title: KOGPR183-1

city: Jinan

first: Qingqing

last: Chu

state: Shandong

address: wenhuaxilu 44

department: School of basic medical science

institute: Shandong University

data_processing:
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence by using Seqtk.
The sample was mapped using Hisat2（version:2.0.4)
The quantification of transcripts expressed for each sequenced samples was performed using Stringtie（version:1.3.0）
Differentially expressed genes were identified using edgeR
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Mus kidney

extract_protocol:
RNA was harvested using MJzol animal RNA Extraction Kit (MagBeads). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The mice were underwent left unilateral nephrectomy. After one week, continuous 21-day release pellets (DOCA, 50mg) were implanted subcutaneously under isoflurane anesthesia，drinking water was replaced with 1.0% NaCl 1 day.

value: Mus renal cortex

value: At 3 months, the mice were euthanized and the kidney tissue samples were harvested for histopathological analysis.


title: WT-3

status: Public on Jun 23 2024

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: genotype

value: WT

tag: treatment


title: WT-2


title: 24M-3

value: Mus glomeruli cortex

value: At 24 months, the mice were euthanized and the kidney tissue samples were harvested for histopathological analysis.


title: KOGPR183-2


title: TCR_Tumor_T1_3

city: Hangzhou

first: Shiqun

last: Wang

state: Zhejiang Province

address: No. 150, Fucheng Road, Hangzhou Economic and Technological Development Zone

institute: Institute of Cancer and Basic Medicine, Chinese Academy of Sciences (CAS)

description: 10X Genomics single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1
Assembly: Mus_musculus (GRCm39)
Supplementary files format and content: Results from Illumina sequencing offline were converted to FASTQ format using bcl2fastq software (version 5.0.1).
Supplementary files format and content: Tab-separated values files and matrix files

source_name: KPC shUbed3-1 tumor tissues

extract_protocol:
The obtained tissues were transferred to a Petri dish (Petri dish was placed on wet ice) pre-spiked with 1×PBS (without RNase and Ca, Mg ions) and washed with 1XPBS to remove blood stains, grease and other adherents from the tissue surface. The tissue was then cut into 0.5 mm2 pieces and washed again with 1×PBS. The washed pieces were added with dissociation solvent (0.35% collagenase IV5, 2 mg/ml papain, 120 Units/ml DNase I) and reacted for 20 min at 37°C in a water bath shaker (100 rpm). PBS (containing 10% fetal bovine serum) was used to terminate the dissociation. The cells were repeatedly puffed 5-10 times with a pipette gun (gentle handling to prevent cell death due to shear force). The cell suspension was filtered through a 70-30um cell sieve and subsequently centrifuged at 300g for 5 min at 4°C. After centrifugation, the cell sediment was collected and the cells were resuspended by adding 100ul of 1× PBS(0.04% BSA)solution. To remove erythrocytes, 1 ml of 1X erythrocyte lysis solution (MACS 130-094-183, 10×) was added and reacted at room temperature or on wet ice for 2-10 min. After lysis, the cells were centrifuged at 300g for 5 min at 4°C, and the cell precipitate was collected after centrifugation. Add 100μl of Dead Cell Removal MicroBeads (MACS 130-090-101), mix well and incubate for 15min at room temperature. At the end of incubation, Binding Buffer was added, after MS Columns (130-042-201) to remove reagents, and dead cells.Cell precipitates were collected by centrifugation at 300g for 5min at 4°C. Subsequently 1×PBS (0.04% BSA) was used to resuspend the cell precipitate and centrifuged at 4°C 300g for 5min (repeated twice). The candidate cells were obtained after tissue dissociation, lysis of erythrocytes and removal of dead cells, and 100 μl of 1×PBS (0.04% BSA) was added to form a cell suspension. The cell activity was detected by trypan blue staining method, and the cell activity was required to be >85%. The number of cells was counted using a hemocytometer or Countess II Automated Cell Counter, and the cell concentration was 700-1200 cells/μ.
Chromium 10x Genomics library and sequencing
For the mRNA library, cDNA was fragmented to 200-300 base pairs, with sequencing adapters and primers added as per traditional library preparation methods, concluding with PCR amplification. For the immune repertoire library, nested PCR targeting the constant region of TCR/BCR enriched TCR sequences. Following fragmentation and controlled interruption for full V(D)J cDNA sequence coverage, the fragments were prepared with A-tailing and adapter ligation, creating a V(D)J library equipped with P5 and P7 adapters.

value: KPC shUbed3-1 tumor tissues

tag: cell type

value: FCM-sorted tumor-inflitrating CD8+ T cells


title: KOGPR183-3


title: mRNA_Tumor_C1_3

description: 10X Genomics single cell

source_name: KPC shScramble tumor tissues

value: KPC shScramble tumor tissues


title: WT-1


title: 3M-3


title: 24M-2


title: 24M-1


title: 3M-2


title: 3M-1


title: DOCA-Z922

value: The mice were underwent left unilateral nephrectomy. After one week, continuous 21-day release pellets (DOCA, 50mg) were implanted subcutaneously under isoflurane anesthesia，drinking water was replaced with 1.0% NaCl 1 day.


title: DOCA-Z923


title: BMDMs, MR_Pu1_2

city: Shanghai

first: Jiahui

last: Du

address: Zhizaoju Road 639

institute: Shanghai Jiao Tong University

library_source: genomic

data_processing:
Clean reads were aligned to the GRCm39 mouse genome using Bowtie 2 (v2.3.5.1)
Multiple aligned reads were filtered out using Picard
Then the unique mapped reads without duplicated reads were called for peaks using MACS2
The peaks were annotated using ChIPseeker
motif analyses were carried out using the MEME
Assembly: Mus_musculus.GRCm39.
Supplementary files format and content: Excel files include peak annotation

molecule: genomic DNA

source_name: bone marrow-derived monocytes (BMDMs)

growth_protocol: Bone marrow cells were harvested from murine femurs and cultured in α-minimum essential medium containing 10% FBS and 1% penicillin-streptomycin overnight.

extract_protocol:
BMDMs were harvested and  fixed with 1% formaldehyde for 10 minutes.The Simple ChIP Plus Enzymatic Chromatin IP Kit (Magnetic Beads; Cell Signaling Technology 9005) were used following the manufacturer’s instructions.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit.

treatment_protocol: For osteoclast induction, BMDMs were cultured into complete media with 50 ng/ml recombinant soluble murine M-CSF (PeproTech, 315-02),100 ng/ml recombinant soluble murine RANKL.

value: CONTROL

value: bone marrow-derived monocytes (BMDMs)

tag: chip antibody

value: PU.1 antibody (Abcam, ab227835)

value: M-CSF and RANKL


title: Sham for DOCA-Z922

value: The mice were underwent left unilateral nephrectomy with normal diet and drinking.


title: BMDMs, MR_Input


title: Sham for DOCA-Z923


title: BMDMs, M_Arid1a

value: ARID1A antibody (Cell signaling, 12345)

value: M-CSF


title: BMDMs, M_Input

description:
M_Arid1a_peaks.annotatePeaks.xlsx
M_Brd4_peaks.annotatePeaks.xlsx


title: E13 mouse head, biological replicate #2

city: Berlin

first: Daniel

last: León-Perinán

address: Hannoversche Str. 28,

country: Germany

institute: Max Delbrück Center

description: Fresh frozen spatial transcriptome sequencing

data_processing:
Assembly: GRCm39
Raw sequencing data were processed with bcl2fastq to generate FASTQ files
Sequences were processed with spacemake v0.7.3 using default configurations for open-ST. Flow cell barcodes were preprocessed with tools from the openst package, and the barcode coordinate files were used in spacemake as puck files
Spatial gene expression quantification was post-processed with the tools included in the openst package, for image alignment and cell segmentation, using default settings.
Assembly: GRCm39 primary assembly with the Gencode vM30 annotation was utilized.
Supplementary files format and content: e13_mouse_head.h5ad.tar.gz: compressed AnnData file containing the spatial transcriptomics data aggregated per segmented cell, with the staining image and the segmentation mask, after filtering for UMIs, genes and % mitochondrial content. Spatial coordinates are aligned to staining image and provided in pixel scale (~0.345 micron/pixel).
Supplementary files format and content: fc_3_coordstar.gz: for fc_3, collection of tsv files containing the barcodes and x,y coordinates for each tile. All tiles are included.
Supplementary files format and content: fc_3_coordinate_system.csv: for fc_3, global offsets for the x,y coordinates of individual tiles, to allow stitching together
Library strategy: Spatial transcriptomics

molecule: polyA RNA

source_name: E13 wild-type mouse

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat
Poly-dT primed reverse transcription, random-primed second strand synthesis, PCR-amplification and adapter addition

value: E13 wild-type mouse


title: TCR_Tumor_C1_3

description: 10X Genomics single cell


title: WT, replicate2, scRNA-seq

city: Shenzhen

first: Chunyan

last: Liao

address: 1068 Xueyuan Avenue, Shenzhen University Town

department: BCBDI

institute: SIAT

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing an gene counting were made using the Cell Ranger software v7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: retina

extract_protocol:
We dissected the retinas from WT and rd1 mice, and obtained retinal single-cell suspensions using Papain Dissociation System Source (Worthington Biochemical Corporation, LK003153) according to the manufacturer’s instructions. Briefly, we collected the eyes from WT and rd1 mice at postnatal day 15 (P15). We immediately isolated the retinas from the eyes, digested the fresh retinas with a papain dissociation kit for 3 min at 37℃,  degrees Celsius, and stopped the papain digestion by adding 10% fetal bovine serum (Thermo, 10091-148). We removed undigested tissue using a 40-μm cell strainer (Falcon, 352340). We counted the cell suspension using a counting chamber and tested cell viability using 0.4% trypan blue. We then filtered the cell suspension with a 40-μm cell strainer (Falcon, 352340) and washed it with ice-cold PBS containing 1% fetal bovine serum. We prepared single cells for use following 10xGenomics Single Cell Protocols.
Library was performed according to the manufacter's instrucion (single cell 3' v3 protocol, 10x Genomics)

value: retina

tag: strain

value: all retina cells

tag: age


title: BMDMs, M_Brd4

value: BRD4 antibody (Bethyl Laboratories, A700-004)


title: RD1, replicate2, scRNA-seq

description: 10x Genomics


title: RD1, replicate1, scRNA-seq

description: 10x Genomics


title: WT, replicate1, scRNA-seq

description: 10x Genomics

value: WT


title: ctl, ip, 24h, 6

city: Homburg

first: QILIN

last: GUO

address: Kirrberger Str. 100, CIPMM, Geb.48

department: Department of physiology

institute: Saarland University

data_processing:
The RNA sequencing reads quality was assessed using FastQC. Reads were aligned to the GRCm38 Mus musculus genome using HISAT2 v2.0.5 with default parameters. Gene count matrix of each sample was generated by featureCounts v1.5.0-p3.
Assembly: mm10
Supplementary files format and content: tab-delimited tex file includes raw counts for each sample

source_name: Cortex

extract_protocol:
After perfusion with ice-cold HBSS, cortical regions samples were dissected from mouse brain and stored at − 80°C until use. Tissues were homogenized in ice-cold lysis buffer (50 mM Tris, pH 7.4, 100 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT, 1x protease inhibitor, 200 units/ml RNasin (Promega) and 0.1 mg/ml cycloheximide (Sigma-Aldrich) in RNase-free deionized H2O) 10% w/v with homogenizer (Precellys 24, PeQlab). Then homogenates were centrifuged at 10,000 g at 4°C for 10 min to remove cell debris. Supernatants were collected and removed: 50 μl were used as input analysis. Anti-HA Ab (1:100, Covance) was added to the supernatant with slow rotation at 4°C. Meanwhile, Dynabeads Protein G (Thermo Fisher Scientific) were equilibrated to the lysis buffer by washing three times. After 4 h of incubation with HA Ab, 100 μl pre-equilibrated beads were added to each sample and incubated overnight at 4°C. After 10-12 h, Dynabeads were washed with high-salt buffer (50 mM Tris, 300 mM KCl, 12 mM MgCl2, 1% NP-40, 1 mM DTT, 1x protease inhibitor, 100 units/ml RNasin and 0.1 mg/ml cycloheximide in RNase-free deionized H2O) three times for 5 min at 4°C. At the end of the washing, beads were magnetized and 350 µl RLT buffer from RNeasy Micro Kit (74004, Qiagen) was added to the beads. RNA was extracted followed with manufacturer's instructions.
The library was prepared and sequenced by Novogene using the following methods. Preliminary quality control was performed on 1% agarose gel electrophoresis to test RNA degradation and potential contamination. Sample purity and preliminary quantitation were measured using Bioanalyser 2100 (Agilent Technologies, USA), which was also used to check the RNA integrity and final quantitation. For library preparation, the mRNA present in the total RNA sample was isolated with magnetic beads of oligos d(T)25. This method is known as polyA-tailed mRNA enrichment. Subsequently, mRNA was randomly fragmented and cDNA synthesis proceeds using random hexamers and the reverse transcriptase enzyme. Once the synthesis of the first chain is finished, the second chain is synthesized with the addition of an Illumina buffer. Together with the presence of dNTPs, RNase H and polymerase I from E.coli, the second chain will be obtained by nick translation. The resulting products go through purification, end-repair, A-tailing and adapter ligation. Fragments of the appropriate size are enriched by PCR, where indexed P5 and P7 primers are introduced, and final products are purified. The library was checked with Qubit 2.0 and real-time PCR for quantification and bioanalyzer Agilent 2100 for size distribution detection. Quantified libraries were pooled and sequenced on Illumina Novaseq 6000 platform, according to effective library concentration and data amount.

value: Cortex

value: astrocyte

value: ctl


title: ctl, ip, 6h, 4


title: E13 mouse head

data_processing:
Assembly: GRCm39
Raw sequencing data were processed with bcl2fastq to generate FASTQ files
Sequences were processed with spacemake v0.7.3 using default configurations for open-ST. Flow cell barcodes were preprocessed with tools from the openst package, and the barcode coordinate files were used in spacemake as puck files
Spatial gene expression quantification was post-processed with the tools included in the openst package, for image alignment and cell segmentation, using default settings.
Assembly: For mouse-origin reads, GRCm39 primary assembly with the Gencode vM30 annotation was utilized. Likewise, the GRCh38 genome reference with the Gencode v43 basic annotation was utilized for alignment of human-origin reads
Supplementary files format and content: e13_mouse_head.h5ad: compressed AnnData file containing the spatial transcriptomics data aggregated per segmented cell, with the staining image and the segmentation mask. Same type of file is provided for the human primary, metastatic and healthy samples. The files for the E13 mouse head, primary HNSCC and healthy lymph node are filtered for UMIs, genes and % mitochondrial content. Spatial coordinates are aligned to staining image and provided in pixel scale (~0.345 micron/pixel).
Supplementary files format and content: adult_mouse_hippocampus.h5ad: compressed AnnData file containing the spatial transcriptomics data at each ~0.6 micron capture spot, with the H&E staining image and the segmentation mask.
Supplementary files format and content: metastatic_lymph_node_S2.tar.gz: compressed AnnData file containing the spatial transcriptomics data aggregated per segmented cell, with the staining image and the segmentation mask - one file for each of the 19 sections of the metastatic lymph node. The files are provided unfiltered (cells & genes).
Supplementary files format and content: metastatic_lymph_node_3d.h5ad: compressed AnnData file containing the spatial transcriptomics data aggregated per segmented cell, upon global alignment of spatial coordinates in 3D. The annotation of cell types is provided here. Cells are filtered for UMIs, genes and % mitochondrial content.
Supplementary files format and content: fc_X_coordstar.gz: for flow cell X, collection of tsv files containing the barcodes and x,y coordinates for each tile. Only tiles used in the samples above are included here.
Supplementary files format and content: fc_X_coordinate_system.csv: for flow cell X, global offsets for the x,y coordinates of individual tiles, to allow stitching together
Library strategy: Spatial transcriptomics


title: cKO, ip, 24h, 4

value: cKO


title: ctl, ip, 6h, 5


title: cKO, ip, 24h, 5


title: ctl, ip, 24h, 4


title: ctl, ip, 24h, 5


title: cKO, ip, 6h, 5


title: ctl, ip, 6h, 6


title: cKO, ip, 0h, 3


title: ctl, ip, 0h, 2


title: cKO, ip, 6h, 6


title: cKO, ip, 24h, 6


title: ctl, ip, 0h, 1


title: cKO, ip, 0h, 2


title: JQ1-2

data_processing:
Raw reads were trimmed using Cutadapt.
Trimmed reads were aligned with the GRCm39 genome using HISAT2
Read count extraction and normalization were performed using htseq.
Assembly: Mus_musculus.GRCm39.
Supplementary files format and content: Excel files include read count and fpkm values for each sample

growth_protocol: Bone marrow cells were harvested from murine tibias and femurs of C57BL/6 mice and cultured in α-minimum essential medium containing 10% FBS and 1% penicillin-streptomycin overnight.

extract_protocol:
BMDMs was collected for RNA isolation using TRIzol.
Libraries were prepared using NEBNext Ultra II RNA Library Prep Kit

value: wild type


title: cKO, ip, 6h, 4


title: cKO, ip, 0h, 1


title: JQ1-1


title: CONTROL-2


title: LAC_MR2

value: CONTROL


title: LAM_MR2

value: bone marrow-derived monocytes (BMDMs)


title: M_Input


title: CONTROL-1


title: LAC_MR1


title: LAM_MR1


title: C_H3K27ac

value: H3K27Ac antibody (Cell signaling, 8173)


title: ctl, ip, 0h, 3


title: M_Brd4

value: M-CSF and RANKL


title: 1_Arid1a


title: C_Input


title: 1_Input


title: MUTANT

description: 10x Genomics

data_processing:
Quality control, alignment, quantification and aggregation of sample count matrices were performed using the 10x Genomics Cell Ranger pipeline according to the manufacturer’s protocol.
Assembly: Mus_musculus.GRCm39.
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Osteoclast induced BMDMs was collected after trypsin digestion, washed and re-suspended in PBS.
Single cells were loaded on a 10X Genomics GemCode Single-cell instrument. Libraries were generated and sequenced from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. and subjected to Illumina NovaSeq 6000.


title: C_Brd4


title: Rela and Stat3 knockout treated 3

city: New Delhi

first: Debasisa

last: Mohanty

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Imunology

data_processing:
The fastp tool was used to remove low qulaity reads and trimming the adapters.
Processed reads were mapped to reference genome (reference: mm9) using hisat2 tool.
Assembly and Quantification were done using stringtie. Further, DESeq2 used for the differential expression analysis.
Assembly: mm9
Supplementary files format and content: processed_count_file.csv

source_name: Liver

extract_protocol: RNA extraction was performend using MN-NucleoSpin RNA

treatment_protocol: 2% DSS was administered in water for a period of 6 days

value: Liver

tag: strain background

value: Rela and Stat3 knockout

value: DSS


title: Rela and Stat3 knockout treated 2


title: Rela and Stat3 knockout treated 1


title: WT treated 2


title: Rela and Stat3 knockout untreated 1

value: Water


title: WT untreated 3


title: WT treated 1


title: Rela and Stat3 knockout untreated 2


title: WT untreated 2


title: JCB-13 E14.5 GFP- GFP

city: Houston

first: Huda

last: Zoghbi

state: Tx

address: 1250 Moursund St

country: USA

institute: Baylor College of Medicine

data_processing:
Adapter trimming with Trimmomatic version 0.36 (2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25) and kseq
Alignment was performed with bowtie2-2.3.4.1 (--dovetail --phred33)
samtools (1.10) used to isolate fragmnets <120bp (for CIC and IgG) and generate BAM files
Bedtools (v2.29.1) was used to process BAM files to BED files, remove blacklist, and generate bigwigs.
Bedtools (v2.29.1) was used to merge replicate BAM files together for peak calling
Peaks called using MACSr (version 1.00, macs3 callpeak parameters “BAMPE”, qvalue = 0.05)
Assembly: mm10 (GRCm38 GCA_000001635.2) and the spike in Ecoli K12 Genomes (GCF_000005845.2_ASM584v2)
Supplementary files format and content: BW
Library strategy: CUT&RUN

source_name: hindbrain

extract_protocol:
The hindbrains of 28 E12.5 and 24 E14.5 Atoh1GFP/GFP embryos were dissected  in ice-cold HEBG media (0.8X B27, 0.25X GlutaMAX in Hibernate E media). Tissues were incubated with Worthington Papain solution at 37°C for 30 min at 800 rpm. At the end of incubation, the samples were transferred to 15 mL falcon tube, followed by gentle trituration with serologic pipette. The cell pellets were collected by centrifuge at 200 rcf for 3 min at 4°C, washed and resuspended in ice-cold sorting buffer (PBS with 0.05% fetal bovine serum). The single-cell resuspension was loaded to 30 µm cell drainer to remove debris, followed by DAPI staining at RT for 5 min. GFP+DAPI- and GFP-DAPI- cells were sorted by Sony SH800S. CUT&RUN was then performed on 200,000 sorted cells with an anti-GFP antibody and IgG antibody for each sample.
Following protocols.IO (dx.doi.org/10.17504/protocols.io.bagaibse) using NEB Next Ultra II DNA Library Prep Kit (E7645S) and NEB Unique Combinatorial Dual index kit (E6442S)
Sequencing at GENEWIZ using Illumina Novaseq S2 lane with 150bp PE reads

value: hindbrain

tag: antibody

value: GFP (Rabbit monoclonal, Invitrogen, G10362; 1:1000)

value: Atoh1 GFP/GFP


title: CONTROL

description: 10x Genomics


title: Rela and Stat3 knockout untreated 3


title: JCB-12 E14.5 GFP+ GFP


title: JCB-10 E14.5 GFP- IgG

value: IgG (Rabbit monoclonal, Millipore, 12-370; 1:100)


title: JCB-9 E14.5 GFP+ IgG


title: JCB-5 E12.5 GFP- GFP


title: JCB-4 E12.5 GFP+ GFP


title: WT untreated 1


title: JCB-2 E12.5 GFP- IgG


title: E16.5, GFP/TdTom, replicate 2

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.1 with default settings.
Assembly: customized genome composed of mouse mm10 reference genome and WPRE sequence
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
The hindbrains of embryos were dissected  in ice-cold HEBG media (0.8X B27, 0.25X GlutaMAX in Hibernate E media). For each timepoint, at least 3 embryos were collected for each two independent replicates. Tissues were incubated with Worthington Papain solution at 37°C for 30 min at 800 rpm. At the end of incubation, the samples were transferred to 15 mL falcon tube, followed by gentle trituration with serologic pipette. The cell pellets were collected by centrifuge at 200 rcf for 3 min at 4°C, washed and resuspended in ice-cold sorting buffer (PBS with 0.05% fetal bovine serum). The single-cell resuspension was loaded to 30 µm cell drainer to remove debris, followed by DAPI staining at RT for 5 min. GFP+DAPI-, GFP+TdTom+DAPI-, or TdTom+DAPI- cells were sorted by Sony SH800S. The cells were pelleted by centrifuge at 200 rcf for 5 min at 4°C and resuspended in sorting buffer to make the final concentration of 1,000 cells/µL.
The cDNA libraries were constructed by 10x Genomics 3’ v3.1 kit following the user guide. Briefly, ~16,500 cells from one sample were mixed with reversed transcription master mix before loaded into Chromium Chip G. GEM containing cells, reversed transcription reagents, and barcoded gel beads were generated by Chromium Controller. The first strand cDNA was amplified, fragmentated, and ligated with sequencing adaptors and sample indices.

value: neurons

tag: condition

value: GFP/TdTom


title: E16.5, TdTom-only, replicate 1

description: 10x Genomics

value: TdTom-only


title: E14.5, TdTom-only, replicate 1

description: 10x Genomics


title: E16.5, GFP/TdTom, replicate 1

description: 10x Genomics


title: WT treated 3


title: E14.5, TdTom-only, replicate 2

description: 10x Genomics


title: E14.5, GFP/TdTom, replicate 2

description: 10x Genomics


title: E16.5, TdTom-only, replicate 2

description: 10x Genomics


title: E13.5, TdTom-only, replicate 1

description: 10x Genomics


title: E12.5, TdTom-only, replicate 1

description: 10x Genomics


title: E13.5, TdTom-only, replicate 2

description: 10x Genomics


title: E13.5, GFP/TdTom, replicate 2

description: 10x Genomics


title: E12.5, TdTom-only, replicate 2

description: 10x Genomics


title: E11.5, TdTom-only, replicate 2

description: 10x Genomics


title: E14.5, GFP/TdTom, replicate 1

description: 10x Genomics


title: E13.5, GFP/TdTom, replicate 1

description: 10x Genomics


title: E11.5, GFP/TdTom, replicate 1

description: 10x Genomics


title: E11.5, TdTom-only, replicate 1

description: 10x Genomics


title: E10.5, GFP-only, replicate 1

description: 10x Genomics

value: GFP-only


title: E12.5, GFP/TdTom, replicate 2

description: 10x Genomics


title: E10.5, GFP-only, replicate 2

description: 10x Genomics


title: WT_res,rep1

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

country: Japan

institute: RIKEN

data_processing:
Adaptor sequences and low quality bases in reads were trimmed using Trim Galore version 0.3.7
The trimmed reads were mapped to the mouse GRCm38 genome assembly using Bismark v0.24.1 with paired-end and non-directional mapping parameters
The methylation level of each CpG site was calculated as follows: number of methylated reads/number of total reads.
Assembly: mm10
Supplementary files format and content: txt

extract_protocol:
Genomic DNA was extracted by phenol chloroform dna extraction
Preparation of genomic DNA. The cells were suspended in a buffer comprising 20 mM Tris-HCl, pH 8.0, 0.4 M NaCl, 10 mM EDTA, 0.5% SDS, and 0.1 mg/ml RNase A, and then incubated at 37℃ for 1 h. Proteinese K was added to the sample at a concentration of 1 mg/ml, and then incubated at 56℃ for overnight. The sample was treated with phenol/chloroform followed by ethanol precipitation. The genomic DNA was dissolved in TE buffer. Preparation of the library. The genomic DNA (1 µg) was sheared by sonication to 100–500 bp using a Covaris S220 and purified by AMPure XP beads (Agencourt Bioscience Corp.). Then, genomic DNA libraries were constructed by KAPA Hyper Prep Kit (Kapa Biosystems) and xGen Stubby Adapter and UDI Primers Pairs kit (Integrated DNA technologies) according to manufacturer instructions. After adapter ligation, the DNA was treated with sodium bisulfite using EZ DNA Methylation GOLD kit (Zymo Research) following the manufacturer's instructions. Enrichment for adapter-ligated DNA was carried out through 17 PCR cycles using KOD One PCR Master mix (Toyobo). The concentration of the WGBS library was quantified by KAPA Library quantification kit (Kapa Biosystems). Paired-end DNA sequencing (2 × 150 bp) was then performed using the Illumina NovaSeq X plus (Illumina). We performed two technical replicates for WGBS. Each library was sequenced with 21–24 M read pairs.
MethylC-seq

tag: cell line

value: mESCs


title: R285C_res,rep2


title: JCB-1 E12.5 GFP+ IgG


title: R285C_res,rep1


title: Dnmt3b_ff,rep2

value: WT


title: E9.5, GFP-only, replicate 2

description: 10x Genomics


title: Dnmt3b_ff,rep1


title: Cdca7KO,rep2


title: Cdca7KO,rep1


title: E12.5, GFP/TdTom, replicate 1

description: 10x Genomics


title: H46K_PBMCs_CMV_TCR

city: Bethesda

first: Jennifer

last: Simpson

state: MD

address: 4 Center Drive

institute: NIAID

description: VDJ

library_source: other

data_processing:
Demultiplexing
CellRanger
Seurat
Assembly: Rhesus Macaque
Supplementary files format and content: For RNAseq: files are filtered barcodes, features and matrix
Supplementary files format and content: For TCRseq: files are filtered contig anotations

molecule: other

organism: Macaca mulatta

source_name: PBMCs

extract_protocol: 10x Genomics pipeline

treatment_protocol: Cells sorted from chronically infected Rhesus Macaques

value: PBMCs

value: primary cells

value: VY9 specific CD8


title: DFT1_Spleen_CMV_RNA

description: RNA

source_name: Spleen

value: Spleen


title: H46K_PBMCs_CMV_RNA

description: RNA


title: H46K_Spleen_CMV_RNA

description: RNA


title: E11.5, GFP/TdTom, replicate 2

description: 10x Genomics


title: DFT1_PBMCs_CMV_TCR

description: VDJ


title: DFT1_Spleen_CMV_TCR

description: VDJ


title: H46K_Spleen_CMV_TCR

description: VDJ


title: DF86_Spleen_CMV_TCR

description: VDJ


title: DFT1_PBMCs_CMV_RNA

description: RNA


title: DF86_Liver_CMV_TCR

description: VDJ

source_name: LIver

value: LIver


title: DF86_Liver_CMV_RNA

description: RNA

value: Liver


title: DF86_PBMCs_CMV_RNA

description: RNA


title: DF86_PBMCs_CMV_TCR

description: VDJ


title: E9.5, GFP-only, replicate 1

description: 10x Genomics


title: WT_res,rep2


title: DGRA_Spleen_Post-treatment controller_RNA

description: RNA

value: CM9 specific CD8


title: CB5X_PBMCs_CMV_RNA

description: RNA


title: DGRA_LNs_Post-treatment controller_TCR

description: VDJ

source_name: LNs

value: LNs


title: DGRA_MeLN_Post-treatment controller_RNA

description: RNA

source_name: MeLN

value: MeLN


title: CB5X_Spleen_CMV_TCR

description: VDJ


title: DGRA_Gut_Post-treatment controller_RNA

description: RNA

source_name: Gut

value: Gut


title: DGRA_Spleen_Post-treatment controller_TCR

description: VDJ


title: CB5X_PBMCs_CMV_TCR

description: VDJ


title: DGRA_LNs_Post-treatment controller_RNA

description: RNA


title: DGRA_MeLN_Post-treatment controller_TCR

description: VDJ


title: CB5X_Spleen_CMV_RNA

description: RNA


title: DGRA_PBMCs_Post-treatment controller_TCR

description: VDJ


title: DGPZ_MeLN_Post-treatment controller_TCR

description: VDJ


title: DGPZ_Spleen_Post-treatment controller_TCR

description: VDJ


title: DGPZ_MeLN_Post-treatment controller_RNA

description: RNA


title: DGPZ_LNs_Post-treatment controller_TCR

description: VDJ


title: DGPZ_Spleen_Post-treatment controller_RNA

description: RNA


title: DGP2_MeLN_Post-treatment controller_TCR

description: VDJ


title: DGPZ_PBMCs_Post-treatment controller_TCR

description: VDJ


title: DGPZ_PBMCs_Post-treatment controller_RNA

description: RNA


title: DGP2_Spleen_Post-treatment controller_TCR

description: VDJ


title: DGP2_MeLN_Post-treatment controller_RNA

description: RNA


title: DGPZ_LNs_Post-treatment controller_RNA

description: RNA


title: DGP2_Gut_Post-treatment controller_TCR

description: VDJ


title: DF86_Spleen_CMV_RNA

description: RNA


title: DGRA_Gut_Post-treatment controller_TCR

description: VDJ


title: Aged

organism: Homo sapiens

source_name: homo kidney

value: homo renal cortex

value: tissues adjacent to cancer from renal cell carcinoma operation


title: DGP2_LNs_Post-treatment controller_TCR

description: VDJ


title: DGP2_Gut_Post-treatment controller_RNA

description: RNA


title: DGP2_LNs_Post-treatment controller_RNA

description: RNA


title: DGP2_PBMCs_Post-treatment controller_RNA

description: RNA


title: DGXJ_Spleen_Noncontroller_RNA

description: RNA


title: DGP2_PBMCs_Post-treatment controller_TCR

description: VDJ


title: LG1_sample1

city: Chengdu

first: Yi

state: Please Select

address: 32 West Frist Ring Rd.,

institute: Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
Preprocessing and Quality Control: (1) Quality Filtering: Remove low-quality sequencing reads or artifacts introduced during library preparation. (2) Spatial Barcode Decoding: Decode spatial barcodes to assign each sequencing read to its spatial location within the tissue section. (3) Normalization: Normalize gene expression data to correct for technical biases and variability between samples.
Spatial Mapping: (1) Registration: Align the spatial coordinates of the tissue sections with a reference map, if available, to accurately map gene expression data onto the tissue structure. (2) Spatial Reconstruction: Reconstruct the spatial organization of gene expression within the tissue, creating spatially resolved expression maps.
Spatial Analysis: (1) Spatial Clustering: Group spatially co-expressed genes or spatially co-located cells into clusters to identify spatially distinct expression patterns. (2) Spatial Visualization: Visualize gene expression patterns within the tissue sections using spatial heatmaps, t-SNE plots, or other dimensionality reduction techniques. (3) Spatial Interaction Analysis: Analyze spatial relationships between genes or cell types to identify spatially co-regulated gene networks or cell-cell interactions.
Spatial Transcriptomics Integration: (1) Integration with Single-Cell Data: Integrate spatial transcriptomic data with single-cell RNA sequencing (scRNA-seq) data, if available, to compare spatially resolved gene expression patterns with single-cell gene expression profiles. (2) Integration with Spatial Imaging Data: Integrate spatial transcriptomic data with imaging data, such as histological stains or immunofluorescence images, to correlate gene expression with tissue morphology or protein localization.
Functional Analysis: (1) Pathway Analysis: Identify enriched biological pathways or gene ontology terms associated with spatially co-expressed gene clusters. (2) Cell Type Annotation: Assign cell type identities to spatially resolved expression patterns using marker genes or cell type-specific signatures. (3) Spatial Gene Expression Profiling: Characterize spatially specific gene expression patterns associated with particular cell types, tissue regions, or biological processes.
Visualization and Interpretation: (1) Spatial Visualization Tools: Utilize specialized software or packages for spatial visualization of gene expression data, allowing researchers to explore and interpret spatial patterns interactively. (2) Spatial Annotation: Annotate spatially resolved expression maps with relevant biological features or annotations to aid interpretation and visualization.
Assembly: GRCh38/hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots

source_name: left temporal lobe

extract_protocol:
The tissues were cut into 4-5 mm pieces and treated with cleanroom wipers. After removing blood stains on the tissue surface, fresh tissue was embedded with OCT then snap frozen. Cryosections were cut at 10-um thickness, mounted onto the ST arrays.Next, the tissue was dehydrated with isopropanol for 1 min followed by staining with HE. Brightfield images were taken on a Leica SCN400 F whole-slide scanner at 40x resolution.
Library preparation slides used were purchased from the Spatial Transcriptomics team. Each of the spots printed onto the array is 55um in diameter and 100um from center to center, covering an area of 6.5x6.5 mm2. Each slide includes 4 Capture Areas, each with ~5,000 unique gene expression spots.
Spatial Transcriptomic

value: left temporal lobe

value: human brain

value: Low-Grade Glioma


title: HG1_sample1

source_name: right temporal lobe

value: right temporal lobe

value: High-Grade Glioma


title: DGXJ_Spleen_Noncontroller_TCR

description: VDJ


title: HG2_sample2


title: LG2_sample2


title: Healthy lymph node

data_processing:
Assembly: GRCh38
Raw sequencing data were processed with bcl2fastq to generate FASTQ files
Sequences were processed with spacemake v0.7.3 using default configurations for open-ST. Flow cell barcodes were preprocessed with tools from the openst package, and the barcode coordinate files were used in spacemake as puck files
Spatial gene expression quantification was post-processed with the tools included in the openst package, for image alignment and cell segmentation, using default settings.
Assembly: For mouse-origin reads, GRCm39 primary assembly with the Gencode vM30 annotation was utilized. Likewise, the GRCh38 genome reference with the Gencode v43 basic annotation was utilized for alignment of human-origin reads
Supplementary files format and content: e13_mouse_head.h5ad: compressed AnnData file containing the spatial transcriptomics data aggregated per segmented cell, with the staining image and the segmentation mask. Same type of file is provided for the human primary, metastatic and healthy samples. The files for the E13 mouse head, primary HNSCC and healthy lymph node are filtered for UMIs, genes and % mitochondrial content. Spatial coordinates are aligned to staining image and provided in pixel scale (~0.345 micron/pixel).
Supplementary files format and content: adult_mouse_hippocampus.h5ad: compressed AnnData file containing the spatial transcriptomics data at each ~0.6 micron capture spot, with the H&E staining image and the segmentation mask.
Supplementary files format and content: metastatic_lymph_node_S2.tar.gz: compressed AnnData file containing the spatial transcriptomics data aggregated per segmented cell, with the staining image and the segmentation mask - one file for each of the 19 sections of the metastatic lymph node. The files are provided unfiltered (cells & genes).
Supplementary files format and content: metastatic_lymph_node_3d.h5ad: compressed AnnData file containing the spatial transcriptomics data aggregated per segmented cell, upon global alignment of spatial coordinates in 3D. The annotation of cell types is provided here. Cells are filtered for UMIs, genes and % mitochondrial content.
Supplementary files format and content: fc_X_coordstar.gz: for flow cell X, collection of tsv files containing the barcodes and x,y coordinates for each tile. Only tiles used in the samples above are included here.
Supplementary files format and content: fc_X_coordinate_system.csv: for flow cell X, global offsets for the x,y coordinates of individual tiles, to allow stitching together
Library strategy: Spatial transcriptomics

source_name: human healthy level III cervical  lymph node from 56-year old male with HNSCC


title: Metastatic lymph node, section #34

source_name: human metastatic level III cervical lymph node from 56-year old male with HNSCC


title: DGXJ_MeLN_Noncontroller_TCR

description: VDJ


title: DGXJ_MeLN_Noncontroller_RNA

description: RNA


title: DGXJ_Liver_Noncontroller_TCR

description: VDJ


title: Metastatic lymph node, section #36

value: human metastatic level III cervical lymph node from 56-year old male with HNSCC


title: DGXJ_LNs_Noncontroller_RNA

description: RNA

value: primary cells


title: Young


title: Metastatic lymph node, section #28


title: DGRA_PBMCs_Post-treatment controller_RNA

description: RNA

value: PBMCs


title: Metastatic lymph node, section #33


title: DGXJ_LNs_Noncontroller_TCR

description: VDJ


title: Metastatic lymph node, section #26


title: DGP2_Spleen_Post-treatment controller_RNA

description: RNA

value: Spleen


title: DGXJ_PBMCs_Noncontroller_TCR

description: VDJ


title: Metastatic lymph node, section #24


title: DGXJ_Liver_Noncontroller_RNA

description: RNA


title: Metastatic lymph node, section #25


title: DGXJ_PBMCs_Noncontroller_RNA

description: RNA


title: Metastatic lymph node, section #23


title: Metastatic lymph node, section #19


title: DGXD_Spleen_Noncontroller_RNA

description: RNA


title: DGXD_Spleen_Noncontroller_TCR

description: VDJ


title: DGXD_MeLN_Noncontroller_TCR

description: VDJ


title: Metastatic lymph node, section #18


title: Flow cell #3 barcodes

description: First sequencing of barcodes from capture oligos

data_processing:
Raw sequencing data were processed with bcl2fastq to generate FASTQ files
Sequences were processed with spacemake v0.7.3 using default configurations for open-ST. Flow cell barcodes were preprocessed with tools from the openst package, and the barcode coordinate files were used in spacemake as puck files
Spatial gene expression quantification was post-processed with the tools included in the openst package, for image alignment and cell segmentation, using default settings.
Assembly: GRCm39 primary assembly with the Gencode vM30 annotation was utilized.
Supplementary files format and content: e13_mouse_head.h5ad.tar.gz: compressed AnnData file containing the spatial transcriptomics data aggregated per segmented cell, with the staining image and the segmentation mask, after filtering for UMIs, genes and % mitochondrial content. Spatial coordinates are aligned to staining image and provided in pixel scale (~0.345 micron/pixel).
Supplementary files format and content: fc_3_coordstar.gz: for fc_3, collection of tsv files containing the barcodes and x,y coordinates for each tile. All tiles are included.
Supplementary files format and content: fc_3_coordinate_system.csv: for fc_3, global offsets for the x,y coordinates of individual tiles, to allow stitching together
Library strategy: Spatial transcriptomics

organism: synthetic construct

source_name: synthetic construct

value: synthetic construct


title: DGXD_LNs_Noncontroller_TCR

description: VDJ


title: Flow cell #2 barcodes

data_processing:
Assembly: NA
Raw sequencing data were processed with bcl2fastq to generate FASTQ files
Sequences were processed with spacemake v0.7.3 using default configurations for open-ST. Flow cell barcodes were preprocessed with tools from the openst package, and the barcode coordinate files were used in spacemake as puck files
Spatial gene expression quantification was post-processed with the tools included in the openst package, for image alignment and cell segmentation, using default settings.
Assembly: For mouse-origin reads, GRCm39 primary assembly with the Gencode vM30 annotation was utilized. Likewise, the GRCh38 genome reference with the Gencode v43 basic annotation was utilized for alignment of human-origin reads
Supplementary files format and content: e13_mouse_head.h5ad: compressed AnnData file containing the spatial transcriptomics data aggregated per segmented cell, with the staining image and the segmentation mask. Same type of file is provided for the human primary, metastatic and healthy samples. The files for the E13 mouse head, primary HNSCC and healthy lymph node are filtered for UMIs, genes and % mitochondrial content. Spatial coordinates are aligned to staining image and provided in pixel scale (~0.345 micron/pixel).
Supplementary files format and content: adult_mouse_hippocampus.h5ad: compressed AnnData file containing the spatial transcriptomics data at each ~0.6 micron capture spot, with the H&E staining image and the segmentation mask.
Supplementary files format and content: metastatic_lymph_node_S2.tar.gz: compressed AnnData file containing the spatial transcriptomics data aggregated per segmented cell, with the staining image and the segmentation mask - one file for each of the 19 sections of the metastatic lymph node. The files are provided unfiltered (cells & genes).
Supplementary files format and content: metastatic_lymph_node_3d.h5ad: compressed AnnData file containing the spatial transcriptomics data aggregated per segmented cell, upon global alignment of spatial coordinates in 3D. The annotation of cell types is provided here. Cells are filtered for UMIs, genes and % mitochondrial content.
Supplementary files format and content: fc_X_coordstar.gz: for flow cell X, collection of tsv files containing the barcodes and x,y coordinates for each tile. Only tiles used in the samples above are included here.
Supplementary files format and content: fc_X_coordinate_system.csv: for flow cell X, global offsets for the x,y coordinates of individual tiles, to allow stitching together
Library strategy: Spatial transcriptomics


title: IMR2_CD45 lo, replicate1

first: Jeffrey

middle: Andrew

last: How

state: TX

address: 1515 Holcombe Blvd. Unit 1362

department: Gyn Onc & Reproductive Med

institute: The University of Texas MD Anderson Cancer Center

data_processing:
STAR 2-pass alignment (v2.7.0f) was performed with default parameters to generate RNA- seq BAM files.
HTSeq-count (v0.11.0) tool was applied to aligned RNA-seq BAM files to count for each gene how many aligned reads overlap with its exons
RNA-Seq gene expression raw read counts generated from HTSeq-count (v0.11.0) were normalized into Transcripts Per Kilobase Million (TPM).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read count of each gene for each Sample

source_name: Brain Tumor

extract_protocol: Illumina Compatible low input mRNA libraries were prepared using the Smart-Seq V4 Ultra Low Input RNA kit (Takara Bio, USA) and KAPA HyperPlus Library Preparation kit (Roche). Briefly, full length, double-stranded cDNA was generated from 8ng of total RNA using Takara’s SMART (Switching Mechanism at 5’ end of RNA Template) technology. The ds cDNA was amplified by nine cycles of LD-PCR, then purified using Ampure Beads (Agencort). Following bead elution, the cDNA was evaluated for size distribution and quantity using the Fragment Analyzer High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies) and the Qubit dsDNA HS Assay Kit (ThermoFisher) respectively. The cDNA was enzymatically fragmented, and 20ng of the fragmented cDNA was used to generate Illumina compatible libraries using the KAPA HyperPlus Library Preparation kit. The KAPA libraries were purified and enriched with 2 cycles of PCR to create the final cDNA library. The libraries were quantified using the Qubit™ dsDNA HS Assay (ThermoFisher), then multiplexed 7 libraries per pool. The pooled libraries were quantified by qPCR using the KAPA Library Quantification Kit (KAPA Biosystems), and assessed for size distribution using the TapeStation 4200 (Agilent Technologies). The libraries were then sequenced, one pool per lane, on the Illumina HiSeq4000 sequencer using the 76bp paired end format.

value: Brain Tumor

value: Leukocytes

tag: diagnosis

value: Glioblastoma

value: IDH Mutant

tag: primary/recurrent

value: Recurrent

value: Standard of care


title: IMP3_CD45 lo, replicate1

value: Oligodendroglioma

value: Primary

value: Treatment Naive


title: IWR5_CD45 hi, replicate1

value: IDH Wild Type


title: DGXD_LNs_Noncontroller_RNA

description: RNA

value: LNs

value: CM9 specific CD8


title: Metastatic lymph node, section #6

value: human metastatic level III cervical lymph node from 56-year old male with HNSCC


title: DGXD_PBMCs_Noncontroller_RNA

description: RNA

value: primary cells


title: Metastatic lymph node, section #5


title: IMP3_CD45 hi, replicate1


title: DGRV_Spleen_Noncontroller_TCR

description: VDJ


title: IWR4, replicate1, mRNASeq


title: Metastatic lymph node, section #4


title: IWR3, replicate1, mRNASeq


title: DGRV_Spleen_Noncontroller_RNA

description: RNA


title: Metastatic lymph node, section #11


title: Metastatic lymph node, section #17


title: DGXD_MeLN_Noncontroller_RNA

description: RNA

value: MeLN


title: IWR1, replicate1, mRNASeq


title: Metastatic lymph node, section #3


title: IWR5_CD45 lo, replicate1


title: Metastatic lymph node, section #9


title: Flow cell #1 barcodes


title: DGRV_MeLN_Noncontroller_TCR

description: VDJ


title: IWP2, replicate1, mRNASeq


title: Metastatic lymph node, section #7


title: DGRV_MeLN_Noncontroller_RNA

description: RNA


title: IMR4, replicate1, mRNASeq


title: Primary HNSCC

source_name: human laryngeal squamous cell carcinoma (pT3 pN2c (2/29) L0 V0 Pn0 G2 R0) from 56-year old male


title: IWP1, replicate1, mRNASeq


title: DGRV_Liver_Noncontroller_TCR

description: VDJ

value: Liver


title: IMR3, replicate1, mRNASeq


title: IMR2_CD45 hi, replicate1


title: IMR2, replicate1, mRNASeq


title: GBM1A KD1 3

city: Jacksonville

first: Hugo

last: Guerrero-Cazares

state: Florida

address: 4500 San Pablo Rd., Griffin Building 111

department: Neurosurgery

institute: Mayo Clinic

data_processing:
Sequencing alignment is performed using STAR v2.6.1c
Fusions calling is performed using STAR-Fusion v1.4
Exon and gene counts were quantified using subread v1.5.1
Variant calling was performed by GATK HaplotypeCaller v3.7
Quality control was performed using a suite of custom tools called RSEQC
Assembly: hg38
Supplementary files format and content: raw counts, FPKM

growth_protocol: BTICs were maintained in DMEM/F12 with B27, antibiotics, 20 ng/mL epidermal growth factor (EGF), and 20 ng/mL FGF in a humidified incubator with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using TriZOL and underwent clean up with the Qiagen Rneasy Mini Kit.
Illumina TruSeq RNA Paired End

treatment_protocol: BTICs were transduced with either EV or KD at an MOI of 100. After 72h, cells were selected with polybrene (0.5 ug/mL) for 1 week. Following selection, cells recovered for an additional 72h and RNA was extracted.

value: Primary brain tumor initiating cells

value: CTSB KD


title: DGRV_Liver_Noncontroller_RNA

description: RNA


title: IWR2, replicate1, mRNASeq

value: Brain Tumor

value: Leukocytes

value: Glioblastoma/Gliosarcoma


title: GBM1A KD1 2


title: IMR1, replicate1, mRNASeq

value: Astrocytoma

value: IDH Mutant

value: Recurrent


title: IMP4, replicate1, mRNASeq

value: Oligodendroglioma

value: Primary


title: DGRV_LNs_Noncontroller_TCR

description: VDJ


title: Adult mouse hippocampus

source_name: male p60 wild-type mouse

value: male p60 wild-type mouse


title: DGRV_LNs_Noncontroller_RNA

description: RNA

value: LNs


title: NGB1, replicate1, mRNASeq

source_name: Quasi-normal Brain

value: Quasi-normal Brain

value: Dysembryoplastic neuroepithelial tumor

value: Not Applicable


title: GBM1A KD1 1


title: IWP3, replicate1, mRNASeq

value: IDH Wild Type

value: Treatment Naive


title: IMP3, replicate1, mRNASeq


title: PLC/PRF/5, tRNA-seq-TARBP1-KO-2

first: Hao

last: Chen

address: 1088 Xueyuan Avenue

institute: Southern University of Science and Technology (SUSTech)

data_processing:
Trimmed reads in FASTQ format were given as input to MINTmap for identifying and quantifying reads associated with tRFs.
The sample normalization and differential expression was performed using the DESeq2 (version 1.32.0)
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include the normalized abundance measurements for each sample.

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium (DMEM, Gibco) containing 10% fetal bovine serum (FBS, BI) and 1% penicillin-streptomycin.

extract_protocol:
Total RNA samples isolated from PLC/PRF/5 cells with or without TARBP1 depletion were first subjected to small RNA purification using the Zymo Research RNA Clean & Concentrator-25 kit (Zymo). The isolated small RNAs were heated at 75°C for 2 min to denature tRNA and then incubated with ALKB-D135S protein in buffer containing 300 mM KCl, 2 mM MgCl2, 50 µM of (NH4)2Fe(SO4)2·6H2O, 300 µM 2-ketoglutarate (2-KG), 2 mM l-ascorbic acid, 50 µg/ml BSA, 50 mM MES buffer (pH 5.0) for 2 hours at room temperature. The demethylated RNAs were purified by the Zymo Research RNA Clean & Concentrator-25 kit and then treated with PNK.
Purified RNA was treated with PNK, and the RNA library was prepared by VAHTSTM Small RNA Library Prep Kit for Illumina®.

value: TARBP1 KO


title: DGRV_PBMCs_Noncontroller_TCR

description: VDJ

value: PBMCs

value: primary cells

value: CM9 specific CD8


title: GBM1A EV 2

value: Primary brain tumor initiating cells

value: EV


title: IMP1, replicate1, mRNASeq

value: Brain Tumor

value: Leukocytes

value: Astrocytoma

value: IDH Mutant


title: PLC/PRF/5, tRNA-seq-TARBP1-KO-1


title: DGRV_PBMCs_Noncontroller_RNA

description: RNA


title: PLC/PRF/5, tRNA-seq-WT-2

value: Wild-type


title: PLC/PRF/5, RNA-seq-TARBP1-KO-rep 3

description:
TARBP.RNA.KO.rep3
TARBP1_RNA-Seq_gene_count_matrix.csv
TARBP1_TE_res.csv

data_processing:
Processed reads were aligned to the reference genome (GRCh38) by the STAR (version 2.7.10a)33, allowing for at most two mismatches.
StringTie (v2.1.7) was used to calculate the raw read count. Both read counts of Ribo-seq and RNA-seq were converted to TPM (transcripts per million).
Quality control was performed by Ribotoolkit. Genes with sufficient expression level (Ribo TPM > 1 and RNA TPM > 5) were subjected to further analysis.
Translation efficiency (TE) and the differentially-TE genes (DTEGs) were calculated by RiboDiff (v0.2.2).
Assembly: GRCh38
Supplementary files format and content: CSV (Comma-Separated Values) files include normalized abundance measurements for all RNA-Seq samples.
Supplementary files format and content: CSV (Comma-Separated Values) files include normalized abundance measurements for all Ribo-Seq samples.
Supplementary files format and content: CSV (Comma-Separated Values) files include differentially translated mRNAs.

source_name: Human liver

extract_protocol:
Two 15-cm plates of PLC/PRF/5 cells with approximately 80-90% confluency were used per group. Cells were incubated with 100 μg/ml Cycloheximide for 8 min at 37°C and were then lysed on ice for 10min in 400uL lysis buffer (20 mM Tris–HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml Cycloheximide, 1% Triton X-100). The supernatant was collected via centrifugation at 12 000 g for 10 min at 4 °C, and its' absorbance at 260nm was measured. The ribosomes with equal A260 in each group were reserved for RNA sequencing. Added 15U RNase1 for each 1OD of lysate, and incubated the reactions at 22°C for 40 min with gentle mixing. Ribosome-protected fragments (RPFs) were collected by MicroSpin S-400 columns (Cytiva) and purified by Zymo Research RNA Clean & Concentrator-25 kit. The RPFs were then separated with 15% polyacrylamide TBE–urea gel, excised the gel slices between 17 and 34 nucleotides and recovered RNA from PAGE gel by ZR small-RNA™ PAGE Recovery Kit (Zymo).
Purified RNA was treated with PNK, and the RNA library was prepared by VAHTSTM Small RNA Library Prep Kit for Illumina®.

value: Human liver

value: Cancer cell

value: Normal culture condition


title: PLC/PRF/5, tRNA-seq-WT-1


title: DG3H_Spleen_Noncontroller_RNA

description: RNA

value: Spleen


title: PLC/PRF/5, RNA-seq-TARBP1-KO-rep 2

description:
TARBP.RNA.KO.rep2
TARBP1_RNA-Seq_gene_count_matrix.csv
TARBP1_TE_res.csv


title: PLC/PRF/5, Ribo-seq-TARBP1-KO-rep 2

description:
TARBP1-Ribo-KO-rep2
TARBP1_Ribo-Seq_gene_count_matrix.csv
TARBP1_TE_res.csv

data_processing:
Processed reads were aligned to the reference genome (GRCh38) by the STAR (version 2.7.10a)33, allowing for at most two mismatches.
StringTie (v2.1.7) was used to calculate the raw read count. Both read counts of Ribo-seq and RNA-seq were converted to TPM (transcripts per million).
Quality control was performed by Ribotoolkit. Genes with sufficient expression level (Ribo TPM > 1 and RNA TPM > 5) were subjected to further analysis.
Translation efficiency (TE) and the differentially-TE genes (DTEGs) were calculated by RiboDiff (v0.2.2).
Assembly: GRCh38
Supplementary files format and content: CSV (Comma-Separated Values) files include normalized abundance measurements for all RNA-Seq samples.
Supplementary files format and content: CSV (Comma-Separated Values) files include normalized abundance measurements for all Ribo-Seq samples.
Supplementary files format and content: CSV (Comma-Separated Values) files include differentially translated mRNAs.
Library strategy: Ribo-seq


title: GBM1A EV 3


title: PLC/PRF/5, RNA-seq-TARBP1-KO-rep 1

description:
TARBP.RNA.KO.rep1
TARBP1_RNA-Seq_gene_count_matrix.csv
TARBP1_TE_res.csv


title: DG3H_MeLN_Noncontroller_TCR

description: VDJ

value: MeLN


title: PLC/PRF/5, Ribo-seq-TARBP1-KO-rep 1

description:
TARBP1-Ribo-KO-rep1
TARBP1_Ribo-Seq_gene_count_matrix.csv
TARBP1_TE_res.csv


title: HD/100CAG_striatum_neuropathology_male4

type: RNA

city: Poznan

first: Agnieszka

last: Fiszer

address: Noskowskiego Str. 12/14

department: Department of Medical Biotechnology

country: Poland

institute: Institute of Bioorganic Chemistry Polish Academy of Sciences

hyb_protocol: Isolated RNA (100ng of toral RNA) was hybridized to the Reporter CodeSet and Capture ProbeSet according to Nanostring manufacture specifications.

scan_protocol: Raw count data were collected and captured by the nCounter Digital Analyzer

data_processing: Following data collection, the raw data were pre-processed using nSolver 4.0 software (NanoString Technologies) for sample quality control (QC), background corection and normalization. The background correction was estimated by a defined threshold count value of 25. The data were normalized to the geometric mean of the average count of six positive controls included in the assay and ten housekeeping genes included in the neuropathology panel.

label: NanoString

source_name: HD/100CAG_striatal tissue04

label_protocol: Gene expression profiling of striatal tissues was conducted using the nCounter® Mouse Neuropathology Gene Expression panel (XT-CSO-MNROP1-12) according to the manufacturer's protocols.

growth_protocol: Male homozygous transgenic mice (HD/100Q and HD/100CAG) and wild-type (WT) littermates at 21 months of age were used in the Nanostring experiment. The animals were housed in the animal facility of the Center for Advanced Technologies Adam Mickiewicz University in Poznan, Poland, at a controlled temperature and humidity under specific pathogen-free (SPF) conditions on a 12-h light/12-h dark cycle and provided access to water and food ad libitum.

extract_protocol: Total RNA was extracted from frozen mouse striatal tissues with an RNeasy Lipid Tissue Mini Kit (Qiagen). Tissues were homogenized in Qiazol Lysis Reagent by being passed through a syringe and needle at least 7–10 times until a homogeneous lysate was obtained.   The genomic DNA was digested on a column with an RNaseFree DNase Set (Qiagen). The RNA concentration and quality were determined using a spectrophotometer (DeNovix) and a fluorometer (Qubit RNA BR Assay Kit, Thermo Fisher Scientific).

tag: Sex

value: male

tag: experimental group

value: HD/100CAG model

value: 21 months

value: striatum


title: PLC/PRF/5, RNA-seq-WT-rep 3

description:
TARBP.RNA.WT.rep3
TARBP1_RNA-Seq_gene_count_matrix.csv
TARBP1_TE_res.csv


title: DG3H_MeLN_Noncontroller_RNA

description: RNA

value: primary cells

value: CM9 specific CD8


title: PLC/PRF/5, Ribo-seq-WT-rep 2

description:
TARBP1-Ribo-WT-rep2
TARBP1_Ribo-Seq_gene_count_matrix.csv
TARBP1_TE_res.csv


title: DG3H_Liver_Noncontroller_TCR

description: VDJ

source_name: Liver

value: Liver


title: PLC/PRF/5, RNA-seq-WT-rep 2

description:
TARBP.RNA.WT.rep2
TARBP1_RNA-Seq_gene_count_matrix.csv
TARBP1_TE_res.csv


title: HD/100CAG_striatum_neuropathology_male1

source_name: HD/100CAG_striatal tissue01


title: HD/100Q_striatum_neuropathology_male4

source_name: HD/100Q_striatal tissue04

value: HD/100Q model


title: PLC/PRF/5, Ribo-seq-WT-rep 1

description:
TARBP1-Ribo-WT-rep1
TARBP1_Ribo-Seq_gene_count_matrix.csv
TARBP1_TE_res.csv


title: DG3H_Liver_Noncontroller_RNA

description: RNA


title: HD/100CAG_striatum_neuropathology_male2

source_name: HD/100CAG_striatal tissue02


title: HD/100CAG_striatum_neuropathology_male3

source_name: HD/100CAG_striatal tissue03


title: GBM1A EV 1

value: Primary brain tumor initiating cells

value: EV


title: PLC/PRF/5, RNA-seq-WT-rep 1

description:
TARBP.RNA.WT.rep1
TARBP1_RNA-Seq_gene_count_matrix.csv
TARBP1_TE_res.csv


title: FST315-GAN-22

city: Boston

first: rongya

last: tao

state: Ma

address: 300 longwood ave

institute: Boston children's hospital

data_processing:
NGS 4.0
Assembly: mm10
Supplementary files format and content: table-delimited xlsx file including the raw counts

extract_protocol:
Total RNAs were isolated from  tissues using TRI Reagent (Sigma).
SMARTER Mrna-aeq library prep kit

value: tissue

value: GAN diet


title: HD/100Q_striatum_neuropathology_male3

source_name: HD/100Q_striatal tissue03


title: Metastatic lymph node, section #2

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat
Poly-dT primed reverse transcription, random-primed second strand synthesis, PCR-amplification and adapter addition

value: human metastatic level III cervical lymph node from 56-year old male with HNSCC


title: DG3H_Spleen_Noncontroller_TCR

description: VDJ

source_name: Spleen


title: HD/100Q_striatum_neuropathology_male2

source_name: HD/100Q_striatal tissue02


title: DG3H_LNs_Noncontroller_TCR

description: VDJ

source_name: LNs

value: LNs


title: IWR4, replicate1, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol: scRNA-seq was performed using 10x Genomics Chromium Single Cell Controller. Sorted cells were washed with 1X PBS and suspended in PBS/0.04% BSA. Cells were double-checked for viability and cell number by using the countess II FL and microscope. All cells were diluted to a concentration of 500-1000 cells/μl in PBS/0.04% BSA before being used for single cell 10X 3’v3. Single cells were captured using the 10X genomic controller according to the bead types and chip used for the experiments. The 10X genomic Chromium Single cell 3’ GEM, library and Gel bead Kit ’v3 (Catalogue #1000075) and chromium chip B single cell kit (Part# 1000073) were used to capture cells on the controller; cell recovery targeted was in a range of 5000 - 10000 cells. Captured cells then undergo a GEM-RT, cDNA amplification, and all purification in accordance to the 10X protocol. Cleanup cDNA was checked via a tape station (Agilent 42000) HSD5000 (Catalogue# Part# 5067-5593) for cDNA traces. 25% of the cDNA was used to generate the library, and the Chromium i7 multiplex kit (Part# 120262) was used to identify each sample. Library cleanup was performed using AMPure beads and QC was done again with tape station D1000 tapes (Part # 5067-5583). Ten libraries of equal amount were pooled to give a final concentration of 10nM and submitted for sequencing with the NovaSeq6000 S2 sequencer, 28 cycles for read1, 8 cycles for i7 index, and 91 cycles for read 2 through the ATGC core at MD Anderson. Sequence data was then put through the 10X genomic cell ranger 3.0 pipeline. QC and Fastq files were obtained and checked for data quality, and Fastq files were used to do further analysis.

value: Brain Tumor

value: Leukocytes

value: Glioblastoma

value: IDH Wild Type

value: Recurrent

value: Standard of care


title: DGXD_PBMCs_Noncontroller_TCR

description: VDJ

source_name: PBMCs

value: PBMCs


title: HD/100Q_striatum_neuropathology_male1

source_name: HD/100Q_striatal tissue01

value: male

value: 21 months

value: striatum


title: FST315-GAN-21

value: Liver


title: IWR3, replicate1, scRNAseq

description: 10x Genomics

source_name: Brain Tumor


title: DG3H_LNs_Noncontroller_RNA

description: RNA

value: primary cells

value: CM9 specific CD8


title: DG3H_PBMCs_Noncontroller_TCR

description: VDJ


title: IWR2, replicate1, scRNAseq

description: 10x Genomics

value: Glioblastoma/Gliosarcoma


title: DG3H_PBMCs_Noncontroller_RNA

description: RNA


title: WT_striatum_neuropathology _male4

source_name: WT_striatal tissue04

value: WT control


title: GFP-GAN-19

value: tissue

value: GAN diet


title: IWR1, replicate1, scRNAseq

description: 10x Genomics

value: Brain Tumor


title: CHOW-18


title: DFH4_Spleen_Noncontroller_TCR

description: VDJ

value: Spleen


title: Patient 3 [IonCode_0124]

first: Kellen

last: Winden

state: MA

address: 300 Longwood Ave

department: Neurology

institute: Boston Children's Hospital

data_processing: Read mapping and preliminary data analysis was completed with the AmpliSeq Plugin available on the ThermoFisher S5 Torrent server. CHP files were loaded into the Transcriptome Analysis Console (TAC) Software from ThermoFisher to complete differential gene expression analysis of the probands versus controls, with 1.2-fold change in expression as cutoff and p-values corrected for multiple comparisons using FDR. Gene ontology analysis was completed using DAVID (https://david.ncifcrf.gov).

source_name: iPSC

growth_protocol: All five iPSC lines were cultured and differentiated in parallel, with a minimum of three independent differentiation batches for each experimental assay. NGN2-induced cortical neurons were differentiated according to the protocol published by Zhang et al. in 2013 [13], with modifications described below. On differentiation day -2, iPSCs were dissociated with Accutase (Innovative Cell Technologies #AT104) and plated at 90,000 cells/cm2 in mTeSR-1 media supplemented with 10uM ROCK inhibitor (Y-27631, Cayman Chemical #10005583), on Geltrex-coated 12-well plates. The following day, on differentiation day -1, iPSCs were transduced with lentiviral vectors expressing NGN2, eGFP, and rtTA along with 8ug/ml polybrene (Sigma-Aldrich #TR-1003-G). High quality lentiviral particles were produced and concentrated at the Viral Core at Boston Children’s Hospital. Plasmids used were gifts from the Thomas Sudhof laboratory, but all components can be purchased from Addgene with the following IDs: 52047, 30130, 20342. On differentiation day 0, NGN2 and eGFP expression was induced via treatment with 2ug/ml doxycycline (Millipore #324385). Cells that were positive for infection with the viral vectors were selected via treatment with 1ug/ml puromycin (Invitrogen #ant-pr-1) for 24-48 hours, depending on cell density. This selection helps to generate a relatively pure population of neurons. For the first 2 days, the following growth factors and supplements were added to the N2 medium: 10ng/ml BDNF (Peprotech #450-02), 10ng/ml NT3 (Peprotech #450-03), and 0.2mg/L laminin (ThermoFisher #23017-015). Differentiating cells were then fed with B27 media containing the following growth factors and supplements every other day until differentiation day 6: 10ng/ml BDNF, 10ng/ml NT3, 0.2mg/L laminin, 2ug/ml doxycycline, and 2uM Ara-C (Sigma-Aldrich #C1768). Contrary to the originally published protocol, on day 2, no mouse glial cells were added. Instead, astrocyte-conditioned media was collected from cultures of iPSC-derived astrocytes (NCardia Astro.4U) and neurons were cultured in this human-astrocyte-conditioned media along with growth factors and supplements after day 6 to avoid astrocyte signals in the RNA analysis. Neurons were matured until day 14 prior to being collected for RNA analysis.

extract_protocol:
At day 14, neurons were collected by removing media and adding a thin layer of lysis buffer from the RNA purification kit and using a cell scraper to collect the cells off the plate. Total RNA was isolated using Clontech RNA isolation kit #740971.50
Isolated total RNA was diluted to 0.95ng/ul and 10.5ul was loaded in each reverse transcription reaction with the SuperScript VILO cDNA Synthesis Kit (Thermo Fisher #11754050). Reverse transcription was completed in a thermocycler with the following temperature settings: 42°C 30minutes, 85°C for 5 minutes, 10°C Hold. After reverse transcription, libraries were prepped using the Ion Chef (ThermoFisher Cat#4484177) and the Ion AmpliSeq Transcriptome Human Gene Expression Panel, Chef-Ready Kit (ThermoFisher Cat#A31446). The AmpliSeq Gene Expression Panel includes one primer pair for almost every gene in the transcriptome, allowing for amplification of a single 100bp amplicon for each gene to be sequenced. Libraries from 8 samples were pooled together, templated, and loaded on the Ion 540 Chip (ThermoFisher Cat#A27765) using the Ion Chef and the Ion 540 Kit Chef (ThermoFisher Cat#A27759). After templated samples were loaded onto the 540 Chips, each Chip was inserted into the Ion Torrent S5 sequencer (ThermoFisher Cat#A27212) and 500 flows were applied for each sequencing run. The second Chip was stored at 4°C during the first sequencing run and removed to room temperature for 30 minutes prior to running the second Chip.

treatment_protocol: no treatments were applied

tag: group

value: Patient

value: iPSC

value: Neuron


title: IWP2, replicate1, scRNAseq

description: 10x Genomics

value: Leukocytes

value: Glioblastoma

value: IDH Wild Type

value: Primary

value: Treatment Naive


title: DFH4_MeLN_Noncontroller_TCR

description: VDJ

source_name: MeLN

value: MeLN


title: Control 2 [IonCode_0123]

value: Control


title: IWP3, replicate1, scRNAseq

description: 10x Genomics

value: Astrocytoma


title: FST315-HFD-16

value: Liver

value: male

value: High fat diet


title: IWP4, replicate1, scRNAseq

description: 10x Genomics


title: FST315-HFD-15

value: tissue


title: WT_striatum_neuropathology_male2

source_name: WT_striatal tissue02

value: WT control

value: 21 months

value: striatum


title: Proband 2 [IonCode_0122]

value: Proband

value: iPSC


title: WT_striatum_neuropathology_male1

source_name: WT_striatal tissue01


title: IWP1, replicate1, scRNAseq

description: 10x Genomics

value: Brain Tumor

value: Leukocytes


title: GFP-HFD-14

source_name: Liver


title: Control 1 [IonCode_0121]

value: Neuron


title: DFH4_Liver_Noncontroller_TCR

description: VDJ

value: primary cells

value: CM9 specific CD8


title: IMR6, replicate1, scRNAseq

description: 10x Genomics

value: IDH Mutant

value: Recurrent

value: Standard of care


title: DFH4_MeLN_Noncontroller_RNA

description: RNA

value: MeLN


title: GFP-HFD-13

value: Liver

value: male


title: GFP-GAN-20

value: tissue

value: GAN diet


title: DFH4_Liver_Noncontroller_RNA

description: RNA


title: WT_striatum_neuropathology_male3

source_name: WT_striatal tissue03

value: WT control

value: 21 months


title: IMR5, replicate1, scRNAseq

description: 10x Genomics

value: Oligodendroglioma


title: LDKO-GAN-12

value: LDKO


title: DFH4_Spleen_Noncontroller_RNA

description: RNA

value: Spleen


title: CHOW-17


title: Control 1 [IonCode_0119]

value: Control

value: iPSC


title: DFH4_LNs_Noncontroller_TCR

description: VDJ

value: LNs

value: primary cells


title: Proband 1 [IonCode_0120]

value: Proband

value: Neuron


title: IMR4, replicate1, scRNAseq

description: 10x Genomics

value: Brain Tumor

value: Leukocytes

value: IDH Mutant

value: Recurrent

value: Standard of care


title: DFH4_LNs_Noncontroller_RNA

description: RNA

value: CM9 specific CD8


title: LDKO-GAN-11

value: Liver

value: tissue

value: male

value: GAN diet


title: IMR3, replicate1, scRNAseq

description: 10x Genomics

value: Oligodendroglioma


title: Proband 1 [IonCode_0118]


title: IRS1/2-GAN-10

value: Control


title: IMR2, replicate1, scRNAseq

description: 10x Genomics

value: Glioblastoma


title: IRS1/2-GAN-9


title: DFH4_PBMCs_Noncontroller_RNA

description: RNA

value: PBMCs


title: Control 2 [IonCode_0115]

value: iPSC


title: DFH4_PBMCs_Noncontroller_TCR

description: VDJ

value: primary cells


title: Patient 3 [IonCode_0116]

value: Patient

value: Neuron


title: LDKO-Fruc-8

value: LDKO

value: High fructose diet


title: Proband 2 [IonCode_0114]

value: Proband


title: IMP4, replicate1, scRNAseq

description: 10x Genomics

value: Brain Tumor

value: Leukocytes

value: IDH Mutant

value: Primary

value: Treatment Naive


title: LDKO-Fruc-7

value: Liver

value: tissue

value: male


title: IMP3, replicate1, scRNAseq

description: 10x Genomics

value: Oligodendroglioma


title: IMR1, replicate1, scRNAseq

description: 10x Genomics

value: Astrocytoma

value: Recurrent

value: Standard of care


title: Patient 3 [IonCode_0113]

value: Patient

value: iPSC


title: DBJK_MeLN_Noncontroller_RNA

description: RNA

value: MeLN

value: primary cells

value: CM9 specific CD8


title: IRS1/2-Fruc-6

value: Control

value: High fructose diet


title: DBJK_MeLN_Noncontroller_TCR

description: VDJ


title: Control 2 [IonCode_0112]

value: Neuron


title: IRS1/2-Fruc-5


title: IMP2, replicate1, scRNAseq

description: 10x Genomics

value: Brain Tumor

value: Leukocytes

value: IDH Mutant

value: Primary


title: DBJK_Liver_Noncontroller_TCR

description: VDJ

value: Liver


title: DBJK_Liver_Noncontroller_RNA

description: RNA


title: IMP1, replicate1, scRNAseq

description: 10x Genomics

value: Treatment Naive


title: Proband 2 [IonCode_0111]

value: Proband


title: LDKO-HFD-4

value: tissue

value: male

value: LDKO

value: High fat diet


title: NGB4, replicate1, scRNAseq

description: 10x Genomics

source_name: Quasi-normal Brain

value: Quasi-normal Brain

value: Type IIIa focal cortical dysplasia

value: Not Applicable


title: Control 1 [IonCode_0110]

value: Control

value: iPSC


title: NGB2, replicate1, scRNAseq

description: 10x Genomics


title: LDKO-HFD-3


title: IRS1/2-HFD-2


title: DBJK_LNs_Noncontroller_TCR

description: VDJ

value: LNs

value: primary cells

value: CM9 specific CD8


title: DBJK_LNs_Noncontroller_RNA

description: RNA


title: Proband 1 [IonCode_0109]

value: Neuron


title: NGB1, replicate1, scRNAseq

description: 10x Genomics

value: Leukocytes

value: Dysembryoplastic neuroepithelial tumor


title: DBJK_PBMCs_Noncontroller_RNA

description: RNA

value: PBMCs


title: DBJK_PBMCs_Noncontroller_TCR

description: VDJ


title: cumulus cells with  pre-incubation  time equals 2 hours, T2

status: Public on Jun 22 2024

city: Tehran

first: Naser

last: Elmi Ghiasi

address: Bioinformatics Deparment, Qods Street, Enghelab Street

department: Bioinformatics

country: Iran

institute: University of Tehran

description: sample 2

data_processing:
Raw data in fastq.gz format downloaded from MGI company FTP address
Quality of the raw data and potential contaminations analyzed by fastqc (Version 0.12.0) software in Linux environment.
The alignment process done using hisat2 (Version 2.2.1).
Stringtie (version 2.2.0) and cuffdiff (version 2.2.1) tools used to extract the gene and transcript counts based on reference GTF file (knowngene) and normalized them using FPKM measure.
EnrichR web application was used for enrichment of upregulated and downlegulated genes
Assembly: hg38
Supplementary files format and content: tab deliminated text file including FPKM normalized expression of samples and differential expression test results such as fold change and adjusted p-value.

source_name: cumulus cells

extract_protocol:
Total RNA extraction was performed using the RNeasy Mini kit (Qiagen, Germany).
RNA libraries for RNA-Seq were prepared using rRNA Depletion stranded Library prep kit by BGI company following the manufacturer's protocols.

treatment_protocol:
The extracted Cumulus-oocyte Complex (COC) samples were washed with GMOPS medium (Vitrolife, Gothenburg, Sweden) to remove the blood contamination.
In the T0 group, COCs were immediately dissected to separate the cumulus cells from around the oocytes and prepare the oocytes for ICSI. Then, CCs related to mature metaphase II (MII) oocyte were centrifuged at 200 g, for 10 min and after washing with phosphate-buffered saline (PBS) stored in liquid nitrogen
In the T2 group, dissection and preparation of CCs were done after 2 hours of incubation. pre-incubation was performed at 37°C, 95% humidity, 6% CO2 and 5% O2 condition. All the media were from Vitrolife (Vitrolife, Gothenburg, Sweden).

value: cumulus cells

value: pre-incubation

tag: time

value: 2 hours


title: Primary HNSCC

type: other

description: Fresh frozen spatial transcriptome imaging

hyb_protocol: Probe hybridization, ligation, amplification, as well as autofluorescence quenching and nuclei staining was performed as specified in CG000582 (Rev E, 10x Genomics) using the pre-designed Xenium Human Multi-Tissue and Cancer Panel (10x Genomics, 1000626), chemistry version v1, created on 05/23/23.

scan_protocol: The slide was loaded onto the Xenium analyzer and the regions of interests (ROIs) selected according to the 10x Genomics protocol CG000584 (Rev E). Xenium Analyzer is fully automated; data was acquired on instrument software version 1.8.2.1, and analysis version xenium-1.7.1.0.

data_processing: Segmentation and transcript aggregation into segmented cells was performed with Xenium Ranger 1.7

source_name: primary human laryngeal squamous cell carcinoma

label_protocol: Fixation and permeabilization was performed as described in protocol CG000581 (Rev C, 10x Genomics).

growth_protocol: Fresh frozen tissue were OCT embedded

extract_protocol: Sectioning of fresh-frozen tissue was performed at 10 μm  with cryostat and placed onto one Xenium slide according to specifications delineated in the 10x Genomics protocol CG000579 (Rev C).

tag: gender

value: male

value: 56 year old

tag: tissue

value: laryngeal squamous cell carcinoma (pT3 pN2c (2/29) L0 V0 Pn0 G2 R0)


title: cumulus cells with pre-incubation time equals zero, control. T0

description: sample 1

tag: treatment

value: 0 hour


title: Ramos_D3_3-_mut

city: Vienna

first: Maximilian

middle: Christian

last: von der Linde

state: Vienna

address: Campus-vienna-biocenter 1, IMP, Pavri GRP

country: Austria

institute: Institute of Molecular Pathology

description:
gen.DNA was purified and used for 2 rounds of PCRs attaching adapters and dual barcoding on 5' and 3' ends of the library
Dual barcoded libraries were multiplexed and sequenced on Illumina platforms with paired-end seq readmode
MutPE-seq

data_processing:
Reads were trimmed for standard adapters with cutadapt. Poor quality (Q<25) 3’ bases were trimmed with trimmomatic by averaging over a sliding window of 5nt. Read pairs were then filtered for minimum remaining length (200nt for read 1, 100nt for read 2) using cutadapt. Read mates were merged down to make combined single-end reads with FLASH allowing 10% mismatch between the mates.
Obvious erroneous mergers were removed by selecting combined reads with lengths within ±30nt of the amplicon length using cutadapt, The remaining combined reads were aligned with Bowtie2, using the “–very-sensitive-local” alignment mode and only the fixed variable region sequence and its immediate vicinity as reference.
Alignments were split into strata by the number of mismatches reported, using a custom Perl script. For each stratum a pile-up was generated with samtools (Li et al., 2009) taking into account only bases with quality of at least 30.
The pileups were then quantified with a custom Python script and the resulting mutation counts were processed and visualized with custom scripts in R (v3.5.1), with the help of additional R packages (ggplot2 , ggrepel, patchwork).
Background mutation profiles were controlled for by subtracting the corresponding mutation frequencies in control samples from the frequencies in the samples of interest, at each position and for each substitution type. Annotation of hot and cold spots was created by means of regex search for the corresponding patterns in the reference sequence.
Code for the workflow and the custom scripts is available on Github at https://github.com/PavriLab/IgH_VDJ_MutPE .
Assembly: NCBI mm9, NCBI HG38, custom IGH genome (see github)
Supplementary files format and content: bedGraph format files showing coverage tracks that can be visualized in genome browser
Library strategy: MutPE-seq

source_name: Ramos

extract_protocol:
cells were harvested and gen.DNA prepared by PCI extraction and EtOH precipitation
2 rounds of PCRs were used to add adapter sequences and dual barcoding for paired-end sequencing on Illumina platform

value: Ramos

tag: genotype

tag: growth protocol

value: full RPMI

value: uninfected

tag: sorted


title: Ramos_D3_1+_mut

value: JP8Bdel infection + Doxicycline/4-HT


title: Ramos_D3_2+_mut


title: Ramos_D3_2-_mut


title: Ramos_D3_3+_mut


title: Ramos_D3_1-_mut


title: Ramos_VH3-30_c1G6-_mut


title: Ramos_VH3-30_c1C6+_mut


title: Ramos_VH3-30_c1C1+_mut


title: Ramos_VH4-59_c2E10+_mut


title: Ramos_VH3-30_c1C1-_mut


title: Ramos_VH3-30_c1C6-_mut


title: Ramos_VH4-59_c2E10-_mut


title: Ramos_VH3-30_c1G6+_mut


title: Metastatic lymph node, section #2

source_name: metastatic lymph node from HNSCC

tag: age

value: metastatic level III cervical lymph node


title: Ramos_VH4-59_c1F8+_mut


title: Ramos_VH4-59_c1E2+_mut


title: Ramos_VH4-59_c1F8-_mut


title: Ramos_B18KI_c2E4+_mut

value: AID-JP8Bdel infection + Doxicycline/4-HT


title: Ramos_VH4-59_c1E2-_mut


title: Ramos_B18KI_c1A7+_mut


title: Ramos_B18KI_c2E4-_mut


title: Ramos_B18KI_c1A7-_mut


title: IRS1/2-HFD-1

value: Liver

value: tissue

tag: cell type

value: Control

value: High fat diet


title: priBd3_B18hi_seq2

description:
RNA was generated by performing transcription run-on on freshly isolated nuclei
5' and 3'linkers with random 8mers were added to allow PCR deduplication
True-seq barcoded RPI primers for multiplexing were used in the PCR step to generate barcoded libraries
PRO-seq

data_processing:
PRO-seq
Reads were trimmed for standard adapters and low quality (Q<30) 3’-end bases and filtered for a remaining length of at least 20nt (excluding the UMI, if applicable) using cutadapt v2.5.
Alignment to the reference genome was done with Bowtie v1.2.3. The NCBI GRCm38.6 assembly was used as the mouse reference. To this we added the fixated sequence of the recombined VDJ locus as an additional chromosome. Similarly, for human data, the Hg38 assembly was used, with the relevant fixed VDJ sequence added as a chromosome.
Where applicable, the dmr6 assembly of Drosophila melanogaster from Flybase (https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase, release version number 6.27) was used as the spike-in reference and was added to the alignment index. During alignment, up to 3 mismatches were allowed.
To accommodate mapping to the repetitive IgH locus, a high degree of multimapping was allowed (194 potential V segments annotated for GRCm38.6). In the case of alignment with spike-ins, only reads mapping exclusively to either genome were considered.
For PCR deduplication, UMIs were identified (8 nucleotides at the 3' end) and filtered with umi-tools v1.0.0. No sequence differences were allowed in UMIs when collapsing the duplicates.
Multimapping reads were then filtered to identify those specific to the VDJ sequence, taking into account the repetitiveness of the reference IgH locus. Reads mapping to the fixed VDJ sequence were allowed to multimap only to the native IgH locus (mouse chr12:113572929-116009954, human ch14:105836764-106875071). The native loci were defined as the region between the earliest position belonging to an annotated V segment and the latest position belonging to an annotated J segment. Reads with a mapped location outside these areas were rejected. This filtering was implemented in a custom Python script. The qualifying reads were then classified as reads mapping uniquely to the particular VDJ sequence and reads mapping to both the VDJ sequence and to the native IgH region.
Genome browser tracks were created by quantifying and scaling read coverage of the VDJ sequence using bedtools v2.29.0. Reads were split by strand, and strand labels for PROseq were inverted in order to match the strand designations of the respective PROcap reads. For both data types, only the first 5' base of the strand-adjusted reads was used for the tracks. Additionlly, the 5' end of PROseq reads was shifted by 1 base downstream, to compensate for the last base in the mRNA being the exogenous termination base. For normalized tracks, read counts were scaled to RPM (reads per million). Finally, “-“ strand coverage tracks were further scaled by -1, for visualization convenience.
Code for the workflow and the custom scripts is available on Github at https://github.com/PavriLab/IgH_VDJ_PROcapseq .
Assembly: NCBI mm9, NCBI HG38, custom IGH genome (see github)
Supplementary files format and content: bigWig of rpm-normalized read densities
Library strategy: PRO-seq

organism:
Drosophila melanogaster
Mus musculus

source_name: spleen

extract_protocol:
Cells were harvested and nuclei isolated. Transcription run-on in the presence of 4 Biotin-11-NTPs. Afterwards Trizol extraction of total RNA
total extraction with trizol, labeled RNA enrichement .3' and 5' linker attachment. cDNA preparation and PCR

value: spleen

value: MACS CD43 depleted primary B cells + S2

value: IL4, LPS, RP105


title: priBd3_B18hi_seq1


title: tobacco NbADCP1+Atlinkers_ChIP_rep2

city: Beijing

first: Weifeng

last: Zhang

address: Zhongguancun Street

institute: Tsinghua University

data_processing:
Illumina RTA software was used for basecalling.
Reads coverage was normalized to RPKM (Reads Per Kilobase Million)
Assembly: TAIR10 for Arabidopsis, Nicotiana benthamiana v2.6.1 for tobacco, S_lycopersicum_chromosomes.4.00 for tomato

organism: Nicotiana tabacum

source_name: leaf

growth_protocol: Arabidopsis surface-sterilized seeds were sown on 1/2 MS medium and cold-imbibed (4 °C) in darkness for 2 days before being transferred to long-day conditions (day/night cycle of 16/8 h) at 22 °C. Tobacco and tomato plants grown in a 22 °C plant culture room.

extract_protocol:
5 g leaves were cross-linked in 1% formaldehyde for 10 min. Then stopped by adding 0.125 M glycine and washed by PBS. The nuclei were extrected by Honda buffer and washed 3 times by NRBT. Then the nuclei were sonicated 4 times for 10 min (30 s on/off intervals) using the Bioruptor® Pico. The sonicated nuclei were centrifuged at 15000rpm for 15 min, and the supernatant was transferred to new tubes and diluted 10 times with ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.0, 167 mM NaCl). 50 μL diluted supernatant was preserved as input. Then 2 μg anti-GFP antibody (Abcam, ab290), anti-mCherry antibody (Abcam, ab213511), or anti-H3K9me2 antibody (Abcam, ab1220) was added into supernatant and rotate at 4 °C overnight. 50 μL washed Protein G Dynabeads (Invitrogen, 10004D) was added to the sample. After rotating for 4 h, the beads were washed sequentially with Low Salt Buffer, High Salt Buffer, LiCl Buffer, TE Buffer (each buffer for a quick wash, and a 10 min wash). Then add 100 μL 10% Chelex resin (Biorad, 1422842) to elute immune complexes by incubating at 95 °C for 10 min at 1300 rpm. After cooled to RT, 2 μL Protease K (10 mg/mL, Amresco 0706) was added into samples and incubated at 45 °C for 1 h, and then boiled at 95 °C and 1300 rpm for 10 min. Then the elution was purified with phenol-chloroform for sequencing.
The library preparation steps were conducted according to the manual (ABclonal, RK20228). Briefly, the first adapter was ligated to the 3’ end of the ssDNA using Adaptase via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified.

value: leaf

value: NbADCP1+Atlinkers-GFP in tobacco transgenic plants


title: priBd3_B18hi_cap2

description:
RNA was generated by performing transcription run-on on freshly isolated nuclei
5' and 3'linkers with random 10mers were added to allow PCR deduplication
True-seq barcoded primers for multiplexing were used in the PCR step to generate barcoded libraries
PRO-cap
SR50

data_processing:
PRO-cap
Reads were trimmed for standard adapters and low quality (Q<30) 3’-end bases and filtered for a remaining length of at least 20nt (excluding the UMI, if applicable) using cutadapt v2.5.
Alignment to the reference genome was done with Bowtie v1.2.3. The NCBI GRCm38.6 assembly was used as the mouse reference. To this we added the fixated sequence of the recombined VDJ locus as an additional chromosome. Similarly, for human data, the Hg38 assembly was used, with the relevant fixed VDJ sequence added as a chromosome.
Where applicable, the dmr6 assembly of Drosophila melanogaster from Flybase (https://wiki.flybase.org/wiki/FlyBase:About#Citing_FlyBase, release version number 6.27) was used as the spike-in reference and was added to the alignment index. During alignment, up to 3 mismatches were allowed.
To accommodate mapping to the repetitive IgH locus, a high degree of multimapping was allowed (194 potential V segments annotated for GRCm38.6). In the case of alignment with spike-ins, only reads mapping exclusively to either genome were considered.
For PCR deduplication, UMIs were identified (10 nucleotides at the 3' end) and filtered with umi-tools v1.0.0. No sequence differences were allowed in UMIs when collapsing the duplicates.
Multimapping reads were then filtered to identify those specific to the VDJ sequence, taking into account the repetitiveness of the reference IgH locus. Reads mapping to the fixed VDJ sequence were allowed to multimap only to the native IgH locus (mouse chr12:113572929-116009954, human ch14:105836764-106875071). The native loci were defined as the region between the earliest position belonging to an annotated V segment and the latest position belonging to an annotated J segment. Reads with a mapped location outside these areas were rejected. This filtering was implemented in a custom Python script. The qualifying reads were then classified as reads mapping uniquely to the particular VDJ sequence and reads mapping to both the VDJ sequence and to the native IgH region.
Genome browser tracks were created by quantifying and scaling read coverage of the VDJ sequence using bedtools v2.29.0. Reads were split by strand, and strand labels for PROseq were inverted in order to match the strand designations of the respective PROcap reads. For both data types, only the first 5' base of the strand-adjusted reads was used for the tracks. Additionlly, the 5' end of PROseq reads was shifted by 1 base downstream, to compensate for the last base in the mRNA being the exogenous termination base. For normalized tracks, read counts were scaled to RPM (reads per million). Finally, “-“ strand coverage tracks were further scaled by -1, for visualization convenience.
Code for the workflow and the custom scripts is available on Github at https://github.com/PavriLab/IgH_VDJ_PROcapseq .
Assembly: NCBI mm9, NCBI HG38, custom IGH genome (see github)
Supplementary files format and content: bigWig of rpm-normalized read densities
Library strategy: PRO-cap

extract_protocol:
Cells were harvested and nuclei isolated. Transcription run-on in the presence of 2 biotinylated NTPs (Bio-UTP and Bio-CTP) and unlabeled ATP and GTP. Afterwards Trizol extraction of total RNA
total extraction with Trizol, labeled RNA enrichment .3' and 5' linker attachment. cDNA preparation and barcoding PCR, gel extraction of ~180-350bp library


title: tobacco NbADCP1+Atlinkers_ChIP_rep1


title: priBd3_B18hi_cap1


title: tobacco NbADCP1_ChIP_rep2

value: NbADCP1-GFP in tobacco transgenic plants


title: tobacco AtADCP1_ChIP_rep2

value: AtADCP1-GFP in tobacco transgenic plants


title: tobacco AtADCP1_ChIP_rep1


title: tobacco H3K9me2_ChIP_rep2

value: tobacco (Nicotiana benthamiana)


title: Monocyte-Specific DNA Methylation Sample 386

type: genomic

city: Honolulu

first: Christian

middle: Ka'ikekuponoaloha

last: Dye

state: HI

address: 641 Ilalo St. BSB 222K

department: Native Hawaiian Health

institute: University of Hawaii at Manoa

description: normal monocyte enriched sample

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC v1.0 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina HiScanSQ System following standard protocols

data_processing:
minfi for quality control, along with ENmix package for normalization in R environment 4.1
average beta value

label: Cy3 and Cy5

source_name: monocyte

label_protocol: Standard Illumina Protocol

extract_protocol: Monocytes were enriched from peripheral blood mononuclear cells using the EasySep Magnetic cell separator for the EasySep Human Monocyte Enrichment Kit without CD16 Depletion following the manufacturers protocols. Enriched monocytes were isolated for genomic DNA using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit following standard protocols.

value: monocyte

value: Male

tag: race

value: Native Hawaiian


title: Monocyte-Specific DNA Methylation Sample 388

description: normal monocyte enriched sample

value: Japanese American


title: Monocyte-Specific DNA Methylation Sample 392

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 387

description: normal monocyte enriched sample

value: Female

value: White


title: Monocyte-Specific DNA Methylation Sample 389

description: normal monocyte enriched sample


title: tobacco H3K9me2_ChIP_rep1


title: Monocyte-Specific DNA Methylation Sample 391

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 390

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 383

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 382

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 378

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 384

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 380

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 379

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 381

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 385

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 376

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 375

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 374

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 373

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 372

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 371

description: normal monocyte enriched sample


title: tobacco NbADCP1_ChIP_rep1


title: Monocyte-Specific DNA Methylation Sample 370

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 369

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 367

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 368

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 365

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 366

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 363

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 360

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 361

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 358

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 377

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 362

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 357

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 355

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 354

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 356

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 347

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 353

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 352

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 349

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 351

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 346

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 348

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 345

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 343

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 344

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 342

description: normal monocyte enriched sample


title: Monocyte-Specific DNA Methylation Sample 341

description: normal monocyte enriched sample