title: Induced Sp1 DNA binding domain line, anti-FLAG, replicate 1

description: Library name: Sp1 DBD, FLAG, R1

value: Sigma F3165

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible Sp1-DBD integrated at the AAVS1 safe harbor locus


title: Induced LacI line, anti-FLAG, replicate 2

status: Public on Mar 20 2026

type: SRA

city: Berkeley

first: Robert

last: Tjian

state: CA

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

country: USA

institute: UC Berkeley

description: Library name: LacI, FLAG, R2

library_source: genomic

data_processing:
Reads trimmed with Cutadapt (version 2.6) with the following parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -m 15
Reads aligned with Bowtie2 (version 2.3.5.1) with the following options:  --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Bowtie2 .sam output converted to .bam with samtools (version 1.9)
.bam files sorted and indexed with samtools (version 1.9)
duplicates removed with samtools (version 1.9)
bigWig coverage files generated with deepTools bamCoverage (version 3.5.4) with the following options: --binSize 10 --samFlagInclude 64 --normalizeUsing RPGC --effectiveGenomeSize 2913022398 --extendReads --ignoreDuplicates, using the hg38 blacklist file published in Doi: 10.1186/s13059-023-03027-3
Irreproducible Discovery Rate (IDR) analysis: macs3 (version 2.2.7.1) peak calling with a liberal p-value cutoff (-p 1e-3) and --nolambda; merged control replicates (CTRL, mAb, R1 + CTRL, mAb, R2; or CTRL, rAb, R1 + CTRL, mAb, R2) used as a control; peaks sorted by pValue before running IDR (version 2.0.4.2) with the following options: --input-file-type narrowPeak --rank p.value
MACS3 bedGraph files used to combine replicates with macs3 cmbreps (--method mean)
Combined bedGraph outputs used for differential peak calling with macs3 bdgdiff with the following options: --cutoff 1.0 --depth1 1.0 --depth2 1.0 -l 120 -g 60, using merged control replicates as a control
Peak coordinates merged and/or intersected with bedtools (version 2.27.1) or bedops (version 2.4.39)
ChIP-Seq heatmaps generated with deepTools (version 3.5.4) computeMatrix and plotHeatmap tools
Assembly: hg38
Supplementary files format and content: *IDR_0.1.txt: peaks highly reproducible between replicates 1 and 2 (IDR score <=0.01). See https://github.com/nboley/idr for a detailed explanation of the output fields
Supplementary files format and content: bdgdiff .bed files: contain coordinates of unchanged (common), depleted (cond 1) or enriched (cond2) ChIP-seq peaks in EPC1 mutants (HSA-6mut or Delta-TRRAP) compared to WT EPC1. The last column in the file represent the log10 likelihood ratio to show how likely the observed signal in one or the other condition in a particular region is from that condition comparing to the other condition.The higher the value, the greater the difference. Only highly reproducible peaks (IDR score <=0.01) are included in the list (reproducible IDR and bdgdiff peaks intersected with bedops --element-of 1)
Supplementary files format and content: *.bw files: coverage files generated with deepTools
Library strategy: CUT&Run

molecule: genomic DNA

organism: Homo sapiens

source_name: U-2 OS

growth_protocol: U-2 OS cells were cultured at 37 °C with 5% CO2 in high-glucose Dulbecco's Modified Eagle Medium (DMEM; Thermo Fisher #12800082) supplemented with 10% fetal bovine serum and penicillin/streptomycin.

extract_protocol:
CUT&Run was performed as previously described (dx.doi.org/10.17504/protocols.io.zcpf2vn), using 0.5x10^6 cells per antibody, 0.02% digitonin and pA/G-MNase digestion (30 minutes on ice). After phenol:chloroform extraction DNA was purified with home-made serapure beads (Doi:10.1101/gr.128124.111).
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®, adapted for short fragments (dx.doi.org/10.17504/protocols.io.bagaibse); adaptors diluted 1:20; 11 PCR cycles

treatment_protocol: Cells were induced for 36 hours with 1 µg/mL doxycycline while also stained with 5 nM of JF549 Halo ligand and 5 nM of JFX650 SNAP ligand. Following induction, cells were trypsinized and resuspended in medium containing 1 µg/mL doxycycline, then subjected to fluorescence-activated cell sorting (FACS) to select for transgene-expressing cells (induction levels typically ranged from ~10% to 50%). Sorted cells were plated into individual wells of six-well plates and cultured for an additional 36 hours in medium with 1 µg/mL doxycycline prior to initiation of the CUT&RUN protocol.

tag: cell line

value: U-2 OS

tag: cell type

value: Osteosarcoma

tag: antibody

tag: genotype

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible LacI integrated at the AAVS1 safe harbor locus

tag: treatment

value: 36 hrs dox induction + cell sorting


title: Induced CTCF DNA binding domain line, anti-FLAG, replicate 2

description: Library name: CTCF DBD, FLAG, R2

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible CTCF DBD integrated at the AAVS1 safe harbor locus


title: Induced wild type Sp1 line, rabbit anti-V5, replicate 1

description: Library name: Sp1 WT, rV5, R1

value: Abcam ab9116

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible wild type Sp1 integrated at the AAVS1 safe harbor locus


title: Induced EWS + Sp1 DNA binding domain chimera line, anti-FLAG, replicate 2

description: Library name: EWS-Sp1 DBD, FLAG, R2

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible EWS-Sp1 DBD chimera integrated at the AAVS1 safe harbor locus


title: Induced wild type Sp1 line, rabbit anti-V5, replicate 2

description: Library name: Sp1 WT, rV5, R2


title: Induced Sp1 activation domain + CTCF DNA binding domain chimera line, mouse anti-V5, replicate 1

description: Library name: Sp1AD-CTCF DBD, mV5, R1

value: Thermo Fisher R960-25

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible Sp1 AD-CTCF DBD chimera integrated at the AAVS1 safe harbor locus


title: Parental cell line, mouse anti-V5, replicate 1

description: Library name: CTRL, mV5, R1

value: Endogenous knock-in V5-Halo-SP1


title: Parental cell line, rabbit anti-FLAG, replicate 1

description: Library name: CTRL, rAb, R1

value: Invitrogen # 740001


title: Induced SNAP-NLS control line, anti-FLAG, replicate 2

description: Library name: SNAP-NLS, FLAG, R2

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible SNAP-NLS integrated at the AAVS1 safe harbor locus


title: Parental cell line, rabbit anti-V5, replicate 1

description: Library name: CTRL, rV5, R1


title: Induced Sp1 DNA binding domain line, anti-FLAG, replicate 2

description: Library name: Sp1 DBD, FLAG, R2


title: Parental cell line, mouse anti-FLAG, replicate 1

description: Library name: CTRL, mAb, R1


title: U-2 OS parental cell line ChIP, rabbit anti-SP1 antibody 1

description: Library name: SP1 ChIP pulldown 1

data_processing:
Reads trimmed with Cutadapt (version 2.6) with the following parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -m 15
Reads aligned with Bowtie2 (version 2.4.5) with the following options:  --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Bowtie2 .sam output converted to .bam with samtools (version 1.15.1)
.bam files sorted and indexed with samtools (version 1.15.1)
duplicates removed with samtools (version 1.15.1)
bigWig coverage files generated with deepTools bamCoverage (version 3.5.4) with the following options: --binSize 20 --normalizeUsing RPGC --effectiveGenomeSize 2913022398 --extendReads --ignoreDuplicates
MACS2 (version 2.2.7.1) peak calling using input samples as control and the following options: macs2 callpeak -B -f BAMPE -g hs
Peak coordinates merged and/or intersected with bedtools (version 2.27.1) or bedops (version 2.4.39)
Assembly: hg38
Supplementary files format and content: *.bw files: coverage files generated with deepTools

growth_protocol: U-2 OS cells were cultured at 37 °C with 5% CO2 in low-glucose Dulbecco's Modified Eagle Medium (DMEM; Thermo Fisher #10567022) supplemented with 10% fetal bovine serum and penicillin/streptomycin.

extract_protocol:
Cells were washed twice with ice-cold PBS, scraped, centrifuged for 10 min at 4000 rpm, resuspended in cell lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, and 0.5% NP-40, 1 ml/15 cm plate) and incubated for 10 min on ice. During the incubation, the lysates were repeatedly pipetted up and down every 5 minutes. Lysates were then centrifuged for 10 min at 4000 rpm. Nuclear pellets were resuspended in 6 volumes of sonication buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 0.1% SDS), incubated on ice for 10 min, and sonicated to obtain DNA fragments below 2000 bp in length (Covaris S220 sonicator, 20% Duty factor, 200 cycles/burst, 100 peak incident power, 11 cycles of 30" on and 30" off). Sonicated lysates were cleared by centrifugation and 500 μg of chromatin was diluted in RIPA buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl) to a final concentration of 0.8 μg/μl, precleared with Protein G Dynabeads (Fisher 1009D) for 2 hours at 4°C and immunoprecipitated overnight with 1.25 μg of normal rabbit IgGs or anti-CTCF antibodies. 10% of the precleared chromatin was saved as input. Immunoprecipitated DNA was purified with the Qiagen QIAquick PCR Purification Kit, eluted in 36 μl of water, 25 ul of which were used used for library prep.
NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (using half of the recommended volumes); adaptors diluted 1:10; 9 PCR cycles; 20 ng starting material for inputs; 25 ul for CTCF ChIP samples.

treatment_protocol: Cells were cross-linked for 6 minutes at room temperature with 1% formaldehyde-containing medium; cross-linking was stopped by PBS-glycine (0.125 M final).

value: 1% formaldehyde crosslinking for 6 minutes


title: Induced Sp1 activation domain + LacI chimera line, rabbit anti-V5, replicate 2

description: Library name: Sp1AD-LacI, rV5, R2

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible Sp1 AD-LacI chimera integrated at the AAVS1 safe harbor locus


title: IMR90 cell, Linker_pre-SnC

city: Novato

first: Qingqing

last: Liu

state: California

address: 8001 Redwood Blvd

institute: Buck Institute - Novato, CA

description: Library name: RNA_QL3

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2Rpackage (1.20.0).
Assembly: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5.
Supplementary files format and content: txt file includes  raw counts for each sample, FPKM for each sample

molecule: total RNA

growth_protocol: IMR90 cells with and without Mito-Lyso linker  were maintained in Dulbecco’s Modified Eagle’s Medium with L-Glutamine and 4.5 g/L Glucose (Corning 10013CV), supplemented with 10% FBS (Gibco) and 1% penicillin-streptomycin (Gibco)  at 37 °C in an atmosphere of 5% CO2.

extract_protocol:
Total RNA was harvested using Rneasy mini kit (Qiagen 74104). 1 ug of total RNA was used for the construction of sequencing libraries.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Senescent IMR90 cells are induced by exposing to a single dose of 10 Gray ionizing radiation (IR) for 9 minutes according to the treatment condition in Campisi lab. After IR, placed cells back to the incubator and changed medium every 48 hrs. Assays for senescent cells were done 10 days after IR.

value: linker

value: pre-SnC


title: Induced LacI line, anti-FLAG, replicate 1

description: Library name: LacI, FLAG, R1

value: U-2 OS

value: Sigma F3165


title: Induced Sp1 activation domain + LacI chimera line, rabbit anti-V5, replicate 1

description: Library name: Sp1AD-LacI, rV5, R1

value: Osteosarcoma


title: Parental cell line, rabbit anti-FLAG, replicate 2

description: Library name: CTRL, rAb, R2

value: 36 hrs dox induction + cell sorting


title: Induced Sp1 activation domain + LacI chimera line, anti-FLAG, replicate 2

description: Library name: Sp1AD-LacI, FLAG, R2


title: Induced SNAP-NLS control line, anti-FLAG, replicate 1

description: Library name: SNAP-NLS, FLAG, R1


title: hiPSC-HSC_P0

city: Tokyo

first: Yunzhong

last: Nie

state: Tokyo

address: Room 330, 3F west, 1st  Bldg, Shirokanedai 4-6-1, Minato

department: Department of Computational Biology and Medical Sciences

country: Japan

institute: The University of Tokyo

description:
Library name: Sample 1
10x Genomics

library_source: transcriptomic single cell

data_processing:
These sequence results were aligned to the GRCh38 human genome and pre-processed using the CellRanger 10x Genomics software for downstream analyses.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values file and matrix files

extract_protocol:
The differentiated hiPSC-HSC_P0  were detached from culture well for scRNA sequencing analysis. For HSC-LO_Day10 dissociation: After 10 days of co-culturing hiPSC-hepatic endoderm, hiPSC-endothelial cells, and hiPSC-HSCs, the liver organoids(LOs) were washed with PBS and collected in one well. 2mL of the dissociation medium (HBSS, 1%HEPS, 0.5%CaCl2, 0.5%MgCl2, and 3mg/mLCOIIV) was added into one well of 6-well plate, incubate the LOs at 37℃ for 30min. Asparite the dissociation medium and add 2mL/well(6-well plate) TrpLE and incubate LOs at the room temperature for 10min. Dissociate LOs by using pippete and collect cells in washing medium (DMEM supplemented with 1% PS and 10% FBS)  The collected cells were filtered through a 100 μm cell strainer and centrifuged at 200 g for 4 minutes. Subsequently, CD31-APC antibody (Miltenyi Biotec) and anti-APC MicroBeads (Miltenyi Biotec) were employed to enrich the endothelial cell population for downstream analyses
Library was prepared by reagents from a Chromium Single Cell 3’v3 reagent kit, according to the 10x Genomics manual.

value: WT

value: hepatic stellate cell differentiation


title: Induced Sp1 mutant line, anti-FLAG, replicate 1

description: Library name: Sp1 mut, FLAG, R1

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible mutant Sp1 integrated at the AAVS1 safe harbor locus


title: HSC-LO_Day10

description:
Library name: Sample 2
10x Genomics

value: Coculturing hiPSC-HE, hiPSC-ECs, and hiPSC-HSCs for 10 days


title: Induced wild type Sp1 line, anti-FLAG, replicate 1

description: Library name: Sp1 WT, FLAG, R1

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible wild type Sp1 integrated at the AAVS1 safe harbor locus


title: MUT.6.9.IgM

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

country: Germany

institute: University clinics Freiburg

description: Library name: MUT.6.9.IgM

data_processing:
Alignments and gene count tables were obtained using STAR (version 2.4.2a)
Assembly: hg38
Supplementary files format and content: raw read count per gene in a tab delimited file

source_name: B lymphocytes

growth_protocol: Ramos cells were cultued in RPMI, 10% FCS, antibiotics Penicillin/Strepomycin, Hepes and beta-meracproethanol in 5% CO2 atmosphere at 37°C

extract_protocol:
RNAs were extracted by RNeasy plus kit (Qiagen cat# 74143). and samples were sequenced 84-bases long on the NextSeq® 550 with high output flowcell (NextSeq® 500/550 High Output Kit v2).
RNA libraries for RNAseq were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB cat # E7760L) according to manufacturer’s instructions

treatment_protocol: Ramos cells were kept unstimulated (resting samples) or stimulated with anti IGM for 4 hours

tag: tissue

value: B lymphocytes

value: Ramos Burkitt Lymphoma

value: CRL-1923, RRID:CVCL 1646

value: PRKCD KO

value: actication anti IgM


title: U-2 OS parental cell line ChIP, input

description: Library name: SP1 ChIP input

value: Endogenous knock-in V5-Halo-SP1

value: 1% formaldehyde crosslinking for 6 minutes


title: Mut.6.22.Resting

description: Library name: Mut.6.22.Resting

value: no


title: Parental cell line, mouse anti-FLAG, replicate 2

description: Library name: CTRL, mAb, R2

value: U-2 OS


title: Mut.6.9.Resting

description: Library name: Mut.6.9.Resting


title: WT.0.2.Resting

description: Library name: WT.0.2.Resting


title: 3control

type: RNA

city: Ciudad de México

first: Julio

last: Granados-Montiel

state: Ciudad de México

address: Las Fuentes 17

department: Investigación

country: Mexico

institute: Universidad La Salle

description: Gene expression data from undifferentiated MSCs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: undifferentiated MSCs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured with DMEM:F12 (Dulbecco´s modified Eagle medium), 10% FCS (fetal calf serum), Pen/Strep 1:100, and glutamine 1:100 (Gibco-Invitrogen, Carlsbad, CA)

extract_protocol: After 21 days of culture, differentiation medium was removed and the cell monolayer was washed twice with phosphate-buffered saline. QIAGEN RNEasy mini kit was used as recommended by the manufacturer. Briefly, monolayers were removed from the tissue culture plates with a 10-minute incubation time at 37°C with Accutase (Sigma); cells were dislodged mechanically with a P1000 tip and transferred to a clean Eppendorf tube. Cells were pelleted and the supernatant removed. They were then lysed with the RLT buffer and processed until the end of the protocol, eluting with 50 µL of RNase-free water.

treatment_protocol: To set up the differentiation assay, 3 technical replicates were cultured in parallel in 24 well plates; 5 × 104 cells per 1 cm2 were seeded. Basal media was supplemented with Kartogenin (KGN) 100 nM (Sigma) and ascorbic acid 50 µM (Sigma).

value: undifferentiated MSCs


title: Induced Sp1 activation domain + LacI chimera line, anti-FLAG, replicate 1

description: Library name: Sp1AD-LacI, FLAG, R1

value: Osteosarcoma

value: Sigma F3165

value: Endogenous knock-in V5-Halo-SP1 + DOX inducible Sp1 AD-LacI chimera integrated at the AAVS1 safe harbor locus


title: Induced wild type Sp1 line, mouse anti-V5, replicate 1

description: Library name: Sp1 WT, mV5, R1

value: Thermo Fisher R960-25

value: 36 hrs dox induction + cell sorting


title: IMR90 cell, Control_SnC

description: Library name: RNA_QL2

value: WT

value: SnC


title: U-2 OS parental cell line ChIP, normal rabbit IgG control

description: Library name: SP1 ChIP rIgG, R1


title: WT.0.1.IgM

description: Library name: WT.0.1.IgM

value: B lymphocytes


title: U-2 OS parental cell line ChIP, rabbit anti-SP1 antibody 2

description: Library name: SP1 ChIP pulldown 2


title: 1condro

description: Gene expression data from Chondrocytes differentiated from MSC

source_name: Chondrocytes differentiated from MSC

value: Chondrocytes differentiated from MSC


title: 0618 cells, DMSO+EZVSET-rep1 (bulkRNA_4)

city: Beijing

first: Jingxiao

last: Cao

state: Beijing

address: No.5 Yiheyuan Road, Yanyuan Street, Haidian District, Beijing

department: Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China.

country: China

institute: Peking University

description:
Library name: DMSO+EZVSET-rep1
counts_bulkRNA_4.txt

data_processing:
Quality control was performed using FastQC.
The raw RNA-seq reads were trimmed using Trimmomatic with parameter ‘ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’ to remove detected adapters.
The clean reads were mapped to human reference genome hg19 using STAR with additional parameter ‘--outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical’.
The number of reads mapped to each gene was counted using program featureCounts of Subread package.
Assembly: hg19
Supplementary files format and content: .txt file containing count values of each gene in each sample.

extract_protocol:
Total RNA was isolated using Direct-zol RNA MiniPrep Kit.
RNA sequencing libraries were constructed using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB England BioLabs, E7775). Fragmented and randomly primed 2 x150 bp pairedend libraries were sequenced using Illumina HiSeq X Ten.

value: induced from hADSC


title: 0618 cells, DMSO+C6NASRJ-rep2 (bulkRNA_4)

description:
Library name: DMSO+C6NASRJ-rep2
counts_bulkRNA_4.txt


title: MUT.6.22.IgM

description: Library name: MUT.6.22.IgM

value: Ramos Burkitt Lymphoma

value: CRL-1923, RRID:CVCL 1646

value: PRKCD KO


title: IMR90 cell, Linker_SnC

description: Library name: RNA_QL4

value: linker


title: NC-N+RA2_rep1_batch2

description: Library name: NC-N+RA2_rep1_batch2

source_name: induced from hADSC

value: Chemical small molecule subtraction and addition samples


title: WT.0.2.IgM

description: Library name: WT.0.2.IgM

value: actication anti IgM


title: 0618 cells, DMSO+C6NAEVZSET-rep2 (bulkRNA_4)

description:
Library name: DMSO+C6NAEVZSET-rep2
counts_bulkRNA_4.txt


title: 0618 cells, DMSO+C6NASRJ-rep1 (bulkRNA_4)

description:
Library name: DMSO+C6NASRJ-rep1
counts_bulkRNA_4.txt


title: 0618 cells, DMSO+C6NAEVZSET-rep1 (bulkRNA_4)

description:
Library name: DMSO+C6NAEVZSET-rep1
counts_bulkRNA_4.txt


title: WT.0.1.Resting

description: Library name: WT.0.1.Resting

value: no


title: NC-N+CH55_rep2_batch2

description: Library name: NC-N+CH55_rep2_batch2


title: NC-N+RA2_rep2_batch2

description: Library name: NC-N+RA2_rep2_batch2


title: NC-N+CH55_rep1_batch2

description: Library name: NC-N+CH55_rep1_batch2


title: 2control

value: undifferentiated MSCs


title: IMR90 cell, Control_pre-SnC

description: Library name: RNA_QL1

value: pre-SnC


title: 3condro


title: 1control


title: NC_rep1_batch2

description: Library name: NC_rep1_batch2

value: Control group


title: NC_rep2_batch2

description: Library name: NC_rep2_batch2


title: S1-AKT_rep2

description:
Library name: S1-AKT_rep2
S1-AKT_rep2

data_processing:
Quality control was performed using FastQC.
The raw RNA-seq reads were trimmed using Trimmomatic with parameter ‘ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’ to remove detected adapters.
The clean reads were mapped to human reference genome hg19 using STAR with additional parameter ‘--outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical’.
The number of reads mapped to each gene was counted using program featureCounts of Subread package.
Assembly: hg19
Supplementary files format and content: .csv file containing count values of fpkm in each sample.

value: Chemical small molecule subtraction samples


title: S1-J_rep2

description:
Library name: S1-J_rep2
S1-J_rep2


title: S1-AKT_rep1

description:
Library name: S1-AKT_rep1
S1-AKT_rep1


title: NC-N_rep2_batch2

description: Library name: NC-N_rep2_batch2


title: 2condro


title: NC-N_rep1_batch2

description: Library name: NC-N_rep1_batch2


title: S1NC_rep2

description:
Library name: S1NC_rep2
S1NC_rep2


title: S1-C_rep2

description:
Library name: S1-C_rep2
S1-C_rep2


title: S1-6_rep2

description:
Library name: S1-6_rep2
S1-6_rep2


title: S1-N_rep1

description:
Library name: S1-N_rep1
S1-N_rep1


title: S1-6_rep1

description:
Library name: S1-6_rep1
S1-6_rep1


title: S1-J_rep1

description:
Library name: S1-J_rep1
S1-J_rep1


title: S1-N_rep2

description:
Library name: S1-N_rep2
S1-N_rep2


title: S1NC_rep1

description:
Library name: S1NC_rep1
S1NC_rep1


title: S1DMSO+J-rep2

description:
Library name: S1DMSO+J-rep2
J-rep2

value: Chemical small molecule addition samples


title: S1DMSO+N-rep2

description:
Library name: S1DMSO+N-rep2
N-rep2


title: S1-C_rep1

description:
Library name: S1-C_rep1
S1-C_rep1


title: S1DMSO+6-rep1

description:
Library name: S1DMSO+6-rep1
6-rep1


title: S1DMSO+6-rep2

description:
Library name: S1DMSO+6-rep2
6-rep2


title: S1DMSO-rep2

description:
Library name: S1DMSO-rep2
DMSO-rep2


title: NC-rep2

description: Library name: NC-rep2

data_processing:
Quality control was performed using FastQC.
The raw RNA-seq reads were trimmed using Trimmomatic with parameter ‘ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:7:1:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36’ to remove detected adapters.
The clean reads were mapped to human reference genome hg19 using STAR with additional parameter ‘--outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical’.
The number of reads mapped to each gene was counted using program featureCounts of Subread package.
Assembly: hg19
Supplementary files format and content: .csv file containing FPKM values of each gene in each sample.

value: NC


title: 0618 cells, DMSO+EZVSET-rep2 (bulkRNA_4)

description:
Library name: DMSO+EZVSET-rep2
counts_bulkRNA_4.txt


title: S1DMSO+N-rep1

description:
Library name: S1DMSO+N-rep1
N-rep1


title: S1DMSO-rep1

description:
Library name: S1DMSO-rep1
DMSO-rep1


title: S1DMSO+A-rep2

description:
Library name: S1DMSO+A-rep2
A-rep2


title: S1DMSO+C-rep1

description:
Library name: S1DMSO+C-rep1
C-rep1


title: NC-N-rep1

description: Library name: NC-N-rep1

value: NC-N


title: DMSO+C6NA-rep1

description: Library name: DMSO+C6NA-rep1


title: NC-N-rep2

description: Library name: NC-N-rep2


title: S1DMSO+J-rep1

description:
Library name: S1DMSO+J-rep1
J-rep1


title: S1DMSO+A-rep1

description:
Library name: S1DMSO+A-rep1
A-rep1


title: DMSO-rep2

description: Library name: DMSO-rep2

value: DMSO


title: L-PGDS KO, biol rep 2, CPZ

city: Houston

first: Jian

last: Hu

state: Texas

address: 1881 East Road

department: Cancer Biology

institute: MD Anderson Cancer Center

description:
Library name: 80193
10x Genomics
Immune_80193

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using Cell Ranger softwaren7.1.0
Assembly: Mouse mm10
Supplementary files format and content: matrix files

molecule: nuclear RNA

organism: Mus musculus

source_name: Brain_corpus callosum

extract_protocol:
RNA was isolated from cells using the Qiagen RNeasy Mini Kit. RNA sequencing and analysis were performed by Novogene.
Library was performed according to the manufacturer's instructions (single cell 3' v3 protocol, 10x Genomics)

treatment_protocol: 11  weeks old WT and L-PGDS KO mice were fed a 0.2% cuprizone diet for 5 weeks. Diet was replenished every two days to ensure effectiveness.

value: Brain_corpus callosum

tag: strain

value: L-PGDS KO

tag: Sex

value: Male

value: 0.5% Cuprizone, 5 weeks


title: neonatal mouse cardiomyocytes, Nrf1 overexpression with H2O2, rep3

city: Boston

first: miao

last: cui

state: Please select region, state or province

address: 300 LONGWOOD AVE

institute: Boston Children's Hospital

description: Library name: Sample12

data_processing:
Raw sequence data were first quality-checked using FastQC (v0.11.4). Reads were aligned to the Rnor 6.0 rat reference genome using HISAT2 (v2.0.4) with default parameters and the option --rna-strandness F. Duplicate reads were removed using Samtools (v0.1.18), and gene-level counts were obtained with featureCounts (v1.6.0) using Ensembl gene annotations. Differential gene expression analysis was conducted using edgeR (v3.20.5) in R, employing a generalized linear model (GLM) framework. Batch effects were accounted for with a design matrix specifying batch and treatment groups.
Assembly: Rnor 6.0
Supplementary files format and content: csv file of FPKM values for each sample

molecule: polyA RNA

source_name: cardiomyocyte

growth_protocol: Neonatal ventricular cardiomyocytes (NRVMs) were isolated from 1- or 2-day-old Sprague-Dawley rats with the Isolation System for Neonatal Rat/Mouse Cardiomyocytes (Cellutron, nc-6031) according to the manufacturer’s instructions. Approximately 30 pups (both male and female) were used for isolation. Isolated NRVMs were plated at a density of 3 × 105 cells/well to gelatin-coated 12-well plates and were maintained in DMEM/199 medium (3:1, 3% FBS) for 48 h before adenoviral infection.

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Cat# 74104) following the manufacturer’s instructions. RNA quality was assessed using an Agilent 2100 TapeStation.
Stranded mRNA-seq libraries were prepared with the KAPA mRNA HyperPrep Kit (Roche, KK8581), according to the provided protocol. Sequencing was performed on an Illumina NextSeq 500 platform using a 75-base single-end high-output run configuration. Sample collection and processing were randomized across groups and performed on the same day to minimize batch effects.

treatment_protocol: Adenoviruses driving expression of LacZ (control) and Nrf1 (encoded by Nfe2l1) were diluted in DMEM/199 medium containing 3% FBS and were added to NRVMs at an MOI of 50. two days after viral infection, NRVMs were treated with 50 μM H2O2 for 1h followed by sample collections for RNA sequencing. Cell seeding, adenovirus infection and H2O2 treatment were randomized across groups.

value: cardiomyocyte


title: DMSO-rep1

description: Library name: DMSO-rep1

value: induced from hADSC


title: WT, biol rep 2, CPZ

description:
Library name: 80168
10x Genomics
Immune_80168

value: WT


title: neonatal mouse cardiomyocytes, Nrf1 overexpression with H2O2, rep1

description: Library name: Sample10


title: neonatal mouse cardiomyocytes, LacZ overexpression with H2O2, rep2

description: Library name: Sample5

value: LacZ


title: neonatal mouse cardiomyocytes, LacZ overexpression with H2O2, rep1

description: Library name: Sample4


title: S1DMSO+C-rep2

description:
Library name: S1DMSO+C-rep2
C-rep2


title: DMSO+TTNPB-rep1

description: Library name: DMSO+TTNPB-rep1

value: DMSO+TTNPB


title: RNA-seq on P28 NR V1 astrocyte GR-KO nuclei, replicate 1

first: Bruno

last: Gegenhuber

state: Massachusetts

address: 220 Longwood Ave

department: Neuroscience

institute: Harvard Medical School

description: Library name: P28_NR_GRKO_RNA_R1

data_processing:
RNA-seq reads were mapped to mm10 using STAR with default parameters. The number of reads mapping to gene bodies (exons and introns) was quantified with Subread featureCounts, using the mm10 UCSC refGene annotation. Differential gene expression analysis between NR GR-Con and NR GR-KO astrocytes and between DR GR-Con and NR GR-Con astrocytes at each time point (P14, P21, P28) was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: Excel file with read counts for each sample.

growth_protocol: Each biological replicate consisted of flash-frozen V1 tissue pooled from 1 male and 1 female GRfl/fl animals that were injected at P0-P1 with AAV2/5-GfaABC1D-ΔCre-T2A-EGFP-KASH-4x6T (GR-Con) or AAV2/5-GfaABC1D-Cre-T2A-EGFP-KASH-4x6T (GR-KO).

extract_protocol:
Mice were deeply anesthetized with isoflurane. Sections of 1 mm spanning V1 were collected in an adult mouse brain matrix (Alto) on ice, and V1 was microdissected. For bulk RNA-seq, tissue samples were immediately flash-frozen in a dry ice ethanol bath and stored at -80°C prior to nuclei extraction. After thawing samples, V1 tissue was transferred to a 1.5 mL tube containing 350 μL of cold homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH pH 7.8 supplemented with 1X PIC, 1 mM DTT, 0.15 mM spermine and 0.5 mM spermidine). For RNA experiments, 0.3 U/μL (bulk RNA-seq) of Protector RNase inhibitor (Sigma) was added. The tissue was dounced in a 2 mL glass homogenizer (Sigma D8938) with a loose pestle for 20 strokes. Samples were supplemented with 0.3% IGEPAL CA-630 and further dounced for an additional 10 strokes with a tight pestle. Homogenate was filtered through a small 40-μm strainer (pluriSelect 43-10040-50) into a 1.5 mL tube before diluting 1:1 with homogenization buffer and adding DRAQ5 (Abcam ab108410) at a 1:500 dilution. Nuclei were then sorted by GFP and/or DRAQ5 signal using the Sony SH800S Cell Sorter (purity mode) with a 100-μm sorting chip. For bulk RNA-seq, 80,000 DRAQ5+/GFP+ events were collected into 350 μL of cold RLT buffer (Qiagen 74004) supplemented 1:100 with β-mercaptoethanol.
After sorting nuclei into RLT buffer, RNA was extracted using the RNeasy Micro Kit (Qiagen 74004). RNA-seq libraries were prepared from 10 ng RNA per sample using the SMARTer Stranded Total RNA-Seq Kit v2 (Takara 634413), according to the manufacturer’s instructions. Libraries were sequenced paired-end on an Illumina NextSeq 500 using a 75-cycle kit.

value: Astrocyte

value: KO

value: NR

tag: age


title: RNA-seq on P28 DR V1 astrocyte GR-KO nuclei, replicate 4

description: Library name: P28_DR_GRKO_RNA_R4

value: DR


title: RNA-seq on P28 DR V1 astrocyte GR-KO nuclei, replicate 3

description: Library name: P28_DR_GRKO_RNA_R3


title: RNA-seq on P28 DR V1 astrocyte GR-Con nuclei, replicate 2

description: Library name: P28_DR_GRCon_RNA_R2

value: Con


title: RNA-seq on P21 NR V1 astrocyte GR-KO nuclei, replicate 1

description: Library name: P21_NR_GRKO_RNA_R1


title: RNA-seq on P21 DR V1 astrocyte GR-KO nuclei, replicate 4

description: Library name: P21_DR_GRKO_RNA_R4


title: RNA-seq on P21 DR V1 astrocyte GR-KO nuclei, replicate 3

description: Library name: P21_DR_GRKO_RNA_R3


title: RNA-seq on P21 DR V1 astrocyte GR-KO nuclei, replicate 1

description: Library name: P21_DR_GRKO_RNA_R1


title: RNA-seq on P28 DR V1 astrocyte GR-KO nuclei, replicate 1

description: Library name: P28_DR_GRKO_RNA_R1


title: RNA-seq on P21 NR V1 astrocyte GR-Con nuclei, replicate 1

description: Library name: P21_NR_GRCon_RNA_R1


title: RNA-seq on P28 NR V1 astrocyte GR-Con nuclei, replicate 3

description: Library name: P28_NR_GRCon_RNA_R3


title: RNA-seq on P21 DR V1 astrocyte GR-Con nuclei, replicate 3

description: Library name: P21_DR_GRCon_RNA_R3


title: RNA-seq on P21 DR V1 astrocyte GR-Con nuclei, replicate 4

description: Library name: P21_DR_GRCon_RNA_R4


title: RNA-seq on P28 NR V1 astrocyte GR-Con nuclei, replicate 1

description: Library name: P28_NR_GRCon_RNA_R1


title: RNA-seq on P21 DR V1 astrocyte GR-Con nuclei, replicate 1

description: Library name: P21_DR_GRCon_RNA_R1


title: RNA-seq on P28 NR V1 astrocyte GR-Con nuclei, replicate 2

description: Library name: P28_NR_GRCon_RNA_R2


title: RNA-seq on P28 DR V1 astrocyte GR-Con nuclei, replicate 4

description: Library name: P28_DR_GRCon_RNA_R4


title: RNA-seq on P28 DR V1 astrocyte GR-Con nuclei, replicate 3

description: Library name: P28_DR_GRCon_RNA_R3


title: RNA-seq on P28 DR V1 astrocyte GR-Con nuclei, replicate 1

description: Library name: P28_DR_GRCon_RNA_R1


title: RNA-seq on P21 NR V1 astrocyte GR-KO nuclei, replicate 3

description: Library name: P21_NR_GRKO_RNA_R3


title: RNA-seq on P21 NR V1 astrocyte GR-KO nuclei, replicate 2

description: Library name: P21_NR_GRKO_RNA_R2


title: RNA-seq on P14 NR V1 astrocyte GR-Con nuclei, replicate 3

description: Library name: P14_NR_GRCon_RNA_R3


title: RNA-seq on P14 NR V1 astrocyte GR-Con nuclei, replicate 2

description: Library name: P14_NR_GRCon_RNA_R2


title: L-PGDS KO, biol rep 1, CPZ

description:
Library name: 80192
10x Genomics
Immune_80192


title: DMSO+C6NA-rep2

description: Library name: DMSO+C6NA-rep2


title: RNA-seq on P14 NR V1 astrocyte GR-Con nuclei, replicate 1

description: Library name: P14_NR_GRCon_RNA_R1


title: RNA-seq on P28 NR V1 astrocyte GR-KO nuclei, replicate 2

description: Library name: P28_NR_GRKO_RNA_R2


title: RNA-seq on P28 NR V1 astrocyte GR-KO nuclei, replicate 3

description: Library name: P28_NR_GRKO_RNA_R3


title: RNA-seq on P21 DR V1 astrocyte GR-KO nuclei, replicate 2

description: Library name: P21_DR_GRKO_RNA_R2


title: neonatal mouse cardiomyocytes, LacZ overexpression, rep2

description: Library name: Sample2

value: no treatment


title: RNA-seq on P14 DR V1 astrocyte GR-Con nuclei, replicate 2

description: Library name: P14_DR_GRCon_RNA_R2


title: RNA-seq on P21 NR V1 astrocyte GR-Con nuclei, replicate 3

description: Library name: P21_NR_GRCon_RNA_R3


title: RNA-seq on P21 NR V1 astrocyte GR-Con nuclei, replicate 2

description: Library name: P21_NR_GRCon_RNA_R2


title: GR CUT&RUN on 250K DEX-treated 3T3 cells, replicate 1

description: Library name: 3T3_250K_DEX_GR_R1

data_processing:
Paired-end reads were trimmed to remove low-quality basecalls and adapters (cutadapt -q 30).
Trimmed reads were aligned to mm10 using Bowtie2 with the following flags: --dovetail --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 --minins 10 --maxins 700.
Duplicate reads were removed using Picard MarkDuplicates. Read pairs with MAPQ < 40 (samtools view) and fragment length > 120 bp were removed (deeptools alignmentSieve). Read pairs aligning to the mitochondrial genome or incomplete assemblies were also removed (samtools view).
Peaks were called against the corresponding IgG control using MACS2 callpeak (q < 0.01). Filtered BAM files were normalized by coverage (bamCoverage -bs 1 --normalizeUsing CPM) to generate bigwig tracks.
Assembly: mm10
Supplementary files format and content: Bigwig files represent normalized genomic coverage. narrowPeak files represent regions of enriched signal.
Library strategy: CUT&Run

source_name: 3T3 cells

growth_protocol: For in vivo CUT&RUN, each biological replicate consisted of P14 V1 tissue pooled from 3-5 mice. To label V1 astrocytes, WT or GRfl/fl animals were injected at P0-P1 with AAV2/5-GfaABC1D-ΔCre-T2A-EGFP-KASH-4x6T (DR vs. NR GR, NR NFIA, and GR-Con samples) or AAV2/5-GfaABC1D-Cre-T2A-EGFP-KASH-4x6T (GR-KO samples), and GFP+ nuclei were isolated via FANS. To label V1 oligodendrocytes, inhibitory neurons, and excitatory neurons, GFP+ nuclei were isolated via FANS from Olig2-Cre;Sun1-GFPfl/fl, Slc32a1-Cre;Sun1-GFPfl/fl, and Slc17a7-Cre;Sun1-GFPfl/fl animals, respectively. For in vitro CUT&RUN, 3T3 cells were grown in phenol-red-free DMEM containing 10% charcoal-stripped FBS for 48 hr.

extract_protocol:
In vivo: Mice were deeply anesthetized with isoflurane. Sections of 1 mm spanning V1 were collected in an adult mouse brain matrix (Alto) on ice, and V1 was microdissected. After dissecting samples, V1 tissue was transferred to a 1.5 mL tube containing 350 μL of cold homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH pH 7.8 supplemented with 1X PIC, 1 mM DTT, 0.15 mM spermine and 0.5 mM spermidine). The tissue was dounced in a 2 mL glass homogenizer (Sigma D8938) with a loose pestle for 20 strokes. Samples were supplemented with 0.3% IGEPAL CA-630 and further dounced for an additional 10 strokes with a tight pestle. Homogenate was filtered through a small 40-μm strainer (pluriSelect 43-10040-50) into a 1.5 mL tube before diluting 1:1 with homogenization buffer and adding DRAQ5 (Abcam ab108410) at a 1:500 dilution. Nuclei were then sorted by GFP and/or DRAQ5 signal using the Sony SH800S Cell Sorter (purity mode) with a 100-μm sorting chip. 175,000 DRAQ5+/GFP+ or DRAQ5+/GFP- events were collected into 1 mL of cold CUT&RUN Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.2% Tween-20, 0.5 mM spermidine, 0.1% bovine serum albumin [BSA], 1X PIC). In vitro:  3T3 cells were washed twice with cold PBS and then scraped in NE1 lysis buffer (20 mM HEPES pH 7.9, 10 mM KCl, 0.1% Triton X-100, 3 mM MgCl2, 0.5 mM spermidine, 1X PIC, 10 mM sodium butyrate). Nuclei were rotated for 10 min at 4°C and centrifuged at 500g for 10 min at 4°C. The nuclei pellet was then resuspended in 1 mL of CUT&RUN Wash Buffer.
Takara SMARTer ThruPlex DNA-seq Kit

treatment_protocol: In vivo: dark-reared or normally-reared from birth to P14. In vitro: 3T3 cells were treated with 200 nM dexamethasone or vehicle (0.01% ethanol) for 2 hr.

value: 3T3 cells

value: DEX


title: GR CUT&RUN on 250K vehicle-treated 3T3 cells, replicate 1

description: Library name: 3T3_250K_Veh_GR_R1

value: Veh


title: IgG CUT&RUN on 250K vehicle-treated 3T3 cells, replicate 1

description: Library name: 3T3_250K_Veh_IgG_R1


title: GR CUT&RUN on 250K vehicle-treated 3T3 cells, replicate 2

description: Library name: 3T3_250K_Veh_GR_R2


title: GR CUT&RUN on 250K DEX-treated 3T3 cells, replicate 2

description: Library name: 3T3_250K_DEX_GR_R2


title: DMSO+C6A-rep2

description: Library name: DMSO+C6A-rep2


title: GR CUT&RUN on 50K vehicle-treated 3T3 cells, replicate 2

description: Library name: 3T3_50K_Veh_GR_R2


title: GR CUT&RUN on 50K vehicle-treated 3T3 cells, replicate 1

description: Library name: 3T3_50K_Veh_GR_R1


title: IgG CUT&RUN on P14 NR V1 GFP+ excitatory neurons, replicate 1

description: Library name: Vglut1_NR_IgG_R1

value: Excitatory neuron


title: IgG CUT&RUN on P14 NR V1 GFP+ oligodendrocytes, replicate 1

description: Library name: Olig2_NR_IgG_R1

value: Oligodendrocyte


title: NFIA CUT&RUN on P14 NR V1 GFP+ excitatory neurons, replicate 3

description: Library name: Vglut1_NR_NFIA_R3


title: NFIA CUT&RUN on P14 NR V1 GFP+ excitatory neurons, replicate 1

description: Library name: Vglut1_NR_NFIA_R1


title: NFIA CUT&RUN on P14 NR V1 GFP+ inhibitory neurons, replicate 3

description: Library name: Vgat_NR_NFIA_R3

value: Inhibitory neuron


title: neonatal mouse cardiomyocytes, LacZ overexpression with H2O2, rep3

description: Library name: Sample6

value: cardiomyocyte


title: NFIA CUT&RUN on P14 NR V1 GFP+ inhibitory neurons, replicate 2

description: Library name: Vgat_NR_NFIA_R2


title: RNA-seq on P14 NR V1 astrocyte GR-KO nuclei, replicate 2

description: Library name: P14_NR_GRKO_RNA_R2


title: NFIA CUT&RUN on P14 NR V1 GFP+ oligodendrocytes, replicate 3

description: Library name: Olig2_NR_NFIA_R3


title: RNA-seq on P14 NR V1 astrocyte GR-KO nuclei, replicate 3

description: Library name: P14_NR_GRKO_RNA_R3


title: WT, biol rep 1, CPZ

description:
Library name: 80167
10x Genomics
Immune_80167

value: Brain_corpus callosum

value: Male

value: 0.5% Cuprizone, 5 weeks


title: NC-rep1

description: Library name: NC-rep1

value: induced from hADSC

value: NC


title: RNA-seq on P21 DR V1 astrocyte GR-Con nuclei, replicate 2

description: Library name: P21_DR_GRCon_RNA_R2

value: Astrocyte


title: NFIA CUT&RUN on P14 NR V1 GFP+ astrocytes, replicate 2

description: Library name: Astro_NR_NFIA_R2

value: WT

value: NR


title: NFIA CUT&RUN on P14 NR V1 GFP+ astrocytes, replicate 1

description: Library name: Astro_NR_NFIA_R1


title: DMSO+TTNPB-rep2

description: Library name: DMSO+TTNPB-rep2

value: DMSO+TTNPB


title: GR CUT&RUN on P14 NR V1 GFP+ excitatory neurons, replicate 2

description: Library name: Vglut1_NR_GR_R2


title: GR CUT&RUN on P14 NR V1 GFP+ inhibitory neurons, replicate 3

description: Library name: Vgat_NR_GR_R3


title: GR CUT&RUN on P14 NR V1 GFP+ inhibitory neurons, replicate 2

description: Library name: Vgat_NR_GR_R2


title: neonatal mouse cardiomyocytes, Nrf1 overexpression with H2O2, rep2

description: Library name: Sample11


title: GR CUT&RUN on P14 NR V1 GFP+ inhibitory neurons, replicate 1

description: Library name: Vgat_NR_GR_R1


title: GR CUT&RUN on P14 NR V1 GFP+ oligodendrocytes, replicate 3

description: Library name: Olig2_NR_GR_R3


title: GR CUT&RUN on P14 NR V1 GFP+ oligodendrocytes, replicate 2

description: Library name: Olig2_NR_GR_R2


title: neonatal mouse cardiomyocytes, Nrf1 overexpression, rep1

description: Library name: Sample7

value: no treatment


title: neonatal mouse cardiomyocytes, LacZ overexpression, rep1

description: Library name: Sample1

value: LacZ


title: RNA-seq on P14 NR V1 astrocyte GR-KO nuclei, replicate 1

description: Library name: P14_NR_GRKO_RNA_R1

value: KO


title: GR CUT&RUN on P14 NR V1 GR-KO astrocytes, replicate 2

description: Library name: Astro_NR_GR_KO_R2

value: GR-KO


title: GR CUT&RUN on P14 NR V1 GR-Con astrocytes, replicate 2

description: Library name: Astro_NR_GR_Con_R2

value: GR-Con


title: neonatal mouse cardiomyocytes, Nrf1 overexpression, rep2

description: Library name: Sample8


title: IgG CUT&RUN on P14 NR V1 GFP+ astrocytes, replicate 1

description: Library name: Astro_NR_IgG_R1


title: neonatal mouse cardiomyocytes, LacZ overexpression, rep3

description: Library name: Sample3


title: GR CUT&RUN on P14 NR V1 GFP+ astrocytes, replicate 3

description: Library name: Astro_NR_GR_R3


title: neonatal mouse cardiomyocytes, Nrf1 overexpression, rep3

description: Library name: Sample9


title: GR CUT&RUN on P14 NR V1 GFP+ astrocytes, replicate 1

description: Library name: Astro_NR_GR_R1


title: RNA-seq on P28 DR V1 astrocyte GR-KO nuclei, replicate 2

description: Library name: P28_DR_GRKO_RNA_R2

value: DR


title: DMSO+C6A-rep1

description: Library name: DMSO+C6A-rep1


title: GR CUT&RUN on P14 DR V1 GFP+ astrocytes, replicate 2

description: Library name: Astro_DR_GR_R2


title: RNA-seq on P14 DR V1 astrocyte GR-KO nuclei, replicate 3

description: Library name: P14_DR_GRKO_RNA_R3


title: GR CUT&RUN on P14 DR V1 GFP+ astrocytes, replicate 3

description: Library name: Astro_DR_GR_R3


title: ATAC-seq on P21 V1 astrocyte GR-Con nuclei, replicate 2

description: Library name: GRCon_ATAC_R2

data_processing:
Fastq files were processed using the ENCODE ATAC-seq pipeline with default parameters.
Assembly: mm10
Supplementary files format and content: Bigwig files represent normalized genomic coverage. narrowPeak files represent regions of enriched signal.

growth_protocol: Each biological replicate consisted of P21 V1 tissue pooled from 3-4 GRfl/fl animals that were injected at P0-P1 with AAV2/5-GfaABC1D-ΔCre-T2A-EGFP-KASH-4x6T (GR-Con) or AAV2/5-GfaABC1D-Cre-T2A-EGFP-KASH-4x6T (GR-KO).

extract_protocol:
Mice were deeply anesthetized with isoflurane. Sections of 1 mm spanning V1 were collected in an adult mouse brain matrix (Alto) on ice, and V1 was microdissected. After dissecting samples, V1 tissue was transferred to a 1.5 mL tube containing 350 μL of cold homogenization buffer (250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH pH 7.8 supplemented with 1X PIC, 1 mM DTT, 0.15 mM spermine and 0.5 mM spermidine). The tissue was dounced in a 2 mL glass homogenizer (Sigma D8938) with a loose pestle for 20 strokes. Samples were supplemented with 0.3% IGEPAL CA-630 and further dounced for an additional 10 strokes with a tight pestle. Homogenate was filtered through a small 40-μm strainer (pluriSelect 43-10040-50) into a 1.5 mL tube before diluting 1:1 with homogenization buffer and adding DRAQ5 (Abcam ab108410) at a 1:500 dilution. Nuclei were then sorted by GFP and/or DRAQ5 signal using the Sony SH800S Cell Sorter (purity mode) with a 100-μm sorting chip. For ATAC-seq, 50,000 DRAQ5+/GFP+ events were collected into 1 mL of cold ATAC-RSB (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2).
After sorting nuclei into ATAC-RSB, 0.1% Tween-20 was added, and the nuclei were centrifuged at 500g for 10 min at 4°C. The nuclei pellet was directly resuspended in the transposition reaction mix, according to the OMNI-ATAC protocol. A 1 μL volume of homemade Tn5 enzyme was used in the transposition reaction. Libraries were prepared with NEBNext High-Fidelity 2X PCR Master Mix (NEB M0541L), following the standard protocol. After an initial five cycles of amplification, another four cycles were added to achieve optimal library concentration, based on qPCR quantification. Libraries were then size-selected (0.5X-1.8X) twice with AMPure XP beads (Beckman Coulter A63880) and sequenced paired-end on an Illumina NextSeq 500 using a 75-cycle kit.


title: ATAC-seq on P21 V1 astrocyte GR-Con nuclei, replicate 1

description: Library name: GRCon_ATAC_R1

value: injected at P0-P1 with AAV2/5-GfaABC1D-ΔCre-T2A-EGFP-KASH-4x6T (GR-Con)


title: Barcode Association Sequencing

city: Huntsville

first: Jesse

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

description: Library name: Barcode Association Sequencing

library_source: other

data_processing:
DNA and RNA Counts as well as DNA and RNA annotations were generated using the MPRAflow count utility as specified in Gordon et al. 2020 using the --mpranalyze flag
The design file was created using custom scripts (https://github.com/HudsonAlpha/Hauser_MAPT_MPRAs). Briefly, reads were alligned to hg38 chr17 using bwa mem. A unique bed file was generated using samtools/bedtools and fasta sequences were obtained from the bedfile using bedtools getfasta.
The barcode association dictionary was created using custom scripts (https://github.com/HudsonAlpha/Hauser_MAPT_MPRAs). Briefly, reads were alligned to hg38 chr17 using bwa mem, and unique barcodes were identified. Barcodes were sorted into 100bp bins based on the location of their associatied insert sequence.
For merged fastqs for replicate 1, fastqs from sequencing runs 1 and 2 were combined into a single file. Because the UMI read was in the header for sequencing run 1 MPRAflow requires reads in fastq format, the UMI seuence was extracted from the header and faux fastqs were generated using a script in (https://github.com/HudsonAlpha/Hauser_MAPT_MPRAs) before merging with the UMI fastqs from sequencing run 2.
Assembly: hg38
Supplementary files format and content: DNA and RNA counts are total barcode counts in csv format
Supplementary files format and content: DNA and RNA annotations are label files for use with mpranalyze in tsv format
Supplementary files format and content: The design file is a fasta file used for MPRAflow's count utility.
Supplementary files format and content: Barcode association dictionary is used for MPRAflow's count utility and is a python pickle file

molecule: other

source_name: NEB 10-beta electrocompetent cells

extract_protocol:
Qiagen Allprep RNA/DNA mini kit for MPRA output sequencing, Qiagen Plasmid Plus Mega kit for Barcode Association Sequencing
Libraries constructed according to LentiMPRA protocol Gordon et al. 2020

value: NEB 10-beta electrocompetent cells

value: not applicable


title: RNA-seq on P14 DR V1 astrocyte GR-KO nuclei, replicate 1

description: Library name: P14_DR_GRKO_RNA_R1


title: HEK293FT, DNA, Replicate 1, merged sequencing runs 1 and 2

description: Library name: HEK_MPRA1_DNA_merged

value: human embryonic kidney cells


title: HEK293FT, RNA, Replicate 1, sequencing 1

description: Library name: HEK_MPRA1_RNA_sequencing1


title: RNA-seq on P14 DR V1 astrocyte GR-KO nuclei, replicate 2

description: Library name: P14_DR_GRKO_RNA_R2


title: HEK293FT, DNA, Replicate 1, sequencing 1

description: Library name: HEK_MPRA1_DNA_sequencing1


title: Neurons, RNA, Replicate 1, merged sequencing runs 1 and 2

description: Library name: Neuron_MPRA1_RNA_merged

value: Neurons


title: RNA-seq on P14 DR V1 astrocyte GR-Con nuclei, replicate 3

description: Library name: P14_DR_GRCon_RNA_R3

value: Con


title: Neurons, DNA, Replicate 1, merged sequencing runs 1 and 2

description: Library name: Neuron_MPRA1_DNA_merged


title: RNA-seq on P14 DR V1 astrocyte GR-Con nuclei, replicate 1

description: Library name: P14_DR_GRCon_RNA_R1


title: IgG CUT&RUN on 250K DEX-treated 3T3 cells, replicate 1

description: Library name: 3T3_250K_DEX_IgG_R1

value: 3T3 cells

value: DEX


title: GR CUT&RUN on 50K DEX-treated 3T3 cells, replicate 1

description: Library name: 3T3_50K_DEX_GR_R1

value: WT


title: PTmixlo2 (RNA-Seq)

first: Kornelia

last: Polyak

address: 450 Brookline Ave. S1070

institute: Dana-Farber Cancer Institute

description:
Library name: PTmixlo2
Cuff_Gene_Counts_mix.csv

data_processing:
RNA-seq data were processed using VIPER pipeline (Cornwell et al., 2018).  Fastq files were aligned to the human reference GRCh37/hg19 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b) (Dobin et al., 2013).
Assembly: hg19
Supplementary files format and content: csv file of FPKM table

source_name: Breast cancer

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen). The total RNA was measured by Agilent 2100 Bioanalyzer.
RNA-seq libraries were prepared using Clontech Low Input mRNA Library (Clontech SMARTer) v4 kit from less than 10ng of purified total RNA according to the manufacturer’s protocol. The concentrations of finished dsDNA library were measured by Qubit Fluorometer, the size of library fragment was measured by Agilent TapeStation 2200, and RT-qPCR for adapted library molar concentration measurement according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500

value: Breast cancer

value: Co-culture


title: IgG CUT&RUN on P14 NR V1 GFP+ inhibitory neurons, replicate 1

description: Library name: Vgat_NR_IgG_R1

value: Inhibitory neuron

value: NR


title: NFIA CUT&RUN on P14 NR V1 GFP+ excitatory neurons, replicate 2

description: Library name: Vglut1_NR_NFIA_R2

value: Excitatory neuron


title: GR CUT&RUN on 50K DEX-treated 3T3 cells, replicate 2

description: Library name: 3T3_50K_DEX_GR_R2


title: PTmixhi1 (RNA-Seq)

description:
Library name: PTmixhi1
Cuff_Gene_Counts_mix.csv


title: NFIA CUT&RUN on P14 NR V1 GFP+ inhibitory neurons, replicate 1

description: Library name: Vgat_NR_NFIA_R1


title: NFIA CUT&RUN on P14 NR V1 GFP+ oligodendrocytes, replicate 2

description: Library name: Olig2_NR_NFIA_R2

value: Oligodendrocyte


title: GR CUT&RUN on P14 NR V1 GFP+ excitatory neurons, replicate 1

description: Library name: Vglut1_NR_GR_R1


title: PTlom1 (RNA-Seq)

description:
Library name: PTlom1
Cuff_Gene_Counts_mix.csv

value: Monoculture


title: NFIA CUT&RUN on P14 NR V1 GFP+ astrocytes, replicate 3

description: Library name: Astro_NR_NFIA_R3

value: Astrocyte


title: HCCmixhi2 (RNA-Seq)

description:
Library name: HCCmixhi2
Cuff_Gene_Counts_mix.csv


title: NFIA CUT&RUN on P14 NR V1 GFP+ oligodendrocytes, replicate 1

description: Library name: Olig2_NR_NFIA_R1


title: HCCmixlo2 (RNA-Seq)

description:
Library name: HCCmixlo2
Cuff_Gene_Counts_mix.csv


title: HCCmixlo1 (RNA-Seq)

description:
Library name: HCCmixlo1
Cuff_Gene_Counts_mix.csv


title: GR CUT&RUN on P14 NR V1 GFP- cells, replicate 1

description: Library name: Astro_NR_GFPneg_GR_R1

value: Non-astrocyte population


title: GR CUT&RUN on P14 NR V1 GFP+ oligodendrocytes, replicate 1

description: Library name: Olig2_NR_GR_R1


title: GR CUT&RUN on P14 NR V1 GFP- cells, replicate 2

description: Library name: Astro_NR_GFPneg_GR_R2


title: GR CUT&RUN on P14 NR V1 GR-Con astrocytes, replicate 1

description: Library name: Astro_NR_GR_Con_R1

value: GR-Con


title: HCChim1 (RNA-Seq)

description:
Library name: HCChim1
Cuff_Gene_Counts_mix.csv


title: GR CUT&RUN on P14 NR V1 GR-KO astrocytes, replicate 1

description: Library name: Astro_NR_GR_KO_R1

value: GR-KO


title: GR CUT&RUN on P14 DR V1 GFP- cells, replicate 2

description: Library name: Astro_DR_GFPneg_GR_R2

value: DR


title: PT_TDM12

description: Library name: PT_TDM12

value: T-DM1 resistant


title: PT_TDM11

description: Library name: PT_TDM11


title: PT_TDXd2

description: Library name: PT_TDXd2

value: T-DXd resistant


title: GR CUT&RUN on P14 NR V1 GFP+ excitatory neurons, replicate 3

description: Library name: Vglut1_NR_GR_R3


title: GR CUT&RUN on P14 NR V1 GFP+ astrocytes, replicate 2

description: Library name: Astro_NR_GR_R2


title: PTlo1

description: Library name: PTlo1


title: PT_DMSO1

description: Library name: PT_DMSO1

value: Control resistant


title: PThi2

description: Library name: PThi2


title: IgG CUT&RUN on P14 DR V1 GFP+ astrocytes, replicate 1

description: Library name: Astro_DR_IgG_R1


title: GR CUT&RUN on P14 DR V1 GFP- cells, replicate 1

description: Library name: Astro_DR_GFPneg_GR_R1


title: ATAC-seq on P21 V1 astrocyte GR-Con nuclei, replicate 3

description: Library name: GRCon_ATAC_R3

value: injected at P0-P1 with AAV2/5-GfaABC1D-ΔCre-T2A-EGFP-KASH-4x6T (GR-Con)


title: ATAC-seq on P21 V1 astrocyte GR-KO nuclei, replicate 2

description: Library name: GRKO_ATAC_R2

value: injected at P0-P1 with AAV2/5-GfaABC1D-Cre-T2A-EGFP-KASH-4x6T (GR-KO)


title: GR CUT&RUN on P14 DR V1 GFP+ astrocytes, replicate 1

description: Library name: Astro_DR_GR_R1

value: WT


title: NT_Tuc2

description: Library name: NT_Tuc2

value: Breast cancer

value: Tucatinib resistant


title: ATAC-seq on P21 V1 astrocyte GR-KO nuclei, replicate 3

description: Library name: GRKO_ATAC_R3


title: PThi1

description: Library name: PThi1


title: NT_Tuc1

description: Library name: NT_Tuc1


title: NT_TDXd1

description: Library name: NT_TDXd1


title: NTlo2

description: Library name: NTlo2


title: NT_DMSO1

description: Library name: NT_DMSO1


title: ATAC-seq on P21 V1 astrocyte GR-KO nuclei, replicate 1

description: Library name: GRKO_ATAC_R1


title: NThi2

description: Library name: NThi2


title: Neurons, RNA, Replicate 1, sequencing 1

description: Library name: Neuron_MPRA1_RNA_sequencing1

value: Neurons


title: PTmixlo1 (RNA-Seq)

description:
Library name: PTmixlo1
Cuff_Gene_Counts_mix.csv

value: Co-culture


title: HEK293FT, RNA, Replicate 1, merged sequencing runs 1 and 2

description: Library name: HEK_MPRA1_RNA_merged

value: human embryonic kidney cells


title: PTlom2 (RNA-Seq)

description:
Library name: PTlom2
Cuff_Gene_Counts_mix.csv

value: Monoculture


title: HCCmixhi1 (RNA-Seq)

description:
Library name: HCCmixhi1
Cuff_Gene_Counts_mix.csv


title: HCClom2 (RNA-Seq)

description:
Library name: HCClom2
Cuff_Gene_Counts_mix.csv


title: PT_Tuc2

description: Library name: PT_Tuc2


title: HCChim2 (RNA-Seq)

description:
Library name: HCChim2
Cuff_Gene_Counts_mix.csv


title: PTmixhi2 (RNA-Seq)

description:
Library name: PTmixhi2
Cuff_Gene_Counts_mix.csv


title: PThim2 (RNA-Seq)

description:
Library name: PThim2
Cuff_Gene_Counts_mix.csv


title: HCClom1 (RNA-Seq)

description:
Library name: HCClom1
Cuff_Gene_Counts_mix.csv


title: Neurons, DNA, Replicate 1, sequencing 1

description: Library name: Neuron_MPRA1_DNA_sequencing1


title: PT_DMSO2

description: Library name: PT_DMSO2


title: HCC_TDXd1

description: Library name: HCC_TDXd1


title: PThim1 (RNA-Seq)

description:
Library name: PThim1
Cuff_Gene_Counts_mix.csv


title: HCC_DMSO1

description: Library name: HCC_DMSO1


title: PTlo2

description: Library name: PTlo2


title: PT_TDXd1

description: Library name: PT_TDXd1


title: PT_Ner2

description: Library name: PT_Ner2

value: Neratinib resistant


title: NT_TDXd2

description: Library name: NT_TDXd2


title: HCChi1

description: Library name: HCChi1


title: HCChi2

description: Library name: HCChi2


title: HCC_Ner1

description: Library name: HCC_Ner1


title: PT_Tuc1

description: Library name: PT_Tuc1


title: NT_Ner1

description: Library name: NT_Ner1


title: PT_Ner1

description: Library name: PT_Ner1


title: HCC_Ner2

description: Library name: HCC_Ner2


title: hiPSC-HE rep2

data_processing:
The libraries were sequenced on Ion Proton system using an Ion PI Hi-Q Sequencing 200 kit and Ion PI Chip v3 (Thermo Fisher Scientific, A26772),
The sequencing reads were aligned to hg19_AmpliSeq_Transcriptome_ERCC_v1 using Torrent Mapping Alignment Program.
Subsequently, the data were analyzed using AmpliSeqRNA plug-in v5.2.0.3, a Torrent Suite Software v5.2.2 (Thermo Fisher Scientific), which provides QC metrics and normalized read counts per gene. Data were analyzed using GeneSpring (Agilent Technologies).
Assembly: hg19
Supplementary files format and content: normalized read counts per gene

extract_protocol:
Total RNA was prepared from indicated samples using a PureLink™ RNA Mini Kit. RNA integrity was evaluated using Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, California), and RNA samples with RNA integrity number > 9.0 were subjected for RNA-seq analysis.
RNA-seq libraries were prepared using 100 ng of total RNA with an Ion AmpliSeq Transcriptome Human Gene Expression kit (Thermo Fisher Scientific, A26326) according to the manufacturer's instructions.

value: Hepatic endoderm

value: Hepatic endoderm differentiation


title: NT_DMSO2

description: Library name: NT_DMSO2


title: NT_TDM12

description: Library name: NT_TDM12


title: hiPSC-HE rep3


title: hiPSC-HE rep1


title: HCC_Tuc2

description: Library name: HCC_Tuc2


title: hiPSC-EC rep1

value: Endothelial cells

value: Endothelial cells  differentiation


title: hiPSC-EC rep3


title: HCC_TDM11

description: Library name: HCC_TDM11

value: T-DM1 resistant


title: NTlo1

description: Library name: NTlo1


title: hiPSC-HSC P3 rep3

value: Hepatic stellate cell

value: Hepatic stellate cell after 3 passage


title: NT_Ner2

description: Library name: NT_Ner2


title: HCC_TDXd2

description: Library name: HCC_TDXd2

value: T-DXd resistant


title: hiPSC-HSC P6 rep2

value: Hepatic stellate cell after 6 passage


title: hiPSC-HSC P6 rep3

value: WT


title: NThi1

description: Library name: NThi1

value: Breast cancer


title: pHSC rep1

source_name: Human primary HSC

value: Human primary HSC


title: hiPSC-HSC P1 rep2

value: Hepatic stellate cell after 1 passage


title: hiPSC-HSC P6 rep1


title: pHSC rep2


title: hiPSC-HSC P0 rep3

value: Hepatic stellate cell  differentiation


title: hiPSC-HSC P1 rep1

value: Hepatic stellate cell  after 1 passage


title: HCC_TDM12

description: Library name: HCC_TDM12


title: hiPSC-STM rep3

value: Septum transversum mesenchyme

value: Septum transversum mesenchyme differentiation


title: hiPSC-HSC P0 rep2

value: Hepatic stellate cell differentiation


title: Uninfected U2, from wt compartment of BMC, cell-pool#6 , Mouse#8 , Left ear [L2002799_U2WT8L]

city: Magdeburg

first: Yan

last: Fu

state: Saxony-Anhalt

address: Haus 26, Institut für Molekulare und Klinische Immunologie, Otto-von-Guericke-Universität Magdeburg, Leipziger Str. 44

institute: Otto-von-Guericke-Universität Magdeburg

description:
SmartSeq2
Uninfected U2, from wt compartment of bone marrow chimeric, cell-pool#6 , Mouse#8 , Left ear [L2002799_U2WT8L]

data_processing:
Raw fastq files were processed with Cutadapt (v3.7) to remove poly-A tails and adapter sequences introduced during library construction (SMART-seq: AAGCAGTGGTATCAACGCAGAGT & Nextera XT: CTGTCTCTTATACACATCT).
The first 15 bases of each read, bases with Qscore < 20 and reads left with less than 25 bases after trimming were also discarded.
Reads were mapped to a reference genome using STAR with default parameters.
The used reference genome has been built by combining the mouse (GRCm38) and Leishmania major (ASM272v2) genomes as well as spike-ins (ERCC92) and the Kikume Green-Red transcript sequences.
The raw count matrix was generated from the mapping results with featureCounts (Subread, v1.6.3)
Assembly: GRCm38,  ASM272v2, ERCC92
Supplementary files format and content: Tab-separated matrix files

source_name: ear tissue

extract_protocol:
Ears of mice were separated in two sheets (ventral and dorsal) using forceps and enzymatically digested in RPMI 1640 medium containing 1 mg/ml collagenase and 50 ng/ml DNase for 60 min at 600 rpm and 37°C and passed through a 70 μm cell strainer. Cells were centrifuged at 4°C with 300 g for 10 min. Cells were washed with PBS and FACS buffer before surface staining of cells was done by using surface marker specific antibodies (PEcy7-CD45.2, PerCPcy5.5-CD45.1, APC-CD11c, APC-cy7-Ly6c, and BV510-CCR2). Samples were blocked with Fc-block using anti-CD16/32 antibody (1:25 in FACS buffer) for 15 min on ice before the antibody staining. Antibodies were applied with a final concentration of 1:200. Leishmania major infections were analyzed with a FACS ARIA III flow cytometer/sorter.
50-100 cells per cell subpopulation per sample were sorted into an individual well from a 96-well plate (Costar) filled with 4.65 µl of Buffer RLT Plus (Qiagen), 0.25 µl of SUPERase-In RNase-Inhibitor (Invitrogen). Sorted cells were immediately frozen and stored at -80 °C. Sequencing libraries were prepared using Smart-seq2 protocol as previous described with minor modifications: Following cDNA amplification, ACTB expression was measured in each cDNA library by qPCR. All cDNA libraries were diluted aiming to an equivalent ct value for ACTB (average = 21.11, SD = 1.05) and were subsequently used as input for a tagmentation-based protocol (Nextera XT, Illumina) using one quarter of the recommended volumes, 10 min for tagmentation at 55°C20. The indexed libraries were quantified using Qubit dsDNA Hs Assay (Life Technologies) and fragment size of libraries was analysed using QIAxcel DNA high resolution Kit (Qiagen) and bioanalyser (Agilent). Libraries were normalized to 2 nM and pooled. Particularly, 87 libraries were sequenced for HiSeq 2500 (Illumina).

value: monocytes

value: ear tissue

value: wt

value: 22 weeks old


title: hiPSC-EC rep2

value: Endothelial cells

value: Endothelial cells  differentiation


title: hiPSC-HSC P1 rep3

value: Hepatic stellate cell


title: hiPSC-HSC P3 rep1

value: Hepatic stellate cell after 3 passage


title: hiPSC-STM rep2

value: WT


title: hiPSC-HSC P0 rep1


title: HCC_Tuc1

description: Library name: HCC_Tuc1

value: Breast cancer

value: Tucatinib resistant


title: Uninfected U2, from wt compartment of BMC, cell-pool#5 , Mouse#7 , Right ear [L2002791_U2WT7R]

department: Institut für Molekulare und Klinische Immunologie

description:
SmartSeq2
Uninfected U2, from wt compartment of bone marrow chimeric, cell-pool#5 , Mouse#7 , Right ear [L2002791_U2WT7R]


title: HCClo2

description: Library name: HCClo2


title: hiPSC rep2

value: Human induced pluripotent stem cells


title: NT_TDM11

description: Library name: NT_TDM11

value: T-DM1 resistant


title: hiPSC-STM rep1


title: HCClo1

description: Library name: HCClo1


title: HCC_DMSO2

description: Library name: HCC_DMSO2

value: Control resistant


title: pHSC rep3

value: Human primary HSC


title: Uninfected U2, from wt compartment of BMC, cell-pool#7 , Mouse#8 , Right ear [L2002807_U2WT8R]

description:
SmartSeq2
Uninfected U2, from wt compartment of bone marrow chimeric, cell-pool#7 , Mouse#8 , Right ear [L2002807_U2WT8R]


title: Uninfected U2, from wt compartment of BMC, cell-pool#2 , Mouse#5 , Right ear [L2002759_U2WT5R]

description:
SmartSeq2
Uninfected U2, from wt compartment of bone marrow chimeric, cell-pool#2 , Mouse#5 , Right ear [L2002759_U2WT5R]


title: Uninfected U2, from wt compartment of BMC, cell-pool#4 , Mouse#7 , Left ear [L2002783_U2WT7L]

description:
SmartSeq2
Uninfected U2, from wt compartment of bone marrow chimeric, cell-pool#4 , Mouse#7 , Left ear [L2002783_U2WT7L]


title: hiPSC-HSC P3 rep2


title: Uninfected U2, from IL7R-/- compartment of BMC, cell-pool#6 , Mouse#8 , Left ear [L2002798_U2KO8L]

description:
SmartSeq2
Uninfected U2, from IL7R-/- compartment of bone marrow chimeric, cell-pool#6 , Mouse#8 , Left ear [L2002798_U2KO8L]


title: Uninfected U2, from IL7R-/- compartment of BMC, cell-pool#4 , Mouse#7 , Left ear [L2002782_U2KO7L]

description:
SmartSeq2
Uninfected U2, from IL7R-/- compartment of bone marrow chimeric, cell-pool#4 , Mouse#7 , Left ear [L2002782_U2KO7L]


title: Uninfected U2, from wt compartment of BMC, cell-pool#1 , Mouse#5 , Left ear [L2002752_U2WT5L]

description:
SmartSeq2
Uninfected U2, from wt compartment of bone marrow chimeric, cell-pool#1 , Mouse#5 , Left ear [L2002752_U2WT5L]


title: Uninfected U2, from IL7R-/- compartment of BMC, cell-pool#2 , Mouse#5 , Right ear [L2002758_U2KO5R]

description:
SmartSeq2
Uninfected U2, from IL7R-/- compartment of bone marrow chimeric, cell-pool#2 , Mouse#5 , Right ear [L2002758_U2KO5R]


title: Uninfected U2, from IL7R-/- compartment of BMC, cell-pool#7 , Mouse#8 , Right ear [L2002806_U2KO8R]

description:
SmartSeq2
Uninfected U2, from IL7R-/- compartment of bone marrow chimeric, cell-pool#7 , Mouse#8 , Right ear [L2002806_U2KO8R]


title: Uninfected U1, from wt compartment of BMC, cell-pool#11 , Mouse#8 , Left ear [L2002797_U1WT8L]

description:
SmartSeq2
Uninfected U1, from wt compartment of bone marrow chimeric, cell-pool#11 , Mouse#8 , Left ear [L2002797_U1WT8L]


title: Uninfected U1, from wt compartment of BMC, cell-pool#10 , Mouse#7 , Right ear [L2002789_U1WT7R]

description:
SmartSeq2
Uninfected U1, from wt compartment of bone marrow chimeric, cell-pool#10 , Mouse#7 , Right ear [L2002789_U1WT7R]


title: Uninfected U1, from wt compartment of BMC, cell-pool#12 , Mouse#8 , Right ear [L2002805_U1WT8R]

description:
SmartSeq2
Uninfected U1, from wt compartment of bone marrow chimeric, cell-pool#12 , Mouse#8 , Right ear [L2002805_U1WT8R]


title: C. trachomatis, EB, BPDL 24hpi, rep1

city: Lausanne

first: Daniel

last: Rodriguez Rozo

address: Avenue de Cour 10

department: IMUL

country: Switzerland

institute: CHUV

description:
Library name: EB_1
RNA-seq of C. trachomatis elementary bodies in infected HEp-2 cells at 72 hpi.

data_processing:
Raw sequencing reads were quality-checked and adapter-trimmed using Trimmomatic v0.36.
Filtered reads were mapped to the C. trachomatis L2/434/Bu reference genome (GCA_000068585.1) using BWA-MEM v0.7.17.
Gene-level read counts were obtained using HTSeq-count v0.11.2 (stranded = no).
Rarefaction analysis was performed to assess gene detection saturation across all samples.
Differential expression analysis was performed using edgeR v3.26.5. Library sizes were normalized using TMM via calcNormFactors, low-abundance genes were filtered using filterByExpr, dispersion was estimated using estimateCommonDisp and estimateTagwiseDisp, and significance was defined as FDR < 0.01. Normalized expression values were reported as RPKM.
Assembly: Chlamydia trachomatis L2/434/Bu, NCBI RefSeq GCA_000068585.1
Supplementary files format and content: Processed data files include tab-delimited text files containing gene-level raw counts and normalized RPKM values for all samples. Rows correspond to ORFs and columns correspond to biological replicates.
Supplementary files format and content: Each processed file contains the C. trachomatis gene identifier, raw counts, and normalized RPKM values for each sample, enabling reproducible downstream analysis.

organism: Chlamydia trachomatis

growth_protocol: HEp-2 cells (ATCC® CCL-23™) were infected with Chlamydia trachomatis at a multiplicity of infection (MOI) of 5.4. Infected cells were incubated until the indicated time points corresponding to reticulate bodies (24 hpi), elementary bodies (72 hpi), or aberrant bodies induced by iron limitation via BPDL treatment (added at 8 hpi and harvested at 24 hpi).

extract_protocol:
Total RNA was extracted from infected HEp-2 cells using TRIzol™ (Invitrogen) followed by DNase I digestion (Invitrogen) and purification according to the manufacturer’s instructions. RNA quality was verified with a Fragment Analyzer (Agilent) and quantity determined using the Qubit™ RNA Broad-Range Assay Kit (Thermo Fisher). RNA was stored at –80°C until library preparation.
rRNA was removed using the Ribo-Zero rRNA Removal Kit (Illumina). cDNA libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit with poly-A negative selection. Libraries were sequenced on an Illumina NovaSeq 6000 platform in paired-end mode.

treatment_protocol: Aberrant bodies (ABs) were induced by the addition of 100 µM 2,2′-bipyridyl (BPDL) at 8 hpi. Untreated infected cells were used to obtain reticulate bodies (RBs) and elementary bodies (EBs).

value: epithelial cell

value: wild type

tag: batch


title: Uninfected U2, from wt compartment of BMC, cell-pool#3 , Mouse#6 , Left ear [L2002767_U2WT6L]

description:
SmartSeq2
Uninfected U2, from wt compartment of bone marrow chimeric, cell-pool#3 , Mouse#6 , Left ear [L2002767_U2WT6L]

value: monocytes


title: C. trachomatis, EB, BPDL 24hpi, rep3

description:
Library name: EB_3
RNA-seq of C. trachomatis elementary bodies in infected HEp-2 cells at 72 hpi.


title: Uninfected U2, from IL7R-/- compartment of BMC, cell-pool#5 , Mouse#7 , Right ear [L2002790_U2KO7R]

description:
SmartSeq2
Uninfected U2, from IL7R-/- compartment of bone marrow chimeric, cell-pool#5 , Mouse#7 , Right ear [L2002790_U2KO7R]

value: ear tissue


title: hiPSC rep1


title: C. trachomatis, RB, BPDL 24hpi, rep2

description:
Library name: RB_2
RNA-seq of C. trachomatis reticulate bodies in infected HEp-2 cells at 24 hpi.


title: C. trachomatis, RB, BPDL 24hpi, rep3

description:
Library name: RB_3
RNA-seq of C. trachomatis reticulate bodies in infected HEp-2 cells at 24 hpi.


title: Uninfected U1, from wt compartment of BMC, cell-pool#7 , Mouse#6 , Left ear [L2002765_U1WT6L]

description:
SmartSeq2
Uninfected U1, from wt compartment of bone marrow chimeric, cell-pool#7 , Mouse#6 , Left ear [L2002765_U1WT6L]

value: wt


title: CaMPARI-red cells moving condition, batch 2

city: Wako

first: Fumi

last: Kubo

address: 2-1 Hirosawa

department: Center for Brain Science

institute: RIKEN

description:
Library name: Moving2
10x Genomics

data_processing:
Initial preprocessing was performed using the Cell Ranger software suite (version v6.0.1, 10X Genomics) following standard guidelines. ‘‘cellranger count’’ was used to align the reads to a custom reference genome created by combining the improved zebrafish transcriptome annotation file (GTF for v4.3.2) (Lawson et al., 2020) and the FATSA file (GRCz11) with CaMPARI2, using ‘‘cellranger mkref’’. Each biological replicate resulted in 3,000-5,000 estimated number of cells with 3,500-5,000 median unique molecular identifier (UMI) counts per cell. Output from cellranger was loaded into Seurat R package 68 (version 4.1.1) using the Read10X function, with each condition representing different experiment: stationary1, stationary2, moving1, and moving2. The data were stored as Seurat objects, with a minimum threshold of 200 genes per cell and a minimum of 3 cells per gene for inclusion. For quality control, cells with greater than 10% mitochondrial gene expression were excluded from further analysis. Cells were also filtered based on the number of detected genes, retaining those with between 200 and 5000 genes. This quality control was applied uniformly to all datasets. The numbers of cells before and after quality control for each dataset were as follows: stationary1, 3117 cells before QC and 3093 cells after QC; stationary2, 3884 and 3869; moving1, 3735 and 3678; moving2, 4812 and 4804, respectively. Following filtering, the datasets were integrated using the SCTransform function. The datasets for stationary1, stationary2, moving1, and moving2 were stored in a list and processed through the SCTransform function. For each transformed dataset, the 3000 most variable genes were selected as possible integration features using SelectIntegrationFeatures. We then followed the standard integration pipeline, employing PrepSCTIntegration to prepare the data for integration. Integration was performed using the FindIntegrationAnchors function, where stationary1 and stationary2 datasets were used as the reference. Normalization was done using the SCTransform. The resulting integration anchors were used to combine the datasets into a single Seurat object using IntegrateData. To reduce dimensionality, principal component analysis (PCA) was performed using the RunPCA function. Subsequently, UMAP was generated using the first 20 principal components (PCs) to visualize the data in a two dimensional space (RunUMAP). Clustering was performed using the FindNeighbors and FindClusters functions with the PCA reduction and a resolution of 0.8. Marker genes for each cluster were identified using the FindAllMarkers function, selecting only positive markers with a log fold change threshold of 0.25. We annotated clusters based on the expression data of marker genes using the Zebrafish Information Network website (zfin.org).
Assembly: GRCz11
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: Brain

extract_protocol:
After photoconversion, larvae were kept at 27.5 degrees for maximally 4 hours until brain dissection. Brain was dissected in ice-cold Neurobasal medium (ThermoFisher Scientific, 21103049) supplemented with B-27 (ThermoFisher Scientific, 17504044). After the eyes were removed from the head, anterior to the habenula and posterior to the otolith was cut away to increase the proportion of pretectal cells. Cell dissociation was performed as previously described with some modifications. Tissues were pooled from 50-60 larvae and digested in 25 U/ml papain, 130 U/ml DNaseI, 2 mM L-cysteine in oxigenated Ames at 37°C for 36 minutes. Every 12 minutes, tissues were triturated by pipetting, followed by a final incubation for 5 minutes. The cell suspension was then passed through a pre-wet 40 µm filter (Falcon, 352340). To stop the digestion, the papain solution was replaced by papain inhibitor solution containing 15 mg/ml ovomucoid and 15 mg/ml BSA. Tissue was gently dissociated by trituration using a broad end tip pipette in the papain inhibitor solution. To wash the cell suspension, cells were pelleted at 300 g for 7 minutes at RT and resuspended in FACS buffer (oxigenated Ames containing 0.25% BSA (Sigma, A4161), 10m M HEPES (Sigma, H0887), 25 U/mL DNase I (Thermofisher, 90083), 5mM MgCl2)). CaMPARI2 red cells were sorted based on green and red fluorescence using SONY Cell Sorter SH800S equipped with 488 nm & 561 nm lasers. First, FACS gates were set after 50,000 recorded events to sort live single-cells. Similar gates were used across experiments. Specifically, a scatter gate was initially set using forward scattering (FSC-A) and back scattering (BSC-A) to select the live cell population. Next, Forward Scatter Area (FSC-A) and Forward Scatter Height (FSC-H) were used to eliminate debris as much as possible and isolate single-cells. Then, CaMPARI2 green and CaMPARI2 red fluorescence were used to collect CaMPARI2 red cells labeled by photoconversion of Tg(elavl3:NLS-CaMPARI2) larvae. The gating was set to include the CaMPARI2 red fluorescent cell population, which was not observed in the Tg(elavl3:NLS-CaMPARI2) control larvae that did not undergo photoconversion. Overall, 60-70% of the population consisted of live single cells, and approximately 8% of those were CaMPARI2 red cells. These cells were sorted using a 100 µm nozzle (20 PSI) and collected to a 2 ml protein LoBind Eppendorf tube filled with 1 ml oxigenated Ames containing 1.0% BSA, 10mM HEPES. A total of 130,000~150,000 CaMPARI2 red cells were collected from 50-60 larvae. After FACS was completed, cell suspension was centrifuged for 5 min at 100 g at RT and the pellet was resuspended in 300 µl of Ames medium/0.5% BSA. This washing step was repeated three times, and finally, the cells were resuspended in 30 μL of Ames/BSA solution. To check cell density and viability, cells were stained with a dead cell stain Trypan Blue (Sigma-Aldrich, T8154) and both live and dead cells were counted using a DIC microscope. Cell density was typically between 300 and 800 cells/µl with a viability rate of over 90%.
Droplet RNA sequencing was performed according to the manufacturer’s instructions with no modifications (10x Genomics Chromium System, Chromium Next GEM Single Cell 3' Reagent Kits v3.1). A single-chromium chip channel was loaded with a cell suspension, aiming to capture 5,000 cells with a doublet rate of <5%. For the “moving” condition, 2 replicates were collected from 2 experiments. For the “stationary” condition, 2 replicates were collected from 2 experiments. cDNA libraries were sequenced on a NovaSeq 6000 (illumina) or DNBSEQ-G400 (MGI Tech) to a depth of ~60,000 reads per cell.

value: Brain


title: Uninfected U2, from IL7R-/- compartment of BMC, cell-pool#1 , Mouse#5 , Left ear [L2002751_U2KO5L]

description:
SmartSeq2
Uninfected U2, from IL7R-/- compartment of bone marrow chimeric, cell-pool#1 , Mouse#5 , Left ear [L2002751_U2KO5L]

value: 22 weeks old


title: CaMPARI-red cells stationary condition, batch 1

description:
Library name: Stationary1
10x Genomics


title: C. trachomatis, RB, BPDL 24hpi, rep1

description:
Library name: RB_1
RNA-seq of C. trachomatis reticulate bodies in infected HEp-2 cells at 24 hpi.


title: Uninfected U2, from IL7R-/- compartment of BMC, cell-pool#3 , Mouse#6 , Left ear [L2002766_U2KO6L]

description:
SmartSeq2
Uninfected U2, from IL7R-/- compartment of bone marrow chimeric, cell-pool#3 , Mouse#6 , Left ear [L2002766_U2KO6L]


title: Uninfected U1, from wt compartment of BMC, cell-pool#8 , Mouse#6 , Right ear [L2002773_U1WT6R]

description:
SmartSeq2
Uninfected U1, from wt compartment of bone marrow chimeric, cell-pool#8 , Mouse#6 , Right ear [L2002773_U1WT6R]


title: C. trachomatis, AB, BPDL 24hpi, rep3

description:
Library name: AB_3
RNA-seq of C. trachomatis aberrant bodies induced by BPDL in infected HEp-2 cells at 24 hpi.

value: BPDL


title: Uninfected U1, from wt compartment of BMC, cell-pool#9 , Mouse#7 , Left ear [L2002781_U1WT7L]

description:
SmartSeq2
Uninfected U1, from wt compartment of bone marrow chimeric, cell-pool#9 , Mouse#7 , Left ear [L2002781_U1WT7L]


title: Uninfected U1, from wt compartment of BMC, cell-pool#6 , Mouse#5 , Right ear [L2002757_U1WT5R]

description:
SmartSeq2
Uninfected U1, from wt compartment of bone marrow chimeric, cell-pool#6 , Mouse#5 , Right ear [L2002757_U1WT5R]


title: Uninfected U1, from wt compartment of BMC, cell-pool#5 , Mouse#5 , Left ear [L2002750_U1WT5L]

description:
SmartSeq2
Uninfected U1, from wt compartment of bone marrow chimeric, cell-pool#5 , Mouse#5 , Left ear [L2002750_U1WT5L]


title: C. trachomatis, AB, BPDL 24hpi, rep2

description:
Library name: AB_2
RNA-seq of C. trachomatis aberrant bodies induced by BPDL in infected HEp-2 cells at 24 hpi.


title: C. trachomatis, AB, BPDL 24hpi, rep1

description:
Library name: AB_1
RNA-seq of C. trachomatis aberrant bodies induced by BPDL in infected HEp-2 cells at 24 hpi.


title: HEK293FT, RNA, Replicate 2

description: Library name: HEK_MPRA2_RNA

value: human embryonic kidney cells


title: C. trachomatis, EB, BPDL 24hpi, rep2

description:
Library name: EB_2
RNA-seq of C. trachomatis elementary bodies in infected HEp-2 cells at 72 hpi.


title: Uninfected U1, from wt compartment of BMC, cell-pool#2 , Mouse#2 , Left ear [L2002736_U1WT2L]

description:
SmartSeq2
Uninfected U1, from wt compartment of bone marrow chimeric, cell-pool#2 , Mouse#2 , Left ear [L2002736_U1WT2L]


title: Uninfected U1, from wt compartment of BMC, cell-pool#3 , Mouse#2 , Right ear [L2002775_U1WT2R]

description:
SmartSeq2
Uninfected U1, from wt compartment of bone marrow chimeric, cell-pool#3 , Mouse#2 , Right ear [L2002775_U1WT2R]


title: Uninfected U1, from IL7R-/- compartment of BMC, cell-pool#7 , Mouse#6 , Left ear [L2002764_U1KO6L]

description:
SmartSeq2
Uninfected U1, from IL7R-/- compartment of bone marrow chimeric, cell-pool#7 , Mouse#6 , Left ear [L2002764_U1KO6L]


title: HEK293FT, DNA, Replicate 1, sequencing 2

description: Library name: HEK_MPRA1_DNA_sequencing2


title: Uninfected U1, from wt compartment of BMC, cell-pool#4 , Mouse#3 , Left ear [L2002744_U1WT3L]

description:
SmartSeq2
Uninfected U1, from wt compartment of bone marrow chimeric, cell-pool#4 , Mouse#3 , Left ear [L2002744_U1WT3L]


title: Neurons, RNA, Replicate 2

description: Library name: Neuron_MPRA2_RNA

value: Neurons


title: HEK293FT, DNA, Replicate 2

description: Library name: HEK_MPRA2_DNA


title: HEK293FT, RNA, Replicate 1, sequencing 2

description: Library name: HEK_MPRA1_RNA_sequencing2


title: Neurons, DNA, Replicate 2

description: Library name: Neuron_MPRA2_DNA


title: Uninfected U1, from IL7R-/- compartment of BMC, cell-pool#12 , Mouse#8 , Right ear [L2002804_U1KO8R]

description:
SmartSeq2
Uninfected U1, from IL7R-/- compartment of bone marrow chimeric, cell-pool#12 , Mouse#8 , Right ear [L2002804_U1KO8R]


title: Uninfected U1, from wt compartment of BMC, cell-pool#1 , Mouse#1 , Right ear [L2002732_U1WT1R]

description:
SmartSeq2
Uninfected U1, from wt compartment of bone marrow chimeric, cell-pool#1 , Mouse#1 , Right ear [L2002732_U1WT1R]


title: Neutro _Virus

city: Montigny-Le-Bretonneux

first: Sophie

last: Dupré

address: 2 av. de la Source de la Bièvre

department: Versailles Saint Quentin University

country: France

institute: Paris Saclay Université

description:
Library name: Sample 2
10xGenomics

data_processing:
QC reads, Pseudo-mapping and quantification Raw BCL-files were demultiplexed and converted to Fastq format using bcl2fastq (version 2.20.0.422 from Illumina).Reads quality control was performed using fastqc (version 0.11.9) and assignment to the expected genome species evaluated with fastq-screen (version 0.14.0).Reads were pseudo-mapped to the Ensembl reference transcriptome v99 corresponding to the homo sapiens GRCH38 build with kallisto (version 0.46.2) using its 'bus' subcommand and parameters corresponding to the 10X Chromium 3' scRNA-Seq v3 chemistry. The index was made with the kb-python (version 0.24.4) wrapper of kallisto. Barcode correction using whitelist provided by the manufacturer (10X Genomics) and gene-based reads quantification was performed with BUStools (version 0.40.0).  QC data on each sample Cell barcode by symbol count table were loaded in R (version 4.1.0) using the BUSpaRse package (version 1.7.1). To call real cells from empty droplets, we used the emptyDrops() function from the dropletUtils package (version 1.12.2), which assesses whether the RNA content associated with a cell barcode is significantly distinct from the ambient background RNA present within each sample. Barcodes with p-value < 0.001 (Benjamini-Hochberg-corrected) were considered as legitimate cells for further analysis. The count matrix was filtered to exclude genes detected in less than 5 cells, cells with less than 1000 UMIs or less than 200 detected genes, as well as cells with mitochondrial transcripts proportion higher than 20%.The proportion of ribosomal gene counts and the proportion of mechanical stress-response gene counts (Thesis of Léo Machado entitled « From skeletal muscle stem cells to tissue atlases: new tools to investigate and circumvent dissociation-induced stress», 2019) were also estimated but not used to filter cells. Cell cycle scoring of each cell was performed using two methods: the CellcycleScoring() function from the Seurat package (version 4.0.4), and the cyclone() function from Scran (version 1.20.1).Barcodes corresponding to doublet cells were identified and discarded using the union of two methods: scDblFinder (version 1.6.0) using default parameters, and scds (version 1.8.0) with its hybrid method using default parameters. We manualy verified that the cells identified as doublets did not systematically correspond to cells in G2M phase.
Assembly: Ensembl reference transcriptome v99 corresponding to the homo sapiens GRCH38 build with kallisto (version 0.46.2)
Supplementary files format and content: Tab-separated value files and matrix files

source_name: blood

extract_protocol:
PMNs (5 × 10^5) per condition were resuspended in HBSS. HBSS, HS or HS-opsonized Ad5 (MOI 10^4 vp/cell) were incubated with PMNs for 30 min at 4°C. After washing with HBSS, samples were incubated 90 min at 37°C then filtered to discard aggregates. PMNs were counted with Trypan Blue to assess cell viability (that was around 80%) then transferred in DNA LoBind tubes
Library was performed according to the manufacturer's instructions 10X Genomics Chromium 3’ single-cell RNAseq

value: blood

value: neutrophil

value: granulocyte

value: Adenovirus pretreated with Human serum


title: Neurons, DNA, Replicate 1, sequencing 2

description: Library name: Neuron_MPRA1_DNA_sequencing2


title: Neurons, RNA, Replicate 1, sequencing 2

description: Library name: Neuron_MPRA1_RNA_sequencing2


title: Uninfected U1, from IL7R-/- compartment of BMC, cell-pool#6 , Mouse#5 , Right ear [L2002756_U1KO5R]

description:
SmartSeq2
Uninfected U1, from IL7R-/- compartment of bone marrow chimeric, cell-pool#6 , Mouse#5 , Right ear [L2002756_U1KO5R]


title: HASMCs,ad-GLS3+PBS

city: Nanjing

first: Hailong

state: Jiangsu

address: 87 Dingjiaqiao

department: Department of Cardiac Surgery

institute: Zhongda hospital

description:
Library name: Sample 9
Column name in genes_fpkm_expression.xlsx: FPKM.C_4

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Homo sapiens GRCh38 . The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. 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 (https://bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: GRCh38
Supplementary files format and content: tab-delimited file include FPKM values for each Samples

source_name: primary cells

growth_protocol: Human aortic smooth muscle cells (HASMCs, 6110, ScienCell) purchased from ScienCell Research Laboratories were cultured in Smooth Muscle Cell Medium (SMCM, 1101, ScienCell).

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen),2μg of RNA was used for construction of sequencing library. Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. 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.
Total RNA was extracted and quantified, requiring a RIN > 7.0. mRNA was purified from 5 µg of total RNA using oligo(d)T beads and fragmented thermally. First-strand cDNA was synthesized using SuperScript™ II Reverse Transcriptase, followed by second-strand synthesis incorporating dUTP. Indexed adapters were ligated to the A-tailed fragments, and size selection was performed. U-labeled second strands were digested using heat-labile UDG enzyme, and the library was amplified via PCR. The final libraries (average insert size 300 ± 50 bp) were subjected to 2 × 150 bp paired-end sequencing on an Illumina Novaseq™ 6000.

treatment_protocol: HASMCs were serum-starved in DMEM without FBS for 12 h, followed by stimulation with PDGF-BB (MedChemExpress, Cat# HY-P7055) at the indicated concentration (20 ng/mL) for 24 h.

value: aorta

value: smooth muscle cell

value: WT


title: Uninfected U1, from IL7R-/- compartment of BMC, cell-pool#10 , Mouse#7 , Right ear [L2002788_U1KO7R]

description:
SmartSeq2
Uninfected U1, from IL7R-/- compartment of bone marrow chimeric, cell-pool#10 , Mouse#7 , Right ear [L2002788_U1KO7R]


title: Uninfected U1, from IL7R-/- compartment of BMC, cell-pool#9 , Mouse#7 , Left ear [L2002780_U1KO7L]

description:
SmartSeq2
Uninfected U1, from IL7R-/- compartment of bone marrow chimeric, cell-pool#9 , Mouse#7 , Left ear [L2002780_U1KO7L]


title: Neutro_HS

description:
Library name: Sample 1
10xGenomics

value: Human serum


title: Uninfected U1, from IL7R-/- compartment of BMC, cell-pool#11 , Mouse#8 , Left ear [L2002796_U1KO8L]

description:
SmartSeq2
Uninfected U1, from IL7R-/- compartment of bone marrow chimeric, cell-pool#11 , Mouse#8 , Left ear [L2002796_U1KO8L]


title: Uninfected U1, from IL7R-/- compartment of BMC, cell-pool#4 , Mouse#3 , Left ear [L2002743_U1KO3L]

description:
SmartSeq2
Uninfected U1, from IL7R-/- compartment of bone marrow chimeric, cell-pool#4 , Mouse#3 , Left ear [L2002743_U1KO3L]


title: Uninfected U1, from IL7R-/- compartment of BMC, cell-pool#3 , Mouse#2 , Right ear [L2002774_U1KO2R]

description:
SmartSeq2
Uninfected U1, from IL7R-/- compartment of bone marrow chimeric, cell-pool#3 , Mouse#2 , Right ear [L2002774_U1KO2R]


title: Uninfected U1, from IL7R-/- compartment of BMC, cell-pool#5 , Mouse#5 , Left ear [L2002749_U1KO5L]

description:
SmartSeq2
Uninfected U1, from IL7R-/- compartment of bone marrow chimeric, cell-pool#5 , Mouse#5 , Left ear [L2002749_U1KO5L]


title: HASMCs,ad-GLS3+PDGF-BB

description:
Library name: Sample 12
Column name in genes_fpkm_expression.xlsx: FPKM.A_3


title: Low-proliferating L. major infected,  wt compartment of BMC, cell-pool#15 , Mouse#8 , Right ear [L2002801_LoWT8R]

description:
SmartSeq2
Low-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#15 , Mouse#8 , Right ear [L2002801_LoWT8R]


title: HASMCs,ad-GLS1+PBS

description:
Library name: Sample 7
Column name in genes_fpkm_expression.xlsx: FPKM.C_1


title: HASMCs,ad-GLS2+PDGF-BB

description:
Library name: Sample 11
Column name in genes_fpkm_expression.xlsx: FPKM.A_2


title: HASMCs,ad-GLS1+PDGF-BB

description:
Library name: Sample 10
Column name in genes_fpkm_expression.xlsx: FPKM.A_1


title: Uninfected U1, from IL7R-/- compartment of BMC, cell-pool#2 , Mouse#2 , Left ear [L2002735_U1KO2L]

description:
SmartSeq2
Uninfected U1, from IL7R-/- compartment of bone marrow chimeric, cell-pool#2 , Mouse#2 , Left ear [L2002735_U1KO2L]


title: Uninfected U1, from IL7R-/- compartment of BMC, cell-pool#8 , Mouse#6 , Right ear [L2002772_U1KO6R]

description:
SmartSeq2
Uninfected U1, from IL7R-/- compartment of bone marrow chimeric, cell-pool#8 , Mouse#6 , Right ear [L2002772_U1KO6R]


title: HASMCs, ad-Vector1+PDGF-BB

description:
Library name: Sample 4
Column name in genes_fpkm_expression.xlsx: FPKM.D_1


title: HASMCs, ad-Vector3+PBS

description:
Library name: Sample 3
Column name in genes_fpkm_expression.xlsx: FPKM.B_4


title: HASMCs,ad-GLS2+PBS

description:
Library name: Sample 8
Column name in genes_fpkm_expression.xlsx: FPKM.C_2


title: HASMCs, ad-Vector1+PBS

description:
Library name: Sample 1
Column name in genes_fpkm_expression.xlsx: FPKM.B_1


title: Low-proliferating L. major infected,  wt compartment of BMC, cell-pool#12 , Mouse#7 , Right ear [L2002785_LoWT7R]

description:
SmartSeq2
Low-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#12 , Mouse#7 , Right ear [L2002785_LoWT7R]


title: Uninfected U1, from IL7R-/- compartment of BMC, cell-pool#1 , Mouse#1 , Right ear [L2002731_U1KO1R]

description:
SmartSeq2
Uninfected U1, from IL7R-/- compartment of bone marrow chimeric, cell-pool#1 , Mouse#1 , Right ear [L2002731_U1KO1R]


title: Low-proliferating L. major infected,  wt compartment of BMC, cell-pool#5 , Mouse#3 , Left ear [L2002742_LoWT3L]

description:
SmartSeq2
Low-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#5 , Mouse#3 , Left ear [L2002742_LoWT3L]


title: HASMCs, ad-Vector2+PDGF-BB

description:
Library name: Sample 5
Column name in genes_fpkm_expression.xlsx: FPKM.D_2


title: Low-proliferating L. major infected,  wt compartment of BMC, cell-pool#9 , Mouse#6 , Right ear [L2002769_LoWT6R]

description:
SmartSeq2
Low-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#9 , Mouse#6 , Right ear [L2002769_LoWT6R]


title: Low-proliferating L. major infected,  wt compartment of BMC, cell-pool#3 , Mouse#2 , Right ear [L2002738_LoWT2R]

description:
SmartSeq2
Low-proliferating L. major infected, from wild type compartment of bone marrow chimeric, cell-pool#3 , Mouse#2 , Right ear [L2002738_LoWT2R]