title: control_H04_1_C93_TP4_S94

description:
Single-cell RNAseq control bone-derived MSCs undergiong osteogenic differentiation for 9 days.
control_expression_matrix.txt

source_name: Control bone-derived primary MSCs

value: Control bone-derived primary MSCs


title: Group 1 LAIV8-IIV5/AS03 Day 92 [P23-6]

status: Public on Dec 13 2022

type: SRA

city: New York

first: Ana

middle: S.

last: Gonzalez-Reiche

state: New York

address: 1 Gustave L. Levy Pl

department: Genetics and Genomic Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

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

library_source: transcriptomic

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

organism: Homo sapiens

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

tag: tissue

value: Blood

tag: cell type

value: Blood cells

tag: gender

value: Female

tag: treatment

tag: time

value: Day 92


title: CAErbB-3-E7

city: Rochester

first: Cameron

last: Baker

state: NY

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

organism: Mus musculus

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

tag: genotype

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


title: Group 1 LAIV8-IIV5/AS03 Day 85 [P23-5]

value: Day 85


title: control_H03_1_C45_TP4_S93

city: Dallas

first: Jonathan

last: Rios

state: TX

address: 2222 Welborn Street

institute: Scottish Rite for Children

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

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


title: EDFig8a_5weekTreatedMouse1_OT16

city: Boston

first: Daniel

last: DeLaughter

state: MA

address: 7 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

library_source: genomic

data_processing: Unprocessed

molecule: genomic DNA

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: control_H02_1_C44_TP4_S92


title: EDFig8a_5weekTreatedMouse1_OT15


title: CAErbB-3-E6


title: CAErbB-3-E5


title: Group 1 LAIV8-IIV5/AS03 Day 29 [P23-4]

value: Day 29


title: EDFig8a_5weekTreatedMouse1_OT14


title: CAErbB-3-E4


title: Group 1 LAIV8-IIV5/AS03 Day 7 [P23-3]

value: Day 7


title: control_F08_1_C35_TP4_S90


title: Group 1 LAIV8-IIV5/AS03 Day 3 [P23-2]

value: Day 3


title: EDFig8a_5weekTreatedMouse1_OT12


title: CAErbB-3-E3


title: control_F05_1_C80_TP4_S89


title: CAErbB-3-E2


title: Group 1 LAIV8-IIV5/AS03 Day 0 [P23-1]

value: Day 0


title: CAErbB-3-E8


title: EDFig8a_5weekTreatedMouse1_OT2


title: control_F04_1_C81_TP4_S1


title: Group 2 LAIV8-IIV5 Day 113 [P22-7]

value: Day 113


title: control_F03_1_C33_TP4_S95


title: CAErbB-3-E1


title: Group 2 LAIV8-IIV5 Day 92 [P22-6]


title: EDFig8a_5weekTreatedMouse1_OT10


title: EDFig8a_5weekTreatedMouse1_OT1


title: CAErbB-3-E11


title: control_F02_1_C32_TP4_S94


title: control_H01_1_C43_TP4_S91


title: Group 2 LAIV8-IIV5 Day 85 [P22-5]


title: CAErbB-3-E10


title: EDFig8a_5weekTreatedMouse1_OT13


title: control_F01_1_C31_TP4_S93


title: EDFig8ab_UntreatedMouse3_OT9

value: UntreatedControl


title: EDFig8ab_UntreatedMouse3_OT8


title: Group 2 LAIV8-IIV5 Day 29 [P22-4]


title: CAErbB-3-D9


title: Group 2 LAIV8-IIV5 Day 7 [P22-3]


title: control_E10_1_C78_TP4_S88

value: Control bone-derived primary MSCs


title: CAErbB-3-D8


title: control_E09_1_C30_TP4_S87


title: EDFig8a_5weekTreatedMouse1_OT11


title: EDFig8ab_UntreatedMouse3_OT6


title: Group 2 LAIV8-IIV5 Day 3 [P22-2]

value: Blood


title: CAErbB-3-D7


title: EDFig8ab_UntreatedMouse3_OT5


title: control_E07_1_C28_TP4_S86


title: CAErbB-3-D6


title: control_E06_1_C73_TP4_S92


title: Group 2 LAIV8-IIV5 Day 0 [P22-1]

value: Blood cells


title: EDFig8ab_UntreatedMouse3_OT4


title: CAErbB-3-D5


title: Group 5 PBS-PBS Day 113 [P21-7]

value: Female

value: PBS-PBS


title: control_E02_1_C26_TP4_S90


title: EDFig8ab_UntreatedMouse3_OT3


title: CAErbB-3-D4

value: Epithelium (organ of Corti)


title: control_E05_1_C74_TP4_S91


title: EDFig8ab_UntreatedMouse3_OT7


title: Group 5 PBS-PBS Day 29 [P21-4]


title: CAErbB-3-D3

value: cochlear supporting cell


title: EDFig8ab_UntreatedMouse3_OT2


title: EDFig8ab_UntreatedMouse3_OT16


title: control_D09_1_C22_TP4_S84


title: EDFig8ab_UntreatedMouse3_OT15


title: CAErbB-3-D2

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


title: Group 5 PBS-PBS Day 7 [P21-3]


title: control_D07_1_C24_TP4_S83


title: Group 5 PBS-PBS Day 3 [P21-2]


title: CAErbB-3-D1


title: EDFig8ab_UntreatedMouse3_OT14


title: control_D06_1_C69_TP4_S89


title: Group 5 PBS-PBS Day 92 [P21-6]

value: Day 92


title: Group 5 PBS-PBS Day 0 [P21-1]


title: EDFig8ab_UntreatedMouse3_OT13

value: Heart (Left Ventricle Apex)


title: CAErbB-3-D11


title: control_D05_1_C68_TP4_S88


title: Group 2 LAIV8-IIV5 Day 113 [P20-7]


title: EDFig8ab_UntreatedMouse3_OT12

value: Myh6 R403Q Heterozygous HCM Model Mouse


title: CAErbB-3-D10


title: control_D11_1_C71_TP4_S85


title: Group 5 PBS-PBS Day 85 [P21-5]

value: Day 85


title: control_D04_1_C67_TP4_S87


title: EDFig8ab_UntreatedMouse3_OT11


title: control_D02_1_C20_TP4_S86


title: CAErbB-3-C9


title: EDFig8ab_UntreatedMouse3_OT10


title: Group 2 LAIV8-IIV5 Day 85 [P20-5]


title: Group 2 LAIV8-IIV5 Day 92 [P20-6]


title: CAErbB-3-C8


title: control_D01_1_C21_TP4_S85


title: Group 2 LAIV8-IIV5 Day 29 [P20-4]

value: Day 29


title: control_C12_1_C66_TP4_S82


title: CAErbB-3-D12


title: EDFig8ab_UntreatedMouse2_OT9


title: EDFig8ab_UntreatedMouse3_OT1


title: CAErbB-3-C7


title: control_C11_1_C65_TP4_S81


title: EDFig8ab_UntreatedMouse2_OT8


title: control_C10_1_C64_TP4_S80


title: EDFig8ab_UntreatedMouse2_OT7


title: CAErbB-3-C6


title: CAErbB-3-C5


title: CAErbB-3-C4


title: control_C09_1_C16_TP4_S79


title: control_C08_1_C17_TP4_S78


title: Group 4 IIV8/AS03-IIV5/AS03 Day 113 [P2-7]

value: Male


title: CAErbB-3-C3


title: Group 4 IIV8/AS03-IIV5/AS03 Day 92 [P2-6]


title: EDFig8ab_UntreatedMouse2_OT6


title: EDFig8ab_UntreatedMouse2_OT5


title: CAErbB-3-C2


title: EDFig8ab_UntreatedMouse2_OT4


title: Group 2 LAIV8-IIV5 Day 7 [P20-3]

value: Day 7


title: Group 4 IIV8/AS03-IIV5/AS03 Day 29 [P2-4]


title: Group 2 LAIV8-IIV5 Day 3 [P20-2]

value: Day 3


title: Group 4 IIV8/AS03-IIV5/AS03 Day 85 [P2-5]


title: EDFig8ab_UntreatedMouse2_OT3

value: UntreatedControl


title: control_C06_1_C63_TP4_S84

value: Control bone-derived primary MSCs


title: control_C04_1_C61_TP4_S83


title: Group 4 IIV8/AS03-IIV5/AS03 Day 7 [P2-3]

value: Blood


title: CAErbB-3-C1


title: control_C07_1_C18_TP4_S77


title: EDFig8ab_UntreatedMouse2_OT2


title: CAErbB-3-C11


title: CAErbB-3-C12


title: Group 2 LAIV8-IIV5 Day 0 [P20-1]

value: Blood cells

value: Day 0


title: CAErbB-3-C10


title: EDFig8ab_UntreatedMouse2_OT16


title: Group 4 IIV8/AS03-IIV5/AS03 Day 0 [P2-1]


title: control_B12_1_C60_TP4_S76


title: EDFig8ab_UntreatedMouse2_OT15


title: control_B11_1_C59_TP4_S75


title: Group 1 LAIV8-IIV5/AS03 Day 113 [P19-7]

value: Female

value: Day 113


title: CAErbB-3-B9

value: Epithelium (organ of Corti)

value: cochlear supporting cell


title: control_B10_1_C58_TP4_S74


title: EDFig8ab_UntreatedMouse2_OT14


title: Group 1 LAIV8-IIV5/AS03 Day 92 [P19-6]

value: Day 92


title: EDFig8ab_UntreatedMouse2_OT13

value: Heart (Left Ventricle Apex)


title: control_C01_1_C15_TP4_S82


title: Group 1 LAIV8-IIV5/AS03 Day 29 [P19-4]


title: control_B07_1_C12_TP4_S73


title: EDFig8ab_UntreatedMouse2_OT11

value: Myh6 R403Q Heterozygous HCM Model Mouse


title: control_B06_1_C57_TP4_S81


title: EDFig8ab_UntreatedMouse2_OT12


title: CAErbB-3-B5

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


title: CAErbB-3-B7


title: CAErbB-3-B4


title: Group 4 IIV8/AS03-IIV5/AS03 Day 3 [P2-2]


title: EDFig8ab_UntreatedMouse2_OT10


title: control_B04_1_C55_TP4_S79


title: CAErbB-3-B6


title: Group 1 LAIV8-IIV5/AS03 Day 3 [P19-2]


title: control_B05_1_C56_TP4_S80


title: EDFig8ab_UntreatedMouse2_OT1


title: Group 1 LAIV8-IIV5/AS03 Day 0 [P19-1]


title: EDFig8ab_UntreatedMouse1_OT9


title: CAErbB-3-B8


title: control_B03_1_C07_TP4_S78


title: control_A06_1_C51_TP4_S77


title: CAErbB-3-B3


title: CAErbB-3-B2


title: Group 4 IIV8/AS03-IIV5/AS03 Day 113 [P18-7]


title: EDFig8ab_UntreatedMouse1_OT8


title: Group 1 LAIV8-IIV5/AS03 Day 85 [P19-5]

value: Day 85


title: Group 1 LAIV8-IIV5/AS03 Day 7 [P19-3]


title: control_A04_1_C49_TP4_S76


title: CAErbB-3-B1


title: Group 4 IIV8/AS03-IIV5/AS03 Day 92 [P18-6]


title: EDFig8ab_UntreatedMouse1_OT7


title: EDFig8ab_UntreatedMouse1_OT6


title: Group 4 IIV8/AS03-IIV5/AS03 Day 85 [P18-5]


title: control_A03_1_C01_TP4_S75


title: control_A02_1_C02_TP4_S74


title: CAErbB-3-B12


title: EDFig8ab_UntreatedMouse1_OT5


title: control_H06_1_C91_TP2_S48

description:
Single-cell RNAseq control bone-derived MSCs undergiong osteogenic differentiation for 3 days.
control_expression_matrix.txt


title: CAErbB-3-B10


title: control_A01_1_C03_TP4_S73


title: Group 4 IIV8/AS03-IIV5/AS03 Day 29 [P18-4]

value: Day 29


title: CAErbB-3-B11


title: Group 4 IIV8/AS03-IIV5/AS03 Day 7 [P18-3]

value: Day 7


title: Group 4 IIV8/AS03-IIV5/AS03 Day 3 [P18-2]

value: Day 3


title: CAErbB-3-A9


title: EDFig8ab_UntreatedMouse1_OT3

value: UntreatedControl


title: CAErbB-3-A8


title: Group 4 IIV8/AS03-IIV5/AS03 Day 0 [P18-1]


title: control_H05_1_C92_TP2_S47

value: Control bone-derived primary MSCs


title: control_H04_1_C93_TP2_S46


title: CAErbB-3-A7


title: Group 2 LAIV8-IIV5 Day 113 [P17-7]

value: Blood


title: CAErbB-3-A6


title: EDFig8ab_UntreatedMouse1_OT4


title: control_H03_1_C45_TP2_S45


title: EDFig8ab_UntreatedMouse1_OT15


title: control_H01_1_C43_TP2_S44


title: EDFig8ab_UntreatedMouse1_OT14


title: CAErbB-3-A5


title: CAErbB-3-A4


title: Group 2 LAIV8-IIV5 Day 29 [P17-4]

value: Blood cells


title: control_G04_1_C87_TP2_S42


title: control_G03_1_C39_TP2_S41


title: EDFig8ab_UntreatedMouse1_OT2


title: Group 2 LAIV8-IIV5 Day 3 [P17-2]


title: EDFig8ab_UntreatedMouse1_OT11


title: EDFig8ab_UntreatedMouse1_OT12


title: CAErbB-3-A3


title: CAErbB-3-A2


title: CAErbB-3-A1


title: EDFig8ab_UntreatedMouse1_OT10


title: Group 2 LAIV8-IIV5 Day 0 [P17-1]

value: Day 0


title: control_F04_1_C81_TP2_S40


title: EDFig8ab_UntreatedMouse1_OT16


title: control_F02_1_C32_TP2_S39


title: Group 2 LAIV8-IIV5 Day 92 [P17-6]

value: Female


title: CAErbB-3-A12


title: Group 1 LAIV8-IIV5/AS03 Day 113 [P16-7]

value: Day 113


title: EDFig8ab_UntreatedMouse1_OT13


title: Group 2 LAIV8-IIV5 Day 85 [P17-5]


title: control_G06_1_C85_TP2_S43


title: control_F01_1_C31_TP2_S38


title: Group 1 LAIV8-IIV5/AS03 Day 92 [P16-6]


title: EDFig8ab_UntreatedMouse1_OT1


title: CAErbB-3-A11

value: Epithelium (organ of Corti)


title: Group 2 LAIV8-IIV5 Day 7 [P17-3]


title: CAErbB-3-A10

value: cochlear supporting cell


title: control_E06_1_C73_TP2_S37


title: EDFig4c_SkMuscle_Mouse6

source_name: Skeletal Muscle

value: Skeletal Muscle

value: SingleDoseABE


title: Group 1 LAIV8-IIV5/AS03 Day 85 [P16-5]


title: EDFig4c_SkMuscle_Mouse5

value: Myh6 R403Q Heterozygous HCM Model Mouse


title: CAErbB-2-E9

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


title: Group 1 LAIV8-IIV5/AS03 Day 7 [P16-3]


title: EDFig4c_SkMuscle_Mouse3


title: EDFig4c_SkMuscle_Mouse4


title: control_E03_1_C27_TP2_S45


title: CAErbB-2-E8


title: Group 1 LAIV8-IIV5/AS03 Day 3 [P16-2]


title: control_E04_1_C75_TP2_S46


title: Group 1 LAIV8-IIV5/AS03 Day 29 [P16-4]


title: control_E02_1_C26_TP2_S44


title: CAErbB-2-E6


title: CAErbB-2-E7


title: Group 1 LAIV8-IIV5/AS03 Day 0 [P16-1]


title: EDFig4c_SkMuscle_Mouse1


title: EDFig4c_SkMuscle_Mouse2


title: CAErbB-2-E5


title: CAErbB-2-E4


title: Group 1 LAIV8-IIV5/AS03 Day 113 [P15-7]


title: Group 1 LAIV8-IIV5/AS03 Day 92 [P15-6]

value: Day 92


title: EDFig4c_Lung_Mouse6

source_name: Lung

value: Lung


title: control_E01_1_C25_TP2_S43


title: EDFig4c_Lung_Mouse5


title: control_D05_1_C68_TP2_S42


title: control_D04_1_C67_TP2_S41


title: control_E05_1_C74_TP2_S47


title: Group 1 LAIV8-IIV5/AS03 Day 85 [P15-5]

value: Day 85


title: EDFig4c_Lung_Mouse4


title: control_D03_1_C19_TP2_S40


title: Group 1 LAIV8-IIV5/AS03 Day 29 [P15-4]

value: Day 29


title: CAErbB-2-E2


title: CAErbB-2-E3


title: EDFig4c_Lung_Mouse3


title: EDFig4c_Lung_Mouse2


title: CAErbB-2-E1


title: control_D01_1_C21_TP2_S38


title: control_D02_1_C20_TP2_S39


title: Group 1 LAIV8-IIV5/AS03 Day 7 [P15-3]

value: Day 7


title: Group 1 LAIV8-IIV5/AS03 Day 3 [P15-2]

value: Day 3


title: EDFig4c_Lung_Mouse1


title: EDFig4c_Liver_Mouse6

source_name: Liver

value: Liver


title: control_C08_1_C17_TP2_S36

value: Control bone-derived primary MSCs


title: CAErbB-2-E10


title: Group 1 LAIV8-IIV5/AS03 Day 0 [P15-1]

value: Blood

value: Blood cells

value: Day 0


title: CAErbB-2-E11

value: Epithelium (organ of Corti)


title: control_C07_1_C18_TP2_S35


title: CAErbB-2-D9

value: cochlear supporting cell


title: EDFig4c_Liver_Mouse5


title: Group 1 LAIV8-IIV5/AS03 Day 113 [P14-7]

value: Female

value: Day 113


title: EDFig4c_Liver_Mouse4

value: Myh6 R403Q Heterozygous HCM Model Mouse

value: SingleDoseABE


title: Group 1 LAIV8-IIV5/AS03 Day 92 [P14-6]

value: Day 92


title: control_C05_1_C62_TP2_S37


title: CAErbB-2-D7

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


title: control_C04_1_C61_TP2_S36


title: CAErbB-2-D6


title: control_C03_1_C13_TP2_S35


title: EDFig4c_Liver_Mouse3


title: CAErbB-2-D8


title: Group 1 LAIV8-IIV5/AS03 Day 29 [P14-4]


title: control_C02_1_C14_TP2_S34


title: EDFig4c_Liver_Mouse1


title: EDFig4c_Liver_Mouse2


title: Group 1 LAIV8-IIV5/AS03 Day 7 [P14-3]


title: CAErbB-2-D4


title: EDFig4c_Gonad_Mouse6

source_name: Gonad

value: Gonad


title: CAErbB-2-D5


title: Group 1 LAIV8-IIV5/AS03 Day 3 [P14-2]


title: CAErbB-2-D3


title: Group 1 LAIV8-IIV5/AS03 Day 85 [P14-5]

value: Day 85


title: control_B12_1_C60_TP2_S34


title: EDFig4c_Gonad_Mouse5


title: Group 1 LAIV8-IIV5/AS03 Day 0 [P14-1]


title: CAErbB-2-D2


title: CAErbB-2-D1


title: Group 5 PBS-PBS Day 113 [P13-7]

value: PBS-PBS


title: control_B10_1_C58_TP2_S32


title: Group 5 PBS-PBS Day 92 [P13-6]


title: CAErbB-2-D12


title: EDFig4c_Gonad_Mouse3


title: control_C01_1_C15_TP2_S33


title: Group 5 PBS-PBS Day 85 [P13-5]


title: Group 5 PBS-PBS Day 29 [P13-4]

value: Day 29


title: EDFig4c_Gonad_Mouse2


title: control_B07_1_C12_TP2_S29


title: control_B09_1_C10_TP2_S31


title: CAErbB-2-D10


title: CAErbB-2-D11


title: EDFig4c_EDFig10_Untreated_Mouse3_Lung

value: Lung

value: UntreatedControl


title: EDFig4c_Gonad_Mouse1


title: Group 5 PBS-PBS Day 3 [P13-2]

value: Blood

value: Day 3


title: Group 5 PBS-PBS Day 7 [P13-3]

value: Blood cells

value: Day 7


title: EDFig4c_EDFig10_Untreated_Mouse3_SkMuscle

value: Skeletal Muscle


title: control_B04_1_C55_TP2_S31

value: Control bone-derived primary MSCs


title: control_B06_1_C57_TP2_S32


title: Group 5 PBS-PBS Day 0 [P13-1]

value: Female

value: Day 0


title: CAErbB-2-C9

value: Epithelium (organ of Corti)

value: cochlear supporting cell


title: EDFig4c_EDFig10_Untreated_Mouse3_Liver

value: Liver

value: Myh6 R403Q Heterozygous HCM Model Mouse


title: control_B02_1_C08_TP2_S30


title: EDFig4c_Gonad_Mouse4

value: Gonad

value: SingleDoseABE


title: CAErbB-2-C7

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


title: Group 4 IIV8/AS03-IIV5/AS03 Day 113 [P12-7]

value: Day 113


title: control_B08_1_C11_TP2_S30


title: control_B01_1_C09_TP2_S29


title: EDFig4c_EDFig10_Untreated_Mouse3_Gonad

value: UntreatedControl


title: CAErbB-2-C6


title: CAErbB-2-C5


title: control_A12_1_C54_TP2_S28


title: Group 4 IIV8/AS03-IIV5/AS03 Day 92 [P12-6]

value: Blood

value: Day 92


title: CAErbB-2-C4


title: control_A09_1_C04_TP2_S26


title: Group 4 IIV8/AS03-IIV5/AS03 Day 7 [P12-3]

value: Blood cells


title: Group 4 IIV8/AS03-IIV5/AS03 Day 3 [P12-2]

value: Day 3


title: Group 4 IIV8/AS03-IIV5/AS03 Day 85 [P12-5]

value: Day 85


title: CAErbB-2-C3


title: control_A11_1_C53_TP2_S27

value: Control bone-derived primary MSCs


title: CAErbB-2-C8


title: EDFig4c_EDFig10_Untreated_Mouse2_SkMuscle

value: Skeletal Muscle


title: EDFig4c_EDFig10_Untreated_Mouse2_Kidney

source_name: Kidney

value: Kidney


title: CAErbB-2-C1

value: Epithelium (organ of Corti)


title: Group 4 IIV8/AS03-IIV5/AS03 Day 0 [P12-1]

value: Female

value: Day 0


title: control_A03_1_C01_TP2_S27


title: control_A04_1_C49_TP2_S28


title: EDFig4c_EDFig10_Untreated_Mouse2_Liver

value: Liver

value: Myh6 R403Q Heterozygous HCM Model Mouse


title: CAErbB-2-C2

value: cochlear supporting cell


title: control_A02_1_C02_TP2_S26


title: EDFig4c_EDFig10_Untreated_Mouse2_Gonad

value: Gonad


title: Group 2 LAIV8-IIV5 Day 113 [P11-7]

value: Male

value: Day 113


title: EDFig4c_EDFig10_Untreated_Mouse3_Kidney

value: UntreatedControl


title: EDFig4c_EDFig10_Untreated_Mouse1_SkMuscle


title: control_A01_1_C03_TP2_S25


title: CAErbB-2-C11

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


title: Group 2 LAIV8-IIV5 Day 92 [P11-6]

value: Blood

value: Blood cells

value: Day 92


title: EDFig4c_EDFig10_Untreated_Mouse1_Lung

value: Lung


title: CAErbB-2-C10


title: Group 4 IIV8/AS03-IIV5/AS03 Day 29 [P12-4]

value: Day 29


title: EDFig4c_EDFig10_Untreated_Mouse2_Lung


title: control_H12_1_C94_TP1_S25

description:
Single-cell RNAseq control bone-derived MSCs undifferentiated
control_expression_matrix.txt

value: Control bone-derived primary MSCs


title: EDFig4c_EDFig10_Untreated_Mouse1_Kidney

value: Kidney


title: control_H06_1_C91_TP1_S24


title: CAErbB-2-C12

value: Epithelium (organ of Corti)


title: CAErbB-2-B8


title: CAErbB-2-B9


title: EDFig4c_EDFig10_Untreated_Mouse1_Liver


title: Group 2 LAIV8-IIV5 Day 85 [P11-5]

value: Day 85


title: Group 2 LAIV8-IIV5 Day 29 [P11-4]


title: control_H02_1_C44_TP1_S23


title: CAErbB-2-B6


title: Fig5a_EDFig9c_30weekMediumDose_Mouse3

value: Heart (Left Ventricle Apex)


title: Group 2 LAIV8-IIV5 Day 0 [P11-1]

value: Day 0


title: control_G04_1_C87_TP1_S21


title: control_H01_1_C43_TP1_S22


title: CAErbB-2-B7

value: cochlear supporting cell


title: Group 2 LAIV8-IIV5 Day 3 [P11-2]

value: Day 3


title: CAErbB-2-B5


title: Fig5a_EDFig9c_30weekMediumDose_Mouse2

value: Myh6 R403Q Heterozygous HCM Model Mouse


title: control_G02_1_C38_TP1_S20


title: Group 5 PBS-PBS Day 113 [P10-7]

value: Male

value: PBS-PBS

value: Day 113


title: Group 5 PBS-PBS Day 92 [P10-6]

value: Blood


title: Fig5a_EDFig9c_30weekMediumDose_Mouse1


title: Fig5a_EDFig9c_30weekLowDose_Mouse3


title: CAErbB-2-B3

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


title: CAErbB-2-B4


title: Group 2 LAIV8-IIV5 Day 7 [P11-3]

value: Blood cells

value: Day 7


title: control_F04_1_C81_TP1_S18


title: EDFig4c_EDFig10_Untreated_Mouse1_Gonad

value: Gonad

value: UntreatedControl


title: Fig5a_EDFig9c_30weekLowDose_Mouse2


title: control_F02_1_C32_TP1_S16

value: Control bone-derived primary MSCs


title: control_F03_1_C33_TP1_S17


title: Group 5 PBS-PBS Day 29 [P10-4]

value: Day 29


title: CAErbB-2-B1

value: Epithelium (organ of Corti)


title: CAErbB-2-B2


title: Fig5a_EDFig9c_30weekLowDose_Mouse1

value: Heart (Left Ventricle Apex)


title: Fig5a_EDFig9c_30weekHighDose_Mouse4


title: Group 5 PBS-PBS Day 3 [P10-2]


title: control_F01_1_C31_TP1_S15


title: CAErbB-2-B12


title: CAErbB-2-B11


title: Group 5 PBS-PBS Day 7 [P10-3]


title: Fig5a_EDFig9c_30weekHighDose_Mouse3


title: Fig5a_EDFig9c_30weekHighDose_Mouse2


title: control_E06_1_C73_TP1_S14


title: Group 5 PBS-PBS Day 0 [P10-1]

value: Day 0


title: control_E05_1_C74_TP1_S13


title: control_F05_1_C80_TP1_S19


title: Fig5a_EDFig9c_30weekHighDose_Mouse1


title: Group 1 LAIV8-IIV5/AS03 Day 113 [P1-7]

value: Female


title: CAErbB-2-B10

value: cochlear supporting cell


title: CAErbB-2-A9


title: control_E04_1_C75_TP1_S12


title: Group 1 LAIV8-IIV5/AS03 Day 92 [P1-6]

value: Day 92


title: Fig3C_EDFig6a_BoostedMouse5

value: Myh6 R403Q Heterozygous HCM Model Mouse

value: BoostedABE


title: Group 5 PBS-PBS Day 85 [P10-5]

value: Male

value: PBS-PBS

value: Day 85


title: control_E02_1_C26_TP1_S22


title: control_E01_1_C25_TP1_S21


title: Group 1 LAIV8-IIV5/AS03 Day 85 [P1-5]

value: Blood

value: Blood cells


title: Fig3C_EDFig6a_BoostedMouse4


title: Group 1 LAIV8-IIV5/AS03 Day 29 [P1-4]


title: Fig3C_EDFig6a_BoostedMouse3


title: Group 1 LAIV8-IIV5/AS03 Day 7 [P1-3]

value: Day 7


title: CAErbB-2-A6

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


title: CAErbB-2-A7


title: Group 1 LAIV8-IIV5/AS03 Day 3 [P1-2]

value: Day 3


title: Fig3C_EDFig6a_BoostedMouse1


title: Fig3C_EDFig6a_BoostedMouse2


title: control_D05_1_C68_TP1_S19

value: Control bone-derived primary MSCs


title: control_D04_1_C67_TP1_S18


title: Group 1 LAIV8-IIV5/AS03 Day 0 [P1-1]


title: control_D02_1_C20_TP1_S17


title: ZAP70 Stim

first: Caleb

last: Lareau

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

library_source: transcriptomic single cell

data_processing:
Fastqs were generated using CellRanger v 6 and aligned to the reference hg38 transcriptome/genome
Cellranger count v6 was run to generate an hdf5 of per-cell gene expression counts
Per-donor genetic demultiplexing was performed using the mgatk v0.6.2 pipeline
Assembly: hg38
Supplementary files format and content: Gene expression counts per cell (hdf5) and meta data per cell (tsv)

molecule: total RNA

source_name: CAR T cells

extract_protocol:
standard 10x Genomics protocol for scRNA-seq
10x Genomics  v3 scRNA-seq

value: CAR T cells

tag: engineered signaling domain

tag: stimulation

value: stimulated in presence of CD19+ cells


title: CAErbB-2-A3

value: Epithelium (organ of Corti)


title: CAErbB-2-A4


title: Fig1C_Fig3C_Fig5a_EDFig4a_EDFig6a_EDFig9bc_Untreated_Mouse3

value: Heart (Left Ventricle Apex)

value: UntreatedControl


title: Fig1C_Fig3C_Fig5a_EDFig4a_EDFig6a_EDFig9bc_Untreated_Mouse2


title: control_D01_1_C21_TP1_S16


title: ZAP70 Unstim

value: unstimulated


title: Fig1C_Fig3C_Fig5a_EDFig4a_EDFig6a_EDFig9bc_Untreated_Mouse1

value: Myh6 R403Q Heterozygous HCM Model Mouse


title: CAErbB-2-A2

value: cochlear supporting cell


title: control_C06_1_C63_TP1_S15


title: CAErbB-2-A1


title: CAErbB-2-A8


title: control_D06_1_C69_TP1_S20


title: CAErbB-2-A5


title: Fig1C_Fig3C_EDFig4a_EDFig6a_UntreatedMouse5


title: BBZ Stim

value: BBZ


title: control_C03_1_C13_TP1_S13


title: BBZ Unstim


title: Fig1c_EDFig4a_SingleDoseABEMouse6

value: SingleDoseABE


title: WT1F8_STAT_REP2

city: Bronx

first: Teresa

last: Bowman

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
basecalling was done with the Picard module IlluminaBasecallsToFastq
Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired-end reads were mapped using STAR aligner (version 2.4.2a) to the reference genome.
FeatureCounts was used to calculate reads per gene.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes feature count values for each sample

source_name: K562 cells

growth_protocol: SF3B1+/K666N and isogenic control K562 cells were maintained in IMDM + 10% FCS + 1% Penicillin/Streptomycin with 20% O2 and 5% CO2.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufactures instructions including DNase digestion. Three independent replicates were isolated and processed for each sample.
RNA quality assessment, library preparation and sequencing were done by the Vanderbilt Technologies for Advanced Genomics core facility. Libraries were generated using the stranded mRNA (polyA-selected) kit (NEB) according to the manufacturer’s protocol.

treatment_protocol: Cells were exposed to DMSO control or 10uM stattic STAT3 inhibitor for 24 hours

value: STATTIC


title: Fig1C_Fig3C_EDFig4a_EDFig6a_UntreatedMouse4


title: CAErbB-1-E9


title: control_C02_1_C14_TP1_S12


title: Fig1c_EDFig4a_SingleDoseABEMouse5


title: Fig1c_EDFig4a_SingleDoseABEMouse4


title: CAErbB-2-A10


title: WT1F8_DMSO_REP3

value: DMSO


title: control_B11_1_C59_TP1_S11


title: control_C01_1_C15_TP1_S11


title: control_B09_1_C10_TP1_S10


title: control_B11_1_C59_TP2_S33


title: CAErbB-2-A11


title: WT1F8_DMSO_REP2


title: CAErbB-1-E7


title: CAErbB-1-E6


title: WT1F8_STAT_REP1


title: control_C05_1_C62_TP1_S14


title: Fig1c_EDFig4a_SingleDoseABEMouse2


title: Fig1c_EDFig4a_SingleDoseABEMouse3


title: WT1F8_DMSO_REP1


title: CAErbB-2-A12


title: control_B08_1_C11_TP1_S9


title: WT1F8_STAT_REP3


title: CAErbB-1-E5


title: K666N_IH2_STAT_REP3


title: control_B07_1_C12_TP1_S8


title: 4007_RA_HighDoseSaCas9Nuclease

data_processing:
Reads were aligned to the mm10 human genome using Spliced Transcripts Alignment to a Reference (STAR) (Dobin et al., 2013). Bam files were mounted onthe  Integrated Genome Viewer (IGV) (Broad Institute, Boston, MA). The percentage of inactivation of the pathogenic variant R403Q was calculated as: (1 – (total number of R403Q reads, divided by total number of WT reads)) multiplied by 100.
Assembly: mm10

source_name: Right Atrium

extract_protocol:
Total RNA (1 ug) underwent two rounds of mRNA purification (polyA-selection) using Dynabeads mRNA DIRECT Kit (Invitrogen, Carlsbad, CA).
Double-stranded cDNA was generated using the Superscript III First-Strand Synthesis System (Invitrogen, Carlsbad, CA). We performed PCR amplification of the targeted MYH6 R403Q allele. PCR products were fragmented using an NEB Fragmentation Kit and Illumina sequencing libraries were prepared. The cDNA products were used to construct libraries with single end 190 bp read and a single I plex 9 bp read.

value: Right Atrium

tag: strain

value: female


title: control_B06_1_C57_TP1_S10


title: CAErbB-1-E8

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


title: CAErbB-1-E4


title: K666N_IH2_STAT_REP2


title: 4007_LA_HighDoseSaCas9Nuclease

source_name: Left Atrium

value: Left Atrium


title: K666N_IH2_STAT_REP1


title: 4007_RV_HighDoseSaCas9Nuclease

source_name: Right Ventricle

value: Right Ventricle


title: control_B04_1_C55_TP1_S9

value: Control bone-derived primary MSCs


title: CAErbB-1-E3


title: K666N_IH2_DMSO_REP3


title: control_B03_1_C07_TP1_S8


title: 4007_LV_HighDoseSaCas9Nuclease

source_name: Left Ventricular Apex

value: Left Ventricular Apex


title: control_B02_1_C08_TP1_S7


title: control_B01_1_C09_TP1_S6


title: Fig1c_EDFig4a_SingleDoseABEMouse1


title: 4006_RA_HighDoseSaCas9Nuclease


title: 4006_LA_HighDoseSaCas9Nuclease


title: CAErbB-1-E1

value: Epithelium (organ of Corti)


title: CAErbB-1-E11


title: K666N_IH2_DMSO_REP1


title: K666N_IH2_DMSO_REP2


title: CAErbB-1-E10


title: control_A12_1_C54_TP1_S7


title: 4006_RV_HighDoseSaCas9Nuclease


title: control_A11_1_C53_TP1_S6


title: K666N_3D1_STAT_REP3


title: K666N_3D1_STAT_REP2


title: CAErbB-1-E2


title: control_A10_1_C52_TP1_S5


title: K666N_3D1_STAT_REP1


title: control_A09_1_C04_TP1_S4


title: control_A08_1_C05_TP1_S3


title: K666N_3D1_DMSO_REP3


title: CAErbB-1-D6


title: control_A07_1_C06_TP1_S2


title: K666N_3D1_DMSO_REP1


title: 4805_RA_MediumDoseSaCas9Nuclease


title: CAErbB-1-D5


title: control_A06_1_C51_TP1_S5


title: 4806_LA_MediumDoseSaCas9Nuclease


title: control_A05_1_C50_TP1_S4


title: 4806_RV_MediumDoseSaCas9Nuclease


title: 4806_LV_MediumDoseSaCas9Nuclease


title: SW480_WT5_B

city: Freiburg

first: Andreas

last: Hecht

address: Stefan-Meier-Str. 17

country: Germany

institute: Albert-Ludwigs-Universität Freiburg

description: replicate B

data_processing:
Base-calling: Base calling was performed by the Illumina sequencer through an integrated primary analysis software called RTA (Real Time Analysis)
FASTQ files: Base calls were converted into FASTQ utilizing illumina package bcl2fastq
Read alignment: All reads were aligned to the human reference genome GRCh37 using RNA STAR Galaxy Version 2.7.5b
Read counts: For counting the reads per gene, featureCounts Galaxy Version 2.0.1 was applied
Differentially expressed genes: DESeq2 Galaxy Version 2.11.40.6+galaxy1 was used for normalization and to identify differentially expressed genes
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files with normalized feature counts for each sample

growth_protocol: All cells were grown in DMEM with 4.5 g/l glucose, stabilized glutamine, sodium pyruvate, and 3.7 g/l NaHCO3, supplemented with 10 % (v/v) fetal calf serum, 10 mM HEPES, 1 % (v/v) MEM non-essential amino acids solution, 1 % (v/v) penicillin/streptomycin at 37°C and 5 % CO2.

extract_protocol:
Total RNA was extracted using the peqGOLD Total RNA kit. For each sample, 1200 ng of total RNA were sent to Macrogen Europe for Sequencing.
The library preparation was performed by Macrogen Europe using the TruSeq RNA Sample Prep Kit v2 and the according protocol (TruSeq RNA Sample Preparation v2 Guide, Part # 15026495 Rev. F)

treatment_protocol: The CTNNB1 gene was inactivated by CRISPR/Cas9-mediated biallelic deletion of exon 7, leading to a frame shift and premature stop codon.

tag: cell line

value: colorectal carcinoma cell line

value: CTNNB1 wild-type

tag: cell clone #

value: SW4809 clone #5


title: CAErbB-1-D9


title: SW480_WT5_A

description: replicate A


title: CAErbB-1-D4


title: 4805_LA_MediumDoseSaCas9Nuclease


title: control_A04_1_C49_TP1_S3


title: CAErbB-1-D2


title: 4806_RA_MediumDoseSaCas9Nuclease


title: 4006_LV_HighDoseSaCas9Nuclease


title: CAErbB-1-D3


title: CAErbB-1-D7


title: CAErbB-1-D8


title: SW480_WT4_B

description: replicate B

value: SW4809 clone #4


title: 4805_RV_MediumDoseSaCas9Nuclease


title: control_A02_1_C02_TP1_S2


title: K666N_3D1_DMSO_REP2


title: CAErbB-1-D1

value: cochlear supporting cell


title: SW480_WT4_A

description: replicate A


title: control_A01_1_C03_TP1_S1


title: CAErbB-1-D12


title: 4805_LV_MediumDoseSaCas9Nuclease


title: 4804_RA_MediumDoseSaCas9Nuclease


title: Hi-c DND41 USP7i+dexamethasone  replicate 2

first: Sonali

last: Narang

address: 435 east 30th street

institute: NYU Langone

data_processing:
Hi-C reads were aligned to the hg19 genome assembly using bwa
reads were filtered using hic-bench
raw hi-c matrices were generated using hic-bench
raw hi-c matrices were normalized using iterative correction
Genome_build: hg19
Supplementary_files_format_and_content: contact matrix in .hic format

growth_protocol: cells in suspension, growing in RPMI

extract_protocol:
Biotinylated DNA was extracted with Arima-HiC kit enrichment beads
Libraries were prepared using the KAPA® Hyper Prep Kit for Illmina®

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

value: human T cell leukemia cells


title: CAErbB-1-D11


title: 4804_LA_MediumDoseSaCas9Nuclease


title: CAErbB-1-D10


title: SW480_KO17_B

description: replicate B

value: CTNNB1 knock-out

value: SW4809 clone #17


title: SW480_KO21_B

description: replicate B

value: SW4809 clone #21


title: Hi-c DND41 dexamethasone  replicate 2


title: Hi-c DND41 dexamethasone  replicate 1


title: 4080_RA_LowDoseSaCas9Nuclease

value: Right Atrium


title: 4804_LV_MediumDoseSaCas9Nuclease

value: female


title: CAErbB-1-C8

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


title: 4080_LA_LowDoseSaCas9Nuclease

value: Left Atrium


title: HT29_WT40_B

description: replicate B

value: HT29 clone #40


title: CAErbB-1-C7


title: SW480_KO17_A

description: replicate A


title: CAErbB-1-C6


title: Hi-c DND41 USP7i  replicate 2


title: HT29_WT11_B

description: replicate B

value: HT29 clone #11


title: 4080_RV_LowDoseSaCas9Nuclease

value: Right Ventricle


title: CAErbB-1-C9

value: Epithelium (organ of Corti)


title: 4080_LV_LowDoseSaCas9Nuclease

value: Left Ventricular Apex


title: Hi-c DND41 Control  replicate 2


title: HT29_WT40_A

description: replicate A

value: colorectal carcinoma cell line

value: CTNNB1 wild-type


title: 4079_RA_LowDoseSaCas9Nuclease


title: Hi-c DND41 USP7i+dexamethasone replicate 1


title: CAErbB-1-C5


title: SW480_KO21_A

description: replicate A


title: HT29_WT11_A

description: replicate A


title: Hi-c DND41 Control  replicate 1


title: CAErbB-1-C4


title: 4079_LA_LowDoseSaCas9Nuclease


title: 4079_RV_LowDoseSaCas9Nuclease


title: HT29_KO38_A

description: replicate A

value: HT29 clone #38


title: HT29_KO38_B

description: replicate B


title: CAErbB-1-C2

value: cochlear supporting cell


title: 4079_LV_LowDoseSaCas9Nuclease


title: HT29_KO28_B

description: replicate B

value: HT29 clone #28


title: Cmg2-KO rep5

city: Beijing

first: Xiaoyan

last: Liu

address: 8 Gongren Tiyuchang Nanlu, Chaoyang District

country: China

institute: Beijing Chao-Yang Hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Rattus_norvegicus_Ensemble_94 whole genome using  HISAT2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.  And then FPKM of each gene was calculated based on the length of the gene and  reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and  is currently the most commonly used method for estimating gene expression levels.
Genome_build: Rattus_norvegicus_Ensemble_94
Supplementary_files_format_and_content: text file include FPKM values and statistics.

organism: Rattus norvegicus

source_name: lung

extract_protocol:
Lungs were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. NEBNext® UltraTM RNA Library Prep Kit for Illumina®  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Sprague Dawley

value: lung

tag: age

value: 8-week old


title: Cmg2-KO rep4


title: CAErbB-1-C3


title: Cmg2-KO rep3


title: HT29_KO28_A

description: replicate A

value: CTNNB1 knock-out


title: CAErbB-1-C1


title: Hi-c DND41 USP7i  replicate 1

value: human T cell leukemia cells


title: 4078_RA_LowDoseSaCas9Nuclease

value: Right Atrium

value: male


title: CAErbB-1-C12

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


title: Cmg2-KO rep2


title: HCT116_WT6_B

description: replicate B

value: HCT116 clone #6


title: 4078_LA_LowDoseSaCas9Nuclease

value: Left Atrium


title: CAErbB-1-C11

value: Epithelium (organ of Corti)


title: HCT116_WT6_A

description: replicate A


title: Cmg2-KO rep1


title: 4078_LV_LowDoseSaCas9Nuclease

value: Left Ventricular Apex


title: CAErbB-1-C10


title: WT rep5

value: WT


title: HCT116_WT4_B

description: replicate B

value: colorectal carcinoma cell line

value: CTNNB1 wild-type

value: HCT116 clone #4


title: 2267_RA_SaCas9Nuclease

value: SvEv


title: CAErbB-1-B9

value: cochlear supporting cell


title: HCT116_WT4_A

description: replicate A


title: WT rep4

value: Sprague Dawley

value: lung


title: CAErbB-1-B8


title: 2267_LA_SaCas9Nuclease


title: HCT116_KO47_B

description: replicate B

value: CTNNB1 knock-out

value: HCT116 clone #47


title: 2267_RV_SaCas9Nuclease

value: Right Ventricle


title: WT rep3

value: 8-week old


title: CAErbB-1-B7

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


title: HCT116_KO47_A

description: replicate A


title: WT rep2


title: 2267_LV_SaCas9Nuclease

value: male


title: CAErbB-1-B6


title: 2264_LA_SaCas9Nuclease

value: Left Atrium


title: WT rep1


title: 2264_RA_SaCas9Nuclease

value: Right Atrium


title: HCT116_KO44_B

description: replicate B

value: HCT116 clone #44


title: CAErbB-1-B4

value: Epithelium (organ of Corti)


title: CAErbB-1-B5


title: AMH3 snRNA-seq

first: qian

middle: qian

last: zhang

address: Datun road, chaoyang district

department: State Key Laboratory of Brain and Cognitive Science

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.

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: HCT116_KO44_A

description: replicate A

value: colorectal carcinoma cell line


title: 2264_RV_SaCas9Nuclease

value: SvEv


title: pCND1_ip_Rep1

city: 广州市

first: 柳

last: 洪

state: 广东省

address: 番禺区

department: 中药学院

institute: 广州中医药大学

data_processing:
Quality control: Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11, Chen et al., 2018) software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
Fragment size estimation:  For a specific ChIP-seq binding site, individual reads mapping to the plus or minus strand and present significant enrich. For single-end sequencing, the fragment size was estimated with MACS2 (Zhang et al., 2008) predicted method with default parameters. MACS2 scan all the genome with a specific window size and calculate the reads enrichment level. A particular number of windows were used as samples to build enrichment model and to predict fragment size. The following peak calling analysis was based on this predicted fragment size.
Peak detection:  After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
Peak annotation and Different peak analysis:  The position of peak summit around transcript start sites of genes can predict the interaction sites between protein and gene. Different peak analysis was based on the fold enrichment of peaks of different experiments. A peak was determined as different peak when the odds ratio between two groups was more than 2. Using the same method, genes associated with different peaks were identified and also do GO and KEGG enrichment analysis. s-Wheeler transform. Bioinformatics, 2
Assembly: TAIR10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

organism: Arabidopsis thaliana

source_name: Arabidopsis seedling

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated
The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Arabidopsis seedling

tag: chip antibody

value: Flag (sigma, #1804)


title: pCND1_input


title: CAErbB-1-B3

value: cochlear supporting cell


title: Col_ip_Rep2


title: AMH2 snRNA-seq

description: 10X genomic snRNA-seq


title: AMH1 snRNA-seq

description: 10X genomic snRNA-seq


title: 2263_RA_SaCas9Nuclease


title: 2264_LV_SaCas9Nuclease

value: Left Ventricular Apex


title: CAErbB-1-B1


title: Col_ip_Rep1


title: CAErbB-1-B12


title: 2263_LA_SaCas9Nuclease


title: Col_input


title: pCND1_ip_Rep2


title: 2263_RV_SaCas9Nuclease

value: Right Ventricle


title: CAErbB-1-B11


title: 2263_LV_SaCas9Nuclease


title: AmiR-mta,chilling,polysome_seq,rep2

city: Nanjing

first: Wang

last: Haiyan

state: Jiangsu

address: Weigang NO.1

department: State Key Laboratory for Crop Genetics and Germplasm Enhancement

institute: Nanjing Agricultural University

description: polysome-mRNA

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence Trim-Galore(version 0.6.6)
Clean reads were aligned to TAIR10 using Hisat2 v2.2.1(http://daehwankimlab.github.io/hisat2).
HTSeq (Anders et al., 2015) and R package DESeq2 (version 1.32.0) were used to calculate the number of reads for each gene and analyse differentially expressed genes.
MeTPeak (Cui et al., 2016) was used to identify m6A peaks.we maintained high confidence peaks on peaks with input FPKM ≥ 1 and peaks enrichment  ≥ 2.
Assembly: TAIR10
Supplementary files format and content: bigWig (m6A-IP and m6A-input), raw counts of sequencing reads (mRNA and polysome-seq)

source_name: leaf

growth_protocol: Plants were grown in a growth chamber at 22 ℃ under long day conditions (16 h light/8 h dark) with a light intensity of 100 µmol m-2 sec-1.

extract_protocol:
m6A-IP，m6A-input and mRNA was isolated with Trizol.Poly(A) RNA selection were performed using the Dynabeads mRNA direct purification kit (MRN10, Sigma-Aldrich).Polysome-mRNA was isolated from polysome with phenol/chloroform/isoamyl alcohol (25:24:1; v/v/v).
NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB, E7770S) was used to construct libraries.
meRIP-seq and polysome-seq

treatment_protocol: chilling treatment, 3-week-old plants were transfer to 4 ℃ for 24 h.

value: leaf

value: AmiR-mta

value: chilling


title: CAErbB-1-B10

source_name: Epithelium (organ of Corti)

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


title: CAErbB-1-A9


title: 2261_RA_SaCas9Nuclease

value: Right Atrium

value: male


title: CAErbB-1-B2

value: Epithelium (organ of Corti)


title: 2261_RV_SaCas9Nuclease


title: 2261_LV_SaCas9Nuclease


title: AmiR-mta,control,polysome_seq,rep1

description: polysome-mRNA

value: control


title: Exp2_RluA_2_rep2_CMC

city: Bloomington

first: W.

middle: Daniel

last: Tracey

state: Indiana

address: 702 N. Walnut Grove

department: Biology

institute: Indiana University

description: CMC treated RluA_2 replicate 2 library from Experiment 2

data_processing:
Raw reads were adapter trimmed and quality filtered using Trimmomatic version 0.33 (Bolger et al. 2014) setting the cutoff threshold for average base quality score at 20 over a window of 3 bases, excluding the reads shorter than 20 bases post-trimming (parameters: leading=20, trailing=20, sliding window=3, Minilen= 20).
Alignment of the reads to the reference sequence was done in two phases. Cleaned reads were first mapped to a sequence reference comprising of the Drosophila melanogaster 18S, 5.8S, 2S and 28S ribosomal RNA gene sequences (accession: M21017.1) and the sequence for RNA spike-in (Schwartz et al. 2014) using bowtie2 (Langmead and Salzberg 2012). The remaining unmapped read pairs were extracted and mapped to the D. melanogaster genome reference version Flybase r6.17 release FB2017_04  (Larkin et al. 2021) using a splice-aware aligner, STAR version 2.6.1a (Dobin et al. 2013).
Inserts were identified by interpolating the concordantly mapped read pairs. For each insert, the 5’ end of the read R2 was identified as the termination site of the product from reverse transcription. For each sample, a Termination Ratio was computed as the ratio of number of reads terminating at the termination site to the total coverage at the site.
Read pairs mapping concordantly and uniquely to the exon regions of the annotated genes were counted using featureCounts tool ver. 2.0.0 of Subread package (Liao et al. 2014). Read alignments to antisense strand, or to multiple regions on the genome or those overlapping with multiple genes were ignored (parameters: -s 2 -p -B -C).
Assembly: Drosophila melanogaster version Flybase r6.17, release FB2017_04
Supplementary files format and content: *.ftcounts.txt contain the counts of read pairs mapping concordantly to the exon regions of the annotated genes. Columns: gene_id, read count
Supplementary files format and content: *.termination_stats.txt contain the read stats at each termination site. Columns: chromosome, position, strand, termination count, coverage, termination ratio
Library strategy: Psi-seq

organism: Drosophila melanogaster

source_name: head

growth_protocol: All flies were reared on yeast, corn meal food in bottles or vials at an incubator with controlled temperature (25°C) and humidity (70%) on a 12h light/12h dark cycle.

extract_protocol:
The flies were then snap frozen in liquid nitrogen and kept at -80°C for 3 days until sufficient number of flies from each genotype had been collected. The frozen flies were then decapitated and 100 heads per replicate homogenized in TRIzol reagent (Invitrogen). Total RNA was prepared according to the manufacturers’ recommendations.
Polyadenylated RNA was enriched from total RNA using two rounds of Oligo(dT) dynabeads (Invitrogen) according to manufacturer’s protocol. To each polyA-RNA sample, spike-in RNA (~3ug) was added and then the samples were split into two equal samples for CMCT or mock treatment.

treatment_protocol: newly eclosed virgins from isow1118 were collected twice every day (once in the morning and once in the afternoon) with less than 8 hours in between. The flies were put into vials with yeast and Bloomington recipe fly medium (20-30 flies in each vial) and aged for 1d in the incubator. The flies were then snap frozen in liquid nitrogen and kept at -80°C for 3 days until sufficient number of flies from each genotype had been collected.

value: head

tag: Sex

value: female

value: 1 day

tag: developmental stage

value: virgin


title: Exp2_RluA_2_rep3_CMC

description: CMC treated RluA_2 replicate 3 library from Experiment 2

tag: tissue


title: Exp2_RluA_2_rep2_mock

description: mock treated RluA_2 replicate 2 library from Experiment 2


title: Exp2_RluA_2_rep4_CMC

description: CMC treated RluA_2 replicate 4 library from Experiment 2


title: Exp2_RluA_2_rep3_mock

description: mock treated RluA_2 replicate 3 library from Experiment 2


title: CAErbB-1-A6

tag: cell type


title: 4823_RA_SingleDoseABE

tag: gender

tag: treatment

value: SingleDoseABE


title: Exp2_RluA_2_rep4_mock

description: mock treated RluA_2 replicate 4 library from Experiment 2

tag: genotype


title: CAErbB-1-A5


title: 4823_LA_SingleDoseABE

value: Left Atrium


title: CAErbB-1-A4

value: cochlear supporting cell


title: Col-0,chilling,polysome_seq,rep1

description: polysome-mRNA


title: AmiR-mta,chilling,polysome_seq,rep1

description: polysome-mRNA


title: Col-0,control,polysome_seq,rep2

description: polysome-mRNA


title: AmiR-mta,control,polysome_seq,rep2

description: polysome-mRNA


title: Exp2_w1118_rep4_mock

description: mock treated w1118 replicate 4 library from Experiment 2


title: Col-0,control,polysome_seq,rep1

description: polysome-mRNA


title: Exp2_RluA_2_rep1_mock

description: mock treated RluA_2 replicate 1 library from Experiment 2


title: 2261_LA_SaCas9Nuclease

value: SvEv


title: CAErbB-1-A3


title: CAErbB-1-A8


title: AmiR-mta,chilling,mRNA-seq,rep2

description: polyA RNA


title: Col-0,chilling,polysome_seq,rep2

description: polysome-mRNA


title: CAErbB-1-A7


title: CAErbB-1-A2


title: AmiR-mta,chilling,mRNA-seq,rep1

description: polyA RNA


title: AmiR-mta,control,mRNA-seq,rep2

description: polyA RNA


title: Exp2_RluA_2_rep1_CMC

description: CMC treated RluA_2 replicate 1 library from Experiment 2


title: CAErbB-1-A1


title: Exp2_w1118_rep3_mock

description: mock treated w1118 replicate 3 library from Experiment 2


title: Exp2_w1118_rep4_CMC

description: CMC treated w1118 replicate 4 library from Experiment 2


title: 4822_RA_SingleDoseABE


title: 4822_LA_SingleDoseABE


title: 4822_RV_SingleDoseABE

value: Right Ventricle


title: 4823_RV_SingleDoseABE


title: AmiR-mta,control,mRNA-seq,rep1

description: polyA RNA

value: leaf


title: CAErbB-1-A12


title: CAErbB-1-A11


title: 40_LV_SingleDoseABE

value: Left Ventricular Apex


title: Col-0,chilling,mRNA-seq,rep2

description: polyA RNA

value: chilling


title: Col-0,chilling,mRNA-seq,rep1

description: polyA RNA


title: 38_RA_SingleDoseABE


title: CAErbB-1-A10

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


title: K_bis

city: Paris

first: Isabelle

last: Leroux

address: 47 Boulevard de l'Hôpital

country: France

institute: Paris Brain Institute

data_processing:
Quality of raw data was evaluated with FastQC.
Poor quality sequences were trimmed or removed with fastp tool, with default parameters, to retain only good quality paired reads.
Illumina DRAGEN bio-IT Plateform (v3.8.4) was used for mapping on mm10 reference genome and quantification with gencode vM25 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files including expecting counts, TPM and FPKM

source_name: WT+GCV

growth_protocol: The lentivirus (1 µL, 6 x 108 PFU/mL) was stereotaxically injected in the right SVZ of brain mice. From the next day, mice were injected i.p. with tamoxifen (TMX, 100 mg/kg) once per day for five consecutive days

extract_protocol:
Total RNA from tumors were extracted following either via the Maxwell RSC simplyRNA Tissue (Promega, #AS1340) or the TRI-reagent (Molecular Center Research, #TR 118) procedures.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: GCV (25 mg/kg) was administered daily via i.p. injections for 5 consecutive days, starting when bioluminescence head/body ratio reached 2.

tag: disease state

value: GBM

value: 129/SVJ x C57BL/6 x FVB

value: GlastCreERT2/+; Ptenfl/fl

tag: injected lentivirus


title: Col-0,control,mRNA-seq,rep2

description: polyA RNA

value: control


title: 38_LA_SingleDoseABE

value: male


title: 38_RV_SingleDoseABE


title: J_bis


title: Exp2_w1118_rep1_mock

description: mock treated w1118 replicate 1 library from Experiment 2

value: head

value: female


title: Exp1_w1118_rep3_mock

description: mock treated w1118 replicate 3 library from Experiment 1

value: 1 day

value: virgin


title: Exp2_w1118_rep3_CMC

description: CMC treated w1118 replicate 3 library from Experiment 2


title: Col-0,control,mRNA-seq,rep1

description: polyA RNA


title: Exp2_w1118_rep2_mock

description: mock treated w1118 replicate 2 library from Experiment 2


title: 38_LV_SingleDoseABE

value: SingleDoseABE


title: Exp2_w1118_rep2_CMC

description: CMC treated w1118 replicate 2 library from Experiment 2


title: Exp2_w1118_rep1_CMC

description: CMC treated w1118 replicate 1 library from Experiment 2


title: AmiR-mta,chilling,input,rep2

description: polyA RNA

value: AmiR-mta


title: EH2362


title: EH2361


title: AmiR-mta,chilling,input,rep1

description: polyA RNA


title: Exp1_w1118_rep3_CMC

description: CMC treated w1118 replicate 3 library from Experiment 1


title: 37_RA_SingleDoseABE

value: Right Atrium

value: SvEv


title: 37_LA_SingleDoseABE

value: Left Atrium


title: W

source_name: p16-3MR +GCV

value: GlastCreERT2/+; Ptenfl/fl; p16-3MR/+


title: AmiR-mta,chilling,m6A-IP,rep2

description: polyA RNA

value: leaf

value: chilling


title: Exp1_w1118_rep1_mock

description: mock treated w1118 replicate 1 library from Experiment 1


title: Exp1_w1118_rep2_mock

description: mock treated w1118 replicate 2 library from Experiment 1


title: EH2360

value: GBM


title: AmiR-mta,chilling,m6A-IP,rep1

description: polyA RNA


title: Exp1_w1118_rep1_CMC

description: CMC treated w1118 replicate 1 library from Experiment 1


title: EH2359

value: 129/SVJ x C57BL/6 x FVB


title: 37_LV_SingleDoseABE

value: Left Ventricular Apex


title: 37_RV_SingleDoseABE

value: Right Ventricle


title: AmiR-mta,control,input,rep2

description: polyA RNA

value: control


title: SARS-CoV-2 infection and Methotrexate treatment_2

city: Hsinchu

first: Jinn-Moon

last: Yang

address: 75 Po-Ai Street

country: Taiwan

institute: National Chiao Tung University

description: Nasal infection of 10000 pfu SARS-CoV-2 and treatment of 2 mg/kg Methotrexate

data_processing:
The quality of reads was examined using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The reads were aligned to the Syrian hamster genome MesAur1.0 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000349665.1/) using HISAT2 (v.2.2.1).
The reads from HISAT2 were mapped and assembled into transcripts using StringTie (v.2.1.4).
The expression proles of whole transcripts were evaluated and calculated based on fragments per kilobase of transcript per million fragments mapped (FPKM) using StringTie and the Ballgown package (v.2.22.0) in R (v. 4.0.4).
Genome_build: MesAur1.0 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000349665.1/)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample using ballgown package

organism: Mesocricetus auratus

source_name: SARS-CoV-2 and Methotrexate

growth_protocol: Male Syrian golden hamsters, aged 7-9 weeks old were obtained from Taiwan National Laboratory Animal Center. The animals were kept in specific-pathogen-free (SPF) housing and were acclimatized at the ABSL-3 facility for 3 days before the experiments. Hamsters were randomly allocated to study groups for antiviral evalution. 100 μL of PBS containing low dose (1x103 pfu) or high dose ((1x104 pfu) of SARSCoV-2 was intranasal instilled under intraperitoneal anesthesia with Zoletil 50 (4mg/kg)/ Xylazine (0.5mg/kg) at day 0, and the mock-infected hamsters were challenged with 100 μL of PBS.

extract_protocol:
Genomic RNA was extracted using RNeasy plus mini kit (Qiagen) according to manufacturer instructions. Hamster tissues were collected after killing and were homogenized using bead disruption (Precellys) in RLT buffer (RNeasy plus Mini kit, Qiagen) and centrifuged (10,000 rpm, 5 min) to pellet the cell debris. RNA was extracted according to the manufacturer’s instructions.
The purified RNA was used for the preparation of the sequencing library by TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations. Briefly, mRNA was purified from total RNA (1 μg) by oligo(dT)-coupled magnetic beads and fragmented into small pieces under elevated temperature. The first-strand cDNA was synthesized using reverse transcriptase and random primers. After the generation of double-strand cDNA and adenylation on 3’ ends of DNA fragments, the adaptors were ligated and purified with AMPure XP system (Beckman Coulter, Beverly, USA). The quality of the libraries was assessed on the Agilent Bioanalyzer 2100 system and a Real-Time PCR system. The qualified libraries were then sequenced on an Illumina NovaSeq 6000 platform with 150 bp paired-end reads generated by Genomics, BioSci & Tech Co., New Taipei City, Taiwan.

treatment_protocol: Treatment groups were intraperitoneally given either MTX (2 mg/kg/day)

tag: agent

value: SARS-CoV-2 and Methotrexate


title: AmiR-mta,control,input,rep1

description: polyA RNA


title: EH2358


title: SARS-CoV-2 infection and Methotrexate treatment_1


title: T

extract_protocol:
Total RNA from tumors were extracted following the Maxwell RSC simplyRNA Tissue procedure (Promega, #AS1340)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: GlastCreERT2/+; Ptenfl/fl


title: AmiR-mta,control,m6A-IP,rep2

description: polyA RNA


title: 36_LV_SingleDoseABE

value: male


title: SARS-CoV-2 infection_2

description: Nasal infection of 10000 pfu SARS-CoV-2


title: SARS-CoV-2 infection_1

description: Nasal infection of 10000 pfu SARS-CoV-2


title: AmiR-mta,control,m6A-IP,rep1

description: polyA RNA


title: Mock_2

description: Control

source_name: Mock

value: Mock


title: Exp1_w1118_rep2_CMC

description: CMC treated w1118 replicate 2 library from Experiment 1

value: head

value: female

value: 1 day

value: virgin


title: Col-0,chilling,input,rep2

description: polyA RNA


title: 2245_LA_BoostedABE

value: Left Atrium

value: BoostedABE


title: N


title: 2245_RA_BoostedABE

value: Right Atrium


title: O_ter


title: Col-0,chilling,input,rep1

description: polyA RNA

value: leaf

value: chilling


title: Col-0,chilling,m6A-IP,rep2

description: polyA RNA


title: M_bis

source_name: miR-ctl

value: GBM

value: 129/SVJ x C57BL/6 x FVB


title: 2245_LV_BoostedABE

value: Left Ventricular Apex


title: F3hrde-1_Hypoxia_rep2

first: Eric

last: Greer

address: 320 Longwood Avenue

department: Newborn Medicine/Department of Pediatrics

institute: Boston Children's Hospital/Harvard Medical School

data_processing:
The fastq files were filtered with Q score 30 or above and were trimmed for the sequencing adaptors using CutAdapt (version 2.5)
The sequencing reads were aligned to the C.elegans genome (WS235) by bowtie2 and the transcripts were quantified by EBSeq.
Transcript and gene expression matrices were built with featurecounts in RSEM pipeline
For calling the significant differentially expressed genes (DEGs), the false discovery rate (FDR) after multiple testing correction was set as 0.05 and analyzed in edgeR
Genome_build: WS235
Supplementary_files_format_and_content: Data matrix was generated in RSEM pipeline

organism: Caenorhabditis elegans

growth_protocol: The worms were kept in 20 °C incubator with sufficient food supply for at least 3 generations before the hypoxic exposure experiments. For single exposure experiments, L4 stage worms were exposed at 0.1% oxygen level in a hypoxic chamber (Eppendorf Galaxy 48R incubator) for 16 hours at 20 °C, then they were returned to ambient oxygen level (~20 %).

extract_protocol:
Whole worms were lysed using tissue homogenizer (Kontes) and total RNA was extracted using mirVana miRNA Isolation kit (life technologies). Messenger RNAs were enriched using NEXTFLEX Poly A Beads 2.0.
In total 32 groups were prepared for RNA-seq libraries with 500 ng mRNA as starting materials using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific)

value: whole worm

value: Hypoxia

tag: generation

tag: genotype/variation


title: Mock_1

description: Control


title: 2245_RV  _BoostedABE

value: Right Ventricle

tag: strain


title: S

value: GlastCreERT2/+; Ptenfl/fl


title: Col-0,chilling,m6A-IP,rep1

description: polyA RNA


title: F3hrde-1_Hypoxia_rep1


title: 2244_RA_BoostedABE

value: male


title: 1900_LV_SingleDoseABE

value: SvEv

value: SingleDoseABE


title: AMBLA3 snRNA-seq

description: 10X genomic snRNA-seq

value: Adult

value: Amygdala

value: nuclear RNA


title: 1899_LV_SingleDoseABE

value: female


title: F3hrde-1_Normoxia_rep2

value: Normoxia


title: 2244_LA_BoostedABE

value: Left Atrium

value: BoostedABE


title: Col-0,control,input,rep2

description: polyA RNA

value: leaf

value: control


title: AMBLA2 snRNA-seq

description: 10X genomic snRNA-seq


title: Col-0,control,input,rep1

description: polyA RNA


title: AMCEA2 snRNA-seq

description: 10X genomic snRNA-seq


title: Col-0,control,m6A-IP,rep2

description: polyA RNA


title: 2244_RV  _BoostedABE


title: F3WT_Hypoxia_rep2

value: WT


title: 2244_LV _BoostedABE

value: Left Ventricular Apex


title: Col-0,control,m6A-IP,rep1

description: polyA RNA


title: F3WT_Hypoxia_rep1

value: whole worm

value: Hypoxia


title: AMCEA1 snRNA-seq

description: 10X genomic snRNA-seq


title: 2243_RA_BoostedABE

value: Right Atrium


title: Q

value: GBM

value: 129/SVJ x C57BL/6 x FVB

value: GlastCreERT2/+; Ptenfl/fl


title: 2243_LA_BoostedABE

value: male


title: 2243_RV  _BoostedABE

value: Right Ventricle


title: AMMS4 snRNA-seq

description: 10X genomic snRNA-seq

value: Adult

value: Amygdala

value: nuclear RNA


title: F3WT_Normoxia_rep1

value: Normoxia


title: AMMS3 snRNA-seq

description: 10X genomic snRNA-seq


title: sib_CAstat3_3

data_processing:
basecalling was done with the Picard module IlluminaBasecallsToFastq
Reads were trimmed using TRIM GALORE software to check for quality of 150bp reads. These paired-end reads were mapped using STAR aligner (version 2.4.2a) to the reference genome.
Differential expression analysis was done using DESeq2 via DEApp. FeatureCounts was used to calculate reads per gene.
Assembly: GRcz10
Supplementary files format and content: tab-delimited text file includes feature count values for each sample

organism: Danio rerio

source_name: endothelial cells

extract_protocol:
kdrl-positive cells were isolated from zebrafish embryos. RNA was extracted with the quick RNA microprep (Zymo). Poly A RNA was selected by oligo dT primer with low-input library generation by Novogene.
Libraries were made following the low-input library prep and sequenced on a Novoseq 6000

tag: time

value: 28 hours post fertilization


title: F2hrde-1_Hypoxia_rep2


title: 2243_LV  _BoostedABE

value: BoostedABE


title: AMMS2 snRNA-seq

description: 10X genomic snRNA-seq

tag: age


title: F3hrde-1_Normoxia_rep1


title: F2hrde-1_Hypoxia_rep1


title: mut_WTstat3_1


title: AMMS1 snRNA-seq

description: 10X genomic snRNA-seq

tag: molecule


title: F2hrde-1_Normoxia_rep2


title: 1096_RV_none

value: SvEv


title: AMBLA1 snRNA-seq

description: 10X genomic snRNA-seq


title: wt_CAstat3_3


title: F2hrde-1_Normoxia_rep1


title: F3WT_Normoxia_rep2

value: WT


title: mut_WTstat3_2


title: 1096_Lva_none

value: Left Ventricular Apex


title: WT+GCV_b [1205]

data_processing:
fastq files were generated using cellranger 3.0.2 mkfastq tool
matrix filles were generated using cellranger 3.0.2 count function, with hg38 + GFP transgene reference transcriptome with 10000 cells as expected-cells number
output from cellranger was processed into Seurat v3.
Genome_build: hg38
Supplementary_files_format_and_content: filtered_feature_bc_matrix : filtered data from cellranger count outputs

extract_protocol:
GFP+ GBMs were macrodissected, papain-based and mechanically dissociated. A debris removal step was performed, and blood cells were removed using a blood lysis buffer. Cells were labeled with eBiosciences Fixable Viability Dye Fluor 450 sorted using the MoFlo Astrios cell sorter. Live cells were collected, centrifuged and resuspended in a final volume of HBSS-0,1%BSA to get a 1200 cells/µL solution.
Libraries were prepared according to Illumina's instructions accompanying the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1. Libraries were sequenced on the Chromium Controller (10X Genomics) following the manufacturer's protocols.
single cell RNAseq 10X 3' v3 kit

treatment_protocol: GCV (25 mg/kg) was administered daily via i.p. injections of 5 consecutive days, when bioluminescence head/body ratio reached 2. Mice were sacrificed 7 days after the last day of GCV injection.

tag: strain background

tag: harvesting

value: early time point (7 days after last GCV injection)

value: GBMs


title: wt_WTstat3_2


title: mut_CAstat3_2


title: sib_WTstat3_2


title: mut_CAstat3_3


title: Somitoid-120h-UNCX-1

first: Yannis

last: Djeffal

state: Massachusetts

address: 60 Fenwood road

department: Pathology/Genetics

institute: Brigham and Women’s Hospital/Harvard Medical School

data_processing:
The sequencing quality was assessed by FastQC (version 0.11.9)
The sequence reads were then mapped to the human transcriptome by Salmon (version 1.4.0) and quantified using the quasi-mapping method.
To assess the quality and origin of the mapped reads, a further quality control step was performed by aligning the reads to the human genome (GRCh38) using STAR (version 2.7.6a) and by subsequently subjecting the resulting alignment data files (BAM files) to further analysis using Qualimap (version 2.2.2a).
The transcript per million (TPM) mapped reads count of each transcript calculated by Salmon was thereafter used for differential gene expression analysis, which was performed using the DESeq2 package.
Assembly: GRCh38
Supplementary files format and content: FASTQ

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared with Genewiz using the polyA selection method

tag: cell line

value: induced pluripotent stem cells

value: paraxial mesoderm differentiation48h


title: F2WT_Hypoxia_rep2

tag: tissue

value: whole worm

value: Hypoxia


title: Somitoid-120h-UNCX-2

tag: cell type


title: p16-3MR+GCV_b [1193]

value: 129/SVJ x C57BL/6 x FVB

value: GlastCreERT2/+; Ptenfl/fl; p16-3MR/+


title: p16-3MR+GCV_a [1191]


title: F2WT_Normoxia_rep2


title: sib_CAstat3_2


title: WT+GCV_a [1198]

value: GlastCreERT2/+; Ptenfl/fl


title: Somitoid-120h-MESP2-3


title: F2WT_Hypoxia_rep1


title: p16-3MR+vhc_997

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads with following parameters : cutoff: '20' leading: '10' minlen: '50' slidingwindow: '4' trailing: '10'
Star v2.5.3a has been used to align reads on  reference genome using standard options
Quantification of gene and isoform abundances has been done with rsem 1.2.28
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including expecting counts, TPM and FPKM

growth_protocol:
GBM mouse model: The lentivirus (1 µL, 6 x 108 PFU/mL) was stereotaxically injected in the right SVZ of brain mice. From the next day, mice were injected i.p. with tamoxifen (TMX, 100 mg/kg) once per day for five consecutive days.
GBM-derived organoids: GBM-derived organoids were generated following Hubert et al. 2016 protocol. Briefly, GFP+ GBM were papain-based and mechanically dissociated. A debris removal step was performed, and blood cells were removed using a blood lysis buffer  when necessary. Cells were resuspended in Neurobasal medium complemented with Glutamax, Penicilline/Streptomycine, Human FGF-basic, Human EGF, B27. An organoid is firstly formed with 8000 cells and made of 16 µL of GelTrex and 4 µL of cell suspension. Pearls of 20 µL cells-Geltrex solution were formed in sterile parafilm molds and let one hour at 37°C, 5% CO2 to solidify. Organoids were then unmolded, placed in Neuro basal complete medium and incubated at 37°C, 5% CO2. After three days in vitro, petri dishes were placed on an orbital shaker (80 rpm). About 40% of the medium was changed every three to four days.

extract_protocol:
GBM mouse model: Total RNA were extracted from GBM samples following TRI-reagent protocol (Molecular Center Research, TR 118).
GBM-derived organoids: Total RNA from 3 pooled GBM-derived organoids were extracted following the Macherey-Nagel Mini kit Nucleospin protocol (Macherey-Nagel, 740955.50).

treatment_protocol:
GBM mouse model: GCV (25 mg/kg) or vhc (PBS, DMSO) was administered daily via i.p. injections of 5 consecutive days, when bioluminescence head/body ratio reached 2. Mice were sacrificed at the endpoints.
GBM-derived organoids: After 14 days in vitro, GBM-derived organoids were treated with either vehicle (vhc) or with ABT263 (2 µM) and were collected 7 days later.

value: end point

tag: tissue/cell type

value: GBM


title: wt_CAstat3_2


title: Somitoid-120h-UNCX-3

tag: treatment


title: Somitoid-120h-MESP2-1

tag: genotype


title: sib_CAstat3_1


title: wt_CAstat3_1


title: mut_CAstat3_1


title: Somitoid-120h-MESP2-2


title: F2WT_Normoxia_rep1

value: Normoxia


title: F1hrde-1_Hypoxia_rep2


title: F1hrde-1_Normoxia_rep2


title: p16-3MR+vhc_869


title: F1hrde-1_Hypoxia_rep1


title: Somitoid-72h-MESP2low-2

value: 72 hr


title: p16-3MR+vhc_861


title: p16-3MR+vhc_765


title: Somitoid-72h-MESP2low-3


title: F1hrde-1_Normoxia_rep1


title: sib_WTstat3_1

value: 28 hours post fertilization


title: Somitoid-72h-MESP2low-1


title: F1WT_Hypoxia_rep2


title: Somitoid-72h-MESP2high-3


title: Somitoid-72h-MESP2high-2


title: p16-3MR+GCV_536


title: p16-3MR+GCV_641


title: p16-3MR+GCV_762


title: beige_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: beige 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: Beige adipose tissue

tag: replicate


title: p16-3MR+GCV_773

tag: injected lentivirus


title: F1WT_Normoxia_rep2

tag: generation

value: WT


title: WAT_RPF2

source_name: white adipose tissue

value: white adipose tissue (WAT)


title: Somitoid-72h-MESP2high-1


title: F1WT_Hypoxia_rep1

tag: genotype/variation


title: beige_RPF2


title: wt_WTstat3_1


title: BAT_RPF2

source_name: brown adipose tissue

value: brown adipose tissue (BAT)


title: Somitoid-120h-3

value: induced pluripotent stem cells


title: P0hrde-1_Hypoxia_rep2


title: F1WT_Normoxia_rep1


title: p16-3MR+GCV_751


title: p16-3MR+GCV_761


title: P0hrde-1_Hypoxia_rep1


title: P0hrde-1_Normoxia_rep2


title: Col-0 Rep3

data_processing:
Quality control—Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts.
Mapping—Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.
Quantification of gene expression level— FeatureCounts (http://subread.sourceforge.net/) was used to count the reads numbers mapped to eachgene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
ifferential expression analysis—Differential expression analysis was performed using the DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html)
Enrichment analysis—The GO and KEGG enrichment analysis of differential genes can explain the functional enrichment of differential genes and clarify the differences between samples at the gene function level. We use clusterProfiler R software package for GO function enrichment and KEGG pathway enrichment analysis.
Assembly: TAIR10
Supplementary files format and content: text files

extract_protocol:
Total RNA was extracted from the seedling of cnd1-3 and Col-0 using TRIzol® Reagent according the manufacturer’s instructions (Magen).
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions. The mRNA was purified from 1 μg total RNA using oligo (dT) magnetic beads followed by fragmentation carried out using divalent cations at elevated temperatures in ABclonal First Strand Synthesis Reaction Buffer. Subsequently, first-strand cDNAs were synthesized with random hexamer primers and Reverse Transcriptase (RNase H) using mRNA fragments as templates, followed by second-strand cDNA synthesis using DNA polymerase I, RNAseH, buffer, and dNTPs. The synthesized double stranded cDNA fragments were then adapterligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system. Finally, the library preparations were sequenced on a MGISEQ-T7 and 150 bp paired-end reads were generated. The data generated from BGI platform were used for bioinformatics analysis. All of the analyses were performed using an in-house pipeline from Shanghai Applied Protein Technology

value: Arabidopsis seedling


title: Somitoid-66h-3

value: paraxial mesoderm differentiation48h

value: 66 hr


title: P0hrde-1_Normoxia_rep1

value: whole worm


title: Col-0 Rep2


title: P0WT_Hypoxia_rep2

value: Hypoxia


title: p16-3MR+GCV_726

value: 129/SVJ x C57BL/6 x FVB

value: GlastCreERT2/+; Ptenfl/fl; p16-3MR/+


title: HDM13375

city: Guiyang

first: Zhibo

last: Zhao

state: China

address: The west campus of Guizhou University

institute: Guizhou University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Illumina Hiseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Fastp v0.19.11; length_required=50, n_base_limit=6.
ChIP-seq reads were aligned to the reference genome (GenBank: CP032631.1) using BWA version 0.7.12-r1039; -T 30, -k 32.
Peaks were called using MACS v2.1.0 with the significance cut-off q-value <=0.05 (--nomode, --call-summits, --nomodel).
Assembly: GenBank: CP032631.1
Supplementary files format and content: bigWig, narrowPeak

organism: Pseudomonas syringae pv. actinidiae

source_name: Bacteria

growth_protocol: HDM13375 and KB13375 indicated bacteria were cultured at 25C for 24 hours in HDM and KB medium, respectively.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. Then a PierceTM Magnetic ChIP Kit (Cat. #: 26157, Thermo Fisher Scientific) and a ChIP-grade Myc-Tag Monoclonal Antibody (Myc.A7, Cat. #: MA121316, Thermo Fisher Scientific) were used for sample pretreatment and immunoprecipitation.
The DNA fragments were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Bacteria

tag: medium

value: hrp-derepressing medium

tag: chip antibody

value: Myc.A7 (Cat. #:MA121316, Thermo Fisher Scientific)


title: KB13375

value: KB


title: Somitoid-66h-1

tag: time


title: Somitoid-120h-1


title: Somitoid-66h-2


title: WT+GCV_1209

value: GlastCreERT2/+; Ptenfl/fl

value: end point

value: GBM


title: p16-3MR+GCV_776


title: Somitoid-120h-2

value: WT


title: Col-0 Rep1


title: cnd1-3 Rep3


title: p16-3MR+GCV_645


title: P0WT_Normoxia_rep2

value: Normoxia


title: P0WT_Hypoxia_rep1


title: P0WT_Normoxia_rep1


title: Somitoid-48h-1

value: induced pluripotent stem cells

value: 48 hr


title: WT+GCV_747


title: WT+GCV_763


title: cnd1-3 Rep2

value: Arabidopsis seedling


title: WT+GCV_995


title: WT+GCV_880


title: Somitoid-48h-2

value: paraxial mesoderm differentiation48h


title: Somitoid-48h-3


title: Dog_SubcorticalWhiteMatter_Male_1005

status: Public on Dec 12 2022

city: North Chicago

first: Terry

last: Van Vleet

state: IL

address: 1 N Waukegan Rd

institute: AbbVie

description:
Dog_SubcorticalWhiteMatter_Male_1005
Dog_FPKM_table_Jun22.xlsx

data_processing:
ArrayStudio
Sequence reads were trimmed for adaptor sequence/low-quality sequence using ArrayStudio
Trimmed sequence reads were mapped to Mouse.B38, Rat.B6.0, Dog.CanFam3.1, and Macaca_fascicularis_5.0
Read count extraction and normalization were performed using ArrayStudio
Assembly: Mouse.B38, Rat.B6.0, Dog.CanFam3.1, and Macaca_fascicularis_5.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Canis lupus familiaris

source_name: White Matter

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). 200-300ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Kit Gold following manufacturer's protocols.

treatment_protocol:
NA
NA

tag: breed

value: Beagle

value: White Matter

tag: Sex

value: Male

value: untreated


title: Dog_SubcorticalWhiteMatter_Male_1003

description:
Dog_SubcorticalWhiteMatter_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_Testes_Male_1001

description:
Dog_Testes_Male_1001
Dog_FPKM_table_Jun22.xlsx

source_name: Testis

value: Testis


description:
Dog_SubmandibularSalivaryGland_Male_1001
Dog_FPKM_table_Jun22.xlsx

source_name: Salivary Glands

value: Salivary Glands


title: Dog_SubcorticalWhiteMatter_Male_1001

description:
Dog_SubcorticalWhiteMatter_Male_1001
Dog_FPKM_table_Jun22.xlsx


description:
Dog_SubmandibularSalivaryGland_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_Testes_Male_1003

description:
Dog_Testes_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_Testes_Male_1005

description:
Dog_Testes_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_Synovium_Male_1001

description:
Dog_Synovium_Male_1001
Dog_FPKM_table_Jun22.xlsx

source_name: Synovial Membrane

value: Synovial Membrane


description:
Dog_SubmandibularSalivaryGland_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_Spleen_Male_1003

description:
Dog_Spleen_Male_1003
Dog_FPKM_table_Jun22.xlsx

source_name: Spleen

value: Spleen


title: Dog_Spleen_Male_1005

description:
Dog_Spleen_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_Synovium_Male_1003

description:
Dog_Synovium_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_Spleen_Male_1001

description:
Dog_Spleen_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: cnd1-3 Rep1

source_name: Arabidopsis seedling


title: Dog_Soleus_Male_1005

description:
Dog_Soleus_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Muscle, Skeletal

value: Muscle, Skeletal


title: Dog_Soleus_Male_1001

description:
Dog_Soleus_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_Soleus_Male_1003

description:
Dog_Soleus_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_Synovium_Male_1005

description:
Dog_Synovium_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_SciaticNerve_Male_1005

description:
Dog_SciaticNerve_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Sciatic Nerve

value: Sciatic Nerve


title: Dog_SciaticNerve_Male_1003

description:
Dog_SciaticNerve_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_Retina_Male_1003

description:
Dog_Retina_Male_1003
Dog_FPKM_table_Jun22.xlsx

source_name: Retina

value: Retina


title: Dog_Retina_Male_1005

description:
Dog_Retina_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_Quadriceps_Male_1005

description:
Dog_Quadriceps_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Quadriceps Muscle

value: Quadriceps Muscle


title: Dog_Retina_Male_1001

description:
Dog_Retina_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_PyloricStomach_Male_1005

description:
Dog_PyloricStomach_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Stomach

value: Stomach


title: Dog_Quadriceps_Male_1001

description:
Dog_Quadriceps_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_Quadriceps_Male_1003

description:
Dog_Quadriceps_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_PyloricStomach_Male_1003

description:
Dog_PyloricStomach_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_Prostate_Male_1001

description:
Dog_Prostate_Male_1001
Dog_FPKM_table_Jun22.xlsx

source_name: Prostate

value: Prostate


title: Dog_ParotidSalivaryGland_Male_1003

description:
Dog_ParotidSalivaryGland_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_PhysisMetaphysis_Male_1005

description:
Dog_PhysisMetaphysis_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Epiphyses

value: Epiphyses


title: Dog_PyloricStomach_Male_1001

description:
Dog_PyloricStomach_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_PhysisMetaphysis_Male_1003

description:
Dog_PhysisMetaphysis_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_Prostate_Male_1003

description:
Dog_Prostate_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_ParotidSalivaryGland_Male_1005

description:
Dog_ParotidSalivaryGland_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_Prostate_Male_1005

description:
Dog_Prostate_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_ParotidSalivaryGland_Male_1001

description:
Dog_ParotidSalivaryGland_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_Pituitary_Male_1001

description:
Dog_Pituitary_Male_1001
Dog_FPKM_table_Jun22.xlsx

source_name: Pituitary Gland

value: Pituitary Gland


title: Dog_Pituitary_Male_1003

description:
Dog_Pituitary_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_Pancreas_Male_1005

description:
Dog_Pancreas_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Pancreas

value: Pancreas


title: Dog_Pituitary_Male_1005

description:
Dog_Pituitary_Male_1005
Dog_FPKM_table_Jun22.xlsx

value: Beagle


title: Dog_Pancreas_Male_1003

description:
Dog_Pancreas_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_SciaticNerve_Male_1001

description:
Dog_SciaticNerve_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_OlfactoryEpithelium_Male_1005

description:
Dog_OlfactoryEpithelium_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Olfactory Mucosa

value: Olfactory Mucosa


title: Dog_Pancreas_Male_1001

description:
Dog_Pancreas_Male_1001
Dog_FPKM_table_Jun22.xlsx

value: Male


title: Dog_OlfactoryEpithelium_Male_1003

description:
Dog_OlfactoryEpithelium_Male_1003
Dog_FPKM_table_Jun22.xlsx

value: untreated


title: Dog_OlfactoryEpithelium_Male_1001

description:
Dog_OlfactoryEpithelium_Male_1001
Dog_FPKM_table_Jun22.xlsx


title: Dog_MesentericAdipose_Male_1001

description:
Dog_MesentericAdipose_Male_1001
Dog_FPKM_table_Jun22.xlsx

source_name: Intra-Abdominal Fat

value: Intra-Abdominal Fat


title: Dog_MesentericAdipose_Male_1003

description:
Dog_MesentericAdipose_Male_1003
Dog_FPKM_table_Jun22.xlsx


title: Dog_MesentericAdipose_Male_1005

description:
Dog_MesentericAdipose_Male_1005
Dog_FPKM_table_Jun22.xlsx


title: Dog_MesentericLymphNode_Male_1005

description:
Dog_MesentericLymphNode_Male_1005
Dog_FPKM_table_Jun22.xlsx

source_name: Lymph Nodes

value: Lymph Nodes