title: CnR_Flx1: Satb2 flx/flx DIV14 primary cortical cultures, 1h bic, rep1

data_processing:
Illumina Universal adapters were trimmed with Trim Galore! with default parameters (--paired --illumina).
The trimmed reads were aligned to mouse genome (mm10) with Bowtie2 (v2.4.5) with the following settings:  bowtie2 --dovetail --local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700 -p 48 -x mm10. Reads with a mapping quality score (MAPQ) < 2 as well as optical and PCR duplicates are excluded. Replicate BAM files were merged and handled as single file for the next steps.
Genome coverage bedgraph files were computed with bamCoverage (bin size 50 bp) and normalized to reads per kilobase per million (RPKM) to minimize bias arising from different sequencing depths and batches. Unspecific noise was filtered out by subtracting the mean signal from each value of the corresponding bedgraph files.
Peaks were called with SEACR v1.4 under relaxed conditions and normalized to the IgG control bedgraph file.
Assembly: mm10
Supplementary files format and content: bed
Library strategy: CUT&RUN

extract_protocol:
For CUT&RUN, nuclei of 106 cells were isolated by addition of nuclei extraction buffer (NEB, 20 mM Hepes (KOH) pH 7.9, 10 mM KCl, 0.5 mM Spermidine, 0.1 % Triton X-100, 20 % Glycerol, 1 tablet cOmplete EDTA-free Protease inhibitor). Cells were incubated at 4 °C for 15 min, lifted from the dish using a cell lifter and gently resuspended. Nuclei suspension was spun down at 600 g at 4 °C for 3 min. Pellet was resuspended in NEB and intact nuclei were counted in a Neubauer chamber. 100 000 nuclei were used for each CUT&RUN reaction. After Concavalin-A conjugated beads activation (21-1401-EPC Epicypher), nuclei were demobilized and blocked in blocking buffer (20 mM Hepes pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.1 % BSA, 2 mM EDTA, 1 tablet cOmplete EDTA-free Protease inhibitor) at RT for 5 min. After washing in washing buffer (20 mM Hepes pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.1 % BSA, 1 tablet cOmplete EDTA-free Protease inhibitor) primary antibody was added and incubated at 4 °C for 2 h. Reaction was washed twice  before adding pAG-MNAse (15-1016-EPC Epicypher) and incubated for 1h at 4°C. Next, beads were washed twice before addition of 100 mM CaCl2 for 30 min at 0 °C in an ice water bath. 2X STOP buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 µg/ml RNAseA, 40 µg/ml Glycogen, 10 pg/ml E.Coli spike-in DNA) was added and beads were incubated for 20 min at 37 °C to release DNA fragments and to digest RNA. DNA was purified by Phenol-Chloroform extraction and precipitated in 95 % EtOH at -80 °C. Pellet was dissolved in TE buffer pH 8.0 (12090015, ThermoFisher) and stored at -20 °C.
Libraries were prepared using the NEBNext Ultra Library prep Kit (E7645S, New England Biolabs) according to the manufacturer’s protocol. Adapters were used according to the DNA input at a working concentration of 1.5 µM. Library was PCR amplified with unique indexes (E7335S, New England Biolabs) for 14 cycles. After clean-up fragment size and concentration was analyzed before sending for sequencing.

value: Cortex

value: DIV14 primary cortical cultures

value: Satb2 flx/flx

value: 1h bicucculine

tag: cut&run antibody

value: SATB2 (Abcam, ab92446)


title: DMS273

status: Public on Jan 22 2024

type: SRA

city: Houston

first: Carl

last: Gay

state: TX

address: 1515 Holcombe Blvd

department: Thoracic-Head & Neck Med Onc

country: USA

institute: The University of Texas MD Anderson Cancer Center

description: NuGEN Ovation RRBS Methyl-Seq

library_source: genomic

data_processing:
Seqeuncing reads were trimmed for adapters using TrimGalore-0.6.5
Trimmed reads were mapped to reference genome using bwa
Mapped reads were deduped using NuGEN nudup tool package
Methylation beta values were computed using Bismark-0.22.3
Assembly: hg38
Supplementary files format and content: gzipped tab delimited text file for CpG locations and beta values

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: RPMI-1640 with 10% fetal calf serum

extract_protocol:
Qiagen AllPrep DNA/RNA Mini Kit
Briefly, approximately 100ng of genomic DNA was digested using MspI, and Illumina-compatible cytosine-methylated adaptor were ligated to the enzyme-digested DNA. RRBS libraries were then visualized using Bioanalyzer High Sensitivity DNA chips (Agilent, Santa Clara, CA), and those passing QC were subsequently sequenced as 100bp paired-end reads on an Illumina NovaSeq instrument.
NuGEN Ovation RRBS Methyl-Seq

treatment_protocol: drugs were diluted in DMSO and directly added to cell culture medium. Medium and drug was replaced every other day during treatment period.

tag: cell line

tag: cell type

value: Small Cell Lung Cancer

tag: genotype

value: WT

tag: treatment

value: untreated

tag: time

value: 0 day


title: H1092

description: NuGEN Ovation RRBS Methyl-Seq


title: H1105

description: NuGEN Ovation RRBS Methyl-Seq


title: miRNAs-M28_AB

city: Mexico City

first: Mariana

last: Flores Torres

address: Periferico Sur 4809

country: Mexico

institute: Instituto Nacional de Medicina Genomica

library_source: transcriptomic

data_processing:
Data quality control analysis was performed before and after adaptor removal using FastQC.
3'-adaptors were trimmed with Cudadapt (Phred score >30, min lenght 18).
Remaining sequences were aligned to the human genome (Hg38p12) with  BWA, miRNA profile was determined using miRDeep2 and miRBase v.22 as miRNA reference.
Reads were tallied to generate total counts for each miRNA.
Genome_build: Hg38p12
Supplementary_files_format_and_content: csv file reports raw counts

molecule: total RNA

source_name: Plasma

extract_protocol:
Total RNA was extracted from pregnant women plasma samples (2 mL) at 1st, 2nd and 3rd trimester (same women for each trimester) using TRI Reagent Solution (Ambion), in a 3:1 sample volume ratio. Samples were mixed and incubated for 5 minutes at room temperature and centrifuged at 12,000 x g for 10 minutes at 4 °C. The remaining aqueous phase was removed and mixed with chloroform (0.2 mL per mL of TRI Reagent), the new aqueous phase was transferred to fresh tubes and isopropanol (0.5 mL per mL of TRI Reagent) was added, mixed, and incubated overnight at -75 °C. After incubation samples were centrifuged at 12,000 x g for 15 minutes at 4 °C. RNA pellet was resuspended in 75% ethanol and centrifuged at 7,500 x g at 4 °C for 5 minutes. RNA pellets were resuspended in 10 uL of RNase-free water and stored at -75 °C.
Library construction for small RNA sequencing analysis was performed with the NextFLEX small RNA-Seq kit v3 (Bioo Scientific), bands in an acrylamide gel, ranging from 50 to 150 bp were processed. Libraries were sequenced for 150 cycles, single-end, on an Illumina NextSeq 500.

value: After birth

tag: tissue

value: Plasma


title: CnR_IgG2: Satb2 flx/flx DIV14 primary cortical cultures, 1h bic, IgG, rep2

city: Innsbruck

first: Nico

last: Wahl

address: Innrain 66

department: Institute for Neuroscience

country: Austria

institute: Medical University Innsbruck

organism: Mus musculus

source_name: Cortex

growth_protocol: Corical tissue was dissected at P0-P1, dissociated with Papain and titurated. Cells were plated in serum-containing medium (MEM, 1% horse serum, 0.1% Pen/Strep, 0.1 % sodium piruvate). After 2h, MEM was excahnged with serum-free feeding medium (Neurobasal-A Medium, containing B-27, 0.1% Pen/Strep and 2 mM Glutamine.  Cells were treated with 5µM cytosine arabinoside on DIV3 to inhibit glial cell proliferation.  At DIV4, one third of the medium was replaced by fresh serum-free feeding medium. Neurons were cultured for 14 days in 5% CO2 at 37°C.

treatment_protocol: Cottical neurons were treated with 20 µM NBQX for 16 h on DIV13. After silencing, neurons were stimulated with 50 µM biccuculine for 1h on DIV14 and then collected.

value: Rabbit IgG Negative Control Antibody (EpiCypher, 13-0042)


title: miRNAs-M30_3T

value: 3rd trimester


title: 17-100 MS NAWM

city: Amsterdam

first: Aletta

last: van den Bosch

address: Meibergdreef 47

country: Netherlands

institute: Netherlands institute of Neuroscience

description:
104343-001-028
allCounts.orig.tab

data_processing:
Putative adapter sequences were removed in the TruSeq adapter sequence set using cutadapt. Trimmed reads were mapped to the human reference genome GRCh37.75 using HiSAT2 v-2-1.0.
Gene levels were obtained using HTSeq v0.11.0.
Genes with more than 2 reads in at least 4 of the samples were retained.
Assembly: GRCh37.75

source_name: NAWM

growth_protocol: Cryosections of 20um were cut, and stained for HLA-DR with IHC.

extract_protocol:
Using the Rneasy micro kit the RNA was extracted.
PolyA-enrichment and low input library prep kit

treatment_protocol: Nodules and surrounding normal appearing white matter was collected with laser capture microdissection and dissociated with Trizure.

value: NAWM

tag: Sex

value: M

tag: age

tag: donor

tag: diagnosis

value: MS


title: DC2.4 cells, EXOuniSTING, Preparation 1

city: Chapel Hill

first: Ying

last: Wang

state: NC

address: 125 Mason Farm Road, 3118G Marsico Hall, Marsico Hall/3118G/3nd

institute: University of North Carolina at Chapel Hill

data_processing:
After removing reads with adapter or of low quality, clean reads were aligned to the mouse GRCm39 reference genome using hisat2 software, and only the uniquely mapped reads were retained for downstream analysis. The gene expression level was quantified using FeatureCounts function from Subread version 2.0.1.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: DC2.4 cells were cultured with RPMI1640 supplemented with 10% FBS, 1× non-essential amino acids (Gibco), 1× HEPES buffer (Gibco), and 0.0054× β-mercaptoethanol (Gibco). 4T1 wild-type cells were cultured in RPMI1640 supplemented with 10% FBS. All the adherent cell lines were cultured at 37 °C and 5% CO2 in a humidified atmosphere.

extract_protocol:
Total RNA was extracted from DC2.4 cells and 4T1 cells after different treatments by using RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. 1.0 µg of total RNA was used for the construction of sequencing libraries.
RNA library was generated by using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB) following manufacturer’s recommendations

treatment_protocol: DC2.4 cells and 4T1 tumor cells were treated with mRNAs (uniSTING mRNA or EGFP mRNA) either mixed with TransIT®-mRNA transfection agent (Mirus Bio) or encapsulated into SS-OP LNPs in DMEM culture medium supplemented with 10% FBS, according to the manufacturer’s instructions or conditions optimized in the Liu lab. For the investigation of the gene regulation in DC2.4 cells by miRNAs, the extracellular vesicles isolated from uniSTING (EXOuniSTING)- or Mock (EXOmock)-treated 4T1 tumor cells were incubated with DC2.4 cells for 24 hours before total RNA extraction.

value: Immortalized murine dendritic cells

value: Extracellular vesicles isolated from uniSTING treated 4T1 tumor cells


title: miRNAs-M32_2T

value: 2nd trimester


title: CnR_IgG1: Satb2 flx/flx DIV14 primary cortical cultures, 1h bic, IgG, rep1

value: Cortex

value: DIV14 primary cortical cultures

value: Satb2 flx/flx


title: DMS114

description: NuGEN Ovation RRBS Methyl-Seq

value: Small Cell Lung Cancer


title: ATAC_cKO3: Satb2 flx/flx::Nes-Cre DIV14 primary cortical cultures, 1h bic, rep3

data_processing:
Pair-end data were mapped by using BWA-MEM (v0.7.17) and the resulting SAM files were converted into sorted and indexed BAM files (SAMtools v1.1).
Peaks were identified per experimental condition by employing Genrich tool (v0.6.1)
Assembly: mm10
Supplementary files format and content: bed

extract_protocol:
For ATAC-seq, 106 primary cortical neurons plated on a 35 mm dish were washed twice with 1X PBS before addition of nuclei isolation buffer (1X PBS, 0.1 % Triton X-100, 5 mM AEBSF Pefabloc, 5 mM Na-Butyrate, 1 tablet cOmplete EDTA-free Protease inhibitor). The dish was incubated on a shaker at 4°C for 7 min before detaching the cells with a cell lifter and gently resuspending them. Cell suspension was spun down at 500 g at 4 °C for 10 min. Supernatant was removed and pellet was gently resuspended in 1X PBS with protease inhibitors. Intact nuclei were counted in a Neubauer chamber. 25 000 nuclei were used for tagmentation in 4X TD buffer (132 mM Tris-acetate pH 7.8, 264 mM Potassium-acetate, 40 mM Magnesium Acetate, 64 % Dimethylformamide, 0.005 % Digitonin and 1.5 µl Tn5 Transposase (15027865 Illumina)). Reaction was incubated at 37 °C for 30 min and purified using the QIAGEN MinElute Kit (28004 QIAGEN) according to the manufacturers protocol.
Each library was given a unique barcode and amplified for 11 cycles. Afterwards, the PCR reaction was purified using 1X AMPURE XP Beads and eluted in 33 µl of 10 mM Tris HCl pH 8.0. Libraries were analyzed with Qubit and fragment size was accessed using the high sensitivity D-5000 screen tapes (5067-5592 Agilent) on a Tapestation.

value: Satb2 flx/flx::Nes-Cre

value: 1h bicucculine


title: DC2.4 cells, EXOmock, Preparation 2

value: WT

value: Extracellular vesicles isolated from Mock treated 4T1 tumor cells


title: 4T1 tumor cells, Mock mRNA, Preparation 2

value: Breast cancer cells

value: Mock (EGFP) mRNA


title: miRNAs-M28_3T

value: 3rd trimester

value: Plasma


title: miRNAs-M28_2T


title: 4T1 tumor cells, Mock mRNA, Preparation 1


title: DC2.4 cells, uniSTING mRNA, Preparation 2

value: uniSTING mRNA


title: DMS53

description: NuGEN Ovation RRBS Methyl-Seq

value: untreated

value: 0 day


title: 14-007 MS nodules

description:
104343-001-025
allCounts.orig.tab

source_name: Nodules

value: Nodules

value: F

value: MS


title: miRNAs-M30_1T

value: 1st trimester


title: miRNAs-M27_AB

value: After birth


title: DC2.4 cells, uniSTING mRNA, Preparation 1

value: Immortalized murine dendritic cells


title: 15-064 MS NAWM

description:
104343-001-024
allCounts.orig.tab

value: NAWM

value: M


title: ATAC_cKO2: Satb2 flx/flx::Nes-Cre DIV14 primary cortical cultures, 1h bic, rep2

value: Cortex

value: DIV14 primary cortical cultures

value: Satb2 flx/flx::Nes-Cre

value: 1h bicucculine


title: ATAC_Flx2: Satb2 flx/flx DIV14 primary cortical cultures, 1h bic, rep2

value: Satb2 flx/flx


title: ATAC_cKO1: Satb2 flx/flx::Nes-Cre DIV14 primary cortical cultures, 1h bic, rep1


title: 4T1 tumor cells, uniSTING mRNA, Preparation 1

value: Breast cancer cells

value: WT


title: 17-100 MS nodules

description:
104343-001-027
allCounts.orig.tab


title: CnR_Flx2: Satb2 flx/flx DIV14 primary cortical cultures, 1h bic, rep2

value: SATB2 (Abcam, ab92446)


title: DC2.4 cells, Mock mRNA, Preparation 2

value: Mock (EGFP) mRNA


title: ATAC_Flx3: Satb2 flx/flx DIV14 primary cortical cultures, 1h bic, rep3


title: HiC_cKO4: Satb2 flx/flx::Nes-Cre DIV14 primary cortical cultures, 1h bic, rep4

data_processing:
Paired-end sequencing reads were mapped to the mouse reference genome assembly (mm10), artefacts were filtered, and libraries were ICED normalized using  HiC-Pro (v.2.11.4) at diffrent resolutions.
Differential compartment analysis was carried out by using dcHiC. Input file was created following dcHiC guidelines using HiC-Pro matrices at 100 kb.
TADs were computed at 25 kb resolution using SpectralTAD. Differential TAD boundaries between cKO and Flx Hi-C contact matrices were identified by TADCompare.
Chromatin loops were called by Mustache (v1.2.0) at 5 kb resolution using pooled replicate Hi-C matrices. The following parameters for differential loop detection were used: P value (-p) of 0.05 and sparsity (-st) of 0.8 thresholds together with KR normalization.
Frequently interacting regions (FIREs) were called using FIREcaller. Briefly, ‘sparseToDense.py’ HiC-Pro utility was used to create quadratic matrices at 10 kb resolution.
Assembly: mm10
Supplementary files format and content: bedgraph / genomic coordinates and EV1 values of called compartments in Flx and cKO samples
Supplementary files format and content: txt / differential TAD boundaries between cKO and Flx samples
Supplementary files format and content: bedpe / genomic coordinates of chromatin loops in Flx and cKO samples called 5kb resolution
Supplementary files format and content: txt / FIRE analysis in Flx and cKO samples

extract_protocol:
For in situ Hi-C, Arima-HiC kit was used, according to the manufacturer’s protocol. Briefly, 2.5x106 primary cortical neurons were fixed directly on the dish by addition of formaldehyde to a final concentration of 1 % for 10 min on RT. After washing twice with 1X PBS cells were detached using a cell lifter and collected in 1X PBS containing protease inhibitors. Cells were pelleted at 500 g for 10 min at 4 °C and pellets were directly snap-frozen in liquid nitrogen. After nuclei isolation and chromatin digestion, biotin was added and filled ends were ligated. After reverse crosslinking and purification, DNA was shared using a M220 Covaris sonicator at duty factor 12 %, PIP 75, CPB 200 for 60 s to achieve input fragment size of 400 bp. Additionally, DNA was size-selected using AMPure XP beads, according to Arima HiC kit manual.
Hi-C libraries were prepared using Swift Biosciences Accel-NGS 2S Plus DNA Library Kit according to Arima-HiC Kit User Guide (November 2018)


title: DC2.4 cells, Mock mRNA, Preparation 1


title: 14-058 MS nodules

description:
104343-001-021
allCounts.orig.tab

value: Nodules


title: miRNAs-M27_1T

value: Plasma


title: miRNAs-M27_2T

value: 2nd trimester


title: 14-058 MS NAWM

description:
104343-001-022
allCounts.orig.tab

value: F

value: MS


title: BK6

city: Lyon

first: Hélène

last: Polvèche

address: 46 allée d'italie

country: France

institute: LBMC - ENS de Lyon

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Trimming with Cutadapt v1.10. Reads were mapped to rRNA sequences using bowtie  (v 2.2.8), and reads mapping to rRNA sequences were removed for further analysis.
Mapping with rna-STAR version 2.5.3a
Gene expression quantification was performed from uniquely aligned reads using htseq-count (v 0.6.1p1), with annotations from Ensembl version 92 and “union” mode.
Assembly: mm10
Supplementary files format and content: Raw counts(.csv)

molecule: polyA RNA

source_name: cortex or hippocampus

extract_protocol:
PureLink TM, RNA minikit, Invitrogen. Cat no.12183018A.
RNA-Seq libraries for poly-A-enriched fractions were generated from total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. High throughput sequencing of 100 bp paired-end reads was carried out on an Illumina HiSeq 2500 platform  (GenomEast Platform, IGBMC, Illkirch, France).

value: cortex or hippocampus

tag: lane

value: B

tag: strain

value: BK

value: neurons


title: miRNAs-M28_1T

value: 1st trimester


title: HiC_cKO3: Satb2 flx/flx::Nes-Cre DIV14 primary cortical cultures, 1h bic, rep3

value: Cortex

value: DIV14 primary cortical cultures

value: Satb2 flx/flx::Nes-Cre


title: 14-007 MS NAWM

description:
104343-001-026
allCounts.orig.tab

value: NAWM


title: miRNAs-M24_AB

value: After birth


title: BQ3

value: A

value: BQ

value: WT


title: 12-032 MS NAWM

description:
104343-001-020
allCounts.orig.tab

value: M


title: miRNAs-M24_3T

value: 3rd trimester

value: Plasma


title: 12-032 MS nodules

description:
104343-001-019
allCounts.orig.tab

value: Nodules

value: MS


title: miRNAs-M27_3T


title: HiC_cKO2: Satb2 flx/flx::Nes-Cre DIV14 primary cortical cultures, 1h bic, rep2

value: 1h bicucculine


title: miRNAs-M24_2T

value: 2nd trimester


title: 15-064 MS nodules

description:
104343-001-023
allCounts.orig.tab


title: HiC_cKO1: Satb2 flx/flx::Nes-Cre DIV14 primary cortical cultures, 1h bic, rep1


title: BK8

value: cortex or hippocampus

value: B

value: BK

value: neurons


title: ATAC_Flx1: Satb2 flx/flx DIV14 primary cortical cultures, 1h bic, rep1

value: Cortex

value: DIV14 primary cortical cultures

value: Satb2 flx/flx


title: 11-089 MS NAWM

description:
104343-001-018
allCounts.orig.tab

value: NAWM


title: BO2

value: A

value: BO


title: HiC_Flx4: Satb2 flx/flx DIV14 primary cortical cultures, 1h bic, rep4


title: miRNAs-M16_AB

value: After birth


title: HiC_Flx3: Satb2 flx/flx DIV14 primary cortical cultures, 1h bic, rep3


title: BJ3

value: BJ

value: KO


title: miRNAs-M16_3T

value: 3rd trimester

value: Plasma


title: 11-089 MS nodules

description:
104343-001-017
allCounts.orig.tab

value: Nodules

value: M

value: MS


title: miRNAs-M16_2T

value: 2nd trimester


title: BK1

value: cortex or hippocampus

value: BK


title: HiC_Flx2: Satb2 flx/flx DIV14 primary cortical cultures, 1h bic, rep2

value: Cortex

value: 1h bicucculine


title: 09-076 MS nodules

description:
104343-001-015
allCounts.orig.tab


title: BJ1

value: neurons


title: BJ2

value: B


title: HiC_Flx1: Satb2 flx/flx DIV14 primary cortical cultures, 1h bic, rep1

value: DIV14 primary cortical cultures

value: Satb2 flx/flx


title: IgE-CAI skin lesion (hashtag library)

city: Bunkyo-ku

first: Kensuke

last: Miyake

state: Tokyo

address: 1-5-45, Yushima

department: Institute of Integrated Research

country: Japan

institute: Institute of Science Tokyo

description: hashtag index A0311: WT Day3,  hashtag index A0312: WT Day5,  hashtag index A0313: CCR2-KO Day3,  hashtag index A0314: CCR2-KO Day5

library_source: transcriptomic single cell

data_processing: After adaptor removal and quality filtering of sequencing data by Cutadapt-2, cDNA reads were mapped to murine reference RNA sequences (GRCm38.p6, release-101) by Bowtie2, and count matrices were generated using the modified python script of BD Rhapsody workflow. Identification of valid cell barcodes were conducted by utilizing the DropletUtils package as previously described (Shichino et al. Commun Biol 2022). Each sample origin and doublets were identified based on fold-change of the normalized read counts of Hashtag antibodies. Distribution-based error correction (DBEC) was performed for subtracting background read counts of each gene derived from RNA diffusion during the lysis step within the BD Rhapsody cartridge and reverse transcription, as described previously (Shichino et al. Commun Biol 2022).

source_name: Skin

extract_protocol: On days 3 and 5 post-challenge, excised ears were cut into small pieces by using razors, and were incubated with Liberase TM (0.25 mg/mL; Roche) in RPMI complete medium at 37 °C for 50 min. The cells were then subjected to density separation with 25% and 65% Percoll PLUS (Cytiva) and cells were recovered from the interphase, to remove dead cells and red blood cells. Recovered cells were subsequently incubated with TotalSeq anti-mouse Hashtag antibodies (clone M1/42, 30-F11; BioLegend). 10,000 labeled cells were trapped and reverse-transcribed using BD Rhapsody (BD) according to the manufacturer’s instructions, followed by the preparation of cDNA libraries and hashtag libraries by TAS-Seq method (Shichino et al. Commun Biol 2022). The sequencing analysis were performed  a Novaseq 6000 sequencer and a Novaseq S4 200 cycles v1.5 kit (Illumina).

treatment_protocol: IgE-CAI was elicited as described previously (Egawa et al. Immunity 2013). In brief, mice were sensitized with intravenous injection of 300 μg of anti-TNP IgE, and on the following day challenged with an intradermal injection of 10 μg TNP12-conjugated ovalbumin (OVA) and control OVA into the right and left ear, respectively.

value: Skin

value: Skin-infiltrating cells

value: Mixed (BALB/c and CCR2-KO)

value: BALB/c and CCR2-/- mice were first treated with 300μg of TNP-specific IgE antibody, followed by intradermal challenge of TNP-conjugated OVA to ear skins


title: 94-124 stroke NAWM

description:
104343-001-014
allCounts.orig.tab

value: NAWM

value: Stroke


title: miRNAs-M11_AB

value: After birth

value: Plasma


title: IgE-CAI skin lesion (cDNA library)


title: 42-21E4, WT

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Trimming with Cutadapt (1.13) & Prinseq (0.20.4)
Mapping & QC-mapped with Tophat2 (2.0.13) & Samtools (0.1.19)
Differential gene expression analysis was carried out using the DESeq2 package, with the following parameters : Log2FC>0.25, p<0.05.
Assembly: mm9
Supplementary files format and content: Raw counts by samples (.csv)
Supplementary files format and content: genes differentially expressed (.xlsx)

source_name: Embryo 42-21E4 WT, female, litter C

tag: embryo

value: Embryo 42-21E4

value: female

tag: litter

value: C

value: WT

value: embryonic cortex


title: 44-9E7, WT

source_name: Embryo 44-9E7 WT, female, litter A

value: Embryo 44-9E7

value: A


title: male_PiC-MeA_neurons_rep3

city: Guangzhou

first: Boxing

last: Li

address: Zhongshan Erlu 74

country: China

institute: Sun Yat-sen University

data_processing:
Paired-end raw reads were first trimmed using Trimmomatic v0.39 to remove the adapter sequence.
Reads were mapped with HISAT2 v2.2.1 with the following options: --no-mixed
Genome-specific reads were extracted and converted into BAM format with samtools view -b -h -q 10
Gene-level counts quantification based on GENCODE release M25 comprehensive gene annotation file was run on aligned reads using featureCounts v2.0.1 with the following parameter -p -B -P -D 1000 -t gene -f
Assembly: mm10
Supplementary files format and content: gzipped tab-delimited text files include raw counts for all samples

source_name: brain tissue

extract_protocol:
EGFP-labeled neurons were collected into a micropipette (tip diameter 60-100um) filled with RNAse-free lysis buffer（0.2% Triton X-100 and 1µl RNase inhibitor）and then promptly transferred to an RNAse-free centrifuge tube containing 2ul of RNAse-free lysis buffer, with later total mRNA extraction. 4-5 cells were collected in one tube as a sample.
RNA libraries for RNA-seq were prepared using SMART-Seq2 Library Prep Kit following manufacturer's protocols.

treatment_protocol: AAVretro-EGFP were injected into PrL or MeA (0.1 μl/injection) to label PrL- or MeA-projecting PiC neurons

value: brain tissue

value: neurons

tag: cell subype

value: EGFP-labeled cells in PiC retrograded from MeA

value: male

value: wild-type

value: rAAV infection


title: miRNAs-M11_3T

value: 3rd trimester


title: 09-012 stroke nodules

description:
104343-001-011
allCounts.orig.tab

value: Nodules

value: M

value: Stroke


title: miRNAs-M11_2T

value: 2nd trimester

value: Plasma


title: miRNAs-M11_1T

value: 1st trimester


title: male_PiC-MeA_neurons_rep2


title: miRNAs-M16_1T


title: 09-076 MS NAWM

description:
104343-001-016
allCounts.orig.tab

value: NAWM

value: MS


title: miRNAs-M10_AB

value: After birth


title: 42-21E1, KO

source_name: Embryo 42-21E1 KO, female, litter C

value: Embryo 42-21E1

value: female

value: C

value: KO

value: embryonic cortex


title: 13-034 stroke NAWM

description:
104343-001-010
allCounts.orig.tab

value: F


title: female_PiC-MeA_neurons_rep3

value: brain tissue

value: neurons

value: EGFP-labeled cells in PiC retrograded from MeA

value: wild-type

value: rAAV infection


title: 44-9E3, KO

source_name: Embryo 44-9E3 KO, female, litter A

value: Embryo 44-9E3

value: A


title: female_PiC-MeA_neurons_rep2


title: miRNAs-M10_2T

value: 2nd trimester

value: Plasma


title: miRNAs-M10_3T

value: 3rd trimester


title: male_PiC-MeA_neurons_rep1

value: male


title: 44-9E2, KO

source_name: Embryo 44-9E2 KO, male, litter A

value: Embryo 44-9E2


title: 13-022 stroke NAWM

description:
104343-001-008
allCounts.orig.tab

value: NAWM

value: Stroke


title: 13-022 stroke nodules

description:
104343-001-007
allCounts.orig.tab

value: Nodules


title: 09-012 stroke NAWM

description:
104343-001-012
allCounts.orig.tab

value: M


title: miRNAs-M10_1T

value: 1st trimester


title: 11-036 stroke NAWM

description:
104343-001-006
allCounts.orig.tab


title: 44-8E17, KO

source_name: Embryo 44-8E17 KO, male, litter D

value: Embryo 44-8E17

value: D

value: KO

value: embryonic cortex


title: 11-036 stroke nodules

description:
104343-001-005
allCounts.orig.tab


title: male_PiC-PrL_neurons_rep4

value: brain tissue

value: neurons

value: EGFP-labeled cells in PiC retrograded from PrL

value: wild-type

value: rAAV infection


title: Dlk ΔMN, Uninjured, biol rep 3

city: Ann Arbor

first: Catherine

last: Collins

address: 1105 N University Ave

institute: University of Michigan

data_processing:
Fastq files were quality checked using FastQC and then trimmed using Illumina Thruseq adaptors and BBDuk, the quality was checked again after the trimming
Trimmed reads were then mapped to the mouse genome (GRCm38.p6) using the STAR/2.5.2a aligner, the output were BAM files sorted by Coordinate
Mapped BAM files from all lanes per sample were then merged using Samtools 1.6
Post mapping quality control using QoRTs
QoRTs provided us with tables with raw read counts suitable to be used for DEseq2 for differential expression analysis (These raw counts are provided). After QC results, sample 121139 was excluded from downstream analysis.
Assembly: GRCm38.p6.genome.fa, gencode.vM21.chr_patch_hapl_scaff.annotation.gtf
Supplementary files format and content: processed.dat files include raw read counts

source_name: Spinal Cord Lumbar

growth_protocol: RiboTag animals expressing tag ribosomes in Chat+ neurons with or without Dlk were raised on a regular chow diet until they were 3 months old

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
Homogenization and immunoprecipitation (IP) of Rpl22-HA-tagged ribosomes were performed according to published protocols (Sanz et al., 2009). RNA was then isolated from the resulting supernatant/eluate using RNeasy Plus Micro Kit (Qiagen) per manufacturer instructions.

treatment_protocol:
3 months old male mice of Dlk ΔMN and control mice received unilateral sciatic nerve crushes. Animals were sacrificed 3 days after the injury
Injured and uninjured sides of the lumbar spinal cord were used to harvest mRNAs. Lumbar spinal cord from aged matched naïve animals of both genotypes were also collected

value: Spinal Cord Lumbar

value: Motoneuron

value: Dlk WT

value: Male

value: D3 post SNC - Uninjured

tag: rip antibody

value: Purified anti-HA.11 Epitope Tag Antibody, Biolegend, MMS-101P


title: 44-9E5, WT

source_name: Embryo 44-9E5 WT, male, litter A

value: Embryo 44-9E5

value: male

value: A

value: WT


title: 13-034 stroke nodules

description:
104343-001-009
allCounts.orig.tab

value: Nodules

value: F

value: Stroke


title: male_PiC-PrL_neurons_rep3

value: brain tissue

value: neurons


title: 94-116 stroke NAWM

description:
104343-001-004
allCounts.orig.tab

value: NAWM


title: male_PiC-PrL_neurons_rep2

value: EGFP-labeled cells in PiC retrograded from PrL

value: wild-type

value: rAAV infection


title: 10-008 stroke NAWM

description:
104343-001-002
allCounts.orig.tab

value: M


title: 94-116 stroke nodules

description:
104343-001-003
allCounts.orig.tab


title: male_PiC-PrL_neurons_rep1


title: miRNAs-NPW16

value: Non pregnant

value: Plasma


title: Control, Naïve, biol rep 2

value: Spinal Cord Lumbar

value: Motoneuron

value: Dlk WT

value: Male

value: 3 Months old, Naïve

value: Purified anti-HA.11 Epitope Tag Antibody, Biolegend, MMS-101P


title: female_PiC-MeA_neurons_rep1

value: EGFP-labeled cells in PiC retrograded from MeA

value: female


title: 10-008 stroke nodules

description:
104343-001-001
allCounts.orig.tab

value: Nodules

value: Stroke


title: female_PiC-PrL_neurons_rep3

value: brain tissue

value: neurons


title: Dlk ΔMN, Naïve, biol rep 3

value: Dlk {delta}MN


title: female_PiC-PrL_neurons_rep2

value: EGFP-labeled cells in PiC retrograded from PrL

value: wild-type

value: rAAV infection


title: Control, Naïve, biol rep 1


title: Prurigo nodularis patient 45 nonlesional

city: Baltimore

first: Shawn

last: Kwatra MD

state: MD

address: 1550 Orleans Street

department: Dermatology

institute: Johns Hopkins School of Medicine

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: 10x Genomics Tab-separated values files
Supplementary files format and content: 10x Genomics Matrix files

source_name: skin punch biopsy

extract_protocol:
Tissues were digested in a pre-warmed dissociation solution (3 mg ml−1 collagenase I (Worthington) and 4 mg ml−1 dispase II (Roche) in PBS) in conical tubes positioned horizontally in a shaking water bath for 1.5 h min at 180 r.p.m. at 37 °C. Samples were then lightly triturated with sterilized Pasteur pipettes (VWR) until the skin samples broke up. They were then run through a 40 μm filter (VWR) and rinsed with 3 ml TSPC medium (αMEM (Gibco) supplemented with 20% FBS, 1%PS) to inactivate the enzymes. Cells were centrifuged at 300g for 30 min at 4 °C. The cell pellet was washed twice with 1 ml PBS and spun for 10 min at 300g at 4 °C.  Cells were then resuspended in HBSS at a concentration of ~1,000 cells/μl.  Cell viability was assessed with Trypan blue exclusion on a Countess II (ThermoFisher Scientific) automated counter and showed a >85% viability.
Library was performed according to the manufacter’s instructions (Chromium Single Cell 5' Reagent Kits User Guide (v1.1 Chemistry) 10x Genomics). Briefly, a maximum volume of 37.8 uL/sample was used for processing to target up to 10,000 cells.  Cells were combined with RT reagents and loaded onto 10X Next GEM Chip G along with 5’ v1.1 gel beads.  The NextGEM protocol was run on the 10X Chromium Controller to create GEMs, composed of a single cell, uniquely barcoded gel bead, and RT reagents.  Approximately 100uL of emulsion is retrieved from the chip and incubated (45 min at 53C , 5 min at 85C, cool to 4C), generating barcoded cDNA from each cell.  The GEMs are broken using Recovery Agent and cDNA is cleaned, following manufacturer’s instructions using MyOne SILANE beads.  The cDNA is amplified for 13 cycles (45sec @ 98C, 13 cycle: 20sec @98C, 30sec @67C, 1min @72C; 1min @ 72C, cool to 4C).  Samples are cleaned using 0.6X SPRIselect beads and the quality control analyses (QC) is completed using Qubit and Bioanalyzer to determine size and concentrations.  Next, 10uL of amplified cDNA is carried into library prep.  Fragmentation, end repair, and A-tailing are completed (5 min @ 32C, 30min @ 65C, cool to 4C), and samples are cleaned up using double sided size selection (0.6X, 0.8X) with SPRIselect beads.  Adaptor ligation (15min @ 20C, cool to 4C), 0.8X cleanup and amplification are performed, with PCR using unique i7 index sequences.  Libraries undergo a final cleanup using double sided size selection (0.6X, 0.8X) with SPRIselect beads.    Library QC for the gene expression libraries is performed using Qubit, Bioanalyzer, and KAPA library quantification qPCR kit.  Libraries are sequenced on the Illumina NovaSeq 6000 using v1.5 kits, targeting 50K reads/cell for GEx libraries, at read lengths of 26 (R1), 8 (i7), 91 (R2).  Demultiplexing and FASTQ generation is completed using Illumina’s BaseSpace software.

value: skin punch biopsy

tag: race

value: African American

tag: matched l/nl_sample

value: Prurigo nodularis patient 45 lesional


title: Prurigo nodularis patient 42 nonlesional

value: Female

value: Caucasian

value: Prurigo nodularis patient 42 lesional


title: female_PiC-PrL_neurons_rep4

tag: cell type


title: Dlk ΔMN, Naïve, biol rep 2

value: Spinal Cord Lumbar

value: Motoneuron

tag: genotype

value: Male

value: 3 Months old, Naïve

value: Purified anti-HA.11 Epitope Tag Antibody, Biolegend, MMS-101P


title: female_PiC-PrL_neurons_rep1

value: brain tissue

value: female

tag: treatment


title: Dlk ΔMN, Naïve, biol rep 1

value: Dlk {delta}MN

tag: time


title: Olfactory bulb, Pmhigh-2nd-3

city: Shanghai

first: Ting

last: Xu

address: No. 1239 Road Siping

institute: Tongji University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2 (hierarchical indexing for spliced alignment of transcripts) v2.0.477.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with FPKMs and raw gene counts for every gene and every sample

source_name: Olfactory bulb

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Strand-specific libraries were prepared using the TruSeq® Stranded Total RNA Sample Preparation kit (Illumina, USA) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: olfactory bulb

value: 7-8 weeks

value: wild type

value: 10 mg/kg/3 day PM2.5


title: Prurigo nodularis patient 34 nonlesional

value: skin punch biopsy

tag: Sex

value: African American

value: Prurigo nodularis patient 34 lesional


title: Olfactory bulb, Pmhigh-2nd-2

tag: age


title: Control, Uninjured, biol rep 3

value: Dlk WT

value: D3 post SNC - Uninjured


title: Control, Naïve, biol rep 3

value: Spinal Cord Lumbar


title: Dlk ΔMN, Injured, biol rep 3

value: Motoneuron

value: D3 post SNC - Injured


title: Prurigo nodularis patient 9 nonlesional

value: Female

value: Prurigo nodularis patient 9 lesional


title: Olfactory bulb, Pmhigh-2nd-1


title: Dlk ΔMN, Uninjured, biol rep 2

value: Male

value: Purified anti-HA.11 Epitope Tag Antibody, Biolegend, MMS-101P


title: Prurigo nodularis patient 1 nonlesional

value: Prurigo nodularis patient 1 lesional


title: Olfactory bulb, Ctrl-2nd-3

value: olfactory bulb


title: Prurigo nodularis patient 45 lesional

value: Prurigo nodularis patient 45 nonlesional


title: Olfactory bulb, Ctrl-2nd-2

value: 7-8 weeks

value: wild type


title: Dlk ΔMN, Uninjured, biol rep 1

value: Dlk {delta}MN


title: Prurigo nodularis patient 42 lesional

value: skin punch biopsy

value: Caucasian

value: Prurigo nodularis patient 42 nonlesional


title: Control, Uninjured, biol rep 1

value: Dlk WT

value: D3 post SNC - Uninjured


title: Olfactory bulb, Pmlow-1st-3

value: 3 mg/kg/3 day PM2.5


title: Olfactory bulb, Ctrl-2nd-1


title: Control, Injured, biol rep 3

value: Spinal Cord Lumbar

value: Motoneuron

value: D3 post SNC - Injured


title: Prurigo nodularis patient 34 lesional

value: Female

value: African American

value: Prurigo nodularis patient 34 nonlesional


title: Olfactory bulb, Pmlow-1st-2

value: olfactory bulb


title: Dlk ΔMN, Injured, biol rep 2

value: Male

value: Purified anti-HA.11 Epitope Tag Antibody, Biolegend, MMS-101P


title: Prurigo nodularis patient 41 lesional

value: Prurigo nodularis patient 41 nonlesional


title: Dlk ΔMN, Injured, biol rep 1

value: Dlk {delta}MN


title: Prurigo nodularis patient 41 nonlesional

value: skin punch biopsy

value: Prurigo nodularis patient 41 lesional


title: Olfactory bulb, Pmlow-1st-1

value: 7-8 weeks

value: wild type


title: Prurigo nodularis patient 9 lesional

value: Prurigo nodularis patient 9 nonlesional


title: Olfactory bulb, Ctrl-1st-4


title: H929 cells, KDM6A KO#2, H3K27me3, CST

city: Boston

first: Jiye

last: Liu

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Low-quality reads and sequencing adapters were removed by Trimmomatic v0.38
the qualified reads were mapped to the human genome (hg38) by bowtie2
Peak calling was performed by MACS2 and visualized in IGV
Assembly: hg38
Supplementary files format and content: bw

growth_protocol: H929 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
DNA was got using SimpleChIP Plus Enzymatic Chromatin IP kit (CST, #9005)
automatedSwift 2S ligation chemistry

treatment_protocol: No treatment

tag: cell line

value: myeloma derived cell line

value: KDM6A KO

tag: chip antibody


title: Prurigo nodularis patient 1 lesional

value: Prurigo nodularis patient 1 nonlesional


title: Control, Injured, biol rep 2

value: Spinal Cord Lumbar

value: Motoneuron

value: Dlk WT

value: D3 post SNC - Injured


title: Control, Injured, biol rep 1


title: H929 cells, KDM6A KO#2, Input


title: Olfactory bulb, Ctrl-1st-3

value: olfactory bulb


title: Olfactory bulb, Ctrl-1st-2


title: Control, Uninjured, biol rep 2

value: Male

value: D3 post SNC - Uninjured


title: H929 cells, KDM6A KO#1, Input


title: Olfactory bulb, Ctrl-1st-1


title: H929 cells, control, Input

value: wildtype


title: H929 cells, KDM6A KO#1, H3K27me3, CST


title: H929 cells, sgKDM6A#2

data_processing:
The raw reads of ATAC-seq were trimmed by Trimmomatic v0.38
aligned to human reference genome hg38 by bowtie2
The alignment was filtered by samtools, screening out reads with mapping quality less than 30, inconsonant alignment, and secondary alignment
PCR duplicates and mitochondria were also filtered out prior to peak calling by Picard v2.18.26
MACS2 v2.1.2 was used for peak calling, and the differential peak analysis was performed by R package Diffbind
Assembly: hg38

extract_protocol: ATAC-Seq workflow established by GENEWIZ


title: H929 cells, control


title: sRNA Fo dark replicate 1

status: Public on Jan 21 2024

city: Sevilla

first: Javier

last: Avalos

address: Av. Reina Mercedes sn

department: Genetica

country: Spain

institute: Universidad de Sevilla

description: small RNA (<150 nt)

data_processing:
Raw reads for all samples were trimmed, filtered, and quality controlled with AfterQC.
Mapping of sRNA reads was done using Bowtie v1.1.1, designed to map short Illumina reads of ~35 nt, or Bowtie2 v2.2.9 for longer reads.
The gff annotation files from both fungi were used to extract fasta files, containing coding, intronic, and intergenic sequences. The extraction was done after creating the corresponding features with the genome browser Artemis 16.0.0.
Assembly: EF1.27 (fusarium fujikuroi)
Assembly: FO2.27 (fusarium oxysporum)
Supplementary files format and content: Ff_sense_raw_read_counts.csv:  Raw reads in Fusarium fujikuroi genes in sense orientation, csv format
Supplementary files format and content: Ff_antisense_raw_read_counts.csv:  Raw reads in Fusarium fujikuroi genes in antisense orientation, csv format
Supplementary files format and content: Fo_sense_raw_read_counts.csv:  Raw reads in Fusarium oxysporum genes in sense orientation, csv format
Supplementary files format and content: Fo_antisense_raw_read_counts.csv:  Raw reads in Fusarium oxysporum genes in antisense orientation, csv format

organism: Fusarium oxysporum f. sp. lycopersici

source_name: Mycelium

growth_protocol: As described in [Ruger-Herreros et al. 2019. BMC Genomics. 20: 67. doi:10.1186/s12864-019-5430-x; GEO Series accession number GSE107342]: 106 conidia were inoculated into 100 ml of DG medium in 500-ml Erlenmeyer flasks and incubated in the dark for three days in an orbital shaker. For illumination 25 ml samples of the cultures were transferred to Petri dishes under red safelight and incubated for one hour either in the dark or under white light The process with F. oxysporum was the same, except that the 3-day cultures were incubated in 145-mm Petri dishes with 80 ml of DGasn medium.

extract_protocol:
RNA samples were extracted with Trizol (Invitrogen, Paisley, UK) using the protocol described by the manufacturer
Libraries constructed selecting transcripts with a size <150 nt from the total RNA samples described in [Ruger-Herreros et al. 2019. BMC Genomics. 20: 67. doi:10.1186/s12864-019-5430-x; GEO Series accession number GSE107342], in which the influence of light and CarS protein in F. fujikuroi and F. oxysporum transcriptomes was analyzed. They were sequenced on Illumina's Hiseq platform in mode 50 bp single read. Raw reads for all samples were trimmed, filtered, and quality controlled with AfterQC.

treatment_protocol: Illumination was achieved with a set of four fluorescent tubes (Philips TL-D 18W/840) at a distance of ca. 60 cm, providing a light intensity of 0.25 m

value: Mycelium

value: Hyphae

value: Wild type

value: Only dark


title: sRNA Fo dark replicate 2

description: small RNA (<150 nt)


title: sRNA Fo  60' light replicate 1

description: small RNA (<150 nt)

value: Dark and 60' light


title: Biol rep 4 CSPG-negative cells

city: Jerusalem

first: Yuval

last: Nevo

address: Ein Kerem Campus

country: Israel

institute: The Hebrew University of Jerusalem

description: processed data columns: A-I, general gene details; J-S, raw counts per sample; T-AC, normalized counts per sample; AD, average signal over all samples; AE-AI, DESeq2 results for comparing CSPG-positive cells to CSPG-negative cells

data_processing:
Fastq files were created with bcl2fastq v2.20.0.422. Cutadapt, v3.4, was used for removal of adapters, polyA and low-quality sequences.
Alignment to GRCg6a (chicken) was done with TopHat, v2.1.1, with annotations from Ensembl release 99. Quantification was done with htseq-count, v0.13.5.
Differential gene expression analysis was performed using the R package DESeq2, v1.30.0. Significance threshold was taken as padj<0.05.
Assembly: GRCg6a
Supplementary files format and content: Excel file with general gene details, raw and normalized counts, and the results of comparing CSPG-positive cells to CSPG-negative cells with DESeq2.

organism: Gallus gallus

source_name: Hindbrain St, 18

growth_protocol: For each biological replicate, 30 hindbrains of st. 18 HH chick embryos were dissected and separated into single cells using collagenase type IV (200 Units\ml, Worthington, 47B9407). Cells were washed in PBS, centrifuged and incubated with mouse anti-CSPG antibody for 75 min (1:50, (#c8053; Sigma-Aldrich), diluted in MACSn MACS® BSA Stock Solution and autoMACS® Rinsing Solution (1:20, Miltenyi Biotec),  washed in PBS, centrifugaed, and incubated with anti-mouse Alexa 488 antibody (1:200, Thermo-Fishe) diluted  in autoMACS® Running Buffer (Miltenyi Biotec).  Cells were washed in PBS , centrifuged and sortes using ARIA III FACS for CSPG-positive and CSPG-negative cell groups.

extract_protocol:
mRNA was extracted from the FACS -isolated CSPG-positive and CSPG-negative cells using Single Cell RNA purification kit (Norgen Biotek Corp). Each RNA sample had a RIN >6.9.
Libraries were prepared using the KAPA Stranded mRNA-Seq Kit (KR0960, Roche, USA) and Illumina platforms sample preparation protocol (v3.15) according to manufacturer's protocoal.  RNA sequencing was conducted by Illumina NextSeq 2000 machine using NextSeq 2000 P2, 100 cycles kit (Illumina, USA). The output was ~25 million single-end- 120bp reads per sample.

value: Hindbrain St, 18

value: Neural ectoderm

tag: isolation

value: FACS isolation for CSPG-


title: Biol rep 4 CSPG-positive cells

value: FACS isolation for CSPG+


title: Biol rep 3 CSPG-positive cells


title: Biol rep 2 CSPG-positive cells


title: Biol rep 3 CSPG-negative cells


title: H929 cells, control, H3K27me3, CST

value: myeloma derived cell line


title: Biol rep 6 CSPG-negative cells


title: Biol rep 1 CSPG-positive cells


title: Biol rep 2 CSPG-negative cells


title: Biol rep 1 CSPG-negative cells


title: sRNA Fo  60' light replicate 2

description: small RNA (<150 nt)


title: Biol rep 5 CSPG-negative cells


title: H929 cells, sgKDM6A#1

value: KDM6A KO


title: P genomic DNA from OML1

type: genomic

city: Chiayi County

first: Jie Ting

last: Low

state: Minxiong Township

address: No. 168, Daxue Road, Section 1

country: Taiwan

institute: National Chung Cheng University

description: tumor cell

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio

label: biotin

source_name: OCSL

label_protocol: Standard Illumina Protocol

growth_protocol: OCSL-P and OCSL-R  cells were grown in RPMI medium supplemented with 10% FBS, and  1% penicillin-streptomycin. Cells were cultured at 37°C and 5% CO2 incubator.

extract_protocol: genomic DNA was  purified from cell extract using genomic DNA mini kit  Kit (Geneaid, GT100, Taiwan) according to standard instructions.Bisulfite conversion of genomic DNA was performed with EZ DNA methylation Kit (Zymo Research,  Orange, CA, #D5002) following the manufacturer's protocol with modifications for the Infinium Methylation Assay.

treatment_protocol: We constructed OCSL-R from OCSL-P cells by using fractionated irradiations. A fraction size of 5 Gy was delivered per 5-7 days. By eight fractions, a total of 40 Gy were delivered on parental OCSL cells (OCSL-P) to construct radioresistant OCSL cells (OCSL-R).

value: gingiva squamous carcinoma


title: KO4

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

data_processing:
Fastq data were uploaded to Banana Slug Analytics Platform (Slug Genomics, 203  UV Santa Cruz) for trimming.
Trimmed sequence reads were mapped to mm10 using Banana Slug Analytics Platform (Slug Genomics, 203  UV Santa Cruz)
Cuffdif were used for differential expression analysis (Slug Genomics, 203  UV Santa Cruz)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include fpkm values for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 0.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Sample Preparation kit following manufacturer's protocols.

treatment_protocol: We immunized CD4cre x Embfl/fl mice with 1ug OmpX and 10ug  LTA1 at Day0 and Day21 intratracheally, and isolated CD4+ cells from Embfl/fl CD4cre-(WT) and Embfl/fl CD4cre+(KO) mice from the lung by magnetic beads on Day28.

value: KO


title: KO5


title: KO3


title: KO2


title: 94-124 stroke nodules

description:
104343-001-013
allCounts.orig.tab

data_processing:
Putative adapter sequences were removed in the TruSeq adapter sequence set using cutadapt. Trimmed reads were mapped to the human reference genome GRCh37.75 using HiSAT2 v-2-1.0.
Gene levels were obtained using HTSeq v0.11.0.
Genes with more than 2 reads in at least 4 of the samples were retained.
Assembly: GRCh37.75

source_name: Nodules

value: Nodules

value: M

tag: donor

tag: diagnosis

value: Stroke


title: R genomic DNA from OML1

description: tumor cell


title: KO1


title: WT4

value: WT


title: WT2


title: WT3


title: Mitochondrial transfer 3

type: RNA

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

institute: Cleveland Clinic

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).
Affymetrix Power Tools (affymetrix-power-tools.html) with RMA using R (https://www.r-project.org/)

source_name: NK-92MI cell after mitochondrial transfer

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: NK-92MI cells were cultured in a-MEM medium supplemented with 12.5% FBS, 12.5% horse serum, 0.1 mM 2-mercaptpethanol, 0.2 mM myo-inositol, 0.02 mM folic acid

extract_protocol: Total RNA from NK-92MI cells was isolated using an easy-spin total RNA extraction kit

treatment_protocol: Transfer of mitochondria isolated from WRL-cells (5 ug) into NK-92MI cells by centrifugation at 1,500 × g for 15 min

value: NK-92MI cell


title: sRNA Ff  60' light replicate 2

description: small RNA (<150 nt)

organism: Fusarium fujikuroi

value: Mycelium

value: Hyphae


title: Control 3

source_name: NK-92MI cell


title: WT5


title: Mitochondrial transfer 1


title: Mitochondrial transfer 2


title: Control 2


title: WT1


title: sRNA Ff  60' light replicate 1

description: small RNA (<150 nt)

value: Wild type


title: sRNA Ff dark replicate 1

description: small RNA (<150 nt)

value: Only dark


title: HK-2 VHL61-A1-2

city: Taichung

first: Tien

last: Hsu

address: No.91, Hsueh-Shih Road

department: Graduate Institute of Biomedical Sciences

institute: China Medical University

description: HK-2 VHL61-A1-2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: Expected count,TPM, FPKM

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human kidney tubule epithelial cell

tag: shRNA


title: HK-2 KIM1-A1-1

description: HK-2 KIM1-A1-1


title: HK-2 VHL61-A1-1

description: HK-2 VHL61-A1-1


title: HK-2 KIM1-A1-3

description: HK-2 KIM1-A1-3


title: Control 1


title: HK-2 VHL61-A1-3

description: HK-2 VHL61-A1-3


title: HK-2 VHL61-3

description: HK-2 VHL61-3


title: HK-2 VHL61-1

description: HK-2 VHL61-1


title: HK-2 Luc976-3

description: HK-2 Luc976-3


title: HK-2 KIM1-A1-2

description: HK-2 KIM1-A1-2


title: HK-2 Luc976-1

description: HK-2 Luc976-1


title: HK-2 Luc976-2

description: HK-2 Luc976-2


title: VEGF_2

city: Freiburg im Breisgau

first: Julian

last: Rapp

address: Killianstraße 5

country: Germany

institute: University Medical Center Freiburg

data_processing:
NextSeq Control Software (NCS) v2.2.0, Image analysis and base calling were done by the Real Time Analysis Software (RTA) v2.4.11, bcl files were converted into .fastq files with the bcl2fastq v2.18 software.
STAR (Galaxy Version 2.7.5b) for aligning
FeatureCounts (Galaxy Version 1.6.4) for assigning reads to genes
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include count values for each Sample

source_name: HUVECs

growth_protocol: Experiments were conducted by using HUVECs for a spheroid sprouting assay with a standard protocol. Spheroids were formed by hanging drops and seeded into a collagen matrix.

extract_protocol:
RNA was harvested using the RNeasy MinElute spin columns (RNeasy Micro Kit, QIAGEN, Hilden, Germany) including proteinase K digestion step
The SMARTer Ultra Low Input RNA Kit for Sequencing v4 (Clontech Laboratories, Inc., Mountain View, CA, USA) was used to generate first strand cDNA from 1 ng total-RNA

treatment_protocol: Spheroids were stimulated with basel endothelial medium or 25 ng/mL VEGF diluted in basel endothelial medium for 18 h.

value: HUVECs

value: VEGF


title: VEGF_5


title: iPSC-derive microglia , 31K biol  rep 2, ATAC

city: Grand Rapids

first: Gerhard

last: Coetzee

state: MI

address: 333 Bostwick Ave NE

department: Center for Neurodegenerative Science

institute: Van Andel Institute

data_processing:
Base-calling was done by Illumina NextSeq Control Software (NCS) v2.0, and the output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.
Using default settings, low quality base calls were trimmed from the 3' end of all reads prior to adapter trimming. Reads were then removed if they were below 20 base-pairs.
Forward and reverse reads were then aligned to the hg19 genome using the default settings for BWA v0.7.17
Multiqc v1.0 was then run on all samples following alignment
Samblaster was used to sort and mark duplicate reads in bam files
Duplicate reads were removed using Samtools
Peaks were called using MACS2 default parameters (narrowPeak files)
bigWig files were generated from bam files using deepTools bamCoverage function
Assembly: hg19
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

growth_protocol: iPSCs were maintained in StemFlex medum (ThermoFisher) on Geltrex growth factor basement membrane (ThermoFisher) in culture conditions of 5% CO2 at 37 °C

extract_protocol:
Samples that yielded the best fragmentation started from a total of 10K, 31K, and 100K cells. Cells were processed according to the Buenrostro et al. 2015 protocol with modifications published by the Kaestner Lab that include the lysis step and transposition buffer published in the Omni ATAC protocol. Breifly, cells were lysed and tagmented using illumina reagents.We also used magnetic beads for purification of libraries.
For library generation, Illumina Nextera DNA unique Dual Indexes plus NEBNext High-Fidelity 2X PCR Master Mix was added to purified transposed DNA. PCR amplified libraries were size selected with KAPA Pure beads. The quality and quantity of libraries were assessed using a combination of Agilent DNA High Sensitivity chip and QuantFluor dsDNA System.

treatment_protocol: iPSCs were differentiated according to the McQuade et al 2018 protocol.

value: iPSC-derived microglai

value: wild-type

tag: starting cell_quantity


title: VEGF_1


title: iPSC-derive microglia,  10K biol rep 1, ATAC


title: VEGF_4


title: VEGF_3


title: iPSC-derive microglia,  100K2 biol  rep 4, ATAC


title: iPSC-derive microglia,  100K biol rep 3, ATAC


title: Control_1

value: basal medium


title: Control_2


title: mtstpLiu131

city: Atlanta

first: James

middle: Gabriel Amor

last: DuBose

state: Georgia

address: 1510 East Clifton Road Northeast 2006

department: Biology

institute: Emory Univeristy

data_processing:
Initial quality control of raw sequences was performed by Novogene, where adapter sequences, reads with ambiguous base calls in greater than 10% of the read, and reads with a phred score of less than or equal to 5 in 50% of the read were removed.
Transcript abundances were calculated using kallisto (v.0.46.2)
Assembly: GCA_000235995.2
Supplementary files format and content: Tab-delimited text files include target gene id, gene length, effective gene length, estimated counts, and TPM normalized count.

organism: Danaus plexippus

source_name: whole body

extract_protocol:
Total RNA was extracted using a Promega SV Total Isolation System kit.
Library construction was implemented by Novogene: "Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification."

value: whole body

value: EJ

tag: developmental stage

value: late-pupa incarnata


title: mtstpLcu56

value: late-pupa curassavica


title: mtstpLiu129


title: mtstpLiu135

value: AT


title: mtstpLcu49


title: Control_3


title: mtstpLcu53


title: mtstpLiu130


title: mtstpLcu52


title: mtstpEiu117

value: early-pupa incarnata


title: mtstpLiu133


title: mtstpLcu50


title: mtstpEiu115


title: Control_5


title: Control_4


title: mtstpEiu113


title: mtstpEcu36

value: early-pupa curassavica


title: mtstpEcu35


title: mtstpEcu34


title: mtstpEcu33


title: mtstpAiu145

value: adult incarnata


title: mtstpAiu149


title: mtstpAcu66

value: adult curassavica


title: mtstpEcu38


title: mtstpAiu148


title: mtstpAcu67


title: mtstpAcu69


title: mtstpEiu116


title: mtstpAcu65


title: mtstpAiu147


title: mtstpAiu146


title: Small Intestine Kras Eif3h Rep2

city: Glasgow

first: Kathryn

last: Gilroy

address: Switchback Road

country: United Kingdom

institute: Cancer Research UK Scotland Institute

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Assembly: GRCm38.98
Supplementary files format and content: matrix of raw counts

source_name: Small Intestine

extract_protocol:
RNA was isolated using the Rneasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
Libraries for cluster generation and DNA sequencing were prepared using an Illumina TruSeq RNA sample kit, then run on an Illumina NextSeq 500 (2x36 cycles, paired end, single index).

treatment_protocol: Induction of genetic recombination was performed by 2 x 80mg/kg intraperitoneal injection of Tamoxifen 24 hrs apart. Tissues  were harvested after 7 days.

value: Male

value: Small Intestine

value: VilCreER KrasG12D/+ Eif3h fl/fl

tag: time point

value: Day 7


title: Small Intestine WT Rep1

value: Wild Type


title: Small Intestine WT Rep3

value: Female


title: Small Intestine WT Rep2


title: Small Intestine Kras Eif3h Rep3


title: Small Intestine WT Rep4


title: Small Intestine Kras Eif3h Rep4


title: mtstpEiu114


title: Small Intestine Kras Eif3h Rep1


title: mtstpAcu68


title: mtstp5iu99

value: fifth-instar incarnata


title: mtstp5iu98


title: mtstp5iu97


title: Small Intestine Kras Rep4

value: VilCreER KrasG12D/+


title: mtstp5iu101

value: whole body


title: Small Intestine Eif3h Rep4

value: VilCreER Eif3h fl/fl


title: mtstp5cu20

value: fifth-instar curassavica


title: mtstp5cu21


title: mtstp5iu100


title: Small Intestine Eif3h Rep3


title: Small Intestine Eif3h Rep1


title: mtstp5cu18

value: EJ


title: mtstp3iu85

value: AT

value: third-instar incarnata


title: 15_HC_Z3Minus_S15_L001_R1_001

city: Chicago

first: Marina

middle: Susana

last: Casalino-Matsuda

state: IL

address: 303 E Superior

institute: Northwestern University

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl2fastq v2.17.1.14.
Reads were trimmed using trimmomatic (version 0.33) to remove primer and adapter sequences.
Reads were then aligned to the Mus musculus reference genome (with mm10 assembly) using the TopHat2 aligner (version 2.1.0). Counts tables were generated using HTSeq (version 0.6.1).
mm10
Assembly: comma-separated values file including raw htseq count

source_name: Lung

growth_protocol: Six- to 10-week-old C57Bl/6 mice were used. Zfhx3fl/flLyzMCre  mice lacking Zfhx3 in the myeloid lineage (Zfhx3-/-)was generated by crossing Zfhx3fl/fl mice with LyzMCre mice from Jackson Laboratories. Zfhx3fl/fl mice (Zfhx3+/+) were used as controls.

extract_protocol:
Total RNA from AT2 cells was extracted using Qiagen RNeasy Plus Mini kit (Qiagen) and quality and quantity were assessed 4200 TapeStation  Agilent
RNA-Seq libraries were prepared using a full-length transcript coverage NEBNext Ultra RNA (New England Biolabs)
DNA libraries sequencing was performed using an Illumina NextSeq 500 instrument (Illumina) of the average dept of 5–10 million aligned reads per sample

treatment_protocol: Mice were exposed to rooom air or normoxic hypercapnia (10% CO2) for 7 days. At the end of the exposure, mice were ansthetized and both lungs were harvested for flow-sorting of AT2 cells.

value: Lung

value: AT2 cells

value: Zfhx3fl/fl LyzMCre  mice

value: 7d 10% CO2 exposure


title: 16_HC_Z3Minus_S16_L001_R1_001


title: 14_HC_Z3Minus_S14_L001_R1_001


title: mtstp3iu83


title: 13_HC_Z3Minus_S13_L001_R1_001


title: mtstp3iu84


title: Small Intestine Kras Rep2

value: Small Intestine


title: 12_HC_Z3Plus_S12_L001_R1_001

value: Zfhx3fl/fl mice


title: Small Intestine Kras Rep3

value: Day 7


title: 11_HC_Z3Plus_S11_L001_R1_001


title: mtstp3cu8

value: third-instar curassavica


title: mtstp3iu82


title: 10_HC_Z3Plus_S10_L001_R1_001


title: Small Intestine Kras Rep1

value: Female


title: mtstp3iu81


title: mtstp3cu5


title: mtstp3cu4


title: 7_Air_Z3Minus_S7_L001_R1_001

value: Room Air exposure


title: mtstp5cu19


title: mtstp3cu3


title: 9_HC_Z3Plus_S9_L001_R1_001


title: mtstp5cu17


title: 6_Air_Z3Minus_S6_L001_R1_001


title: microglia, SNCA enhancer deletion, biol rep 4

data_processing:
Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0
Using default settings, low quality base calls were trimmed from the 3' end of all reads prior to adapter trimming. Reads were then removed if they were below 20 base-pairs.
Paired-end reads were aligned using STAR default parameters and the --quantMode GeneCounts option
Multiqc v1.0 was then run on all samples following alignment
ReadsPerGene.out.tab files were imported and processed in R to generate the table raw counts
Assembly: GRCh38
Supplementary files format and content: RNA_seq_raw_counts.txt contains raw counts in tab delimited format, compiled by importing and organizing the ReadsPerGene.out.tab files output from STAR

growth_protocol: iPSCs were maintained in StemFlex medum (ThermoFisher) on iMatrix-511 (Matrixomme) growth factor basement membrane (ThermoFisher) in culture conditions of 5% CO2 at 37 °C

extract_protocol:
RNA was extracted at three time points across 2 separate differentiations. Biological replicates were differentiated at either separte times or in separate 6-well plates. Total RNA was collected using the Rneasy Mini kit (Qiagen).
Libraries were prepared by the Van Andel Genomics Core from 10 ng of total RNA using Takara SMARTer Stranded Total RNA-Seq Kit v3 Pico Input Mammalian (Takara Bio USA, Moutain View CA) per the manufacturer’s protocol. In brief, RNA was sheared to 300-400 bp, after which dscDNA was generated using a template switching mechanism, and unique dual indexed adapters were added to each sample. Ribosomal cDNA was degraded by scZapR and scrRNA probes, and libraries amplified with 13 cycles of PCR. Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems).  Individually indexed libraries were pooled and 100 bp, paired-end sequencing was performed on an Illumina NovaSeq6000 sequencer (Illumina Inc., San Diego, CA, USA), to return a minimum read depth of 50M read pairs per library.

treatment_protocol: An enhancer in intron two of SNCA was edited in iPSCs using nucleofection of CRISPR/Cas9 guide sequences.

tag: biol replicate

tag: differentiation

tag: sample  name

value: microglia

value: SNCA enhancer deletion

tag: clone

value: clone 2 edited


title: microglia, SNCA enhancer deletion, biol rep 2

tag: cell type

tag: genotype

value: clone 1 edited


title: 5_Air_Z3Minus_S5_L001_R1_001

tag: tissue

tag: treatment


title: mtstp3cu2

value: whole body

value: EJ


title: microglia, WT, biol rep 3

tag: cell line

value: wild-type

value: unedited


title: microglia, SNCA enhancer deletion, biol rep 1


title: 3_Air_Z3Plus__S3_L001_R1_001

value: Lung

value: AT2 cells


title: 4_Air_Z3Plus__S4_L001_R1_001


title: 8_Air_Z3Minus_S8_L001_R1_001

value: Zfhx3fl/fl LyzMCre  mice


title: microglia, SNCA enhancer deletion, biol rep 3


title: microglia, WT, biol rep 2


title: treatment group overexpressed both SAMD4B and APOA2, replicate3,NM-seq

city: Urumqi

first: Zhang

middle: Qing

last: hua

state: Xinjiang

address: Liudao Bay Street

institute: The Second Affiliated Hospital of Xinjiang Medical University

data_processing:
Raw data were generated after sequencing,  image analysis, base calling and quality filtering on Illumina HiSeq4000 sequencer
Firstly, Q30 was used to perform quality control. After adaptor-trimming and low quality reads removing by cutadapt (v1.9.1) software, high quality clean reads were generated.
Then these clean reads were aligned to virus reference genome  (hg19) using bowtie2 software (v2.2.4) with end-to-end mode.
Raw 2'-O-methylation counts and coverage counts were calculated by bedtools (v2.24) software and in-house scripts, then 2'-O-methylation-ratio (define as: count/coverage) and 2'-O-methylation-fc (defined as: 2'-O-methylation-ratio/Input-2'-O-methylation-ratio) were also calculated. 2'-O-methylation sites weree annotated with gene information by bedtools software.
Assembly: hg19
Supplementary files format and content: excel format for methylated level
Library strategy: NM-seq for RNA 2'-O-methylation

source_name: HEK293T cell

extract_protocol:
RNA was harvested using Trizol reagent.
Nm-Seq service was provided by CloudSeq Biotech Inc.(Shanghai, China) by following the published procedures with slight modification (1). Briefly, the RNA samples were fragmented at 95 °C for 5 min with RNA Fragmentation Reagents (GenSeq Inc.). RNA fragments were 3′-end repaired using antarctic phosphatase (New England BioLabs) at 37 °C for 30 min. Then, repaired RNA samples were oxidized/eliminated using 10 mM NaIO4 (Sigma-Aldrich) in 200 mM lysine–HCl buffer (pH 8.5, Sigma-Aldrich) in a total volume of 40 µl at 37 °C for 30 min. The reaction was quenched by ethylene glycol, samples were further dephosphorylated by Shrimp Alkaline Phosphatase (New England BioLabs) at 37 °C for 30 min. Eight cycles of oxidation–elimination–dephosphorylation were performed. A final round of oxidation/elimination reaction was performed, excluding dephosphorylation. Then, purified RNA samples were 5′ phosphorylated by T4 polynucleotide kinase 3′ phosphatase minus (New England BioLabs) at 37 °C for 60 min. Libraries were constructed using GenSeq® Small RNA Library Prep Kit (GenSeq Inc.) and quantified using Qubit fluorometric assay (ThermoFisher).

tag: overexpression

value: SAMD4B and APOA2


title: 44-8E18, WT

city: Lyon

first: Hélène

last: Polvèche

address: 46 allée d'italie

institute: LBMC - ENS de Lyon

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Trimming with Cutadapt (1.13) & Prinseq (0.20.4)
Mapping & QC-mapped with Tophat2 (2.0.13) & Samtools (0.1.19)
Differential gene expression analysis was carried out using the DESeq2 package, with the following parameters : Log2FC>0.25, p<0.05.
Assembly: mm9
Supplementary files format and content: Raw counts by samples (.csv)
Supplementary files format and content: genes differentially expressed (.xlsx)

source_name: Embryo 44-8E18 WT, female, litter D

extract_protocol:
PureLink TM, RNA minikit, Invitrogen. Cat no.12183018A.
RNA-Seq libraries for poly-A-enriched fractions were generated from total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. High throughput sequencing of 100 bp paired-end reads was carried out on an Illumina HiSeq 2500 platform  (GenomEast Platform, IGBMC, Illkirch, France).

tag: embryo

value: Embryo 44-8E18

tag: Sex

value: female

tag: litter

value: D

value: WT

value: embryonic cortex


title: HPCs, SNCA enhancer deletion, biol rep 4

value: HPCs


title: HPCs, SNCA enhancer deletion, biol rep 6

value: SNCA enhancer deletion


title: treatment group overexpressed both SAMD4B and APOA2, replicate2,NM-seq


title: HPCs, SNCA enhancer deletion, biol rep 3


title: treatment group overexpressed both SAMD4B and APOA2, replicate3, input RNA


title: HPCs, SNCA enhancer deletion, biol rep 5

value: clone 2 edited


title: HPCs, WT,  biol rep 4


title: treatment group overexpressed both SAMD4B and APOA2, replicate2, input RNA


title: HPCs, SNCA enhancer deletion, biol rep 1

value: clone 1 edited


title: microglia, WT, biol rep 1

value: microglia


title: M19-AM-Z3--HC

data_processing:
Basecalls performed using Illumina RTA2 software.
Indexed samples were demultiplexed to fastq files with bcl2fastq v2.17.1.14.
Reads were  trimmed using trimmomatic (version 0.33) to remove primer and adapter sequences.
Reads were then aligned to the Mus musculus reference genome (with mm10 assembly) using the TopHat2 aligner (version 2.1.0). Counts tables were generated using HTSeq (version 0.6.1).
Genome_build: mm10
Supplementary_files_format_and_content: comma-separated values file including raw htseq count

extract_protocol:
Total RNA from alveolar macrophages was extracted using Qiagen RNeasy Plus Mini kit (Qiagen) and quality and quantity were assessed 4200 TapeStation  Agilent
RNA-Seq libraries were prepared using a full-length transcript coverage NEBNext Ultra RNA (New England Biolabs)
DNA libraries sequencing was performed using an Illumina NextSeq 500 instrument (Illumina) of the average dept of 5–10 million aligned reads per sample

treatment_protocol: Mice were exposed to rooom air or normoxic hypercapnia (10% CO2) for 7 days. At the end of the exposure, mice were ansthetized and both lungs were harvested for flow-sorting of alveolar macrophages.

tag: strain

value: flow-sorted alveolar macrophages


title: M10-AM-Z3--HC


title: M20-AM-Z3--HC


title: 2_Air_Z3Plus__S2_L001_R1_001

value: Zfhx3fl/fl mice

value: Room Air exposure


title: treatment group overexpressed both SAMD4B and APOA2, replicate1,NM-seq


title: treatment group overexpressed both SAMD4B and APOA2, replicate1, input RNA


title: HPCs, WT, biol rep 2

value: wild-type

value: unedited


title: sRNA Ff dark replicate 2

description: small RNA (<150 nt)

value: Mycelium

value: Hyphae

value: Wild type

value: Only dark


title: KARPAS_P60_1

city: Pamplona

first: Juan

middle: Jose

last: Lasarte

state: Navarra

address: Avda Pio XII, 55

department: Inmunología e Inmunoterapia

institute: Centro de Investigación Médica Aplicada

hyb_protocol: Samples were then processed following Affymetrix recommendations and cRNA was hybridized to the Affymetrix human U133 Plus 2 array.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: Data was normalized using Bioconductor software and RMA algorithm.

label: Biotin

source_name: Karpas 299 human cell line derived from a human lymphoma with a regulatory T cell profile, incubation with P60 peptide

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Karpas299 cells were cultured in RPMI 1640, 10% Fetal Calf Serum (Sigma), 100 U/mL penicillin and 100 μg/mL streptomycin,  Gentamicin and  2 mM L-Glutamine at 37 oC and  6.5% CO2.

extract_protocol: RNA was isolated by using the RNAEasy minikit (Qiagen) according to manufacturer´s instructions

treatment_protocol: Cells were cultured in the presence or absence of the Foxp3 inhibitory peptide P60 (100 uM) for 30 min and then, stimulated with anti-CD3/CD28 coated beads (1 bead/cell)  for additional 6 h.

value: human non-Hodgkin′s T cell lymphoma cell line


title: Bhlhe40 KO, scRNAseq, TCR

city: Little Rock

first: Lin-Xi

last: Li

state: AR

address: 4301 W. Markham St

department: Department of Microbiology and Immunology

institute: University of Arkansas for Medical Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software V6.0.2
Assembly: mm10-3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Female reproductive tract

extract_protocol:
FRTs were collected in RPMI containing 5% fetal bovine serum (FBS), digested with collagenase IV (Sigma) at 37°C by GentleMACS (Miltenyi Biotech), and live cells purified using a Percoll gradient. Purified live cells were surface stained with the following antibodies (CD4, CD44, CD90.2, Dump: CD11b, F4/80, B220, Fixable Viability Dye) for 30 minutes at 4°C. Cells were resuspended in FACS buffer (PBS with 2% FBS) after staining. Live CD90.2+CD4+CD44hidump- CD4 T cells were sorted using a FACSAria (BD Biosciences).
Library constructions were performed according to the manufacturer's protocols (Single Cell 5' v2 Protocol, 10x Genomics). Briefly, purified CD4 T cells were resuspended in the master mix and loaded into the chip with gel beads and partitioning oil. This chip was then placed in a Chromium Controller to generate the Gel Bead-In Emulsions (GEMs). cDNA from poly-A mRNA was generated, followed by amplification for VDJ and 5' Gene Expression library construction. For the VDJ library, VDJ segments are first enriched by PCR amplification with primers specific to TCR constant region. For both VDJ and GEX libraries, enzymatic fragmentation and size selection are performed; lastly, sample indices and an Illumina R2 sequence are added for the final library.

value: Female reproductive tract

value: CD4 T cells

tag: age

value: 6-8 weeks old

value: female


title: KARPAS_2

source_name: Karpas 299 human cell line derived from a human lymphoma with a regulatory T cell profile


title: KARPAS_P60_2


title: KARPAS_1


title: 1_Air_Z3Plus__S1_L001_R1_001

value: Lung

value: AT2 cells


title: iPSCs, SNCA enhancer deletion, biol rep 4

value: iPSCs

value: SNCA enhancer deletion

value: clone 2 edited


title: control group overexpressed APOA2, replicate3, input RNA


title: WT, scRNAseq, TCR

description: 10x Genomics


title: HPCs, SNCA enhancer deletion, biol rep 2

value: HPCs


title: HPCs, WT, biol rep 1

value: wild-type


title: control group overexpressed APOA2, replicate3, NM-seq


title: M16-AM-Z3--Air

value: Room Air exposure

value: Zfhx3fl/fl LyzMCre  mice

value: flow-sorted alveolar macrophages


title: Bhlhe40 KO, scRNAseq, 5' GEX

description: 10x Genomics


title: M07-AM-Z3--Air


title: HK-2 VHL61-2

description: HK-2 VHL61-2

value: Human kidney tubule epithelial cell

tag: shRNA


title: WT, scRNAseq, 5' GEX

description: 10x Genomics


title: control group overexpressed APOA2, replicate2, NM-seq


title: dcl2 deletion, replicate 3

data_processing:
Raw reads for all samples were trimmed, filtered and quality controlled with AfterQC (Chen et al., 2017; doi:10.1186/s12859-017-1469-3)
Read mapping to the reference genome was performed using Star (Dobin et al. 2013)
The annotation used was the corresponding one from the EnsemblFungi database (https://fungi.ensembl.org) for F. fujikuroi IMI58289.
Mapped sequences were analyzed using SeqMonk (version 1.45.4, https://github.com/s-andrews/SeqMonk)
Quantification was performed using the Seqmonk RNAseq quantitation pipeline, merging transcripts and counting reads over exons.
Deseq2 tool (Love et al., 2014; doi:10.1186/s13059-014-0550-8), implemented in SeqMonk, which uses raw counts for quantitation, was used to compare among conditions.
Assembly: EF1.27
Supplementary files format and content: WT_dcl2_raw_counts.csv: Raw counts in Fusarium fujikuroi genes in wild type and dcl2 mutant, csv format

growth_protocol: the strains were grown in 100 ml of DG medium in 500 ml Erlenmeyer flasks, inoculated with 1000000 conidia. The flasks were kept in total darkness for three days at 30°C in an orbital shaker (150 rpm). Then, the cultures were transferred to four 25-ml Petri dishes under safe red light and kept in static conditions in the dark for 240 min. Subsequently, mycelium was obtained by filtration, frozen immediately in liquid nitrogen, and stored at − 80 °C until RNA extraction

extract_protocol:
RNA samples were extracted with Trizol (Invitrogen, Paisley, UK) from 150–200 mg of ground mycelia samples, using the protocol described by the manufacturer
RNA samples were sent for mass sequencing to LifeSequencing S. L. (Valencia, Spain). RIN values were above 8.5 in all the samples. Sequencing was carried out using the Illumina platform. Samples were sequenced on Illumina's NextSeq platform in 75 bp single read mode.

value: Mycelium

value: dcl2 deletion strain

value: Hyphae

value: Grown in dark


title: control group overexpressed APOA2, replicate2 input RNA


title: M17-AM-Z3--Air


title: dcl2 deletion, replicate 2


title: control group overexpressed APOA2, replicate1, NM-seq


title: M05-AM-Z3positive-HC

value: Zfhx3fl/fl mice


title: iPSCs, SNCA enhancer deletion, biol rep 1

value: clone 1 edited


title: dcl2 deletion, replicate 1


title: M03-AM-Z3positive-HC


title: M04-AM-Z3positive-HC


title: control group overexpressed APOA2, replicate1, input RNA


title: iPSCs, SNCA enhancer deletion, biol rep 3


title: HPCs, WT, biol rep 3

value: unedited


title: iPSCs, WT, biol rep 2


title: Wild type, replicate 2

value: wild type


title: Wild type, replicate 3


title: iPSCs, WT biol rep 3

value: iPSCs


title: M13-AM-Z3positive-Air

description: M13-AM-Z3positive-Air-05_S13_L001_R1_001


title: iPSCs, WT, biol rep 1


title: Wild type, replicate 1


title: M02-AM-Z3positive-Air


title: Small Intestine Eif3h Rep2

value: Male

value: Small Intestine

value: VilCreER Eif3h fl/fl

tag: time point

value: Day 7


title: iPSCs, SNCA enhancer deletion, biol rep 2

tag: biol replicate

value: SNCA enhancer deletion


title: M11-AM-Z3positive-Air

description: M11-AM-Z3positive-Air-03_S11_L001_R1_001

value: Room Air exposure


title: P63+ lung progenitor cells from patient #2104

status: Public on Jan 20 2024

city: Shanghai

first: Wei

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAP nuke.
Trimmed sequence reads were mapped to the reference genome (hGRC38) using HISAT 4 (v2.1.0).
Read count extraction and normalization were performed using RSEM (v1.2.8).
Assembly: hGRC38
Supplementary files format and content: csv files includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: The progenitor cells were isolated from a small amount of airway epithelium obtained through bronchoscopic brushing and were expanded to more than 100 million cells within 3-5 weeks.

extract_protocol:
Total RNA was harvested using TRIzol Reagent (Invitrogen, Life Technologies, USA) followed the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using the BGI-NSG platform following manufacturer's protocols.

value: Lung

value: P63+ lung progenitor cells

value: lung progenitor cells

tag: group

value: NR-Patient


title: P63+ lung progenitor cells from patient #8007


title: FaDu cells,shKIF2C,Day2

city: Chongqing

first: Haiyue

last: Zhu

address: No.1 Medical College Road, Yuzhong District, Chongqing

institute: The First Affiliated Hospital of Chongqing Medical University

data_processing:
Bowtie2 was used to align raw data
The bam files was quantify by RSEM
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: FaDu cells

extract_protocol:
The KIF2C knockdown cells and its corresponding negative control cells were collected, total RNA was extracted, and cDNA libraries were then constructed and subjected to RNA-seq analysis
RNA libraries were prepared for sequencing using standard MGI-G400/MGI-2000 protocols

value: FaDu cells

value: hypopharyngeal tumor


title: P63+ lung progenitor cells from patient #8002


title: BEAS-2B-KRAS-G12D-rep1

first: Min

last: Huang

address: 555 Zuchongzhi Road, Pudong

department: State Key Laboratory of Drug Research

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

data_processing:
The raw paired end reads were trimmed and quality controlled by fastp with default parameters.Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software. The mapped reads of each sample were assembled by StringTie in a reference-based approach.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited xlsx file includes TPM values for each Sample

source_name: lung

growth_protocol: BEAS-2B bronchial epithelial cells were maintained in RPMI-1640 supplemented  with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions
RNA-seq transcriptome librariy was prepared following Illumina® Stranded  mRNA Prep, Ligation from Illumina (San Diego, CA) using  1μg of total RNA.

value: lung

value: bronchial epithelial cells


title: BEAS-2B-EV-rep3

value: EV


title: BEAS-2B-KRAS-G12D-rep2


title: BEAS-2B-EV-rep2


title: BEAS-2B-KRAS-G12D-rep3


title: P63+ lung progenitor cells from patient #8001

value: CR-Patient


title: 379TL Rkid | 004 | CD45+

city: Cambridge

first: Sandra

last: Petrus-Reurer

address: Box 202, Level E9 Addenbrooke’s Hospital, Hills Road

department: Department of Surgery

institute: University of Cambridge

description:
379TL_Rkid_004_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule

data_processing:
PCR reactions were pooled, and pooled libraries were paired-sequenced on an Illumina Next Seq 2000 instrument.
FASTQ files for each sample were converted to digital count conversion (DCC) files using the GeoMx DnD pipeline (v.1) of Nanostring according to manufacturer’s pipeline.
DCC files were imported back into the GeoMx DSP instrument for QC and data analyses using GeoMx DSP analysis suite version 2.2.0.111 (Nanostring).
A minimum of 10,000 reads were required for each sample. Probes were checked for outlier status by implementing a global Grubb’s outlier test with alpha set to 0.01.
The counts for all remaining probes for a given target were then collapsed into a single metric by taking the geometric mean of probe counts.
For each sample, an RNA-probe-pool-specific negative probe normalization factor was generated on the basis of the geometric mean of negative probes in each pool.
To ensure good data quality, we calculated the 75th percentile of the gene counts (that is, geometric mean across all non-outlier probes for a given gene) for each AOI, and normalized to the geometric mean of the 75th percentile across all AOIs to give the upper quartile (Q3) normalization factors for each AOI. The distribution of these Q3 normalization factors were then checked for outliers.
Assembly: hg38
Supplementary files format and content: matrix.csv: Q3 normalized signal intensity
Library strategy: Spatial Transcriptomics

source_name: CD45+ cells

growth_protocol: Paraformaldehyde-fixed frozen blocks

extract_protocol:
For GeoMx DSP sample collections, entire slides were imaged at 20X magnification and morphologic markers were used to select ROI using organic shapes. Automatic segmentation of ROI based on KRT7pos markers were used to define AOIs, allowing to separate tumor cells (KRT7pos) from adjacent stromal cells (KRT7neg). AOIs were then exposed to 385 nm light (UV), releasing the indexing oligonucleotides which were collected with a microcapillary and deposited into a 96-well plate for subsequent processing. The indexing oligonucleotides were dried overnight and resuspended in 10 μl of DEPC-treated water.
Spatial Trasncriptomics library were prepared using NanoString human Whole Transcriptome Atlas (WTA) panel probes according to manufacterer's construction.

treatment_protocol: One representative mouse per group was selected, PCO and matrigel-only kidneys were sectioned (5mm) and slides with the NanoString human Whole Transcriptome Atlas (WTA) panel probes overnight, then stained with KRT7 (1:200, abcam, ab215855, clone [KRT7/760]), CD3 (1:100, Origene, UM000048BF, clone [UMAB54]), CD45 (1:200, CST, 13917BF, clone [D9M8I]), in addition to nuclear staining (Syto 83, ThermoFisher Scientific, S11364) as morphology markers to visualize tissue architecture. Stained slides were loaded onto the GeoMx instrument and scanned for region of interest (ROI) selection.

value: CD45+ cells


title: 379TL Rkid | 006 | CD45+

description:
379TL_Rkid_006_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 379TL Rkid | 005 | CD45+

description:
379TL_Rkid_005_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: P63+ lung progenitor cells from patient #8009


title: 379TL Rkid | 008 | CD45+

description:
379TL_Rkid_008_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 379TL Rkid | 007 | CD45+

description:
379TL_Rkid_007_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: FaDu cells,shControl,Day2


title: P63+ lung progenitor cells from patient #8004


title: non-ES_3

city: shanghai

first: Shen

last: Liu

address: Yishan road 600

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
The raw data was handled by Skewer v0.2.2 (https://sourceforge.net/projects/skewer/files/?source=navbar) and data quality was checked by FastQC v0.11.2 (http:// www.bioinformatics.babraham.ac.uk/projects/fastqc/). The read length was 2×150 bp. Clean reads were aligned to the mouse genome (mm10)[1] from ensmble using STAR (https://github.com/alexdobin/STAR), with one mismatch allowed. StringTie (v1.3.1c) was used to generate gene expression data and differential gene expression was analysed by DESeq2 (v1.16.1) (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) . The thresholds for determining DEGs are P < 0.05 and absolute fold change ≥ 2.[2] Then DEGs were chosen for function and signaling pathway enrichment analysis using TopGO (https://www.bioconductor.org/packages/release/bioc/html/topGO.html) and KEGG database (https://www.genome.jp/kegg/pathway.html). The significantly enriched pathways were determined when P < 0.05 .
Assembly: mm10
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

source_name: muscle and connective tissue

extract_protocol:
7. Place the column on 2 ml collection tube, add 400 µ l buffer Rb, centrifuge as described above, discard the filtrate and reuse the collection tube. 8. Place the column on the same 2 ml collection tube, add 600 µ l RNA wash buffer, centrifuge as described above, discard the filtrate and reuse the collection tube. 9. Maximum speed (13000) × g) Centrifuge for 2 min and completely dry the film 10. Transfer the column to a clean 1.5 ml RNase free microfuge tube. Add 50 µ L DEPC treated ddH2O, dissolve RNA, stand at room temperature for 2 min, and centrifuge at the maximum speed for 1 min. 11. Determine the concentration and electrophoretic quality inspection RNA.
Experimental steps: 1. MRNA isolation and fragmentation  take 500ng totalrna, adjust the volume to 50ul with water, add 50ul mrnacapturebeads and mix well  place it on the PCR instrument at 65 ℃ for 5min, and then place it at room temperature for 5min  put it on the magnetic rack for 5min and remove the supernatant  remove it from the magnetic frame, add 200ul wash buffer and mix well  put it on the magnetic rack for 5min and remove the supernatant  remove it from the magnetic frame, add 50ul trisbuffer and mix well  place it on the PCR instrument at 80 degrees for 2min and 25 degrees hold  add 50ul beadbinding buffer, mix well, and place at room temperature for 5min  put it on the magnetic rack for 5min and remove the supernatant  remove it from the magnetic frame, add 200ul wash buffer and mix well  put it on the magnetic rack for 5min and remove the supernatant  add 19ul frame / prime buffer and mix well  put it on the PCR instrument at 94 degrees for 3min and 4 degrees for hold  put it on the magnetic rack for 5min, take out 16ul to a new EP tube, and prepare 0.12mg/ml actinomysin D solution 2.Double stranded cDNA   add 26ul of 1st strand buffer, 22ul of 1st strand enzyme mix and 1ul of actinomycin D (0.12 mg / ml) into 16ul supernatant and mix well  put it on the PCR instrument, 25 degrees for 10min, 42 degrees for 15min and 70 degrees for 15min  add 25ul of 2nd strand buffer 2 (with dUTP) and 15ul of 2nd strand enzyme super mix into the reaction product of the previous step, and mix well  put it on the PCR instrument, 16 degrees for 30min and 65 degrees for 15min 2. Add a connector  add 25ul rapid ligation buffer3, 5ul rapid DNA ligase2, 2 UL connector, 3ul water, mix well, place it on the PCR instrument for 20 degrees and 15min;  add 45ul DNA clean beans, mix well, and place at room temperature for 10min;  place the magnetic rack at room temperature for 5min, remove the supernatant and do not move the beads;  add 200 UL of 80% ethanol for 30 s at room temperature, remove the supernatant and repeat once;  dry at room temperature for 10min;  add 53ul water, remove it from the magnetic frame, fully mix it, and place it at room temperature for 5min;  place it on the magnetic frame and take the supernatant 50ul into a new pipe.  add 35ul DNA clean beans, mix well, and place at room temperature for 10min;  place the magnetic rack at room temperature for 5min, remove the supernatant and do not move the beads;  add 200 UL of 80% ethanol for 30 s at room temperature, remove the supernatant and repeat once; Dry at room temperature for 10min;  add 22ul water, remove it from the magnetic frame, fully mix it, and place it at room temperature for 5min;  place it on the magnetic frame and take the supernatant 19ul into a new pipe.  3. PCR enrichment  add 19uldna, 2.5ul i7 primer+2.5ul i5 primer, 25ulhifi amplification mix and 1ulheat labile UDG successively;  37 ° 10min, 98 ° 30s, 15 cycles (98 ° 10s, 60 ° 30s, 72 ° 30s), 72 ° 5min, 4 ° hold;  add 45ul amurebeads, mix well, and place at room temperature for 15min;  place the magnetic rack at room temperature for 10min, remove the supernatant and do not move the beads;  add 200 UL of 80% ethanol for 30 s at room temperature, remove the supernatant and repeat once,  dry at room temperature for 10min;  add 33ul water, remove it from the magnetic frame, fully mix it, and place it at room temperature for 5min;  place it on the magnetic frame and take the supernatant 30ul into a new pipe. 4. Quantification: qubit quantitative RNA library.(VAHTS® Universal V8 RNA-seq Library Prep Kit for Illumina(Cat.NR605),Vazyme)

treatment_protocol: 1. Grinding treatment: grind the tissue in liquid nitrogen, add 1ml bio reagent to every 50-100mg tissue, and incubate at room temperature for 2min. 2. Add 0.2 ml of chloroform (per 1 ml of biological reagent), cover and shake violently for 15 s. 3．12,000  × g. Centrifugation at 4 ℃ for 3 min. The mixture is divided into lower phenol chloroform phase, intermediate phase and upper aqueous phase. RNA is present in the aqueous phase. 4. Transfer no more than 80% of the aqueous phase to a new tube, add 0.5 times the volume of isopropanol (96-100%, room temperature), and vortex for 15 s. 5. Add no more than 700 µ l of the mixture to an RNA Mini column (the addition of isopropanol in step 5 may form precipitation, vortex and transfer all the mixture to the column). 10,000  × G centrifuge for 30-60 s, discard the filtrate and reuse the collection pipe. 6. Repeat step 6, transfer the remaining sample to the column and centrifuge according to the method in the previous step.(VAHTS mRNA Capture Beads (Cat.N401-02),Vazyme)

value: muscle and connective tissue

value: WT

value: non-ES


title: 379TL Rkid | 003 | CD45+

description:
379TL_Rkid_003_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 379TL Rkid | 002 | CD45+

description:
379TL_Rkid_002_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 208262 TLR 354 Rkid | 013 | CD45+

description:
208262_TLR_354_Rkid_013_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 208262 TLR 354 Rkid | 014 | CD45+

description:
208262_TLR_354_Rkid_014_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: non-ES_2


title: 379TL Rkid | 001 | CD45+

description:
379TL_Rkid_001_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: non-ES_1


title: 2D ES_3

value: 2D ES


title: 2D ES_2


title: P63+ lung progenitor cells from patient #2301


title: 208262 TLR 354 Rkid | 011 | CD45+

description:
208262_TLR_354_Rkid_011_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 208262 TLR 354 Rkid | 012 | CD45+

description:
208262_TLR_354_Rkid_012_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 208262 TLR 354 Rkid | 009 | CD45+

description:
208262_TLR_354_Rkid_009_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 208262 TLR 354 Rkid | 010 | CD45+

description:
208262_TLR_354_Rkid_010_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule


title: 2D ES_1


title: 208262 TLR 354 Rkid | 008 | CD45+

description:
208262_TLR_354_Rkid_008_CD45
FFPE samples from mouse model engrafted with human cholangiocyte organoids under kidney capsule