title: STICR-ST39_T_2, Clonal barcodes library

city: San Francisco

first: Guohua

last: Yuan

address: 1651 4th St Fl 5 521A, Weill Neurosciences Building

institute: UCSF

description: Library name: STICR-ST39_T_2

data_processing:
scRNA-seq analysis 10X transcriptomic libraries were processed using CellRanger (version 7.2.0) and were aligned to the mouse transcriptome mm10-2020-A. Cellranger outputs were processed using Seurat (version 5.2.0). Datasets were processed to remove cells with fewer than 1,000 or greater than 100,000 reads, fewer than 500 or greater than 10,000 genes, or more than 20% of reads corresponding to mitochondrial genes. Doublets were identified and removed by using DoubletFinder (version 2.0.4). Libraries were integrated using Seurat’s “SCTransform” and Harmony (version 0.1.162). Libraries of the seurat project including all regions were integrated by Seurat’s “SCTransform”. Seurat projects of each brain region were integrated by Seurat’s “SCTransform” function and Harmony. To identify clusters, we constructed a shared nearest neighbor (SNN) graph using the 'FindNeighbors' function, and applied clustering through the 'FindClusters' function in Seurat. Iterative clustering to identify subtypes of cells was performed by subsetting into different major cell types (glutamatergic neurons, GABAergic neurons, glia) and using the “FindSubCluster” function in Seurat. Cell identities determined through analysis of iterative clusters were re-assigned to cells in the full Seurat object. Differential expression analysis was conducted using Seurat's “FindMarkers” and “FindAllMarkers” function, and gene expression in clusters was manually analyzed for known markers of given cell types.
STICR barcodes analysis STICR barcode analysis was performed using custom scripts, as previously described in Delgado et al57. First, BBMap (BBMap; sourceforge.net/projects/bbmap/) was used to remove low-quality reads and then extract reads containing STICR barcode sequences. Then, BBMap was used to extract individual STICR barcode fragments that were then aligned to our predefined fragment reference sets using Bowtie59 (version 5.2.1), allowing for up to two mismatches per fragment. Aligned STICR barcodes were compiled into a file containing their corresponding 10X cell barcode and 10X UMI sequences using awk. UMI of STICR barcodes with less than 10 reads were filtered by using awk to remove the noise UMI counts from the sequencing error. Finally, UMI-tools60 (version 0.5.1) was used to remove duplicate STICR barcode/cell barcode (CBC) reads by UMI, allowing for 1-bp mismatches in the UMI. STICR barcodes/CBC) pairings with at least three distinct UMIs were retained. For cells with multiple barcodes detected, only cells with all the same set of barcodes detected are considered as a shared clone, with Jaccard similarity of 1. Barcodes and their corresponding UMI counts were mapped to cells in the Seurat object of transcriptome data by aligning cell barcodes.
Assembly: mm10
Supplementary files format and content: rds
Supplementary files format and content: rds

source_name: Brain

extract_protocol:
Virally injected brains were collected from mouse pups at postnatal day 4. Brains were dissected in ice-cold pre-bubbled artificial cerebrospinal fluid (aCSF), and sectioned into coronal sections. Each brain region was manually dissected out from sliced brains based on the guidance of anatomy atlas from Allen institute. Collected tissue was then dissociated in the solution of papain (Worthington, LK003178) supplemented with 0.5 mg/ml DNase (Sigma Aldrich, DN25-1G) diluted with HBSS (Gibco,14025134) at 37℃. The tissues were incubated at 37℃ for 30-60 min, with gentle trituration every 15 min until samples had no visible chunks.  Papain was quenched by adding 1% BSA (Militeny) to the solution. Samples were spun down and resuspended in HBSS + 0.1% BSA and passed through the 35 um filter into a FACS tube (Falcon, 52235). To isolate and collect virally infected cells, flow cytometry was done using a BD FACSAria III Cell Sorter (BD FACSDiva Software, version 8.0.2) with a 100-µm nozzle. The cell suspensions were first gated on forward scatter, then within this population based on eGFP expression. eGFP-expressing cells were sorted into HBSS + 0.1% BSA for downstream processing on the 10x Genomics Chromium platform. Samples were kept on ice before and after FACS, and the chamber and collection tubes were maintained at 4℃ during sorting.
scRNA-seq library preparation Preparation of scRNA-seq libraries was carried out using a Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, #PN-1000075). We input between 10 and 20k cells per lane on a Chromium Chip G and followed the manufacturer protocol for transcriptomic library preparation.  STICR barcode library preparation STICR barcodes were subamplified from each 10X cDNA library using the Q5 Hot Start High Fidelity 2× master mix (NEB, M0494). In brief, 10 μl of cDNA was used as template in a 50 μl PCR reaction containing STICR barcode read 1 and 2 primers (0.5 μM, each) targeting the region immediately upstream of the STICR viral index/barcode as well as the partial Illumina Read1 sequence added during cDNA library preparation (Extended Data Table 3), using the following program: 1, 98 °C, 30 s; 2, 98 °C, 10 s; 3, 62 °C, 20 s; 4, 72 °C, 10 s; 5, repeat steps 2–4 12 times; 6, 72 °C, 2 min; 7, 4 °C, hold. Following PCR amplification, a 0.8–0.6 dual-sided size selection was performed using Ampure XP beads (Beckman Coulter, A63881). The libraries were quantified by Tapestation (Agilent) and pooled for sequencing.

value: Brain

value: Wild type


title: STICR-ST39_T_1, Clonal barcodes library

status: Public on Jul 31 2026

type: SRA

state: CA

country: USA

description: Library name: STICR-ST39_T_1

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Mus musculus

tag: tissue

tag: genotype


title: SW620cell,SOWAHA,siRNA ,NC1

city: Chengdu

first: Xiaohong

middle: Huang

last: Yi

state: Sichuan

address: 1166 Liutai Avenue, Wenjiang District, Chengdu City

department: School of Basic Medical Science

country: China

institute: CDUTCM

library_source: transcriptomic

data_processing:
A cDNA library constructed by technology from the pooled RNA from < sample description > samples of < researchspecies > was sequenced run with Illumina NovaseqTM 6000 sequence platform.
Using the Illumina paired-end RNA-seq,approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.
get high quality clean reads, reads were further filtered by Cutadapt,(https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9).including the Q20, Q30 and GC-content of the clean data.
The raw sequence data have been extractd and normolizated.
Assembly: GRCh38
Supplementary files format and content: text file including raw read counts for each sample
Supplementary files format and content: text file including raw fpkm values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: colorectum cancer

growth_protocol: Colorectal cells SW620 were obtained from ATCC (Manassas, USA). Cell lines were maintained in DMEM medium (Gibco, ThermoFisher, China) supplemented with 100U/ml penicillin-streptomycin (HyCloneTM, Utah, USA) and 10% fetal bovine serum (FBS, ExCell, China), at 37 ℃ in a 5% CO2 incubator.

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: SOWAHA-siRNA (siSOWAHA)/NC-siRNA (siNC) and transfection reagent (Dharma FECT1, Dharmacon Reagents, USA)  were mixed and left to stand for 30 minutes. The resulting mixture was then evenly added to the bottom of a 10cm plate, with 7× 105 cells seeded in each plate. After 72 hours of transfection, the total mRNA was extracted and the transfection efficiency of siRNA was measured.

value: colorectum cancer

tag: cell line

value: WT

tag: treatment

value: knock-down


title: DKD Glomeruli, rep 1

city: Beijing

first: Lanfang

last: Li

state: State...

address: China-japan Friendship Hospital

institute: China-japan Friendship Hospital

description: Library name: Sample 4

data_processing:
The fastp software  were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
The HISAT2 were used to map reads to the reference genome.
The mapped reads of each sample were assembled using StringTie with default parameters.
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare .
StringTie was used to perform expression level for mRNAs by calculating FPKM(FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and with parametric F-test comparing nested linear models (p value < 0.05) by R package edgeR .
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Glomeruli

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: Glomeruli

value: DKD


title: STICR-ST39_S_2, Clonal barcodes library

description: Library name: STICR-ST39_S_2


title: NO07G02030 knockout, normal light, rep 3

city: Qingdao

first: Yanhai

last: Gong

address: No.189 Songling Road

department: single cell center

institute: qibebt, cas

description:
Library name: NL_KO3
NL_KO3

data_processing:
RNA-seq data were mainly analyzed with the nf-core/rnaseq pipeline (v3.14.0).
Raw reads underwent quality control and adapter trimming using Trim Galore (https://github.com/FelixKrueger/TrimGalore). Ribosomal RNA reads were subsequently removed with SortMeRNA (Kopylova et al., 2012).
The resulting high-quality reads were aligned to the N. oceanica IMET1 reference genome (Gong et al., 2020) using STAR (Dobin et al., 2013), with intron length parameters set to “--alignIntronMin 20 --alignIntronMax 3000”. Duplicate reads were marked using Picard (http://broadinstitute.github.io/picard/).
Transcript abundance was then quantified with Salmon (Patro et al., 2017). Differential gene expression analysis was performed based on the Salmon output using the nf-core/differentialabundance pipeline (v1.5.0).
Assembly: NoIMET1v2
Supplementary files format and content: gene_counts_matrix.txt : tab-delimited text file includes raw counts for genes in each sample
Supplementary files format and content: gene_tpm_matrix.txt : tab-delimited text file includes TPM values for genes in each sample

organism: Nannochloropsis oceanica

source_name: Colonial

growth_protocol: Nannochloropsis oceanica IMET1 was inoculated into the modified f/2 liquid medium, which was prepared with 35 g L-1 sea salt (Realocean, USA), 1 g L-1 NaNO3, 67 mg L-1 NaH2PO4*H2O, 3.65 mg L-1 FeCl3*6H2O, 4.37 mg l-1 Na2EDTA*2H2O, a trace metal mixture (0.0196 mg L-1 CuSO4*5H2O, 0.0126 mg L-1 NaMoO4*2H2O, 0.044 mg L-1 ZnSO4*7H2O, 0.01mg L-1 CoCl2, and 0.36 mg L-1 MnCl2*4H2O), and a vitamin mixture (2.5 µg L-1 VB12, 2.5 µg L-1 biotin, and 0.5 µg L-1 thiamine HCl) (Kang et al., 2015). The cells were first cultured in f/2 medium at 25 °C with 50±5 μmol m-2 s-1 continuous irradiation in a 1 L column reactor (inner diameter: 5 cm). The seed cultures were bubbled with air. At the logarithmic growth phase (OD750=2), the cells were harvested via centrifugation and then washed with fresh medium, before being used for the following experiments.

extract_protocol:
Total RNA was isolated from wild-type (WT) and mutant cells using TRIzol reagent (Invitrogen, CA, USA) following the manufacturer’s standard protocol. RNA purity and concentration were determined with a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA), while RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
For library preparation, 2 μg of qualified total RNA per sample was used as the starting material. RNA-seq libraries were subsequently constructed with the VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) in accordance with the manufacturer’s guidelines. The final library was sequenced on an Illumina instrument with 2×150-bp reads.

treatment_protocol: For both mutant and wild-type (WT) strains, cells were cultured in liquid f/2 medium and maintained at 25 °C under a light intensity of 50 μmol photons m-2 s-1 with aeration until they reached the logarithmic growth phase (OD750 = 2). Subsequently, the cells were harvested and resuspended to an OD750 of 0.5, with three biological replicates. The cultures were then incubated for eight days in flasks at 25 °C, under a fixed light intensity, with shaking at 200 rpm. Two light treatments were set up: high light (about 300 μmol photons·m-2·s-1) and normal light (about 50 μmol photons·m-2·s-1).

tag: cell type

value: Colonial

value: Normal light

tag: strain


title: SVS5 RNA-seq Rep3

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

country: India

institute: Indian Institite of Technology Jammu

data_processing:
BCL files were converted to FASTQ files using bcl2fastq Conversion Software version 2.16.0.10 (Illumina).
FASTQ files were mapped against a reference human genome hg38 with the splice-aware aligner HISAT2 (v2.2.1) to generate BAM files
Obtained aligned files (BAM format) were subjected to quantification using featureCounts from Subread package (v2.0.0). The reads were quantified for Gencode transcript annotation release v38 (corresponds to genome hg38).
Generated matrix file from read quantification was then used for differential expression (DE) analysis. DE analysis was performed using Bioconductor package DESeq2.
Assembly: hg38
Supplementary files format and content: Matrix containing tab-delimited data includes raw read count values for individual genes in each Sample.

growth_protocol: Tissue sections were stored in at least 10 volumes of RNAlater-ICE (AM7030; Ambion) at -80°C before total RNA extraction.

extract_protocol:
Total RNA from cells was extracted using RNeasy Micro Kit  according to the manufacturer’s instructions.
Quality and integrity of total RNA was controlled on 5200 Fragment Analyzer System (Agilent Technologies)). The RNA sequencing library was generated from 50 ng total RNA using NEBNext® Single Cell/Low Input RNA Library to manufacture´s protocols. The libraries were treated with Illumina Free Adapter Blocking and were sequenced on Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit (100 cycles, paired end run 2x 50 bp) with an average of 5 x10 7 reads per RNA sample.

treatment_protocol: For RNA extraction, brain tissue specimens were cut off and further slit to smaller pieces. These pieces were transferred into vials containing ceramic beads (Precellys system, CK14L; Peqlab) and RLT lysis buffer from RNeasy Micro Kit (Qiagen)

value: Solid vestibular schwannoma


title: NO07G02030 overexpression, normal light, rep 1

description:
Library name: NL_OE1
NL_OE1


title: Control Glomeruli, rep 3

description: Library name: Sample 3

value: Control


title: STICR-ST39_S_1, Clonal barcodes library

description: Library name: STICR-ST39_S_1


title: NO07G02030 knockout, normal light, rep 2

description:
Library name: NL_KO2
NL_KO2


title: SVS2 RNA-seq Rep2


title: Control Glomeruli, rep 2

description: Library name: Sample 2


title: STICR-ST39_R, Clonal barcodes library

description: Library name: STICR-ST39_R


title: SVS1 RNA-seq Rep1


title: DU 145 cells, DMOS 48h, rep3

city: shang hai

first: Yi

last: Jiayan

address: pujian road

institute: SHANG HAI JIAO TONG UNIVERSITY

description: Library name: sample6

data_processing:
The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China). Raw data (raw reads) were processed using Trimmomatic
The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count
Gene Set Enrichment Analysis (GSEA) was performed using GSEA software8-9. The analysis waswww.oebiotech.com used a predefined gene set, and the genes were ranked according to the degree of differential expression in the two types of samples. Then it is tested whether the predefined gene set was enriched at the top or bottom of the ranking list.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: prostate

extract_protocol:
Total RNA was extracted using the TRIzol Reagent (Ambion, 15596026) according to the manufacturer’s protocol.l. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: prostate

value: epithelial cell


title: NO07G02030 knockout, normal light, rep 1

description:
Library name: NL_KO1
NL_KO1


title: Control Glomeruli, rep 1

description: Library name: Sample 1


title: STICR-ST39_O, Clonal barcodes library

description: Library name: STICR-ST39_O


title: DU 145 cells, DMOS 48h, rep2

description: Library name: sample5


title: CVS8 RNA-seq Rep3

value: Cystic vestibular schwannoma


title: Environmental Enrichment

city: Tiruchirappalli

first: Koilmani

last: Emmanuvel Rajan

address: School of Life Sciences

department: Animal Science

institute: Bharathidasan University

description:
Library name: EE
Column name in gene_counts.txt: EE

data_processing:
Raw FASTQ reads were pre-processed and assessed for quality using Fastp (v.0.023.4).
The rRNA reads from the trimmed fastq files were filtered using Ribodetector v.0.3.1.
The reads were aligned to the reference genome (Ensembl- GRCm39) using STAR aligner v.2.7.9a.
The total gene counts were obtained FeatureCounts v.2.0.1.
Assembly: GRCm39
Supplementary files format and content: Text file includes raw counts for each sample

organism: Mus booduga

source_name: Hippocampus

extract_protocol:
Total RNA was extracted from the hippocampus using All prep DNA/RNA kit (Cat# 80204; Qiagen). The quantity and quality of RNA were examined using Qubit fluorometer (Cat# Q32855; Thermofisher) and Nanodrop ™1000 respectively.
The library preparation was carried out using NEBNext Ultra II Directional RNA library Prep Kit (NEB#E7770). Final libraries were quantified using Qubit 4.0 fluorometer (Thermofisher #Q32855) using DNA HS assay kit (Thermofisher #Q32851) following manufacturer’s protocol. Obtained results are presented below in the table. To identify the insert size of the library, we queried it on Tapestation 4150 (Agilent) utilizing high sensitive D1000 screentapes (Agilent #5067- 5582) following manufacturers’ protocol.

value: Hippocampus

value: Treated


title: STICR-ST39_H, Clonal barcodes library

description: Library name: STICR-ST39_H


title: CVS4 RNA-seq Rep2


title: DKD kidney, rep 3

description: Library name: Sample 6

source_name: Kidney

value: Kidney


title: Standard Condition

description:
Library name: SC
Column name in gene_counts.txt: SC

value: Stressed


title: DKD kidney, rep 2

description: Library name: Sample 5


title: STICR-ST39_C, Clonal barcodes library

description: Library name: STICR-ST39_C

value: Brain

value: Wild type


title: CVS1 RNA-seq Rep1


title: Direct Wild

description:
Library name: DW
Column name in gene_counts.txt: DW


title: STICR-ST38_S_2, Clonal barcodes library

description: Library name: STICR-ST38_S_2


title: VS1761_MOC1_Tumor_mSuvKO1_S99_rep4_rnaseq

city: ROCKVILLE

first: Vassiliki

last: Saloura

state: MARYLAND

address: 11705 STONEWOOD LN

department: TGMB

institute: NCI

description:
Library name: VS1761
STAR_RG/VS1761_MOC1_Tumor_mSuvKO1_S99.RG.ssAligned.out.s.bam

data_processing:
VS912-VS1049: Base calling was performed with RTA (v3.10.30), and reads were demultiplexed with Bcl2fastq (v2.20). Raw reads were adaptor-trimmed using Cutadapt (v1.18) and aligned to the human genome (hg38; GENCODE 30) using STAR (v2.7.0f). Raw read counts for exon regions were quantified at the gene level using the featureCount function in Subread (v2.0.3) with -s 2 option.
VS1752-VS1761: Reads were demultiplexed by Illumina Dynamic Read Analysis for GENomics (Dragen; v4.2.0_b.29). Raw reads were adaptor-trimmed using Cutadapt (v4.0) and aligned to the mouse genome (GRCm39; GENCODE M39) using STAR (v2.7.11b). Raw read counts for exon regions were quantified at the gene level using the featureCount function in Subread (v2.0.3) with -s 2 option.
Assembly: hg38, GRCm39
Supplementary files format and content: tab-delimited text files contain abundance of gene-level raw read counts.

source_name: Flank tumor tissue

extract_protocol:
RNA was extracted from HN-SCC-151 cells using the Direct-zol RNA miniprep kit (Zymo Research, Irvine, CA). For the mouse tumors, 30mg of tissue were sub-sampled from frozen parent samples into pre-chilled Lysing Matrix A 2.0 ml tubes (MP Biomedical).  RNA lysates were generated by adding 700uL of Buffer RLT (Qiagen) containing 1% 2-mercaptoethanol to each tube containing tissue and homogenizing 2 x 30 sec. at high speed in a Bead Ruptor 12 (Omni, Inc.).  12.5 ug of linear polyacrylamide (LPA) (bioWorld cat#10510000) was added to each sample and total RNA was purified with a QIAcube Connect MDx using the RNeasy Mini reagent and protocol (Qiagen) with DNase I treatment.  RNA was eluted in 50uL of RNase-free water.
VS912-VS1049: Libraries for HN-SCC-151 cells were prepared using the Illumina® Stranded mRNA Prep and sequenced on NextSeq 2000 P2 with 2x51 bp paired-end reads. VS1752-VS1761: Libraries for MOC1 cells were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (E7760) as described in the manufacturer’s manual and sequenced on NextSeq 2000 with 2x101 bp paired-end reads.

value: Flank tumor tissue

value: mouse oral squamous cell carcinoma-derived tumor

value: Suv420h1 knockout


title: lInsula_sample1

first: xiaoqun

last: wang

state: Beijing

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

institute: Chinese Academy of Sciences

data_processing:
data were processed with the scanpy downstream analysising pipeline
Assembly: hg19
Supplementary files format and content: a h5ad file include raw gene expression counts for each sample

source_name: cerebral cortex

extract_protocol: The libraries were generated by using the Chromium Next GEM Single Cell 3' Kit v3 according to the 10x GENOMICS official instructions, and processed on the Illumina platform for sequencing with 150 bp paired-end reads

value: cerebral cortex


title: STICR-ST38_R, Clonal barcodes library

description: Library name: STICR-ST38_R


title: rTP_sample1


title: control  kidney, rep 3

description: Library name: Sample 3


title: VS1760_MOC1_Tumor_mSuvKO1_S97_rep3_rnaseq

description:
Library name: VS1760
STAR_RG/VS1760_MOC1_Tumor_mSuvKO1_S97.RG.ssAligned.out.s.bam


title: control  kidney, rep 2

description: Library name: Sample 2


title: DKD kidney, rep 1

description: Library name: Sample 4

value: DKD


title: STICR-ST38_O, Clonal barcodes library

description: Library name: STICR-ST38_O


title: lTP_sample1


title: VS1759_MOC1_Tumor_mSuvKO1_S96_rep2_rnaseq

description:
Library name: VS1759
STAR_RG/VS1759_MOC1_Tumor_mSuvKO1_S96.RG.ssAligned.out.s.bam


title: control  kidney, rep 1

description: Library name: Sample 1


title: STICR-ST38_H_2, Clonal barcodes library

description: Library name: STICR-ST38_H_2


title: lITGm_sample1


title: VS1757_MOC1_Tumor_mSuvKO1_S93_rep1_rnaseq

description:
Library name: VS1757
STAR_RG/VS1757_MOC1_Tumor_mSuvKO1_S93.RG.ssAligned.out.s.bam


title: Nr3c1_Telencephalon_KO

city: Hangzhou

first: Xiaoping

last: Han

state: Zhejiang

address: Yuhangtang Road 866

department: Center for Stem Cell and Regenerative Medicine

institute: Zhejiang University School of Medicine

description:
Library name: Nr3c1_Telencephalon_KO_CUTnTag
CUT&Tag

library_source: genomic

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were aligned to mm10 using bowtie2 (v2.5.2). Reads with quality > 2 were selected and sorted by query names. BAM files were converted to BEDPE files then to fragment files (sorted BED files). Fragments in the blacklist regions of mm10 (https://www.encodeproject.org/files/ENCFF547MET/) were removed. BED files were converted to BW files for subsequent visualization.
The raw sorted BED files (blacklist regions were not removed) are supported as supplementary files for individual samples.
Assembly: mm10
Supplementary files format and content: BED  files including sorted fragments
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Telencephalon

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Concanavalin A (ConA) coated magnetic beads were freshly activated with Ca²⁺ and Mn²⁺. Nuclei were extracted and a total of 10,000 nuclei were incubated with activated ConA beads. Supernatant was next removed, and beads were incubated with antibody (1:50) on a rotator at 4°C overnight, followed by incubated with secondary antibody (1:100) for 1 hr at room temperature. Beads were washed three times and suspended in dig300-wash buffer pre-mixed with pG-Tn5 (1:100), incubated for 1 hr at room temperature. After washing beads for three times, tag buffer was added to each well, then incubated on a rotator at 37 °C for 1 hr. After centrifugation, beads were washed once and resuspended. Lysis buffer was added to each well, and incubated for 2 hr at 65 °C. After adding 10% Tween20, TruePrep CUT&Tag Amplification Mix (Vazyme), 10 mM MGI-P5, and 10 mM MGI-P7 primer were added. Then PCR program was performed. Finally, 1.5 × VAHTS DNA Clean Beads were used to purify the library.

value: Telencephalon

tag: antibody

value: Mecp2 KO

tag: Sex

value: Male

tag: age

value: 8 weeks


title: STICR-ST38_H_1, Clonal barcodes library

description: Library name: STICR-ST38_H_1


title: rMTGm_sample1


title: Nr3c1_SpinalCord_KO

description:
Library name: Nr3c1_SpinalCord_KO_CUTnTag
CUT&Tag

source_name: SpinalCord

value: SpinalCord


title: STICR-ST38_C, Clonal barcodes library

description: Library name: STICR-ST38_C


title: VS1755_MOC1_Tumor_Suv-WT_S89_rep4_rnaseq

description:
Library name: VS1755
STAR_RG/VS1755_MOC1_Tumor_Suv-WT_S89.RG.ssAligned.out.s.bam


title: VS1756_MOC1_Tumor_Suv-WT_S92_rep5_rnaseq

description:
Library name: VS1756
STAR_RG/VS1756_MOC1_Tumor_Suv-WT_S92.RG.ssAligned.out.s.bam


title: lSTGp_sample1


title: rSTGp_sample1


title: Optic cup, rd10, P10, biol replicate 1

city: Pozzuoli

first: Santiago

last: Negueruela

address: Via Campi Flegrei, 34

department: Genetic Medicie

country: Italy

institute: Telethon Institute of Genetics and Medicine (TIGEM)

description:
Library name: rd10_P10
10X Genomics

data_processing:
10x Genomics Cell Ranger v7.0.0
Assembly: mm10 [refdata version 2020-A from Cell Ranger]
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Optic cup

growth_protocol: Maintenance of the mice was on a regular 12/12-h light/dark cycle, temperature of 20–24°C, and humidity of 54–65%, with ad libitum access to food and water.

extract_protocol:
Eye samples were dissociated using the Worthington Papain Dissociation System, according to the manufacturer's instructions.
Single Cell 3′ Library and Gel Bead Kit V3.1 (10x Genomics)

value: Optic cup

tag: time point

tag: batch


title: Optic cup, WT, P18,  biolreplicate 1

description:
Library name: WT_P18
10X Genomics

value: WT


title: STICR-ST31_T, Clonal barcodes library

description: Library name: STICR-ST31_T


title: VS1754_MOC1_Tumor_Suv-WT_S88_rep3_rnaseq

description:
Library name: VS1754
STAR_RG/VS1754_MOC1_Tumor_Suv-WT_S88.RG.ssAligned.out.s.bam


title: STICR-ST31_S, Clonal barcodes library

description: Library name: STICR-ST31_S


title: Nr3c1_Diencephalon_KO

description:
Library name: Nr3c1_Diencephalon_KO_CUTnTag
CUT&Tag

source_name: Diencephalon

value: Diencephalon


title: Nr3c1_Pituitary_KO

description:
Library name: Nr3c1_Pituitary_KO_CUTnTag
CUT&Tag

source_name: Pituitary

value: Pituitary


title: lMFGps_sample1


title: VS1753_MOC1_Tumor_Suv-WT_S87_rep2_rnaseq

description:
Library name: VS1753
STAR_RG/VS1753_MOC1_Tumor_Suv-WT_S87.RG.ssAligned.out.s.bam


title: Nr3c1_Cerebellum_KO

description:
Library name: Nr3c1_Cerebellum_KO_CUTnTag
CUT&Tag

source_name: Cerebellum

value: Cerebellum


title: VS1752_MOC1_Tumor_Suv-WT_S86_rep1_rnaseq

description:
Library name: VS1752
STAR_RG/VS1752_MOC1_Tumor_Suv-WT_S86.RG.ssAligned.out.s.bam


title: Luhmes + vehicle_diff8 [ATAC-seq]

city: Paris

first: Philippe

last: Ravassard

address: ICM 47 bd de l'hopital

country: France

institute: Paris Brain Institute

data_processing:
Quality of raw data was evaluated with FastQC.
Raw sequences were cleaned by removing low quality trailing bases, technical sequences (adapters) and reads shorter than 50 (after trimming)
ATAC-seq reads were aligned to the hg38 genome using Bowtie2.
Duplicates reads were discared with the Picard tools.
Peaks were called uing MACS with the significance cut-off q-value <=0.05
Assembly: hg38
Supplementary files format and content: Format TSV narrowPeak

source_name: Mid brain

growth_protocol: LUHMES cells were differentiated for 6 days in  Advanced DMEM/F12, 1% N-2 supplement, 1% P/S, L-Glutamine 2 mM,dbcAMP 1 mM, GDNF, 2 ng/mLand tetracycline 1 μg/mL

extract_protocol:
Nuclear were purified by centrifugation after cell lysis in 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2-6H2O, 0.1% IGEPAL CA-630
Nuclear were treated with Tn5 transposase and DNA amplified through 2 rounds of 9 cycle PCR amplification

treatment_protocol: Luhmes cells were treated for 8 hours with a combination of Antimycin A (25µM) and Oligomycin (10µM) and compared to differentiated Luhmes cells  treated with vehicle (DMSO).

value: Mid brain

value: LUHMES

value: Dopaminergic neurons

value: vehicle


title: Luhmes + vehicle_diff7 [ATAC-seq]


title: STICR-ST31_H, Clonal barcodes library

description: Library name: STICR-ST31_H

value: Brain

value: Wild type


title: Infected_8h

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

description:
Library name: 107717
10x Visium HD, FFPE protocol

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files. Deconvolution was carried out using a public single cell reference using the RCTD algorithm.
Sequences were aligned to a mm10 and VEEV (ZPC738-eGFP-Tav) combination genome to gene expression count using Space Ranger's default settings
VEEV designed probes were added to the 10x Visium HD mouse probe set v2 list for transcript identification during alignment
Assembly: mm10
Supplementary files format and content: Cytaimage (H&E) Spatial images in tiff format
Supplementary files format and content: Full Images in tiff format
Supplementary files format and content: Fiducials image registrations in json format
Supplementary files format and content: Barcodes per sample in tsv.gz format (Filtered): list of spatial barcodes
Supplementary files format and content: Features per sample in tsv.gz format (Filtered): list of gene IDs
Supplementary files format and content: Matrix per sample in Matrix Market Exchange format (Filtered): gene expression count data
Supplementary files format and content: Image scale factors per sample in json format
Library strategy: Spatial Transcriptomics

source_name: Lymphoid

extract_protocol:
FFPE tissues were embedded in formalin.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides and Reagent kit according to manufacturer's construction.

value: Lymphoid

value: VEEV-Infected


title: STICR-ST31_C, Clonal barcodes library

description: Library name: STICR-ST31_C

source_name: Brain


title: Nr3c1_BrainStem_KO

description:
Library name: Nr3c1_BrainStem_KO_CUTnTag
CUT&Tag

source_name: BrainStem

value: BrainStem

value: Mecp2 KO


title: Nr3c1_Telencephalon_WT

description:
Library name: Nr3c1_Telencephalon_WT_CUTnTag
CUT&Tag

value: Telencephalon

value: Male

value: 8 weeks


title: Luhmes + vehicle_diff6 [ATAC-seq]

value: WT


title: STICR-ST30_S, Clonal barcodes library

description: Library name: STICR-ST30_S


title: Luhmes + AntimycinA-Oligomycin_diff9 [ATAC-seq]

value: Antimycin-A + Oligomycin


title: Mock_8h

description:
Library name: 107716
10x Visium HD, FFPE protocol

value: Mock


title: Luhmes + AntimycinA-Oligomycin_diff8 [ATAC-seq]


title: Nr3c1_Diencephalon_WT

description:
Library name: Nr3c1_Diencephalon_WT_CUTnTag
CUT&Tag

value: Diencephalon


title: STICR-ST30_T, Clonal barcodes library

description: Library name: STICR-ST30_T


title: STICR-ST30_R, Clonal barcodes library

description: Library name: STICR-ST30_R


title: Luhmes + AntimycinA-Oligomycin_diff7 [ATAC-seq]

value: Mid brain


title: STICR-ST30_OB, Clonal barcodes library

description: Library name: STICR-ST30_OB


title: Mouse #18624, Vehicle, biol rep 4

city: Durham

first: Christine

middle: E

last: Eyler

state: NC

address: 308 Research Dr, LSRC B327C

department: Department of Radiation Oncology

institute: Duke University

description:
Library name: 18624
Column name in raw_counts_AllSamples.txt and TPM_AllSamples.txt: LD_18624

data_processing:
Quality of sequencing reads was assessed with FastQC.
Transcripts were quantified using Salmon 1.10.0 and expression estimates were imported into R with tximport 1.32.0.
Transcripts were aggregated to the gene level using the Mus musculus Ensembl dataset.
Sample data was prefiltered to remove rows with low counts before DESeq2 1.44.0 analysis to identify differentially expressed genes.
Assembly: mm10
Supplementary files format and content: Tab-delineated text file raw_counts_AllSamples.txt includes raw counts for each sample separated by Ensembl unique gene IDs.
Supplementary files format and content: Tab-delineated text file TPM_AllSamples.txt includes TPM values for each sample separated by Ensembl unique gene IDs.

source_name: small intestine crypts

growth_protocol: C57BL/6N (wt) mice were grown under standard housing conditions.  Experiment was conducted at 12 weeks of age. Vehicle mice were housed alongside NCG-023-treated mice in the same cages to minimize the likelihood of cage-by-cage variation biasing the experimental results

extract_protocol:
Total RNA was extracted using the RNEasy Plus Mini Kit (Qiagen, 74134), according to manufacturer's instructions. RNA was quantified with the Qubit RNA Broad Range Assay Kit (Invitrogen, Q10210) and 1 μg of RNA was input into library construction.
Libraries were prepared using the NEBNext rRNA Depletion Kit v2 (NEB, E7400) followed by the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760), according to manufacturer's instructions.

treatment_protocol: Mice were treated with either 50 mg/kg NCGC-023 (Lats1/2 inhibitor) or vehicle (5% DMSO, 19% 2-hydroxypropyl-beta-cyclodextrin, in sterile 1X PBS) at 24 and 2 hours prior to harvest of intestinal crypts.

value: small intestine crypts

value: C57BL/6N (wt)

value: Vehicle (-24, -2) harvested at time of sham-IR

value: Female


title: Luhmes + AntimycinA-Oligomycin_diff6 [ATAC-seq]

value: LUHMES

value: Dopaminergic neurons


title: Nr3c1_BrainStem_WT

description:
Library name: Nr3c1_BrainStem_WT_CUTnTag
CUT&Tag


title: Mouse #18622, Vehicle, biol rep 3

description:
Library name: 18622
Column name in raw_counts_AllSamples.txt and TPM_AllSamples.txt: LD_18622


title: Luhmes + vehicle_diff4 [RNA-seq]

data_processing:
Raw sequences were cleaned by removing low quality trailing bases, technical sequences (adapters) and reads shorter than 50 (after trimming)
Cleaned sequences were map-aligned to the reference genome with HISAT2 and converted to ordered BAM files with Samtools
StringTie was used to assemble transcripts, estimate their abundance and to merge transcripts annotations for all samples into a unified GTF catalog
Custom code was used to merge this unknown transcripts from this unified catalg with the Gencode catalog
The Dragen RNA-seq pipeline was used to quantify transcripts from this merged catalog
Assembly: hg38
Supplementary files format and content: Format TSV: gene and transcript counts in each sample
Supplementary files format and content: Format TSV differential expression of coding genes stress vs control
Supplementary files format and content: Format TSV differential expression of lncRNA genes (including de novo annotated lncRNAs) stress vs control
Supplementary files format and content: GTF file of de novo annotated lncRNAs

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Libraries for RNA-seq were prepared using KAPA mRNA hyperprep (Roche Diagnostic) following manufacturer's protocols.

value: vehicle


title: STICR-ST30_C, Clonal barcodes library

description: Library name: STICR-ST30_C

value: Brain

value: Wild type


title: Mouse #18621, 50 mg/kg NCG-023, biol rep 3

description:
Library name: 18621
Column name in raw_counts_AllSamples.txt and TPM_AllSamples.txt: LD_18621

value: 50 mg/kg NCG-023 IP (-24, -2) harvested at time of sham-IR


title: H3K27ac_Telencephalon_KO

description:
Library name: H3K27ac_Telencephalon_KO_CUTnTag
CUT&Tag

value: Telencephalon

value: Mecp2 KO

value: Male


title: H3K27ac_SpinalCord_KO

description:
Library name: H3K27ac_SpinalCord_KO_CUTnTag
CUT&Tag

value: SpinalCord

value: 8 weeks


title: STICR-ST29_S, Clonal barcodes library

description: Library name: STICR-ST29_S


title: Mouse #18620, Vehicle, biol rep 2

description:
Library name: 18620
Column name in raw_counts_AllSamples.txt and TPM_AllSamples.txt: LD_18620


title: Luhmes + vehicle_diff3 [RNA-seq]

value: WT


title: H3K27ac_Pituitary_KO

description:
Library name: H3K27ac_Pituitary_KO_CUTnTag
CUT&Tag

value: Pituitary


title: STICR-ST29_R, Clonal barcodes library

description: Library name: STICR-ST29_R


title: Mouse #18619, 50 mg/kg NCG-023, biol rep 2

description:
Library name: 18619
Column name in raw_counts_AllSamples.txt and TPM_AllSamples.txt: LD_18619

value: small intestine crypts


title: H3K27ac_Diencephalon_KO

description:
Library name: H3K27ac_Diencephalon_KO_CUTnTag
CUT&Tag

value: Diencephalon


title: STICR-ST29_OB, Clonal barcodes library

description: Library name: STICR-ST29_OB


title: Luhmes + AntimycinA-Oligomycin 4 technical replicates_diff5 [RNA-seq]

value: Mid brain

value: Antimycin-A + Oligomycin


title: Mouse #18618, Vehicle, biol rep 1

description:
Library name: 18618
Column name in raw_counts_AllSamples.txt and TPM_AllSamples.txt: LD_18618

value: C57BL/6N (wt)

value: Vehicle (-24, -2) harvested at time of sham-IR


title: H3K27ac_Cerebellum_KO

description:
Library name: H3K27ac_Cerebellum_KO_CUTnTag
CUT&Tag

value: Cerebellum


title: STICR-ST29_H, Clonal barcodes library

description: Library name: STICR-ST29_H

value: Brain


title: Luhmes + AntimycinA-Oligomycin 4 technical replicates_diff4 [RNA-seq]

value: LUHMES

value: Dopaminergic neurons


title: Mouse #18617, 50 mg/kg NCG-023, biol rep 1

description:
Library name: 18617
Column name in raw_counts_AllSamples.txt and TPM_AllSamples.txt: LD_18617

value: 50 mg/kg NCG-023 IP (-24, -2) harvested at time of sham-IR


title: H3K27ac_BrainStem_KO

description:
Library name: H3K27ac_BrainStem_KO_CUTnTag
CUT&Tag

value: BrainStem

value: Mecp2 KO


title: STICR-ST29_C, Clonal barcodes library

description: Library name: STICR-ST29_C

value: Wild type


title: HT-29 Combo replicate 3

type: RNA

city: miami

first: RIMPI

last: KHURANA

state: FL

address: Room 6112B, Rosenstiel Medical Science Building (RMSB),1600 NW 10th Avenue

institute: University of miami

description: NanoString nCounter Human Tumor Signaling 360 panel

hyb_protocol: RNA hybridized with nCounter Human Tumor Signaling 360 panel according to manufacturer protocol.

scan_protocol: Samples scanned on nCounter Digital Analyzer using standard settings.

data_processing: RCC files processed using nSolver 4.0 Advanced Analysis module with standard normalization and Benjamini–Hochberg correction.

label_protocol: n/a (NanoString uses direct detection, no labeling required)

growth_protocol: HT-29 human colorectal cancer cells were cultured in McCoy’s 5A medium with 10% FBS, penicillin, and streptomycin at 37°C with 5% CO₂.

extract_protocol: RNA extracted using NanoString protocols. RCC files generated for each sample.

treatment_protocol: Cells treated with Vehicle (Ctrl), MV-GFP (GFP), Triptolide (TRP), or MV-GFP + TRP (Combo) for 48 h. Three biological replicates per treatment.

tag: agent

value: Combo


title: STICR-ST28_S, Clonal barcodes library

description: Library name: STICR-ST28_S


title: H3K27ac_SpinalCord_WT

description:
Library name: H3K27ac_SpinalCord_WT_CUTnTag
CUT&Tag

value: SpinalCord

value: WT

value: Male

value: 8 weeks


title: shADAT2_2_Input

city: Boston

first: Qi

last: Liu

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

data_processing:
After adapter-trimming and quality-filtering, the sequences were further filtered to exclude rRNA and tRNA reads by aligning to human rRNA and tRNA sequence which were retrieved from Ensembl and GtRNAdb databases , respectively. The cleaned ribosome-protected fragments (RPFs) were aligned to the human gene models (GENCODE, hg19) using Bowtie with a maximum one mismatch allowed. The translation efficiency (TE) was calculated by dividing RPF abundancy on CDS by its mRNA abundancy. We used 1.5 fold change of TE to define the differential translation genes.
Assembly: hg19
Supplementary files format and content: xls file containing translation efficiency for each sample
Library strategy: Ribo-Seq

growth_protocol: LPS853 cells were cultured in IMDM medium supplemented with 15% FBS and 1X penicillin/streptomycin

extract_protocol:
Ribosome footprinting was performed according to TruSeq® Ribo Profile system (Illumina)
For library preparation the NEBNext Multiplex Small RNA Library Prep set for Illumina (New England Biolabs) was used. In parallel, total RNA input samples were isolated, and fragmented and the library obtained using the TruSeq stranded total RNA Kit (Illumina).

treatment_protocol: 2 shRNAs for ADAT2. shGFP used as a control

tag: molecule subtype

value: RiboMinus mRNA


title: HT-29 Combo replicate 2


title: H3K27ac_Pituitary_WT

description:
Library name: H3K27ac_Pituitary_WT_CUTnTag
CUT&Tag

value: Pituitary


title: HT-29 Combo replicate 1


title: STICR-ST28_R, Clonal barcodes library

description: Library name: STICR-ST28_R

data_processing:
scRNA-seq analysis 10X transcriptomic libraries were processed using CellRanger (version 7.2.0) and were aligned to the mouse transcriptome mm10-2020-A. Cellranger outputs were processed using Seurat (version 5.2.0). Datasets were processed to remove cells with fewer than 1,000 or greater than 100,000 reads, fewer than 500 or greater than 10,000 genes, or more than 20% of reads corresponding to mitochondrial genes. Doublets were identified and removed by using DoubletFinder (version 2.0.4). Libraries were integrated using Seurat’s “SCTransform” and Harmony (version 0.1.162). Libraries of the seurat project including all regions were integrated by Seurat’s “SCTransform”. Seurat projects of each brain region were integrated by Seurat’s “SCTransform” function and Harmony. To identify clusters, we constructed a shared nearest neighbor (SNN) graph using the 'FindNeighbors' function, and applied clustering through the 'FindClusters' function in Seurat. Iterative clustering to identify subtypes of cells was performed by subsetting into different major cell types (glutamatergic neurons, GABAergic neurons, glia) and using the “FindSubCluster” function in Seurat. Cell identities determined through analysis of iterative clusters were re-assigned to cells in the full Seurat object. Differential expression analysis was conducted using Seurat's “FindMarkers” and “FindAllMarkers” function, and gene expression in clusters was manually analyzed for known markers of given cell types.
STICR barcodes analysis STICR barcode analysis was performed using custom scripts, as previously described in Delgado et al57. First, BBMap (BBMap; sourceforge.net/projects/bbmap/) was used to remove low-quality reads and then extract reads containing STICR barcode sequences. Then, BBMap was used to extract individual STICR barcode fragments that were then aligned to our predefined fragment reference sets using Bowtie59 (version 5.2.1), allowing for up to two mismatches per fragment. Aligned STICR barcodes were compiled into a file containing their corresponding 10X cell barcode and 10X UMI sequences using awk. UMI of STICR barcodes with less than 10 reads were filtered by using awk to remove the noise UMI counts from the sequencing error. Finally, UMI-tools60 (version 0.5.1) was used to remove duplicate STICR barcode/cell barcode (CBC) reads by UMI, allowing for 1-bp mismatches in the UMI. STICR barcodes/CBC) pairings with at least three distinct UMIs were retained. For cells with multiple barcodes detected, only cells with all the same set of barcodes detected are considered as a shared clone, with Jaccard similarity of 1. Barcodes and their corresponding UMI counts were mapped to cells in the Seurat object of transcriptome data by aligning cell barcodes.
Assembly: mm10
Supplementary files format and content: rds
Supplementary files format and content: rds

extract_protocol:
Virally injected brains were collected from mouse pups at postnatal day 4. Brains were dissected in ice-cold pre-bubbled artificial cerebrospinal fluid (aCSF), and sectioned into coronal sections. Each brain region was manually dissected out from sliced brains based on the guidance of anatomy atlas from Allen institute. Collected tissue was then dissociated in the solution of papain (Worthington, LK003178) supplemented with 0.5 mg/ml DNase (Sigma Aldrich, DN25-1G) diluted with HBSS (Gibco,14025134) at 37℃. The tissues were incubated at 37℃ for 30-60 min, with gentle trituration every 15 min until samples had no visible chunks.  Papain was quenched by adding 1% BSA (Militeny) to the solution. Samples were spun down and resuspended in HBSS + 0.1% BSA and passed through the 35 um filter into a FACS tube (Falcon, 52235). To isolate and collect virally infected cells, flow cytometry was done using a BD FACSAria III Cell Sorter (BD FACSDiva Software, version 8.0.2) with a 100-µm nozzle. The cell suspensions were first gated on forward scatter, then within this population based on eGFP expression. eGFP-expressing cells were sorted into HBSS + 0.1% BSA for downstream processing on the 10x Genomics Chromium platform. Samples were kept on ice before and after FACS, and the chamber and collection tubes were maintained at 4℃ during sorting.
scRNA-seq library preparation Preparation of scRNA-seq libraries was carried out using a Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, #PN-1000075). We input between 10 and 20k cells per lane on a Chromium Chip G and followed the manufacturer protocol for transcriptomic library preparation.  STICR barcode library preparation STICR barcodes were subamplified from each 10X cDNA library using the Q5 Hot Start High Fidelity 2× master mix (NEB, M0494). In brief, 10 μl of cDNA was used as template in a 50 μl PCR reaction containing STICR barcode read 1 and 2 primers (0.5 μM, each) targeting the region immediately upstream of the STICR viral index/barcode as well as the partial Illumina Read1 sequence added during cDNA library preparation (Extended Data Table 3), using the following program: 1, 98 °C, 30 s; 2, 98 °C, 10 s; 3, 62 °C, 20 s; 4, 72 °C, 10 s; 5, repeat steps 2–4 12 times; 6, 72 °C, 2 min; 7, 4 °C, hold. Following PCR amplification, a 0.8–0.6 dual-sided size selection was performed using Ampure XP beads (Beckman Coulter, A63881). The libraries were quantified by Tapestation (Agilent) and pooled for sequencing.


title: shADAT2_1_Input


title: H3K27ac_Diencephalon_WT

description:
Library name: H3K27ac_Diencephalon_WT_CUTnTag
CUT&Tag

value: Diencephalon


title: STICR-ST28_OB, Clonal barcodes library

description: Library name: STICR-ST28_OB


title: HT-29 TRP replicate 2

value: TRP


title: STICR-ST28_H, Clonal barcodes library

description: Library name: STICR-ST28_H


title: shGFP_1_Input

value: shGFP


title: HT-29 TRP replicate 1


title: H3K27ac_BrainStem_WT

description:
Library name: H3K27ac_BrainStem_WT_CUTnTag
CUT&Tag


title: STICR-ST28_C, Clonal barcodes library

description: Library name: STICR-ST28_C

value: Brain


title: shADAT2_2


title: Mecp2_WhiteFat_WT

description:
Library name: Mecp2_WhiteFat_WT_CUTnTag
CUT&Tag

source_name: WhiteFat

value: WhiteFat

value: MECP2 (Proteintech, 10861-1-AP)


title: STICR-ST27_T, Clonal barcodes library

description: Library name: STICR-ST27_T


title: shADAT2_1


title: HT-29 GFP replicate 3

value: GFP


title: STICR-ST27_S, Clonal barcodes library

description: Library name: STICR-ST27_S


title: STICR-ST31_R, Clonal barcodes library

description: Library name: STICR-ST31_R


title: Nr3c1_SpinalCord_WT

description:
Library name: Nr3c1_SpinalCord_WT_CUTnTag
CUT&Tag


title: HT-29 GFP replicate 2


title: Nr3c1_Pituitary_WT

description:
Library name: Nr3c1_Pituitary_WT_CUTnTag
CUT&Tag


title: Infected_16h

description:
Library name: 107491
10x Visium HD, FFPE protocol

value: Lymphoid

value: VEEV-Infected


title: Mock_16h

description:
Library name: 107492
10x Visium HD, FFPE protocol

value: Mock


title: shGFP_2


title: Mecp2_Uterus_WT

description:
Library name: Mecp2_Uterus_WT_CUTnTag
CUT&Tag

source_name: Uterus

value: Uterus


title: HT-29 GFP replicate 1


title: Mouse #18623, 50 mg/kg NCG-023, biol rep 4

description:
Library name: 18623
Column name in raw_counts_AllSamples.txt and TPM_AllSamples.txt: LD_18623

value: small intestine crypts

value: C57BL/6N (wt)

value: 50 mg/kg NCG-023 IP (-24, -2) harvested at time of sham-IR

value: Female


title: Nr3c1_Cerebellum_WT

description:
Library name: Nr3c1_Cerebellum_WT_CUTnTag
CUT&Tag

value: Cerebellum

value: WT

value: Male

value: 8 weeks


title: Mecp2_Thyroid_WT

description:
Library name: Mecp2_Thyroid_WT_CUTnTag
CUT&Tag

source_name: Thyroid

value: Thyroid


title: STICR-ST27_R, Clonal barcodes library

description: Library name: STICR-ST27_R

value: Brain

value: Wild type


title: STICR-ST30_H, Clonal barcodes library

description: Library name: STICR-ST30_H


title: shGFP_1

value: shGFP

value: RiboMinus mRNA


title: Luhmes + vehicle_diff5 [RNA-seq]

value: Mid brain

value: LUHMES

value: Dopaminergic neurons

value: vehicle


title: Mecp2_Testis_WT

description:
Library name: Mecp2_Testis_WT_CUTnTag
CUT&Tag

source_name: Testis

value: Testis

value: MECP2 (Proteintech, 10861-1-AP)


title: HT-29 Ctrl replicate 3

value: Ctrl


title: STICR-ST27_OB, Clonal barcodes library

description: Library name: STICR-ST27_OB


title: T8,scRNAseq

city: shanghai

first: Dengfeng

last: Huang

address: 301 Yanchang Middle Road

institute: Shanghai Tenth People's Hospital

description: 10x Genomics

data_processing:
Seurat
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: rectum

extract_protocol:
Tumors andadjacent normal tissues were cut into approximately 1 mm3 pieces in the RPMI-1640 medium with 10% FBS. The cancer tissue at the tumor edge and adjacent non-cancerous tissue were digested into single-cell suspension via 1.5 mg/ml collagenase type II and 1.5 mg/ml collagenase type IV treatment for 30 min at 37℃. The dissociated cells were subsequently passed through a 70 mm Cell-Strainer and centrifuged at 300 g for 10 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer and incubated on ice for 2 min to lyse red blood cells. After washing twice with 1X PBS, the cell pellets were re-suspended in sorting buffer (PBS supplemented with 1% FBS).
The 3ʹ Gene Expression Library was constructed with the quality-qualified cDNA. After fragmentation,  adaptor ligation, sample index PCR, etc., the library is finally quantitatively examined.

value: rectum


title: HT-29 Ctrl replicate 2


title: Mecp2_Telencephalon_WT

description:
Library name: Mecp2_Telencephalon_WT_CUTnTag
CUT&Tag

value: Telencephalon


title: T7,scRNAseq

description: 10x Genomics

source_name: Colon

value: Colon


title: STICR-ST27_H, Clonal barcodes library

first: Guohua

last: Yuan

address: 1651 4th St Fl 5 521A, Weill Neurosciences Building

institute: UCSF

description: Library name: STICR-ST27_H


title: Luhmes + vehicle_diff2 [RNA-seq]

value: WT


title: Mecp2_Spleen_WT

description:
Library name: Mecp2_Spleen_WT_CUTnTag
CUT&Tag

source_name: Spleen

value: Spleen

value: Male

value: 8 weeks


title: T6,scRNAseq

description: 10x Genomics


title: STICR-ST27_C, Clonal barcodes library

description: Library name: STICR-ST27_C

value: Brain

value: Wild type


title: HT-29 Ctrl replicate 1

description: NanoString nCounter Human Tumor Signaling 360 panel


title: Late maturing

city: Bergen

first: Simon

last: Henriet

address: Thormøhlensgate 55

country: Norway

institute: University of Bergen

description: Library name: Day7

data_processing:
Genome mapping, counting of barcodes and UMIs with Cellranger 9.0.1
Assembly: ASM20953v1
Supplementary files format and content: Feature Barcode Market Exchange Matrices (MEX), tab-separated values files with lists of barcodes and gene IDs

organism: Oikopleura dioica

source_name: Maturing adults, mixed sexes

extract_protocol:
Pooled individuals were transferred to a glass salier and washed extensively with Calcium-free artificial seawater (CASW) at 15°C to remove debris. Samples were anaesthetized by dropwise addition of 10% MS222-CASW and washed with CASW immediately prior to dissociation to remove houses. Cell dissociation was conducted in glass saliers pre-rinsed with 1% BSA-CASW, by adding to the 0.2 ml sample pellet a 2 ml digestion cocktail pre-warmed at 37°C (2-6phf samples: 0.5% Pronase, 5 mM EDTA, CASW; 8-6hpf samples: 0.25% Pronase, 1.25% Trypsin, 10mg.ml-1 Trichoderma Cellulase, CASW). Samples were digested for 10 minutes at 25°C, and 1 ml of the reaction volume was removed. We produced a cell suspension from digested samples by pipetting the remaining solution in and out a 1 ml plastic tip. Samples were pipetted until complete tissue disruption (usually 5 to 10 minutes) and reactions were stopped by adding 3 ml of ice-cold quenching solution (0.5% BSA, 2mg.ml-1 Glycine, CASW). After an additional 1-minute time of pipetting the sample, complete dissociation of cell aggregates was confirmed under microscope. Cell suspensions were passed on a 20 µm strainer and collected in a 50 ml Falcon tube pre-rinsed with 1% BSA-CASW. Strainers were washed with Magnesium-free CASW (1mM EDTA, CASW) supplemented with 0.5% BSA to maximize cell recovery. Cells were collected after 300g centrifugation for 15 minutes at 25°C and gently resuspended in 1 ml 0.2% BSA-MCASW. We resuspended cells in PBS supplemented with 0.7 M D-Mannitol.
We loaded 20000 cells per well on a Chromium GEM-X chip (10X Genomics) following manufacturer’s recommendations for the Chromium-X controller.

value: Maturing adults, mixed sexes


title: Mecp2_SpinalCord_WT

description:
Library name: Mecp2_SpinalCord_WT_CUTnTag
CUT&Tag

source_name: SpinalCord

value: SpinalCord


title: STICR-ST26_T, Clonal barcodes library

city: San Francisco

description: Library name: STICR-ST26_T


title: T5,scRNAseq

description: 10x Genomics


title: Mid maturing-replicate 2

description: Library name: Day6-2


title: Mecp2_Prostate_WT

description:
Library name: Mecp2_Prostate_WT_CUTnTag
CUT&Tag

source_name: Prostate

value: Prostate


title: T4,scRNAseq

description: 10x Genomics


title: STICR-ST26_S, Clonal barcodes library

description: Library name: STICR-ST26_S


title: Mecp2_Pancreas_WT

description:
Library name: Mecp2_Pancreas_WT_CUTnTag
CUT&Tag

source_name: Pancreas

value: Pancreas


title: STICR-ST26_R, Clonal barcodes library

description: Library name: STICR-ST26_R


title: Mid maturing-replicate 1

description: Library name: Day6-1


title: T3,scRNAseq

description: 10x Genomics


title: Early maturing-replicate 2

description: Library name: Day5-2


title: STICR-ST26_OB, Clonal barcodes library

description: Library name: STICR-ST26_OB


title: H3K27ac_Telencephalon_WT

description:
Library name: H3K27ac_Telencephalon_WT_CUTnTag
CUT&Tag

source_name: Telencephalon


title: Mecp2_LymphNode_WT

description:
Library name: Mecp2_LymphNode_WT_CUTnTag
CUT&Tag

source_name: LymphNode

value: LymphNode


title: T2,scRNAseq

description: 10x Genomics


title: Luhmes + AntimycinA-Oligomycin 4 technical replicates_diff3 [RNA-seq]

source_name: Mid brain

value: Mid brain

value: LUHMES

value: Dopaminergic neurons

value: Antimycin-A + Oligomycin


title: Early maturing-replicate 1

description: Library name: Day5-1


title: STICR-ST28_T, Clonal barcodes library

description: Library name: STICR-ST28_T

source_name: Brain


title: Luhmes + AntimycinA-Oligomycin 4 technical replicates_diff2 [RNA-seq]


title: Mecp2_Liver_WT

description:
Library name: Mecp2_Liver_WT_CUTnTag
CUT&Tag

source_name: Liver

value: Liver

value: MECP2 (Proteintech, 10861-1-AP)


title: T1,scRNAseq

description: 10x Genomics

value: Colon


title: MCF7, NTT-Flag, IgG

city: Rome

first: Valerio

last: Licursi

address: via degli Apuli, 4

department: c/o Dept. Biology and Biotechnologies "C. Darwin", Sapienza University of Rome

institute: Institute of Molecular Biology and Pathology (IBPM), National Research Council (CNR)

description: Library name: S13

data_processing:
FASTQ files were quality-checked using FastQC (v0.12.1) and trimmed with Trim Galore! (v0.6.10). Reads were aligned to the reference genome using Bowtie2 (v2.5.3), then sorted and indexed with SAMtools (v1.20), and duplicates marked with Picard (v3.1.1). Coverage files and signal tracks were generated using deepTools (v3.5.5) and bedGraphToBigWig. Peak calling was performed with SEACR (v1.4), and genomic in-terval operations were conducted using BEDTools (v2.31.1). Quality metrics were summarised with MultiQC (v1.22). Peak merging was performed using the Join tool on Galaxy.
Assembly: GRCh38
Supplementary files format and content: bigWig
Library strategy: CUT&Run

extract_protocol:
The assay was performed using the CUT&RUN Assay Kit (Cell Signalling, #86652), with the anti-H3K4me3 antibody (Cell Signalling Technology, #9751), the anti-FLAG M2 an-tibody (Sigma, #F1804), and the Rabbit IgG isotype control (Cell Signalling Technology, #66362).
Ovation® Ultralow V2 DNA-Seq Library Preparation Kit (Tecan, Redwood City, CA) has been used for library preparation following the manufacturer’s instructions. Immunoprecipitated DNA samples were quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA). Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Bioanalyzer HS DNA assay (Agilent, Santa Clara, CA) Libraries were then prepared for sequencing and sequenced on paired-end 150 bp mode on NovaSeqX Plus (Illumina, San Diego, CA).

tag: transfection

value: NTT-Flag

tag: cut&run antibody

value: Rabbit IgG isotype control


title: MCF7, PLU1-Flag, rep2

description: Library name: S12

value: anti-FLAG M2


title: Mecp2_LargeIntestine_WT

description:
Library name: Mecp2_LargeIntestine_WT_CUTnTag
CUT&Tag

source_name: LargeIntestine

value: LargeIntestine

value: WT

value: Male

value: 8 weeks


title: STICR-ST26_C, Clonal barcodes library

description: Library name: STICR-ST26_C

value: Brain

value: Wild type


title: STICR-ST25_T, Clonal barcodes library

description: Library name: STICR-ST25_T


title: A7,scRNAseq

description: 10x Genomics


title: MCF7, PLU1-Flag, rep1

description: Library name: S11


title: STICR-ST25_S, Clonal barcodes library

description: Library name: STICR-ST25_S


title: A6,scRNAseq

description: 10x Genomics


title: MCF7, NTT-Flag, rep2

description: Library name: S10


title: STICR-ST25_R, Clonal barcodes library

description: Library name: STICR-ST25_R


title: Mecp2_Diencephalon_WT

description:
Library name: Mecp2_Diencephalon_WT_CUTnTag
CUT&Tag

source_name: Diencephalon

value: Diencephalon


title: A5,scRNAseq

description: 10x Genomics


title: MCF7, NTT-Flag, rep1

description: Library name: S9


title: Mecp2_Cerebellum_WT

description:
Library name: Mecp2_Cerebellum_WT_CUTnTag
CUT&Tag

source_name: Cerebellum

value: Cerebellum


title: A4,scRNAseq

description: 10x Genomics


title: MCF7, Empty-Flag, rep2

description: Library name: S8

value: Empty-Flag


title: STICR-ST25_H, Clonal barcodes library

description: Library name: STICR-ST25_H


title: Mecp2_BrainStem_WT

description:
Library name: Mecp2_BrainStem_WT_CUTnTag
CUT&Tag

source_name: BrainStem

value: BrainStem


title: A3,scRNAseq

description: 10x Genomics


title: STICR-ST25_OB, Clonal barcodes library

description: Library name: STICR-ST25_OB


title: Mecp2_Bladder_WT

description:
Library name: Mecp2_Bladder_WT_CUTnTag
CUT&Tag

source_name: Bladder

value: Bladder


title: STICR-ST25_C, Clonal barcodes library

description: Library name: STICR-ST25_C


title: STICR-ST26_H, Clonal barcodes library

description: Library name: STICR-ST26_H


title: A8,scRNAseq

description: 10x Genomics

source_name: rectum

value: rectum


title: A2,scRNAseq

description: 10x Genomics


title: MCF7, PLU1-Flag, H3K4me3, rep2

description: Library name: S6


title: MCF7, Empty-Flag, rep1

description: Library name: S7


title: Mecp2_AdrenalGland_WT

description:
Library name: Mecp2_AdrenalGland_WT_CUTnTag
CUT&Tag

source_name: AdrenalGland

value: AdrenalGland

value: MECP2 (Proteintech, 10861-1-AP)


title: STICR-ST24_T, Clonal barcodes library

description: Library name: STICR-ST24_T


title: A1,scRNAseq

description: 10x Genomics

source_name: Colon

value: Colon


title: E13.5 Fetal liver LK Ddx21-cKO_H3K27me3_ATAC-seq_Rep2

city: Shatin

first: Hoi-Hung

middle: Hoi Hung

last: Cheung

state: NT

address: Rm.707, School of Biomedical Sciences, Area 39, The Chinese University of Hong Kong

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Library name: E13.5 Fetal liver LK Ddx21-cKO_H3K27me3_Rep2

data_processing:
QC was performed with FastQC. Adapter and 3' polyG was removed with fastp -g --detect_adapter_for_pe.
Reads were aligned to UCSC mm10 using bowtie2 (bowtie2 --local --very-sensitive --no-mixed --no-discordant --phred33 --threads 8 -I 20 -X 1000). Alignments with MAPQ <30 (including unmapped and multi-mapped regions) and certain regions (chrM|random|chrUn|chrEBV) were filtered out using samtools.
Duplicate reads were removed with picard.
BAM files were converted to BEDPE using bedtools. Peaks were called with macs2 with FDR cutoff of q<0.01, peaks were extended with (--nomodel --shift 100 --ext 200) to account for Tn5 targetting. Peaks from replicates were merged whenever there is 1bp overlap by bedtools.
Normalized and scaled to per million bigWig tracks were generated using deepTools with scaling factor calculated from 1000000/(EdgeR-TMM scale factor on reads in 10000bp background bin * library size). Blacklist regions of mm10 obtained from ENCODE were also filtered out. BigWig from replicates were merged by wiggleTools-write_bg and then bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: bigWig, broadPeak, bed

source_name: E13.5 fetal liver

extract_protocol:
Dissected fetal livers were washed twice with PBS and kept in fetal liver juice (2%FBS/1mM EDTA/10mMGlucose/PBS) on ice. Cell suspension was obtained by trituration and strained with a sterile 70um cell strainer. Cells were first stained with lineage-biotin antibodies (Gr1, Cd11b, CD3, B220, Ter119) and fixable viability stain 450, washed and subsequently stained with (cKit-APC and streptavidin-APC/Cy7). Live (FVS450-) lineage- (APC/Cy7-) cKit+ (APC+) cells were sorted with BD FACSDiscover™ S8 Cell Sorter. Cells were kept on ice or 4oC throughout harvest and sorting.
ATAC-seq libraries were constructed using Hyperactive ATAC-Seq Library Prep Kit for Illumina (Vazyme #TD711) and TruePrep Index Kit V2 for Illumina (Vazyme #TD202) according to product manual. 65000 cells were used per library with 13 cycle of PCR amplification. Single size exclusion was performed to remove small fragments with beads provided in the kit. Libraries were validated by Agilent high sensitivity dna kit.

value: E13.5 fetal liver

value: Fetal liver Hematopoietic progenitor LK cells (Lineage- Kit+)

value: Ddx21-cKO (Vav-Cre; Ddx21f/f)


title: STICR-ST24_R, Clonal barcodes library

description: Library name: STICR-ST24_R


title: hiPSC-CM, mock , rep4

city: Hong Kong

first: Maxwell

last: Kwok

address: The Chinese University of Hong Kong, Shatin

data_processing:
#Preprocessing: All fastq files were QC'd initially with FastQC (v0.11.9). All files satisfied most QC criteria and therefore trimming was deemed not necessary.
#Alignment: Alignments were performed with STAR (v2.7.9a). A combined genome index of Human (Gencode v39) and the SARS-CoV-2 genome (NCBI Accession ID:NC_045512.2) was used in aligning reads to both the human and viral genomes. Read counts were generated through the in-built counting software of STAR (with arguement --quantMode GeneCounts). Additional parameters specified at the alignment stage included (--outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0)
Assembly: Human (Gencode v39) and the SARS-CoV-2 genome (NCBI Accession ID:NC_045512.2)
Supplementary files format and content: Raw counts of sequencing reads in .csv

source_name: hiPSC-CM

extract_protocol:
Total RNA was harvested using ReliaPrep RNA Miniprep (Promega) following manufacturer's protocols.
500ng of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using TruSeq RNA Kit following manufacturer's protocols.

value: hiPSC-CM


title: E13.5 Fetal liver LK Ddx21-cKO_H3K27me3_ATAC-seq_Rep1

description: Library name: E13.5 Fetal liver LK Ddx21-cKO_H3K27me3_Rep1


title: MCF7, NTT-Flag, H3K4me3, rep1

description: Library name: S3

value: NTT-Flag


title: hiPSC-CM, mock , rep3


title: STICR-ST24_OB, Clonal barcodes library

description: Library name: STICR-ST24_OB


title: hiPSC-CM, mock , rep2


title: MCF7, Empty-Flag, H3K4me3, rep2

description: Library name: S2


title: STICR-ST23_C, Clonal barcodes library

description: Library name: STICR-ST23_C


title: MCF7, Empty-Flag, H3K4me3, rep1

description: Library name: S1


title: E13.5 Fetal liver LK WT_H3K27me3_ATAC-seq_Rep1

description: Library name: E13.5 Fetal liver LK WT_H3K27me3_Rep1

value: WT (Ddx21 f/f)


title: STICR-ST21_T, Clonal barcodes library

description: Library name: STICR-ST21_T

value: Brain


title: hiPSC-CM, omicron BA.2 , rep4


title: hiPSC-CM, mock , rep1


title: FVB_Telencephalon_WT_rep4

description:
Library name: FVB_Telencephalon_WT_rep4_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were then aligned to mm10 using STAR (v2.7.10a).
Read counts were generated using featureCounts.
Transcripts were quantified with Salmon (v1.10.3) in quasi-mapping-based mode.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files including raw count values for individual samples.

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Total RNA was isolated using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme). The extracted RNA was used for reverse transcription. Following the reaction, a PCR amplification program was performed. Purification was then conducted using 0.9× of VAHTS DNA Clean Beads. TruePrep DNA Library Prep Kit for MGI (Vazyme) was used for sequencing library construction.

value: Telencephalon

value: WT

value: FVB/NJ

value: Male

value: 8 weeks

tag: mouse id


title: P15_CPSOXPD1 sample

city: Jinan

first: Lin

address: Wenhuaxi Road #107

institute: Shandong University

description: Library name: P15_CPs1

data_processing:
Raw reads were assessed using FastQC.
Adapters and low-quality bases were trimmed using fastp.
Clean reads were aligned to GRCh38 using STAR.
Gene-level counts were generated using featureCounts with GENCODE vXX annotation.
TPM values were calculated from gene-level counts.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited matrix containing gene-level raw read counts for all samples. Rows represent genes and columns represent samples.

source_name: Stromal

extract_protocol:
Total RNA was extracted from each sample according to the standard RNA extraction protocol provided by the sequencing service provider. RNA quantity and quality were assessed prior to library construction.
RNA sequencing libraries were prepared from total RNA according to the standard bulk RNA-seq library preparation protocol provided by the sequencing service provider. Libraries were sequenced on an Illumina platform using paired-end sequencing.

treatment_protocol: Samples were treated with 5 μM 5-fluorouracil or 5 μM oxaliplatin. Immune checkpoint inhibitor treatment was performed at a concentration of 10 μg/mL. Untreated samples were included as controls.

value: Stromal

value: Chemotherapy combined with immunotherapy


title: STICR-ST21_OB, Clonal barcodes library

description: Library name: STICR-ST21_OB

value: Wild type


title: P15_CPPD-1 sample

description: Library name: P15_CPp1

value: Immunotherapy


title: FVB_Telencephalon_WT_rep3

description:
Library name: FVB_Telencephalon_WT_rep3_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: hiPSC-CM, omicron BA.2 , rep2


title: P15_CPcontrol sample

description: Library name: P15_CPc

value: vehicle


title: FVB_Telencephalon_WT_rep2

description:
Library name: FVB_Telencephalon_WT_rep2_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: STICR-ST20_RT, Clonal barcodes library

description: Library name: STICR-ST20_RT


title: P07_CPSOXPD1 sample

description: Library name: P07_CPs1


title: FVB_Telencephalon_WT_rep5

description:
Library name: FVB_Telencephalon_WT_rep5_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: STICR-ST20_RC, Clonal barcodes library

description: Library name: STICR-ST20_RC


title: FVB_Telencephalon_WT_rep1

description:
Library name: FVB_Telencephalon_WT_rep1_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: hiPSC-CM, omicron BA.1 , rep4


title: FVB_Telencephalon_OE_rep5

description:
Library name: FVB_Telencephalon_OE_rep5_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues

value: MECP2 OE


title: hiPSC-CM, omicron BA.1 , rep3


title: FVB_Telencephalon_OE_rep4

description:
Library name: FVB_Telencephalon_OE_rep4_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: STICR-ST20_CC, Clonal barcodes library

description: Library name: STICR-ST20_CC


title: P03_CPSOXPD1 sample

description: Library name: P03_CPs1


title: FVB_Telencephalon_OE_rep3

description:
Library name: FVB_Telencephalon_OE_rep3_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: P07_CPcontrol sample

description: Library name: P07_CPc


title: STICR-ST18-T, Clonal barcodes library

description: Library name: STICR-ST18-T


title: hiPSC-CM, omicron BA.1 , rep1


title: P03_CPPD1 sample

description: Library name: P03_CPp1


title: FVB_Telencephalon_OE_rep2

description:
Library name: FVB_Telencephalon_OE_rep2_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: STICR-ST17-T, Clonal barcodes library

description: Library name: STICR-ST17-T


title: hiPSC-CM, delta, rep4


title: P03_CPcontrol sample

description: Library name: P03_CPc


title: FVB_Telencephalon_OE_rep1

description:
Library name: FVB_Telencephalon_OE_rep1_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: STICR-ST17-CTX, Clonal barcodes library

description: Library name: STICR-ST17-CTX


title: hiPSC-CM, delta, rep3


title: FVB_AdrenalGland_WT_rep5

description:
Library name: FVB_AdrenalGland_WT_rep5_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues

value: AdrenalGland


title: STICR-ST16-T, Clonal barcodes library

description: Library name: STICR-ST16-T


title: P02_CPPD1 sample

description: Library name: P02_CPp1


title: FVB_AdrenalGland_WT_rep4

description:
Library name: FVB_AdrenalGland_WT_rep4_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: STICR-ST16-R, Clonal barcodes library

description: Library name: STICR-ST16-R


title: hiPSC-CM, delta, rep1


title: P02_CPcontrol sample

description: Library name: P02_CPc


title: FVB_AdrenalGland_WT_rep3

description:
Library name: FVB_AdrenalGland_WT_rep3_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: STICR-ST16-C, Clonal barcodes library

description: Library name: STICR-ST16-C


title: BL MOCK 4

city: New York

first: Justin

middle: J

last: Frere

state: NY

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

institute: NYU Langone Health

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

data_processing:
Base calling and sample deconvolution performed via Illumina BaseSpace
Reads aligned to MesAur1.0 genome assembly using Ensembl GTF file and quantified using Salmon as made available in Illumina BaseSpace "RNA-Seq Alignment" application
Assembly: Mesocricetus Auratus MesAur1.0
Supplementary files format and content: .quant.genes.sf Salmon files (show raw and normalized read counts by gene)
Supplementary files format and content: .csv files show the read count for individual base calls compared to the viral reference sequence

organism: Mesocricetus auratus

source_name: Blood mock 4

growth_protocol: Golden hamstsers were housed in pairs in the ABSL3 facility of NYU-Langone/Mount Sinai Hospital, under 12 hour light/dark cycle. Water and Food (PicoLab Rodent Diet 20 5053) was provided ad libitum.

extract_protocol: RNA was extracted using Trizol reagent and following manufacturer's instructions. 100 ng of RNA were used for the construction ofn libraries.

treatment_protocol: Dexamethasone was prepared fresh each day at a dose of 1 mg/kg in 0.5 mL of 20% DMSO/60% PEG400/20% 2-hydroxypropyl-beta-cyclodextrin in water (w/w), and administered via subcutaneous injection.

value: Blood

tag: time

value: 1 dpi

value: MOCK


title: P15_Cox sample

description: Library name: P15_Cox

tag: tissue

value: Oxaliplatin


title: FVB_AdrenalGland_WT_rep2

description:
Library name: FVB_AdrenalGland_WT_rep2_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues

tag: genotype


title: STICR-ST15_T, Clonal barcodes library

description: Library name: STICR-ST15_T

value: Brain


title: BL MOCK 3

source_name: Blood mock 3


title: P15_Cfu sample

description: Library name: P15_Cfu

value: Fluorouracil


title: P02_CPSOXPD1 sample

description: Library name: P02_CPs1


title: FVB_AdrenalGland_WT_rep1

description:
Library name: FVB_AdrenalGland_WT_rep1_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues

value: WT


title: STICR-ST15_C, Clonal barcodes library

description: Library name: STICR-ST15_C


title: hiPSC-CM, delta, rep2

value: hiPSC-CM


title: BL MOCK 2

source_name: Blood mock 2


title: Mecp2_Heart_WT

description:
Library name: Mecp2_Heart_WT_CUTnTag
CUT&Tag

data_processing:
Adapters in FASTQ files were trimmed using cutadapt with the following command “cutadapt -a CTGTCTCTTATACACATCT -A CTGTCTCTTATACACATCT -j 0 -O 16 -m 20”.
The trimmed reads were aligned to mm10 using bowtie2 (v2.5.2). Reads with quality > 2 were selected and sorted by query names. BAM files were converted to BEDPE files then to fragment files (sorted BED files). Fragments in the blacklist regions of mm10 (https://www.encodeproject.org/files/ENCFF547MET/) were removed. BED files were converted to BW files for subsequent visualization.
The raw sorted BED files (blacklist regions were not removed) are supported as supplementary files for individual samples.
Assembly: mm10
Supplementary files format and content: BED  files including sorted fragments
Library strategy: CUT&Tag

source_name: Heart

extract_protocol:
For the pituitary and spinal cord, subsequent procedures were directly performed after samples were removed. The bone marrow was isolated from femur and tibia bones. Muscles were removed and both ends of bones were carefully trimmed. The bone marrow cavity was flushed 2-3 times with DPBS to collect most of the cells. Tubes were then centrifuged at 300 g for 5 min at 4°C to collect cell pellets. For the stomach, intestine, and bladder, their luminal content was cleaned up before frozen in dry ice. Other tissues were directly frozen once removed. Frozen tissues were ground in liquid nitrogen. The ground powder was used for subsequent library construction and can be stored at -80°C.
Concanavalin A (ConA) coated magnetic beads were freshly activated with Ca²⁺ and Mn²⁺. Nuclei were extracted and a total of 10,000 nuclei were incubated with activated ConA beads. Supernatant was next removed, and beads were incubated with antibody (1:50) on a rotator at 4°C overnight, followed by incubated with secondary antibody (1:100) for 1 hr at room temperature. Beads were washed three times and suspended in dig300-wash buffer pre-mixed with pG-Tn5 (1:100), incubated for 1 hr at room temperature. After washing beads for three times, tag buffer was added to each well, then incubated on a rotator at 37 °C for 1 hr. After centrifugation, beads were washed once and resuspended. Lysis buffer was added to each well, and incubated for 2 hr at 65 °C. After adding 10% Tween20, TruePrep CUT&Tag Amplification Mix (Vazyme), 10 mM MGI-P5, and 10 mM MGI-P7 primer were added. Then PCR program was performed. Finally, 1.5 × VAHTS DNA Clean Beads were used to purify the library.

value: Heart

value: MECP2 (Proteintech, 10861-1-AP)

value: Male


title: P15_Ccon sample

description: Library name: P15_Ccon

value: Stromal


title: FVB_AdrenalGland_OE_rep5

description:
Library name: FVB_AdrenalGland_OE_rep5_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues

value: FVB/NJ

value: 8 weeks


title: Mecp2_Eye_WT

description:
Library name: Mecp2_Eye_WT_CUTnTag
CUT&Tag

source_name: Eye

value: Eye


title: STICR-ST14_T, Clonal barcodes library

description: Library name: STICR-ST14_T

source_name: Brain

value: Wild type


title: BL MOCK 1

source_name: Blood mock 1


title: P07_Cox sample

description: Library name: P07_Cox


title: FVB_AdrenalGland_OE_rep4

description:
Library name: FVB_AdrenalGland_OE_rep4_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues

value: AdrenalGland

value: MECP2 OE


title: STICR-ST14_C, Clonal barcodes library

description: Library name: STICR-ST14_C


title: BL 3DPI IN4

source_name: Blood, SARS-CoV-2, I.N., 3dpi, 4

value: Blood

value: 3 dpi

value: 1000 PFU SARSCOV2 IN


title: P07_Cfu sample

description: Library name: P07_Cfu


title: FVB_AdrenalGland_OE_rep3

description:
Library name: FVB_AdrenalGland_OE_rep3_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: STICR-ST13_T, Clonal barcodes library

description: Library name: STICR-ST13_T

value: Brain


title: P07_Ccon sample

description: Library name: P07_Ccon

value: vehicle


title: FVB_AdrenalGland_OE_rep2

description:
Library name: FVB_AdrenalGland_OE_rep2_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: BL 3DPI IN3

source_name: Blood, SARS-CoV-2, I.N., 3dpi, 3

value: WT


title: MCF7, PLU1-Flag, H3K4me3, rep1

description: Library name: S5

tag: cell line


title: STICR-ST13_C, Clonal barcodes library

description: Library name: STICR-ST13_C


title: BL 3DPI IN2

source_name: Blood, SARS-CoV-2, I.N., 3dpi, 2

tag: treatment


title: P03_Cox sample

description: Library name: P03_Cox

value: Oxaliplatin


title: FVB_AdrenalGland_OE_rep1

description:
Library name: FVB_AdrenalGland_OE_rep1_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: STICR-ST24_C, Clonal barcodes library

description: Library name: STICR-ST24_C


title: MCF7, NTT-Flag, H3K4me3, rep2

description: Library name: S4

value: NTT-Flag


title: E13.5 Fetal liver LK WT_H3K27me3_ATAC-seq_Rep2

description: Library name: E13.5 Fetal liver LK WT_H3K27me3_Rep2

value: E13.5 fetal liver

tag: cell type

value: Fetal liver Hematopoietic progenitor LK cells (Lineage- Kit+)

value: WT (Ddx21 f/f)


title: STICR-ST12_T, Clonal barcodes library

description: Library name: STICR-ST12_T


title: BL 3DPI IN1

source_name: Blood, SARS-CoV-2, I.N., 3dpi, 1


title: P03_Cfu sample

description: Library name: P03_Cfu

value: Stromal

value: Fluorouracil


title: FVB_Thyroid_WT_rep4

description:
Library name: FVB_Thyroid_WT_rep4_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues

source_name: Thyroid

value: Thyroid

tag: strain

value: FVB/NJ

value: Male

value: 8 weeks


title: STICR-ST12_C, Clonal barcodes library

description: Library name: STICR-ST12_C

value: Wild type


title: BL 1DPI IN4

source_name: Blood, SARS-CoV-2, I.N., 1dpi, 4

value: Blood

value: 1 dpi


title: P03_Ccon sample

description: Library name: P03_Ccon


title: P02_Cox sample

description: Library name: P02_Cox


title: STICR-ST11_T, Clonal barcodes library

description: Library name: STICR-ST11_T

value: Brain


title: BL 1DPI IN3

source_name: Blood, SARS-CoV-2, I.N., 1dpi, 3

value: 1000 PFU SARSCOV2 IN


title: FVB_Thyroid_WT_rep3

description:
Library name: FVB_Thyroid_WT_rep3_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues

value: WT


title: hiPSC-CM, omicron BA.2 , rep3

value: hiPSC-CM


title: FVB_Thyroid_WT_rep2

description:
Library name: FVB_Thyroid_WT_rep2_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: STICR-ST11_C, Clonal barcodes library

description: Library name: STICR-ST11_C


title: P02_Cfu sample

description: Library name: P02_Cfu


title: FVB_Thyroid_WT_rep1

description:
Library name: FVB_Thyroid_WT_rep1_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: BL 1DPI IN2

source_name: Blood, SARS-CoV-2, I.N., 1dpi, 2


title: STICR-ST10_T, Clonal barcodes library

description: Library name: STICR-ST10_T


title: BL 1DPI IN1

source_name: Blood, SARS-CoV-2, I.N., 1dpi, 1


title: FVB_Thyroid_OE_rep4

description:
Library name: FVB_Thyroid_OE_rep4_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues

value: MECP2 OE


title: STICR-ST9_T, Clonal barcodes library

description: Library name: STICR-ST9_T


title: hiPSC-CM, omicron BA.2 , rep1

source_name: hiPSC-CM


title: K MOCK 4

source_name: Kidney mock 4

value: Kidney

value: MOCK


title: P15 ox sample

description: Library name: P15ox

source_name: Stromal

value: Oxaliplatin


title: FVB_Thyroid_OE_rep3

description:
Library name: FVB_Thyroid_OE_rep3_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: K MOCK 3

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

source_name: Kidney mock 3


title: FVB_Thyroid_OE_rep2

description:
Library name: FVB_Thyroid_OE_rep2_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: P15 5fu sample

description: Library name: P15fu

value: Stromal


title: STICR-ST8_T, Clonal barcodes library

description: Library name: STICR-ST8_T


title: P07_CPPD1 sample

description: Library name: P07_CPp1

value: Immunotherapy


title: STICR-ST20_CT, Clonal barcodes library

description: Library name: STICR-ST20_CT


title: K MOCK 2

source_name: Kidney mock 2


title: STICR-ST21_C, Clonal barcodes library

description: Library name: STICR-ST21_C


title: HT-29 TRP replicate 3

description: NanoString nCounter Human Tumor Signaling 360 panel

value: TRP


title: FVB_Thyroid_OE_rep1

description:
Library name: FVB_Thyroid_OE_rep1_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues

value: Thyroid

value: FVB/NJ


title: STICR-ST8_C, Clonal barcodes library

description: Library name: STICR-ST8_C


title: P15 control sample

description: Library name: P15con

value: vehicle


title: K MOCK 1

source_name: Kidney mock 1


title: P07 ox sample

description: Library name: P07ox


title: FVB_Thymus_WT_rep5

description:
Library name: FVB_Thymus_WT_rep5_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues

source_name: Thymus

value: Thymus

value: Male

value: 8 weeks


title: 8K

source_name: Kidney, SARS-CoV-2, I.V., 3dpi, 4

value: 3 dpi

value: 100000 PFU SARSCOV2 IV


title: STICR-ST7_T, Clonal barcodes library

description: Library name: STICR-ST7_T

source_name: Brain

value: Brain

value: Wild type


title: STICR-ST7_R, Clonal barcodes library

description: Library name: STICR-ST7_R


title: FVB_Thymus_WT_rep3

description:
Library name: FVB_Thymus_WT_rep3_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues

value: WT


title: 7K

source_name: Kidney, SARS-CoV-2, I.V., 3dpi, 3

value: Kidney


title: STICR-ST7_C, Clonal barcodes library

description: Library name: STICR-ST7_C


title: 6K

source_name: Kidney, SARS-CoV-2, I.V., 3dpi, 2


title: P03 ox sample

description: Library name: P03ox


title: FVB_Thymus_WT_rep2

description:
Library name: FVB_Thymus_WT_rep2_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: STICR-ST6_L1, Clonal barcodes library

description: Library name: STICR-ST6_L1


title: 5K

source_name: Kidney, SARS-CoV-2, I.V., 3dpi, 1


title: P03 5fu sample

description: Library name: P03fu

value: Fluorouracil


title: FVB_Thymus_WT_rep1

description:
Library name: FVB_Thymus_WT_rep1_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: STICR-ST5_L1, Clonal barcodes library

description: Library name: STICR-ST5_L1


title: FVB_Thymus_OE_rep5

description:
Library name: FVB_Thymus_OE_rep5_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues

value: MECP2 OE


title: 4K

source_name: Kidney, SARS-CoV-2, I.N., 3dpi, 4

value: 1000 PFU SARSCOV2 IN


title: P03 control sample

description: Library name: P03con

value: Stromal


title: P02 ox sample

description: Library name: P02ox

value: Oxaliplatin


title: 2K

source_name: Kidney, SARS-CoV-2, I.N., 3dpi, 2


title: P02 5fu sample

description: Library name: P02fu


title: ST39_T_2, Transcriptome library

description: Library name: ST39_T_2


title: FVB_Thymus_OE_rep3

description:
Library name: FVB_Thymus_OE_rep3_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: P07 5fu sample

description: Library name: P07fu


title: P02 control sample

description: Library name: P02con


title: ST39_T_1, Transcriptome library

description: Library name: ST39_T_1


title: FVB_Thymus_OE_rep2

description:
Library name: FVB_Thymus_OE_rep2_RNA-seq
RNA-seq counts of MECP2 OE and WT tissues


title: 1K

source_name: Kidney, SARS-CoV-2, I.N., 3dpi, 1


title: ST39_S_2, Transcriptome library

description: Library name: ST39_S_2


title: 1K12

source_name: Kidney, SARS-CoV-2, I.V., 1dpi, 4

value: 1 dpi


title: 12-Thymoma, MG, Visium HD

city: Chicago

first: Yuanqing

last: Yan

state: IL

address: 303 E Superior Street

institute: Northwestern University

description:
Library name: 12-thymoma
10x Genomics

data_processing:
For scRNA-seq, raw reads were demultiplexed with Cell Ranger (v6.0.0 or v7.1.0) and mapped to the human genome (GRCh38). Ambient RNA was removed using SoupX, and doublets were filtered with scDblFinder. Quality control in Seurat excluded cells with <200 or >7,500 unique features, <400 or >40,000 total RNA counts, or >10% mitochondrial content. For V(D)J sequencing, the djvdj (v0.1.0) package was utilized, retaining only cells with high-quality transcriptomic data. Samples with fewer than 10 cells were excluded for robustness. Clonotypes were defined by CDR3 amino acid sequences, and only those with exactly two chains were retained; cells without an assigned clonotype were removed. For Visium HD, images were aligned in Loupe Browser (v8.0.0), and Space Ranger (v3.1.0) was used for mapping. Bin2cell (v0.3.3) aggregated 2 μm bins to reconstruct single-cell-like profiles based on H&E morphology and gene expression at 0.5 μm per pixel resolution. Downstream analysis was performed in Scanpy, excluding cells with <100 or >40,000 features or >20% mitochondrial content.
Assembly: HG38
Supplementary files format and content: HDF5, csv and tsv of processed data
Library strategy: Spatial Transcriptomics

extract_protocol:
Fresh thymus samples were obtained for scRNA-seq plus V(D)J sequencing and formalin-fixed, paraffin-embedded specimens were used for Visium HD spatial transcriptomics.
For scRNA-seq (3' v3) and scRNA-seq with V(D)J sequencing (5'), libraries were prepared using the 10x Genomics Chromium Single Cell 3' v3 or Single Cell 5' Expression Assay and sequenced on NextSeq 1000/2000 or Illumina NovaSeq 6000 instruments. For Visium HD, samples were sectioned at 5 μm and processed at the Northwestern University NUSeq Core following the manufacturer’s protocol (Visium HD v1). These libraries were subsequently sequenced on an Illumina NovaSeq X Plus.

value: all Thymus cells


title: P02_Ccon sample

description: Library name: P02_Ccon

value: vehicle


title: ST39_S_1, Transcriptome library

description: Library name: ST39_S_1


title: 1K11

source_name: Kidney, SARS-CoV-2, I.V., 1dpi, 3


title: ST39_R, Transcriptome library

description: Library name: ST39_R


title: 6-Thymus, MG, Visium HD

description:
Library name: 6-Thymus
10x Genomics

value: Thymus


title: P20 mouse cortex [hypoxia]

city: Tainan

first: Chih-Yen Wang

last: Wang

address: No.1, University Rd

department: Biotechnology and Bioindustry Sciences

country: Taiwan

institute: National Cheng Kung University

description: Library name: P20_hypoxia

data_processing:
The scRNA-seq data were processed with Cell Ranger Count v7.1.0 (refdata-gex-mm10-2020-A), followed by unbiased clustering using Seurat package in R.
Assembly: mm10
Supplementary files format and content: rds file with integrated data of 2 samples

source_name: brain

extract_protocol:
P20 mouse cortical tissues (3 animals combined per group) were treated with papain and DNase I at 37 degree for 30 min. Unhealthy cells were removed using debris and dead cell removal kit with MS separation columns.
The cell suspension was prepared using single-cell 3’ Library and Gel Bead Kit V3.1 and the Chromium Single Cell G Chip Kit, and then loaded onto the Chromium Single Cell Controller (10x Genomics) to generate single-cell beads in the emulsion according to the manufacturer's protocol.

treatment_protocol: 10.5% oxygen incubation from P3 to P11

value: brain


title: 1K10

source_name: Kidney, SARS-CoV-2, I.V., 1dpi, 2


title: 17-Thymus, no_MG, Visium HD

description:
Library name: 17-Thymus
10x Genomics


title: STICR-ST9_C, Clonal barcodes library

description: Library name: STICR-ST9_C


title: IOMM-Lee cell line genomic DNA methylation profiling

type: genomic

city: Seattle

first: Brendan

middle: F

last: Kohrn

state: WA

address: 1705 NE Pacific St.

department: Department of Laboratory Medicine and Pathology

institute: University of Washington

description: Biosample SAMN61189712

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (v1.0 B5; Illumina) using standard Illumina protocol

scan_protocol: Stained chip was scanned using an Illumina iScan

data_processing: Array sample controls are analyzed using the Illumina BeadArray Controls Reporter Software (v1.1) and analysis is performed using Illumina GenomeStudio software (v2.0.3).  Samples are considered passed if their detected CpG site rate is >98% of the total CpG sites. Resultant idat files were further processed using Sesame to produce beta values

label: Cy3 and Cy5

label_protocol: Standard Illumina Protocol

growth_protocol: IOMM-Lee was propagated in Dulbecco- modified Eagle’s Medium with added 4.5 g/L glucose and L-glutamine (Corning 10-017-CV), supplemented with 10% (v/v) fetal bovine serum (HyClone SH30396.03) and penicillin-streptomycin (Gibco-ThermoFisher 10378016 diluted 100-fold). Conventional tissue culture plasticware used throughout, with growth in a humidified 20% O2/5% CO2 incubator at 37℃.

extract_protocol: Total cellular DNA was extracted using a genomic DNA extraction kit.

treatment_protocol: Cells were not treated during exponential growth prior to DNA extraction.

value: Grade 3 malignant meningioma


title: ST39_O, Transcriptome library

description: Library name: ST39_O


title: 1K9

source_name: Kidney, SARS-CoV-2, I.V., 1dpi, 1