title: Tet TKO chimera plate 26

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190730_P05

value: E7.5 chimera embryo

value: Host cells and injected mESC-derived Control and Tet TKO cells

value: Chimera assay


title: MSC_A5_2

status: Public on Jun 14 2022

type: SRA

city: Mainz

first: Pablo

last: Llavona

state: Rhineland-Palatinate

address: Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4

country: Germany

institute: IMB

library_source: transcriptomic

data_processing:
Adapter sequences were trimmed from paired end RNA-seq reads using TrimGalore (https://github.com/FelixKrueger/TrimGalore).
Quality filtered reads were mapped using STAR against the mouse genome (GRCm39).
Read counts were quantified with HTSeq and differential expression analysis was carried out with these counts using Bioconductor package DESeq2.
Assembly: GRCm39
Supplementary files format and content: RPKM values for each Sample and the comparison of the reads between WT and KO

molecule: total RNA

organism: Mus musculus

source_name: bone marrow

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). 8.7ng of total RNA was used for the construction of sequencing libraries.
Library preparation was performed using NEBNext End Repair module, dA-Tailing module and Quick Ligation module (New England BioLabs).

tag: tissue

value: bone marrow

tag: cell line

value: primary

tag: cell type

value: mesenchymal stromal cells

tag: genotype

value: ANXA5 knockout

tag: treatment


title: MSC_A2_3

value: ANXA2 knockout


title: WT cDC1_untreated_rep2

type: RNA

city: Perugia

first: Marco

last: Gargaro

state: Perugia

address: Polo Unico Sant'Andrea delle Fratte, P.le Gambuli, Bldg C, 4th Floor

department: Medicine and Surgery

country: Italy

institute: University of Perugia

description: WT cDC1_untreated_rep2

hyb_protocol: Following fragmentation and labeling, 2.5 ug of cDNA were hybridized onto the Gene 1.0 ST arrays and placed in GeneChip Hybridization Oven 640 for 18 hr at 45C. Gene Chip’s were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 7G 3000 Scanner.

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

label: biotin

source_name: cDC1 isolated from WT Flt3-BMDCs

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Pico reagent kit from 100pg-2ng total RNA.

extract_protocol: Column extraction of total RNA was performed acording to the manufacturer's instructions.

treatment_protocol: WT Bone marrow derived  cDC1, cDC2 and pDCs sort-purifed were left untreated or treated with E. coli LPS (0.250 μg/ml) for 24 h.

value: Bone marrow derived DCs

tag: strain

value: WT


title: Grp5a db/db+renin+Rosiglitazone rep4

city: St. Louis

first: Haojia

last: Wu

state: Missouri

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

country: USA

institute: Washington University in St. Louis

description:
snRNA-seq using 10X Chromium
I3073

data_processing:
Illumina data were demultiplexed and the resulting fastq files were processed by the 10X Genomics cellranger pipeline (version 6.0.1). Reads were mapped to mouse genome mm10. Both exonic and intronic reads were incorporated in the final molecule counts.
We used CellBender to remove the ambient RNA contamination. In brief, the unfiltered count matrices sampleID.h5 from cellranger were input into CellBender. CellBender remove-background was run (on cuda mode) with parameters “expected-cells” and “total-droplets-included” were chosen for each dataset based on the total UMI per cell vs. cell barcode curve in accordance with CellBender documentation. Other parameters were left at their default values. The CellBender corrected count matrices were then input to DoubletFinder to remove the potential doublets. We used default parameters to run DoubletFinder except for the nExp, which is estimated based on the total cell number of the sample (nNuc) and a linear regression equation derived from the Demuxlet study, i.e. nExp = nNuc * (0.018+8.4e-06* nNuc).
Genome_build: mm10
Supplementary_files_format_and_content: The hdf5 files contain the count matrix generated by CellRanger for each sample. The count_matrix_combined_after_cellbender.tar.gz file contains the gene-by-cell count matrix for all cells combined after data QC. The metadata.csv file is the meta data (e.g. cell type annotation, mouseID, group ID and the UMAP coordinates) for all high-quality cells included in the analysis.

source_name: db/db+renin+Rosiglitazone

extract_protocol:
Single nucleus were isolated using a protocol developed from our lab (dx.doi.org/10.17504/protocols.io.nahdab6).
Single nucleus suspensions at a concentration of 1000 nuclei/ul were loaded into the Chromium Controller as per manufacturer instructions, which target 10,000 nuclei per sample. 12 PCR cycles were used for cDNA synthesis. Each library was sequenced using an Illumina NovaSeq instrument, 8 samples per S4 lane, with one 150 bp read located near the 3′ end of the mRNA.
10x chromium 3' kit version 3 chemistry

treatment_protocol:
To establish the model, female db/db mice (BKS.Cg-Dock7m +/+ Leprdb/J from Jackson, BKS background, Lot 642) were subject to left nephrectomy at 5 weeks of age and, at 12 weeks, infected with a renin expressing adeno-associated virus (ReninAAV, 109 genomic copies) to induce hypertension and accelerate disease progression. In addition to the ReninAAV Unx db/db mice, db/m and Unx db/db mice infected with an empty viral vector (LacZ AAV) were included as healthy and diabetic non-hypertensive controls, respectively.
Drug treatments were given to mice as follows:   1. Vehicle (drinking water)  2. Lisinopril (An ACE inhibitor, 10 mg/kg/d in the drinking water),    3. Rosiglitazone (A PPARꙋ activator, 0.007% w/w via admix diet, p.o. ~10 mg/kg/d)  4. JNJ-39933673 (A SGLT2 inhibitor, 0.0075% w/w via admix diet, p.o. 1 ~ mg/kg/d)  5. ACEi plus SGLT2i (dosed as before).   6. ACEi plus rosiglitazone (dosed as before). Terminal samples were collected 48 hours and 2 weeks after treatment inception

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous

tag: Sex

value: female

value: renin AAV + Rosiglitazone

tag: treatment timepoint

value: 2 days


title: WT cDC1_untreated_rep3

description: WT cDC1_untreated_rep3


title: MSC_A5_4


title: Tet TKO chimera plate 17

city: Rehovot

first: Markus

last: Mittnenzweig

state: Shfela

address: 234 Herzl St.

country: Israel

institute: Weizmann Institute of Science

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190325_P03

library_source: transcriptomic single cell

data_processing:
MARS-seq data was processed as detailed in the MARS-seq2.0 protocol (Keren-Shaul et al. 2019):
1. bcl2fastq/2.15.0.4
2. Pool_barcode (4 bps) and well_barcode (7 bps) plus UMI barcode (8 bps) were removed from Read 1 and Read 2 (respectively) and concatenated to the fastq header.
3. Read 1 sequences were mapped to the mm9 genome using bowtie2.
4. Demultiplexing and construction of mRNA count matrix were based on 4bp plate barcode, 7bp well barcode and 8bp UMI barcode
5. Header structure of labeled Read 1 fastq files: "ORIGINALHEADER_barcode=similar_oligo-pool_barcode_quality-well_barcode_quality-UMI_quality-pool_barcode-well_barcode-UMI". Concatenated entries are separated by "-"
6. well_barcode (7bp), pool_barcode (4bp) and external_barcode (8bp) of each single cell can be found in metadata.
PBAT data was processed as detailed (Meir et al., 2020): PE 150bp or 300bp reads were aligned to the mm9 reference genome using an in-house script based on Bowtie2. In cases where the two reads ends were not aligned in a concordant manner, the reads were discarded. Reads that were mapped to the same genome coordinates where marked as duplicates and were used only once. We subsample methylation of single-cells to have only one methylation call per CpG.
Assembly: mm9
Supplementary files format and content: Tab-separated text file for each 384-well plate containing UMI counts per gene per single cell. metadata_cells_scrna_sequencing.txt file contains metadata for each processed single cell.
Supplementary files format and content: Tab-separated text file for each sample, containing a row per genomic CpG with the following columns: 'chrom','start','end' - coordinates in 0-based form, 'cov' - # of times the CpG was covered, 'meth' # of times the CpG was methylated.

source_name: E7.5 chimera embryo

growth_protocol: Control and mutant mESCs were cultured on irradiated mouse embryonic fibroblasts (MEFs) with standard serum medium for 2-3 days and replaced with 2i+LIF medium containing an additional 1 mM PD0325901 and 3 mM CHIR99021 for another growth of 10-12 hours.

extract_protocol:
Whole-embryo chimera, mixed chimera, and AAV-Cre treated embryos were dissected in ice-cold 1×PBS, followed by imaging in a drop of DMEM medium supplemented with 10% foetal bovine serum (FBS) under a Nikon Eclipse Ti2 inverted microscope. Embryos were then rinsed in ice-cold 1×PBS, transferred into an Eppendorf tube containing 35 µl 0.25% Trypsin/0.02% EDTA Solution A, and incubated at 37 °C for 5 min with 2-3 times pipetting. Trypsinization was stopped by adding 10% FBS/DMEM medium. Cell suspensions were filtered through a 35 µm strainer before sorting.
For MARS-seq analysis, single cells were index-sorted into a pre-barcoded 384-well capture plate that contains 2 µl of lysis solution and barcoded poly (T) reverse-transcription (RT) primers. In each plate, 12 wells at positions C1, C2, D1, D2, J6, J7, K6, K7, O23, O24, P23, and P24 were kept as non-cell controls. Immediately after sorting, each plate was sealed, spun down, snap-frozen on dry ice, and stored at -80 °C until library preparation.
For bisulfite sequencing, Tet-TKO1, Tet-TKO2, Ctrl1, and Ctrl2 cells were sorted from E8.5 chimera embryos respectively. Cell pellets were kept at -80 °C until library preparation. Genomic DNA was extract using commercial kit.
Single-cell cDNA libraries were prepared using the MARS-Seq method as described (Keren-Shaul et al., 2019). Briefly, reverse transcription was performed in individual wells of the sorted 384-well plate to get complementary DNA (cDNA). Subsequently, all liquid from each 384-well plate was pooled and converted to double-stranded DNA, transcribed using T7 RNA polymerase, and fragmented. A unique plate adaptor was added to each library to be sequenced together, and RNA::ssDNA (plate adaptor) ligation was performed. The purified ligates were applied to a second RT step with a primer complementary to the ligated adaptor, and the library is completed by cDNA enrichment through PCR amplification. Library concentration and profile were evaluated before sequencing.  Bulk PBAT library was performed as previously described (Meir et al., 2020). Briefly, genomic DNA was converted with bisulfate, and applied to the first and second strand synthesis. The product was treated by Klenow fragment and purified. A final PCR was performed using a universal primer and indexed primers. The final product was clean and sequenced.

treatment_protocol:
(1) To obtain whole-embryo and mixed chimeric embryos, mESCs were injected into diploid or tetraploid B6D2F x B6D2F1 E3.5 blastocysts and surgically implanted into E2.5 postcoitum pseudo-pregnant Hsd:ICR (CD-1) females following standard procedures. Females were sacrificed at embryonic day 7.5-9.5 based on the design of the experiment.
(2) To obtain AAV-Cre treated Tet knockout embryos, zygotes from Tet triple floxed mice were collected in M2 medium. Following acidic Tryode’s solution treatment, zygotes were rinsed in M2 medium and transferred to KSOM for incubation in a tissue culture incubator. Drops containing 35 µl KSOM medium were placed in 35 mm plates under mineral oil. 6e9 vg AAV1-Cre-GFP viral were added to each drop, followed by a 15 min incubation at 37 °C in the same tissue culture incubator. Subsequently, zygotes were transferred into the viral drop and cultured for 24 hrs. Qualified 2-cell embryos were rinsed in M2 medium and transferred into the oviduct of E0.5 pseudo-pregnant ICR females. Recipient females were allowed to carry the embryos and sacrificed at E7.5.

tag: developmental stage


title: Tet TKO chimera plate 19

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190325_P05


title: WT cDC1_untreated_rep1

description: WT cDC1_untreated_rep1


title: WT pDC_activated (LPS)_rep2

description: WT pDC_activated (LPS)_rep2

source_name: pDC isolated from WT Flt3-BMDCs


title: Tet TKO chimera plate 22

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190730_P01


title: Grp5a db/db+renin+Rosiglitazone rep2

description:
snRNA-seq using 10X Chromium
K3071


title: MSC_A5_3


title: Grp4b db/db+renin+ACEI rep3

description:
snRNA-seq using 10X Chromium
Q3067

source_name: db/db+renin+ACEI

value: renin AAV + ACEI

value: 2 weeks


title: WT pDC_activated (LPS)_rep3

description: WT pDC_activated (LPS)_rep3


title: Tet TKO chimera plate 15

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190325_P01


title: MSC_A2_1


title: Grp4b db/db+renin+ACEI rep5

description:
snRNA-seq using 10X Chromium
H3069


title: MSC_A2_2


title: MSC_WT_1


title: Tet TKO chimera plate 13

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190322_P02


title: Tet TKO chimera plate 12

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190322_P01


title: Grp4b db/db+renin+ACEI rep4

description:
snRNA-seq using 10X Chromium
G3068


title: Grp5a db/db+renin+Rosiglitazone rep1

description:
snRNA-seq using 10X Chromium
E3070


title: Tet TKO chimera plate 14

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190322_P04


title: Tet TKO chimera plate 10

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190318_P11


title: MSC_WT_3


title: Grp4b db/db+renin+ACEI rep2

description:
snRNA-seq using 10X Chromium
P3066


title: WT pDC_untreated_rep3

description: WT pDC_untreated_rep3


title: MSC_WT_2


title: WT pDC_untreated_rep1

description: WT pDC_untreated_rep1


title: Tet TKO chimera plate 9

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190318_P09


title: Tet TKO chimera plate 11

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190318_P12


title: MSC_WT_4


title: WT pDC_untreated_rep2

description: WT pDC_untreated_rep2


title: Grp4b db/db+renin+ACEI rep1

description:
snRNA-seq using 10X Chromium
I3065


title: Grp4a db/db+renin+ACEI rep5

description:
snRNA-seq using 10X Chromium
H3064


title: Grp4a db/db+renin+ACEI rep4

description:
snRNA-seq using 10X Chromium
G3063


title: Grp4a db/db+renin+ACEI rep2

description:
snRNA-seq using 10X Chromium
I3061


title: Grp4a db/db+renin+ACEI rep3

description:
snRNA-seq using 10X Chromium
J3062


title: Ahr f/f Vav iCre_cDC2_activated (LPS)_ plus L-Kyn_rep2

source_name: cDC2 isolated from Ahr f/f Vav iCre Flt3-BMDCs

treatment_protocol: Ahr f/f and Ahr f/f Vav iCre bone marrow derived cDC2 sort-purifed were left untreated or treated with E. coli LPS (0.250 μg/ml)  or  in combination with L-Kynurenine (50 μM)  for 24 h.

value: Ahr f/f Vav iCre


title: Grp4a db/db+renin+ACEI rep1

description:
snRNA-seq using 10X Chromium
D3060


title: WT pDC_activated (LPS)_rep1

description: WT pDC_activated (LPS)_rep1


title: Tet TKO chimera plate 8

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190318_P07

value: E7.5 chimera embryo


title: Grp3b db/db+renin rep5

description:
snRNA-seq using 10X Chromium
B3039

source_name: db/db+renin

value: renin AAV


title: Ahr f/f Vav iCre_cDC2_L-Kyn_rep2

description: Ahr f/f Vav iCre_cDC2_L-Kyn_rep2


title: PRMT1fl/fl; cx3r1cre-ert2 microglia CPZ diet_CD11c_low_Input_rep2

city: Montreal

first: Stephane

last: Richard

state: Quebec

address: Lady Davis Institute, 3755 Cot

country: Canada

institute: Lady Davis Institute- Jewish General Hospital

description: ChIP

library_source: genomic

data_processing:
Single-end reads of length 76 were first trimmed off the adapter sequence as well as the polyA tail and then mapped through the Bowtie2 short read aligner v2.4.1 to the hg19 reference genome from the University of California Santa Cruz (UCSC) (Lander et al., 2001; Langmead and Salzberg, 2012).
Quality control checks on the raw sequence data were carried out through the FASTQC software v0.11.9. BAM files were sorted and indexed, and duplicate reads were removed through Samtools v0.1.19.
Peak calling and motif enrichment for ChIP-seq experiments relative to the input was carried out by the Hypergeometric Optimization of Motif Enrichment (HOMER) software v4.11 in histone or super-enhancer mode using default parameters(Heinz et al., 2010).
Average read coverage profiles across TSS, TTS or gene body regions and corresponding heatmaps were plotted with the NGS PLOT software (Shen et al., 2014). Density plots of reading coverage were made using the Integrative Genomics Viewer (IGV) software.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include normalized tage counts for each Sample

molecule: genomic DNA

extract_protocol:
Chromatin immunoprecipitation for histone modification H3K27ac and was performed as follows, using ~500,000 microglia per assay and n=2 independent biological replicates per conditions. First microglia were briefly thawed on ice and lysed by incubation in 1 ml of lysis buffer (0.5% IGEPAL CA-630, 10 mM HEPES pH 7.9, 85 mM KCl, 1 mM EDTA pH 8.0, in water) for 10 min on ice. Lysates were centrifuged at 800 RCF for 5 min at 4 °C, and pellets were resuspended in 200ul of sonication/ immunoprecipitation buffer (10 mM Tris-HCl pH 7.5, 100 mM NaCl, 0.5 mM EGTA, 0.1% Deoxcycholate, 0.5% Sarkosyl, in water). Sonication was performed with a Bioruptor Standard Sonicator (Diagenode) and consisted of two rounds of 15 min each, alternating stages of 30 sec “sonication-on” with 60 sec “sonication-off”.  Twenty-two microliters of 10% Triton-X were then added to samples (1% final concentration) on ice, and lysates were cleared by centrifugation for 5 min at 18,000 RCF at 4 °C. Two microliters of supernatant were then set aside for input library sequencing controls. Supernatants were then immunoprecipitated on a rotator for two hours at 4 °C with H3K27ac antibody (Active Motif, 39685, 2.5 ug per sample) pre-bound to 17 ul Protein A Dynabeads (Life Technologies 10001D).   Immunoprecipitates were washed three times each on ice with ice-cold wash buffer I (150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA pH 8.0 in water), wash buffer III (10 mM Tris-HCl, 250 mM LiCl, 1% IGEPAL CA-630, 0.7% Deoxycholate, 1mM EDTA in water) and TET (10 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 0.1% Tween-20, in water) and eluted with 1% SDS/TE at RT in a final volume of 100 ul. Reverse-crosslinking was then performed on immunoprecipitates and saved input aliquots. First, 6.38 ul of 5 M NaCl (final concentration 300 mM) was added to each sample immersed in 100 ul SDS/TE. Crosslinking was then reversed by overnight incubation at 65 °C in a hot air oven. Potentially contaminated RNA was then digested for one hour at 37 °C with 0.33 mg/ml RNase A, proteins were digested for one hour at 55 °C with 0.5 mg/ml proteinase K, and DNA was extracted using Sera-Mag SpeedBeads (Thermo Scientific, 6515205050250).
Sequencing libraries were prepared from recovered DNA (ChIP) or generated cDNA (RNA) by blunting, A-tailing, and adapter ligation as previously described using barcoded adapters (NextFlex, Bioo Scientific) (Gosselin et al., 2014; Gosselin et al., 2017). Libraries were PCR-amplified for 12-15 cycles and size selected for fragments (200-400 bp for ChIP-seq) by gel extraction (10% TBE gels, Life Technologies EC62752BOX).  ChIP-seq librairies were single-end sequenced for 76 cycles on an Illumina HiSeq 4000 (Illumina, San Diego, CA) according to manufacturer’s instruction.

treatment_protocol:
0.2% of Cuprizone diet was fed in 4-6 weeks-old wild-type (PRMT1Ifl/fl) and microglia specific knockout (PRMT1fl/fl; cx3r1cre-ert2) mice
Brains were digested, and myelin were removed using 30% percoll gradient. Microglia was sorted using CD45 and CD11B surface markers. RNA in 2X SuperScript III buffer was incubated for 1 min at 50 C on a PCR cycler with 2.5 ul of the following mix: 1.5 ug Random Primer (Life Technologies 48190-011), 10 M Oligo d(T) (Life Technologies 18418020), 10 units SUPERase-In (Ambion AM2696), 4 mM dNTP mix (Life Technologies 18427088), in water. Samples were then immediately placed on ice for 5 min. First-strand synthesis was then performed by incubation at 25 C for 10 min and 50 C for 50 min on a PCR cycler with 7.6 ul of the following mix: 0.2 ug actinomycin (Sigma A1410), 13.15 mM DTT (Life Technologies), 0.026% Tween-20, 100 units SuperScript III (Life Technologies kit 18080-044), in water. After incubation, RNA/DNA complexes were isolated by adding 36 ul of Agencourt RNAClean XP beads (Beckman Coulter A63987) and incubated for 10 min at RT and then 10 min on ice. Samples were then placed on a magnet and beads were washed twice with 150 ul of 75% EtOH. Following washings, beads were air-dried for 10-12 min and eluted with 10 ul of water. Second-strand synthesis was then performed. RNA/DNA samples in 10 ul of water were incubated for 2.5 hours at 16 C with 5 ul of the following mix: 3x Blue Buffer (Enzymatics), 1.0 ul PCR mix (Affymetrix 77330), 2.0 mM dUTP (Affymetrix 77206), 1 unit RNAseH (Ezymatics Y9220L), 10 units DNA Polymerase I (Enzymatics P7050L), 0.03% Tween-20, in water). DNA was then purified by addition of 1.5 ul Sera-Mag SpeedBeads (Thermo Scientific, 651520505025), resuspended in 30 ul 20% PEG 8000/2.5 M NaCl, incubated at RT for 15 min and placed on a magnet for two rounds of bead washing with 80% EtOH. Beads were then air dried for 10-12 min and DNA was eluted from the beads by adding 40 ul of water. Supernatant was then collected on a magnet and placed on ice or stored at -20C until DNA blunting, poly(A)-tailing, and adapter ligation.

value: Microglia

value: PRMT1fl/fl; cx3r1cre-ert2

value: 0.2% cuprizone diet

tag: time

value: 5 weeks

tag: chip antibody

value: none (input)


title: PRMT1Ifl/fl microglia CPZ diet_CD11c_high_Input_rep1

description: ChIP


title: Tet TKO chimera plate 6

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190318_P05

value: Host cells and injected mESC-derived Control and Tet TKO cells

value: Chimera assay


title: Tet TKO chimera plate 5

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190318_P04


title: PRMT1Ifl/fl microglia CPZ diet_CD11c_high_Input_rep2

description: ChIP


title: PRMT1fl/fl; cx3r1cre-ert2 microglia normal diet_Input_rep2

description: ChIP

value: Normal diet

value: 11 weeks


title: Ahr f/f Vav iCre_cDC2_activated (LPS)_rep2

value: Bone marrow derived DCs


title: PRMT1Ifl/fl microglia CPZ diet_CD11c_low_Input_rep2

description: ChIP


title: Tet TKO chimera plate 4

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190318_P03


title: Ahr f/f Vav iCre_cDC2_activated (LPS)_ plus L-Kyn_rep1


title: Grp3b db/db+renin rep4

description:
snRNA-seq using 10X Chromium
A3038

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous

value: female


title: PRMT1Ifl/fl microglia CPZ diet_CD11c_low_Input_rep1

description: ChIP


title: Tet TKO chimera plate 7

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190318_P06


title: PRMT1fl/fl; cx3r1cre-ert2 microglia normal diet_Input_rep1

description: ChIP


title: PRMT1Ifl/fl microglia normal diet_Input_rep2

description: ChIP


title: Grp3b db/db+renin rep2

description:
snRNA-seq using 10X Chromium
J3036


title: Ahr f/f Vav iCre_cDC2_untreated_rep1

description: Ahr f/f Vav iCre_cDC2_untreated_rep1


title: Ahr f/f Vav iCre_cDC2_untreated_rep2

description: Ahr f/f Vav iCre_cDC2_untreated_rep2


title: PRMT1Ifl/fl microglia normal diet_Input_rep1

description: ChIP


title: Tet TKO chimera plate 1

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190303_P02


title: Ahr f/f Vav iCre_cDC2_activated (LPS)_rep1


title: PRMT1fl/fl; cx3r1cre-ert2 microglia CPZ diet_CD11c_low_rep2

description: ChIP


title: Ahr f/f Vav iCre_cDC2_L-Kyn_rep1

description: Ahr f/f Vav iCre_cDC2_L-Kyn_rep1


title: PRMT1fl/fl; cx3r1cre-ert2 microglia CPZ diet_CD11c_low_rep1

description: ChIP


title: Grp3a db/db+renin rep4

description:
snRNA-seq using 10X Chromium
A3033

value: 2 days


title: Tet TKO chimera plate 3

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190318_P02


title: Ahr f/f_cDC2_activated (LPS)_ plus L-Kyn_rep1

source_name: cDC2 isolated from Ahr f/f Flt3-BMDCs

value: Ahr f/f


title: Ahr f/f_cDC2_L-Kyn_rep1

description: Ahr f/f_cDC2_L-Kyn_rep1


title: Tumor1, CD8aapos, WT replicate 3

city: New York

first: Tiago

last: Castro

state: New York

address: 1230 York Avenue

institute: The Rockefeller University

description: Bulk Rnaseq

data_processing:
Data Processing of Single-Cell RNA-Seq and Single Cell TCR-Seq Libraries. Raw fastq files derived from our RNA-seq libraries were processed with cellranger count (v6.0.2) using the 10x Genomics prebuilt human reference (GRCh38 - GENCODE v32/Ensembl 98). The count matrix was processed using Seurat (v4.0.4) (50). Quality control was performed by removing cells with high (> 10%) mitochondrial-derived UMIs. The assembly, alignment, and annotation of TCR sequences were performed using the Cellranger vdj workflow from 10x Genomics and the prebuild human vdj reference (GRCh38 - Ensembl5.0.0). The assignment of gamma/delta T-cell clones was performed using the clonality package (https://github.com/victoraLab/clonality). Paired TCR clones were defined by identical V, (D), J genes, and CDR3 length and nucleotide sequence for delta and gamma chains. Cells with only one successfully TRG or TRD chain sequenced were assigned as part of a paired TCR core if its DNA sequence matched its correspondent chain completely (sticky parameter).
Single Cell RNA-Seq Normalization and Statistical Analysis. The raw UMI counts were normalized using the SCTransform function available in the Seurat (v4.0.4) package (51). The top 3000 variable genes were first used for dimensional reduction by PCA using the scaled data. The first 30 principal components were further used for visualization using the Manifold Approximation and Projection (UMAP) and cell clustering (50, 51). The Wilcoxon rank-sum test detected differentially expressed genes by comparing each cluster against all cells. Genes with adjusted p-values of 0.05 or less were considered for downstream analysis. Finally, we scored each cell based on gene sets for the S and G2M phases using the CellCycleScoring function within the Seurat package (52). Cells that did not score in at least one set were marked as in the G1 phase. GSEA analyses were performed using the fgsea package for R (53) and the Molecular Signatures Database (MSigDB - v7.5.1)[PMID: 16199517]. In short, for each condition or cluster, genes were ranked using their Log2FoldChanges, and enriched pathways were considered significant when having adjusted p-values of 0.05 or less. Heatmap was constructed using the ComplexHeatmap package (54) with the Pearson residuals matrix obtained by GetResidual function from Seurat.
Bulk RNA-Seq Analysis. Raw fastq files were aligned and quantified with STAR (v. 2.7.10a) by using the mouse genome (mm39) and the mouse transcriptome (gencode M29) (58). Next, the count matrix was imported to the R environment and processed by the DESeq2 package (v. 1.34) pipeline (59). Briefly, genes from samples expressing less than ten reads were pre-filtered. Gene expression among samples was normalized by applying a negative binomial distribution model. The Wald test was employed to determine differential gene expression between conditions. Genes containing adjusted pvalues (FDR) less than 0.1 were considered for downstream analysis, and log2 fold changes were shrunk using the ashr algorithm (60).
Assembly: GRCh38
Assembly: GRCm39
Supplementary files format and content: Tab separated files and matrix of UMI counts.

source_name: Colon

extract_protocol:
Single-cell RNA sequencing.  Cryopreserved single cell suspensions of human colon biopsies were thawed at 37 C, washed with RPMI, and rested in complete RPMI in 96-well plate for 1 hour. The cells were subsequently incubated with PMA/ionomycin for 3 hours, washed, blocked in Fc receptor block (TruStain FcX, Biolegend), and tagged with cell hashing antibody. Conjugation of purified antibodies for cell hashing was performed as described by the Technology Innovation Lab at the New York Genome Center (https://cite-seq.com/protocol/). The list of antibodies, clones, and barcodes are available in Table S3. The hashtagged samples were then pooled and stained for FACS sorting with anti-CD3 (clone OKT3, BioLegend) APC, anti-TCRγδ (clone 5A6.E9, Thermo Fisher) PE, and anti-TCRαβ (clone IP26, BioLegend) Alexa Fluor 488. Samples were subsequently stained with Sytox Blue (Thermo Fisher) prior to acquisition to determine cell viability. Viable T cells were sorted in FACS Aria II by gating SytoxBlue- CD3+TCRγδ+TCRαβ- cells and subsequently transferred into RPMI with 10% FBS at 4C. FACS-sorted CD3+ TCRγδ+ cells were loaded onto the Chromium 10x Genomics v1.1 platform (10X Genomics) as described in the manufacturer’s protocol. Single cell 5’ transcript and TCRγδ libraries were prepared using Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 with Feature Barcode Technology for Cell Surface Protein (CG000228). Following cDNA amplification, cell hashing additive oligos were added to amplify cell hashtag oligos. The products were separated using SPRIselect Beads (Beckman Coulter). Cell hashtag library generation was performed as described by the Technology Innovation Lab at the New York Genome Center (https://cite-seq.com/protocol/). TCRγδ libraries were prepared as described in Mimitou et al., 2019. cDNA libraries were quantified using Agilent High Sensitivity D5000 ScreenTape (Agilent, no. 5067-5592). Libraries were sequenced using NovaSeq 6000 platform.
Bulk mRNA-Seq Library Preparation. Sorted cells (300-800 cells) were lysed in a guanidine thiocyanate buffer (TCL buffer, QIAGEN) supplemented with 1% β-mercaptoethanol. RNA was isolated by solid-phase reversible immobilization bead cleanup using RNAClean XP beads (Agentcourt, A63987), reverse transcribed, and amplified as described (57). Uniquely barcoded libraries were prepared using Nextera XT kit (Illumina) following manufacturer’s instructions. Sequencing was performed on an Illumina NextSeq500.

value: Colon (tumor)

value: gd T cells (CD8aapos)


title: Tumor1, CD8aapos, WT replicate 2

description: Bulk Rnaseq


title: Grp3b db/db+renin rep3

description:
snRNA-seq using 10X Chromium
K3037

value: renin AAV

value: 2 weeks


title: Ahr f/f_cDC2_activated (LPS)_ plus L-Kyn_rep2


title: Tumor1, CD8aaneg, WT replicate 3

description: Bulk Rnaseq

value: gd T cells (CD8aaneg)


title: PRMT1Ifl/fl microglia CPZ diet_CD11c_high_rep2

description: ChIP

value: Microglia

value: 0.2% cuprizone diet


title: PRMT1Ifl/fl microglia CPZ diet_CD11c_high_rep1

description: ChIP

value: 5 weeks


title: RNA-seq, 16hr, R2

city: Brookline

first: Sylvan

middle: C

last: Baca

state: MA

address: 450 Brookline Ave

institute: Dana–Farber Cancer Institute, Dana-704

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA for ATAC-seq and ChIP-seq data, and STAR for RNAseq data
bigwig files represent normalized read counts in treatment conditions
Assembly: hg19
Supplementary files format and content: bigwig (normalized read pileup)

organism: Homo sapiens

source_name: LNCaP

growth_protocol: LNCaP cells (ATCC CRL-1740) were cultured in phenol red free RPMI (#11835030, Gibco) with 10% charcoal stripped FBS (#100-119, Gembio) for 3 days

extract_protocol: Total mRNA was collected from 300,000 cells using RNA easy kit (Qiagen 74044) with RNase-Free DNase Set (Qiagen no. 79254) according to the manufacturer instructions. RNA purity and concentration were determined on 2100 Bioanalyzer (Agilent) using Agilent RNA 6000 Nano Kit # 5067-1511). 400ng RNA samples were submitted to Novogene for RNA library preparation.

treatment_protocol: After 3 days, cells were stimulated with either 10 nM DHT (5α-Androstan-17β-ol-3-one, Dihydrotestosterone, A8380, Sigma) or EtOH (Vehicle) for 16 hours.

value: LNCaP

value: DHT


title: Ahr f/f_cDC2_activated (LPS)_rep2

description: Ahr f/f_cDC2_activated (LPS)_rep2


title: Tumor1, CD8aaneg, WT replicate 2

description: Bulk Rnaseq


title: Grp3a db/db+renin rep1

description:
snRNA-seq using 10X Chromium
I3030


title: RNA-seq, 16hr, R1


title: Grp3b db/db+renin rep1

description:
snRNA-seq using 10X Chromium
B3035


title: Ahr f/f_cDC2_L-Kyn_rep2

description: Ahr f/f_cDC2_L-Kyn_rep2


title: Grp3a db/db+renin rep5

description:
snRNA-seq using 10X Chromium
B3034


title: RNA-seq, veh, R2

value: control


title: Grp2 db/db+PBS rep6

description:
snRNA-seq using 10X Chromium
A3029

source_name: db/db+PBS

value: PBS


title: Grp3a db/db+renin rep3

description:
snRNA-seq using 10X Chromium
D3032


title: Grp3a db/db+renin rep2

description:
snRNA-seq using 10X Chromium
C3031


title: PRMT1fl/fl; cx3r1cre-ert2 microglia normal diet_rep2

description: ChIP

value: PRMT1fl/fl; cx3r1cre-ert2

value: Normal diet

value: 11 weeks


title: RNA-seq, veh, R1


title: Tet TKO chimera plate 2

description:
MARS-seq of chimera embryos injected with Tet1/2/3 triple KO cells and control cells
190318_P01

value: E7.5 chimera embryo

value: Host cells and injected mESC-derived Control and Tet TKO cells

value: Chimera assay


title: PRMT1Ifl/fl microglia CPZ diet_CD11c_low_rep2

description: ChIP


title: Tumor1, CD8aapos, WT replicate 1

description: Bulk Rnaseq

value: Colon (tumor)

value: gd T cells (CD8aapos)


title: Ahr f/f_cDC2_activated (LPS)_rep1

description: Ahr f/f_cDC2_activated (LPS)_rep1

value: Bone marrow derived DCs

value: Ahr f/f


title: Grp2 db/db+PBS rep3

description:
snRNA-seq using 10X Chromium
A3026

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous

value: female

value: 2 days


title: Grp2 db/db+PBS rep2

description:
snRNA-seq using 10X Chromium
B3025


title: PRMT1Ifl/fl microglia normal diet_rep2

description: ChIP

value: Microglia


title: Patient 17 MDS

city: Nashville

first: Paul

middle: Brent

last: Ferrell

state: TN

address: 777 Preston Research Bldg., 2220 Pierce Ave.

department: Medicine

institute: Vanderbilt University Medical Center

description:
Sample 3 (Patient 17 MDS)
10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software v3.1 (2020, patient 17) or 6.1 (2021, patient 3) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Patient 3 samples will need to be demultiplexed using hashtag information in the gene matrices. Patient 3 sAML (Sample 2) is hashtag 4 - AGTAAGTTCAGCGTA and patient 3 MDS sample (Sample 1) is hashtag 5 - AAGTATCGTTTCGCA.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow aspirate

extract_protocol:
Bone marrow mononuclear cells were isolated by density gradient centrifugation and cryopreserved. For analysis, cells were thawed, counted and prepared for downstream processing with the 10x kit.
scRNA-seq libraries were created using the 10X Chromium 3' (patient 3) or 5' (patient 17) library preparation kits (10X Genomics) using the manufacturer's recommendations. Next-generation 150 nt paired-end sequencing was performed on an Illumina Novaseq6000.

value: Bone marrow mononuclear cell

value: Bone marrow aspirate

tag: individual

value: Patient 17

tag: disease state

value: MDS


title: Ahr f/f_cDC2_untreated_rep2

description: Ahr f/f_cDC2_untreated_rep2


title: Ahr f/f_cDC2_untreated_rep1

description: Ahr f/f_cDC2_untreated_rep1


title: Tumor1, CD8aaneg, WT replicate 1

description: Bulk Rnaseq

value: gd T cells (CD8aaneg)


title: hCMEC/D3 cells, SiNP, 58 nm, 4

city: Kaifeng

first: Haigang

last: wu

state: Henan province

address: dongjing Road

department: School of Life Sciences

country: China

institute: Henan University

description: SiNP_58 nm_4_fpkm

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimed for adaptor sequence, and masked for low-complexity or low quality sequence, then mapped to the whole genome using bowtie v0.12.2 with parameters set as defaults.
Reads for kilobased of exon per megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Assembly: hg19
Supplementary files format and content: fpkm

growth_protocol: The hCMEC/D3 cells used in the experiments were purchased from BeNa Co., LTD., and cultured in ECM culture medium

extract_protocol:
Cell samples ere lyzed and harvested using RIPA buffer(high) reagent (Cat. R0010, Solarbio life science, China). The purification of RNA was performed using protocol provided by extracting kits (RNAprep FastPure kit, Cat No. TSP413,TSINGKE, China).
RNA library were prepared for sequencnig using standard illumina protocols

treatment_protocol: Cells were treated with 100 μg/mL SiNPs

value: Endothelial cell

tag: phenotype

value: Adherent cell

value: treated with 100μg/mL SiNP_58 nm


title: Grp2 db/db+PBS rep5

description:
snRNA-seq using 10X Chromium
C3028

value: PBS


title: Grp2 db/db+PBS rep4

description:
snRNA-seq using 10X Chromium
B3027


title: PRMT1fl/fl; cx3r1cre-ert2 microglia normal diet_rep1

description: ChIP

value: PRMT1fl/fl; cx3r1cre-ert2

value: Normal diet

value: 11 weeks


title: Patient 17 sAML

description:
Sample 4 (Patient 17 sAML)
10x Genomics

value: sAML


title: PRMT1Ifl/fl microglia normal diet_rep1

description: ChIP


title: Grp1 db/m+PBS rep3

description:
snRNA-seq using 10X Chromium
F3021

source_name: db/m+PBS

value: BKS.Cg-Dock7m +/- Leprdb/J Leprdb- heterozygous


title: PRMT1Ifl/fl microglia CPZ diet_CD11c_low_rep1

description: ChIP

value: 0.2% cuprizone diet

value: 5 weeks


title: Patient 3 MDS and Patient 3 sAML (combined)

description:
Sample 1 (Patient 3 MDS)
Sample 2 (Patient 3 sAML)
10x Genomics

value: Patient 3

value: MDS and sAML


title: Grp2 db/db+PBS rep1

description:
snRNA-seq using 10X Chromium
N3024

value: BKS.Cg-Dock7m +/+ Leprdb/J Leprdb- homozygous

value: female

value: 2 days


title: hCMEC/D3 cells, SiNP, 58 nm, 3

description: SiNP_58 nm_3_fpkm


title: MCF7-BM02-TAM67

city: Tokyo

first: Yuxuan

last: Han

address: 2-2 Wakamatsu-cho, Shinjuku-ku

department: department of advanced science and engineering

country: Japan

institute: Waseda Univ.

data_processing:
Basecalling is performed by Illumina RTA software in sequencer, further demultiplexing is  performed by Illumina bcl2fastq 2.17 software based on index information
reads were mapped according to Ensembl homo sapines, followed the Histat2 and String Tie methods.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: excel file with raw gene count of each sample

extract_protocol:
cells were seeded in 6-well plate and the RNA was extracted by isogen (#319-90211) kit
RNA libraries were prepared for sequencing using standard illumina protocols

value: Breast; Mammary gland

value: c-Jun dominant negative


title: Grp1 db/m+PBS rep4

description:
snRNA-seq using 10X Chromium
G3022


title: Grp1 db/m+PBS rep5

description:
snRNA-seq using 10X Chromium
H3023


title: MCF7-BM02-1

value: WT


title: hCMEC/D3 cells, SiNP, 35 nm, 4

description: SiNP_35 nm_4_fpkm

value: Endothelial cell

value: Adherent cell

value: treated with 100μg/mL SiNP_35 nm


title: Grp1 db/m+PBS rep2

description:
snRNA-seq using 10X Chromium
A3020

value: PBS


title: RPE-1 P53KD WA11 replicate 1

city: Amsterdam

first: Dorine

last: Hintzen

address: Plesmanlaan 121

department: Cell Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: 5386_11_RPE-1_14_20_early_week2_GGCTACA_S11

data_processing:
The reads were sequenced using a stranded RNA protocol
The reads that are of low complexity or repetitive sequences are filtered
The reads are mapped to the transcriptome. Reads that do not map to the transcriptome are used for a whole genome mapping in the last step.
Samples are aligned with HiSat2. settings: --min-intronlen 20 --max-intronlen 500000 --rna-strandness F -k 5 --minins 0 --maxins 500 --fr --new-summary Steps performed: link, count, QCstrandness, eset
Read counts are determined.Count parameters Count library type stranded: true Icount (based on HTSeq-count) GTF version: Homo_sapiens.GRCh38.87.gtf mode -> union: If a read is mapped to a region with overlapping genes, this read will be dismissed. However, when stranded RNA sequencing has been performed, the read can be used there is an overlap of 2 genes which are in opposite direction.
Genome_build: Homo sapiens GRCh38.102
Supplementary_files_format_and_content: read count files: tab-separated gene counts and gene annotation for all samples

source_name: RPE-1 p53KD

growth_protocol: Cells were cultured in DMEM F12 with 12% FBS, glutamine and penicillin/streptomycin (Gibco®) at 37 °C / 5% CO2.

extract_protocol:
polyA RNA
The library was prepared using TruSeq RNA sample prep kit according to the manufacturer’s protocol (Illumina). polyA+ stranded RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Clones were generated by blocking RPE-1 p53kd cells in Thymidine for 14 hours, after which they were released in medium containing a combination of an Mps1 inhibitor (NMS-P715) (480uM) and a CENP-E inhibitor (GSK923295) (50nM) for 8 hours to induce whole chromosome aneuploidies and segmental, then plated single cell to obtain aneuploid clones

value: RPE-1 (human non-transformed cell line)

value: retinal pigment epithelial cell

value: P53KD whole chromosome aneuploid clone

tag: clone


title: hCMEC/D3 cells, SiNP, 35 nm, 3

description: SiNP_35 nm_3_fpkm


title: RPE-1 P53KD WA12 replicate 1

description: 5386_13_RPE-1_14_21_early_week_1_AGTCAAC_S13


title: week-10_rep3 [847-RNA_L8]

city: Wuhan

first: Min

state: Hubei

address: Room 5005, Life Science College, Wuhan University

department: College of Life Science and Technology of Huazhong Agricultural University

institute: Wuhan universioty

data_processing:
Cleaned reads were aligned against the mouse mm10 genome with TopHat (version 2.1.1,  http://ccb.jhu.edu/software/tophat/index.shtml)
Differential expression genes were calculated by Bioconductor package DESeq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html)
the gene expression level was normalized as fragments per kilobase of bin per million mapped reads (FPKM) by Cufflinks (http://cole-trapnell-lab.github.io/cufflinks )
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: The 8-week-old Wild-type C57BL/6J mice were purchased from Beijing HFK Bioscience Co. Ltd.

extract_protocol:
Around 40 mg tissue was used for RNA extraction using Ultrapure RNA Kit (CWBIO, CW0581M). Briefly, tissues were triturated for 30s in 1 mL TRIzon provided in the kit, incubated at room temperature for 5 min, added with 200 μL chloroform and shaken drastically. After centrifugation at 12000 rpm, 4 °C for 10 min, the upper water phase was moved into an adsorption column provided by the kit. The column was then eluted with 50 μL RNase-free water. RNA-seq libraries were constructed by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra II Non-Directional RNA Second Strand Synthesis Module (NEB E6111)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The mice were randomly divided into four experimental groups (2 weeks, 4 weeks, 7 weeks, 10 weeks) and one control group (n = 5 per group). The mice in the experimental groups were given a single intraperitoneal injection of AOM (10 mg/kg body weight). Seven days after the AOM injection, the mice were given 2.5% DSS (w/v) in their drinking water for 7 days. The 2weeks group mice were sacrificed. The other three experimental group mice fed with distilled water for 14 days and then 4 weeks group mice were sacrificed. After that, the remained two experimental group mice were given 2.5% DSS (w/v) in their drinking water for 7 days and next distilled water for 14 days. The 7 weeks group mice were sacrificed. Afterwards the last 10 weeks group mice were given 2.5% DSS (w/v) in their drinking water for 7 days and then distilled water for 14 days and sacrificed. The control group (0 week) mice were fed with distilled water for 70 days and sacrificed. The colorectum of all mice were collected for RNA-seq.

value: Colon


title: RPE-1 P53KD WA12 replicate 2

description: 5735_7_RPE-1_14_21_early-rep2_AGTCAAC_S21


title: MCF7-parent


title: hCMEC/D3 cells, SiNP, 35 nm, 2

description: SiNP_35 nm_2_fpkm


title: hCMEC/D3 cells, SiNP, 58 nm, 2

description: SiNP_58 nm_2_fpkm

value: treated with 100μg/mL SiNP_58 nm


title: week-10_rep2 [841-RNA_L8]


title: hCMEC/D3 cells, SiNP, 58 nm, 1

description: SiNP_58 nm_1_fpkm


title: RPE-1 P53KD WA8 replicate 2

description: 5735_1_RPE-1_14_10_early-rep2_CGATGTA_S14


title: hCMEC/D3 cells, SiNP, 35 nm, 1

description: SiNP_35 nm_1_fpkm


title: RPE-1 P53KD WA8 replicate 1


title: RPE-1 P53KD WA5 replicate 2

description: 5901_11_RPE1_p53KD_clone_15_1_repl2_ACTGATA_S32


title: week-10_rep1 [840-RNA_L8]


title: week-7_rep3 [839-RNA_L8]


title: hCMEC/D3 cells, Control, 3

value: untreated


title: hCMEC/D3 cells, Control, 4


title: Grp1 db/m+PBS rep1

description:
snRNA-seq using 10X Chromium
E3019

value: BKS.Cg-Dock7m +/- Leprdb/J Leprdb- heterozygous


title: RPE-1 P53KD WA11 replicate 2

description: 5735_5_RPE-1_14_20_early-rep2_CAGATCA_S19


title: hCMEC/D3 cells, Control, 2


title: Tgd stimulated cells from healthy and tumor Tcr

description: 10x Genomics

data_processing:
Data Processing of Single-Cell RNA-Seq and Single Cell TCR-Seq Libraries. Raw fastq files derived from our RNA-seq libraries were processed with cellranger count (v6.0.2) using the 10x Genomics prebuilt human reference (GRCh38 - GENCODE v32/Ensembl 98). The count matrix was processed using Seurat (v4.0.4) (50). Quality control was performed by removing cells with high (> 10%) mitochondrial-derived UMIs. The assembly, alignment, and annotation of TCR sequences were performed using the Cellranger vdj workflow from 10x Genomics and the prebuild human vdj reference (GRCh38 - Ensembl5.0.0). The assignment of gamma/delta T-cell clones was performed using the clonality package (https://github.com/victoraLab/clonality). Paired TCR clones were defined by identical V, (D), J genes, and CDR3 length and nucleotide sequence for delta and gamma chains. Cells with only one successfully TRG or TRD chain sequenced were assigned as part of a paired TCR core if its DNA sequence matched its correspondent chain completely (sticky parameter).
Single Cell RNA-Seq Normalization and Statistical Analysis. The raw UMI counts were normalized using the SCTransform function available in the Seurat (v4.0.4) package (51). The top 3000 variable genes were first used for dimensional reduction by PCA using the scaled data. The first 30 principal components were further used for visualization using the Manifold Approximation and Projection (UMAP) and cell clustering (50, 51). The Wilcoxon rank-sum test detected differentially expressed genes by comparing each cluster against all cells. Genes with adjusted p-values of 0.05 or less were considered for downstream analysis. Finally, we scored each cell based on gene sets for the S and G2M phases using the CellCycleScoring function within the Seurat package (52). Cells that did not score in at least one set were marked as in the G1 phase. GSEA analyses were performed using the fgsea package for R (53) and the Molecular Signatures Database (MSigDB - v7.5.1)[PMID: 16199517]. In short, for each condition or cluster, genes were ranked using their Log2FoldChanges, and enriched pathways were considered significant when having adjusted p-values of 0.05 or less. Heatmap was constructed using the ComplexHeatmap package (54) with the Pearson residuals matrix obtained by GetResidual function from Seurat.
Bulk RNA-Seq Analysis. Raw fastq files were aligned and quantified with STAR (v. 2.7.10a) by using the mouse genome (mm39) and the mouse transcriptome (gencode M29) (58). Next, the count matrix was imported to the R environment and processed by the DESeq2 package (v. 1.34) pipeline (59). Briefly, genes from samples expressing less than ten reads were pre-filtered. Gene expression among samples was normalized by applying a negative binomial distribution model. The Wald test was employed to determine differential gene expression between conditions. Genes containing adjusted pvalues (FDR) less than 0.1 were considered for downstream analysis, and log2 fold changes were shrunk using the ashr algorithm (60).
Assembly: GRCh38
Assembly: GRCm39
Supplementary files format and content: Tab separated files and matrix of UMI counts.
Library strategy: TCR-Seq

value: Colon (healthy and tumor)

value: gd T cells

value: PMA/Ionomycin


title: week-4_rep3 [832-RNA_L8]


title: week-7_rep2 [836-RNA_L8]


title: week-4_rep2 [831-RNA_L8]


title: RPE-1 P53KD WA5 replicate 1

description: 5901_10_RPE1_p53KD_clone_15_1_repl1_GAGTGGA_S31


title: SRSF7 siRNA 200uM RPTEC rep3

description:
c12
RPTEC bulk RNA-seq

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a maximum of one mismatch in the indexing read for sample demultiplexing. RNA-seq reads were then aligned to the mm10 (for mouse) or GRCh38 (for human) with STAR version 2.7.9a1. Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3. Raw counts and RPKM were output for downstream analysis.
Assembly: mm10 (GRCm38) and GRCh38
Supplementary files format and content: *csv: Processed files are the raw read counts and RPKM for each gene/sample in comma-separated text format.

source_name: Human primary renal tubular epithelial cells

growth_protocol: Mouse diabetic nephropathy protocol: To establish the model, female db/db mice (BKS.Cg-Dock7m +/+ Leprdb/J from Jackson, BKS background, Lot 642) were subject to left nephrectomy at 5 weeks of age, and at 12 weeks, infected with a renin expressing adeno-associated virus (ReninAAV, 109 genomic copies) to induce hypertension and accelerate disease progression. In addition to the ReninAAV Unx db/db mice, db/m and Unx db/db mice infected with an empty viral vector (LacZ AAV) were included as healthy and diabetic non-hypertensive controls, respectively.

extract_protocol:
Total mRNA were isolated from mouse kidney and human RPTECs using a RNA kit from Qiagen (RNeasy Mini prep kit, Cat# 74104).
Total RNA integrity was determined using Agilent 4200 Tapestation. Library preparation was performed with 500ng to 1ug of total RNA. Ribosomal RNA was removed by an RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.

treatment_protocol:
Drug treatment protocol: Drug treatments were given to mice as follows:  1. Vehicle (drinking water);   2. Lisinopril (An ACE inhibitor, 10 mg/kg/d in the drinking water);    3. Rosiglitazone (A PPARꙋ activator, 0.007% w/w via admix diet, p.o. ~10 mg/kg/d);   4. JNJ-39933673 (A SGLT2 inhibitor, 0.0075% w/w via admix diet, p.o. 1 ~ mg/kg/d);   5. ACEi plus SGLT2i (dosed as before);   6. ACEi plus rosiglitazone (dosed as before). Terminal samples were collected 48 hours and 2 weeks after treatment inception.
In vitro experiment was performed on human primary tubular epithelial cells (RPTEC) purchased from Lonza (cat# CC-2553, lot 0000635750). RPTECs were treated with SRSF7 siRNA (siGenome, cat# M-015909-01-0020) at concentrations of 100 uM and 200 uM. Scrambled siRNA was used as negative control.

value: RPTEC

value: female

value: SRSF7 siRNA

value: 3 days


title: week-2_rep3 [829-RNA_L8]


title: RPE-1 P53KD parental replicate 1

value: parental


title: RPE-1 P53KD parental replicate 2


title: week-2_rep2 [828-RNA_L8]


title: week-7_rep1 [835-RNA_L8]


title: Tgd stimulated cells from healthy and tumor Gex

description: 10x Genomics


title: Input_FOXA2

city: Dallas

first: Ram

last: Mani

state: Texas

address: 5323 Harry Hines Blvd NB6.444

department: Pathology

institute: UT Southwestern Medical Center

data_processing:
The quality of the raw data was checked using fastqc (v0.11.8).
Raw reads were mapped to hg19 using BWA (v 0.7.17-r1188).
Low quality and duplicated reads were removed using Picard (2.20.3, http://broadinstitute.github.io/picard).
Peak calling was performed by MACS2 (v 2.1.0) using default parameters with input DNA as negative control.
Genome_build: hg19
Supplementary_files_format_and_content: Deeptools (2.4.2) was used to generate BigWig files.

source_name: Endometrial cancer cell lines

growth_protocol: Human endometrial cancer cell lines Ishikawa were cultured in standard media per ATCC recommendations supplemented with heat-inactivated FBS and antibiotics (50 U/mL penicillin and 50 mg/L streptomycin) in a humidified atmosphere at 37ᵒC containing 5% CO₂.

extract_protocol:
Crosslinking was carried out using 1% formaldehyde at room temperature. Formaldehyde was quenched with 1.25M glycine. Cells were washed with PBS, lysed, sonicated and the chromatin was used in a Chromatin Immunoprecipitation (ChIP) reaction (HighCell# ChIP kit protein G (Diagenode Inc., NJ) per the manufacturer’s recommendation using the Histone H3 acetyl Lys27 antibody (Active Motif, CA).
The ChIP DNA was reverse crosslinked, eluted and purified, and used to prepare next generation sequencing libraries (KAPA Hyper Prep, KAPA Biosystems, MA). The ChIP sequencing (ChIP-Seq) libraries, after appropriate size selection using AMPure XP Beads (Beckman Coulter Sciences, IN) were sequenced with a read-length of 75bp at the UTSW McDermott Sequencing Core.

treatment_protocol: The H3K27ac mark was analyzed by ChIP-Seq in Ishikawa cells stably transfected with FOXA2, using the empty vector (CMV) as control.

value: Endometrial cancer cell lines

value: Ishikawa cells

value: transfected with FOXA2


title: week-2_rep1 [826-RNA_L8]


title: Input_CMV

value: empty vector


title: RPE-1 P53KD WA1 replicate 2

description: 5901_13_RPE1_p53KD_clone_C23_CGATGTA_S34

value: RPE-1 (human non-transformed cell line)

value: retinal pigment epithelial cell

value: P53KD whole chromosome aneuploid clone


title: Tgd stimulated cells from healthy and tumor Hashtags

description: 10x Genomics

library_source: other

molecule: protein


title: SRSF7 siRNA 100uM RPTEC rep3

description:
c6
RPTEC bulk RNA-seq


title: RPE-1 P53KD WA1 replicate 1


title: SRSF7 siRNA 200uM RPTEC rep1

description:
c10
RPTEC bulk RNA-seq


title: week-4_rep1 [830-RNA_L8]

value: Colon


title: SRSF7 siRNA 200uM RPTEC rep2

description:
c11
RPTEC bulk RNA-seq


title: hCMEC/D3 cells, Control, 1

value: Endothelial cell

value: Adherent cell

value: untreated


title: SRSF7 siRNA 100uM RPTEC rep1

description:
c4
RPTEC bulk RNA-seq


title: RPE-1 P53KD WA2 replicate 2

description: 5901_12_RPE1_p53KD_clone_14_8_ATTCCTT_S33


title: U2940_UT_3_S15

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

data_processing:
Stranded single-end 75bp libraries were run on the NextSeq 500 instrument and converted to FASTQ files using bcl2fastq v1.8.4 software (Illumina)
Partek Flow v9.0
5 bases were trimmed from the 5' end of each read and the 10 base sequence AAAAAAAAAA trimmed from the 3' end of each read using cutAdapt v1.12
miRNAs were identified using Bowtie1.0 alignment with an index built from hg38 miRbase22 mature sequences and normalized using median ratio (DESeq2) method
mRNAs were identified using Bowtie2 v2.2.5 alignment with an index built from hg38 RefSeq v93 sequences and normalized using median ratio (DESeq2) method
Assembly: hg38
Supplementary files format and content: DESeq2 normalized counts (miRNA)
Supplementary files format and content: DESeq2 normalized counts (mRNA)

source_name: U2940 cells, Untreated, 48hrs

growth_protocol: Cells cultured at 37C with 5% C02 in RPMI 1640 + 2mM Glutamine + 10 - 20% Fetal Bovine Serum

extract_protocol:
Cells were lysed in QIAzol lysis reagent (Qiagen). Following aqueous/organic phase separation, RNA was purified with the RNeasy Mini Kit (Qiagen)
For ribosomal depletion, 500ng total RNA was used as input to the NEBNext rRNA Depletion Kit v2 - Human/Mouse/Rat (New England Biolabs). The depleted RNA was used as input to the SEQuoia Complete Stranded RNA Library  Prep Kit (BioRad).

treatment_protocol: Drug treatments performed for 48 hours using empirically determined doses at or near the MIC 50 for each drug and cell line,  diluted in RPMI

value: pleural effusion

value: Primary mediastinal B-cell lymphoma

value: Untreated (UT) RPMI media


title: 4T1_parental_T_8020_NSG_day20_r1

city: Cambridge

first: Dario

last: Bressan

state: Cambridgeshire

address: Li Ka Shing Centre, Robinson Way

department: CRUK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
cellranger v3.0.1 (default parameters)
Genome_build: mm10
Supplementary_files_format_and_content: 10X Cellranger output. Filtered_feature_bc_matrix folder incuding two tab-separated tsv files with a list of identified single cells and measured genes, plus a matrix market mtx file including the cell/gene matrix (zipped). Processed cloupe file (can be visualised using the free cloupe software from 10x genomics)

source_name: Fat-pad tumour

growth_protocol: 4T1 cells were grown in DMEM (Thermo Scientific cat. No 41966029)  + 10% FBS + 1% Pen/Strep (Thermo Scientific), at 37C in presence of 5% CO2, and splitted roughly 1:5 every 2-3 days. Cells were trypsinized when needed using TrypLE express (Thermo Scientific cat. 12604013)

extract_protocol:
10X genomics 3’ single cell gene expression  pipeline (v3)
10X genomics single-cell RNA-seq

treatment_protocol: To induce tumour, cells were trypsinized, washed in PBS, and counted. 50,000 cells were resuspended in approximately 30ul of 1:1 PBS and  Matrigel (Corning, Cat No. 356231) and injected trans-cutaneously into the 4th fat pad (inguinal). Tumours were allowed to develop for 20 days and resected during necropsy, after the animal was euthanised by cervical dislocation.Tumour were dissociated using a Miltenyi Biotech GentleMACS octo w/heaters  dissociatior and the Tumour dissociation kit (cat. 130096730) according to supplier’s instructions.  Cells were washed, counted, and approximately 4000 cells per sample were processed  through the 10X genomics 3’ single cell gene expression  pipeline (v3)

tag: tumour source

value: 4T1 tumour cells

tag: tumour type

value: Triple-negative like mammary tumour

tag: timepoint

value: day 20 post-injection

tag: tumour induction

value: Fat-pad injection

tag: replicate


title: SRSF7 siRNA 100uM RPTEC rep2

description:
c5
RPTEC bulk RNA-seq

tag: cell line

value: RPTEC

value: female

value: SRSF7 siRNA

value: 3 days


title: week-0_rep1 [823-RNA_L8]

tag: tissue


title: RPE-1 P53KD WA2 replicate 1

value: RPE-1 (human non-transformed cell line)

tag: cell type

value: retinal pigment epithelial cell

tag: genotype


title: H3K27ac_CMV

value: Endometrial cancer cell lines

value: Ishikawa cells

tag: treatment

value: empty vector


title: H3K27ac_FOXA2

value: transfected with FOXA2


title: siRNA negative control RPTEC rep3

description:
c3
RPTEC bulk RNA-seq

tag: Sex

value: Scrambled siRNA

tag: treatment timepoint


title: U2940_RmAb_3_S12

source_name: U2940 cells, RmAb treated, 48hrs

value: pleural effusion

value: Primary mediastinal B-cell lymphoma

value: Rituximab (RmAb) 200ug/ml


title: KI (hetero) before UVB irradiation 3

city: Nagoya

first: yuya

last: murase

address: 65 Tsurumai-cho, Showa-ku

institute: Nagoya University Graduate School of Medicine

data_processing:
The sequence reads were aligned to the GENCODE mouse reference transcriptome (version M24)) and transcript-expression levels were calculated using Kallisto (version 0.46.0)
We then used the R package DESeq2 to detect differentially expressed genes before and after UVB irradiation for 5-week-age Nlrp1b KI mice (homo and hetero), and WT mice.

source_name: skin

extract_protocol:
Total RNA extracted from the skin of 5-week-age mice was purified using a RNeasy Mini Kit (QIAGEN, Hiden Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: skin

tag: strain

value: BALB/c

tag: age

value: Nlrp1b knock in (KI) mice - heterozygous

value: before UVB


title: week-0_rep2 [824-RNA_L8]

value: Colon


title: week-0_rep3 [825-RNA_L8]


title: KI (hetero) after UVB irradiation 3

value: after UVB


title: organoid_d28_scRNAseq_2

first: Eva

last: Fast

address: 1 Portland st

institute: Pfizer

data_processing:
Demultiplexing, alignment, and estimation of cell-containing partitions and associated UMIs using Cell Ranger Version 3.0.2
Genome_build: GRCh38
Supplementary_files_format_and_content: For each sample countmatrixes (.mtx) and table files identifying cell barcodes and genes (.tsv)

source_name: IPSC

growth_protocol: High-throughput in vitro kidney organoid generation: For the development of a reproducible scalable protocol, we introduced several key modifications to published protocols5, 7, 13, 14. We started by dispersing iPSCs reaching 80 to 85% confluency into single cell suspensions using Accutase and seeding 275,000 cells per flask in hESC-qualified, matrigel-coated flasks with TeSR1 media plus Y-27632 (Tocris 1254, Bristol, United Kingdom). On the next day, the medium was changed to STEMdiff APEL2 (StemCell Technologies) supplemented with 10 M CHIR99021 (Tocris 4423). After 48 h, the medium was changed to STEMdiff APEL2 supplemented with 8 M CHIR99021. Subsequently, medium was switched to STEMdiff APEL2 with 200 ng/mL FGF9 (R&D Systems, Minneapolis, MN) and 1 g/mL heparin (StemCell Technologies) and changed every other day. On day 7, cells were passaged using Accutase and pelleted by centrifugation at 500,000 cells per pellet. The pellets were placed on transwell plates and STEMdiff APEL2 supplemented with 5 M CHIR99021 was added for 1 h before changing to STEMdiff APEL2 with 200 ng/mL FGF9 and 1 g/mL heparin. Medium was changed every other day for the next 4 days using STEMdiff APEL2 containing 200 ng/mL FGF9 and 1 g/mL heparin. On day 13, the medium was switched to STEMdiff APEL2 with 1 g/mL heparin. Thereafter, organoids were grown in STEMdiff APEL2 and medium was changed every other day.

extract_protocol:
Organoids were rinsed with DPBS, collected into 1.5 ml conical tube containing 500 ml TrypLE Select and incubated for 5 min at 37°C, passed 3 to 4 times through a 27G needle, and incubated for 5 min at 37°C after adding additional 500 ml of TrypLE Select. Organoids were dissociated into single cell suspensions by passing 3 to 4 times through a 30G needle, followed by centrifugation at 600xg for 5 min. Supernatants were discarded, and cell pellets were resuspended in DPBS and filtered through a 40 mm cell strainer. Cell numbers were quantified on a Cellometer cell counter and adjusted to 1000 cells/ml in DPBS.
Single cell cDNA library preparation was performed following manufacturer's protocols (https://www.10xgenomics.com). Single cell suspension were loaded on a Chromium controller to generate single cell GEMS (Gel Beads-In-Emulsions). The scRNA-Seq library was prepared with chromium single cell 3’ reagent kit v3 (10x Genomics)

treatment_protocol: In vitro organoids from growth protocol were grown in parallel and compared to in vivo transplanted organoids. Organoid transplantation protocol:  Prior to initiating transplantation into rats for preclinical studies with stem cell derived organoids, persuasive evidence of promise in in vitro experimental models (Figure 2), were performed in accordance with International Society for Stem Cell Research (ISSCR) guidelines. Organoids differentiated as described above were transplanted into 3-4 weeks old athymic male nude rats (Crl:NIH-Foxn1rnu, Charles River Labs, Wilmington, MA) weighing approximately 100g each, acclimated for at least three days in conventional cage setting with rodent diet 5053 and ad libitum water, at_rat_Research test facility (Worcester, MA) in accordance with an approved IACUC study protocol. 45 rats divided randomly and equally into three experimental groups (Day 10, 12 and 14 differentiated) were anesthetized with ketamine/dexdomitor and an antibiotic (Cephazolin) as well as an analgesic (Buprenorphine-SR) was administered to facilitate post-surgical recovery. The kidneys were exposed by an incision in the abdominal wall. After creating an incision in the kidney capsule, a small niche was created under the kidney capsule to host the organoids. Organoids grown for 10, 12 or 14 days in vitro were aspirated into the tip of an 18-24G catheter (Instech, Plymouth, PA) and placed into the niche, the abdominal wall and skin were closed, and the animals were allowed to recover and followed up with routine cage side observations for general health. At 2 or 4 weeks after transplantation, 6-8 rats per experimental group were euthanized under CO2 as per IACUC approved study protocol, kidneys exposed by an incision in the abdominal wall and organoids (n≥3) were harvested for scRNA-Seq and NanoString mRNA analysis as well as analysis of graft tissue vascularization and functional connectivity in the PK/PD studies.  Organoid differentiation was also evaluated at the protein level by flow cytometry analysis of two podocyte surface proteins, nephrin30 and podocalyxin31. Cells from dissociated organoids were washed with DPBS, blocked in 1% mouse serum for 30 min at 4°C, incubated with anti-nephrin primary antibody (R&D Systems, AF4269) and APC-conjugated anti-podocalyxin antibodies (R&D Systems, FAB1658A) diluted in sorting buffer (HBSS containing 1% BSA and 0.035% NaHCO3). The cells were further incubated for 10 min in Alexa Fluor 488-conjugated donkey anti-sheep LgG (H+L) antibody (ThermoFisher Scientific, A-11015), washed and resuspended in sorting buffer. Unstained cells were utilized to establish background fluorescence. Data acquisition and analysis were performed on a SONY SH800 flow cytometer. Mean fluorescence in live cells was determined for each sample and is presented after subtraction of background fluorescence.

tag: type of organoid

value: in vitro organoid

tag: day of maturation

value: day 28 - in vitro


title: U2940_RmAb_2_S11


title: 4T1_parental_T_8020_NSG_day20_r2

value: 4T1 tumour cells

value: Triple-negative like mammary tumour

value: day 20 post-injection

value: Fat-pad injection


title: U2940_UT_1_S13

value: Untreated (UT) RPMI media


title: organoid_d28_scRNAseq_3


title: U2940_UT_2_S14


title: organoid_d26_scRNAseq_2

value: day 26 - in vitro


title: organoid_d28_scRNAseq_1


title: siRNA negative control RPTEC rep1

description:
c1
RPTEC bulk RNA-seq

value: RPTEC

value: female

value: Scrambled siRNA

value: 3 days


title: siRNA negative control RPTEC rep2

description:
c2
RPTEC bulk RNA-seq


title: organoid_d26_scRNAseq_1


title: organoid_d26_scRNAseq_3


title: U2940_PRED_3_S9

source_name: U2940 cells, PRED treated, 48hrs

value: pleural effusion

value: Primary mediastinal B-cell lymphoma

value: Prednisone (PRED) 60ug/ml


title: U2940_RmAb_1_S10

value: Rituximab (RmAb) 200ug/ml


title: WT after UVB irradiation 3

value: skin

value: BALB/c

value: WT

value: after UVB


title: U2940_PRED_1_S7


title: WT before UVB irradiation 3

value: before UVB


title: U2940_PRED_2_S8


title: organoid_d24_scRNAseq_3

value: in vitro organoid

value: day 24 - in vitro


title: KI (homo) before UVB irradiation 3

value: Nlrp1b knock in (KI) mice - homozygous


title: 5 min post infection, T4Vector, rep2

city: Bethesda

first: Deborah

last: Hinton

state: MD

address: 8 Center drive

institute: NIDDK

data_processing:
Read data in fastq format was demultiplexed and aligned to E. coli E. coli BL21(DE3) (NC_012971.2)  or E. coli virus T4  (NC_000866.4) reference genome using STAR v2.5.2
Default alignment behavior was altered with the following arguments: --outFilterScoreMinOverLread 0 --outFilterMatchNmin 30 --outFilterMatchNminOverLread 0 --clip3pAdapterSeq AGATCGGAAGAGCGTCGTGTA --alignIntronMax 1.
RNA gene counts in both reference genomes were then quantified using the same NCBI gene definitions utilized in mapping index construction using the subread featureCounts v1.4.6-p3 package
Count data was normalized using Deseq2, which utilizes a normalization of means method for sample normalization and comparison.
Differential expression between conditions was represented as a fold change, and genes with both a fold change ≥2 or ≤ 0.5and adjusted p value ≤ 0.05 were considered significant.
Assembly: NC_012971.2  or  NC_000866.4
Supplementary files format and content: Normalized counts

organism: Escherichia coli BL21(DE3)

source_name: Bacteria

growth_protocol: E. coli str. K-12 substr. MG1655 containing either pNW129 or pNW129-MotB were grown to early log phase (OD600 ~ 0.3)  then induced with 0.2% arabinose for 20 minutes. Phage T4 was added to the culture at MOI 10.

extract_protocol:
RNA was isolated  using method II of (Hinton 1989)
The cDNA library was prepared using a modified RNATagSeq workflow as previously described (Shishkin, A.A. et al. 2015 Nat Methods). Optimum fragmentation of the total RNA samples in this library was determined to be 3 min at 94C in FastAP buffer (Thermo Fischer Scientific).  The cDNA Library was run on a Bioanalyzer using the Agilent High Sensitivity DNA Kit to evaluate the quality of the library.  The concentration of the cDNA library was determined by qPCR using the KAPA Library Quantification Kit (Kapa Biosystems, Wilmington, MA, USA) and CFX96 Real-Time PCR Detection System (Bio-Rad, Hercules, CA, USA).

tag: plasmid

tag: infection

value: Bacteriophage T4


title: 5 min post infection, T4motB, rep3


title: 5 min post infection, T4motB, rep2


title: 5 min post infection, T4Vector, rep1


title: KI (homo) after UVB irradiation 3


title: 5 min post infection, T4Vector, rep3


title: organoid_d24_scRNAseq_1


title: organoid_d24_scRNAseq_2


title: 5 min post infection, T4motB, rep1


title: organoid_d14_scRNAseq_3

value: day 14


title: U2940_IBR_3_S6

source_name: U2940 cells, IBR treated, 48hrs

value: Ibrutinib (IBR) 2.5uM


title: WT before UVB irradiation 2


title: U2940_IBR_2_S5


title: MZdnmt3aa_2 dpf_WGBS

city: Higashi-Hiroshima

first: Yutaka

last: Kikuchi

state: Hiroshima

address: 1-3-1, Kagamiyama

institute: Hiroshima University

data_processing:
The read sequences in FASTQ format were first trimmed by removing six bases from random primers of TruSeq DNA Methylation Kit (Illumina) and the last 50 bases of low-quality reads. After trimming, the reads were aligned to the zebrafish genome (danRer10) and lambda phage genome using Bismark (version 0.10.1) and Bowtie (version 1.0.0). Once aligned, reads corresponding to PCR duplicates were removed and methylation calls were performed. The bisulfite conversion rates based on spike control for all samples were over 99%, and the error rates were as follows: WT, 0.3% and MZdnmt3aa-/-, 0.2%. Statistically significant methylated cytosine sites were identified using a binomial distribution with a false discovery rate ≤ 0.05, calculated by the Benjamini-Hochberg (BH) method, and read depth ≥ 5. Data analysis was performed by Takara Bio, Inc. (Shiga, Japan), and based on previous study (Lister et al., 2009). The methylation ratio of CpG sites with a coverage of 5 reads in WT and MZdnmt3aa-/- was calculated from the methylation call data. The methylation ratio was visualized using the Integrative Genomics Viewer (IGV) (version 2.7.2).
Genome_build: danRer10
Supplementary_files_format_and_content: bedGraph, columns: <chromosome> <start position> <end position> <methylation ratio>

organism: Danio rerio

source_name: 2 dpf larvae

extract_protocol:
Zebrafish wild-type (WT) and MZdnmt3aa-/- embryos at 2 days post-fertilization (dpf) were digested with proteinase K and sodium dodecyl sulfate to extract genomic DNA.
DNA samples were prepared by mixing zebrafish genomic DNA and unmethylated lambda DNA (Promega) as spike control, at a ratio of 1000:1. DNA samples (100 ng) were subjected to bisulfite treatment using the EZ DNA Methylation-Gold Kit (Zymo Research). Bisulfite-treated DNA samples (50 ng) were added as adapters in 10 cycles of PCR with random primers in the TruSeq DNA Methylation Kit (Illumina). Libraries with adapters were sequenced on the HiSeq X Five Sequencing System (Illumina) with 150 bp single-end reads. Bisulfite treatment, library preparation, and sequencing were performed by Takara Bio Inc. (Shiga, Japan).

value: whole-body

tag: developmental stage

value: 2 days post-fertilization

value: maternal-zygotic dnmt3aa-/-


title: WT after UVB irradiation 2


title: organoid_d14_scRNAseq_2


title: organoid_d14_scRNAseq_1


title: U2940_IBR_1_S4

value: pleural effusion

value: Primary mediastinal B-cell lymphoma


title: KI (hetero) after UVB irradiation 2

value: Nlrp1b knock in (KI) mice - heterozygous


title: KI (hetero) before UVB irradiation 2

value: skin


title: WT_2 dpf_WGBS

value: wild-type


title: U2940_BV_3_S3

source_name: U2940 cells, BV treated, 48hrs

value: Brentuximab vedotin (BV) 25ng/ul


title: organoid_d12_scRNAseq_3

value: day 12


title: organoid_d12_scRNAseq_1


title: KI (homo) after UVB irradiation 2

value: BALB/c

value: after UVB


title: KI (homo) before UVB irradiation 2

value: before UVB


title: organoid_d12_scRNAseq_2

value: in vitro organoid


title: U2940_BV_2_S2


title: L428_UT_2_S14

source_name: L428 cells, Untreated, 48hrs

value: Hodgkin lymphoma

tag: time

value: 48 hours

value: Untreated (UT) RPMI media


title: U2940_BV_1_S1


title: KI (hetero) before UVB irradiation 1


title: WT after UVB irradiation 1

value: WT


title: L428_UT_3_S15


title: organoid_d10_scRNAseq_2

value: day 10


title: KI (hetero) after UVB irradiation 1


title: L428_UT_1_S13


title: L428_RmAb_3_S12

source_name: L428 cells, RmAb treated, 48hrs

value: Rituximab (RmAb) 200ug/ml


title: L428_RmAb_2_S11

value: pleural effusion


title: organoid_d10_scRNAseq_1


title: KI (homo) before UVB irradiation 1

value: Nlrp1b knock in (KI) mice - homozygous


title: WT before UVB irradiation 1


title: organoid_d10_scRNAseq_3


title: organoid_d7_scRNAseq_3

value: day 7


title: AR_S3_replicate 1

city: VR

first: Alessandra

last: Amato

address: strada le grazie 15

institute: University of Verona

hyb_protocol: Hybridization was carried out in an Agilent custom microarray (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL26142) https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE126052containing 44K probes, corresponding to about 26k annotated genes plus EST and transcripts reported in the literature as candidate genes for important traits and QTLs available at NCBI databases (www.ncbi.nlm.nih.gov/gene/).

scan_protocol: Scanning and Feature Extraction was performed by using an Agilent Scanner following the settings and parameters indicated in the instruction manual

data_processing: A data-matrix was prepared selecting from each single sub-array outcome file the gProcessedSignalvalues, which are the raw fluorescence intensities of each probe.

organism: Vitis vinifera

source_name: Autumn Royal; seeds; pea size phase (BBCH 73-75; E-L 29); replicate 1

label_protocol: The cDNA synthesis, labeling hybridization, and washing were performed according to the Agilent Microarray-Based Gene Expression Analysis Guide (6.9.1)

growth_protocol: Seeded (Red Globe, Italia) and seedless (Autumn Royal, Thompson Seedless) table grapevine varieties were selected from a grape collection grown in the experimental field of the Research Centre Viticulture and Enology (CREA-VE) in Turi (BA) - South of Italy, under conventional vine management and without hormone treatments in the 2013-2014 seasons

extract_protocol: Total RNA was extracted from 0.1 g of ovules or seeds collected at each experimental stage with Total RNA Isolation Mini Kit (Agilent Technologies). RNA integrity was assessed by automated gel electrophoresis on 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Total transcriptome assays were performed on ovules and developing seeds derived from two seeded (Italia and Red globe) and two seedless (Thompson Seedless and Autumn Royal) table grape varieties. Four developing stages were considered: pre-bloom (BBCH 57-60; E-L 17), post-bloom (BBCH 65-68; E-L 19-25), pea size (BBCH 73-75; E-L 29) and veraison (BBCH 81; E-L 35) (Ref. A.A.V.V. 1997; Lorenz D.H. at al.1994)

tag: cultivar

value: Autumn Royal

value: seeds

tag: devepmental stage

value: pea size phase (BBCH 73-75; E-L 29)


title: AR_S4_replicate 3

source_name: Autumn Royal; seeds; veraison phase (BBCH 81; E-L 35); replicate 3

value: veraison phase (BBCH 81; E-L 35)


title: AR_S4_replicate 2

source_name: Autumn Royal; seeds; veraison phase (BBCH 81; E-L 35); replicate 2


title: AR_S3_replicate 3

source_name: Autumn Royal; seeds; pea size phase (BBCH 73-75; E-L 29); replicate 3


title: AR_S3_replicate 2

source_name: Autumn Royal; seeds; pea size phase (BBCH 73-75; E-L 29); replicate 2


title: AR_S4_replicate 1

source_name: Autumn Royal; seeds; veraison phase (BBCH 81; E-L 35); replicate 1


title: organoid_d7_scRNAseq_2


title: KI (homo) after UVB irradiation 1

value: skin

value: BALB/c


title: L428_RmAb_1_S10

tag: cell line


title: LLC1.3Days.DT2

city: Kyoto

first: Shuh

last: Narumiya

state: Kyoto

address: Yoshidahonmachi

department: Department of Drug Discovery Medicine

institute: Kyoto University

description: DT DTR-foxp3-eGFP 2

data_processing:
Illumina Novaseq6000 used for basecalling
CellRanger software package used for alignment, filtering, barcode reading.
Remove ambient mRNA using decontx in celda package (S Yang, 2020)
Data integration and normalization using Seurat package (Stuart, Butler, et al., Cell, 2019)
Genome_build: mm10
Supplementary_files_format_and_content: ExpressionMatrix.csv files are generated from normalized count of RNA assays in seurat object class.
Supplementary_files_format_and_content: Metadata files indicate cell identity from downstream analysis

source_name: Tumor tissue

growth_protocol: Mice were shaved on their right flank and injected with 3x10^5 cells/100 ul of the Lewis Lung Carcinoma line 1 (LLC1) tumor cells.

extract_protocol:
Tumor tissues were harvested and enzymatically digested with the mouse tumor dissociation kit (Miltenyi) and the subjected to agitation and rotation at 37℃ according the manufacturer’s protocol. Cell suspensions were then filtered through a 70 μm filter (Falcon) and wash with FACS buffer containing 1% BSA (Sigma). For scRNAseq experiment of EP2/4 antagonists treated mice, live CD45+ cells were sorted from the dissected LLC1 tumor using BD FACS Aria3. For scRNAseq experiment of Treg-depleted mice, total cells from the dissected LLC1 tumor were used. Single cells were lysed in droplets using the 10X Chromium instrument. Reverse transcription was performed in droplet.
library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kits v3.1 User Guide Rev C

treatment_protocol: Mice were orally administered EP2 and EP4 antagonists treatment for 6 days or  injection intraperitoneally with diphtheria toxin  diphtheria toxin when tumor size reached 20~30 mm3 (day 10 or 11 after transplanted with LLC1 tumor cells)

tag: tissue

value: Tumor

value: post natal 6week

value: 3 days after treated with diphtheria toxin


title: L428_PRED_2_S8

source_name: L428 cells, PRED treated, 48hrs

tag: cell type

value: Hodgkin lymphoma

value: 48 hours

value: Prednisone (PRED) 60ug/ml


title: LLC1.3Days.Control2

description: Control DTR-foxp3-eGFP 2

tag: genotype

value: untreated


title: L428_PRED_3_S9

tag: treatment


title: AR_S2_replicate 2

source_name: Autumn Royal; seeds; post-bloom phase (BBCH 65-68; E-L 19-25); replicate 2


title: LLC1.3Days.DT1

description: DT DTR-foxp3-eGFP 1


title: organoid_d0_scRNAseq_1

source_name: IPSC

value: in vitro organoid

value: day 0


title: organoid_d7_scRNAseq_1


title: organoid_d0_scRNAseq_3


title: organoid_d0_scRNAseq_2


title: L428_PRED_1_S7

value: pleural effusion


title: LLC1.6Days.EP2iEP4i2

description: EP2iEP4i WT 2

source_name: CD45+ tumor-infiltrating immune cells

value: wild type

value: treated with EP2/EP4 antagonists for 6 days


title: LLC1.3Days.Control1

description: Control DTR-foxp3-eGFP 1


title: AR_S2_replicate 3

source_name: Autumn Royal; seeds; post-bloom phase (BBCH 65-68; E-L 19-25); replicate 3

value: Autumn Royal

value: seeds


title: LLC1.6Days.EP2iEP4i1

description: EP2iEP4i WT 1


title: AR_S2_replicate 1

source_name: Autumn Royal; seeds; post-bloom phase (BBCH 65-68; E-L 19-25); replicate 1


title: AR_S1_replicate 1

source_name: Autumn Royal; seeds; pre-bloom phase (BBCH 57-60; E-L 17); replicate 1

value: pre-bloom phase (BBCH 57-60; E-L 17)


title: AR_S1_replicate 2

source_name: Autumn Royal; seeds; pre-bloom phase (BBCH 57-60; E-L 17); replicate 2


title: AR_S1_replicate 3

source_name: Autumn Royal; seeds; pre-bloom phase (BBCH 57-60; E-L 17); replicate 3


title: LLC1.6Days.EP2i

description: EP2i WT 1

value: treated with EP2 antagonists for 6 days


title: L428_IBR_3_S6

source_name: L428 cells, IBR treated, 48hrs

value: Ibrutinib (IBR) 2.5uM


title: TS_S4_replicate 3

source_name: Thompson Seedless; seeds; veraison phase (BBCH 81; E-L 35); replicate 3

value: Thompson Seedless

value: veraison phase (BBCH 81; E-L 35)


title: L428_IBR_2_S5


title: L428_IBR_1_S4


title: L428_BV_3_S3

source_name: L428 cells, BV treated, 48hrs

value: Brentuximab vedotin (BV) 25ng/ul


title: L428_BV_1_S1

value: Hodgkin lymphoma


title: LLC1.6Days.Control2

description: Control WT 2

value: Tumor

value: post natal 6week


title: TS_S4_replicate 1

source_name: Thompson Seedless; seeds; veraison phase (BBCH 81; E-L 35); replicate 1


title: TS_S4_replicate 2

source_name: Thompson Seedless; seeds; veraison phase (BBCH 81; E-L 35); replicate 2


title: K1106P_UT_3_S15

source_name: K1106P cells, Untreated, 48hrs

value: KARPAS 1106P

value: Primary mediastinal B-cell lymphoma

value: 48 hours

value: Untreated (UT) RPMI media


title: LLC1.6Days.EP4i

description: EP4i WT 1

value: wild type

value: treated with EP4 antagonists for 6 days


title: LLC1.6Days.Control1

description: Control WT 1

value: untreated


title: TS_S3_replicate 3

source_name: Thompson Seedless; seeds; pea size phase (BBCH 73-75; E-L 29); replicate 3

value: seeds

value: pea size phase (BBCH 73-75; E-L 29)


title: TS_S3_replicate 1

source_name: Thompson Seedless; seeds; pea size phase (BBCH 73-75; E-L 29); replicate 1


title: TS_S3_replicate 2

source_name: Thompson Seedless; seeds; pea size phase (BBCH 73-75; E-L 29); replicate 2


title: TS_S2_replicate 3

source_name: Thompson Seedless; seeds; post-bloom phase (BBCH 65-68; E-L 19-25); replicate 3


title: K1106P_UT_1_S13

value: pleural effusion


title: K1106P_UT_2_S14


title: L428_BV_2_S2


title: K1106P_PRED_3_S12

source_name: K1106P cells, PRED treated, 48hrs

value: Prednisone (PRED) 60ug/ml


title: K1106P_PRED_2_S11


title: K1106P_IBR_3_S9

source_name: K1106P cells, IBR treated, 48hrs

value: Ibrutinib (IBR) 2.5uM


title: K1106P_PRED_1_S10


title: TS_S1_replicate 3

source_name: Thompson Seedless; seeds; pre-bloom phase (BBCH 57-60; E-L 17); replicate 3

value: Thompson Seedless

value: pre-bloom phase (BBCH 57-60; E-L 17)


title: K1106P_IBR_2_S8


title: THP-1 Cells treated with X_RNA Replicate 3

city: Seattle

first: Richard

last: Green

state: WA

address: 750 Republican St, Seattle, WA 98109

department: Immunology

institute: UW

description: Gene expression in THP-1 Cells after treatment with X_RNA replicate 3

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to Mouse Whole Genome Gene Expression Microarray (G4122F) slides.

scan_protocol: Dry slides were scanned on an Agilent Technologies Scanner (Model G2505C) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess package.

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

extract_protocol: Total RNA purified using RNeasy kit (Qiagen) was submitted to Labcorp Seattle (previously Covance) for microarray analysis using Agilent SurePrint G3 Human Genome Microarrays (version 2).

treatment_protocol: Differentiated THP-1 cells were treated with small molecule compounds (KIN1000 and KIN1148 at 0.625, 2.5 or 10 micromoles/liter) or 25 IU/mL IFN Beta diluted in cRPMI supplemented with 0.5% (v/v) DMSO, or treated with cRPMI supplemented with 0.5% (v/v) DMSO alone (DMSO). Control cells infected with 25 HAU/mL SeV were maintained in cRPMI supplemented with 0.5% (v/v) DMSO after removal of the virus inoculum.

value: THP-1 Cells


title: THP-1 Cells treated with PAMP Replicate 3

description: Gene expression in THP-1 Cells after treatment with PAMP replicate 3


title: K1106P_BV_2_S5

source_name: K1106P cells, BV treated, 48hrs

value: Brentuximab vedotin (BV) 25ng/ul


title: K1106P_IBR_1_S7


title: TS_S1_replicate 2

source_name: Thompson Seedless; seeds; pre-bloom phase (BBCH 57-60; E-L 17); replicate 2


title: THP-1 Cells treated with X_RNA Replicate 2

description: Gene expression in THP-1 Cells after treatment with X_RNA replicate 2


title: K1106P_BV_3_S6


title: TS_S2_replicate 2

source_name: Thompson Seedless; seeds; post-bloom phase (BBCH 65-68; E-L 19-25); replicate 2


title: 18Set5-MNX+S

city: Gothenburg

first: Lars

last: Palmqvist

address: Sahlgrenska University Hospital

department: Institute of Biomedicine

country: Sweden

institute: University of Gothenburg

data_processing:
Rna sequecning was done uwing DNBSEQ with PE100, 40M clean reads paired end
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using STAR (version 2.9.0a) with the following parameters: outSAMtype BAM SortedByCoordinate
Quantification of counts for each gene aligned to exons was carried out using HTSeq-count (Python package HTSeq, python v 3.8.1) software using the following parameters -f bam -r pos -s no -m union with the reference annotation file. The mouse reference genome and annotation files were obtained from the Ensembl database
Differential gene expression was performed using the R package Deseq2 (version "1.31.14").  Genes with log2 (foldchange) 1 and false discovery rate (FDR) adjusted p-value < 0.05 were considered differentially expressed genes
Assembly: GRCm38
Supplementary files format and content: Raw count files obtained from HTSeq

source_name: Fetal liver hematopietic cells E 14.5

growth_protocol: Fetal liver hematopietic cells were obtained at embryonic days 14.5 (E14.5) and maintained in liquid culture (Dulbecco's modified Eagle's medium supplemented with 18% fetal bovine serum, 10 ng/mL human interleukin [IL]-6, 6 ng/mL murine IL-3, and 100 ng/mL murine stem cell factor). All culture media and growth factors were obtained from StemCell Technologies Inc..

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini kit (Qiagen)
mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were load into the patterned nanoarray and single end 50 (pair end 100) bases reads were generated in the way of sequenced by synthesis.

treatment_protocol: For treatment with Sinefungin, cells were kept in daily fresh medium with 5μM Sinefungin (in PBS) for one week after retroviral tranfection

value: C57BL/6 mice

value: Embryonic day 14.5

value: MNX1 overexpression

value: Fetal liver hematopietic cells E 14.16

value: Treated with 5uM Sinefungin


title: RG S4_replicate 2

source_name: Red Globe; seeds; veraison phase (BBCH 81; E-L 35); replicate 2

value: Red Globe

value: veraison phase (BBCH 81; E-L 35)


title: TS_S1_replicate 1

source_name: Thompson Seedless; seeds; pre-bloom phase (BBCH 57-60; E-L 17); replicate 1


title: 14Set4-MNX+S

value: Fetal liver hematopietic cells E 14.15


title: TS_S2_replicate 1

source_name: Thompson Seedless; seeds; post-bloom phase (BBCH 65-68; E-L 19-25); replicate 1

value: seeds


title: THP-1 Cells treated with IFNb Replicate 3

description: Gene expression in THP-1 Cells after treatment with IFNb replicate 3

source_name: IFNb

value: IFNb


title: RG S4_replicate 3

source_name: Red Globe; seeds; veraison phase (BBCH 81; E-L 35); replicate 3


title: RG S4_replicate 1

source_name: Red Globe; seeds; veraison phase (BBCH 81; E-L 35); replicate 1


title: THP-1 Cells treated with PAMP Replicate 2

description: Gene expression in THP-1 Cells after treatment with PAMP replicate 2


title: THP-1 Cells treated with KIN1148 0.625 micromoles/liter Replicate 3

description: Gene expression in THP-1 Cells after treatment with KIN1148 0.625 micromoles/liter replicate 3


title: RG S3_replicate 2

source_name: Red Globe; seeds; pea size phase (BBCH 73-75; E-L 29); replicate 2

value: pea size phase (BBCH 73-75; E-L 29)


title: THP-1 Cells treated with PAMP Replicate 1

description: Gene expression in THP-1 Cells after treatment with PAMP replicate 1


title: RG S3_replicate 3

source_name: Red Globe; seeds; pea size phase (BBCH 73-75; E-L 29); replicate 3


title: K1106P_BV_1_S4

value: pleural effusion

value: KARPAS 1106P

value: Primary mediastinal B-cell lymphoma

value: 48 hours


title: THP-1 Cells treated with KIN1148 10 micromoles/liter Replicate 3

description: Gene expression in THP-1 Cells after treatment with KIN1148 10 micromoles/liter replicate 3

value: THP-1 Cells


title: THP-1 Cells treated with KIN1000 0.625 micromoles/liter Replicate 3

description: Gene expression in THP-1 Cells after treatment with KIN1000 0.625 micromoles/liter replicate 3


title: 10Set3-MNX+S

value: Fetal liver hematopietic cells E 14.14


title: K1106P_RmAb_3_S3

source_name: K1106P cells, RmAb treated, 48hrs

value: Rituximab (RmAb) 200ug/ml


title: THP-1 Cells treated with KIN1000 2.5 micromoles/liter Replicate 3

description: Gene expression in THP-1 Cells after treatment with KIN1000 2.5 micromoles/liter replicate 3


title: RG S3_replicate 1

source_name: Red Globe; seeds; pea size phase (BBCH 73-75; E-L 29); replicate 1


title: THP-1 Cells treated with KIN1148 2.5 micromoles/liter Replicate 3

description: Gene expression in THP-1 Cells after treatment with KIN1148 2.5 micromoles/liter replicate 3


title: THP-1 Cells treated with X_RNA Replicate 1

description: Gene expression in THP-1 Cells after treatment with X_RNA replicate 1


title: 17Set5-Ctr+S

value: C57BL/6 mice

value: Embryonic day 14.5

value: Empty vector

value: Fetal liver hematopietic cells E 14.13


title: RG S2_replicate 3

source_name: Red Globe; seeds; post-bloom phase (BBCH 65-68; E-L 19-25); replicate 3

value: Red Globe


title: 13Set4-Ctr+S

value: Fetal liver hematopietic cells E 14.12

value: Treated with 5uM Sinefungin


title: 9Set3-Ctr+S

value: Fetal liver hematopietic cells E 14.11


title: THP-1 Cells treated with DMSO Replicate 3

description: Gene expression in THP-1 Cells after treatment with DMSO replicate 3

source_name: DMSO

value: DMSO


title: 16Set5-MNX

value: MNX1 overexpression

value: Fetal liver hematopietic cells E 14.10

value: Non-Treated


title: RG S2_replicate 2

source_name: Red Globe; seeds; post-bloom phase (BBCH 65-68; E-L 19-25); replicate 2

value: seeds


title: HDLM2_UT_1_S13

source_name: HDLM2 cells, Untreated, 48hrs

value: pleural effusion

value: Hodgkin lymphoma

value: 48 hours

value: Untreated (UT) RPMI media


title: HDLM2_UT_2_S14


title: K1106P_RmAb_2_S2

value: KARPAS 1106P

value: Primary mediastinal B-cell lymphoma

value: Rituximab (RmAb) 200ug/ml


title: K1106P_RmAb_1_S1


title: HDLM2_UT_3_S15


title: THP-1 Cells treated with KIN1000 10 micromoles/liter Replicate 3

description: Gene expression in THP-1 Cells after treatment with KIN1000 10 micromoles/liter replicate 3

value: THP-1 Cells


title: HDLM2_RmAb_3_S12

source_name: HDLM2 cells, RmAb treated, 48hrs


title: 12Set4-MNX

value: C57BL/6 mice

value: Embryonic day 14.5

value: Fetal liver hematopietic cells E 14.9


title: 8Set3-MNX

value: Fetal liver hematopietic cells E 14.8


title: RG S2_replicate 1

source_name: Red Globe; seeds; post-bloom phase (BBCH 65-68; E-L 19-25); replicate 1

value: Red Globe


title: RG S1_replicate 3

source_name: Red Globe; seeds; pre-bloom phase (BBCH 57-60; E-L 17); replicate 3

value: pre-bloom phase (BBCH 57-60; E-L 17)


title: RG S1_replicate 2

source_name: Red Globe; seeds; pre-bloom phase (BBCH 57-60; E-L 17); replicate 2


title: 2Set1-MNX

source_name: Fetal liver hematopietic cells E 14.5

value: MNX1 overexpression

value: Fetal liver hematopietic cells E 14.6


title: THP-1 Cells treated with SenV Replicate 2

description: Gene expression in THP-1 Cells after treatment with SenV replicate 2

source_name: SenV

value: SenV


title: IT S4_replicate 3

source_name: Italia; seeds; veraison phase (BBCH 81; E-L 35); replicate 3

value: Italia

value: seeds

value: veraison phase (BBCH 81; E-L 35)


title: THP-1 Cells treated with KIN1000 0.625 micromoles/liter Replicate 2

description: Gene expression in THP-1 Cells after treatment with KIN1000 0.625 micromoles/liter replicate 2


title: THP-1 Cells treated with LPS Replicate 2

description: Gene expression in THP-1 Cells after treatment with LPS replicate 2

source_name: LPS

value: LPS


title: THP-1 Cells treated with KIN1148 10 micromoles/liter Replicate 2

description: Gene expression in THP-1 Cells after treatment with KIN1148 10 micromoles/liter replicate 2


title: IT S4_replicate 2

source_name: Italia; seeds; veraison phase (BBCH 81; E-L 35); replicate 2


title: RG S1_replicate 1

source_name: Red Globe; seeds; pre-bloom phase (BBCH 57-60; E-L 17); replicate 1


title: THP-1 Cells treated with KIN1000 2.5 micromoles/liter Replicate 2

description: Gene expression in THP-1 Cells after treatment with KIN1000 2.5 micromoles/liter replicate 2


title: THP-1 Cells treated with KIN1148 0.625 micromoles/liter Replicate 2

description: Gene expression in THP-1 Cells after treatment with KIN1148 0.625 micromoles/liter replicate 2


title: HDLM2_PRED_3_S9

source_name: HDLM2 cells, PRED treated, 48hrs

value: pleural effusion

value: Hodgkin lymphoma

value: 48 hours

value: Prednisone (PRED) 60ug/ml


title: 15Set5-Ctr

value: C57BL/6 mice

value: Empty vector

value: Fetal liver hematopietic cells E 14.5

value: Non-Treated


title: HDLM2_PRED_2_S8


title: HDLM2_RmAb_2_S11

value: Rituximab (RmAb) 200ug/ml


title: 4Set2-MNX

value: Embryonic day 14.5

value: Fetal liver hematopietic cells E 14.7


title: HDLM2_RmAb_1_S10


title: 11Set4-Ctr


title: THP-1 Cells treated with KIN1000 10 micromoles/liter Replicate 2

description: Gene expression in THP-1 Cells after treatment with KIN1000 10 micromoles/liter replicate 2

value: THP-1 Cells


title: IT S3_replicate 3

source_name: Italia; seeds; pea size phase (BBCH 73-75; E-L 29); replicate 3

value: pea size phase (BBCH 73-75; E-L 29)


title: HDLM2_PRED_1_S7


title: IT S4_replicate 1

source_name: Italia; seeds; veraison phase (BBCH 81; E-L 35); replicate 1

value: Italia


title: 7Set3-Ctr


title: HDLM2_IBR_3_S6

source_name: HDLM2 cells, IBR treated, 48hrs

value: Ibrutinib (IBR) 2.5uM


title: IT S3_replicate 2

source_name: Italia; seeds; pea size phase (BBCH 73-75; E-L 29); replicate 2

value: seeds


title: THP-1 Cells treated with LPS Replicate 1

description: Gene expression in THP-1 Cells after treatment with LPS replicate 1

value: LPS


title: Ctr_5

source_name: Bone marrow from mice after transplantation with fetal liver cells

value: C57BL/6 transplanted to NOD.Cg-KitW-41J Tyr + Prkdcscid Il2rgtm1Wjl/ThomJ (NBSGW) mice


title: IT S3_replicate 1

source_name: Italia; seeds; pea size phase (BBCH 73-75; E-L 29); replicate 1


title: THP-1 Cells treated with IFNb Replicate 1

description: Gene expression in THP-1 Cells after treatment with IFNb replicate 1

source_name: IFNb

value: IFNb


title: THP-1 Cells treated with SenV Replicate 1

description: Gene expression in THP-1 Cells after treatment with SenV replicate 1

value: SenV


title: Ctr_2