title: BEAS-2B Steen Glu 4

city: Toronto

first: Jamie

middle: E.

last: Jeon

state: Ontario

address: 101 College St.

institute: University of Toronto

data_processing:
Kallisto used for pseudoalignment and obtaining abundance estimates
BiomaRt used for accessing human gene data set from ensembl
Tximport used for building an annotated gene-level count matrix
DESeq2 used for differential gene expression analysis after loading in unnormalized gene count matrix
Assembly: hsapiens_gene_ensembl (version 107)
Supplementary files format and content: Tab delimited text files containing normalized counts of 21,358 genes for each sample (DESeq2 output)

growth_protocol: Cells were passaged in low glucose Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS) and Pen/Strep (100 U/100μg/ml) (Thermo Fisher Scientific; Burlington, Canada). For HPMEC cells, the flasks and plates were coated with 0.2% gelatin at least 2h before seeding the cells.

extract_protocol:
All wells were washed twice with PBS. Then 1 mL trypsin was added to each well to digest the cells for 2 min at 37°C, and 1 mL media was added for each well before collecting the pellets. Pellets were retrieved after centrifuging at 250g for 5 min, twice, then they were snap-frozen at -80°C before usage. RNeasy Mini Kit was used for RNA isolation according to the manufacturer recommendation (Cat. No.74904, QIAGEN; Hilden, Germany). The isolated RNA samples were purified with PureLink™ DNase Kit (Cat. No. 12185-010, Invitrogen; Carlsbad, CA, USA). RNA purity was measured by using the ratio of absorbance at 260nm/280nm for quality control.
The RNA samples were then sent to Princess Margaret Genomics Centre (Toronto, Canada) for total bulk RNA-sequencing. Illumina NovaSeq 6000 (San Diego, CA, USA) was used to yield FASTQ files after quality assessment of samples using qPCR, BioAnalyzer and TapeStation (Agilent; Santa Clara, CA, USA) as well as quality control of the sequencing data. FASTQ files and their corresponding quality control data were received from the facility.

treatment_protocol: Briefly, 30,000 cells were cultured in 6-well plates until sub-confluent in serum-containing cell culture medium (DMEM + 10% FBS) at 37°C with 5% CO2, and then cold preservation was applied by replacing DMEM + 10% FBS (D10) with 4°C Perfadex® preservation solution (Vitrolife; Englewood, CO) with 0.3 ml/L Tham and 0.6 ml/L CaCl2, and cells were stored at 4°C in a sealed chamber filled with 50% O2 for 18h to mimic cold ischemic time (CIT). IR simulation was done by replacing the cold Perfadex® solution back to the DMEM + 10% FBS (D10) for 4h at 37°C with 5% CO2. Similarly, EVLP simulation was completed by switching from the cold Perfadex® solution to Steen solution (XVIVO; Göteborg, Sweden) for 4h at 37°C with 5% CO2.

value: Human Lung Epithelial Cells

value: Steen + 4mM Glutamax 37°C 5% CO2 4h


title: BEAS-2B Steen Glu 3

status: Public on May 30 2023

type: SRA

department: Physiology

country: Canada

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: treatment


title: BEAS-2B Steen Glu 1


title: BEAS-2B Steen 4

value: Steen 37°C 5% CO2 4h


title: Microglia, Bile_duct_ligation, 14days, rep3

city: Zwijnaarde

first: Roosmarijn

last: Vandenbroucke

state: Gent

address: Technologiepark-Zwijnaarde 71

department: VIB Center for Inflammation Research

country: Belgium

institute: VIB-UGent

description:
B_14_3_MICRO_S45
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt

data_processing:
Illumina software was used for basecalling.
Sequenced reads were inspected with FastQC v0.11.8, trimmed for adaptor sequences with Trimmomatic v0.39, then mapped to mm10 whole genome using STAR v2.7.3a, converted to BAM-files with Samtools v1.9 and finally counted with HTSeqCount v0.11.2
Limma v3.42.2 was used to normalize the count data.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample (one file for microglia samples and another file for astrocyte samples)
Supplementary files format and content: Matrix table with log-CPM values for all biologically meaningfully expressed genes for each sample (one file for microglia samples and another file for astrocyte samples)

organism: Mus musculus

source_name: Microglia

extract_protocol:
After euthanasia using an overdose of ketamine (87.5 mg/kg) and xylazine (12.5 mg/kg), mice were perfused transcardially using 10 ml 0.2 % heparin in ice-cold D‐PBS per mouse  at a flow rate of 4.50 ml/min. Whole brain samples were isolated from the skull, weighed and collected in 1.5 mL ice-cold 1x HBSS -/- . Brains were cut into pieces using spring scissors and slurry was dissociated into single cell suspensions using the Neural Tissue Dissociation Kit (P) (Miltenyi Biotec). Cells were enzymatically dissociated using activated enzyme (P) for 15 min at 37 °C and enzyme (A) for 2x10 min at 37 °C under continuous nutation, with mechanical dissociation by trituration 10 times with a 5 ml serological pipet in between enzymatic dissociation steps. Subsequently, samples were passed through a 70 µM cell strainer. Myelin was removed by centrifugation (300g, 11 min, room temperature, low acceleration/break) of samples in 24 % Percoll PLUS and 75 U/ml DNase. After aspiration of the myelin layer and supernatant, cell pellet was resuspended in 50 µL of FACS buffer (0.5% BSA in D‐PBS). This process was repeated twice. Single cell suspensions were pre-incubated with Fc Block (1/100; BD Biosciences, 553142) for 10 min at 4 °C and stained with appropriate antibodies diluted at 4 °C in the dark for 30 min. After washing and centrifugation (400g, 7min, 4°C), supernatans was removed and pellets were resuspended in FACS buffer and transferred through a 35 µm mesh into a 5 ml Falco®Round‐Bottom Polystyrene Test Tube with Cell Strainer Snap Cap. Cell viability was assessed using DAPI 1/200, added immediately prior to sorting. Cell sorting was performed on the FACSymphony S6 using the 85 µm nozzle.  Cells were sorted into 2 ml Eppendorf tubes containing 450 µL RLT Plus lysis buffer (QIAGEN) containing 1% β-mercaptoethanol. The samples were extensively vortexed and stored at ‐80 °C until RNA isolation. Total RNA from sorted cells was extracted using the RNeasy ®Plus Micro Kit (QIAGEN, 74034) according to the manufacturer’s instructions. The concentration and purity of the RNA was determined using the Agilent RNA 6000 Pico Kit (Agilent) and the Agilent 2100 Bio-Analyzer. A RIN value of 7 or higher was required to proceed. 1 ng of total RNA was used for constructing sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Under isoflurane inhalation anesthesia, a midline abdominal incision was made and the common bile duct was isolated from the flanking portal vein. Next, the common bile duct was occluded with a double ligature of a non-resorbable suture (Mersilk 5-0, Ethicon 682H) and cut in between ligatures to prevent recanalization. In sham mice, the common bile duct was isolated without ligation or resection. All mice received buprenorphine 0.1 mg/kg intraperitoneally for 72 hours to prevent postoperative pain and distress. All mice were sacrificed 14 and 28 days post-surgery.

tag: Sex

value: Male

tag: strain

value: Microglia

tag: timepoint


title: BEAS-2B Steen 3


title: Microglia, Bile_duct_ligation, 14days, rep6

description:
B_14_6_MICRO_S48
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: E10.5 Mx, Twist1

city: Stanford

first: Seungsoo

last: Kim

state: CA

address: 265 Campus Dr

department: Chemical and Systems Biology

country: USA

institute: Stanford University

library_source: genomic

data_processing:
Reads were trimmed of Truseq adapter sequences and low-quality bases (-Q 10) using skewer v0.2.2.
Trimmed reads were mapped to the hg38 analysis set (human), mm39 (mouse), or a combined reference genome using Bowtie2 v2.4.1 with the options --very-sensitive -X 2000.
Reads were deduplicated with samtools v1.10 markdup and uniquely mapped reads (-q 20) mapped to the main chromosomes (excluding mitochondria and unplaced contigs) were retained using samtools view.
MACS2 v2.2.7.1 was used to call peaks using the IgG sample as a negative control, with options -f BAMPE --nomodel --keep-dup all --call-summits -g hs (human) or mm (mouse) with the -B option for H3K27ac.
bigWig tracks were generated with deeptools v3.5.0 bamCoverage -bs 10 --normalizeUsing RPGC --samFlagInclude 64 --samFlagExclude 8 --extendReads with 1h dTAG samples normalized by the fraction of reads mapping to the E. coli genome.
H3K27ac ChIP reads were counted over merged ATAC peaks using deeptools v3.5.0 multiBamSummary with options -e --outRawCounts.
Assembly: hg38 or mm39
Supplementary files format and content: bigWig, narrowPeak (except for input samples, H3K27ac ChIPs, and V5 ChIPs of dTAG-treated samples) for each sample, and tab-delimited text (.txt) files with read counts of H3K27ac ChIPs over merged ATAC peaks

molecule: genomic DNA

source_name: Mouse E10.5 maxillary prominences

growth_protocol: H9 cells (WiCell, WA09, RRID:CVCL_9773) were cultured in feeder-free conditions, in mTeSR1 medium (Stem Cell Technologies, 85850) on Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix (Corning, 356231) and passaged using ReLeSR (Stem Cell Technologies, 05872) every 4-6 days. Cells were switched to mTeSR Plus medium (Stem Cell Technologies, 100-0276) prior to and during genome editing and clonal expansion, but switched back to mTeSR1 before differentiation to CNCC. hESCs were differentiated to CNCC as previously described. Briefly, hESC colonies were partially detached from the plate with collagenase IV (Gibco, 17104019) in Knockout DMEM medium (Gibco, 10829018) for 30-60 min and scraped to break up large colonies, and then cultured in Neural Crest Differentiation Medium (50%-50% v/v mixture of DMEM/F12 1:1 medium with L-glutamine, without HEPES (Cytiva, SH30271.FS) and Neurobasal medium (Gibco, 21103049) with 0.5x N2 NeuroPlex (Gemini Bio, 400-163) and Gem21 NeuroPlex (Gemini Bio, 400-160) supplements and GlutaMAX (Gibco, 35050061), and 1x antibiotic/antimycotic, and 20 ng/ml EGF (Peprotech, AF-100-15), 20 ng/ml bFGF (Peprotech, 100-18B), and 5 ug/ml bovine insulin (Gemini Bio, 700-112P)) for 11 days in bacterial-grade petri dishes, changing the plate to prevent attachment for 4 days and then leaving the cells unfed for two days to allow attachment, and then fed as needed at least every other day. At day 11, cells (now called ‘early hCNCC’) were harvested by treatment with Accutase (Sigma-Aldrich, A6964-100ML), strained to remove residual neuroectodermal spheres, and plated onto plates coated with 7.5 ug/ml human fibronectin (Millipore, FC010-10MG) and cultured in Neural Crest Maintenance Medium (Neural Crest Differentiation Medium with bovine insulin replaced by 1 mg/ml BSA (Gemini Bio, 700-104P)). These hCNCC were then passaged every 2-3 days upon reaching confluency, with cells in the third or subsequent passages defined as ‘late hCNCC’ and cultured with added 50 pg/ml BMP2 (Peprotech, 120-02) and 3 uM CHIR-99021 (Selleck, S2924). dTAGV-1 (Tocris, 6914/5) was dissolved in DMSO at 5 mM and then diluted to 250 uM in 60% DMSO/40% water (v/v) before dilution to 500 nM for acute depletions (up to 1 day) or diluted directly from the 5 mM stock for long-term depletions.  RS4;11 cells (ATCC, CRL-1873, RRID:CVCL_0093) were cultured in RPMI-1640 medium (Gibco, 11875093) supplemented with 10% v/v FBS and 1x antibiotic/antimycotic.  HEK293 cells (ATCC, CRL-1573, RRID:CVCL_0045) and 293FT cells (Invitrogen, R70007, RRID:CVCL_6911) were cultured in DMEM high glucose medium with sodium pyruvate and L-glutamine, supplemented with 10% v/v FBS and 1x GlutaMAX, non-essential amino acids, and antibiotic/antimycotic.  O9-1 cells (Millipore, SCC049, RRID:CVCL_GS42) used for spike-in controls for ChIPs of TWIST1 depletions were cultured in Complete ES Cell Medium with 15% FBS (Millipore, ES-101-B), 25 ng/ml bFGF, and mLIF (Millipore, ESG1107).

extract_protocol:
Cells (about 1 confluent 10-cm plate or ~10-20 million cells) were crosslinked with 1% methanol-free formaldehyde (Pierce, 28908) in PBS for 10 min at room temperature and then quenched by adding 2.5 M glycine to 125 mM final concentration and incubating for 10 min. Cells were washed in PBS with 0.001% v/v Triton X-100, harvested by scraping, and collected by centrifugation for 5 min at 4°C. Cells were washed with PBS and flash frozen for storage at -80°C. Cell pellets were later thawed on ice for 30 min, and then sequentially resuspended in lysis buffer 1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% Igepal CA-630, 0.25% Triton X-100, 1x cOmplete EDTA-free protease inhibitor cocktail (PIC), 1 mM PMSF), lysis buffer 2 (10 mM Tris-HCl pH 8, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1x cOmplete EDTA-free protease inhibitor cocktail, 1 mM PMSF), and lysis buffer 3 (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine, 1x PIC, 1 mM PMSF), with 10 min incubations in each buffer, with rotation. Lysates were sonicated for 10-15 cycles of 30s ON/30s OFF on high power using the Bioruptor Plus (Diagenode), then diluted in additional lysis buffer 3 and clarified by centrifugation for 10 min at max speed at 4°C. Triton X-100 was added to 1%, and a small aliquot was used to extract DNA to check chromatin yield and size distribution, by dilution in elution buffer (1% w/v SDS and 100 mM NaHCO3) and incubation with 200 mM NaCl and RNase A (Thermo, EN0531) at 65°C for 1 h, then proteinase K (Thermo, EO0491) at 65°C for 1 h, and clean up with the ChIP DNA Clean & Concentrator-5 kit (Zymo, D5205). DNA was quantified by Qubit dsDNA high sensitivity kit, and the remaining chromatin was then normalized for immunoprecipitations. For TWIST1 acute depletions, chromatin from O9-1 mouse CNCCs were added prior to ChIP at ~10% of the total chromatin as a spike-in control. For H3K27ac, 5 ug of antibody was used per ChIP; for TFs, 9 ug of antibody was used per ChIP, except for dissected mouse embryos where 4.5 ug was used in half of the total ChIP volume. ChIPs were incubated overnight, then incubated for 4-6h with 100 ul Dynabeads Protein A (Invitrogen, 10002D) or Protein G (Invitrogen, 10004D) prewashed with 0.1% w/v BSA in PBS, then washed 5x with RIPA wash buffer (50 mM HEPES-KOH pH 7.5, 500 mM LiCl, 1 mM EDTA, 1% Igepal CA-630, 0.7% w/v sodium deoxycholate), once with 50 mM Tris-HCl pH 8, 10 mM EDTA, 50 mM NaCl, and eluted in elution buffer at 65°C for 30 min. Eluate was then reverse crosslinked and treated with RNase A and proteinase K, and then DNA was extracted with the ChIP DNA Clean & Concentrator-5 kit.
Libraries were prepared using the NEBNext Ultra II DNA kit (New England Biolabs, E7645S) using up to 50 ng of input or ChIP DNA, with ~4-8 cycles of amplification, with no pre-PCR size selection but a post-PCR double-sided 0.5x/0.9x Ampure XP bead clean-up.

treatment_protocol: DMSO or dTAGV-1 (500 nM) were added by dilution into media before changing media. HEK293 cells were transfected with Lipofectamine 2000 (Invitrogen, 11668019) at a ratio of 2.8 ul lipofectamine per ug of DNA, diluted in Opti-MEM. Cells were transfected with 2.5 ug DNA per well of a 6-well plate or 15 ug DNA per 10-cm plate 1-2 days after seeding, when they reached 70-90% confluency. Media was replaced 4-6h after transfection, and then cells were harvested for Western blot or chromatin immunoprecipitation at 24 h after transfection.

value: Mouse E10.5 maxillary prominences

tag: genotype

value: WT

tag: clone

tag: time

tag: spike-in cell_type

tag: spike-in cell_line

tag: antibody

value: TWIST1 (Abcam, #ab50887)

tag: reference genome_for_alignment

tag: reference genome_for_processed_files


title: BEAS-2B Steen Glu 2


title: Microglia, Bile_duct_ligation, 14days, rep5

description:
B_14_5_MICRO_S47
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: Microglia, Bile_duct_ligation, 14days, rep4

description:
B_14_4_MICRO_S46
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: BEAS-2B D10 2

value: DMEM + 10% FBS 37°C 5% CO2 4h


title: Microglia, Sham, 14days, rep6

description:
S_14_6_MICRO_S42
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt

value: Sham


title: BEAS-2B D10 4


title: E10.5 FNP, Twist1

source_name: Mouse E10.5 frontonasal prominences

value: Mouse E10.5 frontonasal prominences


title: BEAS-2B D10 3


title: Microglia, Bile_duct_ligation, 14days, rep2

description:
B_14_2_MICRO_S44
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: BEAS-2B Steen 2


title: BEAS-2B Steen 1


title: TWIST1FV, 3h dTAG, rep1

data_processing:
Reads were trimmed of Nextera adapter sequences and low-quality bases (-Q 10) using skewer v0.2.2.
Trimmed reads were mapped to the hg38 analysis set reference genome using Bowtie2 v2.4.1 with the options --very-sensitive -X 2000.
Reads were deduplicated with samtools v1.10 markdup and uniquely mapped reads (-q 20) mapped to the main chromosomes (excluding mitochondria and unplaced contigs) were retained using samtools view.
Read ends were shifted inward 5 bp (+5 bp on + strand, -5 bp on - strand) for each fragment.
MACS2 v2.2.7.1 was used to call peaks and generate coverage tracks using the IgG sample as a negative control, with options --shift -100 --extsize 200 -f BED --nomodel --keep-dup all --call-summits -g hs --SPMR.
bedgraph tracks from MACS2 were converted to bigWig format using UCSC bedGraphToBigWig
Reads were counted over merged peaks using bedtools intersect.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak for each sample, tab-delimited text files (.txt) with counts of samples for each comparison (across all replicates), and bed files with coordinates of merged peaks or the top summit from each merged peak with the -log10(pvalue) from MACS2

growth_protocol: H9 cells (WiCell, WA09, RRID:CVCL_9773) were cultured in feeder-free conditions, in mTeSR1 medium (Stem Cell Technologies, 85850) on Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix (Corning, 356231) and passaged using ReLeSR (Stem Cell Technologies, 05872) every 4-6 days. Cells were switched to mTeSR Plus medium (Stem Cell Technologies, 100-0276) prior to and during genome editing and clonal expansion, but switched back to mTeSR1 before differentiation to CNCC. hESCs were differentiated to CNCC as previously described. Briefly, hESC colonies were partially detached from the plate with collagenase IV (Gibco, 17104019) in Knockout DMEM medium (Gibco, 10829018) for 30-60 min and scraped to break up large colonies, and then cultured in Neural Crest Differentiation Medium (50%-50% v/v mixture of DMEM/F12 1:1 medium with L-glutamine, without HEPES (Cytiva, SH30271.FS) and Neurobasal medium (Gibco, 21103049) with 0.5x N2 NeuroPlex (Gemini Bio, 400-163) and Gem21 NeuroPlex (Gemini Bio, 400-160) supplements and GlutaMAX (Gibco, 35050061), and 1x antibiotic/antimycotic, and 20 ng/ml EGF (Peprotech, AF-100-15), 20 ng/ml bFGF (Peprotech, 100-18B), and 5 ug/ml bovine insulin (Gemini Bio, 700-112P)) for 11 days in bacterial-grade petri dishes, changing the plate to prevent attachment for 4 days and then leaving the cells unfed for two days to allow attachment, and then fed as needed at least every other day. At day 11, cells (now called ‘early hCNCC’) were harvested by treatment with Accutase (Sigma-Aldrich, A6964-100ML), strained to remove residual neuroectodermal spheres, and plated onto plates coated with 7.5 ug/ml human fibronectin (Millipore, FC010-10MG) and cultured in Neural Crest Maintenance Medium (Neural Crest Differentiation Medium with bovine insulin replaced by 1 mg/ml BSA (Gemini Bio, 700-104P)). These hCNCC were then passaged every 2-3 days upon reaching confluency, with cells in the third or subsequent passages defined as ‘late hCNCC’ and cultured with added 50 pg/ml BMP2 (Peprotech, 120-02) and 3 uM CHIR-99021 (Selleck, S2924).

extract_protocol:
DNase-treated cells were harvested by Accutase, counted using the Countess II (Invitrogen), and 50,000 cells were collected by centrifugation at 500g for 5 min at 4°C. Cells were resuspended in lysis buffer (resuspension buffer (RSB), or 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2, with 0.1% Igepal CA-630, 0.1% Tween-20, and 0.01% digitonin) for 3 min, then quenched by dilution with RSB with 0.1% Tween-20. Lysate was centrifuged for 10 min at 500g at 4°C and then resuspended in transposition buffer (25 ul TD buffer and 2.5 ul TD enzyme (Illumina, 20034197), 16.5 ul PBS, 0.01% digitonin, 0.1% Tween-20, and water up to 50 ul). Transposition reactions were performed for 30 min at 37°C, and then cleaned up with the DNA Clean & Concentrator-5 kit (Zymo, D4013) and eluted in 21 ul 10 mM Tris-HCl pH 8.
Transposed DNA was pre-amplified 5 cycles with NEBNext Ultra II Q5 master mix (New England Biolabs, M0544) with a cycling protocol of 72°C for 5 min, 98°C for 30s, and 5 cycles of 98°C for 10s, 63°C for 30s, 72°C for 1 min. Then 5 ul of the 50 ul reaction was used to run a qPCR reaction (with the same cycling protocol except the initial 72°C incubation) to determine the optimal number of PCR cycles for each sample. The remaining portion of the reaction was then amplified the appropriate number of cycles, and then subjected to two rounds of double-sided Ampure XP bead cleanup, with 0.5x/1.3x and 0.5x/1.0x bead ratios (numbers indicate bead ratios added in first and second steps). Libraries were quantified by Qubit dsDNA high sensitivity assay (Invitrogen, Q33231), run on a 5% polyacrylamide TBE gel to check the size distribution, and then pooled for sequencing.

treatment_protocol: DMSO or dTAGV-1 (500 nM) were added by dilution into media before changing media. Cells were treated for 30 min with 200 U/ml DNase I (Worthington, LS006331) at 37°C prior to harvesting cells.

value: Human cranial neural crest cells

value: dTAGV-1 (500 nM)


title: Microglia, Bile_duct_ligation, 14days, rep1

description:
B_14_1_MICRO_S43
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: BEAS-2B CIT 6

value: Cold Ischemia Time (CIT) 4°C 50% O2 18h


title: Microglia, Sham, 14days, rep5

description:
S_14_5_MICRO_S41
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: Microglia, Sham, 14days, rep4

description:
S_14_4_MICRO_S40
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: Microglia, Sham, 14days, rep3

description:
S_14_3_MICRO_S39
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: BEAS-2B D10 1


title: BEAS-2B CIT 3


title: BEAS-2B CIT 2


title: Microglia, Sham, 14days, rep2

description:
S_14_2_MICRO_S38
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: BEAS-2B CIT 1


title: Microglia, Sham, 14days, rep1

description:
S_14_1_MICRO_S37
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: HPMEC Steen Glu 4

source_name: HPMEC

value: HPMEC

value: Human Pulmonary Microvascular Endothelial Cells


title: HPMEC Steen Glu 3


title: Microglia, Bile_duct_ligation, 28days, rep4

description:
B_28_4_MICRO_S34
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: Microglia, Bile_duct_ligation, 28days, rep6

description:
B_28_6_MICRO_S36
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: Microglia, Bile_duct_ligation, 28days, rep1

description:
B_28_1_MICRO_S31
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: Microglia, Bile_duct_ligation, 28days, rep3

description:
B_28_3_MICRO_S33
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: Microglia, Sham, 28days, rep6

description:
S_28_6_MICRO_S30
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: Microglia, Sham, 28days, rep3

description:
S_28_3_MICRO_S27
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: Microglia, Sham, 28days, rep5

description:
S_28_5_MICRO_S29
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: Microglia, Sham, 28days, rep2

description:
S_28_2_MICRO_S26
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: Microglia, Bile_duct_ligation, 28days, rep2

description:
B_28_2_MICRO_S32
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: HPMEC D10 4


title: Microglia, Sham, 28days, rep4

description:
S_28_4_MICRO_S28
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: Microglia, Sham, 28days, rep1

description:
S_28_1_MICRO_S25
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt


title: HPMEC D10 2


title: HPMEC Steen Glu 2


title: HPMEC Steen 2


title: HPMEC Steen 4


title: HPMEC Steen Glu 1


title: HPMEC D10 1


title: HPMEC Steen 3


title: HPMEC CIT 4


title: HPMEC D10 3


title: Astrocytes, Bile_duct_ligation, 14days, rep4

description:
B_14_6_ASTRO_S24
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt

source_name: Astrocytes

value: Astrocytes


title: Astrocytes, Bile_duct_ligation, 14days, rep3

description:
B_14_5_ASTRO_S23
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt


title: HPMEC CIT 2


title: HPMEC CIT 3


title: Astrocytes, Bile_duct_ligation, 14days, rep2

description:
B_14_4_ASTRO_S22
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt


title: Astrocytes, Bile_duct_ligation, 14days, rep1

description:
B_14_3_ASTRO_S21
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt


title: HPMEC Steen 1


title: MDA-MB-231, DMSO, 48 hr, rep 2

city: Cleveland

first: Ruth

last: Keri

state: Ohio

address: 9620 Carnegie Ave

institute: Cleveland Clinic Foundation

data_processing:
Libraries were sequenced via Illumina sequencers in “paired-end” mode with 2x150bp read length and a read depth of ~537-781M reads/sample.
The resulting Arima-HiC data was analyzed via Juicer v1.6. TADs at resolutions of 2.5Mb, 1Mb, 500kb, 25kb, 10kb, and 5kb were identified using Arrowhead. Chromatin loops were identified using HiCCUPS with K-R (balanced) normalization. Differential loops were identified using HiCCUPSDiff with default parameters.
Assembly: hg19
Supplementary files format and content: hic, BEDPE files

growth_protocol: MDA-MB-231 cells were seeded into 15 cm dishes at 2 x10^6 cells per plate in 20 mL of complete RMPI media (10% FBS, 1% Pen-strep) on day 0.

extract_protocol:
Per each sample, 7-10 x 106 cells were crosslinked with 4% formaldehyde. Crosslinked chromatin was digested using a proprietary restriction enzyme cocktail and then labeled with biotinylated nucleotide by Arima Genomics.
DNA fragments were subjected to a custom library protocol utilizing Swift Biosciences Accel-NGS 2S Plus DNA Library Kit (Cat # 26148, 26248, 26396, 26596, 26696, 26796, 26896, or 269384) to produce Arima-HiC libraries for sequencing.

treatment_protocol: On day 1, MDA-MB-231 cells were treated with either 75 nM THZ1 in 20 mL complete RPMI media (THZ1 samples) or 20 uL DMSO in 20 mL complete RPMI media (vehicle samples)

value: triple negative breast cancer cells

value: DMSO


title: MDA-MB-231, DMSO, 48 hr, rep 1


title: Astrocytes, Sham, 14days, rep5

description:
S_14_5_ASTRO_S17
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt


title: MDA-MB-231, 75 nM THZ1, 48 hr, rep 2

value: THZ1, 75 nM


title: Astrocytes, Sham, 14days, rep3

description:
S_14_3_ASTRO_S15
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt

value: Male


title: Astrocytes, Sham, 14days, rep2

description:
S_14_2_ASTRO_S14
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt


title: Astrocytes, Sham, 14days, rep1

description:
S_14_1_ASTRO_S13
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt


title: MDA-MB-231, 75 nM THZ1, 48 hr, rep 1


title: scRNA-seq_PDAC 2

city: Shanghai

first: Meilin

last: Xue

state: Shanghai

address: 197 Ruijin 2nd Road

country: China

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic single cell

data_processing:
Basecalls performed using CASAVA version 1.8
Umi-tools was utilized to calculate the raw counts and cell whitelist by default parameter
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. Graphcluster and K-mean 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.
Assembly: GRCh38
Supplementary files format and content: Txt file and TSV file contain counts for each barcodes and genes

source_name: PDAC tumor tissue

extract_protocol:
Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For PDAC tumor tissues, following resection in the operating room, small tissue blocks from ≥3 different sites of tumor were collected and immersed in tissue storage solution (Miltenyi), and transported to the research facility on ice immediately. On arrival, tissues were rinsed with PBS, and necrotic foci, hemorrhagic foci, and blood vessels were removed. Tissues were then minced in into small pieces (<1mm in diameter), and then transferred into 2ml digestion medium containing 100ul enzyme H, 50ul enzyme R, and 12.5ul enzyme A (Tumor Dissociation Kit, Miltenyi, 130-095-929) in RPMI-1640. Tissues were enzymatically digested on a shaker at 37℃ for 20min. The dissociated cells were collected at the interval of 10min to increase viability, and filtered through a 40μm nylon cell strainer to harvest single-cell suspension. Dead cells were removed by dead cell removal kit (Miltenyi). Single-cell RNA sequencing was performed on the single-cell suspensions with viability >70%, including  CD45- non-immune filtrates from tumor tissues isolated by CD45 microbeads (Miltenyi).

tag: tissue

value: human PDAC tumor

tag: celltype

value: non-immune cells (CD45-)

tag: feature

value: with Neural Hypertrophy and Schwann Cells Accumulation


title: Astrocytes, Bile_duct_ligation, 28days, rep5

description:
B_28_6_ASTRO_S12
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt


title: scRNA-seq_PDAC 1


title: ST_PDAC-4

data_processing:
Basecalls performed using CASAVA version 1.8
Read alignment and count summarization were performed using SpaceRanger
Seurat package was used for spot normalization and regression. PCA was constructed based on the scaled data with all high variable genes and top 30 principals were used for tSNE construction. Utilizing graph-based cluster method, we acquired the unsupervised the cell cluster result based the PCA top 30 principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. logFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1. Spatial feature expression plots were generated with the SpatialFeaturePlot function in Seurat (version 3.1.3) and the STUtility R package (version 1.0.0).
Assembly: GRCh38
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

extract_protocol:
ST transcriptomes were collected using 10X Chromium Spatial Gene Expression Slide & Reagent Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PDAC tumors were surgically removed and embedded in optimal cutting temperature (OCT) compound (Sakura). The tissues treated with OCT compound were immediately frozen on dry ice. Tissue sections (10 μm thick) were placed within the frames of capture areas on Visium Spatial slides (10X Genomics) and imaged using a Pannoramic MIDI microscope (3DHISTECH) after H&E staining. Visium spatial tissue optimization slides and reagent kits (10X Genomics) were used for pre-permeabilization to optimize permeabilization time. For tissue permeabilization and spatial transcriptomic sequencing, the stained slides were incubated in RT Master Mix for 45 min at 53°C for reverse transcription after permeabilization. Next, Second Strand mix was added to the tissue sections on the slide and incubated for 15 min at 65°C to initiate second strand synthesis. After transferring the cDNA from the slides, it was purified via the barcode cDNA and amplified. The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors, and amplified using PCR.


title: Astrocytes, Bile_duct_ligation, 28days, rep4

description:
B_28_5_ASTRO_S11
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt


title: ST_PDAC-3


title: Astrocytes, Bile_duct_ligation, 28days, rep3

description:
B_28_4_ASTRO_S10
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt


title: scRNA-seq_PDAC 4


title: Day 4 1-dSA + AA147 treated replicate 3 (AA147 Set)

city: La Jolla

first: R.

middle: Luke

last: Wiseman

address: 10550 N Torrey Pines Rd

department: Dept. of Molecular Medicine

institute: The Scripps Research Institute

description:
11_DSAx147_3
Day_4_AA147_Set_RawGeneCounts.csv

data_processing:
DNAstar Lasergene SeqManPro used to align reads from fastq files
ArrayStar 12.2 QSeq package used to generate read counts per transcript
grch38-r98
.csv of Raw Aligned Read Counts

source_name: iPSC derived retinal organoid

extract_protocol:
Total RNA was purified from frozen tissues using Trizol Reagent
NEB Ultra 2

treatment_protocol: Treated with AA147 + 1-dSA (Avanti) for four days.

value: iPSC derived retinal organoid

tag: agent

value: AA147 + 1-dSA (Avanti)

tag: time point

value: four days


title: Astrocytes, Bile_duct_ligation, 28days, rep2

description:
B_28_3_ASTRO_S9
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt

tag: cell type

tag: treatment


title: HPMEC CIT 1

tag: cell line


title: Day 4 1-dSA + AA147 treated replicate 4 (AA147 Set)

description:
12_DSAx147_4
Day_4_AA147_Set_RawGeneCounts.csv


title: ST_PDAC-2


title: Astrocytes, Bile_duct_ligation, 28days, rep1

description:
B_28_2_ASTRO_S8
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt

tag: Sex

tag: strain

tag: timepoint


title: Astrocytes, Sham, 14days, rep6

description:
S_14_6_ASTRO_S18
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt

value: Sham


title: ST_PDAC-1


title: Day 4 1-dSA treated replicate 4 (AA147 Set)

description:
08_DSA_4
Day_4_AA147_Set_RawGeneCounts.csv

treatment_protocol: Treated with 1-deoxysphinganine (1-dSA) (Avanti) for four days.

value: 1-deoxysphinganine (1-dSA) (Avanti)


title: Astrocytes, Sham, 28days, rep5

description:
S_28_6_ASTRO_S6
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt


title: Day 4 1-dSA treated replicate 3 (AA147 Set)

description:
07_DSA_3
Day_4_AA147_Set_RawGeneCounts.csv


title: Astrocytes, Sham, 14days, rep4

description:
S_14_4_ASTRO_S16
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt


title: Day 4 1-dSA treated replicate 2 (AA147 Set)

description:
06_DSA_2
Day_4_AA147_Set_RawGeneCounts.csv


title: Microglia, Bile_duct_ligation, 28days, rep5

description:
B_28_5_MICRO_S35
Bulk_RNA_seq_raw_counts_Microglia.txt
Bulk_RNA_seq_normalized_counts_Microglia.txt

value: Microglia


title: scRNA-seq_PDAC 3


title: Day 4 1-dSA treated replicate 1 (AA147 Set)

description:
05_DSA_1
Day_4_AA147_Set_RawGeneCounts.csv


title: CAF2_CM

data_processing:
Illumina Casava1.7 software used for basecalling for CAF, and fastp used for CFPAC-1.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole hg18 genome using HISAT2 v2.1.0 with parameters -q -p 1 -e 70 -f -v1 -a-m 10 --best --strata
FPKM (Fragments Per Kilobase Million) were calculated using RSEM v1.2.12.
Assembly: hg18

source_name: CAFs_Cancer associated fibroblasts

extract_protocol:
CFPAC-1 were treated by RSC96 CM or control CM for 72 hours, and CAF1 and CAF2 were treated for 48 hours. After that, CFPAC-1, CAF-1, and CAF-2 were lysed with TRIzol (Invitrogen), and total RNA was extracted using RNeasy Mini Kit (Qiagen, Germany), according to the manufacturer’s instructions. RNA sequencing libraries were generated using KAPA RNA library preparation kit (Illumina) and the KAPA dual- indexed adapter kit (Illumina) for CAFs, and NEBNext® Ultra™ RNA Library Prep Kit (Illumina) for CAFPAC-1. Sequencing was performed on an Illumina HiSeq X10 platform (2 × 150 bp).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: treat w/ RSC96 CM 48 hours

value: primary cancer-associated fibroblasts (CAFs) isolated from patient B


title: CAF2_control


title: Astrocytes, Sham, 28days, rep4

description:
S_28_4_ASTRO_S4
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt


title: Astrocytes, Sham, 28days, rep3

description:
S_28_3_ASTRO_S3
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt


title: Day 4 Control treated replicate 4 (AA147 Set)

description:
04_CONTROL_4
Day_4_AA147_Set_RawGeneCounts.csv

treatment_protocol: Treated with control for four days.

value: control


title: Day 4 Control treated replicate 3 (AA147 Set)

description:
03_CONTROL_3
Day_4_AA147_Set_RawGeneCounts.csv


title: CAF1_CM

value: treat w/ control CM 48 hours

value: primary cancer-associated fibroblasts (CAFs) isolated from patient A


title: Day 4 Control treated replicate 1 (AA147 Set)

description:
01_CONTROL_1
Day_4_AA147_Set_RawGeneCounts.csv


title: Day 4 1-dSA + AA147 treated replicate 1 (AA147 Set)

description:
09_DSAx147_1
Day_4_AA147_Set_RawGeneCounts.csv


title: Day 4 1-dSA + AA147 treated replicate 2 (AA147 Set)

description:
10_DSAx147_2
Day_4_AA147_Set_RawGeneCounts.csv


title: Astrocytes, Sham, 28days, rep1

description:
S_28_1_ASTRO_S1
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt

value: Astrocytes


title: Day 4 1-dSA + ISRIB treated replicate 4 (ISRIB Set)

description:
14idIDrp4-2ID_S16
Day_4_ISRIB_Set_RawGeneCounts.csv

data_processing:
STAR used for alignment
Cutadapt to remove adapter sequences, primers, poly-A tails
featureCounts used to generate reads per transcript
grch38-r98
.csv of Raw Aligned Read Counts

treatment_protocol: Treated with ISRIB + 1-deoxysphinganine (1-dSA) (Avanti) for four days.


title: Astrocytes, Sham, 28days, rep2

description:
S_28_2_ASTRO_S2
Bulk_RNA_seq_raw_counts_Astrocytes_no_outliers.txt
Bulk_RNA_seq_normalized_counts_Astrocytes_no_outliers.txt


title: CFPAC_CM_3

source_name: PDAC cells_CFPAC-1

value: treat w/ RSC96 CM 72 hours

value: pancreatic ductal adenocarcinoma (PDAC)


title: CAF1_control


title: Day 4 1-dSA + ISRIB treated replicate 2 (ISRIB Set)

description:
12idIDrp2-2ID_S14
Day_4_ISRIB_Set_RawGeneCounts.csv

value: ISRIB + 1-deoxysphinganine (1-dSA) (Avanti)


title: Q128__Mtf1_EXP1_rep3

city: Padua

first: Graziano

last: Martello

address: viale Colombo 3

department: Department of Biology

country: Italy

institute: University of Padua

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw counts

source_name: mouse embryo

growth_protocol: ES cell lines (Rex1GFP-d2) were cultured in feeder free conditions (plastic coated with 0.2% gelatine [Sigma, cat. G1890]) and replated every 3–4 days at a split ratio of 1:10 following dissociation with Accutase (GE Healthcare, cat. L11-007) or 0.25% Trypsin (Life Technologies). Cells were cultured in  serum-containing KSR medium (GMEM [Sigma, cat. G5154] supplemented with 10% KSR [Life Technologies], 2%FBS [Sigma, cat. F7524], 100mM 2-mercaptoethanol [Sigma, cat. M7522], 1× MEM non- essential amino acids [Invitrogen, cat. 1140-036], 2mM L-glutamine, 1mM sodium pyruvate [both from Invitrogen]), supplemented with two small-molecule inhibitors (2i) PD (1μM, PD0325901), CH (3mM, CHIR99021) from Axon (cat. 1386 and 1408) and LIF (100 units/ml purchased from Qkine - Cambridge UK).

extract_protocol:
Total RNA was isolated using Total RNA Purification kit (Norgen Biotek), according to manufactorer's protocol.
3'DGE mRNA-seq (research*/clinical**/diagnostic***) grade sequencing service (Next Generation Diagnostics srl)

value: mouse embryonic stem cell

tag: phenotype

value: adherent

tag: genotype

value: Rex1GFP-d2 cells expressing  N-terminal of human huntingtin gene, with 128 CAG repeats and  with CAG-Mtf3


title: CFPAC_CM_2


title: Day 4 1-dSA + ISRIB treated replicate 1 (ISRIB Set)

description:
11idIDrp1-2ID_S13
Day_4_ISRIB_Set_RawGeneCounts.csv

value: iPSC derived retinal organoid


title: Q128__Mtf1_EXP1_rep2

value: Rex1GFP-d2 cells expressing  N-terminal of human huntingtin gene, with 128 CAG repeats and  with CAG-Mtf2


title: CFPAC_CM_1


title: Day 4 1-dSA treated replicate 5 (ISRIB Set)

description:
10idDrp5-1D_S12
Day_4_ISRIB_Set_RawGeneCounts.csv

value: four days


title: CFPAC_control_3

value: treat w/ control CM 72 hours


title: Q128__Mtf1_EXP1_rep1

value: Rex1GFP-d2 cells expressing  N-terminal of human huntingtin gene, with 128 CAG repeats and  with CAG-Mtf1


title: Day 4 1-dSA treated replicate 4 (ISRIB Set)

description:
09idDrp4-1D_S11
Day_4_ISRIB_Set_RawGeneCounts.csv

value: 1-deoxysphinganine (1-dSA) (Avanti)


title: Day 4 1-dSA treated replicate 2 (ISRIB Set)

description:
07idDrp2-1D_S9
Day_4_ISRIB_Set_RawGeneCounts.csv


title: Day 4 1-dSA treated replicate 1 (ISRIB Set)

description:
06idDrp1-1D_S8
Day_4_ISRIB_Set_RawGeneCounts.csv


title: Day 4 1-dSA treated replicate 3 (ISRIB Set)

description:
08idDrp3-1D_S10
Day_4_ISRIB_Set_RawGeneCounts.csv


title: CFPAC_control_2


title: Day 4 1-dSA + ISRIB treated replicate 5 (ISRIB Set)

description:
15idIDrp5-2ID_S17
Day_4_ISRIB_Set_RawGeneCounts.csv


title: Day 4 Control treated replicate 4 (ISRIB Set)

description:
04idCrp4-0C_S6
Day_4_ISRIB_Set_RawGeneCounts.csv


title: Day 4 Control treated replicate 2 (AA147 Set)

description:
02_CONTROL_2
Day_4_AA147_Set_RawGeneCounts.csv


title: Q128_mCherry_EXP1_rep2

value: Rex1GFP-d2 cells expressing  N-terminal of human huntingtin gene, with 128 CAG repeats


title: CFPAC_control_1


title: Day 4 Control treated replicate 5 (ISRIB Set)

description:
05idCrp5-0C_S7
Day_4_ISRIB_Set_RawGeneCounts.csv

value: control


title: Day 4 Control treated replicate 3 (ISRIB Set)

description:
03idCrp3-0C_S5
Day_4_ISRIB_Set_RawGeneCounts.csv


title: Day 4 Control treated replicate 2 (ISRIB Set)

description:
02idCrp2-0C_S4
Day_4_ISRIB_Set_RawGeneCounts.csv


title: Day 4 Control treated replicate 1 (ISRIB Set)

description:
01idCrp1-0C
Day_4_ISRIB_Set_RawGeneCounts.csv


title: Day 3 1-dSA treated replicate 5

description:
15trDSArp005-2DSA_S17
Day_3_RawGeneCounts.csv

data_processing:
STAR used for alignment
Cutadapt to remove adapter sequences, primers, poly-A tails
HTSeq used to generate reads per transcript
grch38-r98
.csv of Raw Aligned Read Counts

treatment_protocol: Treated with 1-deoxysphinganine (1-dSA) (Avanti) for three days.

value: three days


title: Q128_mCherry_EXP1_rep1


title: mild3-S11 D01144

first: Kang

last: Liu

address: Changhai Road

department: Orthopedics

institute: First Affiliated Hospital of the Navy Medical University

data_processing:
fastqc
bwa mapping for the basic reads and alignment
pseudoalignment based on kallisto
deseq2 pipeline for DEG analysis and counts generation
GO, GSEA and downstream analysis by clusterprofiler and GSEA etc.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

source_name: synovitis and  thickening joint capsule

extract_protocol:
Trizol
oligoDT

value: synovitis and joint capsule

tag: Stage

value: mild stage

tag: disease severity

value: mild


title: ctrl4-S10 C99073

value: nomal

value: ctrl


title: Day 3 1-dSA treated replicate 3

description:
13trDSArp003-2DSA_S15
Day_3_RawGeneCounts.csv


title: Q15_mCherry_EXP1_rep2

value: mouse embryonic stem cell

value: Rex1GFP-d2 cells expressing  N-terminal of human huntingtin gene, with 15 CAG repeats


title: Day 3 1-dSA treated replicate 2

description:
12trDSArp002-2DSA_S14
Day_3_RawGeneCounts.csv


title: Day 3 1-dSA treated replicate 1

description:
11trDSArp001-2DSA_S13
Day_3_RawGeneCounts.csv


title: mild1-S9 C98746


title: Q128_mCherry_EXP1_rep3

value: adherent


title: Day 3 1-SA treated replicate 5

description:
10trXSArp005-1XSA_S12
Day_3_RawGeneCounts.csv

treatment_protocol: Treated with sphinganine (1-SA) (Avanti) for two days.

value: iPSC derived retinal organoid

value: sphinganine (1-SA) (Avanti)

value: two days


title: Day 3 1-SA treated replicate 4

description:
09trXSArp004-1XSA_S11
Day_3_RawGeneCounts.csv


title: Day 3 1-SA treated replicate 3

description:
08trXSArp003-1XSA_S10
Day_3_RawGeneCounts.csv


title: Q128_Mtf1+Kdm2b_EXP2_rep4

value: Rex1GFP-d2 cells expressing  N-terminal of human huntingtin gene, with 128 CAG repeats and  with CAG-Mtf1-Kdm2b


title: Q128_Mtf1+Kdm2b_EXP2_rep3


title: mild2-S8 C98588


title: Day 3 1-SA treated replicate 2

description:
07trXSArp002-1XSA_S9
Day_3_RawGeneCounts.csv


title: Day 3 Control treated replicate 5

description:
05trCONrp005-0CON_S7
Day_3_RawGeneCounts.csv

treatment_protocol: Treated with Vehicle for three days.

value: Vehicle


title: ctrl2-S7 C92261


title: mild4-S12 D01737


title: Q15_mCherry_EXP1_rep3


title: Day 3 1-SA treated replicate 1

description:
06trXSArp001-1XSA_S8
Day_3_RawGeneCounts.csv


title: Day 3 1-dSA treated replicate 4

description:
14trDSArp004-2DSA_S16
Day_3_RawGeneCounts.csv

value: 1-deoxysphinganine (1-dSA) (Avanti)


title: severe3-S5 C91656

value: frozen stage

value: severe


title: Day 3 Control treated replicate 3

description:
03trCONrp003-0CON_S4
Day_3_RawGeneCounts.csv

value: three days


title: Q128_Mtf1+Kdm2b_EXP2_rep2


title: Q128_Mtf1+Kdm2b_EXP2_rep1


title: Day 3 Control treated replicate 2

description:
02trCONrp002-0CON_S2
Day_3_RawGeneCounts.csv


title: Day 3 Control treated replicate 1

description:
01trCONrp001-0CON_S1
Day_3_RawGeneCounts.csv


title: Q128_Kdm2b_EXP2_rep3

value: Rex1GFP-d2 cells expressing  N-terminal of human huntingtin gene, with 128 CAG repeats and  with CAG-Kdm2b


title: ctrl3-S4 C72847

value: synovitis and joint capsule


title: Q15_mCherry_EXP1_rep1


title: Day 2 1-SA treated replicate 5

description:
15xSA5
Day_2_RawGeneCounts.csv

treatment_protocol: Treated with 1-deoxysphinganine (1-dSA) (Avanti) for two days.


title: Day 2 1-SA treated replicate 4

description:
14xSA4
Day_2_RawGeneCounts.csv


title: Q128_Kdm2b_EXP2_rep2


title: Q128_Kdm2b_EXP2_rep1


title: Day 2 1-SA treated replicate 3

description:
13xSA3
Day_2_RawGeneCounts.csv


title: Day 2 1-SA treated replicate 2

description:
12xSA2
Day_2_RawGeneCounts.csv


title: severe1-S2 C35481


title: Q128_Mtf1_EXP2_rep3

value: Rex1GFP-d2 cells expressing  N-terminal of human huntingtin gene, with 128 CAG repeats and  with CAG-Mtf1


title: severe2-S6 C92253


title: ctrl1-S3 C72389

value: nomal


title: severe4-S1 958891


title: Day 2 1-dSA treated replicate 4

description:
09dSA4
Day_2_RawGeneCounts.csv


title: Day 2 1-SA treated replicate 1

description:
11xSA1
Day_2_RawGeneCounts.csv


title: Day 2 1-dSA treated replicate 3

description:
08dSA3
Day_2_RawGeneCounts.csv


title: Q128_Mtf1_EXP2_rep2


title: Day 3 Control treated replicate 4

description:
04trCONrp004-0CON_S5
Day_3_RawGeneCounts.csv


title: Day 2 1-dSA treated replicate 2

description:
07dSA2
Day_2_RawGeneCounts.csv


title: Day 2 1-dSA treated replicate 1

description:
06dSA1
Day_2_RawGeneCounts.csv


title: 17_WT _ref_S25

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 124 Science Dr

institute: Duke University

description: Wild-type reference control. Used for in-house batch normalzation. 84% of read pairs mapped to transcipts with appropriate mate pair orientation. 4,589 fragments mapped to pyrF (HAH_2085)

data_processing:
Merged FASTQ files for samples that were loaded onto multiple lanes of a given flowcell, respecting read pair assignment. Ex) cat *_L001_R1_001.fastq.gz *_L002_R1_001.fastq.gz
Adapter sequences were removed with Trim_galore! 0.4.3, cutadapt 2.3, and and sample quality assessed with FastQC 0.11.7 using default parameters.
Reads were aligned to the Haloarcula hispanica ATCC33960 reference genome (GCF_000223905.1, accessed 2018-11-13) with Bowtie2 2.3.5.1 in paired-end mode: only pairs aligning concordantly in the --rf orientation were considered.
Aligned sequence files were converted to binary format, sorted, and indexed using samtools 1.10.
Read paris, or fragments, aligning to ORFs were counted using featureCounts 2.0.1 with arguments -p -B -s 2 and the Haloarcula hispanica ATCC33960 genome annotation (GCF_000223905.1, accessed 2022-10-19). Fragments were required to align concordantly in the correct strand orientation (reverse) to be counted.
In R, counts from 2021 and 2022 experiments were normalized relative to library size and batch corrected with DeSeq2 1.34.0. Pairwise correlations were computed using normalized counts for samples within each genotype+condition group, and samples with average R < 0.7  were considered outliers and were not used in downstream analyses. Only aAWT_B_noglu_24_S19_SP met these requirements for removal. Remaining samples were subjected to differential expression analysis.
Assembly: GCF_000223905.1
Supplementary files format and content: Text file of fragments mapping to genes. Each column is a sample, and rows are counts mapping to a given gene.

organism: Haloarcula hispanica ATCC 33960

source_name: wildtype cell culture

growth_protocol: Four single colonies of DF60 and ASK133 or AKS319 from 10-day old plates were inoculated in 5 mL YPC23 medium supplemented with 0.1% glucose and grown aerobically (250 rpm shaking) at 37C to stationary phase (optical density at 600nm ~ 4). Cells were washed twice with Hh-CA medium without glucose and transferred into fresh 50 mL Hh-CA with or without 0.1\% glucose at an initial optical density of ~ 0.4. After 24 hours cultures were collected and flash frozen with liquid nitrogen.

extract_protocol:
After 24 hours storage in -80C, RNA was extracted from cell pellets using Absolutely RNA Miniprep kit (Agilent Technologies, Santa Clara, CA) followed by additional DNAse treatment with Turbo DNAse (Invitrogen). Total RNA was quantified using Agilent Bioanalyzer RNA Nano 6000 chip (Agilent Technologies, Santa Clara, CA). The absence of DNA contamination was determined on 200 ng samples of RNA in 25 cycles of PCR. Ribosomal RNA was removed from total RNA with the PanArchaea riboPOOL kit according to the manufacturer protocol (siTOOLs Biotech, Germany) and checked for depletion using Agilent Bioanalyzer RNA Nano 6000 chip as described as Described in Pastor et al. 2022.
rRNA-depleted RNA was used to construct the sequencing libraries with KAPA Stranded RNA-seq Library preparation (Kapa Biosystems) following manufacturer protocol. Fragment size of final libraries was measured using Agilent Bioanalyzer DNA 1000 chip and then pooled and sequenced on Illumina NovaSeq 6000 at the Center for Genomic and Computational Biology at Duke University (Durham, NC).

value: wildtype

value: wildtype cell culture

value: YPC23 + uracil

tag: time

value: stationary

tag: used in_de_analysis

value: FALSE

tag: year-flowcell


title: Q128_Mtf1_EXP2_rep1

value: mouse embryonic stem cell

value: adherent


title: 16_TRMB_D_S24

description: 68.6% of read pairs mapped to transcipts with appropriate mate pair orientation. 36 fragments mapped to pyrF (HAH_2085)

source_name: delta-pyrFdelta-trmB cell culture

value: delta-pyrFdelta-trmB

value: delta-pyrFdelta-trmB cell culture

value: Hh-CA + uracil

value: TRUE


title: Day 2 Control treated replicate 5

description:
05xxC5
Day_2_RawGeneCounts.csv

treatment_protocol: Treated with Vehicle for two days.

value: iPSC derived retinal organoid

value: Vehicle

value: two days


title: Q128_mCherry_EXP2_rep4

value: Rex1GFP-d2 cells expressing  N-terminal of human huntingtin gene, with 128 CAG repeats


title: 15_TRMB_C_S23

description: 63.2% of read pairs mapped to transcipts with appropriate mate pair orientation. 5,077 fragments mapped to pyrF (HAH_2085)


title: Day 2 Control treated replicate 4

description:
04xxC4
Day_2_RawGeneCounts.csv


title: Day 2 Control treated replicate 3

description:
03xxC3
Day_2_RawGeneCounts.csv


title: Q128_mCherry_EXP2_rep3


title: Day 2 Control treated replicate 2

description:
02xxC2
Day_2_RawGeneCounts.csv


title: 14_TRMB_B_S22

description: 66% of read pairs mapped to transcipts with appropriate mate pair orientation. 5,214 fragments mapped to pyrF (HAH_2085)


title: Day 2 Control treated replicate 1

description:
01xxC1
Day_2_RawGeneCounts.csv


title: Q128_mCherry_EXP2_rep2


title: Day 2 1-dSA treated replicate 5

description:
10dSA5
Day_2_RawGeneCounts.csv

value: sphinganine (1-SA) (Avanti)


title: snRNAseq Day 3 1-dSA treated replicate 2

description:
snRNA-seq 10X Genomics Single Cell 3' v3 chemistry
nuclear RNA

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v. 6.0.0
GRCh38-2020-A
.tar of barcodes, matrix, and features (raw)

extract_protocol:
Nuclei were isolated following a modified version of 10x Genomics’ Nuclei Isolation from Mouse Brain Tissue (CG000212, Rev. B)
Single Cell 3' v3

treatment_protocol: Treated with 1-deoxysphinganine (1-dSA)(Avanti; cat 860493) for three days.

value: three days


title: snRNAseq Day 3 1-dSA treated replicate 1

value: 1-deoxysphinganine (1-dSA)(Avanti; cat 860493)


title: Q128_mCherry_EXP2_rep1


title: Q15_Mtf1_EXP2_rep4

value: Rex1GFP-d2 cells expressing  N-terminal of human huntingtin gene, with 15 CAG repeats and with CAG-Mtf1


title: 13_TRMB_A_S21

description: 67.6% of read pairs mapped to transcipts with appropriate mate pair orientation. 17 fragments mapped to pyrF (HAH_2085)


title: 11_WT _C_S19

description: 77.9% of read pairs mapped to transcipts with appropriate mate pair orientation. 34 fragments mapped to pyrF (HAH_2085)

source_name: delta-pyrF cell culture

value: delta-pyrF

value: delta-pyrF cell culture


title: 12_WT _D_S20

description: 74% of read pairs mapped to transcipts with appropriate mate pair orientation. 32 fragments mapped to pyrF (HAH_2085)


title: snRNAseq Day 3 control replicate 1

treatment_protocol: Treated with vehicle for three days.

value: vehicle


title: Q15_Mtf1_EXP2_rep3

value: mouse embryonic stem cell


title: 10_WT _B_S18

description: 75.4% of read pairs mapped to transcipts with appropriate mate pair orientation. 43 fragments mapped to pyrF (HAH_2085)


title: Healthy 3 for OA

type: RNA

city: Nashville

first: Juan

middle: M

last: Colazo

state: TN

address: 2301 Vanderbilt Place PMB 351826

department: Biomedical Engineering

institute: Vanderbilt University

description: PTOA

hyb_protocol: standard NanoString protocol

scan_protocol: standard NanoString protocol

data_processing: The raw Nanostring nCounter genes were normalized using nSolver 4.0 (NanoString Technologies Inc., Seattle, WA), adjusting for positive controls, housekeeping genes and background level.

source_name: Knee Joint

extract_protocol: Equal mass of (1) synovial tissue and (2) articular cartilage were stored in RNAlater Stabilization Solution (AM7020, Invitrogen) at -80°C until further processing. Samples were homogenized with the Tissuelyser 2 from Qiagen (Redwood City, CA) before total RNA from the was extracted using Qiagen RNeasy Plus Mini Kit for purification of total RNA according to the manufacturer's instructions. mRNA expression analysis with the NanoString nCounter® Mouse Inflammation v2 Panel was performed according to the manufacturer's protocol (NanoString Technologies Inc., Seattle, WA).

tag: disease model

value: Healthy Control (No PTOA)

tag: tissue

value: Knee Joint

value: No Treatment


title: Healthy 2 for OA

description: PTOA


title: Healthy 1 for OA

description: PTOA


title: OA NT 4

description: PTOA

value: PTOA Mechanical Loading Model


title: 9_WT _A_S17

description: 76.1% of read pairs mapped to transcipts with appropriate mate pair orientation. 62 fragments mapped to pyrF (HAH_2085)

value: Hh-CA + uracil

value: TRUE


title: OA NT 2

description: PTOA


title: Q15_Mtf1_EXP2_rep2

value: adherent


title: OA NT 1

description: PTOA


title: Day 4 1-dSA + ISRIB treated replicate 3 (ISRIB Set)

description:
13idIDrp3-2ID_S15
Day_4_ISRIB_Set_RawGeneCounts.csv

value: iPSC derived retinal organoid

tag: agent

value: ISRIB + 1-deoxysphinganine (1-dSA) (Avanti)

value: four days


title: 8_TRMB_D_S16

description: 83.5% of read pairs mapped to transcipts with appropriate mate pair orientation. 11,180 fragments mapped to pyrF (HAH_2085)

value: delta-pyrFdelta-trmB

value: delta-pyrFdelta-trmB cell culture

value: Hh-CA + uracil + 0.1% glucose (w/v)


title: Q15_Mtf1_EXP2_rep1

value: Rex1GFP-d2 cells expressing  N-terminal of human huntingtin gene, with 15 CAG repeats and with CAG-Mtf1


title: OA siMMP13 3

description: PTOA


title: 7_TRMB_C_S15

description: 82.5% of read pairs mapped to transcipts with appropriate mate pair orientation. 50 fragments mapped to pyrF (HAH_2085)


title: OA siMMP13 2

description: PTOA


title: Healthy 4 for OA

description: PTOA


title: Q15_mCherry_EXP2_rep3

value: Rex1GFP-d2 cells expressing  N-terminal of human huntingtin gene, with 15 CAG repeats


title: Q15_mCherry_EXP2_rep2


title: snRNAseq Day 3 control replicate 2

value: vehicle

tag: time point

value: three days


title: OA siMMP13 4

description: PTOA


title: Healthy 4 for K/BxN

description: K/BxN

source_name: Hindpaw Joint

value: Healthy Control (No K/BxN Arthritis)

value: Hindpaw Joint


title: Healthy 3 for K/BxN

description: K/BxN

value: No Treatment


title: 72_SRC_3ff

city: Houston

first: Prashi

last: Jain

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor college of Medicine

description: Non-tumor bearing

data_processing:
Sequenced reads were trimmed for adaptor sequence using TrimGalore
Reads were mapped to the UCSC mouse reference genome mm10 using STAR
Stringtie was used to evaluate gene expression level as FPKM (Fragments per kilobase of transcript per million read pairs)
Assembly: mm10 GRCm38.101
Supplementary files format and content: tab-delimited text file includes FPKM (Fragments per kilobase of transcript per million read pairs) for each sample

source_name: spleen

extract_protocol:
Tregs were isolated from the spleens of SRC-3KO and WT animals and sorted for YFP. Total RNA was isolated from YFP+ AND YFP- Tregs using Qiagen micro RNAesy plus kit. Quality control of isolated RNA samples was checked using Agilent Bioanalyzer. Takera SMART-Seq v4 kit was used to generate the low throughput sequencing libraries.
RNA libraries were prepared using Takara Bio SMART-seq v4 plus by manufacturer recommended protocol.

tag: mouse strain

value: spleen

tag: cell type

value: Tregs

value: WT Control 2


title: Healthy 2 for K/BxN

description: K/BxN

tag: treatment


title: Healthy 1 for K/BxN

description: K/BxN


title: K/BxN siMMP13 4

description: K/BxN

value: K/BxN Inflammatory Arthritis


title: 5_TRMB_A_S13

description: 81.3% of read pairs mapped to transcipts with appropriate mate pair orientation. 35 fragments mapped to pyrF (HAH_2085)

value: TRUE


title: OA NT 3

description: PTOA

value: PTOA Mechanical Loading Model

value: Knee Joint


title: 3_WT _C_S11

description: 81.7% of read pairs mapped to transcipts with appropriate mate pair orientation. 46 fragments mapped to pyrF (HAH_2085)

value: delta-pyrF

value: delta-pyrF cell culture


title: 68_SRC_3ff

description: Non-tumor bearing


title: K/BxN siMMP13 3

description: K/BxN


title: K/BxN siMMP13 1

description: K/BxN


title: 2_WT _B_S10

description: 82.8% of read pairs mapped to transcipts with appropriate mate pair orientation. 60 fragments mapped to pyrF (HAH_2085)

value: Hh-CA + uracil + 0.1% glucose (w/v)


title: 85_YFP_P

description: Non-tumor bearing

value: C57BL/6 and 129SvEv mixed background

value: Tregs YFP+

value: SRC-3 KO


title: K/BxN NT 4

description: K/BxN


title: 85_YFP_N

description: Non-tumor bearing

value: Tregs YFP-


title: 1_WT _A_S9

description: 81.7% of read pairs mapped to transcipts with appropriate mate pair orientation. 67 fragments mapped to pyrF (HAH_2085)


title: OA siMMP13 1

description: PTOA


title: K/BxN NT 2

description: K/BxN


title: ZWT_A_noglu_24_S47_S1

description: 89.8% of read pairs mapped to transcipts with appropriate mate pair orientation. 58 fragments mapped to pyrF (HAH_2085)

value: Hh-CA + uracil


title: K/BxN NT 1

description: K/BxN

value: Hindpaw Joint


title: 6_TRMB_B_S14

description: 83.1% of read pairs mapped to transcipts with appropriate mate pair orientation. 11,627 fragments mapped to pyrF (HAH_2085)

value: delta-pyrFdelta-trmB

value: delta-pyrFdelta-trmB cell culture


title: Q15_mCherry_EXP2_rep1

value: mouse embryonic stem cell

value: adherent

value: Rex1GFP-d2 cells expressing  N-terminal of human huntingtin gene, with 15 CAG repeats


title: 84_YFP_N

description: Non-tumor bearing

value: spleen


title: YTrmB_D_glu_24_S18_SP

description: 88.1% of read pairs mapped to transcipts with appropriate mate pair orientation. 20,685 fragments mapped to pyrF (HAH_2085)

value: TRUE


title: HEK293, pCAG-TWIST1, TWIST1

value: Human embryonic kidney

tag: cell line

value: WT

tag: clone

value: transfection with pCAG-TWIST1

tag: spike-in cell_type

tag: spike-in cell_line

tag: antibody

value: TWIST1 (Abcam, #ab50887)

tag: reference genome_for_alignment

tag: reference genome_for_processed_files


title: HEK293, pCAG-TWIST1 and pCAG-ALX4-Flag-HA, input

tag: genotype

value: transfection with pCAG-TWIST1 and pCAG-ALX4-Flag-HA

tag: time


title: 24_YFP_P

description: Non-tumor bearing

value: Tregs YFP+

value: WT Control


title: XTrmB_C_glu_24_S26_S1

description: 87.9% of read pairs mapped to transcipts with appropriate mate pair orientation. 5,632 fragments mapped to pyrF (HAH_2085)

tag: strain

value: Hh-CA + uracil + 0.1% glucose (w/v)

tag: used in_de_analysis

tag: year-flowcell


title: 4_WT _D_S12

description: 81.3% of read pairs mapped to transcipts with appropriate mate pair orientation. 38 fragments mapped to pyrF (HAH_2085)

value: delta-pyrF

value: delta-pyrF cell culture


title: HEK293, pCAG-TWIST1, input


title: 23_YFP_P

description: Non-tumor bearing

tag: tissue


title: K/BxN siMMP13 2

description: K/BxN

tag: disease model

value: K/BxN Inflammatory Arthritis

value: Hindpaw Joint


title: WTrmB_B_glu_24_S11_S1

description: 88.4% of read pairs mapped to transcipts with appropriate mate pair orientation.18,022 fragments mapped to pyrF (HAH_2085)

value: delta-pyrFdelta-trmB

value: delta-pyrFdelta-trmB cell culture


title: K/BxN NT 3

description: K/BxN

value: No Treatment


title: WT, 24h dTAG, rep2, input

organism:
Homo sapiens
Mus musculus

value: Human cranial neural crest cell

value: dTAGV-1 (500 nM)

value: Mouse cranial neural crest cell


title: 84_YFP_P

description: Non-tumor bearing

tag: mouse strain

value: C57BL/6 and 129SvEv mixed background

value: spleen

value: SRC-3 KO


title: HEK293, pCAG-TWIST1 and pCAG-ALX4-Flag-HA, TWIST1

tag: cell type

value: Human embryonic kidney

value: WT

value: transfection with pCAG-TWIST1 and pCAG-ALX4-Flag-HA

value: TWIST1 (Abcam, #ab50887)


title: WT, 3h dTAG, rep1, input

tag: treatment


title: WT, 0h dTAG, rep2, input

tag: cell line


title: UWT_D_glu_24_S46_S1

description: 87.8% of read pairs mapped to transcipts with appropriate mate pair orientation. 122 fragments mapped to pyrF (HAH_2085)

value: delta-pyrF

value: Hh-CA + uracil + 0.1% glucose (w/v)

value: TRUE


title: WT, 24h dTAG, rep1, input

tag: clone


title: WT, 0h dTAG, rep1, input

tag: spike-in cell_type


title: WT, 3h dTAG, rep2, input

tag: spike-in cell_line


title: TWT_C_glu_24_S17_SP

description: 88.5% of read pairs mapped to transcipts with appropriate mate pair orientation. 153 fragments mapped to pyrF (HAH_2085)

value: delta-pyrF cell culture


title: WT, 3h dTAG, rep2, TWIST1

tag: antibody


title: SWT_B_glu_24_S16_SP

description: 87.8% of read pairs mapped to transcipts with appropriate mate pair orientation. 116 fragments mapped to pyrF (HAH_2085)


title: WT, 0h dTAG, rep2, TWIST1

tag: reference genome_for_alignment


title: WT, 3h dTAG, rep1, TWIST1

tag: reference genome_for_processed_files


title: WT, 0h dTAG, rep1, TWIST1

tag: genotype


title: WT-tumor_V1G_1d

city: Columbus

first: Xue-Feng

last: Bai

state: OH

address: 281 W. Lane Ave

department: Department of Pathology

institute: Ohio State University Medical Center

description: Chromium™ Controller (10x Genomics)

data_processing:
Using the Cell Ranger software (v.6.0.1), we converted BCL files into FASTQ files, trimmed adapters and primer sequences, mapped reads to the mm10 reference genome, and quantified expression levels. In this step, to eliminate low-quality and dying cells, we filtered out cells with counts less than 200 and those with >5% mitochondrial counts.
Assembly: mm10
Supplementary files format and content: We used the Seurat software (v.4.0.5) for the downstream analysis, based on the count data obtained from Cell Ranger. Specifically, we normalized counts using the LogNormalize approach, visualized cells in a low-dimensional space using the Uniform Manifold Approximation and Projection (UMAP) algorithm, and determined cell clusters using the shared nearest neighbor (SNN) modularity optimization based clustering algorithm.

source_name: Neuroblastoma

growth_protocol: 8 weeks old WT or CD200-/- male C57BL/6 mice were inoculated subcutaneously with 3 × 106 NB9464D tumor cells.

extract_protocol:
On day 28 post inoculation, single cell suspensions were prepared from the tumors after mechanical disruption and enzymatic digestion with 1 mg/mL Type IV Collagenase
Experimental procedures for scRNA-seq followed established techniques using the Chromium Single Cell 3’ Library V3 Kit (10x Genomics). Total tumor cells or FACS-sorted CD45+ tumor infiltrating leukocytes were loaded onto a 10X Genomics Chip A and emulsified with 3’ Single Cell GEM beads using a Chromium™ Controller. Libraries were constructed from the barcoded cDNAs (Ohio State University Comprehensive Cancer Center) and sequenced for approximately 300 million reads/sample on a NovaSeq S4 flow cell (Illumina) at the Core facility (The Ohio State University Comprehensive Cancer Center).

value: Neuroblastoma

value: Wild type

tag: process

value: Total tumor cells


title: KO-tumor_V1G_1a

description: Chromium™ Controller (10x Genomics)


title: WT, 24h dTAG, rep2, H3K27ac

value: Human cranial neural crest cell

tag: time

value: H3K27ac (Active Motif #39133)


title: RWT_A_glu_24_S41_S1

description: 88.6% of read pairs mapped to transcipts with appropriate mate pair orientation. 95 fragments mapped to pyrF (HAH_2085)

tag: strain

tag: used in_de_analysis


title: KO-tumor_V1G_1b

description: Chromium™ Controller (10x Genomics)

tag: tissue


title: WT-tumor_V1G_1c

description: Chromium™ Controller (10x Genomics)


title: KO-tumor_V1G_1c

description: Chromium™ Controller (10x Genomics)


title: HCA_ref_RNA_S7_S1

description: Wild-type reference control. Used for in-house batch normalzation. 86.8% of read pairs mapped to transcipts with appropriate mate pair orientation. 5,294 fragments mapped to pyrF (HAH_2085)

value: wildtype

value: wildtype cell culture

value: YPC23 + uracil

value: stationary

value: FALSE

tag: year-flowcell


title: WT, 0h dTAG, rep2, H3K27ac

value: WT

value: dTAGV-1 (500 nM)

value: Mouse cranial neural crest cell


title: WT-tumor_V1G_1b

description: Chromium™ Controller (10x Genomics)


title: VTrmB_A_glu_24_S25_S1

description: 88.2% of read pairs mapped to transcipts with appropriate mate pair orientation. 11,534 fragments mapped to pyrF (HAH_2085)

value: delta-pyrFdelta-trmB

value: delta-pyrFdelta-trmB cell culture


title: KO-tumor_V1G_1d

description: Chromium™ Controller (10x Genomics)


title: WT, 3h dTAG, rep2, H3K27ac


title: WT, 24h dTAG, rep1, H3K27ac


title: WT, 3h dTAG, rep1, H3K27ac


title: aGTrmB_D_noglu_24_S42_S1

description: 92.8% of read pairs mapped to transcipts with appropriate mate pair orientation. 1,928 fragments mapped to pyrF (HAH_2085)

value: Hh-CA + uracil

value: TRUE


title: TWIST1FV, 24h dTAG, rep2, input


title: WT, 0h dTAG, rep1, H3K27ac


title: aCWT_D_noglu_24_S21_SP

description: 90.5% of read pairs mapped to transcipts with appropriate mate pair orientation. 63 fragments mapped to pyrF (HAH_2085)

value: delta-pyrF

value: delta-pyrF cell culture


title: aFTrmB_C_noglu_24_S48_S1

description: 93.5% of read pairs mapped to transcipts with appropriate mate pair orientation. 7,088 fragments mapped to pyrF (HAH_2085)


title: KO-sorted_V1G_1d

description: Chromium™ Controller (10x Genomics)

value: Neuroblastoma

value: CD45+ sorted cells


title: WT-tumor_V1G_1a

description: Chromium™ Controller (10x Genomics)

value: Wild type

value: Total tumor cells


title: aBWT_C_noglu_24_S20_SP

description: 89.4% of read pairs mapped to transcipts with appropriate mate pair orientation. 80 fragments mapped to pyrF (HAH_2085)


title: TWIST1FV, 3h dTAG, rep2, input

value: Human cranial neural crest cell


title: TWIST1FV, 0h dTAG, rep2, input


title: KO-sorted_V1G_1c

description: Chromium™ Controller (10x Genomics)


title: TWIST1FV, 3h dTAG, rep1, input


title: TWIST1FV, 24h dTAG, rep1, input


title: TWIST1FV, 0h dTAG, rep1, input


title: KO-sorted_V1G_1b

description: Chromium™ Controller (10x Genomics)


title: aAWT_B_noglu_24_S19_SP

description: 93.9% of read pairs mapped to transcipts with appropriate mate pair orientation. 29 fragments mapped to pyrF (HAH_2085)


title: WT-sorted_V1G_1d

description: Chromium™ Controller (10x Genomics)


title: TWIST1FV, 3h dTAG, rep2, TWIST1

value: TWIST1 (Abcam, #ab50887)


title: KO-sorted_V1G_1a

description: Chromium™ Controller (10x Genomics)


title: TWIST1FV, 0h dTAG, rep2, TWIST1


title: TWIST1FV, 3h dTAG, rep2, H3K27ac

value: H3K27ac (Active Motif #39133)


title: TWIST1FV, 0h dTAG, rep2, H3K27ac


title: TWIST1FV, 24h dTAG, rep2, H3K27ac


title: TWIST1FV, 0h dTAG, rep1, TWIST1


title: MPY, day 85

city: Pamplona

first: Emilia

middle: Chuina

last: Tomazeli

state: Navarre

address: Av Calatuña s/n

department: Institute for Multisdisciplinary REsearch in Applied Biology

country: Spain

institute: Public University of Navarra

data_processing:
The quality of mRNA-seq data was checked using FastQC  and trimmed with Trimmomatic to remove reads and sequences containing adapters.
The feature Counts program was used to assign the mapped reads generated from RNA sequencing.
KOG (EuKaryotic Orthologous Groups) and EggnogMapper were used for protein function annotation.
We used the genome of Tuber borchii 3840 as a reference, follow the link on the web page  https://mycocosm.jgi.doe.gov/Tubbor1/Tubbor1.home.html
Assembly: Tbo3840
Supplementary files format and content: The Kallisto program was used to normalize the read data, which generated values of TPMs that were transformed into RPKMs per gene.

organism: Tuber borchii

source_name: mycelium

growth_protocol: The cultivation process was performed in the following culture media: (i) Potato Dextrose Broth 20 g/L (PDB) (Scharlab) or Potato Dextrose Agar (PDA). (ii) Woody Plant (WP) medium (composition per liter: 0.2g KH2PO4, 0.1g CaCl2•2H2O, 0.3g MgSO4•7H2O, 0.9g K2SO4, 0.1g myoinositol, 2.3 g Woody Plant, 1 mL oligo-elements solution containing, per liter, 22.3 mg MnSO4•H2O, 0.014mg FeSO4•7H2O, 8.6 mg ZnSO4•7H2O, 0.25mg Na2MoO4•2H2O, 0.025mg CuSO4•5H2O) [28] modified. The Woody Plant was occasionally supplemented with 20g/L Glucose (WPG), 20g/L glucose plus 5g/L yeast extract (WPGY), 20g/L Dextrose (WPD), 20g/L Dextrose plus 5g/L yeast extract (WPDY) or 20g/L Sucrose (WPS). (iii) Maltose medium (MPY) containing, per liter, 35g Maltose, 5g peptone, 5g yeast extract, 0.5g MgSO4•7H2O, 1g K2SO4, and 0.05 g myoinositol [43] modified. The pH of all culture media was adjusted to 6.3 - 6.4 with NaOH. All liquid cultures were incubated in dark and static conditions at 22±1°C.

extract_protocol:
A fungal RNA EZNA kit (Omega Bio-Tek, Norcross, GA, USA) was used to extract the total RNA
The mRNA libraries were built using TruSeq® RNA (Illumina, Inc., San Diego, CA, USA), following the manufacturer’s instructions.

value: mycelium

tag: growth medium

value: MPY

value: day 85


title: WPGY, day 65

value: WPGY

value: day 65


title: WPG, day 65

value: WPG


title: TWIST1FV, 24h dTAG, rep1, H3K27ac

data_processing:
Reads were trimmed of Truseq adapter sequences and low-quality bases (-Q 10) using skewer v0.2.2.
Trimmed reads were mapped to the hg38 analysis set (human), mm39 (mouse), or a combined reference genome using Bowtie2 v2.4.1 with the options --very-sensitive -X 2000.
Reads were deduplicated with samtools v1.10 markdup and uniquely mapped reads (-q 20) mapped to the main chromosomes (excluding mitochondria and unplaced contigs) were retained using samtools view.
MACS2 v2.2.7.1 was used to call peaks using the IgG sample as a negative control, with options -f BAMPE --nomodel --keep-dup all --call-summits -g hs (human) or mm (mouse) with the -B option for H3K27ac.
bigWig tracks were generated with deeptools v3.5.0 bamCoverage -bs 10 --normalizeUsing RPGC --samFlagInclude 64 --samFlagExclude 8 --extendReads with 1h dTAG samples normalized by the fraction of reads mapping to the E. coli genome.
H3K27ac ChIP reads were counted over merged ATAC peaks using deeptools v3.5.0 multiBamSummary with options -e --outRawCounts.
Assembly: hg38 or mm39
Supplementary files format and content: bigWig, narrowPeak (except for input samples, H3K27ac ChIPs, and V5 ChIPs of dTAG-treated samples) for each sample, and tab-delimited text (.txt) files with read counts of H3K27ac ChIPs over merged ATAC peaks

tag: cell type

value: dTAGV-1 (500 nM)

value: Mouse cranial neural crest cell


title: WT-sorted_V1G_1c

description: Chromium™ Controller (10x Genomics)


title: TWIST1FV, 3h dTAG, rep1, TWIST1

tag: treatment


title: WT-sorted_V1G_1b

description: Chromium™ Controller (10x Genomics)

tag: cell line


title: WT-sorted_V1G_1a

description: Chromium™ Controller (10x Genomics)


title: TWIST1FV, 3h dTAG, rep1, H3K27ac

tag: clone


title: PDB, day 85

value: PDB


title: TWIST1FV, 0h dTAG, rep1, H3K27ac

tag: spike-in cell_type


title: RH2hKO r8 (s013)

city: Dresden

first: Alexander

last: Gerbaulet

state: Saxony

address: Fetscherstr. 74

department: Institute for Immunology

country: Germany

institute: Medical Faculty TU Dresden

data_processing:
Basic quality control of the resulting sequencing reads was performed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and RNA-SeQC (version 1.1.8).
Reads were aligned to the mm10 reference genome using GSNAP (version 2020-12-16)
The Ensembl gene annotation version 98 was used for splice site detection.
Uniquely aligned reads per gene were counted using featureCounts (version 2.0.1) and the respective Ensembl annotation.
Normalisation of raw read counts based on library size, and testing for differential gene expression between conditions was performed using the DESeq2 R package (version 1.30.1, R version 3.5.1).
Supplementary files format and content: Excel

molecule: polyA RNA

source_name: bone marrow

extract_protocol:
Lineage-negative BM cells were prepared from RH2hKO mice and RH2hWT littermate controls (n=4/genotype) and 30,000 – 100,000 GMPs (LE-K CD16/32hiCD34+) were sorted. Total RNA was prepared using the RNeasy Micro Kit (Qiagen). RNA quality was analysed using a Agilent 2100 Bioanalyzer (Agilent Technologies) and samples were frozen at ‑80°C.
mRNA was isolated from 37 – 50 ng total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s instructions. Samples were then directly subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra II Directional RNA Library Prep, NEB). For ligation custom adaptors were used (Adaptor-Oligo 1: 5'-ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT-3', Adaptor-Oligo 2: 5'-P-GAT CGG AAG AGC ACA CGT CTG AAC TCC AGT CAC-3'). After ligation, adapters were depleted by an XP bead purification (Beckman Coulter). Unique dual indexing was done during the following PCR enrichment (15 cycles) using custom amplification primers carrying the same sequence for i7 and i5 index (Primer 1: AAT GAT ACG GCG ACC ACC GAG ATC TAC AC NNNNNNNN ACA TCT TTC CCT ACA CGA CGC TCT TCC GAT CT, Primer 2: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNNNN GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T). After two more XP bead purifications (1:0.9), libraries were quantified using the Fragment Analyzer (Agilent). For Illumina flowcell production, samples were equimolarly pooled and sequenced on Illumina NovaSeq 6000 in 2 x 50 bp paired-end mode, resulting in at least 35 million fragments per sample.

value: Rnaseh2bfl/fl VavCre+


title: RH2hWT r4 (s12)

value: Rnaseh2bfl/fl VavCre-


title: WT_BM_CBE1bait Rep2

city: Boston

first: Frederick

last: Alt

state: MA

address: 1 Blackfan Circle

department: Program in Cellular and Molecular Medicine

institute: Boston Children's Hospital / Harvard Medical School

description: aligned to mm9

data_processing:
Data processing is described in Hu et al., 2016 Nature Protocols (PMC4895203)
Standard basecalling formats for Illumina reads
Illumina reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
Reads were mapped to the indicated reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
We used a best-path searching algorithm to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site. For vector controls and offset nicking with multiple sites, the longest targeted site was used.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
To remove possible mispriming events and other artifacts, the bait alignment must extend 10 nucleotides past the primer.
Post-filter stringency was applied to remove background-prone junctions with gaps larger than 30nt, bait sequences shorter than 50nt and sequences with microhomology larger than 5 bp.
The junctions from Chr12 were extracted and counted for normalization. All 3C-libraires were normalized to the smallest libraries from the same batch of experiments.
Assembly: mm9 or AJ851868/mm9
Supplementary files format and content: bedgraph files were generated for displaying (Jane et al., 2018, PMC6026039)
Library strategy: 3C-HTGTS-Seq

source_name: Primary BM pro-B cells

growth_protocol:
v-Abl pro-B cells were cultured at 37 °C and 5% CO2 in RPMI supplemented with 15% (vol/vol) FCS, 50 U/mL penicillin/streptomycin (ThermoFisher), 2 mM L-glutamine (ThermoFisher), 1× MEM-NEAA (ThermoFisher), 1 mM sodium pyruvate (ThermoFisher), 50 μM 2-mercap- toethanol (Sigma), and 20 mM Hepes (pH 7.4)
Bone marrow pro-B cells were cultured with Opti-MEM; 10% (v/v) FBS plus 10 ng/mL IL-7 and 2 ng/mL SCF for 4-5 days

extract_protocol:
About 10 million cells were crosslinked with 2% formaldehyde for 10 minutes at room temperature and quenched with glycine at a final concentration of 125 mM. Then, the crosslinked cells were lysed in the 3C lysis buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% Triton X-100, protease inhibitors) and nuclei were digested with NlaIII enzyme (NEB, R0125) at 37 ℃ overnight.  They were then brought to 16℃, 100U of T4 ligase added  (Promega, M1801) and they incubated again overnight at 16℃.  The ligated products were de-crosslinked with Proteinase K (Roche, #03115852001) at 56 ℃ overnight and the 3C templates were purified by phenol/chloroform.
Libraries were prepared using 3C samples by HTGTS (Jane et al., 2018, PMC6026039).

treatment_protocol:
G1-arrested Abl cells were treated with STI-571 (3µM) for 96h. 150 μM IAA with 2 µg/mL Dox treatment was added to some of the samples.
Bone marrow pro-B cells were purified via anti-B220 MicroBeads (Miltenyi, #130-049-501)

value: Primary BM pro-B cells

tag: purification

value: Purified via anti-B220 MicroBeads (Miltenyi, #130-049-501)


title: WT_BM_CBE1bait Rep3

description: aligned to mm9

value: Opti-MEM; 10% (v/v) FBS plus 10 ng/mL IL-7 and 2 ng/mL SCF for 4-5 days


title: Mouse liver at P19 of p62 S351E/+ mouse -3

city: Tokyo

first: Keiko

last: Kan-O

address: Kawadacho 8-1, Shinjuku-ku

department: Department of Respiratory Medicine

country: Japan

institute: Tokyo Women's Medical University

data_processing:
Fastq files were processed using TRIMGalore.
Resulting reads were mapped to mm10 using the Spliced Transcripts Alignment to a Reference (STAR) Aligner.
The n umber of reads was calculated using RNA-Seq by Expectation Maximization (RSEM)
Differentially expressed genes (DEGs) between p62+/+ and p62S351E/+ mice were analyzed by DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count values for all Samples

source_name: Liver

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen). Ribosomal RNA was depleted using NEBNext rRNA depletion kit.
cDNA libraries for RNA-seq were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Liver

tag: developmental stage


title: WT_BM_CBE1bait Rep1

description: aligned to mm9


title: WT_DoxIAA_Abl_CBE1bait_Rep3

description: aligned to mm9

source_name: v-Abl pro B cells

value: v-Abl pro B cells

value: RAG1-/-, Emu-Bcl2, WAPL degron, single Igh

value: 3 uM STI 1 day, then 150 μM IAA, 3 uM STI-571 with 2 µg/mL Dox treated for 3 days


title: Mouse liver at P19 of p62 S351E/+ mouse -2


title: RH2hWT r3 (s11)


title: WT_DoxIAA_Abl_CBE1bait_Rep2

description: aligned to mm9


title: Mouse liver at P19 of p62 S351E/+ mouse -1


title: RH2hWT r1 (s09)


title: RH2hWT r2 (s10)


title: RH2hKO r6 (s08)


title: WT_untreat_Abl_CBE1bait_Rep3

description: aligned to mm9

value: 3 uM STI-571 treated for 4 days


title: Mouse liver at P19 of wild-type mouse -2

value: WT


title: RH2hKO r7 (s07)


title: Mouse liver at P19 of wild-type mouse -1


title: WT_DoxIAA_Abl_CBE1bait_Rep1

description: aligned to mm9


title: WT_untreat_Abl_CBE1bait_Rep2

description: aligned to mm9


title: WT_untreat_Abl_CBE1bait_Rep1

description: aligned to mm9


title: 3CBEdel_DoxIAA_Abl_RCbait_Rep3

description: aligned to mm9

value: RAG1-/-, Emu-Bcl2, WAPL degron, single Igh, 3IghCBEs deletion


title: 20T3_DD_Liver

city: Irvine

first: Muntaha

middle: Fatima

last: Samad

address: Campus Dr

department: CS

institute: UC Irvine

data_processing:
Trimming performed using trimmomatic
alignment to reference assembly mm10 using Tuxedo Tophat
Read counting for each gene to FPKM values performed using Tuxedo cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: FPKM value for each gene

extract_protocol:
TRIZOL RNA extraction
Truseq mRNA stranded kit

tag: timepoint

tag: light condition

value: DD

tag: diet

value: Tryptophan depleted


title: RH2hKO r5 (s06)

tag: genotype


title: 3CBEdel_DoxIAA_Abl_RCbait_Rep2

description: aligned to mm9


title: Mouse liver at P19 of wild-type mouse -3


title: 20T2_DD_Liver


title: Flt3L-cultured BM, CD11c-, ST2-KO, IL-33

city: Suwon

first: Myeong-Ho

last: Kang

address: 2066, Seobu-ro

country: South Korea

institute: Sungkyunkwan university

data_processing:
QuantSeq 3’ mRNA-Seq reads were aligned using Bowtie2 (Langmead and Salzberg, 2012).
The alignment file was used for assembling transcripts, estimating their abundances and detecting differential expression of genes.
Differentially expressed gene were determined based on counts from unique and multiple alignments using coverage in Bedtools (Quinlan AR, 2010).
The RC (Read Count) data were processed   based on TMM+CPM normalization method using EdgeR within R (R development Core Team, 2020)   using Bioconductor (Gentleman et al.,2004).
Gene classification was based on searches done by   DAVID (http://david.abcc.ncifcrf.gov/) and Medline databases (http://www.ncbi.nlm.nih.gov/).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include Read count values for each Sample

source_name: Flt3L-cultured bone marrow cells

growth_protocol: The mouse bone marrow cells from WT and ST2-KO mice were suspended at 2 x 10^6/ml in complete RPMI containing 10% fetal bovine serum (FBS) and 100 U/ml penicillin/streptomycin and supplemented with 100ng/ml recombinant human Flt3L, 10 mM HEPES, and 55 μM β-mercaptoethanol. The cells were plated at 1 ml/well on 12-well plates and incubated at 37°C with 5% CO2. On day 5, the cells were collected.

extract_protocol:
Cell lysis was performed using Trizol reagent (Invitrogen) and RNA was harvested using PicoPure RNA Isolation Kit (Applied Biosystems)
RNA libraries for RNA-seq were prepared using QuantSeq 3' mRNA-seq Library Prep Kit (Lexogen, Inc. Austria) according to the manufacturer's instructions.

treatment_protocol: CD11c- cells were isolated and culture for 6h with or without IL-33 at 5 ng/ml.

value: Flt3L-cultured bone marrow cells


title: Flt3L-cultured BM, CD11c-, WT, con

description: WT-con


title: Flt3L-cultured BM, CD11c-, WT, IL-33


title: 3CBEdel_DoxIAA_Abl_RCbait_Rep1

description: aligned to mm9


title: 20T1_DD_Liver


title: Y447_Sham_PCTX3_TER

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: A total of 600 ng Cy3-labeled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microL containing 0.5x Agilent fragmentation buffer and 2x Agilent gene expression blocking agent following the manufacturers instructions.  On completion of the fragmentation reaction, 25 microL of 2× Hi-RPM Hybridization Buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE3 Mouse 8x60k v2 gene expression microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), and dried by slowly removing from Wash buffer 2.

scan_protocol: Following posthybridization rinses, arrays were scanned using an Agilent SureScan microarray Scanner at 5 micron, and hybridization intensity data extracted from the scanned images using Agilent’s Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

data_processing: Raw microarray data were log transformed to yield z-scores. The z-ratio was calculated as the difference between the observed gene z-scores for the experimental and the control comparisons, and dividing by the standard deviation associated with the distribution of these differences. Z-ratio values of ± 1.5 were used as cut-off values and calculated using a 5% false discovery rate (FDR) threshold. The complete set was tested for gene set enrichment using parametric analysis of gene set enrichment. For each pathway z-score, a p-value was computed using JMP 6.0 software to test for the statistical significance.

organism: Rattus norvegicus

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng total RNA using the Low-Input Quick Amp Labeling Kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were evaluated with the NanoDrop ND-1000 Spectrophotometer (Wilmington, DE).

growth_protocol: Male Long–Evans rats (Charles River Laboratories) were individually housed and maintained under specific pathogen-free conditions on a 12-h light/dark cycle at the National Institute on Aging/National Institute on Drug Abuse (NIA/NIDA) animal facilities in the Biomedical Research Center (Baltimore, MD). Standard rat chow and water were available ad libitum throughout the experiments.Baseline cognitive status of the animals was obtained  for individiual rats in a 'place' version of the Morris water maze task as previously described24. Training continued over 8 consecutive days, three training trials per day. Every other day, the third trial was a probe in which the platform was inaccessible for 30 seconds. A learning index score was calculated for each animal from their average proximity to the escape platform during training; lower scores indicate better task performance. Aged rats that performed on par with young animals were denoted aged unimpaired (AU), while rats that scored greater than the young were classified as aged impaired (AI)25. To control for non-mnemonic deficits, rats were tested in a single session of a hippocampus-independent cued water maze protocol the following day. No animals that performed outside the normal range on this version of the task were included in the present experiments.

extract_protocol: RNA was extracted using Qiagen RNeasy Mini kits (#74104). Brain tissues were homogenized using a Precellys 24 Tissue homogenizer (Bertin Instruments, Rockville, MD) at 5500-6000rpm for 30 seconds, using 1 mL cold RLT buffer and glass beads. Homogenates were centrifuged at 12,000 rpm for 4 mins at 4°C to pellet any unhomogenized  tissue and beads, and RNA  isolated according to the manufacturer's instructions. RNA concentration and quality was assayed on an RNA6000 Bioanalyzer chip (Agilent).

treatment_protocol: Prior to rTMS administration,  aged (26-27 months, 714-1150 g) and young male rats (6-7 months, 502-788 g) were lightly anesthetized with isoflurane to reduce restraint stress and head movement during the stimulation procedure. The rats then received an intra-muscular injection of Dexmedetomidine (aged: 0.03 mg kg-1 body weight; young: 0.035 mg kg-1 body weight, the minimum required to prevent movement throughout the stimulation period). Antisedan (aged: 0.03 mg kg-1 body weight; young: 0.035 mg kg-1 body weight) was given after stimulation to reverse the sedation.  Physiological parameters (heart rate, arterial blood oxygen saturation, body temperature) were monitored during anesthesia (Starr Life Sciences MouseOx Plus, Starr Life Sciences Corp. Oakmont, PA, USA) to ensure light and consistent anesthetic depth throughout stimulation. Rats were positioned on a heating pad and body temperature was maintained within 2˚C of the initial measurement.  Rats received either iTBS or sham stimulation: the coil was centered 8 mm above the rat’s skull, oriented with the handle to the left of the rat to produce a mediolaterally oriented electric field, aimed towards maximally stimulating the axons of the corpus callosum. The rat’s head was elevated with a small plastic conical ramp to ensure the skull was roughly parallel with the coil base and to minimize head movement and off-target body stimulation. Stimulator output intensity was adjusted to just below the level that elicited muscle twitching in the neck and head [aged: 15.0 ± 0.9% (11-17%); young: 15.3 ± 1.4% (12-19%) of maximal stimulator output], consistent with earlier preclinical studies in rats. rTMS was applied using a Magstim Rapid¬¬¬2 stimulator with a 70-mm figure-eight coil (The Magstim Company, Whitland, Dyfed, UK). 1 Hz stimulation was applied in 5 blocks of 600 pulses lasting 10 minutes repeated at 15-minute intervals for a total of 3000 pulses in 70 minutes. iTBS was administered in 5 blocks repeated every fifteen minutes with each block consisting of 20 trains of 3 50-Hz pulse bursts repeated at 5 Hz for 2 seconds with a 10-second inter-train interval as described elsewhere30. Each iTBS block consisted of 600 pulses in 192 seconds for a total of 3000 pulses delivered in 63.2 minutes. Sham stimulation was performed with the coil 20 cm away from the rats’ heads. Forty-eight hours later animals were deeply anesthetized with 5% isoflurane and sacrificed, and the neocortex and dorsal hippocampus under the center of the TMS coil during stimulation were freshly microdissected and immediately frozen for storage at -80˚ C.

value: Brain

tag: tissue region

value: Parietal cortex

value: Long-Evans

tag: age

value: Young

value: 6-7 months

tag: Sex

value: Male

tag: cognitive status

value: unimpaired

tag: tms

value: Y

tag: post-treatment (hrs)


title: Y447_Sham_HIPP4_TER

tag: tissue

value: Hippocampus

tag: strain

value: Aged

value: 26-27 months


title: 3CBEdel_untreat_Abl_RCbait_Rep3

description: aligned to mm9

tag: cell type

value: v-Abl pro B cells

value: 3 uM STI-571 treated for 4 days

tag: treatment


title: 16T3_DD_Liver


title: AU_iTBS_PCTX4_TER

value: AU


title: Flt3L-cultured BM, CD11c-, ST2-KO, con

description: KO-con


title: Flt3L-BMDC, GM-CSF, CD103+ cDC1s, rep1

growth_protocol: The mouse bone marrow cells were suspended at 2 x 10^6/ml in complete RPMI containing 10% fetal bovine serum (FBS) and 100 U/ml penicillin/streptomycin and supplemented with 100ng/ml recombinant human Flt3L, 10 mM HEPES, and 55 μM β-mercaptoethanol. The cells were plated at 1 ml/well on 12-well plates and incubated at 37°C with 5% CO2 for 10 days.

treatment_protocol: IL-33 or GM-CSF was treated at 5 ng/ml on day 5 of Flt3L-BMDC culture

value: WT

value: GM-CSF


title: AI_iTBS_PCTX2_TER

value: impaired

value: AI


title: AI_iTBS_HIPP2_TER

value: Brain


title: Y447_Sham_PCTX3_TR

description: Y447-SH-PCTX REPEAT

value: Parietal cortex

value: Long-Evans


title: 3CBEdel_untreat_Abl_RCbait_Rep2

description: aligned to mm9

value: RAG1-/-, Emu-Bcl2, WAPL degron, single Igh, 3IghCBEs deletion


title: 16T2_DD_Liver

value: DD

value: Tryptophan depleted


title: 3CBEdel_untreat_Abl_RCbait_Rep1

description: aligned to mm9


title: Y447_Sham_HIPP3_TER

value: Young

value: 6-7 months

value: Male

value: unimpaired

value: Y


title: Flt3L-BMDC, IL-33, CD103+ cDC1s, rep2

value: Flt3L-cultured bone marrow cells


title: 16T1_DD_Liver


title: AI_iTBS_PCTX3

value: Aged

value: 26-27 months


title: AI_iTBS_PCTX2


title: Flt3L-BMDC, GM-CSF, CD103+ cDC1s, rep2

value: WT

value: GM-CSF


title: Flt3L-BMDC, IL-33, CD103+ cDC1s, rep1


title: Y447_Sham_HIPP3_TR

description: Y447-SH-HIPP REPEAT

value: Hippocampus


title: WT_DoxIAA_Abl_RCbait_Rep3

description: aligned to mm9

value: v-Abl pro B cells

value: RAG1-/-, Emu-Bcl2, WAPL degron, single Igh

value: 3 uM STI 1 day, then 150 μM IAA, 3 uM STI-571 with 2 µg/mL Dox treated for 3 days


title: 12T3_DD_Liver


title: AI_Sham_PCTX3

value: Brain

value: Parietal cortex

value: Long-Evans

value: impaired

value: AI


title: AI_Sham_PCTX4

value: Male


title: WT_DoxIAA_Abl_RCbait_Rep1

description: aligned to mm9


title: AI_iTBS_PCTX1


title: WT_DoxIAA_Abl_RCbait_Rep2

description: aligned to mm9


title: 12T2_DD_Liver

value: DD

value: Tryptophan depleted


title: AI_Sham_PCTX2


title: WT_untreat_Abl_RCbait_Rep3

description: aligned to mm9

value: 3 uM STI-571 treated for 4 days


title: WT3_vent

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Sequencing data were demultiplexed using bcl2fastq2 v.2.2 and aligned to mouse reference genome (mm10).
Alignment and quantification with STAR v.2.5.1 using the default parameters
Normalization using DeSeq2
Genome_build: mm10
Supplementary_files_format_and_content: normalized txt files

extract_protocol:
The samples were frozen in liquid nitrogen (-80° C) and extracted using a RNeasy Micro kit (Qiagen).
The cDNA library was generated according to the SMART-Seq2 protocol.

value: ventricles

value: wild-type

tag: pupid

tag: prepdate

tag: litter


title: KO3_vent

value: MyHC-Creld1 KO


title: KO2_vent


title: AI_Sham_PCTX1

value: Aged

value: 26-27 months


title: 12T1_DD_Liver

tag: timepoint


title: 8T3_DD_Liver

tag: light condition


title: 8T2_DD_Liver

tag: diet


title: AU_iTBS_PCTX5

value: unimpaired

value: AU


title: WT_untreat_Abl_RCbait_Rep1

description: aligned to mm9

value: v-Abl pro B cells

tag: genotype

value: RAG1-/-, Emu-Bcl2, WAPL degron, single Igh

tag: purification


title: 8T1_DD_Liver


title: CBE2inv_Abl_Vh81xbait_C2_Rep6

description: aligned to AJ851868/mm9

value: RAG2-/-, CBE2inv/inv


title: CBE2inv_Abl_Vh81xbait_C2_Rep5

description: aligned to AJ851868/mm9


title: KO1_vent

tag: age