Trp53F/F


title: C.elegans, untreated, batch1 [Ori-06_S18]


title: P12_40d_Xbp1-KO_164, scRNA-seq


title: P9_65, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_163, scRNA-seq


title: P9_64, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: KPPC Vehicle MRTX1133


title: C.elegans, untreated, batch3 [Ori-21_S9]


title: P12_40d_Xbp1-KO_169, scRNA-seq


title: C57BL6J Healthy


title: C.elegans, untreated, batch4 [Ori-24_S12]


title: P9_62, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: C.elegans, untreated, batch5 [Ori-26_S15]


title: C57BL6J KPC689 MRTX849

value: MRTX849 (30 mg/kg)


title: P9_63, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_71, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_162, scRNA-seq


title: P12_40d_Xbp1-KO_161, scRNA-seq


title: C.elegans, untreated, batch2 [Ori-14_S6]


title: C.elegans, UA-treated, batch1 [UA-06_S20]

value: ursolic acid (UA)


title: Megakaryocytes vehicle, biological rep 3

description:
21893_1247_Vehicle_5_Rep_3
Gene expression from in vitro differentiated megakaryocytes treated 6hr with the vehicle for dexamethasone.

value: Bone marrow hematopoietic stem cells


title: P9_60, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_159, scRNA-seq


title: C57BL6J KPC689 MRTX1133


title: P12_40d_Xbp1-KO_158, scRNA-seq


title: C57BL6J KPC689 Vehicle MRTX1133


title: C.elegans, UA-treated, batch3 [UA-21_S11]


title: P9_58, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_157, scRNA-seq


title: P12_40d_Xbp1-KO_160, scRNA-seq


title: C.elegans, UA-treated, batch4 [UA-24_S14]


title: P12_40d_Xbp1-KO_156, scRNA-seq


title: P9_57, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: C.elegans, UA-treated, batch5 [UA-26_S17]


title: NSG KPC689 MRTX849

value: NSG


title: P9_55, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: NSG KPC689 MRTX1133


title: P12_40d_Xbp1-KO_155, scRNA-seq


title: P9_56, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: NSG KPC689 Vehicle MRTX849


title: P9_54, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P9_59, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: P12_40d_Xbp1-KO_154, scRNA-seq


title: P12_40d_Xbp1-KO_153, scRNA-seq


title: P9_53, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv


title: NSG KPC689 Vehicle MRTX1133


title: P12_40d_Xbp1-KO_152, scRNA-seq


title: NSG Healthy


title: Whole blood, healthy control, rep 72

city: Darlington

first: Tracy

last: Chew

state: NSW

address: Merewether Building (H04) City Rd & Butlin Ave

department: Sydney Informatics Hub

institute: University of Sydney

data_processing:
RNASeq-DE workflow (v1.0.0), available online at  https://github.com/Sydney-Informatics-Hub/RNASeq-DE
3’ adapter and polyA tails were trimmed from raw sequence reads with BBDuk (v37.89)
Quality checked, trimmed reads were aligned as pairs to the human reference genome, GRCh38 primary assembly and gene set release 106 (obtained from Ensembl) with STAR, setting –sjdbOverhand to 149
Sequencing batch level binary alignment (BAM) files were merged and indexed with SAMtools (v1.10) to obtain sample level BAMs.
HTSeq-count (v0.12.4) with -s reverse was used to obtain feature level raw counts.
Assembly: GRCh38
Supplementary files format and content: HTSeq-count output, containing raw counts per sample

source_name: Whole blood

extract_protocol:
Total RNA was isolated from whole blood samples stored and stabilized in PAXgene RNA tubes according to the manufacturer's guidelines (PreAnalytiX)
Libraries were prepared with 300ng of total RNA per sample using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus (RZP) as per manufacturer instructions (Illumina, CA, USA).

value: Whole blood

value: control


title: Whole blood, COVID positive, rep 395

value: COVID positive


title: Whole blood, COVID positive, rep 393


title: P9_52, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

value: liver

value: hepatocyte


title: P12_40d_Xbp1-KO_151, scRNA-seq


title: Whole blood, COVID positive, rep 392


title: P12_40d_Xbp1-KO_150, scRNA-seq


title: P9_50, scRNA-seq

description:
mSTRT-seq
readcount.mSTRT-seq.csv

value: Alb-Cre; Rosa-tdTomato


title: Whole blood, COVID positive, rep 394


title: Whole blood, COVID positive, rep 391


title: P12_40d_Xbp1-KO_149, scRNA-seq