title: OK6>mCherry-NLS,unc-13 RNAi(attP2) type I MNs, bio rep 2


title: OK6>mCherry-NLS,unc-13 RNAi(attP2) type I MNs, bio rep 1

status: Public on Aug 28 2024

type: SRA

city: Berkeley

first: Caroline

last: Cypranowska

state: CA

address: 271 Weill Hall #3200

department: Molecular & Cell Biology

country: USA

institute: University of California, Berkeley

library_source: transcriptomic

data_processing:
Fastq files for each library were analyzed with FastQC (version 0.11.7) to check for quality and trimmed with Trimmomatic (version 0.38) with parameters SLIDINGWINDOW:4:20 MINLEN:20 ILLUMINACLIP:nextera.fa:2:40:15 to remove low quality reads and to remove adapter sequences.
Trimmed reads were aligned to a custom reference genome built from Berkeley Drosophila Genome Project (dm6, release 95), including the pUAST-mCherry-NLS vector sequence for the detection of mCherry mRNA reads. Samples with the dsRNA construct were mapped to the custom genome build described along with the sequence of dsRNA construct. Mapping was performed with HISAT2 (version 2.1.0).  The counts matrix was generated with featureCounts from Subread (v1.6.4). Genes with fewer than 5 read counts across two libraries were considered undetectable and removed from downstream analysis.
Differential expression between knockdown conditions was calculated with DESeq2 (version 1.26.0) using the built-in median of ratios method to normalize the read counts for each gene prior to comparison with wild type controls.
Assembly: dm6
Supplementary files format and content: Comma-separated output of featureCounts for each Sample

molecule: total RNA

organism: Drosophila melanogaster

source_name: ventral nerve cord

growth_protocol: Drosophila larvae were raised to the 3rd instar stage on cornmeal and molasses media in an incubator at 25°C. Female parents bearing the OK6-Gal4 driver, UAS-mCherry-NLS and UAS-Dcr2 transgenes were crossed with male parents bearing either the attP2 empty vector or RNAi construct to obtain control and knockdown progeny. Larvae were screened for mCherry fluorescence in the ventral nerve cord immediately prior to dissection of ventral nerve cord.

extract_protocol:
Larvae were washed twice with PBS, followed by a wash in 70% ethanol and a final wash in PBS before being placed in a droplet of Schneider's complete media with 10% FBS for ventral nerve cord dissection. Ventral nerve cord tissue was sequentially recovered for each larva dissected in ice cold Schneider's media with 10% FBS, pooled by the appropriate genotype. Dissected tissue was rinsed three times in Schneider's media containing 1.5 mM EDTA and 1.5 mM L-Cysteine. Cells were dissociated in Schneider's media with 1.5 mM EDTA, 1.5 mM L-Cysteine, papain, and 1.25 mg/mL collagenase type-I at 25C on a nutator for 5 minutes and then triturated 30 times with a P200 pipette. The incubation and trituration step was repeated once before the tissue was sheared 7 times with a 27G1/2 needle. The dissociation reaction was quenched with the addition of Schneider's media with 10% FBS. Dissociated cells were passed through a 40 uM cell strainer, spun down at 0.7xg for 7 minutes before being resuspended in 1 mL of Schneider's media with 5% FBS. Cells were stained with 0.3 uM of Sytox Green to assess viability before being sorted on a BD Influx Cell Sorter or BD FACS Aria. Cells were sorted for high mCherry fluorescence and low Sytox Green fluorescence. Sorted cells were recovered in RLT buffer with 3.5 mM BME from the QIAGEN RNEasy Micro kit and processed according to manufacturer's instruction omitting the DNase digestion step.
Libraries were prepared using a modified SMART-Seq2 protocol (Picelli et al., Nature Protocols, 2014). RNA was annealed with an oligo-dT primer and first-strand synthesis was performed with SuperScriptII kit using a custom template-switching oligo. cDNA preamplification, lambda exonuclease digestion and size-selection were performed as described in Li et al., Cell, 2017. Libraries were constructed with the Nextera XT kit and sequenced on the Illumina Hi-Seq 4000 instrument (PE100).

tag: tissue

value: ventral nerve cord

tag: cell type

value: motor neuron

tag: genotype

value: unc-13 knockdown


title: igg_wt_1

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

institute: Stowers Institute for Medical Research

library_source: genomic

data_processing:
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
CUT&TAG was aligned to genome mm10 using boCtrlie2
Assembly: mm10
Supplementary files format and content: CUT&Tag in bigwig files

molecule: genomic DNA

organism: Mus musculus

source_name: Intestine

extract_protocol:
CUT&TAG is perfomed according to the manufacture's protocol(https://www.epicypher.com/technologies/cutana/cut-and-tag).
Library construction is according to the manufacture's protocol(https://www.epicypher.com/technologies/cutana/cut-and-tag).

value: mouse intestine jejunum part

tag: treatment

value: wildtype


title: igg_fzd5ko_1

value: knockout


title: COV6 (miRNA-seq)

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

data_processing:
Sequencing was performed on NovaSeq 6000 platform in 101-base single-end mode.
Before analysis of the small RNA-Seq data, reads were trimmed the 3' adapter sequence (AGATCGGAAGAGCACACGTCT).
Trimmed reads were mapped on miRBase human miRNA dataset using miRDeep2 software.
Quantification was also performed with miRDeep2 software.
Supplementary files format and content: miRBase human miRNA dataset
Supplementary files format and content: tab-delimited text files include count data for each sample

organism: Homo sapiens

source_name: peripheral blood

extract_protocol:
Total RNA isolation was performed using the PAXgene™ Blood RNA System (BD Bioscience, San Jose, CA, USA). The collection tubes were stored after blood collection until further analysis at -30°C.
Each library was prepared using NEBNext Multiplex Small RNA Library Prep Set for illumina (New England Biolabs).

value: peripheral blood

value: peripheral blood mononuclear cells

tag: disease state


title: COV99 (RNA-seq)

data_processing:
Sequencing was performed on a MGISEQ-2000RS platform in 2 x 100 bp paired-end mode.
The sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat, version 2.0.13, in combination with Bowtie2, version 2.2.3, and SAMtools, version 0.1.19.
Mapped read counts were calculated using featureCounts (in subread-2.0.0) with option -M -O --fraction.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include mapped read counts for each sample

extract_protocol:
Total RNA isolation was performed using the PAXgene™ Blood RNA System (BD Bioscience, San Jose, CA, USA). The collection tubes were stored after blood collection until further analysis at -30°C.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA) according to SMARTer kit instructions. DNA libraries were converted to libraries for DNBSEQ using MGIEasy Universal Library Conversion Kit (App-A).


title: COV102 (RNA-seq)


title: h3k27me3_wt_1


title: OK6>mCherry-NLS,Rbp RNAi(attP2) type I MNs, bio rep 3

value: Rbp knockdown


title: Tumor in combined therapy group

city: Shanghai

first: Changqing

last: Su

state: China

address: 225 Changhai Road, Yangpu District

department: Molecular Oncology

country: China

institute: National Center for Liver Cancer

data_processing:
The Cell Ranger software pipeline (version 5.0.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
We processed the unique molecular identifier (UMI) count matrix using the R package Seurat[1] (version 3.1.1).
To remove low quality cells and likely multiplet captures, which is a major concern in microdroplet-based experiments, we applied a criteria to filter out cells with UMI/gene numbers out of the limit of mean value +/- 2 fold of standard deviations assuming a Guassian distribution of each cells' UMI/gene numbers.
Following visual inspection of the distribution of cells by the fraction of mitochondrial genes expressed, we further discarded low-quality cells where >20% of the counts belonged to mitochondrial genes.
ibrary size normalization was performed with NormalizeData function in Seurat to obtain the normalized count. Specifically, the global-scaling normalization method “LogNormalize” normalized the gene expression measurements for each cell by the total expression, multiplied by a scaling factor (10,000 by default), and the results were logtransformed.
Genome_build: mm10
Supplementary_files_format_and_content: text files containing the raw gene expression count and cell

molecule: polyA RNA

source_name: xenografted tumors

extract_protocol:
Tissue was processed to prepare scRNA-seq libraries by using Chromium Single Cell 3’ Reagent v3 Kits (10x Genomics, Pleasanton, CA, USA). Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/ volume BSA. Then, single-cell suspensions were loaded onto a Chromium Single Cell Controller Instrument (10XGenomics, Pleasanton, CA, USA) to generate single-cell gel beads in emulsions (GEMs).
After generation of GEMs, reverse transcription, cDNA PCR amplification and library preparation were performed accroding to the 10x Genomics 3’ gene expression protocol.

value: MC38 cells

tag: sample type

value: subcutaneous tissue


title: COV97 (RNA-seq)


title: OK6>mCherry-NLS,Rbp RNAi(attP2) type I MNs, bio rep 2


title: Tumor in control group (Visium)

data_processing:
10x genomics pipeline
The Space Ranger software pipeline (version 1.0.0) provided by 10×Genomics   was used to process Visium spatial RNA-seq output and brightfield microscope   images in order to detect tissue, align reads using the STAR aligner, generate  feature-spot matrices, perform clustering and gene expression analysis, and place   spots in spatial context on the slide image.
We processed the unique molecular  identifier (UMI) count matrix using the R package Seurat3(version 3.1.1).
We first normalized the data with sctransform in order to account for variance in sequencing  depth across data points, detecting high-variance features, and stores the data in  the SCT assay.
Briefly, the average expression and dispersion were calculated for  each gene, genes were subsequently placed into x bins based on expression. Principal   component analysis (PCA) was performed to reduce the dimensionality on the log transformed gene-barcode matrices of top variable genes. Cells were clustered based   on a graph-based clustering approach, and were visualized in 2-dimension using tSNE. Likelihood ratio test that simultaneously test for changes in mean expression and in   the percentage of expressed cells was used to identify significantly differentially  expressed genes between clusters.
Genome_build: mm10
Supplementary_files_format_and_content: text files containing gene expression and spatial contents.

extract_protocol:
Tumor were prepared according to Visium spatial protocols of tissue preparation guide (10x genomics). Firstly, freshly obtained tissue samples were snap frozen in liquid nitrogen, then embedded in chilled Optimal Cutting Temperature compound (OCT; Tissue-Tek) and frozen on dry ice, then stored at -80°C in a sealed container for later use. For Visium samples preparation, OCT-embedded tissue blocks were cut to 10 um thick using a LEICA CM1950 machine and mounted on the Visium spatial gene expression slide.
10x genomics visium spatial gene expression pipeline

tag: cell line


title: COV1 (miRNA-seq)


title: KO_6

city: Shinjuku-ku

first: Taeko

last: Hayakawa

state: Tokyo

address: 35 Shinanomachi

department: Division of Tumor Immunology, Institute for Advanced Medical Research

institute: Keio University School of Medicine

data_processing:
Using next-generation sequencing with high-throughput sequencing technology (https://jp.illumina.com/content/dam/illumina-marketing/apac/japan/documents/pdf/2012_illumina_techsupport_session1.pdf), we obtained the nucleotide sequences of library-prepared samples.
The quality of the raw paired-end sequence reads was assessed with FastQC and Low quality (< 20) bases and adapter sequences were trimmed by Trimmomatic software (Version 0.38) with following parameters: ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36.
The trimmed reads for mapping were aligned to the reference genome using RNA-seq aligner HISAT2 (Version 2.1.0)
Assembly: hg38
Supplementary files format and content: The raw read counts were normalized with transcripts per million (TPM).

source_name: T cell + tumor(A549)

extract_protocol:
On day 12, the CD8α+ and CAR+ cells sorted by a cell sorter (Sony) were used as an RNA sequencing of pre-sample. Regarding post-samples, T cells were subjected to the repeated stimulation assay in 6-well plates, transferring T cells to freshly seeded cancer cells (A549) every 48-72 hours. Cultured T cells were sorted after chronic stimulation using cell sorter (Sony) to obtain a pure population of HER2 CAR positive CD8α+ T cells from the co-cultures with target cancer cells. Total RNA from pre and post-CAR T cells was harvested using RNeasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB E7490) and NEBNext Ultra RNA Library Prep Kit for Illumina (E7530) following manufacture's protocol

value: T cell + tumor(A549)

value: CD8+ T cell


title: h3k27me3_fzd5ko_1


title: h3k27me3_wt_2


title: Lgr5GFP

description: 10X scRNA-seq

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed using 10X Genomics Cell Ranger pipeline. Reads were demultiplexed into Fastq file format using cellranger mkfastq. Genome index was built by cellranger mkref using mouse genome mm10. Data were aligned by STAR aligner and cell counts tables were generated using cellranger count function with default parameters.
Assembly: mm10
Supplementary files format and content: single cell RNA-seq expression matrix in h5 format; scATAC-seq peak and fragments file in h5 format

extract_protocol:
Intestinal epithelial cell isolation: The whole intestine was removed and placed into Ca2+/Mg2+-free Hank’s buffered salt solution (CMF-HBSS, Thermo Fisher). For jejunum samples, 10 cm was isolated at the midpoint of the small intestine. The intestine was opened longitudinally and vigorously washed in CMF-HBSS. Samples were then cut into 1-2cm pieces, transferred to CMF-HBSS containing 30 mM EDTA, and rotated for 30 min on ice. Samples were shaken vigorously by hand for 5min, passed over a 70 µm filter and crypts were palleted after centrifuge. Crypts were incubated in TryPLE Express  (Thermo Fisher) containing 0.5mM N-acetyl cysteine ( NAC, Sigma), 10uM Y-27632 dihydrochloride ( Y-27632, Sigma) in a 37ºC water bath with stirring by a P1000 pipette for 20 min. The dissociated samples were transferred to Basal Medium (advanced DMEM/F12 medium containing 1X GlutaMAX, 10 mM HEPES, 1X penicillin/streptomycin (all Thermo Fisher), with 5 mM NAC). 50ml tube was shaken for about 30sec to further promote the dissociation. The supernatant was removed after centrifuge and the pellet was resuspended in 3ml media. 20μm syringe filter was used to separate any remaining mass. Dead cell removal kit (Miltenyi Biotec) was then applied to get live single intestinal epithelial cells.  Nuclei isloation: Single-nucleus suspensions were isolated from ~50 mg fresh mouse intestine using Singulator 100 (genomics) according to the manufacturer's protocol.
ScRNA-seq: Cells were loaded on a Chromium Single Cell Controller (10x Genomics, Pleasanton, CA), based on live cell concentration assessed by Luna-FL cell counter (Logos Biosystems). Libraries were prepared using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (10x Genomics) according to the manufacturer’s directions. ScATAC-seq: High-quality nuclei suspensions were processed to create libraries according to the manufacturer’s instructions for the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit (10x Genomics) using a Chromium Single Cell Controller.


title: h3k27me3_fzd5ko_2


title: OK6>mCherry-NLS,Rbp RNAi(attP2) type I MNs, bio rep 1


title: COV27 (miRNA-seq)


title: OK6>mCherry-NLS,empty(attP2) type I MNs, bio rep 6

value: WT


title: COV87 (RNA-seq)


title: Fzd5KO1Day

description: 10X scRNA-seq


title: OK6>mCherry-NLS,empty(attP2) type I MNs, bio rep 5


title: cont_3


title: COV86 (RNA-seq)


title: WT

description: 10X scRNA-seq


title: COV81 (RNA-seq)


title: Ctrl1Day

description: 10X scRNA-seq

value: Ctrl


title: OK6>mCherry-NLS,empty(attP2) type I MNs, bio rep 4


title: cont_2


title: COV78 (RNA-seq)


title: Fzd5KO1Day_ATAC

description: 10X scATAC-seq

library_source: genomic single cell


title: OK6>mCherry-NLS,empty(attP2) type I MNs, bio rep 3


title: COV90 (RNA-seq)


title: COV75 (RNA-seq)


title: OK6>mCherry-NLS,empty(attP2) type I MNs, bio rep 2


title: Ctrl1Day_ATAC

description: 10X scATAC-seq


title: KO_5


title: Ctrl-Day3-Rep3

data_processing:
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
Raw reads were demultiplexed into Fastq format allowing up to one mismatch using Illumina bcl2fastq2 v2.18. Reads were aligned to UCSC genome mm10 with STAR aligner (version 2.7.3a ), using Ensembl 98 gene models. TPM values were generated using RSEM (version v1.3.0 ).
Assembly: mm10
Supplementary files format and content: TPM expression table in csv file

extract_protocol:
Total RNA was isolated from the intestinal epithelial cells using RNeasy Mini Kit (Qigen).
TruSeq Stranded Total RNA Library Preparation Kit(Illumina) was used in the preparation of sequencing libraries from 10-100 ng total RNA

value: ctrl

tag: time point


title: KO_pre_6

source_name: PBMC

value: PBMC


title: cont_1


title: OK6>mCherry-NLS,empty(attP2) type I MNs, bio rep 1

value: ventral nerve cord


title: COV73 (RNA-seq)


title: KO_4


title: COV72 (RNA-seq)


title: C5

city: Qingdao

first: Minglei

last: Gao

address: No. 217, Liaoyang West Road

institute: Qingdao Women and Children’s Hospital

data_processing:
quality control with MultiQC
adapter and quality trimming with Cutadapt
transcript quantification with featureCounts (GRCh38.primary_assembly.genome.fa)
differential expression analysis (p value <0.05 and |log2foldchange| >1)
Assembly: hg18
Supplementary files format and content: FPKM.tsv

source_name: whole blood

extract_protocol:
A total of 26 blood and serum samples were collected from hospitalized children with CHD in the Dalian Children's Hospital. Blood samples were used for transcriptomic analysis and serum samples were used for metabolomics analysis. Blood and serum samples were collected 24 hours before discharge from the hospital (or after surgery). The children with CHD were divided into three groups according to the nutritional risk and neurodevelopmental status: low nutritional risk combined with normal neurodevelopment (n=14, group A), low nutritional risk combined with neurodevelopmental disorders (n=5, group B), high nutritional risk combined with normal neurodevelopment (n=7, group C).
Total RNA was extracted from the samples with TRIzol. Sequencing By Synthesis (SBS) technology was used to sequence the cDNA library using Illumina's high-throughput sequencing platform.

value: whole blood

value: high nutritional risk combined with neurodevelopmental disorders

tag: Sex

value: male


title: C3


title: COV70 (RNA-seq)


title: Ctrl-Day3-Rep1

value: mouse intestine jejunum part


title: Ctrl-Day3-Rep2


title: KO_pre_5


title: KO_pre_4


title: C1


title: cont_pre_2


title: cont_pre_3


title: COV65 (RNA-seq)


title: COV68 (RNA-seq)


title: T7

value: high nutritional risk combined with normal neurodevelopment


title: Ctrl-Day1-Rep3


title: Ctrl-Day1-Rep2


title: cont_pre_1


title: T6

value: female


title: Ctrl-Day1-Rep1


title: COV62 (RNA-seq)

value: peripheral blood

value: peripheral blood mononuclear cells


title: T5


title: COV59 (RNA-seq)


title: Fzd5KO-Day3-Rep3


title: COV57 (RNA-seq)


title: Fzd5KO-Day3-Rep2


title: COV53 (RNA-seq)


title: A29L overexpression, day 3 of cardiac differentiation, replicate 2

city: Guangzhou

first: Juli

last: Liu

state: Guangdong

address: Zhongshan 2nd road No. 106, Yuexiu District, Guangzhou, Guangdong, China

institute: Guangdong Provincial People's Hospital

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<=0.05 and |log2(foldchange)| >= 1 were set as the threshold for significantly differential expression.
Assembly: hg38
Supplementary files format and content: EXCEL file included gene readcount values for each Sample

source_name: stable cell line

growth_protocol: All hESCs cell lines were maintained in mTesR1 medium (STEM CELL TECHNOLOGIES).

extract_protocol:
Total RNAs were extracted and purified with RNeasy Mini Kit (Qiagen) according to the manual.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained

treatment_protocol: All hESCs cell lines were infected with lenti-virus and screened with puromycin. The stable cell lines were maintained in mTesR1 medium (STEM CELL TECHNOLOGIES). For cardiac differentiation, STEMdiff™ Ventricular Cardiomyocyte Differentiation Kit (STEMCELL Technologies) was used according to the manual.

value: stable cell line

value: human embryonic stem cells, H9

value: H9 hESCs

value: A29L overexpression


title: COV50 (RNA-seq)


title: T2


title: Fzd5KO-Day1-Rep3


title: T1


title: Fzd5KO-Day3-Rep1


title: H3L overexpression, day 3 of cardiac differentiation, replicate 2

description: mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads

value: H3L overexpression


title: Fzd5KO-Day1-Rep2


title: Fzd5KO-Day1-Rep1


title: P7

value: low nutritional risk combined with neurodevelopmental disorders


title: COV45 (RNA-seq)


title: Pol_Ctrl_2

data_processing:
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
CUT&TAG was aligned to genome mm10 using boCtrlie2
Assembly: mm10
Supplementary files format and content: CUT&Tag in bigwig files
Library strategy: CUT&TAG

tag: antibody

value: Pol

value: Ctrl


title: H3L overexpression, day 3 of cardiac differentiation, replicate 1


title: T3


title: P6


title: P5


title: T4


title: COV38 (RNA-seq)


title: Pol_Ctrl_1


title: COV35 (RNA-seq)


title: P3


title: Control, day 3 of cardiac differentiation, replicate 1

value: Control


title: Pol_Fzd5KO_2


title: A29L overexpression, day 3 of cardiac differentiation, replicate 1


title: B52: I1L overexpression, replicate 4

address: Zhongshan 2nd road

department: Medical Research Center

institute: Guangdong provincial people's hospital

growth_protocol: All hESCs cell lines were maintained in mTesR1 medium (STEM CELL TECHNOLOGIES)

treatment_protocol: All hESCs cell lines were infected with lenti-virus and screened with puromycin. The stable cell lines were maintained in mTesR1 medium (STEM CELL TECHNOLOGIES)

value: human embryonic stem cells (hESCs)

value: I1L overexpression


title: COV33 (RNA-seq)


title: COV43 (RNA-seq)


title: Pol_Fzd5KO_1


title: COV41 (RNA-seq)


title: B51: I1L overexpression, replicate 3


title: COV30 (RNA-seq)


title: N19

value: whole blood

value: low nutritional risk combined with normal neurodevelopment


title: Control, day 3 of cardiac differentiation, replicate 2


title: B42: A35R overexpression, replicate 4

value: A35R overexpression


title: N18

value: female


title: COV27 (RNA-seq)

value: peripheral blood


title: COV13 (RNA-seq)

value: peripheral blood mononuclear cells


title: B32: A29L overexpression, replicate 4

value: stable cell line


title: COV6 (RNA-seq)


title: H3K4me3_Fzd5KO_2

value: mouse intestine jejunum part


title: N15


title: B31: A29L overexpression, replicate 3


title: H3K4me3_Fzd5KO_1


title: COV1 (RNA-seq)


title: P1

value: male


title: N14


title: N13


title: 257864010011_2.1ALS112

type: genomic

city: Catania

first: Sebastiano

last: Cavallaro

address: Via Paolo Gaifami, 18

country: Italy

institute: IRIB-CNR

description: Sample 52

hyb_protocol: After probe denaturation and pre-annealing with Cot-1 DNA, hybridization was performed at 65°C with rotation for 24 hr.

scan_protocol: After two washing steps, arrays were scanned at 3 µm resolution using an Agilent G4900DA SureScan Microarray Scanner System.

data_processing:
aCGH image data were processed using Agilent’s Feature Extraction software to assess the array spot quality as well as check signal and background intensity statistics in default setting.Feature extracted raw data was normalized, analyzed and visualized using Agilent CytoGenomics v. 4.0.3.12 and Genomic Workbench v. 7.0.4.0 software (Agilent Technologies, Santa Clara, CA, USA). Briefly, after filtering for saturated and non-uniform probes, data were normalized by GC correction with a window size of 2 kb and Diploid Peak Centralization. The Centralization Normalization Algorithm with a threshold of 6.0 and a bin size of 10 was also used for detecting aberrant regions or regions of constant CNVs. Aberrations were detected by the Aberration Detection Method II algorithm (ADM-2), with a sensitivity threshold of 6.0 and moving average window of 2Mb, which permits to identify all aberrant intervals in a given sample with consistently high or low log ratios based on the statistical score. For chromosome X, only females were used and for chromosome Y only males were used.  An aberration filter was applied for identifying copy number alterations, changes were considered as true positive events with a minimum log2ratio test/control of ±0.5 and a minimum of 3 consecutive probes. Positive statistical score meant amplification, while negative score indicated deletion. Human reference sequence hg19 assembly was used to define the genomic coordinates of detected CNVs.
Normalized log2ratio (Cy5/Cy3) representing test/reference. Changes were considered as true positive events with a minimum log2ratio test/control of ±0.5 and a minimum of 3 consecutive probes.

source_name: Blood

label_protocol: DNA test and a reference of the same sex (Euro Reference, Agilent Technologies, Santa Clara, CA), both at the concentration of 500 ng, were double digested with RsaI and AluI for 2 hours at 37°C. After heat inactivation of the enzymes at 65°C for 20 min, each digested sample was labeled by random priming by using the genomic DNA Enzymatic Labelling Kit (Agilent Technologies, Santa Clara, CA) for 2 hours using Cy5-dUTP for patient DNAs and Cy3-dUTP for reference DNAs. Labeled products were column purified by using the SureTag DNA Labeling Kit Purification Columns (Agilent Technologies, Santa Clara, CA).

extract_protocol: DNA extractions from frozen brain tissues and whole-blood samples were performed using standard procedures.Individual slices of 10 μm were produced from tissue samples at -20°C by a Leica CM1510S cryostat (Leica Microsystems) and stored at -80°C until further processing. Two slices per sample were stained by hematoxylin/eosin staining (Bio Optica) and for Nissl substance (with a microfiltered solution of cresyl violet, Sigma-Aldrich), respectively, to assess integrity of cellular and tissue morphology. Ten adjacent slices per sample were pooled and dissolved in SE buffer (750 m NaCl (pH 8), 250 m EDTA, 1% SDS) containing Proteinase K for DNA isolation. The extracted genomic DNA was quantified by ND-1000 Spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA), and assessed for quality by microcapillary electrophoresis on 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: age at death (in years)

value: Sporadic Amyotrophic Lateral Sclerosis

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

value: caucasian

tag: location of onset

value: Lumbo-sacral region

tag: occupation (job)

tag: smoker or non smoker

tag: alchool use or not

tag: other pathologies

tag: therapy used

tag: vaccination boost

tag: familial anamnesis

source_name: Euro Reference, Agilent Technologies


title: ChinmoST testis, D6-8, scRNAseq

city: Shenzhen

first: Qing

last: Ma

address: 1068 Xueyuan Avenue, Shenzhen University Town, Shenzhen, P.R.China

institute: Shenzhen Institutes of Advanced Technology

description: 10x Genomics v3

data_processing:
For each scRNA-seq dataset, raw data were aligned to D. melanogaster reference genome dm6 and gene-barcode matrices were generated by CellRanger version 4.0.0 . For scRNA-seq datasets of 6-8 and 9-11 days-old testes, we forced the number of cells (--force-cells=5000). Count data were further processed using the R package Seurat version 3.2.2. High-quality cells that expressed 200–6,000 genes and had mitochondrial content <10% were retained for the downstream analysis. Single-cell RNA-seq datasets of wild-type and mutant testes across different time points were integrated using the standard integration workflow (https://satijalab.org/seurat/v3.0/integration.html). Somatic and germline lineage were found in our data and each cell type further is annotated using curated markers by somatic cells and germline cells subclustering analysis.
Assembly: Drosophila melanogaster Release 6 plus ISO1 MT (GCA_000001215.4)
Supplementary files format and content: *.barcodes.tsv.gz, *.features.tsv.gz, *.matrix.mtx.gz : filtered raw counts output by CellRanger count
Supplementary files format and content: combined_WT_ChinmoST_testes_umi_counts.csv.gz : Merged raw counts table for high-quality cells in all scRNA-seq datasets
Supplementary files format and content: combined_WT_ChinmoST_testes_metadata.csv.gz : Metadata for high-quality cells in all scRNA-seq datasets

source_name: Testis

growth_protocol: Fly stocks were raised at 25 °C on standard molasses/yeast medium

extract_protocol:
Approximately 5,000-10,000 cells were washed with 0.04% BSA DPBS for three times and were resuscitated and manually determined to a concentration of 700~1200 cells/ul (viability≥85%). Cells were captured in droplets at a targeted cell recovery of cells. After the reverse transcription step, emulsions were broken and Barcoded-cDNA was purified with Dynabeads, followed by PCR amplification.
Amplified cDNA was then used for 10x Genomics chromium single cell 3ʹ gene expression library construction. For gene expression library construction, 50 ng of amplified cDNA was fragmented and end-repaired, double-size selected with SPRIselect beads.

treatment_protocol: Adult male flies at 3-5, 6-8, 9-11 days of adulthood, and approximately 100 pairs of testes were dissected for each sample preparation. Testes were dissected into Schneider’s medium and then washed twice with cold 0.04% BSA DPBS solution. 500 µL 0.25% Trypsin was added to each tube/sample. Samples were vortexed with 1000rpm for 15-18 minutes at room temperature. The enzymatic reactions were terminated by adding 500 µL DMEM (with >10% FBS). Cell suspensions were filtered through a 40 µm Falcon filter into an Eppendorf tube. Spermatids were filtered out for further enrichment of early germ cells and somatic cyst cells. The efficiency of single cell dissociation methods for fly testes were tested by labeling somatic cells or germline cells with GFP fluorescence. The percentage of each type of GFP-labeled cells were measured, ensuring retrieval of single cell suspensions with reasonable amount of viable germline and somatic cells.

tag: tissue

value: Testis

tag: strain

value: ChinmoST

tag: genotype

tag: developmental stage

value: Adult

tag: age

value: 6-8 days

value: Male


title: B21: H3L overexpression, replicate 3

tag: cell line

tag: cell type

value: human embryonic stem cells (hESCs)

value: H3L overexpression

tag: treatment


title: 257864010011_2.2 ALS113

description: Sample 51

tag: Sex

tag: age at death (in years)

tag: disease state

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

value: Cervical spinal cord


title: ChinmoST testis, D3-5, scRNAseq

description: 10x Genomics v3

value: 3-5 days


title: 257864010014_2.4_ALS949

description: Sample 50

tag: location of onset

value: Upper Limbs

tag: occupation (job)

tag: smoker or non smoker

tag: alchool use or not

tag: other pathologies

tag: therapy used

tag: vaccination boost


title: N12

tag: tissue

value: whole blood

value: low nutritional risk combined with normal neurodevelopment

value: female


title: H3K4me3_Ctrl_2

value: mouse intestine jejunum part

tag: antibody

tag: genotype

value: Ctrl


title: H3K4me3_Ctrl_1


title: B12: Control, replicate 4

value: stable cell line

tag: cell line

tag: cell type

value: Control

tag: treatment


title: N11

tag: disease state

tag: Sex

value: male


title: WT testis, D9-11, scRNAseq

description: 10x Genomics v3

value: Testis

tag: strain

value: Oregon R

value: Wild-type

tag: developmental stage

tag: age

value: 9-11 days


title: B41: A35R overexpression, replicate 3

value: human embryonic stem cells (hESCs)

value: A35R overexpression


title: B11: Control, replicate 3


title: N10


title: WT testis, D6-8, scRNAseq

description: 10x Genomics v3

value: Adult

value: 6-8 days

value: Male


title: 257864010028_1.4_ALS1017

description: Sample 49

tag: age at death (in years)

value: Sporadic Amyotrophic Lateral Sclerosis

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

value: caucasian

tag: location of onset

value: Cervical spinal cord

tag: occupation (job)

tag: familial anamnesis


title: N9

tag: tissue

value: whole blood

value: low nutritional risk combined with normal neurodevelopment

value: female


title: WT testis, D3-5, scRNAseq

description: 10x Genomics v3

tag: genotype

value: 3-5 days


title: 257864010027_2.4_ALS1013

description: Sample 48

value: Lumbo-sacral region

tag: smoker or non smoker

tag: alchool use or not

tag: other pathologies

tag: therapy used

tag: vaccination boost


title: 257864010027_2.2_ALS1010

description: Sample 47

tag: Sex

tag: disease state


title: A51: I1L overexpression, replicate 1

value: stable cell line

tag: cell line

tag: cell type

value: I1L overexpression

tag: treatment


title: ChinmoST testis D9-11, CUT&Tag, Chinmo, rep2

data_processing:
For each CUT &Tag dataset, fastp version 0.21.0 was used to profile quality and remove adapters and low-quality reads. Trimmed reads were aligned to D. melanogaster reference genome dm6 by Bowtie2 version 2.4.3 with the following parameters: --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700. Duplicated reads were removed by Picard version 2.21.1. Uniquely mapped reads were kept by sambamba version 0.8.0 and reads that aligned to blacklist regions were further filtered. These kept reads were shifted by alignmentSieve from deeptools version 3.1.3 as commonly done for ATAC-seq to account for Tn5 insertion offsets. Specifically, plus-stranded reads were shifted by +4bp and minus-stranded reads were shifted by -5bp. BigWig files were generated using the bamCoverage function of deepTools, with RPKM normalization and 10 bp bin size. Peaks were called by MACS2 version 2.2.7.1 with the following parameters: -f BAMPE -g dm --keep-dup all. Peaks that fall in autosomes,chrX and chrY were kept. Replicate reproducibility was assessed by Irreproducibility Discovery Rate (IDR) framework version 2.0.3 and reproducible peaks were defined as peaks with IDR < 0.05.
Assembly: Drosophila melanogaster Release 6 plus ISO1 MT (GCA_000001215.4)
Supplementary files format and content: *_RPKM_normalized.bw : BigWig files generated by the bamCoverage function of deepTools version 3.1.3, with RPKM normalization and 10 bp bin size.
Supplementary files format and content: *_filtered_peaks.narrowPeak : narrowPeak files that contain peaks  in autosomes,chrX and chrY called by MACS2 version 2.2.7.1.
Supplementary files format and content: ChinmoST_vs_WT_DBS.xlsx : An Excel file that contain information about statistically significant differentially Chinmo binding sites (DBSs, Fold change>=1.5, FDR<0.05) between ChinmoST and wild-type testes obtatined by DiffBind version 2.14.0
Library strategy: CUT&Tag

extract_protocol:
Cells were incubated with 10 μL pre-washed ConA beads in a 1.5-ml low-binding tube. Fifty microlitres of antibody buffer with 1 μg antibody (Rabbit anti-Chinmo-PA, 1:50) was added and cultured overnight at 4°C. After washing twice with dig-wash buffer, 50 μl dig-wash buffer with 0.5 μg secondary antibody was added and incubated at room temperature for 1 h. After washing twice with 800 μL dig-wash buffer, 1.0 μM pG–Tn5 was added with 100 μL dig-300 buffer. Samples were incubated at room temperature for 1 h and then washed twice with 800 μL dig-wash buffer. Three hundred microlitres of tagmentation buffer was added and samples were incubated at 37 °C for 1 h. The reaction was stopped with 10 μL 0.5 M EDTA, 3 μL 10% SDS and 2.5 μL 20 mg/ml Proteinase K.
The NovoNGS ® CUT & Tag 2.0 High-Sensitivity Kit (Vazyme, Nanjing, China, N259-YH01) was used to capture Chinmo-binding sites. After extraction with phenol-chloroform and ethanol precipitation, PCR was performed to amplify the libraries according to the manufacturer's instructions. DNA quality and quantity were determined using the Agilent 2100 Bioanalyzer.

treatment_protocol: Adult male flies at 5-7, 9-11 days of adulthood, and approximately 100 pairs of testes were dissected for each sample preparation. Testes were dissected into Schneider’s medium and then washed twice with cold 0.04% BSA DPBS solution. 500 µL 0.25% Trypsin was added to each tube/sample. Samples were vortexed with 1000rpm for 15-18 minutes at room temperature. The enzymatic reactions were terminated by adding 500 µL DMEM (with >10% FBS).

value: Testis

tag: strain

value: ChinmoST

tag: developmental stage

tag: age

tag: antibody

value: Anti-Chinmo


title: N7


title: A42: A35R overexpression, replicate 2

value: human embryonic stem cells (hESCs)

value: A35R overexpression


title: 257864010026_2.4_ALS979

description: Sample 46

value: male

tag: age at death (in years)

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

tag: location of onset

value: Bulbar region

tag: occupation (job)

tag: familial anamnesis


title: ChinmoST testis D9-11, CUT&Tag, Chinmo, rep1

tag: tissue

tag: genotype

value: Adult

value: 9-11 days

tag: Sex

value: Male


title: 257864010026_2.3_ALS978

description: Sample 45

tag: disease state

value: Sporadic Amyotrophic Lateral Sclerosis

value: caucasian

tag: smoker or non smoker

tag: alchool use or not

tag: other pathologies

tag: therapy used

tag: vaccination boost


title: 257864010026_2.2_ALS977

description: Sample 44

value: female

tag: age at death (in years)

value: Cervical spinal cord


title: ChinmoST testis D5-7, CUT&Tag, Chinmo, rep2

tag: strain

tag: developmental stage

tag: age

value: 5-7 days

tag: antibody


title: N5

value: whole blood

value: low nutritional risk combined with normal neurodevelopment


title: 257864010026_1.4_ALS957

description: Sample 43

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

tag: location of onset

value: Upper Limbs


title: A52: I1L overexpression, replicate 2

tag: tissue

value: stable cell line

tag: cell line

tag: cell type

tag: genotype

value: I1L overexpression

tag: treatment


title: A41: A35R overexpression, replicate 1

value: human embryonic stem cells (hESCs)


title: N3

tag: disease state

tag: Sex


title: A32: A29L overexpression, replicate 2

value: A29L overexpression


title: WT testis D9-11, CUT&Tag, Chinmo, rep2

value: Testis

value: Oregon R

value: Wild-type

value: Anti-Chinmo


title: A31: A29L overexpression, replicate 1


title: ChinmoST testis D5-7, CUT&Tag, Chinmo, rep1

value: ChinmoST

value: Adult

value: Male


title: N1

value: male


title: A22: H3L overexpression, replicate 2

value: H3L overexpression


title: N6

value: female


title: 257864010026_1.1_ALS953

description: Sample 42

tag: age at death (in years)

value: Sporadic Amyotrophic Lateral Sclerosis

value: caucasian

value: Lower limbs

tag: occupation (job)

tag: smoker or non smoker

tag: alchool use or not

tag: other pathologies

tag: therapy used

tag: vaccination boost

tag: familial anamnesis


title: Macaca mulatta_Spinalcord_treated with mock rep 1 [23706]

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

data_processing:
CLC workbench v
Raw reads were trimmed of adapter sequence using cutadapt
reads were then filtered for low quality bases and low quality reads using the FASTX-Toolkit
Remaining reads were mapped to the Mmul genome, using HISAT2
Assembly: Mmul_10 (GCF_003339765.1_Mmul_10_genomic.fna)
Supplementary files format and content: tab deliminted text file includes raw data for all samples called  matrix.txt
Supplementary files format and content: tab deliminted text file includes DESEQ2 normalized data for all samples called  normalized_counts.txt

organism: Macaca mulatta

source_name: Spinalcord

growth_protocol: The virus was biologically cloned and amplified to approximately 107 PFU/ml

extract_protocol:
Total RNA was isolated from freshly cut FFPE tissue sections that contained the selected CNS ROIs (see Digital pathology methods below) using the miRNAeasy FFPE kit, following the manufacturer's protocol
Ribosomal RNAs were depleted from 100 ng total FFPE RNA using the QIAseq FastSelect -rRNA MHR kit and following the FastSelect protocol for KAPA RNA HyperPrep kit, with no fragmentation (Qiagen, Valencia, CA).  Sequencing libraries were generated using the Kapa RNA HyperPrep library preparation and technical data sheet KR1350 v3.20, with minor modifications (Roche Sequencing Solutions, Indianapolis, IN).

value: Spinalcord

value: mock


title: B22: H3L overexpression, replicate 4

value: stable cell line

value: human embryonic stem cells (hESCs)


title: ChinmoST testis, D9-11, scRNAseq

description: 10x Genomics v3

value: Testis

tag: strain

tag: developmental stage

tag: age

value: 9-11 days


title: WT testis D9-11, CUT&Tag, Chinmo, rep1

tag: tissue

value: Oregon R

value: Wild-type

tag: antibody


title: Macaca mulatta_Spinalcord_treated with LACV rep 1 [23705]

value: LACV


title: 257864010025_2.3_ALS951

description: Sample 40

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

tag: location of onset

value: Bulbar FTD


title: A12: Control, replicate 2

tag: cell line

tag: cell type

tag: genotype

value: Control

tag: treatment


title: Macaca mulatta_Spinalcord_treated with LACV rep 2 [23704]


title: WT testis D5-7, CUT&Tag, Chinmo, rep2

value: Adult

value: 5-7 days

tag: Sex

value: Male

value: Anti-Chinmo


title: WT testis D5-7, CUT&Tag, Chinmo, rep1


title: 257864010025_2.2_ALS950

description: Sample 39

value: male

tag: age at death (in years)

tag: disease state

value: Sporadic Amyotrophic Lateral Sclerosis

value: caucasian

value: Bulbar region

tag: occupation (job)

tag: smoker or non smoker

tag: alchool use or not

tag: other pathologies

tag: therapy used

tag: vaccination boost


title: A11: Control, replicate 1

tag: tissue

value: stable cell line


title: Macaca mulatta_Spinalcord_treated with mock rep 2 [23703]

value: Spinalcord

value: mock


title: 257864010023_1.2_ALS896

description: Sample 38

value: female

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

value: Lower limbs

tag: familial anamnesis


title: MEC-1 SF3B1 WT rep3

city: Monrovia

first: Lili

last: Wang

state: CALIFORNIA

address: 1218 South Fifth Ave.

department: Systems biology

institute: City of Hope

data_processing:
FASTQ files were analyzed and aligned to hg38 using STAR.
Aligned reads with coordinates are outputted in a BAM format. We used R to create raw count.  No special packages were used.
Assembly: GRCh38/hg38
Supplementary files format and content: raw count

growth_protocol: HG-3 and MEC-1 cells were maintained in RPMI with 10% FBS and 1% PS with 2mM glutamine

extract_protocol:
Total RNAs were extracted using Trizol and mRNAs were enriched using polyA selection
PolyA mRNAs were fragmented and constructed into sequencing libraries per Illumina protocols

value: Blood

tag: cell line

tag: cell type

value: Mature B Cells

value: SF3B1 WT


title: HsSKM_LatB_Rep2

city: Tianjin

first: Yaxin

last: Li

state: Tianjin

address: Building 24 B3, Tianjin University, No 92 Weijin Road, Nankai District

department: SPST

institute: Tianjin University

data_processing:
The fastq data were trimmed with Trim Galore (Galaxy Version 0.6.7+galaxy0)
quality-checked by FastQC(Galaxy Version 0.74+galaxy0)
mapped to human genome hg38 using Bowtie2 (Galaxy Version 2.5.0+galaxy0)
The bigwig files were generated by bamCoverage(Galaxy Version 3.5.1.0.0+galaxy0)
peaks were visualized on integrative genomics viewer (IGV: ver. 2.9.4). Heatmaps for score distributions across genomic regions were created using computeMatrix (Galaxy Version 3.5.1.0.0+galaxy0) and plotHeatmap (Galaxy Version 3.5.1.0.1+galaxy0).
Assembly: hg38
Supplementary files format and content: bigwig file

source_name: Primary Skeletal Muscle Cells

growth_protocol: Human skeletal muscle (hsSKM) cells were cultured in DMEM medium supplemented with 10% FBS in a 5% CO2 incubator, achieving 50-70% confluency on three 10 cm tissue culture dishes for each sample.

extract_protocol:
Control cells and Lat B treated cells were cross-linked with 1 mM dithiobis(succinimidyl propionate) (DSP) in PBS at room temperature for 30 min, quenched with 1 M Tris-HCl pH=8.0 at room temperature for 15 min and washed with PBS for 3 times. Fixed cells were lysed with 400 μl RIPA-G buffer + protease inhibitor cocktail (PIC ) +RNase to extract DNA-protein complex. Isolated DNA-protein complex was rinsed with 400 μl PBS 5 times and then suspended in 400 μl PBS. After centrifugation, the pellet was redissolved in 100 μl RIPA-T buffer +RNase by sonication (1s/1s, for 5s in total). The redissolved DNA-protein complex was digested with 0.5 μl Micrococcal Nuclease ( #10011,CST) at 37°C for 30 mins. After centrifugation, the DNA was loaded on 1.5% agarose gel, and then purified by E.Z.N.A. R Gel Extraction Kit (Omega_D2500-02; Omega BIO-TEK).  The DNA-protein complex absorbed on the column was incubated with digestion buffer (100 μl PBS + 2 μl Proteinase K biosharp#BS080-100mg)  to digest bound protein at 55°C for 2 hours. DNA was collected by centrifugation at 20,000 ✕ g for 1 min.  To de-crosslink DSP, 10 ul of 100 mM DTT was added into the eluate and incubated at 70℃ for 10 min. To remove proteinase K and DTT, the DNA sample was purified using E.Z.N.A. R Gel Extraction Kit.
The library construction was carried out using TruSeq DNA PCR-free prep kit (20015963, illumina). Library was sequenced by NovaSeq Sequencer

treatment_protocol: To depolymerize actin filaments, hsSKM cells were treated with 5μM latrunculin B (Lat B) for 30min.

value: Primary Skeletal Muscle Cells

tag: treatment

value: 5 microM latrunculin B (Lat B) for 30 min


title: Macaca mulatta_Spinalcord_treated with LACV rep 3 [23702]

value: LACV


title: Macaca mulatta_Spinalcord_treated with LACV rep 4 [23701]


title: HsSKM_LatB_Rep1


title: HsSKM_Control_Rep2

value: no treatment


title: 257864010023_1.1_ALS895

description: Sample 37

tag: Sex

tag: race

tag: location of onset

value: Upper limbs


title: MEC-1 SF3B1 WT rep2

tag: genotype


title: 257864010013_1.1_ALS1142

description: Sample 36

value: male

tag: age at death (in years)

tag: disease state

value: Lumbo-sacral region

tag: occupation (job)

tag: smoker or non smoker


title: Macaca mulatta_Spinalcord_treated with mock rep 3 [23700]


title: 257864010012_1.3_ALS1119

description: Sample 35

value: Sporadic Amyotrophic Lateral Sclerosis

value: caucasian

value: Cervical spinal cord

tag: alchool use or not

tag: other pathologies

tag: therapy used

tag: vaccination boost


title: MEC-1 SF3B1 K700E rep3

tag: tissue

value: SF3B1 K700E


title: Macaca mulatta_Spinalcord_treated with LACV rep 5 [23699]

value: Spinalcord


title: 257864010025_2.4_ALS952

description: Sample 41

value: Female

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

value: Upper Limbs

tag: familial anamnesis


title: A21: H3L overexpression, replicate 1

value: stable cell line

tag: cell line

tag: cell type

value: human embryonic stem cells (hESCs)

value: H3L overexpression

tag: treatment


title: HsSKM_Control_Rep1

value: Primary Skeletal Muscle Cells


title: hmSpVO_rep1

first: Jinkui

last: Zhu

state: Shanghai

address: 393 Middle Huaxia Road, Pudong, Shanghai, 201210, China.

department: School of Life Science and Technology

institute: ShanghaiTech University

description: TPM matrix (column name: hdMO_rep1) in the RSEM_gene_tpm.tsv

data_processing:
Cleaned reads were aligned to the reference genome (GRCh38) using STAR v2.7.10a and RSEM v1.3.1 was used to count the reads mapped to each gene. We achieved this through the nf-core/rnaseq pipeline v3.13.2.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited file includes TPM for each sample.

source_name: organoids

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit according to the manufacture's protocol. Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific) was used to determine the concentration and evaluate the purity of RNA samples. Agilent 2100 Bioanalyzer and 2100 RNA nano 6000 assay kit (Agilent Technologies) were used to evaluate the integrity of RNA samples.
For samples of C3,C4,C6 and hdMO_rep1,the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) and were sequenced on Illumina HiSeq X Ten platform. For samples of hdMO_rep2 and hdMO_ventr,, the mRNA was enriched by TIANSeq mRNA Capture Kit (TIANGEN) and the libraries was constructed by TIANSeq Fast RNA Library Kit (Illumina). The libraries were sequenced on Illumina NovaSeq 6000.

value: organoids

value: human embryonic stem cells

tag: genotype

value: WT

value: Differentiation according to protocol


title: 257864010012_1.2_ALS1118

description: Sample 34

tag: Sex

value: female

tag: age at death (in years)

tag: race

tag: location of onset


title: MEC-1 SF3B1 K700E rep2

value: Blood

value: Mature B Cells


title: C6

description: TPM matrix (column name: C6) in the RSEM_gene_tpm.tsv


title: MEC-1 SF3B1 K700E rep1


title: C4

description: TPM matrix (column name: C4) in the RSEM_gene_tpm.tsv


title: HG-3 SF3B1 WT rep3

value: SF3B1 WT


title: 257864010011_2.4_ALS1115

description: Sample 32

value: male

tag: disease state

value: Sporadic Amyotrophic Lateral Sclerosis

value: caucasian

value: Lumbo-sacral region

tag: occupation (job)

tag: smoker or non smoker

tag: alchool use or not


title: Macaca mulatta_Spinalcord_treated with LACV rep 6 [23698]

tag: tissue

value: Spinalcord

value: LACV


title: Macaca mulatta_Spinalcord_treated with LACV rep 7 [23696]


title: Macaca mulatta_Spinalcord_treated with mock rep 4 [23697]

value: mock


title: MEC-1 SF3B1 WT rep1


title: Macaca mulatta_Spinalcord_treated with LACV rep 8 [23695]


title: 257864010011_2.3_ALS1114

description: Sample 31

tag: survival characteristics

tag: other pathologies

tag: therapy used

tag: vaccination boost


title: HG-3 SF3B1 K700E rep3

tag: cell line

value: SF3B1 K700E


title: Macaca mulatta_Cerebellum_treated with mock rep 1 [23694]

source_name: Cerebellum

value: Cerebellum


title: C3

description: TPM matrix (column name: C3) in the RSEM_gene_tpm.tsv

value: organoids

tag: cell type


title: Q_ICV_µ

city: Boston

first: Danilo

last: Pellin

state: MA

address: 300 Longwood Ave

institute: Boston Childrens Hospital

data_processing:
Raw sequencing files were investigated for QC and aligned to the reference mouse genome mm39 (Genome assembly GRCm39) using STAR workflow83, obtaining, as a result, the gene-based count matrices. Poorly-detected genes with a cumulative reads count smaller than 10 or measured (reads count>0) in less than two samples were filtered ou
Assembly: GRCm39
Supplementary files format and content: raw gene counts

source_name: Brain

extract_protocol:
Total RNA was extracted with the RNeasy Plus Micro kit (Qiagen) from sorted myeloid brain populations, RNA quantity was determined using QuantiFluor® RNA system and QuantusTM Fluorometer (Promega)
cDNA was generated starting from 1 ng up to 100ng of purified mRNA by using SuperScript VILO Master mix (Thermo Fisher Scientific)

value: Brain

value: Microglia-like cells

tag: treatment

value: ICV


title: 257864010011_1.4_ALS1078

description: Sample 30

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

value: Cervical spinal cord

tag: familial anamnesis


title: HG-3 SF3B1 WT rep2

value: Blood

tag: genotype


title: HG-3 SF3B1 K700E rep2

value: Mature B Cells


title: HG-3 SF3B1 WT rep1

value: SF3B1 WT


title: Macaca mulatta_Cerebellum_treated with LACV rep 1 [23693]


title: S_CTR_µ

value: CTR


title: N16

value: whole blood

value: low nutritional risk combined with normal neurodevelopment

tag: Sex

value: male


title: 257864010011_1.2_ALS1075

description: Sample 29

value: female

tag: age at death (in years)

tag: disease state

value: Sporadic Amyotrophic Lateral Sclerosis

tag: race

value: caucasian

tag: location of onset

value: Lumbo-sacral region


title: 257864010010_2.4_ALS1073

description: Sample 28

value: Thoracic region

tag: occupation (job)

tag: smoker or non smoker

tag: alchool use or not


title: Macaca mulatta_Cerebellum_treated with LACV rep 2 [23692]

tag: tissue

value: Cerebellum

value: LACV


title: 257864010010_2.3_ALS1068

description: Sample 27

tag: survival characteristics

tag: other pathologies

tag: therapy used

tag: vaccination boost


title: HG-3 SF3B1 K700E rep1

tag: cell line

tag: cell type

value: SF3B1 K700E

tag: treatment


title: 257864010012_1.1_ALS1117

description: Sample 33

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: familial anamnesis


title: O_ICV_µ

value: Brain

value: Microglia-like cells

tag: genotype

value: ICV


title: Macaca mulatta_Cerebellum_treated with mock rep 2 [23691]

value: mock


title: M_ITL_µ

value: ITL


title: Single inactive carrier

city: New Delhi

first: Pramod

last: Upadhyay

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

description: carrier

data_processing:
Quality of reads assessed using FastQC
Trimming of poor-quality bases and adapter sequences using Trimmomatic
Trimmed reads aligned with human reference seqience (hg38) using HiSat2
Read counts generated using featureCounts tool
Differentially expressed genes comapred to healthy control, generated using edgeR software
Assembly: hg38
Supplementary files format and content: Clean_Unpooled_Counts_Control_IC_IT_Carrier.txt : List of gene ID and fearure counts in respective Unpooled groups as .txt files
Supplementary files format and content: Clean_Pooled_Counts_Control_IC_IT.txt : List of gene ID and fearure counts in respective pooled groups as .txt files
Supplementary files format and content: Unpooled_IC_vs_Control.txt : List of differntially expressed genes their Pvalue and respective log2FC values as .txt files
Supplementary files format and content: Pooled_IC_vs_Control.txt : List of differntially expressed genes their Pvalue and respective log2FC values as .txt files
Supplementary files format and content: Unpooled_IT_vs_Control.txt : List of differntially expressed genes their Pvalue and respective log2FC values as .txt files
Supplementary files format and content: Pooled_IT_vs_Control.txt : List of differntially expressed genes their Pvalue and respective log2FC values as .txt files
Supplementary files format and content: Unpooled_Carrier_vs_Control.txt : List of differntially expressed genes their Pvalue and respective log2FC values as .txt files

source_name: blood

extract_protocol:
RNA was isolated using RNAiso Plus (Takara) followed by DNase treatment from MasterPure complete DNA and RNA purification kit (Lucigen).
500ng RNA used to prepare library using TrueSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina Inc.) as per manufacturer's protocol
librabry sample was diluted to 400pM and loaded onto NovaSeq 6000 machine using SP flow cell (Illumina) for sequencing

value: blood

value: CD14+ monocytes

value: WT

tag: disease state

value: HBV inactive


title: 257864010010_2.2_ALS1067

description: Sample 26

tag: Sex

value: male

tag: age at death (in years)

tag: race

tag: location of onset

value: Cervical spinal cord


title: Macaca mulatta_Cerebellum_treated with LACV rep 3 [23690]

tag: tissue


title: Macaca mulatta_Cerebellum_treated with LACV rep 4 [23689]


title: 257864010010_2.1_ALS1065

description: Sample 25

value: Sporadic Amyotrophic Lateral Sclerosis

tag: survival characteristics

value: caucasian

value: Bulbar region

tag: occupation (job)

tag: smoker or non smoker

tag: alchool use or not


title: L_ITL_TAµ


title: Pooled immune-tolerant (IT)

value: HBV immune tolerant


title: P_ICV_TAµ


title: 257864010010_1.4_ALS1064

description: Sample 24

value: Lumbo-sacral region

tag: other pathologies

tag: therapy used

tag: vaccination boost


title: Single immune-tolerant (IT)

tag: cell type

tag: treatment


title: Macaca mulatta_Cerebellum_treated with mock rep 3 [23688]

value: Cerebellum


title: E_ICV_PBS

value: Brain


title: Macaca mulatta_Cerebellum_treated with LACV rep 5 [23687]

value: LACV


title: C_IV_µ

value: Microglia-like cells

value: IV


title: Pooled Immune-clearance (IC)

value: HBV immune clearance


title: 257864010010_1.3_ALS1063

description: Sample 23

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: familial anamnesis


title: B_IV_TAµ

tag: genotype


title: Pooled healthy control

description: control 5

value: blood

tag: disease state

value: healthy


title: Macaca mulatta_Cerebellum_treated with mock rep 4 [23685]

value: mock


title: 257864010010_1.1_ALS1061

description: Sample 21

tag: Sex

tag: age at death (in years)

tag: race


title: Single healthy control

description: control 1

tag: tissue

value: CD14+ monocytes

value: WT


title: 257864010018_2.4_Control

description: Sample 20

value: female

value: Control

tag: survival characteristics

tag: location of onset

tag: occupation (job)


title: Macaca mulatta_Cerebellum_treated with LACV rep 7 [23684]


title: 1% Input

description: 1% Input

data_processing:
The purified DNA was also used for ChIP-seq library preparation. Subsequently, pair-end sequencing of sample was performed on NovaSeq 6000 (Illumina, USA). Raw data (raw reads) of fastq format were firstly processed using fastp software (version 0.19.11). Clean data (clean reads) were obtained for next analysis. Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
After mapping reads to the reference genome, MACS2 (version 2.1.0) was used for peak calling to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets. After peak calling, the distribution of chromosome distribution, peak width, fold enrichment, significant level and peak summit number per peak were all displayed.
ChIPseeker was used to retrieve the nearest genes around the peak and annotate genomic region of the peak. Different peak analysis was based on the fold enrichment of peaks of different experiments.
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: called peaks of each sample in excel format

source_name: H9 hESCs

growth_protocol: All hESCs were cultured in mTesR1 medium.

extract_protocol: Chromatin DNAs were purifed by EZ-Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (Millipore, USA) according to the manual.

treatment_protocol: For chromatin shearing, truChIP® Chromatin Shearing Kit (Covaris, USA) was used according to the manual. All cells were crosslinked and lysed by truChIP® Chromatin Shearing Kit. Then nuclei were isolated and sheared by truChIP® Chromatin Shearing Kit on ME220 Focused-ultrasonicator (Covaris, USA). For ChIP, EZ-Magna ChIP™ A/G Chromatin Immunoprecipitation Kit (Millipore, USA) was used according to the manual.

tag: cell line

value: H9 hESCs

tag: antibody

value: none, 1percent Input


title: I_ITL_µ

value: ITL


title: 257864010018_2.3_Control

description: Sample 19

value: caucasian

tag: smoker or non smoker

tag: alchool use or not

tag: other pathologies

tag: therapy used

tag: vaccination boost


title: Macaca mulatta_Cerebellum_treated with LACV rep 8 [23683]

value: Cerebellum

tag: treatment


title: A29L overexpression, anti-H3K27me3, replicate 3

tag: genotype

value: A29L overexpression


title: VZ_48_Mock_rep3

city: Angers

first: Jerome

last: Verdier

address: Rue Georges Morel

country: France

institute: INRAE / IRHS

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by removing reads containing sequencing adapter; removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
SOAPnuke: version：v1.5.2, parameters: -l 15 -q 0.5 -n 0.1, website: https://github.com/BGI-flexlab/SOAPnuke
Quality control was checked using FastQC
High quality reads were mapped on Phaseolus vulgaris (Pvulgaris_442_v2.1) reference transcriptome using quasi-mapping alignment and quantification methods of Salmon algorithm v.1.2.1 (Patro et al., 2017)
Assembly: Phaseolus vulgaris (Pvulgaris_442_v2.1) from https://phytozome-next.jgi.doe.gov/info/Pvulgaris_v2_1
Supplementary files format and content: Tab-delimited text files corresponding to the Count table of all samples (columns) and all transcripts annotated in Phaseolus vulgaris 442 v2.1(= count.txt)

organism: Phaseolus vulgaris

source_name: Leaf

growth_protocol: The virulent Xanthomonas citri pv. fuscans strain Xcf CFBP4885 (RifR) and its avirulent T3SS-defective hrcV mutant (CFBP13802) (RifR, KanR) were obtained from the French Collection of Plant-associated Bacteria (CFBP, IRHS, Angers, France. DOI: https://doi.org/10.15454/E8XX-4Z18). Bacterial strains were cultured at 28°C on Tryptic Soy Agar medium (17.0 g.L−1 tryptone, 3.0 g.L−1 glucose, 5.0 g.L−1 NaCl, 5 g.L−1 K2HPO4 and 15 g.L−1 agar) supplemented with Rifampicin (100 µg.ml-1) and/or Kanamycin (50 µg.ml-1). For this study, two cultivars of Phaseolus vulgaris were selected: Flavert (susceptible) and Vezer (resistant). The plants were grown in a controlled growth chamberunder LED light (280 µmol·m-2·s-1) with a photoperiod of 16 hours days and 8 hours night. The day temperature was set at 23°C, while the night temperature was set at 20°C. Plants were grown in Traysubstrat 75/25 (Klasmann-Deilmann, Germany) and were watered with standard water until the first trifoliate leaf emerged. Upon appearance of the first trifoliate leaf, fertilized water (N-P-K: 15-10-30; pH 6.5; ec 1300 S.m-1) was used. The relative humidity in the growth chamber was set at 80%. Plants were incubated at 90% relative humidity for 24 hours prior to the inoculation. Following inoculation, the relative humidity was set back to 80%.

extract_protocol:
The collected leaves were ground to a fine powder after inoculation. Total RNA was then extracted from the ground leaves using the Macherey-Nagel NucleoSpin® RNA plus kit (Macherey-Nagel, Düren, Germany).
RNA quality was assessed with a NanoDrop spectrophotometer (Thermo Scientific™ NanoDrop™ One). Samples with acceptable quality (260/280 and 260/230 absorbance ratios of 2) were sent to the Beijing Genomics Institute (BGI, Hong Kong)(https://www.bgi.com) for further quality assessment using a Bio Analyzer. The RNA Integrity Number (RIN) of the 36 samples averaged 7.32, and the 28S/18S ratio averaged 1.8. Library preparation and sequencing were conducted on the BGISEQ-500 platform, generating an average of 24 million reads of 100 base pairs per sample (24M PE100).

treatment_protocol: Inoculation was performed once the plants had fully developed the first trifoliate leaf and had begun developing the second trifoliate leaf, which was approximately 16 days after planting. Bacterial strains were grown overnight at 28°C on Tryptic Soy Agar medium supplemented with the appropriate antibiotics. For the preparation of inocula, bacteria were then resuspended in sterile water to reach an DO600 of 0.1 (equivalent to 1.0x108 cfu.ml-1). Negative control (Mock) consisted in sterile water only. Xanthomonas suspensions and Mock were then infiltrated into the first trifoliate leaf using a vacuum chamber. The homogeneity of the infiltration in leaf tissues was checked visually. In total, 72 plants were inoculated: six plants were inoculated for each inoculation condition (Mock, CFBP4885, CFBP13802), for each timepoint (24hpi and 48hpi), and for each cultivar (Flavert and Vezer). Sampling was performed by collecting leaf discs with a diameter of 1 cm from six plants in each modality. The collected leaf discs were pooled to buffer the variability between the six plant replicates. The whole experiment was carried out on three independent plant lots grown 3 weeks part. Over the three independent repeats of the experiment, 36 samples were collected for total RNA extraction.

value: Leaf

value: Vezer

value: Water

tag: sampling time_(hour_post_inoculation)


title: Macaca mulatta_Brainstem_treated with mock rep 1 [23682]

source_name: Brainstem

value: Brainstem


title: 257864010018_1.4_Control

description: Sample 18

tag: Sex

value: male

tag: disease state

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: familial anamnesis


title: A29L overexpression, anti-H3K27me3, replicate 2


title: FL_48_Mock_rep3

tag: tissue

value: Flavert


title: Single immune-clearance (IC)

value: blood

tag: cell type

value: HBV immune clearance


title: 257864010018_1.3_Control

description: Sample 17

tag: age at death (in years)

tag: survival characteristics

tag: race

tag: location of onset

tag: occupation (job)


title: Macaca mulatta_Cerebellum_treated with LACV rep 6 [23686]

value: LACV


title: A29L overexpression, anti-H3K27me3, replicate 1

tag: cell line

tag: antibody


title: 257864010010_1.2_ALS1062

description: Sample 22

value: Sporadic Amyotrophic Lateral Sclerosis

value: Lumbo-sacral region

tag: smoker or non smoker

tag: alchool use or not

tag: other pathologies

tag: therapy used

tag: vaccination boost


title: Macaca mulatta_Brainstem_treated with LACV rep 1 [23681]

tag: treatment


title: 257864010018_1.2_Control

description: Sample 16

tag: Sex

tag: disease state

value: Control

tag: survival time from date of onset (months)

tag: post-mortem interval in hours


title: VZ_48_hrcv_rep3

tag: tissue

tag: genotype

tag: sampling time_(hour_post_inoculation)


title: A29L overexpression, anti-H3K4me3, replicate 3

value: H9 hESCs


title: A_IV_µ

value: Brain

tag: cell type

value: Microglia-like cells

value: IV


title: Macaca mulatta_Brainstem_treated with LACV rep 2 [23680]


title: FL_48_hrcv_rep3


title: 257864010018_1.1_Control

description: Sample 15

value: female

tag: age at death (in years)

tag: survival characteristics

tag: race

value: caucasian

tag: location of onset

tag: occupation (job)

tag: familial anamnesis


title: Macaca mulatta_Brainstem_treated with mock rep 2 [23679]

value: mock


title: 257864010017_2.4_Control

description: Sample 14

tag: smoker or non smoker

tag: alchool use or not

tag: other pathologies

tag: therapy used


title: VZ_48_4885_rep3

value: Leaf

value: Vezer

tag: treatment


title: A29L overexpression, anti-H3K4me3, replicate 2

tag: cell line

value: A29L overexpression

tag: antibody


title: A29L overexpression, anti-H3K4me3, replicate 1


title: FL_48_4885_rep3

tag: tissue

value: Flavert


title: Macaca mulatta_Brainstem_treated with LACV rep 3 [23678]

value: Brainstem


title: OCS scRNA-seq

city: Hangzhou

first: Junfen

last: Xu

state: Other (Non U.S.)

address: No.1 Xueshi Road

department: Department of Gynecologic Oncology

institute: Women’s Hospital, Zhejiang University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 30%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Genome_build: GRCh38Ensembl91
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Ovarian carcinosarcoma tissue

extract_protocol:
After surgical resection, fresh samples were collected and washed with phosphate-buffered saline (PBS) for three times. Tissue was cut into approximately 1 mm3 pieces and enzymatically digested collagenase IV (Sigma), collagenase I (Sigma) and DNase I (Worthington) at 37°C for 30 min. After digestion, the sample was filtered out with a 35 µm cell strainer. Single cells were stained with AO/PI for viability assessment and live cells were preferentially sorted for single-cell sequencing.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

tag: age

tag: pathology

value: Ovarian carcinosarcoma

tag: tumor stage

value: IIIC


title: 257864010017_2.3_Control

description: Sample 13

tag: Sex

tag: age at death (in years)

tag: disease state

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: vaccination boost


title: Macaca mulatta_Brainstem_treated with LACV rep 4 [23677]

value: LACV


title: A29L overexpression, anti-myc tag, replicate 3

tag: genotype

value: anti-myc tag


title: 257864010017_2.2_Control

description: Sample 12

value: male

value: Control

tag: survival characteristics

tag: race

tag: location of onset

tag: occupation (job)

tag: smoker or non smoker

tag: alchool use or not

tag: familial anamnesis


title: VZ_24_Mock_rep3

tag: tissue

tag: treatment

value: Water

tag: sampling time_(hour_post_inoculation)


title: Macaca mulatta_Brainstem_treated with mock rep 3 [23676]


title: FL_24_Mock_rep3


title: Macaca mulatta_Brainstem_treated with LACV rep 5 [23675]


title: 257864010017_2.1_Control

description: Sample 11

tag: Sex

tag: other pathologies

tag: therapy used


title: A29L overexpression, anti-myc tag, replicate 2

tag: cell line

value: H9 hESCs

tag: antibody


title: A29L overexpression, anti-myc tag, replicate 1


title: 257864010017_1.4_Control

description: Sample 10

tag: age at death (in years)

tag: disease state

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: vaccination boost


title: 257864010017_1.3_Control

description: Sample 9

tag: survival characteristics

tag: race

tag: location of onset

tag: occupation (job)


title: Macaca mulatta_Brainstem_treated with LACV rep 6 [23674]

tag: tissue


title: FL_24_hrcv_rep3

tag: genotype

tag: treatment


title: Macaca mulatta_Brainstem_treated with mock rep 4 [23673]


title: VZ_24_hrcv_rep3

tag: sampling time_(hour_post_inoculation)


title: H3L overexpression, anti-H3K27me3, replicate 3

value: H3L overexpression


title: H3L overexpression, anti-H3K27me3, replicate 1


title: VZ_24_4885_rep3


title: H3L overexpression, anti-H3K27me3, replicate 2


title: 257864010017_1.2_Control

description: Sample 8

tag: Sex

tag: smoker or non smoker

tag: alchool use or not

tag: other pathologies

tag: familial anamnesis


title: 257864010017_1.1_Control

description: Sample 7

value: female

tag: age at death (in years)

tag: disease state

tag: therapy used


title: Macaca mulatta_Brainstem_treated with LACV rep 7 [23672]


title: Macaca mulatta_Brainstem_treated with LACV rep 8 [23671]


title: H3L overexpression, anti-H3K4me3, replicate 3

tag: cell line

tag: antibody


title: 257864010016_2.4_Control

description: Sample 6

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

value: caucasian

tag: vaccination boost


title: H3L overexpression, anti-H3K4me3, replicate 2

tag: genotype


title: VZ_48_Mock_rep2

tag: tissue

tag: treatment

tag: sampling time_(hour_post_inoculation)


title: Macaca mulatta_Basalganglia_treated with mock rep 1 [23670]

source_name: Basalganglia

value: Basalganglia

value: mock


title: FL_48_Mock_rep2

value: Leaf


title: 257864010016_2.2_Control

description: Sample 5

tag: Sex

tag: location of onset

tag: occupation (job)

tag: smoker or non smoker

tag: alchool use or not


title: Macaca mulatta_Basalganglia_treated with LACV rep 1 [23669]


title: H3L overexpression, anti-H3K4me3, replicate 1


title: Macaca mulatta_Basalganglia_treated with LACV rep 2 [23668]


title: VZ_48_hrcv_rep2

value: Vezer


title: 257864010016_2.1_Control

description: Sample 4

tag: age at death (in years)

tag: disease state

tag: other pathologies

tag: therapy used

tag: familial anamnesis


title: FL_48_hrcv_rep2

value: Flavert


title: Macaca mulatta_Basalganglia_treated with mock rep 2 [23667]


title: H3L overexpression, anti-myc tag, replicate 3

tag: cell line

tag: antibody


title: H3L overexpression, anti-myc tag, replicate 2


title: VZ_48_4885_rep2


title: Macaca mulatta_Basalganglia_treated with LACV rep 3 [23666]


title: FL_48_4885_rep2


title: Macaca mulatta_Basalganglia_treated with LACV rep 4 [23665]


title: Macaca mulatta_Basalganglia_treated with mock rep 3 [23664]


title: control-rep3

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: University of Cincinnati, 160 Panzeca Way

institute: University of Cincinnati

data_processing:
Data were de-multiplexed, and appropriate quality control checks were performed before aligning the sequences to the human reference genome (hg19) using STAR TopHat2 aligner
Assembly: hg19
Supplementary files format and content: read counts in the comma separated text file format

source_name: glioma tumor sample

extract_protocol:
Patient tumor samples from 2.5 mg (Group 1), 5 mg (Group 2) and 10 mg (Group 3) dose-cohorts, and three control samples were processed for mRNA isolation via poly-A RNA purification
The mRNA libraries were prepared, indexed, and pooled in order to obtain 50-100 million reads per sample.

value: glioma tumor sample

tag: dose

value: control


title: H3L overexpression, anti-myc tag, replicate 1

tag: genotype


title: FL_24_Mock_rep2

tag: tissue


title: FL_24_4885_rep3

tag: treatment


title: VZ_24_Mock_rep2

tag: sampling time_(hour_post_inoculation)


title: control-rep2


title: Macaca mulatta_Basalganglia_treated with LACV rep 5 [23663]


title: control-rep1


title: VZ_24_hrcv_rep2


title: ∆flaXpflaAX_hcd_rep3

city: Jena

first: Rabea

last: Ghandour

address: Winzerlaer Straße 2

department: Institute of Microbiology

country: Germany

institute: Friedrich Schiller University

data_processing:
cDNA reads were imported into CLC Genomics Workbench v 22.0.2 and analysed using mostly standard parameters.
3'adaptor- and quality trimming was performed using the trim reads command with the following settings: 3´ trim: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA  5' trim: GATCGTCGGACTGTAGAACTCTGAACGTGTAGA; Trim quality scores limit 0.05, Trim ambiguous nucleotides 2
The trimmed reads were checked for quality and mapped to the V.cholerae reference genome: NCBI Acc.number: NC_002505, NC_002506 using the following settings: Mismatch cost =  2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = Yes, Strand specific = forward, Maximum number of hits for a read = 10, expression value: TPM
Read count extraction and normalization were performed using CLC genomic workbench
Assembly: NC_002505, NC_002506
Supplementary files format and content: xlsx file including total reads, TPM from each sample and differential gene expression (fold change and FDR values)

organism: Vibrio cholerae

source_name: bacterial cell

growth_protocol: Vibrio cholerae C6706 WT + pctrl, ∆flaX + pctrl and ∆flaX + pPflaAX were grown overnight in LB media. The following day bacteria were diluted 1:1000 in fresh media. At OD 0.2 and 2.0, cells were collected.

extract_protocol:
Cells equivalent to 50 OD600 units were collected and RNA was isolated using Tri-reagent. DNA contamination was reomved by TurboDNase treatment and RNA was cleaned afterward using standard nucleic acid precipitation procedures. Depletion of ribosomal RNA was performed by custom biotinylated oligos. Binding to magnetic streptavidin-beads removed rRNA. Efficiency of the depletion was verified by Bioanalyzer.  doi.org/10.1128/mBio.00010-20
The rRNA depleted RNAs samples were fragmented using magnesium fragmentation module (NEB). cDNA was synthesized by using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB) following the manufacturer's instructions. cDNA libraries were column-based purified and cleaned left-sided using the Agencourt AMPure XP kit (Beckman Coulter Genomics). The quality and quantity of cDNA libraries was measured by Bioanalyzer and Qubit, respectively.

tag: strain

tag: cell type

value: bacterial cell

value: {delta}flaXpflaAX

tag: cell density

value: hcd


title: ∆flaXpflaAX_hcd_rep1


title: ∆flaXpflaAX_hcd_rep2


title: letrozole-10mg-rep2

value: letrozole


title: 257864010015_2.3_Control

description: Sample 2

tag: Sex

value: Control

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

tag: location of onset

tag: occupation (job)

tag: smoker or non smoker

tag: vaccination boost


title: ∆flaXpctrl_hcd_rep3

value: {delta}flaXpctrl


title: FL_24_hrcv_rep2


title: letrozole-10mg-rep1

tag: dose


title: VZ_24_4885_rep2

tag: genotype


title: 257864010015_2.2_Control

description: Sample 1

tag: age at death (in years)

tag: disease state

tag: alchool use or not

tag: other pathologies

tag: therapy used

tag: familial anamnesis


title: ∆flaXpctrl_hcd_rep2

tag: strain

tag: cell type

tag: cell density


title: ∆flaXpctrl_hcd_rep1


title: Macaca mulatta_Basalganglia_treated with LACV rep 7 [23660]

tag: tissue

tag: treatment

value: LACV


title: FL_24_4885_rep2

tag: sampling time_(hour_post_inoculation)


title: 257864010016_1.3_Control

description: Sample 3

tag: Sex

value: male

tag: survival characteristics

tag: survival time from date of onset (months)

tag: post-mortem interval in hours

tag: race

tag: location of onset

tag: occupation (job)


title: Macaca mulatta_Basalganglia_treated with LACV rep 8 [23659]


title: letrozole-5mg-rep1

tag: dose


title: WTpctrl_hcd_rep3

tag: genotype

value: WTpctrl


title: Macaca mulatta_Basalganglia_treated with LACV rep 6 [23662]


title: VZ_48_Mock_rep1

value: Water


title: FL_48_Mock_rep1


title: letrozole-2.5mg-rep1


title: Macaca mulatta_Cerebralcortex_treated with LACV rep 1 [23657]

source_name: Cerebralcortex

value: Cerebralcortex


title: Macaca mulatta_Basalganglia_treated with mock rep 4 [23661]

value: Basalganglia

value: mock


title: WTpctrl_hcd_rep1


title: Macaca mulatta_Cerebralcortex_treated with LACV rep 2 [23656]


title: VZ_48_hrcv_rep1

value: Leaf

value: Vezer


title: Wild-type, replicate 1, Ly6C low macrophages on Day 4 after muscle injury, ChIP-seq

city: New York

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

department: Department of Oncological Sciences

institute: Mount Sinai Icahn School of Medicine

description: H3K27Ac ChIP-seq

data_processing:
Raw ATAC-seq and ChIP sequencing reads were aligned to the mouse reference genome (mm10) with BWA using default parameters.
Reads with mapping quality less then 10 (MAPQ<10) and duplicated reads are discarded. Furthermore, reads falling into blacklisted regions are also discarded.
To minimize technical variablity across samples we performed upper-quartile normalization using custom scripts. For this, we first generated read number normalized bedgraph files with HOMER and calculated the read distributions for the distal consensus (promoter associated peaks are not considered) ATAC-seq summits.
For each sample, we calculated the top 10% value and divided all values with this normalization factor.
Assembly: mm10
Supplementary files format and content: Processed data files (bedgraph) contains the upper-quartile (UQ) normalized coverage of the samples.

source_name: Muscle

extract_protocol:
Fascia of the injured TA muscle was removed. Muscles were dissociated in RPMI containing 0.2% collagenase B (Roche Diagnostics GmbH) at 37°C for 1 hour and filtered through a 100 µm and a 40 µm filter. CD45+ cells were isolated using magnetic sorting (Miltenyi Biotec). For FACS, macrophages were treated with Fcγ receptor blocking antibodies and with 10% normal rat serum: normal mouse serum 1:1 mix, then stained with a combination of PE-conjugated anti-Ly6C antibody (HK1.4, eBioscience), APC-conjugated F4/80 antibody (BM8, eBioscience) and FITC-conjugated Ly6G antibody (1A8, Biolegend). Cells were isolated for downstream applications on a BD FACSAria III sorter. The monocyte purification procedure was performed as described previously (Houthuys et al., 2010) with slight modifications. In short, the blood from C57BL/6 mice was taken by cardiac puncture to maximize the amount of blood obtained in an endotoxin-free manner. Up to 5.3 × 10^7 ± 4 × 10^6 white blood cells (viability >96%) were obtained from 15 ml of blood from 15 animals after red blood cell lysis (n = 3). To minimize cell aggregation and adhesion to plastic, all purifications were performed at 0–4°C in PBS/BSA/EDTA (MACS buffer). For red blood cell lysis, cells were resuspended in 0.5–1 ml FACS Lysing solution (BD; Cat #349202), incubated for 5 min at room temperature, and then centrifuged (400 g, 5 min, 4°C). For FACS and sorting, MFs were treated with Fcγ receptor blocking antibodies, 5% normal rat serum, and 5% normal mouse serum. They were then stained with a combination of APC-conjugated anti-Ly6C antibody (eBioscience; HK1.4), PE/Cy7-conjugated CD11b antibody (BD Bioscience; M1/70), PE-conjugated Ly6G antibody (BioLegend; 1A8), and PerCP/Cy5.5-conjugated MHCII antibody (BioLegend; M5/114.15.2). Gating and sorting strategy are shown in Patsalos et al. JEM 2022.
ATAC-seq was carried out as described earlier with minor modification (Buenrostro J.D. et al. 2013). 20 000 cells were sorted in ice-cold PBS. Nuclei were isolated with ATAC-Lysis Buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL) and were used for tagmentation using Nextera DNA Library Preparation Kit (Illumina) from 2-3 biological replicates. After tagmentation DNA was purified with MinElute PCR Purification Kit (Qiagen). Tagmented DNA was amplified with Kapa Hifi Hot Start Kit (Kapa Biosystems) using 9 PCR cycles. Amplified libraries were purified again with MinElute PCR Purification Kit. Fragment distribution of libraries was assessed with Agilent Bioanalyzer and libraries were sequenced on a HiSeq 2500 platform.

value: Muscle

tag: chip antibody

value: Muscle infiltrating macrophages

value: Cardiotoxin Injury

tag: time

value: Day 4 after muscle injury


title: ∆flaXpflaAX_lcd_rep3

tag: strain

value: bacterial cell

value: {delta}flaXpflaAX

value: lcd


title: FL_48_hrcv_rep1

value: Flavert


title: Macaca mulatta_Cerebralcortex_treated with mock rep 2 [23655]


title: Wild-type, replicate 1, Ly6C High macrophages on Day 1 after muscle injury, ChIP-seq

description: H3K27Ac ChIP-seq

tag: cell type

value: Day 1 after muscle injury


title: VZ_48_4885_rep1


title: ∆flaXpflaAX_lcd_rep2

tag: cell density


title: Macaca mulatta_Cerebralcortex_treated with LACV rep 3 [23654]

tag: tissue

value: LACV


title: letrozole-2.5mg-rep2

value: glioma tumor sample

tag: treatment

value: letrozole


title: FL_48_4885_rep1

tag: sampling time_(hour_post_inoculation)


title: Macaca mulatta_Cerebralcortex_treated with LACV rep 4 [23653]

value: Cerebralcortex


title: ∆flaXpflaAX_lcd_rep1


title: Wild-type Ly6C High circulating monocytes from uninjured animals, ATAC-seq

description: ATAC-seq

source_name: Blood

value: Blood

value: Circulating monocyte

value: Uninjured


title: WTpctrl_hcd_rep2

value: WTpctrl

value: hcd


title: scr T3

type: RNA

city: rome

first: andrea

last: sacconi

address: via elio chianesi

institute: regina elena cancer institute

hyb_protocol: GeneChip® Hybridization Control Kit and GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix Platform)

scan_protocol: GeneChip® Hybridization, Wash, and Stain Kit Affymetrix platform)

data_processing: the background adjustment and gene expression evaluation of Affymetrix microarray  probe-level data was performed using the Robust Multi-array Average (RMA) procedure. Data was base-2 log trasformed and quantile normalized. Probes not detected in all samples were removed. The HTA-2_0.r1.gene.cdf file was used.

label: Biotin

source_name: sh/scr-  T3

label_protocol: GeneChip® WT PLUS Reagent Kit Affymetrix and GeneChip® WT Terminal Labeling Kit (Affymetrix platform)

growth_protocol: The ECACC-authenticated colorectal cancer line HT29 (ECACC 91072201) derived sh/MKK3 and sh/scr sublines were regularly monitored for mycoplasma contamination every 2 months by PCR, and only mycoplasma-free cells were used for studies. Sublines were used for no more than 15 passages, were were grown in McCoy’s medium (12-688F, Lonza, Burton on Trent, UK) supplemented with 10% heat-inactivated FBS (10099-141, Gibco, Paisley, Scotland, UK), 2 mM L-glutamine (17-606E, Lonza) and 100 U/mL penicillin/streptomycin (DE17-602E Gibco) in humidified conditions at 37°C at 5% CO2.

extract_protocol: Total RNA from biological replicates was extracted using the miRNAeasy® kit (Qiagen, Chatsworth, CA) following the manufacturer’s instructions. The total RNA concentration and purity were assessed with a Nanodrop TM1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA). Reverse transcription and RT‒qPCR were performed with an MMLV RT assay and Sybr Green® or TaqMan Assays (Applied Biosystems, Foster City, CA, USA) according to the manufacturer's protocol.

treatment_protocol: HT29 derived -sh/scr and sh/MKK3 sublines were plated at a density of 3.0x105 cells/60 mm dish, treated 24 h later with doxycycline (DOX) (1 ug/ml, D9891 Sigma‒Aldrich) and collected 60 h later.

value: colorectal cancer

value: sh/scr


title: Macaca mulatta_Cerebralcortex_treated with mock rep 3 [23652]

value: mock


title: ∆flaXpctrl_lcd_rep3

value: bacterial cell

value: {delta}flaXpctrl


title: scr T2

source_name: sh/scr - T2


title: scr T1

source_name: sh/scr - T1


title: VZ_24_Mock_rep1

value: Leaf

value: Vezer

value: Water


title: FL_24_Mock_rep1

value: Flavert


title: ∆flaXpctrl_lcd_rep2

value: lcd


title: Macaca mulatta_Cerebralcortex_treated with LACV rep 5 [23651]

value: LACV


title: ∆flaXpctrl_lcd_rep1


title: VZ_24_hrcv_rep1


title: Macaca mulatta_Cerebralcortex_treated with LACV rep 6 [23650]

value: Cerebralcortex


title: MK80 T3

source_name: sh/MKK3 - T3


title: FL_24_hrcv_rep1


title: MK80 T2

source_name: sh/MKK3 - T2


title: VZ_24_4885_rep1


title: WTpctrl_lcd_rep2


title: Macaca mulatta_Cerebralcortex_treated with LACV rep 7 [23648]


title: WTpctrl_lcd_rep1


title: letrozole-5mg-rep2

value: glioma tumor sample

value: letrozole


title: KO_2M [IgM]

status: Public on Aug 27 2024

type: protein

city: Dallas

first: Chengsong

state: TX

address: 5323 Harry Hines Blvd

department: Immunology

institute: UT Southwestern Medical Center

hyb_protocol: not provided

scan_protocol: not provided

data_processing: NFI were normalized by robust linear model using build-in Ig control with various dilutions

molecule: protein

source_name: Serum

label_protocol:
8 positive controls (4 mouse IgG/IgM controls with different dilutions and 4 human IgG /IgM control with different dilutions) were also imprinted on the arrays as positive controls.
Mouse serum samples were first treated with DNAse I to remove free-DNA and then applied onto antoantigen arrays with 1:50 dilution. The autoantibodies binding to the antigens on the array were detected with cy3-labeled anti-human IgG  and the array slides were scanned with Genepix 4400A scanner with laser wavelengths 532nm for cy3 and 635nm for cy5 to generate Tiff images.  Genepix Pro 7.0 software is used to analyze the image and generate the Genepix report (GPR) files (Molecular Devices, Sunnyvale, California, USA). The net fluorescent intensity (NFI) of each antigen was generated by subtracting the local background and negative control (Phosphate buffered saline or simplified as PBS) signal.

extract_protocol: Serum samples from recipients collected as per routine protocol as defined above were procured from histocompatibility lab after IRB approval. Sera of all subjects were aliquoted and stored at -80ºC.

tag: isotype

value: IgM

tag: gender

value: Male

tag: age (month)

tag: slide

tag: block


title: KO_6M [IgM]


title: NOD_6M [IgM]


title: KO_3M [IgM]


title: PBS [IgM] 2

description:
Slide2_635.gpr
Negative control

organism: synthetic construct

source_name: Negative control


title: NOD_3M [IgM]


title: Macaca mulatta_Cerebralcortex_treated with LACV rep 8 [23647]


title: NOD_2M [IgM]


title: NOD_4M [IgM]


title: KO_1M [IgM]


title: KO_5M [IgM]


title: NOD_5M [IgM]


title: WTpctrl_lcd_rep3

value: WTpctrl


title: KO_4M [IgM]


title: KO_5F [IgM]

value: Female


title: KO_4F [IgM]


title: KO_6F [IgM]


title: PBS [IgM] 1

description:
Slide1_635.gpr
Negative control


title: KO_2F [IgM]


title: KO_1F [IgM]


title: MK80 T1

source_name: sh/MKK3 - T1

value: colorectal cancer


title: FL_24_4885_rep1

source_name: Leaf


title: Het_6F [IgM]

value: Tlr+/-


title: NOD_1M [IgM]


title: Het_4F [IgM]


title: Het_3F [IgM]


title: NOD_5F [IgM]


title: Het_2F [IgM]


title: NOD_6F [IgM]


title: NOD_4F [IgM]


title: NOD_3F [IgM]


title: PBS [IgG] 2

description:
Slide2_532.gpr
Negative control

value: IgG


title: NOD_1F [IgM]


title: KO_3F [IgM]


title: KO_5M [IgG]


title: KO_4M [IgG]


title: NOD_6M [IgG]


title: KO_2M [IgG]


title: KO_3M [IgG]


title: KO_6M [IgG]


title: NOD_5M [IgG]


title: KO_1M [IgG]


title: Het_5F [IgM]


title: NOD_1M [IgG]


title: NOD_4M [IgG]


title: KO_5F [IgG]


title: NOD_2M [IgG]


title: NOD_3M [IgG]


title: KO_6F [IgG]


title: KO_4F [IgG]


title: Het_1F [IgM]


title: PBS [IgG] 1

description:
Slide1_532.gpr
Negative control


title: KO_2F [IgG]


title: KO_1F [IgG]


title: NOD_2F [IgM]


title: Het_6F [IgG]


title: Het_1F [IgG]


title: NOD_6F [IgG]


title: Het_4F [IgG]


title: Het_2F [IgG]


title: Het_3F [IgG]


title: NOD_3F [IgG]


title: NOD_2F [IgG]


title: KO_3F [IgG]


title: NOD_1F [IgG]


title: CONTROL_16

city: Utrecht

first: Joost

last: Koedijk

address: Heidelberglaan 25

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

data_processing:
Raw data were normalized using Quartile 3 count (Q3) normalization in R as per NanoString's recommendations (code: https://bioconductor.org/packages/release/workflows/vignettes/GeoMxWorkflows/inst/doc/GeomxTools_RNA-NGS_Analysis.html)
Batch correction was performed using Combat-seq
Spatial Deconvolution was performed in the GeoMx DSP Analysis suite using scRNAseq reference datasets (see methods in the preprint for references)
Assembly: Human
Supplementary files format and content: There is one spreadsheet (excel) that contains all the Q3-normalized gene expression data for all 143 sequenced regions.
Library strategy: Spatial Transcriptomics

source_name: Non-leukemic bone marrow

extract_protocol:
5 micrometer tissue slices of FFPE bone marrow biopsies (AML or non-leukemic) were cut.
Spatial transcriptomics sequencing libraries were prepared with NanoSTring GeoMx Digital Spatial Profiling slides & reagent kit according to manufacturer's instructions

treatment_protocol: Not applicable (treatment-naïve samples)

value: Non-leukemic bone marrow

tag: disease state

value: treatment-naïve


title: CONTROL_15


title: NOD_5F [IgG]


title: CONTROL_13


title: NOD_4F [IgG]


title: CONTROL_12


title: Het_5F [IgG]


title: CONTROL_9


title: CONTROL_10


title: CONTROL_11


title: CONTROL_8


title: CONTROL_14


title: Macaca mulatta_Cerebralcortex_treated with mock rep 1 [23658]

value: mock


title: CONTROL_7


title: CONTROL_6


title: CONTROL_5


title: CONTROL_4


title: CONTROL_2


title: MIXED2_44

source_name: AML bone marrow

value: AML bone marrow


title: tumor tissue [CIM072T]

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

hyb_protocol: Bisulfite converted DNA was hybridised to Infinium Human Methylation EPIC BeadChip according to the manufacturer’s recommendations.

scan_protocol: The Illumina HiScan system was used to scan the beadchip platform.

data_processing: Data processing was performed with R software. Briefly, probes with low quality (detection p-value > 0.05), mapped in X/Y chromosomes or to SNPs, and cross-reactive were filtered out using the minfi package. Differences in Type-I and Type-II probes and normalization of the β values were adjusted using the Beta MIxture Quantile dilation (BMIQ) method. Batch effect was corrected with ComBat function from sva package (v.3.44.0).

label: Cy5 and Cy3

source_name: inflammatory breast cancer tissue

label_protocol: Cy5 and Cy3

extract_protocol: Genomic DNA was isolated from 24 fresh frozen macrodissected IBC tissue biopsies and six surrounding normal breast frozen tissues using the QIAsymphony kit (Qiagen, Valencia, CA, USA).

tag: donor id

value: inflammatory breast cancer tissue


title: Macaca mulatta_Cerebralcortex_treated with mock rep 4 [23649]


title: tumor tissue [CIM071]


title: CONTROL_3


title: MIXED2_43


title: tumor tissue [CIM022]


title: MIXED2_42


title: MIXED2_41


title: MIXED2_40


title: MIXED2_38


title: tumor tissue [CIM067]


title: tumor tissue [CIM069T]


title: tumor tissue [CIM066]


title: MIXED2_37


title: tumor tissue [CIM009]


title: tumor tissue [CIM024]


title: tumor tissue [CIM016]


title: tumor tissue [CIM068T]


title: tumor tissue [CIM011T]


title: tumor tissue [CIM070T]


title: tumor tissue [CIM014]


title: tumor tissue [CIM017]


title: MIXED2_36


title: tumor tissue [CIM008]


title: MIXED2_34


title: tumor tissue [CIM026]


title: tumor tissue [CIM015T]


title: MIXED2_32


title: MIXED2_31


title: MIXED2_30


title: MIXED2_39


title: MIXED2_28


title: MIXED2_29


title: tumor tissue [CIM004]


title: MIXED2_24


title: tumor tissue [CIM002]


title: MIXED2_26


title: tumor tissue [CIM005]


title: AGGREGATE_35


title: tumor tissue [CIM012]


title: AGGREGATE_34


title: AGGREGATE_32


title: tumor tissue [CIM018]


title: AGGREGATE_31


title: MIXED1_47


title: tumor tissue [CIM001]


title: MIXED1_46


title: AGGREGATE_30


title: AGGREGATE_28