title: TLu-511C, control, replicate 3

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with GRCm38 as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: mm10
Supplementary files format and content: Counts

source_name: primary

extract_protocol:
Immunoprecipitation was performed according to Sanz et al, PNAS 2009. RNA was harvested using RNeasy Micro Plus kit (Qiagen)
RNA libraries for RNA-seq were prepared using SMART-Seq v4 RNA Ultra Low Input (Takara) + Nextera XT (Illumina) following manufacturer's protocols.

treatment_protocol:
Mice were injected with tamoxifen (Aldh1l1-CreERT2 samples, 100mg/kg in corn oil, i.p., daily for 5 days) or virus. Cortical brain tissue was harvested 2 weeks after the last tamoxifen injection.
Virus injections: systemic virus was delivered retroorbitally, 1x10^12 vg/mouse in saline. Intracortical virus was delivered via pulled glass micropipette; 500nl of 1x10^12vg/ml in saline at each of two sites (A/P 0.0mm, M/L 2.0mm, D/V:-0.75mm; A/P -1.2mm, M/L 2.0mm, D/V:-0.65mm)

value: primary

value: oligodendrocyte precursor cells

value: WT

tag: developmental stage

value: no treatment

tag: time

value: 1 hour


title: TLu-511P, PE treatment, replicate 3

status: Public on Jun 26 2023

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell line

tag: cell type

tag: strain

tag: genotype

tag: treatment

value: 20 uM of PE


title: P9_49, scRNA-seq

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

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)

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

value: hepatocyte

value: Alb-Cre; Rosa-tdTomato

tag: age

tag: ploidy

tag: zonation


title: P12_40d_Xbp1-KO_148, scRNA-seq

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


title: TLu-66P, PE treatment replicate 4


title: TLu-49P, PE treatment, replicate 2


title: Whole blood, COVID positive, rep 389

city: Darlington

first: Tracy

last: Chew

state: NSW

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

department: Sydney Informatics Hub

country: Australia

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

organism: Homo sapiens

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: COVID positive


title: P9_48, scRNA-seq

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


title: P12_40d_Xbp1-KO_147, scRNA-seq


title: TLu-49C, control, replicate 2


title: Whole blood, COVID positive, rep 388


title: P9_47, scRNA-seq

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


title: TLu-47C, control, replicate 1


title: TLu-66C, control, replicate 4


title: P12_40d_Xbp1-KO_146, scRNA-seq


title: Whole blood, COVID positive, rep 387


title: P9_51, scRNA-seq

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


title: P9_46, scRNA-seq

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


title: Whole blood, COVID positive, rep 390


title: P12_40d_Xbp1-KO_145, scRNA-seq


title: P12_40d_Xbp1-KO_144, scRNA-seq


title: P9_44, scRNA-seq

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


title: P12_40d_Xbp1-KO_143, scRNA-seq


title: Whole blood, COVID positive, rep 384


title: P9_43, scRNA-seq

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


title: Whole blood, COVID positive, rep 385


title: Whole blood, COVID positive, rep 383


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

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

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: Post-Aire mTEClo

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: Thymus

value: mTEClo


title: Whole blood, COVID positive, rep 386


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


title: C57BL6J KPC689 Vehicle MRTX849

city: Houston

first: Kalluri

state: Texas

address: 1901 East Rd

institute: UT MD Anderson Cancer Center

library_source: transcriptomic single cell

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

source_name: Pancreas

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: Pancreas


title: P12_40d_Xbp1-KO_141, scRNA-seq


title: 4aKO.4gHet.mTEClo.Thy#3


title: P12_40d_Xbp1-KO_142, scRNA-seq


title: Whole blood, COVID positive, rep 382


title: P9_41, scRNA-seq

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


title: P12_40d_Xbp1-KO_140, scRNA-seq


title: 4aKO.4gHet.mTEClo.Thy#2


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


title: P12_40d_Xbp1-KO_139, scRNA-seq


title: 4aKO.4gHet.mTEClo.Thy#1


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


title: Whole blood, COVID positive, rep 380


title: P9_61, scRNA-seq

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


title: P9_42, scRNA-seq

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


title: 4aHet.4gKO.mTEClo.Thy#3


title: P9_38, scRNA-seq

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


title: 4aHet.4gKO.mTEClo.Thy#2


title: Whole blood, COVID positive, rep 378


title: P9_37, scRNA-seq

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


title: P9_36, scRNA-seq

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


title: 4aHet.4gKO.mTEClo.Thy#1


title: Whole blood, COVID positive, rep 379


title: Whole blood, COVID positive, rep 376


title: Whole blood, COVID positive, rep 381


title: Whole blood, COVID positive, rep 377


title: P9_35, scRNA-seq

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


title: P9_45, scRNA-seq

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


title: P12_40d_Xbp1-KO_137, scRNA-seq


title: P12_40d_Xbp1-KO_135, scRNA-seq


title: P12_40d_Xbp1-KO_136, scRNA-seq


title: P12_40d_Xbp1-KO_134, scRNA-seq


title: Whole blood, COVID positive, rep 375


title: P9_34, scRNA-seq

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


title: P12_40d_Xbp1-KO_133, scRNA-seq


title: Whole blood, COVID positive, rep 374


title: P9_33, scRNA-seq

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


title: P12_40d_Xbp1-KO_132, scRNA-seq


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


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


title: C.elegans, Vehicle-treated, batch4 [DMSO-24_S13]

city: Clayton

first: Stuart

middle: Kenneth

last: Archer

state: VIC

address: 15 Innovation Walk, Monash University

department: Monash Bioinformatics Platform

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: 4aHet.4gHet.mTEClo.Thy#2


title: Whole blood, COVID positive, rep 373


title: P12_40d_Xbp1-KO_131, scRNA-seq


title: P9_32, scRNA-seq

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


title: NonEnteroHepato.mTEC.Thy#3

source_name: Non-entero-hepato mTEC

value: mTEC


title: P9_31, scRNA-seq

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


title: KPC689 MRTX849 in vitro


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


title: Whole blood, COVID positive, rep 372


title: NonEnteroHepato.mTEC.Thy#2


title: P9_30, scRNA-seq

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


title: Whole blood, COVID positive, rep 370


title: NonEnteroHepato.mTEC.Thy#1


title: P12_40d_Xbp1-KO_129, scRNA-seq


title: P12_40d_Xbp1-KO_130, scRNA-seq


title: P9_29, scRNA-seq

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


title: P12_40d_Xbp1-KO_128, scRNA-seq


title: EnteroHepato.mTEC.Thy#3

source_name: Entero-hepato mTEC


title: Whole blood, COVID positive, rep 369


title: C.elegans, UA-treated, batch2 [UA-14_S8]

value: ursolic acid (UA)


title: P12_40d_Xbp1-KO_127, scRNA-seq


title: P9_28, scRNA-seq

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


title: Megakaryocytes vehicle, biological rep 1

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description:
21890_1247_Vehicle_1_Rep_1
Gene expression from in vitro differentiated megakaryocytes treated 6hr with the vehicle for 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.

label: biotin

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


title: EnteroHepato.mTEC.Thy#2

value: WT


title: P9_27, scRNA-seq

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

value: liver


title: Whole blood, COVID positive, rep 368


title: Whole blood, COVID positive, rep 371


title: EnteroHepato.mTEC.Thy#1


title: Whole blood, COVID positive, rep 367


title: P9_26, scRNA-seq

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

value: hepatocyte


title: P12_40d_Xbp1-KO_125, scRNA-seq


title: P12_40d_Xbp1-KO_126, scRNA-seq


title: P9_25, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato


title: Control, scRNAseq

city: Belfast

first: Aditi

last: Singh

state: Please Select State

address: 97 Lisburn Road, Belfast

department: The Wellcome-Wolfson Institute for Experimental Medicine, SMDBS

country: United Kingdom

institute: Queen's University Belfast

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The generated cell-by-gene unique molecular identifier (UMI) count matrix was analysed using the Seurat R package v.4.2.0. Only cells expressing at least 250 genes, 500 transcripts and genes with expression in at least 3 cells were kept. The cells were also filtered by the maximum of 20% mitochondrial genes. The UMI counts were then normalized for each cell by the total expression, multiplied by 10,000 and log transformed. Seurat’s default method to identify highly variable genes and scale data for regressing out variation from UMI and mitochondrial genes was used. The scaled data with variable genes were used to perform principal component analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cortex

extract_protocol:
Briefly, cortex samples were digested in papain (20 units/ml) for 45 minutes at 37 °C. After stopping the dissociation with ovomucoid, the cells were resuspended in PBS with 0.04% BSA. Cells were counted and viability was checked using Trypan Blue.
scRNA-seq libraries were generated using the 10x Genomics Chromium Single Cell 3′ Reagent Kit v3 according to the manufacturer’s protocol and sequenced on an Illumina NovaSeq6000 S2 200 flow cell at the Genomics Core Technology Unit (GCTU), Queen’s University Belfast.

value: Cortical cells

value: Cortex

tag: disease state

value: control

value: 16 weeks old


title: P12_40d_Xbp1-KO_124, scRNA-seq


title: Whole blood, COVID positive, rep 366

value: Whole blood

value: COVID positive


title: Diabetic, scRNAseq

description: 10x Genomics

value: diabetic


title: E14_PDS_G4

city: Philadelphia

first: Phillip

last: Wulfridge

state: Pennsylvania

address: 3601 Spruce St

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: CUT&RUN

tag: antibody

value: Pyridostatin


title: Whole blood, COVID positive, rep 365


title: P12_40d_Xbp1-KO_123, scRNA-seq


title: P9_23, scRNA-seq

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


title: P12_40d_Xbp1-KO_122, scRNA-seq


title: Whole blood, COVID positive, rep 363


title: E14_Mock_G4

value: Untreated


title: P9_22, scRNA-seq

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


title: P12_40d_Xbp1-KO_121, scRNA-seq


title: Whole blood, COVID positive, rep 361


title: Whole blood, COVID positive, rep 362


title: P9_21, scRNA-seq

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


title: P9_20, scRNA-seq

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


title: 6792

city: Indianapolis

first: Steven

last: Rhodes

state: IN

address: 1044 W. Walnut St.; Bldg R4, Rm 325

institute: Indiana University

data_processing:
FastQC-passed reads were aligned to the mouse reference genome (mm10) using STAR 2.4.2a and reads were translated to transcriptome coordinates using Salmon 0.60.
Isoform data were collated to single gene IDs using the R package biomaRt, and abundance estimates were upper quartile normalized using R.
Gene values were filtered to include only those with 10 or more reads in at least one sample and values (x + 1) were log2 transformed and used for unsupervised hierarchical clustering (complete linkage) in Morpheus.
DESeq2 was used for differential expression analysis using raw counts.
Assembly: mm10
Supplementary files format and content: Processed file (Nf1_WT_rawcounts.txt) contains raw transcript abundance estimates, organized by gene ID.

molecule: polyA RNA

source_name: Nf1 flox/flox PostnCre+ trigeminal nerve

extract_protocol:
Total RNA was isolated using Qiagen RNeasy Plus Mini kit.
800ng total RNA and 10 cycles of amplification were used for libraries constructed with KAPA Stranded mRNAseq kit.
library preparation kit:  Illumina TruSeq RNA library kit v2

tag: tumor stage

value: plexiform neurofibroma

value: trigeminal nerve

value: Nf1 flox/flox PostnCre+


title: P12_40d_Xbp1-KO_120, scRNA-seq

value: liver


title: P12_40d_Xbp1-KO_119, scRNA-seq

value: hepatocyte


title: P9_24, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato


title: 6436


title: P12_40d_Xbp1-KO_118, scRNA-seq


title: P9_19, scRNA-seq

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


title: 6891


title: Whole blood, COVID positive, rep 364


title: 6264


title: P12_40d_Xbp1-KO_117, scRNA-seq


title: 6491


title: P12_40d_Xbp1-KO_116, scRNA-seq


title: Whole blood, COVID positive, rep 359


title: P9_18, scRNA-seq

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


title: P9_17, scRNA-seq

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


title: Whole blood, COVID positive, rep 358


title: Whole blood, COVID positive, rep 360


title: 6441


title: P9_16, scRNA-seq

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


title: P12_40d_Xbp1-KO_115, scRNA-seq


title: Whole blood, COVID positive, rep 357


title: 6721

source_name: Nf1 flox/flox PostnCre- trigeminal nerve

value: normal nerve

value: Nf1 flox/flox PostnCre-


title: P12_40d_Xbp1-KO_114, scRNA-seq


title: 6616


title: Whole blood, COVID positive, rep 356


title: P9_15, scRNA-seq

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


title: P9_14, scRNA-seq

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


title: P12_40d_Xbp1-KO_113, scRNA-seq


title: Whole blood, COVID positive, rep 355


title: P12_40d_Xbp1-KO_112, scRNA-seq


title: 6385


title: P9_13, scRNA-seq

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


title: P9_10, scRNA-seq

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


title: 6428


title: P12_40d_Xbp1-KO_109, scRNA-seq


title: P12_40d_Xbp1-KO_111, scRNA-seq


title: Whole blood, COVID positive, rep 352


title: 6172


title: Whole blood, COVID positive, rep 354


title: P9_12, scRNA-seq

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


title: Whole blood, COVID positive, rep 353


title: Whole blood, COVID positive, rep 351


title: P9_40, scRNA-seq

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


title: P9_11, scRNA-seq

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


title: Whole blood, COVID positive, rep 350


title: P12_40d_Xbp1-KO_108, scRNA-seq


title: E14_Praf2_GDel2_RNA-Seq_Rep2

value: Praf2 G4 Deletion

value: RNA-Seq


title: Whole blood, COVID positive, rep 349

value: Whole blood


title: E14_Praf2_GDel2_RNA-Seq_Rep1


title: P9_8, scRNA-seq

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


title: P12_40d_Xbp1-KO_107, scRNA-seq


title: Whole blood, COVID positive, rep 348

value: COVID positive


title: 6375


title: E14_Praf2_GDel1_RNA-Seq_Rep2


title: P12_40d_Xbp1-KO_106, scRNA-seq


title: E14_Praf2_GDel1_RNA-Seq_Rep1


title: Whole blood, COVID positive, rep 347


title: P9_7, scRNA-seq

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


title: P9_6, scRNA-seq

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


title: P9_5, scRNA-seq

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


title: E14_Praf2_WT_RNA-Seq_Rep3


title: Whole blood, COVID positive, rep 346


title: Whole blood, COVID positive, rep 345


title: E14_Praf2_WT_RNA-Seq_Rep2


title: P12_40d_Xbp1-KO_103, scRNA-seq


title: P12_40d_Xbp1-KO_105, scRNA-seq


title: P9_9, scRNA-seq

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


title: Whole blood, COVID positive, rep 344


title: P9_4, scRNA-seq

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


title: P9_3, scRNA-seq

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


title: E14_Praf2_WT_RNA-Seq_Rep1


title: E14_Praf2_GDel2_MapR

value: MapR

tag: fusion protein

value: GST-RH-delta-Mnase


title: P12_40d_Xbp1-KO_102, scRNA-seq


title: P9_2, scRNA-seq

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


title: Whole blood, COVID positive, rep 343


title: E14_Praf2_GDel1_MapR


title: P12_40d_Xbp1-KO_101, scRNA-seq


title: P12_40d_Xbp1-KO_110, scRNA-seq


title: Whole blood, COVID positive, rep 342


title: P12_40d_Xbp1-KO_100, scRNA-seq


title: P9_1, scRNA-seq

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


title: E14_Praf2_WT_MapR

value: Wildtype


title: P12_40d_Xbp1-KO_138, scRNA-seq


title: P6_131, scRNA-seq

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


title: P9_39, scRNA-seq

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


title: P12_40d_Xbp1-KO_99, scRNA-seq


title: P6_130, scRNA-seq

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


title: P12_40d_Xbp1-KO_98, scRNA-seq


title: Whole blood, COVID positive, rep 341


title: Whole blood, COVID positive, rep 339


title: P12_40d_Xbp1-KO_97, scRNA-seq


title: Whole blood, COVID positive, rep 340


title: P6_129, scRNA-seq

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


title: E14_Praf2_GDel1_CTCF

value: CUT&RUN

value: CTCF


title: Whole blood, COVID positive, rep 338


title: P12_40d_Xbp1-KO_96, scRNA-seq


title: P6_128, scRNA-seq

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


title: E14_Praf2_WT_CTCF

value: Untreated


title: EN5291_PlusIAA_MapR_GST-MNase_Rep2

value: GST-MNase

value: Auxin


title: Whole blood, COVID positive, rep 337


title: P6_127, scRNA-seq

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

value: liver


title: P12_40d_Xbp1-KO_95, scRNA-seq

value: hepatocyte


title: P6_126, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato


title: Whole blood, COVID positive, rep 336


title: P12_40d_Xbp1-KO_94, scRNA-seq


title: EN5291_PlusIAA_MapR_GST-MNase_Rep1


title: Whole blood, COVID positive, rep 335


title: P6_125, scRNA-seq

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


title: P12_40d_Xbp1-KO_93, scRNA-seq


title: P6_124, scRNA-seq

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


title: Whole blood, COVID positive, rep 334


title: EN5291_MinusIAA_MapR_GST-MNase_Rep1


title: E14_Praf2_GDel2_CTCF


title: P12_40d_Xbp1-KO_92, scRNA-seq


title: P6_123, scRNA-seq

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


title: Whole blood, COVID positive, rep 332


title: Whole blood, COVID positive, rep 333


title: P12_40d_Xbp1-KO_90, scRNA-seq


title: P12_40d_Xbp1-KO_91, scRNA-seq


title: Whole blood, COVID positive, rep 331


title: EN5291_MinusIAA_MapR_Rep2


title: EN5291_PlusIAA_MapR_Rep1


title: P12_40d_Xbp1-KO_89, scRNA-seq


title: P6_121, scRNA-seq

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


title: EN5291_MinusIAA_MapR_Rep1


title: P6_120, scRNA-seq

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


title: Whole blood, COVID positive, rep 330


title: P12_40d_Xbp1-KO_88, scRNA-seq


title: EN5291_MinusIAA_MapR_GST-MNase_Rep2


title: EN5291_PlusIAA_ADNP

value: ADNP


title: P6_119, scRNA-seq

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


title: Whole blood, COVID positive, rep 329


title: Whole blood, COVID positive, rep 328


title: EN5291_MinusIAA_ADNP


title: P12_40d_Xbp1-KO_104, scRNA-seq


title: P6_118, scRNA-seq

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


title: EN5291_PlusIAA_CTCF


title: P6_122, scRNA-seq

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


title: EN5291_PlusIAA_MapR_Rep2


title: P12_40d_Xbp1-KO_86, scRNA-seq


title: Whole blood, COVID positive, rep 327


title: P6_117, scRNA-seq

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


title: EN5291_MinusIAA_CTCF


title: P6_116, scRNA-seq

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


title: Whole blood, COVID positive, rep 325


title: Whole blood, COVID positive, rep 326


title: E14_PlusRNaseH_EZH2_Rep2

value: RNase H


title: P12_40d_Xbp1-KO_84, scRNA-seq


title: P12_40d_Xbp1-KO_83, scRNA-seq


title: E14_PlusRNaseH_EZH2_Rep1


title: P12_40d_Xbp1-KO_87, scRNA-seq


title: P6_115, scRNA-seq

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


title: Whole blood, COVID positive, rep 323


title: Whole blood, COVID positive, rep 324


title: P12_40d_Xbp1-KO_81, scRNA-seq


title: P6_113, scRNA-seq

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


title: E14_MinusRNaseH_EZH2_Rep1


title: P6_114, scRNA-seq

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


title: P12_40d_Xbp1-KO_80, scRNA-seq


title: E14_PlusRNaseH_MapR_GST-MNase_Rep2


title: P12_40d_Xbp1-KO_79, scRNA-seq


title: Whole blood, COVID positive, rep 321


title: Whole blood, COVID positive, rep 322


title: P6_111, scRNA-seq

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


title: P6_112, scRNA-seq

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


title: P12_40d_Xbp1-KO_78, scRNA-seq


title: P12_40d_Xbp1-KO_85, scRNA-seq


title: P6_110, scRNA-seq

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


title: Whole blood, COVID positive, rep 320


title: Whole blood, COVID positive, rep 319


title: P12_40d_Xbp1-KO_77, scRNA-seq


title: E14_MinusRNaseH_MapR_GST-MNase_Rep2


title: E14_PlusRNaseH_MapR_GST-MNase_Rep1


title: P12_40d_Xbp1-KO_82, scRNA-seq


title: P12_40d_Xbp1-KO_76, scRNA-seq


title: P6_108, scRNA-seq

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


title: E14_MinusRNaseH_EZH2_Rep2


title: E14_PlusRNaseH_MapR_Rep2


title: P6_107, scRNA-seq

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


title: P12_40d_Xbp1-KO_75, scRNA-seq


title: E14_PlusRNaseH_MapR_Rep1


title: P6_106, scRNA-seq

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


title: Whole blood, COVID positive, rep 316


title: P12_40d_Xbp1-KO_74, scRNA-seq


title: E14_MinusRNaseH_MapR_Rep2


title: P12_40d_Xbp1-KO_73, scRNA-seq


title: P6_105, scRNA-seq

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


title: E14_MinusRNaseH_MapR_Rep1


title: Whole blood, COVID positive, rep 314


title: P6_104, scRNA-seq

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


title: E14_PlusRNaseH_CTCF_Rep2


title: Whole blood, COVID positive, rep 313


title: P12_40d_Xbp1-KO_72, scRNA-seq


title: P6_103, scRNA-seq

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


title: E14_MinusRNaseH_MapR_GST-MNase_Rep1


title: P6_109, scRNA-seq

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


title: P6_102, scRNA-seq

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


title: Whole blood, COVID positive, rep 312


title: Whole blood, COVID positive, rep 318


title: P12_40d_Xbp1-KO_70, scRNA-seq


title: Whole blood, COVID positive, rep 317


title: E14_MinusRNaseH_CTCF_Rep2


title: P12_40d_Xbp1-KO_69, scRNA-seq


title: Whole blood, COVID positive, rep 311


title: P6_101, scRNA-seq

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


title: E14_MinusRNaseH_CTCF_Rep1


title: Whole blood, COVID positive, rep 310


title: Whole blood, COVID positive, rep 315


title: Whole blood, COVID positive, rep 309


title: E14_ADNPKO_CTCF_Rep2

value: ADNP Knockout


title: P12_40d_Xbp1-KO_68, scRNA-seq


title: P6_100, scRNA-seq

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


title: E14_PlusRNaseH_CTCF_Rep1


title: P12_40d_Xbp1-KO_71, scRNA-seq


title: Whole blood, COVID positive, rep 308


title: P6_98, scRNA-seq

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


title: P12_40d_Xbp1-KO_66, scRNA-seq


title: P6_97, scRNA-seq

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


title: E14_WT_MapR


title: E14_WT_MapR_GST-MNase


title: Whole blood, COVID positive, rep 306


title: P12_40d_Xbp1-KO_65, scRNA-seq


title: E14_ADNPKO_CTCF_Rep1


title: E14_WT_CTCF_Rep2


title: P6_96, scRNA-seq

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


title: Whole blood, COVID positive, rep 305


title: P6_95, scRNA-seq

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


title: P12_40d_Xbp1-KO_63, scRNA-seq


title: E14_WT_CTCF_Rep1


title: P6_94, scRNA-seq

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


title: Whole blood, COVID positive, rep 304


title: P6_99, scRNA-seq

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


title: Whole blood, COVID positive, rep 303


title: 8 h LPS, scATAC-seq

city: Kongens Lyngby

first: Xiao

last: Wang

address: Bagsværdvej 103, ST

country: Denmark

institute: Konge Larsen Aps

description:
transposase-accessible chromatin
10x Genomics

library_source: genomic single cell

data_processing:
Cell Ranger Single-Cell Software Suite (release 3.1.0) was used to process the raw data, demultiplex raw base-call files into FASTQ files by “mkfastq”, perform alignment, filtering, barcode counting, and unique molecular identifier (UMI) counting by “count”, and align raw reads to cattle reference genome (ARS-UCD1.2/bosTau9) by “pipeline.
Assembly: ARS-UCD1.2/bosTau9
Supplementary files format and content: Tab-separated values files and matrix files

organism: Bos taurus

extract_protocol:
On Hanks’ Balanced Salt Solution (Solarbio; Beijing, China), PBMCs were finally isolated from the whole-blood treated replicates by centrifugation at 500 g for 20 min at room temperature.
Following the user guide of Chromium Single Cell 3’ Reagent Kits v3 (CG000183), reverse transcriptase was mixed with the barcoded isolated cells into the Gel Beads-In-Emulsions (GEMs), where read 1 primer sequence (R1) was put into during its incubation. Via end repair, tailing, adaptor ligation, and PCR procedures, the sample index, P5, P7, and read 2 primer sequence (R2) were included in library construction to generate single-cell RNA sequencing (scRNA-seq) library. Following the user guide of Chromium Single Cell ATAC Reagent Kits v1.1 (CG000209), nuclei suspensions were incubated with transposase to preferentially fragment the DNA in open regions of the chromatin and adapter sequences were added to the ends of the DNA fragments instantaneously. The single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) library was constructed via PCR when nuclei were barcoded into the GEMs, where the sample index, P7, and R2 were added.

tag: breed

value: Holstein

value: 2 years

tag: Sex

value: female

value: peripheral blood mononuclear cells

value: 8 h LPS


title: P6_93, scRNA-seq

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

tag: cell type


title: P12_40d_Xbp1-KO_67, scRNA-seq


title: P12_40d_Xbp1-KO_61, scRNA-seq


title: 4 h LPS, scATAC-seq

value: Whole blood

value: 4 h LPS


title: Whole blood, COVID positive, rep 307

value: COVID positive


title: Whole blood, COVID positive, rep 302


title: P6_92, scRNA-seq

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


title: 2 h LPS, scATAC-seq

value: 2 h LPS


title: P6_91, scRNA-seq

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


title: P12_40d_Xbp1-KO_60, scRNA-seq


title: no LPS, scATAC-seq

value: no LPS


title: P12_40d_Xbp1-KO_59, scRNA-seq


title: P12_40d_Xbp1-KO_64, scRNA-seq


title: P12_40d_Xbp1-KO_58, scRNA-seq


title: Whole blood, COVID positive, rep 300


title: 8 h LPS, scRNA-seq

description: 10x Genomics


title: 4 h LPS, scRNA-seq

description: 10x Genomics


title: P6_90, scRNA-seq

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


title: P12_40d_Xbp1-KO_57, scRNA-seq


title: P12_40d_Xbp1-KO_62, scRNA-seq


title: 2 h LPS, scRNA-seq

description: 10x Genomics


title: P6_88, scRNA-seq

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


title: P6_89, scRNA-seq

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


title: Whole blood, COVID positive, rep 299


title: Whole blood, COVID positive, rep 298


title: P6_87, scRNA-seq

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


title: P12_40d_Xbp1-KO_56, scRNA-seq


title: P12_40d_Xbp1-KO_55, scRNA-seq


title: Whole blood, COVID positive, rep 297


title: no LPS, scRNA-seq

description: 10x Genomics


title: P6_86, scRNA-seq

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


title: Whole blood, COVID positive, rep 296


title: P12_40d_Xbp1-KO_54, scRNA-seq


title: Whole blood, COVID positive, rep 301


title: P12_40d_Xbp1-KO_52, scRNA-seq


title: P6_85, scRNA-seq

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


title: Whole blood, COVID positive, rep 294


title: P6_84, scRNA-seq

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


title: H3R17me2 40d w1118-2

first: Pengfei

last: Lv

address: No. 2, Old Summer Palace West Road

institute: China agricultural university

data_processing:
Trim-galore (v0.6.0) was used to trim CHIP-seq reads.
Bowtie2 (v2.5.1) was used to align reads to genome.
SAMtools (v1.19) was used for BAM file processing and merging of replicate BAM files.
PicardTools (v2.8) was used for PCR duplicates removal.
MACS2 (v2.2.7.1) was used for peaking calling.
Assembly: dm6
Supplementary files format and content: bigwig reads
Supplementary files format and content: bed broad peaks

organism: Drosophila melanogaster

source_name: head

growth_protocol: Mated males were collected and maintained at 20 flies per vial at 25˚C under 60% humidity and a 12 hr light/12 hr dark cycle. Flies were transferred to new vials every other day.

extract_protocol:
25 fly heads were lightly triturated in 450 µl 1×PBS, added 6.02 µl 37% formaldehyde for cross-linking before incubating at RT for 10 minutes. After de-crosslinking with 1×glutamate and washing the pellet three times with 1×PBS, added 250 µl SDS lysis buffer (containing protease inhibitor cocktail) and homogenize, centrifuged and the supernatant was taken. Chromatin was sonicated for 2.5 minutes on ice (settings 10s on, 30s off, high power). Sheared chromatin had an average length of 0.1-0.5 kb.
Add the adapter sequence to the end of the DNA fragment that is about to be sequenced.

value: head

value: 40 day

tag: ip target


title: H3R17me2 40d 23382-2

tag: genotype

value: LKRSDHMB01942 mutant


title: H3R17me2 40d w1118-1


title: H3R17me2 40d 23382-1


title: P12_40d_Xbp1-KO_51, scRNA-seq

value: liver

value: hepatocyte

tag: treatment


title: P6_83, scRNA-seq

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

tag: tissue

value: Alb-Cre; Rosa-tdTomato


title: P6_82, scRNA-seq

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

tag: age


title: Whole blood, COVID positive, rep 292


title: P12_40d_Xbp1-KO_50, scRNA-seq

tag: ploidy


title: P6_81, scRNA-seq

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

tag: zonation


title: H3R17me2 3d w1118-2

value: 3 day


title: Whole blood, COVID positive, rep 291


title: H3R17me2 3d w1118-1


title: P12_40d_Xbp1-KO_49, scRNA-seq


title: Whole blood, COVID positive, rep 290


title: Whole blood, COVID positive, rep 289


title: H3R17me2 3d 23382-2


title: P6_79, scRNA-seq

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


title: P12_40d_Xbp1-KO_47, scRNA-seq


title: P12_40d_Xbp1-KO_48, scRNA-seq


title: P6_80, scRNA-seq

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


title: H3R17me2 3d 23382-1


title: P12_40d_Xbp1-KO_53, scRNA-seq


title: Whole blood, COVID positive, rep 288


title: Whole blood, COVID positive, rep 295


title: P6_78, scRNA-seq

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


title: H3K27me3 40d w1118-2


title: P12_40d_Xbp1-KO_46, scRNA-seq


title: Whole blood, COVID positive, rep 293


title: Whole blood, COVID positive, rep 287


title: P6_77, scRNA-seq

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


title: P12_40d_Xbp1-KO_45, scRNA-seq


title: Whole blood, COVID positive, rep 285


title: H3K27me3 40d w1118-1


title: P6_76, scRNA-seq

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


title: P12_40d_Xbp1-KO_44, scRNA-seq


title: H3K27me3 40d 23382-2


title: Whole blood, COVID positive, rep 286


title: P6_75, scRNA-seq

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


title: P12_40d_Xbp1-KO_42, scRNA-seq


title: P6_74, scRNA-seq

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


title: P12_40d_Xbp1-KO_43, scRNA-seq


title: P6_73, scRNA-seq

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


title: H3K27me3 3d w1118-2


title: P12_40d_Xbp1-KO_41, scRNA-seq


title: Whole blood, COVID positive, rep 284


title: P12_40d_Xbp1-KO_40, scRNA-seq


title: H3K27me3 3d 23382-2


title: H3K27me3 3d w1118-1


title: P6_72, scRNA-seq

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


title: Whole blood, COVID positive, rep 281


title: P12_40d_Xbp1-KO_39, scRNA-seq


title: P6_71, scRNA-seq

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


title: H3K27me3 3d 23382-1


title: Whole blood, COVID positive, rep 280


title: P12_40d_Xbp1-KO_38, scRNA-seq


title: P6_70, scRNA-seq

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


title: input 40d w1118-2

value: input


title: H3K27me3 40d 23382-1


title: input 40d w1118-1


title: Whole blood, COVID positive, rep 279


title: P6_68, scRNA-seq

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


title: Whole blood, COVID positive, rep 283


title: P12_40d_Xbp1-KO_37, scRNA-seq


title: Whole blood, COVID positive, rep 278


title: Whole blood, COVID positive, rep 277


title: P12_40d_Xbp1-KO_36, scRNA-seq


title: P6_67, scRNA-seq

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


title: P12_40d_Xbp1-KO_35, scRNA-seq


title: Whole blood, COVID positive, rep 276


title: input 40d 23382-1


title: P6_66, scRNA-seq

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


title: P12_40d_Xbp1-KO_34, scRNA-seq


title: P6_69, scRNA-seq

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


title: Whole blood, COVID positive, rep 275


title: P6_65, scRNA-seq

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


title: input 40d 23382-2


title: input 3d w1118-1


title: P12_40d_Xbp1-KO_33, scRNA-seq


title: input 3d w1118-2


title: P12_40d_Xbp1-KO_32, scRNA-seq


title: Whole blood, COVID positive, rep 274


title: Whole blood, COVID positive, rep 273


title: P6_64, scRNA-seq

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


title: Whole blood, COVID positive, rep 282


title: P12_40d_Xbp1-KO_31, scRNA-seq


title: P6_63, scRNA-seq

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


title: input 3d 23382-2


title: input 3d 23382-1


title: P12_40d_Xbp1-KO_30, scRNA-seq


title: Whole blood, COVID positive, rep 272


title: P6_62, scRNA-seq

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


title: P6_61, scRNA-seq

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


title: P12_40d_Xbp1-KO_29, scRNA-seq


title: P6_60, scRNA-seq

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


title: P12_40d_Xbp1-KO_28, scRNA-seq


title: HiC-71_GAFdegrad_rep3

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

description: High complexity Hi-C library of stage 5 GFP-GAF-degrad embryos

data_processing:
Fastq files were processed using the nfCore Hi-C pipeline
Assembly: BDGP6
Supplementary files format and content: .cool files at 1000, 10000, 100000 bp resolution and .mcool file for each dataset

source_name: stage 5 embryo

extract_protocol:
Embryos were fixed in 5% formaldehyde with hexanes for 30 minutes and frozen, then dounced thoroughly, spun and washed repeatedly to clean nuclei.
TruSeq DNA
in situ Hi-C using MluCI (^AATT) enzyme

value: stage 5 embryo

value: GFP-GAF-degrad


title: P6_59, scRNA-seq

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


title: P12_40d_Xbp1-KO_27, scRNA-seq


title: HiC-69_GAFdegrad_rep2

description: Medium complexity Hi-C library of stage 5 GFP-GAF-degrad embryos


title: Whole blood, COVID positive, rep 269


title: HiC-72_GAFcontrol_rep3

description: High complexity Hi-C library of stage 5 GFP-GAF embryos

value: GFP-GAF


title: Whole blood, COVID positive, rep 268


title: P6_58, scRNA-seq

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


title: HiC-67_GAFdegrad_rep1

description: Low complexity Hi-C library of stage 5 GFP-GAF-degrad embryos


title: P12_40d_Xbp1-KO_26, scRNA-seq


title: P12_40d_Xbp1-KO_25, scRNA-seq


title: HiC-68_GAFcontrol_rep2

description: Medium complexity Hi-C library of stage 5 GFP-GAF embryos


title: P6_57, scRNA-seq

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


title: P6_56, scRNA-seq

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


title: HiC-66_GAFcontrol_rep1

description: Low complexity Hi-C library of stage 5 GFP-GAF embryos


title: P12_40d_Xbp1-KO_24, scRNA-seq


title: Whole blood, COVID positive, rep 266


title: Whole blood, COVID positive, rep 271


title: Whole blood, COVID positive, rep 265


title: P12_40d_Xbp1-KO_23, scRNA-seq


title: Whole blood, COVID positive, rep 270


title: Whole blood, COVID positive, rep 264


title: P6_55, scRNA-seq

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


title: Mef2G4, dSERT-TMKO v WT, day0, scRNAseq

first: Shivan

middle: Luca

last: Bonanno

address: Gonda Rm3335, 695 Charles E. Young Dr.

department: Psychiatry

institute: UCLA

description: 10x Genomics

data_processing:
Standard demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 and a modified GTF file
GEMs were further demulitplexed to genotype-of-origin using demuxlet and SNPs from reads and matching to DGRP reference (see VCF file)
scRNA-seq was further processed and analyzed using Seurat. Please see .RDS files for seurat objects used in publication
Assembly: dm6
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

growth_protocol: Flies were maintained on a standard cornmeal and molasses-based agar media with a 12:12 hour light/dark cycle at room temperature (22–25°C).

extract_protocol:
cells were collected from FACS into Schnieder's Media, and input immediately to a 10x chip for library construction
Library was performed according to the manufacter’s instructions (3'GEX, 10x Genomics).

treatment_protocol: flies were homozygous for either SERT mutant (dSERT16 or SERT-TMKO) or WT (dSERT4 or WT) , or WT flies were fed either CIT (SSRI) or VEH (ctrl)

value: Kenyon cells

value: brain


title: Mef2G4, dSERT-TMKO v WT and CIT v VEH, day4to6, scRNAseq

description: 10x Genomics


title: Mef2G4, dSERT4 v dSERT16, day0, scRNAseq

description: 10x Genomics


title: P6_53, scRNA-seq

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


title: Whole blood, COVID positive, rep 263

value: Whole blood


title: P6_54, scRNA-seq

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


title: P12_40d_Xbp1-KO_21, scRNA-seq


title: P12_40d_Xbp1-KO_22, scRNA-seq


title: Whole blood, COVID positive, rep 267

value: COVID positive


title: Whole blood, COVID positive, rep 262


title: P12_40d_Xbp1-KO_19, scRNA-seq


title: Whole blood, COVID positive, rep 261


title: 4-07_Sert16

data_processing:
fastqs were aligned to Drosophila dm6 genome using STAR aligner and a modified GTF to include intronic sequences from pre-mRNA
Assembly: dm6
Supplementary files format and content: tab-delimited files include raw gene counts for each sample

source_name: Kenyon cells, dSERT16_MUT, day0

extract_protocol:
cells were collected directly off FACS and lysed immediately in Buffer RLT, then RNA isolated using Rneasy kit (Qiagen)
RNA-seq libraries were prepared using SMART-seq v2 using a modified protocol (see manuscript, contact Bonanno S.L.)

treatment_protocol: flies were homozygous for either dSERT16, a p-element-derived imprecise excision mutant allele for SerT, or dSERT4, a genetic-background matched control

tag: time

value: Day 0


title: P6_51, scRNA-seq

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


title: 4-06_Sert16


title: P6_50, scRNA-seq

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


title: Whole blood, COVID positive, rep 260


title: P12_40d_Xbp1-KO_20, scRNA-seq


title: P6_52, scRNA-seq

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


title: Whole blood, COVID positive, rep 259


title: 3-30_Sert16


title: 3-24_Sert16


title: Whole blood, COVID positive, rep 258


title: P6_49, scRNA-seq

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


title: P6_48, scRNA-seq

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


title: P12_40d_Xbp1-KO_16, scRNA-seq


title: P12_40d_Xbp1-KO_17, scRNA-seq


title: P12_40d_Xbp1-KO_18, scRNA-seq


title: 4-07_Sert4

source_name: Kenyon cells, dSERT4_CTRL, day0


title: Whole blood, COVID positive, rep 257


title: P6_47, scRNA-seq

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


title: P12_40d_Xbp1-KO_15, scRNA-seq


title: 4-06_Sert4


title: Whole blood, COVID positive, rep 256


title: P6_44, scRNA-seq

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


title: 3-31_Sert4


title: 3-24_Sert4


title: P6_45, scRNA-seq

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


title: P12_40d_Xbp1-KO_13, scRNA-seq


title: 3-31_Sert16


title: P6_42, scRNA-seq

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


title: sfGFP-GAF control, H3K9me3 Input, 2

data_processing:
ChIP-seq data was aligned using bowtie 2 v2.3.5 without the following default parameters to retain multimapping reads: --no-mixed --no-discordant
Replicates were merged into a single bigWig file. bamCompare was used with the following parameters --scaleFactorsMethod SES, --operation log2, to generate bigWig files of the H3K9me3 IP signal normalized to the input
ChIP-seq peak calling was performed using MACS v2 with the following parameters: -g 1.2e8, --call-summits.
To focus analysis on robust, high-quality peaks, we used 100 bp up- and downstream of peak summits, and retained only peaks that were detected in both replicates and overlapped by at least 100 bp.
Assembly: dm6
Supplementary files format and content: Replicates were merged into a single bigWig file.
Supplementary files format and content: bed files containing peaks. Contains only peaks that were detected in both replicates.

source_name: embryo

growth_protocol: All stocks were grown on molasses food at 25ºC.

extract_protocol:
ChIP was performed as described previously (Blythe and Wieschaus 2015) on hand selected 2-2.5 hr AEL embryos from: sfGFP-GAF/+ and sfGFP-GAFSDPQ/+ females, nos-degradFP/His2Av-RFP (II); sfGFP-GAF (N) (III) and His2Av-RFP (II); sfGFP-GAF (N) (III) females, and nos-DBD-sfGFP/+ females. Briefly, 200-400 embryos were collected, dechorionated in 50% bleach for 3 min, fixed for 15 min in 4% formaldehyde and then lysed in 1 mL of RIPA buffer (50 mM Tris-HCl pH 8.0, 0.1% SDS, 1% Triton X-100, 0.5% sodium deoxycholate, and 150 mM NaCl). The fixed chromatin was then sonicated for 20 s 11 times at 20% output and full duty cycle (Branson Sonifier 250). Chromatin was incubated with 6 μg of anti-GFP antibody (Abcam #ab290) or 10 μl anti-H3K9me3 antibody (Active Motif, # 39162) overnight at 4°C , and then bound to 50 μl of Protein A magnetic beads (Dynabeads Protein A, Thermo Scientific). The purified chromatin was then washed, eluted, and treated with 90 μg of RNaseA (37°C, for 30 min) and 100 μg of Proteinase K (65°C, overnight). The DNA was purified using phenol/chloroform extraction and concentrated by ethanol precipitation. Each sample was resuspended in 25 μl of water.
Sequencing libraries were made using the NEB Next Ultra II library kit. For sfGFP-GAFSDPQ ChIP-seq, libraries were sequenced on the Illumina NextSeq 500 using 75bp single-end reads at the Northwestern Sequencing Core (NUCore). For DBD-sfGFP ChIP-seq, libraries were sequenced on the Illumina HiSeq 4000 using 50bp single-end reads at the Northwestern Sequencing Core (NUCore). For H3K9me3 ChIP-seq, libraries were sequenced on the Illumina NovaSeq 6000 using 150bp paired-end reads at the UW Madison Biotechnology Center.

value: embryo

tag: developmental stage

value: 2-2.5 hr AEL

value: His2Av-RFP (II); sfGFP-GAF(N) (III)

tag: chip antibody

value: none (input)


title: 3-30_Sert4


title: P12_40d_Xbp1-KO_12, scRNA-seq

source_name: liver

value: liver


title: P12_40d_Xbp1-KO_14, scRNA-seq

value: hepatocyte


title: P6_46, scRNA-seq

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

value: Alb-Cre; Rosa-tdTomato


title: Whole blood, COVID positive, rep 254

source_name: Whole blood


title: sfGFP-GAF degrad, H3K9me3 Input, 2

value: nos-degradFP/His2Av-RFP (II); sfGFP-GAF(N) (III)


title: P6_43, scRNA-seq

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


title: Whole blood, COVID positive, rep 250


title: Whole blood, COVID positive, rep 251


title: Whole blood, COVID positive, rep 252


title: Whole blood, COVID positive, rep 249


title: P12_40d_Xbp1-KO_8, scRNA-seq


title: P6_41, scRNA-seq

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


title: P6_39, scRNA-seq

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


title: Whole blood, COVID positive, rep 255


title: P12_40d_Xbp1-KO_9, scRNA-seq


title: Whole blood, COVID positive, rep 253


title: sfGFP-GAF control, H3K9me3 Input, 1


title: P12_40d_Xbp1-KO_10, scRNA-seq


title: P12_40d_Xbp1-KO_11, scRNA-seq


title: P12_40d_Xbp1-KO_7, scRNA-seq


title: sfGFP-GAF control, H3K9me3 IP, 2

value: anti-H3K9me3 (Active motif #39161)


title: P6_40, scRNA-seq

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


title: P6_38, scRNA-seq

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


title: sfGFP-GAF degrad, H3K9me3 Input, 1


title: Whole blood, COVID positive, rep 247


title: P12_40d_Xbp1-KO_5, scRNA-seq


title: P12_40d_Xbp1-KO_6, scRNA-seq


title: P12_40d_Xbp1-KO_3, scRNA-seq


title: P12_40d_Xbp1-KO_4, scRNA-seq


title: P6_37, scRNA-seq

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


title: Whole blood, COVID positive, rep 243


title: P12_40d_Xbp1-KO_1, scRNA-seq


title: sfGFP-GAF degrad, H3K9me3 IP, 2


title: Whole blood, COVID positive, rep 244


title: Whole blood, COVID positive, rep 248


title: sfGFP-GAF degrad, H3K9me3 IP, 1


title: P6_36, scRNA-seq

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


title: sfGFP-GAF control, H3K9me3 IP, 1


title: P6_35, scRNA-seq

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


title: Whole blood, COVID positive, rep 245


title: P6_33, scRNA-seq

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


title: P6_34, scRNA-seq

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


title: P12_40d_Xbp1-KO_2, scRNA-seq


title: P6_32, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_4_32

data_processing:
For scRNA-seq and bulk cell RNA-seq, sequencing reads were aligned to the Mus musculus reference genome (mm10) using TopHat (v2.1.0) with the parameters "-o out_dir -G gtf --transcriptome-index trans_index bowtie2_index input_fastq [input_fastq2]". HTSeq (v0.6.0) was used to quantify the reads that mapped to each gene with the parameters "-f bam -r pos -s no -a 30".
For N-ChIP, sequencing reads were aligned to the Mus musculus genome (mm10) using bowtie2 (v2.2.5)24 with default parameters. Reads with mapping quality ≥30 were retained for downstream analyses. PCR duplicate reads were removed using samtools (v1.3.1) with "samtools sort in_bam | samtools rmdup -s - out_bam". Reads from biological replicates were concatenated. TP10M (tags per 10 million) values were calculated and stored in the bedGraph format using Homer with the parameters "makeUCSCfile out_dir –o out.bdg –name sample_name -color track_color –fragLength 150 –avg -fsize 1e20". Highly enriched regions (peaks) of H3K4me1, H3K4me3 and H3K27ac were identified using MACS (v1.4.2) with default parameters. Peaks of H3K27me3 were identified using MACS2 (v2.1.0) with "—broad" mode. Peaks that overlapped with ENCODE blacklisted genomic regions were excluded.
For CUT&RUN ChIP, index, primer and daptor sequences were identified using FastQC (v0.11.3) with parameters "--extract --o out_dir -t 4 fastqc.file". Next, we trimmed the index, primer and adaptor sequences off from the paired-end reads using Trimmomatic (v0.38) 30 with parameters "java jar trimmoma 0.38.jar PE -phred33 fasq1.file fastq2.file ILLUMINACLIP:fasta.file:2:30:10 LEADING:3 TAILING:3 SLIDINGWINDOW:4:15 MINLEN:36". The trimmed reads were aligned to the Mus musculus genome (mm10) using bowtie2 (v2.2.5) with default parameters. Reads with mapping quality ≥30 were retained for the downstream analysis. Duplicate reads were removed from the PCR results using samtools (v1.3.1) with the command "samtools sort in_bam|samtools rmdup -s - out_bam". Reads generated from biological replicates were pooled. TP10M values were calculated and stored in bedGraph files using Homer with the command "makeUCSCfile out_dir -o out.bdg -name sample_name -avg -fsize 1e20". Peak calling was performed using MACS2 (v2.1.0) with ‘--broad’ mode and default parameters. Genome regions that overlapped with ENCODE blacklist regions (Encode Project Consortium, 2012) were excluded from peak regions.
Genome_build: mm10
Supplementary_files_format_and_content: For scRNA-seq and bulk cell RNA-seq, comma-Separated Values files (.csv) include read count for each sample. For N-ChIP and CUT&RUN ChIP, bedgraph files (.bdg) include scores representing read count per bp per 1 × 10e7 reads; BED files (.bed) include highly enriched regions (peaks).

source_name: Liver

growth_protocol: Liver lobes from E12.5 mouse livers were collected and cultured on Nuclepore Track-Etch Membranes (Whatman, 110414). 12-well plates filled with 2 mL RPMI 1640 medium (Invitrogen, 22400) supplemented with 10% FBS, 1 × ITS-X (Gibco, 51500), 50 ng/mL EGF and 1 × Penicillin-Streptomycin (Gibco, 15140) were used.

extract_protocol:
For scRNA-seq, livers were dissociated into single cells by treatment with 0.25% trypsin at 37°C. The reaction was terminated by the addition of 0.4 volumes of FBS. The single-cell suspensions were centrifuged at 100 × g for 5 min at 4 °C, and the resulting pellets were re-suspended with PBS containing 1% FBS. Cells were incubated with the DLK-FITC antibody (MBL, D187-4, 1:100) and/or EpCAM-APC antibody (eBioscience, 17-5791-82, 1:50) at 4 °C for 20 min. After washing, cells were sorted with a BD FACS Aria SORP cell sorter (BD Bioscience). Dead cells were excluded by DAPI (Sigma, D9564, 0.5 µg/mL). The generation of cDNA were performed according to Smart-seq2 method.
For scRNA-seq, two nanograms of cDNA was used to prepare libraries using a TruePrep DNA Library Prep Kit (Vazyme, TD502). Four-cycle PCR using biotinylated index primers introduced a biotin tag to the 3’ end of the cDNA. After cDNA fragmentation using a Bioruptor Plus sonicator (Diagenode), the 3’ terminals of the cDNA were captured using Dynabeads MyOne Streptavidin C1 (Thermo Fisher, 65002). Thirty nanograms of cDNA was used to construct libraries using a Kapa Hyper Prep Kit (Kapa Biosystems, KK8505).
For N-ChIP and CUT&RUN ChIP, we collected approximately 20,000 cells for each ChIP-seq, and used antibodies against H3K4me3 (Abcam, ab8580, 1ng), H3K27me3 (Millipore, 07-449, 1ng), H3K4me1 (Millipore, 07-436, 1ng), H3K27ac (Active motif, 39133, 1ng) and EZH2 (Cell Signaling Technology, 5246, 1:100). N-ChIP was carried out following the protocol of Brind'Amour et al. (2015), and CUT&RUN ChIP-seq was performed following the protocol of Peter J Skene et al. (2018).
For N-ChIP and CUT&RUN ChIP, libraries of ChIP DNA were constructed with the Ultra DNA Library Prep Kit for Illumina (New England Biolabs, E7370) or the KAPA Hyper Prep Kit (Kapa Biosystems, KK8502). DNA purification was conducted with VAHTS DNA Clean Beads XP beads (Vazyme, N411-03). The quality of the libraries was assessed with an Advanced Analytical Fragment Analyzer (AATI).
For bulk cell RNA-seq, livers were dissociated into single cells by treatment with 0.25% trypsin at 37°C. The reaction was terminated by the addition of 0.4 volumes of FBS. The single-cell suspensions were centrifuged at 100 × g for 5 min at 4 °C, and the resulting pellets were re-suspended with PBS containing 1% FBS. Cells were incubated with the DLK-FITC antibody (MBL, D187-4, 1:100) at 4 °C for 20 min. After washing, cells were sorted with a BD FACS Aria SORP cell sorter (BD Bioscience). Dead cells were excluded by DAPI (Sigma, D9564, 0.5 µg/mL). Total RNA was extracted from approximately 50,000 cells using the RNeasy Micro Kit (Qiagen, 74004).
For bulk cell RNA-seq, libraries were constructed with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, #E7490) and the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs, #E7420).

treatment_protocol: Cultured explants were treated for 2 days with DMSO (control), 2 µM GSKJ4 (Tocris Bioscience, 4594) or 1 µM GSK126.

tag: Stage

tag: protocol

tag: culture

tag: batch

tag: sort

value: EpCAM+

tag: genotype/treatment


title: AlfpCre_P300flfl_P0_Epcam_4_31


title: AlfpCre_P300flfl_P0_Epcam_4_30


title: Whole blood, COVID positive, rep 246


title: Whole blood, COVID positive, rep 241


title: P6_31, scRNA-seq

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

tag: cell type


title: AlfpCre_P300flfl_P0_Epcam_4_3


title: P12_40d_WT_163, scRNA-seq

value: WT


title: AlfpCre_P300flfl_P0_Epcam_4_29


title: P12_40d_WT_162, scRNA-seq


title: Whole blood, COVID positive, rep 242


title: P6_30, scRNA-seq

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


title: Whole blood, COVID positive, rep 239


title: Whole blood, COVID positive, rep 240


title: Whole blood, COVID positive, rep 237


title: P12_40d_WT_159, scRNA-seq


title: P12_40d_WT_161, scRNA-seq


title: AlfpCre_P300flfl_P0_Epcam_4_27


title: AlfpCre_P300flfl_P0_Epcam_4_28


title: P12_40d_WT_160, scRNA-seq


title: Whole blood, COVID positive, rep 236


title: P6_27, scRNA-seq

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


title: P6_28, scRNA-seq

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


title: P6_26, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_4_25


title: P6_29, scRNA-seq

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


title: P12_40d_WT_164, scRNA-seq


title: P6_25, scRNA-seq

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


title: P12_40d_WT_157, scRNA-seq


title: Whole blood, COVID positive, rep 234


title: P12_40d_WT_156, scRNA-seq


title: AlfpCre_P300flfl_P0_Epcam_4_23


title: AlfpCre_P300flfl_P0_Epcam_4_26


title: Whole blood, COVID positive, rep 233


title: P12_40d_WT_155, scRNA-seq


title: P6_23, scRNA-seq

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


title: Whole blood, COVID positive, rep 238


title: AlfpCre_P300flfl_P0_Epcam_4_21


title: P12_40d_WT_153, scRNA-seq


title: P6_22, scRNA-seq

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


title: Whole blood, COVID positive, rep 232


title: P12_40d_WT_158, scRNA-seq


title: P12_40d_WT_154, scRNA-seq


title: AlfpCre_P300flfl_P0_Epcam_4_20


title: AlfpCre_P300flfl_P0_Epcam_4_2


title: AlfpCre_P300flfl_P0_Epcam_4_24


title: P12_40d_WT_152, scRNA-seq


title: Whole blood, COVID positive, rep 235


title: Whole blood, COVID positive, rep 231


title: Whole blood, COVID positive, rep 230


title: Whole blood, COVID positive, rep 229


title: P6_24, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_4_18


title: AlfpCre_P300flfl_P0_Epcam_4_19


title: AlfpCre_P300flfl_P0_Epcam_4_22


title: P12_40d_WT_150, scRNA-seq


title: Whole blood, COVID positive, rep 227


title: P6_21, scRNA-seq

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


title: P12_40d_WT_151, scRNA-seq


title: P12_40d_WT_149, scRNA-seq


title: P6_18, scRNA-seq

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


title: P6_19, scRNA-seq

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


title: P12_40d_WT_148, scRNA-seq


title: P6_16, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_4_17


title: P6_17, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_4_16


title: Whole blood, COVID positive, rep 225


title: P6_15, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_4_14


title: AlfpCre_P300flfl_P0_Epcam_4_15


title: P6_20, scRNA-seq

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


title: Whole blood, COVID positive, rep 224


title: Whole blood, COVID positive, rep 223


title: P6_13, scRNA-seq

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


title: P12_40d_WT_147, scRNA-seq


title: P12_40d_WT_146, scRNA-seq


title: Whole blood, COVID positive, rep 228


title: P12_40d_WT_145, scRNA-seq


title: Whole blood, COVID positive, rep 222


title: AlfpCre_P300flfl_P0_Epcam_4_12


title: P12_40d_WT_144, scRNA-seq


title: P6_12, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_4_11


title: Whole blood, COVID positive, rep 226


title: Whole blood, COVID positive, rep 221


title: AlfpCre_P300flfl_P0_Epcam_4_10


title: AlfpCre_P300flfl_P0_Epcam_4_13


title: P12_40d_WT_143, scRNA-seq


title: P6_14, scRNA-seq

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


title: P6_10, scRNA-seq

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


title: Whole blood, COVID positive, rep 220


title: P12_40d_WT_141, scRNA-seq


title: P6_11, scRNA-seq

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


title: P12_40d_WT_140, scRNA-seq


title: P6_9, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_3_9


title: Whole blood, COVID positive, rep 218


title: AlfpCre_P300flfl_P0_Epcam_3_8


title: P6_7, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_4_1


title: P12_40d_WT_142, scRNA-seq


title: P12_40d_WT_139, scRNA-seq


title: Whole blood, COVID positive, rep 217


title: Whole blood, COVID positive, rep 216


title: P6_6, scRNA-seq

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


title: P12_40d_WT_138, scRNA-seq


title: AlfpCre_P300flfl_P0_Epcam_3_7


title: Whole blood, COVID positive, rep 215


title: AlfpCre_P300flfl_P0_Epcam_3_6


title: P12_40d_WT_137, scRNA-seq


title: Whole blood, COVID positive, rep 214


title: Whole blood, COVID positive, rep 219


title: AlfpCre_P300flfl_P0_Epcam_3_5


title: P6_5, scRNA-seq

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


title: P6_8, scRNA-seq

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


title: P6_4, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_3_4


title: P6_3, scRNA-seq

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


title: P12_40d_WT_136, scRNA-seq


title: P12_40d_WT_135, scRNA-seq


title: P12_40d_WT_134, scRNA-seq


title: AlfpCre_P300flfl_P0_Epcam_3_3


title: Whole blood, COVID positive, rep 210


title: Whole blood, COVID positive, rep 213


title: P6_2, scRNA-seq

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


title: Whole blood, COVID positive, rep 212


title: P12_40d_WT_132, scRNA-seq


title: P12_40d_WT_133, scRNA-seq


title: AlfpCre_P300flfl_P0_Epcam_3_2


title: Whole blood, COVID positive, rep 209


title: P6_1, scRNA-seq

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


title: P12_40d_WT_131, scRNA-seq


title: AlfpCre_P300flfl_P0_Epcam_3_13


title: AlfpCre_P300flfl_P0_Epcam_3_14


title: P3_171, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_3_12


title: Whole blood, COVID positive, rep 208


title: P3_170, scRNA-seq

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


title: P12_40d_WT_130, scRNA-seq


title: P3_169, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_3_11


title: Whole blood, COVID positive, rep 207


title: AlfpCre_P300flfl_P0_Epcam_3_10


title: P12_40d_WT_129, scRNA-seq


title: Whole blood, COVID positive, rep 211


title: Whole blood, COVID positive, rep 206


title: P3_172, scRNA-seq

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


title: P3_168, scRNA-seq

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


title: P12_40d_WT_128, scRNA-seq


title: P12_40d_WT_127, scRNA-seq


title: Whole blood, COVID positive, rep 205


title: P3_167, scRNA-seq

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


title: Whole blood, COVID positive, rep 204


title: P3_165, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_2_8


title: AlfpCre_P300flfl_P0_Epcam_2_9


title: AlfpCre_P300flfl_P0_Epcam_3_1


title: AlfpCre_P300flfl_P0_Epcam_2_7


title: P12_40d_WT_125, scRNA-seq


title: P12_40d_WT_124, scRNA-seq


title: P3_164, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_2_6


title: P3_163, scRNA-seq

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


title: P12_40d_WT_123, scRNA-seq


title: AlfpCre_P300flfl_P0_Epcam_2_5


title: P12_40d_WT_122, scRNA-seq


title: P3_162, scRNA-seq

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


title: P3_161, scRNA-seq

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


title: P12_40d_WT_121, scRNA-seq


title: P3_160, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_2_3


title: AlfpCre_P300flfl_P0_Epcam_2_4


title: P12_40d_WT_120, scRNA-seq


title: P12_40d_WT_126, scRNA-seq


title: P12_40d_WT_119, scRNA-seq


title: P3_166, scRNA-seq

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


title: P3_159, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_2_12


title: AlfpCre_P300flfl_P0_Epcam_2_2


title: P12_40d_WT_118, scRNA-seq


title: AlfpCre_P300flfl_P0_Epcam_2_11


title: P3_157, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_2_10


title: P3_156, scRNA-seq

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


title: P12_40d_WT_116, scRNA-seq


title: P12_40d_WT_115, scRNA-seq


title: P3_154, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_1_9


title: AlfpCre_P300flfl_P0_Epcam_2_1


title: P3_155, scRNA-seq

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


title: P12_40d_WT_114, scRNA-seq


title: P3_153, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_1_8


title: P12_40d_WT_113, scRNA-seq


title: P12_40d_WT_112, scRNA-seq


title: P3_152, scRNA-seq

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


title: P12_40d_WT_111, scRNA-seq


title: P3_151, scRNA-seq

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


title: P3_158, scRNA-seq

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


title: P12_40d_WT_110, scRNA-seq


title: P3_150, scRNA-seq

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


title: P3_149, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_1_6


title: AlfpCre_P300flfl_P0_Epcam_1_5


title: P12_40d_WT_109, scRNA-seq


title: P12_40d_WT_117, scRNA-seq


title: AlfpCre_P300flfl_P0_Epcam_1_4


title: P3_148, scRNA-seq

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


title: P12_40d_WT_108, scRNA-seq


title: AlfpCre_P300flfl_P0_Epcam_1_3


title: P3_147, scRNA-seq

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


title: P12_40d_WT_107, scRNA-seq


title: P3_146, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_1_7


title: AlfpCre_P300flfl_P0_Epcam_1_14


title: P3_144, scRNA-seq

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


title: P12_40d_WT_105, scRNA-seq


title: P12_40d_WT_106, scRNA-seq


title: AlfpCre_P300flfl_P0_Epcam_1_13


title: AlfpCre_P300flfl_P0_Epcam_1_2


title: P12_40d_WT_104, scRNA-seq


title: P3_145, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Epcam_1_11


title: P3_143, scRNA-seq

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


title: P12_40d_WT_103, scRNA-seq


title: AlfpCre_P300flfl_P0_Epcam_1_10


title: P3_142, scRNA-seq

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


title: P12_40d_WT_102, scRNA-seq


title: P3_141, scRNA-seq

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


title: P12_40d_WT_101, scRNA-seq


title: AlfpCre_P300flfl_P0_Epcam_1_1


title: P12_40d_WT_100, scRNA-seq


title: P3_140, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Dlk_3_9

value: DLK+


title: AlfpCre_P300flfl_P0_Dlk_3_8


title: P12_40d_WT_99, scRNA-seq


title: P3_139, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Dlk_3_7


title: P3_138, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Dlk_3_6


title: AlfpCre_P300flfl_P0_Epcam_1_12


title: P3_137, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Dlk_3_5


title: P12_40d_WT_97, scRNA-seq


title: P3_136, scRNA-seq

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


title: P12_40d_WT_95, scRNA-seq


title: AlfpCre_P300flfl_P0_Dlk_3_3


title: P3_134, scRNA-seq

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


title: P3_135, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Dlk_3_4


title: P12_40d_WT_96, scRNA-seq


title: P12_40d_WT_94, scRNA-seq


title: AlfpCre_P300flfl_P0_Dlk_3_2


title: P3_133, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Dlk_3_18


title: P12_40d_WT_92, scRNA-seq


title: AlfpCre_P300flfl_P0_Dlk_3_19


title: P3_132, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Dlk_3_17


title: P12_40d_WT_91, scRNA-seq


title: P3_130, scRNA-seq

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


title: P12_40d_WT_90, scRNA-seq


title: P12_40d_WT_89, scRNA-seq


title: AlfpCre_P300flfl_P0_Dlk_3_15


title: P12_40d_WT_88, scRNA-seq


title: AlfpCre_P300flfl_P0_Dlk_3_16


title: P3_129, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Dlk_3_14


title: P12_40d_WT_87, scRNA-seq


title: P3_128, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Dlk_3_13


title: P3_125, scRNA-seq

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


title: P3_127, scRNA-seq

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


title: P12_40d_WT_98, scRNA-seq


title: P3_126, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Dlk_3_12


title: P12_40d_WT_85, scRNA-seq


title: P12_40d_WT_84, scRNA-seq


title: P3_124, scRNA-seq

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


title: P3_131, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Dlk_3_11


title: AlfpCre_P300flfl_P0_Dlk_3_10


title: P3_123, scRNA-seq

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


title: P3_122, scRNA-seq

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


title: P12_40d_WT_83, scRNA-seq


title: P12_40d_WT_82, scRNA-seq


title: P3_121, scRNA-seq

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


title: P12_40d_WT_81, scRNA-seq


title: AlfpCre_P300flfl_P0_Dlk_2_9


title: P3_120, scRNA-seq

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


title: P12_40d_WT_80, scRNA-seq


title: AlfpCre_P300flfl_P0_Dlk_2_7


title: P12_40d_WT_86, scRNA-seq


title: P3_118, scRNA-seq

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


title: P12_40d_WT_79, scRNA-seq


title: AlfpCre_P300flfl_P0_Dlk_2_5


title: AlfpCre_P300flfl_P0_Dlk_2_6


title: P12_40d_WT_76, scRNA-seq


title: P12_40d_WT_77, scRNA-seq


title: P3_117, scRNA-seq

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


title: P3_116, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Dlk_2_4


title: P3_119, scRNA-seq

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


title: P12_40d_WT_75, scRNA-seq


title: AlfpCre_P300flfl_P0_Dlk_2_2


title: P3_114, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Dlk_2_3


title: AlfpCre_P300flfl_P0_Dlk_3_1


title: P3_115, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Dlk_2_1


title: AlfpCre_P300flfl_P0_Dlk_1_9


title: P12_40d_WT_74, scRNA-seq


title: P12_40d_WT_73, scRNA-seq


title: P3_113, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Dlk_2_8


title: P3_112, scRNA-seq

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


title: P3_111, scRNA-seq

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


title: P12_40d_WT_72, scRNA-seq


title: P12_40d_WT_71, scRNA-seq


title: P3_110, scRNA-seq

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


title: P12_40d_WT_70, scRNA-seq


title: P3_109, scRNA-seq

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


title: P12_40d_WT_69, scRNA-seq


title: P3_107, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Dlk_1_7


title: P12_40d_WT_68, scRNA-seq


title: AlfpCre_P300flfl_P0_Dlk_1_6


title: P3_108, scRNA-seq

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


title: AlfpCre_P300flfl_P0_Dlk_1_5


title: P3_106, scRNA-seq

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


title: P3_105, scRNA-seq

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


title: P12_40d_WT_66, scRNA-seq


title: AlfpCre_P300flfl_P0_Dlk_1_3


title: AlfpCre_P300flfl_P0_Dlk_1_2


title: P12_40d_WT_93, scRNA-seq


title: P12_40d_WT_67, scRNA-seq


title: P12_40d_WT_65, scRNA-seq


title: P3_104, scRNA-seq

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


title: P12_40d_WT_64, scRNA-seq


title: AlfpCre_P300flfl_P0_Dlk_1_4


title: AlfpCre_P300flfl_P0_Dlk_1_8


title: P3_103, scRNA-seq

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


title: P12_40d_WT_63, scRNA-seq


title: AlfpCre_P300flfl_P0_Dlk_1_1


title: AlfpCre_P300flfl_P0_Dlk_1_10


title: AlfpCre_Jmjd3wtwt_P0_Epcam_2_9


title: P3_102, scRNA-seq

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


title: P3_101, scRNA-seq

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


title: AlfpCre_Jmjd3wtwt_P0_Epcam_2_8


title: P12_40d_WT_61, scRNA-seq


title: P12_40d_WT_60, scRNA-seq


title: P3_100, scRNA-seq

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


title: P3_98, scRNA-seq

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


title: AlfpCre_Jmjd3wtwt_P0_Epcam_2_4


title: P12_40d_WT_55, scRNA-seq


title: P3_95, scRNA-seq

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


title: P12_40d_WT_56, scRNA-seq


title: AlfpCre_Jmjd3wtwt_P0_Epcam_2_2


title: AlfpCre_Jmjd3wtwt_P0_Epcam_2_5


title: AlfpCre_Jmjd3wtwt_P0_Epcam_2_12


title: AlfpCre_Jmjd3wtwt_P0_Epcam_2_11


title: P3_96, scRNA-seq

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


title: P3_93, scRNA-seq

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


title: P12_40d_WT_62, scRNA-seq


title: P12_40d_WT_53, scRNA-seq


title: P12_40d_WT_57, scRNA-seq


title: AlfpCre_Jmjd3wtwt_P0_Epcam_2_3


title: P3_94, scRNA-seq

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


title: AlfpCre_Jmjd3wtwt_P0_Epcam_2_10


title: AlfpCre_Jmjd3wtwt_P0_Epcam_2_7


title: AlfpCre_Jmjd3wtwt_P0_Epcam_2_1


title: P3_99, scRNA-seq

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


title: P12_40d_WT_52, scRNA-seq


title: P12_40d_WT_59, scRNA-seq


title: AlfpCre_Jmjd3wtwt_P0_Epcam_2_6


title: P12_40d_WT_58, scRNA-seq


title: P3_91, scRNA-seq

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


title: P12_40d_WT_51, scRNA-seq


title: P3_97, scRNA-seq

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


title: P12_40d_WT_54, scRNA-seq


title: AlfpCre_Jmjd3wtwt_P0_Epcam_1_9


title: AlfpCre_Jmjd3wtwt_P0_Epcam_1_8


title: P12_40d_WT_49, scRNA-seq


title: P12_40d_WT_47, scRNA-seq


title: P12_40d_WT_48, scRNA-seq


title: AlfpCre_Jmjd3wtwt_P0_Epcam_1_6


title: P3_87, scRNA-seq

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


title: AlfpCre_Jmjd3wtwt_P0_Epcam_1_7


title: P12_40d_WT_46, scRNA-seq


title: P3_88, scRNA-seq

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


title: P3_89, scRNA-seq

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


title: AlfpCre_Jmjd3wtwt_P0_Epcam_1_4


title: P3_86, scRNA-seq

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


title: P3_92, scRNA-seq

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


title: AlfpCre_Jmjd3wtwt_P0_Epcam_1_5


title: P12_40d_WT_45, scRNA-seq


title: P12_40d_WT_43, scRNA-seq


title: P3_83, scRNA-seq

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


title: P3_82, scRNA-seq

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


title: AlfpCre_Jmjd3wtwt_P0_Epcam_1_2


title: AlfpCre_Jmjd3wtwt_P0_Epcam_1_3


title: P3_90, scRNA-seq

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


title: P3_84, scRNA-seq

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


title: P12_40d_WT_50, scRNA-seq


title: AlfpCre_Jmjd3wtwt_P0_Epcam_1_12


title: AlfpCre_Jmjd3wtwt_P0_Epcam_1_11


title: P12_40d_WT_42, scRNA-seq


title: P12_40d_WT_41, scRNA-seq


title: AlfpCre_Jmjd3wtwt_P0_Epcam_1_10


title: P3_85, scRNA-seq

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


title: P12_40d_WT_40, scRNA-seq


title: AlfpCre_Jmjd3wtwt_P0_Epcam_1_1


title: P12_40d_WT_44, scRNA-seq


title: AlfpCre_Jmjd3wtwt_P0_Dlk_2_9


title: P3_80, scRNA-seq

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


title: P3_78, scRNA-seq

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


title: AlfpCre_Jmjd3wtwt_P0_Dlk_2_7


title: P12_40d_WT_37, scRNA-seq


title: P12_40d_WT_38, scRNA-seq


title: P12_40d_WT_39, scRNA-seq


title: AlfpCre_Jmjd3wtwt_P0_Dlk_2_8


title: P3_76, scRNA-seq

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


title: P3_77, scRNA-seq

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


title: P12_40d_WT_36, scRNA-seq


title: P3_75, scRNA-seq

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


title: AlfpCre_Jmjd3wtwt_P0_Dlk_2_6


title: P3_74, scRNA-seq

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


title: P12_40d_WT_35, scRNA-seq


title: P3_81, scRNA-seq

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


title: P12_40d_WT_33, scRNA-seq


title: AlfpCre_Jmjd3wtwt_P0_Dlk_2_4


title: AlfpCre_Jmjd3wtwt_P0_Dlk_2_3


title: P12_40d_WT_34, scRNA-seq


title: P3_73, scRNA-seq

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


title: P3_79, scRNA-seq

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


title: P12_40d_WT_31, scRNA-seq


title: P3_71, scRNA-seq

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


title: AlfpCre_Jmjd3wtwt_P0_Dlk_2_2


title: AlfpCre_Jmjd3wtwt_P0_Dlk_2_11


title: P12_40d_WT_78, scRNA-seq


title: P12_40d_WT_30, scRNA-seq


title: AlfpCre_Jmjd3wtwt_P0_Dlk_2_10


title: AlfpCre_Jmjd3wtwt_P0_Dlk_2_12


title: P12_40d_WT_29, scRNA-seq


title: P3_67, scRNA-seq

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


title: AlfpCre_Jmjd3wtwt_P0_Dlk_2_1


title: P3_69, scRNA-seq

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


title: P12_40d_WT_28, scRNA-seq


title: P12_40d_WT_27, scRNA-seq


title: P3_66, scRNA-seq

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


title: AlfpCre_Jmjd3wtwt_P0_Dlk_1_9


title: AlfpCre_Jmjd3wtwt_P0_Dlk_1_8


title: P3_72, scRNA-seq

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


title: P3_64, scRNA-seq

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


title: AlfpCre_Jmjd3wtwt_P0_Dlk_1_7


title: P12_40d_WT_32, scRNA-seq


title: AlfpCre_Jmjd3wtwt_P0_Dlk_1_6


title: P12_40d_WT_24, scRNA-seq


title: P3_70, scRNA-seq

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


title: P12_40d_WT_26, scRNA-seq


title: P12_40d_WT_25, scRNA-seq


title: AlfpCre_Jmjd3wtwt_P0_Dlk_2_5


title: P12_40d_WT_23, scRNA-seq


title: P3_63, scRNA-seq

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


title: P3_68, scRNA-seq

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


title: P3_65, scRNA-seq

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


title: P3_62, scRNA-seq

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


title: P3_61, scRNA-seq

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


title: AlfpCre_Jmjd3wtwt_P0_Dlk_1_4


title: P12_40d_WT_21, scRNA-seq


title: P3_60, scRNA-seq

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


title: P12_40d_WT_20, scRNA-seq


title: P12_40d_WT_22, scRNA-seq


title: P12_40d_WT_19, scRNA-seq


title: AlfpCre_Jmjd3wtwt_P0_Dlk_1_2


title: AlfpCre_Jmjd3wtwt_P0_Dlk_1_3


title: P3_59, scRNA-seq

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


title: P3_58, scRNA-seq

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


title: P3_57, scRNA-seq

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


title: AlfpCre_Jmjd3wtwt_P0_Dlk_1_12


title: AlfpCre_Jmjd3wtwt_P0_Dlk_1_11


title: P3_56, scRNA-seq

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


title: AlfpCre_Jmjd3wtwt_P0_Dlk_1_1


title: P3_55, scRNA-seq

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


title: P12_40d_WT_15, scRNA-seq


title: AlfpCre_Jmjd3wtwt_P0_Dlk_1_10


title: P3_54, scRNA-seq

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


title: AlfpCre_Jmjd3wtwt_P0_Dlk_1_5


title: AlfpCre_Jmjd3flfl_P0_Epcam_2_9


title: P12_40d_WT_17, scRNA-seq


title: AlfpCre_Jmjd3flfl_P0_Epcam_2_8


title: P12_40d_WT_13, scRNA-seq


title: P12_40d_WT_14, scRNA-seq


title: P3_52, scRNA-seq

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


title: AlfpCre_Jmjd3flfl_P0_Epcam_2_7


title: P12_40d_WT_12, scRNA-seq


title: AlfpCre_Jmjd3flfl_P0_Epcam_2_5


title: P3_50, scRNA-seq

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


title: P12_40d_WT_11, scRNA-seq


title: P12_40d_WT_16, scRNA-seq


title: P3_53, scRNA-seq

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


title: AlfpCre_Jmjd3flfl_P0_Epcam_2_4


title: P3_51, scRNA-seq

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


title: P12_40d_WT_18, scRNA-seq


title: P3_49, scRNA-seq

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


title: P12_40d_WT_9, scRNA-seq


title: P12_40d_WT_8, scRNA-seq


title: P3_48, scRNA-seq

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


title: AlfpCre_Jmjd3flfl_P0_Epcam_2_3


title: AlfpCre_Jmjd3flfl_P0_Epcam_2_2


title: P3_47, scRNA-seq

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


title: P3_46, scRNA-seq

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


title: AlfpCre_Jmjd3flfl_P0_Epcam_2_12


title: AlfpCre_Jmjd3flfl_P0_Epcam_2_6


title: AlfpCre_Jmjd3flfl_P0_Epcam_2_11


title: P12_40d_WT_5, scRNA-seq


title: P3_44, scRNA-seq

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


title: P12_40d_WT_7, scRNA-seq


title: P12_40d_WT_3, scRNA-seq


title: P12_40d_WT_6, scRNA-seq


title: P3_42, scRNA-seq

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


title: AlfpCre_Jmjd3flfl_P0_Epcam_2_1


title: P12_40d_WT_2, scRNA-seq


title: P12_40d_WT_4, scRNA-seq


title: P3_43, scRNA-seq

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


title: AlfpCre_Jmjd3flfl_P0_Epcam_1_9


title: NANS-KO iPSCs-derived cerebral organoids, Day35, 3

city: chengdu

first: Qian

last: Bu

state: Sichuan

address: 28 Gaopeng Street, High-tech District

institute: Chengdu  West China-Frontier PharmaTech Co.,Ltd

description: Day35 NANS-KO cerebral organoids.txt

data_processing:
library enrichment： PCR amplification of 15 cycles
recovery of target bands by 2% agarose gel
TBS380 (Picogreen) quantification, mixed on the machine in proportion to the data
bridge PCR amplification on cBot to generate clusters
sequencing on Illumina platform (PE library, read length 2×150bp）
Assembly: Homo_sapiens, GRCh38.p13
Supplementary files format and content: Excel of DEGs in 4 time points include TPM values, Fold change, P value for each Sample

source_name: Cerebral organoids

growth_protocol: two hiPSCs were cultured and differentiated according to the protocol of STEMdiffTM Cerebral Organoid Kit (Stemcell Technologies, 08570)

extract_protocol:
RNA was harvested using miRneasy mini kit (Qiagen). The quantity of RNA samples was analyzed by NanoDrop 2000c (Thermo Scientific). The mRNA was extracted using an RNA sample preparation kit (Illumina).
A double-stranded cDNA synthesis kit (Invitrogen) was used to produce the cDNA and 200–300 bps sheared cDNA was inserted into the library.

value: Cerebral organoids

tag: cell line

value: hiPSCs (NCCSEDi001-A-1)

value: NANS homozygous knockout

value: brain differentiation


title: P12_40d_WT_1, scRNA-seq

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)

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: genotype


title: AlfpCre_Jmjd3flfl_P0_Epcam_1_7


title: P12_40d_Usf1-KO_63, scRNA-seq

tag: treatment


title: AlfpCre_Jmjd3flfl_P0_Epcam_1_6


title: P3_39, scRNA-seq

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

tag: tissue


title: NANS-KO iPSCs-derived cerebral organoids, Day35, 2

description: Day35 NANS-KO cerebral organoids.txt


title: P12_40d_Usf1-KO_62, scRNA-seq

tag: age


title: P3_45, scRNA-seq

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

tag: ploidy


title: AlfpCre_Jmjd3flfl_P0_Epcam_2_10


title: NANS-KO iPSCs-derived cerebral organoids, Day35, 1

description: Day35 NANS-KO cerebral organoids.txt


title: AlfpCre_Jmjd3flfl_P0_Epcam_1_5


title: P3_38, scRNA-seq

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

tag: zonation


title: P12_40d_Usf1-KO_61, scRNA-seq


title: WT iPSCs-derived cerebral organoids, Day35, 3

description: Day35 NANS-KO cerebral organoids.txt

value: hiPSCs (NCCSEDi001-A)


title: P3_37, scRNA-seq

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


title: P12_40d_Usf1-KO_60, scRNA-seq


title: P3_36, scRNA-seq

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


title: P3_40, scRNA-seq

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


title: AlfpCre_Jmjd3flfl_P0_Epcam_1_3


title: P3_41, scRNA-seq

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


title: AlfpCre_Jmjd3flfl_P0_Epcam_1_2


title: P12_40d_Usf1-KO_59, scRNA-seq


title: NANS-KO iPSCs-derived cerebral organoids, Day25, 3

description: Day25 NANS-KO cerebral organoids.txt


title: P12_40d_Usf1-KO_58, scRNA-seq


title: P3_35, scRNA-seq

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


title: WT iPSCs-derived cerebral organoids, Day35, 1

description: Day35 NANS-KO cerebral organoids.txt


title: AlfpCre_Jmjd3flfl_P0_Epcam_1_12


title: P3_34, scRNA-seq

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


title: AlfpCre_Jmjd3flfl_P0_Epcam_1_4


title: NANS-KO iPSCs-derived cerebral organoids, Day25, 2

description: Day25 NANS-KO cerebral organoids.txt


title: AlfpCre_Jmjd3flfl_P0_Epcam_1_11


title: P12_40d_Usf1-KO_57, scRNA-seq


title: P3_33, scRNA-seq

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


title: AlfpCre_Jmjd3flfl_P0_Epcam_1_10


title: NANS-KO iPSCs-derived cerebral organoids, Day25, 1

description: Day25 NANS-KO cerebral organoids.txt


title: P12_40d_Usf1-KO_56, scRNA-seq


title: P3_32, scRNA-seq

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


title: P12_40d_Usf1-KO_55, scRNA-seq


title: AlfpCre_Jmjd3flfl_P0_Epcam_1_1


title: WT iPSCs-derived cerebral organoids, Day35, 2

description: Day35 NANS-KO cerebral organoids.txt


title: WT iPSCs-derived cerebral organoids, Day25, 3

description: Day25 NANS-KO cerebral organoids.txt


title: P3_31, scRNA-seq

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


title: AlfpCre_Jmjd3flfl_P0_Dlk_2_9


title: WT iPSCs-derived cerebral organoids, Day25, 2

description: Day25 NANS-KO cerebral organoids.txt


title: P12_40d_Usf1-KO_54, scRNA-seq


title: P3_30, scRNA-seq

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


title: P12_40d_Usf1-KO_53, scRNA-seq


title: AlfpCre_Jmjd3flfl_P0_Dlk_2_8


title: P12_40d_Usf1-KO_52, scRNA-seq


title: WT iPSCs-derived cerebral organoids, Day25, 1

description: Day25 NANS-KO cerebral organoids.txt