title: MACRO, CSF1R Capture-HiC, rep3

description: Library name: MACRO_CSF1R_Cap_rep3

data_processing:
Capture libraries were sequenced at a depth of at least ~60 million 50bp paired-end reads on the Illumina NextSeq 500 Sequencer. Fastq files were processed using the Capture Hi-C analysis feature of the HiC-Pro pipeline with the addition of a bed file containing the coordinates of the CSF1R target locus to be used as the capture target. Significant chromatin interactions were identified with CHiCAGO. This tool uses a restriction file for hg19 and Arima restriction enzymes, a baitmap file for CSF1R, a design file generated from the restriction fragment and baitmap files, and bam files outputted from the HiC-Pro pipeline as input files to determine significant interactions.  For monocyte and macrophage, differential interactions for 3 biological replicate experiments were detected with the Chicdiff R package .  Chicdiff pipeline was run using the default settings.
Assembly: hg19
Supplementary files format and content: BEDPE file of all capture interactions
Library strategy: Capture-C

extract_protocol:
In situ Hi-C in monocytes and HL60 cells was performed using the Arima HiC kit (Arima Genomics), following the user guide for mammalian cell lines. For the crosslinking step, according to the standard input protocol, 5 million cells were crosslinked then flash-frozen in aliquots of 1 million cells. After estimating the DNA input from crosslinked cells, one aliquot of cells (~2 ug of DNA) per condition was sufficient to proceed with the Hi-C protocol. Digestion and proximity ligation steps were done according to the kit protocol. Proximally ligated DNA underwent quality control checks for ligation, sonicated with the Covaris ME220 sonicator, then purified and size selected with AMPure XP Beads (Beckman Coulter) to obtain a fragment size distribution of 200-600bp prior to the biotin enrichment step.
For library preparation, end repair, dA-tailing, and adaptor ligation were performed using the NEB Next Ultra II DNA Library Prep kit for Illumina, following a protocol tailored for Arima Hi-C DNA. Capture Hi-C of the CSF1R gene locus was performed on Hi-C libraries from either the primary cells or HL-60 CRISPR clones using the myBaits Hybridization Capture for Targeted NGS kit (Arbor Biosciences).  Biotinylated RNA baits were designed to target a 35,413 bp sequence which included the genomic locus of the NM_001288705.2 transcript of CSF1R plus 1000bp upstream and downstream of the transcript. A total of 1,474 70-nucleotide (nt) baits were designed with 3X tiling. Raw sequences were BLASTed against the human genome to filter out 123 baits that did not meet stringent analysis criteria. To amplify and remove residual biotinylated nucleotides from the library samples for myBaits compatibility, Hi-C libraries were first PCR amplified for 7 cycles with the following conditions: 98°C for 2 min, 7 cycles of 98°C for 20 sec, 60°C for 30 sec, and 72°C for 60 sec, then a final extension of 72°C for 5 min. The reaction included 200ng of library DNA, 2X KAPA HiFI HotStart ReadyMix (Roche), and P5 and P7 universal primers (500nM). Amplification reactions were then incubated with prewashed Dynabeads MyOne Streptavidin C1 beads (Invitrogen) for 15 minutes, followed by collection of the supernatant for purification with Ampure XP beads. To the supernatant, 1.8X reaction volume of beads were added then incubated for 5 mins at room temperature. Samples were then placed on a magnetic separator for 10 mins then washed twice with 70% ethanol. Following the washes, beads were air-dried for 20 mins then DNA was eluted in 40uL of 0.1X TE. CSF1R capture of the purified libraries was then performed with the myBaits kit with some modifications to the manufacturer’s protocol. The hybridization step was done at 62°C for 25 hours. The final purification step was done using AMPure XP beads, following the same procedure done after pre-amplification step.


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 24 hours  White light - bio rep #1

status: Public on Jan 21 2026

type: SRA

city: Rehovot

first: Zohar

last: Meir

state: Shfela

address: Herzl 234

department: Mathematics & CS

country: Israel

institute: Weizmann Institute of Science

description:
Library name: White_light_timepoint_24_hours_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in White Light (50-60 μmol m⁻² s⁻¹)

library_source: transcriptomic

data_processing:
.Mapping and counting of transcripts were performed using the nf-core RNA-seq pipeline v3.14.0 (Di Tommaso et al., 2017; Harshil et al., 2024) on the VBC CLIP Batch Environment (CBE) cluster. Raw reads were mapped to the M. polymorpha Tak-1 reference genome assembly MpTak1_v5.1 and its corresponding gene annotation version MpTak1_v5.1_r1 (marchantia.info) using STAR (Dobin., et al., 2013). Reads were normalized by the sequencing depth of each library. After confirming low variability among biological replicates, the average expression value of each gene in each treatment was computed and used for downstream analyses
Assembly: Marchantia polymorpha Takaragaike-1 (MpTak1_v5.1)
Supplementary files format and content: Combined_marchantia_light_transcroptomes_matrix_averaged3replicates.csv; Comma-separated File; A matrix containing gene expression counts normalized by sampling depth (reads per 1 million reads); Each column shows the average computed out of three replicates for each treatment - for particular wavelength (Dark / White / Blue/ Red / Far-Red) for particular time point (0 / 30m / 60m / 180m / 720m-12h / 1440m-24h)
Supplementary files format and content: Combined_marchantia_light_transcroptomes_matrix_3replicates.csv; Comma-separated File; A matrix containing gene expression counts normalized by sampling depth (reads per 1 million reads); Each column indicating one of three replicates for each wavelength (Dark / White / Blue/ Red / Far-Red) for particular time point (0 / 30m / 60m / 180m / 720m-12h / 1440m-24h)

molecule: polyA RNA

organism: Marchantia polymorpha

source_name: Marchantia polymorpha Thallus

growth_protocol: Wild type Tak-1 gemmae were transferred onto medium plates (½ Gamborg, MES, 1% sucrose, and 1% agar), each plate containing three biological replicates. Gemmae were cultured under continuous white light at 23°C for eight days, followed by a 24-hour dark incubation.

extract_protocol:
For each condition, three biological replicates - each containing three individual Tak-1 plants - were collected in 2 mL Eppendorf tubes containing a stainless-steel bead (5 mm) and immediately frozen in liquid nitrogen at the defined timepoints of 0 min, 30 min, 60 min, 180 min, 12 hours, and 24 hours in dark, white light, blue light, red, far-red light, respectively. All samples were stored at -70°C until the full set was collected. Tissue from the samples was disrupted using a mixer mill (RETSCH MM 400) for 4 minutes at 30 Hz, with nitrogen-based cooling breaks during the process. Total RNA was extracted using the High-Performance RNA Bead Isolation kit from the Molecular Biology Service facility at the Vienna BioCenter. The kit employs a guanidine thiocyanate-based lysis method adapted from (Boom et al., 1990), and utilizes carboxylate-modified Sera-Mag Speed beads, with processing done on the KingFisher instrument (Thermo).
mRNA library preparation, including poly(A) capture and NovaSeq S4 PE150 XP RNA sequencing, was performed by the Next Generation Sequencing (NGS) VBC Core Facility. The 78 cDNA libraries, corresponding to 26 treatments with three biological replicates each.

treatment_protocol: After this dark period, the plates were either kept in darkness (control) or exposed to different light conditions: broad white light (WL), monochromatic blue light (BL, λmax = 430 nm), monochromatic red light (RL, λmax = 660 nm), or monochromatic far-red light (FRL, λmax = 730 nm). The light intensity in the monochromatic light treatments was increased by a factor of four, relative to the intensity of the respective wavelength in the standard white light condition.

tag: tissue

value: Marchantia polymorpha Thallus

tag: cell line

tag: genotype

value: Takaragaike-1 (Tak-1, male)

tag: treatment

value: White-light 1440 minutes / 24 hours


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 12 hours  White light - bio rep #2

description:
Library name: White_light_timepoint_12_hours_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in White Light (50-60 μmol m⁻² s⁻¹)

value: White-light 720 minutes / 12 hours


title: Testis_24Month_H3K27ac_Cuttag

city: Guangzhou

first: Jia

middle: Xiao

last: Huang

state: Guangdong

address: Zhongshan 2rd

country: China

institute: GDPH

description: Cuttag

library_source: genomic

data_processing:
reads were aligned to mm9 build of the human genome using Bowtie2 (v2.3.5.1).
Aligned reads were filtered and sorted by Samtools (v1.10) and Bedtools (v2.27.1).
MACS2 (v2.1.1) was applied for peak calling using the p-value cutoff 0.05
ROSE  was applied for the identification of super enhancers using the default parameters: -t 2500.
Assembly: mm9
Supplementary files format and content: bigwig files  includes track information(coverage and depth) of each sample
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: Testis

extract_protocol:
CUT&Tag for profiling histone H3K27ac was performed using Hyperactive Universal CUT&Tag Assay Kit for Illumina (vazyme, TD903-02) according to the instructions, and anti-H3K27ac antibody  (abcam, ab4729) were used to enrich target DNA fragments of Cd34-mesenchymal cells obtained by flow sorting.
TruePrep Index Kit for Illumina (v21.2, vazyme, TD202) were then used to DNA library construction according to the instructions.

value: Testis

tag: cell type

value: mesenchymal cells

tag: age

value: 2-Years old

value: Wild type

tag: chip antibody

value: Anti-Histone H3 (acetyl  K27) antibody (abcam,Cat#ab4729)


title: MACRO, CSF1R Capture-HiC, rep2

city: PHILADELPHIA

first: Sandra

last: Deliard

state: PA

address: 3601 Spruce St

country: USA

institute: The Wistar Institute

description: Library name: MACRO_CSF1R_Cap_rep2

organism: Homo sapiens

source_name: macrophage

value: macrophage


title: Testis_2Month_scRNA

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Single-cell RNA sequencing data of testicular samples was aligned and quantified using the Cell Ranger Software Suite (v3.0.2, 10X Genomics).
We captured approximately 7,000 to 120,000 cells each sample. The reads were aligned to the Mus musculus reference genome mm10, and after alignment, filtering, barcode counting, and UMI counting using the cell count pipeline provided by Cell Ranger, feature-barcode matrices were generated.
We performed quality control using the Seurat R package. Single cells that expressed less than 300 genes and more than 5,000 genes were excluded in case of the potential empty droplets and doublets, and genes expressed in fewer than 20 cells were excluded from further analysis. Individual cells that had less than 25% mitochondrial gene content were retained to remove the dead cells. Only eligible cells will be processed for downstream analysis.
We use the Functions built into Seurat (v4.0) packages to correct for batching effects and merge data sets.
Assembly: mm10
Supplementary files format and content: features.tsv, a file with the gene IDs; representing all genes quantified, barcodes.tsv, a file with the cell IDs, representing all cells quantified; matrix.mtx, a matrix of counts per gene for every cell.

molecule: total RNA

extract_protocol:
Testis samples from C57BL/6j mice were dissected aseptically using sterilized scissors. The samples were washed three times with DPBS (Thermo Fisher Scientific, 14190-144), and the tunica albuginea was carefully removed using sterilized tweezers to isolate the interstitial cells as our previous reported13, 14. The interstitial cells were then digested with 1 mg/ml collagenase type IV (Thermo Fisher Scientific, 17104019) in DMEM-F12 (phenol red-free) (Thermo Fisher Scientific, 21041025) at 37 °C for 10 minutes. During the digestion process, the tissues were gently pipetted up and down. The digestion process was halted by adding 2% FBS, and the resulting cell suspension was filtered through a 40-μm nylon mesh. The cells were then centrifuged at 350 rcf for 5 minutes at room temperature and suspended in DPBS or 2% FBS in DPBS for subsequent fluorescence-activated cell sorting analysis (FACSAria III, BD Bioscience). For the 10x Genomics platform, the cell count for each sample was determined using the Biorad Automated Cell Counter. After GEM generation and barcoding utilizing the Chromium Single Cell Library & Gel Bead Kit v3.1 (10x Genomics) according to User Guide, approximately 20,000 single cells per sample were captured by Chromium Controller (10x Genomics).
For library construction, utilizing the Chromium Single Cell Library & Gel Bead Kit v3.1 (10x Genomics) according to User Guide.

value: Interstitial cell

value: 2-Months old


title: MONO, CSF1R Capture-HiC, rep2

description: Library name: MONO_CSF1R_Cap_rep2

source_name: monocyte

value: monocyte


title: MONO, CTCF (CUT&RUN), rep 2

description: Library name: MONO_CTCF_CR_rep2

data_processing:
For analysis, sequencing files were demultiplexed and QC was performed on FASTQ files with FASTQC. Adaptors were trimmed from sequencing reads with TrimGalore, which were then aligned to the human genome (hg19) with BWA-MEM. Alignment files were sorted, filtered for a mapping quality > 10. Peak calling was done with MACS2. Motif analysis on peaks was done using MEME-ChIP
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Run

extract_protocol:
CUT&RUN was performed according to the published protocol by Skene and Henikoff with some modifications. Experiments were performed with primary monocytes and macrophages using antibodies for CTCF (Cell Signaling), SMC1 (Bethyl), PU.1 (Santa Cruz), and EGR1 (Bethyl). Approximately 250-500, 000 cells were used. For digestion, 1.5uL of pAG-mnase (Cell Signaling) was used. The alternative DNA extraction method was used to extract the final DNA product.
Sequencing libraries were generated with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB).


title: Testis_1Month_scRNA

description: 10x Genomics

value: 1-Month old


title: MONO, CTCF (CUT&RUN), rep 3

description: Library name: MONO_CTCF_CR_rep3


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 12 hours  White light - bio rep #1

description:
Library name: White_light_timepoint_12_hours_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in White Light (50-60 μmol m⁻² s⁻¹)


title: MONO, CSF1R Capture-HiC, rep3

description: Library name: MONO_CSF1R_Cap_rep3


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 180 minutes  White light - bio rep #3

description:
Library name: White_light_timepoint_180_minutes_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in White Light (50-60 μmol m⁻² s⁻¹)

value: White-light 180 minutes


title: HL60, Mutant2, untreated, CSF1R Capture-HiC

description: Library name: HL60_Mutant2_NT_CSF1R_Cap

value: FIRE mutant

value: untreated


title: MACRO, CSF1R Capture-HiC, rep1

description: Library name: MACRO_CSF1R_Cap_rep1


title: Testis_2week_H3K27ac_Cuttag

description: Cuttag

value: 2-Weeks old


title: Testis_3Month_H3K27ac_Cuttag

description: Cuttag

value: 3-Months old


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 180 minutes  White light - bio rep #1

description:
Library name: White_light_timepoint_180_minutes_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in White Light (50-60 μmol m⁻² s⁻¹)

value: Marchantia polymorpha Thallus

value: Takaragaike-1 (Tak-1, male)


title: MACRO, RNA

description: Library name: MACRO_RNA

data_processing:
For Total RNA-Seq, samples were sequenced on Illumina NextSeq 500, producing 42bp PE reads. Sequencing files were demultiplexed (Bcl2fastq, v2.17.1.14) and quality control (QC) was performed on FASTQ files using FASTQC. Adaptors were trimmed from sequencing reads with TrimGalore then aligned to the human genome (hg19) and transcriptome using the Spliced Transcripts Alignment to a Reference (STAR) software .  Alignment files were then filtered with Samtools for a mapping quality >10,  then sorted. Gene expression was quantified with RSEM and featureCounts . For differential gene expression analysis, the R package DESeq2  was used with the thresholds log2 fold change > 1 and FDR < 0.05.
For 3'mRNA-seq, libraries were sequenced on the Illumina NextSeq 500 at 10 million 75bp single-end reads. Following demultiplexing and quality control, sequencing reads were trimmed with TrimGalore then aligned to the human genome (hg19) and transcriptome using the STAR software . Alignment files were then filtered with Samtools for a mapping quality >10,  then sorted. Gene expression was quantified with RSEM  and featureCounts. For differential gene expression analysis, the R package DESeq2  was used with the thresholds log2 Fold Change > 1 and FDR < 0.05.
Assembly: hg19
Supplementary files format and content: raw gene counts

extract_protocol:
For both Total RNA-seq and 3'mRNA-seq, Total RNA was extracted using the Zymo Direct-zol RNA Mini-Prep (50) with TRI Reagent kit (Zymo Research). RNA quality was determined by the RNA Integrity Number (RIN) using TapeStation RNA ScreenTape (Agilent). All retained RNA samples had a RIN > 8. 1 mg of total RNA was depleted of ribosomal RNA using the NEBNext rRNA depletion kit (New England Biolabs) for Total RNA-seq.
rRNA-depleted RNA was purified with the miRNEasy kit (QIAGEN) and used to produce barcoded RNA sequencing libraries with the NEBNext Ultra Directional RNA Library Prep kit (New England Biolabs) for Total RNA-seq. For 3'mRNA-seq, sequencing libraries were prepared using the QuantSeq 3′-mRNA Seq Library Prep Kit for Illumina (Lexogen) from 500ng of total RNA.


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 12 hours  White light - bio rep #3

description:
Library name: White_light_timepoint_12_hours_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in White Light (50-60 μmol m⁻² s⁻¹)

value: White-light 720 minutes / 12 hours


title: Maternal WD diet + I3A mouse 4

city: Oklahoma City

first: Karen

last: Jonscher

address: 975 NE 10th St. BRC North rm 358

department: HHDC

institute: University of Oklahoma Health Sciences Center

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic v 0.39 (default settings)
Trimmed sequence reads were mapped to GRCm38.79/mm10 using gsnap, 2014-12-17 (max mismatches: 0.06, indel: 2)
Gene assembly and abundances were completed and normalized using cufflinks v 2.2.1
Assembly: mm10
Supplementary files format and content: Tab-delimited files containing the estimated gene-level expression values in the generic FPKM Tracking Format for each sample

source_name: liver

extract_protocol:
Direct-zol RNA miniprep kit
100 ng total RNA; Swift RNA Library Kit

value: liver

value: male

value: adult

tag: group

value: Maternal WD diet + I3A


title: MONO, RNA

description: Library name: MONO_RNA


title: HL60, wildtype, untreated, CSF1R Capture-HiC

description: Library name: HL60_Wildtype_NT_CSF1R_Cap

value: wildtype


title: HL-60, mutant2, PMA treated, RNA, rep2

description: Library name: HL60_Mutant2_PMA_RNA_rep2_

value: PMA


title: MONO, CSF1R Capture-HiC, rep1

description: Library name: MONO_CSF1R_Cap_rep1


title: Maternal WD diet + I3A mouse 5


title: HL60, Mutant2, PMA treated, CSF1R Capture-HiC

description: Library name: HL60_Mutant2_PMA_CSF1R_Cap


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 60 minutes  White light - bio rep #3

description:
Library name: White_light_timepoint_60_minutes_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in White Light (50-60 μmol m⁻² s⁻¹)

value: White-light 60 minutes


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 180 minutes  White light - bio rep #2

description:
Library name: White_light_timepoint_180_minutes_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in White Light (50-60 μmol m⁻² s⁻¹)


title: HL60, wildtype, PMA treated, CSF1R Capture-HiC

description: Library name: HL60_Wildtype_PMA_CSF1R_Cap


title: Maternal WD diet + I3A mouse 1


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 60 minutes  White light - bio rep #2

description:
Library name: White_light_timepoint_60_minutes_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in White Light (50-60 μmol m⁻² s⁻¹)


title: HL-60, wildtype, PMA treated, RNA, rep2

description: Library name: HL60_Wildtype_PMA_RNA_rep2_


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 60 minutes  White light - bio rep #1

description:
Library name: White_light_timepoint_60_minutes_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in White Light (50-60 μmol m⁻² s⁻¹)


title: Maternal WD diet + I3A mouse 2


title: HL-60, wildtype, PMA treated, RNA, rep1

description: Library name: HL60_Wildtype_PMA_RNA_rep1_


title: Maternal WD diet + Ind mouse 5

value: Maternal WD diet + Ind


title: HL-60, mutant2, untreated, RNA, rep1

description: Library name: HL60_Mutant2_NT_RNA_rep1_


title: HL-60, mutant2, untreated, RNA, rep2

description: Library name: HL60_Mutant2_NT_RNA_rep2_


title: HL-60, wildtype, untreated, RNA, rep2

description: Library name: HL60_Wildtype_NT_RNA_rep2_


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 30 minutes  White light - bio rep #3

description:
Library name: White_light_timepoint_30_minutes_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in White Light (50-60 μmol m⁻² s⁻¹)

value: White-light 30 minutes


title: Maternal WD diet + Ind mouse 3


title: Maternal WD diet + I3A mouse 3


title: RAW264.7 cells infected with lentiviruses carrying Fbxw11 vector [Fbxw11_3]

city: Tianjin (天津)

first: Siqi

last: Zhang

state: Tianjin (天津市)

address: 劝业场街道

institute: Institute of Hematology & Blood Disease Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

description: Library name: Fbxw11_3

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse genes.
Assembly: mouse mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: RAW264.7 cells were maintained in Dulbecco’s Modified Eagle’s Medium supplemented with 10% fetal bovine serum (FBS) and 1% Penicillin-Streptomycin (Gibco, Gaithersburg, MD).

extract_protocol:
sorted RAW264.7 cells were harvested and resuspended in 350ul RLT and 3.5ul β-Me.Total RNA is exacted by QIAGEN Rneasy Mini Kit(CAT 74103). 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: RAW264.7 cells were infected with lentiviruses carrying Fbxw11 (pMSCV-Fbxw11-pGk-GFP) or control vector


title: RAW264.7 cells infected with lentiviruses carrying control vector [GFP_3]

description: Library name: GFP_3


title: HL-60, wildtype, untreated, RNA, rep1

description: Library name: HL60_Wildtype_NT_RNA_rep1_


title: Maternal WD diet + Ind mouse 4


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 30 minutes  White light - bio rep #2

description:
Library name: White_light_timepoint_30_minutes_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in White Light (50-60 μmol m⁻² s⁻¹)


title: HL-60, mutant2, PMA treated, RNA, rep1

description: Library name: HL60_Mutant2_PMA_RNA_rep1_


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 30 minutes  White light - bio rep #1

description:
Library name: White_light_timepoint_30_minutes_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in White Light (50-60 μmol m⁻² s⁻¹)


title: RAW264.7 cells infected with lentiviruses carrying Fbxw11 vector [Fbxw11_1]

description: Library name: Fbxw11_1


title: chondrocytes, IL-7i-3, 24 hours

city: fuzhou

first: Wenxiu

last: Yuan

state: Fujian Province

address: No. 246 Yangqiao Middle Road, Gulou District

institute: Fujian Medical University

description:
Library name: Sample 15
IL-7i-3

data_processing:
Performed data quality control (QC), such as removing low-quality reads and connector sequences (FASTP, v0.20.1)
Assembly: Use StringTie software (v2.1.2) for assembly of genes or transcripts.
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

source_name: condylar cartilage

growth_protocol: The primary chondrocytes were cultured in low glucose DMEM medium (Gibco) containing 1% penicillin-streptomycin and 10% FBS in a humidified incubator with 5% CO2 and 95% humidity at 37°C

extract_protocol:
total RNA was extracted using TRIzol reagent, and 1 µg of total RNA was applied to construct sequencing libraries.
total RNA was extracted with Trizol (Takara, Japan)

treatment_protocol: Primary condylar chondrocytes were incubated with recombinant IL-1β, tFNAs-143.

value: condylar cartilage

value: primary chondrocytes cells

value: WT


title: chondrocytes, IL-7i-2, 24 hours

description:
Library name: Sample 14
IL-7i-2


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 24 hours darkness - bio rep #3

description:
Library name: Darkness_timepoint_24_hours_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in Darkness

value: Darkness 1440 minutes / 24 hours


title: Maternal WD diet + Ind mouse 2


title: chondrocytes,IL-7i-1, 24 hours

description:
Library name: Sample 13
IL-7i-1


title: RAW264.7 cells infected with lentiviruses carrying control vector [GFP_1]

description: Library name: GFP_1


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 12 hours darkness - bio rep #3

description:
Library name: Darkness_timepoint_12_hours_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in Darkness

value: Darkness 720 minutes / 12 hours


title: chondrocytes, IL-148-2, 24 hours

description:
Library name: Sample 11
IL-148-2


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 24 hours darkness - bio rep #2

description:
Library name: Darkness_timepoint_24_hours_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in Darkness

value: Marchantia polymorpha Thallus


title: chondrocytes, IL-148-1, 24 hours

description:
Library name: Sample 10
IL-148-1


title: chondrocytes,IL-143-3, 24 hours

description:
Library name: Sample 9
IL-143-3


title: Maternal WD diet + Ind mouse 1


title: Maternal WD diet mouse 5

value: Maternal WD diet


title: chondrocytes,IL-148-3, 24 hours

description:
Library name: Sample 12
IL-148-3


title: chondrocytes, IL-143-2, 24 hours

description:
Library name: Sample 8
IL-143-2


title: Maternal WD diet mouse 2


title: Maternal WD diet mouse 4


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 24 hours darkness - bio rep #1

description:
Library name: Darkness_timepoint_24_hours_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in Darkness

value: Takaragaike-1 (Tak-1, male)


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 12 hours darkness - bio rep #1

description:
Library name: Darkness_timepoint_12_hours_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in Darkness


title: Maternal WD diet mouse 3

value: liver


title: chondrocytes,IL-143-1, 24 hours

description:
Library name: Sample 7
IL-143-1


title: Maternal WD diet mouse 1

value: male


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 12 hours darkness - bio rep #2

description:
Library name: Darkness_timepoint_12_hours_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in Darkness


title: chondrocytes, IL-3, 24 hours

description:
Library name: Sample 6
IL-3

value: IL


title: chondrocytes, IL-2, 24 hours

description:
Library name: Sample 5
IL-2


title: RAW264.7 cells infected with lentiviruses carrying control vector [GFP_2]

description: Library name: GFP_2


title: RAW264.7 cells infected with lentiviruses carrying Fbxw11 vector [Fbxw11_2]

description: Library name: Fbxw11_2


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 180 minutes darkness - bio rep #3

description:
Library name: Darkness_timepoint_180_minutes_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in Darkness

value: Darkness 180 minutes


title: chondrocytes, IL-1, 24 hours

description:
Library name: Sample 4
IL-1


title: chondrocytes, con 1, 24 hours

description:
Library name: Sample 1
Con-1


title: chondrocytes, con 3, 24 hours

description:
Library name: Sample 3
Con-3


title: Maternal CH diet mouse 2

value: adult

value: Maternal CH diet


title: Maternal CH diet mouse 5


title: Maternal CH diet mouse 4


title: lncMGC KO high fat diet_7

city: Duarte

first: Rama

last: Natarajan

state: California

address: 1500 E Duarte Rd

department: Department of Diabetes Complications and Metabolism

institute: Beckman Research Institute, City of Hope

description:
Library name: SAMPLE 22
ROI_022

data_processing:
The sequencing data was demultiplexed and converted into FASTQ files with bcl2fastq2 Conversion Software (Illumina, v2.2.0). For QC, negative probes identified as outliers by Grubbs test were excluded in each segment. Raw FASTQ files were subjected to adapter removal, merging of paired-end reads, read alignment to barcode IDs and PCR duplicate removal with GeoMx NGS Pipeline software (NanoString), and resulting DCC files were uploaded into GeoMx DSP Control Center (Nanostring, v.2.4). Signal-to-noise ratio [Q3 / geoMean(Negative probes)] was calculated for each segment and segments with signal-to-noise ratio < 1 were excluded from further analyses. Genes exceeding both the limit of quantitation calculated based on negative probe counts and value 2 in at least 15% of segments were defined as confidently expressed and used in further analyses. For analyses not directly comparing different segment types (differential gene expression and  pathway analyses), this gene filtering was performed separately for UCP1+, CD45+ and UCP1-CD45- segments. Filtered data were normalized by Q3 values calculated based on all genes passing the aforementioned filters. Supplementary files format and content: DCC files that were imported into GeoMx DSP Control Center Supplementary files format and content: .xlsx file containing Initial Dataset (unnormalized and unfiltered) exported from GeoMx DSP Control Center. Supplementary files format and content: .xlsx files containing Q3 normalized count data (four sheets of data: all segments,UCP1+, CD45+ and UCP1-CD45- segments). Library strategy: Spatial Transcriptomics
Mouse GeoMx WTA panel conjugated to unique DNA indexing-oligonucleotides (DSP barcodes) via a Uvphotocleavable linker. After selecting regions of interest (ROIs) on the GeoMx DSP, the DSP barcodes are UV cleaved and collected. During library preparation, the DSP barcodes are tagged with their ROI location, then sequenced on an Illumina sequencer. DNA oligonucleotide sequences contain ROI indices mapping them back to their tissue location, an RNA target identification sequence matching them to their ISH probes, and a unique molecular identifier (UMI) to deduplicate reads. Sequenced oligonucleotides are processed and then imported back into the GeoMx DSP analysis software for integration with the slide images and ROI selections for spatially-resolved RNA expression.
Slides were exposed to aMouse GeoMx WTA panel for overnight at 37 degree and conjugated to unique DNA indexing-oligonucleotides (DSP barcodes) via a Uvphotocleavable linker.
During library preparation, the DSP barcodes are tagged with their ROI location, then sequenced on an Illumina sequencer. DNA oligonucleotide sequences contain ROI indices mapping them back to their tissue location, an RNA target identification sequence matching them to their ISH probes, and a unique molecular identifier (UMI) to deduplicate reads.
Assembly: mm10
Supplementary files format and content: .dcc files and Q3 Normalized values

source_name: Brown adipose tissue

growth_protocol: FFPE section from mouse brown adipose tissue.

extract_protocol:
FFPE blocks were cut into 5μm sections and each samples were placed on the same slide for subsequent simultaneous analysis. Slides were hybridized with RNA probes and stained for UCP-1, CD45, and nuclei. Using the GeoMx DSP instrument, selected regions of interest (ROIs) were segmented into following areas: 1.) UCP1 postive and CD45 negative area, 2.) CD45 postive area and 3.) remaining DNA postive area, and the hybridized RNA probes were collected separately from these three areas.
Following the protocol described (GeoMx® DSP NGS Readout) PCR reactions were purified and libraries were paired-end sequenced (2x50) on a NextSeq 2000.

value: Brown adipose tissue

value: lncMGC KO

value: HFD


title: Kras;M14-/- 3

city: Xi'an

first: Peihua

middle: Second Affiliated Hospital of Xi'an Jiaotong

state: shannxi

address: NO.157 Xiwu Rd

department: National and Local Joint Engineering Research Center of Biodiagnosis and Biotherapy

institute: Xi'an Jiaotong University Second Affiliated Hospital

description: Library name: MY144

data_processing:
CLC Genomics Workbenchv11.0.1
Assembly: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Bone marrow

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-SeqLibrary Prep Kit following manufacturer's protocols.

value: Bone marrow

value: Lin-ckit+ cells

value: Mettl14 fl/fl;Mx1-Cre; KrasLSL G12D/+


title: chondrocytes, con 2, 24 hours

description:
Library name: Sample 2
Con-2

value: condylar cartilage

value: primary chondrocytes cells

value: WT


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 60 minutes darkness - bio rep #2

description:
Library name: Darkness_timepoint_60_minutes_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in Darkness

value: Marchantia polymorpha Thallus

value: Darkness 60 minutes


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 180 minutes darkness - bio rep #1

description:
Library name: Darkness_timepoint_180_minutes_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in Darkness

value: Takaragaike-1 (Tak-1, male)


title: WT_PBS_Ipsi_5

city: Blacksburg

first: Michelle

last: Theus

state: VA

address: 234 Craig Drive

institute: Virginia Polytechnic Institute and State University

data_processing:
The adapter trimming was performed using fastq-mcf program (v1.05) and cutadapt (v2.5)
Contamination removal was performed using Bowtie2 (v2.5.1).
Alignment was performed using STAR (v2.7.3a),  Mouse genome (GRCm38.p6)
The raw read counts were estimated using HTSeq (v0.11.2).
Supplementary files format and content: excel file includes the raw count for each sample
Supplementary files format and content: excel file includes the DESeq2 normalized count for each sample

source_name: Ipsilateral meningeal layer 24hrs stroke WT with PBS

growth_protocol: CD1 male mice (EphA4f/f and VeCad-Cre/EphA4f/f) were subjected to pMCAO. At 24hrs, the meningeal surface was isolated for RNAseq

extract_protocol:
RNA was extracted using Zymo microcolumns
Illumina TruSeq Stranded mRNA HT Sample Prep Kit, enriched by 14 cycles of PCR, validated using Agilent TapeStation and quantified by qPCR

treatment_protocol: pMCAO of the main left MCA at 8-10 weeks of age in male mice

value: brain meningeal layer

value: brain meningeal tissue

value: pMCAO


title: Maternal CH diet mouse 3

value: liver

value: male

value: adult


title: Kras;M14-/- 1

description: Library name: MY129


title: lncMGC KO high fat diet_5

description:
Library name: SAMPLE 20
ROI_020

value: Brown adipose tissue

value: lncMGC KO


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 30 minutes darkness - bio rep #3

description:
Library name: Darkness_timepoint_30_minutes_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in Darkness

value: Darkness 30 minutes


title: lncMGC KO high fat diet_4

description:
Library name: SAMPLE 19
ROI_019

value: HFD


title: lncMGC KO high fat diet_1

description:
Library name: SAMPLE 16
ROI_016


title: Maternal CH diet mouse 1

value: Maternal CH diet


title: Kras;M14-/- 2

description: Library name: MY130

value: Bone marrow

value: Lin-ckit+ cells

value: Mettl14 fl/fl;Mx1-Cre; KrasLSL G12D/+


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 180 minutes darkness - bio rep #2

description:
Library name: Darkness_timepoint_180_minutes_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in Darkness

value: Marchantia polymorpha Thallus

value: Darkness 180 minutes


title: lncMGC KO high fat diet_2

description:
Library name: SAMPLE 17
ROI_017


title: WT_PBS_Ipsi_4

value: WT


title: lncMGC KO high fat diet_3

description:
Library name: SAMPLE 18
ROI_018


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 30 minutes darkness - bio rep #2

description:
Library name: Darkness_timepoint_30_minutes_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in Darkness

value: Takaragaike-1 (Tak-1, male)


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 60 minutes darkness - bio rep #1

description:
Library name: Darkness_timepoint_60_minutes_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in Darkness

value: Darkness 60 minutes


title: lncMGC KO high fat diet_6

description:
Library name: SAMPLE 21
ROI_021


title: WT_PBS_Ipsi_3

value: brain meningeal layer

value: brain meningeal tissue

value: pMCAO


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 60 minutes darkness - bio rep #3

description:
Library name: Darkness_timepoint_60_minutes_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in Darkness


title: lncMGC KO control_4

description:
Library name: SAMPLE 14
ROI_014

value: Control


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness (time-zero of this experiment) - bio rep #2

description:
Library name: Darkness_timepoint_0_replicate_2
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured for 8 days in light then 1 day in darkness (time zero sample) - biological replicate #2

value: Time-Zero


title: WT_PBS_Contra_5

source_name: Contralateral meningeal layer 24hrs stroke WT with PBS


title: Wild-type high fat diet_4

description:
Library name: SAMPLE 8
ROI_008

value: Brown adipose tissue


title: Wild-type high fat diet_5

description:
Library name: SAMPLE 9
ROI_009


title: Wild-type high fat diet_2

description:
Library name: SAMPLE 6
ROI_006


title: M. extorquens AM1, wt, RNA-seq, methanol 2.5%, replicate 2

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

description:
Library name: ME_AM1_wt_2_M_25
Column names in processed data files: WT_Me2.5_2

library_source: other

data_processing:
Raw RNA-seq reads were first evaluated for quality using FastQC v0.12.1. Adapter trimming and quality filtering were performed using Trimmomatic v0.32 with the following parameters: -phred33 LEADING:3 TRAILING:3 CROP:40 MINLEN:40. To remove residual rRNA reads, computational rRNA removal was carried out using the STAR aligner v2.7.10b by first generating an index of rRNA sequences (--runMode genomeGenerate, --genomeSAindexNbases 14) and aligning reads with parameters: --outFilterMismatchNmax 3, --outFilterMultimapNmax 10, --outSAMprimaryFlag AllBestScore, --alignIntronMax 1, --outReadsUnmapped Fastx. Non-rRNA reads were then mapped to each strain’s reference genome (generated via breseq v0.36.1) using STAR with genome-specific indices (--sjdbOverhang 39) and default alignment parameters. The resulting BAM files were sorted using SAMtools v1.19.2, and read counts per gene were obtained using the ‘summarizeOverlaps’ function in R (GenomicAlignments package). Differential expression analysis was performed with DESeq2 v1.36, using a model that incorporated interaction terms to evaluate both strain and methanol concentration effects (design = ~ strains_group * methanol). Normalization was conducted using DESeq2’s size factor estimation. Genes with adjusted p-value < 0.05 and |log₂FoldChange| > 1 were considered significantly differentially expressed.
Assembly: GCF_000022685.1
Supplementary files format and content: Tab-delimited text file containing DESeq2 normalized gene-level counts for all samples.
Supplementary files format and content: Tab-delimited text file including TPM (Transcripts Per Million) values for all genes across all samples, used for relative expression comparison.
Supplementary files format and content: Tab-delimited text file containing differential expression results based on interaction terms between strain and methanol concentration. Includes log2 fold change, p-value, and adjusted p-value for each gene.

molecule: other

organism: Methylorubrum extorquens

source_name: bacterial culture

growth_protocol: Cells were grown in minimal medium with 0.5% or 2.5% methanol as the sole carbon source at 30°C with shaking.

extract_protocol:
The cell culture was treated with the RNAprotect reagent (Qiagen).
RNA libraries were prepared using KAPA RNA Hyper Prep kit for sequencing using standard Illumina protocols

treatment_protocol: Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a Qubit 4.0 (Thermo Scientific Inc., Wilmington, DE, USA).

tag: strain

value: bacterial culture

value: wild-type


title: lncMGC KO control_2

description:
Library name: SAMPLE 12
ROI_012

value: lncMGC KO


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness + 30 minutes darkness - bio rep #1

description:
Library name: Darkness_timepoint_30_minutes_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured in Darkness

value: Darkness 30 minutes


title: WT_PBS_Ipsi_1


title: lncMGC KO control_3

description:
Library name: SAMPLE 13
ROI_013


title: lncMGC KO control_5

description:
Library name: SAMPLE 15
ROI_015


title: Wild-type high fat diet_6

description:
Library name: SAMPLE 10
ROI_010

value: HFD


title: M. extorquens AM1, wt, RNA-seq, methanol 2.5%, replicate 1

description:
Library name: ME_AM1_wt_1_M_25
Column names in processed data files: WT_Me2.5_1


title: Wild-type high fat diet_3

description:
Library name: SAMPLE 7
ROI_007


title: WT_PBS_Contra_1


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness (time-zero of this experiment) - bio rep #1

description:
Library name: Darkness_timepoint_0_replicate_1
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured for 8 days in light then 1 day in darkness (time zero sample) - biological replicate #1


title: RNAseq of Marchantia Thallus after 8 days white light + 1 day in darkness (time-zero of this experiment) - bio rep #3

description:
Library name: Darkness_timepoint_0_replicate_3
poly-A based cDNA profiling of RNA extracted from three homogenized thallus tissues cultured for 8 days in light then 1 day in darkness (time zero sample) - biological replicate #3


title: WT_PBS_Contra_3


title: WT_PBS_Contra_2


title: Wild-type control_1

description:
Library name: SAMPLE 1
ROI_001


title: Control Probes

description: Library name: Control_Blank


title: WT_10nM_Ipsi_5

source_name: ipsilateral meningeal layer 24hrs stroke WT with 10nM vasculotide


title: WT_10nM_Ipsi_4


title: lncMGC KO control_1

description:
Library name: SAMPLE 11
ROI_011


title: Wild-type high fat diet_1

description:
Library name: SAMPLE 5
ROI_005


title: S62675

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

description: Library name: Mut2L2

data_processing:
Cell Ranger is used in the analysis of 10x scRNA-Seq data. Raw reads were demultiplexed into Fastq format using cellranger mkfastq. Alignment, filtering, barcode counting, and UMI counting was done using cellranger’s count pipeline.
Assembly: mm10 Ensembl 98
Supplementary files format and content: single cell  count matrix in hdf5 format, raw data in bam format.

source_name: Craniofacial

extract_protocol:
microdissected craniofacial tissue
Chromium Fixed RNA Profiling for Multiplexed Samples from 10X Genomics Standard Protocol

value: Craniofacial

value: Mutant

value: Tamoxifen


title: WT_ribo_RPF_run3

city: University Park

first: Oluwasegun

middle: Tosin

last: Akinniyi

address: 463 North Frear

department: Biochemistry and Molecular Biology

institute: Pennsylvania State University

description:
Library name: JCR86_run3
JCR86_S1_run3

data_processing:
Adapter sequences and low quality bases were trimmed from Ribo-RPF data with fastap; Split samples into replicates by barcodes;Quality reports were generated and inspected with FastQC;Mapped samples to yeast genome using hisat2.Obtained RPF read counts at CDS of each gene with featureCounts.Metagene analysis was done using Ribominer.
Ribo-RNA samples were mapped to the yeast genome with hisat2; Gene-level read counts were obtained with featureCounts.
Both RPF and RNA-seq data were modeled with DESeq2 and  genes with significant changes in transcription, translation, and translation efficiency were identified.
Transient transcriptome samples were mapped to the reference using STAR aligner;  TPMs were obtained with RSEM
RATE-seq samples were mapped using the ENCODE3 pipeline.  Spike-ins  were mapped to the pombe genome;   Reads were mapped to the reference with STAR aligner and RSEM-1.2.28 was used to get the estimated counts and TPMs ; Differential analysis was done using DESeq2.
Assembly: Saccharomyces cerevisiae S288C assembly R64-4-1
Supplementary files format and content: CSV files with raw read counts for all Ribo-RNA and Ribo-RPF samples
Supplementary files format and content: Tab-delimited text file with read counts for steady state and RATE-seq samples
Library strategy: Ribo-seq ribosome-protected footpfint (RPF)

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: Cells (secondary culture ) were grown in YPD medium  to log phase (OD~0.8-1) and then treated.

extract_protocol:
For RNA-seq, cells were spiked with Schizosaccharomyces pombe cells at an OD ratio of 14:1, followed by RNA extraction using acid(AE-buffered)-phenol chloroform and isopropanol precipitation
For RATE-seq, RNA was isolated using acid(AE-buffered)-phenol chloroform extraction, then precipitated by isopropanol and labeled RNA was captured on streptavidin beads.
For Ribo-seq total RNA, RNA was isolated from cell lysates using acid(AE-buffered)-phenol chloroform followed by isopropanol extraction. For Ribo-seq ribosome-protected footpfint (RPF), cell lysates were treated with 300ug/ml RNaseI, and then resolved on 10-50% sucrose density gradient at 39k rpm and 4C for 3 hours in an SW40Ti Beckmann rotor. Sucrose gradient was fractionated using BRANDEL fractionator (SYN-202). RNA was isolated from monosome fraction by gel electrophoresis (TBE) and used to prepare ribosome-protected footprint (RPF) libraries.
For steady-state RNA-seq, RATE-seq, and Ribo-seq total RNA, libraries were prepared using the Illumina™ Total-stranded RNA library preparation kit. RNA samples were rRNA-depleted with the Qiagen FastSelect™, fractionated and then reverse-transcribed. Complimentary (second) strand DNA was synthesized and cDNA libraries were PCR-amplified. Libraries were quantified on Agilent TapeStation™, then on StepOne Plus™ qPCR machine. Libraries were pooled and sequenced on Illumina NextSeq 2000™.
For Ribo-seq RPF, libraries were prepared according to the widely-used Ribo-seq protocol (McGlincy and Ingolia, 2017). Custom barcodes were ligated using CircLigase I™ and cDNA was generated using Protoscript II™ reverse transcriptase. rRNA was depleted by selective hybridization, and libraries PCR-amplified.

treatment_protocol:
For steady-state RNA-seq, cells were harvested without treating with any agent
For RATE-seq, Cells were labeled with 4-thiouracil for the timepoints 6 min, 9 min, 12 min, 24 min, 90 min and the harvested by transfering to 2-fold volume ice-cold methanol.
For Ribo-seq, cells were treated with 50ug/ml cycloheximide, then harvested by snap-freexing in liquid nitrogen. Lysates were prepared by Cryo-milling.

value: yeast cell

value: Wild type

value: No treatment


title: WT_PBS_Contra_4

value: brain meningeal layer

value: WT


title: Wild-type control_3

description:
Library name: SAMPLE 3
ROI_003


title: Wild-type control_4

description:
Library name: SAMPLE 4
ROI_004


title: WT_10nM_Ipsi_3

value: brain meningeal tissue

value: pMCAO


title: def1_ribo_RPF_run3

description:
Library name: JCR87_run3
JCR87_S2_run3

value: DEF1 knockout


title: Wild-type control_2

description:
Library name: SAMPLE 2
ROI_002

value: Brown adipose tissue

value: Control


title: def1_ribo_RPF_run2

description:
Library name: JCR87_run2
JCR87_S2_run2


title: S62669

description: Library name: Mut1L1


title: dhh1_ribo_RPF_run1

description:
Library name: JCR088_run1
JCR088_S3_run1

value: DHH1 knockout


title: def1_ribo_RPF_run1

description:
Library name: JCR087_run1
JCR087_S2_run1


title: S62674

description: Library name: Mut1L2


title: WT_ribo_RPF_run1

description:
Library name: JCR086_run1
JCR086_S1_run1


title: WT_ribo_RPF_run2

description:
Library name: JCR86_run2
JCR86_S1_run2


title: WT_10nM_Contra_4

source_name: Contralateral meningeal layer 24hrs stroke WT with 10nM vasculotide


title: dhh1_rep3_ribo_RNA

description: Library name: JCR85

data_processing:
Adapter sequences and low quality bases were trimmed from Ribo-RPF data with fastap; Split samples into replicates by barcodes;Quality reports were generated and inspected with FastQC;Mapped samples to yeast genome using hisat2.Obtained RPF read counts at CDS of each gene with featureCounts.Metagene analysis was done using Ribominer.
Ribo-RNA samples were mapped to the yeast genome with hisat2; Gene-level read counts were obtained with featureCounts.
Both RPF and RNA-seq data were modeled with DESeq2 and  genes with significant changes in transcription, translation, and translation efficiency were identified.
Transient transcriptome samples were mapped to the reference using STAR aligner;  TPMs were obtained with RSEM
RATE-seq samples were mapped using the ENCODE3 pipeline.  Spike-ins  were mapped to the pombe genome;   Reads were mapped to the reference with STAR aligner and RSEM-1.2.28 was used to get the estimated counts and TPMs ; Differential analysis was done using DESeq2.
Assembly: Saccharomyces cerevisiae S288C assembly R64-4-1
Supplementary files format and content: CSV files with raw read counts for all Ribo-RNA and Ribo-RPF samples
Supplementary files format and content: Tab-delimited text file with read counts for steady state and RATE-seq samples
Library strategy: Ribo-Seq


title: Sham – Ear - Mouse 3

type: RNA

city: Cambridge

first: Xin

state: Massachusetts

address: 200 Sidney St

institute: AbbVie

description: gene expression from Sham – Ear - Mouse 3

hyb_protocol: Prepared target samples were hybridized to the Clariom S Mouse HT 24 sample array.

scan_protocol: Clariom S Mouse HT arrays were scanned using the GeneTitan MC instrument.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0) using SST-RMA to get summarized gene expression matrix.

label: biotin

source_name: Sham – Ear - Mouse 3

label_protocol: 100ng of mouse RNA samples were processed using the Affymetrix GeneChip WT PLUS Reagent kit

growth_protocol: HDM-treated NC/Nga mice were maintained under SPF condition. 8 mm punches were obtained from back skin and ears for gene analysis.

extract_protocol: Total RNA was isolated from the homogenates via the automated QIAcube Workstation, utilizing the Qiagen RNeasy Fibrous Tissue Mini Kit with DNAse I Digest.

treatment_protocol: RNA within ear and dorsal skin was stabilized by immersion of the samples in Invitrogen RNAlater at 4°C for a minimum of 18 hours, before the samples were stored at -80°C. Thawed samples were disrupted and homogenized in Qiagen RLT lysis buffer utilizing the Qiagen TissueRuptor II (Germantown, Maryland).

value: Ear

tag: agent

value: Sham


title: S62676

description: Library name: CtrL2L2

value: Wildtype


title: dhh1_rep1_ribo_RNA

description: Library name: JCR83


title: p155_ControlTconv_8A

city: Regensburg

first: LIT

last: NGS-Core

address: Franz-Josef-Strauß-Allee 11

department: NGS-Core

country: Germany

institute: Leibniz Institute for Immunotherapy

description:
p155_counts.tsv
p155_RPKM.xls
p155_dds.rds

data_processing:
Demultiplexing was performed with bcl2fastq v2.20.0.422 (NextSeq550), Dragon bclconvert version 3.8.4 (NextSeq200)
Quality control and read mapping to the mouse reference genome (GRCm38, gencode,release23) was performed using an adapted version of the SnakePipes version 2.5.1
Inside the snakePipes Pipeline mapping was performed using STAR  with default values and gene counts were created by featrureCounts.
Quality control of the count matrix and DE-Gene calling was performed with DESeq2. Gene counts were imported and prefiltered with edgeR:filterByExpr and the fdr was set to 0.05. GO-Analysis was performed with genes UP-regulated with a log2FC>1 and fdr<0.05 using goseq. GESA analysis was performed using fgsea. Plots were created with ggplot2 and EnhancedVolcano
Assembly: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/GRCh38.primary_assembly.genome.fa.gz
Assembly: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_29/gencode.v29.primary_assembly.annotation.gtf.gz
Supplementary files format and content: rds files: R version 4.1.1,DESeq2_1.34.0, contains the respective DESeq2DataSet object.

source_name: isolated form spleen

extract_protocol:
Total RNA was isolated using the Qiagen RNeasy Micro Kit and RNA was eluted in 14 µL RNAse-free water. RNA quality was assessed using the Tapestation system 4200 and High-Sensitivity RNA screentape (Agilent).
7 µl of the RNA was used for generating RNA-seq libraries using the SMART-seq Stranded Kit from Takara.
Indexed libraries were pooled in an equimolar ratio and sequenced on an Illumina NextSeq 550 machine with NextSeq 500/550 High Output Kit v2.5 (75 cycles) or NextSeq2000

value: isolated form spleen

value: primary Tcell

value: conventional T-cell

tag: sorting

value: sorted on living H2Kb+TCRbeta+CD4+hCD2-


title: p155_ControlTconv_9A


title: WT_10nM_Contra_1


title: WT_10nM_Ipsi_2


title: p155_ControlTconv_7A


title: S62670

description: Library name: Mut2L1

value: Craniofacial

value: Mutant

value: Tamoxifen


title: WT_10nM_Ipsi_1

value: brain meningeal layer

value: WT


title: p155_GvHDTconv_5A


title: S62673

description: Library name: Ctrl1L2


title: p155_CD40Tconv_15A


title: p155_GvHDTconv_1A


title: S62671

description: Library name: Ctrl1L1


title: def1_rep2_ribo_RNA

description: Library name: JCR81

value: yeast cell

value: No treatment


title: WT_10nM_Contra_5

value: brain meningeal tissue

value: pMCAO


title: dhh1_rep2_ribo_RNA

description: Library name: JCR84

value: DHH1 knockout


title: p155_CD40Tconv_13A


title: p155_GvHDTconv_2A


title: p155_GvHDTconv_3A


title: p155_CD40Tconv_12A


title: KO_PBS_Ipsi_5

source_name: Ipsilateral meningeal layer 24hrs stroke KO

value: EphA4 EC-KO


title: p155_GvHDTconv_4A


title: WT_10nM_Contra_3


title: KO_PBS_Ipsi_3


title: p155_ControlTconv_6A


title: WT_10nM_Contra_2


title: p155_CD40Tconv_11A


title: Cecum, with in situ Polyadenylation

city: Ithaca

first: Iwijn

last: De Vlaminck

state: New York

address: 237 Tower Road

department: Biomedical Engineering

institute: Cornell University

description: Intestial tissue profiled with the 10x Visium platform with and without in situ polyadenylation

data_processing:
Raw sequencing reads were trimmed using Cutadapt to remove polyA, polyG, and TSO sequences (CCCATGTACTCTGCGTTGATACCACTGCTT, both forward and reverse). The trimmed reads were then aligned to the mouse genome using the STAR Solo pipeline (STAR version 2.7.10b), which generates a feature-by-spot barcode expression matrix. The GRCm39 reference genome with GENCODE M28 annotations was used, or alternatively, the same reference was appended with the Reovirus Type 1-Lang sequence and annotations. Unmapped reads were taxonomically classified using Kraken(kraken2.09) to generate a taxon-by-spot barcode matrix.
Assembly: GRCm39
Supplementary files format and content: HDF5 files containing raw gene expression count matrix (UMI counts) per spot barcode and raw microbial ncbi taxid presence count matrix (UMI counts) per spot barcode
Library strategy: Spatial transcriptomics

source_name: Cecum

extract_protocol:
Cryosections were obtained from four distinct locations of the intestine of the same individual (male, 13 weeks old) — the proximal small intestine, ileum, cecum, and large intestine. Tissue sections (10 µm thick) were processed using either the standard Visium protocol or a modified protocol. For the modified protocol, sections were mounted onto Visium Spatial Gene Expression v1 slides and fixed in freshly prepared methacarn (60% methanol, 30% glacial acetic acid, 10% chloroform) for 15 minutes at room temperature. H&E staining was performed following the Visium protocol, and the slides were transferred into the Visium Slide Cassette.  In situ polyadenylation was performed using yeast Poly(A) Polymerase (yPAP; Thermo Scientific). Capture areas were equilibrated with 1X wash buffer, followed by the addition of yPAP enzyme mix. The chambers were sealed and incubated at 37°C for 25 minutes. After enzyme removal, a 30-minute enzymatic permeabilization step was conducted before continuing with the standard Visium library preparation to generate cDNA and sequencing libraries. For the standard Visium protocol, H&E staining and imaging were directly followed by permeabilization.
The cDNA ibraries were prepared following the 10x Visium protocol instructions. Sequencing was performed on a NextSeq 2K platform with a P3 200bp kit, with reads allocated as follows: 28 bp for read 1, 10 bp for index 1, 10 bp for index 2, and 190 bp for read 2.

value: Cecum

value: ApcMin/+

value: 13 weeks


title: p155_ControlTconv_10A

value: isolated form spleen

value: primary Tcell


title: Large Intestine, with in situ Polyadenylation

source_name: Large Intestine

value: Large Intestine


title: def1_rep3_ribo_RNA

description: Library name: JCR82

value: DEF1 knockout


title: KO_PBS_Contra_5

source_name: Contralateral meningeal layer 24hrs stroke KO


title: p155_CD40Tconv_14A

value: conventional T-cell

value: sorted on living H2Kb+TCRbeta+CD4+hCD2-


title: OROV-2024 infected liver organoids, 1 μM NHC treatment for 96 h, biological replicate 3

city: Rotterdam

first: Qiuwei

last: Pan

address: Wytemaweg 80

country: Netherlands

institute: Erasmus University Medical Center

description: Library name: NHC_96H_C

data_processing:
Raw reads (paired-end, 150 bp) were generated on an Illumina platform and converted to FASTQ files by the sequencing provider.
Gene-level read counts were summarized to generate a raw count matrix across all samples. Gene expression values were normalized and reported as FPKM to generate an expression matrix across all samples.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts and FPKM values for each Sample

source_name: Human-derived intrahepatic cholangiocyte organoids

extract_protocol:
Total RNA was extracted from all samples using the MachereyNagel NucleoSpin RNA II Kit (Bioke, Netherlands) and quantified with the Bioanalyzer RNA 6000 Picochip.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads for cDNA synthesis and library construction by Novogene. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. RNA sequencing was conducted using a paired-end 150 bp (PE 150) sequencing strategy via Illumina platforms.


title: KO_PBS_Ipsi_4

value: brain meningeal layer


title: Proximal Small Intestine, with in situ Polyadenylation

source_name: Proximal Small Intestine

value: Proximal Small Intestine


title: WT_rep1_ribo_RNA

description: Library name: JCR77

value: yeast cell

value: Wild type


title: OROV-2024 infected liver organoids, 1 μM NHC treatment for 96 h, biological replicate 2

description: Library name: NHC_96H_B

value: Human-derived intrahepatic cholangiocyte organoids


title: WT_rep2_ribo_RNA

description: Library name: JCR78

value: No treatment


title: OROV-2024 infected liver organoids, 1 μM NHC treatment for 96 h, biological replicate 1

description: Library name: NHC_96H_A


title: DEF1mut_total_RNA_rep1_steady_state

description: Library name: JCR015

data_processing:
Adapter sequences and low quality bases were trimmed from Ribo-RPF data with fastap; Split samples into replicates by barcodes;Quality reports were generated and inspected with FastQC;Mapped samples to yeast genome using hisat2.Obtained RPF read counts at CDS of each gene with featureCounts.Metagene analysis was done using Ribominer.
Ribo-RNA samples were mapped to the yeast genome with hisat2; Gene-level read counts were obtained with featureCounts.
Both RPF and RNA-seq data were modeled with DESeq2 and  genes with significant changes in transcription, translation, and translation efficiency were identified.
Transient transcriptome samples were mapped to the reference using STAR aligner;  TPMs were obtained with RSEM
RATE-seq samples were mapped using the ENCODE3 pipeline.  Spike-ins  were mapped to the pombe genome;   Reads were mapped to the reference with STAR aligner and RSEM-1.2.28 was used to get the estimated counts and TPMs ; Differential analysis was done using DESeq2.
Assembly: Saccharomyces cerevisiae S288C assembly R64-4-1
Supplementary files format and content: CSV files with raw read counts for all Ribo-RNA and Ribo-RPF samples
Supplementary files format and content: Tab-delimited text file with read counts for steady state and RATE-seq samples


title: OROV-2024 infected liver organoids, 96 h post-infection, biological replicate 4

description: Library name: OROV_24_96D


title: KO_PBS_Contra_4

value: brain meningeal tissue

value: pMCAO


title: Ileum, without in situ Polyadenylation

source_name: Ileum

value: Ileum


title: WT_total_RNA_rep2_steady_state

description: Library name: JCR014


title: def1_rep1_ribo_RNA

description: Library name: JCR80


title: OROV-2024 infected liver organoids, 96 h post-infection, biological replicate 3

description: Library name: OROV_24_96C


title: WT_rep3_ribo_RNA

description: Library name: JCR79


title: S62672

description: Library name: Ctrl2L1

value: Craniofacial

value: Wildtype

value: Tamoxifen


title: WT_total_RNA_rep1_steady_state

description: Library name: JCR013


title: KO_PBS_Ipsi_2

value: EphA4 EC-KO


title: OROV-2024 infected liver organoids, 1 μM NHC treatment for 96 h, biological replicate 4

description: Library name: NHC_96H_D


title: Proximal Small Intestine, without in situ Polyadenylation

value: ApcMin/+

value: 13 weeks


title: KO_PBS_Contra_1


title: OROV-2024 infected liver organoids, 96 h post-infection, biological replicate 2

description: Library name: OROV_24_96B


title: KO_PBS_Ipsi_1


title: Ileum, with in situ Polyadenylation


title: 9 months old DBA/2J veins sample 9

city: New York

first: Simon

last: John

state: NY

address: 630 West 168th Street

institute: Columbia University

description: Library name: SC039

data_processing:
Bulk RNA-seq data will be pseudoaligned to Gencode M33 transcriptome and quantified by Kallisto. Transcript quantifications will then be imported into R framework for downstream analysis.
Assembly: GRCm39
Supplementary files format and content: scaled reads per base from Sleuth for each sample

source_name: retinal vein

extract_protocol:
Total RNA was extracted using RNeasy Micro kit (Qiagen, 74004). RNA concentration and quality (RIN) was measured by Bioanalyzer.
About 100 pg total RNA (RIN>9) were reverse transcribed to cDNA using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara). The library is prepared using Nextera XT (Illumina)

value: retinal vein


title: OROV-2024 infected liver organoids, 96 h post-infection, biological replicate 1

description: Library name: OROV_24_96A


title: Maternal WD diet + I3A mouse FMT 5

source_name: liver

extract_protocol:
Direct-zol RNA miniprep kit
100 ng total RNA; NEBNext Poly(A) mRNA Magnetic Isolation Module followed by IDT's xGen Broad Range RNA Library Prep Kit

value: liver

value: male

value: adult


title: Maternal WD diet + I3A mouse FMT 4


title: DEF1mut_total_RNA_rep2_steady_state

description: Library name: JCR016

value: yeast cell

value: DEF1 knockout


title: Cecum, without in situ Polyadenylation

value: Cecum


title: KO_PBS_Contra_3

value: brain meningeal layer


title: 9 months old DBA/2J veins sample 8

description: Library name: SC038


title: OROV-2024 infected liver organoids, 48 h post-infection, biological replicate 4

description: Library name: OROV_24_48D

value: Human-derived intrahepatic cholangiocyte organoids


title: 9 months old DBA/2J veins sample 7

description: Library name: SC037


title: KO_PBS_Contra_2

value: brain meningeal tissue

value: pMCAO


title: Large Intestine, without in situ Polyadenylation

value: Large Intestine


title: DEF1mut_4TU_90min_rep2_RATE_seq

description: Library name: JCR064

data_processing:
Adapter sequences and low quality bases were trimmed from Ribo-RPF data with fastap; Split samples into replicates by barcodes;Quality reports were generated and inspected with FastQC;Mapped samples to yeast genome using hisat2.Obtained RPF read counts at CDS of each gene with featureCounts.Metagene analysis was done using Ribominer.
Ribo-RNA samples were mapped to the yeast genome with hisat2; Gene-level read counts were obtained with featureCounts.
Both RPF and RNA-seq data were modeled with DESeq2 and  genes with significant changes in transcription, translation, and translation efficiency were identified.
Transient transcriptome samples were mapped to the reference using STAR aligner;  TPMs were obtained with RSEM
RATE-seq samples were mapped using the ENCODE3 pipeline.  Spike-ins  were mapped to the pombe genome;   Reads were mapped to the reference with STAR aligner and RSEM-1.2.28 was used to get the estimated counts and TPMs ; Differential analysis was done using DESeq2.
Assembly: Saccharomyces cerevisiae S288C assembly R64-4-1
Supplementary files format and content: CSV files with raw read counts for all Ribo-RNA and Ribo-RPF samples
Supplementary files format and content: Tab-delimited text file with read counts for steady state and RATE-seq samples
Library strategy: RATE-seq

value: 4-thiouracil-labeled for 90 min


title: DEF1mut_4TU_24min_rep2_RATE_seq

description: Library name: JCR063

value: 4-thiouracil-labeled for 24 min


title: 9 months old DBA/2J veins sample 6

description: Library name: SC036


title: DEF1mut_4TU_6min_rep2_RATE_seq

description: Library name: JCR060

value: 4-thiouracil-labeled for 6 min


title: OROV-2024 infected liver organoids, 48 h post-infection, biological replicate 3

description: Library name: OROV_24_48C


title: Maternal WD diet + I3A mouse FMT 3

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trimmomatic v 0.39 (default settings)
Trimmed sequence reads were mapped to GRCm38.79/mm10 using gsnap, 2014-12-17 (max mismatches: 0.06, indel: 2)
Gene assembly and abundances were completed and normalized using cufflinks v 2.2.1
Assembly: mm10
Supplementary files format and content: Tab-delimited files containing the estimated gene-level expression values in the generic FPKM Tracking Format for each sample


title: 9 months old DBA/2J veins sample 4

description: Library name: SC034


title: Maternal WD diet + I3A mouse FMT 2


title: OROV-2024 infected liver organoids, 48 h post-infection, biological replicate 2

description: Library name: OROV_24_48B


title: 9 months old DBA/2J veins sample 5

description: Library name: SC035


title: Maternal WD diet + I3A mouse FMT 1


title: DEF1mut_4TU_12min_rep2_RATE_seq

description: Library name: JCR062

value: 4-thiouracil-labeled for 12 min


title: OROV-2024 infected liver organoids, 1 h post-infection, biological replicate 4

description: Library name: OROV_24_1D


title: Maternal WD diet + Ind mouse FMT 5


title: DEF1mut_4TU_9min_rep2_RATE_seq

description: Library name: JCR061

value: 4-thiouracil-labeled for 9 min


title: DEF1mut_4TU_90min_rep1_RATE_seq

description: Library name: JCR059


title: Maternal WD diet + Ind mouse FMT 3


title: Maternal WD diet + Ind mouse FMT 4


title: 9 months old DBA/2J veins sample 3

description: Library name: SC033

value: retinal vein


title: DEF1mut_4TU_12min_rep1_RATE_seq

description:
Library name: JCR057
did not meet the quality control cutoffs


title: OROV-2024 infected liver organoids, 1 h post-infection, biological replicate 1

description: Library name: OROV_24_1A


title: 9 months old DBA/2J veins sample 2

description: Library name: SC032


title: Maternal WD diet + Ind mouse FMT 2

value: liver


title: DEF1mut_4TU_24min_rep1_RATE_seq

description: Library name: JCR058


title: OROV-2024 infected liver organoids, 48 h post-infection, biological replicate 1

description: Library name: OROV_24_48A


title: OROV-2024 infected liver organoids, 1 h post-infection, biological replicate 3

description: Library name: OROV_24_1C


title: 9 months old DBA/2J veins sample 1

description: Library name: SC031


title: DEF1mut_4TU_9min_rep1_RATE_seq

description: Library name: JCR056


title: OROV-1967 infected liver organoids, 96 h post-infection, biological replicate 4

description: Library name: OROV_67_96D


title: OROV-1967 infected liver organoids, 96 h post-infection, biological replicate 3

description: Library name: OROV_67_96C


title: DEF1mut_4TU_6min_rep1_RATE_seq

description: Library name: JCR055


title: Maternal WD diet mouse FMT 5

value: male


title: 9 months old normotensive control veins sample 5

description: Library name: SC030


title: 9 months old normotensive control veins sample 4

description: Library name: SC028


title: OROV-2024 infected liver organoids, 1 h post-infection, biological replicate 2

description: Library name: OROV_24_1B


title: 9 months old normotensive control veins sample 3

description: Library name: SC018


title: OROV-1967 infected liver organoids, 96 h post-infection, biological replicate 2

description: Library name: OROV_67_96B


title: OROV-1967 infected liver organoids, 96 h post-infection, biological replicate 1

description: Library name: OROV_67_96A


title: Maternal WD diet + Ind mouse FMT 1

value: adult


title: WT_4TU_24min_rep2_RATE_seq

description: Library name: JCR053

value: yeast cell

value: Wild type


title: WT_4TU_12min_rep2_RATE_seq

description: Library name: JCR052


title: WT_4TU_90min_rep2_RATE_seq

description: Library name: JCR054


title: 9 months old normotensive control veins sample 1

description: Library name: SC016


title: Maternal WD diet mouse FMT 1


title: isolated fibroblasts from WT mice, stimulated in vitro with FGF2 and OPN, replicate 3

city: Berlin

first: Gerhard

last: Krönke

address: Virchowweg 11

department: Rheumatology and clinical immunology

institute: Charite Berlin

description: Library name: FGF2_OPN_3

data_processing:
Sequence reads were mapped to GrCM38/mm10 reference genome using the STAR aligner
Read count extraction were performed using featureCounts
Assembly: mm10
Supplementary files format and content: tab delimited text file containing raw read counts for each sample

source_name: Paw

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Cat. No. 74104) according to the manufacturer’s instructions.
RNA samples were submitted to Novogene (Cambridge, UK) for quality control, library preparation, and sequencing. Sequencing was performed on the NovaSeq X Plus platform (paired-end 150 bp), generating approximately 9 Gb of raw data per sample.

treatment_protocol: Sorted synovial fibroblasts were stimulated for three consecutive days with different combinations of 10 ng/mL FGF2 (ImmunoTools, 11343625) and/or 50 ng/mL OPN (R&D Systems, 441-OP-200/CF) prior to assay setup.

value: Paw

value: Fibroblasts

value: WT

value: naïve + in vitro FGF2 and OPN stimulation


title: WT_4TU_90min_rep1_RATE_seq

description: Library name: JCR049


title: WT_4TU_9min_rep2_RATE_seq

description: Library name: JCR051


title: WT_4TU_6min_rep2_RATE_seq

description: Library name: JCR050


title: OROV-1967 infected liver organoids, 48 h post-infection, biological replicate 4

description: Library name: OROV_67_48D

value: Human-derived intrahepatic cholangiocyte organoids


title: OROV-1967 infected liver organoids, 48 h post-infection, biological replicate 3

description: Library name: OROV_67_48C


title: Maternal WD diet mouse FMT 3


title: Maternal WD diet mouse FMT 4


title: 9 months old normotensive control veins sample 2

description: Library name: SC017


title: Maternal CH diet mouse FMT 5


title: isolated fibroblasts from WT mice, stimulated in vitro with FGF2 and OPN, replicate 2

description: Library name: FGF2_OPN_2


title: WT_4TU_24min_rep1_RATE_seq

description: Library name: JCR048


title: OROV-1967 infected liver organoids, 48 h post-infection, biological replicate 2

description: Library name: OROV_67_48B


title: WT_4TU_12min_rep1_RATE_seq

description:
Library name: JCR047
did not meet the quality control cutoffs


title: OROV-1967 infected liver organoids, 1 h post-infection, biological replicate 4

description: Library name: OROV_67_1D


title: Maternal CH diet mouse FMT 2


title: Maternal CH diet mouse FMT 3


title: WT_4TU_6min_rep1_RATE_seq

description: Library name: JCR045


title: isolated fibroblasts from WT mice, stimulated in vitro with OPN, replicate 2

description: Library name: OPN_2

value: naïve + in vitro OPN stimulation


title: OROV-1967 infected liver organoids, 48 h post-infection, biological replicate 1

description: Library name: OROV_67_48A


title: isolated fibroblasts from WT mice, stimulated in vitro with OPN, replicate 3

description: Library name: OPN_3


title: WT_4TU_9min_rep1_RATE_seq

description: Library name: JCR046


title: Maternal WD diet mouse FMT 2


title: OROV-1967 infected liver organoids, 1 h post-infection, biological replicate 3

description: Library name: OROV_67_1C


title: isolated fibroblasts from WT mice, stimulated in vitro with FGF2 and OPN, replicate 1

description: Library name: FGF2_OPN_1


title: OROV-1967 infected liver organoids, 1 h post-infection, biological replicate 2

description: Library name: OROV_67_1B


title: Maternal CH diet mouse FMT 1


title: Uninfected liver organoids, 96 h, biological replicate 3

description: Library name: MOCK_96H_C


title: isolated fibroblasts from WT mice, stimulated in vitro with FGF2, replicate 1

description: Library name: FGF2_1

value: naïve + in vitro FGF2 stimulation


title: OROV-1967 infected liver organoids, 1 h post-infection, biological replicate 1

description: Library name: OROV_67_1A


title: H3K4me1_dleo1-2

city: Chuncheon-si

first: Shinae

last: Park

address: Kangwondaehak-gil

institute: Kangwon National University

description: Library name: 13_H3K4me1 leo1Δ_rep2

data_processing:
The sequencing adapter removal and quality-based trimming on raw data was performed by Trimmomatic v. 0.36 with TruSeq adapter sequences.
Cleaned reads were mapped to reference genome using bowtie v2.4.2 with default parameter
For normalization, S. pombespike-in reads in each sample was calculated.
We assumed that the amount of spike-in added to each sample is same, and the normalization ratio was calculated as "1000000/spike-in reads" for each sample.
The normalized bedGraph was produced by using 'bamCoverage --scaleFactor' and calculated normalization ratio.
bedGraph files were converted to BigWig files and the resulted bw files were averaged by WiggleTools 1.2 (https://github.com/Ensembl/WiggleTools).
Assembly: Saccharomyces cerevisiae S288C genome assembly R64 (sacCer3)
Supplementary files format and content: fastq, bigwig

source_name: Whole cells

growth_protocol: Cells were prepared from exponentially growing at OD600 = 1.0. Harvested cells were resuspended with 4ml of 1XTBS and evenly divided into 4 eppendorf tubes. Cell is harvested by centrifuge 3000 rpm 5min and supernatant was removed. After one more wash step, samples were stored at -80℃.

extract_protocol:
Cells were resuspended with lysis buffer and homogenized with glass beads at cold room. Lysed cells were sonicated and centrifuged to obtain soluble chromatin fraction. S. cerevisiae chromatin lysates, containing 5% of Schizosaccharomyces pombe chromatin extract for control of sample-to-sample normalization, were incubated with antibody and antibody-protein-chromatin complex was captured by Protein A/G agarose. After sequential washing steps and reverse crosslinking, remaining DNA is purified by phenol-chloroform extraction and washing.
ChIP-Seq DNA samples were quantified by Quant-iT PicoGreen dsDNA Assay kit and their quality were assessed Bioanalyzer 2100. ChIP-Seq library was constructed with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions.

treatment_protocol: Before wash the cells with 1XTBS, cells were treated with 1% formaldehyde for 5mins and quenched with 2.5M Glycine for 20mins

value: Whole cells

value: LEO1 Knockout


title: H3K4me1_WT-2

description: Library name: 11_H3K4me1 WT_rep2


title: H3K4me1_dleo1-1

description: Library name: 12_H3K4me1 leo1Δ_rep1


title: FN59_patB10_normal_pre_NR

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Agilent miRNA hybridization protocol

scan_protocol: Standard Agilent scanning protocol

data_processing: The data were processed and normalised using the Bioconductor limma implementation in R

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Agilent MicroRNA Expression Profiling Assay Guide).

extract_protocol: RNA was extracted with FFPE miRNeasy kit in accordance with manufacture's protocol (QIAGEN).

tag: sample type

value: normal

tag: sample class

value: PRE

tag: patient class

value: SR

tag: sample body site

value: LN

tag: drug

value: BRAFi


title: FN60_patB10_tumor_pre_NR

value: tumor


title: isolated fibroblasts from WT mice, stimulated in vitro with OPN, replicate 1

description: Library name: OPN_1


title: FN47_patB32_tumor_pre_LR

value: LR

value: C/SC


title: Maternal CH diet mouse FMT 4

city: Oklahoma City

first: Karen

institute: University of Oklahoma Health Sciences Center

value: liver

value: male

value: adult


title: isolated fibroblasts from STIA mice, stimulated, in vitro with OPN, replicate 3

description: Library name: STIA_OPN_3

value: Paw

value: Fibroblasts

value: WT

value: K/BxN serum induced arthritis + in vitro OPN stimulation


title: isolated fibroblasts from WT mice, replicate 1

description: Library name: unstim_1

value: naïve


title: isolated fibroblasts from WT mice, replicate 2

description: Library name: unstim_2


title: H3K4me2_dleo1-2

description: Library name: 9_H3K4me2 leo1Δ_rep2

value: Whole cells

value: LEO1 Knockout


title: isolated fibroblasts from WT mice, stimulated in vitro with FGF2, replicate 3

description: Library name: FGF2_3

value: naïve + in vitro FGF2 stimulation


title: G5-4

city: Hefei

first: Zheng-sheng

last: Wu

address: 81 Meishan Road

institute: Anhui Medical University

description: Library name: Sample 9

data_processing:
FASTQ file quality control was performed using Trimmomatic (10), where N bases and low-quality (score <15) bases were removed. Reads aligning to rRNA and tRNA sequences were removed.
Assembly: Cleaned reads were aligned to the human reference genome (hg19) using STAR v 2.5.2b
Supplementary files format and content: the format is fastq

extract_protocol:
Total RNA was extracted using the RNeasy FFPE Kit.
RNA sequencing libraries were prepared using KAPA Stranded RNA-Seq Kit with RiboErase (KAPA Biosystems).

tag: classification

value: Grade 5


title: Uninfected liver organoids, 96 h, biological replicate 1

description: Library name: MOCK_96H_A

value: Human-derived intrahepatic cholangiocyte organoids


title: FN50_patB11_tumor_pre_NR

value: PRE

value: SR

value: LN

value: BRAFi


title: Uninfected liver organoids, 96 h, biological replicate 4

description: Library name: MOCK_96H_D


title: H3K4me2_dleo1-1

description: Library name: 8_H3K4me2 leo1Δ_rep1

tag: tissue


title: H3K4me1_WT-1

description: Library name: 10_H3K4me1 WT_rep1

tag: cell line


title: Uninfected liver organoids, 96 h, biological replicate 2

description: Library name: MOCK_96H_B


title: H3K4me3_dset1-1

description: Library name: 5_H3K4me3 set1Δ_rep1

value: SET1 Knockout


title: isolated fibroblasts from STIA mice, stimulated, in vitro with OPN, replicate 1

description: Library name: STIA_OPN_1

tag: genotype


title: H3K4me2_WT-2

description: Library name: 7_H3K4me2 WT_rep2


title: G5-2

description: Library name: Sample 7


title: H3K4me3_dleo1-2

description: Library name: 4_H3K4me3_leo1Δ_rep2


title: isolated fibroblasts from WT mice, stimulated in vitro with FGF2, replicate 2

description: Library name: FGF2_2

tag: treatment


title: isolated fibroblasts from WT mice, replicate 3

description: Library name: unstim_3

tag: cell type


title: FL47_patB14_tumor_pre_NR

value: tumor

value: C/SC


title: FL46_patB13_normal_pre_LR

value: normal

value: LR


title: G5-5

description: Library name: Sample 10


title: isolated fibroblasts from STIA mice, stimulated, in vitro with OPN, replicate 2

description: Library name: STIA_OPN_2

value: Paw

value: Fibroblasts

value: WT


title: FN52_patB24_tumor_pre_NR


title: H3K4me3_WT-2

description: Library name: 2_H3K4me3_WT_rep2

value: Whole cells


title: FN45_patB11_normal_pre_NR


title: G1-5

description: Library name: Sample 5

value: Grade 1


title: isolated fibroblasts from STIA mice, replicate 1

description: Library name: STIA_1

value: K/BxN serum induced arthritis


title: H3K4me2_WT-1

description: Library name: 6_H3K4me2 WT_rep1


title: isolated fibroblasts from STIA mice, replicate 3

description: Library name: STIA_3


title: G5-3

description: Library name: Sample 8

value: Grade 5


title: FL48_patB18_normal_pre_LR

value: BREAST


title: FL41_patB36_tumor_post_NR

value: POST

value: V


title: G5-1

description: Library name: Sample 6


title: H3K4me3_dleo1-1

description: Library name: 3_H3K4me3 leo1Δ_rep1

value: LEO1 Knockout


title: G1-4

description: Library name: Sample 4


title: H3K4me3_WT-1

description: Library name: 1_H3K4me3_WT_rep1


title: isolated fibroblasts from STIA mice, replicate 2

description: Library name: STIA_2


title: FL44_patB26_tumor_post_NR

value: SR

value: BRAFi


title: G1-3

description: Library name: Sample 3


title: FL40_patB33_tumor_pre_LR

value: tumor

value: PRE


title: Stromal cells, K/BxN serum transfer day 5

description:
Library name: F_day5
Novogene

data_processing:
Alignment and gene counting were performed using the cellranger count command (v.7.0.1). Initial analysis and quality control were performed using the Seurat R package (v.4.3.0).
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab seperated value files and matrix file

extract_protocol:
Mice were euthanized and synovial macrophages were isolated from the hind paws. After removal of skin, muscles and tendons, the paws were digested using 2.5 ml RPMI-1640 (Roswell Park Memorial Institute) medium (Life Technologies), 10% heat-inactivated fetal calf serum (FCS, Life Technologies), 2 mg/ml collagenase IV from Clostridium histolyticum (Sigma-Aldrich, C5138), and 0.03 mg/ml desoxyribonuclease I (Sigma-Aldrich, DN25). Tissues were incubated for 30 min in an orbital shaker at 37°C with 300 rpm shaking. Afterwards the solution was filtered through a 40 µm mesh and digestion was stopped using 10 ml ice-cold MACS Buffer containing phosphate buffered saline (PBS, Life Technologies), 2% FCS and 2 mM EDTA (AccuGENETM, Lonza, 12001-382). The cells were then centrifuged for 7 min at 1600 rpm, 4°C. For cell sorting the pellet was resuspended in 3 ml of 40% Percoll (Sigma-Aldrich) solution and centrifuged for 15 min at 2200 rpm, room temperature, without acceleration and brakes. The pellet was washed once in MACS buffer and afterwards incubated for 15 min at 4°C with Fc block (Biolegend) followed by the extracellular antibody staining solution (final dilution of 1:400) for 20 min at 4°C with a washing step in between. Lastly, cells were resuspended in MACS buffer without EDTA for fluorescence-activated cell sorting.
Sorted CD45+CD11b+Ly6G- or CD45- synovial cells from hind paws were used for single-cell sequencing. Cells for single-cell RNA sequencing (scRNAseq) were processed according to the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 User Guide (10x Genomics, CG000204) using the recommended Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1, (PN-1000128). The library was sequenced by Novogene with a depth of 20,000 reads per cell. Reads were aligned to the pre-built 10X mouse reference dataset (refdata-gex-mm10-2020-A)

treatment_protocol: Mice were injected intraperitoneally with 200 µl of serum from K/BxN arthritic mice. Their well-being was monitored daily and the course of arthritis was evaluated using a clinical score together with the measurement of the hind-paw swelling using a thickness gauges (Peacock). The score for each paw ranged from 0 to 4, with 0 = no signs of inflammation; 1 = minor swelling and reddening of a paw, or affecting only single digits; 2 = moderate swelling and erythema, or affecting multiple digits per paw; 3 = severe swelling and erythema affecting the whole paw; 4 = maximum swelling and erythema and was cumulated to a minimal clinical score of 0 and a maximum of 16. The clinical index gave an indication of inflammation in the paws and was used to follow the course of STA at different timepoints after induction.

value: K/BxN serum transfer arthritis day 5


title: dpaf1-1

description: Library name: 7_RNA-seq paf1Δ_rep1

data_processing:
The Illumina Hiseq generates raw images utilizing HCS(HiSeq Control Software v2.2) for system control
Base calling through an integrated primary analysis software called RTA(Real Time Analysis. v1.18)
The BCL(base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq(v1.8.4)
Adapters are not trimmed away from the reads.
bedGraph files were converted to BigWig files and the resulted bw files were averaged by WiggleTools 1.2 (https://github.com/Ensembl/WiggleTools).
Assembly: Saccharomyces cerevisiae S288C genome assembly R64 (sacCer3)
Supplementary files format and content: bigwig

source_name: total cells

growth_protocol: Yeast cells are cultured at 10ml YPD(1% Yeast extract, 2% Peptone, 2% Glucose) in 100ml flask (30℃, 230rpm) and harvested at OD600=1.0

extract_protocol:
RNA was harvested according to the MN RNA-isolation kit(MN;#7409555.50) standard protocols. NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina(NEB #E7420S) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: total cells

value: yeast cell

value: PAF1 knockout


title: FL45_patB22_normal_pre_NR

value: normal

value: LN


title: G1-2

description: Library name: Sample 2

value: Grade 1


title: FL39_patB23_tumor_post_LR

value: LR

value: C/SC


title: G1-1

description: Library name: Sample 1


title: Stromal cells, K/BxN serum transfer day 0

description:
Library name: F_day0
Novogene

value: Paw

value: Steady State


title: dleo1dset1-2

description: Library name: 6_RNA-seq leo1Δset1Δ_rep2

value: LEO1 SET1 double knockout


title: C4_CD40_AIRpos_HEK-CD40L

description:
p138_counts.tsv
CD40L_CAR_RPKM.xlsx
CD40L_CAR_dds.rds

source_name: isolated spleen, then expanded and transduced

value: primary cell

value: regulatory T-cell


title: dleo1dset1-1

description: Library name: 5_RNA-seq leo1Δset1Δ_rep1


title: Myeloid cells, K/BxN serum transfer day 9

description:
Library name: M_day9
Novogene

value: K/BxN serum transfer arthritis day 9


title: FL38_patB27_tumor_post_LR

value: tumor

value: POST

value: V

value: BRAFi


title: Knockdown-KO-Aged-A2-F5_S69_L004

first: Guilherme Henrique

last: Souza Bomfim

address: 1 Washington Square Village 2R

department: Department of Molecular Pathobiology

institute: New York University (NYU)

description:
Library name: Sample 20
Collumn name in raw_counts_all_samples: Knockdown-KO-Aged-A2-F5_S69_L004
03_GHS002 DEG KO Young vs KO Aged.xlsx

data_processing:
Raw paired-end FASTQ files were transferred to the NYU Greene High Performance Computing (HPC) cluster. Adapter sequences and low-quality bases were removed using Fastp (v0.24.0). The cleaned reads were aligned to the mouse reference genome (GRCm39, Ensembl release v113) using STAR (v2.7.11b) to generate BAM files. Gene-level read counts were obtained using featureCounts from the Subread package (v2.0.8). Quality control reports from all steps were aggregated with MultiQC (v1.25.1). Raw counts from all samples were merged into a count matrix. Ensembl gene identifiers were mapped to Entrez Gene IDs, and only genes with valid Entrez IDs were retained. A DESeq2 dataset (DESeq2 v1.42.1) was then constructed from these counts. Genes were further filtered to retain those with at least 10 counts in at least 90% of samples.
Assembly: The cleaned reads were aligned to the mouse reference genome (GRCm39, Ensembl release v113) using STAR (v2.7.11b)
Supplementary files format and content: Tab-delimited text file (csv/xlsx) include normalized values were scaled to convert to z-scores at p< 0.05 with log2FC ˃1. significance at adjusted P < 0.05

source_name: Aorta

extract_protocol:
RNA from cleaned aortic tissues was isolated using RNeasy Mini Kit (Qiagen cat #217004), as indicated by the manufacturer. RNA quality and RNA sequencing (RNA-seq) were conducted at NYU Langone's Genome Technology Center (RRID: SCR_017929). Aortic tissue from 2 different mice (~20mg) were combined, totalizing 5 samples (n=5).
All samples were processed in the same time period, following the same protocol in order to limit the batch effects. Next, the RNASeq enrichment libraries were prepared using the low-input RNA sequencing, TruSeq Stranded RNA Library Prep Gold.

value: Aorta

value: Knockdown-KO

tag: developmental stage

value: Aged

tag: Sex

value: Female


title: Knockdown-KO-Aged-A2-F4_S68_L004

description:
Library name: Sample 19
Collumn name in raw_counts_all_samples: Knockdown-KO-Aged-A2-F4_S68_L004
03_GHS002 DEG KO Young vs KO Aged.xlsx


title: dpaf1-2

description: Library name: 8_RNA-seq paf1Δ_rep1

value: total cells

value: yeast cell

value: PAF1 knockout


title: Knockdown-KO-Aged-A2-F3_S67_L004

description:
Library name: Sample 18
Collumn name in raw_counts_all_samples: Knockdown-KO-Aged-A2-F3_S67_L004
03_GHS002 DEG KO Young vs KO Aged.xlsx


title: FL35_patB14_normal_pre_NR

value: normal

value: PRE

value: SR

value: C/SC


title: C3_CD40_AIR_unstim

value: isolated spleen, then expanded and transduced

value: primary cell

value: regulatory T-cell

value: sorted on CD4+CD25+CD90.1+


title: C2_HLA-A2_CARpos_HEK

description:
p138_counts.tsv
HLA2_CAR_RPKM.xlsx
HLA2_CAR_dds.rds


title: dleo1-1

description: Library name: 3_RNA-seq leo1Δ_rep1

value: LEO1 knockout


title: Knockdown-KO-Aged-A2-F2_S66_L004

description:
Library name: Sample 17
Collumn name in raw_counts_all_samples: Knockdown-KO-Aged-A2-F2_S66_L004
03_GHS002 DEG KO Young vs KO Aged.xlsx


title: FL31_patB36_normal_pre_NR

value: V

value: BRAFi


title: C1_HLA-A2_CAR_unstim


title: WT-2

description: Library name: 2_RNA-seq_WT_rep2

value: WT


title: WT-1

description: Library name: 1_RNA-seq_WT_rep1


title: KT-47 resistance2_3

type: genomic

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

description: genomic DNA from KT-47R2 chemotherapy resistant Wilms tumor patient-derived xenograft

hyb_protocol: Genomic DNA from each KT-47 WTPDX phenotype/timepoint were bisulfite converted using the EZ DNA Methylation kit (Zymo Research). Converted samples were processed and hybridized to the Infinium Methylation EPIC Bead-Chip (v1) system

scan_protocol: Unprocessed IDAT files containing summarized information from the beadchip array were processed using the subset-quantile within array normalization (SWAN) function as previously described.

data_processing: The methylation score of each CpG site in the array is represented as a beta (β) value (methylated signal/methylated +unmethylated signals) and was computed using the R package minifi.

label: Cy3 and Cy5

source_name: kidney tumor

label_protocol: Standard Illumina protocol

growth_protocol: KT-47 was heterotopically engrafted into the flanks of C.B-17 scid (C.B-Igh-1b/IcrTac-Prkdcscid) mice (6–8 weeks old; Taconic Farms, Hudson, NY, USA) without cell culture intermediates.

extract_protocol: Genomic DNA extraction from snap frozen samples of WTPDX tumors at each of the chemotherapy resistance phenotypes / timepoints (Pre-treatment, Pre-resistance, Resistance 1, Resistance 2) was performed using the Qiagen DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany) and confirmed using the Thermo Scientific NanoDrop™ One Microvolume UV-Vis Spectrophotometer (Thermo Fisher Scientific, Waltham, Massachusetts).

treatment_protocol: Tumor-bearing mice were treated with actinomycin-D (0.30 mg/kg intraperitoneal q21 days x 3; Baxter Oncology, Lebanon, NJ), vincristine (1 mg/kg intraperitoneal q7 days x 8; Hospira, Lake Forest, IL), and doxorubicin (4 mg/kg IV q7 days x 8; Pfizer, New York, NY, USA). Three timepoints were selected as experimental groups during this treatment schema for further inquiry: pre-treatment (no VAD chemotherapy exposure in WTPDX model), pre-resistance (VAD chemotherapy exposure without evidence of complete chemoresistance), and resistance (VAD chemotherapy exposure with complete chemotherapy resistance documented). The resistance timepoint was separated into resistance clone 1 and resistance clone 2 (KT-47R1, KT-47R2) which were originally derived from two different mice.

value: kidney tumor

value: Wilms tumor patient-derived xenograft

value: VAD


title: Knockdown-KO-Aged-A2-F1_S65_L004

description:
Library name: Sample 16
Collumn name in raw_counts_all_samples: Knockdown-KO-Aged-A2-F1_S65_L004
03_GHS002 DEG KO Young vs KO Aged.xlsx

value: Aorta

value: Knockdown-KO

value: Aged

value: Female


title: FL30_patB07_normal_pre_NR

value: normal

value: PRE

value: SR

value: LN


title: B3_CD40_AIR_unstim

value: isolated spleen, then expanded and transduced

value: primary cell

value: regulatory T-cell


title: KT-47 resistance2_4


title: FB92_patB18_tumor_pre_LR.

value: tumor

value: LR

value: BREAST


title: KT-47 resistance2_2

value: kidney tumor


title: Knockdown-KO-Young-F3_S62_L004

description:
Library name: Sample 13
Collumn name in raw_counts_all_samples: Knockdown-KO-Young-F3_S62_L004
02_GHS002 DEG KO Young vs WT Aged.xlsx

value: Young


title: B4_CD40_AIRpos_HEK-CD40L


title: A4_CD40_AIRpos_HEK-CD40L


title: FL33_patB06_normal_pre_LR

value: BRAFi


title: FB86_patB25_tumor_pre_LR


title: FB89_patB08_tumor_post_LR

value: POST

value: V


title: Knockdown-KO-Young-F1_S60_L004

description:
Library name: Sample 11
Collumn name in raw_counts_all_samples: Knockdown-KO-Young-F1_S60_L004
02_GHS002 DEG KO Young vs WT Aged.xlsx

value: Aorta

value: Knockdown-KO


title: Knockdown-KO-Young-F4_S63_L004

description:
Library name: Sample 14
Collumn name in raw_counts_all_samples: Knockdown-KO-Young-F4_S63_L004
02_GHS002 DEG KO Young vs WT Aged.xlsx

value: Female


title: Knockdown-KO-Young-F5_S64_L004

description:
Library name: Sample 15
Collumn name in raw_counts_all_samples: Knockdown-KO-Young-F5_S64_L004
02_GHS002 DEG KO Young vs WT Aged.xlsx


title: FB85_patB31_tumor_pre_LR

value: PRE

value: C/SC


title: A2_HLA-A2_CARpos_HEK


title: A1_HLA-A2_CAR_unstim

value: sorted on CD4+CD25+CD90.1+


title: B2_HLA-A2_CARpos_HEK

value: isolated spleen, then expanded and transduced


title: FB91_patB18_tumor_pre_LR.