title: T24 cells, siUSP52, rep3

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
The total reads are compared with the reference genome (clean data were mapped to the reference genome of Homo_sapiens.GRCh38 from NCBI using STRA software (version 2.5.3a) with default parameters.） to obtain comprehensive transcript information.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor)
Assembly: Homo_sapiens.GRCh38

source_name: Tumor

growth_protocol: T24 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:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026). 2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seg were prepared using KCTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

treatment_protocol: Transfection of siRNA followed LipofectamineTM 3000 Reagent’s (L3000015, Invitrogen) protocol.

value: Tumor

value: bladder cancer


title: imgl_S1KO_rep2

status: Public on Dec 09 2024

type: SRA

city: New york

first: Chiara

last: Pedicone

address: 1425 Madison Ave

department: Genetics  and Genomics

country: USA

institute: Icahn School of medicine at Mount Sinai

description: Illumina HiSeq 2x150bp, configuration, with ~30million reads/sample

library_source: transcriptomic

data_processing:
Kallisto indexing
Assembly: Hg38
Supplementary files format and content: aboundance and count files for each sample after Kallisto indexing

molecule: polyA RNA

organism: Homo sapiens

source_name: WTC11 iPSC line

growth_protocol: iPSC microglia were differentiated as McQuade Mol Neurodegeneration (2018)

extract_protocol:
RNeasy Plus  Mini Kit
2x150bp, configuration, with ~30million reads/sample
RNA library preparation with Poly-A selection

tag: cell line

value: WTC11 iPSC line

tag: cell type

value: iPSC derived iMGL

tag: genotype

value: KO


title: Sample 13_Paediatric pneumonia_13

city: Santiago de Compostela

first: Alberto

last: Gómez-Carballa

state: A coruña

address: Choupana sn

department: Pediatrics

country: Spain

institute: GENVIP research group

data_processing:
Quality control of raw data was carried out using fastq.gzC.
Alignment and read counting were performed using STAR, alignment filtering was done with SAMtools and read counting was carried out using FeatureCounts.
Assembly: Ensembl GCh38 genome
Supplementary files format and content: Coma-delimited excell file with raw counts (Counts_raw_data.csv)
Supplementary files format and content: Coma-delimited excell file with normalized counts (Normalized_data.csv)

molecule: total RNA

source_name: Whole blood

extract_protocol:
RNA was extracted using PAXgene Blood RNA Kit (IVD) and Tempus™ Spin RNA Isolation Kit
The Illumina’s TruSeq RNA Sample Preparation Kit was used for library preparation, and ribosomal and globin RNA depletion was performed using the Illumina® Ribo-Zero Gold kit

tag: tissue

value: Whole blood

tag: Sex

value: M

tag: etiology

value: DB

tag: collection tube

value: PAXgene

tag: batch

value: A

tag: condition

value: Pneumonia


title: OAT, donor 3, scRNAseq

city: Milano

first: Silvia

last: Gregori

state: Italy

address: Via Olgettina 60

country: Italy

institute: SR-TIGET

description: OAT, Patient, CD3+ T cells

library_source: transcriptomic single cell

data_processing:
Cellranger 10X demultiplexing (mkfastq)
Cellranger 10X quantification (counts)
Seurat data analysis workflow
Assembly: GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics)
Supplementary files format and content: Tab-separate files of barcodes, features, and matrix counts for each sample
Supplementary files format and content: .xlsx Single-Cell seurat metadata (Full and subset dataset sheet)

source_name: CD3+ T cells purified from peripheral blood(PBMC)

extract_protocol:
CD3+ T cells were isolated from PBMCs obtained by FER (n=5), OAT (n=4), and iNOA (n=6) subjects by magnetic beads negative selection (Miltenyi Biotech, Germany).  After generation of nanoliter-scale Gel bead-in-EMulsions (GEMs), GEMs were reverse transcribed in a T100 Thermal Cycler (Bio-Rad, CA, USA) at 53 °C for 45min, followed by 85 °C for 5min, and held at 4 °C. Single-cell droplets were broken, and the single-strand cDNA was isolated and cleaned with Cleanup Mix containing Dynabeads MyOne SILANE (10x Genomics, CA, USA). cDNA was amplified using 13 PCR cycles, and then fragmented, end-repaired, A-tailed and adaptor ligated, with SPRIselect Reagent Kit (Beckman Coulter, CA, USA) with cleanup in between steps according to the manufacturers’ instructions.
Single-cell libraries were generated through the Chromium Single-Cell Controller using the Chromium Single Cell 3′ Reagent kit v.3.1 according to the manufacturers’ instructions. (10x Genomics, CA, USA). For each donor, samples were loaded to obtain a target cell recovery of 8000 cells. The concentration of the scRNA-seq libraries was determined using Qubit dsDNA HS Assay kit (Invitrogen, MA, USA) at Qubit 3.0, and size distribution was assessed using an Agilent D1000 TapeStation system (Agilent, CA, USA). Libraries were sequenced on an Illumina NovaSeq6000 instruments with a paired-end 150-bp (performed by GENEWIZ, Germany).

value: OAT


title: Sample 12_Paediatric pneumonia_12

value: F

value: U


title: OAT, donor 4, scRNAseq

description: OAT, Patient, CD3+ T cells

value: CD3+ T cells purified from peripheral blood(PBMC)


title: T24 cells, siUSP52, rep2

country: China

tag: treatment


title: Sample 18_Paediatric pneumonia_18


title: imgl_WT_rep2

value: WT


title: imgl_S1KO_rep1


title: T24 cells, siNC, rep3

value: siNC


title: Sample 11_Paediatric pneumonia_11


title: imgl_WT_rep1


title: T24 cells, siUSP52, rep1

value: Tumor


title: OAT, donor 2, scRNAseq

description: OAT, Patient, CD3+ T cells


title: OAT, donor 1, scRNAseq

description: OAT, Patient, CD3+ T cells


title: Sample 9_Paediatric pneumonia_9


title: Pool3_T_3_A

city: Pozzuoli

first: Diego

last: Carrella

state: NAPOLI

address: Via Campi Flegrei 34

institute: TIGEM

description: 0.5mM CuCl2, biological rep3

library_source: genomic

data_processing:
To analyze the NGS datasets, we first performed a demultiplexing step for the highthroughput sequencing output with the bcl2fastq tool (ver. 2.20.0.422) (https://scicrunch.org/resolver/SCR_015058), obtaining one FASTQ file for each sample. To measure the relative quantity of each shRNA in a sample, we aligned the NGS reads to the construct FASTA reference files, provided with the Dharmacon library, using Bowtie2 (ver. 2.4.2). The Bowtie2 output was converted into a single raw count matrix for subsequent analysis using the Python (ver. 2.7.18) script cpuntBowtie2Hits.py, which was provided by Dharmacon. Finally, we normalized raw counts into counts per million (CPM), computed the differential expression analysis between the two conditions of the experimental design, and annotated each shRNA with the corresponding gene. We performed these steps in R environment (ver. 4.2.3), using NOISeq package(ver. 2.42.0) for the normalization, and edgeR package (ver. 3.40.2) for the identification of shRNAs differentially represented in reference and treated cell populations.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

molecule: genomic DNA

source_name: Transcriptome profile of control T sample, biological rep3

growth_protocol: Cells were transfected with each individual Decode Pooled Lentiviral sRNA Screening Libraries and mantained in RPMI with 10%FBS, 1% PS,1% Glu in humidified atmosphere at 37 C with 5% Co

extract_protocol:
DNA was isolated using Quick-DNA Miniprep Plus kit (Zymo Research). 6.6ug of each samples were used for sRNA PCR amplification
For preparation of the library containing single samples, we followed the manufacturer’s instructions (Dharmacon). Purified DNA samples were validated and quantified by microfluidic analysis using the Bioanalyzer High Sensitivity DNA Assay kit (Agilent Technologies) and the 2100 Bioanalyzer with 2100 Expert Software. All samples were pooled with a 10% phiX spike-in.
The library was sequenced using the Next Seq500 system performing single read (SR) runs covering at least 75 nt. (Illumina Inc., San Diego, CA, USA).

treatment_protocol: Cells were left untreated or treated with 0.5 mM CuCl2 for 24h

value: unknown

tag: agent

value: 0.5mM CuCl2


title: FER, donor 5, scRNAseq

description: Fertile, Control, CD3+ T cells

value: FER


title: Pool3_T_2_A

description: 0.5mM CuCl2, biological rep2

source_name: Transcriptome profile of control T sample, biological rep2


title: T24 cells, siNC, rep2

value: bladder cancer


title: Sample 8_Paediatric pneumonia_8

value: Whole blood


title: FER, donor 4, scRNAseq

description: Fertile, Control, CD3+ T cells


title: Pool3_T_1_A

description: 0.5mM CuCl2, biological rep1

source_name: Transcriptome profile of control T sample, biological rep1


title: Sample 7_Paediatric pneumonia_7


title: Sample 6_Paediatric pneumonia_6


title: FER, donor 3, scRNAseq

description: Fertile, Control, CD3+ T cells


title: Sample 10_Paediatric pneumonia_10

value: M


title: Pool3_NT_3_A

description: Control, biological rep3

source_name: Transcriptome profile of control NT sample, biological rep3

value: Control


title: Directed harvested X.kitaake roots no protoplasting Rep #2

city: Los Angeles

first: Rachel

last: Shahan

state: California

address: 610 Charles E. Young Dr. S

institute: University of California, Los Angeles

description: Library name: Sample 2

data_processing:
Reads were aligned to Michigan State University Rice genome v7 with the STAR aligner, deduplicated using UMI-Tools, and counted with HTSeq-Count.
The BAM_COUNTS file were then merged. Reads were normalized, averaged and converted to Log(CPM)  with EdgeR
Assembly: MSU 7.0
Supplementary files format and content: xlsx file (Supplementary Table 2_Protoplast_induced_Genes_with_cp_and_mt_genes_Rice)

organism: Oryza sativa

source_name: Root

growth_protocol: X.kitaake was used as wild type. Rice seeds were dehulled, sterilized with 50% bleach for 10 min, and rinsed four to five times with sterile water. All plant growth was in Yoshida’s nutrient solution solidified with gellan gum (Gelzan, Caisson Inc).Growth boxes were kept at 4°C in the dark for 2-3 days until the seeds germinate, then transferred to a percival growth chamber set to 28°C, and consistant light. Rice seedlings were grown in the percival for 1-3 days before harvesting.

extract_protocol:
Intacted roots (directly harvested from gel grown conditions) and digested roots (protoplasts + undigested chunks) were havested. Samples were frozen in liquid nitrogen and RNA was isolated using the Zymo MagBead RNA Isolation kit. RNA was used as input into the Lexogen QuantSeq 3′ FWD RNA-Seq library preparation procedure. Libraries were indexed and pooled on an Illumina NextSeq. Reads were aligned to Michigan State University Rice genome v7 counted with HTSeq-Count.
RNA was used as input into the Lexogen QuantSeq 3′ FWD RNA-Seq library preparation procedure according to the manufacturer’s protocol, using the Unique Molecular Identifier (UMI) PCR add-on kit. Libraries were indexed and pooled on an Illumina NextSeq.
Lexogen QuantSeq 3′ FWD RNA-Seq

value: Root

value: All cell types of root


title: Directed harvested X.kitaake roots no protoplasting Rep #1

description: Library name: Sample 1


title: Directed harvested X.kitaake roots protoplasting Rep #4

description: Library name: Sample 8

value: Digested by Protoplast cocktail


title: FER, donor 1, scRNAseq

description: Fertile, Control, CD3+ T cells


title: HRMECs,siATF3,rep4

city: Suita

first: Chihiro

last: Ueda

address: l2-2, Yamadaoka

department: Ophthalmology

country: Japan

institute: Osaka University

data_processing:
The Illumina NovaSeq 6000 system was used for 150-base paired-end read sequencing.
Raw FASTQ files were processed using fastp (v0.19.5)  to remove adapter sequences and low-quality reads.
The filtered reads were aligned to the human reference genome (GRCh38) using STAR (v2.7.10b).
Read counts were quantified using RSEM (v1.3.3) with the rsem-calculate-expression function.
Assembly: GRCh38
Supplementary files format and content: Text file includs matrix table with raw gene counts for every gene and every sample

source_name: Human Retinal Microvascular Endothelial Cells

growth_protocol: HRMECs (Cell Systems, Kirkland, WA, USA) were seeded on Attachment Factor (Cell Systems, Kirkland, WA, USA)-coated dishes (Falcon, Franklin Lakes, NJ, USA) in CS-C medium with Defined Cell Boost (Cell Systems, Kirkland, WA, USA), 10% FBS (Gibco, Grand Island, NY, USA)  and antibiotics at 37°C in 5% CO2.

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen, Maryland, MD, USA)
The cDNA library was prepared using  NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit.

treatment_protocol: HRMECs were  transfected for 24 h with Silencer® Select siRNAs targeting human ATF3 (Invitrogen, Carlsbad, CA, USA) and Silencer™ Select Negative Control No. 2 siRNA (Invitrogen, Carlsbad, CA, USA) by using Lipofectamine™ RNAiMAX Transfection Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.

value: Endothelial Cells

value: ATF3 knockdown


title: Sample 5_Paediatric pneumonia_5

value: U

value: PAXgene

value: A

value: Pneumonia


title: FER, donor 2, scRNAseq

description: Fertile, Control, CD3+ T cells

value: CD3+ T cells purified from peripheral blood(PBMC)


title: Sample 3_Paediatric pneumonia_3

value: PB


title: Sample 4_Paediatric pneumonia_4

value: F


title: Pool3_NT_2_A

description: Control, biological rep2

source_name: Transcriptome profile of control NT sample, biological rep2

value: unknown


title: Pool3_NT_1_A

description: Control, biological rep1

source_name: Transcriptome profile of control NT sample, biological rep1


title: Pool1_Pool2_Pool3_Pool4_Pool5_Pool6_Pool7_Pool8_Pool9_Pool10_T_3_A

description: 0.5mM CuCl2, biological rep3

value: 0.5mM CuCl2


title: T24 cells, siNC, rep1

value: Tumor

value: bladder cancer

value: siNC


title: Directed harvested X.kitaake roots protoplasting Rep #3

description: Library name: Sample 7

value: Root

value: WT


title: Directed harvested X.kitaake roots protoplasting Rep #1

description: Library name: Sample 5

value: All cell types of root

value: Digested by Protoplast cocktail


title: Sample 2_Paediatric pneumonia_2

value: Whole blood


title: Directed harvested X.kitaake roots protoplasting Rep #2

description: Library name: Sample 6


title: Directed harvested X.kitaake roots no protoplasting Rep #4

description: Library name: Sample 4


title: HRMECs,siATF3,rep1

value: Human Retinal Microvascular Endothelial Cells

value: Endothelial Cells

value: ATF3 knockdown


title: Pool1_Pool2_Pool3_Pool4_Pool5_Pool6_Pool7_Pool8_Pool9_Pool10_NT_3_A

description: Control, biological rep3

value: Control


title: HRMECs,siNC,rep4


title: Pool1_Pool2_Pool3_Pool4_Pool5_Pool6_Pool7_Pool8_Pool9_Pool10_NT_2_A

description: Control, biological rep2


title: Low mir-243p::GFP sort 4

city: St. Louis

first: Matthew

last: Mosley

state: MO

address: 660 S. Euclid Ave.

department: Developmental Biology

institute: Washington University in St. Louis School of Medicine

description:
Library name: L_243_4
predicted short-lived by mir-243p::GFP expression
L_243_4

data_processing:
Clean reads were obtained by filtereing reads containing adapters, poly-N reads, and low quality reads.
Fastq files were aligned to the reference genome using STAR version 2.7.3a.
Gene counts were determined using the featureCounts function in the R package Rsubread.
Assembly: Caenorhabditis elegans WBcel235.94
Supplementary files format and content: Gene counts for each sample in tab-delimitted text format.

organism: Caenorhabditis elegans

source_name: Whole body

extract_protocol:
Animals were collected in M9 buffer and allowed to settle by gravity. Samples were lysed by addition of TRIzol (ThermoFisher) with repeated flash-freeze/thaw cycles in liquid nitrogen. Total RNA was obtained by phenol chloroform extraction and purified according to the RNeasy Micro kit protocl (Qiagen), including on-column DNase treatment.
mRNA was enriched using oligo(dT) beads, and the Ribo-Zero kit (Illumina) was used to remove rRNA. First, mRNA was fragmented randomly by adding fragmentation buffer, then cDNA was synthesized by using mRNA template and random hexamers primer, after which a second-strand synthesis buffer (Illumina) , dNTPs, RNase H, and DNA polymerase I were added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library was completed through size selection and PCR enrichment.

value: Whole body


title: HRMECs,siNC,rep3


title: HRMECs,siATF3,rep3


title: Low mir-243p::GFP sort 3

description:
Library name: L_243_3
predicted short-lived by mir-243p::GFP expression
L_243_3


title: Pool1_Pool2_Pool3_Pool4_Pool5_Pool6_Pool7_Pool8_Pool9_Pool10_T_2_A

description: 0.5mM CuCl2, biological rep2


title: HRMECs,siNC,rep1


title: Pool1_Pool2_Pool3_Pool4_Pool5_Pool6_Pool7_Pool8_Pool9_Pool10_NT_1_A

description: Control, biological rep1


title: Pool3_Pool4_Pool5_Pool8_Pool10_T_2_A

description: 0.5mM CuCl2, biological rep2


title: Low mir-243p::GFP sort 1

description:
Library name: L_243_1
predicted short-lived by mir-243p::GFP expression
L_243_1


title: HRMECs,siATF3,rep2


title: High mir-243p::GFP sort 4

description:
Library name: H_243_4
predicted long-lived by mir-243p::GFP expression
H_243_4


title: hNMSO_d39-44_spatial

city: Shanghai

first: Jinkui

last: Zhu

state: Shanghai

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

department: School of Life Science and Technology

institute: ShanghaiTech University

description: Fresh frozen Spatial transcriptome sequencing

data_processing:
Raw reads were mapped to the human genome (GRCh38) and filtered using the Space Ranger pipeline (v1.3.0) with default parameters.
Assembly: GRCh38
Supplementary files format and content: barcode.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: algned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json :scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positins_list.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: filtered_feature_bc_matrix.h5: h5 file of the filtered data
Library strategy: Spatial Transcriptomics

source_name: organoids

extract_protocol:
For spatial transcriptome sequencing, organoids were embedded in OCT compound and sectioned at 10 μm thick and were placed on the capture area of the Visium Spatial Gene Expression Slide.
For spatial transcriptome sequencing, Visium Spatial Gene Expression Reagent Kits were applied according to the manufacturer’s instructions. Sections were fixed with formaldehyde, Hematoxylin and Eosin staining were performed, and sections were scanned for collection. Capture Area contains ~5000 gene expression spots that include primers including Illumina TruSeq Read 1, 16 nt Spatial Barcode, 12 nt UMI, and 30 nt poly(dT) sequence required for capture and priming of poly-adenylated mRNA. Once the samples were permeabilized, RT Master Mix containing reverse transcription reagents was added to the permeabilized sections. Cellular mRNA was captured by the primers on the gene expression spots to generate full-length cDNA. Libraries were generated with P5, P7, i7, and i5 sample index, and TruSeq Read 2 was added to each selected cDNA for sequencing.

value: organoids

value: human embryonic stem cells

value: Differentiation according to protocol


title: Pool1_Pool2_Pool3_Pool4_Pool5_Pool6_Pool7_Pool8_Pool9_Pool10_T_1_A

description: 0.5mM CuCl2, biological rep1

value: unknown

value: 0.5mM CuCl2


title: Pool3_Pool4_Pool5_Pool8_Pool10_T_1_A

description: 0.5mM CuCl2, biological rep1


title: Pool3_Pool4_Pool5_Pool8_Pool10_T_3_A

description: 0.5mM CuCl2, biological rep3


title: Directed harvested X.kitaake roots no protoplasting Rep #3

description: Library name: Sample 3


title: Low mir-243p::GFP sort 2

description:
Library name: L_243_2
predicted short-lived by mir-243p::GFP expression
L_243_2


title: HRMECs,siNC,rep2


title: Sample 1_Paediatric pneumonia_1

value: F

value: PB

value: PAXgene

value: A

value: Pneumonia


title: High mir-243p::GFP sort 3

description:
Library name: H_243_3
predicted long-lived by mir-243p::GFP expression
H_243_3


title: hNMSO_d75_snRNA

description: 10X Genomics

data_processing:
To obtain count matrices, reads were aligned to human genome GRCh38 (v 3.0.0, provided by 10X genomics) using Cell Ranger (v 6.1.2) pipeline with the default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
For single-nucleus sequencing, organoids of the same stage were pooled together and were frozen immediately at - 80℃.  The Chromium Nuclei Isolation Kit with RNase Inhibitor was used according to the manufacturer’s instructions to isolate nuclei for subsequent sequencing steps. In short, frozen organoids were homogenized with a pestle in the Lysis Buffer and passed through a column. Next, the debris was removed via centrifugation in the Debris Removal Buffer.
For single-nucleus sequencing, nuclei were used to generate cDNA libraries using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index). Briefly, cell nuclei were partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs), and microfluidic cell nuclei were streamed at limiting dilution into a stream of Single Cell 3’ v3.1 Gel Beads, and then a stream of oil. After lysis, an Illumina TruSeq Read 1, a 16 base pair 10x Barcode, a 12 bp unique molecular identifier (UMI), a 30 nt poly(dT) sequence, and a Capture Sequence 1 were released and mixed with the lysate and the Master Mix containing the RT reagents, full-length cDNA from poly-adenylated messenger RNA was generated. After individual droplets were broken down, homogenized, and cleaned from the remaining noncDNA with silane magnetic beads, the libraries were size-selected, followed by the addition of TruSeq Read 2, P5, P7, i7, and i5 sample indexes sequences to each selected cDNA. Finally, each library was sequenced using the Illumina Novaseq6000, read1 28bp, read2 151bp Mode.

value: WT


title: hNMSO_d38_snRNA

description: 10X Genomics


title: Pool3_Pool4_Pool5_Pool8_Pool10_NT_2_A

description: Control, biological rep2


title: METTL3-knockdown HG-stimulated MPC5 Cell Replicate 2 [HG-m3-1-2(Sup)]

type: RNA

city: Hefei

first: Ling

last: Jiang

state: Anhui

address: Meishan Road

institute: AHMU

hyb_protocol: Cy3 and Cy5 labeled cRNAs were  combined together and hybridized to Arraystar  Mouse mRNA&lncRNA Epitranscriptomic Arrays (8x60K, Arraystar) at 65°C for 17 hours in an Agilent Hybridization Oven.

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

data_processing: Data was extracted using Agilent Feature Extraction software. The probe signals passing P or M QC flags in at least 3 samples were retained for further analysis.

organism: Mus musculus

source_name: METTL3-knockdown HG-stimulated MPC5 Cell_SUP

label_protocol: IP and Sup RNAs were amplified as cRNAs and labeled with Cy5 and Cy3 respectively using Arraystar Super RNA Labeling Kit (IP (Cy5-labelled) and Sup (Cy3-labelled))

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: MPC5 transfected with Si#METTL3 or siNC was stimulated for 24 hours under high glucose conditions (30mmol/L)

value: podocyte

tag: genotype/variation


title: METTL3-knockdown HG-stimulated MPC5 Cell Replicate 1 [HG-m3-1(Sup)]

value: stimulated for 24 hours under high glucose condition


title: Control HG-stimulated MPC5 Cell Replicate 2 [HG-H2-2(Sup)]

source_name: Control HG-stimulated MPC5 Cell_SUP

value: control


title: High mir-243p::GFP sort 2

description:
Library name: H_243_2
predicted long-lived by mir-243p::GFP expression
H_243_2


title: METTL3-knockdown HG-stimulated MPC5 Cell Replicate 3 [S2-2(Sup)]


title: Control HG-stimulated MPC5 Cell Replicate 3 [N2-1(Sup)]


title: Control HG-stimulated MPC5 Cell Replicate 1 [HG-H2-1(Sup)]


title: HK-2 cells ,vector ,3

city: shenyang

first: xiuli

last: Guo

address: No. 155 Nanjing North Street, Heping District, Shenyang, Liaoning Province

institute: The First Hospital of China Medical University

data_processing:
Solexa pipeline version 1.8 (Off-Line Base Caller software, version 1.8) software was used for base calling, and FastQC software was used to evaluate the sequencing quality of the reads after removing adapters (cutadapt was used to remove 3' and 5' adapters).
The trimmed reads (trimmed 5',3'-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 (2.1.0)software.
Transcript abundance was estimated using StringTie software (1.3.3) with reference to official database annotation information.
The R software Ballgown (v2.10.0) was used to calculate the FPKM at the gene level and the transcript level, and the expression differences at the gene level and the transcript level were calculated respectively, and the differentially expressed genes between samples or groups were screened.
The RNA is compared to the reference genome by STAR software, reads count statistics are performed, and differential expression calculation is performed using R software.
Assembly: GRCh37
Supplementary files format and content: FPKM values for each sample

source_name: kidney

growth_protocol: HK-2 cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was enriched using the NEB next®Poly (A) mRNA Magnetic Isolation Module and 1-2 μg of total RNA was used to construct the sequence libraries.
RNA libraries for RNA-seq were prepared using KAPA Stranded RNA-Seq Library Prep Kit following manufacturer's protocols.

value: kidney

value: Renal tubular epithelial cells

value: vector


title: Pool3_Pool4_Pool5_Pool8_Pool10_NT_1_A

description: Control, biological rep1

value: Control


title: METTL3-knockdown HG-stimulated MPC5 Cell Replicate 3 [S2-2(IP)]

source_name: METTL3-knockdown HG-stimulated MPC5 Cell_IP


title: Pool3_Pool4_Pool5_Pool8_Pool10_NT_3_A

description: Control, biological rep3


title: HK-2 cells ,vector ,2


title: Low mir-240/786p::GFP sort 4

description:
Library name: L_240-786_4
predicted long-lived by mir-240/786p::GFP expression
L_240-786_4

value: Whole body


title: HK-2 cells, vector ,1


title: HK-2 cells, shGLIS1, 3

value: GLIS1 knockdown


title: Pool10_NT_1_A

description: Control, biological rep1

value: unknown


title: Pool8_T_1_A

description: 0.5mM CuCl2, biological rep1

value: 0.5mM CuCl2


title: Pool10_T_1_A

description: 0.5mM CuCl2, biological rep1


title: Low mir-240/786p::GFP sort 3

description:
Library name: L_240-786_3
predicted long-lived by mir-240/786p::GFP expression
L_240-786_3


title: HK-2 cells, shGLIS1, 2


title: Low mir-240/786p::GFP sort 1

description:
Library name: L_240-786_1
predicted long-lived by mir-240/786p::GFP expression
L_240-786_1


title: RPT replicate 4

city: Milwaukee

first: Sridhar

last: Rao

state: WI

address: 8797 Watertown Plank Rd

department: Stem Cell Transriptional Regulation

institute: Versiti Blood Research Institte

description:
RPT27
ATAC_RPT_consensus_peaks_signaldata.bigwig

data_processing:
ATAC-seq reads were aligned to the hg38 (human derived sample) and rn7 (rat derived data) genome assembly using bowtie2 and after removing the mitochondrial read and duplicate reads, all replicates from each sample were merged
MACS2 was used to call peak from these merged bam files as well as each replicate bam files using this criteria  -nomodel-extsize200 -shift 100 -q0.01
The alignmed reads was also used to perform motif enrichment by HOMER
Assembly: hg38 and rn7
Supplementary files format and content: NarrowPeak
Supplementary files format and content: bigwig

organism: Rattus norvegicus

source_name: Kidney

growth_protocol: Kidney segments were dissected from human Patients and salt-sensitive rats (SS/JrHsdMcwi; RRID: RGD 61499) are used for this study

extract_protocol:
Small pieces of kidney segments from both human and rat were subjected to multiple rounds of collagenase digestion to isolate mTAL and PT segments
Nuclei were isolated from the PT and mTAL segments and subjected to the transposition reaction with Illlumina transposase in the appropriate buffer. Library fragments were amplified with indexing primers

value: Kidney

value: Proximal tubule


title: METTL3-knockdown HG-stimulated MPC5 Cell Replicate 2 [HG-m3-1-2(IP)]


title: HK-2 cells, shGLIS1, 1


title: High mir-243p::GFP sort 1

description:
Library name: H_243_1
predicted long-lived by mir-243p::GFP expression
H_243_1


title: Pool5_T_2_A

description: 0.5mM CuCl2, biological rep2


title: Pool5_NT_2_A

description: Control, biological rep2


title: METTL3-knockdown HG-stimulated MPC5 Cell Replicate 1 [HG-m3-1(IP)]


title: High mir-240/786p::GFP sort 4

description:
Library name: H_240-786_4
predicted short-lived by mir-240/786p::GFP expression
H_240-786_4


title: Control HG-stimulated MPC5 Cell Replicate 2 [HG-H2-2(IP)]

source_name: Control HG-stimulated MPC5 Cell_IP


title: Control HG-stimulated MPC5 Cell Replicate 3 [N2-1(IP)]


title: RPT replicate 3

description:
RPT26
ATAC_RPT_consensus_peaks_signaldata.bigwig


title: RPT replicate 2

description:
RPT25
ATAC_RPT_consensus_peaks_signaldata.bigwig


title: SBOT1 rep9

first: Cenxi

last: Liu

address: Songhu Road 2005

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for  low-quality sequence, then mapped to mm10 whole genome using Hisat2
Stringtie was used to quantify
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: ovary

extract_protocol:
Total RNA was extracted from tissues by using TRIzol reagent (Invitrogen). Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary

tag: disease state

value: recurrence

tag: disease

value: Serous borderline ovarian tumor


title: Control HG-stimulated MPC5 Cell Replicate 1 [HG-H2-1(IP)]


title: SBOT1 rep8


title: Pool4_T_2_A_Pool10_T_2_A

description: 0.5mM CuCl2, biological rep,2


title: RPT replicate 1

description:
RPT24
ATAC_RPT_consensus_peaks_signaldata.bigwig


title: High mir-240/786p::GFP sort 2

description:
Library name: H_240-786_2
predicted short-lived by mir-240/786p::GFP expression
H_240-786_2


title: Pool8_NT_1_A

description: Control, biological rep1


title: High mir-240/786p::GFP sort 1

description:
Library name: H_240-786_1
predicted short-lived by mir-240/786p::GFP expression
H_240-786_1


title: SBOT1 rep7


title: Low autofluorescence sort 3

description:
Library name: L_AF_3
predicted long-lived by autofluorescence
L_AF_3


title: Pool4_NT_2_A_Pool10_NT_2_A

description: Control, biological rep2


title: Yeast-G2M-WT-2-No_ExoVII-T_END-seq

first: Qingqing

last: Yuan

address: 320 Yueyang Road

department: SIBCB

institute: CEMCS, CAS

description:
Library name: Yeast-G2M-WT-2-No_ExoVII-T_END-seq
PE150

data_processing:
END-seq sequencing reads were firstly trimmed to remove adapters by cutadapt (v4.1) with parameters -e 0.1 -O 3 -m 55 --quality-cutoff 25, then reads were aligned to sacCer3 using bowtie (v1.2.1.1) with parameters -n 3 -l 50 -k 1. To circumvent the interference of internal telomeric sequence, telomeric repeats in sub-telomeric regions are masked with “N”. Functions 'view' and 'sort' of samtools (v.1.9) were used to convert and sort the aligned .sam files to sorted .bam files. The forward reads were retained using samtools 'view' function for subsequent analysis. .bam files were further converted to .bed files using the bedtools (v2.25.0) bamToBed command and bedGraph files were generated using bedtools genomecov, normalized by reads per million (RPM) and then converted into .bigWig files using bedGraphToBigWig from UCSC utilities.
Assembly: own-assembled genome
Supplementary files format and content: bigwig

organism: Saccharomyces cerevisiae

source_name: whole cell

growth_protocol: YP medium,2% galactose

extract_protocol:
~10^8 cells were washed twice by 50 mM EDTA (pH 8.0) and embedded in 0.75% low melting agarose plugs with Lyticase (1 mg/ml, final concentration). Plugs were then treated with Lyticase and Lysing (1 mg/ml, final concentration, 37˚C for 1.5 hours), Proteinase K (50˚C for 2 hours, followed by 37˚C for 7 hours) and RNase A (37˚C for 1 hour) in turn. DNA ends within plugs were either not trimmed (native END-seq) or trimmed (typical END-seq) with Exonuclease T and Exonuclease VII. All samples were followed by A-tailing with Klenow fragment exo- to ligate with 3’ T overhang of biotinylated hairpin adaptors (introducing Illumina p5 primers). After plug melting and sonication, DNA fragments were sheared to 300-500 bp in length and precipitated by ethanol, dissolved in 10 mM  Tris, pH 8.0.
Extract DNA from plugs are enriched by streptavidin beads. End-repair by T4 DNA polymerase, Klenow fragment and T4 polynucleotide kinase was performed before second A-tailing with Klenow fragment exo-, allowing the ligation of distal hairpin adaptors with p7 Illumina primers. Finally, after USER enzyme digestion, libraries were PCR amplified and selected by AMPure XP beads for Illumina sequencing.

treatment_protocol: 10µg/ml nocodozale for 3 hours

value: whole cell

value: hapoloid yeast cell

value: WT


title: SBOT1 rep5


title: Low mir-240/786p::GFP sort 2

description:
Library name: L_240-786_2
predicted long-lived by mir-240/786p::GFP expression
L_240-786_2


title: Low autofluorescence sort 2

description:
Library name: L_AF_2
predicted long-lived by autofluorescence
L_AF_2


title: High mir-240/786p::GFP sort 3

description:
Library name: H_240-786_3
predicted short-lived by mir-240/786p::GFP expression
H_240-786_3


title: Yeast-G2M-WT-No-ExoVII-T_END-seq

description:
Library name: Yeast-G2M-WT-No-ExoVII-T_END-seq
PE150


title: Pool4_NT_1_A_Pool8_NT_2_A

description: Control, biological rep1,2

source_name: Transcriptome profile of control NT sample, biological rep1.2


title: Rat mTAL replicate 3

description:
RmTAL9
ATAC_RmTAL_consensus_peaks_signaldata.bigwig

value: medullary Thick Ascending Limb


title: SBOT1 rep4


title: SBOT1 rep3


title: SBOT1 rep6


title: Yeast-G2M-WT-ExoVII-T_END-seq

description:
Library name: Yeast-G2M-WT-ExoVII-T_END-seq
PE150

value: ExoVII, ExoT


title: 635AP-1923-8

type: genomic

city: Pittsburgh

first: Hisato

last: Yagi

state: PA

address: 530 45th street, Rangos Res Center 8162

institute: University of Pittsburgh

description: Illumina Infinium MouseMethylation array (MouseMethylation-12v1-0_A1)

hyb_protocol: Standard Illuminahybridization protocol

scan_protocol: the beadchip was scanned using an Illumina iSCAN

data_processing:
the data analyzed using Genome Studio. Raw intensities were read into R using the R package minfi (v 1.36.0), and R methylation manifest and annotation packages to use with minfi were created using the Manifest and Annotation files provided by Illumina.
bVals_Brain_sampProbFilt_r2.txt contains average beta

label: Cy3 and Cy5

source_name: Brain

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA was isolated using the QIAamp DNA mini kit (Quiagen)

value: Brain

tag: phenotype


title: High autofluorescence sort 3

description:
Library name: H_AF_3
predicted short-lived by autofluorescence
H_AF_3


title: SBOT1 rep2


title: Pool3_NT_2_A_Pool5_NT_1_A

description: Control, biological rep1,2

source_name: Transcriptome profile of control NT sample, biological rep1,2


title: Yeast-G2M-WT-ExoIII-No-ExoVII-T_END-seq

description:
Library name: Yeast-G2M-WT-ExoIII-No-ExoVII-T_END-seq
PE150

value: ExoIII


title: LFH3, replicated 3, scRNAseq

city: Seoul

first: Hyun Jung

last: Kim

address: 73 Goryeodae-ro, Seongbuk-gu

department: Anatomy

country: South Korea

institute: Korea University

description: 10x Genomics

data_processing:
The number of molecules per barcode of mapped scRNAseq data was quantified using the Cell Ranger 10x softare package (version 5.0.1) with the GRCh38 referece genome as reference.
Cells were than processed following the process of Seurat (version 4).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Ligamentum Flavum

extract_protocol:
Human patients diasgnosed with LSCS accompanied by LF hypertrohpy were collected during elective surgery involving decompressive lumbar laminectormy. LF tissues acquired during surgery were rinsed thoroughly with saline solution an dplaced in a conical tube containing MACS Tissue Storage Solution. The tissue was then transferred to the laboratory for tissue dissociation. The LF tissue was rinsed then dissociated with Hank's balanaced saline solution mixed with 1% penicilin/streptomycin. After remiving bold debris and blood, specimens were minced with a blade on a petri dish, and series of enzymatic digestion reactions were performed using Ham's F-12 medium containing 1% P/S, 5% heat-inactivated fetal bovine serum, and 0.2% protease followed by rinsing. A 70-μm strainer was used to separate the cells from tissue debris after enzymatic digestion. After filtration, the solution with the isolated cells was centrifuged. The remaining cells were counted with a cell counter and stored in a conical tube.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 chemistry, 10x Genomics).

value: Ligamentum Flavum

value: Female

tag: age

value: 67 years old

tag: diagnosis

tag: maximum thickness

tag: lscs grade

value: C

tag: obesity


title: SAP-380-7

tag: tissue

tag: genotype

value: Control


title: High autofluorescence sort 1

description:
Library name: H_AF_1
predicted short-lived by autofluorescence
H_AF_1

value: Whole body


title: High autofluorescence sort 2

description:
Library name: H_AF_2
predicted short-lived by autofluorescence
H_AF_2


title: SBOT1 rep1


title: B6-1257-5


title: LFH1, replicated 1, scRNAseq

description: 10x Genomics

tag: Sex

value: 65 years old

value: LSCS L4/5, L5/S1

value: B


title: LFH2, replicated 2, scRNAseq

description: 10x Genomics

value: 63 years old

value: LSCS L3/4


title: Low lin-4p::GFP sort 5

description:
Library name: L_lin4_5
predicted short-lived by lin-4p::GFP expression
L_lin4_5


title: SBOT2 rep12

value: ovary

value: non-recurrence

value: Serous borderline ovarian tumor


title: Vinblastine_3

description: Treatment, biological rep3

treatment_protocol: Cells were left untreated or treated with 60uM Vinblastine for 24h

tag: cell line

tag: cell type

value: unknown

value: Transcriptome profile of vinblastine treated sample, biological rep3


title: SBOT2 rep10


title: B6-1257-2

value: Brain


title: Low lin-4p::GFP sort 4

description:
Library name: L_lin4_4
predicted short-lived by lin-4p::GFP expression
L_lin4_4


title: Vinblastine_2

description: Treatment, biological rep2

value: Transcriptome profile of vinblastine treated sample, biological rep2


title: Pool3_T_2_A_Pool5_T_1_A

description: 0.5mM CuCl2, biological rep1,2

source_name: Transcriptome profile of control T sample, biological rep1,2

value: 0.5mM CuCl2


title: B6-1257-1


title: SBOT2 rep9


title: Low autofluorescence sort 1

description:
Library name: L_AF_1
predicted long-lived by autofluorescence
L_AF_1


title: 635AP-1877-2

value: m/m

value: Severe


title: Vinblastine_1

description: Treatment, biological rep1

value: Transcriptome profile of vinblastine treated sample, biological rep1


title: Low lin-4p::GFP sort 3

description:
Library name: L_lin4_3
predicted short-lived by lin-4p::GFP expression
L_lin4_3

value: Whole body


title: SBOT2 rep8


title: NT_2

description: Control, biological rep2

value: Transcriptome profile of control NT sample, biological rep2


title: NT_3

description: Control, biological rep3

value: Transcriptome profile of control NT sample, biological rep3


title: 635AP-1923-5


title: Low lin-4p::GFP sort 1

description:
Library name: L_lin4_1
predicted short-lived by lin-4p::GFP expression
L_lin4_1


title: Low lin-4p::GFP sort 6

description:
Library name: L_lin4_6
predicted short-lived by lin-4p::GFP expression
L_lin4_6


title: SAP-380-2


title: SBOT2 rep6


title: SBOT2 rep11


title: 635AP-1923-7

value: Mild


title: NT_1

description: Control, biological rep1

value: Transcriptome profile of control NT sample, biological rep1


title: SBOT2 rep5


title: High lin-4p::GFP sort 6

description:
Library name: H_lin4_6
predicted long-lived by lin-4p::GFP expression
H_lin4_6


title: 635AP-1923-3


title: SETD1AKO_FKBP-SETD1A_dTAG13_1h_EU_30min

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

data_processing:
BCL2FASTQ version2.20.0 software was used for basecalling.
Read were aligned with HISAT v2.1.0.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1. Command line options for cufflinks were '--max-bundle-flags 4000000' for RNA-seq
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

growth_protocol: MOLM-13 cells and MV4-11 cells were cultured in RPMI-1640 containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
Total RNA was collected using Rneasy Mini Kit with DNase (QIAGEN)
Libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: HA-FKBP-hSETD1A expression vector, Cas9 expression vector and SETD1A sgRNA expression vector  were introduced with lentivirus and stable expressing single cell clone was established. Cells were treated with DMSO or 500 nM dTAG-13 for 24 or 96 hours.

tag: stimulation

tag: time


title: High lin-4p::GFP sort 5

description:
Library name: H_lin4_5
predicted long-lived by lin-4p::GFP expression
H_lin4_5


title: SBOT2 rep3


title: High lin-4p::GFP sort 4

description:
Library name: H_lin4_4
predicted long-lived by lin-4p::GFP expression
H_lin4_4


title: SETD1AKO_FKBP-SETD1A_DMSO_1h_EU_30min

value: DMSO


title: SBOT2 rep4

value: ovary


title: SETD1AKO_FKBP-SETD1A_dTAG13_24h_EU_30min


title: Cell_SurfaceP_YA_SVF

city: Urbana

first: Yujun

last: Feng

state: IL

address: 1304 W Green St.

department: Materials Science and Engineering

institute: University of Illinois, Urbana-Champaign

description: HTO: 3' barcode. A read. Read 1 file contains cell barcode and UMI reads. Read 2 file contains barcode reads. L1 and L2 are 2 index reads.

library_source: other

data_processing:
CellRanger v7.1.0 count is used for both transcripts and HTO data all three tests and for each test, CellRanger v7.1.0 generated a single set of barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz that contains both transcripts and HTO data
Assembly: mm39, hg38
Supplementary files format and content: CellRanger Output files for mouse spleen cells mix test: sp_barcodes.tsv.gz, sp_features.tsv.gz, sp_matrix.mtx.gz
Supplementary files format and content: CellRanger Output files for HeLa-SVF mixing test: SVF_barcodes.tsv.gz, SVF_features.tsv.gz, SVF_matrix.mtx.gz
Supplementary files format and content: CellRanger Output files for Young and Aged mouse SVF mixing test: SVF_YA_barcodes.tsv.gz, SVF_YA_features.tsv.gz, SVF_YA_matrix.mtx.gz
Library strategy: CITE-seq

molecule: other

source_name: mouse adipose

extract_protocol:
Cells are loaded to Gel-bead-in-emulsion (GEM) microfluidic device by Chromium Next GEM Single-Cell 3’ dual-index kit version 3.1 with Feature Barcode technology for Cell Surface Protein (10X Genomics, CA) following the manufacturer’s protocols.
The cell transcripts and HTO barcode libraries are prepared per to the manufacturer's protocol:  https://cdn.10xgenomics.com/image/upload/v1666737555/support-documents/CG000317_ChromiumNextGEMSingleCell3-v3.1_CellSurfaceProtein_RevD.pdf

treatment_protocol: For spleen cells and HeLa cells, no sorting or enrichment was implemented, and samples are directly loaded for library preparation after labeling. For SVF cells, live cell enrichment (Miltenyi Biotech) and CD45+ enrichment (Miltenyi Biotech) are implemented after cell labeling, then cells are loaded to single-cell transcript extraction step.

value: mouse adipose

value: CD45+ stromal vascular fraction cell

tag: library type

value: HTO

tag: hto

value: developed Nanocoding method and molecules

tag: treatment

value: mixed sample( 11 month old obese mice, 4 month old young obese mice)


title: Low lin-4p::GFP sort 2

description:
Library name: L_lin4_2
predicted short-lived by lin-4p::GFP expression
L_lin4_2


title: High lin-4p::GFP sort 3

description:
Library name: H_lin4_3
predicted long-lived by lin-4p::GFP expression
H_lin4_3


title: SBOT2 rep2

tag: disease state

value: non-recurrence

tag: disease

value: Serous borderline ovarian tumor


title: SBOT2 rep7


title: High lin-4p::GFP sort 2

description:
Library name: H_lin4_2
predicted long-lived by lin-4p::GFP expression
H_lin4_2


title: GEX_YA_SVF

description: GEX: 3' polyA mRNA read. Read 1 file contains barcode and UMI reads. Read 2 file contains cDNA reads. L1 and L2 are 2 index reads.

data_processing:
CellRanger v7.1.0 count is used for both transcripts and HTO data all three tests and for each test, CellRanger v7.1.0 generated a single set of barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz that contains both transcripts and HTO data
Assembly: mm39, hg38
Supplementary files format and content: CellRanger Output files for mouse spleen cells mix test: sp_barcodes.tsv.gz, sp_features.tsv.gz, sp_matrix.mtx.gz
Supplementary files format and content: CellRanger Output files for HeLa-SVF mixing test: SVF_barcodes.tsv.gz, SVF_features.tsv.gz, SVF_matrix.mtx.gz
Supplementary files format and content: CellRanger Output files for Young and Aged mouse SVF mixing test: SVF_YA_barcodes.tsv.gz, SVF_YA_features.tsv.gz, SVF_YA_matrix.mtx.gz

value: mRNA


title: SBOT2 rep1


title: High lin-4p::GFP sort 1

description:
Library name: H_lin4_1
predicted long-lived by lin-4p::GFP expression
H_lin4_1


title: SETD1AKO_FKBP-SETD1A_DMSO_NoEU


title: SETD1AKO_FKBP-SETD1A_DMSO_24h_EU_30min


title: 635AP-1720-1

description: Illumina Infinium MouseMethylation array (MouseMethylation-12v1-0_A1)

value: Brain

value: m/m

tag: phenotype


title: DnrCL_gCD33_D7_BasoE_0_2284552

status: Public on Dec 08 2024

city: Memphis

first: Lance

last: Palmer

state: TN - Tennessee

address: 262 Danny Thomas Pl

department: Hematology

institute: St. Jude Children's Research Hospital

description: Library name: DnrCL_gCD33_D7_BasoE_0_2284552

data_processing:
RNA-SEQ reads in FASTQ format were mapped to the human genome (hg38) using STAR version 2.7.1a
Counts per gene were determined by STAR using GENCODE v31 (PUBMED: 33270111) for gene annotations.
Differential expression analysis was performed using DESeq2.  Log fold shrinkage was performed using the 'ashr' method.
Assembly: hg38
Supplementary files format and content: Sorted_RNASEQ.counts.txt is a Tab-delimited text file of raw gene counts.

source_name: Day 7 BasoE

growth_protocol: CD34+ cell were edited by CD33 or BCL11A enhancer gRNAs and then cultured in Phase 1 media include IMDM (Thermo Fisher Scientific, Waltham, MA, USA), 3% human AB serum (Atlanta Biologicals, Flowery Branch, GA, USA, S40110), 2% human blood type AB plasma (SeraCare, Milford, MA, USA 1810-0001), 1 penicillin/streptomycin, 3 units/mL erythropoietin (EPOGEN; Amgen, Thousand Oaks, CA, USA # 55513-144-01), 3 units/mL heparin (Sagent Pharmaceuticals, Schaumburg, IL, USA # 25021-401-02), 200 μg/mL holo-transferrin (Millipore Sigma, Burlington, MA, USA T0665), 10 ng/mL human SCF, and 1 ng/mL human interleukin-3 (IL-3; R&D systems, Minneapolis, MN, USA, 203-IL/CF) for 7 days.

extract_protocol:
Cells were collected and stainined with CD235, CD49D and Band3 antibody then separrated by FACs.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Cells were electroporated with CD33 sgRNA or BCL11A enhancer sgRNA+Cas9 RNP complex

value: Day 7 BasoE

tag: donor

value: Donor CL


title: DnrCL_g34_D7_ProE_0_2284557

description: Library name: DnrCL_g34_D7_ProE_0_2284557

source_name: Day 7 ProE

value: Day 7 ProE


title: DnrCL_g1617_D7_BasoE_0_2284555

description: Library name: DnrCL_g1617_D7_BasoE_0_2284555


title: DnrCL_gCD33_D7_ProE_0_2284551

description: Library name: DnrCL_gCD33_D7_ProE_0_2284551


title: Dnr10_UT_NO_D5_Bulk_0_2003906

description: Library name: Dnr10_UT_NO_D5_Bulk_0_2003906

value: Donor 10

value: UT


title: DnrCL_g34_D7_CD71_0_2284556

description: Library name: DnrCL_g34_D7_CD71_0_2284556

source_name: Day 7 CFU-E

value: Day 7 CFU-E


title: Dnr10_UT_NO_D13_PolyE_0_2003930

description: Library name: Dnr10_UT_NO_D13_PolyE_0_2003930


title: DnrCL_g1617_D7_CD71_0_2284553

description: Library name: DnrCL_g1617_D7_CD71_0_2284553


title: DnrCL_g34_D7_BasoE_0_2284558

description: Library name: DnrCL_g34_D7_BasoE_0_2284558


title: DnrCL_gCD33_D7_CD71_0_2284550

description: Library name: DnrCL_gCD33_D7_CD71_0_2284550


title: Dnr11_UT_D7_BasoE_2_2174376

description: Library name: Dnr11_UT_D7_BasoE_2_2174376

value: Donor 11

value: Untreated


title: Dnr11_g34_D7_BasoE_1_2174390

description: Library name: Dnr11_g34_D7_BasoE_1_2174390


title: Dnr11_UT_D7_ProE_2_2174375

description: Library name: Dnr11_UT_D7_ProE_2_2174375


title: Dnr11_UT_D7_CD71_2_2174374

description: Library name: Dnr11_UT_D7_CD71_2_2174374


title: Dnr11_g34_D7_ProE_1_2174389

description: Library name: Dnr11_g34_D7_ProE_1_2174389


title: Dnr11_UT_D7_BasoE_1_2174373

description: Library name: Dnr11_UT_D7_BasoE_1_2174373


title: Dnr11_gCD33_D7_BasoE_2_2174381

description: Library name: Dnr11_gCD33_D7_BasoE_2_2174381


title: Dnr11_g1617_D7_BasoE_1_2174384

description: Library name: Dnr11_g1617_D7_BasoE_1_2174384


title: Dnr11_g1617_D7_ProE_1_2174383

description: Library name: Dnr11_g1617_D7_ProE_1_2174383


title: Dnr11_gCD33_D7_ProE_2_2174380

description: Library name: Dnr11_gCD33_D7_ProE_2_2174380


title: Dnr11_UT_D7_ProE_1_2174372

description: Library name: Dnr11_UT_D7_ProE_1_2174372


title: Dnr11_g34_D7_CD71_1_2174388

description: Library name: Dnr11_g34_D7_CD71_1_2174388


title: Dnr11_g1617_D7_CD71_1_2174382

description: Library name: Dnr11_g1617_D7_CD71_1_2174382


title: Dnr11_gCD33_D7_CD71_2_2174379

description: Library name: Dnr11_gCD33_D7_CD71_2_2174379


title: Dnr11_UT_D7_CD71_1_2174371

description: Library name: Dnr11_UT_D7_CD71_1_2174371


title: Dnr10_g1617_D7_BasoE_0_2003926

description: Library name: Dnr10_g1617_D7_BasoE_0_2003926


title: DnrCL_g1617_D7_ProE_0_2284554

description: Library name: DnrCL_g1617_D7_ProE_0_2284554


title: Dnr10_gCD33_D7_BasoE_0_2003925

description: Library name: Dnr10_gCD33_D7_BasoE_0_2003925


title: Dnr10_UT_D7_BasoE_0_2003924

description: Library name: Dnr10_UT_D7_BasoE_0_2003924


title: Pool4_T_1_A_Pool8_T_2_A

description: 0.5mM CuCl2, biological rep1,2

data_processing:
To analyze the NGS datasets, we first performed a demultiplexing step for the highthroughput sequencing output with the bcl2fastq tool (ver. 2.20.0.422) (https://scicrunch.org/resolver/SCR_015058), obtaining one FASTQ file for each sample. To measure the relative quantity of each shRNA in a sample, we aligned the NGS reads to the construct FASTA reference files, provided with the Dharmacon library, using Bowtie2 (ver. 2.4.2). The Bowtie2 output was converted into a single raw count matrix for subsequent analysis using the Python (ver. 2.7.18) script cpuntBowtie2Hits.py, which was provided by Dharmacon. Finally, we normalized raw counts into counts per million (CPM), computed the differential expression analysis between the two conditions of the experimental design, and annotated each shRNA with the corresponding gene. We performed these steps in R environment (ver. 4.2.3), using NOISeq package(ver. 2.42.0) for the normalization, and edgeR package (ver. 3.40.2) for the identification of shRNAs differentially represented in reference and treated cell populations.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

value: unknown

tag: agent

value: 0.5mM CuCl2


title: Dnr10_g1617_D7_ProE_0_2003920

description: Library name: Dnr10_g1617_D7_ProE_0_2003920


title: Dnr10_g34_D7_ProE_0_2003923

description: Library name: Dnr10_g34_D7_ProE_0_2003923


title: Dnr10_UT_D7_ProE_0_2003918

description: Library name: Dnr10_UT_D7_ProE_0_2003918


title: Dnr10_gCD33_D7_ProE_0_2003919

description: Library name: Dnr10_gCD33_D7_ProE_0_2003919


title: Dnr10_g1617_D7_CD71_0_2003914

description: Library name: Dnr10_g1617_D7_CD71_0_2003914


title: Dnr10_g34_D7_CD71_0_2003917

description: Library name: Dnr10_g34_D7_CD71_0_2003917


title: Dnr10_gCD33_D7_CD71_0_2003913

description: Library name: Dnr10_gCD33_D7_CD71_0_2003913


title: Dnr10_UT_D7_CD71_0_2003912

description: Library name: Dnr10_UT_D7_CD71_0_2003912


title: BCL11AKO_3

description: Library name: BCL11AKO_3

data_processing:
RNA-SEQ reads in FASTQ format were mapped to the human genome (hg38) using STAR version 2.7.1a
Counts per gene were determined by STAR using GENCODE v31 (PUBMED: 33270111) for gene annotations.
Differential expression analysis was performed using DESeq2.  Log fold shrinkage was performed using the 'ashr' method.
Assembly: hg38
Supplementary files format and content: NBSGW_RNAseq.txt is a Tab-delimited text file of raw gene counts.

source_name: CD235a+ erythroid cells

growth_protocol: cells were thawed, prestimulated in X-VIVO 10 medium (Lonza, Basel, Switzerland) with 100 ng/ml human Flt3-Ligand, 100 ng/ml stem cell factor (SCF), 100 ng/ml thrombopoietin (R&D systems, Minneapolis, MN), 1´ penicillin/streptomycin (Thermo Fisher Scientific, Waltham, MA, USA), and 2 mM L-alanyl-L-glutamine (GlutaMaxTM, Gibco, Waltham, MA USA) for 1-2 days, then electroporated with ribonucleoprotein (RNP) consisting of Cas9 + targeting single guide RNA (sgRNA).

extract_protocol:
RNA samples were extracted with QIAGEN RNeasy micro Plus kit
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: 6 to 9-week-old female NBSGW mice were transplanted with 5X105 untreated or BCL11A enhancer gRNA edited CD34+ cells per mouse via tail vein. After 16-17 weeks, mice were euthanized to collect bone marrow (BM) from femurs, tibiae, and hip bones, CD235a+ cells were isolated for RNA-seq analysis.

value: CD235a+ erythroid cells

value: BCL11A Enhancer gRNA


title: BCL11AKO_2

description: Library name: BCL11AKO_2


title: NT_3

description: Library name: NT_3

value: Non-targeting  gRNA


title: BCL11AKO_1

description: Library name: BCL11AKO_1


title: NT_2

description: Library name: NT_2


title: g1617_D7_CD71_2_2196630

description: Library name: g1617_D7_CD71_2_2196630

data_processing:
Reads were mapped to hg38 genome with BWA (v0.7.16a11).
Bigwig (bw) files were generated with bamCoverage from deepTools.
Assembly: hg38
Supplementary files format and content: Bigwig (bw) files.

growth_protocol: CD34+ cell were edited by CD33 or BCL11A enhancer gRNAs and then cultured in Phase 1 media include IMDM (Thermo Fisher Scientific, Waltham, MA, USA), 3% human AB serum (Atlanta Biologicals, Flowery Branch, GA, USA, S40110), 2% human blood type AB plasma (SeraCare, Milford, MA, USA 1810-0001), 1´ penicillin/streptomycin, 3 units/mL erythropoietin (EPOGEN; Amgen, Thousand Oaks, CA, USA # 55513-144-01), 3 units/mL heparin (Sagent Pharmaceuticals, Schaumburg, IL, USA # 25021-401-02), 200 μg/mL holo-transferrin (Millipore Sigma, Burlington, MA, USA T0665), 10 ng/mL human SCF, and 1 ng/mL human interleukin-3 (IL-3; R&D systems, Minneapolis, MN, USA, 203-IL/CF) for 7 days.

extract_protocol:
ATAC-seq was performed using the Omni-ATAC protocol. For each sample, 5-6 × 104 cells were lysed with buffer containing 0.1% NP-40, 0.1% Tween-20, and 0.01% digitonin, then the lysate was washed and incubated with Tagment DNA TDE1 Enzyme (Illumina) for 30 min at 37°C. DNA was purified with a Qiagen MinElute PCR Purification Kit.
Library fragments were amplified using NEBNext® High-Fidelity 2X PCR Master Mix (NEB, M0541) and custom primers (table S4) with unique dual indexes. PCR amplification cycles were in accordance with the manufacturer’s instructions. PCR products were purified using AMPure XP beads (Beckman Coulter, A63881) at a 1:1 ratio according to the manufacturer’s instructions. Purified PCR products sized from 150 bp to 1 kb were purified from E-Gel EX Agarose Gels, 2% (Thermo Fisher, G401002). Libraries were pooled and sequenced in paired-end mode by using an Illumina NovaSeq kit.

treatment_protocol: Cells were electroporated with CD33 sgRNA or BCL11A enhancer sgRNA+Cas9 RNP complex, at day7 of erythroid phase 1 culture, Cells were collected and stainined with CD235, CD49D and Band3 antibody then separrated by FACs.


title: g1617_D7_BasoE_2_2196632

description: Library name: g1617_D7_BasoE_2_2196632


title: g1617_D7_ProE_2_2196631

description: Library name: g1617_D7_ProE_2_2196631


title: g1617_D7_BasoE_1_2196629

description: Library name: g1617_D7_BasoE_1_2196629


title: Dnr10_g34_D7_BasoE_0_2003929

description: Library name: Dnr10_g34_D7_BasoE_0_2003929


title: UT_D7_BasoE_2_2196626

description: Library name: UT_D7_BasoE_2_2196626


title: g1617_D7_CD71_1_2196627

description: Library name: g1617_D7_CD71_1_2196627


title: UT_D7_ProE_2_2196625

description: Library name: UT_D7_ProE_2_2196625


title: UT_D7_CD71_2_2196624

description: Library name: UT_D7_CD71_2_2196624


title: g1617_D7_BasoE_2_2157384

description: Library name: g1617_D7_BasoE_2_2157384

value: Donor 12


title: UT_D7_CD71_1_2196621

description: Library name: UT_D7_CD71_1_2196621


title: UT_D7_ProE_1_2196622

description: Library name: UT_D7_ProE_1_2196622


title: NT_1

description: Library name: NT_1


title: g1617_D7_ProE_2_2157383

description: Library name: g1617_D7_ProE_2_2157383


title: g1617_D7_ProE_1_2157380

description: Library name: g1617_D7_ProE_1_2157380


title: g1617_D7_BasoE_1_2157381

description: Library name: g1617_D7_BasoE_1_2157381


title: g1617_D7_CD71_1_2157379

description: Library name: g1617_D7_CD71_1_2157379


title: UT_D7_BasoE_2_2157378

description: Library name: UT_D7_BasoE_2_2157378


title: g1617_D7_CD71_2_2157382

description: Library name: g1617_D7_CD71_2_2157382


title: UT_D7_ProE_2_2157377

description: Library name: UT_D7_ProE_2_2157377


title: UT_D7_CD71_2_2157376

description: Library name: UT_D7_CD71_2_2157376


title: UT_D7_ProE_1_2157374

description: Library name: UT_D7_ProE_1_2157374


title: UT_D7_CD71_1_2157373

description: Library name: UT_D7_CD71_1_2157373


title: WT_Untreated_2

first: Sijia

last: Zhang

address: 1406 W Green St

department: Bioengineering

institute: Gaj Lab

description: Library name: WT_Unt_2_TAGCGACGAA-TCGATCGCAC_L007_R1_001

data_processing:
Sequenced reads were pseudo-aligned to NCBI’s Annotation Release 110.20220203 (NCBI)  along with the GRCh38 reference genome as the decoy sequence for the Salmon index. Quasi-mapping was then performed in an identical manner for the human and mouse studies with the additional arguments: --seqBias and –gcBias, which were used to correct for sequence- and GC-specific biases, --numBootstraps=30, which was used to compute bootstrap transcript abundance estimates, and –validateMappings and –recoverOrphans, which were used to improve the accuracy of mappings.
The transcript-levels counts were then read into R (v.4.4.1) and gene-level counts were calculated using the "lengthScaledTPM" method from the tximport package (v1.26.1)
Assembly: GRCh38.p14, NCBI Annotation Release 110.20220203
Supplementary files format and content: Gaj_iPSC_Processed_Data.txt : gene level annotations and counts in tab-delimited text format

source_name: Primary

growth_protocol: For  differentiation,  a full volume medium exchange was conducted each day using Complete Motor Neuron Maintenance Medium with 0.2 µM Compound E (Abcam, ab142164), 0.5 µM retinoic acid (Sigma-Aldrich, R2625), 10 ng/mL recombinant human ciliary-derived neurotrophic factor (CNTF) (ax139888), 5 ng/mL recombinant human brain-derived neurotrophic factor (BDNF) (ax139800), 10 ng/mL recombinant human glial cell line-derived neurotrophic factor (GDNF) (ax139855), and motor neuron maturation accelerator supplement (ax0179).

extract_protocol:
RNA was extracted from nuurospheres cells using the PureLink RNA Mini Kit (Invitrogen) and converted to complementary DNA (cDNA) using the iScript cDNA Synthesis Kit (Bio-Rad).
RNA-seq libraries were prepared with the Kapa Hyper Stranded mRNA library kit (Roche). The libraries were pooled; quantitated by qPCR and sequenced on two SP lanes for 101 cycles from one end of the fragments on a NovaSeq 6000 with V1.5 sequencing kits. Fastq files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina).

treatment_protocol: At 14 days in vitro, cells were treated with PHP.eB vector encoding: (i) RfxCas13d-N2V8 with either crRNA-13 or a non-targeted crRNA, both in the presence of 1% (v/v) antibiotic-antimycotic (Gibco). Vector was added to cells at an MOI of ~2 × 10^6.

value: Neural

value: Induced motor neuron

value: Wild-type

value: Untreated Control


title: WT_Untreated_5

description: Library name: WT_Unt_5_AACTCGTTAG-ATGAGGCACC_L007_R1_001


title: g1617_D7_ProE_1_2196628

description: Library name: g1617_D7_ProE_1_2196628

source_name: Day 7  ProE

value: Day 7  ProE


title: WT_Untreated_6

description: Library name: WT_Unt_6_CCTCGGTAGT-TGCATGTTAC_L007_R1_001


title: WT_Untreated_3

description: Library name: WT_Unt_3_TCTATCCTGG-ATGAATGAGC_L007_R1_001


title: UT_D7_BasoE_1_2157375

description: Library name: UT_D7_BasoE_1_2157375

value: Day 7 BasoE


title: WT_NTG_6

description: Library name: WT_NTG_6_TCCATCTGAA-TCTATCCTGG_L007_R1_001

value: RfxCas13d with NTG crRNA


title: WT_Untreated_1

description: Library name: WT_Unt_1_CCGGAACGAA-CATAGTGTAG_L007_R1_001


title: WT_Untreated_4

description: Library name: WT_Unt_4_TTCTATTGCG-GTCGTGACAC_L007_R1_001


title: WT_NTG_5

description: Library name: WT_NTG_5_CGTCTTCGAA-ACCTCAGCTA_L007_R1_001


title: WT_NTG_4

description: Library name: WT_NTG_4_TGGTGAACCT-CTTGGCAGTG_L007_R1_001


title: UT_D7_BasoE_1_2196623

description: Library name: UT_D7_BasoE_1_2196623


title: WT_S13_6

description: Library name: WT_N2V8_S13_6_GCATCAGTCG-CATCACACAA_L007_R1_001

value: RfxCas13d with crRNA 13


title: WT_NTG_2

description: Library name: WT_NTG_2_CGACAGCAGT-ATGGAAGTGG_L007_R1_001


title: WT_NTG_1

description: Library name: WT_NTG_1_AGCTTGTCTC-TACACTCGAA_L007_R1_001


title: WT_NTG_3

description: Library name: WT_NTG_3_AGCAAGACAG-GGATCTTCTT_L007_R1_001


title: WT_S13_5

description: Library name: WT_N2V8_S13_5_CGCCTTGAGA-CTCGTTGCGT_L007_R1_001


title: WT_S13_4

description: Library name: WT_N2V8_S13_4_TATCCATAGC-GAGGTTGTTA_L007_R1_001


title: C9-ALS_Untreated_3

description: Library name: C9_Unt_3_CTAGGCTAGA-CGCCATAGTG_L007_R1_001


title: WT_S13_2

description: Library name: WT_N2V8_S13_2_TCAACACTCT-CCACTTACCG_L007_R1_001


title: WT_S13_3

description: Library name: WT_N2V8_S13_3_GTACAACGAA-AGCTCACTCC_L007_R1_001


title: C9-ALS_Untreated_2

description: Library name: C9_Unt_2_TTGAGTGCGG-CGTCTGCTAG_L007_R1_001


title: C9-ALS_Untreated_1

description: Library name: C9_Unt_1_TCGTCATCTT-TTGTAAGAGG_L007_R1_001


title: WT_S13_1

description: Library name: WT_N2V8_S13_1_GGTTGAATCT-ATACACCGTG_L007_R1_001


title: C9-ALS_NTG_2

description: Library name: C9_NTG_9_AGGCTTACCA-ACAGCGTCAC_L007_R1_001


title: C9-ALS_NTG_3

description: Library name: C9_NTG_10_TCATAACACG-AATTGCCAGA_L007_R1_001


title: CD34_Day7_IgG

description: Library name: CD34_Day7_IgG

data_processing:
CUT&RUN reads were aligned to the hg38 genome using BWA v 0.7.16a11.
MACS2 was used for peak calling.
Assembly: hg38
Supplementary files format and content: Bed files from peak calling
Library strategy: CUT&Run

source_name: Day 7 C34+

extract_protocol:
Cells were collected, dead cells were removed by EasySep Dead Cell Removal (Annexin V) Kit, then process to CUT&RUN process.
Library construction for DNA sequencing was performed using a NEBNext UltraII DNA Library Prep Kit from NEB (E7645S). Indexed samples were analyzed by paired-end NGS using an Illumina NovaSeq (100 cycles) Kit.

treatment_protocol: CD34+ Cells were collected at day 7 or day10 cultured in vitro

value: Day 7 C34+

value: IgG control


title: CD34_Day7_BCL11A_CutRun_1

description: Library name: CD34_Day7_BCL11A_CutRun_1

value: BCL11A Cut & Run


title: C9-ALS_S13_2

description: Library name: C9_N2V8_S13_9_TCACCATACC-TTCTTGCCAA_L007_R1_001


title: CD34_Day7_BCL11A_CutRun_2

description: Library name: CD34_Day7_BCL11A_CutRun_2


title: C9-ALS_S13_3

description: Library name: C9_N2V8_S13_10_AGATGGATGG-ATAGTCAACG_L007_R1_001


title: C9-ALS_NTG_4

description: Library name: C9_NTG_11_TCCAACTTCT-GTTAGCTAGA_L007_R1_001


title: CD34_Day10_BCL11A_CutRun_1

description: Library name: CD34_Day10_BCL11A_CutRun_1


title: C9-ALS_S13_1

description: Library name: C9_N2V8_S13_8_CGCTGTCTAA-CTAACCATCT_L007_R1_001


title: CD34_Day10_BCL11A_CutRun_2

description: Library name: CD34_Day10_BCL11A_CutRun_2


title: CD34_Day10_IgG

description: Library name: CD34_Day10_IgG


title: MAR_3

city: detroit

first: Shailendra

last: Giri

state: MI

address: 2799 W grand boul

department: Neurology Research

institute: henry ford hospital

data_processing:
Using the STAR aligner, paired-end reads of 150 bp were uniquely aligned to GRCm38-mm10, and a mapping rate of approximately 80% STAR was used to count the reads for each sample.
Assembly: mm10
Supplementary files format and content: TXT, RAW COUNTS

source_name: Spinal Cord

extract_protocol:
The disease was induced in the SJL mice (Strain #: 000686 RRID:IMSR_JAX:000686) using proteolipid protein139-151(PLP139-151) peptide (200 μg/mouse) emulsified in Complete Freund’s Adjuvant (CFA, Sigma Chemicals, St. Louis, MO, USA) supplemented with 4 mg/ml heat-killedMycobacterium tuberculosisH37Ra (400 μg; Becton, Dickinson and Company, Sparks, MD, USA). One set of mice was injected with CFA without antigen to serve as a control.It was followed by intraperitoneal treatment with 300ng MaR1 (Cayman) from day 6 till day 70. On day 70, mice were euthanized, and the spinal cord samples were sent for RNAseq (CD-Genomics) for comparative gene expression profiling between the CFA, EAE,and MaR1 treated groups.For RNA-seq, the spinal cords of three mice from each group, CFA, EAE, and MaR1-treated mice, were subjected to RNA-seq via the services of CD-Genomics, NY. RNA wasisolated using the Qiagen RNeasy Lipid Tissue Kit (Qiagen, Hilden, Germany)
Isolated RNA sample quality was assessed by High Sensitivity RNA Tapestation Assay (Agilent Technologies Inc., California, USA)] and quantified by Qubit 2.0 RNA HS assay (ThermoFisher, Massachusetts, USA). Paramagnetic beads coupled with oligo d(T)25 are combined with total RNA to isolate poly(A)+ transcripts based on NEBNext® Poly(A) mRNA Magnetic Isolation Module manual (New England BioLabs Inc., Massachusetts, USA). Prior to first strand synthesis, samples are randomly primed (5´ d(N6) 3´ [N=A,C,G,T]) and fragmented based on manufacturer’s recommendations. The first strand is synthesized with the Protoscript II Reverse Transcriptase with a longer extension period, approximately 30 minutes at 42⁰C. All remaining steps for library construction were performed according to the NEBNext® Ultra™ II Non-Directional RNA Library Prep Kit for Illumina® (New England BioLabs Inc., Massachusetts, USA). Final libraries quantity was assessed by Qubit 2.0 (ThermoFisher, Massachusetts, USA) and quality was assessed by TapeStation HSD1000 ScreenTape (Agilent Technologies Inc., California, USA). The final library size was about 400bp with an insert size of about 250bp. Illumina® 8-nt dual-indices were used. Equimolar pooling of libraries was performed based on QC values and sequenced on an Illumina® NovaSeq 6000 (Illumina, California, USA) with a read length configuration of 150 PE for 40 M PE reads per sample (20M in each direction).

tag: strain

value: SJL

value: Spinal Cord

value: eae+mar

value: Treated with Maresin1  from 6 days through 69 days of EAE daily


title: MAR_2


title: NLGN3_R451C_3D_rep3

city: Piscataway

first: Ziyuan

last: Ma

state: NJ

address: 604 Allison Rd

department: Cell Biology and Neuroscience

institute: Rutgers University

description: Library name: NLGN3_R451C_3D_3

data_processing:
Sequenced reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore (version 0.6.10)
Trimmed sequence reads were mapped to GRCh38 reference genome and GENCODE v44 primary assembly using STAR (version 2.7.11a).
Read count extraction and normalization were performed using RSEM (version 1.3.1)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts, fragments per kilobase per million (FPKM), and transcripts per kilobase million (TPM) for each sample from RSEM output.

source_name: hESC differentiated astroglial cells

growth_protocol: All human ESC and iPSC lines were fully characterized in previous studies (Jin et al. 2022; Wang et al. 2022). The ESC and iPSC lines were cultured on hESC-qualified Matrigel (354277, Corning) coated 6-well plates in mTeSR Plus media (STEMCELL Technologies, 100-0276). Passaging of the ESC and iPSC lines occurred every 5-7 days using ReLeSR media (STEMCELL Technologies, 100-0484) with CEPT (50 nM Chroman 1 (MedChem Express, HY-15392), 5 μM Emricasan (Selleckchem, S7775), Polyamine supplement (Millipore, P8483), 0.7 μM Trans-ISRIB (Tocris, 5284)) added to the medium on the first day (Chen et al. 2021). pNPCs were generated using our previously published protocol (Xu et al., 2019). Briefly, ESCs and iPSCs were detached to form neural embryoid bodies in mTeSR Plus media, followed by a 7-day culture in EB medium (DMEM/F12 (Hyclone, SH3002201), 1x N2 (Thermo Fisher Scientific, 17502048), SB431542 (10 μM, Tocris, 1614), and noggin (40 ng/ml, Peprotech, 120-10C-50UG)). EBs were then cultured on growth factor-reduced Matrigel (Corning, 354230)-coated plates in a medium consisting of DMEM/F12, 1x N2, and laminin (1 μg/ml; Corning, 354232) to form neural rosettes. Neural rosettes were manually isolated and cultured in pNPC medium, which is a 1:1 mixture of Neurobasal (Thermo Fisher Scientific, 21103-049) with 1x GlutaMAX (Thermo Fisher Scientific, 35050061) and DMEM/F12, supplemented with 1x N2, 1x B27-RA (Thermo Fisher Scientific, 12587010), FGF2 (20 ng/ml, Peprotech, 100-18B), human leukemia inhibitory factor (hLIF, 10 ng/ml, Millipore, LIF1005), and CHIR99021 (3 μM, Biogems, 2520691), along with SB431542 (2 μM). pNPCs were passaged and expanded using TrypLE Express (Thermo Fisher Scientific, 12605028), with CEPT added to the medium on the first day of all passaged cells. Organoids were generated from pNPCs within 6 passages. Astroglia were differentiated with minor modifications of our previously published protocols (Chen et al. 2014; Jiang et al. 2013). Briefly, to differentiate pNPCs into astroglia, pNPCs were cultured in suspension for 7 days in NPC medium, which consisted of a 1:1 mixture of Neurobasal with 1× GlutaMAX and DMEM/F12, supplemented with 1× N2, 1× B27-RA, and FGF2 (20 ng/ml). After this period, the neurospheres were dissociated into single cells and plated on growth factor-reduced Matrigel-coated plates in NPC medium for the first two days. The medium was then changed to astroglia differentiation medium containing DMEM/F12, 1× N2, 1× B27-RA, BMP4 (10 ng/ml; Peprotech, 120-05ET), and FGF2 (20 ng/ml). The medium was replaced every other day. Astroglia cultured for 20 to 40 days were used in this study. Brain organoids were generated using ultra-low-attachment 96-well plates, seeding 10,000 pNPCs in NPC medium supplemented with CEPT for three days. After this initial phase, the organoids were transferred to ultra-low-attachment 6-well plates and cultured in NPC medium on an orbital shaker at a speed of 80 rpm until day 14. On day 14, the medium was changed to a neural differentiation medium consisting of a 1:1 mixture of Neurobasal with 1× GlutaMAX and DMEM/F12, supplemented with 1× N2, 1× B27 (Thermo Fisher Scientific), BDNF (10 ng/ml, Peprotech, 450-02), GDNF (10 ng/ml, Peprotech, 450-10), dibutyryl-cyclic AMP (1 μM, Sigma, D0260), and ascorbic acid (200 nM, Sigma, A4403), with or without BMP4 (10 ng/ml). The medium was replaced every other day. The organoids were utilized after three weeks of differentiation. Organoids were dissociated using a 1:1 mixture of TrypLE Express and Accutase (Thermo Fisher Scientific, 00-4555-56) for 30 minutes at 37 °C with 5% CO₂, gently pipetting to assist in the process. DMEM/F12 was then added to stop the digestion, followed by DNase I (Roche, 04536282001) treatment. The cells were filtered through a 0.22 µm filter to obtain a single-cell suspension. To isolate astroglia, a magnetic-based CD44+ MicroBeads system was employed according to the manufacturer's protocol (Miltenyi Biotec, 130-095-194). Briefly, cell pellets were resuspended in 80 µL MACS buffer (0.5% BSA + 2 mM EDTA in PBS) and mixed with 20 µL MicroBeads, incubating at 4 °C in the dark for 15 minutes. The samples were then processed through LS columns using the MidiMACS separator (Miltenyi). Finally, human CD44+ cells were washed into 15 mL tubes for RNA extraction or culture. The purity of the isolated human astroglia was verified through CD44 and S100B staining on cell-seeded coverslips.

extract_protocol:
Total RNA was extracted using RNeasy Micro Kit (QIAGEN).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II DNA Library Prep Kit following manufacturer's protocols.

value: hESC differentiated astroglial cells

value: Isogenic NLGN3 R451C knock-in line (H1)

value: Astroglia

value: NLGN3 R451C knock-in

value: 3D culture


title: NLGN3_R451C_3D_rep2

description: Library name: NLGN3_R451C_3D_2


title: NLGN3_WT_3D_rep2

description: Library name: NLGN3_WT_3D_2

value: Healthy control hESC line (H1)

value: WT


title: NLGN3_R451C_3D_rep1

description: Library name: NLGN3_R451C_3D_1


title: NLGN3_WT_3D_rep1

description: Library name: NLGN3_WT_3D_1


title: NLGN3_WT_3D_rep3

description: Library name: NLGN3_WT_3D_3


title: C9-ALS_S13_4

description: Library name: C9_N2V8_S13_11_GAACATGCAA-TCTGACCTTC_L007_R1_001

value: Neural

value: Induced motor neuron


title: C9-ALS_NTG_1

description: Library name: C9_NTG_8_GCAGGTGATA-TGAAGCCGAG_L007_R1_001

value: RfxCas13d with NTG crRNA


title: EAE_2

value: eae

value: EAE induced with PLP139-151 peptide emulsified in CFA, plus heat-killedMycobacterium tuberculosisH37Ra


title: NLGN3_WT_2D_rep2

description: Library name: NLGN3_WT_2D_2

value: 2D culture


title: MAR_1

value: SJL


title: CFA_3

value: Spinal Cord

value: control

value: control treated with CFA without antigen


title: NLGN3_WT_2D_rep1

description: Library name: NLGN3_WT_2D_1

value: hESC differentiated astroglial cells


title: NLGN3_WT_2D_rep3

description: Library name: NLGN3_WT_2D_3


title: EAE_1


title: CFA_1


title: Hp16_shSet-2

city: Minato-ku

first: Yosuke

last: Igarashi

state: Tokyo

address: 3-25-8, Nishi-Shimbashi

institute: The Jikei University School of Medicine

data_processing:
Sequence reads were checked by using FastQC.
Sequence reads were mapped to GRCm38/mm10 by using STAR.
Read count extraction was performed by using RSEM.
Normalization and differential expression analysis were performed by using DESeq2.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text files include expected_count, TPM and FPKM, which were calculated by using RSEM.

source_name: Liver

extract_protocol:
Total RNA was extracted from cells by using  the RNeasy Plus Mini Kit (QIAGEN, Tokyo, Japan).
RNA libraries for RNA-seq were prepared by using NEBNext Ultra Directional RNA Library Prep Kit for Illumina following manufacturer's protocols.

value: Liver

value: Hepatocellular carcinoma cells

value: Setdb1 knockdown


title: Hp16_shNC-2

value: Setdb1 Wild type


title: NC-2

city: wuxi

first: Kaixiang

last: Ni

state: jiangsu

address: No. 299 Qingyang Road

institute: Wuxi People's Hospital affiliated to the Nanjing Medical University

description:
Library name: NC-2
replicate biosample 2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM counts for each sample

source_name: Glioma cell line

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.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Glioma cell line

value: CBX7 WT


title: OE-1

description:
Library name: OE-1
replicate biosample 1

value: CBX7 overexpression


title: OE-2

description:
Library name: OE-2
replicate biosample 2


title: NC-3

description:
Library name: NC-3
replicate biosample 3


title: MPPH_3

city: Sioux Falls

first: Louis-Jan

last: Pilaz

state: SD

address: 2301 E 60th Street North

department: Pediatrics and Rare Disease

institute: Sanford Research

description: MPPH (Thr280Ala) repeat 3

data_processing:
trimming with Cutadapt
mappping with RNA star
read counts measured with featureCounts
Differential gene expression analysis with DESeq2
Assembly: mm10
Supplementary files format and content: Excel file containing the results of the DEG_seq analysis

source_name: E15.5 embyonic cortex

extract_protocol: RNeasy kit (Qiagen)

value: E15.5 embyonic cortex

value: Wildtype

value: MPPH (Thr280Ala)


title: OE-3

description:
Library name: OE-3
replicate biosample 3


title: MPPH_2

description: MPPH (Thr280Ala) repeat 2


title: MPPH_1

description: MPPH (Thr280Ala) repeat 1


title: GFP_3

description: GFP only control repeat 3


title: Hp16_shNC-1


title: GFP_2

description: GFP only control repeat 2


title: GFP_1

description: GFP only control repeat 1


title: Patient 14

city: Yangsan-si

first: Donghee

last: Kwak

address: 49, Busandaehak-ro

institute: Pusan national university

description: Library name: P14

data_processing:
Quality assessment of paired-end reads from the Illumina sequencer was performed using FastQC
Reads exhibiting a Phred score above 35 were classified as high quality
Adapter sequences were eliminated using Cutadapt
We aligned the processed reads to the Homo sapiens (hg38) genome sequence using HISAT v2.1.0
After alignment, we employed featureCounts v1.6.011 to generate a transcript count table for each sample, which was utilized for subsequent analyses
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Lung

extract_protocol:
RNA was extracted from cell samples using the TRIzol reagent (Invitrogen) and assessed for integrity.
RNA libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Gold Kit and sequenced on an Illumina NovaSeq platform.

value: Lung

tag: subject status

value: Acute Interstitial Pneumonia (AIP) patient


title: Patient 15

description: Library name: P15

tag: tissue


title: Patient 11

description: Library name: P11


title: Patient 9

description: Library name: P9


title: Patient 10

description: Library name: P10


title: Patient 12

description: Library name: P12


title: sipiezo1-mechanical stretch3

city: Nanjing

first: Bin

last: Yan

address: 140Hanzhong Road

institute: Nanjing Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Genome_build: GRCm39
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: BMDMs

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

treatment_protocol: BMDMs transfected with si-NC and si-Piezo1 and exposed to mechanical stretch for 4 h.

value: bone marrow-derived macrophages (BMDMs)

value: transfected with Piezo1 siRNA and exposed to mechanical stretch


title: sipiezo1-mechanical stretch2


title: Hp16_shSet-1

tag: genotype


title: Patient 8

description: Library name: P8


title: Patient 13

description: Library name: P13


title: CFA_2

value: SJL

value: Spinal Cord

value: control


title: NC-1

description:
Library name: NC-1
replicate biosample 1


title: Patient 6

description: Library name: P6


title: EAE_3

value: eae

value: EAE induced with PLP139-151 peptide emulsified in CFA, plus heat-killedMycobacterium tuberculosisH37Ra


title: sipiezo1-mechanical stretch1


title: Patient 5

description: Library name: P5


title: siNC-mechanical stretch3

value: transfected with negative control siRNA and exposed to mechanical stretch


title: siNC-mechanical stretch2


title: siNC-mechanical stretch1


title: METTL3-knockdown HG-stimulated MPC5 Cell Replicate 3 [S2-2]

first: Ling

last: Jiang

address: Meishan Road

institute: AHMU

data_processing:
Solexa pipeline version 1.8
The quality of the raw sequencing data was assessed using FastQC software v0.11.7 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), before the adapter sequences and poor quality bases were trimmed from the reads using the Cutadapt software v1.17
The Hisat2 software v2.0.4 (http://ccb.jhu.edu/software/hisat2) and StringTie software v1.2.2 (http://ccb.jhu.edu/software/stringtie) (33) were used to calculate fragments per kilobase of transcript per million mapped reads (FPKM) values, which represented the final expression levels of the genes. Differential gene expression level analyses were performed using the Ballgown package in R v2.10.0 (https://www.r-project.org) (32). An average FPKM value >0.5 was chosen as the cut-off for gene expression in the samples.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with expression gene counts for every gene and every sample

growth_protocol: MPC5 were purchased from the Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences. MPC5 was cultured at 33 ℃ in RPMI 1640 containing 10% fetal bovine serum and 20 U/ml mouse recombinant interferon-g (IFN-g) medium. In order to induce differentiation, the podocytes were maintained for 7 days under non-permissive conditions without IFN-γ at 37°C for the experiment. SiRNA (Hanbio Biotechnology Co., Ltd, China) was transfected into MPC5 cells by adding Lipofectamine RNAiMAX Reagent (Invitrogen) as recommended by the manufacturer. We used the negative scrambled siRNA (Hanbio Biotechnology Co., Ltd, China) as a control. The diluted siRNA and Lipofectamine RNAiMAX were combined and incubated for 20 min. The mixture was then added to the cells in OPTI-MEM medium. After incubation for 6 h, the cells were replaced by a complete medium. In this study, different treatments were used as followed: NG (5.5 mM glucose), MG (24.5 mM mannitol+ 5.5 mM glucose), HG (30 mM glucose),

extract_protocol:
Total RNA extracted using Trizol following manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

value: kidney podocyte

tag: genotype/variation

tag: treattment

value: HG-stimulated


title: Patient 2

description: Library name: P2


title: METTL3-knockdown HG-stimulated MPC5 Cell Replicate 1 [HG-m3-1]

tag: cell line

tag: cell type


title: METTL3-knockdown HG-stimulated MPC5 Cell Replicate 2 [HG-m3-1-2]


title: Patient 1

description: Library name: P1


title: Patient 4

description: Library name: P4


title: Control 4

description: Library name: C4


title: Control 5

description: Library name: C5


title: Control 3

description: Library name: C3


title: Control 2

description: Library name: C2


title: Patient 7

description: Library name: P7


title: Control HG-stimulated MPC5 Cell Replicate 1 [HG-blank-H2-1]

source_name: Control HG-stimulated MPC5 Cell


title: Control HG-stimulated MPC5 Cell Replicate 2 [HG-blank-H2-2]


title: Control 1

description: Library name: C1


title: CK3_Nthy, control

city: chongqin

first: xiaomeng

last: li

state: nanchong

address: 266 Fangzheng Avenue, Shuitu Street

institute: Chinese Academy of Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing 1 ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate fulllength transcripts representing multiple splice variants for each gene locus.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
(For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed. 2 (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
Gene Set Enrichment Analysis (GSEA) is a computational approach to determine if a pre_x0002_defined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes. We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO, KEGG data set were used for GSEA independently.
GATK (v4.1.1.0) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 ; FS > 30.0; DP < 10.
Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(4.1.0) software was used to analysis the AS event.
PPI analysis of differentially expressed genes was based on the STRING database, which known and predicted Protein-Protein Interactions.
WGCNA (Weighted correlation network analysis) is a systematic biological method used to describe the gene association modes among different samples. it can be used to identify gene sets that are highly synergistic changed, and identify candidate biomarkers or therapeutic targets based on the coherence of gene sets and the correlation between gene sets and phenotypes. The R package WGCNA is a set of functions used to calculate various weighted association analysis, which can be used for network construction, gene screening, gene cluster identification, topological feature calculation, data simulation and visualization. WGCNA is suitable for multisample data. Generally, more than 15 samples are required. One input file is sample information, that is, a matrix describing the traits of the sample: the traits used for association analysis must be numeric; If it is a regional or categorical variable, it needs to be converted to a 0-1 matrix. The other is gene expression data. For transcriptome sequencing, FPKM can be used as gene expression data.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: thyroid

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: thyroid

value: Nthy

value: Normal thyroid cells


title: WT3 [colonic tissues without isolation]

city: Hangzhou

first: Wenlong

last: Lin

state: Zhejiang

address: 66 Yuhang Tang Road

institute: Zhejiang University

description: Library name: Sample 6

data_processing:
Clustering and sequencing (Novogene Experimental Department) The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Quality control Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg18
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Mouse colon

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Eight- to ten-week-old IEC-conditional Nedd4l knockout mice and their littermates were treated with 2% DSS (MP Biomedicals) in drinking water (w/v) for 7 days and sacrificed for further study

value: Mouse colon

value: WT

value: 2% DSS


title: WT1 [colonic tissues without isolation]

description: Library name: Sample 4


title: CK1_Nthy, control


title: cKO3 [colonic tissues without isolation]

description: Library name: Sample 3

value: Nedd4l knockout


title: cKO2 [colonic tissues without isolation]

description: Library name: Sample 2


title: CQ3_Nthy, PM2.5


title: cKO1 [colonic tissues without isolation]

description: Library name: Sample 1


title: Patient 3

description: Library name: P3

value: Lung

value: Acute Interstitial Pneumonia (AIP) patient