title: BBS0050-Z1110046143011421S0


title: BBS0050-Z1110044887011521S0

status: Public on May 01 2026

type: protein

city: Indianapolis

first: Helen

last: Masson

address: 893 S Delaware St.

country: USA

institute: Eli Lilly and Company

description: title describes sample ID used in raw data (NPX.csv)

data_processing:
A set of internal controls (incubation, extension and amplification) was used to assess overall assay quality.  Internal plate controls were used to normalize the data and to calculate the limit of detection (LOD) for each assay.
Protein expression levels are given as normalized protein expression (NPX) values, which are arbitrary units used on a log2 scale that were normalized to the plate controls.

molecule: protein

organism: Homo sapiens

source_name: Whole blood

extract_protocol: Baseline SLE serum samples were collected according to the clinical trial protocols. Blood was collected using a tube containing a clotting agent (BD SST 5ml tube). Circulating proteins were assayed using the Olink Explore 3072 panel, a proteomics platform that combines an antibody-based immunoassay with a proximity oligonucleotide extension assay and signal detection with next-generation sequencing on the NovaSeq6000 instrument (Ilumina Inc.).

tag: Sex

value: F

tag: disease

value: healthy controls


title: BBS0050-Z1110040045011121S0


title: E14.5_scRNA_Control_Male

type: SRA

city: Chcago

first: Gal

last: Finier

state: IL

address: 225 E. Chciago Ave

department: Peditrics

institute: Northwestern University

description:
Library name: Sample A2
10x Genomics

library_source: transcriptomic single cell

data_processing:
E145 scRNA: Raw sequencing data was demultiplexed and processed using  CellRanger with a custom reference combining the mm10 transcriptome with the eGFP and tdTomato RNA sequences.
E185 scRNA: Raw sequencing data was demultiplexed and processed using  CellRanger with a custom reference combining the mm10 transcriptome with the eGFP and tdTomato RNA sequences.
E145 scATAC: Raw sequencing data was demultiplexed and processed using the CellRanger ATAC with the mm10 genome.
E185 bulk-RNA: Raw sequencing data was demultiplexed and mapped to mm10 using HISAT2. Normalized gene expression values (fragments per kilobase million; FPKM) were calculated using Cufflinks.
Assembly: mm10
Supplementary files format and content: E145 scRNA: tab-separated values files and matrix files
Supplementary files format and content: E185 scRNA: tab-separated values files and matrix files
Supplementary files format and content: E145 scATAC: tab-separated values files and matrix files
Supplementary files format and content: E185 bulk-RNA: csv files containing FPKM per sample

molecule: total RNA

organism: Mus musculus

source_name: kidney

extract_protocol:
E145 scRNA: Single cell suspensions were prepared from mouse embryonic kidneys using a cold-active protease cell dissociation protocol (Adam et al. Development 2017). Foxd1+ progenitors and their derivates were subsequently isolated by fluorescence-activated cell sorting (FACS).
E185 scRNA: Single cell suspensions were prepared from mouse embryonic kidneys using a cold-active protease cell dissociation protocol (Adam et al. Development 2017). Foxd1+ progenitors and their derivates were subsequently isolated by fluorescence-activated cell sorting (FACS).
E145 scATAC: Single cell suspensions were prepared as for scRNA-seq. Nuclei was subsequently isolated using the protocol from 10x Genomics.
E185 bulk-RNA: RNA was extracted using the RNeasy Mini Kit (Qiagen 74104).
E145 scRNA: Libraries were constructed using the 10x Genomics Chromium 3' Kit version 3.
E185 scRNA: Libraries were constructed using the 10x Genomics Chromium 3' Kit version 3.
E145 scATAC: Libraries were constructed using the 10x Genomics Chromium Single Cell ATAC Kit version 2.
E185 bulk-RNA: libraries were constructed using the Illumina Stranded mRNA-seq Library Prep Kit.

tag: tissue

value: kidney

tag: genotype

value: Foxd1cre +/- mTmG +/- Tcf21 +/+

tag: developmental stage

value: Male

value: Control


title: BBS0500-Z1110044621092619SS


title: 80216

description: Library name: Sample 559

library_source: transcriptomic

data_processing:
Data was processed using nf-core/rnaseq v3.14.0 of the nf-core collection of workflows, utilizing reproducible software environments from the Bioconda and Biocontainers projects. The pipeline was executed with Nextflow v23.10.1. Resulting count data was pre-processed using the edgeR packagein R, which included filtering out lowly-expressed genes using edgeR filterByExpr (min.count = 10) and performing quantile-normalized voom transformation.
Assembly: GRCh38
Supplementary files format and content: txt file includes normalized gene counts for each sample

molecule: polyA RNA

source_name: whole blood

extract_protocol:
Whole blood RNA was extracted from PAXgene blood RNA tubes. Briefly, frozen tubes were thawed at room temperature and centrifuged according to the manufacturer’s protocol. The resulting pellet was then washed with nuclease free water, resuspended in sterile PBS, and split in half. RNA was extracted from one half of the suspension using the QIAsymphony PAXgene Blood RNA Kit (Qiagen). The other half of the suspension was used for DNA extraction. RNA concentration and integrity were assessed using the Ribogreen Assay (Thermo) and a Fragment Analyzer (Agilent), respectively.
Polyadenylated RNA was enriched using NEBNext Magnetic Oligo(dT)25 Beads and prepared into RNA-seq libraries using the NEBNext mRNA Library Prep Reagent Set for Illumina (New England BioLabs, Ipswich, MA, USA). Unique dual-index barcodes were incorporated as specified per manufacturer’s protocol. Library concentration was measured using the Quant-iT PicoGreen dsDNA Reagent (Thermo), and library size distribution and quality were checked using a DNA chip on Caliper Gx Touch (Revity). Library quantification was further refined by qPCR using the KAPA Library Quantificaiton Kit (Roche). Paired-end sequencing (2 x 100 bp, 100 million reads per sample) was carried out on an Illumina NovaSeq 6000 platform (Illumina) following manufacturer’s recommended protocols.

value: whole blood

value: SLE


title: 80215

description: Library name: Sample 558


title: rna_070425macs_M3_wt_2mo

city: St. Louis

first: India

last: Reiss

state: Missouri

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University in St. Louis

description:
Library name: rna_070425macs_M3_wt_2mo
rep4

data_processing:
Calling Cards FASTQ reads were processed with a custom bash pipeline to generate per-sample insertion files for peak calling. Briefly, reads were first adapter-trimmed and demultiplexed by requiring an exact 5′ match to the OM-piggyBac transposon sequence using cutadapt with zero mismatches/indels and discarding untrimmed reads, then SRT barcodes were extracted with umi_tools extract, followed by an additional exact-match trim of the transposon sequence and trimming of trailing Nextera adapters (cutadapt).  Trimmed reads were aligned to the reference genome with Bowtie2 and converted to BAM; mapped reads were retained, then sorted and indexed. Transposon insertion sites were then computed per read by assigning the insertion point to the alignment start (forward reads) or end (reverse reads), correcting for soft clipping, and encoding the genomic interval immediately preceding the insertion. For piggyBac, reads were optionally filtered to those matching the expected “TTAA” insertion motif.  Finally, unique insertions were aggregated into an insertion table (“qbed” file)  by counting identical insertion sites; these insertion files were then used as input for downstream peak calling.
Differential Calling Cards peak sets were generated using a custom pipeline that (i) defines a unified candidate peak set and (ii) classifies those peaks as condition-enriched (CLN3-specific/WT-specific) or shared. For each condition, peaks were called with PyCallingCards using the MACCs (“cctools”) framework with the parameters  pvalue_cutoffbg=0.05, window_size=800, step_size=400, pvalue_cutoffTTAA=0.005, lam_win_size=1,000,000, pseudocounts=0.4. Peaks from the two TF conditions were then concatenated and collapsed into a nonredundant “union” peak set by sorting and merging intervals with bedtools merge using a 1 kb merge distance (-d 1000).  To call differential peaks, we quantified insertions from the two TF qbed files across the union peak set using pycallingcards.pp.make_Anndata, then tested TF_C1 vs TF_C2 per peak with Fisher’s exact test and ranked peaks by multiple-testing–adjusted p-values. Peaks with adjusted p < 0.05 enriched in TF_C1 were designated CLN3-specific peaks, and peaks enriched in TF_C2 were designated WT-specific peaks (written as separate BED files). Finally, “shared” peaks were defined as the remaining union peaks not assigned to either differential class, implemented with bedtools intersect -v against the condition-specific BED files.
Paired-end MNase-seq FASTQ files were aligned to the mm10 reference genome using Bowtie2 v2.3.5. Alignments were performed in paired-end mode with an expected insert-size range of 110-210 bp (-I 110 -X 210), requiring properly paired reads, and reads were trimmed to 40 bp prior to alignment. SAM files were converted to BAM and unmapped reads were removed, followed by coordinate sorting and indexing. To restrict analyses to canonical chromosomes, BAMs were filtered to chr1-chr19, chrX, chrY, name-sorted, and processed with samtools fixmate.  BAMs were then coordinate-sorted and PCR duplicates were removed with samtools markdup -r.
To generate genome-browser tracks, processed replicate BAMs for each condition were supplied to DANPOS3 for differential analysis using the standard danpos.py. DANPOS3 outputs included pooled per-condition WIG tracks (normalized/smoothed signal) and a differential WIG track (Poisson-based difference). Finally, WIG files were converted to bigWig format using the UCSC wigToBigWig utility. This produced bigWig tracks for each condition’s normalized/smoothed MNase signal and for the DANPOS differential signal.
RNA-seq counts tables produced by GTAC.
Assembly: mm10, hg38
Supplementary files format and content: Calling Cards: qBED, BED. Mnase-seq: bigWig. RNA-seq: counts  csv and metadata csv

source_name: astrocytes

growth_protocol: Hepg2 cells were maintained in DMEM+10% FBS, 1x Penstrep in 6 well plates.

extract_protocol:
For MNase-seq, MNase digestion was performed immediately following astrocyte isolation. Cells were fixed for 10 minutes in 1% formaldehyde and the reaction was quenched for 5 minutes with 2.5 M glycine, added to a final concentration of 0.125 M. The cells were then washed twice in 1x PBS. Nuclei were prepared by adding 100 μl of Nuclei Prep Buffer (Zymo EZ Nucleosome DNA Prep Kit, D5220) per 1 million cells. After centrifugation, the cells were resuspended in 1x Takara MNase Digestion Buffer. Chromatin was digested with 4 units of Takara MNase (2910A) per 1,000,000 cells. The reaction was stopped by adding 5x MN stop buffer from the EZ kit. Subsequently, 4.8 μl of 5 M NaCl and 2 μl of proteinase K were added per 1 million cells, and samples were incubated at 65°C overnight. The following day, DNA was isolated using the EZ kit according to the manufacturer’s instructions. For Calling Cards and RNA-seq, total RNA extraction after MACS was done using the Qiagen RNeasy Plus Mini Kit (Cat no. 74134) according to the manufacturer's protocol. All of the total RNA was used for reverse transcription.
For Calling Cards, First-strand cDNA was generated by oligo(dT) priming with the SMART_dT18VN primer and Maxima H Minus reverse transcriptase in the presence of RNase inhibitor, followed by heat inactivation and RNase H treatment to remove the RNA strand, yielding cDNA for downstream library construction. Self-reporting transposon (SRT) transcripts were then PCR-amplified from cDNA using KAPA HiFi HotStart with a reporter specific primer (tdtomato or puromycin) and SMART reverse primers (cycle number minimized/optimized to avoid over-amplification; typical program uses ~20 cycles with 98°C denaturation, 65°C annealing, and long 72°C extension), and amplicons were size-selected/cleaned with a 0.6× AMPure XP bead cleanup and QC’d by Qubit. Purified SRT PCR products were converted into sequencing-ready libraries by Nextera XT tagmentation (ATM + TD buffer at 55°C), neutralization, and an indexing PCR using a barcoded piggyBac (OM-PB) primer together with a Nextera N7 index primer to enable multiplexing, followed by a final 0.6× bead cleanup and fragment distribution QC prior to pooling and Illumina sequencing. A fraction of the samples were checked for sequencing quality using WashU’s DNA Sequencing Innovation Lab (DSIL)’s spike in program with the Illumina MiSeq or Illumina Miniseq. All samples were then submitted to the the Washington University Genome Technology Access Center (GTAC) to be deeply sequenced with the Illumina NovaSeq X Plus. All sequencing data was combined at the end for each sample. MNase-seq libraries were prepared using the NEBNext Ultra end repair and A-tailing module (NEBNext End Prep, E7442), followed by adapter ligation using the NEBNext Ultra Ligation Module with Quick Ligation (E7445). Libraries were purified using Agencourt AMPure XP beads (Beckman Coulter, A63880). Adapter-ligated DNA was PCR-amplified using Phusion High-Fidelity DNA Polymerase with NEB primers (NEB, E6440S), followed by a second cleanup with Agencourt AMPure XP beads. All samples were then submitted to the the Washington University Genome Technology Access Center (GTAC) to be deeply sequenced with the Illumina NovaSeq X Plus. RNA-seq libraries were prepared in-house from total RNA using the NEBNext UltraExpress® RNA Library Prep Kit (New England Biolabs) according to the manufacturer’s instructions. Indexes used from NEBNext Multiplex Oligos for Illumina® (E6440S).  Final libraries were quantified, pooled, and submitted to the Washington University Genome Technology Access Center (GTAC) for sequencing. GTAC performed sequencing on the Illumina NovaSeq X Plus (paired end reads extending 150 bases) and generated gene-level RNA-seq count tables from the resulting sequencing data using their standard RNA-seq processing workflow; these GTAC-provided count tables were used to assemble the final count matrix for downstream analyses.

treatment_protocol: AAV injections were performed as described in (Yen et al. 2023). Viral titers (viral genomes [vg] per milliliter) were ∼1.0 × 10. Neonatal mice (P0-P1) received intracerebroventricular (ICV) injections of Calling Cards AAVs encoding the piggyBac transposase (unfused or BMAL1 fusion) and donor/self-reporting transposon. AAV stocks were mixed 1:1 immediately prior to injection (6 µL total per pup). Pups were anesthetized by hypothermia on ice (5-8 min; ≤15 min maximum) and injected bilaterally using a Hamilton syringe fitted with a depth guard to ensure a consistent 2 mm insertion depth. Virus was delivered at 1 µL per site at three sites per hemisphere (1 µL/s); after each injection, the needle was held in place for 5 s before withdrawal to minimize backflow. Following injection, pups were placed on a low warming pad for recovery (5-10 min) and returned to the home cage with the dam. For HepG2 cells, calling card constructs (with puro as the marker gene) transfected through neon electroporation (2*10^6 cells/well). Puro selection performed with 3ug/mL puro. Puro selection done over 5 days to allow for cells without insertions to die off, a non-transfected well was used to determine that all cells without insertions had died at that point.

tag: cell type

value: astrocytes


title: BBS0050-Z1110042893010821S0


title: BBS0500-Z1110044838100819SS


title: BBS0500-Z1110040592092419SS


title: 80214

description: Library name: Sample 557


title: BBS0500-Z1110039613092719SS


title: 80310

description: Library name: Sample 560


title: rna_070325macs_M2_wt_2mo

description:
Library name: rna_070325macs_M2_wt_2mo
rep3


title: BBS0500-Z1110040247092419SS


title: BBS0500-Z1110044225092619SS


title: rna_070225macs_M1_wt_2mo

description:
Library name: rna_070225macs_M1_wt_2mo
rep2


title: 80207

description: Library name: Sample 555


title: BBS0500-Z1110042619093019SS


title: BBS0500-Z1110040327092319SS


title: 80213

description: Library name: Sample 556


title: BBS0500-Z1110042972092719SS


title: 80204

description: Library name: Sample 554


title: BBS0050-Z1110040206011321S0


title: rna_063025macs_F_wt_2mo

description:
Library name: rna_063025macs_F_wt_2mo
rep1


title: BBS0500-Z1110040194092319SS


title: BBS0500-Z1110040129102119SS


title: BBS0500-Z1110029997032519S7


title: BBS0500-Z1110029963040519S7


title: 80109

description: Library name: Sample 552


title: BBS0500-Z1110042749032519S7


title: rna_070425macs_M3_cln3_2mo

description:
Library name: rna_070425macs_M3_cln3_2mo
rep4

value: CLN3delta7/8 (C57BL/6J background)


title: BBS0500-Z1110040939031919S7


title: BBS0500-Z1110040651032219S7


title: BBS0500-Z1110040164032619S7


title: rna_070225macs_M1_cln3_2mo

description:
Library name: rna_070225macs_M1_cln3_2mo
rep2


title: rna_063025macs_F_cln3_2mo

description:
Library name: rna_063025macs_F_cln3_2mo
rep1


title: 80106

description: Library name: Sample 550


title: 80111

description: Library name: Sample 553


title: rna_070325macs_M2_cln3_2mo

description:
Library name: rna_070325macs_M2_cln3_2mo
rep3


title: BBS0500-Z1110042636031819S7


title: 80104

description: Library name: Sample 549


title: BBS0500-Z1110042565032119S7


title: BBS0500-Z1110040691031919S7


title: 80101

description: Library name: Sample 548


title: rna_061325macs_M3_wt_1mo

description:
Library name: rna_061325macs_M3_wt_1mo
rep3


title: BBS1000-Z1110036411032719S7


title: rna_061225macs_M2_wt_1mo

description:
Library name: rna_061225macs_M2_wt_1mo
rep2


title: 80108

description: Library name: Sample 551


title: BBS0500-Z1110040001032519S7


title: 76902

description: Library name: Sample 547


title: BBS0500-Z1110036393040419S7


title: BBS0500-Z1110040777032819S7


title: 76801

description: Library name: Sample 545


title: mnase_2mo_032825macs_wt_female1

description:
Library name: mnase_ 032825macs_wt_female1
rep2

library_source: genomic

molecule: genomic DNA


title: BBS1000-Z1110039591032619S7


title: rna_060225macs_F_wt_1mo

description:
Library name: rna_060225macs_F_wt_1mo
rep1


title: rna_060225macs_M2_cln3_1mo

description:
Library name: rna_060225macs_M2_cln3_1mo
rep1


title: SP484302B23


title: SP606313B23


title: rna_061325macs_M3_cln3_1mo

description:
Library name: rna_061325macs_M3_cln3_1mo
rep2


title: 76803

description: Library name: Sample 546


title: BBS0500-Z1110039634032819S7


title: SP484306B23


title: BBS0050-Z1110044290030421S0


title: mnase_2mo_020425macs_cln3_female3

description:
Library name: mnase_020425macs_cln3_female3
rep2


title: 76506

description: Library name: Sample 542


title: mnase_2mo_020425macs_wt_female2

description:
Library name: mnase_020425macs_wt_female2
rep1


title: SP337873B23

description: title describes sample ID used in raw data (NPX.csv)


title: 76508

description: Library name: Sample 544


title: SP484298B23


title: SP545976B23


title: SP337762B23


title: 76507

description: Library name: Sample 543


title: SP484300B23


title: SP545974B23


title: SP545972B23


title: mnase_2mo_020425macs_cln3_female2

description:
Library name: mnase_020425macs_cln3_female2
rep1


title: 76501

description: Library name: Sample 541


title: cc_022825macs_wt_unfused_female3

description:
Library name: cc_022825macs_wt_unfused_female3
Calling Cards Lib Prep, rep7

tag: treatment

value: injected w/ unfused cc aav


title: 76419

description: Library name: Sample 540


title: 76417

description: Library name: Sample 539


title: SP577098B23


title: cc_022425macs_wt_unfused_male4

description:
Library name: cc_022425macs_wt_unfused_male4
Calling Cards Lib Prep, rep4


title: SP489257B23

value: M


title: cc_022825macs_wt_unfused_female2

description:
Library name: cc_022825macs_wt_unfused_female2
Calling Cards Lib Prep, rep6


title: SP514853B23


title: cc_022825macs_wt_unfused_female1

description:
Library name: cc_022825macs_wt_unfused_female1
Calling Cards Lib Prep, rep5


title: 76410

description: Library name: Sample 537


title: SP337734B23


title: 76405

description: Library name: Sample 536


title: SP577095B23


title: SP497225B23


title: cc_022425macs_wt_unfused_male2

description:
Library name: cc_022425macs_wt_unfused_male2
Calling Cards Lib Prep, rep2


title: 76415

description: Library name: Sample 538


title: SP436901B23


title: SP337791B23


title: SP337790B23


title: cc_022425macs_wt_unfused_male1

description:
Library name: cc_022425macs_wt_unfused_male1
Calling Cards Lib Prep, rep1


title: SP337828B23


title: 76403

description: Library name: Sample 535


title: cc_122824_wt_bmal1_male3

description:
Library name: cc_122824_wt_bmal1_male3
Calling Cards Lib Prep, rep17, spike_in fastq files sequenced on Illumina MiniSeq

value: injected w/ bmal1 cc aav


title: 76311

description: Library name: Sample 533


title: SP731442B23


title: 76313

description: Library name: Sample 534


title: SP363972B23


title: cc_022425macs_wt_unfused_male3

description:
Library name: cc_022425macs_wt_unfused_male3
Calling Cards Lib Prep, rep3


title: SP550645B23


title: SP521673B23


title: cc_122824_wt_bmal1_male2

description:
Library name: cc_122824_wt_bmal1_male2
Calling Cards Lib Prep, rep16, spike_in fastq files sequenced on Illumina MiniSeq


title: SP089519B23


title: SP738069B23


title: cc_122824_wt_bmal1_female6

description:
Library name: cc_122824_wt_bmal1_female6
Calling Cards Lib Prep, rep14, spike_in fastq files sequenced on Illumina MiniSeq


title: 76308

description: Library name: Sample 532


title: cc_122824_wt_bmal1_male1

description:
Library name: cc_122824_wt_bmal1_male1
Calling Cards Lib Prep, rep15, spike_in fastq files sequenced on Illumina MiniSeq


title: SP738070B23


title: SP956490B22


title: 76204

description: Library name: Sample 530


title: cc_122824_wt_bmal1_female5

description:
Library name: cc_122824_wt_bmal1_female5
Calling Cards Lib Prep, rep13, spike_in fastq files sequenced on Illumina MiniSeq


title: 76305

description: Library name: Sample 531


title: SP653833B23


title: SP218212B23


title: SP028948B23


title: SP218211B23


title: SP422560B23


title: SP749987B23


title: SP220717B23


title: SP719721B23


title: cc_122024_wt_bmal1_female4

description:
Library name: cc_122024_wt_bmal1_female4
Calling Cards Lib Prep, rep12, spike_in fastq files sequenced on Illumina MiniSeq


title: 76111

description: Library name: Sample 527


title: SP783015B23


title: SP643430B23


title: 76106

description: Library name: Sample 524


title: 76107

description: Library name: Sample 525


title: cc_022525_wt_bmal1_male3

description:
Library name: cc_022525_wt_bmal1_male3
Calling Cards Lib Prep, rep3


title: 76203

description: Library name: Sample 529


title: SP653832B23


title: cc_122024_wt_bmal1_female2

description:
Library name: cc_122024_wt_bmal1_female2
Calling Cards Lib Prep, rep10, spike_in fastq files sequenced on Illumina MiniSeq


title: cc_022525_wt_bmal1_male2

description:
Library name: cc_022525_wt_bmal1_male2
Calling Cards Lib Prep, rep2


title: SP581944B23

description: title describes sample ID used in raw data (NPX.csv)


title: cc_022525_wt_bmal1_male1

description:
Library name: cc_022525_wt_bmal1_male1
Calling Cards Lib Prep, rep1


title: cc_122024_wt_bmal1_female3

description:
Library name: cc_122024_wt_bmal1_female3
Calling Cards Lib Prep, rep11, spike_in fastq files sequenced on Illumina MiniSeq


title: cc_122024_wt_bmal1_female1

description:
Library name: cc_122024_wt_bmal1_female1
Calling Cards Lib Prep, rep9, spike_in fastq files sequenced on Illumina MiniSeq


title: 76007

description: Library name: Sample 522


title: SP177639B23


title: 76002

description: Library name: Sample 521


title: 76112

description: Library name: Sample 528


title: 76011

description: Library name: Sample 523


title: SP937067A23


title: SP177638B23


title: SP714598B23


title: SP598243B23


title: SP471163B23


title: cc_032025macs_cln3_unfused_male2

description:
Library name: cc_032025macs_cln3_unfused_male2
Calling Cards Lib Prep, rep5, spike_in fastq files sequenced on Illumina MiSeq


title: SP189204B23


title: SP287430B23


title: 73605

description: Library name: Sample 519


title: SP767722B23


title: cc_032025macs_cln3_unfused_female3

description:
Library name: cc_032025macs_cln3_unfused_female3
Calling Cards Lib Prep, rep3, spike_in fastq files sequenced on Illumina MiSeq


title: cc_032025macs_cln3_unfused_female2

description:
Library name: cc_032025macs_cln3_unfused_female2
Calling Cards Lib Prep, rep2, spike_in fastq files sequenced on Illumina MiSeq


title: 76109

description: Library name: Sample 526


title: SP168223B23


title: 76001

description: Library name: Sample 520


title: SP398924B23


title: 73506

description: Library name: Sample 518


title: SP189351B23


title: cc_032025macs_cln3_unfused_female1

description:
Library name: cc_032025macs_cln3_unfused_female1
Calling Cards Lib Prep, rep1, spike_in fastq files sequenced on Illumina MiSeq


title: cc_112024macs_cln3_bmal1_female3

description:
Library name: cc_112024macs_cln3_bmal1_female3
Calling Cards Lib Prep, rep9, spike_in fastq files sequenced on Illumina MiSeq


title: 73504

description: Library name: Sample 517


title: SP554160B23


title: PP103648A23


title: 73415

description: Library name: Sample 516


title: cc_112024macs_cln3_bmal1_female2

description:
Library name: cc_112024macs_cln3_bmal1_female2
Calling Cards Lib Prep, rep8, spike_in fastq files sequenced on Illumina MiSeq


title: 73413

description: Library name: Sample 515


title: PP128139A22


title: cc_112024macs_cln3_bmal1_female1

description:
Library name: cc_112024macs_cln3_bmal1_female1
Calling Cards Lib Prep, rep7, spike_in fastq files sequenced on Illumina MiSeq


title: 73412

description: Library name: Sample 514


title: PP128140A22


title: PP125034A23


title: PP122925A23


title: cc_110424macs_cln3_bmal1_male1

description:
Library name: cc_110424macs_cln3_bmal1_male1
Calling Cards Lib Prep, rep6, spike_in fastq files sequenced on Illumina MiSeq


title: 73410

description: Library name: Sample 513


title: PP114518A23


title: cc_110424macs_cln3_bmal1_female1

description:
Library name: cc_110424macs_cln3_bmal1_female1
Calling Cards Lib Prep, rep5, spike_in fastq files sequenced on Illumina MiSeq


title: 73401

description: Library name: Sample 511


title: PP126807A22


title: PP114519A23


title: PP126808A22


title: PP105877A23


title: PP110425A23


title: 73409

description: Library name: Sample 512


title: cc_010825macs_cln3_bmal1_male1

description:
Library name: cc_010825macs_cln3_bmal1_male1
Calling Cards Lib Prep, rep3, spike_in fastq files sequenced on Illumina MiSeq


title: 73302

description: Library name: Sample 510


title: cc_010825macs_cln3_bmal1_male2

description:
Library name: cc_010825macs_cln3_bmal1_male2
Calling Cards Lib Prep, rep4, spike_in fastq files sequenced on Illumina MiSeq


title: PP103425A23


title: PP110426A23


title: PP103417A23


title: cc_010825macs_cln3_bmal1_female1

description:
Library name: cc_010825macs_cln3_bmal1_female1
Calling Cards Lib Prep, rep1, spike_in fastq files sequenced on Illumina MiSeq


title: cc_010825macs_cln3_bmal1_female2

description:
Library name: cc_010825macs_cln3_bmal1_female2
Calling Cards Lib Prep, rep2, spike_in fastq files sequenced on Illumina MiSeq


title: cc_032025macs_cln3_unfused_male1

description:
Library name: cc_032025macs_cln3_unfused_male1
Calling Cards Lib Prep, rep4, spike_in fastq files sequenced on Illumina MiSeq


title: 73201

description: Library name: Sample 509


title: PP103698A23

description: title describes sample ID used in raw data (NPX.csv)


title: PP103420A23


title: E14.5_scRNA_Control_Female

description:
Library name: Sample A1
10x Genomics

value: Female


title: 73003

description: Library name: Sample 507


title: SP581943B23


title: PP103694A23


title: 73002

description: Library name: Sample 506


title: 73005

description: Library name: Sample 508


title: PP103696A23


title: PP103693A23


title: PP122924A23


title: PP121681A23


title: old replicate 4

city: La Jolla

first: Kathryn

last: Lande

state: CA

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute

description:
Library name: MM_1084_2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made in cell ranger
Assembly: mm10
Supplementary files format and content: cellranger filtered_feature_bc_matrix output files

molecule: nuclear RNA

source_name: whole liver

extract_protocol:
Nuclei were isolated, cleaned and sorted using a SH800 (Sony) flow cytometer by the Center for Epigenomics at UC San Diego.
Libraries were generated using the Chromium Single-Cell HT 3′ Library Construction Kit v3.1 (10x Genomics, 1000350, 1000351, 1000352) with the Chromium Single-Cell M Chip Kit (10x Genomics, 1000349) and the Chromium i7 Dual Index Kit TT Set A 96 rxns Kit for sample indexing (10x Genomics, 1000215) according to manufacturer specifications.

value: whole liver

tag: age

value: male


title: 71101

description: Library name: Sample 505


title: young replicate 4

description:
Library name: MM_1085_2
10x Genomics


title: EP871473D23


title: EP759351D23


title: PP101787A23


title: PP110045A23


title: young replicate 3

description:
Library name: MM_1083_2
10x Genomics


title: 71014

description: Library name: Sample 504


title: EP310831D23


title: EP759350D23


title: young replicate 2

description:
Library name: MM_1081_2
10x Genomics


title: EP759354D23


title: 71011

description: Library name: Sample 502


title: young replicate 1

description:
Library name: MM_1079_2
10x Genomics


title: 71012

description: Library name: Sample 503


title: EP311554D23


title: old replicate 3

description:
Library name: MM_1082_2
10x Genomics


title: old replicate 2

description:
Library name: MM_1080_2
10x Genomics


title: EP217887E23


title: EP591231E23


title: 71007

description: Library name: Sample 500


title: 71008

description: Library name: Sample 501


title: EP160848F22


title: EP762152D23


title: old replicate 1

description:
Library name: MM_1078_2
10x Genomics


title: EP712878E23


title: EP217888E23


title: 71006

description: Library name: Sample 499


title: 71005

description: Library name: Sample 498


title: EP160849F22


title: Young Sample 5

description: Library name: s9

data_processing:
Alignment to GrCM38/mm10 using BISMARK aligner. Dyads were condensed using scripts published in Cole et al 2017 (doi: 10.1186/s13059-017-1185-3).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes nReads and %methylated reads for each sample at each measured CpG.

source_name: Hepatocytes

extract_protocol:
Zymo quick-DNA miniprep kit (Zymo D3024)
BGI according to SOP-SS-023 version A0 in which bisulfite treatment followed DNA shearing, end repair, A-tail addition and methylated adapter ligation was conducted

value: Hepatocytes

value: WT

value: Young

tag: strain

tag: dob

tag: cull date


title: EP353700E23

value: F


title: Old Sample 5

description: Library name: s10

value: Old


title: EP712879E23


title: EP353701E23


title: Old Sample 4

description: Library name: s8

value: Male


title: 71003

description: Library name: Sample 497


title: EP353696E23


title: Old Sample 3

description: Library name: s6


title: Young Sample 3

description: Library name: s5


title: EP012784E23


title: Young Sample 4

description: Library name: s7


title: EP844052D23


title: EP121421E23


title: 70901

description: Library name: Sample 493


title: 70911

description: Library name: Sample 495


title: 71001

description: Library name: Sample 496


title: Young Sample 2

description: Library name: s4


title: 70904

description: Library name: Sample 494


title: EP311527D23


title: EP844051D23


title: EP880929E31


title: Old Sample 2

description: Library name: s3


title: EP878412D23


title: 70827

description: Library name: Sample 492


title: 70825

description: Library name: Sample 491


title: Old Sample 1

description: Library name: s2


title: Young Sample 1

description: Library name: s1


title: SP032456B23


title: EP311449D23


title: SP603146B23


title: SP603150B23


title: 70822

description: Library name: Sample 490


title: A74_Young_Ccnd1

description:
Library name: A74
Column name in batch2_raw_counts.txt: ./A74 (20167878.0 total)

data_processing:
Alignment to GrCM38/mm10 using STAR aligner, tag counting using HOMER.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

extract_protocol:
RNA extracted using Trizol-chloroform methodology.
NEB polyA mRNA library prep kits.

value: old

tag: date of_birth

tag: date of_cull


title: SP603145B23


title: 70821

description: Library name: Sample 489

value: whole blood


title: A73_Young_Ccnd1

description:
Library name: A73
Column name in batch2_raw_counts.txt: ./A73 (25818869.0 total)


title: SP603149B23

value: SLE


title: SP603144B23


title: 70815

description: Library name: Sample 488


title: SP527184B23


title: A72_Old_Ccnd1

description:
Library name: A72
Column name in batch2_raw_counts.txt: ./A72 (19506737.0 total)


title: SP584312B23


title: SP603142B23


title: 70811

description: Library name: Sample 486


title: EP353705E23


title: A70_Young_Ccnd1

description:
Library name: A70
Column name in batch2_raw_counts.txt: ./A70 (20792933.0 total)

value: young


title: SP584314B23


title: 70814

description: Library name: Sample 487


title: SP526837B23


title: SP584310B23


title: A71_Young_mApple

description:
Library name: A71
Column name in batch2_raw_counts.txt: ./A71 (20244198.0 total)

value: mApple-AAV


title: 70810

description: Library name: Sample 485


title: SP584307B23


title: A69_Young_mApple

description:
Library name: A69
Column name in batch2_raw_counts.txt: ./A69 (20593578.0 total)


title: A68_Young_mApple

description:
Library name: A68
Column name in batch2_raw_counts.txt: ./A68 (20061179.0 total)


title: SP584306B23


title: SP578926B23


title: 70808

description: Library name: Sample 483


title: EP613193D23


title: 70809

description: Library name: Sample 484


title: SP578925B23


title: SP392294B23


title: SP496787B23


title: A67_Old_Ccnd1

description:
Library name: A67
Column name in batch2_raw_counts.txt: ./A67 (22020701.0 total)


title: SP496788B23


title: BBS0050-Z1110040856011221S0

value: healthy controls


title: SP301653B23


title: SP301654B23


title: 70711

description: Library name: Sample 480


title: A66_Old_Ccnd1

description:
Library name: A66
Column name in batch2_raw_counts.txt: ./A66 (21364656.0 total)


title: 70802

description: Library name: Sample 481


title: EP311555D23


title: SP363384B23


title: A65_Old_mApple

description:
Library name: A65
Column name in batch2_raw_counts.txt: ./A65 (22217700.0 total)


title: EP613192D23


title: SP363382B23


title: 70708

description: Library name: Sample 479


title: A64_Old_mApple

description:
Library name: A64
Column name in batch2_raw_counts.txt: ./A64 (19428030.0 total)


title: SP592322B23


title: 70806

description: Library name: Sample 482


title: SP345130B23


title: SP449191B23


title: SP643431B23


title: SP592323B23


title: 70705

description: Library name: Sample 478


title: A62_Young_Ccnd1

description:
Library name: A62
Column name in batch2_raw_counts.txt: ./A62 (20113807.0 total)


title: SP282521B23


title: SP282520B23


title: A63_Young_Ccnd1

description:
Library name: A63
Column name in batch2_raw_counts.txt: ./A63 (21732323.0 total)


title: SP406437B23


title: A60_Young_mApple

description:
Library name: A60
Column name in batch2_raw_counts.txt: ./A60 (18606584.0 total)


title: 70610

description: Library name: Sample 476


title: SP479462B23


title: A59_Old_Ccnd1

description:
Library name: A59
Column name in batch2_raw_counts.txt: ./A59 (19552571.0 total)


title: A61_Young_mApple

description:
Library name: A61
Column name in batch2_raw_counts.txt: ./A61 (22274919.0 total)


title: 70608

description: Library name: Sample 475


title: SP510313B23

description: title describes sample ID used in raw data (NPX.csv)


title: 70702

description: Library name: Sample 477


title: SP633437B23


title: SP510312B23


title: SP592960B21


title: 70605

description: Library name: Sample 474


title: A58_Old_Ccnd1

description:
Library name: A58
Column name in batch2_raw_counts.txt: ./A58 (20100013.0 total)


title: SP263198B23


title: A57_Old_mApple

description:
Library name: A57
Column name in batch2_raw_counts.txt: ./A57 (19275551.0 total)


title: SP263199B23


title: SP741971B23

value: M


title: SP397480B23


title: 70603

description: Library name: Sample 472


title: 70604

description: Library name: Sample 473


title: 70502

description: Library name: Sample 471


title: SP741980B23


title: A56_Old_mApple

description:
Library name: A56
Column name in batch2_raw_counts.txt: ./A56 (19799881.0 total)


title: 70501

description: Library name: Sample 470


title: SP606706B23


title: SP741984B23


title: SP606709B23


title: A54_anti-IFN

description:
Library name: A54
Column  name  in  raw_counts.txt:  A54  (21650436.0  total)

extract_protocol:
trizol-chloroform extraction methodology
mRNA library preparation (poly A enrichment) with NovaSeq PE150.

value: anti-IFN


title: SP606700B23


title: A55_anti-IFN

description:
Library name: A55
Column  name  in  raw_counts.txt:  A55  (22841625.0  total)


title: 70413

description: Library name: Sample 469


title: 70406

description: Library name: Sample 468


title: SP397481B23


title: SP741982B23


title: A52_IgG

description:
Library name: A52
Column  name  in  raw_counts.txt:  A52  (18030224.0  total)

value: IgG


title: SP397479B23


title: 70404

description: Library name: Sample 467


title: 70208

description: Library name: Sample 466


title: SP555807B23


title: SP555804B23


title: SP397484B23


title: A51_anti-IFN

description:
Library name: A51
Column  name  in  raw_counts.txt:  A51  (21476837.0  total)

value: whole liver


title: SP397476B23


title: 70204

description: Library name: Sample 465


title: SP572786B23


title: A49_anti-IFN

description:
Library name: A49
Column  name  in  raw_counts.txt:  A49  (28379266.0  total)

value: male


title: SP555803B23


title: A50_IgG

description:
Library name: A50
Column  name  in  raw_counts.txt:  A50  (21214236.0  total)


title: 70202

description: Library name: Sample 464


title: SP397477B23


title: SP572783B23


title: SP572785B23


title: SP469613B23


title: SP572784B23


title: SP469616B23


title: 70118

description: Library name: Sample 462


title: SP451917B23


title: A48_anti-IFN

description:
Library name: A48
Column  name  in  raw_counts.txt:  A48  (26968548.0  total)


title: 70201

description: Library name: Sample 463


title: A46_IgG

description:
Library name: A46
Column  name  in  raw_counts.txt:  A46  (21127496.0  total)


title: A47_IgG

description:
Library name: A47
Column  name  in  raw_counts.txt:  A47  (31656900.0  total)


title: SP544277B23


title: SP394982B23


title: SP544276B23


title: 70110

description: Library name: Sample 460


title: 70107

description: Library name: Sample 459


title: 70111

description: Library name: Sample 461


title: WT 2

first: Debashis

last: Sahoo

state: California

address: 9500 Gillman Drive

department: Pediatrics

institute: UCSD

description:
Library name: W2_S2
W2_S2

data_processing:
RNA-seq data was processed using kallisto (version 0.45.0) using Ensembl GRCm38 annotation version 94 mouse genome. Gene-expression levels were quantified by computing Transcripts per Million (TPM) values. Computation of gene-level TPM values and retriveal of gene annotations were performed using a custom PYTHON script. Finally, gene-expression levels were reported either as log2(TPM).
Assembly: Genome assembly: Mus_musculus.GRCm38.rna.fa Ensembl version 94
Supplementary files format and content: Tab-delimited text files report expression levels for each gene in each sample. Gene-expression levels are reported either as log2(TPM) values

source_name: left ventricle

growth_protocol: Left ventricle region of heart was collected from Wildtype, CST-knockout and CST-konockout supplemented with CST mice (strain: C57BL/6J; source: The Jackson Laboratory, stock #000664).

extract_protocol:
RNA was extracted using the Qiagen RNAeasy kit.
RNA seq libraries were prepared using KAPA mRNAHyperprep kit for Illumina platforms.

treatment_protocol: Left ventricles of heart were flash frozen immediately after collection total RNA was extracted using Qiagen RNAeasy kit and DNAseI treatement.

value: left ventricle

value: left ventricle cell

value: C57BL/6J - The Jackson Laboratory [stock #000664]

value: SAL


title: WT 3

description:
Library name: W3_S3
W3_S3


title: A53_IgG

description:
Library name: A53
Column  name  in  raw_counts.txt:  A53  (21264861.0  total)

value: Old


title: AP928769D23

value: F


title: SP333628B23


title: 70103

description: Library name: Sample 458


title: 70102

description: Library name: Sample 457


title: SP333626B23


title: AP754127D23


title: AP667942D23


title: CST-KO+CST 3

description:
Library name: CC4_S18
CC4_S18

value: CST-KO

value: CST


title: AP962231D24

value: SLE


title: CST-KO+CST 4

description:
Library name: CC5_S19
CC5_S19


title: AP766115D23


title: AP908831D23


title: AP766116D23


title: AP908837D23


title: 66311

description: Library name: Sample 456

value: whole blood


title: WT 1

description:
Library name: W1_S1
W1_S1


title: AP766111D23


title: AP289451D23


title: CST-KO 3

description:
Library name: C3_S12
C3_S12


title: AP764630D23


title: CST-KO 2

description:
Library name: C2_S11
C2_S11


title: AP292800E22


title: 65904

description: Library name: Sample 452


title: 66310

description: Library name: Sample 455


title: CST-KO+CST 2

description:
Library name: CC2_S16
CC2_S16


title: 66309

description: Library name: Sample 454


title: CST-KO+CST 1

description:
Library name: CC1_S15
CC1_S15


title: AP289608D23


title: AP908833D23


title: AP289452D23


title: 66202

description: Library name: Sample 453


title: AP595557D23


title: UTX_CUT&Tag_UTX_CD8+ Progenitor_3

city: Los Angeles

first: Ho Chung

last: Chen

address: 609 Charles E Young Dr E

department: MIMG

institute: University of California, Los Angeles

description: Library name: Sample 6

data_processing:
The sequencing quality of the libraries was assessed by FastQC, followed by the trimming process using CutAdapt.
Bowtie2 was used to align the sequencing reads to the mm10 mouse genome
SAMtools was used to convert SAM files into BAM files and sort BAM files.
Picard MarkDuplicates was used to remove duplicate reads in the BAM files.
MACS2 was used for ATAC-seq peak calling (paired-end mode, FDR<0.01).
Assembly: mm10
Supplementary files format and content: The processed data are the differential peak between WT and UTX-deficient progenitor generated by Diffbind package
Library strategy: CUT&Tag

source_name: pancreatic lymph node

extract_protocol:
Sorted cells were performed Epicypher CUT&Tag protocol
After sorting, nuclei were isolated with cold nuclear extraction buffer and incubated with activated concanavalin A-coated magnetic beads (Polysciences, 86057-3) in PCR strip tubes at room temperature for 10 min. A 1:100 dilution of primary antibody (anti-UTX Cell Signaling Rabbit monoclonal antibody no. 33510 or IgG isotype control: Cell Signaling Technology, 3900S) in antibody buffer was added and nuclei were incubated with primary antibodies overnight at 4°C. The next day, the strip tubes were incubated on a magnetic tube holder and supernatants were discarded. Secondary antibody (guinea pig anti-rabbit IgG; Fisher Scientific, NBP172763) was added diluted at 1:100 in Dig-Wash and nuclei were incubated for 1 h at room temperature. Nuclei were washed four times in Dig-Wash and then incubated with a 1:20 dilution of pAG–Tn5 adaptor complex (EpiCypher) in Dig-300 buffer for 1h at room temperature. To stop tagmentation, 25 μl Dig-300 buffer with 10 μl 1M MgCl, 7.5μl 0.5M EDTA, 2.5μl 10% SDS and 5μl 10mg ml−1 proteinase K was added to each reaction and incubated at 55°C for 1h. DNA was extracted by phenol:chloroform:isoamyl alcohol separation. DNA was barcoded and amplified using the following conditions: a PCR mix of 25μl NEBNext 2× mix, 2μl each of barcoded forward and reverse 10μM primers, and 21μl of extracted DNA was amplified at: 58°C for 5min, 72°C for 5min, 98°C for 4 s, 16× 98°C for 15s followed by 63°C for 10s, 72°C for 1min. Amplified DNA libraries were purified by adding a 1.3× volume of KAPA pure SPRI beads (Roche) to each sample and incubating for 10min at 23°C. Samples were placed on a magnet and unbound liquid was removed. Beads were rinsed twice with 80% ethanol, and DNA was eluted with 25 μl TE buffer. All individually i7-barcoded libraries were mixed at equimolar proportions for sequencing on an Illumina Novaseq X Plus sequencer with 50bp pair-end sequencing.

value: pancreatic lymph node

value: CD8+ T cells


title: AP514404D23


title: 65903

description: Library name: Sample 451


title: 65901

description: Library name: Sample 450


title: CST-KO 1

description:
Library name: C1_S10
C1_S10


title: AP514402D23


title: AP041265E23


title: 65732

description: Library name: Sample 448


title: UTX_CUT&Tag_UTX_CD8+ Progenitor_1

description: Library name: Sample 4


title: AP514401D23


title: AP765828D23


title: UTX_CUT&Tag_UTX_CD8+ Progenitor_2

description: Library name: Sample 5


title: AP289610D14


title: AP514400D23


title: 65804

description: Library name: Sample 449


title: AP514405D23


title: AP852330D23


title: UTX_CUT&Tag_WT_CD8+ Progenitor_3

description: Library name: Sample 3

value: WT


title: AP978015D23


title: 65724

description: Library name: Sample 445


title: UTX_CUT&Tag_WT_CD8+ Progenitor_2

description: Library name: Sample 2


title: 65729

description: Library name: Sample 447


title: 65725

description: Library name: Sample 446


title: AP289669D24


title: 65723

description: Library name: Sample 444


title: AP577444D23


title: AP765824D24


title: AP780423D23


title: AP946115D23


title: UTX_CUT&Tag_WT_CD8+ Progenitor_1

description: Library name: Sample 1


title: 65718

description: Library name: Sample 443


title: AP851163D23


title: 65716

description: Library name: Sample 442


title: AP533727D23


title: 65715

description: Library name: Sample 441


title: AP851167D23


title: AP147680D23

value: M


title: 65713

description: Library name: Sample 440


title: AP922152C23


title: AP245895D23


title: 12106-YS-0018,32.5 µg/g NaIO3

city: Nashville

first: Shristi

last: Shrestha

address: 2213 Garland Ave

institute: Vanderbilt University

description: Library name: 12106-YS-0018

data_processing:
RNA sequencing reads were adapter-trimmed and quality-filtered using Trimgalore v0.6.7 (Krueger et al., 2023).
An alignment reference was generated from the mm39 mouse genome and GENCODE comprehensive gene annotations (vM31), to which trimmed reads were aligned and counted using Spliced Transcripts Alignment to a Reference (STAR) v2.7.9a (Dobin et al., 2013) with the –quantMode GeneCounts parameter.
About 69-79 million reads were acquired per sample. DESeq2 package v1.36.0 (Love et al. 2014) was used to perform sample-level quality control, low count filtering, normalization and downstream differential gene expression analysis.
Assembly: mm39
Supplementary files format and content: tab-delimited text file containing raw counts for each sample
Supplementary files format and content: tab-delimited text file containing normalized counts for each sample

source_name: Retinal pigment epithelium

growth_protocol: Young adult mice at 10-11 weeks (both sexes) harboring an inducible Yap overexpression allele (PMID 28943241) (background: C57bl/6J, Swiss Webster) received tamoxifen inducton of RPE-specific Cre (RRID:IMSR_JAX:035973).

extract_protocol:
7 days after SI/saline injection, RPE was collected by removing the retina and incubating posterial eyecup in RNAprotect solution (QIAGEN). RNA was extracted using RNeasy Plus Micro Kit (QIAGEN).
A Quality Control analysis was performed on the RNA samples using the Agilent Bioanalyzer to assess quality and an RNA Qubit assay was used to determine quantity.  Library preparation was completed using the NEBNext® rRNA Depletion kit and protocol (P/N: E7850X, NEB, Ipswich, MA) per manufacturer recommendations (RNA inputs ranging from 74ng-250ng). The kit employs an RNaseH-based method to deplete both cytoplasmic and mitochondrial rRNA. After ribosomal depletion, the RNA samples underwent mRNA enrichment using oligo(dT) beads, followed by thermal fragmentation using divalent cations under elevated temperature.  First-strand cDNA synthesis was performed using random hexamer primers, while second-strand cDNA synthesis was carried out using DNA Polymerase I and RNase H. End repair, A-tailing, and adapter ligation was performed to generate the final cDNA library. The library quality was assessed using a Bioanalyzer and quantified using a qPCR-based method with the KAPA Library Quantification Kit (P/N: KK4873) and the QuantStudio 12K instrument. Prepared library pools are pooled in equimolar ratios based on the qPCR results, and the resulting pool is subjected to cluster generation using the NovaSeq X Plus System, following the manufacturer's protocols. 150 bp paired-end sequencing is performed on the NovaSeq X Plus platform targeting 70M reads per sample.  Raw sequencing data (FASTQ files) obtained from the NovaSeq X Plus is subjected to quality control analysis, including read quality assessment. Real Time Analysis Software (RTA) and NovaSeq Control Software (NCS) (1.8.0; Illumina) is used for base calling. MultiQC (v1.8; Illumina) is used for data quality assessments.

treatment_protocol: Mice were injected intraperitoneally with 32.5 ug/g sodium iodate or saline.

value: Retinal pigment epithelium

value: no Yap overexpression

value: 32.5 µg/g NaIO3

tag: sample group

value: Injury-WT


title: 12106-YS-0019,32.5 µg/g NaIO3

description: Library name: 12106-YS-0019


title: 12106-YS-0020,32.5 µg/g NaIO3

description: Library name: 12106-YS-0020

value: Yap overexpression

value: Injury-Yap


title: 12106-YS-0016,32.5 µg/g NaIO3

description: Library name: 12106-YS-0016


title: AP245897D23


title: 12106-YS-0021,32.5 µg/g NaIO3

description: Library name: 12106-YS-0021


title: 12106-YS-0017,32.5 µg/g NaIO3

description: Library name: 12106-YS-0017


title: 65705

description: Library name: Sample 438


title: AP921101C23


title: 65706

description: Library name: Sample 439


title: AP764629D23


title: 65704

description: Library name: Sample 437


title: AP289668D24


title: 12106-YS-0015,32.5 µg/g NaIO3

description: Library name: 12106-YS-0015


title: LP562333A23


title: AP780419D23


title: LP502218A24


title: LP539008A24


title: 12106-YS-0012,32.5 µg/g NaIO3

description: Library name: 12106-YS-0012


title: 12106-YS-0014,32.5 µg/g NaIO3

description: Library name: 12106-YS-0014


title: 65702

description: Library name: Sample 436


title: 12106-YS-0013,32.5 µg/g NaIO3

description: Library name: 12106-YS-0013


title: LP539011A24


title: LP539010A24


title: 65601

description: Library name: Sample 434


title: LP494297A24


title: LP502217A24


title: 65701

description: Library name: Sample 435


title: LP494296A24


title: LP467222A23


title: LP502215A24


title: 65512

description: Library name: Sample 433


title: 12106-YS-0011,32.5 µg/g NaIO3

description: Library name: 12106-YS-0011


title: 12106-YS-0009,Saline

description: Library name: 12106-YS-0009

value: Saline

value: Sham-Yap


title: LP592986A23

value: F


title: 12106-YS-0010,Saline

description: Library name: 12106-YS-0010

value: Sham-WT


title: 65509

description: Library name: Sample 432


title: 12106-YS-0008,Saline

description: Library name: 12106-YS-0008


title: LP534021A23


title: LP477894A23


title: LP467220A23


title: 65506

description: Library name: Sample 430


title: 65507

description: Library name: Sample 431


title: 12106-YS-0007,Saline

description: Library name: 12106-YS-0007


title: LP498371A23


title: LP423724A24


title: CST-KO 4

description:
Library name: C5_S14
C5_S14

value: left ventricle

value: left ventricle cell

value: CST-KO

value: SAL


title: LP431923A23

value: SLE


title: LP401111A23


title: 12106-YS-0006,Saline

description: Library name: 12106-YS-0006


title: 65504

description: Library name: Sample 429

value: whole blood


title: LP401110A23


title: 65503

description: Library name: Sample 428


title: LP401108A23


title: 12106-YS-0005,Saline

description: Library name: 12106-YS-0005


title: LP401113A23


title: LP370565A23


title: 12106-YS-0004,Saline

description: Library name: 12106-YS-0004


title: LP323439A24


title: LP370567A23


title: LP575667A23


title: 12106-YS-0003,Saline

description: Library name: 12106-YS-0003


title: 65305

description: Library name: Sample 426


title: 65308

description: Library name: Sample 427


title: LP481621A24


title: LP550636A23


title: LP342035A23


title: 64804

description: Library name: Sample 423


title: LP436434A23


title: 65007

description: Library name: Sample 425


title: 12106-YS-0002,Saline

description: Library name: 12106-YS-0002


title: LP432277A23


title: LP436433A23


title: 64802

description: Library name: Sample 422


title: 65002

description: Library name: Sample 424


title: LP533720A23


title: 12106-YS-0001,Saline

description: Library name: 12106-YS-0001


title: LP436435A23


title: 64704

description: Library name: Sample 421


title: LP420325A23


title: LP580205A23


title: 64701

description: Library name: Sample 420


title: LP385055A24


title: 64502

description: Library name: Sample 419


title: LP385057A24


title: LP323311A24


title: 64303

description: Library name: Sample 417


title: LP359558A23


title: LP513917A23


title: LP568709A23


title: 64304

description: Library name: Sample 418


title: 64207

description: Library name: Sample 415


title: LP407584A23

value: M


title: 64208

description: Library name: Sample 416


title: LP483010A24


title: EP999846E22


title: LP407582A23


title: 64101

description: Library name: Sample 413


title: LP407583A23


title: LP323359A23


title: UC_1201 Clinical diagnosis sample study ID#_serum

city: Boston

first: Simon

middle: T

last: Dillon

state: Massachusetts

address: 99 Brookline Ave, Research North Bldg, Room 107

department: IMBIO

institute: BIDMC RESEARCH

hyb_protocol: Hybridized overnight (19 hours) at 55 C as recommended by SomaLogic.

scan_protocol: SOMAmer matching probes printed onto Agilent slides.  After overnight hybridization slides were scanned on an Agilent Microarray SureScan Scanner model D.

data_processing: Standard data processing method as per SomaLogic recommended methods.  Normalized and calibrated using kit control samples.

label: Cy3 labelled SOMAmer

source_name: patient serum_pediatric

label_protocol: Samples run in the manual version of the 1.3k SomaScan assay protocol.

extract_protocol: Human serum was collected at time of in hospital physician visit.

treatment_protocol: Serum samples obtained from 12 pediatric patients with CD, 11 pediatric patients with UC, and 24 non-IBD controls.

value: serum drawn from patient


title: UC_1202 Clinical diagnosis sample study ID#_serum


title: UC_1288 Clinical diagnosis sample study ID#_serum


title: UC_1124 Clinical diagnosis sample study ID#_serum


title: UC_1334 Clinical diagnosis sample study ID#_serum


title: UC_0783 Clinical diagnosis sample study ID#_serum


title: UC_0481 Clinical diagnosis sample study ID#_serum


title: EP632510E23


title: LP323358A23


title: UC_1169 Clinical diagnosis sample study ID#_serum


title: UC_1178 Clinical diagnosis sample study ID#_serum


title: UC_0679 Clinical diagnosis sample study ID#_serum


title: EP941435E22


title: UC_0315 Clinical diagnosis sample study ID#_serum


title: EP004906F22


title: EP500615E23


title: 64016

description: Library name: Sample 412


title: EP632509E23


title: EP136731F22


title: EP500616E23


title: 64015

description: Library name: Sample 411


title: EP089009F22


title: EP089011F22


title: EP733327E23


title: CD_1174 Clinical diagnosis sample study ID#_serum


title: EP733326E23


title: 64013

description: Library name: Sample 410


title: EP733325E23


title: 64011

description: Library name: Sample 409


title: 64010

description: Library name: Sample 408


title: CD_1168 Clinical diagnosis sample study ID#_serum


title: 62704

description: Library name: Sample 407


title: EP241838E23


title: 62703

description: Library name: Sample 406


title: EP241830E23


title: CD_0385 Clinical diagnosis sample study ID#_serum


title: CD_0458 Clinical diagnosis sample study ID#_serum


title: EP241839E23


title: 62406

description: Library name: Sample 405


title: EP089012F22


title: EP241832E23


title: CD_0464 Clinical diagnosis sample study ID#_serum


title: CD_0304 Clinical diagnosis sample study ID#_serum


title: CD_0371 Clinical diagnosis sample study ID#_serum


title: EP241836E23


title: CD_0274 Clinical diagnosis sample study ID#_serum


title: 62403

description: Library name: Sample 404


title: EP241837E23


title: EP468904D23


title: 62401

description: Library name: Sample 403


title: EP468905D23


title: EP472475D23


title: CD_0005 Clinical diagnosis sample study ID#_serum


title: 62210

description: Library name: Sample 399


title: EP993439E22


title: EP084078F22


title: EP472586D23


title: EP084084F22


title: 62301

description: Library name: Sample 402


title: CD_0047 Clinical diagnosis sample study ID#_serum


title: 62216

description: Library name: Sample 401


title: EP084085F22


title: 62211

description: Library name: Sample 400


title: EP112970E23


title: CD_0003 Clinical diagnosis sample study ID#_serum


title: EP734628E23


title: CD_0327 Clinical diagnosis sample study ID#_serum


title: EP021565E23


title: non-IBD_1017 Clinical diagnosis sample study ID#_serum


title: EP543125E23


title: 62209

description: Library name: Sample 398


title: 62205

description: Library name: Sample 397


title: EP543122E23


title: EP956579E22


title: non-IBD_0775 Clinical diagnosis sample study ID#_serum


title: non-IBD_0943 Clinical diagnosis sample study ID#_serum


title: EP288996F22


title: 62204

description: Library name: Sample 396


title: LP323309A23


title: non-IBD_0654 Clinical diagnosis sample study ID#_serum


title: EP548464E23


title: 62011

description: Library name: Sample 393


title: EP528687D23


title: EP252816E23


title: EP232250E23


title: 62203

description: Library name: Sample 395


title: EP256749D23


title: EP253201D23


title: EP748810D23


title: EP232251E23


title: 62010

description: Library name: Sample 392


title: 62009

description: Library name: Sample 391


title: non-IBD_0584 Clinical diagnosis sample study ID#_serum


title: 62007

description: Library name: Sample 389


title: 62202

description: Library name: Sample 394


title: EP108401E23


title: EP439942D23


title: non-IBD_0465 Clinical diagnosis sample study ID#_serum


title: EP239913E23


title: EP037356F22


title: non-IBD_0408 Clinical diagnosis sample study ID#_serum


title: non-IBD_0547 Clinical diagnosis sample study ID#_serum


title: EP834117E22


title: 62008

description: Library name: Sample 390


title: 62004

description: Library name: Sample 387


title: EP277410D23


title: EP037358F22


title: EP239912E23


title: non-IBD_0120 Clinical diagnosis sample study ID#_serum


title: EP238973D23


title: 62005

description: Library name: Sample 388


title: EP999192D23


title: EP239914E23


title: 62003

description: Library name: Sample 386


title: EP277411D23


title: non-IBD_0360 Clinical diagnosis sample study ID#_serum


title: EP724570E24


title: non-IBD_1383 Clinical diagnosis sample study ID#_serum


title: non-IBD_0104 Clinical diagnosis sample study ID#_serum


title: non-IBD_1369 Clinical diagnosis sample study ID#_serum


title: non-IBD_0007 Clinical diagnosis sample study ID#_serum


title: EP229416D23


title: 62001

description: Library name: Sample 385


title: non-IBD_1228 Clinical diagnosis sample study ID#_serum


title: EP320125D23


title: EP206620D23


title: EP320127D23


title: 61501

description: Library name: Sample 384


title: EP206619D23


title: non-IBD_1210 Clinical diagnosis sample study ID#_serum


title: EP046865F22


title: non-IBD_0962 Clinical diagnosis sample study ID#_serum


title: EP750437D23


title: 61401

description: Library name: Sample 383


title: 61304

description: Library name: Sample 382


title: non-IBD_0954 Clinical diagnosis sample study ID#_serum


title: EP320126D23


title: 61105

description: Library name: Sample 381


title: EP844308E22


title: EP660131E23


title: EP548387E23


title: non-IBD_1087 Clinical diagnosis sample study ID#_serum


title: EP844315E23


title: EP529719D23


title: 61003

description: Library name: Sample 380


title: EP165097F23


title: EP529721D23


title: 60702

description: Library name: Sample 379


title: EP263819F31


title: non-IBD_0947 Clinical diagnosis sample study ID#_serum


title: EP228347D23


title: 60506

description: Library name: Sample 378


title: non-IBD_0950 Clinical diagnosis sample study ID#_serum


title: 60503

description: Library name: Sample 377


title: 60301

description: Library name: Sample 376


title: EP099436F22


title: EP529720D23


title: non-IBD_0907 Clinical diagnosis sample study ID#_serum


title: EP976726D23


title: non-IBD_0854 Clinical diagnosis sample study ID#_serum


title: 60101

description: Library name: Sample 375


title: EP147316F22


title: EP891148D23


title: EP794734D23


title: EP713546E23


title: EP367136D23


title: 55611

description: Library name: Sample 374


title: non-IBD_0799 Clinical diagnosis sample study ID#_serum


title: VW17c, McA-RH7777, 83-2-27, NITD008, 3 dpi

city: Bochum

first: Eike

last: Steinmann

address: Universitätsstraße 150

department: Molecular and Medical Virology

country: Germany

institute: Ruhr University

description:
Library name: Sample 9
VW6_S13

data_processing:
Raw FASTQ sequencing reads were assessed for quality using FastQC (version 0.12.1; Andrews, 2010; FastQC: a quality control tool for high-throughput sequence data, available at http://www.bioinformatics.babraham.ac.uk/projects/fastqc), followed by quality trimming using Trimmomatic. Low-quality bases and overrepresented sequences were removed. The trimmed reads were mapped to the brown rat (Rattus norvegicus) reference genome (mRatBN7.2; GCF_015227675.2) obtained from National Center for Biotechnology Information (NCBI. Mapping was performed using STAR version 2.7.11b 58. Optical duplicates were removed using Picard (Picard Toolkit, 2019; Broad Institute, GitHub Repository: https://broadinstitute.github.io/picard/). Gene level read counts were generated using FeatureCounts version 2.0.6 59, and the number of reads mapped to each gene in the reference genome was determined.
Unmapped reads from STAR were aligned to viral genomes using Burrows–Wheeler Aligner (BWA) version 0.7.18. These reads were mapped to the HEV strain Kernow-C1 (GenBank accession no.: HQ709170.1) and strain 83-2-27 (GenBank accession no.: AB740232.1). Alignment files were sorted and indexed, and coverage was calculated using Samtools version 1.21. Viral coverage plots were visualized in R using ggplot2.
Assembly: mRatBN7.2; GCF_015227675.2; HQ709170.1; AB740232.1
Supplementary files format and content: count_data.csv; raw count data

organism: Rattus norvegicus

extract_protocol:
RNA extraction was done using the NucleoSpin RNA kit (Macherey-Nagel)
The RNA sequencing of primary rat hepatocytes was done on the Illumina NovaSeq X Plus platform using the commercial service of Novogene (poly-A enrichment, paired-end 150 base pair reads mode, 20 million reads/sample). For cell line-derived samples, the NEBNext UltraExpress RNA Library Prep Kit (New England Biolabs) and the recommended related reagents were applied for library preparation according to the manufacturer´s instructions. The library was sequenced with P2 reagents (Illumina) on the Illumina NextSeq 1000 sequencing platform.

treatment_protocol: NITD008 (MedChemExpress) 0.5 μM; Baricitinib (MedChemExpress) 2 µM; 100 µl inoculum

tag: cell line

value: hepatoma

value: HEV-3 (83-2-27) infected, NITD008 treated

tag: batch


title: McA-RH7777, p66

description:
Library name: Sample 11
21_MCARH7777p66_S21

value: no treatment

value: passage 66


title: VW17c, McA-RH7777, 83-2-27, Baricitinib, 3 dpi

description:
Library name: Sample 10
VW7_S14

value: HEV-3 (83-2-27) infected, Baricitinib treated


title: EP226565D23


title: 55602

description: Library name: Sample 373


title: AP886597D23


title: VW17c, McA-RH7777, Kernow-C1/p6, Baricitinib, 3 dpi

description:
Library name: Sample 7
VW4_S11

value: HEV-3 (Kernow-C1/p6) infected, Baricitinib treated


title: VW17c, McA-RH7777, 83-2-27, DMSO, 3 dpi

description:
Library name: Sample 8
VW5_S12

value: HEV-3 (83-2-27) infected, DMSO treated


title: AP761510D23

value: F


title: AP811038D24


title: AP886596D23


title: AP710425D23


title: 55601

description: Library name: Sample 372


title: AP045823E23


title: AP540027E22


title: 55505

description: Library name: Sample 371


title: 55502

description: Library name: Sample 370


title: VW17c, McA-RH7777, Kernow-C1/p6, NITD008, 3 dpi

description:
Library name: Sample 6
VW3_S10

value: HEV-3 (Kernow-C1/p6) infected, NITD008 treated


title: 55301

description: Library name: Sample 368


title: VW17c, McA-RH7777,  Mock, DMSO, 3 dpi

description:
Library name: Sample 4
VW1_S8

value: DMSO treated


title: VW17c, McA-RH7777, Kernow-C1/p6, DMSO, 3 dpi

description:
Library name: Sample 5
VW2_S9

value: HEV-3 (Kernow-C1/p6) infected, DMSO treated


title: AP798355D23


title: AP771404D23


title: AP434516E22


title: AP973662D23


title: 55104

description: Library name: Sample 367


title: AP675638D24


title: 55103

description: Library name: Sample 366


title: AP017244E23


title: Run7_Stat1KO_Myc_Young

type: RNA

description: slide 7, segmentation generated in cellpose using DAPI and cell boundary markers. Accelerated clearing was used followed by 24 hours of standard clearing.

hyb_protocol: Encoding-probe hybridization (during tissue prep): Hybridization of the custom v1 encoding probe panel followed the FFPE MERSCOPE MERFISH workflow, including all associated blocking and washing steps.  Cyclical readout-probe hybridization (during imaging rounds): Fluorescent readout probes were hybridized and removed in iterative on/off cycles on the MERSCOPE platform according to the standard MERFISH imaging protocol, including washing and buffer exchanges between cycles.

scan_protocol: Imaging was performed on the MERSCOPE system using default MERFISH acquisition settings. Multi-round imaging, readout-probe cycling, autofocus, and cycle control were handled by the standard MERSCOPE software.

data_processing: Raw files were read into Seurat and SCTransform normalized.

label: per manufacturer's kit

label_protocol: Fresh-frozen tissues were sectioned, fixed, and permeabilized according to the MERSCOPE Fresh Frozen protocol. After permeabilization, tissue processing followed the MERSCOPE FFPE protocol beginning at the Anchoring Pre-Treatment step. Autofluorescence quenching was carried out using the MERSCOPE PhotoBleacher according to the manufacturer’s instructions. Custom v1 encoding probes were hybridized to the tissue according to the FFPE workflow. Nuclear staining with DAPI and poly(T) staining, as well as the associated wash steps, were performed following the instrument user guide.

extract_protocol: fresh-frozen mouse liver sections

value: Male

value: 6 months

value: AAV+Myc

value: whole liver


title: Run7_Rosa26KO_mApple_Young

value: AAV+mApple


title: Run7_Stat1KO_Myc_Old

value: 24 months


title: AP461286E22

value: SLE


title: AP575601E22


title: AP668700D23


title: 55102

description: Library name: Sample 365

value: whole blood


title: Run6_Rosa26KO_mApple_Young

description: slide 6, segmentation generated in cellpose using DAPI and cell boundary markers. Accelerated clearing was used followed by 24 hours of standard clearing.


title: AP328285D24

description: title describes sample ID used in raw data (NPX.csv)


title: AP001989E23


title: AP358407E22


title: AP144728E23


title: AP303945D23


title: Run6_Stat1KO_Myc_Young


title: 55101

description: Library name: Sample 364


title: 54206

description: Library name: Sample 363


title: 54125

description: Library name: Sample 362


title: Run6_Stat1KO_Myc_Old


title: AP996944C23


title: AP114554E23


title: AP931537C23


title: Run2_Old

description: slide 2, segmentation generated in cellpose using DAPI and cell boundary markers. Standard clearing was applied for 72 hours.

value: Untreated

value: WT


title: 54119

description: Library name: Sample 361


title: Run1_Young

description: slide 1, segmentation generated in cellpose using DAPI only. Standard clearing was applied for 72 hours.


title: Run2_Young


title: AP841336D23


title: AP841334D23


title: 53907

description: Library name: Sample 359


title: AP723570D23


title: 54110

description: Library name: Sample 360


title: AP222069E23


title: Run1_Old


title: 55302

description: Library name: Sample 369


title: 53810

description: Library name: Sample 358


title: AP389426D23


title: 53807

description: Library name: Sample 357


title: Brain run 2 control, MERFISH

city: Melbourne

first: Lucas

last: Tobar

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description: VIZGEN MERSCOPE

data_processing:
This experiment was conducted using MERSCOPE 1.0 chemistry, with image processing conducted on the MERSCOPE instrument.
*genome build/assembly: mm10
.vzg files: standard output of processed files to allow full visualisation of transcripts and segmented cells
codebook_0_mouse-vascular-panel_CP1378.csv: gene panel used in experiment

source_name: Brain

extract_protocol: Brain samples were harvested from mice and fixed in 4% PFA for 24h, folowed by embedding in agrose gel and parrafin. Dura samples were harvested and fixed in 4% PFA. Brain sectioning was performed at 10 µm on a Leica RM2255 with a water float temperature of 47 °C. Sections were placed on MERSCOPE slides (Vizgen). Dura samples were not sectioned, rather whole-mounted onto MERSCOPE slides, and left to dry overnight.

value: Brain

value: control (non-tumour bearing) mouse


title: AP389428D23


title: AP489504D23


title: AP619530C23


title: AP476733C23


title: AP671564C24


title: 53803

description: Library name: Sample 355


title: 53805

description: Library name: Sample 356


title: 53601

description: Library name: Sample 354


title: AP821169D24


title: 53005

description: Library name: Sample 353


title: AP527341C23


title: AP270130E23


title: AP535271E22


title: Dura run 2 4T1Br4 Day23, MERFISH

description: VIZGEN MERSCOPE

value: day 23 4T1Br4 bearing mice


title: Dura run 1 4T1Br4 Day17, MERFISH

description: VIZGEN MERSCOPE

value: day17 4T1Br4 bearing mice


title: AP173423E23

value: F


title: AP201590E23


title: Brain TBCP1 Day23, MERFISH

description: VIZGEN MERSCOPE

value: day 23 TBCP-1 bearing mouse


title: AP173424E23


title: Brain control, MERFISH

description: VIZGEN MERSCOPE

value: control (non-tumour bearing)


title: AP599681C23


title: 52910

description: Library name: Sample 351


title: AP200596D24


title: AP200595D24


title: AP475368C24


title: Brain 4T1Br4 Day23, MERFISH

description: VIZGEN MERSCOPE

value: day 23 post-tumour inoculation (4T1Br4) mouse sample


title: 52710

description: Library name: Sample 350


title: AP829923D24


title: AP731841C23


title: Dura run 1 control, MERFISH

description: VIZGEN MERSCOPE


title: 7 months, MERFISH

city: Jerusalem

first: Oren

last: Parnas

address: Faculty of Medicine, Ein-Kerem medical center

department: Immunology

country: Israel

institute: Hebrew University

description: Transcripts were selected for their specificity to immune and epithlial cell types. Importantly, we included marker genes for different metaplastic subpopulations.

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing:
Encoded MERFISH images of RNA spots were de-multiplexed by Vizgen. This pipeline outputs a table with the coordinates and identity of all transcripts, a count matrix of cell_by_gene, a cell metadata table and a parquet file with cell segmentation information. The CellPose algorithm was employed to estimate cell shapes based on DAPI and Vizgen's exclusive fluorescent cell surface marker combination. Individual transcripts located within the boundaries of CellPose segmented cells were allocated to their respective cells, while others were designated to the background.
Processed data includes MERFISH counts per cell

label_protocol: DAPI and Vizgen's exclusive fluorescent cell surface marker combination was employed to estimate cell shapes. For RNA visit https://vizgen.com/technology/#merfish

growth_protocol: Standard mouse housing conditions

extract_protocol: An FFPE mouse pancreas sample was taken from an animal seven months post-induction of Kras mutation with tamoxifen. This sample was sectioned into slices using a microtome and placed onto a 40 mm diameter MERSCOPE Slide. The sample was then shipped and processed by Vizgen

treatment_protocol: Tamoxifen was injected into six-eight weeks old Ptf1a-CreER, LSL-Kras-G12D, LSL-tdTomato (PRT) mice, and the pancreas was collected for single cell purification from mice seven months post-tamoxifen injection (PTI)

value: PTI, Ptf1a-CreER, LSL-Kras-G12D, LSL-tdTomato

tag: time post tamoxifen injection (pti)

value: 7 months

value: Pancreas


title: pooled sample of cell line GS54 with all conditions

city: Austin

first: Stephanie

middle: K

last: Seidlits

state: Texas

address: 107 W. Dean Keeton Street Austin

department: Biomedical Engineering

institute: The University of Texas

description: Library name: GS54

data_processing:
Annotated count matricies were generated using Cell Ranger. Low quality data was removed using a median absolute deviation (MAD) threshold of 3 and a mitochrondrial gene fraction of > 0.2. Data was normalized by application of a shifted logarithm.
Samples in HK177 were assigned ClonMapper cell lineages present in the 'lineage' observation and assigned a migratory phenotype based on a bionomial distribution listed in the 'phenotype' observation.
Assembly: GRCh38
Supplementary files format and content: h5ad anndata

source_name: brain

growth_protocol: Cells were encapsulated in hyaluronic acid-based hydrogels for 2 weeks prior to sequencing and  cultured in DMEM/F12 media containing human FGF, human EGF, Gem21 NeuroPlex supplement and L-Glutamine at 37C 5% O2.

extract_protocol:
Cells were extracted from hydrogels using the human tumor kit and the GentleMACs human tumor dissociator from Miltenyi Biotec (130-095-929). Cells were washed 3X with 1X PBS and stained with 7aad (Invitrogen A1310) according to the manufacturer’s recommendations for dead cell identification. Cells were sorted using FACS to remove hydrogel particles and to ensure that only live cells were submitted for sequencing.
Samples were prepared with 10X Chromium Single Cell 3ʹ v3 kit.

value: brain

value: glioblastoma


title: 52708

description: Library name: Sample 348

value: SLE


title: AP987842C23

extract_protocol: Baseline SLE serum samples were collected according to the clinical trial protocols. Blood was collected using a tube containing a clotting agent (BD SST 5ml tube). Circulating proteins were assayed using the Olink Explore 3072 panel, a proteomics platform that combines an antibody-based immunoassay with a proximity oligonucleotide extension assay and signal detection with next-generation sequencing on the NovaSeq6000 instrument (Ilumina Inc.).

tag: Sex


title: 52709

description: Library name: Sample 349

value: whole blood


title: 52702

description: Library name: Sample 347


title: AP438978D23

tag: disease


title: AP832685D24


title: human OCI-AML4, HOTSCRAMBL CBE2, Day 3 post-editing

first: Peng

last: Lyu

address: 1 Blackfan Street

institute: Boston Children's Hospital

description:
Library name: Sample 8
Column name in chirpRNAseq_featureCounts_all.txt: HOT_CBE2

data_processing:
Featurecount v2.0.6
Assembly: GRCh38
Supplementary files format and content: tab-delimited txt file including: Geneid, Chr, Start, End, Strand, Length, and raw read counts for 8 conditions

source_name: Blood

growth_protocol: MOLM13 cells were cultured in RPMI 1640 Medium supplemented with 20% FBS and 1% Penicillin-Streptomycin. OCI-AML4 cells were cultured in Minimum Essential Medium α (MEM α) supplemented with 20% FBS and 1% Penicillin-Streptomycin.

extract_protocol:
RNA was extract by following ChIRP-RNA isolation protocol. For each sample, 1×10⁷ MOLM13 or OCI-AML4 cells were fixed in 10 mL of freshly prepared 1% glutaraldehyde at room temperature for 10 minutes, then quenched with 125 mM glycine for 5 minutes. Fixed cells were washed in ice-cold DPBS, flash-frozen, and stored at -80 °C. Fixed cell pellets were thawed and resuspended in lysis buffer (1 mL per 10⁷ cells) supplemented with 1× PMSF, 1× protease inhibitor, and RNase inhibitor, then sonicated using a Covaris E220 ultrasonicator to obtain 100-500 bp chromatin fragments. The efficiency of fragmentation was verified by agarose gel electrophoresis after proteinase K digestion and DNA purification (Qiagen). For each ChIRP reaction, lysates were incubated with biotinylated probes (100 pmol per 1 mL lysate) in Hybridization Buffer at 37 °C for 4 hours with rotation. Pre-washed Dynabeads™ MyOne™ Streptavidin C1 beads (100 µL per 100 pmol probe) were added and incubated for an additional 30 min. Beads were washed five times at 37 °C using Wash Buffer to reduce nonspecific binding. For RNA isolation, beads were incubated in RNA PK Buffer with proteinase K at 50 °C for 45 min, followed by heat revere cross-linking at 95 °C for 10 min. RNA was extracted using TRIzol reagent and purified with the miRNeasy Mini Kit (Qiagen). Residual DNA was removed using the TURBO DNA-free™ Kit. 10 ng RNA was used for generating the sequencing library.
SMART-Seq® Total RNA Pico Input Kit (Takara) was used to construction the library according to the manufacturer's instructions.

treatment_protocol: Nucleofection was performed using the SF Cell Line 4D-Nucleofector (100 µL cuvette) for leukemia cell lines at 70%-75% confluence. CRISPR/Cas9 RNPs and cytosine base editors are delivered to cells with guide RNAs. Program DS-100 was used for nucleofection.

tag: tissue

value: Blood

value: Leukemia

value: AML cells

value: HOTSCRAMBL CBE

value: base editing

value: day 3


title: 52508

description: Library name: Sample 346

extract_protocol:
Whole blood RNA was extracted from PAXgene blood RNA tubes. Briefly, frozen tubes were thawed at room temperature and centrifuged according to the manufacturer’s protocol. The resulting pellet was then washed with nuclease free water, resuspended in sterile PBS, and split in half. RNA was extracted from one half of the suspension using the QIAsymphony PAXgene Blood RNA Kit (Qiagen). The other half of the suspension was used for DNA extraction. RNA concentration and integrity were assessed using the Ribogreen Assay (Thermo) and a Fragment Analyzer (Agilent), respectively.
Polyadenylated RNA was enriched using NEBNext Magnetic Oligo(dT)25 Beads and prepared into RNA-seq libraries using the NEBNext mRNA Library Prep Reagent Set for Illumina (New England BioLabs, Ipswich, MA, USA). Unique dual-index barcodes were incorporated as specified per manufacturer’s protocol. Library concentration was measured using the Quant-iT PicoGreen dsDNA Reagent (Thermo), and library size distribution and quality were checked using a DNA chip on Caliper Gx Touch (Revity). Library quantification was further refined by qPCR using the KAPA Library Quantificaiton Kit (Roche). Paired-end sequencing (2 x 100 bp, 100 million reads per sample) was carried out on an Illumina NovaSeq 6000 platform (Illumina) following manufacturer’s recommended protocols.

tag: genotype


title: AP438979D23

data_processing:
A set of internal controls (incubation, extension and amplification) was used to assess overall assay quality.  Internal plate controls were used to normalize the data and to calculate the limit of detection (LOD) for each assay.
Protein expression levels are given as normalized protein expression (NPX) values, which are arbitrary units used on a log2 scale that were normalized to the plate controls.

value: M


title: AP522294C23

value: F


title: AP127886D23


title: AP891625D23


title: human OCI-AML4, AAVS1 CBE2, Day 3 post-editing

description:
Library name: Sample 6
Column name in chirpRNAseq_featureCounts_all.txt: AAVS1_CBE2

value: WT


title: AP127885D23


title: human MOLM13, HOTSCRAMBL CBE1, Day 3 post-editing

description:
Library name: Sample 7
Column name in chirpRNAseq_featureCounts_all.txt: HOT_CBE1


title: 52505

description: Library name: Sample 345


title: AP255739D23


title: AP891624D23


title: human MOLM13, AAVS1 CBE1, Day 3 post-editing

description:
Library name: Sample 5
Column name in chirpRNAseq_featureCounts_all.txt: AAVS1_CBE1


title: 52501

description: Library name: Sample 343


title: human OCI-AML4, HOTSCRAMBL KO2, Day 3 post-editing

description:
Library name: Sample 4
Column name in chirpRNAseq_featureCounts_all.txt: HOT_KO2

value: HOTSCRAMBL KO

value: gene knockout


title: AP581663C23


title: AP291529C23


title: AP471014E22


title: AP581661C23


title: human OCI-AML4, AAVS1 KO2, Day 3 post-editing

description:
Library name: Sample 2
Column name in chirpRNAseq_featureCounts_all.txt: AAVS1_KO2


title: 52001

description: Library name: Sample 341


title: 52504

description: Library name: Sample 344


title: human MOLM13, AAVS1 KO1, Day 3 post-editing

description:
Library name: Sample 1
Column name in chirpRNAseq_featureCounts_all.txt: AAVS1_KO1


title: SP863012B22


title: 51904

description: Library name: Sample 340


title: AP291530C23


title: human MOLM13, HOTSCRAMBL KO1, Day 3 post-editing

description:
Library name: Sample 3
Column name in chirpRNAseq_featureCounts_all.txt: HOT_KO1


title: Brain 4T1Br4 Day17, MERFISH

description: VIZGEN MERSCOPE

value: Brain

value: day 17 post-tumour inoculation (4T1Br4) mouse sample


title: 52406

description: Library name: Sample 342


title: 51902

description: Library name: Sample 339


title: SP111728C22


title: PKP2fl/fl MCM cre/+ mice R1

city: Shanghai

first: Yuze

last: Wang

address: Shanghai Minhang District Dongchuan Road No. 800

country: China

institute: Shanghai Jiao Tong University

description:
Library name: sample2
BD Rhapsody

data_processing:
Raw sequencing reads were demultiplexed and aligned to the Rn7.2 reference rat genome using the BD Rhapsody WTA Analysis Pipeline (v1.11 rev 8, Single-Cell Multiplex Kit - Mouse) on the Seven Bridges Genomics platform. Alignment included introns and exons, and filtered count matrices were generated with recursive substitution error correction (RSEC), based on a liftover from the mm10 mouse genome annotation to the Rn7.2 rat genome. Sample Tag UMIs and calls were generated for each nucleus ID.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: heart

extract_protocol:
Frozen tissue punches were transferred to a prechilled Dounce homogenizer tube, followed by the addition of ice-cold detergent lysis buffer (composition: 0.32 M sucrose, 10 mM HEPES [pH 8.0], 5 mM CaCl₂, 3 mM MgAc, 0.1 mM EDTA, 1 mM DTT, 0.1% Triton X-100). Tissue lysis and nucleus release were performed by homogenization (10 strokes with pestle A, followed by 10 strokes with pestle B).
The lysate was then diluted with chilled low-sucrose buffer (composition: 0.32 M sucrose, 10 mM HEPES [pH 8.0], 5 mM CaCl₂, 3 mM MgAc, 0.1 mM EDTA, 1 mM DTT) and filtered through a 40 μm cell strainer to remove cellular debris. The filtered suspension was centrifuged at 3,200 × g for 10 minutes at 4 °C, and the supernatant was carefully decanted.
The nuclear pellet from each sample was resuspended in 750 μL of chilled resuspension buffer (1× PBS, 0.4 mg/mL BSA, 0.2 U/μL RNase Inhibitor [Biosearch Technologies, Cat. 30281]) containing one of eight unique XPoSE-tags. Each XPoSE-tag consists of a Nucleoporin 62 antibody conjugated to R718 fluorescent dye and one of eight distinct oligo-based Sample Tags (STs), which are custom reagents (BD Biosciences) used at a 1:2000 dilution to uniquely barcode nuclei from individual samples.
For verification of the neuronal nuclei gate, both the XPoSE-tag and the neuronal nuclear marker NeuN (anti-NeuN Mouse mAb, clone A60, MAB377X, Millipore Sigma, RRID: AB_2149209) were added at a 1:500 dilution. Samples were incubated with the antibodies for 15 minutes at 4 °C on a rotating mixer, then transferred to a 5 mL polystyrene round-bottom tube (Falcon) containing 3.5 mL of chilled resuspension buffer.
The samples were centrifuged at 250 × g for 10 minutes at 4 °C, and 4 mL of the supernatant (containing residual XPoSE-tag) was carefully aspirated. The pellet containing XPoSE-tag-labeled nuclei was resuspended in 1–2 mL of chilled resuspension buffer and filtered through a 40 μm cell strainer prior to fluorescence-activated nuclei sorting (FANS).
Single-cell whole transcriptome mRNA and Sample Tag libraries (BD Biosciences, cat. 633801) were generated according to the manufacturer’s protocols for sequencing on Illumina® sequencers. Library concentration was measured using a Qubit 4 fluorometer (ThermoFisher, cat. Q33230) and length distribution via a Bioanalyzer 2100 (Agilent, cat. 5067-4626), following the respective manufacturer’s protocols. Both cartridges were processed in parallel to generate indexed, separate libraries, which were pooled for sequencing. Whole transcriptome libraries were sequenced at 45,000 reads per nucleus and Sample Tag libraries at 1,000 reads per nucleus on an Illumina Novaseq S4 lane (PE 150 bp).

treatment_protocol: tamoxifen injection

value: heart

value: cardiomyocyte

value: pkp2 cko

value: tamoxifen


title: SP751304B23

value: SLE


title: SP751305B23


title: PKP2fl/fl MCM cre/+ mice R2

description:
Library name: sample4
BD Rhapsody


title: 51703

description: Library name: Sample 337

data_processing:
Data was processed using nf-core/rnaseq v3.14.0 of the nf-core collection of workflows, utilizing reproducible software environments from the Bioconda and Biocontainers projects. The pipeline was executed with Nextflow v23.10.1. Resulting count data was pre-processed using the edgeR packagein R, which included filtering out lowly-expressed genes using edgeR filterByExpr (min.count = 10) and performing quantile-normalized voom transformation.
Assembly: GRCh38
Supplementary files format and content: txt file includes normalized gene counts for each sample

value: whole blood


title: SP865999B22


title: SP576570B23


title: SP277364B23


title: SP935792B22


title: 51612

description: Library name: Sample 336


title: MCM cre/+ mice R2

description:
Library name: sample3
BD Rhapsody

value: wt


title: SP798848B23


title: SP660548B23


title: 51706

description: Library name: Sample 338


title: 51608

description: Library name: Sample 334


title: SP059061C22


title: SP059060C22


title: SP884233B22


title: SP820560B23


title: SP311057B23


title: SP096098C22


title: SP055651C22


title: 51610

description: Library name: Sample 335


title: 51602

description: Library name: Sample 333


title: 51408

description: Library name: Sample 332


title: TT-seq in ADNP-FKBP12 mESC, dTAG13, 1h, replicate 2

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Library name: TTseq_ADNP-FKBP12_dTAG13_1h_r2

data_processing:
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
Sequenced reads were aligned using STAR 2.7.3 and repeat sensitive settings according to Teissandier et al (Mobile DNA, 2019) (--outFilterType BySJout --outFilterMultimapNmax 100000  --outFilterMismatchNmax 3 --winAnchorMultimapNmax 20000 --alignMatesGapMax 350 --seedSearchStartLmax 30 alignTranscriptsPerReadNmax 30000  --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300  --seedNoneLociPerWindow 1000--outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax --limitBAMsortRAM 10000000000).
Assembly: GRCm39 / mm39
Supplementary files format and content: bigWig files were generated by using samtools and bedtools to calculate per base coverage, then counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools).

growth_protocol: Mouse embryonic stem cells were grown under standard conditions in medium containing serum, LIF and 2i.

extract_protocol:
For RNA-seq, RNA was collected using Absolutely RNA miniprep kit (Agilent) according to manufacturer's instructions. For TT-seq, RNA was isolated using Trizol according to manufacturer's instructions.
Libraries were prepared using TruSeq Ilumina total RNA-seq

value: hybrid 129-C57BL/6

value: embryonic stem cells (ESC)


title: TT-seq in ADNP-FKBP12 mESC, dTAG13, 1h, replicate 3

description: Library name: TTseq_ADNP-FKBP12_dTAG13_1h_r3


title: SP489400B23


title: SP757986B23


title: TT-seq in ADNP-FKBP12 mESC,  dTAG13, 1h, replicate 1

description: Library name: TTseq_ADNP-FKBP12_dTAG13_1h_r1


title: SP627721B23


title: 51407

description: Library name: Sample 331


title: 51404

description: Library name: Sample 330


title: SP627722B23


title: TT-seq in ADNP-FKBP12 mESC, dTAG13, 4h, replicate 3

description: Library name: TTseq_ADNP-FKBP12_dTAG13_4h_r3


title: SP332838B23


title: TT-seq in ADNP-FKBP12 mESC, dTAG13, 4h, replicate 2

description: Library name: TTseq_ADNP-FKBP12_dTAG13_4h_r2


title: TT-seq in ADNP-FKBP12 mESC, dTAG13, 4h, replicate 1

description: Library name: TTseq_ADNP-FKBP12_dTAG13_4h_r1


title: EP241752F22

description: title describes sample ID used in raw data (NPX.csv)


title: SP332837B23


title: 51403

description: Library name: Sample 329


title: EP266079E23


title: EP934784D23


title: 51103

description: Library name: Sample 328


title: TT-seq in ADNP-FKBP12 mESC, dTAG13, 24h, replicate 3

description: Library name: TTseq_ADNP-FKBP12_dTAG13_24h_r3


title: EP408822E23


title: TT-seq in ADNP-FKBP12 mESC, dTAG13, 24h, replicate 2

description: Library name: TTseq_ADNP-FKBP12_dTAG13_24h_r2


title: EP374334E30


title: EP340073E23


title: TT-seq in ADNP-FKBP12 mESC, dTAG13, 24h, replicate 1

description: Library name: TTseq_ADNP-FKBP12_dTAG13_24h_r1


title: 50707

description: Library name: Sample 327


title: EP371966D23


title: EP908182D23


title: EP907317D23


title: TT-seq in ADNP-FKBP12 mESC, ctrl, 24h, replicate 3

description: Library name: TTseq_ADNP-FKBP12_ctrl_r3

value: 24h DMSO ctrl


title: EP908183D23


title: EP938879E22


title: EP129465E23


title: 50608

description: Library name: Sample 325


title: TT-seq in ADNP-FKBP12 mESC, ctrl, 24h, replicate 2

description: Library name: TTseq_ADNP-FKBP12_ctrl_r2


title: EP907252D23


title: 50510

description: Library name: Sample 323


title: 50606

description: Library name: Sample 324


title: EP983164D23


title: EP316148D23


title: EP367472E24

value: M


title: 50609

description: Library name: Sample 326


title: EP280808E23

value: F


title: POL3 Input for ADNP-FKBP12 3F-HALO-BRF1 mESC, DMSO, 24h, replicate 2

description: Library name: Pol3_In_AdnpFKBP_Brf1HALO_ctrl_r2

data_processing:
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
Sequenced reads were aligned using STAR 2.7.3 with repeat sensitive settings based on Teissandier et al (Mobile DNA, 2019)  ( --outFilterMultimapNmax 100000 --outSAMmultNmax 1 --outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 2000 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 100000 --alignWindowsPerReadNmax 100000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 1000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000  --outBAMsortingBinsN 100 --limitBAMsortRAM 10000000000  --alignSJDBoverhangMin 999).
Assembly: GRCm39 / mm39
Supplementary files format and content: bigWig files were generated by first using samtools to filter out only uniquely mapping reads, then per base coverage was calculated using bedtools, counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (UCSC tools).

extract_protocol:
10^6 mES cells were crosslinked, chromatin was extracted and sonicated to an average size of 300bp. 5% of chromatin was set aside as Input control. The chromatin was incubated with antibody and protein A/G coupled Dynabeads, washed and de-crosslinked. Purified DNA was subsequently used for library preparation. For a detailed protocol, see Schnabl et al. 2025.
Libraries were prepared using the NEB Next Ultra II DNA library prep kit according to manufacturers instructions.


title: MCM cre/+ mice R1

description:
Library name: sample1
BD Rhapsody


title: EP221870E23


title: POL3 Input for ADNP-FKBP12 3F-HALO-BRF1 mESC, DMSO, 24h, replicate 1

description: Library name: Pol3_In_AdnpFKBP_Brf1HALO_ctrl_r1


title: 50507

description: Library name: Sample 321


title: POL3 Input for ADNP-FKBP12 3F-HALO-BRF1 mESC, dTAG13+PROTAC3, 24h, replicate 2

description: Library name: Pol3_In_AdnpFKBP_Brf1HALO_24h_r2

value: 24h dTAG13 [500nM] PROTAC3 [500nM]


title: TT-seq in ADNP-FKBP12 mESC, ctrl, 24h, replicate 1

description: Library name: TTseq_ADNP-FKBP12_ctrl_r1


title: EP668150E23


title: EP157219E23


title: SP641421B46


title: SP340514B23


title: SP574694B23


title: SP479586B23


title: 50508

description: Library name: Sample 322


title: POL3 ChIP in ADNP-FKBP12 3F-HALO-BRF1 mESC, DMSO, 24h, replicate 1

description: Library name: Pol3_ChIP_AdnpFKBP_Brf1HALO_ctrl_r1


title: POL3 Input for ADNP-FKBP12 3F-HALO-BRF1 mESC, dTAG13+PROTAC3, 24h, replicate 1

description: Library name: Pol3_In_AdnpFKBP_Brf1HALO_24h_r1


title: 50207

description: Library name: Sample 319


title: 50203

description: Library name: Sample 318


title: POL3 ChIP in ADNP-FKBP12 3F-HALO-BRF1 mESC, DMSO, 24h, replicate 2

description: Library name: Pol3_ChIP_AdnpFKBP_Brf1HALO_ctrl_r2


title: SP750521B23


title: SP296596B23


title: POL3 ChIP in ADNP-FKBP12 3F-HALO-BRF1 mESC, dTAG13+PROTAC3, 24h, replicate 2

description: Library name: Pol3_ChIP_AdnpFKBP_Brf1HALO_24h_r2


title: SP011571B23


title: SP932889B22


title: 50107

description: Library name: Sample 316


title: POL3 ChIP in ADNP-FKBP12 3F-HALO-BRF1 mESC, dTAG13+PROTAC3, 24h, replicate 1

description: Library name: Pol3_ChIP_AdnpFKBP_Brf1HALO_24h_r1


title: 50111

description: Library name: Sample 317


title: SP721107B23


title: SP710562B23


title: SP191236B23


title: SP405533B23


title: 50103

description: Library name: Sample 314


title: 50104

description: Library name: Sample 315


title: SP277772B23


title: SP629730B23


title: Resident airway macrophages, engulfing, rep2

city: Denver

first: Alexandra

last: McCubbrey

state: CO

address: 1400 Jackson St

institute: National Jewish Health

description: Library name: ResAM_4_plus

data_processing:
FASTQ files were generated from BCL files using Illumina bcl2fastq converter without adapter trimming.
Nf-core RNA-seq pipeline (version v3.9) run with Nextflow version 20.04.1
Assembly: GRCm38
Supplementary files format and content: raw_gene_counts.tsv: Gene-level counts; genes are rows and columns are library names

source_name: Resident airway macrophages

extract_protocol:
RNA was isolated using the RNeasy Plus Micro isolation kit (QIAGEN) per the manufacturer’s instructions with addition of β-mercaptoethanol to RLT Plus buffer. RT-PCR was performed using the SensiFast Hi-ROX One-Step Kit (Meridian Bioscience) per the manufacturer’s instructions.
Libraries were built using the standard Kapa Biosystems library preperation kit.

value: Resident airway macrophages

tag: engulfment

value: engulfing

tag: replicate


title: 49809

description: Library name: Sample 312


title: 50305

description: Library name: Sample 320


title: Resident airway macrophages, engulfing, rep3

description: Library name: ResAM_5_plus

tag: cell type


title: Resident airway macrophages, engulfing, rep5

description: Library name: ResAM_8_plus


title: Resident airway macrophages, engulfing, rep1

description: Library name: ResAM_3_plus


title: SP277775B23


title: Resident airway macrophages, engulfing, rep4

description: Library name: ResAM_7_plus


title: 50101

description: Library name: Sample 313


title: AP926030D23


title: SP472478B23


title: SP224467B23


title: 49808

description: Library name: Sample 311


title: Resident airway macrophages, non-engulfing, rep5

description: Library name: ResAM_8_minus

value: non-engulfing


title: AP926029D23


title: AP518144E22


title: AP250193E23


title: 49807

description: Library name: Sample 310


title: AP250192E23


title: Resident airway macrophages, non-engulfing, rep4

description: Library name: ResAM_7_minus


title: Resident airway macrophages, non-engulfing, rep3

description: Library name: ResAM_5_minus


title: 53001

description: Library name: Sample 352


title: 49805

description: Library name: Sample 308


title: AP921062D23


title: AP921061D23


title: AP462110E22


title: Resident airway macrophages, non-engulfing, rep2

description: Library name: ResAM_4_minus


title: AP462108E22


title: AP603753E22


title: AP926087D23


title: 49703

description: Library name: Sample 307


title: Recruited airway macrophages, engulfing, rep4

description: Library name: CD11b_8_plus

source_name: Recruited airway macrophages

value: Recruited airway macrophages


title: 49701

description: Library name: Sample 306


title: AP603755E22


title: Resident airway macrophages, non-engulfing, rep1

description: Library name: ResAM_3_minus


title: Recruited airway macrophages, engulfing, rep3

description: Library name: CD11b_7_plus


title: 49601

description: Library name: Sample 305


title: AP462106E22


title: AP894057D23


title: 49806

description: Library name: Sample 309


title: AP462109E22


title: AP642994E22


title: AP894058D23