title: WT_C2

status: Public on Dec 31 2024

type: SRA

city: Trondheim

first: Katja

last: Scheffler

address: Edvard Griegs Gate 8

department: Department of Neuromedicine and Movement Sciences

country: Norway

institute: Norwegian University of Science and Technology

description: 24 hours post H2O2 treatment

library_source: transcriptomic

data_processing:
Quality was assessed using FastQC (v0.11.9) & Fastq-Screen (v0.15.2)
Files were mapped to GRCh38 using Hisat2 (v.2.2.1)
Reads wre counted using Rsubread (v.2.2.6) in R (v4.2.2) using the Enseml GRCh38.p13 annotation (release 103)
Differential enrichment analysis performed using edgeR (v.3.42.4) in R (v4.2.2)
Assembly: GRCh38
Supplementary files format and content: Tab-deliminated text file with raw counts for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cell culture in IMDM with 10% FBS and 1% Penicillin/Streptomycin

extract_protocol:
RNeasy kit (Qiagen) according to manufacture's protocol with 0.1mM butylated hydroxytoluene and 0.1mM deferoxamine added to prevent oxidative damage during isolation.
Standard library preparation by BGI Tech solutions

treatment_protocol: Cells were treated with 100 µM H2O2 and collected after 24 hours.

tag: cell line

tag: cell type

value: near-haploid

tag: genotype

value: WT


title: WT_C11

description: 24 hours post H2O2 treatment


title: Human brain organoid, 2 months sample 1

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: human iPSC derived brain organoid

extract_protocol:
Dissociated cells were resuspended in PBS containing 1% BSA, immediately followed by a library preparation targeting single cells using the Chromium Single Cell 3’ Reagent Kit v3 (10×Genomics) and Chromium Controller (10×Genomics) according to the manufacturer’s instructions. A total of 6,000 cells were analyzed. The library was sequenced on a HiSeq2500 TruSeq SBS v3 reagent.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

tag: tissue

value: human iPSC derived brain organoid

value: brain organoids

value: wild type

tag: treatment


title: Dicty, whole organism, 8h, rep2

city: Moscow

first: Irina

middle: V

last: Zhegalova

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology

library_source: genomic

data_processing:
Hi-C paired-end reads were processed with distiller-nf pipeline (v 0.3.3) with default parameters. Briefly, read were mapped to Dictyostelium reference genome with bwa mem (v0.7.17-r1188), then processed into pairs of aligned reads by pairtools (v0.3.1-dev.1) with walks-policy "mask".
Only reads mapped with MAPQ not smaller than 30 were considered as potential contact pairs. Multimappers, one-sided mapped reads and potential PCR duplicates were excluded.
The resulting conact pairs were binned into contact matrices with resolution=100 bp by cooler (v0.8.7).
The maps were subsampled to the same number of conacts, and maps with lower resolution was constructed. The iterative correction. was applied using cooler balance
The resolution for loop calling was set to 2000.
Assembly: dicty_2.7
Supplementary files format and content: mcool filtered - only 6 chromosomes are included, maps subsampled to equal amoun of contact pairs, replicates are merged
Supplementary files format and content: mcool with contigs — contatin the output from distiller pipeline with all contigs present
Supplementary files format and content: bed file - loop annotation for merged replicates

molecule: genomic DNA

organism: Dictyostelium discoideum

source_name: whole organism

growth_protocol: Dictyostelium discoideum AX4 strain was obtained from the dictyBase Stock Center (strain ID: DBS0237637). Culture was started from the frozen stock on SM agar plates (1 g of anhydrous glucose, 1 g of Proteose Peptone A (Lab M; #MC011), 0.1 g of yeast extract, 1.5 g of agar, 8.62 10× KK2 buffer, MilliQ water to 100 ml; after autoclaving, 415 μl of 1M MgSO4 were added [17545967]). 10× KK2 buffer composition (for 50 ml): 1.1 g of KH2PO4, 0.458 g of K2HPO4×3H2O, MilliQ water to 50 ml. Frozen stock was thawed and mixed with 10 ml of the modified HL5 axenic growth medium [5530749] in a 100-mm plastic Petri dish (2.5 g of Tryptose (Lab M; #MC008), 2.5 g of Proteose Peptone A (Lab M; #MC011), 2.5 g of yeast extract, 5 g of anhydrous glucose, 1.27 ml of 1M KH2PO4, 0.65 ml of 1M Na2HPO4, MilliQ water to 500 ml; note that in our experience, not all Tryptoses and Peptones are suitable for the Dictyostelium axinic growth). The dish was incubated for 30 minutes at 20oC. The medium was removed, and attached cells were rinsed off from the dish by pipetting in 10 ml of fresh HL5 medium. Cells were harvested for 5 minutes at 400 g (room temperature; hereinafter 20oC). 100 μl of the mixture of fresh overnight culture of E. coli DH5α and 0.5-2×106 Dictyostelium cells was spread on 100-mm SM agar plates using sterile glass spatula. Plates were inverted, placed in a humid chamber (plastic bag with wet filter paper) and incubated at 20oC for 5-7 days. After the appearance of growth plaques, cells were scraped using a bacteriological loop and inoculated in 100 ml of modified HL5 axenic growth medium supplemented with 1× penicillin/streptomycin (Thermo Fisher Scientific; #15140122) or kanamycin (Thermo Fisher Scientific; #15160054) in a 500-ml glass flask and incubated at 20oC with shaking at 200 rpm. Cultures were maintained at a density of 0.2-1×106 cells per ml for no more than 3 weeks. For long-term storage, cells from fresh culture were harvested for 5 minutes at 400 g (4oC) and resuspended in ice-cold HL5 medium supplemented with 5% of dimethylsulfoxide (DMSO, Sigma-Aldrich; #D8418) to a concentration of 5×106 cells per ml. Suspension was aliquoted into 1.8-ml cryovials, incubated at -80oC for 12 hours in an alcohol-free cell freezing container and stored in liquid nitrogen.

extract_protocol:
Hi-C libraries were prepared as described in [22652625] with several modifications. Cells were cross-linked in 50 ml of 1× KK2 buffer supplemented with fresh 2% formaldehyde (Sigma-Aldrich; #F8775) for 10 minutes at room temperature. Excess of formaldehyde was quenched with 125mM glycine for 5 min. Cells were centrifuged (1,000 g, 10 minutes, 4oC), resuspended in 100 μl of 1× PBS, snap-frozen in liquid nitrogen, and stored at -150oC. Defrozen cells were lysed in 1.5 ml of Isotonic buffer (50 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.5 % (v/v) NP-40 substitute, 1 % (v/v) Triton X-100, 1× Protease Inhibitor Cocktail (Bimake; #B14001)) on liquid ice for 15 minutes. Cells were centrifuged at 5,000 g for 7 minutes, resuspended in 100 μl of 1.12× DpnII buffer (NEB; #B0543S), and pelleted again. The pellet was resuspended in 200 μl of 0.1% SDS in 1.12× DpnII buffer and incubated at 65oC for 10 minutes without shaking. Then, 330 μl of 1.12× DpnII buffer and 52.7 μl of 20% Triton X-100 were added, and the suspension was incubated at 37oC for 1 hour with shaking (1,400 rpm). Next, 600 U of DpnII restriction enzyme (NEB; #R0543M) were added, and the chromatin was digested overnight (14 - 16 hours) at 37oC with shaking (1,400 rpm). On the following day, 200 U of DpnII restriction enzyme were added, and the cells were incubated for 2 hours. DpnII was then inactivated by incubation at 65oC for 20 minutes. After DpnII inactivation, the nuclei were harvested for 10 minutes at 5,000 g in a pre-cooled centrifuge (4oC), washed twice with 200 μl of 1,2× NEBuffer 2.1 (NEB; #B7202S), and resuspended in 125 μl of 1,2× NEBuffer 2.1. Cohesive DNA ends were biotinylated by the addition of 25 μl of the biotin fill-in mixture (0.025 mM dCTP (Thermo Fisher Scientific; #R0151), 0.025 mM dGTP (Thermo Fisher Scientific; #R0161), 0.025 mM dTTP (Thermo Fisher Scientific; #R0171), 0.025 mM biotin-14-dATP (Thermo Fisher Scientific; #19524-016), and 0.8 U/μl Klenow enzyme (NEB; #M0210L)). The samples were incubated at 37oC for 90 minutes with shaking (900 rpm). Nuclei were pelleted at 5,000 for 5 minutes, resuspended in 100 μl of 1× T4 DNA ligase buffer (Thermo Fisher Scientific; #EL0011), and pelleted again. The pellet was resuspended in 400 μl of 1× T4 DNA ligase buffer, and 50 U of T4 DNA ligase (Thermo Fisher Scientific; #EL0011) were added. Chromatin fragments were ligated at 22oC for 6 hours with shaking (1,400 rpm). The cross-links were reversed by overnight incubation at 65oC in the presence of Proteinase K (100 μg/ml; Sigma-Aldrich; #P2308) and 1% of SDS. After cross-link reversal, the DNA was purified by single phenol-chloroform extraction followed by ethanol precipitation with 20 μg/ml of glycogen (Thermo Scientific Scientific; #R0561) as a co-precipitator. After precipitation, the pellets were dissolved in 100 μl of 10 mM Tris-HCl (pH8.0). To remove residual RNA, samples were treated with 20 μg of RNase A (Thermo Fisher Scientific; #R1253) for 45 minutes at 37oC. To remove residual salts and DTT, the DNA was additionally purified using Agencourt AMPure XP beads (Beckman Coulter; #A63881). Biotinylated nucleotides from the non-ligated DNA ends were removed by incubating the Hi-C libraries (2 μg) in the presence of 6 U of T4 DNA polymerase (NEB; #M0203L) in NEBuffer 2.1 supplied with 0.025 mM dATP (Thermo Fisher Scientific; #R0141) and 0.025 mM dGTP at 20oC for 4 hours. Next, the DNA was purified using Agencourt AMPure XP beads. The DNA was then dissolved in 500 μl of sonication buffer (50 mM Tris-HCl (pH8.0), 10 mM EDTA, 0.1 % SDS) and sheared to a size of approximately 100 - 500 bp using a VirSonic 100 (VerTis). The samples were concentrated (and simultaneously purified) using AMICON Ultra Centrifugal Filter Units (Millipore; #UFC503096) to a total volume of approximately 50 μl. The DNA ends were repaired by adding 62.5 μl of MilliQ water, 14 μl of 10× T4 DNA ligase reaction buffer, 3.5 μl of 10mM dNTP mix (Thermo Fisher Scientific; #R0191), 5 μl of 3 U/μl T4 DNA polymerase, 5 μl of 10 U/μl T4 polynucleotide kinase (NEB; #M0201L), 1 μl of 5 U/μl Klenow DNA polymerase, and then incubating at 25oC for 30 min. The DNA was purified with Agencourt AMPure XP beads and eluted with 60 μl of 10mM Tris-HCl (pH 8.0). To perform an A-tailing reaction, the DNA samples were supplemented with 7.5 μl of 10× NEBuffer 2.1, 1.5 μl of 10mM dATP, 1,5 μl of MilliQ water, and 4.5 μl of 5 U/μl Klenow (exo-) (NEB; #M0212S). The reactions were carried out for 30 minutes at 37oC in a PCR machine, and the enzyme was then heat-inactivated by incubation at 65oC for 20 minutes. The DNA was purified using Agencourt AMPure XP beads and eluted with 100 μl of 10mM Tris-HCl (pH8.0). Biotin pulldown of the ligation junctions: 10 μl of MyOne Dynabeads Streptavidin C1 (Thermo Fisher Scientific; #65001) beads washed 2 times with the TWB buffer (5 mM Tris-HCl (pH8.0), 0.5 mM EDTA (pH8.0), 1 M NaCl, 0.05 % Tween-20), resuspended in 200 μl of 2× Binding buffer (10 mM Tris-HCl (pH8.0), 1 mM EDTA, 2 M NaCl) and added to 200 μl of DNA. Biotin pulldown was performed for 30 minutes at 25oC with shaking. Next, beads with captured ligation junctions were washed once with 1× Binding buffer, once with 1× T4 DNA ligase buffer, and then resuspended in 50 μl of adapter ligation mixture comprising of 41.5 μl of MilliQ water, 5 μl of 10× T4 DNA ligase reaction buffer, 2.5 μl of Illumina TruSeq adapters, and 1 μl of 5 U/μl T4 DNA ligase. Adapter ligation was performed at 22oC for 2.5 hours, and the beads were sequentially washed twice with 200 μl of TWB, twice with 200 μl of CWB (10 mM Tris-HCl (pH8.0) and 50 mM NaCl), and then resuspended in 25 μl of MilliQ water.
Test PCR reactions containing 4 μl of the streptavidin-bound Hi-C library were performed to determine the optimal number of PCR cycles required to generate an amount of PCR products sufficient for sequencing. The PCR reactions were performed using KAPA High Fidelity DNA Polymerase (Kapa Biosystems; #08201595001) and Illumina PE1.0 and PE2.0 PCR primers (10 pmol each). The temperature profile was 5 minutes at 95oC, followed by 6, 9, 12, 15, and 18 cycles of 20 sec at 98oC, 15 sec at 65oC, and 20 ses at 72oC. The PCR reactions were separated on a 2 % agarose gel containing ethidium bromide, and the number of PCR cycles necessary to obtain a sufficient amount of DNA was determined based on the visual inspection of gels (typically 8 - 12 cycles). Four preparative PCR reactions were performed for each sample. The PCR mixtures were combined, and the products were purified with Agencourt AMPure XP beads. Libraries were sequenced on an Illumina Novaseq 6000 by 100-bp paired-end reads.

treatment_protocol: Induction of multicellular development was performed by starvation on KK2 agar plates according to previously published protocol [17545967] with several modifications. 3×108 of cells from fresh axinic culture in HL5 medium (1-2 days, 0.5-1×106 cells per ml) were harvested for 10 minutes at 400 g (room temperature), washed once with 50 ml of ice-cold 1× KK2 buffer and once with 50 ml of ice-cold Development buffer (5 mM Na2HPO4, 5 mM KH2PO4, 1 mM CaCl2, 2 mM MgCl2). The pellet was resuspended in 1 ml of Development buffer. The suspension was spreaded on 150-mm Petri dishes with 1.5% agar prepared on a 1× KK2 buffer. Dishes were wrapped with the Parafilm, placed in a humid chamber and incubated at 22oC for 2 (starvation), 5 (early aggregation) and 8 hours (late aggregation). The development progress accompanied by the appearance of characteristic spiral-like patterns formed by migrating cells has been monitored by visual inspection of the cell layer at the agar surface. At each time point, cells were rinsed off from the agar surface by pipetting in 10 ml of ice-cold 1× KK2 buffer. Cells were then harvested for 5 minutes at 400 g (4oC). Pellet was resuspended in 10 ml of ice-cold 1× KK2 buffer, the suspension was splitted into two aliquots in a ratio of 1:4, and cells were harvested as described above. The cell pellet from the smaller aliquot was snap-frozen in a liquid nitrogen for the subsequent RNA isolation. The cell pellet from the larger part was resuspended in 50 ml of 1× KK2 buffer and used for the Hi-C library preparation.

value: whole organism

tag: induction time


title: Dicty, whole organism, 5h, rep2


title: Dicty, whole organism, 8h, rep1


title: Dicty, whole organism, 2h, rep1


title: Dicty, whole organism, 2h, rep2


title: Dicty, whole organism, 0h, rep1


title: Dicty, whole organism, 5h, rep1


title: Dicty, whole organism, 0h, rep2


title: Nucleus pulposus cells control-3

city: Hangzhou

first: Tianyuan

last: Gu

state: Zhejiang

address: 3 Qingchun East Road, Shangcheng District, Hangzhou City, Zhejiang Province, China

department: Department of Orthopedic Surgery

country: China

institute: Zhejiang University School of Medicine Sir Run Run Shaw Hospital

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp  with default parameters
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software
The mapped reads of each sample were assembled by StringTie in a reference- based approach.
Assembly: hg38
Supplementary files format and content: excel file

source_name: Nucleus pulposus cells

growth_protocol: To isolate NPCs, the nucleus pulposus was cut into small pieces and treated with 10ml DMEM media (Gibco-Thermo Fisher Scientific, Waltham, MA, USA) with 0.1% collagenase type II (Biosharp, Hefei, China) for 4 to 6 hours at 37℃. Liberated cells were filtered through a 40 µm cell strainer, and the filtrate was centrifuged for 5 minutes at 1,200 rpm. The supernatant was aspirated, and the cell pellets were washed with sterile phosphate-buffered saline (PBS), then cultured in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS) (Thermo Fisher Scientific, Waltham, MA, USA) at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’ s instructions.
The RNA-seq transcriptome librariy was prepared following Illumina® Stranded mRNA Prep Ligation from Illumina (San Diego, CA) using 1μg of total RNA

treatment_protocol: Adenovirus harboring the circFUNDC1 (pAdeasy-EF1- hsa_circ_0007290-CMV-EGFP-N) was generated and purified by Hanheng Biotechnology (Shanghai, China) and transfected into NPCs.

value: Nucleus pulposus cells

value: transfected with Ad-NC


title: Nucleus pulposus cells control-2


title: mnn9D/D grown in yeast form at 28ºC Rep 1

type: RNA

city: Salamanca

first: Angel

last: Domínguez

state: Salamanca

address: Plaza de los Doctores de la Reina

department: Microbiology and Genetics/CIETUS/IBSAL

country: Spain

institute: University of Salamanca

description: mutant clone 1, WT pool WT. Data matrix B200H

hyb_protocol: The C. albicans oligo-microarrays (Eurogentec) were prehybridised for 45 min at 42ÂºC in 5x SSC, 1% SDS and 1% BSA. Prehybridised microarrays were washed five times with water, once with isopropanol and the washed arrays were air dried.  Before hybridization, concentrated Cy5- and Cy3-labeled cDNA from mutant and parental cells was mixed. Then 5 microl of denatured herring sperm salmon DNA (10mg/ml) was added. After DNA denaturation for 5 min at 95ÂºC, DIG easy hybridisation buffer (50% formamide, 10x SSC, 0.2% SDS, ROCHE) was incorporated up to a final volume of 60 microl. The mixture was applied on the prehybridised microarray, covered with a LifterSlip (60x24 mm, Sigma-Aldrich) and incubated overnight in a humidified chamber (Corning) in a water bath at 42ÂºC. Hybridised microarrays were washed for 15 min in 2x SSC, 1% SDS, for 8 min in the same solution and twice for 5 min in 0.2x SSC. Then microarrays were dried by centrifugation at 1100 rpm at room temperature.

scan_protocol: The microarrays were scanned with a GenePix4000B scanner and intensity data were captured using the GenePix Pro version 6.0 software package (Axon Instruments).

data_processing: Data were analysed in GeneSpring 5.0 sofware (Axon Instruments). Data were per-chip and per-spot normalized by intensity dependent (LOWESS) normalization applied to the print-tip region. Genes with differential expression were obtained by first filtering genes with a fold change ≥ 1.5 in at least one hybridisation and then applying a “statistical group comparison” (Wilconxon-Mann-Whitney test) and the multiple testing correction Benjamini and Hochberg False Discovery Rate (FDR) with p-value  0.02. The second filter was introduced to control the stringency of the FDR correction, which is directly influenced by the number of genes analysed. Among genes selected by the test we considered only genes as being significantly regulated, if they were differentially expressed by at least a mean factor of 1.5 considering the three replicates.

organism: Candida albicans

source_name: cDNA, WT 28ºC

label_protocol: 15 micrograms of total RNA was labelled using the CyScribe First-Strand cDNA labeling kit (RPN 6200, Amersham, GE Healthcare) following manufacturer’ s instructions, with 1 micrograms anchored oligo-dT-primer (Amersham Biosciences) and 0.1 pmol C. albicans-specific primer mix (provided by Eurogentec).  Labelled cDNA was purified using “CyScribe GFX Purification Kit (GE Healthcare)”. cDNA was checked for proper labelling measuring the amount of probe and incorporated dye using a NanoDrop 1000 device and calculating the frequency of incorporation. Then it was stored at -20ºC until further use.

growth_protocol: For transcriptional profile analysis of cells grown in yeast form, strains were grown to mid exponential phase in Lee’ s medium (pH 6.8, 1.25% glucose) (Lee et al., 1975) at 28ºC. recovered and frozen in liquid nitrogen and stored at -80ºC until further use.

extract_protocol: The isolation of total RNA were performed according to Galar Fungail standard operating procedures (www.pasteur.fr/recherche/unites/Galar_Fungail/)

tag: strain

source_name: cDNA, mutant 28ºC


title: mnn9D/D grown in yeast form at 28ºC Rep 2


title: mnn1D/D grown under hypha-inducing conditions for 15 min. Rep 3

description: mutant clone 1, WT pool WT. Data matrix I180H

source_name: cDNA, mutant 37ºC, 15 min

growth_protocol: For transcriptional profile analysis of cells grown in yeast form, strains were grown to mid exponential phase in Lee’ s medium (pH 6.8, 1.25% glucose) (Lee et al., 1975) at 28ºC. recovered and frozen in liquid nitrogen. To induce the yeast-to-hypha transition, first, cells were incubated in Lee medium at 28ºC until the OD600 reached 0.5, collected, washed and resuspended in distilled water at a final concentration of 2x 107 cells/ml. In order to synchronize cells in G1, they were incubated with shaking at 200 rpm for 2 hours at 28ºC and next maintained without shaking for 24 hours at 4ºC. Finally, they were collected and inoculated at 1x 107 cells/ml into pre-warmed Lee’s pH 6.8 and incubated at 37ºC. Samples of cells were extracted after 15, 60 and 180 min and then centrifuged and the resulting pellet was immediately frozen in liquid nitrogen and stored at -80ºC until further use.

source_name: cDNA, WT 37ºC, 15 min


title: Nucleus pulposus cells treatment-3

value: transfected with Ad-CircFUNDC1


title: OP_pil3

city: Fuzhou

first: Meiyuan

last: Chen

state: Fujian Province

address: No.10.95th Lane, Qianheng Rd

department: Institute of Edible Fungi

institute: Fujian Academy of Agricultural Sciences

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS(Illumia)according to the manufacturer's instruction
The library preparations were sequenced on an Illumina Hiseq platform
Raw data(raw reads)of fastq format were firstly processed through in-house perl scripts
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene
Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced was calculated based on the length of the geneand reads count mapped to this gene.
Genome_build: The genome sequence of A.blazei was submitted to DDBJ/ENA/GenBank under the accession SSNC00000000
Supplementary_files_format_and_content: text file include RPKM values for each Sample

organism: Agaricus blazei

extract_protocol:
The total RNA from mycelium and fruiting body primodium  was isolated usingTriZol reagent
Sequencing libraries were generated using NEBNext®UltraTM RNA Library Prep Kit for Illumina®(NEB,USA) following manufacturer’s instruction

value: JA

value: pileus of fruit body at  Maturation stage


title: OP_sti2

value: stipe of fruit body at  Maturation stage


title: OP_sti1


title: OP_pil1


title: Nucleus pulposus cells treatment-2


title: OP_pil2


title: mnn1D/D grown under hypha-inducing conditions for 180 min. Rep 3

description: mutant clone 2, WT pool WT. Data matrix I180H

source_name: cDNA, mutant 37ºC, 180 min

source_name: cDNA, WT 37ºC, 180 min


title: mnn1D/D grown under hypha-inducing conditions for 60 min. Rep 3

source_name: cDNA, mutant 37ºC, 60 min

source_name: cDNA, WT 37ºC, 60 min


title: mnn1D/D grown under hypha-inducing conditions for 60 min. Rep 2


title: mnn1D/D grown under hypha-inducing conditions for 15 min. Rep 2


title: mnn1D/D grown in yeast form at 28ºC Rep 2


title: Nucleus pulposus cells control-1


title: mnn1D/D grown under hypha-inducing conditions for 180 min. Rep 2

description: mutant clone1, WT pool WT. Data matrix I180H


title: mnn1D/D grown under hypha-inducing conditions for 60 min. Rep 1


title: Nucleus pulposus cells treatment-1


title: OP3

source_name: OP

value: fruit body harvested at Maturation stage


title: OP_sti3


title: mnn1D/D grown in yeast form at 28ºC Rep 1


title: PA treated HepG2 cells for co-administration of HQF and copper_3

city: Wuhan

first: Xiang

last: Li

address: Youyi Road

institute: Hubei University

data_processing:
Through removing low quality, ploy-N, and adapter contained reads by in-house perl scripts, high-quality clean data were used for further analysis.
After building index of the reference genome (GRCh38.p13), paired-end clean reads were aligned to the human genome using Hisat (v2.1.0).
RSEM (v1.3.3) was used to quantify gene abundances, and the TPM value of each gene was obtained according to the transcript length and reads count.
Assembly: GRCh38.p13
Supplementary files format and content: Text file include all TPM values for each sample

source_name: liver

growth_protocol: HepG2 (ATCC® HB-8065) cells were procured from American Type Culture Collection and cultured in complete DMEM (Gibco; C11995500BT) at 37 oC within a saturating humidity atmosphere containing 5% CO2. The complete DMEM contained 10% FBS (Gibco; 26140079), and 1% penicillin/streptomycin (Gibco; 15140122).

extract_protocol:
RNA was harvested using TRIzolTM Reagent. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina® Stranded mRNA Prep, Ligation kit according to manufacturer’s recommendations.

treatment_protocol: For PA group, HepG2 cells were pre-treated with 750 μM PA for 24h. For PA_CuCl2_HQF group, the PA-treated HepG2 cells were further co-treated with HQF (0.5 µM) and CuCl2 (5 µM) for 24 h.

value: liver

value: Human hepatocellular carcinomas

value: cancer cell


title: OP2


title: PA treated HepG2 cells for co-administration of HQF and copper_2


title: OP1


title: mnn1D/D  grown in yeast form at 28ºC Rep 3


title: mnn1D/D grown under hypha-inducing conditions for 15 min. Rep 1


title: PA treated HepG2 cells for co-administration of HQF and copper_1


title: PA treated HepG2 cells_3

value: PA


title: HA_sti3

value: stipe of fruit body at Harvested  stage


title: HA_sti1


title: HA_sti2


title: HA_pil3

value: pileus of fruit body at Harvested  stage


title: PA treated HepG2 cells_2


title: ChIP_seq_MCF7_H_Input

city: Bhopal

first: Sanjeev

last: Shukla

state: Madhya Prades

address: Bhopal Bypass Road, Bhauri Bhopal 462 066 Madhya Pradesh, INDIA

department: Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Bhopal

data_processing:
Quality control of raw ChIP-seq, CUT&RUN and 4C-seq reads was performed using Fastqc.
CTCF-ChIP-seq paired-end sequencing fastq files were mapped to human hg38 genome using Bowtie2 (Langmead and Salzberg, 2012). Sam files were converted into bam files and sorted by Samtools (Li et al., 2009). Peaks were called using MACS v2.1.2. Each bam file was converted into bigwig files using DeepTools bamCoverage (Ramirez et al., 2014).
The CUT&RUN reads were mapped to the human genome hg38 utilizing Bowtie2. To call peaks, we used MACS2 using an IgG bam file as a control. Each bam file was converted into bigwig files using DeepTools bamCoverage (Ramirez et al., 2014).
4C-seq reads were processed using pipe4C (Krijger P.H.L. et al., 2020) using default parameters in the configuration file.
Assembly: GRCh38
Supplementary files format and content: bigWig

growth_protocol: MCF7 cells were cultured in media recommended by American Type Cell Culture in a humidified incubator at 37 ⁰C and 5% CO2

extract_protocol:
MCF7 breast cancer cell line was kept in duplicate under Normoxia (21% oxygen) or Hypoxia (1% oxygen) for 24 hours before performing CTCF-ChIP-seq (Shukla et al., 2011; Khoury et al., 2020) and CTCF-CUT&RUN assay (Skene et al., 2018; Sharma et al, 2023). For 4C-seq, MCF7 cells  transduced with lentivirus expressing either shRNA control (shControl) or shRNA specific for CTCF (shCTCF) were kept in Normoxia or Hypoxia and the 4C-seq experiment was performed based on (Splinter et al., 2012; Krijger et al., 2020)  using NlaIII and DpnII as restriction enzymes.
All the DNA libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.
150 bp paired-end ChIP-seq using Illumina NovaSeq X Plus, 50 bp paired-end CUT&RUN using Illumina NovaSeq 6000, 100 bp paired-end 4C-seq using Illumina NovaSeq 6000

treatment_protocol: MCF7 breast cancer cell line was kept under Normoxia (21% oxygen) or Hypoxia (1% oxygen) for 24 hours before performing CTCF-ChIP-seq or CTCF-CUT&RUN or 4C-seq

value: Breast cancer cell line (luminal)

tag: chip antibody


title: ChIP_seq_MCF7_H_CTCF_2

value: CTCF (CST, #3418S)


title: HA_pil2


title: ChIP_seq_MCF7_N_Input


title: ChIP_seq_MCF7_N_CTCF_2


title: ChIP_seq_MCF7_H_CTCF_1


title: HA1

source_name: HA

value: fruit body harvested at Harvested  stage


title: ChIP_seq_MCF7_N_CTCF_1


title: HA3


title: BU_sti1

value: stipe of fruit body at Button  stage


title: HA_pil1


title: BU_sti2


title: Eyestalk_3

city: Kansas City

first: Alejandro

last: Sanchez Alvarado

state: MO

address: 1000 East 50th Street

country: USA

institute: Stowers Institute for Medical Research

data_processing:
Alignment with STAR aligner
Assembly: GCF_003073045.1
Supplementary files format and content: read counts from STAR aligner

organism: Pomacea canaliculata

source_name: eye stalk

extract_protocol:
Trizol Extraction
PoylA selected RNA

value: eye stalk


title: Eyestalk_2


title: BU_sti3


title: Eyestalk_1


title: BU_pil3

value: pileus of fruit body at Button  stage


title: PA treated HepG2 cells_1


title: Oral_3

source_name: oral tentacle

value: oral tentacle


title: BU_pil1

value: JA

value: pileus of fruit body at Button stage


title: HA2


title: BU_pil2


title: BU2

source_name: BU

value: fruit body harvested at Button stage


title: Oral_1


title: mnn1D/D grown under hypha-inducing conditions for 180 min. Rep 1

source_name: cDNA, mutantT 37ºC, 180 min


title: BU3


title: Oral_2


title: BU1


title: Cephalic_2

source_name: cephalic tentacle

value: cephalic tentacle


title: Cephalic_3


title: primodium2

source_name: primodium

value: primodium stage equivalent to pinhead stage in A. bisporus whose velum not differentiated


title: primodium3


title: Retina_3

source_name: retina

value: retina


title: primodium1


title: Retina_4


title: mycelium3

source_name: mycelium

value: mycelium harvested at 20 days after casing


title: Retina_1


title: Cephalic_1


title: mycelium1


title: 28dpa_4

data_processing:
Alignment with STAR aligner
Assembly: GCF_003073045.1
Supplementary files format and content: regen_star_count.csv.gz

tag: group


title: TBP mice, radio, scRNA

city: Chengdu

first: Heng

last: Xu

state: Sichuan

address: 17#, section 3, South Renmin Road

institute: Sichuan University

description: 10x Genomics

data_processing:
Raw bcl files were demultiplexed using mkfastq (Cell Ranger v3.1.0) to generate FASTQ files. FASTQ were mapped to the reference genome (GRCm38) using count application (Cell Ranger v6.0.2) with default settings. Read10× function from the Seurat package (version 4.1.1) was used to merge all sample data into an aggregate Seurat object. Cells were filtered by several criteria: less than 15% of mitochondrial gene expression, minimal expression of 200 genes per cell, and nFeature RNA less than 4000. After filtering, we obtained 11,256 cells. We ran Seurat ScaleData and NormalizeData with default parameters. The variable genes were identified by the FindVariableFeatures function of Seurat package. We corrected batch effects between samples with RunHarmony function in harmony (version 0.1.0) R packages. Last, we clustered cells using the FindNeighbors and FindClusters functions and performed nonlinear dimensional reduction with the RunUMAP (resolution = 0.8) function with default settings. Differentially expressed genes (DEGs) between every pair of clusters were identified by using FindMarkers with default settings.
Assembly: genome GRCm38
Supplementary files format and content: The count matrix of all cells

organism: Mus musculus

source_name: Thyroid

extract_protocol: The Chromium Single Cell 3′ Library & Gel Bead Kit v2 (PN120237), Chromium Single Cell 3’ Chip Kit v2 (PN-120236), and Chromium i7 Multiplex Kit (PN-120262) were used according to the manufacturer’s instructions in the Chromium Single Cell 3′ Reagents Kits v2 User Guide. The single-cell suspension was washed twice with 1× phosphate-buffered saline (PBS) + 0.04% BSA. Cell number and concentration were confirmed with TC20 Automated Cell Counter. Cells were subjected immediately onto a 10× Genomics Chromium Controller machine for gel beads-in-emulsion (GEM) generation. Barcoded complementary DNAs (cDNAs) were prepared using a 10× Genomics Chromium Single Cell 3′ reagent kit (V2 chemistry), which was subsequently recovered, purified, and amplified to generate sufficient quantities for library preparation. Library quality and concentration were assessed using Agilent Bioanalyzer 2100. Libraries were run on the NovaSeq platform of Illumina for PE150 sequencing.

value: TBP (Tpo-Cre, Braftm1Mmcm/wz TrP53tm1Brn/tm1Brn)

value: Thyroid

value: radiotherapy


title: 28dpa_3


title: 28dpa_1


title: 28dpa_2


title: TBP mice, immune, scRNA

description: 10x Genomics

value: immunotherapy


title: 21dpa_4


title: 21dpa_3


title: TBP mice, combine, scRNA

description: 10x Genomics

value: combined (radiation+immunotherapy)


title: TBP mice, control, scRNA

description: 10x Genomics

value: control


title: 21dpa_2


title: 53HET

city: Washington

first: Leilei

last: Qi

state: DC

address: 2300 I St NW

institute: The George Washington University

data_processing:
Basecalls performed using Illuminal CASAVA software.
Tophat2 alignment
HTseq-DEseq to find differentially expressed genes
R package ‘DESeq’ was used to normalize data and find group-pairwise differential gene expression
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include reads counts for each Sample

source_name: Naïve CD8 T cell

extract_protocol:
naive CD8 + T cells were directly isolated from mouse splenocytes, total RNA was extracted with RNeasy Mini Kit.
total RNA was used for library preparation following the protocol for Illumina TruSeq stranded mRNA-seq.

value: spleen

tag: age

value: 3 month old

value: Het


title: 56HET


title: 21dpa_1

value: eye stalk


title: 15dpa_4


title: 15dpa_3


title: 139HET


title: 31HET


title: 15dpa_2


title: 65WT

value: wild type


title: 57WT


title: 54WT


title: 12dpa_4


title: mycelium2

value: JA


title: 15dpa_1


title: WholeBlood-MDD-F-914

type: genomic

city: Strasbourg

first: Pierre-Eric

last: Lutz

address: 8 allée du général Rouvillois

country: France

institute: Institut des Neurosciences Cellulaires et Intégratives, INCI CNRS UPR3212

hyb_protocol: Performed by Diagenode, following Illumina’s recommendations (Illumina, San Diego, CA)

data_processing:
The R package ChAMP (v2.16.2) was used for data processing (see manuscript for details)
normalized Average Beta computed using the BMIQ (Beta MIxture Quantile dilation) normalisation from the ChAMP package
Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: WholeBlood, MDD, F

growth_protocol: Not applicable

extract_protocol: DNA extraction from venous blood collected in EDTA-tubes, using PureLink TM genomic DNA mini kit (Invitrogen), and deaminated using the EZ-96 DNA Methylation Kit (Zymo Research)

treatment_protocol: Not applicable

value: MDD

tag: Sex

value: Female


title: WholeBlood-Control-M-1100

scan_protocol: Performed by Diagenode, following Illumina’s recommendations (Illumina, San Diego, CA)

source_name: WholeBlood, Control, M

value: Control

value: Male


title: 12dpa_2


title: WholeBlood-MDD-M-913

source_name: WholeBlood, MDD, M

label_protocol: Performed by Diagenode, following Illumina’s recommendations (Illumina, San Diego, CA)


title: 12dpa_1


title: 45WT


title: 12dpa_3


title: 9dpa_3


title: 9dpa_4


title: WholeBlood-MDD-F-912


title: 9dpa_2


title: WholeBlood-MDD-F-911


title: WholeBlood-MDD-F-910


title: 9dpa_1


title: WholeBlood-MDD-F-909


title: 6dpa_4


title: WholeBlood-MDD-F-908


title: 6dpa_2


title: WholeBlood-MDD-F-906


title: 6dpa_3


title: WholeBlood-MDD-F-905


title: WholeBlood-MDD-F-904


title: 3dpa_4


title: 6dpa_1


title: WholeBlood-MDD-M-901


title: 3dpa_3


title: 3dpa_2


title: 3dpa_1


title: WholeBlood-MDD-F-903


title: WholeBlood-MDD-F-820


title: WholeBlood-MDD-F-822


title: 1dpa_1


title: WholeBlood-MDD-M-813


title: 1dpa_4


title: 1dpa_2


title: WholeBlood-MDD-F-817


title: WholeBlood-MDD-M-823


title: Intact_3

value: Intact


title: 1dpa_3


title: WholeBlood-MDD-F-811


title: Intact_2


title: Intact_4


title: Intact_1


title: WholeBlood-MDD-F-807


title: WholeBlood-MDD-F-802


title: WholeBlood-MDD-F-806


title: WholeBlood-MDD-F-804


title: husAB_3

city: Wrocław

first: Michał

last: Śmiga

address: Fryderyka Joliot-Curie 14a

country: Poland

institute: Faculty of Biotechnology, University of Wrocław

data_processing:
data processing was performed by Novogene (Cambridge, United Kingdom) according to the company standard protocols.
Assembly: GCF_001263815.1
Supplementary files format and content: tab-delimited text file include raw counts for each sample

organism: Porphyromonas gingivalis

source_name: bacteria cells

growth_protocol: Porphyromonas gingivalis was cultured in heme and iron-rich conditions (Basal medium supplemented with 7.7 µM heme; Hm) or heme and iron-depleted conditions (Basal medium supplemented with 160 μM 2,2-dipyridyl; DIP) until the mid-exponential growth phase (OD600 = 0.5-0.6).

extract_protocol:
RNA was isolated from the bacteria pellet received from 1 ml of the culture (OD600 = 0.5-0.6). RNA isolation was performed by Novogene (Cambridge, United Kingdom) according to the company standard protocols.
RNA libraries were constructed by Novogene (Cambridge, United Kingdom) according to the company standard protocols.

value: bacteria cells

value: husA{delta}Tcr husB{delta}Emr

value: heme and iron rich conditions

tag: optical density_at_600_nm


title: husAB_2


title: WholeBlood-MDD-F-801


title: WholeBlood-MDD-M-633


title: husAB_1


title: hmuYR_3

value: hmuY{delta}Tcr hmuR{delta}Emr


title: WholeBlood-MDD-M-631


title: WholeBlood-MDD-F-629


title: hmuYR_2


title: WholeBlood-MDD-F-623


title: WT-DIP_3

value: wild-type

value: heme and iron starvation


title: WholeBlood-MDD-F-620


title: hmuYR_1


title: WholeBlood-MDD-M-621


title: WholeBlood-MDD-F-618


title: WholeBlood-MDD-F-611


title: WT_3


title: WholeBlood-MDD-M-619


title: WT-DIP_1


title: WT-DIP_2


title: WholeBlood-MDD-M-608


title: WT_1


title: WT_2


title: WholeBlood-MDD-F-603


title: WholeBlood-MDD-F-516


title: WholeBlood-MDD-M-514


title: SCHU_P9_rep2

city: Shinjuku-ku

first: Akihiko

last: Uda

state: Tokyo

address: Toyama 1-23-1

department: Department of Veterinary Science

institute: National Institute of Infectious Diseases

description: Gene expression in Francisella tularensis subsp. tularensis SCHU P9 replicate2

hyb_protocol: The microarray to determine the gene expression of F. tularensis (Agilent) was immediately placed on the gasket slide, and hybridization was conducted in a Hybridization Oven (Agilent) at 50°C for 17 h. After completion of hybridization, the slides were washed according to the Agilent protocol ver. 6.5.

scan_protocol: Microarrays slides were scanned at 5 micrometer resolution on a microarray scanner (Agilent) with excitation of the fluorophores Cy3.

data_processing: The image files were analyzed using Feature Extraction software ver. 10.7.3.1 (Agilent), and data mining was performed using GeneSpring GX version 11.5.1 (Agilent).

organism: Francisella tularensis

source_name: Cultured bacteria

label_protocol: The total RNAs were denatured at 65°C for 5 min, stood on ice for 5 min, and labeled by Ulysis Alexa Fluor 546 Nucleic Acid Labeling Kit (Molecular Probes) at 80°C for 15 min. The labeled RNAs were ethanol precipitated, washed twice with 70% ethanol, dried, and then dissolved in 10 μl DW. After treatment with fragmentation buffer (Agilent) at 60°C for 30 min, the samples were mixed with 2x Hi-RPM Gene Expression Hybridization Buffer (Agilent) and loaded on a gasket slide (Agilent).

growth_protocol: F. tularensis SCHU P0, P5, and P9 cultured sub-confluently on chocolate Eugon agar plates at 37°C were duplicated.

extract_protocol: Total RNAs were extracted from bacterial pellets of SCHU P0, P5, and P9 (n=2) using the RNeasy mini kit (Qiagen) following the manufacturer's instructions. Purified RNAs from each strain were dissolved in 5 mM Tris-HCl (pH 8.0) containing 1 mM EDTA.

value: subsp. tularensis SCHU P9


title: WholeBlood-MDD-F-511


title: WholeBlood-MDD-M-513


title: SCHU_P9_rep1

description: Gene expression in Francisella tularensis subsp. tularensis SCHU P9 replicate1


title: WholeBlood-MDD-F-510


title: SCHU_P5_rep1

description: Gene expression in Francisella tularensis subsp. tularensis SCHU P5 replicate1

value: subsp. tularensis SCHU P5


title: SCHU_P0_rep2

description: Gene expression in Francisella tularensis subsp. tularensis SCHU P0 replicate2

value: subsp. tularensis SCHU P0


title: SCHU_P5_rep2

description: Gene expression in Francisella tularensis subsp. tularensis SCHU P5 replicate2


title: WholeBlood-MDD-M-509


title: WholeBlood-MDD-F-503


title: WholeBlood-MDD-M-504


title: Rep1_IWRR, 1day

city: Jinan

first: YAO

last: XIAO

state: Shandong

address: 23788 Gong Ye Bei Road

department: Institute of Animal Science and Veterinary Medicine

institute: Shandong Academy of Agricultural Sciences

description:
The sample was collected from bESC1 co-culturing with MEF and treated with the IWR-1 removed medium. Reads were mapped to the bovine genome ARS-UCD1.3 as well as the mouse genome GRCm39 respectively to analyze distinct repsonses of  the two different cell type.
IWRRL1

data_processing:
Samples were sequenced with 150 bp pair-end reads on an illumina Novaseq 6000 platform.
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: ARS-UCD1.3
Assembly: GRCm39
Supplementary files format and content: tab-delimited tex file includes read counts for each sample

organism:
Bos taurus
Mus musculus

source_name: Cell line

growth_protocol: The bESC-MEF co-culture was cultured with the mTeSR1 medium supplemented with 2.5 µM IWR-1 and 1% (v/v) penicillin-streptomycin solution. The MEF were derived from E13.5 CD-1 mouse fetuses and cultured with DMEM supplemented with 10% (v/v) fetal bovine serum and 1% (v/v) penicillin-streptomycin solution. Before serving as feeder cells, MEF were treated with mitomycin C for 2h to disrupt their growth.

extract_protocol:
Total RNA was extracted using Trizol reagent according to the manufacturer’s instructions. RNA concentration was determined using a Qubit 2.0 Flurometer. All samples passed the RNA integrity tests assessed with an Agilent 5400 Bioanalyzer.
Total RNA was subjected to mRNA purification using poly-T oligo-attached magnetic beads. The RNA sequencing library was constructed using NEBNext Ultra RNA Library Prep Kit following the manufacturer’s protocol. After synthesis of the first and second strand cDNA, library fragments were purified by AMPure XP system.

treatment_protocol: On the day 0 of the experiment, culture medium was removed and rinsed with DPBS 3 times. Then, each line of bESC were treated with either the complete medium that supplemented with 2.5 µM IWR-1 (IWR) or the IWR-1 removed medium (IWRR).

value: Cell line

tag: bovine cell_type

value: Embryonic stem cells

tag: mouse cell_type

value: Embryonic fibroblasts

value: WT

value: IWR-1 removed medium


title: Rep4_IWRR, 1day

description:
The sample was collected from bESC4 co-culturing with MEF and treated with the IWR-1 removed medium. Reads were mapped to the bovine genome ARS-UCD1.3 as well as the mouse genome GRCm39 respectively to analyze distinct repsonses of  the two different cell type.
IWRRL4


title: Rep2_IWRR, 1day

description:
The sample was collected from bESC2 co-culturing with MEF and treated with the IWR-1 removed medium. Reads were mapped to the bovine genome ARS-UCD1.3 as well as the mouse genome GRCm39 respectively to analyze distinct repsonses of  the two different cell type.
IWRRL2


title: Rep11_IWRR, 1day

description:
The sample was collected from bESC11 co-culturing with MEF and treated with the IWR-1 removed medium. Reads were mapped to the bovine genome ARS-UCD1.3 as well as the mouse genome GRCm39 respectively to analyze distinct repsonses of  the two different cell type.
IWRRL11


title: WholeBlood-MDD-M-502

value: MDD


title: Rep8_IWRR, 1day

description:
The sample was collected from bESC8 co-culturing with MEF and treated with the IWR-1 removed medium. Reads were mapped to the bovine genome ARS-UCD1.3 as well as the mouse genome GRCm39 respectively to analyze distinct repsonses of  the two different cell type.
IWRRL8


title: WholeBlood-MDD-F-404

value: Female


title: WholeBlood-MDD-F-408


title: WholeBlood-MDD-M-501

value: Male


title: Rep4_IWR, 1day

description:
The sample was collected from bESC4 co-culturing with MEF and treated with the complete ESC medium. Reads were mapped to the bovine genome ARS-UCD1.3 as well as the mouse genome GRCm39 respectively to analyze distinct repsonses of  the two different cell type.
IWRL4

value: Complete medium with IWR-1


title: WholeBlood-MDD-M-401


title: Rep8_IWR, 1day

description:
The sample was collected from bESC8 co-culturing with MEF and treated with the complete ESC medium. Reads were mapped to the bovine genome ARS-UCD1.3 as well as the mouse genome GRCm39 respectively to analyze distinct repsonses of  the two different cell type.
IWRL8


title: Rep1_IWR, 1day

description:
The sample was collected from bESC1 co-culturing with MEF and treated with the complete ESC medium. Reads were mapped to the bovine genome ARS-UCD1.3 as well as the mouse genome GRCm39 respectively to analyze distinct repsonses of  the two different cell type.
IWRL1


title: Rep11_IWR, 1day

description:
The sample was collected from bESC11 co-culturing with MEF and treated with the complete ESC medium. Reads were mapped to the bovine genome ARS-UCD1.3 as well as the mouse genome GRCm39 respectively to analyze distinct repsonses of  the two different cell type.
IWRL11


title: Rep2_IWR, 1day

description:
The sample was collected from bESC2 co-culturing with MEF and treated with the complete ESC medium. Reads were mapped to the bovine genome ARS-UCD1.3 as well as the mouse genome GRCm39 respectively to analyze distinct repsonses of  the two different cell type.
IWRL2


title: WholeBlood-MDD-F-323


title: WholeBlood-MDD-M-515


title: WholeBlood-MDD-M-315


title: WholeBlood-MDD-M-322


title: SCHU_P0_rep1

description: Gene expression in Francisella tularensis subsp. tularensis SCHU P0 replicate1


title: WholeBlood-MDD-F-314


title: WholeBlood-MDD-M-313


title: WholeBlood-MDD-M-303


title: WholeBlood-MDD-F-309


title: WholeBlood-MDD-M-302


title: WholeBlood-MDD-F-222


title: 24hr CpG Stimulated CD23+ Follicular B Cells, Xist cKO, Biological Rep 4

city: PHILADELPHIA

first: MONTSERRAT

last: ANGUERA

state: PA

address: 380 S. University Ave, Room 390EB

department: Biomedical Sciences

institute: University of Pennsylvania

description: Library name: Sample 15

data_processing:
Data quality was assessed using FastQC
Reads were aligned to a C57BL/6J reference genome (GRCm38) using STAR (v2.7.1a).
Read counts were calculated using STAR quantMode “GeneCounts”.
Assembly: GRCm38
Supplementary files format and content: Tab separated file type containing reads per gene as output by STAR.

source_name: Spleen

growth_protocol: B cell subsets were isolated from the spleens of mice using fluorescence-activated cell sorting (FACS)

extract_protocol:
RNA was extracted using the QIAGEN RNeasy Micro Kit according to manufacturer's protocol.
RNA libraries were prepared with Takara/Clontech SMARTer-seq Pico V3 (low input total transcriptome; FFPE/degraded)

treatment_protocol: Freshly sorted cells or cells stimulated in vitro with CpG (TLR9 agonist) for 24 hours were stored in 500ul TRIzol LS Reagent and frozen at -80C until RNA extraction.

value: Spleen

value: CD23+ B Cell

value: Xist cKO

value: CpG (24hr)


title: 24hr CpG Stimulated CD23+ Follicular B Cells, WT, Biological Rep 2

description: Library name: Sample 9

value: None (naïve)


title: 24hr CpG Stimulated CD23+ Follicular B Cells, Xist cKO, Biological Rep 2

description: Library name: Sample 13


title: 24hr CpG Stimulated CD23+ Follicular B Cells, Xist cKO, Biological Rep 3

description: Library name: Sample 14


title: WholeBlood-MDD-M-219


title: Naïve CD23+ Follicular B Cells, Xist cKO, Biological Rep 4

description: Library name: Sample 7


title: WholeBlood-MDD-F-216


title: 24hr CpG Stimulated CD23+ Follicular B Cells, Xist cKO, Biological Rep 1

description: Library name: Sample 12


title: Naïve CD23+ Follicular B Cells, Xist cKO, Biological Rep 2

description: Library name: Sample 5


title: 24hr CpG Stimulated CD23+ Follicular B Cells, WT, Biological Rep 3

description: Library name: Sample 10


title: WholeBlood-MDD-F-211


title: 24hr CpG Stimulated CD23+ Follicular B Cells, WT, Biological Rep 1

description: Library name: Sample 8


title: Naïve CD23+ Follicular B Cells, Xist cKO, Biological Rep 3

description: Library name: Sample 6


title: Naïve CD23+ Follicular B Cells, WT, Biological Rep 1

description: Library name: Sample 1


title: Mouse neocortex, single-cell gene expression library, batch 10

city: Chapel Hill

first: Hyejung

last: Won

state: NC

address: 116 Manning Dr #6110

department: Genetics

institute: UNC Chapel Hill

description:
Library name: sc20230613inlt1M
10x Genomics 3' (version 3.1) library

data_processing:
Single-cell gene and gRNA library sequencing files were processed using the cellranger count 6.1.2 pipeline for demultiplexing, barcoded processing, gene counting and aggregation.
Assembly: mm10
Supplementary files format and content: Tab-separated value files, matrices, comma-separated values and cloupe files.

source_name: Brain, neocortex

extract_protocol:
Briefly, minced neocortical tissue was incubated in papain/DNase solution with constant agitation for 90 min at 37ºC in a 5% CO2 incubator. After chemical digestion, the tissue was gently triturated using a serological pipet. Dissociated cells were filtered through a 70-μm cell strainer, and protease inhibitor and DNase were added before pelleting at 300g for 5 min. Cells were resuspended in Hibernate A (BrainBits, cat. no. HALF500) / B27 (ThermoFisher, cat. no. A3582801) / 10% FBS resuspension buffer. Y-27632 ROCK inhibitor (Selleck Chemicals, cat. no. S1049) was added to media in 1:1000 ratio to reduce cell death during single-cell prep. Next, live RFP-expressing cells were sorted by FACS and processed using the 10x Genomics 3' v3.1 Dual Index workflow for scRNA-seq library generation by the UNC Advanced Analytics (AA) Core. gRNA reads were separately enriched from cDNA using custom-design primers targeting the CROP-seq backbone sequence for assigning gRNAs to cells. The resulting libraries were sequenced with Illumina high-throughput sequencers (NextSeq2000 P2 or P3 for gene expression library, NovaSeq6000 SP for gRNA library). We used cycles R1 x i1 x i2 x R2 = 28 x 10 x 10 x 90, with 1% PhiX for gene library,  and cycles R1 x i1 x i2 x R2 = 28 x 10 x 10 x 42, with 20% PhiX for gRNA library.
Library preparation was done by UNC Advanced Analytics Core according to manufacturer instructions (Chromium 10x Genomics 3' v3.1 Dual Index Workflow).

value: Brain, neocortex

value: Cas9 heterozygous


title: WholeBlood-MDD-F-205


title: 24hr CpG Stimulated CD23+ Follicular B Cells, WT, Biological Rep 4

description: Library name: Sample 11


title: WholeBlood-MDD-M-207


title: WholeBlood-MDD-M-215


title: WholeBlood-Control-F-199

source_name: WholeBlood, Control, F

value: Control


title: WholeBlood-MDD-M-202


title: Mouse neocortex, single-cell gene expression library, batch 8

description:
Library name: sc20230502inlt2M
10x Genomics 3' (version 3.1) library


title: Naïve CD23+ Follicular B Cells, Xist cKO, Biological Rep 1

description: Library name: Sample 4


title: Mouse neocortex, single-cell gene expression library, batch 7

description:
Library name: sc20230502inlt1M
10x Genomics 3' (version 3.1) library


title: WholeBlood-MDD-F-210


title: Mouse neocortex, single-cell gene expression library, batch 9

description:
Library name: sc20230516inlt1F
10x Genomics 3' (version 3.1) library


title: Naïve CD23+ Follicular B Cells, WT, Biological Rep 3

description: Library name: Sample 3


title: WholeBlood-Control-F-196


title: WholeBlood-Control-M-195


title: Mouse neocortex, single-cell gene expression library, batch 5

description:
Library name: sc20230418inlt1F
10x Genomics 3' (version 3.1) library


title: WholeBlood-Control-F-193


title: Naïve CD23+ Follicular B Cells, WT, Biological Rep 2

description: Library name: Sample 2


title: WholeBlood-Control-M-197


title: WholeBlood-Control-F-194


title: Mouse neocortex, single-cell gene expression library, batch 2

description:
Library name: sc20230130inlt1F
10x Genomics 3' (version 3.1) library


title: Mouse neocortex, single-cell gene expression library, batch 3

description:
Library name: sc20230130inlt2M
10x Genomics 3' (version 3.1) library


title: WholeBlood-MDD-M-208


title: WholeBlood-Control-F-192


title: Mouse neocortex, single-cell gene expression library, batch 4

description:
Library name: sc20230131inlt1M
10x Genomics 3' (version 3.1) library


title: WholeBlood-Control-F-191


title: Young, male, biological replicate 3, YY1 CUT&RUN

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
male_Y3_YY1

data_processing:
Briefly, Illumina sequencing reads (~107 million paired end reads per sample) were de-multiplexed generating compressed FASTQ files by bcl-convert (v4.1.50).
Paired-end reads were trimmed using Trim Galore (v0.6.7) to remove the adapter and qualities of the FASTQs assessed using FASTQC (v0.11.9).
Reads were then aligned to the mouse genome (mm10) using Bowtie2 (v2.5.3).
SAM output files from Bowtie2 were filtered to retain alignments with a minimum mapping quality of 2 using samtools (v1.19) and aligned reads mapping to ENCODE blacklist regions were removed using intersect function in bedtools (v2.30.0).
RPKM normalized bigWig files were generated using the bamCoverage function in deepTools (v3.5.4).
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: microglia isolated from fresh whole brain

extract_protocol:
CUT&RUN was performed using the CUT&RUN Assay Kit (cell signaling technology, 86652) following the manufacturer's instructions. Briefly, 500,000 microglia isolated from one biological replicate were used for each reaction. The cells and concanavalin A-coated magnetic beads slurry were incubated with antibodies overnight at 4 °C. DNA was purified from enriched chromatin samples using NEB Monarch® DNA Cleanup Kit(NEB, T1130) following the manufacturer's instructions.
Libraries were constructed using all CUT&RUN-enriched DNA with the NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S).The libraries were size-selected and purified with SPRIselect (Beckman, Coulter B23318), and quality checked on Agilent Bioanalyzer® High Sensitivity DNA chip (Agilent Technologies,5067-4626).  Equimolar amounts of each library were combined, and the pooled library was further quantified using a NEBNext Library Quant Kit (New England Biolabs).

value: 16 weeks

value: YY1 (Cell Signaling Technology, 46395s,Lot 1)


title: WholeBlood-Control-M-190


title: Young, male, biological replicate 3, cebpb CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
male_Y3_cebpb

value: microglia isolated from fresh whole brain

value: C/EBP beta (Santa cruz, sc-7962,Lot 1623)


title: WholeBlood-Control-M-189


title: WholeBlood-Control-F-198


title: Young, male, biological replicate 2, igg CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
male_Y2_igg


title: Mouse neocortex, single-cell gene expression library, batch 6

description:
Library name: sc20230425inlt1M
10x Genomics 3' (version 3.1) library


title: Young, male, biological replicate 2, YY1 CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
male_Y2_YY1


title: Mouse neocortex, single-cell gene expression library, batch 1

description:
Library name: sc20221114inlt1F
10x Genomics 3' (version 3.1) library


title: WholeBlood-Control-M-188


title: Young, male, biological replicate 1, igg CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
male_Y1_igg


title: WholeBlood-Control-F-187


title: Young, male, biological replicate 1, YY1 CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
male_Y1_YY1


title: Young, male, biological replicate 2, cebpb CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
male_Y2_cebpb


title: WholeBlood-Control-F-182


title: WholeBlood-Control-M-183


title: WholeBlood-Control-F-180


title: Old, male, biological replicate 3, YY1 CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
male_O3_YY1

value: 90 weeks


title: Old, male, biological replicate 2, igg CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
male_O2_igg


title: WholeBlood-Control-F-184


title: WholeBlood-Control-F-178


title: Young, male, biological replicate 1, cebpb CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
male_Y1_cebpb


title: Old, male, biological replicate 2, cebpb CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
male_O2_cebpb


title: WholeBlood-Control-F-185


title: Old, male, biological replicate 1, igg CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
male_O1_igg


title: WholeBlood-Control-M-181


title: WholeBlood-Control-M-177


title: Old, male, biological replicate 2, YY1 CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
male_O2_YY1


title: WholeBlood-Control-M-175


title: Old, male, biological replicate 1, cebpb CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
male_O1_cebpb


title: Old, male, biological replicate 1, YY1 CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
male_O1_YY1


title: WholeBlood-Control-F-174


title: Young, female, biological replicate 2, cebpb CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
female_Y2_cebpb

value: 14 weeks


title: WholeBlood-Control-M-186


title: Young, female, biological replicate 1, YY1 CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
female_Y1_YY1


title: WholeBlood-Control-M-171


title: Young, female, biological replicate 1, cebpb CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
female_Y1_cebpb


title: Old, female, biological replicate 3, igg CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
female_O3_igg

value: 88 weeks


title: WholeBlood-Control-F-168

value: Female


title: Old, female, biological replicate 3, YY1 CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
female_O3_YY1


title: WholeBlood-Control-F-167


title: Old, female, biological replicate 2, YY1 CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
female_O2_YY1


title: WholeBlood-Control-M-162

value: Male


title: Old, female, biological replicate 1, cebpb CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
female_O1_cebpb


title: WholeBlood-Control-F-161


title: WholeBlood-Control-F-159


title: RUN1_KO_mRNA

city: Marseille

first: Romain

last: Fenouil

address: Parc Scientifique et Technologique de Luminy - Case 906

department: CIML

institute: CNRS

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
FASTQ raw files were aligned to the mouse genome reference (mm10) using 10x Genomics Cell Ranger 7.0.1, which performs filtering, barcode counting, and unique molecular identifier (UMI) counting.
After individual quality control, all count matrices were loaded and processed together using R package Seurat (4.1.0).
Assembly: mm10
Supplementary files format and content: Cellranger output: barcodes.tsv is a list of filtered barcodes associated with count matrix
Supplementary files format and content: Cellranger output: features.tsv is a list of filtered features associated with count matrix
Supplementary files format and content: Cellranger output: matrix.mtx is the (sparse) matrix containing feature counts across all selected barcodes

source_name: Small intestine

extract_protocol:
The small intestine was collected from WT or VilCreIfnlr1fl/fl mice three days after targeted irradiation. The luminal content was removed by flushing with HBSS (without Mg2+/Ca2+). The epithelial tissue was then dissociated by incubating with HBSS containing Pen/Strep (100X), 10 mM HEPES, 2% FBS, and 15 mM EDTA in a shaking incubator. The intestinal crypt cells were isolated by passing through 100 µm and 70 µm strainers and then stained with an anti-EPCAM Biotin and an anti-CD45 FITC antibody. The cells were washed with FACS buffer (PBS, 5% BSA, 2 mM EDTA), followed by staining with TotalSeqB PE Streptavidin. After washing, the cells were resuspended in PBS, stained with a viability dye, and then washed and resuspended in FACS buffer. Live epithelial cells were sorted using a FACSAria III (Becton Dickinson) based on the presence of the PE signal and the absence of the FITC signal. The sorted cells from different samples were pooled into one WT and one VilCreIfnlr1fl/fl sample in PBS supplemented with 0.04% BSA.
HTO and DNA libraries were sequenced at the CIML genomic facility using a P3 flowcell in Illumina NextSeq 2000. 2 independent experiments were performed and analyzed separately.

treatment_protocol: WT or VilCreIfnlr1fl/fl mice were sedated with a mix of ketamine (100 mg/ml) and xylazine (20 mg/ml) intraperitoneally. Mice then received gamma irradiation in a Best Theratronics Gammacell 40 Cesium 137-based irradiator with lead shielding of the head, thorax, and upper extremities to prevent bone marrow failure. Mice received either 11 Grey of gamma irradiation to assess tissue restitution in small intestinal crypts.

value: Small intestine

value: Epithelial

tag: library type

value: mRNA

tag: antibodies/tags

value: Irradiation


title: Old, male, biological replicate 3, cebpb CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
male_O3_cebpb


title: Old, female, biological replicate 1, YY1 CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
female_O1_YY1


title: WholeBlood-Control-F-158


title: RUN1_WT_HTO

description: Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

library_source: other

molecule: protein

value: HTO

value: WT1 TotalSeq-B0952 PE Streptavidin / WT2 TotalSeq-B0953 PE Streptavidin / WT3 TotalSeq-B0954 PE Streptavidin

value: WT


title: WholeBlood-Control-F-157

value: Control


title: WholeBlood-Control-M-170


title: ScRNA-seq, hashtag library

first: Magali

last: IRLA

address: 163, avenue de Luminy - Case 906

institute: Center of Immunology Marseille Luminy (CIML)

description: 220126_VH00228_82_AAAV3TVM5_LtaTReg_EXP1_TregSpl_HTO

data_processing:
Raw fastq files from gene expression libraries and Hashtag libraries were processed using 10x Genomics Cell Ranger v6.0.1 software, with alignment on the GRCm38 reference genome.
For each experiment, cells with less than 200 genes detected and genes detected in less than 3 cells were removed. We further excluded bad quality cells expressing less than 603 and more than 4,128 UMI, more than 9.94% mitochondrial genes or less than 11.5% ribosomal genes. These threshold values were set manually using the ShIVA interface (Aussel, 2022-bioarxiv).  The QC filtering removed 717 cells and leav 4151 cells for downstream analysis.
HTO barcodes for sample demultiplexing after hashing were normalized for each cell using a centered log ratio (CLR) transformation across cells implemented in the Seurat function NormalizeData. Cells were demultiplexed using Seurat MULTIseqDemux function and barcodes assigned as doublets or negative were excluded from further analysis.
The resulting filtered UMI count matrices were log-normalized with Seurat NormalizeData with a scale factor of 10,000 and centered using the Seurat ScaleData function.
Assembly: GRCm38
Supplementary files format and content: Gzipped tab separated value and matrix files containing the cellular bacrodes (barcodes.tsv.gz), the liste of features (features.tsv.gz) and the matrix count of UMI (matrix.mtx.gz).

extract_protocol:
Single cell suspensions of spleens were obtained by pressing organs through a 70-μm nylon mesh cell strainer with a plastic plunge in PBS 5%BSA 1mM EDTA. Splenic cell suspensions were incubated with red blood cell lysis buffer for 3 minutes at room temperature and enriched for CD4+ T cells by depletion of CD8+ and CD19+ cells using the autoMACS® Pro Separator with the Deplete program (Miltenyi). We used cell hashing with hashtag oligonucleotides (HTO) to multiplex the two samples from 2 individual mice. Cell surface staining used for gating Foxp3+ Treg cells and staining for distinct barcoded anti-mouse CD45 antibody (Biolegend; A0308 and A0307 for WT and Lta-/- Treg cells, respectively) were performed in PBS 5%BSA 1mM EDTA for 30 min on ice. For each sample, Foxp3+ Treg cells (Live Dead-CD4+Foxp3eGFP+) were bulk-sorted with BD FACS Aria II. Sorted cell samples (20,000 WT Treg cells and 20,000 Lta-/-Treg cells) were pooled and loaded in a single capture well for subsequent 10x Genomics Single Cell 3’ v3.1 workflow.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics). Briefly, Foxp3+ Treg cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. The resulting libraries were pooled and sequenced together on an Illumina NextSeq2000 platform with P2 flow cells (100 cycles).

value: Spleen

value: Treg cells

value: C57BL/6 Foxp3eGFP Lta WT/WT or Lta-/-


title: WholeBlood-Control-F-169


title: WholeBlood-Control-F-155


title: WholeBlood-Control-M-154


title: ScRNA-seq, mRNA library

description: 220126_VH00228_82_AAAV3TVM5_LtaTReg_EXP1_TregSpl_mRNA


title: WholeBlood-Control-F-165


title: Old, female, biological replicate 2, cebpb CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
female_O2_cebpb

value: microglia isolated from fresh whole brain

value: C/EBP beta (Santa cruz, sc-7962,Lot 1623)


title: WholeBlood-Control-M-149


title: RUN1_KO_HTO

value: KO1 TotalSeq-B0952 PE Streptavidin / KO2 TotalSeq-B0953 PE Streptavidin / KO3 TotalSeq-B0954 PE Streptavidin


title: WholeBlood-Control-F-150


title: WholeBlood-Control-F-151


title: WholeBlood-Control-M-166


title: WholeBlood-Control-F-160


title: Old, female, biological replicate 1, igg CUT&RUN

description:
Cleavage Under Targets & Release Using Nuclease (CUT&RUN)
female_O1_igg

value: 88 weeks


title: Non-inflammatory dilated cardiomyopathy 10367

city: Maastricht

first: Maurits

last: Sikking

address: Universiteitssingel 50

country: Netherlands

institute: Maastricht University

data_processing:
Bcl2fastq 1.20 used for base-calling and fastq generation
Alignment was performed using STAR, default settings
Assembly: UCSC Hg38
Supplementary files format and content: tab delimeted raw reads per RefSeq annotated gene-transcript

source_name: Endomyocardial biopsy

extract_protocol:
miRVana
Illumina TruSeq LT stranded, Samples random pooled per 12.

value: Endomyocardial biopsy

value: Frozen endomyocardial biopsy in bulk


title: Non-inflammatory dilated cardiomyopathy 10299


title: Non-inflammatory dilated cardiomyopathy 10297


title: Non-inflammatory dilated cardiomyopathy 10327


title: Inflammatory dilated cardiomyopathy 10248


title: Inflammatory dilated cardiomyopathy 10239


title: WholeBlood-Control-F-145

value: Female


title: Inflammatory dilated cardiomyopathy 10168


title: WholeBlood-Control-M-147

value: Male


title: Inflammatory dilated cardiomyopathy 10162


title: RUN1_WT_mRNA

value: Small intestine

value: Epithelial

value: mRNA


title: WholeBlood-Control-M-144


title: Inflammatory dilated cardiomyopathy 10152


title: WholeBlood-Control-F-141


title: WholeBlood-Control-M-140


title: Non-inflammatory dilated cardiomyopathy 10149


title: Inflammatory dilated cardiomyopathy 10086


title: WholeBlood-Control-F-139


title: WholeBlood-Control-F-137


title: Inflammatory dilated cardiomyopathy 10085


title: WholeBlood-Control-M-135


title: WholeBlood-Control-F-134


title: Inflammatory dilated cardiomyopathy 10076


title: Inflammatory dilated cardiomyopathy 835


title: WholeBlood-Control-M-133


title: Inflammatory dilated cardiomyopathy 10053


title: WholeBlood-Control-M-146


title: WholeBlood-Control-F-136


title: Inflammatory dilated cardiomyopathy 823


title: WholeBlood-Control-F-132


title: Non-inflammatory dilated cardiomyopathy 762


title: Non-inflammatory dilated cardiomyopathy 730


title: WholeBlood-Control-F-130


title: WholeBlood-Control-F-173


title: Inflammatory dilated cardiomyopathy 691


title: Inflammatory dilated cardiomyopathy 699


title: WholeBlood-Control-F-127


title: WholeBlood-Control-F-129


title: WholeBlood-Control-F-126


title: WholeBlood-Control-M-143


title: WholeBlood-Control-F-124


title: WholeBlood-Control-F-125


title: Inflammatory dilated cardiomyopathy 603


title: Inflammatory dilated cardiomyopathy 616


title: WholeBlood-Control-F-123


title: Inflammatory dilated cardiomyopathy 586


title: Inflammatory dilated cardiomyopathy 579


title: WholeBlood-Control-M-122


title: WholeBlood-Control-F-121


title: Inflammatory dilated cardiomyopathy 505


title: Inflammatory dilated cardiomyopathy 602


title: Inflammatory dilated cardiomyopathy 516


title: WholeBlood-Control-F-131


title: WholeBlood-Control-M-116


title: WholeBlood-Control-F-118


title: Non-inflammatory dilated cardiomyopathy 434


title: Inflammatory dilated cardiomyopathy 732


title: WholeBlood-Control-F-113


title: Inflammatory dilated cardiomyopathy 328


title: Inflammatory dilated cardiomyopathy 502


title: WholeBlood-Control-F-110


title: WholeBlood-Control-F-109


title: Inflammatory dilated cardiomyopathy 293


title: Inflammatory dilated cardiomyopathy 326


title: WholeBlood-Control-F-107


title: Non-inflammatory dilated cardiomyopathy 685


title: WholeBlood-Control-M-106


title: Non-inflammatory dilated cardiomyopathy 287


title: Inflammatory dilated cardiomyopathy 214


title: WholeBlood-Control-F-105


title: Inflammatory dilated cardiomyopathy 141


title: WholeBlood-Control-M-104


title: UBP_3

city: Seoul

first: Nagendra

middle: Kumar

last: Kaushik

state: Nowon-Gu

address: 20 Kwangwoongil, Wolgye Dong 447-1

department: Biophysics

country: South Korea

institute: Kwangwoon University

description: UBP1-overexpressed MCF7 cells, Day 2

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hsa (mirbase) whole genome using Bowtie2
Read count extraction using bedtools.
Quantile normalization was performed by EdgeR.
Assembly: hsa
Supplementary files format and content: tab-delimited text files include normalized values for each Sample

source_name: UBP1-overexpressed MCF7 cells, Day 2

growth_protocol: Cells were cultured in DMEM media supplemented in 10% FBS with antibiotics.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). Total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using NEBNext Multiplex Small RNA Library Prep kit (New England BioLabs, Inc., USA) according to the manufacturer’ instructions.

treatment_protocol: Cells were overexpressed with UBP1 and incubated for two additional days for the analysis.

value: Breast Cancer cells

value: UBP-1 overexpression


title: WholeBlood-Control-M-103

value: Control


title: UBP_2

description: UBP1-overexpressed MCF7 cells, Day 2


title: WholeBlood-Control-F-111


title: WholeBlood-Control-M-102


title: Dicty, whole organism, 8h, rep2

city: Moscow

first: Irina

last: Zhegalova

address: 34/5 Vavilova Street

institute: Institute of Gene Biology

data_processing:
reads were aligned using hisat2 (v2.1.0) with default parameters except maximum intro length set to 3100 bp
only uniquely maped reads were selected.
count matrix was obtained by htseq-count (v0.11.1) using gff-file from dictyBase with gene coordinates.
Assembly: dicty_2.7
Supplementary files format and content: Tab-delimited file contains raw-counts for each Sample
Supplementary files format and content: bigwig with reads normalized on library size

source_name: whole organism

extract_protocol:
108 of cells from fresh culture (1-2 days, 0.5-1×106 cells per ml) or from development plates were harvested for 5 minutes at 400 g (room temperature), washed with 5 ml of 1× KK2 buffer and snap-frozen in a liquid nitrogen. RNA extraction was carried out using an RNeasy Mini kit (Qiagen) following the manufacturer’s instructions. RNA quality was assessed using capillary electrophoresis with a Bioanalyzer 2100 (Agilent).
For library preparation, a TruSeq RNA Sample Prep kit v2 (Illumina) was used following the manufacturer’s instructions. After preparation, libraries were quantified using a Qubit fluorometer and quantitative PCR and sequenced with HiSeq 2000 with read lengths of 51 nt.

value: whole organism

tag: time


title: UBP_1

description: UBP1-overexpressed MCF7 cells, Day 2

tag: cell line


title: control2

description: MCF7 cells, control, Day 2

source_name: MCF7 cells, control, Day 2

tag: cell type

value: No overexpression


title: control3

description: MCF7 cells, control, Day 2


title: Dicty, whole organism, 8h, rep1


title: WholeBlood-Control-M-101


title: Dicty, whole organism, 5h, rep2


title: A5_pooled_Input

city: Tempe

first: Vel

last: Murugan

state: Arizona

address: 727 E. Tyler St.

department: Biodesign Institute

institute: Arizona State University

data_processing:
Cutadapt (v 1.18) was used to trim raw sequencing reads.
BWA (v 0.7.17 50) was used to align reads to the human reference genome (GRCh38.p12, hg38).
MethylQA (v 0.2.1) was used to generate genome density for MeDIP-Seq data and reads mapping and CpG coverage statistics.
MACS2 (v 2.2.6) were used to call peaks with input as a control.
Assembly: hg38
Supplementary files format and content: narrowPeak (except for Input sample) (http://genome.ucsc.edu/FAQ/FAQformat.html#format12)

source_name: PBMC

extract_protocol:
Frozen PBMCs were centrifuged twice at 600x g for 10 minutes at 20°C and washed with RPMI+ 20% FBS. The cell pellet was resuspended in PBS to achieve a final volume of 7,500 cells per 1µL of suspension. An equal volume of the MNase digestion buffer (0.02 U/µL MNase (Thermo Scientific, Cat. No: 88216) in 2x lysis buffer was added to the cell suspension and gently vortexed. The cell suspension was then incubated on ice for 20 minutes, followed by incubation at 55°C water bath for 10 minutes. The digestion reaction was terminated using 30 mM EGTA. Then the digested chromatin was protease k (Ambion™) treated at 55°C and then pre-cleared with 1:2 KAPA Pure beads (Roche Cat. No: 07983298001). The quality and quantity of fragmented DNA were verified using agarose gel (1.5%) electrophoresis and Qubit® 4.0 Fluorometer (Thermo Fisher Scientific, Waltham, Massachusetts, U.S), respectively.
Illumina KAPA LTP Library Preparation Kit was employed for library construction (Cat. No: KK8233). Purified, fragmented DNA was end-repaired to produce 5′-phosphorylated and blunt-ended dsDNA fragments. Unique Dual Indexes (UDIs) were ligated to 3'-A-tailed library fragments holding appropriate adapter sequences on both ends. DNA fragments were subjected to methylated DNA immunoprecipitation, followed by library amplification.

value: PBMC

value: Input


title: control1

description: MCF7cells, control, Day 2


title: Dicty, whole organism, 5h, rep1


title: Dicty, whole organism, 2h, rep2


title: A7_pooled_Input


title: Dicty, whole organism, 2h, rep1


title: A4_pooled_Input


title: Dicty, whole organism, 0h, rep1


title: A19_pooled_Input


title: A18_pooled_Input


title: A2_pooled_Input


title: A16_pooled_Input


title: A15_pooled_Input


title: A13_pooled_Input


title: A12_pooled_Input


title: A5_pooled_IP

value: 5 methylcytosine


title: A7_pooled_IP


title: A4_pooled_IP


title: A19_pooled_IP


title: Dicty, whole organism, 0h, rep2


title: A16_pooled_IP


title: A18_pooled_IP


title: A2_pooled_IP


title: A15_pooled_IP


title: sin3 vs. WT (grown in hyphae-inducing conditions at 37ºC for 180 min.) Rep 2

city: Salamanca

first: Angel

last: Domínguez

address: Plaza de los Doctores de la Reina

institute: University of Salamanca

description: mutant colony 5, WT pool WT

hyb_protocol: For transcriptional profiling C. albicans microarrays (Eurogentec) were prehybridised for 45 min at 42ºC in 5x SSC, 1% SDS and 1% BSA. Prehybridised microarrays were washed 5x with water, once with isopropanol and the washed arrays were air dried.  Before hybridization, concentrated Cy5- and Cy3-labeled cDNA from mutant and parental cells was mixed. Then 5 µl of denatured herring sperm salmon DNA (10mg/ml) was added. After DNA denaturation for 5 min at 95ºC, DIG easy hybridisation buffer (50% formamide, 10x SSC, 0.2% SDS, ROCHE) was incorporated up to a final volume of 60 µl. The mixture was applied on the prehybridised microarray, covered with a LifterSlip (60x24 mm, Sigma-Aldrich) and incubated over night in a humidified chamber (Corning) in a water bath at 42ºC. Hybridised microarrays were washed for 15 min in 2x SSC, 1% SDS, for 8 min in the same solution and twice for 5 min in 0,2x SSC. Then microarrays were dried by centrifugation at 1100 rpm at room temperature. Hybridisation for each strain was done in quadruplicate including one dye swap.

scan_protocol: The microarrays were scanned with a GenePix4000B scanner and intensity data were captured using the GenePix Pro version 6.0 software package(Axon).

data_processing: Data were analyzed in GeneSpring 5.0 sofware (Axon). Data were per-chip and per-spot normalized by intensity dependent (LOWESS) normalization applied to the print-tip region. Genes with differential expression were obtained by first filtering genes with a fold change >= 1.5 in at least one hybridisation and then applying a "satistical group comparison" (Wilconxon-Mann-Whitney test) and the multiple testing correction Benjamini and Hochberg False Discovery Rate (FDR) with p-value < 0.02. The second filter was introduced to control the stringency of the FDR correction, which is directly influenced by the number of genes analysed. Among genes selected by the test we considered only genes as being significantly regulated, if they were differentially expressed by at least a mean factor of 1.5 considering the four replicates.

source_name: cDNA, WT 37ºC, 180 min

label_protocol: 15 µg of total RNA were resuspended in 20 µl of RNase free H20 along with 40 U of Rnasin Ribonuclease Inhibitor (Promega) and then used for labelled cDNA synthesis following the protocol provided by Eurogentec with minor modifications. Total RNA of each strain was incubated with 0.5 mg oligo-d(T)-primer (Amersham Biosciences) and 0.1 pmol Candida albicans specific RT primer (Eurogentec) at 65º for 10 min. After adding 1x First-strand buffer, 10 mM dithiotreithol, 500 µM dATP, 500 µM dGTP, 500 µM dTTP, 25 µM dCTP (Roche), and 37,5 µM Cyanine 3-dCTP or Cyanine 5-dCTP (Amersham Biosciences),labelling occurred after addition of 200 U SuperScript II RTTM enzyme (Invitrogen) and incubation for 3 h at 42ºC in a dark environment. After 1h of incubation 200 U of fresh reverse transcriptase were added. The reaction was stopped by adding 5 µl EDTA (50 mM, pH8) and RNA was degraded by addition of 2 µl NaOH (10 N) following an incubation at 65ºC for 20 min. The reaction was neutralised by adding 4 µl acetic acid (5 M). Labelled cDNA was purified using Qia-quick PCR purification kit (Qiagen). cDNA was checked for proper labelling by spectrophotometric analysis measuring the amount of probe and incorporated dye and calculating the frequency of incorporation. Then it was stored at -20ºC until further use.

growth_protocol: For transcriptional profiling in exponential growth, strains were grown up to 5 x 107 cells/ml in a minimal medium YNB  (0,67% yeast nitrogen base-Difco, 10% glucose) at 28ºC.  For transcriptional profiling under hyphae-inducing conditions, strains were precultured in Lee´s medium at 28ºC (Lee et al., 1975) and then cells were washed, resuspended in water at 2 x 107 cells/ml, incubated at 28ºC during 2 hours, and starved during 24-48 h at 4ºC. 107 starved cells/ml were inoculated in Lee medium  and incubated at 37ºC. Samples of cells were extracted after 15, 60 and 180 min and then centrifuged and the resulting pellet was immediately frozen in liquid nitrogen and stored at -80ºC until further use.

extract_protocol: The isolation of total RNA were performed according to Galar Fungail standard operating procedures (www.pasteur.fr/recherche/unites/Galar_Fungail/)

tag: temperature

value: 37C for 180 min

source_name: cDNA, mutant 37ºC, 180 min


title: sin3 vs. WT (grown in hyphae-inducing conditions at 37ºC for 180 min.) Rep 1

description: mutant colony 5, WT pool WT


title: sin3 vs. WT (grown in hyphae-inducing conditions at 37ºC for 60 min.) Rep 4

description: mutant colony 5, WT pool WT

source_name: cDNA, mutant 37ºC, 60 min

value: 37C for 60 min

source_name: cDNA, WT 37ºC, 60 min


title: sin3 vs. WT (grown in hyphae-inducing conditions at 37ºC for 180 min.) Rep 3

description: mutant colony 6, WT pool WT


title: A13_pooled_IP

tag: tissue


title: sin3 vs. WT (grown in hyphae-inducing conditions at 37ºC for 180 min.) Rep 4

description: mutant colony 6, WT pool WT


title: sin3 vs. WT (grown in hyphae-inducing conditions at 37ºC for 60 min.) Rep 1

description: mutant colony 6, WT pool WT


title: A12_pooled_IP

tag: treatment


title: sin3 vs. WT (grown in hyphae-inducing conditions at 37ºC for 60 min.) Rep 3

description: mutant colony 5, WT pool WT


title: sin3 vs. WT (grown in hyphae-inducing conditions at 37ºC for 60 min.) Rep 2

description: mutant colony 6, WT pool WT


title: sin3 vs. WT (grown in yeast form at 28ºC) Rep 4

description: mutant colony 5, WT pool WT

source_name: cDNA, WT 28ºC

source_name: cDNA, mutant 28ºC


title: sin3 vs. WT (grown in hyphae-inducing conditions at 37ºC for 15 min.) Rep 3

description: mutant colony 5, WT pool WT

source_name: cDNA, mutant 37ºC, 15 min

value: 37C for 15 min

source_name: cDNA, WT 37ºC, 15 min


title: sin3 vs. WT (grown in hyphae-inducing conditions at 37ºC for 15 min.) Rep 4

description: mutant colony 5, WT pool WT


title: sin3 vs. WT (grown in hyphae-inducing conditions at 37ºC for 15 min.) Rep 2

description: mutant colony 6, WT pool WT


title: sin3 vs. WT (grown in hyphae-inducing conditions at 37ºC for 15 min.) Rep 1

description: mutant colony 6, WT pool WT


title: Memory D3

city: Bethesda

first: Farhat

last: Parween

state: MD

address: 10 Center Drive

department: NIAID

institute: NIH

description: Library name: Sample 25

data_processing:
Each library was down sampled to equivalent sequencing depth and libraries were merged with cellranger aggr v2.0.2 pipeline (10X Genomics). Data were imported into R Studio (R 3.6.2), and the Seurat package (Seurat 3.1.4, https://github.com/satijalab/seurat) was used to process and analyze the gene expression data.
Assembly: GRCh38
Supplementary files format and content: raw_feature_bc_matrix.h5

source_name: Human Blood

growth_protocol: After FACS sorting, cells were maintained in RPMI medium supplemented with 10% FBS in a 37 degree CO2 incubator

extract_protocol:
Human memory as well as CCR6highCCR2pos CD4+ T cells were isolated from the elutriated lymphocytes to approximately 90% purity by negative selection using RosetteSep human CD4+ T cell enrichment cocktail using Ficoll/Hypaque density centrifugation. After staining with the antibodies, cells were sorted by FACS.
Cells were loaded onto the Chromium Single Cell Library & Gel Bead Kit v3.1 (10x Genomics), to generate libraries for scRNA-seq .

treatment_protocol: After FACS prification, Memory  as well as CCR6highCCR2pos CD4+ T cells were stimulated with PMA for 3 hours.

value: Human Blood

value: Primary cells

value: CD4 T cells


title: CCR6highCCR2pos CD4 T cells D3

description: Library name: Sample 26


title: sin3 vs. WT (grown in yeast form at 28ºC) Rep 3

description: mutant colony 5, WT pool WT


title: sin3 vs. WT (grown in yeast form at 28ºC) Rep 2

description: mutant colony 3, WT pool WT


title: Hepatic Ly6C low macrophage, RNaseT2 deficient, replicate2

city: Tokyo

first: Ryota

last: Sato

address: 4-6-1 Shirokanedai, Minato-ku

institute: The Institute of Medical Science, The University of Tokyo

description:
Ion Ampliseq Transcriptome
Liver_RNaseT2KO-Ly6C low_2

data_processing:
The sequencing reads were aligned to mm10_AmpliSeq_Transcriptome_ERCC_v1 using Torrent Mapping Alignment Program (TMAP).
QC metrics and normalized read counts per gene were obtained using AmpliSeqRNA plug-in v5.2.0.3, a Torrent Suite Software v5.2.2 (Thermo Fisher Scientific).
Assembly: mm10
Supplementary files format and content: Comma-delimited text files include RPM values for each Sample.

source_name: Liver

growth_protocol: Splenic and hepatic macrophages were subjected to RNAseq analysis soon after FACS sorting.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kits (Qiagen). 1 ng of total RNA with RIN value of more than 7.0 was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using an Ion AmpliSeq Transcriptome Mouse Gene Expression kit (Thermo Fisher Scientific) according to the manufacturer's instructions.

treatment_protocol: No Treatment

value: Liver

value: Ly6C low CD11b(+) Fcgr4(+) Ly6G(-) SiglecF(-) NK1.1(-)

value: macrophage

tag: genotype

value: Rnaset2 -/-


title: sin3 vs. WT (grown in yeast form at 28ºC) Rep 1

description: mutant colony 3, WT pool WT

tag: strain


title: PaCa-44 tumor tissue, hRabMab1 + chemo 3

city: Cincinnati

first: Xiang

last: Zhang

state: OH

address: 160 Panzeca Way, Kettering Room 336

department: Environmental and Public Health Sciences

institute: University of Cincinnati

description:
BV12-3949
controlBV789_vs_comparisonBV101112.genes.deseq.counts.csv
controlBV789_vs_comparisonBV101112.genes.deseq.res.csv

data_processing:
Demultiplexing was performed using Illumina BaseSpace DRAGEN Analysis (v1.3.0). Adapter-trimmed fastq files were generated.
Reads alignment was perfomred via BaseSpace RNA-Seq Alignment app v2.0.2 with Mark Duplicates unchecked.
BaseSpace RNA-Seq Differential Expression app v1.0.1 was then used for differential gene expression analysis. The analyses used STAR for alignment and Salmon for quantification (Transcripts Per Million, TPM), followed by DESeq2 to identify differentially expressed genes.
Assembly: Homo sapiens (PAR-masked)/hg19 (RefSeq)
Supplementary files format and content: cvs files include gene counts for each Sample
Supplementary files format and content: cvs files include TPM values for each Sample (https://support.illumina.com/help/BS_App_RNASeq_DE_OLH_1000000071939/Content/Source/Informatics/Apps/DESeq2ResultFile_swBS.htm)

source_name: experimental tumor (orthotopic, pancreas)

growth_protocol: Tumor tissue was harvested at sacrifice and flash frozen in LN2.

extract_protocol:
Total RNA was harvested using RNAeasy kit (Qiagen); 1 ug of total RNA was used for library construction.
Using good quality of total RNA as input, NEBNext Poly(A) mRNA Magnetic Isolation Module combined with NEBNext Ultra II Directional RNA Library Prep kit was used for library construction.

treatment_protocol: We used KRAS mutant human PDAC cell line PaCa44 to generate aggressive primary orthotopic tumors. Experimental design featured orthotopic tumors formed by implantation of luciferase-labeled PaCa44 cells into the pancreata of mice. Four groups of mice were treated with vehicle; hRabMab1 alone; gemcitabine/paclitaxel (gem/PTX) alone; and the combination of hRabMab1 and gem/PTX).

tag: host

value: mouse

value: human pancreatic adenocarcinoma, ductal

value: WT

value: hRabMab1 + gemcitabine/paclitaxel


title: PaCa-44 tumor tissue, hRabMab1 + chemo 1

description:
BV10-3949
controlBV789_vs_comparisonBV101112.genes.deseq.counts.csv
controlBV789_vs_comparisonBV101112.genes.deseq.res.csv

value: experimental tumor (orthotopic, pancreas)


title: PaCa-44 tumor tissue, hRabMab1 + chemo 2

description:
BV11-3949
controlBV789_vs_comparisonBV101112.genes.deseq.counts.csv
controlBV789_vs_comparisonBV101112.genes.deseq.res.csv


title: Hepatic Ly6C high macrophage, RNaseT2 deficient, replicate2

description:
Ion Ampliseq Transcriptome
Liver_RNaseT2KO-Ly6C hi_2

value: Ly6C high CD11b(+) Ly6G(-) SiglecF(-) NK1.1(-)


title: Hepatic Ly6C low macrophage, RNaseT2 deficient, replicate3

description:
Ion Ampliseq Transcriptome
Liver_RNaseT2KO-Ly6C low_3


title: Hepatic Ly6C high macrophage, RNaseT2 deficient, replicate3

description:
Ion Ampliseq Transcriptome
Liver_RNaseT2KO-Ly6C hi_3


title: PaCa-44 tumor tissue, chemo alone 1

description:
BV7-3949
controlBV123_vs_comparisonBV789.genes.deseq.counts.csv
controlBV123_vs_comparisonBV789.genes.deseq.res.csv

value: gemcitabine/paclitaxel


title: PaCa-44 tumor tissue, chemo alone 3

description:
BV9-3949
controlBV123_vs_comparisonBV789.genes.deseq.counts.csv
controlBV123_vs_comparisonBV789.genes.deseq.res.csv


title: PaCa-44 tumor tissue, hRabMab1 alone 3

description:
BV6-3949
controlBV123_vs_comparisonBV456.genes.deseq.counts.csv
controlBV123_vs_comparisonBV456.genes.deseq.res.csv


title: Hepatic Ly6C low macrophage, WT, replicate1

description:
Ion Ampliseq Transcriptome
Liver_Wild-Ly6C low_1

value: wildtype


title: PaCa-44 tumor tissue, hRabMab1 alone 1

description:
BV4-3949
controlBV123_vs_comparisonBV456.genes.deseq.counts.csv
controlBV123_vs_comparisonBV456.genes.deseq.res.csv


title: Hepatic Ly6C low macrophage, RNaseT2 deficient, replicate1

description:
Ion Ampliseq Transcriptome
Liver_RNaseT2KO-Ly6C low_1


title: Hepatic Ly6C high macrophage, RNaseT2 deficient, replicate1

description:
Ion Ampliseq Transcriptome
Liver_RNaseT2KO-Ly6C hi_1


title: Hepatic Ly6C low macrophage, WT, replicate2

description:
Ion Ampliseq Transcriptome
Liver_Wild-Ly6C low_2


title: PaCa-44 tumor tissue, chemo alone 2

description:
BV8-3949
controlBV123_vs_comparisonBV789.genes.deseq.counts.csv
controlBV123_vs_comparisonBV789.genes.deseq.res.csv


title: Hepatic Kupffer cells, WT, replicate4

description:
Ion Ampliseq Transcriptome
Liver_Wild-Kupffer_4

value: F4/80(+) CD11b(int) Tim4(+) PDCA-1 low


title: PaCa-44 tumor tissue, vehicle 1

description:
BV1-3949
controlBV123_vs_comparisonBV456.genes.deseq.counts.csv
controlBV123_vs_comparisonBV456.genes.deseq.res.csv

value: vehicle


title: TS603 cells, Treated, 48 hours, Biological replicate 2

city: BETHESDA

first: Zachary

last: Sergi

address: 37 CONVENT DR

department: Neuro-Oncology Branch

institute: National Cancer Institute

data_processing:
The samples have 51 to 67 million pass filter reads with more than 96% of bases above the quality score of Q30
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (hg38) and the annotated transcripts using STAR
the gene expression quantification analysis was performed for all samples using STAR/RSEM tools
Assembly: Human hg38
Supplementary files format and content: tab-delimited text file includes raw count values for each sample

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen) and passed the quality control of the Agilent RNA ScreenTape syste
TruSeq Stranded mRNA Kit

value: IDH Mut

value: ZTR


title: TS603 cells, Treated, 48 hours, Biological replicate 3


title: PaCa-44 tumor tissue, vehicle 2

description:
BV2-3949
controlBV123_vs_comparisonBV456.genes.deseq.counts.csv
controlBV123_vs_comparisonBV456.genes.deseq.res.csv


title: Hepatic Ly6C low macrophage, WT, replicate3

description:
Ion Ampliseq Transcriptome
Liver_Wild-Ly6C low_3


title: PaCa-44 tumor tissue, hRabMab1 alone 2

description:
BV5-3949
controlBV123_vs_comparisonBV456.genes.deseq.counts.csv
controlBV123_vs_comparisonBV456.genes.deseq.res.csv


title: PaCa-44 tumor tissue, vehicle 3

description:
BV3-3949
controlBV123_vs_comparisonBV456.genes.deseq.counts.csv
controlBV123_vs_comparisonBV456.genes.deseq.res.csv


title: Hepatic Kupffer cells, WT, replicate1

description:
Ion Ampliseq Transcriptome
Liver_Wild-Kupffer_1


title: TS603 cells, Control, 48 hours, Biological replicate 3

value: Control


title: Splenic Ly6C low macrophage, RNaseT2 deficient, replicate4

description:
Ion Ampliseq Transcriptome
Spleen_RNaseT2KO-Ly6C low_4

source_name: Spleen

value: Spleen


title: Hepatic Ly6C high macrophage, WT, replicate3

description:
Ion Ampliseq Transcriptome
Liver_Wild-Ly6C hi_3

value: Liver


title: TS603 cells, Control, 48 hours, Biological replicate 1


title: Splenic Ly6C low macrophage, RNaseT2 deficient, replicate3

description:
Ion Ampliseq Transcriptome
Spleen_RNaseT2KO-Ly6C low_3

value: Ly6C low CD11b(+) Fcgr4(+) Ly6G(-) SiglecF(-) NK1.1(-)

value: macrophage


title: Hepatic Ly6C high macrophage, WT, replicate2

description:
Ion Ampliseq Transcriptome
Liver_Wild-Ly6C hi_2


title: GSC923 cells, Treated, 48 hours, Biological replicate 3

value: IDH WT


title: Hepatic Kupffer cells, WT, replicate2

description:
Ion Ampliseq Transcriptome
Liver_Wild-Kupffer_2


title: TS603 cells, Treated, 48 hours, Biological replicate 1


title: Splenic Ly6C low macrophage, RNaseT2 deficient, replicate1

description:
Ion Ampliseq Transcriptome
Spleen_RNaseT2KO-Ly6C low_1

value: Rnaset2 -/-


title: Splenic Ly6C high macrophage, RNaseT2 deficient, replicate2

description:
Ion Ampliseq Transcriptome
Spleen_RNaseT2KO-Ly6C hi_2


title: Hepatic Kupffer cells, WT, replicate3

description:
Ion Ampliseq Transcriptome
Liver_Wild-Kupffer_3


title: Hepatic Ly6C high macrophage, WT, replicate1

description:
Ion Ampliseq Transcriptome
Liver_Wild-Ly6C hi_1


title: TS603 cells, Control, 48 hours, Biological replicate 2


title: GSC923 cells, Treated, 48 hours, Biological replicate 2


title: Splenic Ly6C high macrophage, RNaseT2 deficient, replicate3

description:
Ion Ampliseq Transcriptome
Spleen_RNaseT2KO-Ly6C hi_3


title: GSC923 cells, Treated, 48 hours, Biological replicate 1


title: Splenic Ly6C high macrophage, RNaseT2 deficient, replicate1

description:
Ion Ampliseq Transcriptome
Spleen_RNaseT2KO-Ly6C hi_1


title: GSC923 cells, Control, 48 hours, Biological replicate 3


title: Splenic Ly6C low macrophage, WT, replicate3

description:
Ion Ampliseq Transcriptome
Spleen_Wild-Ly6C low_3


title: Splenic Ly6C low macrophage, WT, replicate2

description:
Ion Ampliseq Transcriptome
Spleen_Wild-Ly6C low_2


title: TS603 cells, Treated, 24 hours, Biological replicate 2


title: GSC923 cells, Control, 48 hours, Biological replicate 2


title: Splenic Ly6C low macrophage, RNaseT2 deficient, replicate2

description:
Ion Ampliseq Transcriptome
Spleen_RNaseT2KO-Ly6C low_2


title: GSC923 cells, Control, 48 hours, Biological replicate 1


title: Splenic Ly6C low macrophage, WT, replicate1

description:
Ion Ampliseq Transcriptome
Spleen_Wild-Ly6C low_1


title: Splenic Ly6C high macrophage, WT, replicate3

description:
Ion Ampliseq Transcriptome
Spleen_Wild-Ly6C hi_3


title: Splenic Ly6C high macrophage, WT, replicate1

description:
Ion Ampliseq Transcriptome
Spleen_Wild-Ly6C hi_1


title: TS603 cells, Control, 24 hours, Biological replicate 2


title: Splenic Ly6C high macrophage, WT, replicate2

description:
Ion Ampliseq Transcriptome
Spleen_Wild-Ly6C hi_2


title: TS603 cells, Treated, 24 hours, Biological replicate 3


title: TS603 cells, Control, 24 hours, Biological replicate 1


title: TS603 cells, Treated, 24 hours, Biological replicate 1


title: TS603 cells, Control, 24 hours, Biological replicate 3


title: GSC923 cells, Treated, 24 hours, Biological replicate 2


title: GSC923 cells, Treated, 24 hours, Biological replicate 3


title: GSC923 cells, Treated, 24 hours, Biological replicate 1