title: MOLM13 RNA-seq 24h Quizartinib replicate 2

description: RNA-seq


title: Primary AML Sample 2555 24h Combination replicate 2

status: Public on Mar 21 2024

type: SRA

city: Portland

first: William

middle: Montgomery

last: Yashar

state: OR

address: 3181 SW Sam Jackson Park Rd

department: Knight Cancer Institute

country: USA

institute: OHSU

description: RNA-seq

library_source: transcriptomic

data_processing:
Raw reads were trimmed with Trimmomatic and aligned with STAR
Differential expression analysis was performed using DESeq2
Genome_build: hg38

molecule: total RNA

organism: Homo sapiens

extract_protocol:
Total RNA was isolated using a RNeasy Plus Mini Kit (Qiagen)
The OHSU Massively Parallel Sequencing Shared Resource (MPSSR) performed the sequencing at 100 BP single end

tag: cell type

value: primary AML blasts

tag: treatment

value: 500 nM quizartinib + 500 nM GSK2879552

tag: time point

value: 24 hours

tag: antibody


title: p300KD 2

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

description: p300KD Astrocytes

data_processing:
The raw sequences are aligned to the GRCm38 reference genome and quantified using kallisto.
Assembly: GRCm38
Supplementary files format and content: tar gzipped kallisto quantification output.

organism: Mus musculus

source_name: p300KD Astrocytes

growth_protocol: Mice. C57BL/6J mice (The Jackson Laboratory, 000664) were used as a genetic background for all in vivo experiments. Mice were housed in a conventional, pathogen-free facility at the Hale Building for Transformative Medicine under a standard 12h light/dark cycle at 20–23°C and 50% humidity with access to water and food ad libitum, in accordance with guidelines for care and experimentation defined by the Institutional Animal Care and Use Committee (IACUC). Transgenic mouse genotypes were confirmed by PCR (Transnetyx). When Aldh1l1Cre-ERT2/TdTomato astrocyte reporter mice (The Jackson Laboratory, #031008 and #007909) were used, 200mg/kg Tamoxifen (Sigma-Aldrich, T5648) diluted in corn oil (Sigma-Aldrich, C8267) was administered intraperitoneally 2-4 weeks before starting the experiment and TdTomato induction was confirmed by flow cytometry at the time of measurement.

extract_protocol:
Sorted cells were lysed and RNA isolated using the Qiagen RNeasy Micro kit (Qiagen, #74004) with on-column DNase I digestion (Qiagen, #79254). RNA was suspended in 10 µL of nuclease free water at 0.5-1 ng/µL and sequenced using SMARTSeq279 at the Broad Institute Technology Labs and the Broad Genomics Platform. Processed RNA-seq data was filtered by removing genes with low read counts. Read counts were normalized using TMM normalization and CPM (counts per million) were calculated to create a matrix of normalized expression values. The fastq files of each RNA-seq data sample were aligned to the Mus musculus GRCm38 transcriptome using Kallisto (v0.46.1), and the same software was used to quantify the alignment results. Differential expression analysis was conducted using DESeq2, and the log2 fold change was adjusted using apeGLM for downstream analysis.
Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al 2014).

tag: strain

tag: Sex

value: Female


title: MLVQ16

city: ILLKIRCH

first: Delphine

last: Duteil

address: 1 rue Laurent Fries

country: France

institute: IGBMC

description: GR 24h starved

library_source: genomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Assembly: mm10

molecule: genomic DNA

source_name: Chromatin extrated after immunoprecipitation with various antibodies.

extract_protocol:
P2727
P2727 AND 2731: ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 2-20 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.  , P2731 : ChIP samples were purified using SPRIselect beads (Beckman-Coulter, Villepinte, France) and quantified using the Qubit 4 fluorimeter (Thermo Fischer Scientific, Illkirch, France). ChIP-seq libraries were prepared from 1-10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v3 (C05010001, Diagenode, Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using SPRIselect beads (Beckman Coulter) to remove unincorporated primers and other reagents.

tag: tissue

value: Skeletal muscle

tag: age

value: 10 weeks


title: Primary AML Sample 2555 24h Combination replicate 1

description: RNA-seq


title: Day12 daf-2 mutant feed with E. coli OP50

city: Ashburn

first: Shihong

middle: Max

last: Gao

address: 19700 Helix Dr

institute: Janelia Research Campus

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
We used Cell ranger (6.0, 10x Genomics) to align Raw base call (BCL) sequence files or FASTQ files to the C. elegans genome (WS282, Wormbase), and generated feature-barcode matrices. Doublets were removed based on the recommended ratio provided by the 10X Genomics Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 user guide (CG000204 Rev D), with a score calculated by Doubletfinder (Github/chris-mcginnis-ucsf). The feature-barcode matrices for each sample were constructed into a Seurat (R package, 4.0.5) object for downstream analysis. Cells were filtered by requiring a minimum of 100 genes to be expressed, and genes were filtered by being expressed in at least 3 cells. Integration of samples was performed with Seurat canonical correlation analysis (CCA) method to remove the batch effects. We tested CCA, reciprocal principal component analysis (PCA) and Harmony (0.1) for integration and chose the method with the best performance. The top 2,000 variable features were used for integration anchor identification. UMAP and tSNE dimension reduction were performed with the first 50 dimensions from PCA. Clustering was performed at multiple Leiden resolutions.
Assembly: WS282
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

organism: Caenorhabditis elegans

source_name: whole body

extract_protocol:
Worms were washed three times with PBS and collected in a 1.5 mL tube. We then added 100 μl of homogenization buffer {10.1126/science.abk2432} and grind the worms with a pestle motor for 30 seconds on ice. To minimize nuclei adhesion on the surface, all the pestles, tubes and filters were pre-coated with a homogenization buffer or 1x PBS. 900 μl of homogenization buffer was added to wash the pestle, and the total 1mL homogenized sample was transferred into a 1mL Dounce tissue grinder (Wheaton 357538). The grinder was autoclaved overnight in a 220℃ oven to deactivate ribonuclease. After placing the grinder on ice, 20 strokes were applied using a loose pestle, followed by another 20 strokes using a tight pestle, while avoiding generating foams. The 1000μl samples were filtered through a cell strainer (35 μm) and then through a Flowmi cell strainer (BelArt, H13680-0040) into a new 1.5 mL tube. The tubes were centrifuged for 10 minutes at 1000 g at 4°C, and the supernatant was removed while not disturbing the pellet, which was hardly visible. The pellet was resuspended with 500 μl 1x PBS with 0.5% BSA and RNAase inhibitor and filtered with a Flowmi cell strainer (BelArt, H13680-0040) again into a 5 mL flow cytometer tube. A total of 20 μl was transferred into another flow cytometer tube and diluted with 180 μl 1x PBS with 0.5% BSA and RNAase inhibitor as an unstained control. Hoechst (Invitrogen 33342) was used to stain the nuclei in 1:1000 working concentration. We coated the 1.5 mL sorting collection tube with 1x PBS with 0.5% BSA and RNAase inhibitor and ~300,000 nuclei were sorted with Hoechst 33342 positive gating, which indicates DNA content, and forward scatter area (FSC-A) gating, representing the particle size above threshold. The intestinal nuclei, which are polypoid (32N), usually form an obvious cluster separating from the other 2N somatic nuclei, and these were also included in our collection. The collection tube was centrifuged at 800g for 8 minutes at 4℃ and the sheath buffer supernatant was carefully removed before resuspending the sorted nuclei with 40-50 μl 1x PBS with 0.5% BSA and RNAase inhibitor. The concentration and morphology of the nuclei were checked under a microscope to ensure high-quality nuclei isolation. If the results were desirable, we proceeded to generate gel emulsion with 10X Chromium Controller. For sorting the nuclei, we used either DB LSR II or Sony MA800 sorter. To obtain the best nuclei morphology and the least RNA degradation, it is recommended to minimize the sorting time. Two researchers could simultaneously set up the sorter and perform nuclei processing.
Library preparation was carried out using the published 10X Chromium Single Cell 3’ v2/v3 Solution protocol (Single/dual index). The resulting libraries were sequenced on the NextSeq550 or NovaSeq6000 or NextSeq 2000 platforms, with a depth ranging from 6,306 to 29,862 reads/cell, with the recommended cycle numbers: 26 cycles for Read 1, 8 cycles for i7 index, and 98 cycles for Read 2.

value: whole body


title: MOLM13 RNA-seq 24h Quizartinib replicate 1

description: RNA-seq

source_name: MOLM13 cell line

extract_protocol:
Total RNA was isolated using a RNeasy Plus Mini Kit (Qiagen)
BGI performed the library preparation and sequencing at 50 base pair single end

value: 1 nM quizartinib


title: MOLM13 RNA-seq 24h DMSO replicate 3

description: RNA-seq

value: DMSO


title: MOLM13 RNA-seq 24h DMSO replicate 2

description: RNA-seq


title: NPC_deletion_hic

city: Berlin

first: Ana

last: Pombo

address: Hannoversche Strasse 28

country: Germany

institute: Max Delbrueck Center for Molecular Medecine

description: heterozygous 7qF3 deletion

data_processing:
Hi-C data was processed using the TADbit pipeline as described (Serra et al., 2017). Raw Hi-C contact frequencies were normalized at 50 kb resolution using the iterative correction pipeline (Imakaev et al., 2012) for one iteration.
Genome_build: mm9

source_name: neuronal progenitor cells

growth_protocol: Control and mutant cell lines harboring heterozygous deletion (del) or duplication-deletion (dupdel) of 7qF3 locus which is synteny conserved with human 16p11.2 locus were kindly provided by Alea Mills (Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA). Generation of cell lines described in Horev et al., 2011 (doi: 10.1073/pnas.1114042108). Embryonic stem cells (ESCs) were cultured directly on gelatine-coated plates in M15 medium, supplemented with 15% FBS and 2000 U/ml LIF. Cells were grown for one week before plating them for harvest or for subsequent differentiation. Cells were split every 48 h and media was changed every 24 h. Cell harvest was performed at 70 – 80 % confluency. For generating neuronal precursor cells commited to ventral midbrain lineage or immature dopaminergic neurons, cells were differentiated according to Ferrai et al. (2017). Briefly, the differentiation of ESCs to immature midbrain dopaminergic neurons starts with differentiating ESCs into epiblast stem cells (EpiSCs) by growing them for 4 weeks in N2B27 basal medium containing Activin and FGF2. The EpiSCs were kept in culture for one week, followed by differentiation towards midbrain-specific dopamine neurons. After 5 days of differentiation neuronal progenitor cells were harvested, and after 16 days of differentiation immature dopaminergic neurons were harvested.

extract_protocol:
Cells were grown on a 100-mm cell culture dish to 70-80 % confluency on the day of harvest. A technical replicate was grown for counting cell numbers. Typically, 25 million cells were used for one Hi-C library. Cells in adherent cell culture were fixed in 14 ml fresh culture media, supplemented with 2% formaldehyde for 10 min at RT, while gently rocking the plate every 2 min. Crosslinking was stopped by adding 781 µl of 2.5 M glycine, and incubation at RT for 5 min, followed by 15 min on ice. Cells were scraped off the plate with a cell scraper and transferred into a 15 ml conical tube. Cells were spun down with 872xg for 10 min at 4°C, media was removed and the cell pellet was frozen in liquid nitrogen for storage at -80°C.
Hi-C library preparation was performed as previously described (Lieberman-Aiden et al., 2009) with modifications. In brief, isolated nuclei were divided in 5 aliquots and digested overnight with 1500U of HindIII per aliquot. After biotin-fill in, in each aliquot proximity ligation was carried with 100 units of T4 DNA ligase (Invitrogen) at 16°C overnight. DNA was purified by reverse crosslinking and DNA precipitation, and biotinylated nucleotides were removed from unligated fragments ends with 1U T4 DNA polymerase per µg DNA for 4 hours at 12°C. DNA was sonicated to 300 – 500 bp, using the Bioruptor Plus and size selected for fragments between 300 and 500 bp with AmPure XP beads. Biotinylated DNA fragments were pulled down with MyOne Streptavidin C1 beads (Invitrogen), end-repaired, a-tailed, and TruSeq sequencing adapters were ligated to the DNA fragments with 15U T4 DNA ligase (Invitrogen) overnight at 16°C, shaking at 750 rpm. Adapter-ligated DNA was amplified for 6-8 cycles using Herc II Fusion DNA polymerase (Agilent). PCR products were purified with AMPure XP beads and sequenced with paired-end sequencing (2x 75 bp).

tag: background strain

tag: genotype

tag: developmental stage

value: neuronal progenitor cells

tag: restriction enzyme

value: HindIII


title: NPC_duplication_deletion_hic

description: heterozygous 7qF3 duplication, heterozygous 7qF3 deletion

value: 129Sv df/dp


title: Primary AML Sample 2555 24h GSK2879552 replicate 3

description: RNA-seq


title: Day12 lipl-4 intestinal overexpression line feed with E. coli OP50

description: 10x Genomics

value: MCW14 raxIs3 [ges-1p::lipl-4::SL2GFP]


title: NPC_control_hic

description: control


title: p300KD 1

description: p300KD Astrocytes


title: MOLM13 RNA-seq 24h DMSO replicate 1

description: RNA-seq


title: Day14 Wild-type(N2) feed with E. coli OP50, replicate 3

description: 10x Genomics


title: Wild-type 4h post fertilization biol rep 2

city: Bergen

first: Simon

last: Henriet

address: Thormøhlensgate 55

country: Norway

institute: University of Bergen

data_processing:
Adaptor trimming with flexbar 3.4.0
Alignment to transcript models from annotated genes with kallisto 0.46.0
Differential gene expression analysis with DESeq2
Assembly: Oikopleura dioica genome assembly version 3.0
Supplementary files format and content: tab-delimited text files includes raw read counts produced by kallisto for each library

molecule: polyA RNA

organism: Oikopleura dioica

source_name: whole animal

growth_protocol: Animals from single crosses between Pax37b+/- parents were raised until 4, 8 and 6 hours post-fertilization. Individual animals were collected and transferred in RNA extraction buffer, and 10% of the lysate was used for genotyping Pax37b.

extract_protocol:
Animals with the same genotype were pooled together, and we extracted RNA with Nucleospin RNA XS kit (Macherey-Nagel)
Libraries were prepared with the NEBNext Single-cell/Low-input RNA library prep kit for Illumina (New England Biolabs), following the manufacturer's protocol

value: whole animal


title: Primary AML Sample 2555 24h GSK2879552 replicate 1

description: RNA-seq


title: Primary AML Sample 2555 24h GSK2879552 replicate 2

description: RNA-seq


title: ESC_duplication_deletion_hic

source_name: embryonic stem cells

value: embryonic stem cells


title: Day14 Wild-type(N2) feed with E. coli OP50, replicate 2

description: 10x Genomics


title: ESC_deletion_hic

description: heterozygous 7qF3 deletion


title: Primary AML Sample 2555 24h Quizartinib replicate 3

description: RNA-seq

value: 500 nM quizartinib


title: Day6 Wild-type(N2) feed with E. coli OP50, replicate 3

description: 10x Genomics


title: Pax37b mutant 4h post fertilization biol rep 2


title: Day6 Wild-type(N2) feed with E. coli OP50, replicate 2

description: 10x Genomics


title: Pax37b mutant 4h post fertilization biol rep 1


title: Primary AML Sample 2555 24h Quizartinib replicate 2

description: RNA-seq


title: Primary AML Sample 2555 24h Quizartinib replicate 1

description: RNA-seq


title: ESC_control_hic

description: control


title: NEU_dupdel_4

data_processing:
Sequencing reads were mapped to mm9 with STAR v2.6.0c (Dobin et al., 2013), transcripts were quantified with RSEM v1.3.0 (Li and Dewey, 2011), and analysis of count data was performed with DEseq2 v1.22.2 (Love et al., 2014).
Genome_build: mm9

source_name: dopaminergic neurons

extract_protocol:
Cell lysis was performed on the culture dish, in TRIzol Reagent (Invitrogen, 15596026) at room temperature, and lysate was frozen in liquid nitrogen and stored at -80°C upon processing. Samples were incubated at RT for 5 min and homogenized with 200 ml chloroform per 1 ml of TRIzol, by shaking for 15 s and incubating 3 min at RT. After centrifugation at 12,000xg for 15 min at 4°C, the upper aqueous phase containing the RNA was transferred to a new tube and RNA was precipitated by adding 500 µl HPLC-grade isopropanol, incubating for 10 min at RT, and centrifugation at 12,000xg for 10 min at 4°C. Supernatant was removed and RNA pellet is washed with 75 % ethanol, air-dried for 10 min, resuspended in RNase-free water, and incubated at 55°C for 10 min. DNA was removed by DNase treatment using Turbo DNase (AM2238, Thermo Fisher) according to the manufacturer’s instructions.
RNA-seq libraries were generated from 1 µg of clean RNA using the TruSeq Stranded total RNA library preparation kit according to the manufacturer’s (Sample prep guide 15031048). Samples were sequenced on the NextSeq500, paired end 75 bp, with the NextSeq 500/550 High Output v2 kit (150 cycles), following the manufacturer’s instructions for denaturing, dilution, and sequencing of the libraries.

value: Immature dopaminergic neurons


title: Primary AML Sample 2555 24h DMSO replicate 3

description: RNA-seq

value: primary AML blasts


title: Day12 rsks-1 mutant feed with E. coli OP50

description: 10x Genomics


title: NEU_dupdel_2


title: LE9 assay timepoint 3 (36h without geneticin)

city: Edinburgh

first: Grzegorz

last: Kudla

address: Crewe Road

department: MRC HGU

country: United Kingdom

institute: University of Edinburgh

description:
High-Output v2.5 (75 cycles) Kit (#20024906). PhiX Control v3 Library (Illumina Inc, # FC-110-3001) was spiked in at a concentration of 10%. Custon rd1 primer at a final concentration of 0.3μM.
le9_0to03_cont.tsv

library_source: other

data_processing:
For pax6_le9_assay, Data from the run was transferred from the NextSeq 550 instrument to a computer running Linux and a sample sheet was created to allow the generation of demultiplexed FASTQ files using Bcl2fastq2 v2.20.0.422, using adapter stringency 0.9.
For pax6_blx_assay, Basecall data was produced by the NextSeq 1000/2000 Control Software (Version 1.4.1.39716).
Following demultiplexing of the pax6_le9_assay and pax6_blx_assay, the regions flanking the 30 nt barcodes were trimmed using trimgalore then barcodes counted and variant fitness scores calculated using the Enrich2 tool (Rubin et al. 2017)
Assembly: NA
Supplementary files format and content: barcode counts calculated with the Enrich2 tool (Rubin et al. 2017)
Supplementary files format and content: Barcode:variant phasing was achieved using the alignparse Python package (Crawford et al. 2016)
Library strategy: Barcode amplicon sequencing

molecule: other

organism: Saccharomyces cerevisiae

source_name: cell

growth_protocol: Competition assays were performed using a complete supplement mixture without histidine (Formedium) and yeast nitrogen base without amino acids (Formedium) media, supplemented with 2% glucose. To begin, the barcoded PAX6 variant library was transformed into two separate strains, LE9 and BLX, in two independent assays. The transformation process followed the protocol described in the Yeastmaker™ Yeast Transformation System 2 User Manual (Takara Bio), yielding approximately 2 x 106 and 7 x 106 transformants for LE9 and BLX strains, respectively. Transformed cells were then inoculated into 500 ml of liquid media and incubated at 30°C and 230 RPM for 12-24 hours until reaching an OD600 of approximately 1.0. Subsequently, approximately 7.5 x 108 cells were transferred to fresh media and grown for an additional 12 hours (T0). The T0 cultures were then split into two parallel lineages. All cultures were then maintained between an OD600 of 0.05 and 1.0 by passaging every 12 hours for a total of 36 hours (Timepoints 1-3).

extract_protocol:
Plasmid isolation was achieved using the protocol described by Fowler et al. (2014), which in summary used a freeze-thaw cycle and zymolyase cell wall digestion steps were coupled with Qiaprep spin miniprep kit (Qiagen) column purification
Samples from each timepoint were prepared for next-generation sequencing using a single limited-cycle PCR. Barcodes were amplified using primers possessing overhangs that contained sequencing primer annealing sequences, unique dual indexes, and P5/P7 Illumina adapter sequences (Table S1). 50 µl PCR reactions were performed for each timepoint using Phusion High-Fidelity PCR Master Mix with HF Buffer (NEB) with 20 to 50ng of template isolated plasmid DNA. Each reaction was then thermocycled using the following conditions: (1) initial denaturation at 98°C for 30 seconds, (2) incubation at 98°C for 8 seconds, (3) incubation at 69°C for 20 seconds, (4) incubation at 72°C for 8 seconds, (5) incubation at 72°C for 7 minutes. Steps 2 to 4 were repeated for 12 to 19 cycles (< 20). Multiple replicate 50 µl reactions were performed for each timepoint to ensure enough PCR product was generated. 2.5ul of Exo I nuclease (NEB) was then added directly to each ‘dirty’ PCR product and incubated at 37°C for 1 hour, followed by purification using QIAquick PCR Purification Kit (Qiagen). Samples were further purified by 2% E-Gel SizeSelect agarose gel (Invitrogen). The resulting products were purified using QIAquick PCR Purification Kit (Qiagen), after which all samples were pooled at equimolar amounts (quantified by QuBit [Invitrogen]) and then quantitated by Bioanalyzer (Agilent).

treatment_protocol: Geneticin was  added to one lineage of each strain (LE9; 400 µg/ml, BLX; 500 µg/ml) starting from timepoint 0

value: cell

tag: cell line

value: Y1HGold (Takara Bio)


title: NEU_del_3

description: heterozygous 7qF3 deletion


title: Primary AML Sample 2555 24h DMSO replicate 2

description: RNA-seq

value: 24 hours


title: Day12 Wild-type(N2) feed with E. coli OP50 , replicate 2

description: 10x Genomics


title: LE9 assay timepoint 1 (12h without geneticin)


title: Primary AML Sample 2555 24h DMSO replicate 1

description: RNA-seq


title: NEU_con_4

description: control


title: Primary AML Sample 2307 24h Combination replicate 3

description: RNA-seq

value: 500 nM quizartinib + 500 nM GSK2879552


title: NEU_con_3

description: control


title: Primary AML Sample 2307 24h Combination replicate 2

description: RNA-seq


title: LE9 assay timepoint 3 (36h with geneticin)

description:
High-Output v2.5 (75 cycles) Kit (#20024906). PhiX Control v3 Library (Illumina Inc, # FC-110-3001) was spiked in at a concentration of 10%. Custon rd1 primer at a final concentration of 0.3μM.
le9_0to03_g418.tsv

value: Geneticin sulfate


title: LE9 assay timepoint 2 (24h with geneticin)


title: NEU_con_2

description: control


title: Wild-type 4h post fertilization biol rep 1


title: Primary AML Sample 2307 24h Combination replicate 1

description: RNA-seq


title: NEU_con_1

description: control


title: LE9 assay timepoint 0


title: NPC_dupdel_5

description: heterozygous 7qF3 deletion


title: Day12 Wild-type(N2) feed with E. coli OP50 , replicate 3

description: 10x Genomics

value: whole body


title: Lats1/2 KO adipocyte derived cells (tdT+).

city: Daejeon

first: Sungwoo

last: Choi

address: 291 Daehak-ro

country: South Korea

institute: KAIST

description: 10X genomics

data_processing:
STAR genome index was generated for GRCm38 mouse genome assembly with Gencode M23 annotations. STARsolo was run with the parameters: --soloType CB_UMI_Simple --soloUMIlen 12 --soloBarcodeReadLength 0 --soloStrand Forward --soloUMIfiltering MultiGeneUMI --soloCellFilter CellRanger2.2 3000 0.99 10 --soloFeatures Gene GeneFull; all other parameters used default values.
Assembly: GRCm38
Supplementary files format and content: Cellranger barcodes and gene count matrices

source_name: iWAT

extract_protocol:
iWAT was minced and incubated in KRH buffer containing 1.5% bovine serum albumin (160069, MP Biomedicals), 1 mg/ml of collagenase type 1 (LS004194, Worthington Biochemical Corporation) and 2.4 units/ml Dispase I (354235, Corning) for 30-45min in 37’C shaking water bath. After mixing it with DMEM 10% FBS at 1:1 volume ratio, dissociated cells were filtered through series of 100µm and 40 µm nylon mesh strainer, followed by RBC lysis (11814389001, Roche) for 3minutes. After washing with HBSS 3% BSA, cells were incubated with APC-CD45 antibody (559864, BD Pharmingen) at 1:200 ratio diluted in HBSS 3% BSA for 20min on ice. Then the cells were washed with HBSS 3% BSA, and resuspended in FACS buffer (PBS 0.5% BSA). DAPI was added at 1:1000 right before flow-sorting to exclude dead cell. Singlets were selected based on gating. CD45-& tdT+ cells from AKO SVF and CD45-& tdT- cells from Con SVF were sorted for single cell RNA-sequencing.
10X Chromium Single cell 3’ reagent kit v3 (10X genomics), following manufacturer’s protocols

value: iWAT

value: SVF

value: KO


title: Primary AML Sample 2307 24h GSK2879552 replicate 2

description: RNA-seq


title: NPC_dupdel_2

description: heterozygous 7qF3 deletion

value: neuronal progenitor cells


title: LE9 assay timepoint 2 (24h without geneticin)


title: Primary AML Sample 2307 24h Quizartinib replicate 3

description: RNA-seq


title: Con CD45- SVF cells.

description: 10X genomics

value: Control


title: NPC_del_5

description: heterozygous 7qF3 deletion


title: NEU_del_1

description: heterozygous 7qF3 deletion


title: NPC_dupdel_4

description: heterozygous 7qF3 deletion

value: 129Sv df/dp


title: Primary AML Sample 2307 24h GSK2879552 replicate 1

description: RNA-seq


title: Day1 Wild-type(N2) feed with OP50 bacteria, replicate 3

description: 10x Genomics

extract_protocol:
Worms were washed three times with PBS and collected in a 1.5 mL tube. We then added 100 μl of homogenization buffer {10.1126/science.abk2432} and grind the worms with a pestle motor for 30 seconds on ice. To minimize nuclei adhesion on the surface, all the pestles, tubes and filters were pre-coated with a homogenization buffer or 1x PBS. 900 μl of homogenization buffer was added to wash the pestle, and the total 1mL homogenized sample was transferred into a 1mL Dounce tissue grinder (Wheaton 357538). The grinder was autoclaved overnight in a 220℃ oven to deactivate ribonuclease. After placing the grinder on ice, 20 strokes were applied using a loose pestle, followed by another 20 strokes using a tight pestle, while avoiding generating foams. The 1000μl samples were filtered through a cell strainer (35 μm) and then through a Flowmi cell strainer (BelArt, H13680-0040) into a new 1.5 mL tube. The tubes were centrifuged for 10 minutes at 1000 g at 4°C, and the supernatant was removed while not disturbing the pellet, which was hardly visible. The pellet was resuspended with 500 μl 1x PBS with 0.5% BSA and RNAase inhibitor and filtered with a Flowmi cell strainer (BelArt, H13680-0040) again into a 5 mL flow cytometer tube. A total of 20 μl was transferred into another flow cytometer tube and diluted with 180 μl 1x PBS with 0.5% BSA and RNAase inhibitor as an unstained control. Hoechst (Invitrogen 33342) was used to stain the nuclei in 1:1000 working concentration. We coated the 1.5 mL sorting collection tube with 1x PBS with 0.5% BSA and RNAase inhibitor and ~300,000 nuclei were sorted with Hoechst 33342 positive gating, which indicates DNA content, and forward scatter area (FSC-A) gating, representing the particle size above threshold. The intestinal nuclei, which are polypoid (32N), usually form an obvious cluster separating from the other 2N somatic nuclei, and these were also included in our collection. The collection tube was centrifuged at 800g for 8 minutes at 4℃ and the sheath buffer supernatant was carefully removed before resuspending the sorted nuclei with 40-50 μl 1x PBS with 0.5% BSA and RNAase inhibitor. The concentration and morphology of the nuclei were checked under a microscope to ensure high-quality nuclei isolation. If the results were desirable, we proceeded to generate gel emulsion with 10X Chromium Controller.  For sorting the nuclei, we used either DB LSR II or Sony MA800 sorter. To obtain the best nuclei morphology and the least RNA degradation, it is recommended to minimize the sorting time. Two researchers could simultaneously set up the sorter and perform nuclei processing.
Library preparation was carried out using the published 10X Chromium Single Cell 3’ v2/v3 Solution protocol (Single/dual index). The resulting libraries were sequenced on the NextSeq550 or NovaSeq6000 platforms, with a depth ranging from 6,306 to 29,862 reads/cell, with the recommended cycle numbers: 26 cycles for Read 1, 8 cycles for i7 index, and 98 cycles for Read 2.

value: day1(55~60h after L1)


title: Day6 rsks-1 mutant feed with E. coli OP50

description: 10x Genomics


title: Day1 rsks-1 mutant feed with E. coli OP50

description: 10x Genomics


title: NPC_del_1

description: heterozygous 7qF3 deletion


title: NPC_del_3

description: heterozygous 7qF3 deletion


title: NPC_con_4

description: control


title: Day6 Wild-type(N2) feed with E. coli HT115

description: 10x Genomics


title: Primary AML Sample 2307 24h Quizartinib replicate 2

description: RNA-seq


title: Primary AML Sample 2307 24h DMSO replicate 3

description: RNA-seq

value: DMSO


title: NPC_con_5

description: control


title: Primary AML Sample 2307 24h GSK2879552 replicate 3

description: RNA-seq


title: Primary AML Sample 2307 24h DMSO replicate 2

description: RNA-seq


title: LE9 assay timepoint 1 (12h with geneticin)


title: NPC_con_3

description: control


title: Day6 Wild-type(N2) feed with E. coli OP50

description: 10x Genomics


title: Primary AML Sample 2307 24h DMSO replicate 1

description: RNA-seq


title: Day1 Wild-type(N2) feed with E. coli OP50, replicate 2

description: 10x Genomics


title: Day1 Wild-type(N2) feed with E. coli HT115

description: 10x Genomics


title: Day14 Wild-type(N2) feed with E. coli OP50

description: 10x Genomics


title: NPC_con_2

description: control


title: Primary AML Sample 2307 24h Quizartinib replicate 1

description: RNA-seq

value: 500 nM quizartinib


title: Day1 Wild-type(N2) feed with E. coli OP50

description: 10x Genomics


title: NPC_con_1

description: control


title: Decidua Normal 2

city: shanghai

first: ql

last: zheng

address: xiangyin

country: China

institute: immunity

data_processing:
Basecalls performed using CASAVA version 1.8
1. We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria:   MT% < 20%;    Cell Gene Number < Median Gene Number * 2;   Cell Gene Number > 200.  PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples.  Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Genome_build: Ensembl/GRCh38
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Decidual macrophage

growth_protocol: Decidua samples were collected from RSA patients or control women undergoing elective terminations of first trimester pregnancies.

extract_protocol: dMCs were washed in complete medium. Cells were then counted and distributed at approximately 1×106 cells/mL in 200 μL FACS wash (FW, 1×PBS, 2% FCS). Cells were stained with CD14 and CD45 antibody for 15 min at 4 °C. Viability was assessed using DAPI staining incubated for 5 min at 4 °C. Cells were then analyzed on a LSR Fortessa (BD Biosciences). Macrophages were gated on as live CD14+CD45+ lymphocytes.

treatment_protocol: To isolate decidual mononuclear cells (dMCs), decidual tissue pieces were first washed, remaining tissue was then minced and digested by Collagenase IV (0.1 g/100 mL, sigma) and DNase I (150 U/mL, Sigma) for 40 min at 37°C whilst being gently shaken. The collagenase was quenched by addition of DMEM/F12 with 10% FCS and then filtered through 100 μm and then 40 μm filters. dMCs were isolated following a percoll gradient centrifugation step

value: Normal decidual tissue

value: Decidual macrophage

tag: method

value: flow cytometry

tag: markers

value: CD14 CD45


title: Decidua RSA 2

value: Decidual tissue of recurrent spontaneous abortion


title: Decidua RSA 1


title: ESC_dupdel_3

value: embryonic stem cells


title: Day12 Wild-type(N2) feed with E. coli OP50

description: 10x Genomics


title: Day6 Wild-type(N2) feed with E. coli delta lon(Keio collection)

description: 10x Genomics


title: ESC_dupdel_2


title: Decidua Normal 1


title: BLX assay timepoint 3 (36h without geneticin)

description:
NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811) with custon rd1 primer and PhiX Control v3 spiked in to the sequencing library at a concentration of 10%
blx_0to03_cont.tsv

value: cell

value: Y1HGold (Takara Bio)


title: Day6 lipl-4 intestinal overexpression line feed with E. coli OP50

description: 10x Genomics

value: whole body

value: MCW14 raxIs3 [ges-1p::lipl-4::SL2GFP]


title: BLX assay timepoint 1 (12h without geneticin)


title: ESC_del_1

description: heterozygous 7qF3 deletion


title: BLX assay timepoint 2 (24h without geneticin)


title: ESC_del_3

description: heterozygous 7qF3 deletion


title: Day6 daf-2 mutant feed with E. coli OP50

description: 10x Genomics


title: BLX assay timepoint 2 (24h with geneticin)

description:
NextSeq 1000/2000 P2 Reagents (100 cycles) v3 Kit (#20046811) with custon rd1 primer and PhiX Control v3 spiked in to the sequencing library at a concentration of 10%
blx_0to03_g418.tsv

value: Geneticin sulfate


title: BLX assay timepoint 1 (12h with geneticin)


title: BLX assay timepoint 3 (36h with geneticin)


title: ESC_con_2

description: control


title: Day6 Wild-type(N2) feed with E. coli K-12 BW25113

description: 10x Genomics


title: Day1 Wild-type(N2) feed with E. coli delta lon(Keio collection)

description: 10x Genomics


title: Day1 daf-2 mutant feed with E. coli OP50

description: 10x Genomics


title: Day1 Wild-type(N2) feed with E. coli K-12 BW25113

description: 10x Genomics


title: BLX assay timepoint 0


title: ESC_con_1

description: control


title: TG microglia (Me-X04 pos) 4

status: Public on Mar 20 2024

city: Kuopio

first: Flavia

last: Scoyni

address: Neulaniementie 2

department: A.I. Virtanen Institute for Molecular Sciences

country: Finland

institute: University of Eastern Finland

data_processing:
Raw reads were trimmed and filtered using Trim Galore (v.0.4.4) with Phred quality score cutoff 30. Processed reads were aligned to the genome assembly GRCm38 using STAR version 2.5.4b with options --outFilterMismatchNoverLmax 0.04 and --outFilterMultimapNmax 10.
Aligned reads mapping to features were assigned using featureCounts (Rsubread 1.32.4) with the Gencode M16 GTF.
Transcripts with low counts of CPM < 1 not present in at least 2 libraries above this threshold were considered not expressed and removed from the analysis.
Library sizes were subsequently normalised using TMM, batch corrected, and quasi-likelihood F-testing was used to estimate differential expression using edgeR (3.24.3).
Transcripts with a log2 FC of ≥ 1 or ≤ -1 and FDR < 0.01 were considered differentially expressed.
Assembly: GRCm38

source_name: Brain

growth_protocol: Ex vivo microglia obtained from 5xFAD mouse brain

extract_protocol:
RNA extraction was performed with Qiagen Micro RNA kit (Qiagen)
RNA libraries for RNA-seq were prepared using Ovation RNA-Seq System V2 followed by Ovation Ultralow System V2 using  Nugen protocols M01114 v5 and M01379v3.1.

treatment_protocol: Mice were injected with Methoxy-X04 amyloid beta staining previous to microglia isolation

value: Brain

value: Microglia (Cd11b-Cd45 positive)

value: Methoxy-X04(amyloid beta), Cd11b, Cd45 stained single cell sorting

tag: time

value: 6 months old mice


title: TG microglia (Me-X04 pos) 2


title: TG microglia (Me-X04 pos) 3


title: ESC_dupdel_1

value: 129Sv df/dp


title: Day1 lipl-4 intestinal overexpression line  feed with E. coli OP50

description: 10x Genomics


title: TG microglia (Me-X04 pos) 1


title: WT microglia (Me-X04 neg) 6

value: 2 months old mice


title: ESC_del_2

description: heterozygous 7qF3 deletion


title: ESC_con_3

description: control


title: TG microglia (Me-X04 neg) 5


title: TG microglia (Me-X04 neg) 4


title: WT microglia (Me-X04 neg) 2


title: TG microglia (Me-X04 neg) 3


title: WT microglia (Me-X04 neg) 7


title: TG microglia (Me-X04 neg) 1


title: WT microglia (Me-X04 neg) 4


title: WT microglia (Me-X04 neg) 1


title: WT microglia (Me-X04 neg) 5


title: Young_Replicate2

city: Villigen

first: Shivashankar

last: GV

state: Aargau

address: Forschungsstrasse 111

department: LNB

country: Switzerland

institute: Paul Scherrer Institut

data_processing:
Al the raw files were processed for QC using FASTAQC
All the trimmed reads were mapped back to genome using TopHat tool
Mapped reads were processed to derive FPKM using Cufflinks
DE-seq2 was used to derive fold change differences between the samples
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

growth_protocol: Cells were cultured in MEM media containing 15%FBS, 1% Penstrep, 1% Non essential amino acids and 1% GlutaMAX in a cell culture incubator with 5% Co2 and 37C.

extract_protocol:
Total RNA was isolated using Qiagen plus micro kit and 200 ng of RNA used for sequencing
RNA libraires were constructed using RiboZero depletion followed library construcuon using Illumina Stranded Total RNA Prep with Ribo-Zero Plus

treatment_protocol: For Rejuvenation we took the GM08401 cells and cultured on fixed micropattern size 78*190 for 8 days with MEM complete medium and for re-differentiation or rejuvenation we kept thte collagen gel with 1mg/ml concentration on these day 8 spheroid and cultured for 48 hours.

value: Dermal Fibroblast

value: Wild type


title: TG microglia (Me-X04 neg) 2


title: RF_8401_Replicate2

value: Reprogrammed and re-differentiaed


title: RF_8401_Replicate1


title: WT microglia (Me-X04 neg) 3


title: Old_Replicate2


title: Old_Replicate1


title: Young_Replicate1


title: Rutaecarpine C83-3

type: RNA

city: Riyadh

first: Meshail

last: Okla

country: Saudi Arabia

institute: King Saud University

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul following the manufacturer’s instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0 (Agilent) using default parameters. Data were analyzed using Agilent GeneSpring X software.

source_name: hBMSC-osteoblast, day 21

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng RNA using the Low Input Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: The hBMSC cell line was created by the overexpression of the human telomerase reverse transcriptase gene (hTERT).These cells were cultured in basal culture medium of Dulbecco’s modified Eagle’s medium (DMEM) supplemented with D-glucose 4,500 mg/L, 4 mM l-glutamine, 110 mg/L sodium pyruvate, 10% fetal bovine serum, 1% penicillin–streptomycin (Pen-Strep), and 1% nonessential amino acids.

extract_protocol: Total RNA was extracted from hBMSC-derived osteoblasts on day 21 using the Total RNA Purification Kit (Norgen Biotek Corp., Thorold, ON, Canada)

treatment_protocol: hBMSCs were subjected to osteogenic differentiation after reaching 80-90% confluency. Osteogenesis was induced using 50 mg/ml L-ascorbic acid ( Wako-chemicals), 10mM b-glycerophosphatase (Sigma-Aldrich), 10 nM calcitriol (1a,25-dihydroxyvitamin D3; Sigma Aldrich), and 100 nM dexamethasone (Sigma-Aldrich). Treatments: DMSO (as a control), Apigenin, or Rutaecarpine were added at 1uM on day 0 of osteblast differentiation and continuously replaced till day 21.

tag: agent

value: Rutaecarpine C83


title: Apigenin C10-3

value: Apigenin C10


title: Rutaecarpine C83-1


title: DMSO-1

value: DMSO


title: Apigenin C10-1


title: C18-Q

city: Philadelphia

first: Umadevi

last: Sajjan

state: PA

address: 3500 N Broad street, 1157 MERB, 115, 1157 MERB,

institute: Temple University

hyb_protocol: Purified and quantified cRNA was hybridized to affymetrix Human Gene ST 2.1 test chips and the microarrays were performed following instructions from the manufacturer.

scan_protocol: Peg Arrays were scanned using the Affymetrix GeneTitan system (software version 4.3.0.1592).

data_processing: The data were analyzed with Transcriptome Analysis Console (software version 4.0) using default analysis settings (Gene-Level Fold Change < -2 or > 2, Gene-Level p-value < 0.05, ebayes ANOVA method) and Gene Level RMA as normalization method.

label: Biotin

source_name: Airway basal cells from COPD subjects

label_protocol: Double stranded cDNA was synthesized from 2 µg of total RNA followed by clean up with GeneChip Sample Cleanup Module. Biotin-labeled cRNA was then synthesized by in vitro transcript reaction using GeneChip IVT labeling kit.

extract_protocol: Cells were washed once with PBS, lysed in TRIZOL and total RNA was isolated by using miRNeasy kit (Qiagen, Valencia, CA) involving DNAse treatment step.

treatment_protocol: Basal cells were cultured in collagen coated 10 cm dishes in Bronchial Life medium (LifeLine Cell Technologies, Frederick, MD) until 80% confluent. Cells wereflow sorted based on the expression of basal cell marker nerve growth factor receptor and seeded in transwells at a density of 1 x 10^5/well. Cells were grown under submerged conditions in Bronchial Life medium until confluent (5 to 7 days), treated with 1 uM  quercetin for 3 days. Cells were then harvested.

value: Basal cells treated with quercetin

tag: disease state

value: COPD


title: C15-Q

tag: treatment


title: C10-Q


title: C11-Q


title: DMSO-3


title: C14-Q


title: C19-Q


title: Rutaecarpine C83-2


title: Apigenin C10-2


title: C18

value: Basal cells treated with vehicle


title: C6-Q


title: DMSO-2


title: C12-Q


title: Ah20mirS2_AGO4-IP

city: Villeneuve d'Ascq

first: Vincent

last: Castric

address: Batiment SN2, bureau 207

institute: CNRS / Universite de Lille - Sciences et Technologies

description: small RNAs from IP experiment - AGO4 bound fraction

data_processing:
read trimming: trim_galore --fastqc --length 18 --max_length 25
mapping to TAIR10 genome: ShortStack --bowtie_cores 4 --mismatches 1 --bowtie_m 50 --mmap u
mapping to S locus: ShortStack --bowtie_cores 2 --mismatches 1 --bowtie_m 50 --mmap u
only reads that mapped only to S locus and not to TAIR10 were kept for further analysis
reads from different samples of the same genotype were poooled to generate a smallRNA dabase for that genotype (see processed data file)
Assembly: for all libraries: TAIR10; for libraries AVBR-14, AVBR-5 and AVBR-6: Ah04 S locus (GenBank ID: KJ461484); for libraries AVBR-15, AVBR-8 and AVBR-9: Ah20 S locus (GenBank ID KJ772400)
Supplementary files format and content: smallRNA database columns: sRNA_chr/sRNA_start/sRNA_end/sRNA_id/sRNA_size /sRNA_strand/sRNA_seq/mir_of_origin/allele_of_origin/sample_of_origin

organism: Arabidopsis thaliana

source_name: immature floral buds

growth_protocol: Arabidopsis thaliana plants used in this study were grown in a greenhouse, using standard growth conditions (16 h light/8 h dark; 110 μmol/s/m2; 21°C; 70% humidity)

extract_protocol:
AGO1 and AGO4 immunoprecipitation (IP) assays were performed on immature buds of plants carrying an homozygous Ah04mir1887, Ah20mirS3 or Ah20mirS2 transgene, using a protocol adapted from (Schott et al., 2012), with the following modifications: IPs were performed on 1.4 g of finely ground powder of frozen immature buds. The anti-AGO1 (AS09 527, Agrisera) and anti-AGO4 (AS09 617, Agrisera) antibodies were added at a 1/500 dilution for the incubation step and their immobilization was performed using Dynabeads Protein G (Invitrogen). The IP products were washed six times with PBS prior to sRNA extraction using the Trizol reagent (Ambion). In parallel, an aliquot of each input extract was used for total sRNA isolation using the Trizol LS reagent (Invitrogen), according to the supplier instructions. For each genotype three sRNA fractions were obtained: AGO1-IP, AGO4-IP and input. These three sRNA fractions were subjected to an acrylamide gel-based size selection for sRNAS.
TruSeq Small RNA library kit (Illumina)

value: immature floral buds

value: C24 Ah20mirS2

tag: fraction

value: AGO4-IP fraction


title: RXRAChIP_MVEH8

city: Innsbruck

first: Jose Miguel

last: Ramos Pittol

address: Innrain 80-82

department: Institute of Biochemistry

country: Austria

institute: University of Innsbruck

data_processing:
Alignment was carried out using Bowtie2 allowing for up to 2 mismatches. FXR and RXRA peaks were identified using MACS2 narrowPeak with parameters “--nomodel --extsize 150”, and additionally “-q 0.1” for RXRA. GSM1899657 was used as input.
Coverage was computed with DeepTools2 bamCoverage with options “--binsize 50 --normalizeUsing RPGC --effectiveGenomeSize 1865500000 --extendReads 300”
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: Liver

extract_protocol:
Lysates were clarified from sonicated nuclei foxated with Formaldehyde/DSG, and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to the instructions accompanying the SOLiD ChIP-seq kit for library preparation. Libraries were sequenced on the SOLiD 5500 WG following the manufacturer's protocols.

treatment_protocol: Male mice were treated daily by oral gavage for 7 days with OCA/INT-747 (10mg/kg/day) or vehicle (1% methyl cellulose). This study used material from a mouse from the vehicle group

value: Liver

tag: chip antibody

value: RXRa (SantaCruz, sc-553)


title: C19


title: exosome from nicorandil-pretreated msenchymal stem cell, rep3

city: Beijing

first: Zhaoting

last: Gong

address: No.167 North Lishi Road, Xicheng District

institute: Fuwai Hospital

data_processing:
The raw reads were processed by filtering out containing adapter, poly 'N', low quality, smaller than 17nt reads by FASTQC to get clean reads. Mapping reads were obtained by mapping clean reads to reference genome of by bowtie.
miRDeep2 was used to identify known mature miRNA based on miRBase21 (www.miRBase.org) and predict novel miRNA. Databases of Rfam12.1 (www.rfam.xfam.org) and pirnabank (www.pirnabank.ibab.ac.in) were used to identify rRNA, tRNA, snRNA, snoRNA and piRNA by BLAST. The miRNA expression were calculated by RPM (Reads Per Million) values (PRM=(number of reads mapping to miRNA/ number of reads in Clean data)×106 ).
The expression levels were normalized by RPM, RPM is equal to (number of reads mapping to miRNA/ number of reads in Clean data)×10^6 . Differential expression between two sets of samples was calculated by edgeR algorithm according to the criteria of |log2（Fold Change）|≥1 and P-value < 0.05.
TargetScan, miRDB, miRTarBase and miRWalk were used to predict targets gene of selected miRNA. KOBAS was used to further Gene Ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway analysis.
Supplementary files format and content: RPM values

organism: Rattus norvegicus

source_name: RBMSC

extract_protocol:
Exosome was isolated from cell supernatants using the RiboTM Exosome Isolation Reagent (Ribobio, China), and Exosomal RNA was extracted by the MagZol (Magen) according to the manufacturer's protocol.
Briefly, RNAs were ligated with 3'RNA adapter, and followed by 5'adapter ligation. Subsequently, the adapter-ligated RNAs were subjected to RT-PCR and amplified with a low-cycle. Then the PCR products were size selected by PAGE gel according to instructions of NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Illumina, USA). The purified library products were evaluated using the Agilent 2200 TapeStation, The libraries were sequenced by HiSeq 2500(Illumina, USA) with single-end 50bp at Ribobio Co. Ltd (Ribobio, China).

value: RBMSC

tag: cell type

value: mesenchymal stem cells

value: WT

value: Nicorandil pretreatment


title: C12


title: C15


title: exosome from non-pretreated msenchymal stem cell, rep3


title: C11


title: C6


title: Rat1A Cells, Mutant R323, rep1

city: Riverside

first: Ernest

last: Martinez

address: 900 University Ave.

department: Biochemistry

institute: University of California Riverside

data_processing:
systemPipeR v1.4.4
Sequence reads were mapped to Rnor_6.0.82 using TopHat v.2.1.0
Read count extraction was performed with GenomicFeatures v.1.22.4 and the smarizeOverlaps function
Assembly: Rnor_6.0.82
Supplementary files format and content: tab-delimited text files include read-count values for each sample

growth_protocol: Rat1a cells were grown under adherent conditions in DMEM (high glucose) complemented with 10% FBS

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen, Germantown, MD, USA).  RNA was quantified using Thermoscientific Nanodrop2000 spectrophotometer and quality was assessed using Agilent 2100 bioanalyzer.
cDNA libraries were constructed using the TruSeq Stranded (dUTP) mRNA Library Prep Kit (Illumina, San Diego, CA, USA).
stranded mRNA-seq

value: Normal Primary Fibroblast Cells


title: C10


title: Ah20mirS2_AGO1-IP

description: small RNAs from IP experiment - AGO1 bound fraction

value: AGO1-IP fraction


title: exosome from nicorandil-pretreated msenchymal stem cell, rep1


title: exosome from nicorandil-pretreated msenchymal stem cell, rep2


title: exosome from non-pretreated msenchymal stem cell, rep2


title: Rat1A Cells, Mutant R158, rep1


title: exosome from non-pretreated msenchymal stem cell, rep1


title: Rat1A Cells, Mutant R149, rep3


title: Rat1A Cells, Mutant R149, rep1


title: Rat1A Cells, Wild Type, rep3


title: Rat1A Cells, Wild Type, rep2


title: Rat1A Cells, Mutant R323, rep3


title: Rat1A Cells, Mutant R158, rep2


title: Rat1A Cells, Mutant R158, rep3


title: ShRictor_2

type: genomic

city: Shinjuku

first: Kenta

last: Masui

state: Tokyo

address: 8-1 Kawada-cho

department: Department of Pathology

country: Japan

institute: Tokyo Women's Medical University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan System using standard recommended Illumina scanner setting

data_processing: IDAT files were processed using ChAMP R packages

label: Cy3, Cy5

source_name: mTORC2-suppressed glioblastoma cells

label_protocol: Genomic DNA was bisulfite converted using the Zymo Research EZ DNA Methylation kit following standard Illumina protocol

growth_protocol: Adherent cells (U87-EGFRvIII) were cultured in a 100-mm dish with DMEM (Thermo Fisher; Waltham, MA) supplemented with 10% FBS (Omega Scientific; Tarzana, CA), and 1% Penicillin-Streptomycin (Thermo Fisher).  Gibco™  Penicillin-Streptomycin (Sigma).

extract_protocol: Genomic DNA from each cell line was extracted using the QIAamp DNA mini Kit (Qiagen, Hilden, Germany) and quantified using Nanodrop (Thermo Fisher).

treatment_protocol: Control U87-EGFRvIII and mTORC2-suppressed (Rictor knockdown) cells were prepared with lentivirus-mediated delivery of shRNA targeting scramble sequences or human Rictor from Addgene (Watertown, MA). Cells were infected in the presence of 12.5 μg/ml Polybrene (Santa Cruz; Dallas, TX) and selected with puromycin (Sigma; St. Louis, MO).

value: glioblastoma cell line

tag: RNAi

value: Rictor


title: Rat1A Cells, Mutant R323, rep2


title: GS134_Placenta

city: Miami

first: Augusto

middle: F

last: Schmidt

state: FL

address: 1611 NW 12th ave

institute: University of Miami Miller School of Medicine

data_processing:
Alignment with RN6.0 genome build with Kallisto
Gene summarization and feature counts with tximport
Differental expression with DESeq2
Assembly: Rn6.0

source_name: Placenta, LPS exposed, 24hrs post intra-amniotic injection

extract_protocol:
Total RNA was extracted from tissue homogenates with QIAGEN Rneasy kit per manufacturer's intructions
After polyA selection, paired-end RNA-sequencing with 150bp was done with a depth of 30M reads.Library was generated at BGI Genomics.

tag: strain

value: Sprague-Dawley

tag: tissue

value: placenta

tag: gestational day

value: Day 18

value: LPS O55:B5 1- micrograms

value: 24 hrs post-injection


title: Rat1A Cells, Mutant R149, rep2

tag: genotype


title: GS123_Placenta

source_name: Placenta, placebo exposed, 24hrs post intra-amniotic injection

value: PBS


title: GS122_Placenta


title: ShScramble_2

source_name: Control glioblastoma cells

value: Scramble


title: ShRictor_1


title: Fetal lung, LPS exposed, 24hrs post intra-amniotic injection 2

source_name: lung

extract_protocol:
Total RNA was extracted from tissue homogenates with QIAGEN Rneasy kit per manufacturer's intructions
Afer polyA selection, paired-end RNA-sequencing with 150bp was done with a depth of 30M reads.
Library was generated at BGI Genomics

tag: breed

value: lung

tag: developmental stage

value: fetus, E18


title: Rat1A Cells, Empty, rep3

tag: cell line

value: E


title: Rat1A Cells, Wild Type, rep1


title: GS136_Placenta


title: Fetal lung, placebo exposed, 24hrs post intra-amniotic injection 2


title: Fetal lung, placebo exposed, 24hrs post intra-amniotic injection 3


title: Fetal lung, placebo exposed, 24hrs post intra-amniotic injection 1


title: Rat1A Cells, Empty, rep2


title: GS133_Placenta


title: spo mutant, stage 14, rep3

city: DALLAS

first: Zhi-Rong

last: Ruan

state: Texas

address: 6000 Harry Hines Blvd. NA8.102

department: Molecular Biology

institute: UTSouthwestern Medical Center

data_processing:
Single-end 100 bp read length Fastq files were checked for quality using fastqc (v0.11.2) and fastq_screen (v0.4.4)
Reads were quality trimmed using fastq-mcf (ea-utils, v1.1.2-806).
Trimmed fastq files were mapped to Drosophila genome using STAR(2.5.3a)
Read counts were generated using featureCounts (subread) for coding genes from gencode (v19)
Normalized read counts generated using edgeR
Assembly: dm6
Supplementary files format and content: tab delimited txt files that includes normalized read counts for each sample per gene

organism: Drosophila melanogaster

source_name: whole embryo

extract_protocol:
RNeasy Mini Kit (Qiagen)
KAPA mRNA HyperPrep Kit (Roche)

value: whole embryo

value: stage 14

value: spo mutant


title: GS124_Placenta


title: Fetal lung, LPS exposed, 24hrs post intra-amniotic injection 4


title: Fetal lung, LPS exposed, 24hrs post intra-amniotic injection 3


title: wild-type, stage 14, rep1

value: wild-type


title: spo mutant, stage 14, rep2


title: wild-type, stage 14, rep3


title: spo mutant, stage 14, rep1


title: wild-type, stage 14, rep2


title: Primary human BM cells, TP53 mutation, patient 1

city: Chicago

first: Yan

last: Liu

state: IL

address: 303 E. Superior Street, Lurie 5-107, Northwestern University

department: Department of Medicine

institute: Northwestern University

data_processing:
Replicate Multivariate Analysis of Transcript Splicing (rMATS, version 4.1.0) was used to identify alternative splicing events differentially observed between the control and mutation samples, given the RNA-seq alignment data (BAM) of the respective groups. Cutoff: FDR < 0.05.
Five types of splicing events: skipping exon (SE), mutually exclusive exon (MXE), alternative 5' splice site (A5SS), alternative 3' splice site (A3SS), and intron retention (RI) were considered, based on Gencode annotation (GRCh38.p13, hg38).
Assembly: hg38
Supplementary files format and content: A zip file contains 5 txt files of alternative splicing analysis
IJC_SAMPLE_1: Junction read counts (per each sample) supporting the inclusion form of splicing event, in sample group 1 (control)
SJC_SAMPLE_1: Junction read counts (per each sample) supporting the exclusion form of splicing event, in sample group 1 (control)
IJC_SAMPLE_2: Junction read counts (per each sample) supporting the inclusion form of splicing event, in sample group 2 (mutation)
SJC_SAMPLE_2: Junction read counts (per each sample) supporting the exclusion form of splicing event, in sample group 2 (mutation)
The junction read count (JC) values in each of these columns were in the same order of the provided sample files, i.e., *.BAM 1, 2, 3, ...

source_name: Bone marrow

extract_protocol:
RNAswere isolated using Rneasy Plus Micro or mini Kit
Srandard RNA-Seq Library Preparation

value: Bone marrow

value: primary human cells

value: hematopoietic stem and progenitor cells

value: Mutant p53


title: Ah20mirS2_Input

description: small RNAs from IP experiment - input fraction

value: immature floral buds

value: C24 Ah20mirS2

value: input fraction


title: Primary human BM cells, no-TP53 mutations, patient 2

value: WT p53


title: THA004

city: Boston

first: Shenglin

last: Mei

state: MA

address: 10 Shattuck Street

institute: Harvard medical school (DMBI)

description: Affymetrix CytoScan HD

hyb_protocol: DNA extraction from neuroblastoma samples was performed using the DNeasy blood and tissue kit (Qiagen) according to the manufacturer’s protocol. DNA quality was assessed using the Tapestation platform (Agilent).

scan_protocol: The Arrays were washed using affymetrix fluidics stations FS450 and scanned using the Gene Chip Scanner 3000.

data_processing: SNP microarray analysis was performed using the Cytoscan HD Array (Affymetrix) and data was processed using the Chromosome Analysis Suite version 3.3.0.139.

label: biotin

source_name: neuroblastoma

label_protocol: Sample DNA was digested by restriction enzymes NspI, adaptors were ligated to the diagested DNA to perform a PCR amplification. Amplified DNA was labeled and further fragmented using Affymetrix Cytoscan HD array kit and reagent kit bundle, (Affymetrix, Santa Clara, CA,US) to obtain biotin labeled DNA, as per manufacturer’s instruction.

tag: age (month)

tag: risk group

value: Low

tag: tumor type

value: Primary


title: CD34_R248W_3

source_name: Cord Blood

growth_protocol: CD34 cells were culture in Stem cell media: 50ml StemSpan, 500ul 100X anti-anti, 50ul of  human 100ng/ul TPO, FLT3 and SCF respectively. Adding 0.75uM or 1uM SR1. In humidified atmosphere with 5% of CO2 at 37C

extract_protocol:
RNAs were isolated using Rneasy Plus Micro Kit
Srandard RNA-Seq Library Preparation

treatment_protocol: CD34 cells were transduced with MIGR1 or p53R248W retroviruses, Cells were sorted for GFP, 48 hours after retroviral transduciton,

value: Cord Blood

value: CD34+ cells

value: HSPCs


title: CD34_R248W_2


title: CD34_MIGR1_4


title: CD34_MIGR1_3


title: THA018

description: Affymetrix CytoScan HD

extract_protocol: DNA extraction from neuroblastoma samples was performed using the DNeasy blood and tissue kit (Qiagen) according to the manufacturer’s protocol. DNA quality was assessed using the Tapestation platform (Agilent).

value: High


title: CD34_MIGR1_2


title: NB34

description: Affymetrix CytoScan HD


title: Primary human BM cells, TP53 mutation, patient 2


title: CD34_MIGR1_1


title: THA016

description: Affymetrix CytoScan HD


title: Primary human BM cells, no-TP53 mutations, patient 1


title: CD34_R248W_1


title: Primary human BM cells, TP53 mutation, patient 5


title: C14

value: Basal cells treated with vehicle

value: COPD


title: Turk-C33

city: Los Angeles

first: Matteo

last: Pellegrini

address: 610 Charles Young Drive East

institute: University of California, Los Angeles

data_processing:
Adapter sequences were trimmed off from the raw reads using Cutadapt (Martin, 2011) and only reads with minimum 10bp were kept for downstream analysis. Reads were aligned to GRCh38 reference genome using bsbolt align function and the duplicated reads were marked with samtools markdup function before calling methylation using bsbolt callmethylation function (Farrell et al, 2021). CGmaps from all samples were aggregated into one methylation count matrix using bsbolt aggregatematrix function with parameters -min-coverage 30 -min-sample 1.0.
Assembly: hg38
Supplementary files format and content: comma-separated text file containing methylation level per CpG site for each sample.

source_name: Buccal Swab

extract_protocol:
500 ng of extracted DNA were used for TBS-seq library preparation. Fragmented DNA was subject to end repair, dA-tailing and adapter ligation using the NEBNext Ultra II Library prep kit using custom pre-methylated adapters (IDT). Pools of 16 purified libraries were hybridized to the biotinylated probes according to the manufacturer’s protocol. Captured DNA was treated with bisulfite prior to PCR amplification using KAPA HiFi Uracil+(Roche) with the following conditions: 2 min at 98◦C; 14 cycles of (98◦C for 20 sec; 60◦C for 30 sec; 72◦C for 30 sec); 72◦C for 5 minutes; hold at 4◦C.
Library QC was performed using the High-Sensitivity D1000 Assay on a 2200 Agilent TapeStation. Pools of 96 libraries were sequenced on a NovaSeq6000 (S1 lane) as paired-end 150 bases.

value: Buccal Swab

value: PBMC

tag: age


title: Turk-C37


title: Turk-C32


title: Turk-C42


title: Turk-C26


title: THA019

description: Affymetrix CytoScan HD


title: Turk-C24


title: Turk-C16


title: Turk-C17


title: CD34_R248W_4


title: Turk-C40


title: Turk-C39


title: Turk-C14


title: Turk-C13


title: THA020

description: Affymetrix CytoScan HD


title: Turk-C12


title: Turk-9


title: Turk-C21


title: Turk-8


title: Turk-63


title: Turk-C31


title: Turk-9R


title: Turk-C18


title: Turk-C34


title: Turk-C28


title: Turk-5


title: Turk-58


title: Turk-8R


title: Turk-56


title: Turk-7R


title: Turk-67


title: Fetal lung, LPS exposed, 24hrs post intra-amniotic injection 1

value: Sprague-Dawley

value: lung

value: fetus, E18

value: LPS O55:B5 1- micrograms

tag: time

value: 24 hrs post-injection


title: Turk-46


title: Turk-54


title: Turk-48


title: Turk-47


title: Turk-60


title: Turk-64


title: Turk-52


title: Turk-44


title: Turk-5R


title: Turk-66


title: Turk-21R


title: Turk-51


title: Turk-53


title: Turk-20


title: Turk-50


title: Turk-22R


title: Turk-22


title: Turk-21


title: Turk-20R


title: Turk-19R


title: Turk-19


title: Turk-17


title: Turk-16


title: ShScramble_1

value: glioblastoma cell line

value: Scramble


title: Turk-15


title: Turk-15R


title: Turk-18


title: Turk-12


title: Turk-11R


title: HEK293T cells, KDtr Input

city: Gandhinagar

first: Umashankar

last: Singh

state: Gujarat

address: Acad Block 4 Room 317 IIT Gandhinagar Palaj

department: Biological Sciences and Engineering

country: India

institute: IIT Gandhinagar

description: Sample 16

data_processing:
For the samples 1 to 3, the raw sequenced reads were subjected to proprietary quality trimming (minimum Q20) for the IonTorrent platform. Quality-filtered reads with minimum length of 100 bases were used for further analysis. For the rest of the samples, the sequenced reads on the ONT platform were basecalled in real-time (minimum Qscore = 8) using guppy basecaller. The failed reads were subjected to basecalling in a locally installed guppy basecaller. The qualified reads were combined and subjected removal of sequencing adapters using Porechop with default options.
The reads were aligned using minimap2 against the unmasked hg38 (annotated chromosomes except chromosomes Y and M). The uniquely aligned reads were further analyzed for coverage on 0.2 kb genomic bins. Bins with coverage <3 and > 100 were eliminated for downstream analyzes.
Broadpeaks were called using MACS2 callpeak on the datasets against the inputs. A broadpeak q-value cutoff of 0.01 was used to call the peaks with a fixed background local lambda.
Assembly: hg38 (unmasked)
Supplementary files format and content: BED, broadpeaks discovered using MACS2 callpeak

source_name: HEK293T (stable cell line; CGGBP1-targeting shRNA)

growth_protocol: HEK293T cells, transduced with non-targeting lentiviral (CT) or CGGBP1-targeting (KD) shRNA, as described elsewhere (PMID 31547883), were cultured in DMEM supplemented with 10% fetal bovine serum and 1% antibiotic-antimycotic solution at 5% CO2 and 80% RH.

extract_protocol:
For all the G4-quadruplex immunoprecipitations, the cells were processed from two 10 cm dishes for each sample. The inputs were derived either from respective samples or by pooling from CT and KD samples. The immunoprecipitated DNA was purified using ethanol precipitation follwed by dissolution nuclease-free water.
Libraries were synthesized as follows:
(i) End-repair and pre-processing: As per the manufacturer’s instruction for Ion Express Plus Fragment Library kit (Cat. No. 4471269) from ThermoFisher Scientific for samples 1 to 3.
(ii) Sequencing library preparation: As per the manufacturer’s instruction for PCR sequencing kit (SQK-PSK004) from Oxford Nanopore Technologies for samples 4 to 16.
For samples 4 to 16, 4 – 8 ng of DNA were subjected to end-repair, ligation of PCR-adapters followed by fragment size selection using 0.4x AMPure XP beads. The adapter-ligated fragments were subjected to PCR amplification followed by size selection using 0.6x AMPure XP beads. The library was then subjected to sequencing adapter ligation followed by sequencing on MinION device using flow cells (R9.4.1). The mean length of the sequenced reads was in the range of 0.8 – 1 kb.
G4-quadruplex immunoprecipitation
Ion Torrent S5, ONT MinION Mk1B

treatment_protocol: Samples 1 and 2 were processed for G4-quadruplex immunoprecipitation using the AbC G4-ChIP protocol. The corresponding pooled input was also processed (Sample 3). Sample 4 was processed using the conventional G4-quadruplex immunoprecipitation (PMID: 29470465) alongside the corresponding input (Sample 5). For samples 6 and 7, the genomic DNA were extracted from untransduced HEK293T cells. The sonicated genomic DNA were  processed for in vitro G4-quadruplex immunoprecipitation directly (Sample 6) or after heat-denaturation and snap-chilling (Sample 7). The input (Sample 8) corresponding to the Samples 6 and 7 was the genomic DNA without any immunoprecipitation. Samples 9 and 11 were processed using AbC G4-ChIP without any transfection of control DNA (pGEMT Easy vector carrying an insert with G4-quadruplex-forming signature sequence). For samples 9 and 11, 500ng of each of the control DNA and a carrier DNA (vector carrying an insert devoid of G4-quadruplex-forming sequence signature) were first mixed, treated with 150 mM KCl, incubated with 1H6 antibody, crosslinked and added to the respective cell lysates for sonication and subsequent steps. Samples 10 and 12 were the inputs for samples 9 and 11 respectively. Samples 13 and 15 were transfected with 1.25 ug of each of control and carrier DNA mix per 10 cm dish using calcium-phosphate transfection method. Following 12 hours of transfection, the cells were processed for G4-quadruplex immunoprecipitation using AbC G4-ChIP. Samples 14 and 16 were the inputs for samples 13 and 15 respectively. From the step of reverse-crosslinking till elution, the inputs were treated the same way as the immunoprecipitated samples.

tag: treatment

value: CGGBP1-targeting shRNA

tag: antibody

value: Chromatin


title: Turk-14R


title: Turk-18R


title: Turk-11


title: HEK293T cells, KDtr

description: Sample 15

value: Anti-G4 1H6 antibody (Sigma; MABE1126)

tag: fraction


title: Turk-110

tag: cell type


title: Turk-10R


title: Turk-10


title: HEK293T cells, KDut Input

description: Sample 12


title: Turk-108


title: Turk-107


title: Turk-17R


title: HEK293T cells, KDut

description: Sample 11


title: Turk-105


title: HEK293T cells, CTtr Input

description: Sample 14

source_name: HEK293T (stable cell line; non-targeting shRNA)

value: non-targeting shRNA


title: Turk-104


title: Turk-14


title: HEK293T cells, CTut

description: Sample 9


title: Turk-16R


title: HEK293T cells, CTtr

description: Sample 13


title: SalivaDiabetes_20094


title: SalivaDiabetes_20092


title: HEK293T cells, CTut Input

description: Sample 10


title: Turk-12R


title: HEK293T cells, G4-ChIP

description: Sample 4


title: Turk-109


title: HEK293T cells, In vitro Input

description: Sample 8

value: Genomic DNA


title: SalivaDiabetes_20093


title: SalivaDiabetes_20091


title: HEK293T cells, G4-ChIP Input

description: Sample 5


title: HEK293T cells, In vitro G4 DNA-IPnat

description: Sample 6


title: SalivaDiabetes_20089


title: SalivaDiabetes_20085


title: BMDMs, Petri_IL_4_DMSO_4

city: New Haven

first: Scott

middle: Dean

last: Pope

state: Connecticut

address: 300 Cedar St

department: Immunobiology

institute: Yale School of Medicine

data_processing:
Paired-end sequencing was performed with Illumina instrument with paired end reads of 38 base pairs. Illumina fastq files were downloaded from Illumina Basespace, and adapters were removed with Cutadapt using the option “-a CTGTCTCTTATA -A CTGTCTCTTATA -m 23”. Reads were then mapped to the mm9 mouse genome with Bowtie2 using the option “-k 10 -X 1000 –end-to-end –very-sensitive”. Sam files were converted to Bam files, and read duplicates were removed using Picard. Blacklist regions and mitochondrial genomic reads were removed using BEDTools and Picard, respectively. Bam files were converted to Bed files also using BEDTools, and macs2 was used to call peaks using the converted bed file. Macs2 call-peak options used were “-f BED -g mm -q 0.05 --nomodel --shift -75 --extsize 150 --keep-dup all”. To count the number of reads in each peak, featureCounts was used. Read counts were normalized using the TMM method in EdgeR.
Assembly: mm9
Supplementary files format and content: peaks_annotate_NCBI.csv (normalized counts)
Supplementary files format and content: narrowPeak

source_name: bone marrow-derived macrophage

growth_protocol: BMDMs were differentiated from mouse bone marrow cells in macrophage growth media (MGM) composed of 30% L929-cell conditioned media and 70% complete RPMI media (cRPMI), which consisted of RPMI-1640 (Corning) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Gibco), 2 mM L-glutamine, 200 U/mL penicillin/streptomycin, 1 mM sodium pyruvate, and 10 mM HEPES. Bone marrow was prepared by crushing C57BL/6J mouse femurs and tibias to release marrow, followed by ACK (ammonium-chloride-potassium) lysis of red blood cells and passage through a 70-μm cell strainer. Bone marrow was plated at 5 × 106 cells in 20 mL of MGM in a non-tissue culture (non-TC) dish (Day 0). Every three days, cells were supplemented with 10 mL of MGM. After day 6, adherent cells were lifted with cold phosphate-buffered saline (PBS) containing 5 mM EDTA and used for experiments.

extract_protocol:
ATAC-seq was performed according to the protocol detailed by Buenrostro and colleagues.
ATAC-seq library was created according to the protocol detailed by Buenrostro and colleagues.
fragmented DNA

treatment_protocol: For stimulation of BMDMs, recombinant murine IL-4 (Peprotech, 214-14) was used at 20 ng/mL, recombinant murine MCSF (Cell Signaling Technologies, 5228) at 100 ng/mL and latrunculin A (Cayman Chemical, 10010630 or Sigma, 428021) at 1 uM.

value: bone marrow-derived macrophage

value: wild-type

value: DMSO+24 hrs. IL-4


title: SalivaDiabetes_20090

value: Buccal Swab


title: BMDMs, Petri_IL_4_2

value: 24 hrs. IL-4


title: HEK293T cells, In vitro G4 DNA-IPdenat

description: Sample 7


title: BMDMs, Petri_IL_4_LatA_6

value: LatA+24 hrs. IL-4


title: SalivaDiabetes_20086

value: PBMC


title: SalivaDiabetes_20080


title: SalivaDiabetes_20081


title: SalivaDiabetes_20084


title: BMDMs, Petri_Untx_DMSO_3

value: DMSO


title: SalivaDiabetes_20083


title: SalivaDiabetes_20078


title: 20200923_Hide092320_8hrCIS-AJ3_12

city: cleveland

first: Hidetoshi

last: Tsuda

state: ohio

address: 9500 euclid ave

institute: cleveland clinic

description: Pancancer panel includes 784 probes including 6 positive control and 8 negative control.

hyb_protocol: Hybridization was followed NanoString nCounter XT gene expression assay protocol. Briefly,  for pereparation of master mix,  hybridization buffer was mixed with the Reporter CodeSet, the master mix, samples and Rnase-fee water were added to each tube and then Panel Capture codeset was added.All samples were incubated for 16 hours at 65 degree.

scan_protocol: Targeted mRNA hybridized with the capture probe was counted using the NanoString nCounter instrument (Nanostring)

data_processing: Raw Data  was normalized and analyzed in the nCounter Advanced Analysis 2.0 software (Nanostring)

source_name: Apex of  the graft

label_protocol: Total RNA was reverse-transcribed using the High-Capacity cDNA Reverse Transcription Kit (Applied Biosystem) according to the instructions.

extract_protocol: Total RNA was extracted using an RNeasy Fibrous Tissue Mini kit (QIAGEN) for  grafts  according to the instructions.

value: mouse heart

tag: status

value: Alive

tag: Sex

value: Male

value: 8hrs cold ischemic storage

tag: cartridgeid


title: SalivaDiabetes_20082

tag: tissue


title: BMDMs, Petri_Untx_1

tag: strain

tag: genotype


title: 20200923_Hide092320_8hrCIS-AJ1_10


title: SalivaDiabetes_20075


title: BMDMs, Petri_IL_4_MCSF_10

value: MCSF+24 hrs. IL-4


title: SalivaDiabetes_20087


title: 20200923_Hide092320_8hrCIS-AJ2_11


title: SalivaDiabetes_20074


title: SalivaDiabetes_20073


title: 20200923_Hide092320_30minCIS-AJ2_05

value: 30mins cold ischemic storage


title: SalivaDiabetes_20077


title: 20200923_Hide092320_30minCIS-AJ1_04


title: 20200923_Hide092320_30minCIS-AJ3_06


title: SalivaDiabetes_20076


title: 20200923_Hide092320_30minCIS+p40-2_08

value: Recombinant p40 homo dimers


title: X99.144.6.brca1.mutated

first: Olufunmilayo

middle: I

last: Olopade

address: 900 E. 57th Street

institute: University of Chicago

description: RNA expression from breast tumors

hyb_protocol: Extracted RNA samples were hybridized to capture and reporter probes for the measured genes. These multiplexed hybridizations were carried out in a single-tube for 15-21 hours at 65˚C using 100 ng RNA.

scan_protocol: The signals were scanned on the nCounter Analysis system according to the manufacture’s protocols.

data_processing:
For the algorithm to produce precise results, data for the test samples had to meet a minimum threshold for expression of normalizing genes.
The normalized gene expression profile of each breast tumor sample was correlated to the prototypical gene expression profiles of the main breast cancer intrinsic subtypes.

source_name: Breast Tumor

label_protocol: The target-probe complexes were processed on the nCounter Analysis system according to the manufacture’s protocols.

extract_protocol: Total RNA was extracted from FFPE breast tumors using an RNA extraction kit (Roche)

treatment_protocol: Formalin-fixed paraffin-embedded (FFPE) tumor blocks from the surgical specimen

value: Breast Tumor

tag: gender

value: Female

tag: ethnicity

value: Cau

value: Basal


title: SalivaDiabetes_20072


title: 20200923_Hide092320_30minCIS+p40-1_07


title: SalivaDiabetes_20067


title: X99.094.1.brca1.mut

description: RNA expression from breast tumors


title: 20200923_Hide092320_30minCIS+p40-3_09


title: SalivaDiabetes_20071


title: SalivaDiabetes_20064


title: Rat1A Cells, Empty, rep1

tag: cell line

value: Normal Primary Fibroblast Cells

value: E


title: X99.021.42.brca1.mutated

description: RNA expression from breast tumors


title: SalivaDiabetes_20062

value: Buccal Swab


title: X98.151.6

description: RNA expression from breast tumors

value: AA


title: SalivaDiabetes_20070

value: PBMC


title: SalivaDiabetes_20060


title: SalivaDiabetes_20069


title: SalivaDiabetes_20059


title: X99.144.1.brca1.mut

description: RNA expression from breast tumors


title: SalivaDiabetes_20068


title: X94.13.1.brca1.mut

description: RNA expression from breast tumors


title: SalivaDiabetes_20066


title: SalivaDiabetes_20063


title: X98.19284

description: RNA expression from breast tumors

value: LumB


title: X99.229.6

description: RNA expression from breast tumors


title: X98.11.6.brca2.mut

description: RNA expression from breast tumors


title: SalivaDiabetes_20061


title: X95.42.1.brca1.mut

description: RNA expression from breast tumors


title: SalivaDiabetes_20054


title: X93.8676S

description: RNA expression from breast tumors


title: X3_bx_ng

description: RNA expression from breast tumors

value: Nig


title: SalivaDiabetes_20052


title: SalivaDiabetes_20051


title: X2006.35.1

description: RNA expression from breast tumors


title: X2006.148.1.brca1.methyl

description: RNA expression from breast tumors


title: X6_BX_NG

description: RNA expression from breast tumors


title: SalivaDiabetes_20057


title: SalivaDiabetes_20055


title: X99.009.01.brca1.methyl

description: RNA expression from breast tumors

value: LumA


title: X2005.54.1

description: RNA expression from breast tumors


title: X2006.53.1

description: RNA expression from breast tumors


title: SalivaDiabetes_20046


title: X2005.349.1.brca1.mutated

description: RNA expression from breast tumors


title: SalivaDiabetes_20053


title: SalivaDiabetes_20050


title: SalivaDiabetes_20058


title: X2005.259.1

description: RNA expression from breast tumors


title: X2006.108.1.brca1.methyl

description: RNA expression from breast tumors


title: X2005.238.1

description: RNA expression from breast tumors


title: SalivaDiabetes_20049


title: X2005.89.1.brca1.mutated

description: RNA expression from breast tumors


title: SalivaDiabetes_20043


title: SalivaDiabetes_20042


title: SalivaDiabetes_20041


title: X2005.35.1

description: RNA expression from breast tumors


title: SalivaDiabetes_20048


title: X2004.87.1.brca1.mut

description: RNA expression from breast tumors


title: SalivaDiabetes_20040


title: X5_bx_ng

description: RNA expression from breast tumors


title: SalivaDiabetes_20056


title: SalivaDiabetes_20045


title: X2006.75.1

description: RNA expression from breast tumors


title: SalivaDiabetes_20044


title: SalivaDiabetes_20038


title: SalivaDiabetes_20047


title: X2004.59.1.brca2.mut

description: RNA expression from breast tumors


title: X2005.117.1

description: RNA expression from breast tumors


title: X2005.184.1.brca1.methyl

description: RNA expression from breast tumors


title: X2004.59.1.brca2.mut.2

description: RNA expression from breast tumors


title: X2004.59.1.brca2.mut.1

description: RNA expression from breast tumors


title: SalivaDiabetes_20039


title: SalivaDiabetes_20032

source_name: Blood

value: Blood


title: X2004_04_1.brca2.mut

description: RNA expression from breast tumors


title: SalivaDiabetes_20033


title: SalivaDiabetes_20037


title: X2004.400.1

description: RNA expression from breast tumors


title: X2004.229.1

description: RNA expression from breast tumors


title: X2004.418.1

description: RNA expression from breast tumors


title: X2004.101.1

description: RNA expression from breast tumors


title: SalivaDiabetes_20028


title: SalivaDiabetes_20034


title: SalivaDiabetes_20035


title: SalivaDiabetes_20029


title: X2004.406.1

description: RNA expression from breast tumors


title: SalivaDiabetes_20030


title: SalivaDiabetes_20026


title: SalivaDiabetes_20025


title: SalivaDiabetes_20024


title: X2003.85.1

description: RNA expression from breast tumors


title: SalivaDiabetes_20031


title: X2003.21.1.brca1.mutated

description: RNA expression from breast tumors


title: X2003.168.1.brca1.mutated

description: RNA expression from breast tumors


title: X2003.166.1

description: RNA expression from breast tumors


title: X2003.133.1

description: RNA expression from breast tumors

value: Normal


title: SalivaDiabetes_20022


title: X2002.97.41

description: RNA expression from breast tumors


title: SalivaDiabetes_20020


title: X2002.59.1.brca2.mut

description: RNA expression from breast tumors


title: X2004.261.1

description: RNA expression from breast tumors


title: SalivaDiabetes_20021


title: SalivaDiabetes_20019


title: SalivaDiabetes_20018


title: SalivaDiabetes_20016


title: X2002.217.1

description: RNA expression from breast tumors


title: SalivaDiabetes_20015


title: SalivaDiabetes_20014


title: X2002.161.1.brca2.mut

description: RNA expression from breast tumors


title: X2002.212.1

description: RNA expression from breast tumors


title: X2002.228.1

description: RNA expression from breast tumors


title: X2001.70.1.brca1.mut

description: RNA expression from breast tumors


title: X2001.263.1

description: RNA expression from breast tumors


title: SalivaDiabetes_20012


title: SalivaDiabetes_20011


title: SalivaDiabetes_20013


title: X2001.239.1

description: RNA expression from breast tumors


title: X2001.228.1

description: RNA expression from breast tumors


title: SalivaDiabetes_20010


title: SalivaDiabetes_20009


title: X2001.188.1

description: RNA expression from breast tumors


title: X2001.221.1.brca1.mut

description: RNA expression from breast tumors


title: SalivaDiabetes_20006


title: SalivaDiabetes_20008


title: SalivaDiabetes_20007


title: X2001.062.1

description: RNA expression from breast tumors


title: SalivaDiabetes_20005


title: X16_BX_NG

description: RNA expression from breast tumors


title: X14_BX_NG

description: RNA expression from breast tumors


title: SalivaDiabetes_20003


title: X15_BX_NG

description: RNA expression from breast tumors


title: X10_BX_Ng

description: RNA expression from breast tumors


title: SalivaDiabetes_20004


title: X13_BX_NG

description: RNA expression from breast tumors


title: SalivaDiabetes_20002


title: SalivaDiabetes_20001


title: SalivaDiabetes_20000


title: TB310.FFPE

description: RNA expression from breast tumors


title: TB280.FFPE

description: RNA expression from breast tumors


title: TB283

description: RNA expression from breast tumors


title: TB313

description: RNA expression from breast tumors


title: Neonate1075


title: X2003.130.1.brca1.mutated

description: RNA expression from breast tumors


title: Neonate1074


title: TB263.FFPE

description: RNA expression from breast tumors


title: Neonate1073


title: TB251

description: RNA expression from breast tumors


title: TB251.FFPE.REPEAT

description: RNA expression from breast tumors


title: TB245

description: RNA expression from breast tumors


title: Neonate1069


title: Neonate1072


title: TB217.FFPE

description: RNA expression from breast tumors


title: TB189

description: RNA expression from breast tumors


title: Neonate1050


title: Neonate1057


title: Neonate1052


title: Neonate1051


title: Neonate1048


title: TB170.FFPE.REPEAT

description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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title: PN0249.1S.T

description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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title: PN0247.G.T

description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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title: PN0236.G.T

description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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title: 130029


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title: PN0114.T.T

description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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title: PFitness_95


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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title: PFitness_91


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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title: PFitness_86


title: PFitness_87


title: PFitness_84


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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title: PFitness_92


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description: RNA expression from breast tumors


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title: N010842

description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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title: H500.12_206422550217_01_05

description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors


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description: RNA expression from breast tumors