title: normal_Control_S7

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

data_processing:
Sequencing data was analyzed on the Galaxy web platform (usegalaxy.eu). Quality control was performed with FastQC (Galaxy Version 0.73, http://www. bioinformatics.babraham.ac.uk/projects/fastqc/, last access on 6th November 2022).
Reads were mapped to the human reference genome (Gencode, GRCh38.p13, all regions, release 42) with RNA STAR (Galaxy Version 2.7.8a, default parameters).
Reads mapped to the human reference genome were counted by featureCounts (Galaxy Version 2.0.1, default parameters).
The output of featureCounts was imported to RStudio (version 1.4.1103, R Version 4.0.3). Gene symbols and gene types were determined based on Ensembl (Release 108, download on 5 November 2022). Principal component analysis (PCA) was applied to check for potential outlier and batch effects.
Normalized reads and differential gene expression were calculated using the R package DESeq2 (version 1.34) with default parameters (Benjamini-Hochberg adjusted p-values). Transcripts with log2 fold change (log2FC) >2 or <-2 and adjusted p-value <0.05 were considered as differentially expressed genes (DEG).
Assembly: Gencode GRCh38.p13, all regions, release 42
Supplementary files format and content: csv, normalized reads (DESeq2)

source_name: cornea

extract_protocol:
A total of 14 corneal specimens from 14 patients who underwent corneal transplantation at the Eye Center of the University of Freiburg, Germany, were included in this study (Table 1). The indication for surgery was made by an experienced cornea consultant. 7 healthy corneas from 7 patients who underwent enucleation due to choroidal melanoma at our institution served as controls. After surgery, corneal tissue was immediately fixed in formalin and processed for paraffinembedding followed by routine histopathological examination. The clinical diagnosis was confirmed histologically by at least two experienced ophthalmic pathologists (Suppl. Figure 1). There was no evidence of tumor-induced alterations in any of the healthy corneal specimens. Fifteen FFPE sections, each 4 µm thick, were taken from each corneal sample and stored in RNase-free tubes prior to RNA extraction
RNA extraction from corneal samples was performed by a commercial provider (GenXPro, Frankfurt am Main, Germany). Briefly, total RNA was isolated from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, CA, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, Madison, WI, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorometer (Life Technologies, Carlsbad, CA, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, MA, USA). RNA sequencing was performed by GenXPro using massive analysis of cDNA ends (MACE), a 3′-RNA sequencing method, as previously described (Wolf et al., 2022c). We recently demonstrated that MACE allows sequencing of FFPE samples with high accuracy (Boneva et al., 2020). Briefly, barcoded libraries comprising unique molecule identifiers were sequenced on the NextSeq 500 (Illumina, San Diego, CA, USA) with 1 × 75 bp. PCR bias was removed using unique molecular identifiers.

tag: tissue

value: cornea

tag: diagnosis

value: healthy  normal control


title: normal_Control_S6

status: Public on Jan 30 2024

type: SRA

country: Germany

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens


title: normal_Control_S4


title: normal_Control_S3


title: normal_Control_S1


title: smRNA Col0_HS1

city: Davis

first: Patricia

last: Baldrich Gonzalez

state: CA

address: 451 Health Sciences Dr., Davis, CA 95616

department: Genome Center

country: USA

institute: University of California - Davis

data_processing:
we trimmed adapters and low-quality reads using Cutadapt v2.9 software (Martin, 2011) and retaining only reads between 18- and 34-nt long.
Reads were then mapped to the Arabidopsis genome version 10 (available at www.arabidopsis.org/download/) and its corresponding TAIR10 blastsets for all the features, using Bowtie2 (Langmead and Salzberg, 2012).
Assembly: Arabidopsis TAiR 10

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis seeds were surface-sterilized using ethanol and plated on MS agar (MES-buffered MS salts medium [Duchefa, Murashige & Skoog medium inc. vitamins/MES- MO255)], 1% sucrose, and 0.8% agar, pH 5.7). The seeds were then stratified for 2 days at 4°C in the dark and then transferred in 16h light/8h dark (20,5/17°C,70% humidity) growth chamber, under fluorescent light (Osram Biolux 58W/965)

extract_protocol:
Total RNA was extracted using Tri-Reagent according to the manufacturer’s instructions. For AGO1-loaded sRNA samples, AGO1-IPs were performed as described above from 1g of 1-week-old Arabidopsis seedlings grown on MS-agar plates and following similar HS and recovery treatments. AGO1-loaded sRNAs were then extracted by adding Tri-Reagent directly on the magnetic beads and extraction of RNA was performed according to the manufacturer’s instructions. RNAs were precipitated O/N at -20°C in 2 volumes of isopropanol + 40 μg glycogen as described above.
Small RNA seq libraries were generated using RealSeq v2 kit (Barberán-Soler et al., 2018), following manufacturer’s instructions, with 100ng as initial input and 15 cycles PCR amplification.

treatment_protocol: 7-day old Col-0 seedling +/- 1hour treatment at 37°C (HS) and after an additional 2H period back at 22°C (Recovery)

value: Seedlings

tag: genotype

value: Col 0

tag: developmental stage

tag: treatment

value: Heat shock

tag: ip antibody


title: normal_Control_S5


title: smRNA Col0_C3

value: Control


title: normal_Control_S2


title: Yuuki_1

city: Bethesda

first: Stefan

last: Ambs

state: MD

address: Building 37, Room 3050B

department: CCR

institute: NCI

description: Panc 10.05 control

data_processing:
mRNA-Seq samples were pooled and sequenced on NextSeq using Illumina Stranded mRNAseq ligation and paired-end sequencing. The samples have 32 to 60 million pass filter reads with more than 93% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Human - hg38) and the annotated transcripts using STAR.
The gene expression quantification analysis was performed using STAR/RSEM tools. Differential expression analysis was done using DESeq2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each Sample

source_name: Pancreatic cancer cell line

extract_protocol:
RNA isolation was done using TRIzol. Integrity of isolated RNA was evaluated with the Agilent 2100 Bioanalyzer (Agilent Technologies), and sequencing was performed on an Illumina NextSeq machine at the Sequencing Facility, Leidos Biomedical Research, Inc.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: condition

value: Panc 10.05_Ctrl_1

tag: cell lines

tag: outcome

value: Panc 10.05 control


title: smRNA Col0_C2


title: SbGhd7, Myc, Sigma, Rep 1

city: Upton

first: Meng

last: Xie

state: NY

address: 50 Bell Ave

institute: Brookhaven National Laboratory

library_source: genomic

data_processing:
Raw reads were filtered by SOAPnuke
clean reads were mapped to the reference genome Sorghum bicolor v3.1.1 (Phytozome) using BWA-MEM package (v0.7.17.2)
Mapped data of ChIP samples and Input samples from two biological replicates with >50% correlation was then pooled for peak calling using MACS2 (v2.2.7.1)
Assembly: Sorghum bicolor v3.1.1 (Phytozome)
Supplementary files format and content: narrowPeak (except for Input sample)

molecule: genomic DNA

organism: Sorghum bicolor

source_name: protoplast

growth_protocol: Freshly isolated mesophyll protoplasts, transiently expressed SbGhd7 for overnight at 24 degree

extract_protocol:
Cells were fixed with 1% formaldehyde for 8 minutes. After quenching and cell lysis, chromatin was sonicated using a Bioruptor Plus sonicator (Diagenode).
ChIP-seq libraries were prepared using the ThruPLEX DNA-Seq Kit complemented with DNA Unique Dual Index Kit (Takara). 50-100 pg of DNA was used as starting material for input and ip samples. Libraries were amplified using 18 cycles on the thermocycler. Post amplification libraries were size selected at 200-500bp in length using agarose gel. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: cell type

value: protoplast

tag: chip antibody

value: Myc (Sigma, #C3956)


title: Yuuki_8

description: Panc 10.05 ELAPOR1 transgene

value: Panc 10.05_ELAPOR1 overexpression_4

value: Panc 10.05 ELAPOR1 transgene


title: SbGhd7, Myc, Sigma, Rep 2


title: smRNA Col0_Rec3

value: Recovery


title: Bacterial_fungal_S4

value: bacterial/fungal keratitis


title: Keratoconus_S4

value: keratoconus


title: Keratoconus_S3


title: smRNA Col0_C1


title: Keratoconus_S2


title: Keratoconus_S1


title: Viral_S5

value: viral keratitis


title: SbGh7, Input, Rep 2


title: healthy, seedling, rep3

city: HangZhou

first: Xiaoqi

last: Gao

address: 548 Binwen Road, Binjiang District, Hangzhou City, Zhejiang Province

country: China

institute: zhejiang chinese medical university

data_processing:
A cDNA library was sequenced run with Illumina Novaseq 6000 sequence platform.
Firstly, Cutadapt [1] and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). including the Q20, Q30 and GC-content of the clean data.
De novo assembly of the transcriptome was performed with Trinity 2.4.0 [2]. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a 'gene'. The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).
Salmon [4] was used to perform expression level for Unigenes by calculating TPM
Assembly: de novo assembly
Supplementary files format and content: xlsx files include TPM values for each Sample

organism: Atractylodes macrocephala

source_name: Healthy seedlings of Atractylodes macrocephala

extract_protocol:
SMARTer cDNA synthesis starts with picogram amounts of total RNA or single cell/several cells. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribe™ Reverse Transcriptase reaches the 5’ end of the mRNA, the enzyme’s terminal transferase activity adds a few additional nucleotides to the 3’ end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5’ end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.
cDNA was fragmented by dsDNA Fragmentase(NEB, M0348S) by incubate at 37°C for 30min.Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand,indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR.

value: rhizome


title: healthy, seedling, rep1


title: HUVEC, siCTRL

city: Münster

first: Kai

last: Kruse

state: North Rhine-Westphalia

address: Roentgenstr. 20

department: Bioinformatics Core Facility

institute: Max Planck Institute for Molecular Biomedicine

library_source: transcriptomic single cell

data_processing:
Raw FASTQ reads were quality and adapter trimmed using TrimGalore! (version 0.6.4 length cutoff 66, quality cutoff 20).
The UMI, complex barcode, and sample tags were extracted and demultiplexed using custom scripts. The first mate (R1) in the FASTQ files contains the barcode (1-27) and UMI (28-35) of the BD Rhapsody Express experiment.
Reads were mapped to the human reference genome version GRCh38.p13, with Gencode annotations v35, and counted using STAR version 2.7.3a (--soloType Droplet –soloCellFilter None –soloFeatures Gene –soloCBstart 1 –soloCBlen 27 –soloUMIstart 28 –soloUMIlen 8 –outFilterMultimapNmax 1 –soloCBwhitelist rhapsody_whitelist.txt)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: HUVEC

growth_protocol: Human umbilical venous endothelial cells (HUVECs, Thermo Fisher, C0035C) were cultured in ECPM (endothelial cell proliferation medium) (Provitro, 211 0001) supplemented with 7% FCS, 10 µg/ml heparin, 10 ng/ml EGF, 5 ng/ml bFGF, 5 ng/ml R3-IGF-1, 0.5 ng/ml VEGF, 1 µg/ml ascorbic acid and 0.2 µg/ml hydrocortisone, and kept in a humidified incubator at 37°C, 5% CO2.

extract_protocol:
For multiplexed scRNA-sequencing of cultured ECs, HUVECs were labeled with sample tag human antibodies using the BD Human Sample Multiplexing Kit (BD Bioscience, 633781). Briefly, cells were trypsinized, centrifuged and resuspended in 2% FBS/PBS and incubated with 10 µl sample tag antibody per 1.5x10^5 cells for 20min on ice. After several washes with 2% FBS/PBS, cells were loaded into a BD Rhapsody Cartridge (BD Bioscience, 633733) and captured on the BD Rhapsody Express Single-Cell Analysis System (BD Bioscience).
Whole transcriptome mRNA and Sample Tag libraries were created using the BD Rhapsody Whole Transcriptome Analysis (WTA) Amplification Kit (BD Bioscience, 633801) and DNA sequencing was performed on a NextSeq500 (Illumina).

treatment_protocol: Cells were transfected with siRNA using Lipofectamine RNAiMAX (Invitrogen, 13778) according to the manufacturer’s protocol. siRNAs: Negative control (Ambion, 4390844), EPHB4 s244 (Ambion, 4390824), EFNB2 s4514 (4392420). After four hours the medium was changed to fresh culture medium and analysis was performed 48 h post transfection.

tag: cell line

value: HUVEC

value: siCTRL


title: Viral_S2

value: cornea


title: SbGh7, Input, Rep 1


title: Viral_S1


title: Root rot seedlings, Positive pesticide (TM) treatment, rep2

source_name: FS infects healthy Atractylodes macrocephala seedlings, followed by positive pesticide (TM) treatment, rep2

value: Positive pesticide (TM) treatment


title: CD4_T_Cells_Neonate_1_CD3CD28_RNA-seq [N2-2]

city: Cuernavaca

first: LInda

middle: AImara

last: Kempis

state: Morelos

address: Avenida Universidad 1001

department: CIDC

country: Mexico

institute: UAEM

data_processing:
The quality of the data was evaluated with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).  Adapters and low-quality sequences were trimmed or discarded using Trimmomatic. Quality check using FastQC was performed again on the trimmed sequences.
Reads were aligned to the human reference genome GRCh38/hg38 version 99 to generate the Binary Alignment Map (BAM) files with STAR (v2.4.2a).
Adaptors and low quality reads were cut using Trimmomatic version 0.39 . The reads were aligned against reference transcriptome GRCh38/hg38, using the STAR 2.4.2ª software . Read counting per gene was obtained using the software HTSeq-count. To identify differentially expressed genes, we used the DESeq2 package in R (Bioconductor).
DESeq2 (v1.27.32) was used to screen differentially expressed genes and normalization of the count data.
Assembly: hg38
Supplementary files format and content: fastq

source_name: CD4+ T cells

extract_protocol: RNA-seq libraries were constructed at the Transcriptomic & Genomic Platform Marseille Luminy (Aix-Marseille University, TAGC) using the TruSeq RNA Library Prep Kit v2 (Illumina; California, USA). Libraries were single end sequenced on an Illumina NextSeq 500 sequencer.

treatment_protocol:
CD4+T cells were cultured in RPMI 1640 medium supplemented with 2 mM glutamine, commercial antibiotics (50 U/mL penicillin,50lg/mL streptomycin) and 5% fetal coalf serum. Cells were activated with 1µg/mL anti-CD3 (OKT3; TONBO Bio-sciences) and 1µg/mL anti-CD28 (CD28.2;TONBO Biosciences) , cross-linked with 1ug/mL goat anti-mouse (Polyclonal,Bioss) and incubated for 6 h under 5% CO2 at 37°C
Total RNA from CD4+ T cells was extracted using TRIZOL® Reagent, following the manufacturer’s protocol.

tag: age

value: Neonate

value: CD4+ T cells

tag: time

value: 6 hours


title: CD4_T_Cells_Neonate_2_CD3CD28_RNA-seq [N3-2]


title: Bacterial_fungal_S5


title: Spleen from PBS-treated and challenged mouse 4

city: Columbia

first: Jerod

last: Skyberg

state: MO

address: Veterinary Pathobiology, 1500 Bouchelle

institute: University of Missouri

data_processing:
OnestopRNASeq
FastQC and MultiQC were used for raw reads quality control and QoRTs for post-alignment quality control
Reads were aligned to the reference genome assembly mm10 with star_2.7.5a and annotated with gencode.vM25.
Aligned exon reads were counted toward gene expression with featureCounts_2.0.0 with default settings.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM  values for each Sample

organism: Mus musculus

source_name: whole spleen

extract_protocol:
RNA was isolated via Trizol and further purified with an Rneasy kit.
Stranded mRNA libaries were constructed by the University of Missouri Genomics Core facility using a poly A enrichment method

value: whole spleen

value: WT

value: PBS and then challenge


title: Spleen from PBS-treated and challenged mouse 3


title: Bacterial_fungal_S3


title: CD4_T_Cells_Adult_3_CD3CD28_RNA-seq [A4-2]

value: adult


title: healthy, seedling, rep2


title: Spleen from S19 vaccinated and challenged mouse 3

value: S19 vaccination and then challenge


title: Bacterial_fungal_S1


title: Spleen from PBS-treated and challenged mouse 5


title: CD4_T_Cells_Adult_1_CD3CD28_RNA-seq [A1-2]


title: Spleen from S19 vaccinated and challenged mouse 2


title: HUVEC, siEPHB4


title: HUVEC, siEFNB2


title: CD4_T_Cells_Adult_2_Basal_RNA-seq [A3-1]

value: BASAL

value: 0 hours


title: Viral_S4


title: Root rot seedlings, treated with AM201, rep3

source_name: FS infection of healthy Atractylodes macrocephala seedlings, treatment with endophytic bacteria AM201 in Atractylodes macrocephala, rep3

value: treated with AM201


title: Viral_S3

value: viral keratitis


title: HC11_vangl2_knockout02_rep03

city: Santa cruz

first: Chad

middle: Steven

last: Cockrum

address: 329 sinsheimer labs

institute: University of California at Santa Cruz

data_processing:
Raw reads were trimmed for adapter sequences and quality filtered average read quality > Q20 using fastp.
Processed reads were mapped to the GRCm38 mouse genome assembly using HISAT2 with parameters: --no-unal --no-mixed —no-discordant
Mapping QC was performed using qualimap.
Mapped reads were counted over exons in transcripts annotated in the GRCm38 GTF annotation file v23 to acquire gene-level counts using featureCounts from the Subread package.
Differential expression was performed using the raw gene-level counts and DESeq2 Wald tests. Differentially expressed genes were qualified by an FDR <0.05 and an absolute fold change >2.
Assembly: GRCm38
Supplementary files format and content: CSV file of raw read counts over transcripts annotated in GRCm38 for each sample.

growth_protocol: HC11 cells were cultured in RPMI-1640, supplemented with 10% FBS, 5 µg/mL insulin (Millipore-Sigma, Burlington VT, USA; I6634), 10 ng/mL epidermal growth factor (EGF; Thermo-Fisher Scientific,, Waltham, MA, USA; AF-100-15), and 1× AntiAnti  at 37 °C with 5% CO2.

extract_protocol:
HC11 cells were harvested in 500 µL trizol and flash frozen in liquid nitrogen. Upon thawing, samples were mixed with 100 µL of 1-bromo-3-chloropropane (BCP) (Sigma, #B9673), transferred to phase lock heavy gel tubes, and stored at room temperature for 10 minutes. To separate the phases samples were centrifuged at 13,000 × g and 4°C for 15 min. The aqueous top phase was transferred to a fresh tube and mixed with 0.7x volumes of ice-cold isopropanol and 1.5 µL of GlycoBlue Coprecipitant (15 mg/mL). Samples were stored at -80C overnight followed by another centrifugation at 13,000 × g at 4°C for 30 min. RNA pellets were washed 3× with ice-cold 75% ethanol and finally resuspended in 15 µL water.
NEB Ultra RNA library prep kit for Illumina

treatment_protocol: N/A all cells were just grown in normal conditions

value: Mouse mammary gland

value: Vangl2 knockout 2


title: HC11_vangl2_knockout02_rep02


title: Root rot seedlings, Positive pesticide (TM) treatment, rep3

source_name: FS infects healthy Atractylodes macrocephala seedlings, followed by positive pesticide (TM) treatment, rep3

value: rhizome


title: CD4_T_Cells_Neonate_3_Basal_RNA-seq [N5-1]


title: CD4_T_Cells_Neonate_2_Basal_RNA-seq [N3-1]


title: CD4_T_Cells_Neonate_1_Basal_RNA-seq [N2-1]


title: CD4_T_Cells_Adult_3_Basal_RNA-seq [A4-1]


title: Root rot seedlings, treated with sterile water, Rep3

source_name: FS infects healthy Atractylodes macrocephala seedlings, followed by sterile water treatment, rep3

value: treated with sterile water


title: AKI2

city: Lugano

first: Anna

last: Rinaldi

state: Ticino

address: Tesserete

department: Nephrology

country: Switzerland

institute: Ente Ospedaliero Cantonale

data_processing:
Sequencing data were processed by CellRanger (version 3.1.0) and reads were aligned to human pre-mRNA reference genome (GRCh38-2020) with STAR (v.2.5.1b)
The Cell Ranger cellranger count function output filtered gene–cell expression matrices, removing cell barcodes not represented in cells.
UMI count table utilizing both exonic and intronic reads was generated for downstream analysis.
Nuclei with less than 150 nFeature_RNA detected or more than 4 times the absolute median of nFeature_RNA were excluded
Nuclei with a relatively high percentage of UMIs mapped to mitochondrial genes (>1 and only for one human case >5) and ribosomal genes (>1) were ecluded
SoupX to remove ambient RNA contamination was applied
Genome_build: human pre-mRNA reference genome (GRCh38-2020)
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: renal biopsy

extract_protocol:
Renal biopsy was performed before planned withdrawal of resuscitation measures and directly frozen at -80. Frozen biopsies were processed to extract sinlge nuclei and perform single nucleus RNA sequencing using 10X Chromium single cell platform (10X Genomics)
Barcoded single-cell gel beads in emulsion (GEMs) were created by 10x Genomics Chromium TM and then reverse transcribed to generate single-cell RNA-seq libraries using Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10X Genomics) according to manufacturer’s instructions

tag: disease

value: Acute kidney injury

tag: covid status

value: COVID positive


title: HC11_vangl2_knockout01_rep03

value: Vangl2 knockout 1


title: CD4_T_Cells_Adult_2_CD3CD28_RNA-seq [A3-2]

value: CD4+ T cells

value: 6 hours


title: Spleen from PBS-treated and challenged mouse 2

value: whole spleen

value: WT


title: Root rot seedlings, treated with sterile water, Rep2

source_name: FS infects healthy Atractylodes macrocephala seedlings, followed by sterile water treatment, rep2


title: Spleen from PBS-treated and challenged mouse 1

value: PBS and then challenge


title: siDHX15_2 (biol rep 2)

city: Göttingen

first: Katherine

last: Bohnsack

address: Humboldtallee 23

institute: University Medical Centre Göttingen

description: Trimmed reads

data_processing:
Library strategy: RiboMeth-seq
Barcode separation using python script
Adaptor trimming using Cutadapt v. 2.0
Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1
Counting read ends and calculating RiboMeth-seq scores using python scripts
Assembly: Human rDNA reference sequence from Krogh et al, NAR 2016 and snRNA sequences from genome build hg38
Supplementary files format and content: MS Excel file contains 5' and 3' read count and calculated RiboMeth-seq score at all positions in the rRNA sequence.
Library strategy: RiboMeth-seq

source_name: Flp-In T-Rex HEK293

growth_protocol: Wild-type (WT) and GPATCH4 knockout (GP4KO) HEK293 Flp-In T-Rex cells or HEK293 Flp-In T-Rex cells transfected with non-target siRNAs (siNT) or those targeting DHX15 (siDHX15) were grown at 37°C in 5% CO2 in high glucose DMEM supplemented with 10% foetal calf serum .

extract_protocol:
Total RNA was extracted using TRI Reagent (Sigma-Aldrich) according to the manufacturer's instructions.
RiboMeth-seq: 5-10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20-40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2',3' cyclic phosphate and 5' phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U, Christensen-Dalsgaard M, Krogh N, Sabarinathan R, Gorodkin J, Nielsen H. Profiling of ribose methylations in RNA by high-throughput sequencing. Angewandte Chemie. 2015;54(2):451-5 for detailed description

value: Flp-In T-Rex HEK293

value: WT, siDHX15


title: Root rot seedlings, Positive pesticide (TM) treatment, rep1

source_name: FS infects healthy Atractylodes macrocephala seedlings, followed by positive pesticide (TM) treatment, rep1

value: Positive pesticide (TM) treatment


title: siDHX15_1 (biol rep 1)

description: Trimmed reads


title: Root rot seedlings, treated with sterile water, Rep1

source_name: FS infects healthy Atractylodes macrocephala seedlings, followed by sterile water treatment, rep1


title: siNT_3 (biol rep 3)

description: Trimmed reads

value: WT, siNon-Target


title: siNT_2 (biol rep 2)

description: Trimmed reads


title: Root rot seedlings, treated with AM201, rep1

source_name: FS infection of healthy Atractylodes macrocephala seedlings, treatment with endophytic bacteria AM201 in Atractylodes macrocephala, rep1

value: treated with AM201


title: CD4_T_Cells_Adult_1_Basal_RNA-seq [A1-1]

value: adult

value: BASAL

value: 0 hours


title: CTRL3


title: Root rot seedlings, treated with AM201, rep2

source_name: FS infection of healthy Atractylodes macrocephala seedlings, treatment with endophytic bacteria AM201 in Atractylodes macrocephala, rep2

value: rhizome


title: HC11_vangl2_knockout02_rep01

value: Mouse mammary gland

value: Vangl2 knockout 2


title: CTRL1

value: Acute kidney injury

value: COVID positive


title: HC11_rep02


title: WT_2 (biol rep 2)

description: Trimmed reads


title: AKI1


title: CTRL2


title: siDHX15_3 (biol rep 3)

description: Trimmed reads


title: HC11_rep03


title: WT_1 (biol rep 1)

description: Trimmed reads


title: FHFR46

city: Illkirch

first: Manuel

last: Mendoza

address: 1 rue Laurent Fries

country: France

institute: INSTITUTE OF GENETICS AND MOLECULAR AND CELLULAR BIOLOGY

description: Nascent RNA extracted from mouse embryonic stem cells, labelled with 4sU

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Alignment : Reads were mapped onto a hybrid genome composed of mm10 and BDGP6 assemblies of Mus musculus and Drosophila melanogaster respectivement using STAR v.2.5.3a.
Quantification : Gene expression was quantified using HTSeq v.0.6.1p1 (union mode and "type" option set to "gene") and Ensembl release 102 annotations for M. musculus and Ensembl release 93 annotations for D. melanogaster.
Differential gene expression analysis was performed using R 3.3.2 and DESeq2 v1.16.1. Counts was normalized with size factors estimated by the median-of-ratios method based on the spike-in counts.
Assembly: mm10
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

source_name: TIP60-AID transgenic mESC line

growth_protocol: The auxin-inducible TIP60KI/KI mouse Embryonic Stem Cell (ESC) line was grown on 0.1% gelatinized (Sigma-Aldrich, Cat# G1890) tissue-culture plates in 2i medium, DMEM (4.5g/L glucose) with GlutaMAX-I supplemented with ES-tested 15% fetal calf serum (FCS, ThermoFisher Scientific, Cat# 10270-106), 2 mM L-glutamine (ThermoFisher Scientific, Cat# 25030-024), 0.1% β-mercaptoethanol (ThermoFisher Scientific, Cat# 31350-010), 100 UI/ml penicillin, 100 μg/ml streptomycin (ThermoFisher Scientific, Cat# 15140-122), 0.1 mM non-essential amino acids (ThermoFisher Scientific, Cat# 11140-035), 1500 U/ml leukemia inhibitory factor (produced in-house) and 2i, 3 μM CHIR99021 (Axon Medchem, Cat# 1386) and 1 μM PD0325901 (Axon Medchem, Cat# 1408) were added freshly to the medium.

extract_protocol:
P2625
RNA extraction was performed using TRI Reagent® (Molecular Research Center Inc., Cat# TR 188), following the manufacturer's instructions. DNase I treatment was performed to prevent genomic DNA contamination using the TURBO DNA-free™ Kit (ThermoFisher Scientific, Cat# AM1907) manufacturer's instructions.
P2625 : Total RNA-Seq libraries were generated from 50 ng of total RNA using Illumina Stranded Total RNA Prep, Ligation with Ribo-Zero Plus kit and IDT for Illumina RNA UD Indexes, Ligation (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, abundant ribosomal RNAs were depleted by hybridization to specific DNA probes and enzymatic digestion. The depleted RNAs were purified and fragmented using divalent cations at 94oC for 2 minutes. After random hexamers annealing, fragmented RNAs were then reverse transcribed into first strand complementary DNA (cDNA). Second strand cDNA synthesis further generated blunt-ended double-stranded cDNA and incorporated dTTP in place of dUTP to achieve strand specificity by quenching the second strand during amplification. Following A-tailing of DNA fragments and ligation of pre-index anchors, PCR amplification was used to add indexes and primer sequences and to enrich DNA libraries (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 13 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using SPRIselect beads (Beckman-Coulter, Villepinte, France) and the final libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: KI cells were treated with Auxin for 24 hours

value: TIP60-AID transgenic mESC line

value: stem cell

tag: replicate

value: Auxin


title: Mid thoracic spinal cord, 106_D (spatial)

city: Geneve

first: Alan Yue Yang

last: Teo

address: Chem. des Mines 9, Campus Biotech

department: SV

institute: EPFL

description: 10x v3

data_processing:
For the snRNA-seq, reads were aligned using Cellranger v 4.0.0 and the final data matrix is generated as per Cellranger pipeline. For the spatial transcriptomics, reads were aligned with SpaceRanger v 1.0.0 and the final data matrix is generated as per Spaceranger pipeline
Data were analyzed using Seurat v3
Assembly: mm10-1.2.0 (GRCm38.101)
Supplementary files format and content: tab-delimited text files include UMI values for each cell with tab delimeters
Library strategy: Spatial Transcriptomics

source_name: Mid thoracic spinal cord

extract_protocol:
For snRNA-seq experiment, single-nucleus dissociation of the mouse lumbar spinal cord was performed according to our established procedures. Following euthanasia by isoflurane inhalation and cervical dislocation, the spinal cord injury site was immediately dissected and frozen on dry ice. Spinal cords were doused in 500 µL sucrose buffer (0.32 M sucrose, 10 mM HEPES [pH 8.0], 5 mM CaCl2, 3 mM Mg acetate, 0.1 mM EDTA, 1 mM DTT) and 0.1% Triton X-100 with the Kontes Dounce Tissue Grinder. 2 mL of sucrose buffer was then added and filtered through a 40 µm cell strainer. The lysate was centrifuged at 3200 g for 10 min at 4°C. The supernatant was then decanted, and 3 mL of sucrose buffer was added to the pellet for 1 min. We homogenized the pellet using an Ultra-Turrax and 12.5 mL of density buffer (1 M sucrose, 10 mM HEPES [pH 8.0], 3 mM Mg acetate, 1 mM DTT) was added below the nuclei layer. The tube was centrifuged at 3200 g at 4°C and supernatant poured off. Nuclei on the bottom half of the tube wall were collected with 100 µL PBS with 0.04% BSA and 0.2 U/µL RNase inhibitor. Finally, nuclei were resuspended through a 30 µm strainer, and adjusted to 1000 nuclei/µL. snRNA-seq library preparation was carried out using the 10x Genomics Chromium Multiome ATAC + Gene Expression Kit Version 3. The nuclei suspension was added to the Chromium RT mix to achieve loading numbers of 10,000 nuclei. For downstream cDNA synthesis (13 PCR cycles), library preparation and sequencing, the manufacturer’s instructions were followed. For spatial transcriptomics, we carried out two separate experiments to study the cytoarchitecture of the lesion microenvironment after SCI. First, we prepared sections from uninjured mice, 7 days and 2 months after crush SCI. For each experimental condition, we prepared sections from the lesion epicenter of three independent biological replicates. Second, to prepare our four-dimensional spatiotemporal atlas, we collected sections throughout the entire spinal cord of mice from each of the three experimental conditions. The spinal cord injury sites of mice were embedded in OCT and cryosections were generated at 10 µm at −20 °C. For the four-dimensional atlas, every fifth section was collected throughout the entire dorsoventral axis of each spinal cord. Sections were immediately placed on chilled Visium Tissue Optimization Slides or Visium Spatial Gene Expression Slides.
We used 10x Genomics Chromium Single Cell Gene Expression Kit Version 3.1 kit to profile the snRNA sequencing and Visium Spatial Gene Expression to profile the spatial transcriptomics.

tag: strain

tag: tissue

value: spinal cord

value: Mixture of uninjured, 7 days post SCI, 2 months post SCI

value: wild type


title: HC11_vangl2_knockout01_rep02

tag: genotype

value: Vangl2 knockout 1


title: KO-1

type: RNA

city: Baltimore

first: Lan

last: Xiao

state: Maryland

address: HSF II S-211, 20 Penn Street

department: Surgery

institute: University of Maryland School of Medicine

description: miRNA-profiling

hyb_protocol: Cy3 labeled small RNAs were hybridized to Arraystar Mouse Small RNA Arrays in Agilent Hybridization Oven.

scan_protocol: After washing, the slides were scanned with Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. To compare two groups for differential small RNA expression, the fold change (FC) and statistical significance of the difference (p-value) were calculated for each small RNA. The default thresholds are |FC| 1.5 and p < 0.05. One can adjust the stringency thresholds and rank the differentially expressed small RNAs further by the Data/Sort & Filter functionality in Microsoft Excel.

source_name: small intestine

label_protocol: For each sample, 100ng total RNAs were dephosphorylated to form a unified 3-OH end. 3-OH ended RNA were then denaturated by DMSO and enzymatically labeled with Cy3.

extract_protocol: RNA quantity was measured by using NanoDrop ND-1000 spectrophotometer and RNA integrity was assessed by Bioanalyzer 2100 or gel electrophoresis. Results were provided in Sample QC report

value: small intestine

value: cdr1as knockout


title: HC11_vangl2_knockout01_rep01


title: glutamatergic neurons, homozygous, clone 44, rep 2

city: London

first: Laura

last: Sichlinger

address: 5 Cutcombe Rd

country: United Kingdom

institute: King's College London

description:
LSI02_44-RP2
LSI02_44-RP2

data_processing:
Sequence reads were aligned to reference genome and indexed using STAR (2.7.3a)
Duplicates were tagged and removed using MarkDuplicates of picard (2.25.1)
Count table was generated using htseq-count
Assembly: GRCh38
Supplementary files format and content: tab-limited csv file contains raw counts for each sample

growth_protocol: Doxycycline-inducible NGN2 overexpression system was paired with Wnt and SMAD inhibition for 3 days to generate patterend cortical glutamtamatergic neurons. After Day 4 base medium B27 was supplemented with growth factors BDNF and GDNF, and DAPT. RNA was harvested at Day 7. Please refer to publication for more detailed information.

extract_protocol:
TRIzol reagent was used to extract, chloroform for phase separation of, and ethanol to clean total RNA. Total RNA was used for library preparation.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina following manufacturer's instructions (NEB, Ipswich, MA, USA).

treatment_protocol: A dual-sgRNA CRISPR/Cas9 approach was designed to excise exon 3 of ZNF804A; two clones per genotype (wt, het hom) were validated prior to differentiation

value: hiPSCs

tag: differentiation

value: dox-induced NGN2 overexpression + Wnt/SMADi

value: CRISPR/Cas9 treated - homozygous


title: HC11_differentiated_antiVangl2_rep02

data_processing:
Reads were aligned to the GRCm38 mouse genome with bowtie 2  v2.4.1 tool --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700
Reads were filtered by best quality reads with samtools and minQualityScore=2
Signal coverage files BigWig were obtained with bamCoverage from deeptools package and normalized with RPKM
Peaking calling was perfomed with MACS v2.2.9.1 with the significance cut-off q-value <= 0.01 and default settings
Assembly: GRCm38
Supplementary files format and content: BigWig RPKM
Supplementary files format and content: narrowPeak except for Input sample
Library strategy: CUT&RUN

growth_protocol: Undifferentiated HC11 cells were cultured in RPMI-1640, supplemented with 10% FBS, 5 µg/mL insulin (Millipore-Sigma, Burlington VT, USA; I6634), 10 ng/mL epidermal growth factor (EGF; Thermo-Fisher Scientific,, Waltham, MA, USA; AF-100-15), and 1× AntiAnti  at 37 °C with 5% CO2.

extract_protocol:
We collected 100,000 cells from three independent dishes of HC11 cells at undifferentiated, confluent, and differentiated states. CUT&RUN was performed on HC11 cells using a rabbit anti-VANGL2 antibody (1:50, Millipore-Sigma, Burlington VT, USA; ABN2242) and isotype control IgG (Cell Signaling Technologies, Danvers, MA, USA;  2729) and the CUT&RUN Assay Kit (Cell Signaling Technologies, Danvers, MA, USA;  86652).
The resulting DNA fragment samples were generated into libraries using the SimpleChIP® ChIP-seq DNA Library Prep Kit for Illumina® (Cell Signaling Technologies, Danvers, MA, USA;  56795) and SimpleChIP® ChIP-seq Multiplex Oligos for Illumina® (Dual Index Primers) (Cell Signaling Technologies, Danvers, MA, USA;  47538). Samples were sequenced using the NovaSeq 6000, 50PE (UC Berkeley, Berkeley, CA, USA).

treatment_protocol: To differentiate HC11 cells, first the cells were made competent by growing them to confluency and then maintaining them in growing medium for 2 days. Next, the cells were primed by culturing them in priming medium [RPMI-1640 supplemented with 5% charcoal-stripped-FBS (Equitech Bio, Kerrville, TX, USA; SFBM31) 5 µg/mL insulin, 1 µM dexamethasone (Millipore-Sigma, Burlington VT, USA; D4902-1G), and 1× Anti-Anti] for 18 h at 37 °C with 5% CO2. To induce differentiation, primed HC11 cells were cultured in DIP Medium [RPMI-1640, supplemented with 10% FBS, 1 µM dexamethasone, 5 µg/mL insulin, 3 µg/mL Prolactin (National Hormone and Pituitary Program, Los Angeles, CA, USA; oPRL-21) and 1× anti-anti] at 37 °C with 5% CO2.

tag: treatment

value: Dexamethasone/Insulin/Prolactin (DIP)

tag: cut&run antibody

value: Rabbit anti-Vangl2


title: Bacterial_fungal_S2

source_name: cornea

value: cornea

tag: diagnosis

value: bacterial/fungal keratitis


title: FHFR44


title: glutamatergic neurons, homozygous, clone 44, rep 1

description:
LSI02_44-RP1
LSI02_44-RP1


title: Mid thoracic spinal cord, 106_B (spatial)

description: 10x v3

tag: condition


title: siNT_1 (biol rep 1)

description: Trimmed reads

value: Flp-In T-Rex HEK293

value: WT, siNon-Target


title: FHFR43

value: TIP60-AID transgenic mESC line

value: stem cell

value: DMSO


title: WT-2

description: miRNA-profiling

value: wildtype


title: KO-3

description: miRNA-profiling


title: GP4KO_3 (biol rep 3)

description: Trimmed reads

value: GPATCH4 KO


title: KO-2

description: miRNA-profiling


title: FHFR42


title: WT-1

description: miRNA-profiling


title: Spleen from S19 vaccinated and challenged mouse 1

value: whole spleen

value: WT

value: S19 vaccination and then challenge


title: GP4KO_2 (biol rep 2)

description: Trimmed reads


title: WT_3 (biol rep 3)

description: Trimmed reads


title: HC11_undifferentiated_antiVangl2_rep01

value: Mouse mammary gland


title: WT-3

description: miRNA-profiling

value: small intestine


title: HC11_undifferentiated_antiIgG_rep01

value: Rabbit anti-IgG


title: glutamatergic neurons, heterozygous, clone 42.13, rep3

description:
LSI02_42-13-RP3
LSI02_42-13-RP3

value: hiPSCs

value: dox-induced NGN2 overexpression + Wnt/SMADi

value: CRISPR/Cas9 treated - heterozygous


title: FHFR5

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto mm10 assembly of Mus musculus genome using STAR v.2.5.3a
Quantification : Gene expression was quantified using HTSeq v.0.6.1p1 (union mode) and Ensembl release 102 annotations.
Assembly: mm10
Supplementary files format and content: Tabulated text file containing raw read counts in each sample.

extract_protocol:
P2423
RNA extraction was performed using TRI Reagent® (Molecular Research Center Inc., Cat# TR 188), following the manufacturer's instructions. DNase I treatment was performed to prevent genomic DNA contamination using the TURBO DNA-free™ Kit (ThermoFisher Scientific, Cat# AM1907) manufacturer's instructions.
P2423: Total RNA-Seq libraries were generated from 500 ng of total RNA. Before cDNA synthesis, cytoplasmic and mitochondrial ribosomal RNA (rRNA) were removed using a biotin-streptavidin magnetic bead-based procedure with the riboPOOL kit targeting HMR ribosomal rRNA (siTOOLs Biotech, Planegg/Martinsried, DE) according to manufacturer's instructions.  Total RNA-seq libraries were then generated using TruSeq Stranded mRNA Library Prep kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA) omitting the poly-A selection step and starting from the fragmentation step. Briefly, following clean up by ethanol precipitation, the depleted RNA was fragmented into small pieces using divalent cations at 94oC for 2 minutes. Cleaved RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Strand specificity was achieved by replacing dTTP with dUTP during second strand synthesis. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single 'A' nucleotide was added to the 3' ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC). Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: Auxin


title: glutamatergic neurons, homozygous, clone 44, rep 3

description:
LSI02_44-RP3
LSI02_44-RP3

value: CRISPR/Cas9 treated - homozygous


title: Mid thoracic spinal cord, 105_A (spatial)

description: 10x v3

value: spinal cord

value: Mixture of uninjured, 7 days post SCI, 2 months post SCI

value: wild type


title: HC11_rep01


title: GP4KO_1 (biol rep 1)

description: Trimmed reads

value: Flp-In T-Rex HEK293


title: FHFR6

value: TIP60-AID transgenic mESC line

value: stem cell


title: HC11_differentiated_antiVangl2_rep03

value: Dexamethasone/Insulin/Prolactin (DIP)

value: Rabbit anti-Vangl2


title: FHFR45


title: Mid thoracic spinal cord, 106_C (spatial)

description: 10x v3


title: OVX-EPC-2

city: Philadelphia

first: Charan

middle: Thej

last: Gurrala

state: Pennsylvania

address: 3500 N Broad St, MERB 983

department: Aging + Cardiovascular Discovery Center

institute: Temple University

data_processing:
Data quality statistics were assessed and filtered clean reads were mapped to reference genome using HISAT2.
Cuffquant and Cuffnorm components of Cufflinks software were used to quantify gene expression levels using mapped reads positional information on the gene.
DEseq was used to analyze the differentially expressed genes (DEG) for samples with biological replicates.
Fold change ≥2 and FDR>0.05 were set as screening criteria. Gene enrichment analyses of upregulated and downregulated genes were performed using KEGG and GO databases.
Assembly: mm10
Supplementary files format and content: Excel Workbook

source_name: Bone marrow

growth_protocol: Cultured in EGM-2 medium

extract_protocol:
RNA was extracted using Rneasy mini kit (Qiagen), quantity was assessed with Qubit RNA HS assay (ThermoFisher) and quality was assessed using Bioanalyzer 2100 Eukaryote total RNA nano (Agilent)
Illumina mRNA seq TruSeq
DNA libraries generated using NEBNext Ultra II

value: Bone marrow

value: freshly isolated

value: Mouse Female Ovariectomized Endothelial Progenitor Cells

value: Sca-1/CD31 + magnetic sorting


title: glutamatergic neurons, heterozygous, clone 10.23, rep3

description:
LSI02_10-23-RP3
LSI02_10-23-RP3

value: hiPSCs


title: M-EPC-3

value: Mouse Male Endothelial Progenitor Cells


title: Mid thoracic spinal cord, 103_C (spatial)

description: 10x v3


title: HC11_differentiated_antiVangl2_rep01

value: Mouse mammary gland


title: FHFR3

value: DMSO


title: Mid thoracic spinal cord, 106_A (spatial)

description: 10x v3


title: glutamatergic neurons, heterozygous, clone 10.23, rep2

description:
LSI02_10-23-RP2
LSI02_10-23-RP2

value: dox-induced NGN2 overexpression + Wnt/SMADi

value: CRISPR/Cas9 treated - heterozygous


title: M-EPC-2


title: glutamatergic neurons, homozygous, clone 20, rep 2

description:
LSI02_20-RP2
LSI02_20-RP2

value: CRISPR/Cas9 treated - homozygous


title: FHFR41


title: CD4_T_Cells_Neonate_3_CD3CD28_RNA-seq [N5-2]

source_name: CD4+ T cells

value: Neonate

value: CD4+ T cells

value: 6 hours


title: glutamatergic neurons, homozygous, clone 20, rep 1

description:
LSI02_20-RP1
LSI02_20-RP1


title: M-EPC-1


title: Mid thoracic spinal cord, 103_A (spatial)

description: 10x v3

value: spinal cord

value: Mixture of uninjured, 7 days post SCI, 2 months post SCI

value: wild type


title: Mid thoracic spinal cord, 105_D (spatial)

description: 10x v3


title: DSRCT-2

city: Houston

first: Danh

last: Truong

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

data_processing:
Libraries from each sample were pooled together and sequenced on the Illumina HiSeq 4000 (Illumina).
Reads were mapped to the hg19 reference genome using GSNAP.
For calculation of gene expression, raw counts were obtained using featureCounts.
Assembly: hg38
Supplementary files format and content: tab-delimited text file

source_name: Patient-derived xenograft

extract_protocol:
Total RNA of DSRCT PDX frozen samples were extracted using RNeasy Mini Kit (Qiagen).
Libraries were made using the KAPA Stranded RNA-Seq Library Preparation Kit (KAPA Biosystems).

value: Patient-derived xenograft

tag: subtype

value: desmoplastic small round cell tumor


title: Mid thoracic spinal cord, 105_C (spatial)

description: 10x v3


title: F-EPC-3

value: Bone marrow

value: freshly isolated

tag: cell type

value: Mouse Female Endothelial Progenitor Cells


title: glutamatergic neurons, homozygous, clone 20, rep 3

description:
LSI02_20-RP3
LSI02_20-RP3

value: hiPSCs


title: glutamatergic neurons, wildtype, clone 4, rep3

description:
LSI02_4-RP3
LSI02_4-RP3

value: CRISPR/Cas9 treated - locus not edited


title: DSRCT-4


title: glutamatergic neurons, wildtype, clone 4, rep2

description:
LSI02_4-RP2
LSI02_4-RP2


title: Mid thoracic spinal cord, 105_B (spatial)

description: 10x v3


title: F-EPC-2

value: Sca-1/CD31 + magnetic sorting


title: HC11_undifferentiated_antiVangl2_rep02

value: Mouse mammary gland

value: Rabbit anti-Vangl2


title: glutamatergic neurons, heterozygous, clone 42.13, rep2

description:
LSI02_42-13-RP2
LSI02_42-13-RP2

value: dox-induced NGN2 overexpression + Wnt/SMADi

value: CRISPR/Cas9 treated - heterozygous


title: OVX-EPC-3

value: Mouse Female Ovariectomized Endothelial Progenitor Cells


title: HC11_undifferentiated_antiVangl2_rep03


title: FHFR4

value: TIP60-AID transgenic mESC line

value: stem cell

value: Auxin


title: glutamatergic neurons, heterozygous, clone 42.13, rep1

description:
LSI02_42-13-RP1
LSI02_42-13-RP1


title: OVX-EPC-1


title: Mid thoracic spinal cord, 078_B (spatial)

description: 10x v3

value: spinal cord

value: Mixture of uninjured, 7 days post SCI, 2 months post SCI

value: wild type


title: Mid thoracic spinal cord, 103_D (spatial)

description: 10x v3


title: F-EPC-1

value: Bone marrow


title: Mid thoracic spinal cord, 078_D (spatial)

description: 10x v3


title: Mid thoracic spinal cord, 077_D (spatial)

description: 10x v3


title: Mid thoracic spinal cord, 103_B (spatial)

description: 10x v3


title: RS_3

city: stockholm

first: wenteng

last: He

state: **Non-US resident**

address: solnavagen

country: Sweden

institute: karolinska institutet

library_source: other

data_processing:
miRanda-3.3a was used to predict miRNA target genes and known miRNA analysis was performed by Mirdeep2
mirdeep2 and miREvo were used for novel miRNA prediction
Biological repeat analysis was performed by DEseq2
Target gene candidate enrichment in pathways was performed by KOBAS
Assembly: Bowtie-0.12.9 was used to map small RNA tags to the reference sequence
Supplementary files format and content: tab-delinted txt file including raw counts of each sample

molecule: other

source_name: testes spermatids

growth_protocol: mAG-haESC derivation and culture were conducted as previously described (He et al., 2018). Briefly, all mAG-haESCs were derived in 15% KSR knockout DMEM (Gibco) supplemented with 0.1 mM mercaptoethanol (Merck Millipore), 1 mM L-glutamine (Merck Millipore), nucleosides (100×, Merck Millipore), 1% nonessential amino acid stock (Merck Millipore), penicillin/streptomycin (100×, Merck Millipore), 2i (1 μM PD0325901 and 3 μM CHIR99021), and 1,000 U/mL mouse LIF (Merck Millipore). Haploid cells were sorted after outgrowth cells expanded to one 12-well plate. Then, mAG-haESCs were propagated in 15% FBS ES medium supplemented with 1 mM L-glutamine, 0.1 mM mercaptoethanol, nucleosides (100×), 1% nonessential amino acid stock, penicillin/streptomycin (100×), 2i, and 1,000 U/mL mouse LIF. Periodic enrichment (every 3～5 weeks, depending on the cell lines) of haploid cells treated with staining buffer (15 µg/mL Hoechst 33342 and 2.5 µM verapamil) was conducted with a BD FACS Aria II cell sorter.

extract_protocol:
RNA was extracted using a QIAGEN RNA kit or off-site at Novogene (for sRNA extraction). Small RNA quality was checked prior to library construction, and samples of small RNA without degradation and genomic DNA contamination were considered appropriate for use.
Three micrograms of total RNA from each sample were used for library construction with the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA). Briefly, the 3’ adapter was first ligated to the small RNAs, followed by ligation of the 5’ adapter. Then, the ligation-reconstructed small RNAs were reverse transcribed into small cDNAs. After amplification by PCR, a library with a length of 140~160 bp was purified by gel excision. Library quality was checked on an Agilent Bioanalyzer 2100 system before sequencing. Small RNA sequencing was conducted on the NovaSeq 6000 SE50 platform, and at least 10 M clean reads were obtained for each sample.

treatment_protocol: Haploid germ cells were collected from the testes of male 129Sv mice. The testes were collected with scissors, and the surrounding fatty tissue was removed. After opening the testicular capsule under a microscope, seminiferous tubules were released and placed into a 1.5 mL Eppendorf tube. After cutting the seminiferous tubules with scissors for 1 minute, 400 μL of 0.05% trypsin-EDTA was added, and the tissue was digested for 4 minutes and then neutralized with 600 μL feeder medium. Germ cells were filtered through a 70 μm filter and then centrifuged at 1000 rpm for 5 minutes. Then, germ cells were stained with Hoechst 33342 at 37 °C for 30 minutes, centrifuged and resuspended in FACS buffer. Finally, mRS were sorted with a BD FACS Aria II cell sorter after filtration through a 40 μm filter.  mRS, mAG-haESCs and R1 were collected in 15 ml tubes with 1 mL DPBS. Cell sorting was finished in 2 hr to avoid cell death. Samples of more than 5×106 cells from each mAG-haESC line, R1 and mRS were collected in 2-3 independent replicates by FACS sorting. Samples were lysed in TRIzol to isolate small RNAs after centrifugation at 1400 rpm for 5 min to remove the cell culture medium (supernatant).

value: testes spermatids

value: mRS

value: spermatids

value: WT

value: Sorting


title: Mid thoracic spinal cord, 077_C (spatial)

description: 10x v3


title: RS_1


title: FHFR1

value: DMSO


title: glutamatergic neurons, heterozygous, clone 10.23, rep1

description:
LSI02_10-23-RP1
LSI02_10-23-RP1

value: hiPSCs


title: R1_2

source_name: diploid ESCs

value: diploid ESCs


title: Mid thoracic spinal cord, 077_B (spatial)

description: 10x v3


title: FHFR2


title: R1_1


title: Mid thoracic spinal cord, 078_C (spatial)

description: 10x v3


title: Mid thoracic spinal cord, 078_A (spatial)

description: 10x v3


title: GPATCH4-His-Flag_ChIP

data_processing:
Raw data were quality checked using FastQC (v0.11.9). The average Phred score is 35.
Single-end reads were aligned to the human rDNA using default bowtie2 (v2.3.5.1) arguments.
Duplicated reads were marked with Picard  (v3.0.0) using the following arguments: MarkDuplicates  VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true REMOVE_DUPLICATES=FALSE
Using samtools (v1.10), .bam files were filtered to remove duplicated, unmapped, not primary alignment, and low-quality reads with the following arguments: view -F 1804 -q 30
Bedgraph files were generated using bedtools (version 2.27.1) with the following arguments genomecov -ibam .bg -scale RPM. Bedgraph files were then converted to bigwig files using bedGraphToBigWig (v4)
Assembly: Human ribosomal DNA (accesion number U13369.1)
Supplementary files format and content: Aligned reads in bigwig format

growth_protocol: HEK293 Flp-In T-Rex cell lines expressing GPATCH4-His-FLAG or the His-FLAG tag alone were grown at 37°C in 5% CO2 in high glucose DMEM supplemented with 10% foetal calf serum .

extract_protocol:
ChIP was performed usign the ChIP-IT High Seneitivity kit (Active Motif 53040). Chromatin shearing to 200-500 bp fragments was performed by sonication. 30 µg of sheared chromatin was subjected to immunoprecipitations using  anti-FLAG M2 beads (Sigma-Aldrich M8823). Eluates were treated with Proteinase K.
Libraries were constructed using the TruSeq ChIP Library Preparation Kit (Illumina) according to the maufacturer's instructions.

treatment_protocol: Expression of tagged proteins was induced by addition of tetracycline for 24 h before crosslinking with 1.5 mM EGS for 10 min at room temperature and 1% PFA for 45 min at 4°C.

value: Flp-In T-Rex HEK293

value: WT with Flp-In locus modified fro expression of GPATCH4-His-FLAG

tag: chip antibody

value: anti-FLAG M2 (Sigma-Aldrich Cat#M8823)


title: ES-4

value: Patient-derived xenograft

value: Ewing sarcoma


title: DSRCT-1

value: desmoplastic small round cell tumor


title: glutamatergic neurons, wildtype, clone 4, rep1

description:
LSI02_4-RP1
LSI02_4-RP1

tag: cell line

value: dox-induced NGN2 overexpression + Wnt/SMADi

value: CRISPR/Cas9 treated - locus not edited


title: CDS-1

value: CIC-DUX4 sarcoma


title: ES-1


title: glutamatergic neurons, wildtype, clone 61, rep3

description:
LSI02_61-RP3
LSI02_61-RP3


title: Mid thoracic spinal cord, 075_D (spatial)

description: 10x v3

value: spinal cord

value: Mixture of uninjured, 7 days post SCI, 2 months post SCI

value: wild type


title: NOLC1-His-Flag_ChIP


title: pbmc withdrawa stage

city: ShenZhen

first: jiao

last: zhao

state: US and Canada only

address: 1088 Xueyuan Avenue, Shenzhen 518055, P.R. China

institute: Southern University of Science and Technology

description: 10x Genomics

data_processing:
Sequencing-generated fastq files were processed using Cellranger (version 5.0.1) and run with default parameters for comparison, filtering, barcode separation, and UMI counting.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pbmc

extract_protocol:
5 mL of blood was collected from the patients who develop paroxysmal　atrial fibril-lation after using crizotinib . PBMCs were prepared using the density gradient cen-trifugation method. In brief, whole blood cells were diluted with 1× DPBS (1:1 ratio), layered on top of Ficoll-Paque Plus, and then centrifuged at 500g for 20 minutes at room temperature (RT). The white layer containing PBMCs was isolated and washed twice with DPBS. Subsequently, erythrocytes were removed using red blood cell lysate on ice. PBMCs were prepared using the density gradient centrifugation method at 1000 rpm for 5 minutes. The cells were successfully resuspended and filtered through a 40 μm cell strainer.
The cell suspensions underwent library preparation using the 10× Chromium Single Cell 3′ library kit and the Chromium Single Cell 30 v3 reagent (from 10× Ge-nomics) immediately after preparation.

value: pbmc

tag: Sex

value: female

tag: age

tag: treament

value: Discontinuation of crizotinib

value: Paroxysmal atrial fibrillation


title: Pericyte_iPSC_mesoderm_3

city: HOBART

first: Brad

middle: A.

last: Sutherland

state: TAS

address: Medical Sciences Precinct, 17 Liverpool Street

country: Australia

institute: University of Tasmania

data_processing:
The primary sequence data was generated using the Illumina DRAGEN BCL Convert 07.021.609.3.9.3 pipeline.
Reads were screened for the presence of any Illumina adapter/overrepresented sequences and cross-species contamination
The STAR aligner (v2.7.10a) was used to map reads to the genomic sequences.
Assembly: HG38
Supplementary files format and content: Tab-delimted text file including raw counts for each sample

source_name: Mesoderm iPericytes from TOB-00220 iPSC line

extract_protocol:
Cells grown to 95% confluence were collected and extracted using an Rneasy mini kit (Qiagen).
Libraries were generated using an Illumina Stranded mRNA workflow with polyA capture.


title: GPATCH4-His-Flag_Input


title: Mid thoracic spinal cord, 077_A (spatial)

description: 10x v3


title: pbmc use stage

description: 10x Genomics

value: crizotinib


title: Pericyte_iPSC_mesoderm_2

value: Mesoderm iPericytes from TOB-00220 iPSC line


title: glutamatergic neurons, wildtype, clone 61, rep2

description:
LSI02_61-RP2
LSI02_61-RP2

value: hiPSCs

tag: time


title: glutamatergic neurons, wildtype, clone 61, rep1

description:
LSI02_61-RP1
LSI02_61-RP1


title: RS_2

value: testes spermatids

value: mRS

value: spermatids

value: WT

value: Sorting


title: Pericyte_iPSC_mesoderm_1


title: A129_172

source_name: haploid ESCs

value: haploid ESCs


title: Mid thoracic spinal cord, 075_C (spatial)

description: 10x v3


title: NOLC1-His-Flag_Input

source_name: Flp-In T-Rex HEK293

value: Flp-In T-Rex HEK293

value: WT with Flp-In locus modified fro expression of GPATCH4-His-FLAG


title: A129_171


title: Mid thoracic spinal cord, 075_B (spatial)

description: 10x v3

value: spinal cord

value: Mixture of uninjured, 7 days post SCI, 2 months post SCI


title: Mid thoracic spinal cord, 075_A (spatial)

description: 10x v3

value: wild type


title: A129_6_2


title: Pericyte_iPSC_neuralcrest_2

source_name: Neural Crest iPericytes from TOB-00220 iPSC line


title: RIP_GPATCH4-His-Flag_B

data_processing:
3'  Adaptor seuquences (AACTGTAGGCACCATCAAT) were  Clipped using  Flexbar (version 3.5.0) with the following arguments  -qf i1.8 -qt 13 -u 0 -m 15 -n 8 -at RIGHT -z GZ -o -ao 2 -ae 0.1 -as AACTGTAGGCACCATCAAT
Clipped reads were aligned to the human genome using STAR (Version 2.7.10a) with the following arguments  --alignEndsType EndToEnd  --outFilterMismatchNmax 10  --outFilterMultimapScoreRange 10   --quantMode TranscriptomeSAM GeneCounts  --outReadsUnmapped Fastx  --outSAMtype BAM SortedByCoordinate  --outFilterMultimapNmax 30  --outSAMunmapped Within  --outFilterScoreMinOverLread 0  --outFilterMatchNminOverLread 0  --outFilterMatchNmin 16  --alignSJDBoverhangMin 1000  --alignIntronMax 1  --outWigType wiggle  --outWigStrand Stranded  --outWigNorm RPM  --readFilesCommand zcat
Bedgraphs were  generated using bedtools (version 2.27.1) with the following arguments genomecov -ibam .bg
Assembly: Homo_sapiens.GRCh38.108
Supplementary files format and content: Aligned reads in bedgraph format

extract_protocol:
Crosslinked RNA-protein complexes were purified and RNAs associated with His-FLAG-tagged proteins were recovered.
Small RNAs <200 nt were enriched and libraries were constructed using the  QIAseq miRNA Library Kit Catalog no.331502  according to the maufacturer's instructions.

treatment_protocol: Expression of tagged proteins was induced by addition of tetracycline for 24 h before crosslinking. Cells were UV crosslinked using light at 254 nm as previously described (Sloan et al., 2015; Memet et al., 2017).


title: His-Flag_Input

value: WT with Flp-In locus modified fro expression of His-FLAG


title: Mid thoracic spinal cord, uninjured_3 (rnaseq)

description: 10x v3

data_processing:
For the snRNA-seq, reads were aligned using Cellranger v 4.0.0 and the final data matrix is generated as per Cellranger pipeline. For the spatial transcriptomics, reads were aligned with SpaceRanger v 1.0.0 and the final data matrix is generated as per Spaceranger pipeline
Data were analyzed using Seurat v3
Assembly: mm10-1.2.0 (GRCm38.101)
Supplementary files format and content: tab-delimited text files include UMI values for each cell with tab delimeters

value: Uninjured mice


title: A129_6_1


title: RIP_GPATCH4-His-Flag_A


title: Mid thoracic spinal cord, uninjured_10 (rnaseq)

description: 10x v3


title: Pericyte_Primary_HBVP_6

source_name: Human Brain Vascular Pericytes (ScienCell)

tag: passage


title: A129_2_2


title: Pericyte_iPSC_neuralcrest_1

value: Neural Crest iPericytes from TOB-00220 iPSC line


title: Pericyte_iPSC_neuralcrest_3


title: Mid thoracic spinal cord, uninjured_2 (rnaseq)

description: 10x v3

tag: strain


title: RIP_His-Flag_B


title: RIP_His-Flag_A


title: APOE-/- NMOSD mice + APOE130-149

city: Beijing

first: Wei-Na

last: Jin

state: Beijing

address: NO.119, Southwest of the Fourth Ring Road, Fengtai District

department: China National Clinical Research Center for Neurological Diseases

institute: Beijing Tiantan Hospital, Capital Medical University

data_processing:
Raw files (FASTQ format) were processed with Cell Ranger software (v5.0.1), which performed mapping to the mm10 transcriptome, filtering, barcode counting, and UMI counting and finally generated feature-by-barcode UMI matrix. Seurat (v4.3.0) was used for downstream analysis. Low-quality cells, with < 1000 genes expressed or < 1000 UMIs, were excluded at the initial quality-control step. Cells > 10% mitochondrial UMIs were removed. Doublets were identified by the R package DoubletFinder with default settings. We first used the “SCTransform” function to perform the workflow of data normalization, identification of highly variable genes (HVGs), and data scaling, and then used the “RunPCA” function to perform PCA dimensionality reduction. Selected top PCs were retained using the elbow method for computing the UMAP dimensional reduction. Cells were clustered with Seurat’s “FindClusters” function.
Assembly: mm10
Supplementary files format and content: tsv and mtx file

source_name: Brain

extract_protocol:
Single-cell suspensions were prepared from pooled mouse brain tissues at day 4 after sham or NMOSD induction. CD45intCD11b+ cells were isolated at 4°C using flow-cytometry.
Library was performed according to the manufacter’s instructions (single-cell 3' v.2 kit, 10× Genomics).

tag: tissue

value: Brain

value: CD45intCD11b+ cells

value: APOE konckout

value: NMOSD induction + APOE130-149


title: Pericyte_Primary_HBVP_5

value: Human Brain Vascular Pericytes (ScienCell)


title: A129_2_1

tag: genotype


title: Mid thoracic spinal cord, timecourse_OLD_3 (rnaseq)

description: 10x v3

value: Old mice


title: His-Flag_ChIP

value: anti-FLAG M2 (Sigma-Aldrich Cat#M8823)


title: A129_6_3

value: WT

value: Sorting


title: Mid thoracic spinal cord, timecourse_OLD_2 (rnaseq)

description: 10x v3


title: GPATCH4-His-Flag_A

data_processing:
Sequencing reads for each experimental sample were demultiplexed using their 5' barcode sequences NNNNNAGC. Using pyBarcode Filter (pyCRAC version 1.4.5).
3' adaptor sequences (TGGAATTCTCGGGTGCCAAGG) were removed using Flexbar (version 3.5.0). flexbar', '-r', , '-t', '-q', 'TAIL', '-qf', u'i1.8', '-qt', '13', '-u', '0', '-m', '21', '-n', '8', '-at', 'RIGHT', '-z', 'GZ', '-o', '-ao', '2', '-ae', '0.1', '-as'
Identical sequence reads containing the same UMI were collapsed using pyFastqDuplicateRemover (PyCRAC version 1.4.5).
Aligment STAR (version 2.7.0d):params=' --runThreadN 8  --alignEndsType EndToEnd  --outFilterMismatchNoverLmax 0.3  --outFilterMultimapScoreRange 10   --outReadsUnmapped Fastx  --outSAMtype BAM SortedByCoordinate  --outFilterMultimapNmax 60  --outSAMunmapped Within  --outFilterScoreMinOverLread 0  --outFilterMatchNminOverLread 0  --outFilterMatchNmin 15  --alignSJDBoverhangMin 1000  --alignIntronMax 1  --outWigType wiggle  --outWigStrand Stranded  --outWigNorm RPM  --readFilesCommand zcat  '
Bedgraphs were  generated using bedtools (version 2.27.1) with the following arguments genomecov -ibam .bg
Assembly: Homo_sapiens.GRCh38.29
Supplementary files format and content: Aligned reads in bedgraph format
Library strategy: CRAC

growth_protocol: HEK293 Flp-In T-Rex cell lines expressing GPATCH4-His-FLAG or the His-FLAG tag alone were grown at 37°C in 5% CO2 in hihg glucose DMEM supplemented with 10% foetal calf serum .

extract_protocol:
Crosslinked RNA-protein complexes were purified under denaturing conditions and RNAs associated with His-FLAG-tagged proteins were trimmed (Bohnsack et al., 2012).
3' and 5' adapters were ligated and a cDNA library was prepared by reverse transcription and amplified by PCR (Haag et al., 2017).

value: Flp-In T-Rex HEK293


title: GPATCH4-His-Flag_B


title: APOE-/- NMOSD mice + control peptide

value: NMOSD induction+ control peptide


title: Pericyte_Primary_HBVP_3


title: Pericyte_Primary_HBVP_4


title: Mid thoracic spinal cord, timecourse_OLD_1 (rnaseq)

description: 10x v3

value: spinal cord


title: Pericyte_Primary_HBVP_2


title: Mid thoracic spinal cord, timecourse_2m_9 (rnaseq)

description: 10x v3

value: 2 months post SCI


title: His-Flag_B


title: APOE-/- sham mice + PBS

value: Sham induction + PBS


title: Mid thoracic spinal cord, timecourse_2m_3 (rnaseq)

description: 10x v3

value: wild type


title: cKO_2, scRNAseq

city: Wuhan

first: chuan

last: he

state: China

address: Fruit lake street

department: Medical Research Institute

institute: Wuhan University

description: 10x Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
Cellranger was utilized to calculate the raw counts and cell whitelist by default parameter
We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers under following criteria: MT% < 30%; Cell Gene Number < Median Gene Number * 2; Cell Gene Number > 200. PCA and tSNE analysis was used for the single cell to cell relation description. The fastMNN function  (k = 5, d = 50, approximate = TRUE, auto.order = TRUE) from R package scran (v1.10.2) was used to apply mutual nearest neighbor method to correct for batch effect among samples. Graphcluster was utilized for cell clustering and based on the marker gene achieved some cluster was combined. Wilcox rank sum test was then used for marker gene analysis.
Assembly: mmu10(Ensembl release 100)
Supplementary files format and content: MIX file and TSV file contain counts for each barcodes and genes

source_name: Subcutaneous MC38 tumors

growth_protocol: MC38 tumors were established by subcutaneously injecting 1×105 MC38 cells into 8-week-old WT and Ufl1 cKO mice. 16 days after injection, tumors were isolated from the subcutaneous body of mice.

extract_protocol:
Each sample was placed in a sterile Petri dish on ice. Fat, fibrous and necrotic areas were removed, and the tissue was subsequently minced to smaller pieces of less than 3 mm. Samples were first washed with phosphate-buffered saline (PBS), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with collagenase Ⅱ (Worthington) for 60 min at 37°C, with agitation. Subsequently, the sample was filtered using a 70-mm nylon mesh (Miltenyi #130-095-823). 10 ml of this cell suspension was counted by Trypan Blue to determine the concentration of live cells. The sample was then centrifuged at 300g and 4℃ for 5 min, and the supernatant was discarded. The cell pellet was resuspended in 1 ml freezing media (Gibco) for long term cryopreservation in liquid nitrogen. Throughout the dissociation procedure, cells were maintained on ice whenever possible, and the entire procedure was completed in less than 1 hr.
Cryopreserved single-cell suspensions were promptly thawed and prepared as outlined by the 10x Genomics Single Cell 3 v3.1 Reagent Kit user guide.

value: Subcutaneous MC38 tumors

value: CD45+ immune cells

value: Immune cells

value: cKO


title: Pericyte_Primary_HBVP_1


title: HBL1_ULK2_then1_24hr_ACAL

city: Bethesda

first: David

last: Huang

address: 9000 Rockville Pike

institute: National Cancer Institute

description:
S1 flow cell
12_HBL1_ULK2_then1_24hr_ACAL_S47

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 human genome using STAR2
Raw read counts per gene were called with Htseq-Count
Assembly: hg19
Supplementary files format and content: Tab-delimited text files of median-shift normalized count of each gene and each sample

growth_protocol: DLBCL cell liness were grown in advanced RPMI supplemented with 5% FBS with pen/strep and glutamine.

extract_protocol:
RNA wass extracted using the Qiagen AllPrep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The DLBCL cell lines were grown at 0.5 x 10^6 cells/ml and either treated  with vehicle (DMSO) or 25 nM acalabrutinib  for  24 hours. 2 x 10^6 cells were collected for each sample.

value: human DLBCL cell line

value: Cas9 engineered, ULK1 and ULK2 KO

value: 100 nM acalabrutinib_24h


title: His-Flag_A


title: Mid thoracic spinal cord, timecourse_2m_2 (rnaseq)

description: 10x v3


title: cKO_1, scRNAseq

description: 10x Genomics


title: siEXOSC10_2xFlag-His6-EXOSC10K583R_biol rep 2

data_processing:
Raw data were quality checked using FastQC, no reads had to be removed due to low quality. Most reads had a Phred score higher than 30.
For mapping the aligner STAR v2.7.10a with the following settings was used: --sjdbOverhang 50 --outSAMtype BAM SortedByCoordinate --outWigType bedGraph --outWigStrand Stranded --quantMode GeneCounts --outReadsUnmapped Fastx --outFilterMismatchNmax 1 --outFilterMultimapNmax 1 --outWigNorm RPM
Assembly: GRCh38.p13
Supplementary files format and content: bigWig, unstranded genome coverage

source_name: HeLa

growth_protocol: HeLa cells were grown at 37°C in 5% CO2 in DMEM supplemented with 10% foetal bovine serum.

extract_protocol:
Total RNA was extracted using TRI reagent (Sigma) according to the manufacturer's instructions. DNase treatment was performed using TURBO DNase at 37°C for 15 min and RNA was re-purified using the RNA clean and concentrator kit (Zymo Research) according to the manufacturer's instructions.
Total RNA was depleted of rRNA and libraries were constructed by TruSeq total RNA library preparation (Illumina) according to the maufacturer's instructions.

treatment_protocol: For hypoxia treatment, cells were grown as above with 1% O2 for 24 h. Where indicated cells were transfected with siRNAs (50 nmol) using RNAiMAX transfection reagent and harevested after 72 h. Expression of Flag-tagged proteins was induced by treatement with 1ug/ml tetracycline for 24 h before harvesting.

value: HeLa


title: siEXOSC10_2xFlag-His6-EXOSC10K583R_biol rep 1


title: WT_2, scRNAseq

description: 10x Genomics


title: siEXOSC10_2xFlag-His6-EXOSC10WT_biol rep 2


title: WT_1, scRNAseq

description: 10x Genomics


title: HBL1_ULK1_then2_24hr_ACAL

description:
S1 flow cell
11_HBL1_ULK1_then2_24hr_ACAL_S46


title: HBL1_ATG9A_24hr_ACAL

description:
S1 flow cell
10_HBL1_ATG9A_24hr_ACAL_S45

value: Cas9 engineered, ATG9A KO


title: Mid thoracic spinal cord, timecourse_1m_9 (rnaseq)

description: 10x v3

source_name: Mid thoracic spinal cord

extract_protocol:
For snRNA-seq experiment, single-nucleus dissociation of the mouse lumbar spinal cord was performed according to our established procedures. Following euthanasia by isoflurane inhalation and cervical dislocation, the spinal cord injury site was immediately dissected and frozen on dry ice. Spinal cords were doused in 500 µL sucrose buffer (0.32 M sucrose, 10 mM HEPES [pH 8.0], 5 mM CaCl2, 3 mM Mg acetate, 0.1 mM EDTA, 1 mM DTT) and 0.1% Triton X-100 with the Kontes Dounce Tissue Grinder. 2 mL of sucrose buffer was then added and filtered through a 40 µm cell strainer. The lysate was centrifuged at 3200 g for 10 min at 4°C. The supernatant was then decanted, and 3 mL of sucrose buffer was added to the pellet for 1 min. We homogenized the pellet using an Ultra-Turrax and 12.5 mL of density buffer (1 M sucrose, 10 mM HEPES [pH 8.0], 3 mM Mg acetate, 1 mM DTT) was added below the nuclei layer. The tube was centrifuged at 3200 g at 4°C and supernatant poured off. Nuclei on the bottom half of the tube wall were collected with 100 µL PBS with 0.04% BSA and 0.2 U/µL RNase inhibitor. Finally, nuclei were resuspended through a 30 µm strainer, and adjusted to 1000 nuclei/µL. snRNA-seq library preparation was carried out using the 10x Genomics Chromium Multiome ATAC + Gene Expression Kit Version 3. The nuclei suspension was added to the Chromium RT mix to achieve loading numbers of 10,000 nuclei. For downstream cDNA synthesis (13 PCR cycles), library preparation and sequencing, the manufacturer’s instructions were followed. For spatial transcriptomics, we carried out two separate experiments to study the cytoarchitecture of the lesion microenvironment after SCI. First, we prepared sections from uninjured mice, 7 days and 2 months after crush SCI. For each experimental condition, we prepared sections from the lesion epicenter of three independent biological replicates. Second, to prepare our four-dimensional spatiotemporal atlas, we collected sections throughout the entire spinal cord of mice from each of the three experimental conditions. The spinal cord injury sites of mice were embedded in OCT and cryosections were generated at 10 µm at −20 °C. For the four-dimensional atlas, every fifth section was collected throughout the entire dorsoventral axis of each spinal cord. Sections were immediately placed on chilled Visium Tissue Optimization Slides or Visium Spatial Gene Expression Slides.
We used 10x Genomics Chromium Single Cell Gene Expression Kit Version 3.1 kit to profile the snRNA sequencing and Visium Spatial Gene Expression to profile the spatial transcriptomics.

value: 1 month post SCI


title: Mid thoracic spinal cord, timecourse_1m_10 (rnaseq)

description: 10x v3


title: siEXOSC10_2xFlag-His6-EXOSC10WT_biol rep 1


title: LN-Red

city: New York

first: Vanessa

last: Cristaldi

address: 522 First Avenue

department: Dermatology

institute: NYU Langone Health

description: scRNA-Seq + Cite-seq

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

source_name: P14 CD8 T cells from draining lymph nodes after skin vaccinia-GP33 infection

extract_protocol: CD8 T cells were isolated from mouse draining lymph nodes of ears 12 days post ear infection with vaccinia-GP33. Draining lymph nodes were pooled from 29 mice (male and female). Mouse lymph nodes  were smashed on a 70um filter. Lymph node suspension was filtered and then cells were stained with CD8a PE-Cy7. Cells were then enriched using Miltenyi magnetic enrichment kit. CD8 cells were then fluorescence activated cell sorted for CD8+ , CD45 intravenous negative, CD44+, DAPI-

value: Lymph node

value: CD8 T cell


title: Mid thoracic spinal cord, timecourse_14d_10 (rnaseq)

description: 10x v3

value: 14 days post SCI


title: HBL1_ATG101_24hr_ACAL

description:
S1 flow cell
9_HBL1_ATG101_24hr_ACAL_S44

value: Cas9 engineered, ATG101 KO


title: Mid thoracic spinal cord, timecourse_1m_5 (rnaseq)

description: 10x v3

value: spinal cord


title: HBL1_A20_24hr_ACAL_R2

description:
S1 flow cell
8_HBL1_A20_24hr_ACAL_S43

value: Cas9 engineered, TNFAIP3 KO


title: HeLa_Hypoxia_biol rep 3

value: WT


title: HBL1_NT_24hr_ACAL_R2

description:
S1 flow cell
7_HBL1_NT_24hr_ACAL_S42

value: Cas9 engineered, control KO


title: HeLa_Hypoxia_biol rep 2


title: HeLa_Hypoxia_biol rep 1


title: CB67 WT

city: Bunkyo-ku

first: Naoko

last: Yokota

state: Tokyo

address: 1-1-1 yayoi

department: Department of Cell and Molecular Biology

country: Japan

institute: The University of Tokyo

data_processing:
Sequence reads were mapped to the reference genome with the bowtie mapping tool. The reads mapped to each 10-bp genome bin were counted with the parse2qig comand in DROMPA3.
Assembly: R64 (sacCer3)
Supplementary files format and content: wig, the number of RNA-seq reads mapped to the indicated genome bins.
Supplementary files format and content: Gene expression files (*.genes.results.txt) were generated using STAR version 2.7.3a with default parameters and RSEM v1.3.1 with the option "--estimate-rspd --strandedness reverse".

organism: Saccharomyces cerevisiae

growth_protocol: Cells were cultured in YEP medium (1 % yeast extract, 2 % peptone, 40 μg ml-1 adenine) supplemented with 2 % glucose

extract_protocol:
Total RNA was prepared from 2.5x108 yeast cells with Trizol (Invitrogen) and RNA extraction was performed according to the manufacture’s description. Briefly, 1 ml of Trizol reagent was added to the cells and cell disruption was achieved through vortexing (2 minutes) in the presence of glass beads. Then, 0.2 ml of chloroform was added to the cell suspension and incubated for 2 minutes at room temperature. Samples were centrifuged at 12,000 g for 15 minutes at 4˚C and the aqueous phase was transferred to a fresh tube and mixed with 0.5 ml isopropanol. For RNA precipitation, samples were incubated at room temperature for 10 minutes and centrifuged at 12,000 g for 10 minutes at 4˚C. RNA pellets were then washed with 70 % ethanol, air-dried and dissolved in 50 µl RNase-free water.
RNA-seq samples were prepared according to the manufacture's standard protocol (TruSeq Standard Total RNA Sample Prep Kit, Illumina).

treatment_protocol: For G2/M cell cycle arrest, benomyl (Merck, 381586) was added to the YEPD media for a final concentration 80 µg ml-1. For G2/M-arrest following synchronization in G1-phase, cells were released into benomyl-containing YEPD for 60 minutes.

value: G2/M-arrest following an S-phase at 35°C


title: Mid thoracic spinal cord, timecourse_14d_9 (rnaseq)

description: 10x v3

value: wild type


title: HBL1_ULK2_then1_24hr_DMSO

description:
S1 flow cell
6_HBL1_ULK2_then1_24hr_DMSO_S41


title: Mid thoracic spinal cord, timecourse_14d_8 (rnaseq)

description: 10x v3


title: HBL1_ULK1_then2_24hr_DMSO

description:
S1 flow cell
5_HBL1_ULK1_then2_24hr_DMSO_S40


title: TJ1 -32hrs-replicate-3

city: Buffalo

first: Johnny

last: Cruz Corchado

address: Elm & Carlton Streets Buffalo,L3-L125

department: Cell Stress

institute: Roswell Park Comprehensive Cancer Institue

data_processing:
The quality of the RNA sequences was assessed with FastQC
Adapters sequences and reads with a quality lower than Q25 were trimmed by using Trimgalore version 0.67.
Sequencing reads were aligned to the C. elegans genome WBcel235  using the Star aligner v2.7.9a2
Aligned reads were quantified with FeatureCounts v2.0.1 from the package Rsubread3 .
Differential expression analysis was performed using DESeq2
Assembly: WBcel235
Supplementary files format and content: csv file include DESeq2 normalized counts for all Samples
Supplementary files format and content: csv file include CPM values for all Samples
Supplementary files format and content: csv File Raw normalized counts include raw values for all  Samples

organism: Caenorhabditis elegans

source_name: Whole Animal

growth_protocol: Day-one adult worms were bleach-hatched and ~3200 eggs/genotype (~800 eggs/plate and 4 plates/genotype) were seeded on fresh OP50 plates and allowed to grow for either 15 hours or 32 hours at 25 C.

extract_protocol:
Worms were washed with sterile water and total RNA was extracted from biological triplicates using the Direct-zol RNA Miniprep Kits Worms were washed with sterile water and total RNA was extracted from biological triplicates using the Direct-zol RNA Miniprep Kits
Libraries were prepared using Illumina TruSeq Stranded mRNA kit.

value: Whole Animal

value: Growth Time :32 hrs


title: CB980 top2-4


title: HeLa_Normoxia_biol rep 3


title: Mid thoracic spinal cord, timecourse_7d_9 (rnaseq)

description: 10x v3

value: 7 days post SCI


title: TJ1 -32hrs-replicate-2


title: HBL1_ATG9A_24hr_DMSO

description:
S1 flow cell
4_HBL1_ATG9A_24hr_DMSO_S39

value: human DLBCL cell line


title: HeLa_Normoxia_biol rep 2

value: HeLa


title: Mid thoracic spinal cord, timecourse_7d_4 (rnaseq)

description: 10x v3


title: LN-Green

description: scRNA-Seq + Cite-seq


title: HBL1_ATG101_24hr_DMSO

description:
S1 flow cell
3_HBL1_ATG101_24hr_DMSO_S38


title: HBL1_A20_24hr_DMSO_R2

description:
S1 flow cell
2_HBL1_A20_24hr_DMSO_S37


title: Mid thoracic spinal cord, timecourse_4d_6 (rnaseq)

description: 10x v3

value: 4 days post SCI


title: Mid thoracic spinal cord, timecourse_4d_8 (rnaseq)

description: 10x v3


title: TJ1 -15hrs-replicate-2

value: Growth Time :15 hrs


title: HBL1_NT_24hr_DMSO_R2

description:
S1 flow cell
1_HBL1_NT_24hr_DMSO_S36


title: Mid thoracic spinal cord, timecourse_4d_5 (rnaseq)

description: 10x v3


title: HBL1_WIPI2_24hr_DMSO

description:
S1 flow cell
HBL1_Wipi_plusDMSO_24h

value: Cas9 engineered, WIPI2 KO


title: Balilla-4x, normal,rep2 [E250_2]

city: Suzhou

first: Shiqin

last: Yang

address: No.1 Jianxiong Road, Taicang, Suzhou

institute: Suzhou Chien-Shiung Institute of Technology,

data_processing:
SeqPrep was used to remove splices or merge overlapping paired reads into a single read (https://github.com/jstjohn/SeqPrep), and use Sickle to remove low-quality reads (https://github.com/najoshi/sickle).
Then calibrate the data with the reference genome of rice using HISAT2 v2.1.0.
Assembly: MSU_7
Supplementary files format and content: raw counts, RPKM for each sample.

organism: Oryza sativa

source_name: leaves

growth_protocol: The rice plants (Balilla-2x and Balilla-4x) used in this study, grew in the paddy field of experimental fields in Shanghai during the natural growing seasons.

extract_protocol:
The leaves of Balilla-2x and Balilla-4x plants were sampled for RNA isolation. According to the manufacturer's instructions, total RNA was extracted from rice leaves using Trizol reagent (LifeTechnologies).
Qualified RNA samples were used for library construction according to Tru®Seq RNA Library Preparation Kit v2(Illumina).

value: leaves

value: four week old

value: normal


title: TJ1 -15hrs-replicate-1


title: TJ1 -15hrs-replicate-3


title: Balilla-4x, normal,rep1 [E250_1]


title: Mid thoracic spinal cord, timecourse_1d_8 (rnaseq)

description: 10x v3

value: spinal cord

value: 1 day post SCI


title: Balilla-4x, normal,rep3 [E250_3]


title: VP14/TJ1-32hrs-replicate-3

growth_protocol: Day-one adult worms were bleach-hatched and ~3200 eggs/genotype (~800 eggs/plate and 4 plates/genotype) were seeded on fresh OP50 plates and allowed to grow for either 15 hours or 32 hours at 25C.


title: HBL1_WIPI2_24h_ACAL

description:
S1 flow cell
HBL1_Wipi_plusACAL_24h

value: 100 nM acalabrutinib_24h


title: Balilla-2x, normal,rep3 [E251_3]


title: Mid thoracic spinal cord, timecourse_1d_3 (rnaseq)

description: 10x v3


title: Mid thoracic spinal cord, timecourse_1d_2 (rnaseq)

description: 10x v3


title: HBL1_NT_24h_DMSO_R1

description:
S1 flow cell
HBL1_NT_plusDMSO_24h

value: Cas9 engineered, control KO


title: Balilla-2x, normal,rep2 [E251_2]


title: VP14 -32hrs-replicate-3


title: Balilla-2x, normal,rep1 [E251_1]


title: cep-1-OE-32hrs-replicate-3


title: HeLa_Normoxia_biol rep 1

city: Göttingen

first: Katherine

last: Bohnsack

address: Humboldtallee 23

institute: University Medical Centre Göttingen

source_name: HeLa Flp-In  T-REx

value: HeLa Flp-In  T-REx

value: WT


title: TJ1 -32hrs-replicate-1

value: Whole Animal


title: HBL1_ATG5_24hr_DMSO

description:
S1 flow cell
HBL1_ATG5_plusDMSO_24h

value: Cas9 engineered, ATG5 KO


title: HBL1_NT_24hr_ACAL_R1

description:
S1 flow cell
HBL1_NT_plusACAL_24h


title: N2 -32hrs-replicate-3

value: Growth Time :32 hrs


title: Huh7 cells, sgMETTL16-2

city: Duarte

first: Rui

last: Su

address: 1500 E Duarte Rd

institute: City of Hope

description:
Ribozero RNA
MX_Su70

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were mapped to the human GRCh38 using the STAR aligner.
The aligned reads were then assigned to genes using RSEM
Assembly: GRCh38
Supplementary files format and content: TPM of each gene were calculated by RSEM.

growth_protocol: Huh7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using RNA Clean & Concentrator-5 Kit (R1015, Zymo Research). 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded mRNA-Seq Kit  following manufacturer's protocols.

treatment_protocol: Huh7 Cas9 single clone cells were infect with lentiviral guide RNA, and selected by hygromycin B at 1mg/mL to obtain stable cell lines.

value: liver cancer cells

value: METTL16 knockdown


title: HBL1_ATG5_24hr_ACAL

description:
S1 flow cell
HBL1_ATG5_plusACAL_24h

value: human DLBCL cell line


title: Huh7 cells, sgMETTL16-1

description:
Ribozero RNA
MX_Su69


title: Mid thoracic spinal cord, sex_male_13 (rnaseq)

city: Geneve

first: Alan Yue Yang

last: Teo

address: Chem. des Mines 9, Campus Biotech

institute: EPFL

description: 10x v3

value: Male

value: wild type


title: Mid thoracic spinal cord, sex_male_11 (rnaseq)

description: 10x v3


title: cep-1-OE-32hrs-replicate-2


title: Huh7 cells, sgNS-2

description:
Ribozero RNA
MX_Su68


title: VP14 -32hrs-replicate-2


title: Mid thoracic spinal cord, severity_1_4 (rnaseq)

description: 10x v3

value: SCI at 1 mm space


title: Mid thoracic spinal cord, severity_1_2 (rnaseq)

description: 10x v3


title: HBL1_ATG14_24h_ACAL

description:
S1 flow cell
HBL1_ATG14_plusACAL_24h

value: Cas9 engineered, ATG14 KO


title: HBL1_ATG14_24hr_DMSO

description:
S1 flow cell
HBL1_ATG14_plusDMSO_24h


title: N2 -32hrs-replicate-2


title: HBL1_A20_24hr_DMSO_R1

description:
S1 flow cell
HBL1_A20_plusDMSO_24h

value: Cas9 engineered, TNFAIP3 KO


title: FMN_14h_CTRL 3

city: Rehovot

first: Shay

last: Covo

state: Central District

address: POB 12

department: Plant Pathology and Microbiology

country: Israel

institute: Hebrew University of Jerusalem

data_processing:
Raw data quality was assessed using FASTQC (Babraham Bioinformatics)
Raw reads were mapped against the F. mangiferae [GCA_900044065.1] reference genome using STAR version 2.5 (Dobin et al., 2013).
Reads were counted with with HTSeq (Anders et al., 2014).
Reads were assembled, normalized and gene-expression level was quantified using the DESeq2 R package (version 1.3.4) data-normalization method
Assembly: GCA_900044065.1
Supplementary files format and content: Excel file contaning normalized reads of all samples. file includes two sheets, each sheet contains samples for one of two time points; 8 h post innoculation (fmn_uv_8h_norm_counts) and 14 h post innoculation (fmn_uv_14h_norm_counts)

organism: Fusarium mangiferae

source_name: Germinating conidia

growth_protocol: Spores of F. mangiferae strain MRC7560 were incubated in KNO3-based medium on an orbital shaker (250 rpm) at 25 °C for 5 days. Microconidia were obtained by filtering the culture through a nylon cell strainer (mesh size 40 µm, Corning, USA) and resuspended in sterile water. Conidia were then inoculated into potato dextrose broth (PDB; BD Sparks, USA) at 1 x 108 conidia/ml. The cultures were incubated on an orbital shaker at 25 °C for either 8 or 14 h and then harvested immediately or treated as specified.

extract_protocol:
Germinating conidia / filaments were disrupted in a Minilys bead beater (Bertin Instruments, France) for 30 s at medium speed. Total RNA was extracted with the Qiagen (USA) RNeasy micro kit and was treated on-column with RQ1 RNase-free DNase (Promega, USA) to remove additional residues of genomic DNA. RNA quality was quantified by Agilent 2200 TapeStation machine using an RNA kit (Agilent Technologies, USA). For quantification, 1 µl RNA was quantified with a Qubit 2.0 Fluorometer and RNA BR kit (Life Technologies, USA).
cDNA libraries were prepared using 0.5 µg RNA with a QuantSeq 3ʹ mRNA-Seq Library Prep Kit FWD (Lexogen GmbH, Austria) and were sequenced using the NextSeq 500 system (Illumina, USA) at the Center for Genomic Technologies of the Hebrew University of Jerusalem.

treatment_protocol: Spores or germlings of F. mangiferae (8 and 14 h post-inoculation) were obtained by filtering 10 ml of the cultures, and suspensions with 2 x 107 conidia/ml were irradiated with either 50 -200 J/m2 UV light (254 nm, 15 W lamp, Osram, Germany); the incident fluence was measured with a radiometer (YK-35UV, Digital Instruments, USA).

value: Germinating conidia

value: Fungal asexual spore

value: Untreated at 14 hpi


title: Mid thoracic spinal cord, sex_male_20 (rnaseq)

description: 10x v3

value: spinal cord


title: VP14/TJ1-32hrs-replicate-2


title: FMN_14h_200J_60m 3

value: 200J UVC + 60 m recovery at 14 hpi


title: TMD8_ATG7_24hr_ACAL

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
52_TMD8_ATG7_24hr_ACAL_S87

source_name: cell line

growth_protocol: TMD8 cells were grown in advanced RPMI supplemented with 5% FBS with pen/strep and glutamine.

treatment_protocol: The DLBCL cell line TMD8 was grown at 0.5 x 10^6 cells/ml and either treated  with vehicle (DMSO) or 25 nM acalabrutinib  for  24 hours. 2 x 10^6 cells were collected for each sample.

value: cell line

value: Cas9 engineered, ATG7 KO

value: 25 nM acalabrutinib_24h


title: FMN_14h_200J_30m 3

value: WT

value: 200J UVC + 30 m recovery at 14 hpi


title: Mid thoracic spinal cord, severity_0_25_4 (rnaseq)

description: 10x v3

value: SCI at 0.25 mm space


title: Huh7 cells, sgNS-1

description:
Ribozero RNA
MX_Su67

value: liver cancer cells


title: cep-1-OE-32hrs-replicate-1

value: Whole Animal

value: Growth Time :32 hrs


title: Mid thoracic spinal cord, severity_0_25_3 (rnaseq)

description: 10x v3

value: wild type


title: FMN_14h_200J_0m 3

value: 200J UVC + 0 m recovery at 14 hpi


title: Mid thoracic spinal cord, severity_0_25_2 (rnaseq)

description: 10x v3


title: TMD8_ATG5_24hr_ACAL

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
51_TMD8_ATG5_24hr_ACAL_S86

value: human DLBCL cell line

value: Cas9 engineered, ATG5 KO


title: VP14 -32hrs-replicate-1


title: VP14/TJ1-32hrs-replicate-1


title: N2 -32hrs-replicate-1


title: FMN_14h_50J_60m 3

value: Germinating conidia

value: Fungal asexual spore

value: 50J UVC + 60 m recovery at 14 hpi


title: HBL1_A20_24hr_ACAL_R1

description:
S1 flow cell
HBL1_A20_plusACAL_24h

value: Cas9 engineered, TNFAIP3 KO

value: 100 nM acalabrutinib_24h


title: TMD8_WIPI2_24hr_ACAL

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
50_TMD8_WIPI2_24hr_ACAL_S85

value: cell line

value: Cas9 engineered, WIPI2 KO


title: VP14/TJ1-15hrs-replicate-3

value: Growth Time :15 hrs


title: TMD8_ATG14_24hr_ACAL

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
48_TMD8_ATG14_24hr_ACAL_S83

value: Cas9 engineered, ATG14 KO

value: 25 nM acalabrutinib_24h


title: Mid thoracic spinal cord, severity_0_5 (rnaseq)

description: 10x v3

value: spinal cord

value: SCI with no space


title: FMN_14h_50J_30m 3

value: WT

value: 50J UVC + 30 m recovery at 14 hpi


title: Mid thoracic spinal cord, severity_0_2 (rnaseq)

description: 10x v3

value: wild type


title: cep-1-OE-15hrs-replicate-3

value: Whole Animal


title: Mid thoracic spinal cord, severity_0_3 (rnaseq)

description: 10x v3


title: FMN_14h_CTRL 2

value: Untreated at 14 hpi


title: TMD8_RB1CC1_24hr_ACAL

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
46_TMD8_RB1CC1_24hr_ACAL_S81

value: human DLBCL cell line

value: Cas9 engineered, RB1CC1 KO


title: Mid thoracic spinal cord, mechanism_hemi_3 (rnaseq)

description: 10x v3

value: Hemisection injury model


title: N2 -15hrs-replicate-3


title: Mid thoracic spinal cord, mechanism_hemi_2 (rnaseq)

description: 10x v3


title: Mid thoracic spinal cord, severity_1_1 (rnaseq)

description: 10x v3

value: SCI at 1 mm space


title: FMN_14h_50J_0m 3

value: Germinating conidia

value: Fungal asexual spore

value: 50J UVC + 0 m recovery at 14 hpi


title: VP14 -15hrs-replicate-3

value: Growth Time :15 hrs


title: VP14/TJ1-15hrs-replicate-2


title: TMD8_ULK2_then1_24hr_ACAL

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
45_TMD8_ULK2_then1_24hr_ACAL_S80

value: cell line

value: Cas9 engineered, ULK1 and ULK2 KO


title: FMN_14h_200J_30m 2

value: 200J UVC + 30 m recovery at 14 hpi


title: cep-1-OE-15hrs-replicate-2


title: Mid thoracic spinal cord, mechanism_hemi_1 (rnaseq)

description: 10x v3

value: spinal cord


title: FMN_14h_200J_60m 2

value: WT

value: 200J UVC + 60 m recovery at 14 hpi


title: VP14 -15hrs-replicate-2


title: FMN_14h_50J_60m 2

value: 50J UVC + 60 m recovery at 14 hpi


title: TMD8_ULK1_then2_24hr_ACAL

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
44_TMD8_ULK1_then2_24hr_ACAL_S79

value: 25 nM acalabrutinib_24h


title: FMN_14h_50J_30m 2

value: 50J UVC + 30 m recovery at 14 hpi


title: TMD8_ATG9A_24hr_ACAL

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
43_TMD8_ATG9A_24hr_ACAL_S78

value: human DLBCL cell line

value: Cas9 engineered, ATG9A KO


title: Mid thoracic spinal cord, mechanism_contusion_1 (rnaseq)

description: 10x v3

value: Contusion injury model

value: wild type


title: Mid thoracic spinal cord, mechanism_contusion_4 (rnaseq)

description: 10x v3


title: TMD8_NT_24hr_ACAL

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
39_TMD8_NT_24hr_ACAL_S74

value: Cas9 engineered, control KO


title: VP14/TJ1-15hrs-replicate-1

value: Whole Animal


title: TMD8_ATG7_24hr_DMSO

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
38_TMD8_ATG7_24hr_DMSO_S73

value: Cas9 engineered, ATG7 KO


title: Mid thoracic spinal cord, mechanism_contusion_2 (rnaseq)

description: 10x v3


title: N2 -15hrs-replicate-2

value: Growth Time :15 hrs


title: TMD8_A20_24hr_ACAL

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
40_TMD8_A20_24hr_ACAL_S75

value: cell line

value: Cas9 engineered, TNFAIP3 KO


title: FMN_14h_200J_0m 2

value: Germinating conidia

value: Fungal asexual spore

value: 200J UVC + 0 m recovery at 14 hpi


title: TMD8_ATG101_24hr_ACAL

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
42_TMD8_ATG101_24hr_ACAL_S77

value: Cas9 engineered, ATG101 KO


title: FMN_14h_50J_0m 2

value: WT

value: 50J UVC + 0 m recovery at 14 hpi


title: Mid thoracic spinal cord, drug_mino_9 (rnaseq)

description: 10x v3

value: spinal cord

value: Minocycline treatment


title: cep-1-OE-15hrs-replicate-1


title: VP14 -15hrs-replicate-1


title: TMD8_ATG5_24hr_DMSO

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
37_TMD8_ATG5_24hr_DMSO_S72

value: human DLBCL cell line

value: Cas9 engineered, ATG5 KO


title: FMN_14h_CTRL 1

value: Untreated at 14 hpi


title: Mid thoracic spinal cord, drug_mino_5 (rnaseq)

description: 10x v3

value: wild type


title: N2 -15hrs-replicate-1

value: Whole Animal


title: Mid thoracic spinal cord, drug_mino_7 (rnaseq)

description: 10x v3


title: FMN_14h_200J_60m 1

value: 200J UVC + 60 m recovery at 14 hpi


title: FMN_14h_200J_30m 1

value: 200J UVC + 30 m recovery at 14 hpi


title: Mid thoracic spinal cord, drug_meth_7 (rnaseq)

description: 10x v3

value: Methylprednisolone treatment


title: TMD8_ATG14_24hr_DMSO

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
34_TMD8_ATG14_24hr_DMSO_S69

value: cell line

value: Cas9 engineered, ATG14 KO


title: FMN_14h_200J_0m 1

value: Germinating conidia

value: Fungal asexual spore


title: TMD8_RB1CC1_24hr_DMSO

description:
S1 flow cell
TMD8_RNAseq_22_MedianShift_Normalized_log2.txt
32_TMD8_RB1CC1_24hr_DMSO_S67

value: Cas9 engineered, RB1CC1 KO