title: Mdr2-/-3

city: shanghai

first: Jiamei

last: Chen

address: zhangheng road,pudong district,shanghai

institute: shuguang hospital

data_processing:
1. Quality control and mapping The transcriptome sequencing and analysis were conducted by OE biotech Co., Ltd. (Shanghai, China). Raw data (raw reads) were processed using Trimmomatic[1] . The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference genome using hisat2 [2] .
2. Gene-level quantification, analysis of differentially expressed genes (DEGs), cluster analysis, GO and KEGG enrichment FPKM[3] value of each gene was calculated using cufflinks[4] , and the read counts of each gene were obtained by htseq-count[5] . DEGs were identified using the DESeq[6](2012) R package functions estimateSizeFactors and nbinomTest. Pvalue < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG[7] pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
3. Transcript-level quantification, analysis of differentially expressed transcript (DEGs), cluster analysis, GO and KEGG enrichment If it was transcript-level quantification, FPKM[2] and read counts value of each transcript (protein_coding) was calculated using bowtie2 [8] and eXpress[9] . DEGs were identified using the DESeq[6] (2012) functions estimateSizeFactors and nbinomTest. P value < 0.05 and foldChange >2 or foldChange < 0.5 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore transcripts expression pattern. GO enrichment and KEGG[7] pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
4. Gene structure extension and novel transcripts identification The reads were reassembled using StringTie[10] . Then gene structure extension and novel transcripts identification were performed by comparing the reference genome and the known annotated genes using cuffcompare software.
5. Alternatively splicing analysis and SNP-INDEL calling The alternatively splicing analysis of differentially regulated transcripts isoforms or exons was performed using ASprofile[11] . SNP and INDEL were called using samtools[12] and bcftools[13] , and the details were shown on samtools webpage (http://samtools.sourceforge.net/mpileup.shtml). Then snpeff[14] annotates and predicts the effects of variants on genes (such as amino acid changes)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: liver

extract_protocol:
A. Add 600 μL Lysis/Binding Buffer to the cell or tissue lysate. Then add 30 μL miRNA Homogenate Additive to homogenate, and mix well by vortexing or inverting the tube several times. Leave the mixture on ice for 10 min. B. Add a volume of Acid-Phenol: Chloroform that is equal to the lysate volume before addition of the miRNA Homogenate Additive. Centrifuge for 5 min at maximum speed (10,000 x g) to separate the aqueous and organic phases. Carefully remove the aqueous (upper) phase without disturbing the lower phase, and transfer it to a fresh tube. C. Add 1.25 volumes of room temperature 100% ethanol to the aqueous phase. D. Pipet the lysate/ethanol mixture (from the previous step) onto the Filter Cartridge (Note: Up to 700 μL can be applied to a Filter Cartridge at a time.). Centrifuge for 30 sec at 13,000 rpm to pass the mixture through the filter. Discard the flow-through.E. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube. F. The 10 μL DNase I and 70 μL Buffer RDD QIAGEN (#79254) were mixed. Then the mixture was added to the Filter Cartridge. Leave it at the room temperature for 15 min. G. Apply 350 μL miRNA Wash Solution 1 to the Filter Cartridge and centrifuge for 30 sec at 13,000 rpm. Discard the flow-through from the Collection Tube, and replace the Filter Cartridge into the same Collection Tube. H. Apply 500 μL Wash Solution 2/3 and centrifuge for 30 sec at 13,000 rpm. Draw it through the Filter Cartridge as in the previous step. Repeat with a second 500 μL aliquot of Wash Solution 2/3.  I. Spin the assembly for 1 min to remove residual fluid from the filter. Transfer the Filter Cartridge into a fresh Collection Tube. Apply 100 μL of pre-heated (95°C) Elution Solution to the center of the filter. Leave it at the room temperature for 2 min. Spin for ~20–30 sec at maximum speed to recover the RNA. Collect the eluate (which contains the RNA) and store it at –70°C.
2.1 Purify and Fragment mRNA a. Add 50 μL RNA Purification Beads to each well with 50 μL total RNA (4μg) and mix thoroughly. b. Incubate at 65°C for 5 min, remove at 4°C, and then place at room temperaturefor 5 min. c. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well. d. Remove the magnetic stand, add 200 μL of Bead Washing Buffer in each well, and mix thoroughly. e. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well. f. Add 50 μL of Elution Buffer in each well and mix thoroughly. g. Incubate at 80°C for 2 min, remove at 25°C, and then place at room temperature. h. Add 50 μL of Beads Binding Buffer in each well and mix thoroughly. The mixture was placed at room temperature for 5 min. i. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well. j. Remove the magnetic stand, add 200 μL of Bead Washing Buffer in each well, and mix thoroughly. k. Place it on the magnetic stand at room temperature for 5 min. Remove and discard all of the supernatant from each well. l. Remove the magnetic stand, add 19.5 μL of Elute, Primer,Fragment Mix in each well and mix thoroughly. m. Incubate at 94°C for 8 min, remove at 4°C, and then centrifuge. 2.2 Synthesize First Strand cDNA a. Add 8 μL First Strand Synthesis Act D Mix and SuperScript II Reverse Transcriptase in each well and mix thoroughly.b. The mixture was incubated in the following progress: 25°C for 10 min, 42°C for 15 min, 70°C for 15 min, hold at 4°C. 2.3 Synthesize Second Strand cDNA a. Add 5 μL End Repair Control (2 μL End Repair Control + 98 μL Resuspension Buffer) in each well. b. Add 20 μL Second Strand Marking Master Mix and mix thoroughly. b. The mixture was incubated at 16°C for 60 min. 2.3.1 Purification a. Add 90 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min. b. Place it on the magnetic stand at room temperature for 5 min. c. Remove and discard all of the supernatant from each well. d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well. e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well. f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand. g. Add 17.5 μL Resuspension Buffer and mix thoroughly. h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min.i. Transfer 15 μL the supernatant from each well into the new PCR plate. 2.4 Adenylate 3’Ends a. Add 2.5 μL diluted A-Tailing Control (1 μL A-Tailing Control + 99 μL Resuspension Buffer) in each well. b. Add 12.5 μL A-Tailing Mix and mix thoroughly. c. The mixture was incubated in the following progress: 37°C for 30 min, 70°C for 5 min, hold at 4°C. 2.5 Ligate Adapters a. Add 2.5 μL diluted Ligation Control (1 μL Ligation Control + 99 μL Resuspension Buffer) in each well. b. Add 2.5 μL Ligation Mix. c. Add 2.5 μL RNA Adapter Index and mix thoroughly. d. The mixture was incubated at 30°C for 10 min. e. Add 5 μL Stop Ligation Buffer in each well and mix thoroughly. 2.5.1 Purification a. Add 42 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min. b. Place it on the magnetic stand at room temperature for 15 min. c. Remove and discard 79.5 μL of the supernatant from each well. d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well. e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well. f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand. g. Add 52.5 μL Resuspension Buffer and mix thoroughly. h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min. i. Transfer 50 μL the supernatant from each well into the new PCR plate. j. Add 50 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min. k. Place it on the magnetic stand at room temperature for 15 min. l. Remove and discard 95 μL of the supernatant from each well. m. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well. n. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well. o. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand. p. Add 22.5 μL Resuspension Buffer and mix thoroughly. q. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min. r. Transfer 20 μL the supernatant from each well into the new PCR plate. 2.6 Enrich DNA Fragments a. Add 5 μL PCR Primer Cocktail. b. Add 25 μL PCR Master Mix and mix thoroughly. c. The mixture was incubated in the following progress: 1 cycle 98°C for 30 sec; 15 cycles 98°C for 10 sec, 60°C for 30 sec, 72°C for 30 sec; 1 cycle 72°C for 5 min; hold at 10°C. 2.7.1 Purification a. Add 50 μL mixed AMPure XP beads, mix thoroughly, and then place at room temperature for 15 min. b. Place it on the magnetic stand at room temperature for 15 min. c. Remove and discard 95 μL of the supernatant from each well. d. Place the plate on the magnetic stand. Add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec. Remove and discard all of the supernatant from each well. e. Repeat the above progress: place the plate on the magnetic stand; add 200 μL of 80% ethyl alcohol and place at room temperature for 30 sec; remove and discard all of the supernatant from each well. f. Place at room temperature for 15 min for air drying. Remove the plate from the magnetic stand. g. Add 32.5 μL Resuspension Buffer and mix thoroughly. h. Incubate the mixture at room temperature for 2 min. Place it on the magnetic stand at room temperature for 5 min. i. Transfer 30 μL the supernatant from each well into the new PCR plate. 2.8 Validate library a. Load 1 μL sample on an Agilent 2100 Bioanalyzer. b. Check the size and purity of the library.

value: liver

value: Mdr2 knockout


title: hOBS, control (titanium surface), rep 2

status: Public on Aug 01 2025

type: SRA

city: Seattle

first: Xinru

last: Wang

state: Washington

address: 3946 W Stevens Way NE

department: Biochemistry

country: USA

institute: University of Washington

library_source: transcriptomic

data_processing:
demultiplexing was performed with bcl2fastq. Alignment was done through biojupies with standard parameters to hg38. Raw counts were normalized to log10-Counters per million (logCPM) by dividing each column by the total sum of its counts, multiplying it by 10^6, followed by the application of a log10-transform.
Assembly: hg38
Supplementary files format and content: fastqs

molecule: polyA RNA

organism: Homo sapiens

source_name: bone

growth_protocol: MCF10A cells were cultured in media described previously50,51; briefly, the media consisted of DMEM/F12 (Gibco, 11330032), 5% horse serum (Gibco, 16050130), 20 ng/mL EGF (Sigma-Aldrich, SRP3027), 0.5 mg/mL hydrocortisone (Sigma-Aldrich, H4001), 100 ng/mL cholera toxin (Millipore, C8052), 10 µg/mL insulin (Sigma-Aldrich,11070-73-8) and 1% penicillin–streptomycin (Gibco, 15140122). MCF10A cells were starved in the same media without EGF and contained 2% horse serum (assay media) for 16 hours before signaling experiments. Human bone marrow-derived mesenchymal stem cells (MSCs; ATCC) and human osteoblasts (OBs; Sigma-Aldrich) were cultured in Advanced DMEM medium supplemented with 10% FBS, 20 mM HEPES, penicillin/streptomycin (50 U/mL and 50 µg/mL, respectively) and 2 mM L-glutamine (all components from ThermoFisher Scientific). Cells from passage 5 were used in all experiments. Human foreskin fibroblasts (FFs; Millipore) were cultured in DMEM medium supplemented with 10% FBS, 20 mM HEPES, 50 U mL-1 penicillin, 50 µg mL-1 streptomycin and 2 mM L-glutamine, all from ThermoFisher Scientific. FFs from passage 10 were used in all experiments.

extract_protocol:
RNAeasy plus (Qiagen)
Illumina Stranded mRNA prep

treatment_protocol: MCF10A cells (5X 103) were plated onto 12 wells plate in assay media. These cells were treated with the increasing concentration (0, 20, 200, 500 nM) of integrin mini binder (mb) after 12 h of attachment.MSCs, FFs, and OBs were cultured in serum-free conditions at a concentration of 25,000 cells/disc and allowed to adhere for 4 h on the grafted titanium discs.

tag: tissue

value: bone

tag: cell line

value: osteoblasts

tag: cell type

tag: genotype

value: WT

tag: treatment

value: control


title: PBMCs, IL15, 6h, 40ng/ml, 32062, Three

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

description: Library name: 036_O10_32062_40_6h_3

data_processing:
Trimgalorev0.6.10 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.4.4
Aligned reads with STARv2.7.10b to rhesus macaque genome
Assembly: Macaca mulatta version 10 Ensembl annoation v110
Supplementary files format and content: individual count files for each sample

molecule: total RNA

organism: Macaca mulatta

source_name: PBMCs

extract_protocol:
RNeasy Micro Kit
TruSeq mRNA / Biomek

treatment_protocol: Ex-vivo PBMCs from rhesus macaques  were treated with IL-15/IL-15Ra at 4ng and 40ng/ml

value: PBMCs

tag: time

tag: animal id

tag: Sex

value: male

tag: replicate

value: Three

tag: dose


title: Mdr2-/-2

country: China

organism: Mus musculus


title: replicate-3.snRNA-seq

city: Nanjing

first: shunkai

last: Hu

state: Jiangsu Province

address: Nanjing Agricultural University, Weigang No. 1, Xuanwu District, Nanjing

department: College of Horticulture

institute: Nanjing Agricultural University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The raw data was processed using the Cell Ranger analysis software from 10x Genomics to perform data filtering, mapping to the Tea Plant Information Archive, quantification, and identification of recovered cells, resulting in a gene expression matrix for each nucleus
Assembly: Shuchazao
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

molecule: nuclear RNA

organism: Camellia sinensis

source_name: root

extract_protocol:
Approximately 1 g of fresh, tender tea plant root tips, specifically from 'Shuchazao' (Camellia sinensis ' Shuchazao '), were excised using a sterile razor blade and immediately placed into a pre-cooled petri dish containing 500 μl of Nuclear Isolation Buffer (NIB; Sigma-Aldrich, Catalog No. CELLYTPN1)
Chromium™ Single Cell 3' Solution utilized GemCode technology within a microfluidic platform, precisely controlling the concentration of cell nuclei within the suspension between 700-1200 nuclei per microliter.
cDNA was enzymatically segmented into approximately 200-300 bp fragments. Following this segmentation, standard library preparation steps were undertaken, including the attachment of sequencing adapters and primers. A final round of PCR amplification was conducted to finalize the DNA library. This library was then sequenced on the Illumina NovaSeq 6000 platform by LC-Bio Technology Co., Ltd., based in Hangzhou, China, ensuring high-throughput results.

value: root

value: root cells


title: alveolar macrophages, G1-1, control, biol rep1

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

data_processing:
All sequencing data were analyzed using the Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data (ARMOR v1.5.4) pipeline48.
In this pipeline, reads underwent a quality check using FastQC (Babraham Bioinformatics). Quantification and quality control results were summarized in a MultiQC report before being mapped using Salmon to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Mus_musculus.GRCm39.cdna.all.fa file.
Assembly: Mus_musculus.GRCm39.cdna.all.fa
Supplementary files format and content: excell file with the counts matrix

source_name: Primary alveolar macrophages

growth_protocol: Primary alveolar macrophages were maintained during 5 days in DMEM supplemented with 10% fetal bovine serum (FBS) and 1 % antibiotic-antimycotic (AA) in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. Residual DNA was removed by on-column DNase digestion using the RNAse-Free DNase Set (Qiagen)
The Libraries were prepared starting from 150 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems, KK8560) following the manufacturer’s recommendations (KR1351 – v1.16).

treatment_protocol: Cells were exposed during 4 days to control, non-overload or overload conditions of G1-1 or Printex90 particles

value: Primary alveolar macrophages

tag: strain

value: Male

value: 4 days


title: PBMCs, IL15, 6h, 40ng/ml, 32062, Two

description: Library name: 035_O10_32062_40_6h_2

value: Two


title: replicate-2.snRNA-seq

description: 10x Genomics


title: d3, hiPSC,TC1133

city: Maastricht

first: Jana

last: Hegenbarth

state: Limburg

address: Universiteitssingel 50

department: Department of Molecular Genetics

country: Netherlands

institute: Maastricht University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processig, gene counting and aggregation were made using the Cell Ranger software v5.0.0
Assembly: GrCh38/Ensembl98
Supplementary files format and content: Cell Ranger feature matrix and value files

source_name: hiPSC

extract_protocol:
For single cell dissociation, d3, d10, d25 and EHM were treated with digestion medium (Accutase, Trypsin and DNase1) for up to 30 min at room temperature. Cell suspensions were gently dissociated by pipetting, centrifuged (100xg, 10min @RT) and resuspended in PBS. Similarly, hiPSC (d0) were washed with PBS twice and incubated in Versene for 5-10 min, arrested with pre-warmed medium, mechanically dissociated, centrifuged and resuspended in PBS. All cell suspensions were checked for viability (>90%), counted and passaged through a 30 μm mesh to ensure compatibility with the 10x Genomics pipeline.
Library was constructed according to manufacter's instructions (Chromium Single Cell 3’ Gene Expression Solution v2, 10x Genomics).

value: hiPSC

value: mesodermal cells


title: Mdr2-/-1

value: liver


title: PBMCs, IL15, 2h, 40ng/ml, 32062, Three

description: Library name: 033_O10_32062_40_2h_3


title: Blood, Age-matched cerulein treated, rep7

city: Edinburgh

first: Alan

last: Serrels

address: Crewe Road South

department: Institute of Genetics and Cancer

country: United Kingdom

institute: University of Edinburgh

description: Library name: Pancreatitis_47

data_processing:
Data was processed using nf-core/rnaseq v3.14.0 (doi: https://doi.org/10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
Assembly: Ensembl/GRCm38
Supplementary files format and content: A tab-separated text file with counts per Ensembl transcript (salmon quant format)
Supplementary files format and content: A tab-separated table of gene-level counts, for all samples, that have been corrected for effective gene length, generated by the tximport package from Salmon quantification files.

source_name: Blood

growth_protocol: Tumours were established by intrapancreatic injection of 1x10e5 cells into the pancreas of a C57BL/6 mouse. Mice were euthanised 3 weeks post injection and blood drawn via cardiac puncture.

extract_protocol:
Total RNA was extracted from blood using Mouse RiboPure Blood RNA isolation kit (Ambion Inc), following manufacturer’s instructions.
Libraries were prepared from totalRNA using the NEBNext Ultra2 directional RNA library prep kit (Illumina, Cat# E7760) and NEBNext globin and rRNA depletion kit (Cat#E7750) according to the manufacturers protocol.

treatment_protocol: To induce pancreatitis, cerulein (80µg/kg) was administered via intraperitoneal injection a total of 6 times at 1-hour intervals. Mice were euthanised two days after the first cerulein dose.

value: Blood

value: Cerulein

tag: batch

value: total RNA


title: Blood, Age-matched cerulein treated, rep6

description: Library name: Pancreatitis_46


title: WT3

value: WT


title: replicate-1.snRNA-seq

description: 10x Genomics


title: Blood, Age-matched cerulein treated, rep5

description: Library name: Pancreatitis_45


title: PBMCs, IL15, 2h, 40ng/ml, 32062, Two

description: Library name: 032_O10_32062_40_2h_2


title: d10, hiPSC,TC1133

description: 10x Genomics

value: cardiac cells


title: Blood, Age-matched cerulein treated, rep4

description: Library name: Pancreatitis_44


title: WT1


title: Blood, Age-matched cerulein treated, rep2

description: Library name: Pancreatitis_42


title: PBMCs, IL15, 2h, 40ng/ml, 32062, One

description: Library name: 031_O10_32062_40_2h_1

value: PBMCs

value: One


title: PBMCs, IL15, 48h, 4ng/ml, 32062, Three

description: Library name: 030_O10_32062_4_48h_3

value: male

value: Three


title: PBMCs, IL15, 12h, 40ng/ml, 32062, One

description: Library name: 037_O10_32062_40_12h_1


title: Blood, Age-matched cerulein treated, rep1

description: Library name: Pancreatitis_41


title: mouse ovarian stromal tissues, Sema3E injected, 8 h post-hCG, rep3

city: Ithaca

first: Yi

last: Ren

address: 203 Morrison Hall

department: Animal Science

institute: Cornell University

data_processing:
Raw RNA-seq reads were aligned to the mouse (GRCm38/mm10) genome using HISAT2 (version 2.0.5) by default parameters.
Raw read counts for each gene were generated using featureCounts (v1.5.0-p3) and Transcripts Per Million (TPM) values of each gene were generated using EdgeR (version 1.3.3).
Assembly: mm10
Supplementary files format and content: excel sheet file includes TPM values for each sample

source_name: ovary

extract_protocol:
Total messenger RNA (mRNA) was extracted using RNeasy Micro Kit.
Library preparation and transcriptome sequencing were conducted by Novogene Co., LTD

treatment_protocol: One ovary was injected with 2 μg of Sema3E  in 10 μL of PBS (0.2 μg/μL) supplemented with 0.1% BSA (Sema3E group). The contralateral ovary was injected with 2 μg of IgG in 10 μL of PBS with 0.1% BSA (IgG group).

value: ovary

value: ovarian stromal cells

value: intraovarian injection of Sema3E


title: Blood, Age-matched cerulein treated, rep8

description: Library name: Pancreatitis_48


title: mouse ovarian stromal tissues, Sema3E injected, 8 h post-hCG, rep2


title: Blood, Age-matched healthy control, rep6

description: Library name: NT_38


title: Blood, Age-matched healthy control, rep7

description: Library name: NT_39


title: PBMCs, IL15, 48h, 4ng/ml, 32062, Two

description: Library name: 029_O10_32062_4_48h_2


title: mouse ovarian stromal tissues, Sema3E injected, 8 h post-hCG, rep1


title: Blood, Age-matched healthy control, rep5

description: Library name: NT_37


title: PBMCs, IL15, 48h, 4ng/ml, 32062, One

description: Library name: 028_O10_32062_4_48h_1


title: Blood, Age-matched healthy control, rep3

description: Library name: NT_35


title: Blood, Age-matched cerulein treated, rep3

description: Library name: Pancreatitis_43


title: mouse ovarian stromal tissues, IgG injected, 8 h post-hCG, rep3

value: intraovarian injection of IgG


title: PBMCs, IL15, 24h, 4ng/ml, 32062, Two

description: Library name: 026_O10_32062_4_24h_2

value: Two


title: Blood, KrasG12Dp53-/-Cdkn2a-/-Smad4-/- tumour bearing mouse, rep8

description: Library name: 2KO_32

value: KrasG12D p53-/- Cdkn2a-/- Smad4-/-

value: Injection of tumour cells into the pancreas


title: Blood, Age-matched healthy control, rep2

description: Library name: NT_34


title: mouse ovarian stromal tissues, IgG injected, 8 h post-hCG, rep2


title: PBMCs, IL15, 24h, 4ng/ml, 32062, One

description: Library name: 025_O10_32062_4_24h_1


title: mouse ovarian stromal tissues, IgG injected, 8 h post-hCG, rep1


title: PBMCs, IL15, 12h, 4ng/ml, 32062, Three

description: Library name: 024_O10_32062_4_12h_3


title: Blood, KrasG12Dp53-/-Cdkn2a-/-Smad4-/- tumour bearing mouse, rep6

description: Library name: 2KO_30


title: Blood, Age-matched healthy control, rep1

description: Library name: NT_33


title: Blood, KrasG12Dp53-/-Cdkn2a-/-Smad4-/- tumour bearing mouse, rep5

description: Library name: 2KO_29


title: Blood, KrasG12Dp53-/-Cdkn2a-/-Smad4-/- tumour bearing mouse, rep7

description: Library name: 2KO_31


title: mouse ovarian granulosa cells, Sema3E injected, 8 h post-hCG, rep3

value: ovarian granulosa cells


title: Blood, KrasG12Dp53-/-Cdkn2a-/-Smad4-/- tumour bearing mouse, rep4

description: Library name: 2KO_28

value: Blood


title: Blood, Age-matched healthy control, rep8

description: Library name: NT_40


title: PBMCs, IL15, 12h, 4ng/ml, 32062, Two

description: Library name: 023_O10_32062_4_12h_2


title: Blood, KrasG12Dp53-/-Cdkn2a-/-Smad4-/- tumour bearing mouse, rep3

description: Library name: 2KO_27


title: Blood, Age-matched healthy control, rep4

description: Library name: NT_36


title: PBMCs, IL15, 24h, 4ng/ml, 32062, Three

description: Library name: 027_O10_32062_4_24h_3


title: Blood, KrasG12Dp53-/-Cdkn2a-/-Smad4-/- tumour bearing mouse, rep2

description: Library name: 2KO_26


title: mouse ovarian granulosa cells, Sema3E injected, 8 h post-hCG, rep2


title: PBMCs, IL15, 6h, 4ng/ml, 32062, Three

description: Library name: 021_O10_32062_4_6h_3


title: Blood, KrasG12Dp53-/-Cdkn2a-/-Smad4-/- tumour bearing mouse, rep1

description: Library name: 2KO_25


title: PBMCs, IL15, 6h, 4ng/ml, 32062, Two

description: Library name: 020_O10_32062_4_6h_2


title: Blood, KrasG12Dp53-/-Smad4-/- tumour bearing mouse, rep7

description: Library name: SMAD4_23

value: KrasG12D p53-/- Smad4-/-


title: mouse ovarian granulosa cells, Sema3E injected, 8 h post-hCG, rep1


title: mouse ovarian granulosa cells, IgG injected, 8 h post-hCG, rep3


title: WT2

value: liver


title: Blood, KrasG12Dp53-/-Smad4-/- tumour bearing mouse, rep5

description: Library name: SMAD4_21

value: total RNA


title: PBMCs, IL15, 6h, 4ng/ml, 32062, One

description: Library name: 019_O10_32062_4_6h_1


title: Blood, KrasG12Dp53-/-Smad4-/- tumour bearing mouse, rep6

description: Library name: SMAD4_22


title: mouse ovarian granulosa cells, IgG injected, 8 h post-hCG, rep2

value: WT


title: PBMCs, IL15, 2h, 4ng/ml, 32062, Three

description: Library name: 018_O10_32062_4_2h_3

value: PBMCs


title: Blood, KrasG12Dp53-/-Smad4-/- tumour bearing mouse, rep4

description: Library name: SMAD4_20


title: Blood, KrasG12Dp53-/-Smad4-/- tumour bearing mouse, rep3

description: Library name: SMAD4_19


title: Blood, KrasG12Dp53-/-Smad4-/- tumour bearing mouse, rep2

description: Library name: SMAD4_18


title: PBMCs, IL15, 2h, 4ng/ml, 32062, Two

description: Library name: 017_O10_32062_4_2h_2


title: PolyIC_NK2

city: Hefei

first: Qi

middle: wu

last: Bian

state: Anhui

address: Division of Life Sciences and Medicine, 443 Huangshan Road

department: Life sciences and medicine

institute: University of Science and Technology of China

data_processing:
Illumina Casava software used for basecalling.
Raw sequencing data were first processed by Trimmomatic (version 0.36) to remove adaptor sequences and low-quality reads.
Clean reads were aligned to the GRCm38 mouse genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include RPKM values for each Sample

source_name: deccidua

extract_protocol:
Total RNAs were extracted from NK cells using TRIzol Reagent (Invitrogen), mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Decidua NK cells isolated from E13.5 dams 24 hours after injection with polyIC or saline.

value: deccidua

value: NK cell

value: polyIC


title: Blood, KrasG12Dp53-/-Smad4-/- tumour bearing mouse, rep1

description: Library name: SMAD4_17


title: mouse ovarian granulosa cells, IgG injected, 8 h post-hCG, rep1

value: ovary


title: Blood, KrasG12Dp53-/-Cdkn2a-/- tumour bearing mouse, rep8

description: Library name: CDKN2A_16

value: KrasG12D p53-/- Cdkn2a-/-


title: Blood, KrasG12Dp53-/-Cdkn2a-/- tumour bearing mouse, rep7

description: Library name: CDKN2A_15


title: PBMCs, IL15, 2h, 4ng/ml, 32062, One

description: Library name: 016_O10_32062_4_2h_1

value: male

value: One


title: Blood, KrasG12Dp53-/-Smad4-/- tumour bearing mouse, rep8

description: Library name: SMAD4_24


title: PolyIC_NK1


title: PBMCs, Control, 48h, 0ng/ml, 32062, Three

description: Library name: 015_O10_32062_0_48h_3

value: Control

value: Three


title: Blood, KrasG12Dp53-/-Cdkn2a-/- tumour bearing mouse, rep6

description: Library name: CDKN2A_14

value: Injection of tumour cells into the pancreas


title: Blood, KrasG12Dp53-/-Cdkn2a-/- tumour bearing mouse, rep4

description: Library name: CDKN2A_12


title: Blood, KrasG12Dp53-/-Cdkn2a-/- tumour bearing mouse, rep5

description: Library name: CDKN2A_13


title: PBMCs, Control, 48h, 0ng/ml, 33047, One

description: Library name: 058_O10_33047_0_48h_1


title: Blood, KrasG12Dp53-/-Cdkn2a-/- tumour bearing mouse, rep3

description: Library name: CDKN2A_11


title: Ctrl_NK1

value: Saline


title: PBMCs, Control, 48h, 0ng/ml, 32062, One

description: Library name: 013_O10_32062_0_48h_1


title: PolyIC_4

extract_protocol:
Total RNAs were extracted from decidua tissues using TRIzol Reagent (Invitrogen), mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Decidua tissues isolated from E13.5 dams 24 hours after injection with polyIC or saline.


title: Blood, KrasG12Dp53-/-Cdkn2a-/- tumour bearing mouse, rep1

description: Library name: CDKN2A_9

value: Blood


title: Blood, KrasG12Dp53-/-Cdkn2a-/- tumour bearing mouse, rep2

description: Library name: CDKN2A_10


title: PBMCs, Control, 24h, 0ng/ml, 32062, One

description: Library name: 010_O10_32062_0_24h_1


title: PolyIC_2


title: PBMCs, Control, 24h, 0ng/ml, 32062, Three

description: Library name: 012_O10_32062_0_24h_3


title: Blood, KrasG12Dp53-/- tumour bearing mouse, rep4

description: Library name: Pac5_4

value: KrasG12D p53-/-


title: Blood, KrasG12Dp53-/- tumour bearing mouse, rep3

description: Library name: Pac5_3


title: Blood, KrasG12Dp53-/- tumour bearing mouse, rep2

description: Library name: Pac5_2


title: Ctrl_4


title: PBMCs, Control, 12h, 0ng/ml, 32062, One

description: Library name: 007_O10_32062_0_12h_1


title: Blood, KrasG12Dp53-/- tumour bearing mouse, rep5

description: Library name: Pac5_5


title: Blood, KrasG12Dp53-/- tumour bearing mouse, rep7

description: Library name: Pac5_7


title: PolyIC_3


title: PBMCs, Control, 24h, 0ng/ml, 32062, Two

description: Library name: 011_O10_32062_0_24h_2

value: Two


title: Blood, KrasG12Dp53-/- tumour bearing mouse, rep6

description: Library name: Pac5_6

value: total RNA


title: BL/6NZB female 19M_1

city: New York

first: Edmund

middle: C

last: Jenkins

state: NY

address: 1468 Madison Avenue

department: Heme/Onc

institute: Icahn School of Medicine at Mt. Sinai

data_processing:
raw sequencing data was processed by Azenta using the cellranger count pipeline
Assembly: GRCm39
Supplementary files format and content: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: mammary gland

extract_protocol:
Nuclear isolation
Freshly isolated snap frozen Inguinal mammary glands were submitted to GENEWIZ, LLC, NJ, USA for nuclei isolation and GEM (Gel Bead-based Emulsion) single cell RNA seq analysis on the 10x Genomics platform

value: mammary gland

value: female

tag: age


title: Ctrl_NK2

value: deccidua

value: WT


title: PBMCs, Control, 12h, 0ng/ml, 32062, Three

description: Library name: 009_O10_32062_0_12h_3

value: PBMCs


title: BL/6NZB female 14M_2


title: Blood, KrasG12Dp53-/- tumour bearing mouse, rep1

description: Library name: Pac5_1


title: Ctrl_3


title: PBMCs, Control, 12h, 0ng/ml, 32062, Two

description: Library name: 008_O10_32062_0_12h_2


title: BL/6NZB female 14M_1


title: PolyIC_1

value: polyIC


title: BL/6NZB female 19M_2


title: PBMCs, Control, 6h, 0ng/ml, 32062, Three

description: Library name: 006_O10_32062_0_6h_3


title: BL/6NZB female 14M_3


title: BL/6NZB female 11M_2


title: Ctrl_1


title: BL/6NZB female 11M_1


title: BL/6NZB female 19M_3


title: PBMCs, Control, 6h, 0ng/ml, 32062, Two

description: Library name: 005_O10_32062_0_6h_2


title: Blood, KrasG12Dp53-/- tumour bearing mouse, rep8

description: Library name: Pac5_8


title: BL/6NZB female 11M_3


title: BV2_G_AF2

data_processing:
Illumina Casava software used for basecalling.
Raw sequencing data were first processed by Trimmomatic (version 0.36) to remove adaptor sequences and low-quality reads.
Clean reads were aligned to the GRCm38 mouse genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file include FPKM values for each Sample

growth_protocol: The murine microglial BV2 cells were cultured with RPMI 1640 medium containing 10% FBS and 1% penicillin/streptomycin at 37°C in a 5% (v/v) humidified CO2 incubator.

extract_protocol:
Total RNAs were extracted from BV2 cells using TRIzol Reagent (Invitrogen), mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Murine microglial BV2 cells were stimulated for 20 hours using different treatments, including Ctrl, GZMB (500 ng/ml), amniotic fluid (AF, 50 μl), and AF (50 μl) + GZMB (500 ng/ml).

value: Murine microglial

value: AF (50 ul) + GZMB (500 ng/ml)


title: BL/6NZB female 3M_1


title: BL/6NZB female 3M_2


title: BV2_G_AF1


title: BV2_GZMB2

value: GZMB (500 ng/ml)


title: PBMCs, Control, 2h, 0ng/ml, 32062, One

description: Library name: 001_O10_32062_0_2h_1

value: Control

value: male

value: One


title: PBMCs, Control, 2h, 0ng/ml, 32062, Two

description: Library name: 002_O10_32062_0_2h_2


title: BV2_AF2

value: AF (50 ul)


title: TET TKO PGCLC aggregates, plus cytokines, day 2 Rep1

city: Edinburg

first: Sara

last: Gonzalez Brito

email: saraglezbr@gmail.com, s1659595@ed.ac.uk

state: Scotland

address: 5 Little France Dr

description: Column in raw_count_matrix - TKO_D2_PLUSCYT_1

data_processing:
Generation of FASTQ files was performed using Illumina's BaseSpace. TrimGalore 0.5.0 and cutadapt 1.16 were used for quality treaming and reads were alligned to the mouse genome (mm10) using STAR 2.7.1a. Count matrices were then generated using subread 1.5.2 and differential expression analysis was performed by Deseq2.
Assembly: mm10
Supplementary files format and content: Processed data file (raw_count_matrix.csv) contains the raw reads as produced by subread. Each column corresponds to a different sample and each row corresponds to a gene, identified by gene symbol.

growth_protocol: Cells were routinely cultued in S/L media on gelatin plates. PGCLC differentiation was perfomed as previosly descrbied (Hayashi et al, 2011). Cells were first kept in 2i/LIF (N2B27 supplemented with CHIR99021  and PD0325901 ) for at least three passages prior to EpiLC and PGCLC differentiation. EpiLCs were derived for 44 hours in EpiLC medium (N2B27 supplemented with human Activin A and Fgf) and then cultured in suspension in GK15 (GMEM 15% KOSR) for 6 days. Cultures with cytokines were also supplemented with BMP4, BMP8a, SCF, LIF and EGF.

extract_protocol:
Direct-zol RNA MiniPrep kit (Zymo Research, cat. R2052)
100ng of starting material used for NEBNext rRNA Depletion kit (Human/Mouse/Rat) (cat. E6310). rRNA-depleted RNA was then Dnase treated  and purified (Agencourt RNA clean XP beads - Beckman Coulter Inc, cat. 6651) and libraries were generated using the NEBNext Ultra II Directional RNA library prep kit for Illumina (cat. E7760)

value: TET TKO

value: PGCLC aggregates

tag: time point

value: Day 2

value: plus cytokines


title: PBMCs, Control, 6h, 0ng/ml, 32062, One

description: Library name: 004_O10_32062_0_6h_1


title: green stage tomato_control_2

city: Bunkyo-ku

first: Tomiko

last: Asakura

state: Tokyo

department: Applied Biological Chemistry Graduate School of Agricultural and Life Sciences

country: Japan

institute: The University of Tokyo

data_processing:
CLC Genomics Workbench 20
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to miRBase using CLC genomic benchwork
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: SL3.1
Supplementary files format and content: Excel file

organism: Solanum lycopersicum

source_name: fruit

growth_protocol: Plants were cultivated in a greenhouse under controlled conditions consisting of 12 h of light at 25°C and 12 h of darkness at 20°C. Liquid fertilizer (Sumitomo Chemical Co., Ltd.) diluted 500× was mixed into the irrigation water until the seedlings developed one or two true leaves. The seedlings were then placed in plastic pots (15 cm in diameter and 12.5 cm depth) and filled with Hyuga soil up to 80%. Plants were then watered only with distilled water until flowering.

extract_protocol:
Prior to extract total RNA using RNAiso Plus (#9108; Takara), polysaccharides and polyphenols were eliminated with Fruit-mate (#9192; Takara, Shiga, Japan) according to the manufacturer’s protocol. After DNase I treatment, the extracted RNA was purified again using an RNeasy Mini Kit (Qiagen, Hilden, Germany).240ng of total RNA was used for the construction of sequencing libraries.
Libraries for small RNA sequencing were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Massachusetts, USA), following the manufacturer’s protocol.

treatment_protocol: After flowering, the control pots were watered with liquid fertilizer (diluted 500×) on the first day and with water the following day. This cycle was repeated until cultivation was completed. Drought-stressed pots were watered with liquid fertilizer (diluted 500×) only once per week.

value: fruit

tag: Stage

value: green

value: normal condition


title: TET TKO PGCLC aggregates, plus cytokines, day 6, Rep1

description: Column in raw_count_matrix - TKO_D6_PLUSCYT_1

value: Day 6


title: TET TKO PGCLC aggregates, plus cytokines, day 6,  Rep2

description: Column in raw_count_matrix - TKO_D6_PLUSCYT_2


title: BV2_AF1

value: WT


title: green stage tomato_control_3


title: Ctrl_2

value: deccidua

value: Saline


title: TET TKO PGCLC aggregates, no cytokines, day 2 Rep2

description: Column in raw_count_matrix - TKO_D2_NOCYT_2

value: no cytokines


title: BV2_GZMB1

value: Murine microglial

value: GZMB (500 ng/ml)


title: green stage tomato_control_1


title: TET TKO PGCLC aggregates, no cytokines, day 6, Rep2

description: Column in raw_count_matrix - TKO_D6_NOCYT_2


title: TET TKO PGCLC aggregates, no cytokines, day 2 Rep1

description: Column in raw_count_matrix - TKO_D2_NOCYT_1


title: TET TKO PGCLC aggregates, no cytokines, day 6, Rep1

description: Column in raw_count_matrix - TKO_D6_NOCYT_1


title: TET TKO PGCLC aggregates, plus cytokines, day 2 Rep2

description: Column in raw_count_matrix - TKO_D2_PLUSCYT_2


title: BV2_ctrl2

value: Ctrl


title: TET TKO EpiLCs, Rep2

description: Column in raw_count_matrix - TKO_EPI_2

value: EpiLCs

value: Day 0 (EpiLCs)


title: green stage tomato_dorought stress_3

value: drought stress


title: TET TKO EpiLCs, Rep1

description: Column in raw_count_matrix - TKO_EPI_1

value: TET TKO


title: green stage tomato_dorought stress_2


title: Wild type PGCLC aggregates, plus cytokines, day 6, Rep2

description: Column in raw_count_matrix - WT_D6_PLUSCYT_2

value: Wild type

value: PGCLC aggregates


title: Wild type PGCLC aggregates, plus cytokines, day 6, Rep1

description: Column in raw_count_matrix - WT_D6_PLUSCYT_1

value: plus cytokines


title: BMSCs, Control, day9, rep1

city: Changsha

first: bin

last: guo

address: Xiangya street

institute: Xiangya Hospital

data_processing:
CLC Genomics Workbenchv 11.0.1
Sequence reads w ere trimmed for adaptor sequence/low-quality sequence using CLC genomic benchw ork (parameter- Quality limit: 0.05)
Trimmed sequence reads w ere mapped to GrCM38/mm10 using CLC genomic benchw ork (parameters- mis math cost 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization w ere performed using CLC genomic benchw ork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts and FPKMs for each Sample

source_name: bone marrow

growth_protocol: mesenchymal stem cells were martained in DMEM supplemented w th 10% fetal bovine serum (FBS) and antiblotics in humidfied atmosphere w th 5% C02 at 37℃

extract_protocol:
RNA was harvested using Trizol. 1.5 ug of total RNA w as used for the construction of sequencing ibraries.
library preparation according to Illumina standard instruction (VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® ).

treatment_protocol: Osteogenic differentiation induction solution formula: complete medium (containing 10% FBS ,89% MEM and 1% penicillin-streptomycin solution). Add to 50μM ascorbic acid, 10mM β- Glycerol phosphate and 100nM dexamethasone. Additional added to the experimental group 0.5μ M melanin concentration hormone.

value: bone marrow

value: Purified primary bone marrow cells

value: mesenchymal stem cells

tag: differentiation

value: osteogenic differentiation

value: Control


title: LW,fruit, 35d-2

city: Shenyang

first: Hongyan

last: Qi

state: Liaoning

address: No.120 Dongling Road, Shenhe District

institute: Shenyang Agricultural University

data_processing:
To obtain clean data, the adapter sequences, poly-N reads, and low-quality reads were removed using Fastp software.
The clean reads were mapped to theC. melogenomeusing Hisat2 v2.0.5 and gene expression levels are presented as FPKM.
The DEGs between the two groups were identified using the DESeq2 R package (1.20.0). We screened and filtered the DEGs according to the thresholds of |log2FC| > 1 and padj ≤0.05.
GO and KEGG enrichment analyses were performed using the Cluster Profiler R package.
Assembly: http://cucurbitgenomics.org/organism/18
Assembly: Melon (DHL92) genome 3.6.1
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Cucumis melo

growth_protocol: The high-sucrose cultivar ‘HS’ and low-sucrose cultivar ‘LW’ melon seedlings were exclusively grown in matrix sacks containing soil, peat, and fertilizer in a greenhouse under a temperature range of 25-35 ℃ at Shenyang Agricultural University, Shenyang, China.

extract_protocol:
The total RNA was extracted and purified utilizing the RNA isolation kit.1.0 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: fruit

tag: cultivar

value: LW

value: 35 days


title: Wild type PGCLC aggregates, no cytokines, day 2, Rep1

description: Column in raw_count_matrix - WT_D2_NOCYT_1

value: Day 2

value: no cytokines


title: Wild type PGCLC aggregates, no cytokines, day 6, Rep1

description: Column in raw_count_matrix - WT_D6_NOCYT_1

value: Day 6


title: BMSCs, Control, day9, rep2

tag: tissue

value: WT


title: BMSCs, MCH, day9, rep3

tag: cell line

value: melanin concentration hormone


title: LW,fruit, 35d-1


title: LW,fruit, 35d-3


title: Wild type PGCLC aggregates, no cytokines, day 6, Rep2

description: Column in raw_count_matrix - WT_D6_NOCYT_2

tag: cell type


title: BMSCs, Control, day9, rep3

tag: genotype


title: PDX2263_sgGAP45_1_Lexogen_2

city: PHILADELPHIA

first: Zhendong

last: Cao

state: PA

address: BRB Rm620, 421 Curie Blvd

department: Cancer biology

institute: university of pennsylvania

description: Library name: Sample 4

data_processing:
Sequencing reads were aligned to human genome hg38 using STAR Aligner. Raw read counts were generated via HTSeq-count.
Assembly: hg38
Supplementary files format and content: txt, tab, raw read counts

source_name: human AML PDX-2263

growth_protocol: PDX-2263 cells were cultured in BM media (IMDM supplemented with 15% Fetal Bovine Serum (FBS), 1% P/S, 1% GlutaMAX) and human cytokines, including 1:1000 dilution of the10ng/μl human IL-3 (Peprotech#200-03), 10ng/μl human FLT3 (Peprotech#300-19), 100ng/μl human SCF (Peprotech#300-07), 20ng/μl human IL-6 (Peprotech#200-06), and 10 ng/μl human TPO (Peprotech#300-18) stock.

extract_protocol:
Total RNA was isolated from 0.5~5 million cells using Direct-zol RNA Miniprep Plus kit (ZYMO) or RNeasy Mini Kit (Qiagen) with DNase I treatment in column.
RNA-seq libraries were prepared using QuantSeq 3’ mRNA-seq Library Prep Kit (Lexogen) with 0.5-2 µg of total RNA according to the manufacturer's protocol.  Library quality was checked by High Sensitivity Bioanalyzer (Agilent) and libraries with different barcodes were pooled and sequenced on the Nextseq 500 platform with 75 bp single-end reads.

treatment_protocol: PDX-2263  cells were harvested on day 5 post-infection of sgRNA for GAP45-KO.

value: human AML PDX-2263

tag: treatment

value: day 5 after sgRNA infection


title: LW,fruit, 30d-3

tag: time

value: 30 days


title: PDX2263_sgGAP45_3_Lexogen_1

description: Library name: Sample 5


title: Wild type PGCLC aggregates, no cytokines, day 2, Rep2

description: Column in raw_count_matrix - WT_D2_NOCYT_2

value: Wild type

value: PGCLC aggregates


title: green stage tomato_dorought stress_1

value: green

value: drought stress


title: BMSCs, MCH, day9, rep2

value: bone marrow

value: Purified primary bone marrow cells

value: mesenchymal stem cells

value: osteogenic differentiation


title: Wild type EpiLCs, Rep1

description: Column in raw_count_matrix - WT_EPI_1

value: EpiLCs

value: Day 0 (EpiLCs)


title: PDX2263_sgGAP45_1_Lexogen_1

description: Library name: Sample 3


title: PDX2263_sgGAP45_4_Lexogen_2

description: Library name: Sample 6


title: BL/6NZB female 3M_3

value: mammary gland

value: female


title: BV2_ctrl1

value: Murine microglial

value: WT

value: Ctrl


title: PDX2263_sgNeg_Lexogen_2

description: Library name: Sample 2

value: human AML PDX-2263

value: day 5 after sgRNA infection


title: BMSCs, MCH, day9, rep1

value: melanin concentration hormone


title: LW,fruit, 30d-2

value: fruit

value: LW

value: 30 days


title: Wild type EpiLCs, Rep2

description: Column in raw_count_matrix - WT_EPI_2

value: Wild type


title: PDX2263_sgNeg_Lexogen_1

description: Library name: Sample 1


title: XS0311-1-Gi

first: Xiangming

state: Hunan

address: Xiangya Road，88

department: Department of Orthopedic

institute: Xiangya Hospital of Central South University

data_processing:
Raw reads were processed using CeleScope v1.5.2 (Singleron Biotechnologies) with default parameters to generate gene expression profiles. The R1 reads were used to extract barcodes and UMIs, which were then corrected. Adapter sequences and poly A tails were trimmed from the R2 reads, and the trimmed R2 reads were aligned against transcriptome using STAR (v2.6.1b). Uniquely mapped reads were assigned to exons using.FeatureCounts (v2.0.1). Successfully assigned reads with the same cell barcode, UMI, and gene were grouped together to generate the gene expression matrix for further analysis.
Supplementary files format and content: Tab-separated values fles and matrix fles

source_name: bone marrow cells

extract_protocol:
The tissue dissociation and preparation process involved the following steps. First, the ascites sample was filtered through sterile 40-micronstrainers and centrifuged to separate the cells from the supernatant. The cell sediment was then resuspended in PBS and treated with erythrocytelysis buffer to remove erythrocytes. Fresh tissues obtained during surgery were preserved in a tissue preservation solution and subsequently washed,minced, and digested using a tissue dissociation solution. After centrifugation, the pellet was suspended in PBS. Finally, the samples were stained with Trypan Blue to assess cell viability.
For reverse transcription, amplification, and library construction, single-cell suspensions were loaded onto the microwell chip by a single-cell processing system. Barcoding     beads were used to capture mRNA fromthe cells. Reverse transcription was performed to generate cDNA,followed by PCR amplification. After that, the amplified cDNA wasfragmented and ligated with sequencing adapters. scRNA-seq libraries were prepared using a specific kit and diluted to a concentration of 4 nM.The individual libraries were pooled together and sequenced on anIllumina NovaSeq 6000 platform with paired-end reads of 150 bp.Raw reads were processed using CeleScope v1.5.2 (Singleron Biotechnologies) with default parameters to generate gene expression profiles. The R1 reads were used to extract barcodes and UMIs, which were then corrected. Adapter sequences and poly A tails were trimmed from the R2 reads, and the trimmed R2 reads were aligned against  transcriptome using STAR (v2.6.1b). Uniquely mapped reads were assigned to exons using.FeatureCounts (v2.0.1). Successfully assigned reads with the same cell barcode, UMI, and gene were grouped together to generate the gene expression matrix for further analysis.

value: bone marrow cells

value: Gi


title: MV411-shUBR5_F6_RNA_KO539_25nM_3d_REP3_240626_NANOVO_S39

city: Boston

first: Scott

last: Armstrong

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

description: Library name: Sample 18

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human (Gencode GRCh38/hg38) reference genome using STAR (v2.7.5a, sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl).
Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
Assembly: GRCh38/hg38
Supplementary files format and content: Raw per-gene counts (from HTSeq; .txt format) and .tdf files (for visualization in Broad IGV)

growth_protocol: MV4;11 cells were cultured in RPMI supplemented with 1xL-glutamine, 10% Fetal Bovine Serum, and 1xPenStrep

extract_protocol:
For cell line experiments, RNA was extracted using the RNeasy Mini kit (Qiagen). For RT–qPCR, cDNA was synthesized using the Applied Biosystems™ High-Capacity cDNA Reverse Transcription Kit.
RNA integrity was evaluated using the Agilent TapeStation 4200 (Agilent Technologies), and libraries were prepared using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs). Sequencing was performed on an Illumina NextSeq™ 550 system (Illumina), producing 37-bp, paired-end reads.

treatment_protocol: MV4;11 cells were plated at 2X10^5 cells/mL in the culture medium and were treated with DMSO, JNJ-6617 (25 nM), KO-539 (25 nM) for 72h.

tag: timepoint

value: 3 days

tag: shRNA

value: shUBR5 #2


title: LW,fruit, 30d-1


title: XS0311-1-control

value: control


title: MV411-shUBR5_F6_RNA_KO539_25nM_3d_REP1_240626_NANOVO_S37

description: Library name: Sample 16


title: LW,fruit, 25d-2

value: 25 days


title: C57_liver_ad-egfp1

city: Shanghai

first: Lianju

last: Li

state: China

address: Xujiahui Road

institute: Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases

data_processing:
Paired-end clean reads were mapped to the reference genome. Gene abundance was expressed as fragment per kilobase of transcript per million mapped reads (FPKM). Differential expression analysis was performed using DESeq2 software. Genes with a false discovery rate below 0.05 and an absolute fold change > 1.5 were considered as differentially expressed genes.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

source_name: Liver

extract_protocol:
Total RNA was isolated using RNA extraction kits (LS1040; Promega).
The enriched mRNA was fragmented and transcribed into cDNA using NEBNext Ultra RNA Library Prep Kit for Illumina (7530, New England Biolabs). The purified double-stranded cDNA fragments were end repaired, ‘A’ base added, and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads and enriched by PCR amplification to create the final cDNA library. The resulting cDNA library was sequenced using Illumina Novaseq 6000.

value: Liver

value: ad-egfp

value: infected with control adenovirus (Ad-EGFP)


title: MV411-shUBR5_F6_RNA_KO539_25nM_3d_REP2_240626_NANOVO_S38

description: Library name: Sample 17


title: MV411-shUBR5_F6_RNA_JNJ_25hM_3d_REP2_240626_NANOVO_S41

description: Library name: Sample 14


title: MV411-shUBR5_F6_RNA_JNJ_25hM_3d_REP1_240626_NANOVO_S40

description: Library name: Sample 13


title: LW,fruit, 25d-3


title: MV411-shUBR5_F6_RNA_DMSO_3d_REP3_240626_NANOVO_S36

description: Library name: Sample 12

value: DMSO


title: C57_liver_ad-egfp2


title: C57_liver_ad-egfp3


title: MV411-shLuc-2_RNA_KO539_25nM_3d_REP3_240626_NANOVO_S30

description: Library name: Sample 9


title: LW,fruit, 15d-3

value: 15 days


title: C57_liver_ad-dyrk1b3

value: infected with adenovirus overexpressing mouse Dyrk1b (Ad-Dyrk1b)


title: MV411-shLuc-2_RNA_KO539_25nM_3d_REP2_240626_NANOVO_S29

description: Library name: Sample 8


title: MV411-shUBR5_F6_RNA_DMSO_3d_REP1_240626_NANOVO_S34

description: Library name: Sample 10


title: LW,fruit, 25d-1


title: C57_liver_ad-dyrk1b2


title: LW,fruit, 15d-2


title: MV411-shLuc-2_RNA_KO539_25nM_3d_REP1_240626_NANOVO_S28

description: Library name: Sample 7


title: MV411-shLuc-2_RNA_JNJ_25hM_3d_REP3_240626_NANOVO_S33

description: Library name: Sample 6


title: LW,fruit, 15d-1


title: MV411-shLuc-2_RNA_JNJ_25hM_3d_REP2_240626_NANOVO_S32

description: Library name: Sample 5


title: C57_liver_ad-dyrk1b1


title: MV411-shUBR5_F6_RNA_JNJ_25hM_3d_REP3_240626_NANOVO_S42

description: Library name: Sample 15


title: PBMCs, Control, 2h, 0ng/ml, 32062, Three

description: Library name: 003_O10_32062_0_2h_3

data_processing:
Trimgalorev0.6.10 used to remove low quality reads and bases
Filtered out globin and rRNA reads using bowtie2v2.4.4
Aligned reads with STARv2.7.10b to rhesus macaque genome
Assembly: Macaca mulatta version 10 Ensembl annoation v110
Supplementary files format and content: individual count files for each sample

extract_protocol:
RNeasy Micro Kit
TruSeq mRNA / Biomek

value: PBMCs

value: Control

tag: animal id

tag: Sex

value: male

tag: replicate

value: Three


title: MV411-shLuc-2_RNA_JNJ_25hM_3d_REP1_240626_NANOVO_S31

description: Library name: Sample 4


title: MV411-shUBR5_F6_RNA_DMSO_3d_REP2_240626_NANOVO_S35

description: Library name: Sample 11


title: HS,fruit, 35d-3

value: fruit

value: HS

value: 35 days


title: MV411-shLuc-2_RNA_DMSO_3d_REP3_240626_NANOVO_S27

description: Library name: Sample 3

value: 3 days


title: HS,fruit, 35d-2


title: ATAC_Monos_OMV-SIRP-G_rep3

city: Beijing

first: Jie

last: Liang

address: beiyitiao 11, zhognguancun, beijing

institute: National Center for Nanoscience and Technology, Chinese Academy of Sciences

library_source: genomic

data_processing:
Nextera adaptor sequences were firstly trimmed from the reads using skewer (0.2.2). These reads were aligned to a reference genome using BWA, with standard parameters. These reads were then filtered for high quality (MAPQ≥ 13), non mitochondrial chromosome, and properly paired reads (longer than 18 nt).
All peak calling was performed with macs2 using ‘macs2 callpeak --nomodel --keepdup all --call-summits’. For simulations of peaks called per input read, aligned and de-duplicated BAM files were used without any additional filtering.
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: GRCm38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

extract_protocol:
Nuclei was extracted from samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix
ATAC-seq libraries were purified with the AMPure beads and library quality was assessed with Qubit.

value: bone marrow

value: bone marrow cells

value: WT

value: OMV-SIRP-G


title: MV411-shLuc-2_RNA_DMSO_3d_REP1_240626_NANOVO_S25

description: Library name: Sample 1


title: HS,fruit, 30d-3

value: 30 days


title: MV411-shUBR5_F6_ChIP_MLL1_DMSO_72h_REP1_230927_CAGATC_S15

description: Library name: Sample 63

data_processing:
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human (Gencode GRCh38/hg38) genome using STAR (v2.7.5a; params --alignIntronMax 1 --alignEndsType EndToEnd --alignM atesGapMax 2000 for ChIPseq analysis), sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
ChIP-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75) and deeptools (pileup heatmaps). ChIPseq peaks were called using MACS2 with appropriate input samples used as controls.
TSS- and other interval-associated signals were assessed using bedtools coverage (v2.28.0).
Assembly: Gencode GRCh38/hg38
Supplementary files format and content: MACS2 called peaks (.xls format) or TSS locus signal (from bedtools; .txt format) and .tdf files (for visualization in Broad IGV)

extract_protocol:
First, cells were crosslinked with disuccinimidyl glutarate (DSG) by resuspending 20 million cells in 2 mL room-temperature PBS and adding 0.5 M DSG to a final concentration of 2 mM. The reaction was rocked at room temperature for 30 minutes, then quenched by pelleting the cells via centrifugation and washing twice with ice-cold PBS. Next, cells were resuspended in PBS and crosslinked with 2% formaldehyde for 8 minutes at room temperature with rocking. Formaldehyde was quenched by sequentially adding Tris-HCl (pH 8.0) to a final concentration of 100 mM, followed by glycine to a final concentration of 125 mM. Crosslinked cells were washed twice with PBS. Cells were then lysed by centrifuging for 15000 rpm for 10 minutes in SDS buffer containing 50 mM Tris-HCl (pH 8.0), 100 mM NaCl, 5 mM EDTA, and 1% SDS, supplemented with protease inhibitors. The opaque pellet was resuspended in cold IP buffer (1/3 Triton dilution buffer and 2/3 SDS buffer). Chromatin was sonicated using a Covaris sonicator, with optimized settings to shear DNA to fragments between 150–1000 bp. The sonicated chromatin was clarified by centrifugation at 15,000 x g for 10 minutes at room temperature. A small amount of the resulting input after sonication was de-crosslinked and quantified using Qubit, and immunoprecipitations (IPs) were normalized to equal amounts of DNA. Protein A Dynabeads were prepared by washing in ChIP dilution buffer and blocking with BSA. Antibodies specific to, manufacturer listed above, Menin (5 µg per IP), KMT2A (10 µg per IP) IKAROS (Cell signaling Technology, 14859, 5ug per IP), MEIS1 (5ug per IP) and UBR5 (10 µg per IP) were conjugated to the beads by incubation at 4°C overnight. For Menin, KMT2A, IKAROS, and MEIS1, 20-30 µg of sheared chromatin per sample was loaded into each IP. 50 ug of sheared chromatin was loaded for each UBR5 IP. The sheared chromatin was diluted 2X with ChIP dilution buffer, then incubated with the antibody-conjugated beads at 4°C overnight on a rotating platform. Beads were washed 6 times sequentially with 3 different buffers, 2X washes with Mixed Micelle Wash buffer (150 mM NaCl, 20 mM Tris-HCl pH 8.0, 5 mM EDTA, 5.2% Sucrose, 1.25% Triton X-100, 0.2% Sodium Dodecyl Sulfate), 2X washes with Buffer 500 (0.1% w/v deoxycholic acid, 1 mM EDTA, 50 mM Tris-HCl ph 8.0, 1% Triton X-100), and 2X washes with LiCl Detergent Wash Buffer (0.5% w/v deoxycholic acid, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 10 mM Tris-HCl ph=8) followed by two washes with 1× Tris-EDTA buffer (10 mM Tris pH 8.0, 1 mM EDTA). Chromatin was then eluted in elution buffer (50 mM Tris-HCl at pH 8.0, 10 mM EDTA, and 1% SDS). De-crosslinking of chromatin was performed overnight at 65°C in a buffer containing 100 mM NaHCO₃, 100 mM NaCl, and 1% SDS. DNA was purified using AMPureXP beads, following the manufacturer’s recommendations, with a 1.2X bead-to-sample ratio. DNA concentration was quantified using a Qubit fluorometer, and fragment size was verified using a Tapestation system. All buffers, including SDS buffer, Triton dilution buffer, and mixed micelle wash buffer, were prepared according to standard formulations detailed in the supplementary section.
ChIP and input DNA were processed for library preparation using the ThruPlex DNA-Seq kit (Takara Bio), employing single-index barcodes and 12–14 PCR cycles for amplification. Libraries were sequenced as paired-end reads (37 bp) on the NextSeq500 system (Illumina).

treatment_protocol: MV4;11 cells were plated at 2X10^5-5x10^5 cells/mL in the culture medium and were treated with DMSO, MI-3454 (50nM), SNDX-5613 (50nM), DS-1594 (50nM), JNJ-6617 (50 nM), KO-539 (50 nM) for 72h.

value: 72 hours

tag: chip target

tag: chip antibody

tag: antibody vendor

value: Bethyl

tag: antibody catalog_number

value: shUBR5 #2


title: MV411-shUBR5_F6_ChIP_MLL1_MI3454_50nM_72h_REP1_230927_ACTTGA_S16

description: Library name: Sample 64


title: ATAC_Monos_OMV-SIRP_rep3

value: OMV-SIRP


title: HS,fruit, 35d-1


title: MV411-shUBR5_F6_ChIP_MEN1_MI3454_50nM_72h_REP1_230927_CCGTCC_S24

description: Library name: Sample 62

value: Menin

value: Anti-Menin


title: MV411-shUBR5_F6_ChIP_input_MI3454_50nM_72h_REP1_230927_ATTCCT_S8

description: Library name: Sample 60

value: Input


title: ATAC_Monos_OMV-SIRP-G_rep1


title: HS,fruit, 30d-2


title: ATAC_Monos_OMV-SIRP-G_rep2


title: MV411-shUBR5_F6_ChIP_MEN1_DMSO_72h_REP1_230927_ATGTCA_S23

description: Library name: Sample 61

value: DMSO


title: MV411-shUBR5_B4_ChIP_MLL1_MI3454_50nM_72h_REP1_230927_GCCAAT_S14

description: Library name: Sample 58

value: shUBR5 #1


title: HS,fruit, 30d-1

value: fruit

value: HS


title: MV411-shUBR5_F6_ChIP_input_DMSO_72h_REP1_230927_ACTGAT_S7

description: Library name: Sample 59


title: MV411-shUBR5_B4_ChIP_MEN1_MI3454_50nM_72h_REP1_230927_AGTTCC_S22

description: Library name: Sample 56


title: MV411-shUBR5_B4_ChIP_MLL1_DMSO_72h_REP1_230927_ACAGTG_S13

description: Library name: Sample 57


title: ATAC_Monos_OMV-SIRP_rep2


title: ATAC_Monos_PBS_rep3

value: PBS


title: HS,fruit, 25d-3

value: 25 days


title: MV411-shUBR5_B4_ChIP_input_DMSO_72h_REP1_230927_CGTACG_S5

description: Library name: Sample 53


title: MV411-shLuc-2_RNA_DMSO_3d_REP2_240626_NANOVO_S26

description: Library name: Sample 2

value: 3 days


title: ATAC_Monos_PBS_rep2

value: bone marrow

value: bone marrow cells

value: WT


title: MV411-shUBR5_B4_ChIP_MEN1_DMSO_72h_REP1_230927_AGTCAA_S21

description: Library name: Sample 55

value: 72 hours


title: MV411-shUBR5_B4_ChIP_input_MI3454_50nM_72h_REP1_230927_GAGTGG_S6

description: Library name: Sample 54


title: HS,fruit, 25d-1


title: MV411-shLuc-2_ChIP_MLL1_DMSO_72h_REP1_230927_TTAGGC_S11

description: Library name: Sample 51

value: Bethyl

value: shLuc #2


title: ATAC_Monos_PBS_rep1


title: MV411-shLuc-2_ChIP_MEN1_MI3454_50nM_72h_REP1_230927_CTTGTA_S20

description: Library name: Sample 50


title: MV411-shLuc-2_ChIP_MEN1_DMSO_72h_REP1_230927_GGCTAC_S19

description: Library name: Sample 49


title: HS,fruit, 15d-2

value: 15 days


title: ATAC_GMPs_OMV-SIRP-G_rep3

value: OMV-SIRP-G


title: MV411-shLuc-2_ChIP_input_MI3454_50nM_72h_REP1_230927_GTTTCG_S4

description: Library name: Sample 48


title: MV411-shLuc-2_ChIP_input_DMSO_72h_REP1_230927_GTGGCC_S3

description: Library name: Sample 47


title: HS,fruit, 15d-3


title: ATAC_Monos_OMV-SIRP_rep1

value: OMV-SIRP


title: ATAC_GMPs_OMV-SIRP-G_rep2


title: ATAC_GMPs_OMV-SIRP-G_rep1


title: MV411-shLuc-1_ChIP_MLL1_DMSO_72h_REP1_230927_ATCACG_S9

description: Library name: Sample 45

value: shLuc #1


title: MV411-shLuc-1_ChIP_MLL1_MI3454_50nM_72h_REP1_230927_CGATGT_S10

description: Library name: Sample 46


title: HS,fruit, 15d-1


title: MV411-shLuc-1_ChIP_MEN1_DMSO_72h_REP1_230927_GATCAG_S17

description: Library name: Sample 43

value: DMSO

value: Menin

value: Anti-Menin


title: ATAC_GMPs_OMV-SIRP_rep3


title: CRACUPF1, plus UV, replicate 3

city: Paris

first: Gwenael

last: Badis

address: 46 rue d'Ulm

department: Genomique fonctionnelle (Section 2)

country: France

institute: IBENS

description:
Library name: CRACUPF1_plus_R3
SR75

data_processing:
demultiplexing using Flexbar
Mapping to the SC288 reference genome Saccer3.fa using STAR standard configuration with option  --alignIntronMax 1500 --alignMatesGapMax 1500 --alignSJoverhangMin 25
Assembly: Saccer3.fa
Supplementary files format and content: wig files contain the profile of each experiment (strand 1 and strand 2 per replicate)
Supplementary files format and content: Fastq files contains the raw data sequences after demultiplexing.

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: 30°C in YPD, exponential phase (OD 600=0,7)

extract_protocol:
Double Immunoprecipitation (Protein A, TEV elution then Nickel), Denaturing SDS page, Transfer on nitrocellulose, Proteinase K elution, Phenol Chloroform extraction.
CRAC (Illumina)

treatment_protocol: Immunoprecipitiation of the HIS6 tag after eventual UV crosslink (CRAC +UV vs -UV)

value: yeast

value: MATa, ura3 delta 0, his3 delta 1, leu2 delta 0, met15 delta 0, UPF1(YMR080W)-HTP:URA3MX6

tag: batch

value: November 2015


title: HS,fruit, 25d-2

value: fruit

tag: cultivar

value: HS

value: 25 days


title: CRACUPF1, plus UV, replicate 2

description:
Library name: CRACUPF1_plus_R2
SR75

tag: tissue


title: MV411-shLuc-1_ChIP_input_DMSO_72h_REP1_230927_GTCCGC_S1

description: Library name: Sample 41

value: Input


title: MV411-shLuc-1_ChIP_input_MI3454_50nM_72h_REP1_230927_GTGAAA_S2

description: Library name: Sample 42

value: 72 hours


title: CRACUPF1, plus UV, replicate 1

description:
Library name: CRACUPF1_plus_R1
SR75

tag: cell line


title: MV411-sgUBR5_ChIP_MEN1_MI3454_50nM_72h_REP1_220916_GTGAAA_S8

description: Library name: Sample 39

tag: cell type

value: Bethyl

tag: sgrna


title: MV411-sgUBR5_ChIP_MEN1_MI3454_50nM_72h_REP1_221219_GTGAAA_S8

description: Library name: Sample 40

tag: treatment


title: MV411-shLuc-2_ChIP_MLL1_MI3454_50nM_72h_REP1_230927_TGACCA_S12

description: Library name: Sample 52

value: shLuc #2


title: MV411-shLuc-1_ChIP_MEN1_MI3454_50nM_72h_REP1_230927_TAGCTT_S18

description: Library name: Sample 44


title: ATAC_GMPs_OMV-SIRP_rep1

value: bone marrow

value: bone marrow cells

tag: genotype

value: WT


title: ATAC_GMPs_OMV-SIRP_rep2

value: OMV-SIRP


title: MV411-sgUBR5_ChIP_MEN1_DMSO_72h_REP1_221219_GTCCGC_S7

description: Library name: Sample 38

value: DMSO

tag: timepoint


title: CRACUPF1, minus UV, replicate 3

description:
Library name: CRACUPF1_minus_R3
SR75


title: MV411-sgUBR5_ChIP_input_MI3454_50nM_72h_REP1_220916_AGTTCC_S4

description: Library name: Sample 36


title: ATAC_GMPs_PBS_rep3

value: PBS


title: CRACUPF1, minus UV, replicate 2

description:
Library name: CRACUPF1_minus_R2
SR75


title: ATAC_GMPs_PBS_rep2


title: MV411-sgLuc_ChIP_MEN1_MI3454_50nM_72h_REP1_221219_CCGTCC_S6

description: Library name: Sample 33

value: Menin

value: Anti-Menin

value: sgLuc


title: MV411-sgUBR5_ChIP_input_DMSO_72h_REP1_220916_AGTCAA_S3

description: Library name: Sample 35


title: MV411-sgUBR5_ChIP_MEN1_DMSO_72h_REP1_220916_GTCCGC_S7

description: Library name: Sample 37


title: MV411-sgLuc_ChIP_UBR5_DMSO_72h_REP1_221219_GTGGCC_S1

description: Library name: Sample 34

value: Steady state

value: CST


title: LSECs; Hb-injected mouse, rep. 4

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

description: 55vivo HB8

data_processing:
The raw reads were processed with Ion Torrent RNASEQAnalysis pipeline (Torrent Suite version 5.0.4)
htseq-count, version 0.6.0, default parameters
DESeq2, version 1.18.1, normalization
Assembly: AmpliSeq Mouse Transcriptome v1
Supplementary files format and content: htseq normalized count

extract_protocol:
RNA from sorted LSECs was extracted using TRIzol™ LS Reagent (ThermoScientific, #10296028) according to the manufacturer’s instructions with an additional step of RNA precipitation with glycogen (ThermoScientific, #R0551).
Library was prepared using Ion AmpliSeq™ Transcriptome Mouse Gene Expression Kit according to the manufacturer’s protocol (Thermo Fisher Scientific)

tag: strain

value: Balb/c

tag: gender

value: female

value: Liver

value: LSECs

value: FACS-sorted LSECs (CD45-dim, STAB2-high, CD146-high)

value: wild type

value: intravenous injection with Hb (10 mg) for 5 hours


title: MV411-sgLuc_ChIP_MEN1_MI3454_50nM_72h_REP1_220916_CCGTCC_S6

description: Library name: Sample 32

value: 72 hours

value: Bethyl


title: MV411-sgLuc_ChIP_MEN1_DMSO_72h_REP1_220916_ATGTCA_S5

description: Library name: Sample 30


title: MV411-sgLuc_ChIP_MEN1_DMSO_72h_REP1_221219_ATGTCA_S5

description: Library name: Sample 31


title: RNA_Monos_OMV-SIRP-G_rep3

data_processing:
Quality control, raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reads mapping to the reference genome,paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Novel transcripts prediction were assembled by StringTie and quantification of gene expression level were obtained using featureCounts v1.5.0-p3.
Differential expression analysis
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using TRIzol and RNA integrity was assessed using the RNA Nano 6000 Assay Kit.
RNA libraries for RNA-seq were prepared using NEBNext mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: bone marrow

value: bone marrow cells

value: WT

value: OMV-SIRP-G


title: MV411-sgLuc_ChIP_input_MI3454_50nM_72h_REP1_220916_CTTGTA_S2

description: Library name: Sample 29

value: Input


title: RNA_Monos_OMV-SIRP-G_rep2


title: LSECs; Hb-injected mouse, rep. 3

description: 55vivo HB7


title: MV411-sgLuc_ChIP_input_DMSO_72h_REP1_220916_GGCTAC_S1

description: Library name: Sample 28

value: DMSO

value: sgLuc


title: LSECs; Hb-injected mouse, rep. 2

description: 55vivo HB6


title: MV411_ChIP_MLL1_JNJ_50nM_72h_REP1_230913_TTAGGC_S3

description: Library name: Sample 25


title: RNA_Monos_OMV-SIRP_rep3

value: OMV-SIRP


title: LSECs; Hb-injected mouse, rep. 1

description: 55vivo HB5

value: Balb/c


title: MV411_ChIP_MLL1_KO539_50nM_72h_REP1_230913_CGATGT_S2

description: Library name: Sample 26


title: MV411_ChIP_MLL1_SNDX_50nM_72h_REP1_230913_TGACCA_S4

description: Library name: Sample 27


title: RNA_Monos_OMV-SIRP-G_rep1


title: LSECs; PBS-injected mouse, rep. 4

value: female

value: intravenous injection with PBS for 5 hours


title: MV411_ChIP_MLL1_DS1594b_50nM_72h_REP1_230913_GCCAAT_S5

description: Library name: Sample 24


title: ATAC_GMPs_PBS_rep1

value: PBS


title: CRACUPF1, minus UV, replicate 1

description:
Library name: CRACUPF1_minus_R1
SR75

value: yeast

value: MATa, ura3 delta 0, his3 delta 1, leu2 delta 0, met15 delta 0, UPF1(YMR080W)-HTP:URA3MX6

value: November 2015


title: LSECs; PBS-injected mouse, rep. 3

value: Liver

value: LSECs

value: FACS-sorted LSECs (CD45-dim, STAB2-high, CD146-high)

value: wild type


title: MV411_ChIP_MEN1_SNDX_50nM_72h_REP1_230913_CTTGTA_S9

description: Library name: Sample 22

value: 72 hours

value: Menin

value: Anti-Menin

value: Bethyl


title: MV411_ChIP_MEN1_KO539_50nM_72h_REP1_230913_ACTTGA_S7

description: Library name: Sample 21


title: RNA_Monos_OMV-SIRP_rep1

value: bone marrow

value: bone marrow cells

value: WT


title: RNA_Monos_PBS_rep3


title: LSECs; PBS-injected mouse, rep. 2

value: Balb/c

value: female


title: MV411_ChIP_MEN1_DS1594b_50nM_72h_REP1_230913_ATGTCA_S10

description: Library name: Sample 19


title: MV411_ChIP_MEN1_JNJ_50nM_72h_REP1_230913_GATCAG_S8

description: Library name: Sample 20


title: LSECs; PBS-injected mouse, rep. 1

value: intravenous injection with PBS for 5 hours


title: MV411_ChIP_input_untreated_DSG_REP1_210129_ATCACG_S1

description: Library name: Sample 16

value: Steady state

value: Input


title: MV411_ChIP_input_SNDX_50nM_72h_REP1_230913_CGTACG_S14

description: Library name: Sample 15


title: RNA_Monos_PBS_rep1

value: PBS


title: MV411_ChIP_input_KO539_50nM_72h_REP1_230913_GTGGCC_S12

description: Library name: Sample 14


title: MV411_ChIP_MLL1_DMSO_72h_REP1_230913_ATCACG_S1

description: Library name: Sample 23

value: DMSO


title: Norm2 iPSC-pericytes

city: Los Angeles

first: Ruslan

last: Rust

state: CA

address: 1501 San Pablo Street

institute: University of Southern California

description:
Library name: Sample4
Pericytes cultured in normoxia 2

data_processing:
Raw reads were quality-checked with FastQC and trimmed using Trimmomatic.
Reads were aligned to the GRCh38 human genome using STAR.
Gene counts were generated with featureCounts.
Assembly: GRCh38
Supplementary files format and content: csv counts

source_name: iPSC-pericytes

growth_protocol: iPSC-derived pericytes were cultured on Matrigel-coated plates in defined pericyte medium under standard conditions until confluence.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit with on-column DNase digestion.
Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit and sequenced on an Illumina platform

treatment_protocol: Cells were exposed to normoxia (21% O₂) or severe hypoxia (0.2% O₂) for 48 hours prior to RNA collection.

value: iPSC-pericytes

value: pericytes

value: normoxia


title: RNA_GMPs_OMV-SIRP-G_rep3

value: OMV-SIRP-G


title: Norm1 iPSC-pericytes

description:
Library name: Sample3
Pericytes cultured in normoxia 1


title: Hyp2 iPSC-pericytes

description:
Library name: Sample2
Pericytes cultured in hypoxia 2

value: hypoxia


title: MV411_ChIP_input_JNJ_50nM_72h_REP1_230913_GTTTCG_S13

description: Library name: Sample 13

value: 72 hours


title: RNA_Monos_OMV-SIRP_rep2

value: OMV-SIRP


title: RNA_GMPs_OMV-SIRP-G_rep2

value: bone marrow


title: MV411_ChIP_input_DMSO_72h_REP1_230913_GTGAAA_S11

description: Library name: Sample 11


title: Hyp1 iPSC-pericytes

description:
Library name: Sample1
Pericytes cultured in hypoxia 1


title: MV411_ChIP_IKZF1_untreated_DSG_REP1_210129_CGATGT_S2

description: Library name: Sample 10

value: anti-IKAROS

value: CST


title: MV411_ChIP_input_DS1594b_50nM_72h_REP1_230913_GAGTGG_S15

description: Library name: Sample 12


title: RNA_GMPs_OMV-SIRP-G_rep1

value: bone marrow cells

value: WT


title: MV411_ChBID_ZNF692_steadystate_REP1_200907_GAGTGG_S2

description: Library name: Sample 9

value: Biotin

value: Dynabeads™ MyOne™ Streptavidin T1

value: Invitrogen


title: adr-2(-) germlines rep3

city: BLOOMINGTON

first: Emily

middle: Ann

last: Erdmann

state: IN

address: 1001 E Third Street

department: Biology

institute: Indiana University

description: Library name: Sample6_GSF3037

data_processing:
Reads were aligned to C. elegans reference genome using STAR (v.2.7.10b)
Differential gene expression analysis was performed using Feature counts and DeSeq2
A-to-I editing site identification was performed using SAILOR
Assembly: C. elegans WS275
Supplementary files format and content: diff_exp.csv files include DeSeq2 analysis with normalized read counts. sites.csv files include SAILOR A-to-I editing site analysis.

organism: Caenorhabditis elegans

source_name: germline

extract_protocol:
Worms were collected in Trizol (Invitogen) and purified using TURBO Dnase(Ambion) followed by Rneasy extraction kit (Qiagen)
Poly-A selected mRNA library preparation was done using KAPA stranded library preparation kit

value: germline


title: MV411_ChBID_NRF1_steadystate_REP1_200907_CGTACG_S1

description: Library name: Sample 8

value: Steady state


title: MV411_ChBID_MEN1_steadystate_REP1_200907_ACTGAT_S3

description: Library name: Sample 7


title: RNA_GMPs_OMV-SIRP_rep3


title: MV411_ChIP_MEN1_DMSO_72h_REP1_230913_CAGATC_S6

description: Library name: Sample 18

value: DMSO

value: Menin

value: Anti-Menin

value: Bethyl


title: adr-2(-) germlines rep2

description: Library name: Sample5_GSF3037


title: RNA_GMPs_OMV-SIRP_rep2


title: RNA_Monos_PBS_rep2

value: PBS


title: MV411_ChIP_MEIS1_untreated_DSG_REP1_210129_GCCAAT_S6

description: Library name: Sample 17

value: Abcam


title: MV411_ChBID_input_untreated_REP1_200717_GTCCGC_S7

description: Library name: Sample 4

value: Input


title: adr-2(-) germlines rep1

description: Library name: Sample4_GSF3037


title: MV411_ChBID_input_steadystate_REP1_200907_ATTCCT_S4

description: Library name: Sample 3


title: RNA_GMPs_OMV-SIRP_rep1

value: bone marrow

value: OMV-SIRP


title: N2 germlines rep3

description: Library name: Sample3_GSF3037

value: wildtype


title: MV411_ChBID_IKZF1_untreated_REP1_200717_AGTCAA_S3

description: Library name: Sample 2


title: RNA_GMPs_PBS_rep3

value: bone marrow cells


title: N2 germlines rep2

description: Library name: Sample2_GSF3037


title: patient_I3__bb21217 CAR T cells__DoseCohort_450x10^6 cells

city: Seattle

first: Daniel

last: Zak

state: WA

address: 188 East Blaine Street, Suite 300

institute: Regeneron

description:
Library name: I3
75bp PE

data_processing:
Sequences were aligned to the human genome using STAR aligner (Dobin et al., 2013).
Gene features were only determined for uniquely mapped reads and these were annotated with the GENCODE version 29 gene transfer format (gtf) file using RNA-Seq by Expectation Maximization (RSEM) (Li & Dewey, 2011). For each gene feature, RSEM provides read counts and transcripts per million reads.
Assembly: human genome: GRCh38, GENCODE version 29; gene annotations: GENCODE version 29 gene transfer format (gtf) file.
Supplementary files format and content: Three processed data files include comma-delimited text files that contain (1) RSEM TPMs, (2) RSEM expected counts, and (3) batch corrected RSEM expected counts for each sample.  The batch corrected counts were used in the WGCNA analyses.

source_name: autologous CAR T cells manufactured from PBMCs obtained from leukapheresis

growth_protocol: bb21217 Drug Product (DP) was manufactured by transducing autologous T cells with an anti-BCMA02 CAR lentiviral vector as described by Friedman et al. and culturing in the presence of bb007.    DP T cells were otherwise untreated.

extract_protocol:
Total RNA was isolated using the Qiagen 96-well RNeasy Prep Kit.
RNA was extracted from each sample containing 1–2 × 106 cells and quality was assessed using the Agilent 2200 TapeStation system with High Sensitivity RNA ScreenTape Assay (Agilent, Santa Clara, CA). Samples with at least 5 ng/μL of RNA and an RNA integrity number score >7 were used in the library preparation following the exact protocol in the Kapa RNA HyperPrep Kit with RiboErase (Roche, Pleasanton, CA). Final libraries with a concentration greater than 4 nM and an average fragment size between 300 and 500 bases were pooled in equimolar ratio and volume to make a final sample of 4 nM.
The pooled library was sequenced on a NextSeq 500/550 sequencer (Illumina, San Diego, CA) using a High Output Kit providing 150 cycles with 75 base pair paired-end reads to a minimum depth of 20 million reads per sample.

tag: disease state

value: relapsed/refractory multiple myeloma

value: bb21217 CAR T cells

tag: transgene

value: anti-BCMA02 CAR

value: manufactured by transducing autologous T cells with an anti-BCMA02 CAR lentiviral vector as described by Friedman et al. (2018) and culturing in the presence of bb007

tag: dose cohort

tag: randomized id


title: RNA_GMPs_PBS_rep1

value: WT


title: N2 germlines rep1

description: Library name: Sample1_GSF3037

value: germline


title: patient_T5__bb21217 CAR T cells__DoseCohort_300x10^6 cells

description:
Library name: T5
75bp PE

value: autologous CAR T cells manufactured from PBMCs obtained from leukapheresis


title: RNA_GMPs_PBS_rep2


title: patient_I1__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: I1
75bp PE


title: MV411_ChBID_IKZF1_untreated_DSG_REP1_200717_AGTTCC_S4

description: Library name: Sample 1

value: Steady state

tag: chip target

value: Biotin

tag: chip antibody

value: Dynabeads™ MyOne™ Streptavidin T1

tag: antibody vendor

value: Invitrogen


title: patient_Q3__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: Q3
75bp PE


title: patient_U1__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: U1
75bp PE


title: MCF7_WT_E2_INPUT

city: Amsterdam

first: Wilbert

last: Zwart

state: Noord-Holland

address: Plesmanlaan 121

department: Oncogenomics

institute: Netherlands Cancer Institute

description: Library name: U8

data_processing:
Reads were aligned to the human genome build Hg38/GRCh38 using BWA
Reads with a mapping quality (MAPQ) < 20 were removed from further analysis and duplicates were marked by PICARD/GATK markDuplicates
Enrichment over input control was determined using MACS2 (q < 0.001, narrowPeak mode). Only peaks not overlapping with the ENCODE hg38/GRCh38 blacklisted regions, were retained.
BigWigs have been generated using bamCoverage from Deeptools using reads extension, RPGC normalization and a average bin of 50bp.
Assembly: hg38/GRCh38
Supplementary files format and content: .bed, narrowPeaks
Supplementary files format and content: .bw, bigWigs

source_name: Breast cancer

growth_protocol: MCF7 cells have been cultured in DMEM (no phenol-red) + 5% DCC+ 1% Pen/Strep, at 5% CO2 and 37°C.

extract_protocol:
Chromatin immunoprecipitation followed by sequencing (ChIP)-seq was performed as previously described (Schmidt, D. et al. Methods 48, 240–248 (2009). In brief, cells were fixed in 1% formaldehyde for 10 min and quenched with 0.125M glycine. Nuclear lysates were extracted as previously described and sonicated for 15 cycles (30 sec on/30 sec off) using the Bioruptor® Pico (B01060001, Diagenode). Per ChIP, 50 µL of magnetic Protein A beads (10008D, Thermo Fisher Scientific) were conjugated to 5µg TRIM24 antibody.
Illumina

treatment_protocol: After three days in DCC media, cells were treated either with DMSO or 10nM E2, for 3 hours.

value: Breast cancer

value: DCC + E2 (10nM)


title: MV411_ChBID_MEIS1_untreated_REP1_200717_GGCTAC_S1

description: Library name: Sample 6

tag: antibody catalog_number


title: MV411_ChBID_MEIS1_untreated_DSG_REP1_200717_CTTGTA_S2

description: Library name: Sample 5


title: patient_G8__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: G8
75bp PE

tag: tissue


title: patient_A8__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: A8
75bp PE


title: patient_R7__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: R7
75bp PE


title: RNA_MC38_OMV-SIRP-G_rep2

source_name: tumor

value: tumor

value: tumor-associated macrophages

value: OMV-SIRP-G


title: RNA_MC38_OMV-SIRP-G_rep3


title: MCF7_WT_E2_TRIM24_rep3

description: Library name: U6

tag: cell line

value: TRIM24 (NB100-2596, NovusBio)


title: patient_G0__bb21217 CAR T cells__DoseCohort_300x10^6 cells

description:
Library name: G0
75bp PE

value: relapsed/refractory multiple myeloma

tag: cell type


title: RNA_MC38_OMV-SIRP-G_rep1


title: patient_B8__bb21217 CAR T cells__DoseCohort_150x10^6 cells

description:
Library name: B8
75bp PE

value: bb21217 CAR T cells


title: MCF7_WT_E2_TRIM24_rep2

description: Library name: U5


title: patient_S2__bb21217 CAR T cells__DoseCohort_150x10^6 cells

description:
Library name: S2
75bp PE

value: anti-BCMA02 CAR


title: RNA_MC38_OMV-SIRP_rep3

value: OMV-SIRP


title: patient_F8__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: F8
75bp PE

value: manufactured by transducing autologous T cells with an anti-BCMA02 CAR lentiviral vector as described by Friedman et al. (2018) and culturing in the presence of bb007


title: RNA_MC38_OMV-SIRP_rep2

value: WT


title: MCF7_WT_E2_TRIM24_rep1

description: Library name: U4


title: patient_L6__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: L6
75bp PE

value: autologous CAR T cells manufactured from PBMCs obtained from leukapheresis


title: patient_X6__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: X6
75bp PE


title: MCF7_WT_DMSO_TRIM24_rep3

description: Library name: U3

value: DCC + DMSO


title: patient_N2__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: N2
75bp PE


title: RNA_MC38_OMV-SIRP_rep1


title: patient_O6__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: O6
75bp PE


title: RNA_MC38_PBS_rep3

value: PBS


title: MCF7_WT_DMSO_TRIM24_rep2

description: Library name: U2


title: RNA_MC38_PBS_rep2


title: MCF7_WT_DMSO_INPUT

description: Library name: U7


title: patient_B7__bb21217 CAR T cells__DoseCohort_300x10^6 cells

description:
Library name: B7
75bp PE


title: MCF7_WT_DMSO_TRIM24_rep1

description: Library name: U1


title: patient_C0__bb21217 CAR T cells__DoseCohort_300x10^6 cells

description:
Library name: C0
75bp PE


title: patient_C7__bb21217 CAR T cells__DoseCohort_300x10^6 cells

description:
Library name: C7
75bp PE


title: patient_X4__bb21217 CAR T cells__DoseCohort_300x10^6 cells

description:
Library name: X4
75bp PE


title: patient_Q9__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: Q9
75bp PE


title: RNA_MC38_PBS_rep1


title: patient_T3__bb21217 CAR T cells__DoseCohort_150x10^6 cells

description:
Library name: T3
75bp PE


title: RNA_B16_F10_OMV-SIRP-G_rep3


title: patient_A7__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: A7
75bp PE


title: RNA_B16_F10_OMV-SIRP-G_rep2


title: patient_C3__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: C3
75bp PE


title: patient_G9__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: G9
75bp PE


title: RNA_B16_F10_OMV-SIRP-G_rep1


title: patient_O0__bb21217 CAR T cells__DoseCohort_300x10^6 cells

description:
Library name: O0
75bp PE


title: patient_E5__bb21217 CAR T cells__DoseCohort_300x10^6 cells

description:
Library name: E5
75bp PE


title: RNA_B16_F10_OMV-SIRP_rep3


title: patient_L0__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: L0
75bp PE


title: patient_C6__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: C6
75bp PE


title: patient_K1__bb21217 CAR T cells__DoseCohort_150x10^6 cells

description:
Library name: K1
75bp PE


title: patient_M7__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: M7
75bp PE


title: patient_D2__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: D2
75bp PE


title: RNA_B16_F10_OMV-SIRP_rep2


title: patient_S1__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: S1
75bp PE


title: RNA_B16_F10_OMV-SIRP_rep1


title: patient_Q4__bb21217 CAR T cells__DoseCohort_300x10^6 cells

description:
Library name: Q4
75bp PE


title: patient_H1__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: H1
75bp PE


title: patient_K2__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: K2
75bp PE


title: RNA_B16_F10_PBS_rep2


title: patient_N7__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: N7
75bp PE


title: RNA_B16_F10_PBS_rep3


title: patient_K3__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: K3
75bp PE


title: patient_W6__bb21217 CAR T cells__DoseCohort_150x10^6 cells

description:
Library name: W6
75bp PE


title: patient_J8__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: J8
75bp PE


title: patient_J9__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: J9
75bp PE


title: patient_U6__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: U6
75bp PE


title: patient_E0__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: E0
75bp PE


title: P19, shCtrl, No antibody

city: Jinan

first: Yongze

last: Yu

email: lwyyzsdu@163.com, lwyyzsdu@hotmail.com

state: Shandong

address: 文化西路44号国家辅助生殖与优生工程技术研究中心

institute: Shandong University

data_processing:
library strategy:CUT&Tag
The library preparations were sequenced on Illumina Novaseq platform at Novogene Science and Technology Co., Ltd (Beijing, China) and 150bp paired-end reads were generated
The read sequences produced by the Illumina pipeline in FASTQ format were pre-processed through Trimmomatic software, and all low-quality reads and PCR adapters were removed
CUT&Tag reads were aligned to the UCSC mm10 genome using Bowtie v0.7.12.
All peak calling was performed with MACS2 v2.1.2 using ‘macs2 -q 0.05 --call-summits --nomodel --shift -100 --extsize 200 --keep-dupall’.
bigWig files were generated using the genomicRanges R package. narrowPeak files were generated using MACS v2.1.2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: embryo

growth_protocol: α-MEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
The genome DNA were extracted by the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, China; TD903).
CUT&Tag libraries were prepared using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme Biotech, China; TD903). Libraries were amplified using 11 cycles on the thermocycler. Libraries were purified with the AMPure beads and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: embryo

value: Mouse embryo carcinoma

value: Wild-type

value: Knockdown with control adenovirus, no primary antibody used


title: patient_H7__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: H7
75bp PE


title: patient_X8__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: X8
75bp PE


title: patient_B2__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: B2
75bp PE


title: P19, shUbe2t #1, S9.6

address: 文化西路44号国家辅助生殖与优生工程技术研究中心

value: Ube2t knockdown

value: Knockdown with shUbe2t #1 adenovirus, S9.6 antibody used


title: P19, shCtrl, S9.6

address: 文化西路44号国家辅助生殖与优生工程技术研究中心

value: Knockdown with control adenovirus, S9.6 antibody used


title: MDA-MB-231/tet-off/EV clone H3_biol_rep_4

city: Baltimore

first: Julia

middle: L

last: Rutherford

address: 108 N Greene St

institute: University of Maryland, Baltimore

description: Library name: TTP-H3-4

data_processing:
Data was processed by Azenta Biosciences according to established protocols.
Sequenced reads were trimmed using Trimmomatic v.0.36.
Trimmed reads were mapped to the Homo sapiens GRCh38 reference genome using STAR aligner v.2.5.2b.
Unique gene hit counts were calculated using featureCounts from the Subread package v.1.5.2.
Differential expression analysis was performed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: csv file including ENSEMBL ID, gene symbol, log2(fold change) values, p-values, adjusted p-values, and raw counts

growth_protocol: All cells were maintained in DMEM, 10% FBS, 100 IU/mL pencillin, 100 ug/mL streptomycin, 400 ug/mL G418 sulfate, and 100 ug/mL Hygromycin B. 2 ug/mL doxycycline was added to cells expressing TTP.

extract_protocol:
RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel)
Libraries were constructed by Azenta Biosciences using the NEBNext Ultra II RNA library preparation kit.

treatment_protocol: Before experiements, selection agents and doxycycline were washed out for at least 24 hours to allow expression of TTP.

value: TNBC cell line


title: patient_P0__bb21217 CAR T cells__DoseCohort_450x10^6 cells

description:
Library name: P0
75bp PE

value: relapsed/refractory multiple myeloma


title: ST8814 cell line, 10nM trametinib 48h, replicate 3

city: Select

first: Angelina

middle: V.

last: Vaseva

state: Oregon

address: Pediatrics

institute: Oregon Health Science University

description:
Library name: GSM250722036
T3_ST

data_processing:
Trim Galore was applied to raw sequencing data to remove the adapter and poor-quality reads.
STAR were used to align DNA and RNA sequencing data to the reference genome.
To remove mouse-derived reads in PDXs, we mapped the sequencing data to the human (GRCh38, GENCODE v29) and mouse (GRCm38, GENCODE vM19) reference genomes. Disambiguate was then employed on the BAM files to remove mouse reads. RSEM5 was applied to calculate raw read counts.
Assembly: GRCh38
Supplementary files format and content: Expression Matrix, in TPM

growth_protocol: cells were plated in tissue culture dishes in RPMI medium supplemented with 10% FBS

extract_protocol:
RNA was isolated using RNeasy Mini Kit (QIAGEN). The quality of Total RNA was checked by Agilent Fragment Analyzer (Agilent Technologies, Santa Clara, CA), and only high-quality RNA samples (RQN >7) were used for mRNA-seq library preparation and sequencing.
Following the Illumina TruSeq stranded mRNA sample preparation guide, we used approximately 500ng Total RNA for RNA-seq library preparation. fter RNA-seq libraries were quantified, they were pooled and subsequently loaded for 101bp paired read sequencing run on the Illumina NovaSeq 6000 platform.

treatment_protocol: Treatment was done the next next day after plating. Cells were treated with either 250 nM LXH254, 10 nM trametinib, or 250 nM LXH254 + 10 nM trametinib for 48 hours. Each treatment was done in triplicate. Three MPNST cell lines were used: ST8814, S462, and NF90.8

value: MPNST

value: 10 nM trametinib 48h