title: AC16 IFN-α repeat regimen replicate 1

city: Beverly Hills

first: Caroline

last: Jefferies

address: 121 N San Vicente Blvd

department: Kao Autoimmunity Institute

institute: Cedars-Sinai Medical Center

description:
Library name: IL1
Harvested day 7 after second pulse

data_processing:
Adapter and low-quality bases were removed with Trim Galore v0.6.10 (cutadapt v4.3, minimum length 20 bp, default quality settings).
Trimmed reads were aligned to the human reference genome GRCh38.p13 using STAR v2.7.11a with two-pass mode and output sorted BAM files.
Gene-level counts were obtained with featureCounts v2.0.3 using Gencode release 41 annotation (parameters: -t exon -g gene_id -s 2).
TPM values were calculated from raw counts with tximport v1.30.0 and edgeR’s rpkm function; quality metrics (duplication, rRNA content, insert size) were assessed with Picard v2.27.5 and RSeQC v4.0.0.
Assembly: GRCh38.p13 (Gencode release 41)
Supplementary files format and content: Tab-delimited text file containing raw gene-level counts (rows = Ensembl gene IDs, columns = samples): ANK-30306--02-15-2024_COUNTS.tsv
Supplementary files format and content: Tab-delimited text file containing TPM-normalized expression values in matching order: ANK-30306--02-15-2024_TPM.tsv

source_name: heart

growth_protocol: AC16 human ventricular cardiomyocytes (ATCC CRL-4021) were maintained in RPMI 1640 supplemented with 10 % fetal bovine serum and 1 % Antibiotic-Antimycotic at 37 °C in a humidified 5 % CO₂ incubator. Cultures were passaged at 70–80 % confluence and seeded at 1 × 10⁶ cells per 10 cm dish 24 h before interferon treatment.

extract_protocol:
Culture medium was aspirated, cells were rinsed twice with ice-cold PBS, and total RNA was isolated using the Qiagen RNeasy Plus Kit following the manufacturer’s protocol (gDNA Eliminator spin columns included). RNA integrity was assessed on an Agilent 2100 Bioanalyzer (RNA 6000 Nano), and samples with RIN ≥ 8 were quantified with the Qubit RNA HS Assay prior to library preparation.
Poly(A) RNA (from 325 ng total RNA) was purified using the NEBNext Poly(A) Magnetic Isolation Module. Stranded libraries were prepared with the IDT xGen Broad-Range RNA Library Prep Kit using 12 PCR cycles and unique dual indexes. Library size was verified on an Agilent 4200 TapeStation HS D1000 ScreenTape, concentration measured with the Qubit 1X dsDNA HS assay, pooled equimolarly at 4 nM, and sequenced on an Illumina NovaSeq X generating 1 × 75 bp reads at ~30 million reads per sample.

treatment_protocol: Cells were exposed to recombinant human IFN-α2a (1 000 U mL⁻¹) or PBS vehicle under three regimens: (i) acute: single 24 h pulse, (ii) chronic-hold: 24 h pulse followed by 5 d recovery without cytokine, and (iii) repeat: 24 h pulse, 4 d recovery, second 24 h pulse. Vehicle controls received PBS for equivalent intervals. Cells were harvested immediately after the final incubation.

value: heart

value: cardiomyocyte

value: WT

value: IFN-α 24 h → 4 d hold → second 24 h

tag: batch


title: AC16 IFN-α repeat regimen replicate 2

status: Public on Aug 29 2025

type: SRA

state: CA

country: USA

description:
Library name: IL2
Harvested day 7 after second pulse

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: PI8 day3

city: Lund

first: Ilia

last: Kurochkin

state: Skane

address: BMC A12, Sölvegatan 17

country: Sweden

institute: Lund University

library_source: transcriptomic single cell

data_processing:
The Cell Ranger v6.0.1 pipeline was used to process data generated using the 10x Chromium platform. Using Cell Ranger, the reads were converted to fastq format, processed, filtered, and then the aligned reads were generated. This pipeline was used with a mm10 genome.
R1 read is technical; R2 is biological. Barcode position in R1 is 1-16bp; UMI - 17-28bp.
The resulting expression matrix was used as input to the Seurat library v4.3.0
Assembly: mm10
Supplementary files format and content: 10x Gene Expression matrix

organism: Mus musculus

source_name: MEF

growth_protocol: After transduction with lentivirus, MEFs were cultured in gelatin-coated plates in DMEM+10%FBS.

extract_protocol:
Single cells were isolated using 10x Chromium by 10x Genomics.
scRNA-seq libraries were prepared with Dual Index Chromium Next GEM Single Cell 3ʹ Kit v3.1 (Dual Index) (10x Genomics) according to manufacturer’s instructions. Library size and quality check was performed using High Sensitivity D1000 ScreenTape with High Sensitivity D1000 Reagents (Agilent) in a 4200 TapeStation System (Agilent), according to the manufacturer’s protocol.

treatment_protocol: Cells were sorted by FACS.

value: MEF

value: mouse embryonic fibroblast

tag: transduction

value: Cells were transduced with Pu.1, Irf8 (PI8)

tag: time

value: Cells were collected 3 days after viral transduction

tag: sorted cell_type

value: sorted live(DAPI-) and tdTomato+


title: AC16 IFN-α repeat regimen replicate 3

description:
Library name: IL3
Harvested day 7 after second pulse


title: At root, control, biol rep2

city: taipei

first: Yitze

last: Chen

address: 128 Academia Road, Section 2, Nankang,

country: Taiwan

institute: Academia Sinica

description: Library name: Sample 4

data_processing:
CLC-Genomics Workbench 11
Before mapping to the Arabidopsis thaliana TAIR10 transcriptome, removal of low quality sequences and reads smaller than 25 bp, and adaptor trimming was conducted. Expression levels of genes were determined by reads per kilobase of transcript, per million mapped reads (RPKM).
Assembly: TAIR 10
Supplementary files format and content: Excel files (xlsx, xls) include gene reads and RPKM.

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Roots

growth_protocol: Plants were grown in hydroponic system with half-strength Hoagland nutrient solution (3 mM KNO3, 2 mM Ca(NO3)2, 0.5 mM NH4H2PO4, 1 mM MgSO4, 46.2 mM H3BO3, 9.1 μM MnCl2, 0.8 μM ZnSO4, 0.3 μM CuSO4, 0.08 μM Na2MoO4, and 10 μM NaFeEDTA).

extract_protocol:
Root RNA was extracted in 1 mL of TRIzol reagent. Samples were mixed briefly and incubated for 30 min at room temperature. Subsequently, chloroform (200 μL) was added to the sample and the mixture was vigorously shaken for 30 s. The samples were centrifuged at 15,000g at 4°C for 15 min, and the upper aqueous phase was carefully transferred to a new tube. RNA was precipitated by the addition of 0.5 mL of isopropanol and incubation at −80°C for 30 min. Following centrifugation at 15,000g at 4°C for 15 min, the resulting pellet was washed twice with 75% ethanol. The residual ethanol was evaporated in a chemical fume hood for 10 min. RNA was redissolved in 30 μL of diethyl pyrocarbonate-treated water.
Libraries were prepared using TrueSeq Illumina kit, following manufacturer's protocol.

value: Roots


title: MEF rep2

value: wildtype

value: sorted live(DAPI-)


title: PIP day3

value: Cells were transduced with Pu.1, Irf4, Prdm1 (PIP)


title: NO116_S79

city: Taichung

first: Wei-Chung

last: Cheng

address: No.91, Hsueh-Shih Road

department: Research Center for Tumor Medical Science

institute: China Medical University

data_processing:
1. Reads Alignment: HISAT2 (default)
2. Expression profiling: Stringtie (default)
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: text file containing gene expression profiles

source_name: hepatocellular carcinoma tissue

extract_protocol:
All of specimens were lysed with 1 ml TRIzol. Phenol-chloroform pH 6.7/8.0 was then added for phase separation, and RNA-rich layers were separated by centrifugation. Soluble RNA was precipitated with 2-propanol. The salt was washed away with 75% ethanol and RNA was dissolved in RNase-free water.
TruSeq

value: hepatocellular carcinoma tissue


title: AC16 IFN-α 24 h + 5 d recovery replicate 3

description:
Library name: IC3
Harvested day 6 post-pulse

value: IFN-α 24 h → 5 d hold


title: Fig4BC:apoCas9 truncation:Control: No Cas9

city: Ann Arbor

first: Zhonggang

last: Hou

state: Michigan

address: 1150 W Medical Center Dr.

department: Biological Chemistry

institute: University of Michigan

description:
Library name: 202303-37
previous GSM: GSM8208992

library_source: other

data_processing:
Read processing: Sequencing reads were assessed for quality with fastQC (version 0.11.8) and multiQC (version 0.92) to ensure the general quality of the datasets. For the newly acquired spacer sequences, the Read 1 sequences reads were trimmed to extract new spacer instances using Cutadapt (version 2.6) by identifying the flanking Repeat 26 sequences (attgtagcactgcgaaatgagaaagggagctacaac).
Deduplication: For samples with UMIs, the Read 2 sequences of the paired-end reads were processed with Cutadapt to extract the 8-nt UMI sequences by trimming known construct sequences. The newly spacer-UMI sequence combinations were paired with fastq-pair (version 0.4) and processed with UMI-tools (version 1.0.1) for deduplication after alignment. For samples with no UMIs during library construction, no UMI processing was performed (see the next step for an alternative approach to minimize PCR artifacts). For Miseq sample, UMIs are extracted from Read1.
Spacer source identification: The preprocessed spacer sequences were aligned by bowtie2 (version 2.4.1) with the "very-sensitive" preset to the combined alignment reference containing the N.meningitidis 8013 genome sequence (RefSeq accession number NC_017501.1, assembly: GCF_000026965.1) and the MDA phage genome sequence. For samples with UMIs, aligned spacers were deduplicated using UMI-tools with the directional-adjacency method as noted above. For samples with no UMIs, to handle technical artifacts such as PCR jackpot sites that can over-amplify a subset of spacer sequences, a maximum cap of 5% of the total detected spacer counts on the corresponding Neisseria or phage genome was applied to each unique spacer sequence, i.e., for each unique spacer sequence, if its abundance among total spacers exceeded 5%, its abundance was set to 5% of the total detected spacer count of the given source genome.
Genomic context extraction: Any reads that mapped ambiguously were removed from further analysis using samtools (version 1.9). For each genomic location aligned with the 5' end of any new spacer, the genomic context was extracted as the reference genome sequences flanking the alignment location, including the sequence upstream 10 bp from the alignment sites.
Spacer counting: The numbers of spacers at each unique spacer-aligned location were counted using bedtools2 (version 2.26.0) and custom codes were used to format the genomic context sequences for sequence logo inputs.
Assembly: N.meningitidis 8013 genome sequence (RefSeq accession number NC_017501.1, assembly: GCF_000026965.1) MDA phage genome: J. Meyer et al., Characterization of MDAPhi, a temperate filamentous bacteriophage of Neisseria meningitidis. Microbiology (Reading) 162, 268-282 (2016).
Supplementary files format and content: For *.MDA.fa files: format: FASTA files, with each header formatted as ">MDA_kan:<start on genome>:<end on genome>(<strand>)[<spacer count>](rc)"; content: unique spacer sequences and their genomic contexts, with their source on MDA phage genome and counts listed in the headers
Supplementary files format and content: For *.Nme.fa files: format: FASTA files, with each header formatted as ">NC_017501.1:<start on genome>:<end on genome>(<strand>)[<spacer count>](rc)"; content: unique spacer sequences and their genomic contexts, with their source on Neisseria genome and counts listed in the headers

molecule: other

organism: Neisseria meningitidis 8013

source_name: bacteria

growth_protocol: N. meningitidis (aka meningococcal) strains MC58, 8013, and 8013 mutant derivatives are used in this study. These strains were grown on GC Medium Base (GCB) (BD, 228950) plates with appropriate antibiotics and Kellogg’s supplements I and II (22.2 mM glucose [Fisher Scientific, D16-1], 0.68 mM glutamine [Sigma, G3126], 0.45 mM co-carboxylase [aka thiamine pyrophosphate, Sigma, C8754], 1.23 mM Fe(NO3)3 [Sigma, F8508]). Antibiotic concentrations used were 2.5 μg/mL for erythromycin (Erm), 100 μg/mL for kanamycin (Kan), 100 μg/mL for streptomycin (strp), 2.5 μg/mL for chloramphenicol (cm), and 100 μg/mL for spectinomycin (spc). All solid cultures were incubated at 37 ̊C in a 5% CO2 humidified atmosphere.  JM109 (Promega, L2005) and Mach1 (Invitrogen, C862003) chemically competent E. coli cells were used for plasmid cloning. E. coli BL21 (DE3) (Novagen, 69450-3) cells were used for protein purification. E. coli cells were grown at 37 ̊C in LB broth Lennox or on LB agar plates supplemented, when needed, with 50 μg/mL kanamycin, 50 μg/mL carbenicillin, 20 μg/mL for chloramphenicol or 100 μg/mL spectinomycin.

extract_protocol:
To detect spacer acquisition, 10 ng genomic DNA was used as template to PCR amplify CRISPR’s downstream end using Q5 DNA Polymerase with with primers described in Supplemental Table 1. The following PCR conditions were used: 98 ̊C for 30 s; 98 ̊C for 10 s, 60 ̊C for 10 s, 72 ̊C for 20 s (25 cycles); 72 ̊C for 2 min. PCR products were resolved on 2% agarose gel, stained by SYBR Safe (Invitrogen, S33102), and visualized using a Bio-Rad Chemidoc MP imager (12003154). The adapted “+1” “+2” bands are 66- and 132- nts larger than the un-adapted “0” product derived from parental CRISPR array, due to addition of repeat-spacer units (66-nt each). Adaptation efficiency was measured as the percentage of total CRISPR amplicons with new spacers. Quantification of PCR band intensity was done using Image Lab 6.0 software (Bio-Rad).
UMI library construction: Ligated products from above were used as template for 1st step Q5 PCR to amplify the leader-end of CRISPR array with primers OYZ3624+593 containing partial adaptor. Cycling conditions are 98 ̊C for 30 s; 98 ̊C for 10 s, 60 ̊C for 10 s, 72 ̊C for 25 s (25 cycles); 72 ̊C for 2 min. Following 2% agarose gel electrophoresis, the “+1” adapted band was gel extracted with QIAquick Gel Extraction Kit (Qiagen, 28706). Eluate is used as template for 2nd step Q5 PCR amplification using I5 and I7 index primers to add full Illumina adapter and indexes. 2nd PCR conditions are: 98 ̊C for 30 s; 98 ̊C for 10 s, 65 ̊C for 10 s, 72 ̊C for 25 s (15 cycles); 72 ̊C for 2 min.  Non-UMI library construction: For mutant strains carrying the del_crispr::R26, del_crispr::crispr(sp1), del_crispr::crispr(sp1-2), del_crispr::crispr(sp1-3), del_crispr::crispr(sp1-5), del_crispr::crispr(sp1-7), del_crispr::crispr(sp1-8), del_crispr::crispr(sp1-17), del_crispr::crispr(sp1-25), del_crispr::crispr(sp1-49) alleles, a non-UMI method was used due to the lack of unique restriction site (e.g., FatI) close enough to the newly acquired spacer. 10 ng of total genomic DNA from an adaptation experiment was used as template for 1st step PCR with primers are described in Supplemental Table 1. The following steps for “+1” adapted band gel extraction and 2nd step Q5 PCR were as described in the earlier paragraph.  All final libraries from 2nd step PCR were pooled together, cleaned up using QIAquick PCR Purification Kit, and then purified as one sample by agarose gel electrophoresis and gel extraction. This final pooled library was sequenced on an Illumina sequencing platform, NovaSeq (2x150 bp) at the Univ. of Michigan Advanced Genomics Core.

treatment_protocol: A phage transduction assay was initially performed. Rather than culturing cells on GCB plates with kanamycin, the cells were back-diluted to a concentration of 0.1 OD, and kanamycin was added at a concentration of 40 µg/mL to enrich for transductants. Adaptation assay was performed by incubating diluted culture with or without appropriate inducers, at 37 ̊C in a 5% CO2 humidified atmosphere. Inducer concentrations used were 0.1mM for IPTG (Fisher scientific, BP1755-10). After 24 hrs of induction, genomic DNA was isolated using QIAamp DNA Mini Kit (Qiagen, 51306) per manufacturer’s instructions with the following minor modification. After cell lysis at 56 ̊C for 40 min, RNase A (1mg/mL, Qiagen 19101) treatment was performed at RT for 2 min.

value: bacteria

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::empty

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG


title: At root, control, biol rep1

description: Library name: Sample 3


title: Fig3CD:apoCas9 complement by CRISPR-tracr pair:apoCas9+CRISPR+tracr

description:
Library name: 202303-36
previous GSM: GSM8208991

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9+CRISPR del_40nt leader+pTR tracr


title: AC16 IFN-α 24 h + 5 d recovery replicate 2

description:
Library name: IC2
Harvested day 6 post-pulse

value: heart

value: cardiomyocyte

value: WT


title: Fig3CD:apoCas9 complement by CRISPR-tracr pair:apoCas9+sgRNA

description:
Library name: 202303-35
previous GSM: GSM8208990

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9+pTR sgRNA


title: Fig4BC:apoCas9 truncation:apoCas9del_REC1/2

description:
Library name: 202303-40
previous GSM: GSM8208995

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9del_REC1/2-FLAG


title: CFTR_WT-Leu558_within_High-abc_02

city: Lexington

first: Jae Seok

last: YOON

state: MA

address: 44 Hartwell Avenue

department: CFFT Lab

institute: Cystic Fibrosis Foundation

description: Library name: Sample 14

data_processing:
Basecalling with Illumina NCS software
3' adaptor sequence of each read was trimmed by FastX-toolkit.
Reads mapped to four rRNA sequences (RNA5S1, RefSeq: NR_023363; RNA5-8SN5, RefSeq: NR_003285; RNA18SN5, RefSeq: NR_003286 and RNA28SN5, RefSeq: NR_003287) by HISAT2 were eliminated.
Assembly: hg38, CFTR CDS seq
Supplementary files format and content: txt, Read count mapped to individual CFTR residues
Library strategy: Ribo-Seq

extract_protocol:
RNase I footprinting, ribosome pelleting, TRIZOL extraction of riboseom-protected mRNA fragments
Preadenylated linker ligation, reverse transcription, cDNA circularization, rRNA depeletion, PCR amplification

value: Immortalized human embryonic cell line


title: CFTR_WT-Leu558_within_High-abc_01

description: Library name: Sample 13


title: CFTR_High-Leu558(UUA-to-CUC)_02

description: Library name: Sample 12


title: Intact_MMP1pos_3

city: Kansas City

first: Shiyuan

middle: (Cynthia)

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description: mmp-1 positive cellsfrom intact worms

data_processing:
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl-convert 3.10.5 Reads were aligned to UCSC genome smed_20140614 with STAR aligner (version 2.7.3a ), using Ensembl 106 gene models. TPM values were generated using RSEM (version v1.3.0 ).
Supplementary files format and content: Gene Counts using STAR aligner

organism: Schmidtea mediterranea

source_name: planaria

growth_protocol: Animals was starved for 11 days before the experiment

extract_protocol:
Worms were dissociated and fixed with ACME buffer. Then HCR was performed to label cells with mmp-1 probe. The mmp-1 positive and mmp-1 negative populations were seperated using flow cytometry. 1000 cells for each population were sorted directly into lysis buffer.
cDNA was generated using 10 cycles of PCR with the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara, cat. no. 634890). Libraries were generated from 1 ng of cDNA using 12 cycles of PCR with the Nextera XT DNA Library Preparation Kit (Illumina, cat. no. FC-131-1096) according to the manufacturer’s directions and using IDT for Illumina DNA/RNA UD Indexes for Tagmentation, Set A (Illumina, cat. no. 20027213)
Clontech(poly A)/Nextera Non-stranded RNA-Seq

treatment_protocol: There are three conditions, intact animals, tail fragments at 6 hours and 48 hours post amputation. Each conditions had three biological replicates and 100 worms for each replicate.

value: wildtype cells

value: mmp-1 positive


title: AC16 IFN-α 24 h + 5 d recovery replicate 1

description:
Library name: IC1
Harvested day 6 post-pulse


title: Intact_MMP1pos_2

description: mmp-1 positive cellsfrom intact worms


title: Fig4BC:apoCas9 truncation:apoCas9 WT

description:
Library name: 202303-38
previous GSM: GSM8208993

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9-FLAG


title: AC16 IFN-α acute 24 h replicate 3

description:
Library name: CI3
1 000 U mL⁻¹ IFN-α, harvested at 24 h

value: IFN-α 24 h


title: Intact_MMP1pos_1

description: mmp-1 positive cellsfrom intact worms


title: CFTR_High-Leu558(UUA-to-CUC)_01

description: Library name: Sample 11


title: Fig3CD:apoCas9 complement by CRISPR-tracr pair:apoCas9+tracr

description:
Library name: 202303-33
previous GSM: GSM8208988

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9+pTR tracr


title: AC16 IFN-α acute 24 h replicate 2

description:
Library name: CI2
1 000 U mL⁻¹ IFN-α, harvested at 24 h


title: Fig3CD:apoCas9 complement by CRISPR-tracr pair:apoCas9+CRISPR

description:
Library name: 202303-34
previous GSM: GSM8208989

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9+CRISPR del_40nt Leader


title: AC16 IFN-α acute 24 h replicate 1

description:
Library name: CI1
1 000 U mL⁻¹ IFN-α, harvested at 24 h


title: Fig3CD:apoCas9 complement by CRISPR-tracr pair:apCas9

description:
Library name: 202303-32
previous GSM: GSM8208987

value: bacteria

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::pTet Nmecas9


title: Intact_MMP1neg_3

description: mmp-1 negative cellsfrom intact worms

value: mmp-1 negative


title: CFTR_High-abc_03

description: Library name: Sample 8

value: CFTR_High-abc overexpression


title: CFTR_High-abc_04

description: Library name: Sample 9


title: CFTR_High-abc_05

description: Library name: Sample 10


title: Intact_MMP1neg_1

description: mmp-1 negative cellsfrom intact worms


title: AC16 vehicle control 24 h replicate 3

description:
Library name: CC3
Vehicle 24 h, RNA collected at 24 h

value: PBS 24 h


title: Fig4EF:CRISPR role:del_CRISPR::R26

description:
Library name: 202303-24
previous GSM: GSM8208979

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG


title: Fig3CD:apoCas9 complement by CRISPR-tracr pair:No Cas9

description:
Library name: 202303-31
previous GSM: GSM8208986

value: del_tracrdel_cas9, del_CRISPR::R26, NICS::pLacNmecas1-cas2, iga-trpB::empty


title: AC16 vehicle control 24 h replicate 2

description:
Library name: CC2
Vehicle 24 h, RNA collected at 24 h

value: heart

value: cardiomyocyte

value: WT


title: 6hpa_MMP1pos_3

description: mmp-1 positive cells, 6 hours post amputation

value: wildtype cells


title: CFTR_High-abc_02

description: Library name: Sample 7

value: Immortalized human embryonic cell line


title: MEF rep1

value: MEF

value: mouse embryonic fibroblast

value: wildtype

value: sorted live(DAPI-)


title: Fig4EF:CRISPR role:WT, FigS3C:spacer preference analysis:WT+pLac-Cas1-Cas2 with induction repeat-3

description:
Library name: 202303-23
previous GSM: GSM8208978

value: bacteria


title: AC16 vehicle control 24 h replicate 1

description:
Library name: CC1
Vehicle 24 h, RNA collected at 24 h


title: CFTR_High-abc_01

description: Library name: Sample 6


title: IX-2MRC

city: Minato-ku

first: Yuta

last: Hirano

state: Tokyo

address: 3-25-8 Nishi-shimbashi

department: Internal Medicine

country: Japan

institute: The Jikei University School of Medicine

description: Library name: IX-2MRC

data_processing:
Pair-end sequenced reads were checked by FastQC.
Estimation of transcripts was performed using Kallisto.
The expression matrix was constructed and normlized by Tximport in R
Assembly: Assembly: hg19
Supplementary files format and content: tab-delimited text file include TPM values for each sample

growth_protocol: The cell lines were maintained in Dulbecco’smodified Eagle’smedium (Nacalai tesque, Kyoto, Japan) supplemented with 10% heat-inactivated fetal bovine serum (FBS; Thermo Fisher Scientific, MA, USA) and 1 x Antibiotic and Antimycotic Solution (Thermo Fisher Scientific) and grown at 37 °C in a 5% CO2 incubator.

extract_protocol:
RNA was isolated by an RNeasy Mini Kit (Qiagen) from each cell lysate.
cDNA libraries for RNA sequencing were established from total RNA usingNEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760)  (New England Biolabs) for selecting poly-A mRNA .

treatment_protocol: For trans-well co-cultures, 2.5x104 of Calu-3 or LC1-sq cell lines were seeded into the top of trans-well membrane (0.4 μm pore size, Corning Life Science, Tewksbury, MA) with MRC-5 (5x104) growing in the lower compartment

value: fibroblast

value: monoculture


title: CFTR_WT_05

description: Library name: Sample 5

value: CFTR_WT overexpression


title: 6hpa_MMP1pos_2

value: mmp-1 positive


title: cDC1

value: splenic dendritic cell type 1

value: sorted live(DAPI-) and CD11c+MHC-II+CD8alpha+


title: 6hpa_MMP1pos_1


title: FigS4EF:CRISPR role:del_CRISPR::R26 with pLac-Cas1-Cas2 induction

description:
Library name: 202303-21
previous GSM: GSM8208977

value: endo dcas9, del_CRISPR::R26, iga-trpB::pLacNmecas1-cas2

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG


title: FigS4EF:CRISPR role:endo dCas9 with pLac-Cas1-Cas2 induction

description:
Library name: 202303-19
previous GSM: GSM8208975

value: endo dcas9, iga-trpB::pLacNmecas1-cas2


title: Intact_MMP1neg_2

description: mmp-1 negative cellsfrom intact worms

value: wildtype cells

value: mmp-1 negative


title: CFTR_WT_04

description: Library name: Sample 4

value: Immortalized human embryonic cell line


title: 6hpa_MMP1neg_3

description: mmp-1 negative cells, 6 hours post amputation


title: FigS3GH:tracr role:endo dCas9, del_tracr+tracr with pLac-Cas1-Cas2 induction

description:
Library name: 202303-18
previous GSM: GSM8208974

value: endo dcas9, del_tracr, iga-trpB::pLacNmecas1-cas2, NICS::tracr


title: IX-2LC1

description: Library name: IX-2LC1

value: co-cultured with LC1


title: IX-2Calu3

description: Library name: IX-2Calu3

value: co-cultured with Calu3


title: 6hpa_MMP1neg_2


title: IX-1MRC

description: Library name: IX-1MRC


title: CFTR_WT_03

description: Library name: Sample 3


title: CFTR_WT_02

description: Library name: Sample 2


title: 6hpa_MMP1neg_1


title: FigS3GH:tracr role:endo dCas9, del_tracr with pLac-Cas1-Cas2 induction

description:
Library name: 202303-16
previous GSM: GSM8208972

value: bacteria

value: endo dcas9, del_tracr, iga-trpB::pLacNmecas1-cas2


title: FigS3GH:tracr role:endo dCas9, del_tracr w/o induction

description:
Library name: 202303-17
previous GSM: GSM8208973


title: IX-1LC1

description: Library name: IX-1LC1

value: fibroblast


title: CFTR_WT_01

description: Library name: Sample 1

value: CFTR_WT overexpression


title: 48hpa_MMP1pos_3

description: mmp-1 positive cells, 48 hours post amputation

value: mmp-1 positive


title: FigS3GH:tracr role:endo dCas9 with pLac-Cas1-Cas2 induction

description:
Library name: 202303-15
previous GSM: GSM8208971


title: IX-1Calu3

description: Library name: IX-1Calu3


title: 48hpa_MMP1pos_2


title: Fig2BC:tracr role, FigS3GH:tracr role:del_tracrdel_cas9 with pLac-Cas1-Cas2 induction

description:
Library name: 202303-14
previous GSM: GSM8208970


title: SII-HDF-Input

library_source: genomic

data_processing:
ChIP-seq analysis was performed on the raw FASTQ files. FASTQ reads were aligned to the human genome (hg38) using the BWA v0.7.12. Only uniquely mapped reads (mapping quality >= 25) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome
Mapped output files were processed through MACS v2.1.0 software to determine peaks.
Bigwig files were created from bam files with deeptools v2.5.4.
Assembly: hg38
Supplementary files format and content: bigwig, bed

molecule: genomic DNA

source_name: HDFa

extract_protocol:
Cells were collected 2 days after viral transduction. Cultured cells were fixed in 11 % formaldehyde for 15 min at room temperature on a rotating platform. The formaldehyde was quenched by adding 125 nM glycine. The chromatin was sheared and immunoprecipitated with the antibody of interest. A control sample consisting of sonicated chromatin that was not immunoprecipitated was also sequenced.
Illumina sequencing libraries were prepared from ChIP and Input DNAs by standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara). After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single-end).

treatment_protocol: Cells were transduced overnight twice in consecutive days and media replaced in between. After the second transduction, culture media was replaced by normal growth media and this was considered day 0.

value: HDFa

value: adult human dermal fibroblast

value: wildtype

tag: antibody


title: HDF-Pooled-Input


title: 48hpa_MMP1pos_1


title: FigS1D:MDA insertion

description:
Library name: 202202
previous GSM: GSM8209055

value: WT

value: MDAΦ transducants


title: PIP-HDF-Input


title: IKZF2-HDF-IKZF2

value: Helios (IKZF2) (CST, 42427)


title: 48hpa_MMP1neg_3

description: mmp-1 negative cells, 48 hours post amputation

value: wildtype cells


title: SPIB-HDF-SPIB

value: SPIB (Custom)


title: Fig2BC:tracr role:del_tracr w/o pLac-Cas1-Cas2 induction

description:
Library name: 202303-11
previous GSM: GSM8208967

value: MDAΦ 3+21 hr


title: GBM12 cells, SR-2

city: new york city

first: Jeongyeon

last: Mun

state: NY

institute: Columbia University Irving Medical Center

description:
Library name: GBM12-SR-2
replicate 2

data_processing:
Raw sequencing data (FASTQ files) were uploaded and analyzed using the SciDAP platform (https://scidap.com). Quality control, transcript quantification, and normalization were performed using the default SciDAP RNA-seq pipeline. Transcript-level quantification was conducted using Salmon against the human reference transcriptome (GRCh38). Gene-level counts and TPM values were generated using tximport. Differential expression analysis was performed using DESeq2, and downstream gene ontology and pathway enrichment analyses were conducted using integrated SciDAP tools.
Assembly: GRCh38 (human)
Supplementary files format and content: Processed data files include gene-level expression matrices and differential expression results. Gene expression matrices are provided as tab-delimited text files containing either raw counts or TPM-normalized values, with genes as rows and samples as columns. Differential expression results include log2 fold changes, p-values, and adjusted p-values (FDR), generated using DESeq2. All files are in plain text (.txt or .tsv) format.

source_name: Brain

growth_protocol: GBM12 cells were cultured in DMEM supplemented with 10% FBS and 100 μg/ml primocin. This cells were maintained at 37˚C with 5% CO2.

extract_protocol:
RNA samples for sequencing were isolated using the Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. The library’s quality and quantity were measured by a Bioanalyzer Nanochip.
Libraries were prepared according to the manufacturer’s instructions. Briefly, poly(A)+ RNA was fragmented and reverse transcribed to synthesize first-strand cDNA, followed by second-strand synthesis. After end-repair, A-tailing, and adapter ligation, the libraries were PCR amplified and purified. Library quality and quantity were assessed using the Bioanalyzer at the Columbia Genomics Center. Sequencing was performed on the Element AVITI platform using paired-end 2x150 bp reads.

treatment_protocol: For the treatment, cells were treated with 20 nM SR-4835 in DMEM containing 1.5% FBS and 100 μg/ml of Primocin for 24h.

value: Brain

value: PDX GBM cells


title: GBM12 cells, SR-1

description:
Library name: GBM12-SR-1
replicate 1


title: Fig2BC:tracr role, FigS3C:spacer preference analysis:WT+pLac-Cas1-Cas2 with induction repeat-2

description:
Library name: 202303-09
previous GSM: GSM8208966

value: 0.1 mM IPTG


title: 48hpa_MMP1neg_1

value: mmp-1 negative


title: GBM12 cells, DMSO-3

description:
Library name: GBM12-DMSO-3
replicate 3

value: DMSO


title: PRDM1-HDF-PRDM1

value: BLIMP1 (CST, 9115BF)


title: iBAT_20d_Ucp1KO

city: Freising

first: Katharina

last: Küllmer

state: Bavaria

address: Gregor-Mendel Straße 2

country: Germany

institute: Technical University of Munich

description: Library name: Sample 2

data_processing:
Alignmet was done using the Galaxy Europe Server. Before, reads got trimmed using TrimGalore. Mapping was done using HISAT2.
Assembly: mm39
Supplementary files format and content: countmatrix as txt file

source_name: iBAT

growth_protocol: iBAT tissue was dissected from mice.

extract_protocol:
RNA was extracted using the Promega Kit (SV Total RNA Isolation System )
directional mRNA library preparation (poly A enrichment), strand specific

treatment_protocol: No treatment

value: iBAT

value: Bl6N, Ucp1 KO

value: untreated


title: GBM12 cells, DMSO-2

description:
Library name: GBM12-DMSO-2
replicate 2


title: Fig1FG: Cas9 role:Cas9-Nme2PI

description:
Library name: 202303-08
previous GSM: GSM8208965

value: bacteria

value: del_cas9, iga-trpB::pLacNmecas1-cas2, NICS::Nmecas9 PID swap


title: iBAT_20d_wt

description: Library name: Sample 1

value: Bl6N, wild-type


title: IRF4-HDF-IRF4

value: HDFa

value: adult human dermal fibroblast

value: wildtype


title: GBM12 cells, DMSO-1

description:
Library name: GBM12-DMSO-1
replicate 1

value: WT


title: SII-HDF-IKZF2

value: Helios (IKZF2) (CST, 42427)


title: brown adipocytes (iBAT), untreated, wild-type

description: Library name: Sample 6

growth_protocol: Primary brown preadipocytes (iBAT) were maintained in high-glucose DMEM medium supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere at 5% CO2 and 37°C.

extract_protocol:
RNA was extracted using the Promega Kit (SV Total RNA Isolation System )
Library preparation was performed using the Illumina Kit following the instructions.

treatment_protocol: Cells were treated upon 70-80% confluency with 5.5 nM FGF2, 250 nM FGFR-inhibitor or left untreated. Preadipocytes were then induced and differentiated into mature brown adipocytes.

value: SVF from iBAT, differentiated

value: brown adipocytes


title: GBM12 cells, SR-3

description:
Library name: GBM12-SR-3
replicate 3

value: Brain

value: PDX GBM cells


title: Fig2BC:tracr role:del_tracr+tracr with pLac-Cas1-Cas2 induction

description:
Library name: 202303-13
previous GSM: GSM8208969

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG


title: Fig1FG: Cas9 role:dCas9

description:
Library name: 202303-06
previous GSM: GSM8208963

value: del_cas9, iga-trpB::pLacNmecas1-cas2, NICS::Nme dcas9


title: Half-size3.fastq.bz2

city: Moscow

first: Fedor

middle: M

last: Eroshkin

address: 16/10 Miklukho-Maklaya str.

country: Russia

institute: IBCH RAS

data_processing:
The reads obtained from sequencing the samples were aligned to the reference genome Spur_5.0 using Bowtie2 version 2.2.2 software with default alignment parameters.
The RefSeq NCBI annotation for Strongylocentrotus purpuratus (Annotation Release 102) was used for mapping genomic regions and identifying functional elements.
Statistics of differential expression (stretched vs control explants) were caluclated via DEseq R package.
Assembly: RefSeq NCBI annotation for Strongylocentrotus purpuratus (Annotation Release 102)
Supplementary files format and content: excel file (.xlsx) containing output from edgeR (for each transcript (gene))

organism: Strongylocentrotus droebachiensis

source_name: embryonic tissue explants, mesenchymal blastula embryos

growth_protocol: Adult sea urchins (Strongylocentrotus droebachiensis) were collected during three breeding seasons of this species in the Barents (near) and White Seas, near Murmansk and the White Sea Biological Station of Moscow State University, respectively. Sea urchins collected near Murmansk were transported by plane to Moscow, where embryos were obtained for experiments conducted at the Institute of Bioorganic Chemistry. Embryos from sea urchins collected in the White Sea were obtained and used in further experiments in the White Sea Biological Station of Moscow State University. Gametes were obtained via intra-coelomic injections of 1ml 0.5M KCl into adults.

extract_protocol:
Total RNA was extracted on NucleoSpin RNA columns (Macherey-Nagel).The obtained RNA samples were tested on integrity on Aligent 4200 TapeStation instrument.
For preparation for sequencing, the samples were processed with TruSeq Stranded mRNA Library Prep Kit (Illumina) according to a manufacturer’s protocol. The resulted libraries were tested by qPCR and Aligent 4200 TapeStation.

treatment_protocol: For blastomeres separation experiment eggs were fertilized, then washed three times and kept in 1 mM 3-amino-1,2,4-triazole (ATA) in artificial seawater (ASW) to prevent envelope hardening until the first cleavage. 2-cell-stage embryos (3,5 hpf) were washed in calcium- and magnesium-free artificial seawater twice for 15 minutes in total. Then they were pushed through a 21Gx1,5” syringe needle with a moderate force to separate blastomeres. Control and half-size embryos were cultured in ASW in glass Petri dishes at 8°C until mesenchyme blastula stage (46 hpf).

value: wild type

value: half-size embryos


title: SII-HDF-IRF8

value: IRF8 (Custom)


title: Fig2BC:tracr role, FigS3C:spacer preference analysis:del_tracr with pLac-Cas1-Cas2 induction repeat-1

description:
Library name: 202303-12
previous GSM: GSM8208968

value: bacteria


title: brown adipocytes (iBAT), LY-treated, wild-type

description: Library name: Sample 5

value: iBAT

value: Bl6N, wild-type

value: LY


title: 48hpa_MMP1neg_2

value: wildtype cells

value: mmp-1 negative


title: brown adipocytes (iBAT), FGF2-treated, wild-type

description: Library name: Sample 4


title: Half-size1.fastq.bz2

value: embryonic tissue explants, mesenchymal blastula embryos


title: Fig1FG: Cas9 role:No Cas9

description:
Library name: 202303-04
previous GSM: GSM8208961


title: PIP-HDF-PRDM1

value: HDFa

value: adult human dermal fibroblast

value: wildtype

value: BLIMP1 (CST, 9115BF)


title: brown adipocytes (iBAT), untreated, Ucp1_KO

description: Library name: Sample 3

value: SVF from iBAT, differentiated

value: brown adipocytes

value: Bl6N, Ucp1_KO

value: untreated


title: Fig1E:pLac-Cas1-Cas2 with induction, FigS3C:spacer preference analysis:WT+pLac-Cas1-Cas2 with induction repeat-1

description:
Library name: 202303-03
previous GSM: GSM8208960

value: MDAΦ 3+21 hr

value: 0.1 mM IPTG


title: brown adipocytes (iBAT), LY-treated, Ucp1_KO

description: Library name: Sample 2


title: Wild-size3.fastq.bz2

value: wild type

value: control embryos


title: PIP-HDF-IRF4


title: Wild-size2.fastq.bz2


title: Fig1FG: Cas9 role:Cas9 H1024A

description:
Library name: 202303-07
previous GSM: GSM8208964

value: bacteria

value: del_cas9, iga-trpB::pLacNmecas1-cas2, NICS::Nmecas9 H1024A


title: Ah root, control, biol rep2

description: Library name: Sample 2

organism: Arabidopsis halleri subsp. gemmifera

value: Roots


title: Ah root, control, biol rep1

description: Library name: Sample 1


title: brown adipocytes (iBAT), FGF2-treated, Ucp1_KO

description: Library name: Sample 1

value: iBAT


title: Wild-size1.fastq.bz2

value: embryonic tissue explants, mesenchymal blastula embryos


title: Bulk mRNA sequencing of adjacent normal lung tissue and tumor tissue from patient 1

status: Public on Aug 28 2025

city: Irvine

first: Stephanie

middle: Jeanelle

last: Hachey

address: 2400 Biological Sciences III

institute: UC Irvine

description: Library name: P001_RNAseq

data_processing:
Raw WES reads were aligned to the human reference genome (GRCh38) using BWA-MEM, and somatic variants were identified using GATK Mutect2. RNA-seq reads were aligned to GRCh38 using STAR, and gene expression levels were quantified with featureCounts.
Assembly: GRCh38
Supplementary files format and content: tab separated values (normalized counts and DE results, RNAseq; copy number variations, WES), png chromosomal view CNV WES

source_name: healthy adjacent lung and tumor

extract_protocol:
DNA and RNA were extracted from freshly collected primary tumor and matched adjacent normal tissues using the QIAGEN Quick-DNA and Quick-RNA Microprep Kits, respectively.
Whole-exome sequencing (WES) was performed on tumor and matched normal DNA using the Agilent SureSelect Human All Exon V7 kit for library preparation, followed by 150 bp paired-end sequencing on the Illumina NovaSeq 6000 platform. Bulk RNA sequencing (RNA-seq) was conducted on tumor tissue using the Clontech SMARTer Stranded Total RNA-Seq Pico Input Mammalian v3 Kit and paired-end sequenced on the Illumina NovaSeq X Plus.

value: healthy adjacent lung and tumor

value: epithelial, lung

value: age 49, F, never smoker, Vietnamese


title: Bulk mRNA sequencing of adjacent normal lung tissue and tumor tissue from patient 2

description: Library name: P002 RNAseq

value: age 64, F, never smoker, White


title: Bulk mRNA sequencing of adjacent normal lung tissue and tumor tissue from patient 4

description: Library name: P004_RNAseq

value: age 69, F, never smoker, Hispanic


title: Bulk mRNA sequencing of adjacent normal lung tissue and tumor tissue from patient 3

description: Library name: P003_RNAseq

value: age 63, F, former smoker (10 pack years), White


title: Fig1FG: Cas9 role:wtCas9

description:
Library name: 202303-05
previous GSM: GSM8208962


title: Half-size2.fastq.bz2

value: half-size embryos


title: SII-HDF-SPIB

value: HDFa

value: adult human dermal fibroblast

value: wildtype

value: SPIB (Custom)


title: hiEC+hiBPC_inf_3

city: Amsterdam

first: Henrique

last: Nogueira Pinto

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam UMC

description: Library name: iEC.TW.INF.3

data_processing:
Raw RNA sequencing data were first assessed for quality using FastQC (110) and then aligned to the human genome using STAR (version 2.7.10a) (111). Genome indices were generated from the reference FASTA and GTF annotation files prior to alignment. Post-alignment, the resulting SAM files were converted to BAM format, sorted, and indexed using Samtools (version 1.13) (112). Gene-level read quantification was performed using featureCounts (version 2.0.3) (113) from the Subread package (114), employing the corresponding GTF annotation file. For differential gene expression analysis, raw count data were imported into R (version 4.4.1) and analyzed using the DESeq2 package (version 1.44.0) (115). Genes with less than 5 counts in at least 3 different samples were filtered prior to normalization.
Assembly: GRCh38
Supplementary files format and content: raw transcript counts for all samples

source_name: GB4d hiPSC line

extract_protocol:
Total RNA from cells was isolated in TRIzol (Invitrogen) and a TapeStation RNA ScreenTape assay (Agilent) was performed to assess RNA integrity.
RNA libraries were prepared and multiplexed using KAPA mRNA Hyperprep (Roche), and used as the input for high-throughput sequencing via NovaSeq X Plus platform (Illumina).

value: GB4d hiPSC line

value: 25 IU/mL TNFa + 25 IU/mL IFNg (16h)


title: hiEC+hiBPC_inf_2

description: Library name: iEC.TW.INF.2


title: hiBMEC_inf_3

description: Library name: iEC.TW.CHIR.INF.3

value: 4 uM CHIR (48h) & 25 IU/mL TNFa + IFNg (16h)


title: hiEC+hiBPC_inf_1

description: Library name: iEC.TW.INF.1


title: hiBMEC_3

description: Library name: iEC.TW.CHIR.3

value: 4 uM CHIR (48h)


title: hiBMEC_inf_2

description: Library name: iEC.TW.CHIR.INF.2


title: hiBMEC_1

description: Library name: iEC.TW.CHIR.1


title: hiEC_inf_3

description: Library name: iEC.INF.3


title: PIP-HDF-PU.1

value: PU.1 (Santa Cruz, sc-352)


title: hiEC+hiBPC_2

description: Library name: iEC.TW.2


title: hiBMEC_2

description: Library name: iEC.TW.CHIR.2


title: hiEC+hiBPC_1

description: Library name: iEC.TW.1


title: hiEC_inf_2

description: Library name: iEC.INF.2


title: hiEC_CHIR_inf_2

description: Library name: iEC.CHIR.INF.3


title: hiEC_CHIR_inf_1

description: Library name: iEC.CHIR.INF.2


title: hiEC+hiBPC_3

description: Library name: iEC.TW.3


title: hiEC_CHIR_3

description: Library name: iEC.CHIR.3


title: hiEC_CHIR_1

description: Library name: iEC.CHIR.1


title: hiEC_3

description: Library name: iEC.3


title: hiEC_CHIR_2

description: Library name: iEC.CHIR.2


title: hiBPC+hiEC_inf_1

description: Library name: iBPC.TW.INF.1


title: hiBPC+hiEC_inf_2

description: Library name: iBPC.TW.INF.2


title: hiBMEC_inf_1

description: Library name: iEC.TW.CHIR.INF.1


title: hiBPC+hiBMEC_inf_1

description: Library name: iBPC.TW.CHIR.INF.2


title: hiBPC+hiBMEC_inf_2

description: Library name: iBPC.TW.CHIR.INF.3


title: hiBPC+hiBMEC_2

description: Library name: iBPC.TW.CHIR.2


title: hiEC_1

description: Library name: iEC.1


title: hiBPC+hiBMEC_1

description: Library name: iBPC.TW.CHIR.1


title: BECs, Tgfbr1-CKO

city: Baltimore

first: Amir

last: Rattner

state: MD - Maryland

address: 725 North Wolfe St.

institute: Johns Hopkins University

description:
Library name: AR9
PIPseq 4PLUS
Tgfbr1_BECs_features.tsv.gz
Tgfbr1_BECs_barcode.tsv.gz: barcode-1
Tgfbr1_BECs_matrix.mtx.gz
Tgfbr1_BECs_clusters.csv
Tgfbr1_BECs_umap.csv

data_processing:
Reads were aligned with the PIPseeker program (Fluent BioSiences, version 3.3.0). The CellBender program was used to detect empty droplets and remove background (version 0.3.2; Fleming et al., 2023). The SOLO program was used to remove doublets (scVI-tools 1.2.2-post2; Bernstein et al., 2020). Manual curation was used to further remove potentially mixed (doublet) nuclei as well as clusters with multiple nuclei from samples AR7 and AR8. The data were normalized using a regularized negative binomial regression algorithm implemented with the SCTransform function (Hafemeister and Satija, 2019). Batch effects were corrected using the Seurat RPCAIntegration function. UMAP dimensional reduction was performed using the R uwot package (https://github.com/jlmelville/uwot) integrated into the Seurat R package (Melville, 2022).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files, comma-separated values files, and matrix files.

molecule: nuclear RNA

source_name: brain endothelial cells

extract_protocol:
The minced brain tissue was suspended in 10 ml of ice-cold DPBS supplemented with 5 mM EDTA (Invitrogen, AM9262) and 60 U/ml of RNasin-Plus RNase Inhibitor (Promega, N2615), and gently homogenized using a smooth pestle in a Thomas Pestle Tissue Grinder (3431E45) on ice with 5 strokes. The sample was incubated on ice for 10 minutes, and then gently homogenized with 40 more strokes. The brain vascular fragments were pelleted by two rounds of centrifugation through 15% Ficoll PM 400 (Sigma-Aldrich, F4375). For the first round of centrifugation, 10 ml of the homogenate was vigorously mixed with 10 ml of 30% Ficoll PM 400. The sample was aliquoted into three 50 ml heavy-walled glass centrifuge tubes with round bottoms (Marienfeld, 3933041) and each tube was loaded with 6.7 ml of sample and then centrifuged at 5,800 x g for 20 min at 4ÅãC. The pellets, containing enriched vascular fragments, were saved. For the second round of centrifugation, the supernatant from the first round of centrifugation, which included a layer of myelin at its top, was transferred to a fresh 50 ml glass tube and vigorously mixed. The sample was aliquoted into three heavy-walled glass centrifuge tubes and centrifuged as described for the first round. The pellets from the two rounds of centrifugation were resuspended and pooled in a total volume of 10 ml of DPBS supplemented with 1% BSA and 40 U/ml of RNasin-Plus RNase Inhibitor (“DPBS+BR”). The sample was centrifuged in a heavy-walled glass centrifuge tube with a round bottom at 300 x g for 10 min at 4C. The pellets were resuspended and pooled in a total volume of 1 ml of DPBS+BR by gently pipetting 10 times with a 1 ml pipette tip.  The 1 ml suspension was filtered through a Nylon Mesh Filter (Tisch Scientific; 300 μm mesh, ME17240) to remove large tissue fragments. The material trapped by the filter was rinsed one time with 1 ml of DPBS+BR. The resulting 2-ml suspension was then filtered through a PluriStrainer 20 μm filter (Cell Strainer, 43-50020-03) to capture vascular fragments. The PluriStrainer 20 μm filter was placed on top of a 50-ml tube and loaded in several steps with the suspension, which was allowed to drain by gravity flow. The vascular fragments retained on the filter were then washed once with 1 ml of DPBS+BR. The vascular fragments were recovered from the surface of the filter with several washes with 1 ml of DPBS+BR. The resulting 3-ml sample was centrifuged in a 12 ml heavy-walled glass centrifuge tube with a round bottom (Marienfeld, 3933011, 12 ml) at 300 x g for 10 min at 4ÅãC. The pellet was resuspended in 500 ul of DPBS buffer with 40 U/ml of RNasin Plus RNase Inhibitor using a 1 ml Low Retention Pipette Tip (1000 uL Filtered Pipette Tips for Rainin LTS Pipette - RNase and DNase Free; 3840/CS, LTS-1000FTCS). The suspended vascular fragments were placed in a 1.5-ml Low Retention tube (Thermo Scientific, 3451) and centrifuged at 300 x g for 10 min at 4C. The supernatant was removed, and the pellet was frozen on dry ice and stored at -80C.
Single nucleus (sn)RNA-seq libraries were prepared using the PIPseq T20 3’ Single Cell RNA Kit v4.0 PLUS or the PIPseq T10 Single Cell RNA Kit v5.0 (Fluent BioSiences; Clark et al., 2023; Fontanez et al., 2024). Frozen tissue was suspended in homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH,pH 7.8) supplemented with 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, EDTA free protease inhibitor (Roche 11836 170 001), 0.5% IGEPAL-630, and 40 U/mL Protector RNase Inhibitor (Sigma, 03335402001). Samples were homogenized in a 2 mL Dounce homogenizer, using 15 strokes with a loose-fitting pestle followed by 30 strokes with a tight-fitting pestle. The sample was filtered through a 10 μm filter (CellTrix, Sysmex, 04-004-2324), and nuclei were pelleted in Low Retention 1.5 mL microcentrifuge tubes for 5 min at 500 x g at 4oC. Nuclei were washed twice with Nuclei Suspension Buffer (supplied in the Fluent BioSciences kit) supplemented with 1% BSA and 40 U/mL Protector RNase Inhibitor. Nuclei were counted, and ~40,000 nuclei (for the T20 kit) or ~20,000 nuclei (for the T10 kit) were used for library production following the Fluent BioSiences protocol. The resulting snRNA-seq libraries were sequenced on an Illumina NovaSeq X Plus sequencer. Vascular fragments from two mouse brains were pooled for each snRNAseq library.

value: brain endothelial cells


title: hiBPC+hiBMEC_3

description: Library name: iBPC.TW.CHIR.3


title: BECs, WT

description:
Library name: AR10
PIPseq 4PLUS
Tgfbr1_BECs_features.tsv.gz
Tgfbr1_BECs_barcode.tsv.gz: barcode-2
Tgfbr1_BECs_matrix.mtx.gz
Tgfbr1_BECs_clusters.csv
Tgfbr1_BECs_umap.csv

value: wild type


title: Whole retina, Tgfbr1-CKO, repeat 11

description:
Library name: AR16
PIPseq 5
Tgfbr1_retina_features.tsv.gz
Tgfbr1_retina_barcode.tsv.gz: barcode-12
Tgfbr1_retina_matrix.mtx.gz
Tgfbr1_retina_mata_data.csv
Tgfbr1_retina_umap.csv

source_name: retina

value: retina


title: hiBPC+hiEC_3

description: Library name: iBPC.TW.3


title: hiEC_inf_1

description: Library name: iEC.INF.1


title: hiBPC+hiEC_2

description: Library name: iBPC.TW.2


title: Whole retina, Tgfbr1-CKO, repeat 9

description:
Library name: AR14
PIPseq 5
Tgfbr1_retina_features.tsv.gz
Tgfbr1_retina_barcode.tsv.gz: barcode-10
Tgfbr1_retina_matrix.mtx.gz
Tgfbr1_retina_mata_data.csv
Tgfbr1_retina_umap.csv


title: hiBPC+hiEC_1

description: Library name: iBPC.TW.1


title: hiBPC_inf_3

description: Library name: iBPC.INF.3


title: Whole retina, Tgfbr1-CKO, repeat 8

description:
Library name: AR13
PIPseq 5
Tgfbr1_retina_features.tsv.gz
Tgfbr1_retina_barcode.tsv.gz: barcode-9
Tgfbr1_retina_matrix.mtx.gz
Tgfbr1_retina_mata_data.csv
Tgfbr1_retina_umap.csv


title: Whole retina, Tgfbr1-CKO, repeat 10

description:
Library name: AR15
PIPseq 5
Tgfbr1_retina_features.tsv.gz
Tgfbr1_retina_barcode.tsv.gz: barcode-11
Tgfbr1_retina_matrix.mtx.gz
Tgfbr1_retina_mata_data.csv
Tgfbr1_retina_umap.csv


title: Whole retina, Tgfbr1-CKO, repeat 5

description:
Library name: AR8
PIPseq 4PLUS
Tgfbr1_retina_features.tsv.gz
Tgfbr1_retina_barcode.tsv.gz: barcode-6
Tgfbr1_retina_matrix.mtx.gz
Tgfbr1_retina_mata_data.csv
Tgfbr1_retina_umap.csv


title: hiEC_2

description: Library name: iEC.2


title: hiBPC_inf_2

description: Library name: iBPC.INF.2


title: hiBPC_inf_1

description: Library name: iBPC.INF.1


title: hiBPC_3

description: Library name: iBPC.3


title: Whole retina, Tgfbr1-CKO, repeat 6

description:
Library name: AR11
PIPseq 4PLUS
Tgfbr1_retina_features.tsv.gz
Tgfbr1_retina_barcode.tsv.gz: barcode-7
Tgfbr1_retina_matrix.mtx.gz
Tgfbr1_retina_mata_data.csv
Tgfbr1_retina_umap.csv


title: hiBPC_2

description: Library name: iBPC.2


title: Whole retina, Tgfbr1-CKO, repeat 4

description:
Library name: AR7
PIPseq 4PLUS
Tgfbr1_retina_features.tsv.gz
Tgfbr1_retina_barcode.tsv.gz: barcode-5
Tgfbr1_retina_matrix.mtx.gz
Tgfbr1_retina_mata_data.csv
Tgfbr1_retina_umap.csv


title: hiBPC+hiEC_inf_3

description: Library name: iBPC.TW.INF.3


title: Whole retina, Tgfbr1-CKO, repeat 2

description:
Library name: AR5
PIPseq 4PLUS
Tgfbr1_retina_features.tsv.gz
Tgfbr1_retina_barcode.tsv.gz: barcode-3
Tgfbr1_retina_matrix.mtx.gz
Tgfbr1_retina_mata_data.csv
Tgfbr1_retina_umap.csv


title: hiBPC_1

description: Library name: iBPC.1


title: Whole retina, Tgfbr1-CKO, repeat 3

description:
Library name: AR6
PIPseq 4PLUS
Tgfbr1_retina_features.tsv.gz
Tgfbr1_retina_barcode.tsv.gz: barcode-4
Tgfbr1_retina_matrix.mtx.gz
Tgfbr1_retina_mata_data.csv
Tgfbr1_retina_umap.csv


title: Purified NKX2-5-positive/TBX5-negative cardiomyocytes derived from human induced pluripotent cells (biol rep 2)

city: Okayama

first: Yukihiro

last: Sato

address: 2-5-1 Shikata-cho Kita-ku

institute: Okayama University

description: Library name: 379

data_processing:
We use fastqc for quality check, fastp for preprocessing, and Star-RSEM-DEseq2 pipeline for mapping, annotation, and extraction of expression variation genes.
TPM is used for expression analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: induced pluripotent stem cell-derived cardiomyocytes

extract_protocol:
Total RNA was extracted with Monarch® Total RNA Miniprep Kit (NEB).
1 µg of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using  NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB) and NEBNext® Ultra RNA Library Prep Kit for Illumina® (NEB).

value: cardiomyocytes

value: WT

value: Modified GiWi


title: Purified NKX2-5-positive/TBX5-negative cardiomyocytes derived from human induced pluripotent cells (biol rep 1)

description: Library name: 378

value: induced pluripotent stem cell-derived cardiomyocytes


title: Purified NKX2-5-positive/TBX5-negative cardiomyocytes derived from human induced pluripotent cells (biol rep 3)

description: Library name: 380


title: Purified NKX2-5-positive/TBX5-positive cardiomyocytes derived from human induced pluripotent cells (biol rep 2)

description: Library name: 376

value: Standard GiWi


title: Crypt Organoids, IL25 treated wild type mice, proximal small intestine, biol rep 3

city: San Francisco

first: Victor

middle: S

last: Cortez

address: 513 Parnassus Avenue

department: Medicine

institute: University of California, San Francisco

description:
Library name: VC_F
Active Motif ATACseq Kit

data_processing:
Raw reads were assessed for quality using FastQC(v0.12.1) and trimmed for adapter sequences and low-quality bases with Trim Galore(0.6.2). Trimmed reads were aligned to the mouse reference genome(mm10) using bwa-mem (v0.7.17). Alignment files were converted from SAM to BAM format with Samtools (v1.19.2), sorted, and duplicates were marked using Picard (v2.27.3). Peak regions were identified using MACS2 (v2.2.9.1) and read counts per peak were generated using featureCounts (v2.0.8). Differential chromatin accessibility was analyzed using the edgeR package (v4.0.16) in R and the resulting p-values adjusted for multiple testing using the Benjamini-Hochberg algorithm to obtain the false discovery rate (FDR). Differentially accessible regions were considered significant if FDR was < 0.05 and logFC > 1 for upregulated peaks and logFC < -1 for downregulated peaks. Gene annotation was performed with ChIPseeker(v1.42.0).
Assembly: Trimmed reads were aligned to the mouse reference genome(mm10) using bwa-mem (v0.7.17).
Supplementary files format and content: bigWig

source_name: Small Intestine

growth_protocol: 1000 crypts were plated per well in preheated 24-well plates in 50 uL Matrigel domes in ENR medium (Basal Medium, B27 Supplement, N2 Supplement, hrEGF (50 ng/mL), Noggin (100 ng/mL), and R-spondin conditioned medium). 6 days after plating, matrigel domes were washed with 1x PBS, then incubated with 0.5 pre-warmed TrypLE for ~10 min, with trituration to promote organoid dissociation. The reaction was stopped with 1 mL of Basal medium + 10% FBS

extract_protocol:
Epithelial crypts were isolated from the proximal small intestinal of C57BL/6J (from 3 IL-25-treated and 3 PBS-treated) mice +50 days after the last treatment, grown under standard organoid conditions for 6 days, and organoids isolated from Matrigel and dissociated as detailed below. Tissue was cut open and rinsed twice in PBS + Pen/Strep on ice, then incubated in Harvest Buffer (PBS + Pen/Strep + 2 mM DTT + 10 uM Y-27632+ 1 mM EDTA) with rocking on ice for 15 min. After 15 min, the tissue was shaken for 1 min, transferred to Crypt Dissociation Buffer (PBS + Pen/Strep + 2 mM DTT + 10 uM Y-27632+ 5 mM EDTA), and incubated for 1 hr with gentle rocking on ice. The tissue was manually shaken for 1-3 min, filtered through a 70 µm filter, rinsed with 5 mL of ice cold Basal Medium (Advanced DMEM/F12 High Glucose, N-acetyl-L-cysteine, Pen/Strep, Glutamax, HEPES) and enumerated. Cells were washed with basal medium containing 10% FBS, stained in FACS wash buffer containing antibodies for flow cytometry (EpCAM+), then resuspended in FACS wash buffer containing DAPI. Single, live EpCAM+ cells were sorted and 100k cells per sample were used as input for ATAC libraries.
Libraries were prepared using the Active Motif ATAC-Seq kit according to manufacturer instructions. Right side size selection clean-up of ATAC libraries was performed with a 0.5x ratio of SPRIselect beads according to the SPRIselect User Guide. Final libraries were sequenced with Novogene on NovaSeq X Plus with 50M paired end reads per libary..

value: Small Intestine

value: Crypt Organoids (day 6)

value: Wild type

tag: strain

value: IL25 treated


title: Crypt Organoids, IL25 treated wild type mice, proximal small intestine, biol rep 2

description:
Library name: VC_E
Active Motif ATACseq Kit


title: Whole retina, Tgfbr1-CKO, repeat 7

description:
Library name: AR12
PIPseq 4PLUS
Tgfbr1_retina_features.tsv.gz
Tgfbr1_retina_barcode.tsv.gz: barcode-8
Tgfbr1_retina_matrix.mtx.gz
Tgfbr1_retina_mata_data.csv
Tgfbr1_retina_umap.csv


title: Crypt Organoids, IL25 treated wild type mice, proximal small intestine, biol rep 1

description:
Library name: VC_D
Active Motif ATACseq Kit


title: Whole retina, WT

description:
Library name: AR3
PIPseq 4PLUS
Tgfbr1_retina_features.tsv.gz
Tgfbr1_retina_barcode.tsv.gz: barcode-1
Tgfbr1_retina_matrix.mtx.gz
Tgfbr1_retina_mata_data.csv
Tgfbr1_retina_umap.csv


title: Whole retina, Tgfbr1-CKO, repeat 1

description:
Library name: AR4
PIPseq 4PLUS
Tgfbr1_retina_features.tsv.gz
Tgfbr1_retina_barcode.tsv.gz: barcode-2
Tgfbr1_retina_matrix.mtx.gz
Tgfbr1_retina_mata_data.csv
Tgfbr1_retina_umap.csv


title: Purified NKX2-5-positive/TBX5-positive cardiomyocytes derived from human induced pluripotent cells (biol rep 3)

description: Library name: 377


title: Crypt Organoids, PBS treated wild type mice, proximal small intestine, biol rep 1

description:
Library name: VC_A
Active Motif ATACseq Kit

value: PBS treated


title: Sham, ATAC

city: New York

first: Michael

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

description: Library name: Sham ATAC

library_source: genomic single cell

data_processing:
Reads were processed through the Cellranger count pipeline
Assembly: GRCm38 GENCODE vM23/Ensembl98
Supplementary files format and content: Cellranger filtered matrix output files

source_name: Bone marrow

growth_protocol: Cells were isolated from mice at the time of experiment.

extract_protocol:
On day nine after femoral artery ligation or sham surgery, bone marrow was FACS-purified and enriched for Lineage– cKit+ Sca1+/- hematopoietic progenitors.
Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Kit (10x Genomics)

treatment_protocol: Mice were injected with E0771 breast cancer cells three days prior to receiving sham or femoral artery ligation surgery.

value: Bone marrow

value: Primary

value: Hematopoietic stem and progenitor

tag: library type

value: ATAC

value: Sham surgery


title: FAL, GEX

description: Library name: FAL RNA

value: mRNA

value: Femoral artery ligation


title: Crypt Organoids, PBS treated wild type mice, proximal small intestine, biol rep 2

description:
Library name: VC_B
Active Motif ATACseq Kit


title: Purified NKX2-5-positive/TBX5-positive cardiomyocytes derived from human induced pluripotent cells (biol rep 1)

description: Library name: 375

value: cardiomyocytes


title: heads, elav-Gal4/+;UAS-tauR406W/+, rep2

city: Providence

first: Bess

last: Frost

state: RI

address: 185 Meeting St

institute: Center for Alzheimer’s Disease Research, Brown University

description: Library name: tau_2

data_processing:
Basecalling was performed with Guppy (v5.1.12)31. Reads with a quality value of 9 or more were used for further analysis.
Assembly: dm6
Supplementary files format and content: Long read TPM counts of reference transcriptome (dm6.43) were generated by NanoCount.

organism: Drosophila melanogaster

source_name: head

extract_protocol:
Total RNA was extracted from 500 10-day-old adult Drosophila heads using TRIzol (Invitrogen, 15596026); RNA concentrations were measured on a Nanodrop 8000 spectrophotometer. Total RNA isolated from Drosophila heads was analyzed via RNA ScreenTape prior to ONT library generation; all samples achieved an RIN >9.8. 75 g of total RNA was enriched for full-length polyA RNA using the Dynabeads mRNA Purification kit (Invitrogen, 61005). For Illumina, 10 fly heads (five female and five male) per biological replicate were homogenized in radioimmunoprecipitation buffer (50 mM tris-HCL, 0.5% Nonidet-P40, 1.5 mM MgCl, 140 nM NaCl, and 1 mM dithiothreitol) with 1 μL (40 units/μL) of RNaseOUT (Invitrogen) and precleared with 40 μl of protein A Dynabeads (Invitrogen) for one hour at 4°C. After bead clearance, precleared lysate was split in two aliquots and diluted to a volume of 200 μl with cold binding buffer (0.0025% Triton X-100 in 1× PBS). Precleared lysate (200 μl) was stored at −80°C for RNA extraction via TRIzol.
500 ng polyA tailed RNA was used for library preparation using the Direct RNA Sequencing kit (SQK-RNA002) and protocol from ONT.RNA quality of the libraries was assessed using a Qubit 4 fluorometer (Invitrogen) prior to sequencing using the MinION Mk1C with R9.4 flow cells. For Illumina, RNA libraries from 0.7-1 μg of RNA were generated using the TruSeq Stranded mRNA Library Prep Kit and accompanying Index Set (Illumina Inc).

value: head


title: heads, elav-Gal4/+, rep3

description: Library name: control_3


title: heads, elav-Gal4/+;UAS-tauR406W/+, rep1

description: Library name: tau_1


title: heads, elav-Gal4/+, rep2

description: Library name: control_2


title: heads, elav-Gal4/+, rep1

description: Library name: control_1


title: Sham, GEX

description: Library name: Sham RNA

value: WT


title: Sham, HTO

description: Library name: B HTO

molecule: protein

extract_protocol:
On day nine after femoral artery ligation or sham surgery, bone marrow was FACS-purified and enriched for Lineage– cKit+ Sca1+/- hematopoietic progenitors.
PIPseq T20 V4.0PLUS Supplemental Enrichment of Synthetic Nucleotide Tags

tag: hto

value: ACCCACCAGTAAGAC sham_1_batch_2, GGTCGAGAGCATTCA sham_2_batch_2, CTTGCCGCATGTCAT surgery_1_batch_2, AAAGCATTCTTCACG surgery_2_batch_2

value: HTO


title: FAL, ATAC

description: Library name: FAL ATAC


title: FAL, HTO

description: Library name: A HTO

value: ACCCACCAGTAAGAC sham_1_batch_1, GGTCGAGAGCATTCA sham_2_batch_1, CTTGCCGCATGTCAT surgery_1_batch_1, AAAGCATTCTTCACG surgery_2_batch_1


title: Sham, RNA

description: Library name: B RNA


title: FAL, RNA

description: Library name: A RNA


title: root2, 2 weeks

city: Weifang

first: haiying

last: yang

state: Shandong

address: 699 Binhu Road, Xiaoshan Ecological Economic Development Zone

country: China

institute: Weifang Modern Agriculture Laboratory of Shandong Province

description: Library name: W82_root_2

data_processing:
The total RNA was treated with T4 polynucleotide kinase (M0201L, NEB, USA) and subsequently digested with Terminator™ 5´-Phosphate-Dependent Exonuclease (TER51020, Epicentre, USA) to enrich the capped mRNA. Next, reverse transcription (RT) primer harboring a 3'-adaptor sequence and randomized hexamer was used to conduct RT. Subsequently, the 5' adaptor, which contained three additional guanine residues (rG) at its 3' terminus, was added to the RT reaction. The mixture was then incubated for another 30 minutes to facilitate template switching and the tagging of the 5' adaptor.
Assembly: Wm82-NJAUT2T genome
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes TPM for merged Sample
Supplementary files format and content: tab-delimited text file includes TCs for merged Sample

organism: Glycine max

source_name: root

extract_protocol:
RNA extraction was conducted by using RNA extraction Kit (DP441, TIANGEN, China) by following the manufacturer’s instructions. NanoCAGE-seq libraries were prepared from 1 µg of total RNA of each sample.
NanoCAGE-seq assays were performed by Wuhan Ruixing Biotechnology Co.Ltd, China (http://www.rxbio.cc).

value: root

value: Williams 82


title: shoot1, 2 weeks

description: Library name: W82_shoot_1

source_name: shoot

value: shoot


title: root1, 2 weeks

description: Library name: W82_root_1


title: heads, elav-Gal4/+;UAS-tauR406W/+, rep3

description: Library name: tau_3


title: Crypt Organoids, PBS treated wild type mice, proximal small intestine, biol rep 3

description:
Library name: VC_C
Active Motif ATACseq Kit

value: Small Intestine

value: Crypt Organoids (day 6)

value: Wild type

value: PBS treated


title: Aorta, Tagln Cre +, Prdm16 fl/fl, Baseline

city: Philadelphia

first: Ryan

middle: Patrick

last: Calhoun

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

description:
Library name: Tagln_KO
Prdm16_SMC_cKO_Baseline.rds

data_processing:
Illumina sequencing was demultiplexed using cellranger mkfastq (version 7.2.0)
Fastq files were processed with cellranger multi function against the mm10 genome with default parameters and a custom probe-list containing our extra designed gene-probes to generate counts
Unfiltered count files were read into R (version 4.3.0)  and DropletUtils (version 1.20.0) and SoupX (version 1.6.2) removed empty droplets and ambient RNA removal was performed to produce the processed files
Seurat (version 4.3.0) was utilized for quality control filtering, data analysis, and integration and package scDblFinder (version 1.14.0) was used for doublet detection and harmony (version 1.2.0) for evaluation of batch effects
Assembly: mm10, customized chromium mouse transcriptome probe set (version 1.0.1) to include designed probes for TdTomato and Prdm16 Exon 9
Supplementary files format and content: The processed features, barcodes, and matrix files are thee processed files after running DropletUtils and SoupX on the raw cellranger outpus
Supplementary files format and content: Prdm16_SMC_iKO_Athero.rds is a seurat processed R object for Myh11 CreER Prdm16 +/+ and fl/fl samples integrated together
Supplementary files format and content: Prdm16_SMC_cKO_Baseline.rds is a seurat processed R object for Tagln Cre - and Cre + samples integrated together
Supplementary files format and content: Baseline_Athero_FixedcellscRNAseq.rds is a seurat processed R object for Myh11 CreER Prdm16 +/+ and Tagln Cre - samples integrated together

source_name: Fixed Aorta

extract_protocol:
scRNAseq was performed using the 10x Flex Platform with the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (1000414). Aortae were dissected from the root to the ileac bifurcation, washed twice in cold RPMI. The tissue was then sliced in 1 mm rings on a chilled glass slide and fixed in 1 mL fixation buffer per 25 mg tissue for 16h at 4°C without agitation. The fixation buffer consisted of 4% PFA combined with 10x concentrated fixation/permeabilization buffer). The following day, tissue pieces were centrifuged at 850 x g for 5 min and washed with 2 mL cold PBS. Samples were then resuspended in 1 mL quenching buffer with 0.1 volume of Enhancer, and adjusted to a final glycerol concentration of 10% before being stored at -80°C. For enzymatic digestion, aortae were processed individually in 2 mL pre-warmed RPMI 1640 containing 1 mg/mL Liberase TM (Roche 05401020001) using a Miltenyi GentleMACS at 37°C with the following program: (spin 50 rpm for 20 min, [spin 1000 rpm for 30s, spin -1000 rpm for 30s (2x)]). Digested tissue suspensions were pooled and filtered through a 30 µm strainer. The strainer and collection tube were rinsed with PBS to maximize cell recovery. Cells were centrifuged at 1200 × g for 10 minutes and resuspended in 250 µL quenching buffer
Probe hybridization and cell capture were performed using the 10x Chromium Fixed RNA Kit, Mouse Transcriptome kit (1000495) according to the manufacturer's instructions except for an increase in centrifugation speed (1200 x g for 10 min).

treatment_protocol: For iKO experiments, tamoxifen (Sigma, T5648; stock 20 mg/mL in corn oil) was injected intraperitoneally at a dose of 100 mg/kg for 4 consecutive days. To induce atherosclerosis, mice were retro-orbitally injected at 8 weeks with AAV8-PCSK9 D377Y (Vector Biolabs) at a dose of 5 x 1011 GC/mouse, as described by to Bjørklund et al.41. Following injection, mice were fed a Western Diet containing 40% fat and 0.15% cholesterol (Research Diets, D12079B) for 18 weeks.

value: Fixed Aorta

tag: disease

value: baseline

tag: Sex

value: male

tag: tamoxifen status

tag: cre status

value: Tagln Cre

tag: floxed allele

value: Prdm16 fl/fl


title: Aorta, Tagln Cre -, Prdm16 fl/fl, Baseline

description:
Library name: Tagln_Ctrl
Prdm16_SMC_cKO_Baseline.rds

tag: tissue

value: No Cre


title: Z2FH_D3_ChIP_ZIC2_rep2

city: Santander

first: Alvaro

last: Rada-Iglesias

state: Cantabria

address: Albert Einstein 22, PCTCAN

country: Spain

institute: Institute of Biomedicine and Biotechnology of Cantabria

description: Library name: Sample 74

data_processing:
ChIP-Seq data was generated for (i) transcription factors (TFs) (i.e. ZIC3) and (ii) different histone marks (H3K27me3, H3K27ac, H3K4me1, H3K4me2, H3K4me3) in WT and Zic2-/- cells. In addition, ChIP-seq data for ZIC2 was generated in Zic2FLAG-HA cells. For all ChIP-seq samples, reads quality control and removal of low quality regions and/or adapters was performed with fastqc, MultiQC and Trimmomatic. Regarding the ChIP-seq samples concerning TFs, reads were mapped to the mouse reference assembly (mm10) using Bowtie2. Subsequently, reads with a mapping quality below 10 and duplicated reads were discarded with Samtools. For each sample, a BigWig based on RPKM normalization was generated. Finally, for conditions in which multiple replicates were available (i.e. ZIC2 ChIPs), an average BigWig file was created using Wiggletools mean and bedGraphToBigWig tools, to be used as consensus/reference in the different visualizations/quantifications in which BigWig files were used. Regarding the ChIP-seq samples for histone marks, in order to handle the exogenous DNA (human) added to the samples during their preparation, and following published guidelines, reads were mapped to a mm10-hg19 concatenated genome using Bowtie2. Subsequently, reads with a mapping quality below 10 and duplicated reads were discarded with Samtools. Next, reads mapping to each of the genomes (mm10 and hg19) were identified using split_bam.py from Spiker (https://spiker. readthedocs.io/en/latest/index.html). The bam file with the reads mapping exclusively to mm10 was the only one considered for downstream analyses. ChIP BigWigs were generated applying a quantile normalization between samples of the same histone mark (e.g., H3K27ac) and differentiation time point (e.g., D3). Regarding the particularities to generate them, first, the mm10 genome was split in bins of 100 bps with bedtools makeWindows and the resulting coordinates were converted into saf (simplified annotation format) format, to be accepted as an annotation file in featureCounts. Next, for each sample, considering their bam file and the saf file, the number of reads in each of the 100 bp genome windows was counted with featureCounts. The resulting counts matrix was loaded in R where two main steps were applied. In the first one, read counts per bin were converted to RPKMs. Next, the resulting values were quantile normalized among samples using the function normalize.quantiles() from the preprocessCore package. Then, bedgraphs with the quantile normalized values per 100 bp window were generated and subsequently converted to BigWigs with the usage of UCSC bedGraphToBigWig tool. Finally, a reference BigWig file per condition was created averaging the information of the different replicates with Wiggletools mean and bedGraphToBigWig tools.
Assembly: mm10
Supplementary files format and content: BigWig

source_name: Z2FH E14Tg2a D3 cells

growth_protocol: mESC maintenance and AntNPCs differentiation protocol. E14Tg2a (E14) mouse ESC were cultured on gelatin-coated plates using Knock-out DMEM (Life Technologies, 10829018) supplemented with 15% FBS (Life Technologies, 10082147), leukemia inhibitory factor (LIF), antifungal and antibiotics (Sigma-Aldrich, A5955), β-mercaptoethanol (ThermoFisher Scientific, 21985023), Glutamax (ThermoFisher Scientific, 35050038) and MEM NEAA (ThermoFisher Scientific, 11140035). Cells were cultured at 37°C with 5% CO2. For the AntNPC differentiation, mESCs were plated at 20.000 cells/cm2 on geltrex-coated plates (ThermoFisher, A1413302) and grown in N2B27 medium: Advanced Dulbecco’s Modified Eagle Medium F12 (Life Technologies, 21041025) and Neurobasal medium (Life Technologies,12348017) (1:1), supplemented with 1 × N2 (R&D Systems, AR009), 1 × B27 (Life Technologies, 12587010), 2mM l-glutamine (Life Technologies, 25030024) and 0.1 mM 2-mercaptoethanol (Life Technologies, 31350010)). During the six days of differentiation, the N2B27 medium was additionally supplemented with the following components: bFGF (ThermoFisher Scientific, PHG0368) 10 ng/ml from day 0 to day 2, Xav939 (Sigma-Aldrich, X3004-5MG) 5 µM from day 2 to day 6, BSA (ThermoFisher Scientific, 15260037) 1 mg/ml at day 0 and 40 µg/mL the remaining days.

extract_protocol:
For TF ChIPs (ZIC2, ZIC3), one confluent 10 cm plate (~40–50 × 106 cells) was used; for histone mark ChIPs, 1/5 of a 10 cm plate was used (~10 × 106 cells). Cells were cross-linked directly on the tissue culture plate in 1% formaldehyde (Sigma-Aldrich, 252549-100ML) for 10 min at room temperature, followed by quenching with 0.125M Glycine (Sigma-Aldrich, G8898-1KG) during 5–10 min. After two washes with 1X PBS supplemented with cOmpleteª Protease Inhibitor ULTRA Tablets (SigmaAldrich, 5892791001), cell pellets were snap-frozen and stored at –80°C prior to use. Chromatin was extracted by sequential re-suspension in three lysis buffers (Lysis Buffer 1: 50 mM Hepes (pH 7.5), 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.2% TX-100, dH20 ;Lysis Buffer 2: 10 mM Tris pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, dH20; Lysis Buffer 3: 10 mM Tris pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, dH20), followed by centrifugation (5 min, 1350 g, 4 °C) between steps. Chromatin was sonicated using an EpiShear Probe Sonicator (Active Motif, 53052) under the following conditions: • Histone marks: 30% amplitude, 20 sec on / 30 sec off, 10 min total. • Transcription factors: 35% amplitude, 20 sec on / 30 sec off, 4 min 40 sec total. These conditions aimed to obtain chromatin with sizes 200-500 bp for histone ChIPs and 500-1000 bp for TF ChIPs. After sonication, samples were cleared by centrifugation (10 min, 16000 g, 4 °C), and supernatants were aliquoted. Each aliquot was incubated overnight at 4 °C with 3–5 µg antibody (for histone marks) or 10 µg (for TFs). A 10% aliquot was reserved as input control. The next day, pre-blocked Dynabeads™ Protein G (Thermo Fisher Scientific, 10004D) were added (100 µl for TFs; 75 µl for histone marks) and incubated for 4 h at 4 °C. Beads were washed five times with RIPA buffer (50 mM Hepes pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate, dH2O) and once with TE buffer containing 50 mM NaCl (Sigma-Aldrich, S9888). Chromatin was eluted from the beads by heating at 65°C with occasional vortex. After this, crosslinking was reversed by overnight incubation at 65°C. DNA was purified using DNA Clean & Concentrator kit (Zymo Research, D4034) for inputs and ChIP DNA Clean & Concentrator kit (Zymo Research, D5205) for ChIP samples. Purified DNA concentration was measured with a Qubit 4 Fluorimeter (Thermo Fisher Scientific, Q33238) using the Qubit™ dsDNA HS Assay Kit (Thermo Scientific, Q32854) for ChIP DNA, and the Qubit™ dsDNA BR Assay Kit (Thermo Scientific, Q32853) for input samples.
Libraries were prepared for the ChIP and input samples from D0, D3, and D6 by Macrogen Inc. (Korea) using the Illumina TruSeq ChIP-seq protocol. Libraries were sequenced (paired-end 150 bp, 40M reads/sample) on a NovaSeq6000 platform.

treatment_protocol: Zic2 and Zic3 deletions using CRISPR-Cas9.Pairs of sgRNAs were designed to flank Zic2 coding region using Benchling’s genome engineering toolbox (https://www. benchling.com/). Guides were selected for high on target efficiency and minimal off target potential. Complementary oligonucleotides containing BbsI (NEB, R0539L) overhangs were synthesized and annealed (see Supplementary Data 4) by heating to 95°C for 5 min, followed by gradual cooling down to 25°C at -5 °C/min. Annealed oligos were ligated into BbsI-digested pX330A-hCas9-longchimeric-gRNA-G2P vector using T4 DNA ligase (NEB, M0202L) and transformed into chemically competent E. coli (TOP10) via heat shock. Colonies were plated on LB-ampicillin agar and screened by colony PCR to confirm the presence of the desired insert (see Colony PCR section). Plasmids were purified using the NZY Miniprep Kit (NZYTech, MB01001) and verified by Sanger sequencing using the pX330A_R reverse primer (see Supplementary Data 4). Verified clones were stored as glycerol stocks at -140°C. mESCs were plated on gelatin-coated 12- or 6-well plates and co-transfected with Lipofectamine 3000 transfection reagent (Thermo Fisher Scientific, L3000001) and one or two sgRNA-expressing pX330A vectors. For 12-well plates, 150.000 mESC were transfected with 1.5 µl of Lipofectamine 3000. Transfection efficiency was assessed via GFP fluorescence 24 h later. Cells with 70–90% transfection efficiency underwent puromycin (Sigma-Aldrich, P8833-25MG) selection (2 µg puromycin/ml during 48 h). Puromycin-resistant cells were serially diluted and plated in 96-well plates for clonal expansion. After 10–12 days, individual colonies were split into duplicate wells: one for gDNA extraction and PCR based genotyping and another for expansion and maintenance of each clone. Positive knock-out mESC clones were expanded and cryopreserved at -140 °C for future use.Genomic insertions by CRISPR-Cas9-mediated homology directed repair (HDR). To generate the DNA double strand break that would favour a genomic insertion through homology directed repair (HDR), a single gRNA was designed in order to cut as close as possible to the insertion site according to the instructions of the genome engineering toolbox from Benchling (https://www.benchling.com/). The steps followed for the design were the same as the ones described previously. In order to introduce the desired insertion, a ssDNA repair template was designed and synthesized as an Ultramer™ (for fragments up to 200 bp; IDT) or as a Megamer™ (for fragments up to 500 bp; IDT). The repair template contained the sequence of the epitope (i.e. Flag-HA, FKBPV36-HA) flanked with two homology arms, complementary to the sequences upstream and downstream of the gRNA-Cas9 cutting site. mESC were transfected as described above, including the ssDNA sequence as an additional component of the transfection reactions. Subsequent steps to derive mESC clonal lines with the desired genomic insertion were as the ones described for genomic deletions.

tag: cell line

value: Z2FH E14Tg2a D3 cells

value: Differentiation to AntNPCs (sample collection at D3); HA antibody (Abcam, ab9110)


title: Z2FH_D6_ChIP_ZIC2_rep2

description: Library name: Sample 77

source_name: Z2FH E14Tg2a D6 AntNPCs

value: Z2FH E14Tg2a D6 AntNPCs

value: Differentiation to AntNPCs (sample collection at D6); HA antibody (Abcam, ab9110)


title: Aorta, Tamoxifen Treated, Myh11 CreER +, Prdm16 fl/fl, Atherosclerosis

description:
Library name: Myh11_KO
Prdm16_SMC_iKO_Athero.rds

value: atherosclerosis

value: Myh11 CreER

value: Prdm16 fl/fl, Rosa26 tdTomato/+


title: Z2FH_D6_ChIP_ZIC2_rep1

description: Library name: Sample 76


title: Z2FH_D6_Input_ZIC2_rep1

description: Library name: Sample 75

value: Differentiation to AntNPCs (sample collection at D6); no antibody


title: monocyte_sia_donor16-9

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

description: Library name: Sample 6

data_processing:
Basecalling on the raw Nanopore data was performed using the Guppy GPU basecaller using FLO-MINI106 flowcell and SQK-PCS109 kit. Sample debarcoding was done using Guppy GPU based on SQK-PBK004 barcoding kit. FASTQ files were obtained and mapped to the human genome GRCh38 using minimap2. Gene counts were then obtained using featureCounts (part of the Subread package) based on GENCODE V31 annotations.
Assembly: Human GRCh38
Supplementary files format and content: log2 RPKM values provided as rpkm.csv

source_name: Human pimary monocytes

extract_protocol:
Total RNA was isolated from primary human monocytes using a RNeasy Micro Kit (Qiagen), following the manufacturer's instructions.
cDNA libraries were generated from a total of 50 ng RNA according to the Oxford Nanopore Technologies (Oxford Nanopore Technologies Ltd, Oxford, UK) protocol “cDNA-PCR Barcoding Sequencing”60 with 18 cycles of PCR (4.5 min elongation time). ONT adapters were ligated to the amplified cDNA library.

treatment_protocol: Primary monocytes were isolated from human whole blood and  stimulated with a 10 UM concentration of sialokinin or PBS

tag: timepoint

value: 24 hours post-treatment

tag: cell type

value: Human pimary monocytes

value: Sialokinin 10uM


title: shoot2, 2 weeks

description: Library name: W82_shoot_2

value: shoot

tag: genotype

value: Williams 82


title: Z2FH_D3_ChIP_ZIC2_rep1

description: Library name: Sample 73

tag: treatment


title: monocyte_sia_donor12

description: Library name: Sample 5


title: monocyte_sia_donor9

description: Library name: Sample 4


title: monocyte_mock_donor16-9

description: Library name: Sample 3

value: PBS


title: monocyte_mock_donor12

description: Library name: Sample 2


title: Z2FH_D3_Input_ZIC2_rep1

description: Library name: Sample 72

value: Differentiation to AntNPCs (sample collection at D3); no antibody


title: Z2FH_D0_Input_ZIC2_rep1

description: Library name: Sample 69

source_name: Z2FH E14Tg2a mESC D0

value: Z2FH E14Tg2a mESC D0

value: Culture in S+LIF; no antibody


title: Z2FH_D0_ChIP_ZIC2_rep2

description: Library name: Sample 71

value: Culture in S+LIF; HA antibody (Abcam, ab9110)


title: monocyte_mock_donor9

description: Library name: Sample 1


title: Z2KO_D6_ChIP_H3K27me3_rep1

description: Library name: Sample 67

source_name: Z2KO E14Tg2a D6 AntNPCs

value: Z2KO E14Tg2a D6 AntNPCs

value: Differentiation to AntNPCs (sample collection at D6);  H3K27me3 antibody (Active Motif, 39155)


title: Z2KO_D6_ChIP_H3K27ac_rep1

description: Library name: Sample 65

value: Differentiation to AntNPCs (sample collection at D6); H3K27ac antibody (Active Motif, 39133)


title: Z2KO_D6_ChIP_H3K27ac_rep2

description: Library name: Sample 66

value: Differentiation to AntNPCs (sample collection at D6);  H3K27ac antibody (Active Motif, 39133)


title: Z2KO_D6_ChIP_H3K4me3_rep2

description: Library name: Sample 64

value: Differentiation to AntNPCs (sample collection at D6);  H3K4me3 antibody (Active Motif, 39159)


title: DSP.1001660039493.B.H11.dcc

city: London

first: Jack

last: Wood

state: County

address: Gower Street

department: Neuroscience, Physiology and Pharmacology

country: United Kingdom

institute: University College London

description: Library name: DSP.1001660039493.B.H11.dcc

data_processing:
Demultiplex to FASTQ and convert to DCC with GeoMx NGS Pipeline/GUI.
Map oligo barcodes to human gene symbols using the GeoMx Human WTA PKC annotation.
AOI QC thresholds: ≥1,000 reads/AOI; ≥80% trimmed; ≥80% stitched; ≥75% aligned; ≥50% sequencing saturation. Failing AOIs were excluded.
Assembly: Gene identifiers derived from the GeoMx Human Whole Transcriptome (WTA) probe annotation (PKC file): Hs_R_NGS_WTA_v1.0.pkc
Supplementary files format and content: dcc/ - one .dcc file per AOI (barcode counts). dcc_stats/ - per-AOI .stats.txt files generated by GeoMx NGS.
Library strategy: Spatial Transcriptomics

source_name: Hippocampus

extract_protocol:
FFPE blocks were sectioned at 8 μm using a rotary microtome. Three of these tissue squares were mounted per SuperFrost Plus slide within the designated GeoMx scan area.
Slide preparation followed the standard GeoMx Slide Preparation protocol . Probe mic: GeoMx Whole Transcriptome Probe Mix. Library quality was verified on an Agilent TapeStation D1000. Sequencing was performed on an Illumina NextSeq 2000 (X-LEAP chemistry), paired-end.

value: Hippocampus

value: Microglia

value: A

tag: batch

tag: group

value: AD

tag: age

tag: braak

tag: pmd

tag: ph

tag: weight

tag: csf

tag: area

tag: slide

tag: apoe

value: M


title: DSP.1001660039493.B.H09.dcc

description: Library name: DSP.1001660039493.B.H09.dcc

tag: tissue

tag: Sex


title: DSP.1001660039493.B.H10.dcc

description: Library name: DSP.1001660039493.B.H10.dcc


title: DSP.1001660039493.B.H08.dcc

description: Library name: DSP.1001660039493.B.H08.dcc

value: PP


title: Aorta, Tamoxifen Treated, Myh11 CreER +, Prdm16 +/+, Atherosclerosis

description:
Library name: Myh11_Ctrl
Prdm16_SMC_iKO_Athero.rds

value: Fixed Aorta

tag: strain

tag: disease

value: atherosclerosis

value: male

tag: tamoxifen status

tag: cre status

value: Myh11 CreER

tag: floxed allele

value: Prdm16 +/+, Rosa26 tdTomato/+


title: DSP.1001660039493.B.H07.dcc

description: Library name: DSP.1001660039493.B.H07.dcc

tag: cell type

tag: treatment

value: P

tag: batch

tag: group


title: Z2KO_D6_ChIP_H3K4me3_rep1

description: Library name: Sample 63

tag: cell line

value: Z2KO E14Tg2a D6 AntNPCs

tag: genotype


title: Z2KO_D6_ChIP_H3K4me2_rep2

description: Library name: Sample 62

value: Differentiation to AntNPCs (sample collection at D6);  H3K4me2 antibody (Active Motif, 39141)


title: DSP.1001660039493.B.H06.dcc

description: Library name: DSP.1001660039493.B.H06.dcc

tag: age

tag: braak

tag: pmd

tag: ph

tag: weight

tag: csf


title: Z2KO_D6_ChIP_H3K4me2_rep1

description: Library name: Sample 61


title: DSP.1001660039493.B.H02.dcc

description: Library name: DSP.1001660039493.B.H02.dcc

tag: tissue

tag: area

tag: slide

tag: apoe

tag: Sex

value: F


title: DSP.1001660039493.B.H03.dcc

description: Library name: DSP.1001660039493.B.H03.dcc

tag: cell type


title: Z2FH_D0_ChIP_ZIC2_rep1

description: Library name: Sample 70

value: Z2FH E14Tg2a mESC D0

tag: treatment

value: Culture in S+LIF; HA antibody (Abcam, ab9110)


title: Z2KO_D6_Input_HistoneMarks_rep1

description: Library name: Sample 59

value: Differentiation to AntNPCs (sample collection at D6); no antibody


title: WT_D6_ChIP_H3K27me3_rep2

description: Library name: Sample 58

source_name: E14Tg2a D6 AntNPCs

value: E14Tg2a D6 AntNPCs

value: WT

value: Differentiation to AntNPCs (sample collection at D6);  antibody (Active Motif, 39155)


title: Z2KO_D6_ChIP_H3K27me3_rep2

description: Library name: Sample 68

value: Differentiation to AntNPCs (sample collection at D6);  H3K27me3 antibody (Active Motif, 39155)


title: Z2KO_D6_ChIP_H3K4me1_rep1

description: Library name: Sample 60

value: Differentiation to AntNPCs (sample collection at D6);  H3K4me1 antibody (Active Motif, 39297)


title: DSP.1001660039493.B.H04.dcc

description: Library name: DSP.1001660039493.B.H04.dcc

value: Hippocampus

value: Microglia

value: PP

tag: batch

value: AD

value: M


title: WT_D6_ChIP_H3K27me3_rep1

description: Library name: Sample 57

value: Differentiation to AntNPCs (sample collection at D6); H3K27me3 antibody (Active Motif, 39155)


title: WT_D6_ChIP_H3K27ac_rep2

description: Library name: Sample 56

value: Differentiation to AntNPCs (sample collection at D6); H3K27ac antibody (Active Motif, 39133)


title: DSP.1001660039493.B.G09.dcc

description: Library name: DSP.1001660039493.B.G09.dcc

tag: group


title: WT_D6_ChIP_H3K27ac_rep1

description: Library name: Sample 55

tag: cell line


title: DSP.1001660039493.B.G10.dcc

description: Library name: DSP.1001660039493.B.G10.dcc

value: P


title: DSP.1001660039493.B.G11.dcc

description: Library name: DSP.1001660039493.B.G11.dcc

value: F


title: DSP.1001660039493.B.G08.dcc

description: Library name: DSP.1001660039493.B.G08.dcc


title: WT_D6_ChIP_H3K4me3_rep2

description: Library name: Sample 54

tag: genotype

value: Differentiation to AntNPCs (sample collection at D6); H3K4me3 antibody (Active Motif, 39159)


title: DSP.1001660039493.B.H05.dcc

description: Library name: DSP.1001660039493.B.H05.dcc

tag: age


title: WT_D6_ChIP_H3K4me2_rep2

description: Library name: Sample 52

value: Differentiation to AntNPCs (sample collection at D6); H3K4me2 antibody (Active Motif, 39141)


title: DSP.1001660039493.B.G03.dcc

description: Library name: DSP.1001660039493.B.G03.dcc

value: CU-AP

tag: braak


title: WT_D6_ChIP_H3K4me2_rep1

description: Library name: Sample 51

value: E14Tg2a D6 AntNPCs


title: DSP.1001660039493.B.G04.dcc

description: Library name: DSP.1001660039493.B.G04.dcc

tag: pmd


title: DSP.1001660039493.B.G02.dcc

description: Library name: DSP.1001660039493.B.G02.dcc

tag: ph


title: DSP.1001660039493.B.G05.dcc

description: Library name: DSP.1001660039493.B.G05.dcc

tag: weight


title: WT_D6_ChIP_H3K4me3_rep1

description: Library name: Sample 53

value: WT


title: DSP.1001660039493.B.G06.dcc

description: Library name: DSP.1001660039493.B.G06.dcc

tag: csf


title: Z2KO_D3_ChIP_H3K27me3_rep2

description: Library name: Sample 48

source_name: Z2KO E14Tg2a D3 cells

value: Z2KO E14Tg2a D3 cells

value: Differentiation to AntNPCs (sample collection at D3);  H3K27me3 antibody (Active Motif, 39155)


title: WT_D6_ChIP_H3K4me1_rep1

description: Library name: Sample 50

value: Differentiation to AntNPCs (sample collection at D6); H3K4me1 antibody (Active Motif, 39297)


title: WT_D6_Input_HistoneMarks_rep1

description: Library name: Sample 49

value: Differentiation to AntNPCs (sample collection at D6); no antibody


title: Z2KO_D3_ChIP_H3K27me3_rep1

description: Library name: Sample 47


title: DSP.1001660039493.B.G01.dcc

description: Library name: DSP.1001660039493.B.G01.dcc

tag: tissue

value: Hippocampus

value: Microglia


title: DSP.1001660039493.B.F12.dcc

description: Library name: DSP.1001660039493.B.F12.dcc

tag: area


title: Z2KO_D3_ChIP_H3K27ac_rep2

description: Library name: Sample 46

value: Differentiation to AntNPCs (sample collection at D3);  H3K27ac antibody (Active Motif, 39133)


title: Z2KO_D3_ChIP_H3K4me3_rep2

description: Library name: Sample 44

value: Differentiation to AntNPCs (sample collection at D3);  H3K4me3 antibody (Active Motif, 39159)


title: DSP.1001660039493.B.F11.dcc

description: Library name: DSP.1001660039493.B.F11.dcc

value: A

tag: slide


title: DSP.1001660039493.B.G12.dcc

description: Library name: DSP.1001660039493.B.G12.dcc

value: AD

tag: apoe


title: DSP.1001660039493.B.F10.dcc

description: Library name: DSP.1001660039493.B.F10.dcc

tag: Sex


title: Z2KO_D3_ChIP_H3K27ac_rep1

description: Library name: Sample 45


title: Z2KO_D3_ChIP_H3K4me3_rep1

description: Library name: Sample 43


title: DSP.1001660039493.B.F06.dcc

description: Library name: DSP.1001660039493.B.F06.dcc

tag: cell type

value: PP


title: Z2KO_D3_ChIP_H3K4me2_rep2

description: Library name: Sample 42

tag: treatment

value: Differentiation to AntNPCs (sample collection at D3);  H3K4me2 antibody (Active Motif, 39141)


title: DSP.1001660039493.B.F07.dcc

description: Library name: DSP.1001660039493.B.F07.dcc

tag: batch

value: Non-AD

value: F


title: DSP.1001660039493.B.G07.dcc

description: Library name: DSP.1001660039493.B.G07.dcc

tag: group


title: Z2KO_D3_ChIP_H3K4me2_rep1

description: Library name: Sample 41

tag: cell line


title: DSP.1001660039493.B.F08.dcc

description: Library name: DSP.1001660039493.B.F08.dcc


title: Z2KO_D3_ChIP_H3K4me1_rep2

description: Library name: Sample 40

tag: genotype

value: Differentiation to AntNPCs (sample collection at D3);  H3K4me1 antibody (Active Motif, 39297)


title: DSP.1001660039493.B.F05.dcc

description: Library name: DSP.1001660039493.B.F05.dcc

value: P

tag: age


title: Z2KO_D3_ChIP_H3K4me1_rep1

description: Library name: Sample 39


title: DSP.1001660039493.B.F03.dcc

description: Library name: DSP.1001660039493.B.F03.dcc

tag: braak


title: Z2KO_D3_Input_HistoneMarks_rep1

description: Library name: Sample 38

value: Differentiation to AntNPCs (sample collection at D3); no antibody


title: DSP.1001660039493.B.F02.dcc

description: Library name: DSP.1001660039493.B.F02.dcc

tag: pmd


title: WT_D3_ChIP_H3K27me3_rep2

description: Library name: Sample 37

source_name: E14Tg2a D3 cells

value: E14Tg2a D3 cells

value: WT

value: Differentiation to AntNPCs (sample collection at D3); H3K27me3 antibody (Active Motif, 39155)


title: DSP.1001660039493.B.E12.dcc

description: Library name: DSP.1001660039493.B.E12.dcc

tag: ph


title: DSP.1001660039493.B.F01.dcc

description: Library name: DSP.1001660039493.B.F01.dcc

tag: weight


title: WT_D3_ChIP_H3K27ac_rep2

description: Library name: Sample 35

value: Differentiation to AntNPCs (sample collection at D3); H3K27ac antibody (Active Motif, 39133)


title: DSP.1001660039493.B.F04.dcc

description: Library name: DSP.1001660039493.B.F04.dcc

value: Hippocampus

tag: csf


title: WT_D3_ChIP_H3K27me3_rep1

description: Library name: Sample 36


title: DSP.1001660039493.B.F09.dcc

description: Library name: DSP.1001660039493.B.F09.dcc

tag: tissue

value: Microglia

value: CU-AP


title: WT_D3_ChIP_H3K27ac_rep1

description: Library name: Sample 34


title: DSP.1001660039493.B.E10.dcc

description: Library name: DSP.1001660039493.B.E10.dcc

tag: area


title: WT_D3_ChIP_H3K4me3_rep2

description: Library name: Sample 33

value: Differentiation to AntNPCs (sample collection at D3); H3K4me3 antibody (Active Motif, 39159)


title: DSP.1001660039493.B.E08.dcc

description: Library name: DSP.1001660039493.B.E08.dcc

value: A

tag: slide


title: DSP.1001660039493.B.E11.dcc

description: Library name: DSP.1001660039493.B.E11.dcc

value: AD

tag: apoe


title: WT_D3_ChIP_H3K4me2_rep2

description: Library name: Sample 31

value: Differentiation to AntNPCs (sample collection at D3); H3K4me2 antibody (Active Motif, 39141)


title: WT_D3_ChIP_H3K4me3_rep1

description: Library name: Sample 32


title: DSP.1001660039493.B.E09.dcc

description: Library name: DSP.1001660039493.B.E09.dcc

tag: Sex


title: WT_D3_ChIP_H3K4me2_rep1

description: Library name: Sample 30


title: DSP.1001660039493.B.E07.dcc

description: Library name: DSP.1001660039493.B.E07.dcc

tag: cell type


title: WT_D3_ChIP_H3K4me1_rep2

description: Library name: Sample 29

tag: treatment

value: Differentiation to AntNPCs (sample collection at D3); H3K4me1 antibody (Active Motif, 39297)


title: DSP.1001660039493.B.E05.dcc

description: Library name: DSP.1001660039493.B.E05.dcc

tag: batch


title: WT_D3_ChIP_H3K4me1_rep1

description: Library name: Sample 28


title: WT_D3_Input_HistoneMarks_rep1

description: Library name: Sample 27

source_name: Z2KO E14Tg2a mESC D0

value: Z2KO E14Tg2a mESC D0


title: DSP.1001660039493.B.E04.dcc

description: Library name: DSP.1001660039493.B.E04.dcc

value: PP

tag: group

value: F


title: DSP.1001660039493.B.E02.dcc

description: Library name: DSP.1001660039493.B.E02.dcc


title: DSP.1001660039493.B.E03.dcc

description: Library name: DSP.1001660039493.B.E03.dcc

value: P


title: Z2KO_D0_ChIP_H3K27me3_rep1

description: Library name: Sample 25

tag: cell line

value: Culture in S+LIF; H3K27me3 antibody (Active Motif, 39155)


title: Z2KO_D0_ChIP_H3K27ac_rep2

description: Library name: Sample 24

tag: genotype

value: Culture in S+LIF; H3K27ac antibody (Active Motif, 39133)


title: Z2KO_D0_ChIP_H3K27ac_rep1

description: Library name: Sample 23


title: Z2KO_D0_ChIP_H3K4me2_rep2

description: Library name: Sample 20

value: Culture in S+LIF; H3K4me2 antibody (Active Motif, 39141)


title: DSP.1001660039493.B.E01.dcc

description: Library name: DSP.1001660039493.B.E01.dcc

tag: age


title: Z2KO_D0_ChIP_H3K4me3_rep2

description: Library name: Sample 22

value: Culture in S+LIF;H3K4me3 antibody (Active Motif, 39159)


title: DSP.1001660039493.B.D12.dcc

description: Library name: DSP.1001660039493.B.D12.dcc

value: Non-AD

tag: braak