title: Day 15 endothelial cells RNA-seq rep 2

city: Philadelphia

first: Rajan

last: Jain

address: 09-102 Smilow TRC 3400 Civic Center Blvd

department: Departments of Medicine and Cell and Developmental Biology, Penn CVI

institute: Perelman School of Medicine, University of Pennsylvania

data_processing:
adapters trimmed with Trimmomatic v0.39
sequencing reads aligned to human hg38 with BWA-MEM v0.7.17
aligned reads converted to BAM and sorted with Samtools v0.1.19, quality filter ("-F") set to 1804
duplicates were removed with Picard MarkDuplicates v2.18.7
ENCODE blacklist features filtered from the BAM files with Bedtools v2.29.0
Bigwig files generated for ChIP-seq datasets using deepTools bamCompare v3.3.2 with 20kb bins and signal extraction scaling (SES) normalization method
RNAseq quantification was performed using Kallisto quant v0.44.0 with fragment length identified by BioAnalyzer, standard deviation of 10, and 30 bootstraps
RNAseq quantified tpm values were quantile normalized between tissues using pandas v0.25.2 in Python v3.7.7
Differentially expressed transcripts from RNAseq analysis were identified using Sleuth v0.30.0
Genome_build: hg38
Supplementary_files_format_and_content: BED files with LAD or KDD calls per cell type
Supplementary_files_format_and_content: bigwig files with ChIP-seq signal per cell type
Supplementary_files_format_and_content: Tab-separated file with transcript abundance generated as described above
Supplementary_files_format_and_content: Combined quantile-normalized transcript abundance generated as described above

growth_protocol: Human pluripotent stem cell maintenance: Human pluripotent stem cells (hPSCs) were maintained in E8 media and passaged every 4 days onto matrigel-coated plates (Roche). ESCs, cardiomycoytes, epicardium, and endothelium were H9 hESC derived. The remainder of the cells were H7 hESC derived. hPSC cardiomyocyte differentiation: On Day 0 (start of differentiation) hPSCs were treated with 1mg/ml Collagenase B (Roche) for 1 hour, or until cells dissociated from plates, to generate embryoid bodies (EBs). Cells were collected and centrifuged at 300 rcf for 3 mins, and resuspended as small clusters of 50–100 cells by gentle pipetting in differentiation media containing RPMI (Gibco), 2 mM/L L-glutamine (Invitrogen), 4×104 monothioglycerol (MTG, Sigma-Aldrich), 50 µg/ml ascorbic acid (Sigma-Aldrich). Differentiation media was supplemented with 2ng/ml BMP4 and 3 µmol Thiazovivin (Milipore). EBs were cultured in 6cm dishes (USA Scientific) at 37°C in 5% CO2, 5% O2, and 90% N2. On Day 1, the media was changed to differentiation media supplemented with 30 ng/ml BMP4 (R&D Systems) and 30 ng/ml Activin A (R&D Systems), 5ng/ml bFGF (R&D Systems) and 1 µM Thiazovivin (Milipore). On Day 3, EBs were harvested and washed once with DMEM (Gibco). Media was changed to differentiation media supplemented with 5 ng/ml VEGF (R&D Systems) and 5 µmol/L XAV (Stemgent). On Day 5, media was changed to differentiation media supplemented with 5 ng/ml VEGF (R&D Systems). After Day 8, media was changed every 3-4 days to differentiation media without supplements. hPSC epicardium differentiation: The hPSC cardiomyocyte protocol was followed up to Day 3. At Day 3 EBs were dissociated with TrypLE Express (Gibco). Dissociated cells were washed with Wash media (DMEM, 0.1% BSA) + 1mg/ml DNase (VWR) twice and centrifuged at 300 rcf for 3 mins. Cells were resuspended in differentiation media supplemented with 1ng/ml BMP4 (R&D Systems), filtered and counted using a hemocytometer. Cells were plated onto a matrigel-coated 96 well plate at 80,000 cells per well. On Day 5, the media was changed to differentiation media supplemented with 5ng/ml VEGF (R&D Systems) and 1nM all-trans Retinoic Acid (Sigma-Aldrich). After Day 5, media was changed every 2 days with the same Day 5 differentiation media composition. On Day 11, the media was changed to differentiation media supplemented with 5ng/ml VEGF (R&D Systems) and cells were fed with the same differentiation media every 2 days until Day 15. On Day 15, cells were dissociated with 1mg/ml Collagenase B (Roche) for 1 hour, washed with Wash media (DMEM, 0.1% BSA) + 1mg/ml DNase (VWR) and centrifuged at 300 rcf for 3 mins. Cells were further dissociated with 3ml TrypLE Express, washed with Wash media (DMEM, 0.1% BSA) + 1mg/ml DNase (VWR) and centrifuged at 300 rcf for 3 mins. Cells were resuspended in differentiation media supplemented with 1 µM Thiazovivin (Millipore), filtered and counted using a hemocytometer. Cells were plated in a matrigel-coated 6 well-plate at 100,000 cells per well. On Day 16 media was changed to differentiation media supplemented with 5ng/ml VEGF (R&D Systems) and cells were fed every 2 days until they reached confluence (approximately Day 22). hPSC endothelial cell differentiation: The hPSC cardiomyocyte protocol was followed up to Day 5. At day 5 EBs were dissociated with TrypLE Express (Gibco). Dissociated cells were washed with Wash media (DMEM, 0.1% BSA) + 1mg/ml DNase (VWR) twice and centrifuged at 300 rcf for 3 mins. Cells were resuspended in differentiation media supplemented with 100ng/ml VEGF (R&D Systems) and 50ng/ml bFGF (R&D Systems), filtered and counted using a hemocytometer. Cells were plated onto a matrigel-coated 96 well plate at 80,000 cells per well. Media was changed every 2 days using differentiation media supplemented with 100ng/ml VEGF (R&D Systems) and 50ng/ml bFGF (R&D Systems). Cells were harvested and sorted on Day 15. Cardiomyocyte dissociation: EBs were incubated overnight with 0.6mg/ml Collagenase Type II (Worthington) at 37ºC. Dissociated cells were harvested and washed with Wash media (DMEM, 0.1% BSA) + 1mg/ml DNase (VWR) twice and centrifuged at 300 rcf for 3 mins. Cells were resuspended in differentiation media supplemented with 1 µM Thiazovivin (Millipore) and filtered. Basal media for hPSC differentiation: All differentiation was conducted in serum-free media, either Chemically Defined Medium 2 (CDM2) or Chemically Defined Medium 3 (CDM3). The composition of CDM2 basal medium (Loh et al., 2014; Loh et al., 2016) is: 50% IMDM + GlutaMAX (Thermo Fisher, 31980-097) + 50% F12 + GlutaMAX (Thermo Fisher, 31765-092) + 1 mg/mL polyvinyl alcohol (Sigma, P8136-250G) + 1% v/v chemically defined lipid concentrate (Thermo Fisher, 11905-031) + 450 μM 1-thioglycerol (Sigma, M6145-100ML) + 0.7 μg/mL recombinant human insulin (Sigma, 11376497001) + 15 μg/mL human transferrin (Sigma, 10652202001) + 1% v/v penicillin/streptomycin (Thermo Fisher, 15070-063). Polyvinyl alcohol was brought into suspension by gentle warming and magnetic stirring, and the media was sterilely filtered (through a 0.22 μm filter) prior to use. The composition of CDM3 basal medium (Ang et al., 2018) is: 45% IMDM + GlutaMAX (Thermo Fisher, 31980-097) + 45% F12 + GlutaMAX (Thermo Fisher, 31765-092) + 10% KnockOut serum replacement (Thermo Fisher, 10828028) + 1 mg/mL polyvinyl alcohol (Sigma, P8136-250G) + 1% v/v chemically defined lipid concentrate (Thermo Fisher, 11905-031) + 1% v/v penicillin/streptomycin (Thermo Fisher, 15070-063). Polyvinyl alcohol was brought into suspension by gentle warming and magnetic stirring, and the media was sterilely filtered (through a 0.22 μm filter) prior to use. hPSC ectodermal differentiation: The day prior to beginning differentiation, H7 hESCs were dissociated with Accutase (Thermo Fisher) for 10 minutes at 37°C. Accutase was neutralized through the addition of excess DMEM/F12 media, and then hESCs were pelleted via centrifugation and the supernatant was aspirated. Pelleted hESCs were resuspended in mTeSR1 + 1% penicillin/streptomycin + 1 μM of the ROCK inhibitor Thiazovivin (Tocris) (henceforth referred to “cell-plating media”), and plated onto onto Geltrex-coated tissue culture plastics at a density of 4 x 105 cells/cm2 (i.e., 2.1 x 106 cells per 10-cm dish). 24 hours after seeding, the cell-plating media was aspirated, and cells were briefly washed with DMEM/F12 to remove all traces of cell-plating media. hESCs were then differentiated into definitive ectoderm through the addition of CDM2 basal medium supplemented with A8301 (1 μM; Tocris), LDN193189 (100 nM, Stemgent), C59 (1 μM; Tocris), and Trametinib (250 nM; Selleck Chem), which was added for 24 hours. For border ectoderm induction, hESCs were differentiated into definitive ectoderm in 24 hours (as described above), and then definitive ectoderm was briefly washed (with DMEM/F12) and then treated with CDM2 basal media supplemented with BMP4 (30 ng/mL; R&D Systems), PD0325901 (100 nM; Tocris), CHIR99021 (3 μM; Tocris), and A8301 (1 μM; Tocris) for an additional 2 days, to generate day 3 border ectoderm progenitors. Differentiation media was aspirated and added fresh every 24 hours. For midbrain induction, hESCs were differentiated into definitive ectoderm in 24 hours (as described above), and then definitive ectoderm was briefly washed (with DMEM/F12) and then treated with CDM2 basal media supplemented with A8301 (1 μM; Tocris), LDN193189 (100 nM; Stemgent), and Trametinib (250 nM; Selleck Chem) for an additional 2 days to generate neural progenitors. Day 3 neural progenitors were briefly washed (with DMEM/F12) and were then treated with CDM2 basal media supplemented with CHIR99021 (4 μM; Tocris), SB-505124 (2 μM; Tocris) and FGF2 (20 ng/mL; R&D Systems) for 2 days, to generate day 5 midbrain progenitors. Differentiation media was aspirated and added fresh every 24 hours. hPSC endodermal differentiation: The day prior

extract_protocol:
ChIP and RNA-seq libraries were prepared with the NEBNextUltra II DNA library prep kit and the NEBNext Poly(A) mRNA Magnetic Isolation Module/NEBNext Ultra II library prep kit.
Libraries were quantified with Kapa and/or NEB qPCR-based library quantification systems and pooled for sequencing; input libraries were always run with associated ChIP samples. If possible, replicate samples were run together on the same sequencing run. RNAseq replicate samples were all run on the same sequencing run.

treatment_protocol: ChIP and ChIP-seq Library Preparation: Undifferentiated ESCs and all differentiated cell types were crosslinked in culture by addition of methanol-free formaldehyde (ThermoFisher, final 1% v/v) and incubated at room temperature for 10 minutes with gentle rotation. Crosslinking was quenched by addition of glycine (final 125mM) and incubated at room temperature for 5 minutes with gentle rotation. Media was discarded and replaced with PBS; cells were scraped and transferred to conical tubes and pelleted by centrifugation (250xg, 5 minutes at room temperature). Resulting pellets were flash frozen on dry ice and stored at -80C. For ChIP, 30uL protein G magnetic beads (per ChIP sample; Dynal) were washed 3 times in blocking buffer (0.5% BSA in PBS); beads were resuspended in 250uL blocking buffer and 2ug antibody (LaminB1: ab16048 [abcam]; H3K9me2: ab1220 [Abcam]) and rotated at 4C for at least 6 hours. Crude nuclei were isolated from frozen crosslinked cells as follows: cell pellet (from 10cm plate) was resuspended in 10mL cold Lysis Buffer 1 (50mM HEPES-KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% Glycerol, 0.5% NP‐40, 0.25% Triton X‐100, and protease inhibitors), and rotated at 4C for 10 minutes, followed by centrifugation (250xg, 5 minutes at room temperature). Supernatant was discarded and the pellet was resuspended in 10mL cold Lysis Buffer 2 (10mM Tris‐HCl pH 8.0, 200mM NaCl, 1mM EDTA, 0.5mM EGTA, and protease inhibitors), and rotated at room temperature for 10 minutes, followed by centrifugation (250xg, 5 minutes at room temperature). Supernatant was discarded and nuclei were resuspended/lysed in 1mL cold Lysis Buffer 3 (10mM Tris‐HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na‐Deoxycholate, and protease inhibitors) and transferred to pre-chilled 1mL Covaris AFA tubes (Covaris) Samples were sonicated using a Covaris S220 sonicator (high cell chromatin shearing for 15 minutes; Covaris). Lysates were transferred to tubes and Triton X-100 was added (final 1%) followed by centrifugation (top speed, 10 minutes at 4C in microcentrifuge). Supernatant was transferred to a new tube; protein concentration was measured by Bradford assay. Antibody-conjugated beads were washed 3 times in blocking buffer, resuspended in 50uL blocking buffer and added to 500ug input protein for overnight incubation with rotation at 4C. 50ug lysate was aliquoted and stored at -20C for input. On day 2, beads were washed 5 times in 1mL RIPA buffer (50mM HEPES‐KOH pH 7.5, 500mM LiCl, 1mM EDTA, 1% NP‐40, 0.7% Na‐Deoxycholate) with 2-minute incubation at room temperature with rotation for each wash. Beads were washed in 1mL final wash buffer (1xTE, 50mM NaCl) for 2 minutes with rotation at room temperature before final resuspension in 210uL elution buffer (50mM Tris‐HCl pH 8.0, 10mM EDTA, 1% SDS). To elute, beads were incubated with agitation at 65C for 30 minutes. 200uL eluate was removed to a fresh tube, and all samples (ChIP and reserved inputs) were reverse-crosslinked overnight at 65C with agitation for a minimum of 12 hours, but not more than 18 hours. 200uL 1xTE was added to reverse crosslinked DNA to dilute SDS, and samples were RNaseA treated (final 0.2mg/mL RNase; 37C for 2 hours) and Proteinase K (final 0.2mg/mL Proteinase K; 55C for 2 hours) before phenol:chloroform extraction and resuspension in 10mM Tris-HCl pH 8.0.  ChIP and input DNA was quantified by Qubit (ThermoFisher) before library preparation using the NEBNext Ultra II DNA library prep kit (NEB). Samples were indexed for multiplex sequencing. Library quality was analyzed by BioAnalyzer (Agilent Genomics) and quantified using qPCR (Kapa Biosystems). Libraries were pooled for multiplex sequencing, re-quantified, and sequenced on the Illumina NextSeq500 platform (vII; 75bp single-end sequencing; Illumina). RNA Isolation and RNA-seq Library Preparation: Undifferentiated ESCs or differentiated cells were scraped from tissue culture plates with 1xPBS, and centrifuged at 1500g for 5 minutes at room temperature. After discarding supernatant, cell pellets were flash frozen in dry ice and stored at -80C until processing. RNA was isolated using QIAGEN RNeasy total RNA extraction kit (QIAGEN). RNA quality was analyzed by BioAnalyzer; samples with RIN scores >8 were chosen for further processing. RNA libraries were prepared using the NEBNext Ultra II DNA Library Prep kit (NEB) with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) to enrich for poly-A tailed RNA molecules. RNA-seq library quality was analyzed by BioAnalyzer (Agilent Genomics) and quantified using qPCR (Kapa Biosystems). Libraries were pooled for multiplex sequencing, re-quantified, and sequenced on the Illumina NextSeq500 platform (vII; 75bp single end sequencing; Illumina).

value: ES-derived endothelial cells


title: Day 15 endothelial cells RNA-seq rep 1

status: Public on Dec 13 2022

type: SRA

state: PA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

source_name: endothelial cells

tag: cell type


title: Embryonic stem cells RNA-seq rep 2

source_name: embryonic stem cells (H9)

value: H9 embryonic stem cells


title: Embryonic stem cells RNA-seq rep 1


title: Skin tissue, Postnatal day P28, Wildtype

city: hyderabad

first: Sivapriya

last: Pavuluri

address: uppal

country: India

institute: cdfd

data_processing:
Libraries are sequenced in HiSeq X10 for 150bp read length using Sequencing Chemistry v4.0.
Adapter sequences are removed using cutadapt tool (v-2.6).
Reads are mapped to the reference genome.
Cuffdiff was used to analyze differential expression of genes and transcripts, thus aiding in understanding transcriptional and post transcriptional regulation under different conditions.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include RPKM values for each Sample.

organism: Mus musculus

source_name: Skin

extract_protocol:
RNA was isolated using RNeasy mini kit (Qiagen).
RNA libraries were prepared for RNA-seq using TruSeq sample preparation Kit following manufacturer's protocols.

tag: tissue

value: Skin

tag: genotype

value: Wild type

tag: age

value: Postnatal day P28


title: Skin tissue, Postnatal day P28, Hairloss

value: Hairloss


title: Day 15 endothelial cells RNA-seq rep 3


title: Ventricular cardiac myocytes RNA-seq rep 2

source_name: ventricular cardiac myocytes

value: ES-derived ventricular cardiac myocytes


title: Embryonic stem cells RNA-seq rep 3


title: Ventricular cardiac myocytes RNA-seq rep 3


title: Group 2 LAIV8-IIV5 Day 92 [P8-6]

city: New York

first: Ana

middle: S.

last: Gonzalez-Reiche

state: New York

address: 1 Gustave L. Levy Pl

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: average read depth ~30 million pairs of 2 × 95 bp reads

data_processing:
Illumina’s Real-Time Analysis (RTA) software was used for base-calling and quality scoring of RNA-sequencing (RNA-seq) data.
Adapters were removed with cutadapt and base quality trimming to remove 3′ read sequences if more than 20 bases with Q ≥ 20 were present
QC-passed paired-end reads were mapped to the human hg38 reference genome using STAR
A combined matrix of mapped paired end read raw counts (genes x samples) was generated with featureCounts
Assembly: hg38 (Release 23 GRCh38.p3)
Supplementary files format and content: A single tab-delimited text file includes all FPKM values for each Sample

molecule: polyA RNA

source_name: Blood

extract_protocol:
RNAdvance Blood Kit (Beckman Coulter)
Libraries were prepared from 300 ng of total RNA were using the Universal Plus mRNA-Seq kit (Tecan Genomics, San Carlos, CA, United States)

treatment_protocol: Blood samples collected with PAXgene tubes

value: Blood

value: Blood cells

tag: gender

value: Male

tag: treatment

tag: time

value: Day 92


title: Ventricular cardiac myocytes RNA-seq rep 1


title: paraxial mesoderm ChIP-seq input 2

library_source: genomic

molecule: genomic DNA

source_name: paraxial mesoderm

value: ES-derived paraxial mesoderm


title: Skin tissue, Postnatal day P19, Hairloss

value: Postnatal day P19


title: paraxial mesoderm H3K9me2 ChIP-seq rep 1


title: Group 2 LAIV8-IIV5 Day 85 [P8-5]

value: Day 85


title: Skin tissue, Postnatal day P19, Wildtype


title: Group 2 LAIV8-IIV5 Day 29 [P8-4]

value: Day 29


title: Group 4 IIV8/AS03-IIV5/AS03 Day 0 [P9-1]

value: Day 0


title: Skin tissue, Postnatal day P16, Hairloss

value: Postnatal day P16


title: Group 4 IIV8/AS03-IIV5/AS03 Day 3 [P9-2]

value: Day 3


title: paraxial mesoderm LB1 ChIP-seq rep 2


title: Group 2 LAIV8-IIV5 Day 7 [P8-3]

value: Day 7


title: mid-hindgut ChIP-seq input 2

source_name: mid-hindgut

value: ES-derived mid-hindgut


title: Skin tissue, Postnatal day P16, Wildtype

value: Skin

value: Wild type


title: paraxial mesoderm LB1 ChIP-seq rep 1


title: Group 2 LAIV8-IIV5 Day 3 [P8-2]


title: Skin tissue, Postnatal day P0, Hairloss

value: Hairloss

value: Postnatal day P0


title: paraxial mesoderm H3K9me2 ChIP-seq rep 2


title: mid-hindgut H3K9me2 ChIP-seq rep 2


title: mid-hindgut H3K9me2 ChIP-seq rep 1


title: mid-hindgut ChIP-seq input 1


title: paraxial mesoderm ChIP-seq input 1


title: mid-hindgut LB1 ChIP-seq rep 2


title: Group 1 LAIV8-IIV5/AS03 Day 113 [P7-7]

value: Blood

value: Day 113


title: Group 2 LAIV8-IIV5 Day 0 [P8-1]

value: Blood cells

value: Male


title: Skin tissue, Postnatal day P0, Wildtype


title: Group 1 LAIV8-IIV5/AS03 Day 92 [P7-6]

value: Day 92


title: AMMA3 snRNA-seq

city: Beijing

first: qian

middle: qian

last: zhang

address: Datun road, chaoyang district

department: State Key Laboratory of Brain and Cognitive Science

country: China

institute: Institute of Biophysics

description: 10X genomic snRNA-seq

data_processing:
All snRNA-seq raw fastq data were processed through Cell Ranger Single-Cell Software Suit (v3.1.0), which performed sequencing reads alignment and gene expression quantification. The sequencing reads from human were aligned to GRCh38 human reference genome, while mouse, monkey (macaque mulatta) and chicken sequencing reads were aligned to mm10-3.0.0, Macaca_mulatta.Mmul_10.102, GRCg6a species reference genome respectively.
We used CellRanger aggr pipeline to merge cells from the same species under different samples, with parameter “normalize=none”.
We computed the highest density interval of total UMI count (total_counts), detected genes number () and the percentage of mitochondrial gene expressed, by using hdi() function from HDInterval R packages with parameter “credMass=0.98”, and filtered cells outside of the confidence interval
Then, we removed potential doublets reported by Scrublet, with default parameter. With strict quality control procedure, we retained 91,699 nuclei with a median of 9417 unique molecular identifiers (UMIs) and 3617 genes in human datasets, 45,626 nuclei with a median of 4631 UMIs and 2373 genes in monkey datasets, 54,186 nuclei with a median of 5020 UMIs and 2316 genes in mouse datasets, while 12,460 nuclei with a median of 3660 UMIs and 1716 genes in chicken
We performed normalize_total and log1p function in SCANPY to normalize (library-size correct) and logarithmize the raw count matrix (filtered after quality control). Next, we detected highly variable genes (HVGs) using scanpy.pp.highly_varible_genes function with parameter “min_mean=0.0125, max_mean=3, min_disp=0.5” and selected all the HVGs for downstream analysis. Finally, we performed scanpy.pp.regress_out function to regress out effects of total counts and mitochondrial genes expression percentage.
Genome_build: GRCh38;Macaca_mulatta.Mmul_10.102;GRCg6a;mm10-3.0.0,
Supplementary_files_format_and_content: metadata.csv.gz file was metadata for each datasets. And  normalized_count.csv was normalized gene expression file.

organism: Macaca mulatta

source_name: Amygdala

growth_protocol: Human samples were from postmortem donors with very short postmortem interval (within 6 hours), and macaque, mouse and chicken amygdala were freshly dissected.All the fresh dissected sample were quick-frozen by liquied nitrogen and stored for nuclei isolation

extract_protocol:
Frozen tumor tissue was homogenized into small cell pellets using a glass tissue grinder in ice-cold EZ buffer   and incubated on ice for 5 min. Then nuclei were centrifuged at 500 × g for 5 min at 4 °C. Repeat the wash and centrifuge step again. After that, nuclei were resuspended with PBS, and Debris Removal Solution (MACS) was added to effectively remove cell debris. Isolated nuclei were suspended in Nuclei Suspension Buffer (NSB; consisting of 1× PBS, 0.01% BSA and 0.1% RNase inhibitor. A final nuclei suspension was filtered through a 35-μm cell strainer (Corning, Cat #352235) and used for single-cell libraries preparation.
Single nuclei were processed using Chromium Single  V3 Chemistry Library Kits (10× Genomics) and  according to the manufacturer’s instructions.

treatment_protocol: Without any treatment

value: Adult

value: Amygdala

tag: molecule

value: nuclear RNA


title: liver ChIP-seq input 2

source_name: liver

value: ES-derived liver progenitors


title: mid-hindgut LB1 ChIP-seq rep 1


title: liver H3K9me2 ChIP-seq rep 1


title: liver ChIP-seq input 1


title: Group 1 LAIV8-IIV5/AS03 Day 85 [P7-5]

value: Day 85


title: AMMA1 snRNA-seq

description: 10X genomic snRNA-seq


title: Group 1 LAIV8-IIV5/AS03 Day 29 [P7-4]

value: Day 29


title: AMC2 snRNA-seq

description: 10X genomic snRNA-seq

organism: Gallus gallus


title: Group 1 LAIV8-IIV5/AS03 Day 7 [P7-3]

value: Day 7


title: AMC1 snRNA-seq

description: 10X genomic snRNA-seq


title: embryonic stem cells ChIP-seq input 2

source_name: embryonic stem cells

value: Embryonic stem cells


title: liver LB1 ChIP-seq rep 2


title: embryonic stem cells H3K9me2 ChIP-seq rep 2


title: liver H3K9me2 ChIP-seq rep 2


title: Group 1 LAIV8-IIV5/AS03 Day 3 [P7-2]

value: Day 3


title: embryonic stem cells H3K9me2 ChIP-seq rep 1


title: AMMA2 snRNA-seq

description: 10X genomic snRNA-seq


title: Group 1 LAIV8-IIV5/AS03 Day 0 [P7-1]

value: Day 0


title: embryonic stem cells LB1 ChIP-seq rep 1


title: 1897_RV_SingleDoseABE

city: Boston

first: Daniel

last: DeLaughter

state: MA

address: 7 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

library_source: transcriptomic single cell

data_processing:
Reads were aligned to the mm10 genome using the Cell Ranger software (Genomics 10x, Pleasanton, CA ) command mkfastq.
Assembly: mm10
Supplementary files format and content: h5

source_name: Right Ventricle

extract_protocol:
Single nuclei were obtained from flash-frozen tissues using mechanical homogenization folled by FACs sorting to remove debris. Nuclei were then loaded on the Chromium Controller (10X Genomics) with a targeted  nuclei recovery of 4,000–10,000 per reaction.
Gene expression libraries were prepared according to the manufacturer’s instructions of the v3 Chromium Single Cell Reagent Kits (10X Genomics).

value: Right Ventricle

tag: strain

value: SvEv

value: male

value: SingleDoseABE


title: 35_RV_SingleDoseABE


title: embryonic stem cells LB1 ChIP-seq rep 2


title: 1898_LV_SingleDoseABE

source_name: Left Ventricular Apex

value: Left Ventricular Apex


title: epicardium H3K9me2 ChIP-seq rep 1

source_name: epicardium

value: ES-derived epicardium


title: Group 4 IIV8/AS03-IIV5/AS03 Day 113 [P6-7]

value: Blood

value: Blood cells

value: Male

value: Day 113


title: epicardium LB1 ChIP-seq rep 1


title: epicardium ChIP-seq input 1


title: epicardium LB1 ChIP-seq rep 2


title: epicardium H3Kme2 ChIP-seq rep 2


title: Group 4 IIV8/AS03-IIV5/AS03 Day 92 [P6-6]

value: Day 92


title: endothelial progenitors ChIP-seq input 2

source_name: endothelial progenitors

value: ES-derived endothelial progenitors


title: liver LB1 ChIP-seq rep 1

value: ES-derived liver progenitors


title: embryonic stem cells ChIP-seq input 1


title: A549 HCoV-OC43 infected, treated with SBI-756 rep1

city: La Jolla

first: Ze'ev

middle: A.

last: Ronai

state: CA

address: 10901 North Torrey Pines Road

department: Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center

institute: Sanford Burnham Prebys Medical Discovery Institute

data_processing:
Illumina Truseq adapter, polyA, and polyT sequences were trimmed using cutadapt version 2.3.
Trimmed reads were aligned to human genome version hg38 and Ensembl gene annotations version 84 using STAR aligner version 2.7.0d_0221 and ENCODE long RNA-seq pipeline parameters (https://github.com/ENCODE-DCC/long-rna-seq-pipeline). Gene expression levels were quantified using RSEM version 1.3.1.
Assembly: hg38
Supplementary files format and content: Matrix table with normalized gene expression (TPM)

source_name: A549 cell line

growth_protocol: A549 cells were obtained from the American Type Culture Collection (ATCC) and maintained in high-glucose Dulbecco's modified Eagle's medium (HyClone) with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted using a total RNA miniprep kit (Sigma) with the On-column DNase I digestion step included.
Libraries were prepared from isolated total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen (Vienna, Austria). Barcoded libraries were pooled, and single end sequenced (1X75) on the Illumina NextSeq 500 system using the High output V2.5 kit (Illumina Inc., San Diego, CA). Read data was processed and multiplexed with the BlueBee Genomics Platform (BlueBee, San Mateo, CA).

treatment_protocol: Cells were seeded in 6-well (2 x 105) or 96-well (1 x 104) plates. The next day, cells were incubated 1 h with a dilution of OC43 virus stock at a MOI of 0.1.  Media supplemented with 2% FBS and test compounds at various concentrations were then added to infected cells. Cells were collected for Western blotting analysis and RNA-seq (6-well plate) after 24 h or subjected to IF staining (96-well plate) after 48 h

tag: cell line

value: A549 cell line

tag: infection

value: infected

tag: treatment concentration

value: 1 uM


title: JM8.N4 mESC, WT, Xinput, rep2

city: Cambridge

first: Viraat

middle: Y

last: Goel

address: Building 56 Room 787B, 32 Vassar Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for NovaSeq output.
Paired end reads were aligned to the a concatenation of the UCSC mm39 and hg38 genomes using bowtie2 v2.3.5.1 with --no-mixed --no-discordant.
Uniquely aligned reads were filtered for PCR duplicates using Sambamba markdup. Reads for each condition were randomly subsambled using normalization factors based on hg38 spike-in. Normalization factors were corrected using the ratio of human to mouse read counts in corresponding input samples.
Assembly: mm39; hg38
Supplementary files format and content: bigwig file with data based on all uniquely aligning non-duplicate reads

growth_protocol: Mouse embryonic stem cells (JM8.N4 mESCs) were cultured on plates coated with 0.1% gelatin solution (Sigma-Aldrich) under feeder-free conditions in medium consisting of KnockOut DMEM (Thermofisher) with 15% FBS (HyClone, SH30396.03, Lot. No. AE28209315) and 1000U/mL LIF (home-made), 1 mM MEM Non-Essential Amino Acid Solution (Thermofisher), 2 mM GlutaMAX (Thermofisher), 100 μg/ml Penicillin-Streptomycin (Thermofisher), and 0.1 mM 2-mercapoethanol (Sigma) supplemented with 2i, 10 μM MEK inhibitor (Tocris) and 3 μM GSK inhibitor (Sigma). mESCs were fed daily by replacing half the medium and passaged every two days with 0.05% Trypsin-EDTA (Thermo Fisher Scientific). 1 day prior to harvesting, cells were swapped to medium as described above without 2i.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 mins. Following quenching, chromatin was sonicated and then reverse crosslinked. Naked DNA was further sonicated to the 400-800bp range.
DNA from RPB1 ChIP or input chromatin was used to prepare libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with a number of PCR cycles according to the manufacturer's protocol on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified twice using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR. Following qPCR quantification, libraries were submitted for sequencing.

treatment_protocol: Transcription inhibition was performed by adding triptolide to the media of confluent cells at 1 µM for 45 minutes.

value: Mouse embryonic stem cell

tag: spike-in reference_organism

value: Homo sapiens

tag: spike-in cell_line

tag: chip antibody

tag: antibody info

value: WT


title: Group 4 IIV8/AS03-IIV5/AS03 Day 85 [P6-5]

value: Day 85


title: Group 4 IIV8/AS03-IIV5/AS03 Day 29 [P6-4]

value: Day 29


title: epicardium ChIP-seq input 2


title: endothelial progenitors H3K9me2 ChIP-seq rep 2


title: endothelial progenitors ChIP-seq input 1


title: 1897_LV_SingleDoseABE

value: Left Ventricular Apex

value: SvEv

value: male

value: SingleDoseABE


title: JM8.N4 mESC, Triptolide 4hr, RCMC, rep2

data_processing:
Basecalls were performed using bcl2fastq v2.20.0.422 for NovaSeq output.
Paired end reads were aligned to the UCSC mm39 genome using bowtie2 v2.3.5.1 with --local --reorder --very-sensitive-local. Aligned paired end reads were then parsed with pairtools (v0.3.0) parse with --add-columns mapq --walks-policy mask --min-mapq 2.
Parsed reads were filtered for PCR duplicates and unmapped/mutiply mapping reads with pairtools dedup with --max-mismatch 1. Remaining reads were indexed (pairix v0.3.7) and filtered to retain only those reads where both read mates lie in a locus of interest. These filtered reads were subsequently converted to .cool format using cooler (v0.8.11) cload pairs, and then to .mcool format with cooler zoomify, including the --balance option.
Assembly: mm39
Supplementary files format and content: mcool file contains all valid Micro-C pairs stored in HDF5 format with multiple resolutions
Library strategy: Micro-C

extract_protocol:
Cells were fixed with 3 mM DSG for 35 minutes, followed by an additional 10 minutes with 1% formaldehyde. Following quenching, nuclei were prepared from fixed cells. Chromatin was digested in situ using MNase, DNA 3' ends were chewed back and biotinylated, and then free DNA ends were proximity ligated. Unligated ends were digested, and followed by reverse crosslinking of the chromatin and Protease K digestion. DNA was purified by phenol chloroform extraction and DNA Clean and Concentrator kit (Zymo), and then size selected for dinucleosomal fragments on an agarose gel. Following end polishing of DNA fragments, a streptavidin pulldown was used to enrich for ligated dinucleosomal fragments.
Size selected DNA fragments bound to streptavidin coated beads were used to prepare Micro-C libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with 7-8 PCR cycles on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR and pooled in a 1:1 ratio to a total of 2-4 µg of DNA. Following the Twist Standard Hybridization Target Enrichment Protocol (Twist Biosciences) with the inclusion of Mouse Cot-1 DNA (Invitrogen) blocker solution, this library pool was hybridized to custom probe panels for loci of interest and bound to streptavidin coated beads. Bead-bound fragments were pulled down, amplified with 6 PCR cycles on the thermocycler using Equinox Library Amp Mix (Twist), and purified using Twist Binding and Purification Beads (Twist). Following qPCR quantification, the target enriched library pool was submitted for sequencing.

value: Triptolide

value: 4 hours


title: Group 4 IIV8/AS03-IIV5/AS03 Day 7 [P6-3]

value: Blood

value: Blood cells

value: Male

value: Day 7


title: endothelial progenitors LB1 ChIP-seq rep 2

value: ES-derived endothelial progenitors


title: Group 4 IIV8/AS03-IIV5/AS03 Day 3 [P6-2]

value: Day 3


title: early somite H3K9me2 ChIP-seq rep 2

source_name: early somite

value: ES-derived early somite


title: endothelial progenitors LB1 ChIP-seq rep 1


title: Group 4 IIV8/AS03-IIV5/AS03 Day 0 [P6-1]

value: Day 0


title: JM8.N4 mESC, F1 RAD21-mAID DMSO, RCMC, rep2

treatment_protocol: RAD21 degradation was induced by addition of IAA at 500 µM to the media of confluent cells for 3 hours.

value: Mouse embryonic stem cell

value: Homozygous RAD21-mAID-BFP-V5

value: DMSO

value: 3 hours


title: JM8.N4 mESC, F1 RAD21-mAID IAA 3hr, RCMC, rep2

value: IAA


title: early somite H3K9me2 ChIP-seq rep 1


title: Group 4 IIV8/AS03-IIV5/AS03 Day 113 [P53-7]

value: Day 113


title: early somite LB1 ChIP-seq rep 1


title: early somite LB1 ChIP-seq rep 2


title: definitive ectoderm ChIP-seq input 2

source_name: definitive ectoderm

value: ES-derived definitive ectoderm


title: early somite ChIP-seq input


title: JM8.N4 mESC, WT, RCMC, rep2

value: WT


title: Group 4 IIV8/AS03-IIV5/AS03 Day 92 [P53-6]

value: Day 92


title: definitive ectoderm H3K9me2 ChIP-seq rep 2


title: JM8.N4 mESC, Triptolide 4hr, RCMC, rep1

value: Triptolide

value: 4 hours


title: endothelial progenitors H3K9me2 ChIP-seq rep 1


title: Group 4 IIV8/AS03-IIV5/AS03 Day 85 [P53-5]

value: Blood

value: Blood cells

value: Male

value: Day 85


title: Group 4 IIV8/AS03-IIV5/AS03 Day 29 [P53-4]

value: Day 29


title: definitive ectoderm LB1 ChIP-seq rep 2


title: Group 4 IIV8/AS03-IIV5/AS03 Day 7 [P53-3]

value: Day 7


title: definitive ectoderm H3K9me2 ChIP-seq rep 1


title: Group 4 IIV8/AS03-IIV5/AS03 Day 3 [P53-2]

value: Day 3


title: Day-5 Midbrain H3K9me2 ChIP-seq rep 2

source_name: midbrain progenitors

value: ES-derived midbrain progenitors


title: definitive ectoderm ChIP-seq input 1


title: Day-5 Midbrain H3K9me2 ChIP-seq rep 1


title: Day-5 Midbrain ChIP-seq input


title: Day-5 Midbrain LB1 ChIP-seq rep 2


title: definitive ectoderm LB1 ChIP-seq rep 1


title: MAD-60

city: Houston

first: Stephanie

middle: Lynn

last: Coffin

state: TX

address: 1250 Moursund St

institute: Baylor College of Medicine

description: CIC_WT_EnCKO_Merged_peaks_under120_peaks.blacklistRemoved.sorted.narrowPeak

data_processing:
Adapter trimming with Trimmomatic version 0.36 (2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25) and kseq
Alignment was performed with bowtie2-2.3.4.1 (--dovetail --phred33)
samtools (1.10) used to isolate fragmnets <120bp (for CIC and IgG) and generate BAM files
Bedtools (v2.29.1) was used to process BAM files to BED files, remove blacklist, and generate bigwigs.
Bedtools (v2.29.1) was used to merge replicate BAM files together for peak calling
Peaks called using MACSr (version 1.00, macs3 callpeak parameters “BAMPE”, qvalue = 0.05)
Assembly: mm10 (GRCm38 GCA_000001635.2) and the spike in Ecoli K12 Genomes (GCF_000005845.2_ASM584v2)
Supplementary files format and content: bigwig files, some peaks
Library strategy: CUT&RUN

source_name: Cerebellum

extract_protocol:
Nuclear Extraction (Mo et. al 2015) followed by CUT&RUN
Following protocols.IO (dx.doi.org/10.17504/protocols.io.bagaibse) using NEB Next Ultra II DNA Library Prep Kit (E7645S) and NEB Unique Combinatorial Dual index kit (E6442S)
Sequencing at GENEWIZ using Illumina Novaseq S2 lane with 150bp PE reads

value: Cerebellum

tag: cut&run antibody

value: CIC (Rabbit polyclonal, in house; 1:2000)

value: Engrailed1-Cre;Cicfl/fl (CIC KO)


title: MAD-58

value: H3K27ac (Rabbit monoclonal, D5E4 #8173 Cell Signaling; 1:100)


title: MAD-54


title: Day-5 Midbrain LB1 ChIP-seq rep 1

tag: cell type


title: JM8.N4 mESC, Triptolide 45min, RCMC, rep2

value: Mouse embryonic stem cell

value: 45 minutes


title: Group 4 IIV8/AS03-IIV5/AS03 Day 0 [P53-1]

tag: tissue

value: Day 0


title: border ectoderm ChIp-seq input

source_name: border ectoderm

value: ES-derived border ectoderm


title: MAD-57

value: IgG (Rabbig monoclonal, Millipore, 12-370; 1:100)

tag: genotype


title: MAD-56

tag: age


title: MAD-53


title: border ectoderm LB1 ChIp-seq rep 2


title: border ectoderm H3K9me2 ChIp-seq rep 2


title: border ectoderm H3K9me2 ChIp-seq rep 1


title: border ectoderm LB1 ChIp-seq rep 1


title: Group 4 IIV8/AS03-IIV5/AS03 Day 113 [P52-7]

value: Blood

tag: gender

value: Female

value: Day 113


title: Group 4 IIV8/AS03-IIV5/AS03 Day 85 [P52-5]

value: Blood cells

tag: treatment

value: Day 85


title: anterior primitive streak H3K9me2 ChIP-seq rep 2

source_name: anterior primitive streak

value: ES-derived anterior primitive streak


title: MAD-52

description: CIC_154Q_AXH_EnCKO_Merged_peaks_under120_peaks.blacklistRemoved.sorted.narrowPeak


title: anterior primitive streak H3K9me2 ChIP-seq rep 1


title: Group 4 IIV8/AS03-IIV5/AS03 Day 92 [P52-6]

source_name: Blood

tag: time

value: Day 92


title: MAD-49


title: Group 4 IIV8/AS03-IIV5/AS03 Day 29 [P52-4]

value: Day 29


title: MAD-48

value: Cerebellum

value: wildtype


title: Group 4 IIV8/AS03-IIV5/AS03 Day 7 [P52-3]

value: Day 7


title: anterior primitive streak LB1 ChIP-seq rep 2


title: MAD-46

value: H3K27ac (Rabbit monoclonal, D5E4 #8173 Cell Signaling; 1:100)


title: ATAC-seq DND41 USP7i+dexamethasone replicate 3

first: Sonali

last: Narang

state: NY

address: 435 east 30th street

institute: NYU Langone

data_processing:
Aigned to reference genome (hg19) using Bowtie2
Filtering of duplicate reads by Sambamba
Peak-calling conducted with MACS2
Genome_build: hg19
Supplementary_files_format_and_content: bed files consisting of peak calls for each sample with 3replicates

growth_protocol: cells in suspension, growing in RPMI

extract_protocol:
Zymo DNA Clean & Concentrator Kit
Transposed libraries were prepped with NEBNext master mix and ATAC-seq dual index adapters

treatment_protocol: cells treated with USP7 inhibitor with or without dexamethasone for 72hr.

value: human T cell leukemia cells


title: anterior primitive streak LB1 ChIP-seq rep 1


title: cardiac myocytes H3K9me2 ChIP-seq rep 2

source_name: cardiac myocytes

value: ES-derived cardiac myocytes


title: cardiac myocytes LB1 ChIP-seq rep 1


title: Group 4 IIV8/AS03-IIV5/AS03 Day 0 [P52-1]

value: Day 0


title: MAD-45


title: cardiac myocytes H3K9me2 ChIP-seq rep 1


title: ATAC-seq DND41 dexamethasone  replicate 3


title: Group 4 IIV8/AS03-IIV5/AS03 Day 3 [P52-2]

value: Day 3


title: cardiac myocytes LB1 ChIP-seq rep 2


title: ATAC-seq DND41 USP7i+dexamethasone replicate 1


title: cardiac myocytes ChIP-seq input


title: MAD-44

description: CIC_154Q_EnCKO_Merged_peaks_under120_peaks.RepeatMasked.blacklistRemoved.sorted.summits_v3.narrowPeak

value: CIC (Rabbit polyclonal, in house; 1:2000)


title: anterior primitive streak ChIP-seq input


title: MAD-50


title: MAD-42


title: MAD-41

value: IgG (Rabbig monoclonal, Millipore, 12-370; 1:100)


title: ATAC-seq DND41 dexamethasone  replicate 2


title: Group 2 LAIV8-IIV5 Day 85 [P51-5]

value: Blood

value: Male


title: ATAC-seq DND41 dexamethasone  replicate 1


title: Group 2 LAIV8-IIV5 Day 113 [P51-7]

value: Blood cells

value: Day 113


title: ATAC-seq DND41 USP7i+dexamethasone  replicate 2


title: Group 2 LAIV8-IIV5 Day 92 [P51-6]


title: ATAC-seq DND41 USP7i  replicate 3


title: Group 2 LAIV8-IIV5 Day 29 [P51-4]


title: MAD-40


title: ATAC-seq DND41 USP7i  replicate 1


title: ATAC-seq DND41 Control  replicate 3


title: ATAC-seq DND41 Control  replicate 2


title: Group 2 LAIV8-IIV5 Day 3 [P51-2]


title: ATAC-seq DND41 USP7i  replicate 2


title: MAD-38


title: RNA-seq CUTLL1 shUSP11 Dex 24hr replicate 1

data_processing:
Basecalls performed using bcl2fastq
RNA-seq reads were aligned to the hg19 genome assembly using Tophat
Reads were counted on the exons of hg19 genes using htseq
Differential gene expression analysis was performed using edgeR.
Genome_build: hg 19
Supplementary_files_format_and_content: TAB-delimited text, edgeR output containing normalized expression values.

extract_protocol:
Aurum Total RNA Mini Kit (Bio-Rad)
Poly-A+ (magnetic oligodT-containing beads (Invitrogen)) RNA was used for library preparation. cDNA preparation and strand-specific library construction was performed using the dUTP method. Libraries were sequenced on the Illumina NextSeq 500 using 75bp single-read method.

treatment_protocol: cells treated with Dasatinib and the control for 24hr.


title: MAD-37


title: Group 2 LAIV8-IIV5 Day 0 [P51-1]


title: RNA-seq CUTLL1 shUSP11 Dex 24hr replicate 2


title: RNA-seq CUTLL1 Dex 24hr replicate 3

value: Dex


title: RNA-seq CUTLL1 shUSP11 Dex 24hr replicate 3


title: Group 2 LAIV8-IIV5 Day 113 [P50-7]

value: Female


title: MAD-34


title: MAD-36


title: RNA-seq CUTLL1 Dex 24hr replicate 1


title: RNA-seq CUTLL1 Dex 24hr replicate 2


title: Group 2 LAIV8-IIV5 Day 85 [P50-5]

value: Day 85


title: Group 2 LAIV8-IIV5 Day 92 [P50-6]

value: Day 92


title: Group 2 LAIV8-IIV5 Day 7 [P51-3]


title: ATAC-seq DND41 Control  replicate 1


title: MAD-33

value: Cerebellum

value: wildtype


title: RNA-seq DND41 Dex USP7i 72hr replicate 1

value: Dex and USP7i


title: MAD-32


title: MAD-30

value: H3K27ac (Rabbit monoclonal, D5E4 #8173 Cell Signaling; 1:100)


title: RNA-seq DND41 Dex USP7i 72hr replicate 2

value: human T cell leukemia cells


title: RNA-seq DND41 USP7i 72hr replicate 3


title: RNA-seq DND41 USP7i 72hr replicate 2


title: Group 2 LAIV8-IIV5 Day 7 [P50-3]

value: Day 7


title: Group 2 LAIV8-IIV5 Day 29 [P50-4]

value: Day 29


title: MAD-28

value: CIC (Rabbit polyclonal, in house; 1:2000)


title: RNA-seq DND41 Dex 72hr replicate 2


title: RNA-seq DND41 USP7i 72hr replicate 1


title: MAD-29

value: IgG (Rabbig monoclonal, Millipore, 12-370; 1:100)


title: RNA-seq DND41 Dex 72hr replicate 1


title: Group 2 LAIV8-IIV5 Day 3 [P50-2]

value: Blood

value: Day 3


title: Group 2 LAIV8-IIV5 Day 0 [P50-1]

value: Blood cells

value: Day 0


title: RNA-seq DND41 Dex 72hr replicate 3

value: Dex


title: MAD-26


title: RNA-seq DND41 DMSO 72hr replicate 3

value: DMSO


title: RNA-seq DND41 DMSO 72hr replicate 2


title: MAD-25


title: Group 4 IIV8/AS03-IIV5/AS03 Day 113 [P5-7]

value: Female

value: Day 113


title: RNA-seq DND41 Dex USP7i 72hr replicate 3


title: Group 4 IIV8/AS03-IIV5/AS03 Day 92 [P5-6]

value: Day 92


title: RNA-seq DND41 Dex USP7i 48hr replicate 3


title: RNA-seq DND41 Dex USP7i 48hr replicate 2


title: RNA-seq DND41 Dex USP7i 48hr replicate 1


title: MAD-24

value: Cerebellum

value: Engrailed1-Cre;Cicfl/fl (CIC KO)


title: Group 4 IIV8/AS03-IIV5/AS03 Day 85 [P5-5]

value: Day 85


title: Group 4 IIV8/AS03-IIV5/AS03 Day 29 [P5-4]


title: RNA-seq DND41 USP7i 48hr replicate 1

value: human T cell leukemia cells


title: MAD-22

value: H3K27ac (Rabbit monoclonal, D5E4 #8173 Cell Signaling; 1:100)


title: RNA-seq DND41 USP7i 48hr replicate 3


title: RNA-seq DND41 USP7i 48hr replicate 2


title: MAD-21


title: Group 4 IIV8/AS03-IIV5/AS03 Day 7 [P5-3]

value: Day 7


title: Group 4 IIV8/AS03-IIV5/AS03 Day 3 [P5-2]


title: RNA-seq DND41 Dex 48hr replicate 2


title: RNA-seq DND41 DMSO 72hr replicate 1


title: RNA-seq DND41 Dex 48hr replicate 1


title: RNA-seq DND41 Dex 48hr replicate 3


title: MAD-18

value: wildtype


title: RNA-seq DND41 DMSO 48hr replicate 2


title: RNA-seq CUTLL1 shUSP11 replicate 2


title: Group 4 IIV8/AS03-IIV5/AS03 Day 0 [P5-1]


title: RNA-seq DND41 DMSO 48hr replicate 1


title: RNA-seq CUTLL1 shUSP11 replicate 3


title: RNA-seq CUTLL1 shUSP11 replicate 1


title: Group 5 PBS-PBS Day 92 [P49-6]

value: PBS-PBS


title: RNA-seq CUTLL1 Control replicate 3

value: control


title: MAD-14


title: RNA-seq CUTLL1 Control replicate 2


title: RNA-seq CUTLL1 Control replicate 1


title: RNA-seq CUTLL1 Dasatinib 24hr replicate 3

value: dasatininb


title: Group 5 PBS-PBS Day 85 [P49-5]

value: Blood

value: Blood cells


title: Group 5 PBS-PBS Day 29 [P49-4]

value: Day 29


title: RNA-seq DND41 DMSO 48hr replicate 3

value: DMSO


title: RNA-seq CUTLL1 Dasatinib 24hr replicate 2


title: MAD-20

value: CIC (Rabbit polyclonal, in house; 1:2000)


title: MAD-17

value: IgG (Rabbig monoclonal, Millipore, 12-370; 1:100)


title: MAD-12


title: RNA-seq CUTLL1 Dasatinib 24hr replicate 1


title: Group 5 PBS-PBS Day 113 [P49-7]

value: Female

value: Day 113


title: MAD-10

value: Cerebellum


title: RNA-seq CUTLL1 Control 24hr replicate 2


title: Group 5 PBS-PBS Day 7 [P49-3]


title: Group 5 PBS-PBS Day 3 [P49-2]

value: Day 3


title: RNA-seq CUTLL1 Control 24hr replicate 1

value: human T cell leukemia cells


title: 154Q-AXH-CTX-218

data_processing:
Raw reads were trimmed before mapping by Trimmomatic-0.36 using the adapter reference TruSeq3-PE.fa.
STAR v2.7.2d was used to align trimmed reads to the Mus musculus genome (GRCm38.p6, https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26) and to obtain read counts with default parameters
Differential gene expression analysis using DESeq2 package v1.28.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Cortex Tissue

extract_protocol:
Qiagen miRNeasy Kit
RNA libraries were prepared by Genewiz using standard Illumina protocols

value: Cortex Tissue


title: MAD-16


title: Group 2 LAIV8-IIV5 Day 113 [P48-7]

value: Male


title: Group 5 PBS-PBS Day 0 [P49-1]

value: Day 0


title: MAD-9


title: MAD-8

value: wildtype


title: MAD-13


title: 154Q-AXH-CTX-207


title: 154Q-AXH-CTX-209


title: SCA1-CTX-76


title: Group 2 LAIV8-IIV5 Day 92 [P48-6]

value: Day 92


title: MAD-5


title: RNA-seq CUTLL1 Control 24hr replicate 3

value: control


title: MAD-6

value: H3K27ac (Rabbit monoclonal, D5E4 #8173 Cell Signaling; 1:100)


title: SCA1-CTX-75


title: SCA1-CTX-69


title: Group 2 LAIV8-IIV5 Day 85 [P48-5]

value: Blood

value: Blood cells

value: Day 85


title: MAD-4

value: CIC (Rabbit polyclonal, in house; 1:2000)

value: Engrailed1-Cre;Cicfl/fl (CIC KO)


title: WT-CTX-221


title: Group 2 LAIV8-IIV5 Day 29 [P48-4]

value: Day 29


title: 154Q-AXH-CTX-217


title: SCA1-CTX-71


title: WT-CTX-220


title: MAD-1

value: IgG (Rabbig monoclonal, Millipore, 12-370; 1:100)


title: MAD-2

value: Cerebellum


title: Group 2 LAIV8-IIV5 Day 7 [P48-3]

value: Day 7


title: WT-CTX-77


title: WT-CTX-70


title: Group 2 LAIV8-IIV5 Day 3 [P48-2]

value: Day 3


title: 154Q-AXH-STR-218

source_name: Striatal Tissue

value: Striatal Tissue


title: PD-1- T-ALL cells, PDX recipients, RNA-seq 3

city: Guangzhou

first: Guo

last: Qiu

state: Guangdong

address: Guangzhou Avenue

institute: Nanfang Hospital, Southern Medical University

description:
human readcount.txt
PTEN-P-jian-3

data_processing:
Low-quality reads were removed, and the adaptor sequences were trimmed by Trim Galore (v0.6.2).
The remaining pair-end reads were mapped to the reference genome (mouse genome GRCm38 or human genome GRCh38) by Salmon (v0.03.1) with ENCODE options and gene annotated from the Ensembl database
Transcripts per million (TPM) and read counts were quantified by Salmon.
Assembly: GRCm38 or GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: bone marrow

extract_protocol:
Fresh primary T-ALL cells were isolated by Ficoll gradient centrifugation to obtain mononuclear cells, and sorted by FAC sorter (InFlux Cell or FACSARIA III, BD Biosciences), BM cells were markered as SSCAlowCD45dimPD-1- or SSCAlowCD45dimPD-1+. Total mRNA(1 million cells ) was isolated using the RNeasy plus mini kit (74134, QIAGEN) and Performed transcriptome sequencing.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: bone marrow

value: T-ALL cells


title: Group 2 LAIV8-IIV5 Day 0 [P48-1]

value: Male

value: Day 0


title: 154Q-AXH-STR-217


title: AAV8-TBG-Activin A 3

first: Huan

last: Liu

state: Massachusetts

address: 185 Cambridge Street

department: CVRC

institute: Massachusetts General Hospital

data_processing:
Trimmed sequence reads were mapped to GRCm38 (mm10)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values and counts

source_name: Liver

growth_protocol: we studied LDLR-/- mice on a Western diet for 12 weeks and used adeno-associated viral vectors with a liver-specific thyroxine binding globulin (TBG) promoter to express Activin A or GFP (control)

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
TruSeq stranded mRNA kit (Illumina Corp.)  following manufacturer's protocols.

value: Liver

value: LDLR-/-

tag: Sex

value: western diet

value: 12 weeks


title: PD-1- T-ALL cells, PDX recipients, RNA-seq 2

description:
human readcount.txt
PTEN-P-jian-2


title: 154Q-AXH-STR-209

tag: strain


title: AAV8-TBG-Activin A 2


title: AAV8-TBG-Activin A 1


title: PD-1- T-ALL cells, PDX recipients, RNA-seq 1

description:
human readcount.txt
PTEN-P-jian-1


title: Group 1 LAIV8-IIV5/AS03 Day 113 [P47-7]

value: Blood

value: Blood cells

value: Day 113


title: PD-1+ T-ALL cells, PDX recipients, RNA-seq 3

description:
human readcount.txt
PTEN-P-jia-3


title: 154Q-AXH-STR-207


title: AAV8-TBG-Control 3


title: Group 1 LAIV8-IIV5/AS03 Day 85 [P47-5]

value: Day 85


title: PD-1+ T-ALL cells, PDX recipients, RNA-seq 2

description:
human readcount.txt
PTEN-P-jia-2


title: Group 1 LAIV8-IIV5/AS03 Day 92 [P47-6]

value: Day 92


title: SCA1-STR-76


title: AAV8-TBG-Control 2


title: Group 1 LAIV8-IIV5/AS03 Day 29 [P47-4]

value: Day 29


title: PD-1+ T-ALL cells, PDX recipients, RNA-seq 1

description:
human readcount.txt
PTEN-P-jia-1


title: AAV8-TBG-Control 1


title: SCA1-STR-75


title: Group 1 LAIV8-IIV5/AS03 Day 7 [P47-3]

value: Day 7


title: SCA1-STR-71


title: pseudarthrosis_G05_1_C86_TP4_S89

city: Dallas

first: Jonathan

last: Rios

address: 2222 Welborn Street

institute: Scottish Rite for Children

description:
Single-cell RNAseq pseudarthrosis-derived MSCs undergiong osteogenic differentiation for 9 days.
Pseudarthrosis_expression_matrix.txt

data_processing:
Read alignment: HISAT2 v2.1.0
Alignment filtering: Removed duplicates with same start and sequence, keeping read withhighest mapping scoring
Abundance measurement: Raw gene expression counts were calculated relative to RefSeq v93
Genome_build: hg38
Supplementary_files_format_and_content: Expression matrix of raw gene expression counts

molecule: nuclear RNA

source_name: Pseudarthrosis-derived primary MSCs

growth_protocol: MEM-alpha with 10% FBS + antibiotic

extract_protocol:
Cells were isolated and cDNA generated using the Fluidigm C1 instrument and SMARTer Ultra Low RNA Kit, respectively.
Sequencing libraries were generated using the Nextera XT Library Preparation Kit and sequenced using the Illumina HiSeq 2500 generating paired-end 100 bp reads.

treatment_protocol: 100μg/ml L-ascorbic acid 2-phosphate, 10mM β-glycerophosphate, and 100nM Dexamethasone

tag: osteogenesis day

tag: msc source

value: Pseudarthrosis bone

value: Pseudarthrosis-derived primary MSCs


title: pseudarthrosis_D04_1_C67_TP4_S83


title: SCA1-STR-69

value: Striatal Tissue


title: Group 1 LAIV8-IIV5/AS03 Day 3 [P47-2]

value: Day 3


title: Control-FgCre-3-E9

city: Rochester

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
basecalling - bcl2fastq version 2.19.1
read cleaning and filtering - FastP version 0.20.1 with the following parameters: "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y -r".
alignment - STAR_2.7.6a with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM SortedByCoordinate – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReads UnmappedFastx".
read counting - subread-2.0.1 package (featureCounts) and the following parameters: "-s 2 -t exon -g gene_name"
analysis - R v4.0.5, Seurat v4.0.4
Assembly: GRCm38 + Gencode-M25 Annotation
Supplementary files format and content: gene counts

source_name: Epithelium (organ of Corti)

growth_protocol: The following mouse strains were used: Fgfr3-iCre, TetON-CA-ErbB2, and ROSA-floxed-rtTA/GFP.  Fgfr3-iCre and TetON-CA-ERBB2 mice were crosses to generate double heterozygous transgenic mice that were subsequently used as breeders.  In a second breeding, double heterozygous were crossed with homozygous ROSA-floxed-rtTA/GFP mice.  For scRNA-seq experiments, generated pups were genotyped at P0 to identify triple-transgenic mice that harbor Fgfr3-iCre, ROSA-floxed-rtTA/GFP, and TetON-CAERBB2 (named here as CA-ERBB2).  Littermates with Fgfr3-iCre and ROSA-floxed-rtTA/GFP were used as Controls.

extract_protocol:
Cochlea (2-4) from P3 pups were collected and incubated with 1 mL Accutase solution (Innovative Cell Technologies) for 15 minutes at 37°C.  The Accutase solution was removed and cochlea were gentle washes in ice cold Ca2+, Mg2+ - free HBSS buffer.  Organs were dissociated by trituration for 2-3 minutes.  Cells were then filtered with a 40 μm cell strainer (BD Biosciences) and kept on ice until sorted.  For the exclusion of dead cells and debris from the samples during sorting, a single-cell suspension was stained with DAPI.  Sorting was performed at 4°C in a FACSAria II cell sorter (BD Biosciences) using a 130 μm nozzle.  Scatter discrimination was used to eliminate doublets and samples were negatively selected with DAPI to remove dead cells and debris.  For scRNA-seq, single GFP+ cells were captured into 96-well plate with 11.5 ml lysis buffer and RNase Inhibitor without the CDS IIA Oligo (Takara Bio, Mountain View, CA), and stored at -80°C until used for construction of cDNA libraries.
Single-cell RNA-seq libraries were constructed according to the SMART-Seq Single PLUS protocol (Takara Bio, Mountain View, CA).  Frozen 96-well plates with single cells were thawed on ice.  Next, cDNA was generated with the addition of the 3’ SMART-Seq CDS Primer II A and SMARTScribe II RT reagents.  cDNA was amplified via 20 cycles of PCR, purified, and assessed for quantity and quality by Qubit dsDNA assay (ThermoFisher, Waltham, MA) and Fragment Analyzer (Agilent, Santa Clara, CA) analysis, respectively.  For each well, 1 ng amplified cDNA was fragmented and prepared for library construction with the addition of stem-loop adapters.  Final library amplification and indexing was performed through 16 cycles of PCR amplification.  Following bead purification, individual library profiles were assessed by Fragment Analyzer and quantified by Qubit dsDNA assay.  Libraries were diluted, pooled in equimolar amounts, and sequenced on a NovaSeq S1 flowcell (Illumina, San Diego, CA) to generate an average of 10 million reads per cell.

treatment_protocol: The iCRE activity was induced in pups by tamoxifen injections (75 mg/kg) at P0/P1 to label supporting cells with GFP and rtTA.  Doxycycline injections (100 mg/kg) were performed at P2 to drive CA-ERBB2 expression in GFP+ supporting cells.

value: Epithelium (organ of Corti)

value: cochlear supporting cell

value: Fgfr3-iCre, ROSA-floxed-rtTA/GFP


title: Control-FgCre-3-E8


title: pseudarthrosis_A07_1_C06_TP4_S73


title: WT-STR-221

value: wildtype


title: pseudarthrosis_A03_1_C01_TP4_S76


title: WT-STR-220


title: Group 1 LAIV8-IIV5/AS03 Day 0 [P47-1]

value: Male

value: Day 0


title: Control-FgCre-3-E7


title: Control-FgCre-3-E6


title: WT-STR-77


title: pseudarthrosis_A01_1_C03_TP4_S70


title: Group 5 PBS-PBS Day 92 [P46-6]

value: Blood

value: PBS-PBS


title: pseudarthrosis_F07_1_C34_TP4_S77


title: Control-FgCre-3-E5


title: Group 5 PBS-PBS Day 29 [P46-4]

value: Blood cells


title: WT-STR-70


title: Group 5 PBS-PBS Day 85 [P46-5]

value: Day 85


title: Control-FgCre-3-E4


title: pseudarthrosis_G12_1_C88_TP4_S91


title: Control-FgCre-3-E3


title: pseudarthrosis_B05_1_C56_TP4_S85


title: Group 5 PBS-PBS Day 7 [P46-3]


title: pseudarthrosis_A09_1_C04_TP4_S80


title: 154Q-AXH-hipp-218

source_name: Hippocampal Tissue

value: Hippocampal Tissue


title: Group 5 PBS-PBS Day 3 [P46-2]


title: Control-FgCre-3-E2


title: 154Q-AXH-hipp-217


title: pseudarthrosis_E05_1_C74_TP4_S87


title: 154Q-AXH-hipp-209


title: Control-FgCre-3-E1


title: Group 5 PBS-PBS Day 0 [P46-1]


title: pseudarthrosis_G03_1_C39_TP4_S79


title: Control-FgCre-3-E11


title: Group 5 PBS-PBS Day 113 [P46-7]

value: Day 113


title: SCA1-hipp-75


title: Group 4 IIV8/AS03-IIV5/AS03 Day 92 [P45-6]

value: Female

value: Day 92


title: Control-FgCre-3-E10


title: pseudarthrosis_H11_1_C95_TP4_S87

value: Pseudarthrosis bone

value: Pseudarthrosis-derived primary MSCs


title: Control-FgCre-3-D9


title: pseudarthrosis_E11_1_C77_TP4_S85


title: SCA1-hipp-71


title: Control-FgCre-3-D8


title: Group 4 IIV8/AS03-IIV5/AS03 Day 85 [P45-5]


title: pseudarthrosis_E12_1_C76_TP4_S90


title: Group 4 IIV8/AS03-IIV5/AS03 Day 29 [P45-4]

value: Day 29


title: pseudarthrosis_D01_1_C21_TP4_S73


title: SCA1-hipp-69


title: Group 4 IIV8/AS03-IIV5/AS03 Day 3 [P45-2]

value: Day 3


title: WT-hipp-221


title: Control-FgCre-3-D7

value: Epithelium (organ of Corti)

value: cochlear supporting cell


title: SCA1-hipp-76


title: 154Q-AXH-hipp-207


title: Group 4 IIV8/AS03-IIV5/AS03 Day 7 [P45-3]

value: Day 7


title: Control-FgCre-3-D5

value: Fgfr3-iCre, ROSA-floxed-rtTA/GFP


title: Group 4 IIV8/AS03-IIV5/AS03 Day 0 [P45-1]

value: Day 0


title: pseudarthrosis_H04_1_C93_TP4_S84


title: pseudarthrosis_H12_1_C94_TP4_S92


title: WT-hipp-77

value: wildtype


title: Control-FgCre-3-D4


title: Control-FgCre-3-D6


title: Group 4 IIV8/AS03-IIV5/AS03 Day 113 [P45-7]

value: Blood


title: Group 1 LAIV8-IIV5/AS03 Day 113 [P44-7]

value: Blood cells


title: WT-hipp-70


title: Control-FgCre-3-D3


title: pseudarthrosis_F03_1_C33_TP4_S78


title: Control-FgCre-3-D2


title: Group 1 LAIV8-IIV5/AS03 Day 92 [P44-6]


title: 154Q-AXH-BS-218

source_name: Brainstem Tissue

value: Brainstem Tissue


title: Group 1 LAIV8-IIV5/AS03 Day 85 [P44-5]

value: Day 85


title: 154Q-AXH-BS-209


title: Control-FgCre-3-D1


title: WT-hipp-220

value: Hippocampal Tissue


title: pseudarthrosis_H06_1_C91_TP4_S72


title: Control-FgCre-3-D12


title: Control-FgCre-3-D11


title: Group 1 LAIV8-IIV5/AS03 Day 7 [P44-3]

value: Female


title: SCA1-BS-76


title: pseudarthrosis_C07_1_C18_TP4_S75


title: SCA1-BS-71


title: SCA1-BS-75


title: Group 1 LAIV8-IIV5/AS03 Day 29 [P44-4]


title: Control-FgCre-3-D10


title: 154Q-AXH-BS-207


title: Group 1 LAIV8-IIV5/AS03 Day 3 [P44-2]


title: pseudarthrosis_F08_1_C35_TP4_S79


title: pseudarthrosis_C05_1_C62_TP4_S86


title: pseudarthrosis_G01_1_C37_TP4_S74


title: pseudarthrosis_F11_1_C83_TP4_S86


title: pseudarthrosis_H10_1_C96_TP4_S83


title: SCA1-BS-69


title: Control-FgCre-3-C8


title: WT-BS-221


title: Control-FgCre-3-C9


title: Control-FgCre-3-C7


title: Group 4 IIV8/AS03-IIV5/AS03 Day 113 [P43-7]

value: Day 113


title: pseudarthrosis_C11_1_C65_TP4_S84

value: Pseudarthrosis bone


title: pseudarthrosis_F06_1_C79_TP4_S70

value: Pseudarthrosis-derived primary MSCs


title: Group 4 IIV8/AS03-IIV5/AS03 Day 85 [P43-5]


title: WT-BS-220


title: pseudarthrosis_B09_1_C10_TP4_S81


title: Group 1 LAIV8-IIV5/AS03 Day 0 [P44-1]


title: Control-FgCre-3-C6


title: Group 4 IIV8/AS03-IIV5/AS03 Day 29 [P43-4]

value: Day 29


title: WT-BS-77


title: pseudarthrosis_G07_1_C40_TP4_S78


title: Group 4 IIV8/AS03-IIV5/AS03 Day 7 [P43-3]


title: Control-FgCre-3-C5


title: WT-BS-70


title: Control-FgCre-3-C4


title: pseudarthrosis_B01_1_C09_TP4_S71


title: 154Q-AXH-CB-218

source_name: Cerebellar Tissue

value: Cerebellar Tissue


title: Group 4 IIV8/AS03-IIV5/AS03 Day 92 [P43-6]

value: Day 92


title: pseudarthrosis_C04_1_C61_TP4_S82


title: 154Q-AXH-CB-217


title: Control-FgCre-3-C3

value: Epithelium (organ of Corti)

value: cochlear supporting cell


title: Group 4 IIV8/AS03-IIV5/AS03 Day 0 [P43-1]


title: Control-FgCre-3-C2

value: Fgfr3-iCre, ROSA-floxed-rtTA/GFP


title: pseudarthrosis_B07_1_C12_TP4_S74


title: Group 2 LAIV8-IIV5 Day 92 [P42-6]


title: 154Q-AXH-CB-209


title: pseudarthrosis_F05_1_C80_TP4_S88


title: Control-FgCre-3-C1


title: pseudarthrosis_H03_1_C45_TP4_S80


title: 154Q-AXH-CB-207


title: Control-FgCre-3-C12


title: SCA1-CB-76


title: Group 2 LAIV8-IIV5 Day 85 [P42-5]


title: Group 4 IIV8/AS03-IIV5/AS03 Day 3 [P43-2]

value: Day 3


title: Control-FgCre-3-C11


title: pseudarthrosis_H05_1_C92_TP4_S90


title: Group 2 LAIV8-IIV5 Day 29 [P42-4]


title: pseudarthrosis_C06_1_C63_TP4_S91


title: Control-FgCre-3-C10


title: SCA1-CB-71


title: Control-FgCre-3-B9


title: Group 2 LAIV8-IIV5 Day 7 [P42-3]

value: Day 7


title: pseudarthrosis_D12_1_C72_TP4_S89


title: Control-FgCre-3-B8


title: SCA1-CB-69


title: Group 2 LAIV8-IIV5 Day 113 [P42-7]

value: Blood


title: pseudarthrosis_D09_1_C22_TP4_S82


title: Group 2 LAIV8-IIV5 Day 3 [P42-2]

value: Blood cells


title: Group 2 LAIV8-IIV5 Day 0 [P42-1]

value: Day 0


title: pseudarthrosis_G02_1_C38_TP4_S75


title: Group 4 IIV8/AS03-IIV5/AS03 Day 113 [P41-7]


title: WT-CB-221

value: wildtype


title: Control-FgCre-3-B7


title: pseudarthrosis_B12_1_C60_TP4_S88


title: Group 4 IIV8/AS03-IIV5/AS03 Day 92 [P41-6]


title: Control-FgCre-3-B6


title: SCA1-CB-75


title: WT-CB-77


title: WT-CB-70


title: pseudarthrosis_G06_1_C85_TP4_S71


title: Group 4 IIV8/AS03-IIV5/AS03 Day 85 [P41-5]

value: Day 85


title: Control-FgCre-3-B5


title: pseudarthrosis_D06_1_C69_TP4_S92


title: Group 4 IIV8/AS03-IIV5/AS03 Day 29 [P41-4]

value: Female


title: PD-1- T-ALL cells, Pten null, RNA-seq 3

description:
mose readcount.txt
H-PD1-jian-3

value: bone marrow

value: T-ALL cells


title: Control-FgCre-3-B4


title: Control-FgCre-3-B3


title: pseudarthrosis_D03_1_C19_TP4_S77

value: Pseudarthrosis bone

value: Pseudarthrosis-derived primary MSCs


title: Group 4 IIV8/AS03-IIV5/AS03 Day 7 [P41-3]


title: pseudarthrosis_A04_1_C49_TP4_S81


title: WT-CB-220

value: Cerebellar Tissue


title: Control-FgCre-3-B1


title: Control-FgCre-3-B12


title: pseudarthrosis_C01_1_C15_TP4_S72


title: pseudarthrosis_D07_1_C24_TP4_S76


title: PD-1+ T-ALL cells, Pten null, RNA-seq 3

description:
mose readcount.txt
H-PD1-jia-3


title: Control-FgCre-3-B11


title: Group 4 IIV8/AS03-IIV5/AS03 Day 3 [P41-2]


title: PD-1- T-ALL cells, Pten null, RNA-seq 2

description:
mose readcount.txt
H-PD1-jian-2


title: pseudarthrosis_H06_1_C91_TP3_S62

description:
Single-cell RNAseq pseudarthrosis-derived MSCs undergiong osteogenic differentiation for 6 days.
Pseudarthrosis_expression_matrix.txt


title: PD-1+ T-ALL cells, Pten null, RNA-seq 2

description:
mose readcount.txt
H-PD1-jia-2


title: PD-1- T-ALL cells, NOTCH1 induced, RNA-seq 3

description:
notch1 T-ALLmodel fpkm.txt
N1-PD1-jian-3


title: pseudarthrosis_H05_1_C92_TP3_S56


title: Group 4 IIV8/AS03-IIV5/AS03 Day 85 [P40-5]


title: PD-1+ T-ALL cells, Pten null, RNA-seq 1

description:
mose readcount.txt
H-PD1-jia-1


title: Control-FgCre-3-A9


title: PD-1- T-ALL cells, NOTCH1 induced, RNA-seq 2

description:
notch1 T-ALLmodel fpkm.txt
N1-PD1-jian-2


title: Group 4 IIV8/AS03-IIV5/AS03 Day 29 [P40-4]

value: Day 29


title: Control-FgCre-3-A8

value: Epithelium (organ of Corti)


title: Control-FgCre-3-B2

value: cochlear supporting cell


title: pseudarthrosis_H04_1_C93_TP3_S49


title: pseudarthrosis_H02_1_C44_TP3_S59


title: PD-1- T-ALL cells, Pten null, RNA-seq 1

description:
mose readcount.txt
H-PD1-jian-1


title: Group 4 IIV8/AS03-IIV5/AS03 Day 7 [P40-3]


title: Control-FgCre-3-A7

value: Fgfr3-iCre, ROSA-floxed-rtTA/GFP


title: Group 4 IIV8/AS03-IIV5/AS03 Day 0 [P41-1]


title: PD-1- T-ALL cells, NOTCH1 induced, RNA-seq 1

description:
notch1 T-ALLmodel fpkm.txt
N1-PD1-jian-1


title: Group 4 IIV8/AS03-IIV5/AS03 Day 113 [P40-7]

value: Day 113


title: pseudarthrosis_G07_1_C40_TP3_S66


title: Group 4 IIV8/AS03-IIV5/AS03 Day 3 [P40-2]

value: Day 3


title: PD-1+ T-ALL cells, NOTCH1 induced, RNA-seq 3

description:
notch1 T-ALLmodel fpkm.txt
N1-PD1-jia-3


title: Group 1 LAIV8-IIV5/AS03 Day 113 [P4-7]

value: Blood


title: Control-FgCre-3-A6


title: Control-FgCre-3-B10


title: pseudarthrosis_G06_1_C85_TP3_S61


title: Group 4 IIV8/AS03-IIV5/AS03 Day 0 [P40-1]

value: Blood cells


title: Control-FgCre-3-A5


title: Group 4 IIV8/AS03-IIV5/AS03 Day 92 [P40-6]

value: Day 92


title: PD-1+ T-ALL cells, NOTCH1 induced, RNA-seq 1

description:
notch1 T-ALLmodel fpkm.txt
N1-PD1-jia-1


title: pseudarthrosis_G04_1_C87_TP3_S48


title: Control-FgCre-3-A4


title: PD-1+ T-ALL cells, NOTCH1 induced, RNA-seq 2

description:
notch1 T-ALLmodel fpkm.txt
N1-PD1-jia-2


title: pseudarthrosis_G01_1_C37_TP3_S53


title: Group 1 LAIV8-IIV5/AS03 Day 92 [P4-6]


title: WAT_RPF1

city: San Diego

first: April

middle: Elizabeth

last: Williams

state: California

address: 10010 N Torrey Pines Rd

department: IGC

institute: Salk Institute for Biological Studies

data_processing:
Library strategy: Ribo-Seq
Raw sequencing data was quality assessed using fastqc (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
After trimming adapters with Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), removal of mm10 rRNA and tRNA sequences, and alignment to the mm10 genome with STAR v2.53b (Dobin et. al., 2014)
Stringtie v2.1.4 (PMCID: PMC4643835) and MAPS v1.0(PMCID: PMC5870951) were run using default parameters on combined alignments from total and mRNA RNA-Seq libraries from BAT, beige, and WAT adipocytes, followed by 3-frame translated using a custom script GTFtoFasta (see PMC7085969 for details).
The resulting 3-frame translated ORF databases were then scored for translation using ribORF (PMCID: PMC6168376) with the pipeline described by Martinez et al (PMC7085969), which briefly included shifting reads of each length to obtain base-pair resolution, and then scoring each candidate smORF using ribORF, keeping only highly scoring (score ≥ 0.7), short (≤ 150 aa), and novel (not overlapped with known coding regions in RefSeq, and a maximum blastp alignment evalue  to SwissProt (Bairoch and Apweiler, 1997) of 100).
The resulting microproteins were then collated into a non-redundant table and were further annotated using HOMER (Heinz et al, PMID: 20513432; genomic location of their ORFs), and using PhyloCSF (Lin et al, 2014; conservation from a multi-way alignment of mammals) as described previously (PMC7085969).
Candidate microproteins were then split into categories based on the genomic location of their ORF with respect to genomic features: uORFs exist upstream of known genes, non-uORFs are all other ORFs, iORFs specifically exist in intergenic regions, while dORFs exist downstream of known genes. These categories of ORFs were then further tested for expression in RNA-Seq datasets and visualized using read pileup tracks.
Genome_build: mm10
Supplementary_files_format_and_content: Excel table containing annotated microproteins

source_name: white adipose tissue

growth_protocol: Twenty female C57Bl6/J mice aged 7 weeks old were sacrificed using an overdose of anaesthesia. Interscapular and subscapular BAT was excised with dissecting scissors, being careful to avoid surrounding muscle and white adipose tissue. For white adipose tissue, subcutaneous (scWAT) depots were excised bilaterally. Fat pads were placed collectively in a 50 mL falcon containing ice-cold DMEM.  DMEM was carefully decanted through a mesh filter, and the pads washed briefly in HBSS. Most of the HBSS was then decanted, before transferring each tube of fat pads to a single well of a 6-well culture plate. Dissecting scissors were then used to thoroughly mince each collection of pooled fat explants. Digests were performed in the following solutions (pre-warmed to 37 ºC): 1) for scWAT, 40 mg Collagenase Type I with 80 mg Collagenase Type II in 28 mL Hanks BSS and 12 mL 7.5% w/v BSA (Sigma); 2) for BAT, 80 mg Collagenase Type I with 80 mg Collagenase Type II in 28 mL Hanks BSS and 12 mL 7.5% w/v BSA (Sigma). Digests were incubated at 37 ºC for 15-20 mins with shaking (225 rpm), resulting in complete dissociation of adipose tissue. Digests were then filtered through a 100 μm mesh (yellow) into 50 ml falcon tubes and allowed to sit on ice for 20 minutes. Visible fat floating as a layer was carefully aspirated. Working from the top, the supernatant was pipetted into a clean 50 ml Falcon tube, leaving behind the lowest 10 ml of digested material. This fraction is enriched for pre-adipocytes and was mixed 1:1 with 10% newborn calf serum. Cells were spun down at 700 g for 15 minutes and resuspended in growth media consisting of: 1) for scWAT (“scWAT media”), DMEM plus 10% NCS with Pen/Strep, 4 mM Glutamax, 150 μM sodium ascorbate, 30 nM insulin, and 1 μM rosiglitazone; and 2) for BAT (“BAT media”) DMEM plus 10% NCS with Pen/Strep, 4 mM Glutamax, 150 μM sodium ascorbate, 4 nM insulin, and 2 nM T3. Cells were spun again for 10 minutes and resuspended ready for plating in the following volumes (based on 2 ml of media for each well seeded): 1) for scWAT, a ratio of 5 mice in 38 mL of plating media with suspended cells, and 2) for BAT, a ratio of 5 mice in 25 mL of plating media with suspended cells. Cells were plated into 6-well dishes with 2 mL of cell suspension per well. Cells cultured as the “Beige” phenotype represent the scWAT cultures that were switched to the BAT media 24 hours after plating in the scWAT media. Media was changed daily for days 1-4 and every other day from days 4-8. On day 6, media was changed to phenol red free DMEM and rosiglitazone was removed from the scWAT cultures to allow wash out before harvest. All cultures were treated or harvested or both on day 8

extract_protocol:
For sample collection of BAT/WAT/Beige cultures for Ribo-Seq and total mRNA-Seq used for smORF discovery, each culture was washed directly out of the incubators 3x with ice-cold PBS supplemented with 100μg/mL cyclohexamide (Fisher Scientific #AAJ66004X). After the last wash, liquid nitrogen was gently ladled onto the surfaces of the cells and plates were stored at -80 °C prior to Ribo-Seq analysis. Each biological replicate for Ribo-Seq in our experiments represents 11 wells of a 6-well dish leaving one well to be lysed with Trizol reagent (Thermo #15596026) for the bulk mRNA-Seq used int the de novo transcriptome assembly of the cells under analysis. Cells were lysed with 400 μl of ice-cold lysis buffer (20 mM Tris–HCl, pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1% Triton X-100, with 1 mM DTT, 25 U ml−1 Turbo DNase (Thermo Fisher, catalog no. AM2238) and 100 μg ml−1 CHX added fresh) was dripped onto the plate. Cells were incubated on ice in lysis buffer for 10 min with periodic vortexing and pipetting to disperse the cells. The lysate was then clarified by centrifugation at 15,000g for 10 min. Cell lysates were flash-frozen in liquid nitrogen and stored at −80 °C for up to 7 d before ribosome footprinting. For each cell type, ribosome footprinting was carried out by digesting 40-60 μg of RNA in 200-300 μL lysate with 0.375 U/μg−1 RNase I (Lucigen, N6901K) for 50 min at room temperature. Digestion reactions were quenched with 200 U Superase-In RNase I inhibitor (Thermo Fisher, AM2694) on ice. Following digestion, monosomes were purified from small RNA fragments using MicroSpin S-400 HR columns (GE Life Sciences), and ribosome protected RNA fragments (RPFs) were extracted by acid phenol chloroform and isopropanol precipitation.
Sequencing libraries were prepared as in (McGlincy et al. 2017) with some modifications. First, the Ribo-Zero Mammalian Kit (Illumina) was used to deplete rRNA after RPF extraction and just prior to RPF size selection by gel extraction. Second, the Zymo clean & concentrator step after adaptor ligation is omitted and the reaction was carried over straight into reverse transcription. For the reverse transcription step to form cDNA, Episcript RT(Lucigen, ERT12910K) was used. Following reverse transcription, excess primer was degraded using Exonuclease I (Lucigen, X40520K) and the RNA templates were degraded using Hybridase (Lucigen, H39500). For the cDNA circularization step, CircLigase I (Lucigen, CL4111K) was used. PCR amplification was then carried out using Phusion Hot Start II High-Fidelity Master Mix (Thermo Fisher, F565L) for 9-12 cycles. The adapters and primers for library construction used were as follows: 3’ adapter – 5’-/5phos/AGATCGGAAGAGCACACGTCTGAA/3ddC/-3’; RT primer – 5’-/5Phos/AGATCGGAAGAGCGTCGTGTAGGGAAAGAG/iSp18/GTGACTGGAGTTCAGACGTGTGCTC-3’; PCR forward primer – 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’; Illumina TruSeq Ribo Profile (Mammalian) Library Prep Kit index primers 1 – 12.
Ribosome footprinting

value: adipose tissue

tag: tissue subtype

value: white adipose tissue (WAT)

tag: replicate


title: Control-FgCre-3-A3


title: BAT_RPF1

source_name: brown adipose tissue

value: brown adipose tissue (BAT)


title: pseudarthrosis_F07_1_C34_TP3_S65


title: Group 1 LAIV8-IIV5/AS03 Day 85 [P4-5]

value: Female

value: Day 85


title: Control-FgCre-3-A2


title: Group 1 LAIV8-IIV5/AS03 Day 29 [P4-4]


title: Control-FgCre-3-A1


title: Control-FgCre-3-A12


title: pseudarthrosis_G05_1_C86_TP3_S55

value: Pseudarthrosis bone


title: Group 1 LAIV8-IIV5/AS03 Day 7 [P4-3]

value: Day 7


title: pseudarthrosis_F05_1_C80_TP3_S54

value: Pseudarthrosis-derived primary MSCs


title: EDFig10_MediumDose_Mouse3_Lung

data_processing: Unprocessed

source_name: Heart (Left Ventricle Apex)

extract_protocol:
Genomic DNA was extracted using the Qiagen DNeasy blood and tissue kit
PCR of the target region of DNA was conducted, followed by an additional short barcoding PCR for Illumina Sequencing

treatment_protocol: AAV vectors encoding ABE8e-NG and sgRNA targeting the editor to the target R403Q mutation were injected into disease model mice intrathoracically.

value: Heart (Left Ventricle Apex)

value: Myh6 R403Q Heterozygous HCM Model Mouse


title: Group 1 LAIV8-IIV5/AS03 Day 3 [P4-2]


title: EDFig10_MediumDose_Mouse3_SkMuscle


title: EDFig10_MediumDose_Mouse3_Liver


title: EDFig10_MediumDose_Mouse3_Kidney


title: Control-FgCre-3-A10

value: Epithelium (organ of Corti)

value: cochlear supporting cell


title: pseudarthrosis_F03_1_C33_TP3_S65


title: pseudarthrosis_F02_1_C32_TP3_S58


title: Group 1 LAIV8-IIV5/AS03 Day 0 [P4-1]

value: Day 0


title: Group 5 PBS-PBS Day 113 [P39-7]

value: Male

value: PBS-PBS

value: Day 113


title: Control-FgCre-3-A11

value: Fgfr3-iCre, ROSA-floxed-rtTA/GFP


title: Group 5 PBS-PBS Day 92 [P39-6]

value: Blood

value: Blood cells

value: Day 92


title: EDFig10_MediumDose_Mouse3_Gonad


title: EDFig10_MediumDose_Mouse2_SkMuscle


title: Control-FgCre-2-E9


title: Control-FgCre-2-E8


title: Group 5 PBS-PBS Day 85 [P39-5]


title: EDFig10_MediumDose_Mouse2_Lung


title: pseudarthrosis_E07_1_C28_TP3_S64


title: pseudarthrosis_F06_1_C79_TP3_S60


title: Control-FgCre-2-E6


title: pseudarthrosis_E06_1_C73_TP3_S59


title: Group 5 PBS-PBS Day 29 [P39-4]

value: Day 29


title: Control-FgCre-2-E7


title: Group 5 PBS-PBS Day 7 [P39-3]


title: Control-FgCre-2-E5


title: pseudarthrosis_E05_1_C74_TP3_S53


title: EDFig10_MediumDose_Mouse2_Kidney


title: pseudarthrosis_E03_1_C27_TP3_S64


title: EDFig10_MediumDose_Mouse2_Gonad


title: pseudarthrosis_F01_1_C31_TP3_S52


title: Group 5 PBS-PBS Day 3 [P39-2]

value: Day 3


title: pseudarthrosis_E02_1_C26_TP3_S57

value: Pseudarthrosis bone


title: Control-FgCre-2-E3


title: Group 5 PBS-PBS Day 0 [P39-1]


title: pseudarthrosis_E01_1_C25_TP3_S51


title: Group 4 IIV8/AS03-IIV5/AS03 Day 92 [P38-6]


title: pseudarthrosis_D05_1_C68_TP3_S52


title: Group 4 IIV8/AS03-IIV5/AS03 Day 113 [P38-7]


title: Group 4 IIV8/AS03-IIV5/AS03 Day 85 [P38-5]

value: Day 85


title: Control-FgCre-2-E1


title: EDFig10_MediumDose_Mouse1_Kidney


title: EDFig10_MediumDose_Mouse1_Gonad


title: pseudarthrosis_D04_1_C67_TP3_S69

value: Pseudarthrosis-derived primary MSCs


title: pseudarthrosis_E04_1_C75_TP3_S47


title: Control-FgCre-2-E10


title: Control-FgCre-2-E11


title: Group 4 IIV8/AS03-IIV5/AS03 Day 29 [P38-4]


title: EDFig10_LowDose_Mouse3_SkMuscle

value: Heart (Left Ventricle Apex)


title: pseudarthrosis_D03_1_C19_TP3_S63


title: EDFig10_MediumDose_Mouse2_Liver

value: Myh6 R403Q Heterozygous HCM Model Mouse


title: Group 4 IIV8/AS03-IIV5/AS03 Day 7 [P38-3]

value: Day 7


title: Control-FgCre-2-E4

value: Epithelium (organ of Corti)

value: cochlear supporting cell


title: EDFig10_MediumDose_Mouse1_SkMuscle


title: Group 4 IIV8/AS03-IIV5/AS03 Day 3 [P38-2]

value: Male


title: pseudarthrosis_D01_1_C21_TP3_S50


title: Control-FgCre-2-D9


title: EDFig10_MediumDose_Mouse1_Lung


title: Control-FgCre-2-E2


title: Control-FgCre-2-D8


title: pseudarthrosis_C08_1_C17_TP3_S69


title: EDFig10_LowDose_Mouse3_Liver


title: Group 4 IIV8/AS03-IIV5/AS03 Day 0 [P38-1]

value: Day 0


title: EDFig10_LowDose_Mouse3_Lung


title: pseudarthrosis_C05_1_C62_TP3_S51


title: Group 4 IIV8/AS03-IIV5/AS03 Day 113 [P37-7]

value: Female

value: Day 113


title: EDFig10_MediumDose_Mouse1_Liver


title: Control-FgCre-2-D6

value: Fgfr3-iCre, ROSA-floxed-rtTA/GFP


title: pseudarthrosis_C04_1_C61_TP3_S68


title: Group 4 IIV8/AS03-IIV5/AS03 Day 92 [P37-6]

value: Blood

value: Blood cells


title: EDFig10_LowDose_Mouse3_Gonad


title: EDFig10_LowDose_Mouse3_Kidney


title: Control-FgCre-2-D5


title: Group 4 IIV8/AS03-IIV5/AS03 Day 85 [P37-5]


title: pseudarthrosis_C03_1_C13_TP3_S62


title: Control-FgCre-2-D4


title: EDFig10_LowDose_Mouse2_SkMuscle


title: Group 4 IIV8/AS03-IIV5/AS03 Day 29 [P37-4]

value: Day 29


title: Group 4 IIV8/AS03-IIV5/AS03 Day 7 [P37-3]


title: EDFig10_LowDose_Mouse2_Lung


title: pseudarthrosis_C01_1_C15_TP3_S49


title: Control-FgCre-2-D3


title: pseudarthrosis_C02_1_C14_TP3_S56


title: EDFig10_LowDose_Mouse2_Liver


title: pseudarthrosis_B08_1_C11_TP3_S68


title: Group 4 IIV8/AS03-IIV5/AS03 Day 3 [P37-2]

value: Day 3


title: Control-FgCre-2-D7


title: Control-FgCre-2-D2


title: pseudarthrosis_B07_1_C12_TP3_S63

value: Pseudarthrosis bone


title: Control-FgCre-2-D12


title: EDFig10_LowDose_Mouse2_Gonad


title: Control-FgCre-2-D1


title: EDFig10_LowDose_Mouse2_Kidney


title: Group 4 IIV8/AS03-IIV5/AS03 Day 0 [P37-1]


title: Group 2 LAIV8-IIV5 Day 113 [P36-7]


title: EDFig10_LowDose_Mouse1_SkMuscle


title: Control-FgCre-2-D11


title: pseudarthrosis_B06_1_C57_TP3_S58


title: Group 2 LAIV8-IIV5 Day 92 [P36-6]

value: Day 92


title: pseudarthrosis_B05_1_C56_TP3_S50

value: Pseudarthrosis-derived primary MSCs


title: Control-FgCre-2-D10


title: EDFig10_LowDose_Mouse1_Lung

value: Heart (Left Ventricle Apex)


title: Group 2 LAIV8-IIV5 Day 85 [P36-5]

value: Day 85


title: pseudarthrosis_B04_1_C55_TP3_S67


title: pseudarthrosis_B03_1_C07_TP3_S61


title: Control-FgCre-2-C9


title: EDFig10_LowDose_Mouse1_Liver

value: Myh6 R403Q Heterozygous HCM Model Mouse


title: Group 2 LAIV8-IIV5 Day 29 [P36-4]


title: EDFig10_LowDose_Mouse1_Kidney


title: pseudarthrosis_B02_1_C08_TP3_S55


title: Control-FgCre-2-C8

value: Epithelium (organ of Corti)


title: EDFig10_LowDose_Mouse1_Gonad


title: Group 2 LAIV8-IIV5 Day 7 [P36-3]

value: Day 7


title: pseudarthrosis_B01_1_C09_TP3_S48


title: Group 2 LAIV8-IIV5 Day 3 [P36-2]

value: Male


title: EDFig10_HighDose_Mouse2_SkMuscle


title: Control-FgCre-2-C6

value: cochlear supporting cell


title: pseudarthrosis_A08_1_C05_TP3_S67


title: Group 2 LAIV8-IIV5 Day 0 [P36-1]

value: Day 0


title: Control-FgCre-2-C7


title: EDFig10_HighDose_Mouse2_Lung


title: Control-FgCre-2-C5


title: pseudarthrosis_A06_1_C51_TP3_S57


title: Group 1 LAIV8-IIV5/AS03 Day 113 [P35-7]

value: Female

value: Day 113


title: Control-FgCre-2-C4

value: Fgfr3-iCre, ROSA-floxed-rtTA/GFP


title: Control-FgCre-2-C3


title: EDFig10_HighDose_Mouse2_Kidney


title: Group 1 LAIV8-IIV5/AS03 Day 92 [P35-6]

value: Blood

value: Blood cells


title: Group 1 LAIV8-IIV5/AS03 Day 85 [P35-5]


title: pseudarthrosis_A04_1_C49_TP3_S66


title: pseudarthrosis_A03_1_C01_TP3_S60


title: EDFig10_HighDose_Mouse2_Gonad


title: EDFig10_HighDose_Mouse1_SkMuscle


title: Group 1 LAIV8-IIV5/AS03 Day 29 [P35-4]

value: Day 29


title: Control-FgCre-2-C1


title: Group 1 LAIV8-IIV5/AS03 Day 7 [P35-3]


title: pseudarthrosis_A02_1_C02_TP3_S54

value: Pseudarthrosis bone


title: pseudarthrosis_A01_1_C03_TP3_S47


title: Control-FgCre-2-C12


title: EDFig10_HighDose_Mouse1_Lung


title: Group 1 LAIV8-IIV5/AS03 Day 3 [P35-2]

value: Day 3


title: Control-FgCre-2-C11


title: Group 1 LAIV8-IIV5/AS03 Day 0 [P35-1]


title: EDFig10_HighDose_Mouse1_Liver


title: Group 1 LAIV8-IIV5/AS03 Day 113 [P34-7]


title: pseudarthrosis_H04_1_C93_TP2_S30

description:
Single-cell RNAseq pseudarthrosis-derived MSCs undergiong osteogenic differentiation for 3 days.
Pseudarthrosis_expression_matrix.txt

value: Pseudarthrosis-derived primary MSCs


title: pseudarthrosis_H03_1_C45_TP2_S46


title: EDFig10_HighDose_Mouse1_Gonad

value: Heart (Left Ventricle Apex)


title: Control-FgCre-2-C10


title: EDFig10_HighDose_Mouse1_Kidney


title: pseudarthrosis_H05_1_C92_TP2_S36


title: EDFig10_HighDose_Mouse2_Liver


title: pseudarthrosis_H02_1_C44_TP2_S38


title: pseudarthrosis_H01_1_C43_TP2_S31


title: Group 1 LAIV8-IIV5/AS03 Day 92 [P34-6]

value: Day 92


title: EDFig9c_5weekMediumDose_Mouse3

value: Myh6 R403Q Heterozygous HCM Model Mouse


title: Control-FgCre-2-C2

value: Epithelium (organ of Corti)


title: Group 1 LAIV8-IIV5/AS03 Day 85 [P34-5]

value: Day 85


title: EDFig9c_5weekMediumDose_Mouse2


title: Group 1 LAIV8-IIV5/AS03 Day 29 [P34-4]


title: pseudarthrosis_G06_1_C85_TP2_S42


title: EDFig9c_5weekMediumDose_Mouse1


title: pseudarthrosis_G04_1_C87_TP2_S29


title: Group 1 LAIV8-IIV5/AS03 Day 7 [P34-3]

value: Day 7


title: Control-FgCre-2-B6

value: cochlear supporting cell


title: EDFig9c_5weekLowDose_Mouse2


title: pseudarthrosis_G03_1_C39_TP2_S45


title: Control-FgCre-2-B9


title: Group 1 LAIV8-IIV5/AS03 Day 3 [P34-2]


title: pseudarthrosis_G02_1_C38_TP2_S37


title: EDFig9c_5weekLowDose_Mouse1


title: Control-FgCre-2-B4


title: EDFig9c_5weekHighDose_Mouse3


title: Control-FgCre-2-B3


title: pseudarthrosis_G01_1_C37_TP2_S30


title: EDFig9c_5weekHighDose_Mouse2


title: Group 5 PBS-PBS Day 113 [P33-7]

value: Male

value: PBS-PBS


title: Control-FgCre-2-B2


title: Control-FgCre-2-B8


title: Group 5 PBS-PBS Day 92 [P33-6]


title: Control-FgCre-2-B7


title: pseudarthrosis_F06_1_C79_TP2_S41


title: pseudarthrosis_F05_1_C80_TP2_S35


title: EDFig9a_Treated_WithGuide_Mouse2

value: WT


title: Control-FgCre-2-B1

value: Fgfr3-iCre, ROSA-floxed-rtTA/GFP


title: Group 5 PBS-PBS Day 85 [P33-5]

value: Blood


title: pseudarthrosis_F04_1_C81_TP2_S28


title: Control-FgCre-2-B5


title: Group 5 PBS-PBS Day 29 [P33-4]

value: Blood cells


title: EDFig9a_Treated_WithGuide_Mouse1


title: pseudarthrosis_F03_1_C33_TP2_S44


title: Group 5 PBS-PBS Day 7 [P33-3]


title: Group 1 LAIV8-IIV5/AS03 Day 0 [P34-1]

value: Female

value: Day 0


title: Control-FgCre-2-B11


title: Control-FgCre-2-B10


title: EDFig9a_Treated_NoGuide_Mouse2


title: pseudarthrosis_F01_1_C31_TP2_S29

value: Pseudarthrosis bone


title: Group 5 PBS-PBS Day 3 [P33-2]

value: Day 3


title: EDFig9a_Treated_NoGuide_Mouse1

value: Heart (Left Ventricle Apex)


title: EDFig8b_30weekTreatedMouse3_OT9


title: Control-FgCre-2-A9


title: Group 5 PBS-PBS Day 0 [P33-1]


title: pseudarthrosis_E04_1_C75_TP2_S27

value: Pseudarthrosis-derived primary MSCs


title: Control-FgCre-2-A8


title: EDFig9c_5weekHighDose_Mouse1

value: Myh6 R403Q Heterozygous HCM Model Mouse


title: Control-FgCre-2-A7

value: Epithelium (organ of Corti)


title: EDFig8b_30weekTreatedMouse3_OT8


title: pseudarthrosis_E03_1_C27_TP2_S43


title: Group 1 LAIV8-IIV5/AS03 Day 92 [P32-6]

value: Day 92


title: pseudarthrosis_E02_1_C26_TP2_S36


title: Control-FgCre-2-A6


title: Group 1 LAIV8-IIV5/AS03 Day 113 [P32-7]

value: Day 113


title: EDFig8b_30weekTreatedMouse3_OT6


title: Control-FgCre-2-B12

value: cochlear supporting cell


title: EDFig8b_30weekTreatedMouse3_OT7


title: pseudarthrosis_E01_1_C25_TP2_S28


title: Control-FgCre-2-A5


title: Group 1 LAIV8-IIV5/AS03 Day 29 [P32-4]

value: Male

value: Day 29


title: EDFig8b_30weekTreatedMouse3_OT5


title: Control-FgCre-2-A4


title: pseudarthrosis_E06_1_C73_TP2_S40


title: EDFig8b_30weekTreatedMouse3_OT4


title: Group 1 LAIV8-IIV5/AS03 Day 7 [P32-3]

value: Day 7


title: Group 1 LAIV8-IIV5/AS03 Day 0 [P32-1]


title: pseudarthrosis_D05_1_C68_TP2_S34


title: Group 1 LAIV8-IIV5/AS03 Day 85 [P32-5]

value: Day 85


title: pseudarthrosis_D06_1_C69_TP2_S39


title: EDFig8b_30weekTreatedMouse3_OT3


title: EDFig8b_30weekTreatedMouse3_OT2


title: Control-FgCre-2-A2

value: Fgfr3-iCre, ROSA-floxed-rtTA/GFP


title: Control-FgCre-2-A3


title: Control-FgCre-2-A1


title: pseudarthrosis_D03_1_C19_TP2_S42


title: EDFig8b_30weekTreatedMouse3_OT16


title: Group 2 LAIV8-IIV5 Day 113 [P31-7]

value: Blood

value: Blood cells


title: pseudarthrosis_D02_1_C20_TP2_S35


title: Control-FgCre-2-A12


title: EDFig8b_30weekTreatedMouse3_OT15


title: Control-FgCre-2-A11


title: Group 2 LAIV8-IIV5 Day 85 [P31-5]

value: Female


title: pseudarthrosis_D01_1_C21_TP2_S27

value: Pseudarthrosis bone


title: EDFig8b_30weekTreatedMouse3_OT14


title: Control-FgCre-2-A10


title: pseudarthrosis_D07_1_C24_TP2_S46


title: Control-FgCre-1-E9


title: Group 2 LAIV8-IIV5 Day 29 [P31-4]


title: EDFig8b_30weekTreatedMouse3_OT13


title: pseudarthrosis_C07_1_C18_TP2_S45


title: pseudarthrosis_C06_1_C63_TP2_S38


title: Group 1 LAIV8-IIV5/AS03 Day 3 [P32-2]

value: Day 3


title: EDFig8b_30weekTreatedMouse3_OT12

value: Heart (Left Ventricle Apex)


title: Group 2 LAIV8-IIV5 Day 7 [P31-3]


title: Control-FgCre-1-E8


title: Group 2 LAIV8-IIV5 Day 92 [P31-6]


title: pseudarthrosis_C04_1_C61_TP2_S26

value: Pseudarthrosis-derived primary MSCs


title: Group 2 LAIV8-IIV5 Day 3 [P31-2]


title: EDFig8b_30weekTreatedMouse3_OT11

value: Myh6 R403Q Heterozygous HCM Model Mouse


title: pseudarthrosis_C05_1_C62_TP2_S33


title: pseudarthrosis_C03_1_C13_TP2_S41


title: EDFig8b_30weekTreatedMouse3_OT10


title: Control-FgCre-1-E7

value: Epithelium (organ of Corti)


title: Control-FgCre-1-E5


title: Control-FgCre-1-E4


title: Group 2 LAIV8-IIV5 Day 0 [P31-1]

value: Day 0


title: pseudarthrosis_C02_1_C14_TP2_S34


title: Group 1 LAIV8-IIV5/AS03 Day 92 [P30-6]

value: Day 92


title: Group 1 LAIV8-IIV5/AS03 Day 113 [P30-7]

value: Day 113


title: pseudarthrosis_C01_1_C15_TP2_S26


title: EDFig8b_30weekTreatedMouse2_OT9


title: Group 1 LAIV8-IIV5/AS03 Day 29 [P30-4]


title: EDFig8b_30weekTreatedMouse2_OT8


title: Control-FgCre-1-E3

value: cochlear supporting cell


title: Group 1 LAIV8-IIV5/AS03 Day 85 [P30-5]


title: Control-FgCre-1-E2


title: pseudarthrosis_B05_1_C56_TP2_S32


title: EDFig8b_30weekTreatedMouse2_OT6


title: EDFig8b_30weekTreatedMouse2_OT7


title: Group 1 LAIV8-IIV5/AS03 Day 7 [P30-3]


title: Control-FgCre-1-E1


title: Control-FgCre-1-E6


title: EDFig8b_30weekTreatedMouse3_OT1


title: pseudarthrosis_B04_1_C55_TP2_S25


title: Control-FgCre-1-E11


title: Group 1 LAIV8-IIV5/AS03 Day 3 [P30-2]


title: EDFig8b_30weekTreatedMouse2_OT5


title: Group 1 LAIV8-IIV5/AS03 Day 0 [P30-1]


title: EDFig8b_30weekTreatedMouse2_OT4


title: pseudarthrosis_B03_1_C07_TP2_S40


title: EDFig8b_30weekTreatedMouse2_OT3


title: pseudarthrosis_B07_1_C12_TP2_S44


title: pseudarthrosis_B01_1_C09_TP2_S25


title: Group 5 PBS-PBS Day 113 [P3-7]

value: PBS-PBS


title: Control-FgCre-1-D8


title: pseudarthrosis_A07_1_C06_TP2_S43


title: EDFig8b_30weekTreatedMouse2_OT2


title: Group 5 PBS-PBS Day 85 [P3-5]


title: Control-FgCre-1-D7


title: pseudarthrosis_A06_1_C51_TP2_S37


title: Group 5 PBS-PBS Day 29 [P3-4]

value: Day 29


title: pseudarthrosis_A05_1_C50_TP2_S31


title: Group 5 PBS-PBS Day 7 [P3-3]

value: Day 7


title: Control-FgCre-1-D6

value: Fgfr3-iCre, ROSA-floxed-rtTA/GFP


title: EDFig8b_30weekTreatedMouse2_OT14


title: Group 5 PBS-PBS Day 3 [P3-2]

value: Blood


title: Control-FgCre-1-E10


title: pseudarthrosis_B02_1_C08_TP2_S33


title: pseudarthrosis_A03_1_C01_TP2_S39


title: Control-FgCre-1-D4


title: pseudarthrosis_A04_1_C49_TP2_S24


title: Control-FgCre-1-D5


title: Control-FgCre-1-D9


title: Group 5 PBS-PBS Day 92 [P3-6]

value: Blood cells


title: EDFig8b_30weekTreatedMouse2_OT13


title: EDFig8b_30weekTreatedMouse2_OT12


title: Group 5 PBS-PBS Day 0 [P3-1]

value: Female


title: pseudarthrosis_A02_1_C02_TP2_S32

value: Pseudarthrosis bone


title: Group 4 IIV8/AS03-IIV5/AS03 Day 113 [P29-7]

value: Male


title: EDFig8b_30weekTreatedMouse2_OT16

value: Heart (Left Ventricle Apex)


title: Control-FgCre-1-D3


title: EDFig8b_30weekTreatedMouse2_OT11


title: Control-FgCre-1-D2


title: pseudarthrosis_A01_1_C03_TP2_S24

value: Pseudarthrosis-derived primary MSCs


title: EDFig8b_30weekTreatedMouse2_OT10

value: Myh6 R403Q Heterozygous HCM Model Mouse


title: pseudarthrosis_H11_1_C95_TP1_S19

description:
Single-cell RNAseq pseudarthrosis-derived MSCs undifferentiated.
Pseudarthrosis_expression_matrix.txt


title: Group 4 IIV8/AS03-IIV5/AS03 Day 92 [P29-6]


title: EDFig8b_30weekTreatedMouse2_OT15


title: Group 4 IIV8/AS03-IIV5/AS03 Day 85 [P29-5]

value: Day 85


title: EDFig8b_30weekTreatedMouse2_OT1


title: pseudarthrosis_H10_2_C96_TP1_S11


title: Group 4 IIV8/AS03-IIV5/AS03 Day 29 [P29-4]


title: EDFig8b_30weekTreatedMouse1_OT9


title: Control-FgCre-1-D12

value: Epithelium (organ of Corti)


title: Control-FgCre-1-D11


title: Group 4 IIV8/AS03-IIV5/AS03 Day 3 [P29-2]

value: Day 3


title: Group 4 IIV8/AS03-IIV5/AS03 Day 0 [P29-1]

value: Day 0


title: Group 4 IIV8/AS03-IIV5/AS03 Day 7 [P29-3]


title: pseudarthrosis_H08_1_C47_TP1_S20


title: EDFig8b_30weekTreatedMouse1_OT7


title: pseudarthrosis_H09_1_C48_TP1_S3


title: Control-FgCre-1-D10

value: cochlear supporting cell


title: pseudarthrosis_H07_1_C46_TP1_S15


title: pseudarthrosis_H01_1_C43_TP1_S7


title: EDFig8b_30weekTreatedMouse1_OT6


title: Control-FgCre-1-D1


title: EDFig8b_30weekTreatedMouse1_OT5


title: Control-FgCre-1-C8


title: Control-FgCre-1-C7


title: Control-FgCre-1-C9


title: pseudarthrosis_G11_1_C89_TP1_S18


title: pseudarthrosis_G10_1_C90_TP1_S10


title: Control-FgCre-1-C6


title: EDFig8b_30weekTreatedMouse1_OT4


title: Group 2 LAIV8-IIV5 Day 85 [P28-5]


title: Group 2 LAIV8-IIV5 Day 113 [P28-7]

value: Day 113


title: EDFig8b_30weekTreatedMouse1_OT3


title: Control-FgCre-1-C5


title: pseudarthrosis_G08_1_C41_TP1_S19


title: EDFig8b_30weekTreatedMouse1_OT2


title: EDFig8b_30weekTreatedMouse1_OT8


title: Group 2 LAIV8-IIV5 Day 7 [P28-3]


title: pseudarthrosis_F11_1_C83_TP1_S17


title: Group 2 LAIV8-IIV5 Day 3 [P28-2]


title: EDFig8b_30weekTreatedMouse1_OT15


title: Control-FgCre-1-C3


title: EDFig8b_30weekTreatedMouse1_OT16


title: pseudarthrosis_F09_1_C36_TP1_S2


title: Control-FgCre-1-C2


title: pseudarthrosis_F07_1_C34_TP1_S14


title: Group 2 LAIV8-IIV5 Day 0 [P28-1]


title: Group 1 LAIV8-IIV5/AS03 Day 113 [P27-7]


title: Control-FgCre-1-C1


title: Control-FgCre-1-C12


title: Group 2 LAIV8-IIV5 Day 92 [P28-6]

value: Day 92


title: EDFig8b_30weekTreatedMouse1_OT13


title: Control-FgCre-1-C11


title: pseudarthrosis_E11_1_C77_TP1_S16


title: Control-FgCre-1-C4


title: Control-FgCre-1-C10


title: EDFig8b_30weekTreatedMouse1_OT11


title: EDFig8b_30weekTreatedMouse1_OT12


title: Group 2 LAIV8-IIV5 Day 29 [P28-4]

value: Day 29


title: Group 1 LAIV8-IIV5/AS03 Day 85 [P27-5]


title: Group 1 LAIV8-IIV5/AS03 Day 29 [P27-4]


title: Group 1 LAIV8-IIV5/AS03 Day 92 [P27-6]


title: EDFig8b_30weekTreatedMouse1_OT10


title: pseudarthrosis_E10_1_C78_TP1_S8


title: pseudarthrosis_G01_1_C37_TP1_S6


title: Control-FgCre-1-B9

value: Fgfr3-iCre, ROSA-floxed-rtTA/GFP


title: EDFig8b_30weekTreatedMouse1_OT14


title: pseudarthrosis_E07_1big_C28_TP1_S13


title: Group 1 LAIV8-IIV5/AS03 Day 7 [P27-3]

value: Blood

value: Day 7


title: EDFig8b_30weekTreatedMouse1_OT1


title: pseudarthrosis_E01_1_C25_TP1_S4


title: pseudarthrosis_F01_1_C31_TP1_S5


title: Group 1 LAIV8-IIV5/AS03 Day 3 [P27-2]

value: Blood cells

value: Female


title: Control-FgCre-1-B8


title: EDFig8a_5weekTreatedMouse2_OT9


title: Group 1 LAIV8-IIV5/AS03 Day 0 [P27-1]


title: pseudarthrosis_D12_1_C72_TP1_S23

value: Pseudarthrosis bone


title: Group 1 LAIV8-IIV5/AS03 Day 113 [P26-7]

value: Male


title: EDFig8a_5weekTreatedMouse2_OT8

value: Heart (Left Ventricle Apex)


title: EDFig8a_5weekTreatedMouse2_OT7

value: Myh6 R403Q Heterozygous HCM Model Mouse


title: pseudarthrosis_D10_1_C70_TP1_S7

value: Pseudarthrosis-derived primary MSCs


title: Control-FgCre-1-B5

value: Epithelium (organ of Corti)


title: Control-FgCre-1-B6


title: EDFig8a_5weekTreatedMouse2_OT6


title: EDFig8a_5weekTreatedMouse2_OT5


title: pseudarthrosis_D09_1_C22_TP1_S23


title: pseudarthrosis_D11_1big_C71_TP1_S15


title: pseudarthrosis_D08_1_C23_TP1_S18


title: Control-FgCre-1-B4


title: Control-FgCre-1-B3


title: Group 1 LAIV8-IIV5/AS03 Day 85 [P26-5]

value: Day 85


title: EDFig8a_5weekTreatedMouse2_OT4


title: Control-FgCre-1-B2


title: Group 1 LAIV8-IIV5/AS03 Day 92 [P26-6]


title: Group 1 LAIV8-IIV5/AS03 Day 29 [P26-4]


title: Control-FgCre-1-B7


title: pseudarthrosis_C12_1_C66_TP1_S22


title: pseudarthrosis_D01_1_C21_TP1_S3


title: Control-FgCre-1-B1


title: EDFig8a_5weekTreatedMouse2_OT2


title: Group 1 LAIV8-IIV5/AS03 Day 7 [P26-3]


title: Group 1 LAIV8-IIV5/AS03 Day 3 [P26-2]

value: Day 3


title: Control-FgCre-1-B12

value: cochlear supporting cell


title: pseudarthrosis_C11_1_C65_TP1_S14


title: Group 1 LAIV8-IIV5/AS03 Day 0 [P26-1]

value: Day 0


title: EDFig8a_5weekTreatedMouse2_OT16


title: Control-FgCre-1-B11


title: pseudarthrosis_C09_1_C16_TP1_S22


title: Control-FgCre-1-B10


title: Group 5 PBS-PBS Day 113 [P25-7]

value: PBS-PBS

value: Day 113


title: EDFig8a_5weekTreatedMouse2_OT15


title: EDFig8a_5weekTreatedMouse2_OT3


title: Group 5 PBS-PBS Day 85 [P25-5]


title: pseudarthrosis_B12_1_C60_TP1_S21


title: EDFig8a_5weekTreatedMouse2_OT13


title: Control-FgCre-1-A9

value: Fgfr3-iCre, ROSA-floxed-rtTA/GFP


title: EDFig8a_5weekTreatedMouse2_OT14


title: pseudarthrosis_B11_1_C59_TP1_S13


title: Control-FgCre-1-A8


title: Group 5 PBS-PBS Day 92 [P25-6]

value: Blood

value: Day 92


title: Group 5 PBS-PBS Day 29 [P25-4]

value: Blood cells

value: Day 29


title: EDFig8a_5weekTreatedMouse2_OT12


title: pseudarthrosis_B10_1_C58_TP1_S5

value: Pseudarthrosis bone


title: Control-FgCre-1-A7


title: Group 5 PBS-PBS Day 7 [P25-3]

value: Male

value: Day 7


title: EDFig8a_5weekTreatedMouse2_OT11

value: Heart (Left Ventricle Apex)

value: Myh6 R403Q Heterozygous HCM Model Mouse


title: Group 5 PBS-PBS Day 3 [P25-2]


title: pseudarthrosis_B08_1_C11_TP1_S17

value: Pseudarthrosis-derived primary MSCs


title: EDFig8a_5weekTreatedMouse2_OT10


title: Control-FgCre-1-A6

value: Epithelium (organ of Corti)


title: pseudarthrosis_B01_1_C09_TP1_S2


title: Control-FgCre-1-A5


title: Control-FgCre-1-A4


title: EDFig8a_5weekTreatedMouse2_OT1


title: Group 5 PBS-PBS Day 0 [P25-1]


title: pseudarthrosis_C10_1_C64_TP1_S6


title: Control-FgCre-1-A3


title: pseudarthrosis_A12_1_C54_TP1_S20


title: Group 2 LAIV8-IIV5 Day 113 [P24-7]

value: Female


title: pseudarthrosis_A11_1_C53_TP1_S12


title: EDFig8a_5weekTreatedMouse1_OT9


title: pseudarthrosis_A10_1_C52_TP1_S4


title: Group 2 LAIV8-IIV5 Day 92 [P24-6]


title: Control-FgCre-1-A2

value: cochlear supporting cell


title: Control-FgCre-1-A1


title: pseudarthrosis_A08_1_C05_TP1_S16


title: EDFig8a_5weekTreatedMouse1_OT8


title: EDFig8a_5weekTreatedMouse1_OT6


title: Group 2 LAIV8-IIV5 Day 85 [P24-5]

value: Day 85


title: EDFig8a_5weekTreatedMouse1_OT5


title: Control-FgCre-1-A11


title: Control-FgCre-1-A12


title: Group 2 LAIV8-IIV5 Day 7 [P24-3]


title: Control-FgCre-1-A10


title: pseudarthrosis_A07_1_C06_TP1_S9


title: Group 2 LAIV8-IIV5 Day 3 [P24-2]

value: Day 3


title: Group 2 LAIV8-IIV5 Day 0 [P24-1]

value: Day 0


title: pseudarthrosis_A01_1_C03_TP1_S1


title: EDFig8a_5weekTreatedMouse1_OT3


title: EDFig8a_5weekTreatedMouse1_OT4


title: CAErbB-3-E9

value: Tamoxifen injection at day 0/day 1 of age (P0/P1); Doxycycline injection at P2; collected tissue at P3


title: pseudarthrosis_A03_1_C01_TP1_S8


title: pseudarthrosis_A09_1_C04_TP1_S21


title: EDFig8a_5weekTreatedMouse1_OT7


title: Group 2 LAIV8-IIV5 Day 29 [P24-4]

value: Blood


title: Group 1 LAIV8-IIV5/AS03 Day 113 [P23-7]

value: Day 113