title: TCR-seq, B16-F10 melanoma cells, Mettl5 KO, rep5

description: Library name: TCRseq-C28


title: RNA-seq of Atf4 exon2 Control mice  E11.5  heart replicate 2

status: Public on Feb 18 2026

type: SRA

city: San Diego

first: Zeyu

last: Chen

state: CA

address: 9500 Gilman Drive, BFRII 1217

department: School of Medicine

country: USA

institute: UCSD

description:
Library name: Atf4_e2_Ctrl_rep2
Atf4.Batch2.CT2

library_source: transcriptomic

data_processing:
Raw RNA-seq reads were assessed for quality using FastQC.
Adapter sequences and low-quality bases were trimmed using Trim Galore (v0.6.7).
Clean reads were aligned to the mouse reference genome (GRCm38, Mus musculus) using HISAT2 (v2.2.1) with default parameters.
Gene expression quantification was performed using StringTie (v2.2.1).
Gene counts were obtained with featureCounts and used for differential expression analysis with DESeq2.
Assembly: GRCm38 (Mus musculus)
Supplementary files format and content: normalized bigWig files (*.bw) representing RNA-seq read coverage for each sample
Supplementary files format and content: a text file (merge.TPM.txt) containing  TPM expression values across all samples.

molecule: total RNA

organism: Mus musculus

source_name: Ventricular heart

growth_protocol: All mice were housed in a pathogen-free facility under standard laboratory conditions with a 12-hour light/dark cycle. Mice were maintained on a standard rodent chow diet with water provided ad libitum. Timed matings were set up, and noon on the day of vaginal plug detection was considered embryonic day 0.5 (E0.5). Pregnant dams were euthanized at E11.5 to collect embryonic heart tissues.

extract_protocol:
Total RNA was extracted from cultured primary cortical neurons using the Quick-RNA Miniprep Kit (Zymo Research; Cat# R1054) following the manufacturer's instructions. RNA concentration and purity were assessed using a Nanodrop spectrophotometer. For downstream applications, equal amounts of RNA were used for either RNA-seq library preparation or reverse transcription into cDNA using the High-Capacity cDNA Reverse Transcription Kit (Invitrogen™).
RNA-seq libraries were constructed following ribosomal RNA (rRNA) depletion protocols to enrich for non-rRNA transcripts. Total RNA was subjected to rRNA depletion using a commercial RNA depletion kit according to the manufacturer’s instructions. Libraries were then generated from the rRNA-depleted RNA and sequenced on an Illumina NovaSeq 6000 platform using paired-end sequencing.

treatment_protocol: No chemical or pharmacological treatments were applied in this study. All embryos were harvested under baseline physiological conditions without experimental perturbation.

tag: tissue

value: Ventricular heart

tag: cell type

tag: genotype

value: C57BL/6 WT

tag: treatment

value: Control

tag: batch


title: TCR-seq, B16-F10 melanoma cells, Mettl5 KO, rep2

city: Shenzhen

first: Hao

address: 1088 Xueyuan Avenue

country: China

institute: Southern University of Science and Technology (SUSTech)

description: Library name: TCRseq-C12

data_processing:
Processed reads were aligned to the reference genome (gencode GRCm39) by the STAR (v2.7.10a)80, allowing for at most two mismatches. For Ribo-seq data, quality control and translational profiles was analyzed by RiboseQC. Transcriptome assembly and quantification were performed using StringTie (v2.1.7)81. For TCR-seq, data were analysed using ImmunoSEQ Analyzer 3.0, an Adaptive Biotechnologies online analysis platform. For scRNA-seq, Single-cell RNA sequencing (scRNA-seq) data were processed using standardized bioinformatics workflows. Raw sequencing data were aligned to the Mouse reference genome (GRCm39) and converted into unique molecular identifier (UMI) count matrices using Cell Ranger.
Assembly: GRCm39.genome.fa
Library strategy: TCR-Seq

source_name: B16-F10 melanoma cells

growth_protocol: The B16-F10 melanoma cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, Gibco) supplemented with 10% fetal bovine serum (FBS, Biological Industries), 1% penicillin-streptomycin (Thermo Fisher Scientific), and 1% SaveIt mycoplasma inhibitor (Hanbio Biotechnology). Cells were maintained in a humidified incubator at 37°C with 5% CO₂ and routinely tested for bacterial and mycoplasma contamination.

extract_protocol:
For Ribo-Seq, cells were incubated with 100 μg/ml Cycloheximide (MCE) for 8 min at 37°C and were then lysed on ice for 10min in 400uL lysis buffer (20 mM Tris–HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml Cycloheximide, 1% Triton X-100). The supernatant was collected via centrifugation at 12 000 g for 10 min at 4 °C, and its' absorbance at 260nm was measured. The ribosomes with equal A260 in each group were reserved for RNA sequencing. For TCR-Seq, PBMCs were isolated from whole blood of C57BL/6N mice that had been inoculated with either control B16F10 cells or Mettl5-KO cells 12 days prior.   For scRNA-Seq,  Tumors were surgically resected and preserved in MACS Tissue Storage Solution, then transferred to the laboratory at low temperature. Following the manufacturer's instructions for the Miltenyi Biotec dissociation kit, the tumors were dissociated into a single-cell suspension. Post-dissociation, cells were resuspended in MACS Tissue Storage Solution to maintain viability. Cell counting and concentration adjustment were performed, followed by labeling with Zombie NIR viability dye to distinguish live and dead cells. Subsequently, cells were incubated with Fc blocker in FACS buffer to prevent non-specific antibody binding. Cells were then incubated with an antibody cocktail containing anti-CD45 antibodies. After incubation, cells were washed, filtered through a 70-μm Macs SmartStrainer to remove aggregates and debris, ensuring a high-quality single-cell suspension. Finally, CD45+ live immune cells were sorted using a BD FACSAria II instrument for downstream scRNA-seq analysis with the 10X Genomics 5' platform. This method ensures the isolation of viable immune cells, crucial for studying the tumor immune microenvironment.
For Ribo-Seq, added 15U RNase1 (Thermo Fisher Scientific) for each 1OD of lysate, and incubated the reactions at 22°C for 40 min with gentle mixing. Ribosome-protected fragments (RPFs) were collected by MicroSpin S-400 columns (Cytiva) and purified by Zymo Research RNA Clean & Concentrator-25 kit (Zymo). The RPFs were then separated with 15% polyacrylamide TBE–urea gel, excised the gel slices between 17 and 34 nucleotides and recovered RNA from PAGE gel by ZR small-RNA™ PAGE Recovery Kit (Zymo). Purified RNA was treated with PNK(NEB), and the RNA library was prepared by VAHTSTM Small RNA Library Prep Kit for Illumina®(Vazyme). The library concentration was analyzed using the VAHTSTM Library Quantification Kit for Illumina®, and equimolar pools of libraries were sequenced. For TCR-Seq, DNA was extracted from PBMC using a QIAamp DNA Blood Mini Kit (Qiagen), and the concentration was tested using NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific). The DNA was used as a template for PCR amplification, which was performed to generate the library of TCR and BCR. The step 1 PCR amplification protocol was as follows: 95 °C for 5 min; 95 °C for 30 s, 59 °C for 30 s; 72 °C for 1 min for 30 cycles; and 72 °C for 10 min. The step 2 PCR amplification protocol was as follows: 98 °C for 2 min; 98 °C for 30 s, 65 °C for 30 s; 72 °C for 30 s for 10 cycles; and 72 °C for 5 min. The PCR products were purified, and the barcodes were confirmed. The annealed region of these primers was the CDR3 region, as shown by Multiplex PCR Amplifies. The CDR3 regions were sequenced on Illumina NextSeq500 (MyGenostics).  For scRNA-Seq, Following cell sorting, live CD45+ immune cells were resuspended in PBS + 0.04% BSA at 1,000 cells/μL. Libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 5' v2 Kit according to manufacturer protocol, targeting 10,000 cells per sample. cDNA amplification and fragmentation were performed before Illumina adapter ligation.

tag: cell line

value: B16-F10 melanoma cells

value: Mettl5 KO


title: ConA-1

city: Beijing

first: Xiyu

last: Wang

address: No. 8 Gongren Tiyuchang South Road

institute: Beijing Chaoyang Hospital, Capital Medical University

description: Library name: Sample 1

data_processing:
HISAT2 2.1.0 --dta –t –p 4
RNA samples were purified, fragmented, reverse transcribed, end-repaired. After sequenced adapters were added, the target fragments were recovered by magnetic bead screening, and PCR amplification was performed to complete the entire library preparation work.
After the library construction was completed, use Agilent2100 to detect the insert size of the library.
If insert size met the expectation, Bio-RAD CFX 96 fluorescent quantitative PCR instrument and Bio-RAD KIT iQ SYBR GRN were used to perform q-PCR to accurately quantify the effective concentration of the library (the effective concentration of the library was > 10nM) to ensure the quality of the library.
Assembly: Mus_musculus.GRCm38.91
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: liver

extract_protocol:
Mice were performed oral gavage with a 30 mg/kg body weight mixed solution of simvastatin or PBS per day before 5 days of ConA injection and 1 h before the injection. An additional oral gavage was administered to the mice 24 h after ConA injection.. CD4+ T cells in liver samples were stained and detected by fluorescence activated cell sorting (FACS) cells Aria II (BD Biosciences, CA, USA), CD3+ NK1.1-CD4+ CD8- cells were selected.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: liver

value: Primary cells

value: T cell

value: Wild type


title: TCR-seq, B16-F10 melanoma cells, scrambled control (SCR) , rep3

description: Library name: TCRseq-C25

value: scrambled control (SCR)


title: TCR-seq, B16-F10 melanoma cells, Mettl5 KO, rep3

description: Library name: TCRseq-C13


title: TCR-seq, B16-F10 melanoma cells, scrambled control (SCR) , rep4

description: Library name: TCRseq-C29


title: TCR-seq, B16-F10 melanoma cells, scrambled control (SCR) , rep2

description: Library name: TCRseq-C24


title: Male mice, inoculated with UTI, biol rep 1

city: Cambridge

first: Ashlee

middle: M

last: Earl

state: MA

address: 415 Main Street

department: Infectious Disease and Microbiome Program

institute: Broad Institute

description: Library name: Oil_UTI_Male_1

library_source: transcriptomic single cell

data_processing:
Initial analysis of sequencing data was performed using 10X Genomics CellRanger software (version 6.0.1).
CellBender (version 0.1.0) was used to remove ambient RNA signals, using stringent thresholds (CellBender expected number of cells 10,000; CellRanger Total_droplets_included 100%).
Assembly: mm10
Supplementary files format and content: h5 files, after filtering with cellbender

molecule: nuclear RNA

source_name: kidney

extract_protocol:
Kidney nuclear preparation was completed as described previously (Wilson et al., 2019 [PMID 31506348]; Humphreys et al., 2018 [dx.doi.org/10.17504/protocols.io.nahdab6])
Library prep, barcoding, and pooling were performed on the 10X Chromium platform.

value: kidney


title: RNAseq, B16-F10 melanoma cells, Mettl5 KO, rep2

description: Library name: RNAseq-Mettl5-KO2

data_processing:
Processed reads were aligned to the reference genome (gencode GRCm39) by the STAR (v2.7.10a)80, allowing for at most two mismatches. For Ribo-seq data, quality control and translational profiles was analyzed by RiboseQC. Transcriptome assembly and quantification were performed using StringTie (v2.1.7)81. For TCR-seq, data were analysed using ImmunoSEQ Analyzer 3.0, an Adaptive Biotechnologies online analysis platform. For scRNA-seq, Single-cell RNA sequencing (scRNA-seq) data were processed using standardized bioinformatics workflows. Raw sequencing data were aligned to the Mouse reference genome (GRCm39) and converted into unique molecular identifier (UMI) count matrices using Cell Ranger.
Assembly: GRCm39.genome.fa


title: RNAseq, B16-F10 melanoma cells, scrambled control (SCR), rep2

description: Library name: RNAseq-Mettl5-SCR2


title: RNAseq, B16-F10 melanoma cells, Mettl5 KO, rep1

description: Library name: RNAseq-Mettl5-KO1


title: Male mice, inoculated with PBS (control), biol rep 1

description: Library name: Oil_PBS_Male_1


title: RNAseq, B16-F10 melanoma cells, scrambled control (SCR)  , rep1

description: Library name: RNAseq-Mettl5-SCR1


title: Male mice, inoculated with UTI, biol rep 2

description: Library name: Oil_UTI_Male_2


title: Male mice, inoculated with UTI, biol rep 3

description: Library name: Oil_UTI_Male_3


title: ConA-3

description: Library name: Sample 3


title: Female mice, inoculated with PBS (control), biol rep 1

description: Library name: Oil_PBS_Female_1


title: Female mice, inoculated with PBS (control), biol rep 3

description: Library name: Oil_PBS_Female_3


title: Female mice, inoculated with UTI, biol rep 1

description: Library name: Oil_UTI_Female_1


title: Androgen-exposed female mice, inoculated with UTI, biol rep 3

description: Library name: Depo_UTI_Female_3


title: Female mice, inoculated with UTI, biol rep 3

description: Library name: Oil_UTI_Female_3


title: TCR-seq, B16-F10 melanoma cells, scrambled control (SCR) , rep1

description: Library name: TCRseq-C3


title: Androgen-exposed female mice, inoculated with UTI, biol rep 1

description: Library name: Depo_UTI_Female_1


title: Female mice, inoculated with PBS (control), biol rep 2

description: Library name: Oil_PBS_Female_2


title: Male mice, inoculated with PBS (control), biol rep 2

description: Library name: Oil_PBS_Male_2


title: Female mice, inoculated with UTI, biol rep 2

description: Library name: Oil_UTI_Female_2


title: Androgen-exposed female mice, inoculated with PBS (control), biol rep 2

description: Library name: Depo_PBS_Female_2


title: Androgen-exposed female mice, inoculated with PBS (control), biol rep 3

description: Library name: Depo_PBS_Female_3


title: Heart ventricles, Cre control male 1, Day12

city: Houston

first: Romain

last: Harmancey

state: Texas

address: 1881 East Rd.

department: Internal Medicine - Division of Cardiology

institute: The University of Texas Health Science Center at Houston

description:
Library name: Sample 31
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.CTRL_VEN_D12_M1

data_processing:
Cutadapt and proprietary Perl scripts (LC Sciences) were used to filter reads.
Sequence quality was verified using FastQC and HISAT was employed to map reads to GrCM38/mm10.
The mapped reads of each sample were assembled using StringTie.
All transcriptomes were merged to reconstruct a comprehensive transcriptome using Perl scripts (LC Sciences)and gffcompare.
After the ﬁnal transcriptome was generated, StringTie and Ballgown were used to estimate the expression levels of all transcripts as FPKM.
Assembly: mm10
Supplementary files format and content: Genes_fpkm_expression.xlsx file includes normalized gene counts (FPKM) for each sample.
Supplementary files format and content: Isoforms_fpkm_expression.xlsx file includes normalized mRNA isoforms counts (FPKM) for each sample

source_name: Heart, ventricle

growth_protocol: Mice with cardiomyocyte-specific, tamoxifen-inducible overexpression of NR4A2 (Nr4a2-icTg) were generated by crossing Nr4a2-reporter conditional knockin EGE-GJ-095 ROSA26-KI mice with B6.FVB(129)-A1cfTg(Myh6-cre/Esr1*)1Jmk/J mice (The Jackson Laboratory; Strain #005657).

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen). Approximately 1 µg of total RNA was used for the construction of sequencing libraries.
Poly(A) RNA libraries were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: The expression of NR4A2 was induced in 8- to 9-week-old mice through a single intraperitoneal injection of 40 mg/kg body weight tamoxifen; αMHC-MerCreMer, Cre recombinase inducible littermates were used to control for potential tamoxifen-dependent effects.

value: Heart, ventricle

value: aMHC-MerCreMer

value: Tamoxifen

tag: time

value: Day 12


title: Heart ventricles, Cre control female 2, Day12

description:
Library name: Sample 30
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.CTRL_VEN_D12_F2


title: Androgen-exposed female mice, inoculated with UTI, biol rep 2

description: Library name: Depo_UTI_Female_2


title: Male mice, inoculated with PBS (control), biol rep 3

description: Library name: Oil_PBS_Male_3


title: Heart ventricles, Nr4a2-icTg male 2, Day12

description:
Library name: Sample 28
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_VEN_D12_M2


title: Heart ventricles, Nr4a2-icTg male 1, Day12

description:
Library name: Sample 27
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_VEN_D12_M1


title: Heart ventricles, Nr4a2-icTg female 2, Day12

description:
Library name: Sample 26
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_VEN_D12_F2


title: Heart ventricles, Cre control female 1, Day12

description:
Library name: Sample 29
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.CTRL_VEN_D12_F1


title: Heart ventricles, Nr4a2-icTg male 2, Day6

description:
Library name: Sample 24
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_VEN_D6_M2

value: Day 6


title: Heart ventricles, Cre control male 2, Day12

description:
Library name: Sample 32
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.CTRL_VEN_D12_M2


title: Androgen-exposed female mice, inoculated with PBS (control), biol rep 1

description: Library name: Depo_PBS_Female_1


title: Heart ventricles, Nr4a2-icTg female 1, Day12

description:
Library name: Sample 25
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_VEN_D12_F1


title: Heart ventricles, Nr4a2-icTg male 1, Day6

description:
Library name: Sample 23
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_VEN_D6_M1


title: Heart ventricles, Nr4a2-icTg female 2, Day6

description:
Library name: Sample 22
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_VEN_D6_F2


title: Heart ventricles, Nr4a2-icTg female 2, Day3

description:
Library name: Sample 18
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_VEN_D3_F2

value: Day 3


title: Heart ventricles, Nr4a2-icTg male 1, Day3

description:
Library name: Sample 19
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_VEN_D3_M1


title: Heart ventricles, Nr4a2-icTg female 1, Day3

description:
Library name: Sample 17
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_VEN_D3_F1


title: Heart ventricles, Nr4a2-icTg male 2, Day3

description:
Library name: Sample 20
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_VEN_D3_M2


title: Heart ventricles, Nr4a2-icTg female 1, Day0

description:
Library name: Sample 13
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_VEN_D0_F1

value: Day 0


title: Heart atria, Nr4a2-icTg female 2, Day0

description:
Library name: Sample 10
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_ATR_D0_F2

source_name: Heart, atrium

value: Heart, atrium


title: Heart atria, Nr4a2-icTg male 1, Day0

description:
Library name: Sample 11
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_ATR_D0_M1


title: Heart ventricles, Nr4a2-icTg male 1, Day0

description:
Library name: Sample 15
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_VEN_D0_M1


title: Heart ventricles, Nr4a2-icTg male 2, Day0

description:
Library name: Sample 16
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_VEN_D0_M2


title: Heart ventricles, Nr4a2-icTg female 2, Day0

description:
Library name: Sample 14
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_VEN_D0_F2


title: Heart ventricles, Cre control female 1, Day0

description:
Library name: Sample 5
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.CTRL_VEN_D0_F1


title: Heart atria, Nr4a2-icTg male 2, Day0

description:
Library name: Sample 12
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_ATR_D0_M2


title: Heart ventricles, Nr4a2-icTg female 1, Day6

description:
Library name: Sample 21
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_VEN_D6_F1


title: Heart ventricles, Cre control male 2, Day0

description:
Library name: Sample 8
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.CTRL_VEN_D0_M2


title: Heart atria, Cre control male 1, Day0

description:
Library name: Sample 3
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.CTRL_ATR_D0_M1


title: Heart atria, Cre control female 2, Day0

description:
Library name: Sample 2
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.CTRL_ATR_D0_F2


title: Heart ventricles, Cre control female 2, Day0

description:
Library name: Sample 6
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.CTRL_VEN_D0_F2


title: Heart ventricles, Cre control male 1, Day0

description:
Library name: Sample 7
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.CTRL_VEN_D0_M1


title: Heart atria, Nr4a2-icTg female 1, Day0

description:
Library name: Sample 9
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.NR4A2_ATR_D0_F1


title: DM_ZT20_1

city: Zhengzhou

first: Xiao-Qian

last: Li

state: Henan

address: No. 1, East of Jianshe Street, Erqi District

department: Nephrology Hospital

institute: the First Affiliated Hospital of Zhengzhou University

description: Library name: Sample 44

data_processing:
The raw sequencing data were processed using Trimmomatic to remove low-quality reads and those containing ploy-N sequences, resulting in clean reads. The fragments per kilobase million (FPKM) value of each gene was calculated using cufflinks, and the read count of each gene was obtained by htseq-count.The rhythmicity of transcriptome genes in both control and diabetic mice was analyzed using JTK_CYCLE
Assembly: GRCm39
Supplementary files format and content: txt files include FPKM values and meta2d analysis for each sample in both control and diabetic group.

source_name: renal cortex

growth_protocol: Ten-week-old male C57BLKS/J background m/m and db/db mice were supplied by GemPharmatech Co., Ltd. (Nanjing, China). Mice were accommodated in the Laboratory Animal Center of Henan Province with a 12-hour light/12-hour dark cycle (light on at 8:00 AM was specified as zeitgeber time (ZT) 0 and light off at 8:00 PM was defined as ZT12). They had unrestricted access to food and water.

extract_protocol:
mirVana miRNA Isolation Kit. The RNA isolation were handled by OE Biotech Co., Ltd. (Shanghai, China).
Library construction was performed with the TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA).

treatment_protocol: Kidney tissues were harvested every 4-hour, rapidly frozen in liquid nitrogen and then stored at -80℃.

value: renal cortex

tag: strain

value: C57BLKS db/db

tag: Sex

value: male


title: DM_ZT16_4

description: Library name: Sample 43


title: DM_ZT20_3

description: Library name: Sample 46


title: Heart atria, Cre control male 2, Day0

description:
Library name: Sample 4
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.CTRL_ATR_D0_M2


title: DM_ZT20_4

description: Library name: Sample 47


title: DM_ZT16_2

description: Library name: Sample 41


title: DM_ZT16_3

description: Library name: Sample 42


title: DM_ZT16_1

description: Library name: Sample 40


title: Heart atria, Cre control female 1, Day0

description:
Library name: Sample 1
column name in Isoforms_fpkm_expression.xlsx and genes_fpkm_expression.xlsx: FPKM.CTRL_ATR_D0_F1


title: DM_ZT20_2

description: Library name: Sample 45


title: DM_ZT12_2

description: Library name: Sample 37


title: DM_ZT12_3

description: Library name: Sample 38


title: DM_ZT8_4

description: Library name: Sample 35


title: DM_ZT8_2

description: Library name: Sample 33


title: DM_ZT4_4

description: Library name: Sample 31


title: DM_ZT8_1

description: Library name: Sample 32


title: DM_ZT8_3

description: Library name: Sample 34


title: DM_ZT12_4

description: Library name: Sample 39


title: DM_ZT12_1

description: Library name: Sample 36


title: DM_ZT4_2

description: Library name: Sample 29


title: DM_ZT0_1

description: Library name: Sample 24


title: DM_ZT0_2

description: Library name: Sample 25


title: DM_ZT0_3

description: Library name: Sample 26


title: Ctrl_ZT20_3

description: Library name: Sample 22

value: C57BLKS m/m


title: DM_ZT4_3

description: Library name: Sample 30


title: DM_ZT0_4

description: Library name: Sample 27


title: Ctrl_ZT20_4

description: Library name: Sample 23


title: Ctrl_ZT16_2

description: Library name: Sample 17


title: Ctrl_ZT20_1

description: Library name: Sample 20


title: Ctrl_ZT16_4

description: Library name: Sample 19


title: Ctrl_ZT16_1

description: Library name: Sample 16


title: Ctrl_ZT12_4

description: Library name: Sample 15


title: DM_ZT4_1

description: Library name: Sample 28


title: Ctrl_ZT12_3

description: Library name: Sample 14


title: Ctrl_ZT16_3

description: Library name: Sample 18


title: Ctrl_ZT20_2

description: Library name: Sample 21


title: Ctrl_ZT8_3

description: Library name: Sample 11


title: Ctrl_ZT8_2

description: Library name: Sample 10


title: Ctrl_ZT12_1

description: Library name: Sample 12


title: Ctrl_ZT8_1

description: Library name: Sample 9


title: Ctrl_ZT4_3

description: Library name: Sample 7


title: Ctrl_ZT4_4

description: Library name: Sample 8


title: Ctrl_ZT12_2

description: Library name: Sample 13


title: Ctrl_ZT4_1

description: Library name: Sample 5


title: Ctrl_ZT4_2

description: Library name: Sample 6


title: Ctrl_ZT0_4

description: Library name: Sample 4


title: Ctrl_ZT0_3

description: Library name: Sample 3


title: Ctrl_ZT0_2

description: Library name: Sample 2


title: scRNAseq, barcode, Gastruloids 2, Day 6

city: Barcelona

first: Yolanda

last: Andres Lopez

address: C/ Baldiri Reixac, 4-8

country: Spain

institute: Institute of Molecular Biology of Barcelona

description: 10x Genomics 3'

data_processing:
Raw RNA-seq reads were processed using the Cell Ranger pipeline.
For the Barcode data FASTQ files were processed to extract nucleotide sequences and corresponding quality scores.
Assembly: mm10
Supplementary files format and content: The tab-delimited text file includes raw counts for each sample.

molecule: polyA RNA

source_name: mouse embryonic stem cells (mESC)

growth_protocol: Mouse embryonic stem cells (mESCs) were cultured at 37°C in a 5% CO2 atmosphere on gelatin-coated culture plates under standard serum/LIF conditions.

extract_protocol:
RNA was extracted using the RNeasy Micro Kit (Qiagen, 74004).
Single-cell RNA libraries were constructed using the 10X Genomics platform (Single-Cell 3’ Library & Gel Bead Kit v2).

treatment_protocol: For pZscan4-CreERT2 cells, tamoxifen (1 µM) was used for 12 days to activate Cre recombinase.

value: mouse embryonic stem cells (mESC)


title: scRNAseq, barcode, Gastruloids 3, Day 6

description: 10x Genomics 3'


title: Ctrl_ZT0_1

description: Library name: Sample 1


title: scRNAseq, transcriptome, Gastruloids 3, Day 6

description: 10x Genomics 3'


title: scRNAseq, barcode, Gastruloids 1, Day 6

description: 10x Genomics 3'


title: scRNAseq, transcriptome, Gastruloids 1, Day 6

description: 10x Genomics 3'


title: scRNAseq, transcriptome, Gastruloids 2, Day 6

description: 10x Genomics 3'


title: scRNAseq, transcriptome, Timecourse, Day 0 and Day 4

description: 10x Genomics 3'

value: Day 0-4


title: scRNAseq, transcriptome, Timecourse, Day 10

description: 10x Genomics 3'

value: Day 10


title: western diet, AAV8siAATF, replicate 2

city: Mysore

first: Divya

middle: P

last: Kumar

state: Karnataka

address: SS Nagar

department: Biochemistry

country: India

institute: JSS Medical College

data_processing:
High quality reads were mapped to reference genome using STAR (v.2.7.11.a) and further quantified using FeatureCounts (v2.0.1). Differential expression analysis was carried out using DESeq2 (version 1.42.0) in R (version 4.3.2). Genes with read counts less than 10 across the samples were removed prior to downstream analysis. Raw read counts were normalized by DESeq2. The magnitude (log 2 transformed fold change) and significance (P-value) of differential expression between groups were calculated, and genes with P-values <0.05 were considered as significant. We obtained DEGs with the following criteria: PValue <0.05 and |log 2 fold change|≥2.
Assembly: GRCm39: GCF_000001635.27
Supplementary files format and content: Raw Read Counts per gene.

growth_protocol: Male C57Bl/6NCrl mice aged 6 weeks were fed either a chow diet normal water (CD) or a western diet sugar water (WD)

extract_protocol:
RNA extraction was carried out by All prep DNA/RNA kit (Qiagen). RNA was quantified on a Qubit fluorometer and RIN was obtained using Tapestation 4150 using HS RNA screen tape.
The library preparation was carried out using the SMART-Seq Library Prep Kit

treatment_protocol: After 12 weeks of dietary intervention, mice were injected via the tail vein with 1×1011 genome copies of AAV8 serotype particles and randomized into four groups: (i) CDNW with AAV8-TBG-Null, (ii) CDNW with AAV8-TBG-siAATF, (iii) WDSW with AAV8-TBG-Null, and (iv) WDSW with AAV8-TBG-siAATF.

value: liver

value: KD

value: siAATF AAV


title: western diet, AAV8siAATF, replicate 1


title: western diet, AAV8 Control, replicate 3

value: WT

value: control AAV


title: western diet, AAV8siAATF, replicate 3


title: scRNAseq, barcode, Timecourse, Day 10

description: 10x Genomics 3'


title: scRNAseq, transcriptome, pZscan4c, Day 12

description: 10x Genomics 3'

value: Day 12


title: scRNAseq, barcode, pZscan4c, Day 12

description: 10x Genomics 3'


title: scRNAseq, barcode, Timecourse, Day 0 and Day 4

description: 10x Genomics 3'


title: chow diet, AAV8siAATF, replicate 3


title: chow diet, AAV8siAATF, replicate 2


title: chow diet, AAV8siAATF, replicate 1


title: chow diet, AAV8 Control, replicate 2


title: chow diet, AAV8 Control, replicate 1


title: Actg1-NMD rep2

first: Mohamed

middle: A.

last: El-Brolosy

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

data_processing:
The first three nucleotides of Read 2 were trimmed as per the Pico RNA-seq protocol and reads were aligned against the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.5.3a. The numbers of reads that aligned to genes were counted with featureCounts 1.6.0 from the Subread package with the following parameters -B -C -s 2 -t exon. Only reads mapping at least partially inside exons were admitted, and these reads were aggregated per gene. Reads overlapping with multiple genes or aligning to multiple regions were excluded. Only protein-coding genes were considered for the analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited file with raw readcounts for each sample, and DeSeq2 analysis file

source_name: Mouse embryonic fibroblasts

growth_protocol: WT MEFs were transduced with either Actg1-NMD or GFP-2A-RFP-NMD vectors. After puromycin selection, cells were then treated with doxycyline (2ug/ml) for 3 days before RNA extraction

extract_protocol:
RNA was extracted using the RNA Clean & Concentrator-5 kit (Zymo) with on-colomn DNA digestion
10 ng of the total RNA was used as input for the SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech), and libraries were prepared as per the manufacturer's protocol.

value: Mouse embryonic fibroblasts

value: Fibroblast

value: GFP-2A-RFP NMD


title: chow diet, AAV8 Control, replicate 3


title: western diet, AAV8 Control, replicate 2


title: GFP-2A-RFP rep3


title: Actg1-NMD rep1


title: western diet, AAV8 Control, replicate 1


title: GFP-2A-RFP rep2


title: GFP-2A-RFP rep1

data_processing:
The first three nucleotides of Read 2 were trimmed as per the Pico RNA-seq protocol and reads were aligned against the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.5.3a. The numbers of reads that aligned to genes were counted with featureCounts 1.6.0 from the Subread package with the following parameters -B -C -s 2 -t exon. Only reads mapping at least partially inside exons were admitted, and these reads were aggregated per gene. Reads overlapping with multiple genes or aligning to multiple regions were excluded. Only protein-coding genes were considered for the analysis.
Assembly: mm10
Supplementary files format and content: tab-delimited file with raw readcounts for each sample, and DeSeq2 analysis file.


title: Actg1 crosslinked input rep 3

data_processing:
Reads were then trimmed followed by mapping to Ensembl mouse genome version mm10 (GRCm38) as described above. The number of reads aligning to genes were counted with featureCounts with the following parameters -B -C -s 0 -t exon, where only reads mapping at least partially inside exons were admitted, and these reads were aggregated per gene. Reads overlapping with multiple genes or aligning to multiple regions were excluded.
Assembly: mm10
Supplementary files format and content: tab-delimited file with raw readcounts for each sample, and DeSeq2 analysis file.

extract_protocol:
Cross-linked RIP was performed using the Magna Nuclear RIP (Cross-Linked) Nuclear RNA-Binding Protein Immunoprecipitation Kit (Millipore Sigma) according to the manufacturer’s protocol using at least 2x 107 WT or rescued Actg1-NSD MEFs per replicate. For the cross-linked RIP, fixed nuclei were subjected to sonication using Bioruptor (Diagenode) to generate fragments of 200–600 bp in size prior to IP. Enriched ‘input’ samples were generated by reserving 10% of the starting lysate; the remaining volume was subjected to IP using the with 10 µg Anti-ILF3 antibody (abcam; ab92355 and BD Biosciences; Clone 21/DRBP76) coated onto protein A/G magnetic beads as described in the Magna RIP technical manual. RNA purified from both IP and input samples was concentrated by ethanol precipitation and resuspended in equivalent volumes of RNase-free water to be used to generate RNA-seq libraries
sequencing libraries were generated using 10 ng of RNA from input and IP samples using the SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Clontech).


title: Actg1 crosslinked input rep 2


title: WT crosslinked input rep3


title: Actg1 crosslinked input rep 1


title: Actg1-NMD rep3


title: WT crosslinked input rep1


title: Actg1 NSD crosslinked RIP rep 3

library_source: other

molecule: other


title: WT crosslinked input rep2


title: Actg1 NSD crosslinked RIP rep 1


title: WT ILF3 crosslinked RIP rep3


title: Actg1 NSD crosslinked RIP rep 2


title: WT ILF3 crosslinked RIP rep1


title: WT ILF3 crosslinked RIP rep2


title: Actg1-NSD;∆Ilf3 -bach2-rep2

data_processing:
Reads were processed and aligned to the Ensembl mouse genome version mm10 (GRCm38) as described before (Mahat et al., 2016; Mimoso and Adelman, 2023).
Assembly: mm10
Supplementary files format and content: tab-delimited file with normalized readcounts for each sample in each batch, DeSeq2 analysis file, and spike and normalized bedGraphs.
Library strategy: PRO-seq

extract_protocol:
2 million cells that were permeabilized, followed by library construction as described before (Mahat et al., 2016; Mimoso and Adelman, 2023).
2 million cells  were permeabilized, followed by library construction as described before (Mahat et al., 2016; Mimoso and Adelman, 2023).

value: Actg1-NSD;ILF3 KO


title: Actg1-NSD-bach2-rep1


title: Actg1-NSD-bach1-rep2


title: Actg1-NSD-bach1-rep1


title: Actg1-NSD;∆Ilf3 -bach2-rep1


title: WT-batch1-rep1


title: Actg1 NSD native RIP rep 1_seq2

data_processing:
RNA sequencing was performed on a NovaSeq S1 instrument (Illumina), with 150 × 150 bp paired-end setup (only Read 1, however, was used in downstream analysis). Cutadapt was then used to trim Read 1 using the following criteria m 15 -u 3 -a AAAAAAAAAAAAAAA as per the kit’s manufacturer’s recommendation followed by mapping to Ensembl mouse genome version mm10 (GRCm38)
Assembly: mm10
Supplementary files format and content: bedgraph

extract_protocol:
native RIP was performed using the Magna Nuclear RIP (Native) Nuclear RNA-Binding Protein Immunoprecipitation Kit (Millipore Sigma) according to the manufacturer’s protocol using at least 2x 107 WT or rescued Actg1-NSD MEFs per replicate. Enriched ‘input’ samples were generated by reserving 10% of the starting lysate; the remaining volume was subjected to IP using the with 10 µg Anti-ILF3 antibody (abcam; ab92355 and BD Biosciences; Clone 21/DRBP76) coated onto protein A/G magnetic beads as described in the Magna RIP technical manual. RNA purified from both IP and input samples was concentrated by ethanol precipitation and resuspended in equivalent volumes of RNase-free water to be used to generate RNA-seq libraries.
10ng of RNA was used to generate small RNA-seq libraries using the SMARTer smRNA-Seq Kit (Clonetech). RNA was treated with T4 Polynucleotide Kinase for 1 hr prior to library preparation to capture various potential mRNA decay intermediates that may not have a 5’P or 3’OH.


title: WT-batch1-rep3


title: WT-batch1-rep2


title: Actg1-NSD-bach2-rep2


title: Actg1 NSD native RIP rep 2


title: Actg1 NSD native RIP rep 1_seq1


title: 122_H12

city: Bethesda

first: Maxwell

last: Lee

state: MD

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

description: Expression_CountValue.tsv,Expression_FPKM.tsv,Expression_TPM.tsv,Mutations.tsv

data_processing:
We used GATK Best Practices to call mutations from scRNAseq, bWTS and bWES datasets. Depends on the data there are some modifications in the pipeline. Briefly, after trimming and quality control of reads by FastQ (v0.11.9) and Trim Galore (v0.6.5), raw reads were mapped to the mouse genome (GRCm38, mm10) using STAR (v2.7.3a) in two-pass mode which improves the mapping quality at junction sites. Then Picard (v2.22.3) was used for removing duplicated mapped reads and doing indel realignment and base re-calibration. During base quality recalibration, dbSNP variants were used as known sites. In the next step, HaplotypeCaller (v3.8) was used to call the mutations for every single cell separately in GVCF mode. After that, GenotypeGVCFs was used to call the mutations in a joint mode (as pseudo-bulk). These steps keep specificity and sensitivity of calling mutations high. Afterward, the mutations were annotated using ANNOVAR (v2019.10.24). Following that, mutations that were marked as unknown and non-exonic were filtered out. For further confidence, mouse SNPs/Indels filtration was applied to the VCF files based on normal mouse spleen SNPs in addition to a curated in-house database. Finally, somatic-mutations associated with less than 10 reads in at least 2 cells were filtered out. RSEM (v1.3.2) was used to extract expected counts, TPM and FPKM information.
Assembly: mouse mm10
Supplementary files format and content: tab-delimited text files include expression matrix where rows are samples and columns are genes
Supplementary files format and content: tab-delimited text file include all exonic mutations in the samples

source_name: Tumor #122

extract_protocol: Smart-seq2 (Nature Protocol, 2014, 9: 171)

value: Melanoma cell line-derived tumor

value: HGF-tg C57BL6

tag: microbiota status

tag: sorting strategy

value: CD45-, CD31-, alive, nucleated cells


title: 122_H08


title: Actg1 NSD native RIP rep 3


title: 122_H10


title: 122_H11


title: 122_H05


title: 122_H09


title: 122_H04


title: 122_H03


title: 122_H02


title: 122_H06


title: 122_G11


title: 122_H07


title: 122_H01


title: 122_G10


title: 122_G09


title: 122_G07


title: 122_G08


title: 122_G04


title: 122_G12


title: 122_G01


title: 122_F10


title: 122_G03


title: 122_F11


title: 122_G06


title: 122_F12


title: 122_F08


title: 122_G02


title: 122_G05


title: 122_F09_S70


title: 122_F06


title: 122_F05


title: 122_F03


title: 122_F07


title: 122_F01


title: 122_E12


title: 122_E08


title: 122_E09


title: 122_E11


title: 122_E10


title: 122_E05


title: 122_E07


title: 122_E04


title: 122_E06


title: 122_F02


title: 122_E03


title: 122_E02


title: 122_D10


title: 122_E01


title: 122_D12


title: 122_D09


title: 122_D07


title: 122_D03


title: 122_D01


title: 122_D04


title: 122_C09


title: 122_D08


title: 122_D06


title: 122_F04


title: 122_D05


title: 122_C11


title: 122_D02


title: 122_C12


title: 122_C01


title: 122_C03


title: 122_C10


title: 122_D11


title: 122_C05


title: 122_B11


title: 122_B09


title: 122_B12


title: 122_C08


title: 122_B07


title: 122_C06


title: 122_C07


title: 122_B08


title: 122_C04


title: 122_B04


title: 122_B06


title: 122_B10


title: 122_A10


title: 122_B05


title: 122_A11


title: 122_C02


title: 122_A12


title: 122_A07


title: 122_B01


title: 122_A05


title: 122_B02


title: 122_A09


title: 122_A02


title: 122_A06


title: 122_A08


title: 117_P10_H10

source_name: Tumor #117


title: 122_A03


title: 117_P10_H12


title: 122_A01


title: 117_P10_H11


title: 117_P10_H06


title: 117_P10_H08


title: 117_P10_H01


title: 117_P10_H02


title: 122_A04_S25


title: 117_P10_H04


title: 122_B03


title: 117_P10_G12


title: 117_P10_G09


title: 117_P10_H09


title: 117_P10_G08


title: 117_P10_H05


title: 117_P10_H07


title: 117_P10_H03


title: 117_P10_G07


title: 117_P10_G10


title: 117_P10_G06


title: 117_P10_G05


title: 117_P10_G11


title: 117_P10_G03


title: 117_P10_G04


title: 117_P10_G02


title: 117_P10_F09


title: 117_P10_F11


title: 117_P10_G01


title: 117_P10_F08


title: 117_P10_F07


title: 117_P10_F10


title: 117_P10_F12


title: 117_P10_F06


title: 117_P10_F01


title: 117_P10_E12


title: 117_P10_F02


title: 117_P10_F04


title: 117_P10_E07


title: 117_P10_F05


title: 117_P10_E11


title: 117_P10_F03


title: 117_P10_E03


title: 117_P10_E10


title: 117_P10_E06


title: 117_P10_D12


title: 117_P10_E01


title: 117_P10_D11


title: 117_P10_E08


title: 117_P10_E05


title: 117_P10_E04


title: 117_P10_E09


title: 117_P10_D09


title: 117_P10_D10


title: 117_P10_D03


title: 117_P10_D01


title: 117_P10_E02


title: 117_P10_D06


title: 117_P10_D07


title: 117_P10_D02


title: 117_P10_D08


title: 117_P10_C11


title: 117_P10_C10


title: 117_P10_C09


title: 117_P10_D05


title: 117_P10_C12


title: 117_P10_C08


title: 117_P10_D04


title: 117_P10_C05


title: 117_P10_C04


title: 117_P10_C07


title: 117_P10_C03


title: 117_P10_C02


title: 117_P10_C01


title: 117_P10_C06


title: 117_P10_B09


title: 117_P10_B08


title: 117_P10_B06


title: 117_P10_B05


title: 117_P10_B03


title: 117_P10_A11


title: 117_P10_B11


title: 117_P10_B12


title: 117_P10_B01


title: 117_P10_B07


title: 117_P10_A08


title: 117_P10_A12


title: 117_P10_A04


title: 117_P10_B10


title: 117_P10_B04


title: 117_P10_A07


title: 117_P10_A06


title: 117_P10_A09


title: 117_P10_A03


title: 117_P10_A10


title: 117_P10_A02


title: 117_P04_H11


title: 117_P10_A01


title: 117_P10_B02


title: 117_P04_H08


title: 117_P04_H12


title: 117_P04_H07


title: 117_P10_A05


title: 117_P04_H06


title: 117_P04_H09


title: 117_P04_H10


title: 117_P04_H03


title: 117_P04_H05


title: 117_P04_H04


title: 117_P04_H01


title: 117_P04_H02


title: 117_P04_G11


title: 117_P04_G12


title: 117_P04_G09


title: 117_P04_G10


title: 117_P04_G07


title: 117_P04_G01


title: 117_P04_G04


title: 117_P04_G08


title: 117_P04_G03


title: 117_P04_G05


title: 117_P04_F11


title: 117_P04_F12


title: 117_P04_G02


title: 117_P04_F06


title: 117_P04_F08


title: 117_P04_G06


title: 117_P04_F03


title: 117_P04_F04


title: 117_P04_F01


title: 117_P04_F09


title: 117_P04_F07


title: 117_P04_F02


title: 117_P04_F10


title: 117_P04_E12


title: 117_P04_E08


title: 117_P04_E10


title: 117_P04_E11


title: 117_P04_E06


title: 117_P04_E09


title: 117_P04_F05


title: 117_P04_E07


title: 117_P04_E05


title: 117_P04_E04


title: 117_P04_E01


title: 117_P04_D08


title: 117_P04_E03


title: 117_P04_D07


title: 117_P04_D10


title: 117_P04_D12


title: 117_P04_D11


title: 117_P04_D06


title: 117_P04_C11


title: 117_P04_D02


title: 117_P04_C10


title: 117_P04_E02


title: 117_P04_D01


title: 117_P04_D09


title: 117_P04_C09


title: 117_P04_D04


title: 117_P04_D05


title: 117_P04_D03


title: 117_P04_C07


title: 117_P04_C06


title: 117_P04_C08


title: 117_P04_C04


title: 117_P04_C05


title: 117_P04_C01


title: 117_P04_C02


title: 117_P04_C12


title: 117_P04_B11


title: 117_P04_B12


title: 117_P04_B09


title: 117_P04_B08


title: 117_P04_B05


title: 117_P04_B06


title: 117_P04_B07


title: 117_P04_B03


title: 117_P04_B04


title: 117_P04_A11


title: 117_P04_A12


title: 117_P04_B02


title: 117_P04_A09


title: 117_P04_B01


title: 117_P04_B10


title: 117_P04_A08


title: 117_P04_A06


title: 117_P04_A05


title: 117_P04_A07


title: 117_P04_A01


title: 117_P04_A03


title: 117_P04_A04


title: 117_P04_A02


title: 117_P04_C03


title: 115_P07_H06

source_name: Tumor #115


title: 115_P07_H07


title: 117_P04_A10


title: 115_P07_H10


title: 115_P07_H12


title: 115_P07_H08


title: 115_P07_H04


title: 115_P07_H05


title: 115_P07_H03


title: 115_P07_H01


title: 115_P07_G09


title: 115_P07_H09


title: 115_P07_H11


title: 115_P07_G06


title: 115_P07_G10


title: 115_P07_H02


title: 115_P07_G11


title: 115_P07_G04


title: 115_P07_G12


title: 115_P07_G08


title: 115_P07_G02


title: 115_P07_G05


title: 115_P07_G03


title: 115_P07_G01


title: 115_P07_F11


title: 115_P07_F12


title: 115_P07_F07


title: 115_P07_F06


title: 115_P07_F10


title: 115_P07_F04


title: 115_P07_F05


title: 115_P07_F09


title: 115_P07_E12


title: 115_P07_F02


title: 115_P07_F08


title: 115_P07_E10


title: 115_P07_F03


title: 115_P07_E09


title: 115_P07_E11


title: 115_P07_E07


title: 115_P07_E08


title: 115_P07_E04


title: 115_P07_E06


title: 115_P07_E03


title: 115_P07_E05


title: 115_P07_E01


title: 115_P07_E02


title: 115_P07_D12


title: 115_P07_F01


title: 115_P07_D10


title: 115_P07_D11


title: 115_P07_D03


title: 115_P07_D08


title: 115_P07_D06


title: 115_P07_D09


title: 115_P07_D05


title: 115_P07_D04


title: 115_P07_D02


title: 115_P07_C10


title: 115_P07_C12


title: 115_P07_D07


title: 115_P07_C08


title: 115_P07_D01


title: 115_P07_C04


title: 115_P07_C06


title: 115_P07_C07


title: 115_P07_C03


title: 115_P07_C05


title: 115_P07_B12


title: 115_P07_C11


title: 115_P07_C01


title: 115_P07_B07


title: 115_P07_B08


title: 115_P07_C02


title: 115_P07_B10


title: 115_P07_B09


title: 115_P07_B11


title: 115_P07_C09


title: 115_P07_G07


title: 115_P07_B06


title: 115_P07_A10


title: 115_P07_B04


title: 115_P07_B03


title: 115_P07_B02


title: 115_P07_B01


title: 115_P07_A11


title: 115_P07_A07


title: 115_P07_A06


title: 115_P07_B05


title: 115_P07_A03


title: 115_P03_H12


title: 115_P07_A05


title: 115_P07_A02


title: 115_P03_H11


title: 115_P07_A01


title: 115_P07_A08


title: 115_P07_A04


title: 115_P03_H09


title: 115_P03_H10


title: 115_P07_A09


title: 115_P03_H05


title: 115_P03_H03


title: 115_P03_H04


title: 115_P03_H07


title: 115_P03_G09


title: 115_P03_H01


title: 115_P03_G08


title: 115_P03_G07


title: 115_P03_G06


title: 115_P03_H08


title: 115_P03_G12


title: 115_P07_A12


title: 115_P03_H02


title: 115_P03_G05


title: 115_P03_G11


title: 115_P03_G10


title: 115_P03_F11


title: 115_P03_F12


title: 115_P03_G01


title: 115_P03_F10


title: 115_P03_G03


title: 115_P03_F08


title: 115_P03_F05


title: 115_P03_F09


title: 115_P03_F07


title: 115_P03_F04


title: 115_P03_F03


title: 115_P03_F06


title: 115_P03_G02


title: 115_P03_F02


title: 115_P03_E12


title: 115_P03_E11


title: 115_P03_E08


title: 115_P03_H06


title: 115_P03_E05


title: 115_P03_E09


title: 115_P03_E04


title: 115_P03_E06


title: 115_P03_E01


title: 115_P03_E07


title: 115_P03_E03


title: 115_P03_D10


title: 115_P03_F01


title: 115_P03_E02


title: 115_P03_E10


title: 115_P03_D12


title: 115_P03_D08


title: 115_P03_D03


title: 115_P03_D11


title: 115_P03_D09


title: 115_P03_G04


title: 115_P03_C12


title: 115_P03_D05


title: 115_P03_D01


title: 115_P03_C08


title: 115_P03_D07


title: 115_P03_C06


title: 115_P03_D04


title: 115_P03_C07


title: 115_P03_C09


title: 115_P03_C05


title: 115_P03_C03


title: 115_P03_C11


title: 115_P03_D06


title: 115_P03_C10


title: 115_P03_B10


title: 115_P03_C02


title: 115_P03_B08


title: 115_P03_B11


title: 115_P03_B07


title: 115_P03_B12


title: 115_P03_D02


title: 115_P03_B09


title: 115_P03_B06


title: 115_P03_B01


title: 115_P03_B03


title: 115_P03_A12


title: 115_P03_A11


title: 115_P03_C04


title: 115_P03_B02


title: 115_P03_C01


title: 115_P03_B05


title: 115_P03_B04


title: 115_P03_A05


title: 115_P03_A07


title: 115_P03_A09


title: 115_P03_A06


title: 115_P03_A08


title: 115_P03_A01


title: 115_P03_A02


title: 115_P02_H11


title: 115_P03_A10


title: 115_P02_H08


title: 115_P02_H05


title: 115_P02_H09


title: 115_P02_H06


title: 115_P02_H04


title: 115_P02_H10


title: 115_P02_H07


title: 115_P03_A03


title: 115_P02_H03


title: 115_P02_H12


title: 115_P02_H02


title: 115_P02_G10


title: 115_P02_H01


title: 115_P02_G12


title: 115_P02_G09


title: 115_P02_G08


title: 115_P02_G05


title: 115_P02_G06


title: 115_P02_G04


title: 115_P02_G01


title: 115_P02_G03


title: 115_P02_G11


title: 115_P02_F11


title: 115_P02_F09


title: 115_P02_G07


title: 115_P02_F07


title: 115_P02_F10


title: 115_P02_F04


title: 115_P03_A04


title: 115_P02_F02


title: 115_P02_F08


title: 115_P02_E12


title: 115_P02_F01


title: 115_P02_E11


title: 115_P02_E10


title: 115_P02_F03


title: 115_P02_E07


title: 115_P02_E09


title: 115_P02_E06


title: 115_P02_G02


title: 115_P02_F06


title: 115_P02_F12


title: 115_P02_E05


title: 115_P02_F05


title: 115_P02_E02


title: 115_P02_E08


title: 115_P02_E03


title: 115_P02_E01


title: 115_P02_D12


title: 115_P02_D10


title: 115_P02_D11


title: 115_P02_D09


title: 115_P02_D05


title: 115_P02_E04


title: 115_P02_D08


title: 115_P02_D04


title: 115_P02_D03


title: 115_P02_D07


title: 115_P02_D01


title: 115_P02_C11


title: 115_P02_D06


title: 115_P02_C12


title: 115_P02_C09


title: 115_P02_C10


title: 115_P02_D02


title: 115_P02_C07


title: 115_P02_C08


title: 115_P02_C04


title: 115_P02_C03


title: 115_P02_C01


title: 115_P02_C05


title: 115_P02_C02


title: 115_P02_C06


title: 115_P02_B11


title: 115_P02_B12


title: 115_P02_B07


title: 115_P02_B10


title: 115_P02_B09


title: 115_P02_B08


title: 115_P02_B06


title: 115_P02_B05


title: 115_P02_B03


title: 115_P02_B04


title: 115_P02_A12


title: 115_P02_A11


title: 115_P02_B02


title: 115_P02_A09


title: 115_P02_A08


title: 115_P02_A10


title: 115_P02_A04


title: 115_P02_A07


title: 115_P02_A06


title: 115_P02_A05


title: 115_P02_A01


title: 115_P02_B01


title: 115_P02_A02


title: 115_P02_A03


title: 109_P12_H09

source_name: Tumor #109


title: 109_P12_H11


title: 109_P12_H12


title: 109_P12_H08


title: 109_P12_H06


title: 109_P12_H10


title: 109_P12_H02


title: 109_P12_H04


title: 109_P12_H05


title: 109_P12_G11


title: 109_P12_H01


title: 109_P12_H03


title: 109_P12_G12


title: 109_P12_G07


title: 109_P12_G10


title: 109_P12_G08


title: 109_P12_G05


title: 109_P12_G06


title: 109_P12_H07


title: 109_P12_G09


title: 109_P12_F12


title: 109_P12_G02


title: 109_P12_G01


title: 109_P12_F09


title: 109_P12_F11


title: 109_P12_F10


title: 109_P12_F08


title: 109_P12_F07


title: 109_P12_F06


title: 109_P12_G03


title: 109_P12_F04


title: 109_P12_F05


title: 109_P12_G04


title: 109_P12_E12


title: 109_P12_F03


title: 109_P12_E08


title: 109_P12_E10


title: 109_P12_E09


title: 109_P12_F01


title: 109_P12_E11


title: 109_P12_E04


title: 109_P12_E07


title: 109_P12_E06


title: 109_P12_E03


title: 109_P12_F02


title: 109_P12_E02


title: 109_P12_E01


title: 109_P12_E05


title: 109_P12_D11


title: 109_P12_D09


title: 109_P12_D12


title: 109_P12_D06


title: 109_P12_D08


title: 109_P12_D04


title: 109_P12_D07


title: 109_P12_D10


title: 109_P12_D05


title: 109_P12_D02


title: 109_P12_C12


title: 109_P12_D03


title: 109_P12_C11


title: 109_P12_C10


title: 109_P12_C09


title: 109_P12_D01


title: 109_P12_C08


title: 109_P12_C07


title: 109_P12_C02


title: 109_P12_C03


title: 109_P12_B12


title: 109_P12_C06


title: 109_P12_B10


title: 109_P12_B11


title: 109_P12_C04


title: 109_P12_C01


title: 109_P12_B09


title: 109_P12_C05


title: 109_P12_B08


title: 109_P12_B07


title: 109_P12_B04


title: 109_P12_B06


title: 109_P12_A10


title: 109_P12_A09


title: 109_P12_A11


title: 109_P12_B01


title: 109_P12_A12


title: 109_P12_A08


title: 109_P12_A05


title: 109_P12_A04


title: 109_P12_B03


title: 109_P12_B02


title: 109_P12_B05


title: 109_P12_A06


title: 109_P12_A07


title: 109_P08_H10


title: 109_P08_H09


title: 109_P08_H11


title: 109_P12_A02


title: 109_P08_H07


title: 109_P12_A01


title: 109_P08_H05


title: 109_P08_H06


title: 109_P08_H04


title: 109_P12_A03


title: 109_P08_H01


title: 109_P08_H12


title: 109_P08_H03


title: 109_P08_G12


title: 109_P08_H08


title: 109_P08_G05


title: 109_P08_G09


title: 109_P08_G02


title: 109_P08_G11


title: 109_P08_G07


title: 109_P08_G08


title: 109_P08_G06


title: 109_P08_G01


title: 109_P08_H02


title: 109_P08_F12


title: 109_P08_G10


title: 109_P08_G04


title: 109_P08_F09


title: 109_P08_F10


title: 109_P08_F03


title: 109_P08_F11


title: 109_P08_F08


title: 109_P08_G03


title: 109_P08_F07


title: 109_P08_F06


title: 109_P08_F05


title: 109_P08_E12


title: 109_P08_F02


title: 109_P08_F04


title: 109_P08_E08


title: 109_P08_E07


title: 109_P08_F01


title: 109_P08_E11


title: 109_P08_E04


title: 109_P08_E06


title: 109_P08_E10


title: 109_P08_E03


title: 109_P08_E09


title: 109_P08_E02


title: 109_P08_D12


title: 109_P08_D07


title: 109_P08_D10


title: 109_P08_E01


title: 109_P08_E05


title: 109_P08_D04


title: 109_P08_D06


title: 109_P08_C11


title: 109_P08_C12


title: 109_P08_C10


title: 109_P08_D02


title: 109_P08_D01


title: 109_P08_C09


title: 109_P08_D11


title: 109_P08_D09


title: 109_P08_D08


title: 109_P08_D05


title: 109_P08_C07


title: 109_P08_C08


title: 109_P08_C05


title: 109_P08_D03


title: 109_P08_C02


title: 109_P08_C01


title: 109_P08_C04


title: 109_P08_B07


title: 109_P08_C03


title: 109_P08_B12


title: 109_P08_B11


title: 109_P08_B02


title: 109_P08_B09


title: 109_P08_B04


title: 109_P08_C06


title: 109_P08_A12


title: 109_P08_B08


title: 109_P08_A10


title: 109_P08_A07


title: 109_P08_B06


title: 109_P08_B03


title: 109_P08_B05


title: 109_P08_A06


title: 109_P08_A11


title: 109_P08_B10


title: 109_P08_A03


title: 109_P08_A02


title: 109_P08_B01


title: 109_P08_A01


title: 109_P08_A09


title: 109_P08_A05


title: 109_P08_A04


title: 109_P01_H11


title: 109_P08_A08


title: 109_P01_H08


title: 109_P01_H10


title: 109_P01_H07


title: 109_P01_H06


title: 109_P01_H04


title: 109_P01_H03


title: 109_P01_G11


title: 109_P01_H01


title: 109_P01_G10


title: 109_P01_H02


title: 109_P01_H12


title: 109_P01_H09


title: 109_P01_G09


title: 109_P01_G07


title: 109_P01_G05


title: 109_P01_G04


title: 109_P01_G06


title: 109_P01_G08


title: 109_P01_G03


title: 109_P01_G01


title: 109_P01_G02


title: 109_P01_H05


title: 109_P01_F12


title: 109_P01_G12


title: 109_P01_F11


title: 109_P01_F10


title: 109_P01_F07


title: 109_P01_F08


title: 109_P01_F05


title: 109_P01_F09


title: 109_P01_F03


title: 109_P01_F06


title: 109_P01_F01


title: 109_P01_E10


title: 109_P01_F02


title: 109_P01_E11


title: 109_P01_E12


title: 109_P01_E09


title: 109_P01_E04


title: 109_P01_E08


title: 109_P01_E07


title: 109_P01_D10


title: 109_P01_F04


title: 109_P01_D07


title: 109_P01_E06


title: 109_P01_E05


title: 109_P01_D08


title: 109_P01_D03


title: 109_P01_D01


title: 109_P01_D09


title: 109_P01_D12


title: 109_P01_D11


title: 109_P01_D02


title: 109_P01_E02


title: 109_P01_C10


title: 109_P01_E03


title: 109_P01_D04


title: 109_P01_D06


title: 109_P01_C08


title: 109_P01_C07


title: 109_P01_C12


title: 109_P01_D05


title: 109_P01_C02


title: 109_P01_E01


title: 109_P01_C05


title: 109_P01_C09


title: 109_P01_C11


title: 109_P01_C03


title: 109_P01_C04


title: 109_P01_C06


title: 109_P01_B11


title: 109_P01_B07


title: 109_P01_B12


title: 109_P01_B08


title: 109_P01_B05


title: 109_P01_B04


title: 109_P01_C01


title: 109_P01_A10


title: 109_P01_A12


title: 109_P01_A09


title: 109_P01_B02


title: 109_P01_B03


title: 109_P01_B09


title: 109_P01_A11


title: 109_P01_B06


title: 109_P01_B10


title: 109_P01_A08


title: 109_P01_B01


title: 109_P01_A06


title: 109_P01_A05


title: S026_Tumor_Pre_R1

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

description: Library name: S026T1R1

data_processing:
Libraries were sequenced using the NovaSeq6000 Illumina sequencer in 100 bp paired-end.
Standard Illumina bioinformatics analysis were used to generate fastq files, followed by quality assessment [MultiQC].
Reads were trimmed with TrimGalore!. Rsubread was used for mapping to the hg38 genome and creating a matrix of RNA-Seq counts
edgeR was used for all downstream preprocessing steps
Assembly: hg38
Supplementary files format and content: raw counts for all samples

organism: Homo sapiens

source_name: Tumor

extract_protocol:
Microdissected material was collected in 0.5 ml Zeiss adhesive cap tubes (Carl Zeiss Microscopy, Jena, Germany; one tube per slide). Dissections were completed within 60 min, with dissected areas ranging from ~7 × 10⁴ to 1.4 × 10⁶ µm². RNA was extracted in 150 µl PKD buffer using the RNeasy FFPE Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. RNA integrity (RIN) and DV200 were assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Whole transcriptome was captured from 1ng of tumoral RNA. Libraries were prepared using Takara Bio SMART-Seq mRNA LP reagents following the manufacturer's recommendations.

treatment_protocol: Tumors samples were Formalin-fixed paraffin-embedded (FFPE) for further histologic analysis. Laser capture microdissection was performed on a PALM MicroBeam system (v4.6, P.A.L.M. Microlaser Technologies AG, Bernried, Germany) with RoboSoftware. Regions of interest were identified on serial scans at 5× magnification and precisely dissected at 20×.

tag: id paired

value: Tumor

tag: timepoint

value: Pre

tag: response

value: PR

tag: pfs time

tag: pfs status

tag: OS time

tag: OS status


title: 109_P01_A02

tag: tissue


title: S028_Tumor_Pre_R1

description: Library name: S028T1R1


title: 109_P01_A01


title: 109_P01_A03


title: 109_P01_A07


title: 109_P01_A04


title: S027_Tumor_Pre_R1

description: Library name: S027T1R1


title: S025_Tumor_Pre_R1

description: Library name: S025T1R1


title: S022_Stroma_Post_R1

description: Library name: S022S2R1

source_name: Stroma

value: Stroma

value: Post


title: S022_Tumor_Post_R2

description: Library name: S022T2R2


title: 107_P06_H12

source_name: Tumor #107


title: 107_P06_H11


title: 107_P06_H10


title: S022_Tumor_Post_R1

description: Library name: S022T2R1


title: S021_Tumor_Pre_R1

description: Library name: S021T1R1

value: SD


title: S017_Tumor_Pre_R1

description: Library name: S017T1R1


title: S020_Tumor_Pre_R1

description: Library name: S020T1R1


title: 107_P06_H08


title: 107_P06_H09


title: S018_Tumor_Pre_R1

description: Library name: S018T1R1


title: S016_Tumor_Pre_R1

description: Library name: S016T1R1


title: 107_P06_H07


title: S019_Tumor_Pre_R1

description: Library name: S019T1R1


title: 107_P06_H06


title: 107_P06_H05


title: 107_P06_H03


title: 107_P06_H04


title: S015_Tumor_Pre_R1

description: Library name: S015T1R1


title: S013_Tumor_Pre_R1

description: Library name: S013T1R1


title: S013_Tumor_Post_R1

description: Library name: S013T2R1


title: 107_P06_G12


title: 107_P06_H01


title: S014_Tumor_Pre_R1

description: Library name: S014T1R1


title: 107_P06_G11


title: S013_Stroma_Pre_R1

description: Library name: S013S1R1


title: 107_P06_G09


title: S012_Tumor_Pre_R1

description: Library name: S012T1R1


title: S011_Tumor_Pre_R1

description: Library name: S011T1R1


title: S011_Tumor_Post_R1

description: Library name: S011T2R1


title: 107_P06_H02


title: S009_Tumor_Post_R1

description: Library name: S009T2R1


title: 107_P06_G10


title: 107_P06_G07


title: S010_Tumor_Pre_R1

description: Library name: S010T1R1


title: S009_Stroma_Pre_R1

description: Library name: S009S1R1


title: 107_P06_G08


title: S007_Tumor_Post_R1

description: Library name: S007T2R1


title: 107_P06_G02


title: 107_P06_G03


title: S009_Tumor_Pre_R1

description: Library name: S009T1R1


title: S009_Stroma_Post_R1

description: Library name: S009S2R1


title: 107_P06_G01


title: 107_P06_G05


title: S006_Tumor_Pre_R1

description: Library name: S006T1R1


title: 107_P06_G04


title: 107_P06_F11


title: S005_Tumor_Pre_R1

description: Library name: S005T1R1


title: S003_Tumor_Pre_R1

description: Library name: S003T1R1


title: 107_P06_G06


title: S002_Tumor_Post_R1

description: Library name: S002T2R1


title: S001_Tumor_Pre_R1

description: Library name: S001T1R1


title: 107_P06_F07


title: 107_P06_F09


title: 107_P06_F12


title: 107_P06_F06


title: 9954 2 DMSO

city: London

first: Kevin

last: Blighe

address: 207 Regent Street

country: United Kingdom

institute: Clinical Bioinformatics Research Ltd.

description:
Library name: Sample 63
PrimaryPatientDerivedSamplesRawCounts.tsv

data_processing:
For the MOLM-16 cell line-derived xenograft (CDX) samples, raw count data was provided directly by the service provider (Sequanta Technologies), whereas the patient-derived samples—specifically the ex vivo primary AML cells rather than the in vivo PDX tumors—underwent a specific processing pipeline where raw FASTQ files were pseudo-aligned to the Homo sapiens GENCODE ‘comprehensive’ reference transcriptome using Salmon.  Following alignment, transcript-level counts for the patient samples were summarized to gene-level counts using the tximport package in R, filtered to retain only protein-coding genes, and cleaned by removing genes with zero counts; finally, the count data for both experimental groups were normalized using DESeq2 to generate negative binomial-distributed counts, which were subsequently transformed into regularized log (rlog) and variance-stabilized (vst) expression levels for downstream analysis.
Assembly: GRCh38.p12
Supplementary files format and content: Tab-Separated Values; Raw Counts

source_name: Patient-Derived Xenograft

growth_protocol: For the RNA-sequencing analysis, the study employed two distinct growth protocols corresponding to the MOLM-16 cell line-derived xenografts (CDX) and the ex vivo primary patient cells (not to be confused with the in vivo PDX model, which was assessed via flow cytometry).  The MOLM-16 CDX tumors were established by injecting 10^7 cells suspended in 100 µl of a 1:1 mixture of PBS and Matrigel subcutaneously into the flanks of female 6- to 8-week-old NOD/SCID mice; these tumors were allowed to grow to a volume of 100–200 mm^3 before treatment and subsequent harvesting, after which the tissue was stored in RNALater at 4C overnight and then frozen at -80C. In contrast, the patient-derived material used for sequencing consisted of primary AML cells cultured ex vivo at a density of 0.5-1 x 10^6 cells per ml in SFEMII medium supplemented with 1% Antibiotic-Antimycotic, 35 nM UM729, 750 nM SR1, and 100 ng/ml each of TPO, FLT3L, SCF, IL-6, and IL-3, maintained at 37C in a 5% CO2 humidified incubator.

extract_protocol:
For the MOLM-16 cell line-derived xenograft (CDX) samples specifically, the tumor tissue was first harvested and preserved in RNALater (Sigma) at 4C overnight and stored at -80C prior to sequencing by Sequanta Technologies, while the patient-derived samples—which the text identifies as the ex vivo primary AML cells rather than the in vivo PDX tumors—were processed using the described TRIzol and RNeasy extraction method before being sequenced by Azenta.
RNA sequencing was conducted as an outsourced service, with Sequanta Technologies handling the MOLM-16 CDX samples and Azenta handling the patient cells experiment.

treatment_protocol: For the MOLM-16 cell line-derived xenograft (CDX) samples subjected to RNA sequencing, the treatment protocol entailed orally dosing the mice once daily with APL-4098 formulated in 0.5% methylcellulose and 0.2% Tween80 (or a vehicle control) after the subcutaneous tumors reached a volume of 100–200 mm^3. Regarding the patient-derived samples, the text indicates that molecular profiling was performed on the ex vivo primary AML cells rather than the in vivo PDX tumors; therefore, the treatment for the sequenced patient samples involved exposing the cultured cells to APL-4098 at indicated doses within the SFEMII-based medium, distinct from the 15 mg/kg oral regimen described for the in vivo PDX efficacy experiments which relied on flow cytometry for assessment.

value: Patient-Derived Xenograft

tag: donor

value: DMSO


title: S004_Tumor_Pre_R1

description: Library name: S004T1R1

value: PD


title: S002_Tumor_Pre_R1

description: Library name: S002T1R1


title: 107_P06_F10


title: 9954 1 DMSO

description:
Library name: Sample 62
PrimaryPatientDerivedSamplesRawCounts.tsv

tag: treatment


title: 107_P06_F02


title: 107_P06_F01


title: 107_P06_E12


title: 9794 2 DMSO

description:
Library name: Sample 57
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 107_P06_F08


title: 107_P06_E10


title: S002_Stroma_Pre_R1

description: Library name: S002S1R1


title: 107_P06_E09


title: 107_P06_E08


title: 9794 1 APL-4098

description:
Library name: Sample 53
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 107_P06_F05


title: S001_Stroma_Pre_R1

description: Library name: S001S1R1


title: 9395 2 DMSO

description:
Library name: Sample 51
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 9395 3 DMSO

description:
Library name: Sample 52
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 107_P06_E04


title: 9954 3 DMSO

description:
Library name: Sample 64
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 107_P06_F04


title: 9395 1 DMSO

description:
Library name: Sample 50
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 107_P06_E02


title: 107_P06_F03


title: 107_P06_E01


title: 9395 1 APL-4098

description:
Library name: Sample 47
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 9954 3 APL-4098

description:
Library name: Sample 61
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 8799 2 DMSO

description:
Library name: Sample 45
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 9954 1 APL-4098

description:
Library name: Sample 59
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 8799 3 APL-4098

description:
Library name: Sample 43
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 9954 2 APL-4098

description:
Library name: Sample 60
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 9794 3 DMSO

description:
Library name: Sample 58
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 107_P06_D06


title: 107_P06_E11


title: 107_P06_D07


title: 9794 1 DMSO

description:
Library name: Sample 56
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 9794 3 APL-4098

description:
Library name: Sample 55
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 107_P06_E07

description: Expression_CountValue.tsv,Expression_FPKM.tsv,Expression_TPM.tsv,Mutations.tsv


title: 49049 Group03 96h

description:
Library name: Sample 39
CelllineDerivedXenograftsRawCounts.tsv

source_name: Cell-lline-Derived Xenograft

value: Cell-lline-Derived Xenograft


title: 9794 2 APL-4098

description:
Library name: Sample 54
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 107_P06_E06


title: 107_P06_E05


title: 107_P06_D03


title: 49045 Group03 96h

description:
Library name: Sample 37
CelllineDerivedXenograftsRawCounts.tsv


title: 107_P06_E03


title: 9395 2 APL-4098

description:
Library name: Sample 48
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 9395 3 APL-4098

description:
Library name: Sample 49
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 107_P06_D12


title: 107_P06_D11


title: 8799 3 DMSO

description:
Library name: Sample 46
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 107_P06_C11


title: 107_P06_D09


title: 107_P06_D10


title: 8799 1 DMSO

description:
Library name: Sample 44
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 49024 Group03 48h

description:
Library name: Sample 31
CelllineDerivedXenograftsRawCounts.tsv


title: 107_P06_D08


title: 8799 1 APL-4098

description:
Library name: Sample 41
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 49052 Group03 96h

description:
Library name: Sample 40
CelllineDerivedXenograftsRawCounts.tsv


title: 107_P06_D04


title: 49047 Group03 96h

description:
Library name: Sample 38
CelllineDerivedXenograftsRawCounts.tsv


title: 8799 2 APL-4098

description:
Library name: Sample 42
PrimaryPatientDerivedSamplesRawCounts.tsv


title: 107_P06_D02


title: 107_P06_D05


title: 107_P06_D01


title: 49018 Group03 24h

description:
Library name: Sample 28
CelllineDerivedXenograftsRawCounts.tsv


title: 49041 Group03 48h

description:
Library name: Sample 35
CelllineDerivedXenograftsRawCounts.tsv


title: 107_P06_C07


title: 107_P06_C12


title: 107_P06_C04


title: 49014 Group03 24h

description:
Library name: Sample 27
CelllineDerivedXenograftsRawCounts.tsv


title: 49039 Group03 48h

description:
Library name: Sample 34
CelllineDerivedXenograftsRawCounts.tsv


title: 49044 Group03 96h

description:
Library name: Sample 36
CelllineDerivedXenograftsRawCounts.tsv


title: 49036 Group03 48h

description:
Library name: Sample 33
CelllineDerivedXenograftsRawCounts.tsv


title: 107_P06_C09

description: Expression_CountValue.tsv,Expression_FPKM.tsv,Expression_TPM.tsv,Mutations.tsv


title: 107_P06_C10


title: 49027 Group03 48h

description:
Library name: Sample 32
CelllineDerivedXenograftsRawCounts.tsv


title: 107_P06_C02


title: 107_P06_C08


title: 49006 Group03 8h

description:
Library name: Sample 23
CelllineDerivedXenograftsRawCounts.tsv


title: 49008 Group03 8h

description:
Library name: Sample 24
CelllineDerivedXenograftsRawCounts.tsv


title: 49023 Group03 24h

description:
Library name: Sample 30
CelllineDerivedXenograftsRawCounts.tsv


title: 49002 Group03 8h

description:
Library name: Sample 22
CelllineDerivedXenograftsRawCounts.tsv


title: 49019 Group03 24h

description:
Library name: Sample 29
CelllineDerivedXenograftsRawCounts.tsv


title: 107_P06_C06


title: 107_P06_C05


title: 107_P06_C03


title: 49009 Group03 8h

description:
Library name: Sample 25
CelllineDerivedXenograftsRawCounts.tsv


title: 49060 Group02 96h

description:
Library name: Sample 18
CelllineDerivedXenograftsRawCounts.tsv

value: Vehicle


title: 107_P06_B07


title: 107_P06_B12


title: 107_P06_B06


title: 107_P06_B08


title: 107_P06_C01


title: 107_P06_B10


title: 107_P06_B05


title: 49059 Group02 96h

description:
Library name: Sample 17
CelllineDerivedXenograftsRawCounts.tsv


title: 48996 Group03 8h

description:
Library name: Sample 21
CelllineDerivedXenograftsRawCounts.tsv


title: 107_P06_B04


title: 107_P06_B11


title: 49010 Group03 24h

description:
Library name: Sample 26
CelllineDerivedXenograftsRawCounts.tsv


title: 107_P06_B09


title: 49053 Group02 96h

description:
Library name: Sample 16
CelllineDerivedXenograftsRawCounts.tsv


title: 107_P06_B02


title: 49066 Group02 96h

description:
Library name: Sample 20
CelllineDerivedXenograftsRawCounts.tsv


title: 107_P06_B03


title: 49048 Group02 48h

description:
Library name: Sample 15
CelllineDerivedXenograftsRawCounts.tsv


title: 49064 Group02 96h

description:
Library name: Sample 19
CelllineDerivedXenograftsRawCounts.tsv


title: 49042 Group02 48h

description:
Library name: Sample 13
CelllineDerivedXenograftsRawCounts.tsv


title: 49033 Group02 48h

description:
Library name: Sample 12
CelllineDerivedXenograftsRawCounts.tsv


title: 107_P06_B01

description: Expression_CountValue.tsv,Expression_FPKM.tsv,Expression_TPM.tsv,Mutations.tsv


title: 107_P06_A12


title: 49028 Group02 48h

description:
Library name: Sample 11
CelllineDerivedXenograftsRawCounts.tsv


title: 49046 Group02 48h

description:
Library name: Sample 14
CelllineDerivedXenograftsRawCounts.tsv


title: 107_P06_A11


title: 107_P06_A10


title: 49025 Group02 24h

description:
Library name: Sample 9
CelllineDerivedXenograftsRawCounts.tsv


title: 49021 Group02 24h

description:
Library name: Sample 7
CelllineDerivedXenograftsRawCounts.tsv


title: 49022 Group02 24h

description:
Library name: Sample 8
CelllineDerivedXenograftsRawCounts.tsv


title: 107_P06_A07


title: 107_P06_A09


title: 107_P06_A08


title: 49013 Group02 8h

description:
Library name: Sample 4
CelllineDerivedXenograftsRawCounts.tsv


title: 49026 Group02 24h

description:
Library name: Sample 10
CelllineDerivedXenograftsRawCounts.tsv


title: 49007 Group02 8h

description:
Library name: Sample 3
CelllineDerivedXenograftsRawCounts.tsv


title: 49005 Group02 8h

description:
Library name: Sample 2
CelllineDerivedXenograftsRawCounts.tsv


title: 49015 Group02 8h

description:
Library name: Sample 5
CelllineDerivedXenograftsRawCounts.tsv


title: 107_P06_A05


title: 107_P06_A03


title: 49016 Group02 24h

description:
Library name: Sample 6
CelllineDerivedXenograftsRawCounts.tsv


title: 107_P06_A01


title: 49000 Group02 8h

description:
Library name: Sample 1
CelllineDerivedXenograftsRawCounts.tsv


title: 103_P11_H12

source_name: Tumor #103


title: RNA-seq of human Breast cancer: docetaxel-sensitive group BC1311G3

city: Guiyang

first: jianjun

last: huang

state: Guizhou

address: 9, Beijing Road

department: School of Clinical Medicine

institute: Guizhou Medical University

description:
Library name: BC1311G3
Column name in gene_count.xls: BC1311G3

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: hg39
Supplementary files format and content: txt file includes gene counts for all Sample

source_name: Breast cancer

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Vazyme) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Breast cancer

tag: batch


title: RNA-seq of human Breast cancer: docetaxel-sensitive group BC1311G2

description:
Library name: BC1311G2
Column name in gene_count.xls: BC1311G2


title: 107_P06_A02


title: RNA-seq of human Breast cancer: docetaxel-sensitive group BC1311G1

description:
Library name: BC1311G1
Column name in gene_count.xls: BC1311G1


title: 107_P06_A06


title: RNA-seq of human Breast cancer: docetaxel-sensitive group BC514G1

description:
Library name: BC514G1
Column name in gene_count.xls: BC514G1


title: 103_P11_H07

description: Expression_CountValue.tsv,Expression_FPKM.tsv,Expression_TPM.tsv,Mutations.tsv


title: 103_P11_H08


title: RNA-seq of human Breast cancer: docetaxel-resistant group BC106G3

description:
Library name: BC106G3
Column name in gene_count.xls: BC106G3


title: RNA-seq of human Breast cancer: docetaxel-sensitive group BC514G2

description:
Library name: BC514G2
Column name in gene_count.xls: BC514G2


title: 103_P11_H05


title: 103_P11_H09


title: 103_P11_H06


title: RNA-seq of human Breast cancer: docetaxel-resistant group BC49G2

description:
Library name: BC49G2
Column name in gene_count.xls: BC49G2


title: RNA-seq of human Breast cancer: docetaxel-resistant group BC49G1

description:
Library name: BC49G1
Column name in gene_count.xls: BC49G1


title: 103_P11_H03


title: 103_P11_H04


title: RNA-seq of human Breast cancer: docetaxel-resistant group BC49G3

description:
Library name: BC49G3
Column name in gene_count.xls: BC49G3


title: 103_P11_H02


title: 103_P11_H10


title: 103_P11_H11


title: RNA-seq of human Breast cancer: docetaxel-sensitive group BC514G3

description:
Library name: BC514G3
Column name in gene_count.xls: BC514G3


title: 107_P06_A04


title: RNA-seq of human Breast cancer: docetaxel-resistant group BC106G2

description:
Library name: BC106G2
Column name in gene_count.xls: BC106G2


title: 103_P11_G12


title: 103_P11_H01


title: THP-1 cells,  (Input)

city: Hengyang

first: Qin-Yi

last: Zhou

state: Hunan

address: Institute of Cardiovascular Disease, Affiliated Nanhua Hospital, 336 S Dongfeng Road, Hengyang, Hunan 421002, China

institute: University of South china

description: Library name: THP-1, INPUT

library_source: genomic

data_processing:
Data Collection and Analysis Raw data  FastQC  Human genome (hg19) alignment  Peak detection  Peak annotation.
Assembly: hg19
Supplementary files format and content: Peak_Annotation.xlsx

molecule: genomic DNA

growth_protocol: THP-1 cells were subcultured using a semi-retention method. The culture medium consisted of RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and was maintained in a humidified incubator at 37°C with 5% CO2.

extract_protocol:
Following C18-3OH treatment, the cells were washed to remove the culture medium and stored at −80°C for subsequent analysis. Frozen cell pellets were thawed and subjected to chromatin immunoprecipitation sequencing (ChIP-Seq) to identify PAX-8 target genes. Cell samples were processed through lysis, sonication, immunoprecipitation, and cross-linking to obtain DNA. The purified DNA fragments, after precipitation and dilution, were used to construct a ChIP-seq library for sequencing. The ChIP-seq experiment was independently repeated once . The experimental procedures were performed by Shanghai Kangcheng Biotechnology Co., Ltd., with standardized protocols executed by trained personnel.
ChIP DNA QC: The purity and concentration of DNA samples were determined with Qubit® Fluorometer. Results are provided in this report. Sequencing Library Preparation: DNA samples were end-repaired, A tailed, and adaptor ligated using TruSeq Nano DNASample Prep Kit (#FC-121-4002, Illumina), following the manufacturer’s instructions. ~200-1500 bp fragments were size selected using AMPure XP beads. The final size of the library was confirmed by Agilent 2100 Bioanalyzer. Cluster Generation: The samples were diluted to a final concentration of 8 pM and cluster generation was performed on the Illumina cBot following NovaSeq 6000 S4 Reagent Kit manufacturer’s instructions.Sequencing on Illumina NovaSeq 6000: Sequencing was performed on Illumina NovaSeq 6000 using NovaSeq 6000 S4 Reagent Kit (300 cycles), according to the manufacturer’s instructions.

treatment_protocol: To differentiate THP-1 cells into macrophages, the culture medium was supplemented with 160 nmol/L phorbol 12-myristate 13-acetate (PMA) for 24 h. Subsequently, the cells were cultured in fresh medium for 6–12 h, followed by incubation with 50 mg/mL oxidized low-density lipoprotein (ox-LDL) for 48 h to induce foam cell formation.

tag: cell line

tag: cell type

value: THP-1 cells

value: Input


title: P3HR1-ZHT_Pan

city: Durham

first: Micah

last: Luftig

state: NC

address: 213 Research Dr

institute: Duke University

description:
Library name: P3HR1-ZHT_Pan
10x Genomics; Site: Duke

data_processing:
Read assembly, demultiplexing, barcode processing, and counting were performed using the cellranger pipeline (v3) from 10x Genomics
Assembly: Assembly: hg38 + NC009338 (EBV type 2)
Supplementary files format and content: Supplementary files format and content: Tab-separated values (tsv) and matrix (.mtx) files

growth_protocol: Cell line grown in R10 (RPMI+10% heat inactivated FBS)

extract_protocol:
Cells were harvested from culture at specified times after specified treatments and enriched to >90% viability by Ficoll gradient prior to single-cell library preparation
Library preparation was performed according to manufacturer's protocol -- 10x Genomics v2 3' Gene Expression Kit

treatment_protocol: Treatments in culture as described above

value: B cell

value: 50 nM panobinostat, 48h


title: RNA-seq of human Breast cancer: docetaxel-resistant group BC106G1

description:
Library name: BC106G1
Column name in gene_count.xls: BC106G1


title: 103_P11_G10

value: Melanoma cell line-derived tumor

tag: strain

value: HGF-tg C57BL6

value: CD45-, CD31-, alive, nucleated cells


title: 103_P11_G11


title: 103_P11_G08


title: CRISPRi; D11+IFNg+T, Rep3

city: Brisbane

first: Jonathan

last: Beesley

state: QLD

address: 300 Herston Rd Herston

country: Australia

institute: QIMR Berghofer

description: Library name: DoDi_18

data_processing:
Raw sequencing reads were processed by trimming adaptors and vector sequences using cutadapt v1.13 with parameter '-g TTGTGGAAAGGACGAAACACCG'.
sgRNA barcodes were counted using MAGeCK (v0.5.9.4) and the significance of treatment-dependent abundances calculated using maximum-likelihood estimation implemented in the MLE module, with 10 rounds of permutation (each round corresponding to 2 × gene number), correcting for MCF7 gene copy number using CNV array data from the Broad Institute Cancer Cell Line Encyclopedia and normalizing by counts of negative control sgRNAs.
Assembly: hg38
Supplementary files format and content: Normalised count matrix generated using the MAGeCK count command.

growth_protocol: MCF7 cells stably expressing Cas9 or KRAB-dCas9 were established by transduction of the virus at MOI<0.7, selected in 10 μg/ml blasticidin and maintained in 5 μg/ml blasticidin. MCF7 cells were transduced with CRISPRko or CRISPRi library virus at a MOI of 0.3 to ensure one guide per cell and obtain 1000 cells per sgRNA. Library infection was carried out in triplicate. Twenty-four hours after infection, cells were selected using puromycin (1 μg/ml) for 7 days.

extract_protocol:
Target cells were harvested and genomic DNA extracted using NucleoSpin Blood XL kit (Clontech).
Libraries were generated using one-step PCR to amplify the integrated sequence within the construct and the addition of sample barcodes. PCR products were purified using AMPure beads and samples sequenced using Novaseq6000.

treatment_protocol: Library-infected MCF7 cells were cultured for 24 hours with interferon-gamma (IFNγ) at 10 ng/ml followed by co-culturing with HER2-restricted T cells at an Effector:Target ratio of 1:1. When the cytolysis rate reached 70% in the co-culture flask (MCF7+T cells), media was removed. After three washes with PBS, the cells were maintained with blasticidin (10 μg/ml) and puromycin (1 μg/ml) for another 48 hours.


title: 103_P11_G09


title: CRISPRi; Input

description: Library name: DoDi_19


title: 103_P11_G06


title: THP-1 cells, PAX-8 target genes (ChIP)

description: Library name: THP-1, ChIP

value: PAX-8 target genes (ChIP)


title: CRISPRi; D11+IFNg+T, Rep1

description: Library name: DoDi_16


title: 103_P11_G05


title: CRISPRi; D11+T, Rep3

description: Library name: DoDi_15


title: P3HR1-ZHT_UT

description:
Library name: P3HR1-ZHT_UT
10x Genomics; Site: Duke

value: Untreated


title: 103_P11_G04


title: CRISPRi; D11+T, Rep1

description: Library name: DoDi_13


title: 103_P11_G03


title: CRISPRi; D11+IFNg, Rep3

description: Library name: DoDi_12


title: 103_P11_G02


title: CRISPRi; D11+T, Rep2

description: Library name: DoDi_14


title: 103_P11_G01


title: CRISPRi; D11+IFNg, Rep1

description: Library name: DoDi_10


title: CRISPRi; D11+IFNg, Rep2

description: Library name: DoDi_11


title: CRISPRi; D11, Rep3

description: Library name: DoDi_9


title: 103_P11_F12


title: 103_P11_F10


title: CRISPRi; D11+IFNg+T, Rep2

description: Library name: DoDi_17


title: 103_P11_F08


title: CRISPRi; D11, Rep2

description: Library name: DoDi_8


title: 103_P11_G07


title: 103_P11_F09


title: CRISPRi; D7, Rep3

description: Library name: DoDi_6


title: 103_P11_F07


title: CRISPRi; D7, Rep1

description: Library name: DoDi_4


title: CRISPRi; D7, Rep2

description: Library name: DoDi_5


title: 103_P11_F11


title: CRISPRi; D11, Rep1

description: Library name: DoDi_7


title: 103_P11_F05


title: 103_P11_F04


title: CRISPRi; D3, Rep2

description: Library name: DoDi_2


title: 103_P11_F03


title: CRISPRi; D3, Rep1

description: Library name: DoDi_1


title: 103_P11_F02


title: 103_P11_F01


title: CRISPRko; Input

description: Library name: HER2_WS_19


title: 103_P11_E11


title: 103_P11_F06


title: SF3A1_3

city: Asahikawa

first: Hiroaki

last: Konishi

address: 2-1-1-1, Midorigaoka-higashi

country: Japan

institute: Asahikawa Medical University

description:
IonXpressRNA_016 SF3A1_3
IgG vs. SF3A1.xlsx

data_processing:
CLC Genomics Workbench software program 24
Assembly: hg38
Supplementary files format and content: xlsx files include RPKM values for each sample.

growth_protocol: HCT116 cells were cultured in McCoy's 5A medium supplemented with 10% (vol/vol) fetal bovine serum (FBS) and 50 U/ml penicillin, and cells were maintained at 5% CO2 and 37°C under humidified conditions.

extract_protocol:
Total RNA was isolated utilizing the RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
RNA libraries were generated using the Ion Total RNA-Seq Kit v2 (ThermoFisher Scientific) following the manufacturer’s instructions.

treatment_protocol: Transfection was carried out in triplicate using Lipofectamine RNAiMAX (Thermo Fisher Scientific) following the manufacturer's instructions for reverse transfection methods.

value: colorectal cancer cells

tag: genotype

value: Pulldowned using SF3A1 antibody

tag: time


title: CRISPRko; D11+IFNg, Rep3

description: Library name: HER2_WS_16


title: CRISPRko; D11+IFNg+T, Rep3

description: Library name: HER2_WS_18


title: SF3A1_1

description:
IonXpressRNA_014 SF3A1_1
IgG vs. SF3A1.xlsx


title: CRISPRko; D11, Rep3

description: Library name: HER2_WS_15


title: CRISPRko; D11+T, Rep3

description: Library name: HER2_WS_17


title: 103_P11_E12

tag: microbiota status

tag: sorting strategy


title: 103_P11_E10


title: IgG_3

description:
IonXpressRNA_013 IgG_3
IgG vs. SF3A1.xlsx

value: Pulldowned using IgG antibody


title: SF3A1_2

description:
IonXpressRNA_015 SF3A1_2
IgG vs. SF3A1.xlsx


title: IgG_2

description:
IonXpressRNA_012 IgG_2
IgG vs. SF3A1.xlsx


title: 103_P11_E08


title: CRISPRko; D11+IFNg+T, Rep2

description: Library name: HER2_WS_14


title: CRISPRko; D11+T, Rep2

description: Library name: HER2_WS_13


title: siSF3A1_3

description:
IonXpressRNA_016 siSF3A1_3
Scramble vs. siSF3A1.xlsx

value: SF3A1 knockdown


title: 103_P11_E09

description: Expression_CountValue.tsv,Expression_FPKM.tsv,Expression_TPM.tsv,Mutations.tsv


title: siSF3A1_2

description:
IonXpressRNA_015 siSF3A1_2
Scramble vs. siSF3A1.xlsx


title: 103_P11_E07


title: siSF3A1_1

description:
IonXpressRNA_014 siSF3A1_1
Scramble vs. siSF3A1.xlsx


title: 103_P11_E06


title: IgG_1

description:
IonXpressRNA_011 IgG_1
IgG vs. SF3A1.xlsx


title: 103_P11_E05


title: Scramble3

description:
IonXpressRNA_013 Scramble_3
Scramble vs. siSF3A1.xlsx

value: WT


title: Scramble2

description:
IonXpressRNA_012 Scramble_2
Scramble vs. siSF3A1.xlsx


title: CRISPRko; D11, Rep2

description: Library name: HER2_WS_11


title: Scramble1

description:
IonXpressRNA_011 Scramble_1
Scramble vs. siSF3A1.xlsx


title: CRISPRko; D11+IFNg+T, Rep1

description: Library name: HER2_WS_10


title: CRISPRko; D11+IFNg, Rep2

description: Library name: HER2_WS_12


title: P14_CD1_OE_L35292_0_1_HK7KCBCX2

city: Cleveland

first: Davin

middle: J

last: Marro

state: Ohio

address: 2210 Circle Dr

department: Neurosciences

institute: Case Western Reserve University

description:
Library name: L35292
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software.
Assembly: mouse mm10
Supplementary files format and content: Processed h5 files containing gene counts per cell barcode.

source_name: Olfactory Epithelium

extract_protocol:
Animals were euthanized with standard protocols in Stowers Institute for Medical Research, olfactory epithelium was dissected and bones were removed in the ice cold HBSS. Dissected epitheliums were dissociated in papain solution (20 mg/mL papain and 3 mg/mL L-cysteine in HBSS) with RNase-free DNase I (10unit) at 37 °C for 15–20 mins. 0.01% BSA in PBS was added to the digestion solution before filtering with 70 µm and 30 µm filters (pluriSelect).  Dissociated cells were washed twice in 0.01% BSA with final volume 1 mL, followed by Draq5 (25 µM) and DAPI (0.5 µg/mL) staining 5 min on ice. Draq5+/DAPI- cells (live/nucleated cells) were sorted on BD Influx cytometer (BD Bioscience) with 100 µm nozzle.
Note: Library protocol will be specified for each batch present in study.  MOLNG-2453: Cells deemed to be 45-85% viable were loaded based on live cell concentration onto a Chromium Controller instrument (10x Genomics) and libraries prepared using the Chromium Single Cell 3' Library & Gel Bead Kit v2 (10x Genomics) according to manufacturer’s directions.  Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer (Agilent Technologies) and Qubit Fluorometer (Thermo Fisher Scientific).  With cells captured estimated at ~1,300-9,000 cells per sample, libraries were pooled and sequenced to a depth necessary to achieve at least 19,000 mean reads per cell on an Illumina HiSeq 2500 instrument in Rapid Run mode utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 26*8*98bp
MOLNG-2407: Cells deemed to be at least 69% viable were loaded based on live cell concentration onto a Chromium Controller instrument (10x Genomics) and libraries prepared using the Chromium Single Cell 3' Library & Gel Bead Kit v2 (10x Genomics) according to manufacturer’s directions.  Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer (Agilent Technologies) and Qubit Fluorometer (Thermo Fisher Scientific).  With cells captured estimated at ~1,500-4,000 cells per sample, libraries were pooled and sequenced to a depth necessary to achieve at least 20,000 mean reads per cell on an Illumina HiSeq 2500 instrument in Rapid Run mode utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 26*8*98bp.
MOLNG-3334: Cells deemed to be at least 90% viable were loaded on a Chromium Single Cell Controller (10x Genomics), based on live cell concentration.  Libraries were prepared using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics) according to manufacturer’s directions.  Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer (Agilent Technologies) and Qubit Fluorometer (Thermo Fisher Scientific).  With cells captured estimated at ~3,100-7,400 cells per sample, libraries were pooled as needed and sequenced to a depth necessary to achieve at least 38,000 mean reads per cell on an Illumina NovaSeq 6000 instrument utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 28*10*10*90bp.
MOLNG-3650: Dissociated, sorted cells were assessed for concentration and viability using a Luna-FL cell counter (Logos Biosystems).   Cells deemed to be at least 95% viable were loaded based on live cell concentration onto a Chromium X Series instrument (10x Genomics) and libraries prepared using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics) according to manufacturer’s directions.  Resulting cDNA and short fragment libraries were checked for quality and quantity using a 2100 Bioanalyzer (Agilent Technologies) and Qubit Fluorometer (Thermo Fisher Scientific).  With cells captured estimated at ~4,000-10,000 cells per sample, libraries were pooled and sequenced to a depth necessary to achieve at least 30,000 mean reads per cell on an Illumina NextSeq 2000 instrument utilizing RTA and instrument software versions current at the time of processing with the following paired read lengths: 28*10*10*90bp.

value: Olfactory Epithelium

value: Multiple


title: P7_CD1_OSNs_L34688_0_1_HKLHCBCX2

description:
Library name: L34688
10x Genomics


title: P21_CD1_OSNs_L34690_0_1_HKLHCBCX2

description:
Library name: L34690
10x Genomics


title: CRISPRko; D11+IFNg, Rep1

description: Library name: HER2_WS_8


title: 103_P11_E04


title: Adult_CD1_OE_L35293_0_1_HK7KCBCX2

description:
Library name: L35293
10x Genomics


title: E18_5_CD1_OE_L35290_0_1_HK7KCBCX2

description:
Library name: L35290
10x Genomics


title: EpiSC Setd1a WT biol rep 2

city: Dresden

first: Anna

middle: R

last: Poetsch

address: Tatzberg 47/49

country: Germany

institute: TU Dresden

description:
Library name: Sample 36
Column name in bfx754.mm10.e87.txt: RNA36

data_processing:
Reads were mapped to GRCm38/mm10 with GSNAP version 2017-03-17
Read counts extraction and normalization were performed using featureCounts v1.5.2
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Epiblast-like Stem Cells

extract_protocol:
Total RNA was isolated with Trizol (Invitrogen) according to the manufacturer's recommendations. 100 μg total RNA was subjected to two rounds of poly(A) selection (Oligotex mRNA Mini Kit; QIAGEN), followed by DNaseI treatment (QIAGEN).
100–200 ng mRNA was fragmented by hydrolysis (5× fragmentation buffer: 200mM Tris acetate, pH8.2, 500mM potassium acetate and 150mM magnesium acetate) at 94°C for 90 s and purified (RNAeasy Minelute Kit; QIAGEN). cDNA was synthesized with 5 μg random hexamers by Superscript III Reverse Transcriptase (Invitrogen). Ds cDNA synthesis was performed in second strand buffer (Invitrogen) according to the manufacturer's recommendations and purified (Minelute Reaction Cleanup Kit; QIAGEN). Strand-specific rRNA depleted ds cDNA profiling was performed with the ScriptSeq kit (cat. no. SS10924) from Illumina, according to the instructions of the manufacturer. rRNA depletion was performed with the Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat; cat. no. RZH110424).

value: Epiblast-like Stem Cells

value: Media with Activin A and FGF2


title: 103_P11_E02


title: CRISPRko; D7, Rep3

description: Library name: HER2_WS_6


title: E13_5_CD1_OE_L35289_0_1_HK7KCBCX2

description:
Library name: L35289
10x Genomics


title: CRISPRko; D11, Rep1

description: Library name: HER2_WS_7


title: 103_P11_E03


title: 103_P11_E01


title: P3_CD1_OSNs_L34687_0_1_HKLHCBCX2

description:
Library name: L34687
10x Genomics


title: CRISPRko; D7, Rep2

description: Library name: HER2_WS_5


title: 103_P11_D12


title: P0_CD1_OSNs_L34689_0_1_HKLHCBCX2

description:
Library name: L34689
10x Genomics


title: CRISPRko; D11+T, Rep1

description: Library name: HER2_WS_9


title: EpiSC Setd1a WT biol rep 1

description:
Library name: Sample 34
Column name in bfx754.mm10.e87.txt: RNA34


title: 103_P11_D11


title: EpiSC Mll2 WT biol rep 2

description:
Library name: Sample 32
Column name in bfx754.mm10.e87.txt: RNA32


title: EpiSC Setd1a KO Tamoxifen biol rep 2

description:
Library name: Sample 35
Column name in bfx754.mm10.e87.txt: RNA35

value: Setd1a KO


title: CRISPRko; D7, Rep1

description: Library name: HER2_WS_4


title: CRISPRi; D3, Rep3

description: Library name: DoDi_3


title: EpiSC Mll2 KO Tamoxifen biol rep 2

description:
Library name: Sample 31
Column name in bfx754.mm10.e87.txt: RNA31

value: Mll2 KO


title: CRISPRko; D3, Rep3

description: Library name: HER2_WS_3


title: EpiSC Mll2 WT biol rep 1

description:
Library name: Sample 30
Column name in bfx754.mm10.e87.txt: RNA30


title: 103_P11_D10


title: 103_P11_D09


title: EpiSC Mll2 KO Tamoxifen biol rep 1

description:
Library name: Sample 29
Column name in bfx754.mm10.e87.txt: RNA29


title: EpiSC Bod1L WT biol rep 2

description:
Library name: Sample 28
Column name in bfx754.mm10.e87.txt: RNA28


title: 103_P11_D08


title: EpiSC Setd1a KO Tamoxifen biol rep 1

description:
Library name: Sample 33
Column name in bfx754.mm10.e87.txt: RNA33


title: CRISPRko; D3, Rep2

description: Library name: HER2_WS_2


title: CRISPRko; D3, Rep1

description: Library name: HER2_WS_1


title: 103_P11_D07


title: EpiSC Bod1L KO Tamoxifen biol rep 2

description:
Library name: Sample 27
Column name in bfx754.mm10.e87.txt: RNA27

value: Bod1L KO


title: 103_P11_D06

description: Expression_CountValue.tsv,Expression_FPKM.tsv,Expression_TPM.tsv,Mutations.tsv

value: Melanoma cell line-derived tumor


title: EpiSC Bod1L KO Tamoxifen biol rep 1

description:
Library name: Sample 25
Column name in bfx754.mm10.e87.txt: RNA25


title: ESCFCS Setd1a KO Tamoxifen biol rep 2

description:
Library name: Sample 23
Column name in bfx754.mm10.e87.txt: RNA23

source_name: Cycling Embryonic Stem Cells

value: Cycling Embryonic Stem Cells

value: Media with LIF and FCS


title: 103_P11_D05

value: HGF-tg C57BL6

value: CD45-, CD31-, alive, nucleated cells