title: HepG2, Flash Freezing, OmniATAC

city: Freiburg im Breisgau

first: Thomas

last: Manke

address: Stuebeweg 51

department: Bioinformatics Core Facility

institute: Max-Planck-Institute of Immunobiology and Epigenetics

description: 10x Genomics scATAC-seq

library_source: genomic single cell

data_processing:
BCL files were converted to fastq format using bcl2fastq2. Demultiplexing was performed using either Illumina p7 barcodes or sample barcodes introduced via multiplexing.
Fastq files served as input for individual runs of the cellranger-atac pipeline (v2.1.0) per sample (https://software.10xgenomics.com/single-cell-atac/software/overview/welcome)
Assembly: GRCh38
Supplementary files format and content: fragments.tsv.gz - fragment files from cellranger output
Supplementary files format and content: fragments.tsv.gz.tbi - index files for fragment files from cellranger output
Supplementary files format and content: singlecell.csv - metadata information from cellranger output

growth_protocol: EMEM with 10% FBS, 2 mM GlutaMAX, and 1mM sodium pyruvate

extract_protocol:
Cells were pelleted and resuspended in 1 ml of fixative buffer (0.1% Formaldehyde in DMEM) and incubated at room temperature for 5 minutes. Afterwards, cells were pelleted and washed in DMEM + 0.1% BSA, pelleted again, and either snap-frozen by submerging the tubes in liquid nitrogen or cryopreserved.
Cells and nuclei were permeabilized in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630, 0.1% Tween-20, 0.01% Digitonin, 1% BSA) and incubated for 5 minutes on ice. Ice-cold wash buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA) was added and mixed by inversion. Nuclei were pelleted and resuspended inin 1x Nuclei Dilution Buffer (10x Genomics). Transposition mix for multiplexed scATAC (comprising 7.5 μl of 2x Diagenode Tn5 reaction buffer and 1.5 μl of 10x Genomics 1x Nuclei Dilution Buffer) was added. To each transposition reaction, 1 μl of custom barcoded Tn5 at a 1:4 dilution was added, ensuring the selection of Tn5 barcodes to avoid overlap after pooling. All reactions were mixed by pipetting and incubated at 37°C for 30 minutes.Transposition was quenched by adding 1 μl of 300 mM EDTA, followed by incubation at 37°C for 15 minutes. The reactions were then cooled and pooled on ice. The pooled cells were centrifuged, washed and resuspended with 1x Nuclei Dilution Buffer. 15 μl of the diluted cell suspension were aliquoted into a PCR tube strip on ice for loading into the Chromium Controller, with a total of 15,600 cells loaded according to 10x Genomics recommendations. The single-cell ATAC v2 protocol was then continued from step 2.1 of the manufacturer’s manual (Chromium Next GEM Single Cell ATAC Reagent Kits v2 User Guide, CG000496 rev B).  For final PCR amplification at step 4.1 of the User Guide, the "individual single index set N" was replaced with 2.5 μl of 25 μM custom oligo (MUXscATAC_i7_n, sequences in Additional File 1), selecting library indices appropriately to prevent equal index assignment. Library amplification was performed using 9 PCR cycles.

value: liver

value: hepatocellular carcinoma


title: siCtrl normoxia 4

status: Public on Jul 01 2025

type: SRA

city: Frankfurt

first: Andreas

last: Weigert

address: Theodor-Sern-Kai 7

department: Medicine

country: Germany

institute: Goethe-University

description:
Library name: norm_ctrl_4
norm_ctrl_4

library_source: transcriptomic

data_processing:
data were processed using the blue-bee pipeline (https://lexogen.bluebee.com/quantseq/)
umi2index
Trimming: bbduk v35.92
Alignment: STAR Aligner with modifi_x001E_ed ENCODE settings
Gene Read Counting: HTSeq-count with kit-specic options (FWD)
differential analysis: log2 fold change and p-adjusted FDR
Assembly: human genome GRCh38
Supplementary files format and content: text files containing the normalized read counts for hypoxic, normoxic, siRNA control and siSCD1 treated macrophages.

molecule: total RNA

organism: Homo sapiens

source_name: blood

growth_protocol: Peripheral blood mononuclear cells (PBMC) were isolated using Pancoll gradientsand seeded onto high-adherence culture dishes in RPMI 1640 medium supplemented with 100 U/mL penicillin and 100 µg/mL streptomycin. Non-adherent cells were washed away after 1 h and the remaining cells were maintained in  RPMI 1640 medium supplemented with 100 U/mL penicillin, 100 µg/mL streptomycin and 5% human serum for 7 days to allow for differentiation to MΦ.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit.
cDNA libraries were generated with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD with UDI for Illumina (Lexogen).

treatment_protocol: Macrophages were transfected with SCD1 (ON-TARGETplus SMART pool, human #6319) and siRNA control (ON-TARGETplus Non-targeting Pool Cat#D-001810-10-50) using Hiperfect transfection reagent (Qiagen) and harvested 5 days after transfection. A group of samples was cultured under normoxia and another under hypoxia during the 5 days treatment.

tag: tissue

value: blood

tag: cell line

value: human primary macrophages

tag: cell type

value: immune cells

tag: treatment

value: Control transfection normoxia


title: de-diff SC-EV microRNA biol rep 3

city: Cincinnati

first: Leyla

last: Esfandiari

state: OH

address: 2600 Clifton Ave

country: USA

institute: University of Cincinnati

description:
Library name: Sample 18
Leyla Esfandiari_PE507 Project 10239 small RNA-seq_part 2 of 2 LE12
miRNA_rawCounts.csv

data_processing:
For mRNA seq, RNA-seq reads in FASTQ format were subsampled and standedness of the FASTQ files were auto-inferred using fq. This was followed by quality control analysis using FastQC, adapter and quality trimming using Trim Galore and cutadapt. Reads were aligned using STAR to the reference genome and options were provided for using HISAT2 aligner. SAMtools was used to sort and index alignments followed by marking of PCR duplicates using Picard MarkDuplicates. Transcript assembly and quantification were done using StingTie. BEDTools and bedGrapgToBigWig were used to generate bigWig files. We performed extensive quality control analysis of the RNA-Seq data using RSeQC, Qualimap, dupRadar, and DESeq2. Salmon and tximport were used as the default quantification tools for transcript quantification and conversion of transcript counts to gene counts respectively. Differential gene expressions between groups of samples were assessed with the R package DESeq2 v1.26.0.  Summary report of the analysis was performed using MultiQC.
For miRNA seq, the QC and quantification of miRNA-Seq data was performed using nf-core/smrnaseq (version 2.3.1) pipeline. The pipeline generated raw and normalized (CPM) gene count files. Differential gene expression analysis between groups of samples were assessed with the R package DESeq2 v1.26.0. Summary report of the analysis was performed using MultiQC.
For lncRNA seq, RNA sequencing reads were assessed for quality using FastQC  and subsequently trimmed to remove adapter sequences using Trim Galore and Cutadapt. The cleaned reads were aligned to the rat reference genome using the STAR aligner. Raw counts and lncRNA expression (Transcripts Per Million, TPM) were generated.
Assembly: Rn6
Supplementary files format and content: salmon.merged.gene_counts.tsv
Supplementary files format and content: miRNA_rawCounts.csv
Supplementary files format and content: lncRNA_raw_readcounts.tsv

organism: Rattus norvegicus

growth_protocol: Primary Rat Schwann cells (RSC) (Catalog R842-05a) were purchased from CELL Applications (San Diego, CA, USA) and maintained according to the manufacturer’s protocol. Briefly, Schwann cells were cultured in RSC growth medium (Catalog R825-500) (CELL Applications, San Diego, CA, USA) at 37°C in 5% CO2. The culture medium was replaced every 48 h. Sub-culturing was performed when the cells reached 80% confluency and cells were maintained for no longer than 5 passages. Passages 3 to 5 were used for experiments.

extract_protocol:
1. Whole-transcriptome RNA sequencing was performed by the Genomics, Epigenomics, and Sequencing Core (GESC) at the University of Cincinnati following updated protocols. Total RNA was isolated from Schwann cells for mRNA-seq and SC-EVs for lncRNA-seq, and quality control was assessed using the Agilent Bioanalyzer with the RNA 6000 Pico Kit. 2. For MicroRNA-Sequencing, total RNA was extracted from SC-EVs using the miRNeasy Micro kit as per the manufacturer’s suggested protocol and was quality control-assessed using the RNA 6000 Pico Kit on the Agilent Bioanalyzer
1. For whole RNA sequencing for mRNA and lncRNA, 10 ng of total RNA was used as input for library preparation using the NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA).  2. For microRNA-Sequencing, ~5 ng of total RNA was used for library construction with the NEBNext Multiplex Small RNA Library Prep Kit (New England BioLabs, Ipswich, MA), incorporating a protocol modification to increase sensitivity and specificity for small RNA detection.

treatment_protocol: Six-well plates and 11 mm glass coverslips were incubated with Schwann Cells Coating solution (Cat036-20) CELL Applications (San Diego, CA, USA) at 37°C overnight. The remaining solution was aspirated, rinsed twice with PBS, and dried. RSC samples were prepared according to a modified protocol (Zou, 2023).  Cells were seeded into a coated 6-well plate at a density of 2´105 cells/well for western blot and RNA sequencing and seeded into a 24-well plate (covered with coated glass coverslips) at a density of 1´104 cells/well for immunofluorescence staining. Cells were cultured in RSC complete growth medium (R825-500) for 24 h and the medium was changed into the complete medium-RSC basal media containing 10% Exosome-Depleted FBS (Fisher), 2mM of Foskolin (Sigma-Aldrich, catalog number: F6886), 10 ng/mL of human neuregulin 1-β1/heregulin (R&D Systems, Catalog Number: 396-HB/CF), and 100 mg/mL penicillin-streptomycin (Gibco) for 24 h. Then the medium was removed and replaced by a medium containing DMEM, 1% Exosome-depleted FBS, and 100 mg/mL penicillin-streptomycin (starvation medium) overnight to limit mitogenic stimulation.  Cells were then differentiated into myelinating SC by removing the starvation medium and replacing it with medium containing DMEM, 1% Exosome-depleted FBS, 100 mg/mL penicillin-streptomycin, and 1 mM db-cAMP (Sigma, USA).  After 72 h, the medium was replaced with the Exosome-depleted complete medium for an additional 72 h to induce dedifferentiation. Cells maintained in the absence of db-cAMP-inducing agents served as a control for undifferentiated cells.  Cells were monitored daily to observe changes in morphology. At the end of the assay, cells were harvested for SC stage-specific markers for characterization of Schwann cell differentiation stages, and the supernatant was collected for EV isolation.

value: Schwann cell de-differentiation


title: MEF-silencer-output3_MEF-silencer-output3-3

city: shenzhen

first: Guoli

last: Li

address: penfei street

country: China

institute: Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences

data_processing:
bowtie2 aligns sequencing data to the hg38 genome, samtools filters comparison data, and CRADLE software identifies silencer.
Assembly: hg38
Supplementary files format and content: bed file records silencer location and silencer activity
Library strategy: STARR-seq

organism: Mus musculus

source_name: MEFs

extract_protocol:
MEFs were inoculated with 10 % FBS (Gibco; Cat 10437028) and 1% penicillin streptomycin P/S (Sigma; cat P0781) in DMEM (Thermo Fisher; Cat 10566024), MEFs are induced in iCD1 medium(Delicell, Cat 820250). iPSCs and mESCs were cultured in N2B27-2i/LIF medium (Neural Basal, F12,1%Glutamax, 1%NEAA, 1%Sodium pyruvate, 0.1mM β-me, 1%B27, 0.5% N2, 0.5% P/s(optional), mLif(1:8000), 3uM CHIR99021(1:4000), 1 uM PD0325901). The culture conditions of all cells were 37 °C, 5 % carbon dioxide.
The construction of the random input DNA library involves three main steps: creating insert fragments, preparing the linearized vector, and seamless assembly cloning. First, the genome is fragmented into 300-400 base pair segments using an ultrasonic disruptor. The library construction kit (Roche; KK8514) is used to add homologous arms and Illumina adapters to these fragments. Next, the Ss-STARR-seq vector is digested with AgeI-HF and SalI-HF enzymes (NEB). The fragmented DNA is then recombined with the linearized vector using Gibson's homologous recombination enzyme (NEB). The quality of the library clones is verified through Sanger sequencing. Forty recombination reactions are set up, and the products are purified using a DNA purification kit (ZYMO; d4013). The purified DNA is transformed into competent cells (Thermo Fisher Scientific; c6400) and cultured in 15 liters of LB medium. When the bacterial culture reaches an optical density (OD) between 1.0 and 1.2, PCR amplification is performed using 100 ng of plasmid as a template. The PCR conditions include initial denaturation at 98°C for 45 seconds, followed by 20 cycles of denaturation at 98°C for 15 seconds, annealing at 60°C for 30 seconds, and extension at 72°C for 30 seconds. The amplified products are recovered through 2% agarose gel electrophoresis and prepared for high-throughput sequencing. Cells transfected with the input library were harvested for RNA extraction using TURBOTM DNase (Thermo Fisher Scientific) and Dynabeads Oligo (dT)25 (Thermo Fisher Scientific). The enriched mRNA was reverse transcribed into cDNA using SuperScript TM IV Reverse Transcriptase (Thermo Fisher Scientific) and specific primers. AmbionTM RNase H was then used to degrade any remaining RNA in the cDNA product. The cDNA was purified and amplified via PCR using the HiFi high fidelity enzyme Ready Mix (Roche). The PCR protocol involved initial denaturation at 98°C for 45 seconds, followed by 20 cycles of 98°C for 15 seconds, 60°C for 30 seconds, and 72°C for 30 seconds. The PCR products were separated by 2% agarose gel electrophoresis to create the output library for high-throughput sequencing.

value: MEFs


title: MEF-silencer-output3_MEF-silencer-output3-2

growth_protocol: MEFs were inoculated with 10 % FBS (Gibco; Cat 10437028) and 1% penicillin streptomycin P/S (Sigma; cat P0781) in DMEM (Thermo Fisher; Cat 10566024), MEFs are induced in iCD1 medium(Delicell, Cat 820250). iPSCs and mESCs were cultured in N2B27-2i/LIF medium (Neural Basal, F12,1%Glutamax, 1%NEAA, 1%Sodium pyruvate, 0.1mM β-me, 1%B27, 0.5% N2, 0.5% P/s(optional), mLif(1:8000), 3uM CHIR99021(1:4000), 1 uM PD0325901). The culture conditions of all cells were 37 °C, 5 % carbon dioxide.


title: siCtrl normoxia 3

description:
Library name: norm_ctrl_3
norm_ctrl_3


title: HepG2, fresh, OmniATAC

description: 10x Genomics scATAC-seq

molecule: genomic DNA

source_name: liver

tag: genotype

value: WT


title: diff SC-EV microRNA biol rep 3

description:
Library name: Sample 17
Leyla Esfandiari_PE507 Project 10239 small RNA-seq_part 2 of 2 LE11
miRNA_rawCounts.csv

source_name: Primary Rat Schwann cells (RSC) (Catalog R842-05a)

value: Schwann cell differentiation


title: MEF-silencer-output3_MEF-silencer-output3-1


title: siCtrl normoxia 2

description:
Library name: norm_ctrl_2
norm_ctrl_2


title: MEF-silencer-output2_MEF-silencer-output2-16


title: HepG2, fresh, DirectATAC

description: 10x Genomics scATAC-seq


title: HepG2, Cryopreservation, OmniATAC

description: 10x Genomics scATAC-seq


title: diff SC-EV microRNA biol rep 2

description:
Library name: Sample 14
Leyla Esfandiari_PE507 Project 10239 small RNA-seq_part 2 of 2 LE8
miRNA_rawCounts.csv

value: Primary Rat Schwann cells (RSC) (Catalog R842-05a)


title: de-diff SC-EV microRNA biol rep 2

description:
Library name: Sample 15
Leyla Esfandiari_PE507 Project 10239 small RNA-seq_part 2 of 2 LE9
miRNA_rawCounts.csv


title: siCtrl normoxia 1

description:
Library name: norm_ctrl_1
norm_ctrl_1


title: MEF-silencer-output3_MEF-silencer-output3-4


title: YNN4 replicate 2

city: State College

first: Shane

middle: Douglas

last: Stoeber

state: Pennsylvania

address: 406 South Frear Building

department: BMMB

institute: Penn State

description: Library name: YNN4 replicate 2

library_source: other

data_processing:
Paired-end reads were aligned to the corresponding reference sequence (Widom 601 or YNN with or without factor binding site) with Bowtie2 on galaxy (https://usegalaxy.org/) in paired-end mode.
Unpaired and unmapped reads were removed using samtools view in galaxy (https://usegalaxy.org/).
Nucleosome coverage was calculated from the read counts normalized to total reads in BPM using bamCoverage. The minimum and maximum fragment length was set to 130 bp and 160 bp respectively unless otherwise stated to enrich reads for mono-nucleosome fragments. Files were outputted as a bedgraph and plotted to visualize nucleosome occupancy.
The dyad position for each sequence was calculated using bamCoverage –MNase in which only the three center bp of each fragment was used for analysis and were normalized to total reads in BPM. Files were outputted as a bedgraph and plotted to visualize dyad location.
Supplementary files format and content: All nucleosome coverage and dyad analysis are bedgraph

molecule: other

organism: synthetic construct

source_name: PCR generated DNA molecule

extract_protocol:
Nucleosome binding experiments were performed by incubating 60 nM nucleosome with 0 nM or 60 nM of TFs (Reb1, Cbf1, or Pho4) for 20 minutes at room temperature. Nucleosomes-TF binding was confirmed on a 5% acrylamide native gel. The incubated samples were then digested with 0.3 U, 1 U, 3 U, 10 U of MNase (New England Biolabs) for 8 minutes at 37 ⁰C and immediately quenched by adding quench buffer (0.1 % SDS, 20 mM EDTA pH8.0, 0.01 U proteinase K). Proteinase K digestion was carried out by incubating the quenched samples for 1 hour at 50 ⁰C. The final digested samples were analyzed by agarose gel electrophoresis with a 1.5% gel in 0.5x TAE buffer (20 mM Tris base, 10 mM acetic acid, 0.5 mM EDTA pH 8.0) (Figure S4). The digest DNA samples were then purified by agarose gel electrophoresis and then gel extraction with a Freeze 'N Squeeze DNA extraction kit (Bio-Rad).
After gel purification of the MNase digested samples, sequencing libraries were prepared using NEBNext ® Ultra™ II DNA Library Prep Kit for Illumina® (Catalog # E7645L) according to the manufacturer’s instructions. The sequencing libraries were sequenced on a NextSeq 2000 machine in 2 x 50 bp paired-end sequencing mode at the Genomics Research Incubator at The Pennsylvania State University.

value: 1 unit micrococcal nuclease


title: HepG2, Cryopreservation, DirectATAC

description: 10x Genomics scATAC-seq


title: YNN5 replicate 2

description: Library name: YNN5 replicate 2


title: HepG2, 0.1% FA + Flash Freezing, OmniATAC

description: 10x Genomics scATAC-seq


title: undiff SC-EV microRNA biol rep 2

description:
Library name: Sample 13
Leyla Esfandiari_PE507 Project 10239 small RNA-seq_part 2 of 2 LE7
miRNA_rawCounts.csv

value: Schwann cell undifferentiation


title: YNN3 replicate 2

description: Library name: YNN3 replicate 2


title: HepG2, 0.1% FA + Flash Freezing, DirectATAC

description: 10x Genomics scATAC-seq


title: HepG2, Flash Freezing, DirectATAC

description: 10x Genomics scATAC-seq


title: MEF-silencer-output2_MEF-silencer-output2-13


title: YNN2 replicate 2

description: Library name: YNN2 replicate 2


title: MEF-silencer-output2_MEF-silencer-output2-12


title: diff SC-EV microRNA biol rep 1

description:
Library name: Sample 11
Leyla Esfandiari_PE507 Project 10239 small RNA-seq_part 2 of 2 LE5
miRNA_rawCounts.csv


title: HepG2, 0.1% FA + Cryopreservation, OmniATAC

description: 10x Genomics scATAC-seq


title: MEF-silencer-output2_MEF-silencer-output2-11


title: YNN1 replicate 2

description: Library name: YNN1 replicate 2


title: undiff SC-EV microRNA biol rep 1

description:
Library name: Sample 10
Leyla Esfandiari_PE507 Project 10239 small RNA-seq_part 2 of 2 LE4
miRNA_rawCounts.csv


title: undiff SC-EV microRNA biol rep 3

description:
Library name: Sample 16
Leyla Esfandiari_PE507 Project 10239 small RNA-seq_part 2 of 2 LE10
miRNA_rawCounts.csv


title: HepG2, 0.1% FA + Cryopreservation, DirectATAC

description: 10x Genomics scATAC-seq


title: MEF-silencer-output2_MEF-silencer-output2-15


title: 601 replicate 2

description: Library name: 601 replicate 2


title: MEF-silencer-output2_MEF-silencer-output2-14


title: de-diff SC mRNA biol rep 3

description:
Library name: Sample 9
Leyla Esfandiari _PE512_Project 11026 LE12
salmon.merged.gene_counts.tsv


title: MEF-silencer-output2_MEF-silencer-output2-9


title: HepG2, 5.0%FA + flash freezing

library_source: genomic

data_processing:
BCL files were converted to fastq format using bcl2fastq2. Demultiplexing was performed using either Illumina p7 barcodes or sample barcodes introduced via multiplexing.
DNA-mapping pipeline from snakePipes (v2.7.2) using the GRCh38 reference genome with cutadapt options: "--trimmerOptions -a nexteraF=CTGTCTCTTATA -A nexteraR=CTGTCTCTTATA"
bamCoverage from deepTools (v3.5.5) with RPKM normalization and a bin size of 1bp
For bed file: ATACseq pipeline from snakePipes (v2.7.2) with the hg38 genome. This runs MACS2 which yields the peak file.
Assembly: GRCh38
Supplementary files format and content: bigWig (bw)
Supplementary files format and content: narrowPeaks (bed) called for sample cryo_0.1FA

extract_protocol:
Cells were pelleted and resuspended in 1 ml of fixative buffer (0.1-5% Formaldehyde in DMEM) and incubated at room temperature for 5 minutes. Afterwards, cells were pelleted and washed in DMEM + 0.1% BSA, pelleted again, and either snap-frozen by submerging the tubes in liquid nitrogen or cryopreserved.
Cells and nuclei were permeabilized in lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal CA-630, 0.1% Tween-20, 0.01% Digitonin, 1% BSA) and incubated for 5 minutes on ice. Ice-cold wash buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA) was added and mixed by inversion. Nuclei were pelleted and resuspended in transposition mix (25 μl of Diagenode 2x Tn5 reaction buffer, 0.5 μl of 1% Digitonin, 0.5 μl of 10% Tween-20, 16.5 μl of PBS, 5 μl of water, and 2.5 μl of Custom Tn5 at a 1:4 dilution). The mixture was thoroughly mixed by pipetting and incubated for 30 minutes at 37°C. Transposition was quenched by adding 50 μl of 2x Tn5 stop solution (40 mM EDTA, 2 mM spermidine), followed by incubation at 37°C for 15 minutes. The reactions were then cooled and pooled on ice. The pooled cells were centrifuged and resuspended in buffer EB. Samples were de-crosslinked at 68°C for 30 minutes. DNA was purified using the MinElute PCR purification kit according to the manufacturer's instructions. For PCR amplification, 10 μl of each transposed DNA was mixed with 2.5 μl of 25 μM i5 primer, 2.5 μl of 25 μM i7 primer, and 25 μl of 2x NEBNext Ultra II Q5 Master Mix. The mixture was amplified (72°C for 5 min, 98°C for 30 s, followed by 10 cycles of 98°C for 10 s, 63°C for 30 s, 72°C for 1 min, hold at 4°C). Final libraries were cleaned using Ampure XP at a 0.8x ratio (40 μl of beads per 50 μl of reaction) and eluted in EB (Qiagen).


title: de-diff SC-EV microRNA biol rep 1

description:
Library name: Sample 12
Leyla Esfandiari_PE507 Project 10239 small RNA-seq_part 2 of 2 LE6
miRNA_rawCounts.csv


title: HepG2, 1.0%FA + flash freezing


title: diff SC mRNA biol rep 3

description:
Library name: Sample 8
Leyla Esfandiari _PE512_Project 11026 LE11
salmon.merged.gene_counts.tsv


title: Placental EV from Nodal^Δ/Δ mice at embryonic day 10.5, replicate 3

city: Montreal

first: Bioinformatics

last: Platform

state: Quebec

address: 1001 Decarie Blvd

country: Canada

institute: RI-MUHC

description: Library name: KO-3

data_processing:
fastp version 0.23.4
exceRpt smallRNA version 4.6.3
Assembly: mm10
Supplementary files format and content: TSV format with columns ReferenceID, uniqueReadCount, totalReadCount, multimapAdjustedReadCount, multimapAdjustedBarcodeCount

source_name: placenta

extract_protocol:
To extract total RNA, the EV samples were first treated with 20 μg/μL of proteinase K for 30 min at 37 to purify the samples of non-EV protein contamination. The samples were then treated with 20 μg/μL of RNAse A (FEREN0531, Fisher Scientific International) for 2 min at room temperature to eliminate any non-EV RNA contamination. The QIAZol Lysis Reagent from the Qiagen miRNeasy Micro Kit (217084, QIAGEN N.V.) was added to the samples in a 5:1 ratio and vortexed for 5 sec before being kept at room temperature for 5 min. Chloroform was then added to the samples in a 1:5 volume ratio, vortexed for 15 sec, and left to incubate for 3 min at room temperature. The samples were centrifuged for 15 min at 12,000g at 4, and the resulting aqueous phase was removed and mixed with 1.5 100% ethanol. The samples were transferred to the MinEluteTM columns from the Qiagen miRNeasy Micro Kit and the instructions outlined in kit were then followed to complete the RNA extraction.
NEBNext Multiplex Small RNA Library Prep Kit for Illumina

value: placenta

value: Nodal Knockout


title: MEF-silencer-output2_MEF-silencer-output2-8


title: HepG2, 0.5%FA + flash freezing


title: undiff SC mRNA biol rep 3

description:
Library name: Sample 7
Leyla Esfandiari _PE512_Project 11026 LE10
salmon.merged.gene_counts.tsv


title: Placental EV from Nodal^Δ/Δ mice at embryonic day 10.5, replicate 1

description: Library name: KO-1


title: HepG2, 0.1%FA + flash freezing


title: Placental EV from Nodal^Δ/Δ mice at embryonic day 10.5, replicate 2

description: Library name: KO-2


title: MEF-silencer-output2_MEF-silencer-output2-7


title: MEF-silencer-output2_MEF-silencer-output2-5


title: de-diff SC mRNA biol rep 2

description:
Library name: Sample 6
Leyla Esfandiari_PE500_PE503_PE504_Project 9987 LE9
salmon.merged.gene_counts.tsv


title: MEF-silencer-output2_MEF-silencer-output2-6


title: MEF-silencer-output2_MEF-silencer-output2-10


title: HepG2, 5.0%FA + cryopreservation


title: diff SC mRNA biol rep 2

description:
Library name: Sample 5
Leyla Esfandiari_PE500_PE503_PE504_Project 9987 LE8
salmon.merged.gene_counts.tsv


title: Placental EV from Nodal^loxP/loxP mice at embryonic day 10.5, replicate 3

description: Library name: CTL-3


title: MEF-silencer-output2_MEF-silencer-output2-4


title: undiff SC mRNA biol rep 2

description:
Library name: Sample 4
Leyla Esfandiari_PE500_PE503_PE504_Project 9987 LE7
salmon.merged.gene_counts.tsv


title: HepG2, 0.5%FA + cryopreservation


title: Placental EV from Nodal^loxP/loxP mice at embryonic day 10.5, replicate 2

description: Library name: CTL-2


title: Placental EV from Nodal^loxP/loxP mice at embryonic day 10.5, replicate 1

description: Library name: CTL-1


title: MEF-silencer-output2_MEF-silencer-output2-3


title: cochlear mambranous labyrinth, treated hMPZL2Q74X/Q74X, biol rep 3

city: Seoul

first: Sohyang

last: Jeong

address: 71, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University Hospital

description: Library name: treated_3

data_processing:
Confirming the library size (approximately 300–500 bp) and fluorophore-based quantification of each library concentration (Quantus; Promega, USA), the samples were sequenced on a Nextseq 2000 under paired-end conditions (Illumina).
After filtering, fastq files were mapped against the reference genome GRCm39 (ensemble) and pseudo-aligned by Kallisto (version 0.51.0).
Transcript counts were imported at the gene level using txiimport.
DEGs were identified using DEseq.
Individual samples were further analyzed to list genes with a fold change greater than 1.5 and a p-value < 0.05.
DAVID GO analysis was performed to examine GO terms for biological processes, cellular components, and molecular functions.
Representative GO terms were summarized and visualized using REVIGO.
DEGs were further compared with the mouse cochlear single-cell RNA-seq database (http://umgear.org) and the SHIELD database (http://shield.hms.harvard.edu) in order to refine the list of genes implicated in specific cellular pathways.
Assembly: NC_000075.7, NM_007962.4 for hMPZL2Q74X, and NM_005797.4 for human MPZL2 transcript.
Supplementary files format and content: text file includes raw counts for samples.

source_name: cochlear mambranous labyrinth

growth_protocol: The temperature and humidity of the breeding environment were maintained at 22 ± 1 °C and 50%, with a 12-hour light:dark cycle

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen, USA) following the manufacturer's protocol.
RNA sequencing libraries were prepared using a SMARTER stranded total RNA-seq in accordance with the manufacturer’s protocols (Takara, Japan).

treatment_protocol: treated hMPZL2Q74X/Q74X group were injected AAV-ie-ABE8eWQ-SpRY:sgRNA3 into cochlear Round Window Membrane route at P2.

value: cochlear mambranous labyrinth

value: treated hMPZL2Q74X/Q79X

tag: age


title: HepG2, 0.1%FA + cryopreservation

value: liver


title: de-diff SC mRNA biol rep 1

description:
Library name: Sample 3
Leyla Esfandiari_PE500_PE503_PE504_Project 9987 LE6
salmon.merged.gene_counts.tsv


title: diff SC mRNA biol rep 1

description:
Library name: Sample 2
Leyla Esfandiari_PE500_PE503_PE504_Project 9987 LE5
salmon.merged.gene_counts.tsv


title: cochlear mambranous labyrinth, treated hMPZL2Q74X/Q74X, biol rep 2

description: Library name: treated_2

value: treated hMPZL2Q74X/Q78X


title: MEF-silencer-output2_MEF-silencer-output2-1


title: HepG2, 1.0%FA + cryopreservation

value: hepatocellular carcinoma


title: MEF-silencer-output1_MEF-silencer-output1-16


title: CM-SHED

city: Shijiazhuang

first: Jiayu

last: Zhang

address: No. 361 Zhongshan East Road

institute: Hebei Medical University

library_source: transcriptomic single cell

data_processing:
Processing was performed with the 10X Chromium cellranger pipeline version 6.0.1 using default settings
Assembly: GRCh38
Supplementary files format and content: Supplementary files format and content: tsv.gz of Filtered feature-barcode matrix with raw counts for each sample

molecule: polyA RNA

source_name: in vitro

extract_protocol:
Using the Chromium Single Cell 3′ Reagent Kit v3User Guide, single cell suspensions were partitioned into nanoliter droplets called Gel-bead-in-Emulsions (GEMs) to achieve single cell resolution. The cDNA generated within each individual GEM is tagged with a common 16nt 10x barcode and a 12nt unique molecular barcode during the RT reaction. Purified cDNA was amplified for 11 cycles before being purified using SPRIselect beads. Samples were then run on a Agilent Bioanalyzer to determine cDNA concentration. 10uL of purified cDNA was used to generate the Illumina library for sequencing.
For sample preparation on the 10x Genomics platform, the Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 16 rxns (PN-1000075), Chromium Chip B Single Cell Kit, 48 rxns (PN-1000073) and Chromium i7 Multiplex Kit (PN-120262) were used. The single cell libraries were then sequenced on the Illumina NovaSeq 6000 S4 200 cycle flow cell generating 28x98 reads. A median sequencing depth of 50,000 reads/cell was targeted for each sample.

value: in vitro

value: Stem cells

value: intestinal organoid medium cultured


title: SHED

value: Control


title: met-2(n4256) hpl-2(tm1489)_3

city: Mainz

first: Jan

last: Padeken

address: Ackermannweg 4

institute: Institute of Molecular Biology

data_processing:
Adapter were trimmed using Trimmomatic v0.39. Reads were aligned to the C. elegans genome (ce10) with the R package QuasR v1.42.1, (www.bioconductor.org/packages/2.12/bioc/html/QuasR.html). The command “proj <-qAlign(“samples.txt“,“BSgenome. Celegans.UCSC.ce10”, splicedAlignment=TRUE)” instructs hisat296 to align using default parameters, considering unique reads for genes and genome wide distribution.
Count Tables of reads mapping within annotated exons in WormBase (WS220) (expr_mRNA.tab) were constructed using the qCount function of the QuasR package to quantify the number of reads in each window (qCount(proj, GRange_object,orientation=“same”)) and normalized by division by the total number of reads in each library and multiplied by the average library size. Transformation into log2 space was performed after the addition of a pseudocount of 8 to minimize large changes in abundance fold change (FC) caused by low count numbers.
Assembly: ce10
Supplementary files format and content: Tab delimited table with first column indicating the WormBase ID followed by coumns with the read counts for each condition and replica

organism: Caenorhabditis elegans

source_name: yeast cells

growth_protocol: RNA was extracted from early wild-type (N2 Bristol), hpl-2 (hpl-2(tm1489)), hpl-2-ffaa (hpl-2-FFAA(px112)), and hpl-2 met-2 (met-2(n4256) hpl-2(tm1489) III/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III)) C. elegans embryos from a synchronized culture grown at 20°C

extract_protocol:
RNA was extracted from early wild-type (N2 Bristol) C. elegans embryos from a synchronized culture grown at 20°C and exposed to indicated temperatures for 2 h, using Trizol. Embryos were freeze cracked five times, then RNA was extracted with choloroform followed by isopropanol precipitation. Further purification was performed with the RNA Clean and Concentrator kit (Zymo).
Libraries were produced using the Stranded Total RNA Prep Ligation with Ribo-Zero Plus Kit (Illumina). rRNA was depleted using the Ribo-Zero Plus kit supplemented with custom made C. elegans specific rDNA oligos (IDT).
Libraries were profiled in a DNA 1000 Chip on a 2100 Bioanalyser (Agilent technologies) and quantified using the Qubit 1x dsDNA HS Assay Kit, in a Qubit 4.0 Fluorometer (Life technologies). Equimolar amounts of indexed libraries were pooled and sequenced on a NextSeq 2000 (Illumina).

tag: developmental stage

value: embryo

value: yeast cells


title: hCiCMs_scRNA

city: shanghai

first: Chenwen

last: Huang

state: shanghai

address: 600 Yi Shan Road

department: Department of Joint Clinical Research Centre

institute: Shanghai Sixth People's Hospital

description: 10X Genomics，scRNA

data_processing:
Raw reads were processed to generate gene expression profiles using CeleScope v1.5.2 (Singleron Biotechnologies) with default parameters. Briefly, Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were aligned against the Homo_sapiens_ensembl_92 transcriptome using STAR(v2.6.1b). Uniquely mapped reads were then assigned to exons  with FeatureCounts(v2.0.1). Successfully Assigned Reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis.
Assembly: hg38
Supplementary files format and content: tab-separated values files and matrix files

source_name: cardiomyocytes

extract_protocol:
The cells were collected by trypsinization. The ascites samples went through filtering by 40-micron sterile strainers and were  centrifuged at 350× g for 5 min. Then the supernatant was discarded, and the sediment was resuspended in 1ml PBS (HyClone). Finally, the samples were stained with Trypan Blue and the cell viability was evaluated microscopically. Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron)1. Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.Raw reads were processed to generate gene expression profiles using CeleScope v1.5.2 (Singleron Biotechnologies) under default setting. Briefly, Barcodes and UMIs were extracted from R1 reads and corrected. Adapter sequences and poly A tails were trimmed from R2 reads and the trimmed R2 reads were aligned against the Homo_sapiens_ensembl_92 transcriptome using STAR(v2.6.1b). Uniquely mapped reads were then assigned to exons with FeatureCounts(v2.0.1). Successfully Assigned Reads with the same cell barcode, UMI and gene were grouped together to generate the gene expression matrix for further analysis.
Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) (Ref) . Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

value: cardiomyocytes

value: cardiac cells


title: MEF-silencer-output1_MEF-silencer-output1-15

value: MEFs


title: MIA PaCa-2_DMPatA_rep3

city: Angers cedex 02

first: Agnes

last: Basseville

address: 15 rue André Boquel

country: France

institute: Institut de Cancerologie de l'Ouest

data_processing:
RTA (Illumina) was used for base calling and bcl2fastq2 (version 2.19) for converting BCL to fastq format, coupled with adaptor trimming
Pseudoalignment was performed to a kallisto index created from transcriptomes (Human: GRCh38) using kallisto (0.44.0)
Assembly: Human GRCh38
Supplementary files format and content: tab-delimitated text file including tpm values for each sample
Supplementary files format and content: tab-delimitated text file including raw counts for each sample

source_name: MIA PaCa-2

growth_protocol: Cells were cultured in appropriate medium (RMPI for KLM, and DMEM for MIA PaCa-2) supplemented with 10% fetal bovine serum , 100-units/L penicillin-streptomycin and 1% glutamine in a 5% CO2 atmosphere at 37°C.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (Qiagen), and stored at -80°C before its use for the construction of sequencing libraries.
RNA-seq libraries for RNA-seq were prepared using poly-A pull-down to enrich mRNAs from total RNA samples, then proceed with library construction using Illumina TruSeq chemistry.

treatment_protocol: Cells were treated 18 hours with either vehicule control (DMSO 0,3 %, 18h continuously), 15 nM romidepsin (6h + 12 h washout), 2 nM DMPatA (18h continuously), or a combination of romidepsin and DMPatA (following the same dose and time exposure than in monotherapy).

value: MIA PaCa-2

value: pancreatic cancer cell line

value: DMPatA

tag: time


title: met-2(n4256) hpl-2(tm1489)_1


title: MEF-silencer-output1_MEF-silencer-output1-14


title: cochlear mambranous labyrinth, hMPZL2Q74X/Q74X , biol rep 2

description: Library name: HOMO_2

value: cochlear mambranous labyrinth


title: cochlear mambranous labyrinth, hMPZL2Q74X/Q74X , biol rep 3

description: Library name: HOMO_3


title: cochlear mambranous labyrinth, hMPZL2Q74X/Q74X , biol rep 1

description: Library name: HOMO_1


title: cochlear mambranous labyrinth, treated hMPZL2Q74X/Q74X, biol rep 1

description: Library name: treated_1

value: treated hMPZL2Q74X/Q77X


title: MIA PaCa-2_DMPatA_rep2


title: hpl-2-FFAA(px112)_4


title: MEF-silencer-output1_MEF-silencer-output1-13


title: MIA PaCa-2_DMPatA_rep1


title: MEF-silencer-output1_MEF-silencer-output1-12


title: MEF-silencer-output2_MEF-silencer-output2-2


title: hpl-2-FFAA(px112)_3


title: undiff SC mRNA biol rep 1

description:
Library name: Sample 1
Leyla Esfandiari_PE500_PE503_PE504_Project 9987 LE4
salmon.merged.gene_counts.tsv

value: Primary Rat Schwann cells (RSC) (Catalog R842-05a)

value: Schwann cell undifferentiation


title: cochlear mambranous labyrinth, Mpzl2 WT, biol rep 3

description: Library name: WT_3

value: Mpzl4 WT


title: cochlear mambranous labyrinth, Mpzl2 WT, biol rep 2

description: Library name: WT_2

value: Mpzl3 WT


title: MIA PaCa-2_romi_rep3

value: romidepsin


title: hpl-2-FFAA(px112)_2


title: MEF-silencer-output1_MEF-silencer-output1-11


title: met-2(n4256) hpl-2(tm1489)_2


title: MIA PaCa-2_romi_rep2


title: cochlear mambranous labyrinth, Mpzl2 WT, biol rep 1

description: Library name: WT_1

value: Mpzl2 WT


title: hpl-2-FFAA(px112)_1


title: MEF-silencer-output1_MEF-silencer-output1-10


title: hpl-2(tm1489)_4


title: MIA PaCa-2_romi_rep1


title: MEF-silencer-output1_MEF-silencer-output1-9


title: MEF-silencer-output1_MEF-silencer-output1-8


title: MIA PaCa-2_romi_DMPatA_rep3

value: romidepsin+DMPatA


title: hpl-2(tm1489)_3

value: embryo


title: LSK, ND, IgG, rep4

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio

description: Library name: LSK_ND_IgG_rep4

data_processing:
Paired-end FASTQ files were processed using the nf-core-cutandrun pipeline (v3.0).
Adapter sequences were removed with Trim Galore.
Reads were aligned with Bowtie2 to GRCm39 (NCBI, release 109) and duplicates were removed for only control samples using picard6.
Generally speaking, "peaks" refer to regions where at least one of the target samples significantly exceeds its matched control for a given genomic region. Here, peaks were called with seacr (normalization mode: CPM).
Peaks were defined as regions where at least one of the target samples significantly exceeds its matched IgG control for a given genomic region. Consensus peaks were merged across all samples using BEDTools and annotated to the nearest gene transcriptional start site using HOMER.
Peak counts were generated using featureCounts.
Downstream analysis was performed using Pluto Bio software (https://pluto.bio).
Assembly: GRCm39
Supplementary files format and content: comma-delimited text files include consensus peak counts for each Sample
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: LSK

growth_protocol: The male B6 mice were fed by either high fat (60% kcal) or low fat (10% kcal) diet from 4 week-old to 20 week-old of age.

extract_protocol:
The bone marrow cells were isolated and separated by magnetic sorting and subsequently further sorted by flow cytometory sorting. Cells were collected in 30% fetal bovine serum containing RPMI media. After washing, nucleus is isolated followed by CUT&Tag using a custom kit.
We performed CUT&Tag using a modified protocol based on Kaya-Okur et al. (2019) and consults with Dr. Henikoff (Fred Hutch). Approximately 10,000 cells were incubated with primary antibodies, followed by secondary antibodies and pA-Tn5 fusion protein. After tagmentation, DNA was extracted and amplified by PCR for 14 cycles. Libraries were sequenced on an Illumina NextSeq 2000 platform with paired-end 75 bp reads.

value: LSK

tag: cut&tag antibody

value: IgG

tag: diet

value: ND

tag: plx259429 sample_id


title: MIA PaCa-2_romi_DMPatA_rep2


title: LSK, HFD, IgG, rep7

description: Library name: LSK_HFD_IgG_rep7

value: HFD


title: MIA PaCa-2_romi_DMPatA_rep1

value: MIA PaCa-2


title: MEF-silencer-output1_MEF-silencer-output1-7

value: MEFs


title: LSK, ND, H3K4me3, rep8

description: Library name: LSK_ND_H3K4me3_rep8

tag: plx259429 input_control


title: MEF-silencer-output1_MEF-silencer-output1-6


title: MIA PaCa-2_ctl_rep3

value: pancreatic cancer cell line

value: vehicule control


title: wild-type_3

value: yeast cells

value: wild-type (N2 Bristol)


title: LSK, ND, H3K4me3, rep4

description: Library name: LSK_ND_H3K4me3_rep4


title: MEF-silencer-output1_MEF-silencer-output1-5


title: MEF-silencer-output1_MEF-silencer-output1-4


title: MIA PaCa-2_ctl_rep2


title: GMP, ND, H3K4me3, rep8

description: Library name: GMP_ND_H3K4me3_rep8

source_name: GMP

value: GMP

tag: plx176062 sample_id

tag: plx176062 input_control


title: LSK, ND, IgG, rep8

description: Library name: LSK_ND_IgG_rep8


title: GMP, ND, IgG, rep8

description: Library name: GMP_ND_IgG_rep8


title: MEF-silencer-output1_MEF-silencer-output1-2


title: GMP, HFD, H3K4me3, rep8

description: Library name: GMP_HFD_H3K4me3_rep8


title: WTcornLightD

city: seattle

first: Ethan

middle: D

last: Buhr

state: WA

address: 750 Republican St

department: Ophthalmology

institute: University of Washington

description: Library name: Sample 8

data_processing:
Barcoded libraries are pooled using liquid handling robotics prior to loading. Massively parallel sequencing-by-synthesis with fluorescently labeled, reversibly terminating nucleotides is carried out on the Dnb machine
Assembly: Gene level expression quantification is generated with RNA-SeQC (v2.3.3) and RSEM (v1.3.1). RPKM and TPM for transcript isoforms are quantitated on the merged lane-level data with RSEM (v1.3.1). Gene-level RPKMs are quantitated with RNA-SeQC (v2.3.3) on a standard collapsed reference annotation.
Supplementary files format and content: FASTQ
Supplementary files format and content: xls

source_name: cornea

extract_protocol:
Total RNA was extracted using Qiagen RNAeasy kit.
Total RNA is normalized to 30ng/ul in a total volume of 10ul on the Perkin Elmer Janus Workstation (Perkin Elmer, Janus II).  Ribosomal depletion via hybridization and cDNA synthesis are performed using the TruSeq Stranded Total RNA LP Globin kit as outlined by the manufacturer (Illumina, cat#20020612).  All steps are automated on the Perkin Elmer Sciclone NGSx Workstation to reduce batch to batch variability and to increase sample throughput.  Final RNASeq libraries are quantified using the Quant-it dsDNA High Sensitivity assay, and library insert size distribution is checked using a fragment analyzer (Advanced Analytical; kit ID DNF474).  Samples where adapter dimers constitute more than 4% of the electopherogram area are failed prior to sequencing.  Technical controls (K562,Thermo Fisher Scientific, cat# AM7832), are compared to expected results to ensure that batch to batch variability is minimized.  Successful libraries are normalized to 10nM for submission to sequencing.

treatment_protocol: Corneas were given an epithelial debridement 12 hours before collection. They were immediately flash frozen.

value: cornea

value: whole tissue

value: wild-type

value: epithelial debridement

tag: batch

value: 12 hour post wound


title: MIA PaCa-2_ctl_rep1


title: MEF-silencer-output1_MEF-silencer-output1-1


title: WTcornLightC

description: Library name: Sample 7


title: LSK, ND, IgG, rep2

description: Library name: LSK_ND_IgG_rep2

tag: plx032702 sample_id


title: MEF-silencer-output1_MEF-silencer-output1-3


title: WTcornLightB

description: Library name: Sample 6


title: wild-type_1

value: embryo


title: LSK, HFD, H3K4me3, rep7

description: Library name: LSK_HFD_H3K4me3_rep7

value: LSK


title: KLM_DMPatA_rep3

source_name: KLM

value: KLM

value: DMPatA


title: hPGK-mouse-input_hPGK-mouse-input-20

description:
mESCs_silencer.bed
MEFs_silencer.bed

source_name: mESCs

value: mESCs


title: LSK, ND, IgG, rep1

description: Library name: LSK_ND_IgG_rep1

value: IgG

value: ND


title: hpl-2(tm1489)_2


title: KLM_DMPatA_rep2

value: pancreatic cancer cell line


title: KLM_romi_rep3

value: romidepsin


title: hPGK-mouse-input_hPGK-mouse-input-18

description:
mESCs_silencer.bed
MEFs_silencer.bed


title: O5cornLightC

description: Library name: Sample 3


title: KLM_romi_rep1


title: KLM_DMPatA_rep1


title: hPGK-mouse-input_hPGK-mouse-input-17

description:
mESCs_silencer.bed
MEFs_silencer.bed


title: KLM_romi_DMPatA_rep3

value: romidepsin+DMPatA


title: hpl-2(tm1489)_1

value: yeast cells


title: wild-type_2

value: wild-type (N2 Bristol)


title: WTcornLightA

description: Library name: Sample 5

value: cornea


title: KLM_romi_DMPatA_rep2


title: KLM_romi_DMPatA_rep1


title: LSK, HFD, H3K4me3, rep2

description: Library name: LSK_HFD_H3K4me3_rep2

value: HFD

tag: plx032702 input_control


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 078

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_078
sci-RNA-seq3
L1_rice_combined.RData

data_processing:
Demultiplexing, barcoded processing, and gene counting were preformed using the Cell Ranger software. Data filtering was performed with Seurat
Assembly: Os-Nipponbare-Reference-IRGSP-1.0  and Sorghum bicolor v3.0.1
Supplementary files format and content: Seurat object
Library strategy: sci-RNA-seq3

molecule: nuclear RNA

organism: Sorghum bicolor

source_name: seedling

growth_protocol: 5 day old seedlings grown on soil were exposed to light and harvested at different time points during de-etiolation.

extract_protocol:
Frozen tissue from each time point was crushed using a bead bashing approach, and nuclei released from homogenate by resuspending in Nuclei Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2). The resulting suspension was passed through a 30-um filter. To enrich the filtered solution for nuclei, an Optiprep (Sigma) gradient was used. Enriched nuclei were then stained with Hoechst, before being FACS purified.
Library construction was performed according to the manufacturer's specification (Chromium Next GEM Single Cell 3' HT Kit v3.0, 10x Genomics)

tag: tissue

value: seedling


title: hPGK-mouse-input_hPGK-mouse-input-19

description:
mESCs_silencer.bed
MEFs_silencer.bed

tag: cell line


title: O5cornLightB

description: Library name: Sample 2

value: whole tissue

value: epithelial debridement


title: GMP, ND, IgG, rep1

description: Library name: GMP_ND_IgG_rep1

tag: cell type

value: GMP


title: LSK, HFD, IgG, rep2

description: Library name: LSK_HFD_IgG_rep2

value: LSK


title: B_IFNa

city: London

first: Efstathios

last: Giotis

address: Norfolk Place

department: Infectious Diseases

country: United Kingdom

institute: Imperial College London

data_processing:
Sequencing data (Fastq raw files) were imported into Partek Flow (version 10.0, build 10.0.23.0531; Partek Inc., St. Louis, MO, USA), quality-controlled, and thereafter processed.
Paired-end reads were trimmed based on the Phred quality score threshold of >20 and aligned to the human genome (hg38) with the STAR - 2.7.8a aligner.
Quantification was done using the transcript model Ensembl Transcripts release 104 v2, subsequently normalised by the median ratio method.
Differential expressed genes were identified with the DESeq2 package.
Genes were called differentially expressed if FDR < 0.05, and fold change ≥ 2 or ≤ -2.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file include output of DESeq2 analysis of the virus-infected versus mock samples comparison (total counts per gene, FDR, fold change of gene expression).

source_name: hNECs stimulated with IFNa

growth_protocol: Primary human nasal epithelial cells (hNECs) cultured under air–liquid interface conditions were purchased from Epithelix and maintained in Mucilair cell culture medium (Epithelix). Cells were grown and infected at 5% CO2, 37oC.

extract_protocol:
RNA was harvested using the Rneasy Mini Plus Kit (Quiagen). A total of ~1ug of RNA was used for construction of sequencing libraries.
According to the manufacturers protocol (Novogene): Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina NovaSeq 6000, according to effective library concentration and data amount.
Library preparation and sequencing was performed by Novogene (mRNA library preparation (poly A enrichment))

treatment_protocol: Before infection or stimulation, hNECs were washed with serum-free DMEM (Gibco) for 10 min at 37oC to remove mucus. Cells were infected with 200 µL of virus-containing serum-free DMEM and incubated at 37oC for 1 h. Inoculum was then removed, and cells were washed twice. Cells stimulated with recombinant interferon alpha (IFNa; 1000 U/ml) for 24 hours were also included as a positive control to ensure the immune responsiveness of the cells.

value: Primary cells

value: Nasal epithelial cells

value: WT

tag: treatment

value: Stimulated


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 074

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_074
sci-RNA-seq3
L1_rice_combined.RData


title: KLM_romi_rep2

value: KLM


title: O5cornLightD

description: Library name: Sample 4

tag: genotype

value: 12 hour post wound


title: LSK, HFD, H3K4me3, rep1

description: Library name: LSK_HFD_H3K4me3_rep1


title: A_IFNa


title: LSK, HFD, IgG, rep1

description: Library name: LSK_HFD_IgG_rep1

value: IgG


title: GMP, ND, H3K4me3, rep1

description: Library name: GMP_ND_H3K4me3_rep1

value: ND


title: LSK, ND, H3K4me3, rep2

description: Library name: LSK_ND_H3K4me3_rep2


title: hPGK-mouse-input_hPGK-mouse-input-16

description:
mESCs_silencer.bed
MEFs_silencer.bed

value: mESCs


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 075

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_075
sci-RNA-seq3
L1_rice_combined.RData

tag: age


title: KLM_ctl_rep1

value: pancreatic cancer cell line

value: vehicule control


title: LSK, ND, H3K4me3, rep1

description: Library name: LSK_ND_H3K4me3_rep1


title: hPGK-mouse-input_hPGK-mouse-input-15

description:
mESCs_silencer.bed
MEFs_silencer.bed


title: hPGK-mouse-input_hPGK-mouse-input-14

description:
mESCs_silencer.bed
MEFs_silencer.bed


title: GMP, HFD, IgG, rep2

description: Library name: GMP_HFD_IgG_rep2

value: HFD


title: KLM_ctl_rep3


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 077

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_077
sci-RNA-seq3
L1_rice_combined.RData

value: seedling


title: C_BA5_72

source_name: hNECs infected with Omicron BA.5

value: Infected


title: GMP, HFD, H3K4me3, rep2

description: Library name: GMP_HFD_H3K4me3_rep2


title: hPGK-mouse-input_hPGK-mouse-input-7

description:
mESCs_silencer.bed
MEFs_silencer.bed


title: GMP, HFD, IgG, rep1

description: Library name: GMP_HFD_IgG_rep1


title: hPGK-mouse-input_hPGK-mouse-input-13

description:
mESCs_silencer.bed
MEFs_silencer.bed


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 070

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_070
sci-RNA-seq3
L1_rice_combined.RData


title: hPGK-mouse-input_hPGK-mouse-input-12

description:
mESCs_silencer.bed
MEFs_silencer.bed


title: GMP, ND, IgG, rep2

description: Library name: GMP_ND_IgG_rep2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 076

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_076
sci-RNA-seq3
L1_rice_combined.RData


title: GMP, ND, H3K4me3, rep2

description: Library name: GMP_ND_H3K4me3_rep2


title: hPGK-mouse-input_hPGK-mouse-input-11

description:
mESCs_silencer.bed
MEFs_silencer.bed


title: O5cornLightA

description: Library name: Sample 1

value: cornea

value: whole tissue

value: epithelial debridement


title: hPGK-mouse-input_hPGK-mouse-input-5

description:
mESCs_silencer.bed
MEFs_silencer.bed


title: KLM_ctl_rep2


title: hPGK-mouse-input_hPGK-mouse-input-10

description:
mESCs_silencer.bed
MEFs_silencer.bed


title: C_BA5_24

value: Primary cells


title: hPGK-mouse-input_hPGK-mouse-input-4

description:
mESCs_silencer.bed
MEFs_silencer.bed


title: A_BA5_24

value: Nasal epithelial cells


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 073

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_073
sci-RNA-seq3
L1_rice_combined.RData


title: hPGK-mouse-input_hPGK-mouse-input-9

description:
mESCs_silencer.bed
MEFs_silencer.bed


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 072

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_072
sci-RNA-seq3
L1_rice_combined.RData


title: hPGK-mouse-input_hPGK-mouse-input-8

description:
mESCs_silencer.bed
MEFs_silencer.bed


title: C_BA1_72

source_name: hNECs infected with Omicron BA.1

value: WT


title: B_BA5_72


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 066

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_066
sci-RNA-seq3
L1_rice_combined.RData


title: chrX-KO_H1_biol_rep_2

city: Berlin

first: Amit

last: Pande

address: Robert-Rössle-Straße 10

institute: Max Delbruck Center for Medicine

description:
Library name: KO2
rRNA deplted

data_processing:
Sequenced libraries were filtered for quality with fastp in default parameter setting. Expression was quantified with kallisto by ‘kallisto quant –bias‘. GENCODE version 44 transcriptome annotation and  hg38 genome assembly  were used for indexing transcripts with ‘kallisto index –make-unique’. TPMs were converted to gene level counts with tximport. DESeq2 was used for differential expression analysis between KO and control samples.
genes with p-adj value < 0.05 were considered significant
presence of genes specific for molecular processes (EMT, defence etc) was marked in the additional, process-specific columns
Assembly: hg38
Supplementary files format and content: tab separated values for each gene, differentially expressed between chrX-KO_H1 and chrX-ctrl_H1

growth_protocol: full mTESR media, vitronectin coating, passaging in clumps with versene

extract_protocol:
Direct-zol RNA Miniprep (Zymo Research), in column DNAse treatment
Illumina Stranded Total RNA protocol

value: human embryonic stem cells

value: knock out

value: differentiated cells

value: replicate 2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 071

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_071
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 065

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_065
sci-RNA-seq3
L1_rice_combined.RData


title: hPGK-mouse-input_hPGK-mouse-input-1

description:
mESCs_silencer.bed
MEFs_silencer.bed


title: hPGK-mouse-input_hPGK-mouse-input-6

description:
mESCs_silencer.bed
MEFs_silencer.bed


title: chrX-KO_H1_biol_rep_1

description:
Library name: KO1
rRNA deplted

treatment_protocol: Direct-zol RNA Miniprep (Zymo Research), in column DNAse treatment

value: replicate 1


title: GMP, HFD, H3K4me3, rep1

description: Library name: GMP_HFD_H3K4me3_rep1

value: GMP


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 064

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_064
sci-RNA-seq3
L1_rice_combined.RData


title: DSS_TGM2neg_CD45

description: 10x genomics

data_processing:
Processing was performed with the 10X Chromium cellranger pipeline version 6.0.1 using default settings
Assembly: mm10
Supplementary files format and content: Supplementary files format and content: tsv.gz of Filtered feature-barcode matrix with raw counts for each sample

source_name: Colon

extract_protocol:
Using the Chromium Single Cell 3′ Reagent Kit v2 or v3User Guide, single cell suspensions were partitioned into nanoliter droplets called Gel-bead-in-Emulsions (GEMs) to achieve single cell resolution. The cDNA generated within each individual GEM is tagged with a common 16nt 10x barcode and a 12nt unique molecular barcode during the RT reaction. Purified cDNA was amplified for 11 cycles before being purified using SPRIselect beads. Samples were then run on a Agilent Bioanalyzer to determine cDNA concentration. 10uL of purified cDNA was used to generate the Illumina library for sequencing.
For sample preparation on the 10x Genomics platform, the Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 16 rxns (PN-1000075), Chromium Chip B Single Cell Kit, 48 rxns (PN-1000073) and Chromium i7 Multiplex Kit (PN-120262) were used. The single cell libraries were then sequenced on the Illumina NovaSeq 6000 S4 200 cycle flow cell generating 28x98 reads. A median sequencing depth of 50,000 reads/cell was targeted for each sample.

value: Colon

value: CD45 positive immune cells

value: wild type

value: DSS treatment with TGM2 negtive cells transferred


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 069

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_069
sci-RNA-seq3
L1_rice_combined.RData

value: seedling


title: chrX-KO_H1_biol_rep_5

description:
Library name: KO5
rRNA deplted

value: replicate 5


title: B_BA5_24

value: Infected


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 068

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_068
sci-RNA-seq3
L1_rice_combined.RData


title: B_BA1_24


title: A_BA1_24


title: A_BA5_72


title: chrX-KO_H1_biol_rep_4

description:
Library name: KO4
rRNA deplted

value: replicate 4


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 067

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_067
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 060

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_060
sci-RNA-seq3
L1_rice_combined.RData


title: hPGK-mouse-input_hPGK-mouse-input-3

description:
mESCs_silencer.bed
MEFs_silencer.bed

value: mESCs


title: hPGK-mouse-input_hPGK-mouse-input-2

description:
mESCs_silencer.bed
MEFs_silencer.bed


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 059

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_059
sci-RNA-seq3
L1_rice_combined.RData


title: A_BA1_72

value: Primary cells

value: Nasal epithelial cells


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 063

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_063
sci-RNA-seq3
L1_rice_combined.RData


title: chrX-KO_H1_biol_rep_3

description:
Library name: KO3
rRNA deplted

value: human embryonic stem cells

value: replicate 3


title: C_BA1_24

value: WT


title: B_BA1_72


title: chrX-ctrl_H1_biol_rep_4

description:
Library name: ctrl4
rRNA deplted

value: differentiated cells


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 058

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_058
sci-RNA-seq3
L1_rice_combined.RData


title: DSS_TGM2pos_CD45

description: 10x genomics

value: DSS treatment with TGM2 positive cells transferred


title: i11w-mNC iNeurons, BORCS6 sgRNA sample 1

city: Rockville

first: Veronica

last: Ryan

state: MD

address: 9000 Rockville Pike

department: Center for Alzheimer's and Related Dementias, Alzheimer's and Related Dementias Independent Scholar

institute: National Institute on Aging

description: Library name: KD1

data_processing:
Fastq files were quality inspected using the FastQC (https://www.bioinformatics.babraham.ac.uk) and MultiQC (https://multiqc.info) tools. For reference mapping (hg38) and gene length adjusted count enumeration, the nf-core RNA-Seq pipeline (v3.10.1) was used (https://nf-co.re/rnaseq) in conjunction with select parameters (--clip_r1 10 --clip_r2 10).
Assembly: hg38
Supplementary files format and content: csv, gene-length adjusted counts, gene symbols

source_name: i11w-mNC (derivative of WTC11)

growth_protocol: iPSCs were grown as established in Essential 8 media. sgRNAs were transduced and iPSCs were selected for cells with successful transduction. Cells were split with accutatse and replated in doxycycline-containing induction media to initiate neuronal differentation, as established. On d3 post dox induction, neurons were replated to final plate in neuron maturation media, also containing dox. On day 7 post dox induction, neurons were harvested.

extract_protocol:
RNA was extracted using the Zymo Direct-zol-96 MagBead RNA kit, following manufacturer's instructions and using a Kingfisher APEX for magnetic steps.
Strand-Specific RNA-seq library preparation was performed with rRNA depletion using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and the NEBNext Globin & rRNA Depletion Kit.

value: i11w-mNC (derivative of WTC11)

value: iNeuron

value: BORCS6 KD

value: iNeuron differentation (d7 post dox)


title: B_Delta_24

source_name: hNECs infected with Delta


title: chrX-ctrl_H1_biol_rep_3

description:
Library name: ctrl3
rRNA deplted


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 061

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_061
sci-RNA-seq3
L1_rice_combined.RData


title: chrX-ctrl_H1_biol_rep_2

description:
Library name: ctrl2
rRNA deplted

value: replicate 2


title: WT_CD45

description: 10x genomics

value: Colon

value: CD45 positive immune cells

value: wild type

value: Control


title: DSS_CD45

description: 10x genomics

value: DSS treatment


title: chrX-ctrl_H1_biol_rep_1

description:
Library name: ctrl1
rRNA deplted

value: replicate 1


title: B_Delta_72

value: Primary cells

value: Nasal epithelial cells

value: Infected


title: CMOTagLibrary

city: Bochum

first: Carlos

last: Plaza Sirvent

address: Universitätstr. 150

institute: Ruhr University Bochum

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing and gene counting were made using CellRanger multi software (cellranger-7.0.0, 10x Genomics).
Assembly: mm10, refdata-cellranger-mm10-3.0.0
Supplementary files format and content: matrix file (h5, 10X Genomics), rds file (seurat object)

source_name: CMOTagOligo

extract_protocol:
RNAesay (Qiagen)
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 3'v3.1 + Cell Surface Protein (Dual Index), 10x Genomics). Cellular mRNA and Cell Multiplexing Oligos(CMO) were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were amplified by PCR according to the Chromium Single Cell 3’ v3.1 protocol.

value: CMOTagOligo


title: 48pos

data_processing:
Before alignment to reference genome each sequence in the raw FASTQ files were trimmed on base call quality and sequencing adapter contamination using Trim Galore! wrapper tool. Reads shorter than 20 bp were removed from FASTQ file. Trimmed reads were aligned to the reference genome using open source short read aligner STAR (https://code.google.com/p/rna-star/) with settings according to log file. Feature counts were determined using R package “Rsubread”.
Assembly: mm10
Supplementary files format and content: raw counts, Excel format

source_name: Spleen and lymph nodes

extract_protocol:
RNAesay (Qiagen)
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany). The RNA sequencing library was generated from 100ng total RNA using NEBNext Single Cell/Low Input RNA Library Prep (New England BioLabs) according to manufacture´s protocols.

value: Spleen and lymph nodes

value: CD4+ CD25+ Treg cells

value: Ripk1 -/-


title: i11w-mNC iNeurons, BORCS6 sgRNA sample 6

description: Library name: KD6

value: i11w-mNC (derivative of WTC11)

value: iNeuron


title: A_Delta_72

value: WT


title: RIPK1

description: 10x Genomics


title: i11w-mNC iNeurons, BORCS6 sgRNA sample 2

description: Library name: KD2

value: BORCS6 KD

value: iNeuron differentation (d7 post dox)


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 057

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_057
sci-RNA-seq3
L1_rice_combined.RData

value: seedling


title: 53pos


title: i11w-mNC iNeurons, non-targeting sgRNA sample 1

description: Library name: NT1

value: NT


title: C_Delta_24


title: B_Beta_72

source_name: hNECs infected with Beta


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 062

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_062
sci-RNA-seq3
L1_rice_combined.RData


title: A_Beta_72


title: A_Delta_24


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 056

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_056
sci-RNA-seq3
L1_rice_combined.RData


title: 53neg


title: i11w-mNC iNeurons, non-targeting sgRNA sample 6

description: Library name: NT6


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 052

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_052
sci-RNA-seq3
L1_rice_combined.RData


title: A_Beta_24


title: i11w-mNC iNeurons, non-targeting sgRNA sample 3

description: Library name: NT3


title: C_Beta_72


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 053

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_053
sci-RNA-seq3
L1_rice_combined.RData


title: 48neg


title: i11w-mNC iNeurons, non-targeting sgRNA sample 2

description: Library name: NT2


title: HMEC-1, DDP1

city: Chengdu

first: Fangqi

last: Jing

address: No14, the third part ren min road, wuhou district

institute: West China Hospital of Stomatology

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 system by OE Biotech Co., Ltd. (Shanghai, China).
Assembly: GRCh38
Supplementary files format and content: The processed data files are provided in tab-delimited text format.

growth_protocol: HMEC-1 were cultured in complete growth medium for HMEC-1 (Procell, CM-0576, China) and were maintained at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions.
Transcriptome libraries were constructed following the protocols provided with the VAHTS Universal V5 RNA-seq Library Prep Kit.

treatment_protocol: Exposed to 0 μg/ml (control) and 1 μg/ml cisplatin for 48 hours and changed into complete medium without cisplatin. HMEC-1 was characterized by analysis of typical senescence phenotypes.

value: Human microvascular endothelium endothelial cells

value: cisplatin (DDP)


title: C_Alpha_72

source_name: hNECs infected with Alpha


title: 46pos


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 054

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_054
sci-RNA-seq3
L1_rice_combined.RData


title: B_Beta_24


title: 46neg


title: 21pos


title: HMEC-1, DDP3


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 051

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_051
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 055

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_055
sci-RNA-seq3
L1_rice_combined.RData


title: B_Alpha_72


title: HMEC-1, DDP2


title: GBM mouse treated with IFN - rep3

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger v7.2.0 software (10X Genomics)
Assembly: mm10
Supplementary files format and content: Tab-separated features and barcodes, and matrix of each sample

source_name: GBM Brain Tumor

extract_protocol:
After tumor dissociation, sample processing and staining were performed at 4°C. Cells were stained with anti-mouse FcγIII/II receptor (CD16/CD32) blocking antibody (1:100 dilution) for 10 minutes and then incubated in the presence of ⍺CD45.2-PB and ⍺CD45.1-APC-Cy7 antibodies for 30 minutes in the dark. 7-AAD was added to each sample just before sorting to label dead cells. CD45.2+ adoptive and both CD45.1+ and CD45.1+/CD45.2+ endogenous immune cells were then sorted using a BD FACSAria Fusion Cell Sorter (BD Biosciences), resuspended in 1% BSA-PBS at a concentration of 1000 cells/µL.
Library was constructed using a microfluidics-based approach on Chromium Controller (10X Genomics) using the Chromium Next-GEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics) according to the manufacturer’s instructions. Briefly, 16500 cells were added to each channel to achieve a recovery rate of 10000 cells per sample. Cells were partitioned in Gel Beads in Emulsion (GEMs, 10X Genomics) and lysed, followed by RNA barcoding, reverse transcription and PCR amplification (12 cycles). The concentration and size distribution of the scRNAseq libraries were determined using 4200 TapeStation system (Agilent).

value: GBM Brain Tumor

value: Immune inflitrate

value: IFN


title: GBM mouse treated with IFN - rep2


title: 21neg


title: GBM mouse treated with IFN - rep1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 047

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_047
sci-RNA-seq3
L1_rice_combined.RData


title: HMEC-1, control3


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 050

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_050
sci-RNA-seq3
L1_rice_combined.RData


title: A_Alpha_72

value: Primary cells

value: Nasal epithelial cells

value: Infected


title: HMEC-1, control2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 048

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_048
sci-RNA-seq3
L1_rice_combined.RData


title: HMEC-1, control1


title: B_Alpha_24


title: HUVEC, DDP3

source_name: Umbilical vein

growth_protocol: HUVECs were cultured in DMEM supplemented with 10% FBS and were maintained at 37°C in a humidified atmosphere containing 5% CO₂.

treatment_protocol: Exposed to 0 μg/ml (control) and 1 μg/ml cisplatin for 48 hours and changed into complete medium without cisplatin. HUVECs was characterized by analysis of typical senescence phenotypes.

value: HUVEC

value: Human umbilical vein endothelial cells


title: A_Alpha_24


title: GBM mouse treated with IFN+oIL2 - rep3


title: GBM mouse treated with IFN+oIL2 - rep1


title: D_IC19_72

source_name: hNECs infected with IC19


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 046

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_046
sci-RNA-seq3
L1_rice_combined.RData


title: GBM mouse treated with oIL2 - rep3


title: F_IC19_72


title: GBM mouse treated with IFN+oIL2 - rep2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 045

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_045
sci-RNA-seq3
L1_rice_combined.RData


title: HUVEC, DDP2


title: E_IC19_72


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 042

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_042
sci-RNA-seq3
L1_rice_combined.RData


title: GBM mouse treated with oIL2 - rep2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 049

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_049
sci-RNA-seq3
L1_rice_combined.RData


title: HUVEC, DDP1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 044

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_044
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 040

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_040
sci-RNA-seq3
L1_rice_combined.RData


title: D_IC19_24


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 039

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_039
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 043

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_043
sci-RNA-seq3
L1_rice_combined.RData


title: HUVEC, control3


title: GBM mouse treated with Empty LV - rep1

value: Empty


title: HUVEC, control2


title: C_IC19_72


title: Pooled WT colon scRNA-seq

city: Novato

first: Daniel

middle: A

last: Winer

address: 8001 Redwood Blvd

institute: Buck Institute for research in Aging

description: 10X genomics

data_processing:
The resulting sequencing data was processed using Cell Ranger (6.0.1).
Assembly: mm10
Supplementary files format and content: Comma-separated values files

extract_protocol:
Single cell suspensions of colons from 9-month-old littermate WT and 5XFAD female mice were generated using a lamina propria dissociation kit (Miltenyi Biotec, 130-097-410) with the gentleMACS Dissociator (Miltenyi Biotec, 130-093-235). Cells were stained with LIVE/DEAD Fixable Blue cell stain (Thermofisher, L23105) for viability assessment and blocked with FcBlock with CD16/32 (Biolegend, 101320). Cells were then stained with anti-mouse CD45 (Biolegend, 30-F11). Live CD45+ cells were sorted using the FACS Aria sorter at the Buck Institute for Aging Research flow cytometry core facility and collected into RPMI-1640 (Wisent) with 10% FBS (Wisent).
Samples were processed utilizing a Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1. The resulting libraries were sequenced at UC Davis Genome Center Bioinformatics Core using Illumina NovaSeq 6000 sequencing.

value: Colon

value: 9 months

value: Immune cells CD45+

value: 3 mice pooled


title: M120 colonised poplar root 1

city: Champenoux

first: Annegret

last: Kohler

address: Centre Grand Est Nancy

institute: INRAE

description:
Library name: M120_ECM_1
This sample ist from P.microcarpus strain M120 colonised poplar roots. It is the first of three biological replicates used in this experiment.

data_processing:
Illumina software was used by the Genotoul sequencing facilities (Toulouse, France) to generate fastq raw data files.
raw reads were paired, trimmed (quality limit=0.05, automatic read through adapter trimming, discard short reads) and mapped against Pisolithus microcarpus 441  v2 primary scaffolds transcripts (https://mycocosm.jgi.doe.gov/Pismi2/Pismi2.home.html) using CLC Genomics Workbench v23.0.5 (Qiagen, Courtaboeuf, France).
For mapping, the minimum length fraction was 0.9, the minimum similarity fraction 0.8, and the maximum number of hits for a read was set to 10.
Differentially expressed genes (DEGs) were calculated using DESeq2 (v1.32) and unique mapped gene reads as entry .
Condition-specific differentially expressed genes (DEGs) were identified for each pairwise condition, using a false discovery rate (FDR) < 0.05 and a log2 fold-change (Log2FC) ≥ |1| as cut-off.
Assembly: https://mycocosm.jgi.doe.gov/Pismi2/Pismi2.home.html
Supplementary files format and content: tab-delimited text files include Protein ID, raw counts, RPKM, TPM and CPM values for each sample

organism: Pisolithus microcarpus

source_name: colonised poplar root

growth_protocol: In vitro interactions were established between the hybrid poplar clone and parental dikaryon and sibling monokaryons of P. microcarpus. The MMN medium used had low phosphorus and nitrogen content and was lined with cellophane membranes. Ten to twelve agar discs containing fungal mycelia were placed on cellophane membranes and kept at 25°C for 20 days. Two poplar plants were transferred to the fungal mycelium. Petri dishes were incubated in a growth chamber at 25°C with 16 h of light per day for 30 days. Fungal controls (free-living mycelium, FLM) were included in the experiment. Minimum three replicates were performed for each isolate.

extract_protocol:
Total RNAs was extracted from ECM tissues and FLM of the parental dikaryon (D002) and three selected monokaryons (M057, M091, and M120) using a CTAB and lithium chloride-based method (Chang et al., 1993). We selected these monokaryon strains based on their ability to form ECMs with poplar clones. Total RNA was quantified, and integrity waschecked using an Experion Automated Electrophoresis Station (Bio-Rad, Hercules, CA, USA).
Preparation of libraries from total RNA (TruSeq Stranded mRNA Kit Illumina) and 2 x 125 bp Illumina HiSeq2500 sequencing was performed at the GET platform (Gé-nopole Toulouse Midi-Pyrénées, Auzeville, France) following their standard protocol.

value: colonised poplar root

tag: strain


title: M120 free-living mycelium 3

description:
Library name: M120_FLM_3
This sample ist from P.microcarpus strain M120 free-living mycelium. It is the third of three biological replicates used in this experiment.

source_name: free-living mycelium

value: free-living mycelium


title: Pooled 5XFAD colon scRNA-seq

description: 10X genomics


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 036

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_036
sci-RNA-seq3
L1_rice_combined.RData

value: seedling


title: B_IC19_72

value: WT

tag: time


title: HUVEC, control1


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 041

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_041
sci-RNA-seq3
L1_rice_combined.RData


title: A_IC19_72


title: M120 colonised poplar root 3

description:
Library name: M120_ECM_3
This sample ist from P.microcarpus strain M120 colonised poplar roots. It is the third of three biological replicates used in this experiment.


title: GBM mouse treated with oIL2 - rep1

value: GBM Brain Tumor


title: M120 colonised poplar root 2

description:
Library name: M120_ECM_2
This sample ist from P.microcarpus strain M120 colonised poplar roots. It is the second of three biological replicates used in this experiment.


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 034

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_034
sci-RNA-seq3
L1_rice_combined.RData


title: M091 colonised poplar root 3

description:
Library name: M091_ECM_3
This sample ist from P.microcarpus strain M091 colonised poplar roots. It is the third of three biological replicates used in this experiment.


title: GBM mouse treated with Empty LV - rep2

value: Immune inflitrate


title: D_Mock

source_name: hNECs uninfected

value: Uninfected


title: WT

city: Nanjing

first: LU

last: CHEN

address: Longmian Road 101

institute: Nanjing Medical University

description: 10× Genomics

data_processing:
Single cell RNA-seq data processing Reads were processed using the Cell Ranger 3.0.1 pipeline with default and recommended parameters. FASTQs generated from Illumina sequencing output were aligned to the mouse genome, version mm10, using the STAR algorithm. Next, Gene-Barcode matrices were generated for each individual sample by counting UMIs and filtering non-cell associated barcodes. Finally, we generate a gene-barcode matrix containing the barcoded cells and gene expression counts. This output was then imported into the Seurat (v3.0.2) R toolkit for quality control and downstream analysis of our single cell RNAseq data. All functions were run with default parameters, unless specified otherwise. We excluded cells with fewer than 200 or more than 6000 detected genes (where each gene had to have at least one UMI aligned in at least three cells). The expression of mitochondria genes was calculated using PercentageFeatureSet function of the seurat package. To remove low activity cells, cells with more than 10 percent expression of mitochondria genes were excluded. The normalized data (NormalizeData function in Seurat package) was performed for extracting a subset of variable genes. Variable genes were identified while controlling for the strong relationship between variability and average expression. Next, we integrated data from different samples after identifying ‘anchors’ between datasets using FindIntegrationAnchors and IntegrateData in the seurat package. Then we performed principal component analysis (PCA) and reduced the data to the top 30 PCA components after scaled the data. We visualized the clusters on a 2D map produced with t-distributed stochastic neighbor embedding (t-SNE). Identification of cell types and subtypes by nonlinear dimensional reduction (t-SNE) Cells were clustered using graph-based clustering of the PCA reduced data with the Louvain Method after computing a shared nearest neighbor graph. For sub-clustering, we applied the same procedure of scaled, dimensionality reduction, and clustering to the specific set of data (usually restricted to one type of cell.) For each cluster, we used the Wilcoxon Rank-Sum Test to find significant deferentially expressed genes comparing the remaining clusters. SingleR and known marker genes were used to identify cell type.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: colon

extract_protocol:
Colon tissues were transported in sterile culture dish with 10 ml 1x Dulbecco's Phosphate-Buffered Saline (DPBS; Thermo Fisher, Cat. no. 14190144) on ice to remove the residual tissue storage solution, then minced on ice. We used dissociation enzyme 0.25% Trypsin (Thermo Fisher, Cat. no.25200-072) and 10 ug/mL lDNase I (Sigma, Cat. no. 11284932001) dissolved in PBS with 5% Fetal Bovine Serum (FBS; Thermo Fisher, Cat. no. SV30087.02) to digest the tissues. Colon tissues were dissociated at 37 ℃ with a shaking speed of 50 r.p.m for about 40 min.We repeatedly collected the dissociated cells at interval of 20 min to increase cell yield and viability. Cell suspensions were filtered using a 40 um nylon cell strainer and red blood cells were removed by 1X Red Blood Cell Lysis Solution (Thermo Fisher, Cat. no. 00-4333-57). Dissociated cells were washed with 1x DPBS containing 2% FBS. Cells were stained with 0.4% Trypan blue (Thermo Fisher, Cat. no. 14190144) to check the viability on Countess® II Automated Cell Counter (Thermo Fisher).
On cDNA synthesis, each cDNA molecule was tagged on the 5’end (that is, the 3’end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Briefly, 10× beads that were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using randomly interrupted whole-transcriptome amplification products to enrich the 3’ end of the transcripts linked with the cell barcode and UMI. All the remaining procedures including the library construction were performed according to the standard manufacturer’s protocol (CG000206 RevD). Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.

value: colon


title: Foxp3YFPcreNOtch3Fl/Fl3

city: Boston

first: Mehdi

last: Benamar

state: MA

address: 1 Blackfan Circle, Karp Family Building

institute: Harvard medical school/Boston children's Hospital

description: 10X genomics

data_processing:
The Fastq data were analysis with Cell Ranger Count v7.1.0 (10x cloud analysis)
Assembly: genome used was  Mouse (mm10) 2020-A
Supplementary files format and content: processed data files contains: matrix.h5, barcodes, features and matrix.mtx

source_name: CNS

extract_protocol:
CNS Cells were cell sorted based on CD4 expression
Library construction were perforned based on Chromium Next GEM Single Cell 3ʹ v3.1: Dual Index Libraries protocol
Chromium Next GEM Single Cell 3ʹ v3.1: Dual Index Libraries

value: CNS

tag: strain _background

value: Treg Cell

value: Foxp3YFPcre NOtch3Fl/Fl

value: EAE


title: GBM mouse treated with Empty LV - rep3

value: Empty


title: C_IC19_24

value: Primary cells

value: Nasal epithelial cells

value: Infected


title: B_IC19_24


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 038

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_038
sci-RNA-seq3
L1_rice_combined.RData

source_name: seedling


title: M091 colonised poplar root 2

description:
Library name: M091_ECM_2
This sample ist from P.microcarpus strain M091 colonised poplar roots. It is the second of three biological replicates used in this experiment.


title: M120 free-living mycelium 2

description:
Library name: M120_FLM_2
This sample ist from P.microcarpus strain M120 free-living mycelium. It is the second of three biological replicates used in this experiment.


title: C_Mock


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 033

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_033
sci-RNA-seq3
L1_rice_combined.RData


title: A_IC19_24


title: B_Mock


title: M120 free-living mycelium 1

description:
Library name: M120_FLM_1
This sample ist from P.microcarpus strain M120 free-living mycelium. It is the first of three biological replicates used in this experiment.


title: E_Mock


title: A_Mock


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 035

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_035
sci-RNA-seq3
L1_rice_combined.RData


title: AD

description: 10× Genomics

value: transgenic Alzheimer's disease (AD) model


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 037

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_037
sci-RNA-seq3
L1_rice_combined.RData


title: Foxp3YFPCRE2

description: 10X genomics


title: Foxp3YFPCRE1

description: 10X genomics


title: M091 colonised poplar root 1

description:
Library name: M091_ECM_1
This sample ist from P.microcarpus strain M091 colonised poplar roots. It is the first of three biological replicates used in this experiment.

value: colonised poplar root


title: M091 free-living mycelium 3

description:
Library name: M091_FLM_3
This sample ist from P.microcarpus strain M091 free-living mycelium. It is the third of three biological replicates used in this experiment.

value: free-living mycelium


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 031

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_031
sci-RNA-seq3
L1_rice_combined.RData

value: seedling


title: M091 free-living mycelium 1

description:
Library name: M091_FLM_1
This sample ist from P.microcarpus strain M091 free-living mycelium. It is the first of three biological replicates used in this experiment.


title: M091 free-living mycelium 2

description:
Library name: M091_FLM_2
This sample ist from P.microcarpus strain M091 free-living mycelium. It is the second of three biological replicates used in this experiment.


title: TAM-OE3

city: Guanzghou

first: Zihang

last: Yu

state: Please Select

address: GuangZhou Avenue

institute: Southern Medicla University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: hg38
Supplementary files format and content: tab-delimited text files includes raw counts and TPM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
Then the enriched mRNAwasfragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).

value: monocytic leukemia cells

value: WT

value: supernatant of H1299-DCBLD2, PMA


title: M057 colonised poplar root 3

description:
Library name: M057_ECM_3
This sample ist from P.microcarpus strain M057 colonised poplar roots. It is the third of three biological replicates used in this experiment.


title: RNA_tumor_Smarca5_888

city: Beijing

first: Jing

last: Han

address: qinghuayuan

institute: Tsinghua university

data_processing:
The adaptors of paired-end reads were trimmed by trim-galore (v.0.6.4) with the parameters set as: -q 25 --phred33 --length 50 -e 0.1 --fastqc --stringency 5 --paired.
Adaptor-trimmed reads were aligned to the mm10 genome with the following parameters: --readFilesCommand zcat --outFilterMismatchNoverLmax 0.2 by STAR (v.2.7.9a)
Aligned reads stored in SAM format were converted to BAM files using SAMtools with parameter: samtools view -bS -h -F 4 -f 2 -q 7.
FeatureCounts counted reads stored in BAM format to exon sites of genes included in GTF files from Ensembl
Assembly: mm10
Supplementary files format and content: raw counts

source_name: pancreas

extract_protocol:
300 GFP-positive cells and 10,000 GFP-positive cells were sorted by FACS for small scale RNA-seq and ATAC-seq. 10% HEK-293T cells were mixed in ATAC-seq samples for spike-in normalization. ATAC-seq was performed with Chromatin Profile Kit for Illumina (Novoprotein, N248-01A). Small scale RNA-seq library was constructed using Smart-seq2 method with modifications allowing higher quality library generation from pancreatic cells. Briefly, mouse pancreatic cells were directly sorted into 8 μl of denaturing lysis buffer (6 M guanidine HCl, 0.2% (vol/vol) Triton X-100 and 1% (vol/vol) β-mercaptoethanol). RNA SPRI beads (RNA Clean XP beads, Beckman A63987) were added (2.2X) to the lysis buffer and RNA was purified, followed by library preparation by the standard Smart-seq2 protocol, except with a 12-cycle PCR pre-amplification step.
Smart-seq2 protocol.

value: pancreas

value: PDAC


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 028

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_028
sci-RNA-seq3
L1_rice_combined.RData


title: TAM-OE2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 032

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_032
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 027

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_027
sci-RNA-seq3
L1_rice_combined.RData


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 029

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_029
sci-RNA-seq3
L1_rice_combined.RData


title: TAM-OE1


title: RNA_tumor_Smarca5_893


title: Foxp3YFPcreNOtch3Fl/Fl2

description: 10X genomics

value: CNS


title: TAM-C3

value: supernatant of H1299-Control, PMA


title: M057 colonised poplar root 2

description:
Library name: M057_ECM_2
This sample ist from P.microcarpus strain M057 colonised poplar roots. It is the second of three biological replicates used in this experiment.


title: M057 colonised poplar root 1

description:
Library name: M057_ECM_1
This sample ist from P.microcarpus strain M057 colonised poplar roots. It is the first of three biological replicates used in this experiment.


title: RNA_tumor_Rosa_993

value: control


title: Foxp3YFPcreNOtch3Fl/Fl1

description: 10X genomics

value: Treg Cell

value: Foxp3YFPcre NOtch3Fl/Fl

value: EAE


title: M057 free-living mycelium 3

description:
Library name: M057_FLM_3
This sample ist from P.microcarpus strain M057 free-living mycelium. It is the third of three biological replicates used in this experiment.


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 030

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_030
sci-RNA-seq3
L1_rice_combined.RData


title: TAM-C2


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 025

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_025
sci-RNA-seq3
L1_rice_combined.RData


title: TAM-C1


title: M057 free-living mycelium 2

description:
Library name: M057_FLM_2
This sample ist from P.microcarpus strain M057 free-living mycelium. It is the second of three biological replicates used in this experiment.


title: RNA_D7_Smarca5_770

value: pancreatitis


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 024

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_024
sci-RNA-seq3
L1_rice_combined.RData


title: M057 free-living mycelium 1

description:
Library name: M057_FLM_1
This sample ist from P.microcarpus strain M057 free-living mycelium. It is the first of three biological replicates used in this experiment.


title: OE2

value: cancer cell

value: DCBLD2 overexpression


title: 7-day-old sorghum seedlings undergoing deetiolation for 48h - technical replicate 023

description:
Library name: 7_1_22_JS_Sorghum_vegetative_shoot_Light_48h_023
sci-RNA-seq3
L1_rice_combined.RData


title: RNA_D7_Smarca5_722