title: SVG+SOX10_R176_R177insPQPR_2_input

city: Urbana

first: Jun

middle: S

last: Song

email: songj@illinois.edu, jssong137@gmail.com

state: IL

address: 1110 West Green Street, MC 704

institute: University of Illinois, Urbana-Champaign

data_processing:
Paired-end reads were aligned to the human genome (hg38) with Bowtie2 using the command bowtie2 -X 1000
Aligned reads were filtered using Samtools with the command samtools view -h -F 4 -q 10
Read duplicates were removed using Samtools with the commend samtools markdup -r
Peak locations were determined from deduplicated reads using MACS2 with the command macs2 callpeak --format BAMPE -g hs -q 0.3
Peak locations derived from replicate samples were combined into a single consensus set of peak locations using IDR with the command idr --input-file-type narrowPeak --rank q.value
Peak locations with IDR < 0.1 were removed
Assembly: hg38
Supplementary files format and content: Thresholded peak file returned by IDR.  Tab delimited text file. Columns are: chromosome, start position (1-based), end position (1-based), IDR value, -log10(merged peak q-value), merged peak summit relative to start position, -log10(local IDR value), -log10(global IDR value), replicate 1 start position (1-based), replicte 1 end position (1-based), replicate 1 average enrichment, replicate 1 peak summit relative to start replicate 1 start position, replicate 2 start position (1-based), replicte 2 end position (1-based), replicate 2 average enrichment, replicate 1 peak summit relative to start replicate 2 start position

growth_protocol: SVG-p12 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 degrees Celsius.

extract_protocol:
Cells were fixed with 1% formaldehyde for 9 minutes. After quenching and cell lysis, chromatin was sonicated using a Corvaris S2 focused-ultrasonicator.  Chromatin immunoprecipitation was performed with the mouse anti-FLAG2 clone M2 antibody (Sigma cat # F1804) using the SimpleChIP Plus Sonication Chromatin IP Kit (Cell Signaling cat # 56383) following the manufacturer's instructions.
Sequencing libraries were prepared from both total input DNA and following anti-FLAG immunoprecipitation using the KAPA Hyper Prep Kit (KAPA cat # KK8502) complemented with DNA adapter barcodes (KAPA UDI Adapters KK8727). 20 ng of DNA was used as starting material for input and IP samples. Adapter-ligated libraries were amplified for 8 cycles with HiFi Polymerase. Post-amplification cleanup and double-sided size selection was performed with KAPA cleanup beads. Sequencing library size and quality were checked by Agilent Bioanalyzer profiling, and sequencing libraries were also validated by qPCR using the KAPA Library Quant kit KK4824) before pooling for sequencing.

treatment_protocol:
Lentiviral supernatants generated from pCDF1-SOX10-3xFLAG wildtype and mutant vectors were used to infect parental SVG-p12 cells in the presence of 10 μg/mL polybrene.
Following lentiviral infection, SVG-p12 cells were selected for stable transduction using 2 ug/mL puromycin, and thereafter maintained in 1 ug/mL puromycin.  Expression of FLAG-tagged wildtype and mutant SOX10 protein was subsequently confirmed by Western blot using both anti-FLAG and anti-SOX10 antibodies.

value: immortalized fetal glial cells

value: +SOX10 R176_R177insPQPR


title: Root Control, Replicate 2

status: Public on Jul 13 2023

type: SRA

city: Invergowrie / Dundee

first: Raul

last: Huertas

state: Perth and Kinross

address: Errol Road

department: Environmental and Biochemical Sciences

country: United Kingdom

institute: The James Hutton Institute

library_source: transcriptomic

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence and mapped using to reference genome (v4.1) using HISAT2 2.0.5 and Stringtie 1.2.4 using default parameters.
Read count extraction and normalization were performed using Cuffdiff software.
Assembly: Panicum virgatum v4.1
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

molecule: total RNA

organism: Panicum virgatum

source_name: Root

growth_protocol: Germinated seedling were growth in cones (6.9 cm in diameter X 25.4 cm in depth) filled with 40% all-purpose sand, 40% Q-ROK silica sand and 20% fine (2-4 mm particle size) perlite.

extract_protocol:
Total RNA was extracted using a cetyltrimethylammonium bromide (CTAB) and LiCl method (Chang, Puryear, & Cairney, 1993). RNA was treated with DNase I to remove genomic DNA.
RNA libraries were prepared using Illumina TruSeq RNA library preparation kit following manufacturer's protocols

treatment_protocol: Plants were watered daily to field capacity during a 4-week growth period with a modified nutrient solutions

tag: tissue

value: Root

tag: genotype

value: WT cv. Alamo

tag: treatment

value: Optimal nutrition


title: 7E_M_210

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age

tag: strain


title: B2_S28

city: Ramat Gan

first: Talia

last: Golan

state: <None>

address: Tel Hashomer

department: Oncology Institute

country: Israel

institute: Sheba Medical Center

data_processing:
STAR alignment, output sorted genomes.
XenofilteR on sorted genomes.
Unsort filtered bams to fastqs.
Realign filtered FASTQs with STAR,   output   unsorted transcriptome
RSEM on realigned bam.
Assembly: Create CPM matrix.
Supplementary files format and content: BRCA_CPM.csv - cvs file including CPM data for each sample

organism: Homo sapiens

source_name: Human;PDX

growth_protocol: Tumor tissue from patient derived xenograft (PDX) was snaped frozen in liquie nitrogen

extract_protocol:
NucleoSpin® RNA, MACHEREY-NAGEL
Bulk MARS-seq

treatment_protocol: No treatment in vivo

value: PDAC

value: Patient derived xenofraft

value: BRCA

value: No


title: SVG+SOX10_R176_R177insPQPR_1_input

tag: cell line

tag: cell type


title: ATAC_WT_aOrg 1

city: Copenhagen N

first: Laura

middle: Maarit

last: Pikkupeura

address: Ole Maaloes vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

description:
ATAC-seq
Enh_ATAC_counts.txt
wt_aOrg_1_S1

data_processing:
The NextSeq bcl format sequence data was downloaded from BaseSpace and using Illumina's blc2fastq (v2.20.0.422) base-called and demultiplexed. The raw 76 bp paired-end (PE) reads were first trimmed for Nextera transposase adapter sequences using Trimmomatic in palindrome mode. FastQC (v0.11.7) of reads before and after trimming confirmed the removal of any 3’-end adapter sequences, while also clearly showing the known insertion Tn5 motif in the 5’-end. FastQ Screen (v0.11.4) was furthermore used to check for sample contamination. The trimmed PE reads were mapped to the mouse genomes (mm10 assembly, canonical chromosomes only) using bowtie2 v.2.2.9 with default settings except -k 2 -X 2000 --no-mixed --no- discordant and finally converted to bam format using samtools (v1.10).  After sorting (SortSam) and labeling duplicates (MarkDuplicates) with Picard tools and adding a NH tag (number of reported alignments), reads were filtered to exclude unmapped, multimapping, and mitochondrial reads (samtools view -f 2 -F 4 and custom filter). The filtered bam files were converted to bed format using bedtools bamtobed.
Mapped reads were imported from bed files as ‘Datasets’ into EaSeq[50] (v. 1.2, http://easeq. net) for subsequent analysis using its integrated tools and default settings where nothing else is stated. A list of previously identified organoid enhancers including values from differential accessibility analysis as previously described (Pikkupeura and Bardini Bressan et al, 2022, submitted) was imported as a ‘Regionset’. ATAC-seq signal was quantified in 1 kbp windows centred at the previously identified regions using the ‘Quantify’ tool with all normalization disabled to give raw read-counts and the Regionset was exported. Based on this, a subset of regions was filtered having a signal above the 0.9 fractile in at least two of eight samples (two replicates of Smarca4, two replicates of Smarcc1, and four replicates of negative controls) and termed ‘filtered enhancers’.
Assembly: mm10
Supplementary files format and content: A tab delimited text file containing a matrix of sgRNA read counts in T0 and the three populations CD117+, CD117NegSca1Neg, and CD117NegSca1High in T1, T2, and T3

source_name: Adult proximal small intestine

growth_protocol: Standard 3D Matrigel culture of organoids. ENR medium: adv.DMEM/F12, GlutaMAX, Hepes, Pencillin/Streptomycin (all from Thermo Fisher), EGF (Peprotech; 50 ng/mL), Noggin (Peprotech; 100 ng/mL) and conditioned R-spondin1 media (10%)

extract_protocol:
Organoids were isolated and dissociated to single cells and 50,000 live cells were sorted in 200 mL 0.1% BSA/PBS for generation of ATAC-seq libraries. Briefly, sorted cells were lysed and incubated with Tn5 Transposase (Illumina) for 30 minutes at 37C for DNA tagmentation
The tagged DNA was PCR amplified with sequence-compatible and barcoded primers for a total of 13 cycles. The concentration and quality of the libraries was analysed with Qubit and Bioanalyzer. The libraries were diluted to 2 nM in EB buffer and a final dilution of 1.5 pM was sequenced with Illumina High Output 150 pair-end  cycles kit on an Illumina NextSeq 500 sequencer.

value: Adult proximal small intestine

value: Epithelial organoids

value: WT

value: Untreated, 5 days in culture


title: Root Control, Replicate 1


title: 7E_M_209


title: SVG+SOX10_R176_R177insPQPR_2

tag: chip antibody

value: anti-FLAG clone M2 (Sigma cat # F1804)


title: ATAC_Neg2-ctrl high 2

description:
ATAC-seq
Enh_ATAC_counts.txt
Neg2_2_high_S6

source_name: E16.5 fetal proximal small intestine

value: E16.5 fetal proximal small intestine

value: Cas9-blasticidin plasmid transduced WT organoids transduced with scrambled sgRNA


title: 7E_M_208


title: 7E_M_207


title: THP1, TET2KO

city: Hangzhou

first: Yixiang

last: Hu

address: 866 Yuhangtang Rd, Hangzhou 310058, P.R. China

country: China

institute: Zhejiang University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
hMeDIP-seq  reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.36, discarding reads left with < 36 bp
hMeDIP-seq reads were aligned to the UCSC hg19 genome using BWA-0.7.17.
To create hMeDIP-seq coverage plots, the locations of the mapped hMeDIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the Wig file format.
Peaks between IP sample and input sample were called uing MACS-1.4.2 with the significance cut-off p-value <=e-5
DiffPeaks between the IP samples were called uing MACS-1.4.2 with the significance cut-off q-value <=e-5,and merge pos peaks and neg peaks.Statistical features of peaks and GO and KEGG enrichment of diff-genes
Assembly: hg19
Supplementary files format and content: Peaks, DiffPeaks between the IP samples
Library strategy: hMeDIP-seq

growth_protocol: RPMI-1640, 10% fetal bovine serum, 1 × penicillin/streptomycin. Cells were cultured at 37 ℃ at 5% CO2.

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood & Tissue Kit (Qiagen) and fragmented by sonication to a mean size of approximately 200-400 bp
hMeDIP-seq libraries were prepared using the KAPA HyperPrep Kit (KAPA, KK8505) according to the manufacturer’s protocol. The anti-5hmC antibody (Diagenode) was used to immunoprecipitate the adaptor-ligated DNA. This captured DNA was then purified with Zymo DNA Clean & Concentrator™-5 (Zymo Research) and subsequently amplified by 13-15 cycles of PCR using Illumina 8-bp dual index primers. Libraries were validated using Qubit.

treatment_protocol: Cells were infected with influenza virus A/swine/Jiangsu/C1/2008 (H9N2) at an MOI of 3 for 6 hours

value: human mononuclear cells

value: 5hmc (Active Motif, #39791)


title: Root 200 μM Phosphorus (mild stress), Replicate 2

value: Pi limitation (mild)


title: Smarca4-mut

description:
scRNA-seq
smarca4.csv
Smarca4_S2

library_source: transcriptomic single cell

data_processing:
Raw reads were processed with Cell Ranger (v3.0.1) software from 10x Genomics[34] to generate bam files. Read alignment was based on the refdata-cellranger-mm10-3.0.0 reference downloaded from the 10x Genomics website (https://support.10xgenomics. com/). Raw base call files were demultiplexed into FASTQ files and then aligned and filtered using cellranger’s mkfastq and count functions.
The bulk of the analysis was done in Python using scanpy. Adult organoid and fetal spheroid samples were treated separately to filter out low quality cells. The first metrics were per cell distributions of spliced counts, unspliced counts and genes. Based on visual tracing of a Gaussian curve, the cut-off values for those three characteristics were determined. Secondly, cells with a high ratio of counts originating from mitochondrial features (more than 0.08%) were filtered out. Lastly, doublets were removed using scrublet and Doublet Detection packages. The expected doublet rate in scrublet was set to 0.06, and DoubletFinder was used with default parameters. Cells predicted to be doublets by either of the tools were filtered out. After concatenating the samples together, genes expressed in less than 5 cells or with less than 20 counts were filtered out. Count data was normalised and log-transformed, without genes that account for more than 0.05 of total counts.
Assembly: mm10
Supplementary files format and content: A tab delimited text file containing a matrix of sgRNA read counts in T0 and the three populations CD117+, CD117NegSca1Neg, and CD117NegSca1High in T1, T2, and T3

extract_protocol:
Organoids were isolated on day 5 after passaging and dissociated into single cells using TrypLE incubation. 20,000 live cells were sorted into 10 mL of ultra clean 0.8% BSA/PBS
For scRNA-seq of mutant FEnS (Smarca4mut, Smarcc1mut and Scramble-ctrl) TotalSeq™ hashtag antibodies (A0301-A0305; Biolegend) were used to multiplex samples. Cells isolated from two individual organoid lines from each perturbation were sequenced. Cells were isolated on day 5 after passaging and dissociated to single cells. Each sample was incubated with 0.5 mg of unique hashtag antibody for 20 minutes on ice. Before sorting, cells were incubated with DAPI (0.2 mg/mL) for 10 minutes on ice. 10,000-15,000 events/cells from each sample were sorted on an ARIAIII sorter (BD Biosciences) and pooled directly into four tubes. Single cell libraries were prepared using 10X Genomics v3 Chemistry as described above with implementation of hashtag libraries for demultiplexing. An additive primer (HTO primer) was added in the step for cDNA amplification. The hashtag-cDNA and endogenous cDNA were separated after cDNA amplification using SPRIselect beads (Beckman Coulter) for size separation. Here hashtag-cDNA was isolated in the supernatant containing smaller DNA fragments and collected to generate the hashtag-library following the protocol from Stoeckius et al and CiteSeq (https://cite-seq.com). Briefly, the supernatant was cleaned using SPRIselect beads (Beckman Coulter) and 30 ng cDNA was used as input for PCR amplification (20 cycles). Illumina-indexes for sequencing was subsequently added using Kapa HiFi HotStart Ready Mix (Roche Diagnostics). For the endogenous cDNA library, the 10X protocol was followed. The dual index kit set AA (10X genomics) was used for sample indexing and 11-12 cycles were used during the final amplification step. The four hashtag cDNA- and four endogenous cDNA libraries were diluted to 2 nM and combined into two pooled libraries for sequencing (5% hashtag + 95 % endogenous cDNA). The two final libraries for sequencing were further diluted to 1.7 pM before being sequenced with Illumina High Output 150 cycles kit on an Illumina NextSeq500 sequencer.

value: Cas9-blasticidin plasmid transduced WT organoids transduced with smarca4 sgRNA


title: THP1, TET2KO, Input


title: SVG+SOX10_R176_R177insPQPR_1

value: immortalized fetal glial cells

value: +SOX10 R176_R177insPQPR


title: SVG+SOX10_K172_Y173dup_2_input


title: SVG+SOX10_K172_Y173dup_2


title: 7E_M_205


title: Neg-ctrl

description:
scRNA-seq
ctrl.csv
Neg-ctrl_S1

value: Cas9-blasticidin plasmid transduced WT organoids transduced with scramble sgRNA


title: 7E_M_211


title: 7E_M_206


title: Smarcc1-mut

description:
scRNA-seq
smarcc1.csv
Smarcc-WT_S2

value: Cas9-blasticidin plasmid transduced WT organoids transduced with Smarcc1 sgRNA


title: THP1, Control, Input

value: control


title: ATAC_WT_aOrg 2

description:
ATAC-seq
Enh_ATAC_counts.txt
wt_aOrg_2_S2


title: WT_FEnS

description:
scRNA-seq
aOrg.csv
aOrg_S1

extract_protocol:
Organoids were isolated on day 5 after passaging and dissociated into single cells using TrypLE incubation. 20,000 live cells were sorted into 10 mL of ultra clean 0.8% BSA/PBS
scRNA libraries were prepared using 10X Genomics v3 Chemistry according to manufacturer’s guidelines. Cells were loaded on the 10X Genomics Single Cell Chip for formation of Gel Bead-in-Emulsions (GEMs) and followed by reverse transcriptase. cDNA was amplified with 10 PCR cycles, while sample indexing PCR was performed with 11 cycles. Libraries were diluted to 2 nM in elution buffer, and a final dilution of 1.7 pM was sequenced with Illumina High Output 150 cycles kit on an Illumina NextSeq 500 sequencer.


title: SVG+SOX10_K172_Y173dup_1_input


title: SVG+SOX10_K172_Y173dup_1


title: T3_ENR4

description:
RNA-seq
all_CRISPR_samples.count.txt
T3_ENR4

data_processing:
Raw reads were processed with Cell Ranger (v3.0.1) software from 10x Genomics[34] to generate bam files. Read alignment was based on the refdata-cellranger-mm10-3.0.0 reference downloaded from the 10x Genomics website (https://support.10xgenomics. com/). Raw base call files were demultiplexed into FASTQ files and then aligned and filtered using cellranger’s mkfastq and count functions.
The bulk of the analysis was done in Python using scanpy. Adult organoid and fetal spheroid samples were treated separately to filter out low quality cells. The first metrics were per cell distributions of spliced counts, unspliced counts and genes. Based on visual tracing of a Gaussian curve, the cut-off values for those three characteristics were determined. Secondly, cells with a high ratio of counts originating from mitochondrial features (more than 0.08%) were filtered out. Lastly, doublets were removed using scrublet and Doublet Detection packages. The expected doublet rate in scrublet was set to 0.06, and DoubletFinder was used with default parameters. Cells predicted to be doublets by either of the tools were filtered out. After concatenating the samples together, genes expressed in less than 5 cells or with less than 20 counts were filtered out. Count data was normalised and log-transformed, without genes that account for more than 0.05 of total counts.
Assembly: mm10
Supplementary files format and content: A tab delimited text file containing a matrix of sgRNA read counts in T0 and the three populations CD117+, CD117NegSca1Neg, and CD117NegSca1High in T1, T2, and T3
Library strategy: CRISPR screen

extract_protocol:
DNA from all timepoints was isolated using the DNeasy Blood and Tissue Kit (Qiagen)
sgRNAs were amplified from genomic DNA using KAPA HiFi HotStart Library Amplification Kit (Kapa Biosystems) with 20 cycles of PCR. A second PCR was used to add sample unique Illumina sequencing barcodes. The amplified sgRNA libraries were run in an agarose gel and isolated with Gel Extraction Kit (Qiagen) and cleaned with DNA Clean & Concentrator kit (Zymo Research). The concentrations of the sgRNA libraries were measured using KAPA Library Quantification kit (Kapa Biosystems), and diluted to 2 nM before libraries were pooled. A final dilution of 1.7 pM pooled libraries were sequenced with Illumina High Output 75 cycles kit and sequenced on Illumina NextSeq500 sequencer.

value: Cas9-blasticidin plasmid transduced WT organoids transduced with sgRNA library

value: 10 days in culture + 7 days in culture after passaging + 7 days in culture after passaging (T3)


title: 7E_M_204


title: WT_aOrg

description:
scRNA-seq
fens.csv
FEnS_S2

value: Epithelial organoids


title: THP1, Control


title: Vd592_rep 2

city: Tübingen

first: Chenlei

last: Hua

address: Auf der Morgenstelle 32

department: Department of Plant Biochemistry, Centre of Plant Molecular Biology (ZMBP)

country: Germany

institute: University of Tübingen

data_processing:
Primary sequencing data that produced by Illumina HiSeqTM 2000, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences.
QC of alignment is performed to determine if resequencing is needed. The alignment data is utilized to calculate distribution of reads on reference genes and perform coverage analysis.
Results of gene expression include gene expression levels and differential expression analysis.
Further, we perform Gene Ontology (GO) enrichment analysis and Pathway enrichment analysis.
Assembly: GCA_000723945.1Ni_benscaffolds:100,480contigs:100,480N50:776L50:22,990
Supplementary files format and content: .xls file containing all the gene expression reads and relative expression levels

organism: Verticillium dahliae

source_name: fungal mycelia

extract_protocol:
Total RNA was isolated using a Nucleospin® RNA Plant Kit (Macherey-Nagel, Germany) according to the manufacturer’s instructions.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA or by removing rRNAs from the total RNA. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates.

value: fungal mycelia

value: wild-type


title: 7E_M_203


title: SVG+SOX10_wildtype_2_input

value: +SOX10 wildtype


title: Vd171_rep 2


title: Vd592_rep 1


title: 7E_M_202


title: SVG+SOX10_wildtype_1_input


title: SVG+SOX10_wildtype_2

value: anti-FLAG clone M2 (Sigma cat # F1804)


title: T3_ENR3

description:
RNA-seq
all_CRISPR_samples.count.txt
T3_ENR3

data_processing:
The screen sequencing data was analysed with MAGeCK (model-based analysis of genome-wide CRISPR/Cas9 knockout)[42]. Briefly, the sequencing reads were mapped to the sgRNA design library and read counts were calculated for all individual sgRNAs.
Screen hits were identified by integrating fold changes and P-values of individual sgRNAs targeting the same gene using robust ranking aggregation (RRA) for comparison between any two conditions to identify positively or negatively selected genes between time points or cell populations. The counts were normalised based on 100 non-targeting sgRNAs. All sgRNAs were present at T0 and positive control sgRNAs targeting essential genes were depleted over time. To identify significant screen hits, FDR <0.05 and absolute log2 fold change >1 cut-offs were used.
Assembly: mm10
Supplementary files format and content: A tab delimited text file containing a matrix of sgRNA read counts in T0 and the three populations CD117+, CD117NegSca1Neg, and CD117NegSca1High in T1, T2, and T3
Library strategy: CRISPR screen

value: E16.5 fetal proximal small intestine


title: 7E_M_201


title: Vd171_rep 1


title: T3_ENR2

description:
RNA-seq
all_CRISPR_samples.count.txt
T3_ENR2


title: 7E_M_200


title: T3_ENR1

description:
RNA-seq
all_CRISPR_samples.count.txt
T3_ENR1


title: 7E_M_199


title: HR1a, pahT mutant replicate 2

city: Little Rock

first: Zulema

last: Udaondo

state: AR

address: 501 Jack Stephens Drive

department: Biomedical Informatics

institute: UAMS

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts (Novogen, Hong Kong). In this step, clean data (clean reads) were obtained by removing reads containing adapters and reads in which uncertain nucleotides (N) were more than the 10% of the read length. Reads with low quality nucleotides (base quality <20) in more than 50% of the read length were also discarded. Read data were deposited in the Gene Expression Omnibus repository (accession number GSE163593)
Paired-end clean reads were mapped to the reference genome (RAST Genome ID: 6666666.92368) using HISAT2 software v.0.6.1. HISAT2 uses a large set of small GFM indexes that collectively cover the whole genome. These small indexes (called local indexes), combined with several alignment strategies, enable rapid and accurate alignment of sequencing reads. A table with the gene names as in RAST and the equivalent genes in GenBank (JABXWS000000000) is included in Supplementary Table 6.
HTSeq software was used to count the read mapped to each gene, including known and novel genes.
Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 package v1.20.0 in R. DESeq2 provides 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 (FDR). Genes with an adjusted P value (Padj) < 0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: RAST Genome ID: 6666666.92368

organism: Novosphingobium sp. HR1a

source_name: bacterial cells

growth_protocol: Overnight cultures grown in M9 minimal medium plus glucose of Novosphingobium sp. HR1a and the pahT mutant were diluted in 10 mL of fresh M9 minimal medium plus glucose or plus glucose and phenanthrene (0.05 mg) to an initial OD 660nm of 0.1 and incubated at 30 ºC for seven hours at 200 rpm in an orbital shaker. 5 ml of these cultures were centrifuged (6000 rpm during 10 minutes) and the pellets were immediately frozen in liquid N2 and stored a -80ºC.

extract_protocol:
Total RNA was extracted using the Trizol method (TRIzol RNA Isolation Reagents, Thermofisher Scientist) and further DNAse treatment and purification with RNeasy Mini Kit (Qiagen). RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). RNA integrity and quantification were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
One μg RNA per sample was used to prepare the sequencing libraries which were generated by Novogen (Hong Kong) using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.

value: bacterial cells

value: pahT mutant


title: HR1a, pahT mutant replicate 1


title: SVG+SOX10_wildtype_1


title: ETIS, WI38, VPF72h, scRNA-seq

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: 10x Genomics

data_processing:
Cell Ranger software version 6.0.0 was used for demultiplexing, barcoded processing, sequence alignment, and for generating matrix files
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Etoposide-induced senescent (ETIS) cells

extract_protocol:
ETIS cells (untreated or VPF-treated) were trypsinized, washed and resuspended in PBS, and subjected to single-cell GEM (Gel Bead-Emulsion) generation with Chromium Controller (10x Genomics)
scRNA-seq library was performed according to the manufacter’s instructions (10x Genomics Chromium Next Gem Single Cell 3' Regent Kits v3 protocol, 10x Genomics). In brief, single cell suspension was loaded into a Chromium Next GEM Chip G (10x Genomics), and GEMs were generated using the Chromium Single Cell Controller (10x Genomics). We used 11 and 13 cycles for cDNA amplification and Sample Index PCR (Single Index Kit T Set A, 10x Genomics), respectively


title: 7E_M_223


title: 7E_M_198


title: HR1a, wt replicate 2

value: wild type


title: T2_ENR4

description:
RNA-seq
all_CRISPR_samples.count.txt
T2_ENR4

value: 10 days in culture + 7 days in culture after passaging (T2)


title: T2_ENR3

description:
RNA-seq
all_CRISPR_samples.count.txt
T2_ENR3


title: ETIS, WI38, untreated, scRNA-seq

description: 10x Genomics

value: Etoposide-induced senescent (ETIS) cells

value: untreated


title: HR1a, wt replicate 1


title: 7E_M_197


title: T2_ENR2

description:
RNA-seq
all_CRISPR_samples.count.txt
T2_ENR2


title: BY_K27me3_KHRM3_5cpw_(220817_DJ_Hs_BY_K27me3_KHRM3_5cpw_220802)

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: sciCUT&Tag for H3K27me3 run on a mixture of Human Cell Lines and mouse 3T3 cells and dispensed on the ICELL8 at a concentration of 5 nuclei per nanowell

data_processing:
Genome_build: hg38
Genome_build: mm10
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads. 2. We used Bowtie2 2.4.2 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the repeat-masked hg38 Homo sapiens reference sequence obtained from UCSC. 3. We used samtools 1.14 "view" to extract properly paired reads from the D. melanogaster alignments. 4. We used bedtools 2.30.0 "genomecov" to make a normalized count hg38 track which is the fraction of counts at each base pair scaled by the size of the hg38 reference sequence (3210038034) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .hg38.bw) 5. We repeated steps 2-4 to map the paired reads to mm10 Mus Musculus. (Supplementary file .mm10.bw)

organism:
Homo sapiens
Mus musculus

source_name: sciCUT&Tag

tag: scicut&tag antibody

value: H3K27me3 Cell Signaling Technologies cat# C36B11

tag: human cell lines

tag: mouse cell line


title: T2_ENR1

description:
RNA-seq
all_CRISPR_samples.count.txt
T2_ENR1


title: 7E_M_195


title: BY_K27me3_KHRM3_40cpw_(220817_DJ_Hs_BY_K27me3_KHRM3_40cpw_220802)

description: sciCUT&Tag for H3K27me3 run on a mixture of Human Cell Lines and mouse 3T3 cells and dispensed on the ICELL8 at a concentration of 40 nuclei per nanowell


title: 7E_M_196


title: S_VPF_2_Etop8d_VPF48h_S20

data_processing:
BCL files were de-multiplexed and converted to FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to human genome hg19 Ensembl v82 using STAR software v2.4.0j.  featureCounts (v1.6.4) software was used to generate gene counts.
Assembly: hg19 Ensembl v82

extract_protocol:
Samples were harvested by directly lysing cells on the plate with RLT buffer (QIAGEN) plus beta-mercaptoethanol, and RNA  extracted with the QIACUBE using the RNeasy plus Mini kit protocol.
High-quality RNA (125 ng) was used for sequencing the library prep using Illumina TruSeq Stranded mRNA Library prep kit following the manufacturer’s protocol (Illumina, San Diego, CA), and the quality and quantity of the libraries were checked using the Agilent DNA 1000 Screen Tape on the Agilent Tapestation.

treatment_protocol: WI-38 fibroblasts (N=6 biological repeats) were induced to senesce by etoposide treatment (50 µM for 8 days, medium refreshed every 3 days). Untreated proliferating WI-38 cells were used a control (N=3 biological repeats). Senescent cells were either treated with vehicle (DMSO) (3 samples) or VPF (1.5 µM) for 48 hours (3 samples).

tag: Sex

value: Female

value: Etoposide+Verteporfin (1.5 μM, 48 h, 8 days into senescence)


title: S_VPF_1_Etop8d_VPF48h_S19


title: 7E_M_194


title: T1_ENR4

description:
RNA-seq
all_CRISPR_samples.count.txt
T1_ENR4

value: Cas9-blasticidin plasmid transduced WT organoids transduced with sgRNA library

value: 10 days in culture (T1)


title: S_3_Etop8d_S18

value: Etoposide-induced senescent (8 days)


title: BY_K27me3_KHRM3_20cpw_(220817_DJ_Hs_BY_K27me3_KHRM3_20cpw_220802)

description: sciCUT&Tag for H3K27me3 run on a mixture of Human Cell Lines and mouse 3T3 cells and dispensed on the ICELL8 at a concentration of 20 nuclei per nanowell


title: T1_ENR3

description:
RNA-seq
all_CRISPR_samples.count.txt
T1_ENR3

value: Epithelial organoids


title: BY_K27me3_KHRM3_10cpw_(220817_DJ_Hs_BY_K27me3_KHRM3_10cpw_220802)

description: sciCUT&Tag for H3K27me3 run on a mixture of Human Cell Lines and mouse 3T3 cells and dispensed on the ICELL8 at a concentration of 10 nuclei per nanowell


title: S_2_Etop8d_S17


title: 7E_M_192


title: T1_ENR2

description:
RNA-seq
all_CRISPR_samples.count.txt
T1_ENR2


title: T1_ENR1

description:
RNA-seq
all_CRISPR_samples.count.txt
T1_ENR1


title: 7E_M_191


title: S_VPF_3_Etop8d_VPF48h_S21


title: P_3_PDL20_S15

value: Proliferating controls


title: T0_seq2

description:
RNA-seq
all_CRISPR_samples.count.txt
T0_seq2

growth_protocol: T=0 was taking 40 h after library transduction. ENR medium: adv.DMEM/F12, GlutaMAX, Hepes, Pencillin/Streptomycin (all from Thermo Fisher), EGF (Peprotech; 50 ng/mL), Noggin (Peprotech; 100 ng/mL) and conditioned R-spondin1 media (10%)

value: Control (T0)


title: Mcpip1 DN_replicate3

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

country: Poland

institute: Maria Skłodowska-Curie National Research Institute of Oncology

data_processing:
Signal processing and basecalling was performed with Torrent Suite version 5.14.0.
Raw reads were mapped to Danio rerio Ensembl genome version GRCz11 using STAR (version 2.7.10a)  (PMID: 23104886) and bowtie2 (version 2.4.4) (PMID: 22388286) for unmapped reads.
Gene counts were created with htseq-count (PMID: 25260700), using Ensembl gene model.
Differential expression was tested with DESeq2 version (version 1.40.1) (PMID: 2551628)
Assembly: Danio rerio Ensembl genome version GRCz11
Supplementary files format and content: DESeq2 normalized count

organism: Danio rerio

source_name: embryo (6 hpf)

growth_protocol: AB/TL zebrafish were maintained in a continuous recirculating closed system aquarium with a light/dark cycle of 14/10 hours at 280C. Larvae were incubated in E3 medium at 28°C according to standard protocols.

extract_protocol:
Zebrafish embryos were collected in Fenozol (A&A Biotechnology, Gdansk, Polska) and stored at -80°C  prior to analysis. For RNA isolation, the samples were homogenized in Fenozol using a tissue homogenizer (OMNI International, Kennesaw, GA, USA).
The poly (A) mRNA fraction from total RNA was isolated with Dynabeads® mRNA DIRECT™ Micro Kit (Thermo). The sequencing library for each RNA sample was prepared according to the protocol provided by the manufacturer using the Ion Total RNA-Seq Kit v2 (Thermo). The libraries were generated from 1-15 ng of mRNA by fragmenting the mRNA with RNaseIII, purifying the fragmented RNA, and hybridizing and ligating it with Ion adaptors. Subsequently, the RNA products were reverse transcribed and amplified to double-stranded cDNA, and then purified using a magnetic bead-based method. The molar concentration and size of each cDNA library was determined using the DNA HS Kit on Bioanalyzer 2100 (Agilent). Each library was diluted to ~53 pM concentration before template preparation. Up to three barcoded libraries were mixed in equal volume and used for automatic template preparation on the Ion Chef instrument (Thermo) using reagents from the Ion PI Hi-Q 200 Kit (Thermo) and Ion PI v3 Proton Chip.

treatment_protocol: Zebrafish eggs at 1-cell stage were microinjected with mRNA using WPI Picopump PV820 microinjector.

value: embryo (6 hpf)

value: AB/TL

value: microinjection with mRNA encoding zebrafish Mcpip1 D112N


title: Mcpip1 DN_replicate2


title: 7E_M_190


title: Mcpip1 DN_replicate1


title: P_1_PDL20_S13


title: T0_seq1

description:
RNA-seq
all_CRISPR_samples.count.txt
T0_seq1

value: E16.5 fetal proximal small intestine


title: Mcpip1 WT_replicate3

value: microinjection with mRNA encoding zebrafish Mcpip1


title: Mcpip1 WT_replicate2


title: plusDOX-rep3

data_processing:
Reads were aligned using qAlign function from Bioconductor package QuasR (Gaidatzis et al),with default parameters.
Mapped reads were assigned to known UCSC genes and  quantified with qCount function from QuasR.
Assembly: mm10
Supplementary files format and content: Gene counts for each sample as comma separated text file

source_name: Proximal small intestine

growth_protocol: Epithelial fragments from fetal intestine (intestines from three fetuses were pooled for each sample) and scraped adult crypts (from one individual per sample) were harvested from the proximal parts of the small intestine using EDTA (2mM). Harvested epithelial fragments adult crypts were embedded in Matrigel droplets and cultured in advanced DMEM/F12 with GlutaMAX and Penicillin/Streptomycin supplemented with EGF (Peprotech; 50 ng/ml), Noggin (Peprotech; 100ng/mL), and R-spondin1 (R&D Systems; 500 ng/ml). When indicated, the growth medium was supplemented with CHIR99021 (Stemgent; 3μM) and Nicotinamide (Sigma; 10 mM).

extract_protocol:
RNA was collected using RNAeasy Microkit (Qiagen). The samples were sequenced with Illumina NextSeq. 2015).
Libraries were prepared using TruSeq RNA kit (Illumina) following manufacturer instructions.

treatment_protocol: For transgene induction and the TetON-YAP-H2B-mCherry, doxycycline (Sigma #D9891, 1ug/ml) was added for 48h immediately after passaging.

value: Proximal small intestine

value: Doxycyclin


title: P_2_PDL20_S14


title: 7E_M_189


title: 7E_M_188


title: 7E_M_193


title: 7E_M_187


title: SVG+SOX10_R176_R177insPQPR_replicate#2

city: Stanford

first: David

middle: A.

last: Solomon

address: 300 Pasteur Dr, Lane L216

department: Pathology

institute: Stanford University School of Medicine

description:
SVG+SOX10_R176_R177insPQPR_S85
Matrix processed SVG+SOX10 RNA-seq.txt

data_processing:
FastQC version 0.11.9
Trimmomatic version 0.39
Sequence reads were trimmed for adaptor sequence/low-quality sequence using FastQC and Trimmomatic (default parameters).
HISAT2 version 2.2.1
Trimmed sequence reads were mapped to GRCh38 using HISAT2 (default parameters).
featureCounts function in subread package version 2.0.3
Read count extraction was performed using the featureCounts function in the subread package (non-default parameters used: cutoff for base calling quality scores = 2; attribute type used to group features = exons)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file including raw peak counts per gene for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Lentiviral supernatants generated from empty pCDF1 vector or pCDF1-SOX10-3xFLAG wildtype and mutant vectors were used to infect parental SVG-p12 cells in the presence of 10 μg/mL polybrene.
Following lentiviral infection, SVG-p12 cells were selected for stable transduction using 2 ug/mL puromycin, and thereafter maintained in 1 ug/mL puromycin.  Expression of FLAG-tagged wildtype and mutant SOX10 protein was subsequently confirmed by Western blot using both anti-FLAG and anti-SOX10 antibodies.

value: immortalized fetal glial cells

value: +SOX10 R176_R177insPQPR


title: plusDOX-rep2


title: Mcpip1 WT_replicate1


title: S_1_Etop8d_S16

value: Female


title: plusDOX-rep1


title: 7E_M_186


title: minusDOX-rep3

value: Control


title: SVG+SOX10_R176_R177insPQPR_replicate#1

description:
SVG+SOX10_R176_R177insPQPR_S84
Matrix processed SVG+SOX10 RNA-seq.txt


title: 7E_M_185


title: 7E_M_184


title: SVG+SOX10_K172_Y173dup_replicate#3

description:
SVG+SOX10_K172_Y173dup_S81
Matrix processed SVG+SOX10 RNA-seq.txt


title: SVG+SOX10_K172_Y173dup_replicate#2

description:
SVG+SOX10_K172_Y173dup_S80
Matrix processed SVG+SOX10 RNA-seq.txt


title: minusDOX-rep1


title: 7E_M_183


title: 7-days old pre-treated 43°C 30 min 3

city: BEAUCOUZE

first: Sandra

last: Pelletier

address: 42, rue Georges Morel - BP 60057

country: France

institute: INRAE

description:
Ribosomal depletion
PH3

data_processing:
Alignment was performed using bowtie2 and SAMtools
DESeq2 was used for differential analysis
Assembly: TAIR10

organism: Arabidopsis thaliana

source_name: Priming + heat shock 3

growth_protocol:
Liquid culture in Evian natural mineral water (Réthoré et al., 2019, The Plant Journal 99: 302–315).
20 mg of seeds were germinated for 6 or 7 days in 6 mL Evian mineral water under rotary shaking (135 rpm) at 21°C 16h 150 µmol photons.m-2.s-1/19°C 8h dark according to Réthoré et al. (2019)  The Plant Journal 99: 302–315.

extract_protocol:
Total RNAs were extracted using NucleoSpin RNAPlus (Macherey-Nagel) kit
Strand-specific RNA library (rRNA removed with Ribo-Zero Plus rRNA Depletion Kit)

treatment_protocol: Heat treatments (38°C or 43°C 2h) were performed in a water bath (in Schott bottle  25mL), under illumination 50 µmol photons.m-2.s-1,  after 2h of photoperiod.

tag: tissus

value: Whole seedling

tag: Stage

value: 1.0 (Boyes) cotyledons fully opened

value: Wild-type

tag: harvest date


title: SVG+SOX10_R176_R177insPQPR_replicate#3

description:
SVG+SOX10_R176_R177insPQPR_S86
Matrix processed SVG+SOX10 RNA-seq.txt


title: 7-days old pre-treated 43°C 30 min 2

description:
Ribosomal depletion
PH2

source_name: Priming + heat shock 2


title: 7-days old pre-treated 43°C 30 min 1

description:
Ribosomal depletion
PH1

source_name: Priming + heat shock 1


title: 7-days old non pre-treated 43°C 30 min 2

description:
Ribosomal depletion
H2

source_name: Heat shock 2

value: 43°C 30 min


title: SVG+SOX10_wildtype_replicate#3

description:
SVG+SOX10_wildtype_S83
Matrix processed SVG+SOX10 RNA-seq.txt

value: +SOX10 wildtype


title: Mouse_HOMER_3

city: Boston

first: I-Hsiu

last: Lee

state: Massachusetts

address: 185 Cambridge Street

department: Center for Systems Biology

institute: Mass General Hospital/Harvard University

description:
FACS-purified left atrial non-cardiomyocytes
mRNA

data_processing:
Illumina proprietary software used for basecalling.
10X Genomics Cell Ranger (version 6.0.2 for human samples, version 3.0.2 for mouse samples) was used to demultiplex raw base call files from the Illumina sequencer to produce fastq files.
Cell Ranger was used to align the reads, filter out background-associated-barcodes, count barcodes and UMIs, and generate gene-barcode matrices.
Genome_build: GRCh38 for human samples, GRCm38 (mm10) for mouse samples.
Supplementary_files_format_and_content: *_filtered_feature_bc_matrix.tar.gz: tar archives include matrix.mtx.gz, features.tsv.gz, and barcodes.tsv.gz files; Count matrices in Market Exchange Format for sparse matrices and gzipped tsv files for genes and barcodes corresponding to row and column indices of the count matrices.

source_name: Heart

extract_protocol:
Viable (DAPI-), metabolically active (Calcein+), nucleated (VDR+), single cells were FACS-purified from digested left atrial tissues, and subsequently loaded on a 10X Genomics Chromium Single Cell B chip as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent Kits v3 user guide.
Libraries were prepared as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent Kits v3 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics). Constructed libraries were validated and quantified with the Agilent High Sensitivity DNA chip and by real-time qPCR, and subsequently sequenced on an Illumina NextSeq 500 in high-output mode.

tag: disease status

value: HOMER

value: male

value: left atrial tissue

value: non-cardiomyocytes


title: 7E_M_181

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq2


title: 7-days old non pre-treated 43°C 30 min 3

description:
Ribosomal depletion
H3

source_name: Heat shock 3


title: SVG+SOX10_K172_Y173dup_replicate#1

description:
SVG+SOX10_K172_Y173dup_S79
Matrix processed SVG+SOX10 RNA-seq.txt


title: 7E_M_182


title: SVG+SOX10_wildtype_replicate#2

description:
SVG+SOX10_wildtype_S82
Matrix processed SVG+SOX10 RNA-seq.txt


title: Mouse_HOMER_2

tag: tissue


title: 7E_M_180


title: Mouse_sham_LV_1

description: FACS-purfied left ventricular non-cardiomyocytes

data_processing:
10X Genomics Cell Ranger ( version 3.0.2) was used to demultiplex raw base call files from the Illumina sequencer to produce fastq files.
Cell Ranger was used to align the reads, filter out background-associated-barcodes, count barcodes and UMIs, and generate gene-barcode matrices.
Assembly: mm10
Supplementary files format and content: Count matrices in Market Exchange Format for sparse matrices and gzipped tsv files for genes and barcodes corresponding to row and column indices of the count matrices

source_name: left vetricular tissue

extract_protocol:
Viable (DAPI-), metabolically active (Calcein+), nucleated (VDR+), single cells were FACS-purified from digested left ventricular tissues, and subsequently loaded on a 10X Genomics Chromium Single Cell B chip as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent Kits v3 user guide.
Libraries were prepared as outlined by the 10X Genomics Chromium Single Cell 3’ Reagent Kits v3 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics). Constructed libraries were validated and quantified with the Agilent High Sensitivity DNA chip and by real-time qPCR, and subsequently sequenced on an Illumina NextSeq 500 in high-output mode.

value: left vetricular tissue

tag: group

value: sham


title: SVG+SOX10_wildtype_replicate#1

description:
SVG+SOX10_wildtype_S78
Matrix processed SVG+SOX10 RNA-seq.txt

tag: genotype


title: Mouse_HOMER_1


title: 7-days old non pre-treated 43°C 30 min 1

description:
Ribosomal depletion
H1

source_name: Heat shock 1

tag: treatment


title: 7E_M_179

source_name: C57BL/6J Male P56 Mouse Brain

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

tag: age


title: 6-days old 38°C 30min 2

description:
Ribosomal depletion
P2

source_name: Priming 2

value: 38°C 30 min


title: minusDOX-rep2

value: Proximal small intestine

value: Epithelial organoids


title: Mouse_sham_4


title: Mouse_sham_3


title: Mouse_HOMER_4


title: 7E_M_178

tag: strain


title: SVG+empty_vector_replicate#1

description:
SVG+empty_vector_S75
Matrix processed SVG+SOX10 RNA-seq.txt

tag: cell line

tag: cell type

value: immortalized fetal glial cells

value: +empty pCDF1 vector


title: 6-days old control 2

description:
Ribosomal depletion
C2

source_name: Control 2


title: 6-days old control 3

description:
Ribosomal depletion
C3

source_name: Control 3


title: Mouse_sham_2


title: SVG+empty_vector_replicate#2

description:
SVG+empty_vector_S76
Matrix processed SVG+SOX10 RNA-seq.txt


title: 6-days old 38°C 30min 1

description:
Ribosomal depletion
P1

source_name: Priming 1


title: Patient 2 CITE

city: Leiden

first: Mirjam

last: van der Burg

address: Albinusdreef 2

country: Netherlands

institute: LUMC

description:
10x Genomics
processed data available on associated GEX sample, GSM6614333

library_source: other

data_processing:
For library demultiplexing, fastq file generation, and read alignment, CellRanger software version 3.1 was used with feature barcoding function. Resulting matrices contained the number of Unique Molecular Identifiers (UMI) per genes or per antibody for each cell. The gene expression and antibody matrices of the 4 samples were imported in Seurat v3 (Stuart et al., 2019), retaining only genes expressed in at least 3 cells, and merged into a combined Seurat object. Cells with less than 250 UMI or less than 3000 genes and more than 25% of mitochondrial RNAs were filtered out. Random selection of an equal amount of cells per subject was chosen to minimize sample bias. Antibody UMI counts were centered using log ratio (CLR) normalization to account for unspecific background.   In order to identify shared clusters of cells collected from different groups (patient and controls), the gene-barcode matrix was integrated according to the integration workflow in Seurat (Stuart et al., 2019), using SCT-transform to normalize and scale the gene-expression. Next, principal components analysis (PCA) and UMAP was performed and 30 PCs were used as input for graph-based clustering (resolution = 0.8). In order to assign the resulting 19 clusters to a cell type, we analyzed the results of the “FindAllMarkers” function next to known gene-markers expression. Clusters 5, 9, and 12 were merged into a pre-BII large cluster based on their gene expression signature and similar expression of pre-BII cell large cell markers as well as genes associated with proliferation. Clusters 0 and 1 were merged into a pre-BII small cluster based on their gene expression signature and similar expression of pre-BII small cell markers. The “late-stage” cluster contained cells with weak expression of B-cell markers and could represent cells with unsuccessful IgH or IgL rearrangements or pre-apoptotic cells. It was therefore excluded from additional analyses.   Clusters  “CLP/pro-B1”, “pro-B2”, “pro-B3”, and “pro-B4/pre-BI” displayed the typical signature of early B cell-precursors and constituted the “early BCP” subset. Clusters “pro-B4/pre-BI”, “pre-BII large”, “pre-BII small”, and “immature” were defined as the “late BCP” subset. The two subsets were subjected to pseudotime analysis using the monocle3 package (Cao et al., 2019). The UMAP embedding was then used as input for pseudotime analysis: the “CLP/pro-B1” cluster was used as a starting point for the commitment subset and cluster “pro-B4/preBI” was chosen as a starting point for the differentiation subset. After calculating the pseudotime, the cells were ordered along the resulting trajectories. To analyze how the progression along the pseudotime is affected by IL-7RA deficiency, we performed a univariate analysis of the pseudotime values between the two group (patient and controls) using slingshot v 2.2.1 (Street et al., 2018) and the latest tradeSeq package (v 1.7.07) (Van den Berge et al., 2020) following the TGFb example (de Bézieux et al., 2021).   In order to identify differentially expressed genes between conditions in each cell type, a combined metadata field was added to the two subsets, which contained the combination of the cluster name and the condition (patient/control). For this analysis, we used the FindMarkers function in Seurat.
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq

molecule: protein

source_name: bone marrow

extract_protocol:
Analysis was performed with previously frozen material that was enriched for BM mononuclear cells by Ficoll density centrifugation prior to freezing. BM mononuclear cells of the two aforementioned pediatric controls and the two IL7RA-deficient SCID patients were thawed and dead cells were removed with the Dead Cell Removal Kit (Miltenyi Biotec) according to the manufacturer’s instructions. Subsequently, non-B cells were depleted using the MojoSort Human Pan B Cell Isolation Kit (BioLegend). After the addition of Fc block (eBioscience), cells were labeled in PBS with 1% BSA using the following TotalSeq-C antibodies (BioLegend): 0050 anti-human CD19 (clone HIB19); 0054 anti-human CD34 (clone 581); 0136 anti-human IgM (clone MHM-88); 0390 anti-human CD127 (clone A019D5).
Single cell gene expression libraries were generated on the 10x Genomics Chromium platform using the Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 and Chromium Next GEM Chip G Single Cell Kit (10x Genomics) according to the manufacturer’s protocol. Targeted B cell receptor libraries were generated using the Chromium Single Cell V(D)J Enrichment Kit for Human B Cells and the Chromium Single Cell 5’ Library Construction Kit (10x Genomics) according to the manufacturer’s protocol. CITE-seq libraries were generated using the Chromium Single Cell 5' Feature Barcode Library Kit (10x Genomics) according to the manufacturer’s protocol. Gene expression, targeted B cell receptor, and CITE-seq libraries were sequenced on a NovaSeq 6000 S4 flow cell using v1 chemistry (Illumina).

value: bone marrow

tag: subject

value: Patient 2

value: sorted mononuclear cells


title: 6-days old 38°C 30min 3

description:
Ribosomal depletion
P3

source_name: Priming 3

value: Whole seedling

value: 1.0 (Boyes) cotyledons fully opened

value: Wild-type


title: 7E_M_177


title: Mouse_sham_1


title: 7E_M_173


title: org_adult_rep2_hic

data_processing:
Sequencing reads were converted by using bcf2fastq and demultiplexed according to the indexes
The reads were quality trimmed with Trim Galore and mapped and processed with HiC-Pro.
We used MAPQ score threshold 30 and excluded read pairs mapping within 1kb, to retain valid pairs and generate ICE normalised contact maps at 100kb resolution.
Genome_build: mm10
Supplementary_files_format_and_content:  Contact matrixes of all valid read pairs are stored in Juicebox viable .hic file.

source_name: small intestinal epithelium derived organoids

growth_protocol: Fetal spheroids and adult organoids derived from E16.5 fetal epithelial fragments or scraped adult crypts harvested from proximal small intestine using 2mM EDTA were embedded in Matrigel droplets and cultured in advanced DMEM/F12 with GlutaMAX and Penicillin/Streptomycin supplemented with 50 ng/ml EGF, 100 ng/ml Noggin, and 500 ng/ml, R-Spondin1, 3 µM CHIR99021 and 10 mM Nicotinamide.

extract_protocol:
Fetal spheroids and adult organoids corresponding to approximately one million cells per replicate were released from Matrigel and fragmented by repeated washing with cold PBS with 0.1% BSA. The organoid fragments were cross-linked in 2% formaldehyde for 20 minutes, quenched, and washed. Following, the cells were lysed and chromatin was digested with 2 units of DNase I for 5 minutes.
The nuclei were purified with AMPure XP beads and washed followed by end repair and dA-tailing reactions. Biotin-labeled bridge adapters were then ligated overnight to the fragments followed by another round of purification with AMPure XP beads and washing. The nuclei were treated with PNK to phosphorylate adapters and ligation prior to reversal of cross-linking, DNA precipitation and purification. The ligation products with biotin were then pulled down with MyOne C1 beads followed by washing and end repair, dA-tailing, and ligation of sequencing adapters. The libraries were amplified for 14 PCR cycles with primers containing Nextera barcodes for sample multiplexing: N701 (TCGCCTTA), N702 (CTAGTACG), N703 (TTCTGCCT), and N704 (GCTCAGGA). Libraries were then purified and quantified with Qubit and Fragment Analyzer (Agilent) and the four libraries were pooled and paired-end sequenced with Illumina NextSeq.

tag: developmental state

value: Adult

value: untreated


title: Patient 1 CITE

description:
10x Genomics
processed data available on associated GEX sample, GSM6614332

value: Patient 1


title: 6-days old control 1

description:
Ribosomal depletion
C1

source_name: Control 1


title: Control 2 CITE

description:
10x Genomics
processed data available on associated GEX sample, GSM6614331

value: Control 2

value: wild type


title: org_adult_rep1_hic

value: small intestinal epithelium derived organoids


title: PBS-6

city: Chicago

first: Leonid

last: Feferman

state: Illinois

address: 1737 West Polk St

department: Research Resources Center

institute: University of Illinois at Chicago

data_processing:
Raw reads were aligned to the reference genome using STAR.
ENSEMBL gene expression was quantified using FeatureCounts.
Assembly: mm39
Supplementary files format and content: tab-delimited text tables

source_name: cerebral cortex

growth_protocol: bEnd.3 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
100ng/ml LPS (Sigma) was used to treat Raw 264.7 cells co-cultured with bEnd.3 cells. RNA was harvested using Direct-zol RNAkit (Zymo) and purified from total RNA using oligo(Dt)-attached magnetic beads.
DNBSEQ Eukaryotic Stranded Transcriptome library preparation

treatment_protocol: Inflammation was induced by co-culture with LPS-treated Raw 264.7 cells.

tag: cells

value: bEnd.3 cells

value: cerebral cortex

value: co-cultured with PBS-treated Raw 264.7


title: SVG+empty_vector_replicate#3

description:
SVG+empty_vector_S77
Matrix processed SVG+SOX10 RNA-seq.txt

value: immortalized fetal glial cells


title: PBS-4


title: PBS-5


title: Control 1 CITE

description:
10x Genomics
processed data available on associated GEX sample, GSM6614330

value: Control 1


title: org_fetal_rep2_hic


title: 7E_M_172


title: Patient 2 GEX

description: 10x Genomics

data_processing:
For library demultiplexing, fastq file generation, and read alignment, CellRanger software version 3.1 was used with feature barcoding function. Resulting matrices contained the number of Unique Molecular Identifiers (UMI) per genes or per antibody for each cell. The gene expression and antibody matrices of the 4 samples were imported in Seurat v3 (Stuart et al., 2019), retaining only genes expressed in at least 3 cells, and merged into a combined Seurat object. Cells with less than 250 UMI or less than 3000 genes and more than 25% of mitochondrial RNAs were filtered out. Random selection of an equal amount of cells per subject was chosen to minimize sample bias. Antibody UMI counts were centered using log ratio (CLR) normalization to account for unspecific background.   In order to identify shared clusters of cells collected from different groups (patient and controls), the gene-barcode matrix was integrated according to the integration workflow in Seurat (Stuart et al., 2019), using SCT-transform to normalize and scale the gene-expression. Next, principal components analysis (PCA) and UMAP was performed and 30 PCs were used as input for graph-based clustering (resolution = 0.8). In order to assign the resulting 19 clusters to a cell type, we analyzed the results of the “FindAllMarkers” function next to known gene-markers expression. Clusters 5, 9, and 12 were merged into a pre-BII large cluster based on their gene expression signature and similar expression of pre-BII cell large cell markers as well as genes associated with proliferation. Clusters 0 and 1 were merged into a pre-BII small cluster based on their gene expression signature and similar expression of pre-BII small cell markers. The “late-stage” cluster contained cells with weak expression of B-cell markers and could represent cells with unsuccessful IgH or IgL rearrangements or pre-apoptotic cells. It was therefore excluded from additional analyses.   Clusters  “CLP/pro-B1”, “pro-B2”, “pro-B3”, and “pro-B4/pre-BI” displayed the typical signature of early B cell-precursors and constituted the “early BCP” subset. Clusters “pro-B4/pre-BI”, “pre-BII large”, “pre-BII small”, and “immature” were defined as the “late BCP” subset. The two subsets were subjected to pseudotime analysis using the monocle3 package (Cao et al., 2019). The UMAP embedding was then used as input for pseudotime analysis: the “CLP/pro-B1” cluster was used as a starting point for the commitment subset and cluster “pro-B4/preBI” was chosen as a starting point for the differentiation subset. After calculating the pseudotime, the cells were ordered along the resulting trajectories. To analyze how the progression along the pseudotime is affected by IL-7RA deficiency, we performed a univariate analysis of the pseudotime values between the two group (patient and controls) using slingshot v 2.2.1 (Street et al., 2018) and the latest tradeSeq package (v 1.7.07) (Van den Berge et al., 2020) following the TGFb example (de Bézieux et al., 2021).   In order to identify differentially expressed genes between conditions in each cell type, a combined metadata field was added to the two subsets, which contained the combination of the cluster name and the condition (patient/control). For this analysis, we used the FindMarkers function in Seurat.
Supplementary files format and content: Tab-separated values files and matrix files

value: bone marrow


title: 7E_M_176


title: PBS-3


title: 7E_M_174


title: Patient 1 GEX

description: 10x Genomics


title: PBS-2


title: org_adult_rep2_atac

data_processing:
Sequencing reads were converted by using bcf2fastq and demultiplexed according to the indexes
Paired-end reads were mapped with Bowtie2 against the mm10 assembly and only uniquely mapping reads were retained using samtools
Duplicate reads were removed and regions highly contaminated by duplicate reads (99.9th percentile) and reads within ENCODE black-list regions were masked. Reads aligning to plus strand were offset by +4 bp and reads aligning to minus strand with -5bp. The peaks were called for each replicate using MACS2 without a shifting model and the background lambda as local lambda.
Genome_build: mm10
Supplementary_files_format_and_content:  ATAC bigwig files where the score represents per-base genome coverage normalized to the library size.

extract_protocol:
Fetal spheroids and adult organoids were released from Matrigel and resuspended in TrypLE Express Enzyme (GIBCO) and incubated at 37°C until a single cell suspension was obtained. After centrifugation, cells were resuspended in PBS with 1% BSA and incubated with fluorescent-conjugated primary antibody EpCAM-APC (Supplementary table 1), for 30 min on ice. After washing, DAPI (Sigma; 1 µM) was added and 50 000 live (EpCAM+ DAPI-) cells were subsequently sorted on a FACS Aria I (BD Bioscience) cell sorter.
The cells were lysed and after centrifugation resuspended in transposase reaction mix and incubated for 30 min at 37°C. After purification, the eluted DNA was PCR amplified with unique barcode (TAAGGCGA, CGTACTAG, TCCTGAGC and TAGGCATG) containing PCR primers for multiplexing of samples: and purified. The samples were paired-end sequenced with Illumina NextSeq.


title: Control 2 GEX

description: 10x Genomics


title: 7E_M_169


title: PBS-1


title: Control 1 GEX

description: 10x Genomics


title: org_adult_rep1_atac


title: org_fetal_rep2_atac


title: 7E_M_171


title: Osteoarthritis, Condylar cartilage cells, Biol rep 2 [PPCC_2]

city: New York

first: Ikue

last: Tosa

state: New York

department: College of Dental Medicine

institute: Columbia University

data_processing:
MultiQC (1.13) for quality check. Trim Galore (0.6.7) for adapter and quality trimming.
First time read alignment with STAR (2.7.9a) with parameters of: --chimSegmentMin 10 --alignEndsType Local --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 70 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outSAMstrandField intronMotif --outFilterType BySJout --twopassMode Basic.
Mapping restuls from the first time read alignment then passed to StringTie (2.1.0) for reference-based (Sscrofa11.1 Eensembl release-105) de novo transcriptome assembly with parameters of: -m 100 -a 5 -j 0.1 -c 0.5 -f 0.005
Finally, trimmed sequence reads were mapped to de novo transcriptome assembly using Salmon software (1.1.0).
The estimated TPM and read counts from Salmon software was converted to gene-level following the DESeq2 (1.26.0) manual.
Assembly: Sscrofa11.1
Supplementary files format and content: excel file include TPM and read counts for each sample

organism: Sus scrofa

source_name: Temporomandibular Joint

extract_protocol:
Total RNA was extracted from tissue samples using RNeasy Micro kit (Qiagen).
QIAseq FastSelect rRNA HMR Kit (Qiagen) was used for rRNA depletion, followed by library preparation using NEBNext Ultra II Directional RNA Library Prep Kit (NEB).

treatment_protocol: An oblique incision was created superior to the zygomatic process. Tissue was elevated and retracted to access the TMJ superior joint space and the disc was retracted posteriorly. A periosteal elevator was placed under the disc to protect the condyle from injury. A punch biopsy was used to create a 5.0 mm perforation in the posterior-lateral portion of the TMJ disc and the perforated disc tissue was excised (Supplemental Figure 1). No disc attachments were severed and the disc reduced to its normal anatomical location upon release of disc retraction.

value: Temporomandibular Joint

value: Condylar cartilage cells

value: WT

value: Osteoarthritis


title: Osteoarthritis, Condylar cartilage cells, Biol rep 1 [PPCC_1]


title: Osteoarthritis, Condylar cartilage cells, Biol rep 4 [PPCC_4]


title: Osteoarthritis, Condylar cartilage cells, Biol rep 3 [PPCC_3]


title: LPS-5

value: co-cultured with LPS-treated Raw 264.7


title: cell HCT116 shFBL,Mitomycin C overnight,rep3

city: baoding

first: chen

last: wu

state: hebei

address: wusidong road

institute: hebei university

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: colon

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: shNC or shFBL HCT116 cells were treated with 5 μM MMC

value: colon

value: human colorectal carcinoma cells

value: FBL knockdown

value: Mitomycin C,overnight


title: org_fetal_rep1_atac

value: untreated


title: Control, Condylar cartilage cells, Biol rep 4 [PHCC_4]

value: Control


title: LPS-4

value: bEnd.3 cells


title: org_fetal_rep1_hic

value: small intestinal epithelium derived organoids


title: cell HCT116 shFBL,Mitomycin C overnight,rep1


title: Control, Condylar cartilage cells, Biol rep 3 [PHCC_3]


title: LPS-3

value: cerebral cortex


title: cell HCT116 shFBL,Mitomycin C overnight,rep2


title: MCF7 Y537S cells, Fulvestrant treatment, sample 4

city: Urbana

first: Zeynep

last: Madak Erdogan

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger (v1.3) pipeline to generate FASTQ files
Sequences were aligned to a custom combined reference of hg38 and mm10 genomes (Ensembl 104) and gene expressison quantified using Space Ranger's default settings
Assembly: hg38 and mm10
Supplementary files format and content: 08.12.2021.ZME.GE.*.Li.tif: brightfield image of tissue and spots
Supplementary files format and content: *_aligned_fiducials.jpg - aligned fiducials of the tissue image
Supplementary files format and content: *_detected_tissue_image.jpg - image of tissue and spots
Supplementary files format and content: *_scalefactors_json.json - scale factors in json format
Supplementary files format and content: *_tissue_hires_image.png - hi-res image of tissue
Supplementary files format and content: *_tissue_lowres_image.png - low res image of tissue
Supplementary files format and content: *_tissue_positions_list.csv
Supplementary files format and content: *_barcodes.tsv.gz - list of spatial barcodes
Supplementary files format and content: *_features.tsv.gz - list of gene IDs
Supplementary files format and content: *_matrix.mtx.gz UMI count data in Matrix Market Exchange format
Library strategy: Spatial Transcriptomics

source_name: Liver metastatic breast tumor

growth_protocol: 1x106 MCF7 Y537S cells resuspended in 1% PBS were injected to ovariectomized, NOD SCID gamma (NSG) immunodeficient female mice via tail vein

extract_protocol:
Fresh frozen tissue were OCT embedded, and 10µm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's construction

treatment_protocol: Fulvestrant (Sigma) was dissolved in 10% DMSO and 90% corn oil

value: Liver metastatic breast tumor

value: MCF7 Y537S

value: metastatic tumor cells

value: NOD scid gamma

value: Fulvestrant

tag: slide serial_and_position


title: cell HCT116 shControl,Mitomycin C,overnight,rep3

value: WT


title: LPS-2


title: Control, Condylar cartilage cells, Biol rep 2 [PHCC_2]

value: Temporomandibular Joint

value: Condylar cartilage cells


title: MCF7 Y537S cells, no treatment, sample 2


title: LPS-6

value: co-cultured with LPS-treated Raw 264.7


title: cell HCT116 shControl,Mitomycin C,overnight,rep2

value: colon

value: human colorectal carcinoma cells


title: Control, Condylar cartilage cells, Biol rep 1 [PHCC_1]


title: MCF7 Y537S cells, no treatment, sample 1


title: cell HCT116 shControl,Mitomycin C,overnight,rep1

value: Mitomycin C,overnight


title: CY-5day-02 miRNA-Seq

status: Public on Jul 12 2023

city: Guangzhou

first: Danni

last: Lin

address: 388 Guangxin Road, Baiyun District

institute: Zhongkai University of Agriculture and Engineering

data_processing:
Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Sequence quality was verified using FastQC, including the Q20, Q30 and GC-content of the clean data.
De novo assembly of the transcriptome was performed with Trinity 2.4.0.
All assembled Unigenes were aligned against the non-redundant (Nr) protein database,Gene ontology (GO), SwissProt, Kyoto Encyclopedia of Genes and Genomes (KEGG) and eggNOG databases using DIAMOND with a threshold of Evalue<0.00001.
Salmon was used to perform expression level for Unigenes by calculating TPM. The differentially expressed Unigenes were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files

organism:
Auxenochlorella pyrenoidosa
Yarrowia lipolytica

source_name: whole cells

extract_protocol:
Total RNA was extracted from C. pyrenoidesa and the co-culture system using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) with the manufacturer’s protocol.
The mRNA sequencing libraries were generated using the NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA), and the miRNA sequencing library was generated using the Next Ultra-small RNA Sample Library Prep Kit for Illumina (NEB, USA)
miRNA-Seq、mRNA-Seq

value: whole cells


title: LPS-1


title: CY-5day-03 miRNA-Seq


title: CY-5day-01 miRNA-Seq


title: CY-3day-03 miRNA-Seq


title: CY-3day-02 miRNA-Seq


title: MCF7 Y537S cells, Fulvestrant treatment, sample 3


title: CY-3day-01 miRNA-Seq


title: CY-5day-03 RNA-Seq


title: CY-5day-02 RNA-Seq


title: CY-5day-01 RNA-Seq


title: CY-3day-03 RNA-Seq


title: CY-3day-02 RNA-Seq


title: CY-3day-01 RNA-Seq


title: Bulk Tumor 2

type: RNA

city: Aarhus

first: Juan Luis

last: Garcia-Rodriguez

address: Høegh-Guldbergs Gade 10

department: Biomedicine

institute: Aarhus University

description: Normalized Nanostring nCounter counts

data_processing: nSolver software analysis

source_name: Bulk Tumor 2

extract_protocol: Rneasy Plus Mini Kit (Qiagen) and Trizol for the cells lines

value: Bulk human colon adenocarcinoma tissue

value: Stage II


title: Bulk Tumor 4

description: Normalized Nanostring nCounter counts

source_name: Bulk Tumor 4


title: Bulk Tumor 3

description: Normalized Nanostring nCounter counts

source_name: Bulk Tumor 3


title: Bulk Tumor 5

description: Normalized Nanostring nCounter counts

source_name: Bulk Tumor 5


title: Bulk Normal 4

description: Normalized Nanostring nCounter counts

source_name: Bulk Normal 4

value: Bulk human colon adjacent normal tissue


title: Bulk Tumor 1

description: Normalized Nanostring nCounter counts

source_name: Bulk Tumor 1


title: Bulk Normal 5

description: Normalized Nanostring nCounter counts

source_name: Bulk Normal 5


title: Bulk Normal 2

description: Normalized Nanostring nCounter counts

source_name: Bulk Normal 2


title: Caco-2

description: Normalized Nanostring nCounter counts

value: Colon adenocarcinoma cell line


title: Muscularis propria 2

description: Normalized Nanostring nCounter counts

source_name: Muscularis propria 2

value: Laser capture microdissected Adjacent normal muscularis propria cells


title: Bulk Normal 3

description: Normalized Nanostring nCounter counts

source_name: Bulk Normal 3


title: COLO320-HSR

description: Normalized Nanostring nCounter counts


title: Bulk Normal 1

description: Normalized Nanostring nCounter counts

source_name: Bulk Normal 1


title: HT-29

description: Normalized Nanostring nCounter counts


title: HCT-116

description: Normalized Nanostring nCounter counts


title: Muscularis propria 3

description: Normalized Nanostring nCounter counts

source_name: Muscularis propria 3


title: Caco-2 Mock

description: Raw Nanostring nCounter counts

source_name: Caco-2 Mock

value: Caco-2 Mock


title: Caco-2 RNaseR

description: Raw Nanostring nCounter counts

source_name: Caco-2 RNaseR

value: Caco-2 RNaseR


title: Muscularis propria 1

description: Normalized Nanostring nCounter counts

source_name: Muscularis propria 1


title: Muscularis propria 4

description: Normalized Nanostring nCounter counts

source_name: Muscularis propria 4


title: Epithelium 4

description: Normalized Nanostring nCounter counts

source_name: Epithelium 4

value: Laser capture microdissected Adjacent normal epithelial cells


title: Epithelium 1

description: Normalized Nanostring nCounter counts

source_name: Epithelium 1


title: Tumor stroma 5

description: Normalized Nanostring nCounter counts

source_name: Tumor stroma 5

value: Laser capture microdissected tumor stroma cells


title: Epithelium 2

description: Normalized Nanostring nCounter counts

source_name: Epithelium 2


title: Tumor stroma 4

description: Normalized Nanostring nCounter counts

source_name: Tumor stroma 4


title: Tumor stroma 2

description: Normalized Nanostring nCounter counts

source_name: Tumor stroma 2


title: Tumor stroma 1

description: Normalized Nanostring nCounter counts

source_name: Tumor stroma 1


title: Cancer cells 5

description: Normalized Nanostring nCounter counts

source_name: Cancer cells 5

value: Laser capture microdissected cancer cells


title: Cancer cells 3

description: Normalized Nanostring nCounter counts

source_name: Cancer cells 3


title: Muscularis propria 5

description: Normalized Nanostring nCounter counts

source_name: Muscularis propria 5


title: Cancer cells 2

description: Normalized Nanostring nCounter counts

source_name: Cancer cells 2


title: Epithelium 5

description: Normalized Nanostring nCounter counts

source_name: Epithelium 5


title: Cancer cells 1

description: Normalized Nanostring nCounter counts

source_name: Cancer cells 1


title: Epithelium 3

description: Normalized Nanostring nCounter counts

source_name: Epithelium 3


title: Omikron_P2_MAN21_II_T

city: Munich

first: Stefan

last: Engelhardt

address: Biedersteiner Str. 29

department: Institute of Pharmacology and Toxicology

institute: Technical University Munich

data_processing:
paired-end run was performed using a NextSeqHigh
Most steps of this pipeline were performed using the Galaxy platform.
Reads were trimmed with Flexbar 3.5.0. and aligned to human reference genome (hg38) using HISAT 2.1.0. and for transcript assembly and quantification StringTie 2.1.1 was used.
Assembly: hg38
Supplementary files format and content: raw gene counts in txt.format

source_name: lung

extract_protocol:
Total RNA was prepared with Trizol reagent according to manufacturer's instructions.
low-input mRNA-Seq; Libraries were generated using  NEBNext® NEBNext Single Cell/Low Input RNA Library Prep Kit according to manufacturer's instructions.

value: lung

value: hPCLS


title: Omikron_P2_MAN21_I_T


title: Omikron_P2_MAN21_III_T


title: Tumor stroma 3

description: Normalized Nanostring nCounter counts

source_name: Tumor stroma 3


title: Omikron_P1_MAN21_III_T


title: Omikron_P2_MOI1_I_T


title: Omikron_P2_MOI1_III_T


title: Omikron_P2_MOI1_II_T


title: Omikron_P1_MOI1_II_T


title: Plants from Oliver cultivar, repetition 1, Agilent slide S39

city: Villeneuve d'Ascq

first: Anca

last: Lucau-Danila

address: Cité Scientifique SN2 303

department: Biology

institute: University of Lille

description:
A 5 cm fragment of the stem was collected at 5 cm from the cotyledons
Gene expression in field conditions

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Wheat Gene Expression Microarrays GE 4x44 (Agilent, Santa Clara, CA, USA) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Scanner GenePix 4200B (Molecular Device) using one color scan setting

data_processing: The scanned images were analyzed with GenePix Pro Software 6.0 (Molecular Device) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Linum usitatissimum

source_name: Flax plants, Oliver cultivar, area R1 (repetition 1)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Seven flax cultivars (Diane, Hermes, Drakkar, Belinka, Adelie, Violin, and Oliver) were grown under field conditions by LINEA, Grandvilliers France. The plant material was harvested from three randomly distributed areas (R1, R2, R3) of the field at the budding stage. A 5 cm fragment of the stem was collected at 5 cm from the cotyledons.  Stem outer tissues (i.e. containing bast fibers) were manually separated from the inner tissues and frozen in liquid nitrogen before storing at -80° C until use for transcriptomic and proteomic analyses.

extract_protocol: Total RNA was extracted from three pools of outer stem tissues for each of the 7 varieties using Tri-Reagent (MRC, Inc., Dundee, Scotland, UK). RNA integrity and concentration were evaluated with RNA StdSens Chips using the Experion automated electrophoresis system (Bio-Rad, Marnes-la-Coquette, France).

treatment_protocol: Field coordinate, reference to agricultural approaches.

value: outer stem tissues

tag: cultivar

value: Oliver


title: Plants from Oliver cultivar, repetition 2, Agilent slide S43

source_name: Flax plants, Oliver cultivar, area R2 (repetition 2)


title: Plants from Violin cultivar, repetition 2, Agilent slide S39

source_name: Flax plants, Violin cultivar, area R2 (repetition 2)

value: Violin


title: Omikron_P1_MOI1_I_T


title: Plants from Oliver cultivar, repetition 3, Agilent slide S44

source_name: Flax plants, Oliver cultivar, area R3 (repetition 3)


title: Cancer cells 4

description: Normalized Nanostring nCounter counts

source_name: Cancer cells 4

tag: Stage


title: Plants from Drakkar cultivar, repetition 3, Agilent slide S42

source_name: Flax plants, Drakkar cultivar, area R3 (repetition 3)

value: Drakkar


title: Plants from Violin cultivar, repetition 1, Agilent slide S37

source_name: Flax plants, Violin cultivar, area R1 (repetition 1)


title: Omikron_P2_uninfected_I_T


title: Plants from Drakkar cultivar, repetition 1, Agilent slide S38

source_name: Flax plants, Drakkar cultivar, area R1 (repetition 1)


title: Omikron_P1_uninfected_III_T


title: Omikron_P1_MOI1_III_T


title: Plants from Belinka cultivar, repetition 2, Agilent slide S38

source_name: Flax plants, Belinka cultivar, area R2 (repetition 2)

value: Belinka


title: Plants from Hermes cultivar, repetition 2, Agilent slide S38

source_name: Flax plants, Hermes cultivar, area R2 (repetition 2)

value: Hermes


title: Plants from Diane cultivar, repetition 1, Agilent slide S38

source_name: Flax plants, Diane cultivar, area R1 (repetition 1)

value: Diane


title: Plants from Diane cultivar, repetition 3, Agilent slide S42

source_name: Flax plants, Diane cultivar, area R3 (repetition 3)


title: HaCaT_Switched_rep3

first: Richard

last: White

state: NY

department: Cancer Biology and Genetics

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Quality control of the raw reads from RNA-seq fastq files was performed using FASTQC
Low quality and adapter sequences were trimmed using TRIMMOMATIC
Trimmed reads were mapped to the human (hg38) genome using STAR
Gene counts of aligned reads were calculated using the feature counts algorithm
Differential gene expression analysis was performed using DeSeq2
Assembly: hg38
Supplementary files format and content: tab delimited text file contains raw counts for each sample

source_name: HaCaT

growth_protocol: HaCaT keratinocytes were maintained in DMEM with 10% FBS, supplemented with 1X penicillin/streptomycin in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted from the FACS isolated HaCaT keratinocytes post-recovery using the Quick RNA miniprep kit (Zymo).
RNA libraries were prepared using the TruSeq RNA V2 kit according to the manufacturers instructions.

treatment_protocol: HaCaT keratinocytes expressing the switch cassette (CMV-lsl-dsRED-lsl-GFP) were grown in monoculture or in co-culture with A375 melanoma cells (expressing Cre) for 21 days following which dsRED positive (non-switched) and GFP positive (switched) keratinocytes were isolated using FACS.

value: HaCaT

value: Keratinocyte

value: Wild-type

value: Co-culture, switched


title: Plants from Belinka cultivar, repetition 1, Agilent slide S37

source_name: Flax plants, Belinka cultivar, area R1 (repetition 1)


title: Plants from Adelie cultivar, repetition 1, Agilent slide S37

source_name: Flax plants, Adelie cultivar, area R1 (repetition 1)

value: Adelie


title: Omikron_P2_uninfected_II_T

source_name: lung


title: Omikron_P1_MAN21_II_T


title: HaCaT_Switched_rep2


title: Plants from Adelie cultivar, repetition 3, Agilent slide S44

source_name: Flax plants, Adelie cultivar, area R3 (repetition 3)


title: HaCaT_Switched_rep1


title: EC_AHR_KO_Rep2

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

data_processing:
RTA version 3.9.25 with default filter and quality setting running under NextSeq 1000/2000 Control Software 1.4.1.39716 was used for basecalling.
The reads were demultiplexed with DRAGEN GenerateFastQ 3.7.4 (allowing 1 mismatches).
Reads were aligned to GENCODE mouse genome (GRCm38) using STAR (2.7.7a) with argument “----quantMode TranscriptomeSAM GeneCounts".
Gene-based read counts were performed by STAR as well.
Assembly: GENCODE mouse genome (GRCm38)
Supplementary files format and content: csv file includes Gene counts for each Sample

source_name: Small intestine

extract_protocol:
Cells were snap frozen in TRIzol and RNA purified using the TRIzol plus RNA Purification kit (both Thermo Fisher)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Following tamoxifen-mediated Cre induction (100mg/kg tamoxifen 5 doses every 2 days) in VeciCre x Ahr fl/fl x NuTRAP mice (experimental), or Veci Cre x NuTRAP (control), 2 weeks later mice were injected with 10mg/Kg 6-Formylindolo(3,2-b)carbazole (FICZ) or corn-oil vehicle control intraperitoneally, 3h prior to culling

value: Small intestine

value: FICZ

value: VeciCre x AHRflfl x NuTRAP

tag: Sex

value: Male


title: EC_AHR_KO_Rep3


title: EC_AHR_KO_Rep4


title: Plants from Hermes cultivar, repetition 1, Agilent slide S37

source_name: Flax plants, Hermes cultivar, area R1 (repetition 1)


title: EC_AHR_KO_Rep1


title: HaCaT_Monoculture_rep3

value: Monoculture


title: Omikron_P1_uninfected_II_T

value: lung

value: hPCLS


title: EC_AHR_WT_Rep2


title: Plants from Adelie cultivar, repetition 2, Agilent slide S39

source_name: Flax plants, Adelie cultivar, area R2 (repetition 2)

value: outer stem tissues


title: Omikron_P1_uninfected_I_T


title: RRBS Dentate Gyrus cells, Mother Group, Rep 3

city: Tallahassee

first: Nicholas

middle: James

last: Waddell

state: FL

address: 319 Stadium Dr

department: Biological Sciences

institute: Florida State University

data_processing:
Basecalls were performed using bcl2fastq for Novaseq output.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore (minimum quality 20, minimum length 20)
Sequences were aligned to the prairie vole genome using Bismark methylation alignment software.
Methylation calls were extracted using the built-in methylation extractor program provided in the Bismark suite.
Values were not normalized prior to import into DSS general for differential methylation analysis.
Assembly: MicOch1.0
Supplementary files format and content: files per sample are formatted for use in DSS-general for differential methylation analysis.  Columns are as follows: Chromosome, Position, N = number of reads covering this position, X = number of reads with methylation call at this position.

organism: Microtus ochrogaster

source_name: Dentate Gyrus

extract_protocol:
DNA and RNA were isolatted from the same tissue using the Qiagen AllPrep DNA/RNA Mircro Kit (Qiagen, #80284) according to the manufacturer's protocol.
100ng of genomic DNA was digested using MspI, and RRBS libraries were constructed using the Premium RRBS Kit (Diagenode, #C02030032)

treatment_protocol: Adult Voles were exposed to conspecific pups and their behavioral response was recorded. Samples were separated based on this response for virgin animals or based on sex for pair-bonded individuals.

value: Dentate Gyrus

value: Female

value: WT

tag: behavioral group

value: Mother


title: RRBS Dentate Gyrus cells, Mother Group, Rep 5

tag: tissue


title: RRBS Dentate Gyrus cells, Mother Group, Rep 2


title: HaCaT_Coculture_rep2

value: HaCaT

value: Co-culture, not switched


title: HaCaT_Coculture_rep1

value: Keratinocyte

value: Wild-type


title: RRBS Dentate Gyrus cells, Mother Group, Rep 1


title: RRBS Dentate Gyrus cells, Father Group, Rep 5

value: Father


title: RRBS Dentate Gyrus cells, Father Group, Rep 3


title: HaCaT_Monoculture_rep2


title: RRBS Dentate Gyrus cells, Attacker Group, Rep 6

value: Attacker


title: IC-A46GBM-III-4782-4796_S19

city: Cincinnati

first: Frank

last: Huang

state: OHIO

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Bowtie for reads alignment
HTSeq for mapping reads to each gene.
Assembly: hg38

organism: Homo sapiens/Mus musculus xenograft

source_name: NOD SCID mouse

extract_protocol:
RNA was extracted using AllPrep DNA/RNA/Protein Mini Kit according to manufacturer's instructions (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mus musculus Xenograft

value: Tumor


title: HaCaT_Monoculture_rep1


title: EC_AHR_WT_Rep4

value: Small intestine

value: FICZ

value: VeciCre x AHRflfl x NuTRAP

value: Male


title: V0914-17318-Untreated-sur_S17


title: EC_AHR_WT_Rep3


title: EC_AHR_WT_Rep1


title: RRBS Dentate Gyrus cells, Mother Group, Rep 6


title: RRBS Dentate Gyrus cells, Father Group, Rep 1


title: HaCaT_Coculture_rep3


title: RRBS Dentate Gyrus cells, Mother Group, Rep 4


title: FPD_21.1

city: Philadelphia

first: Alexandra

last: Zezulin

address: 421 Curie Blvd 544 BRB II/III

institute: University of Pennsylvania

data_processing:
Sequencing reads were demultiplexed using Bcl2Fastq v2.20 then trimmed and filtered for quality using Trim Galore v0.6.4 with the following settings: fastqc, paired, and trim1. Reads were then aligned to the human genome (hg38) using bowtie 2.3.5.1. Only uniquely mapped reads with fewer than 2 mismatches were used for downstream analyses. Samtools v.1.1 was used to convert SAM files to BAM files, and Sambamba v0.6.6 was used to filter out duplicates, multi-mappers, reads mapped to ChrM or blacklist regions, and unmapped reads. MACS2 2.2.7.1 was used for peak calling using the following parameters: BAMPE, q: 0.05. Peaks from the patient and control samples were called individually. For downstream analysis, we compared the patient and unaffected family members individually. The peaks from the patient sample and the corresponding control sample were merged for each comparison and RPKM per merged peak was calculated using BEDtools. Peaks with RPKM less than 0.5 in both control and patient were filtered from downstream analysis. Control or patient  specific peaks were called if the RPKM fold change between control and patient peaks was greater than 2. Individual samples were used to create bigwig files for visualization using Deeptools v3.3.0 and the  following parameters: normalized to Bins Per Million mapped reads (BPM), bin size: 50.
see SAMPLES section
Assembly: hg38
Supplementary files format and content: BigWig files provided are normalized tracks
Supplementary files format and content: Bed files provided are the output of merged MACS2 peak calling: the peaks from the patient sample and the corresponding control sample were merged for each comparison and RPKM per merged peak was calculated using BEDtools. Peaks with RPKM less than 0.5 in both control and patient were filtered from downstream analysis. Control or patient specific peaks were called if the RPKM fold change between control and patient peaks was greater than 2

source_name: PB Neutrophils

extract_protocol:
Neutrophils from human patient/control peripheral blood were isolated using the EasyStep Human Neutrophil Isolation Kit (Stem Cell). 50,000 cells were collected and washed with cold PBS. Cell pellets were resuspended in 50 µl of lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% Tween-20, 0.1% NP-40, 0.01% Digitonin, 1% BSA) and incubated on ice for 4 min. Lysis was halted with the addition of 50 uL of wash buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% Tween-20, 0.1%, 1% BSA). Samples were centrifuged at  500 x g, 4 °C for 5 min. Nuclei pellets were resuspended in 50 µl of wash buffer and centrifuged at  500 x g, 4 °C for 5 min.  Nuclei pellets were resuspended in 50 µl of transposition reaction mix (1× Tagment DNA Buffer, 2.5 µl of Tagment DNA Enzyme 1) and incubated for 30 min at 37 °C
Libraries were purified using SPRI-Select bead purification and the concentrations were measured using both Qubit and KAPA qPCR. 2100 Bioanalyzer was used to check the quality of libraries. Libraries were sequenced on the Illumina NextSeq 250, with 75-bp paired-end reads.

tag: disease state

value: FPDMM

tag: organ

value: Peripheral Blood

tag: treatment protocol

value: PB was collected and neutrophils were isolated on the same day


title: IC-A129GBM-I-13058_S12

tag: genotype


title: RRBS Dentate Gyrus cells, Attacker Group, Rep 5

value: Dentate Gyrus

value: WT