title: siControl HUVEC (0h) rep1


title: Control_replicate_10

status: Public on Feb 09 2026

type: RNA

city: Vienna

first: Matthias

last: Hackl

state: Austria

address: Leberstrasse 20

country: Austria

institute: TAmiRNA GmbH

description: Sample name: K27

data_processing:
Cycle of quantification values (Cq-values) were determined using the second derivative method as provided by the Roche LC480 software. RT-qPCR miRNA data were normalized to the Cq-value of the RNA Spike-In (UniSp4) to account for analytical variability (CqUniSp4 – CqmiRNA = normalized deltaCq). Missing miRNA data below the detection limit were not imputed.
Matrix normalized worksheet reports normalized signal (against RNA spike-in control).
Fold Change file reports T1D/control ratios.

label: SYBR green

molecule: total RNA

organism: Homo sapiens

source_name: EDTA Plasma

label_protocol: Reverse transcription (RT) quantitative PCR (qPCR) analysis of 23 distinct miRNAs and 5 controls was performed as previously described [11-14]. In brief, cDNA was synthesized using the miRCURY RT kit (Qiagen, Germany, catalog number 339340) where 2 µL of total RNA were used as input per 10 µL RT reaction mix. Cel-miR-39-3p was added to each RT reaction to monitor RT efficiency. PCR amplification was performed in a 384-well plate format using custom Pick&Mix plates (Qiagen, Germany) in a Roche LC480 II instrument (Roche, Germany) and miRCURY SYBR(R) Green Mix (Qiagen, Germany, catalog number 339347) with the following settings: 95 °C for 10 min, 45 cycles of 95 °C for 10 s and 60 °C for 60 s, followed by melting curve analysis. miRCURY LNA miRNA PCR Assay (Qiagen, catalog number 339306).

extract_protocol: For sample lysis, 200 µL of plasma were mixed with 1000 µL Qiazol to which 1 µL spike-in controls had been added (Qiagen, Germany). Following incubation at room temperature for 10 min, 200 µL chloroform were added to the lysates. After centrifugation at 12,000×g for 15 min at 4 °C, 650 µL of the upper aqueous phase were obtained and mixed with 7 µL glycogen (50 mg/mL) to enhance precipitation. RNA washing and clean-up was performed using the miRNeasy mini kit (Qiagen, Germany): the aqueous phase was transferred to a column, and RNA was precipitated by adding 750 µL ethanol. Washing with RPE and RWT buffer was performed in a QiaCube liquid handling robot (Qiagen, Germany). In the last step, total RNA was eluted in 30 µL nuclease free water and stored at −80 °C until further analysis.

tag: disease state

value: Control

tag: tissue

value: plasma

tag: gender

value: F


title: 8021, plasma sample, pegIFNβ-1a, 0.125days

type: SRA

city: Silver Spring

first: Lakshmi Manasa

middle: Sakuntala

last: Chekka

state: Maryland

address: 10903 New Hampshire Avenue

department: DARS, CDER

country: USA

institute: U.S. FDA

description: Library name: F11644120

library_source: other

data_processing:
CLC Genomics Workbench v21.0.1
Samples were processed using Toolbox "Ready to use workflow" for "Small RNA sequencing" and "Qiaseq miRNAquantification"
Sequence reads were trimmed for adapters and size, UMI reads are generated from grouping greads with the same or similar UMI and similar sequence.
Mature miRNA reads are considered as expression counts.
Raw data was normalized using Deseq2 R package
Assembly: mirBase v22
Supplementary files format and content: csv file includes raw counts for each sample

molecule: other

source_name: plasma

growth_protocol: EDTA Plasma from healthy subjects was collected and stored at -80 degrees centigrade.

extract_protocol:
EDTA plasma from whole blood. RNA was extracted using miRNeasy® Serum/Plasma Kit (Cat. 217184, Qiagen LLC).
Library preparations were carried out using the QIAseq miRNA Library Kit [96] (# 331505) together with QIAseq miRNA [96] Index IL (#331565), and an automated liquid handling method developed for preparation of 96 cDNA using the Biomek i7 Automated Liquid Handler (Beckman).

treatment_protocol: Subjects were randomized between IFNβ-1a, pegIFNβ-1a and placebo groups

tag: time

value: Healthy

tag: treatment


title: 8018, plasma sample, IFNβ-1a_placebo, 9days

description: Library name: F11639747


title: L. donovani infected non-parenchymal liver cells, SI3 [scRNA-seq]

city: York

first: Paul

middle: M

last: Kaye

state: North Yorkshire

address: University of York, Heslington

country: United Kingdom

institute: Hull York Medical School, University of York

description:
Library name: SI3
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data was used to generate FASTQ files using default settings
10x 3' v1 chemistry using spaceranger-1.3.0 was used to align reads to GRCm38 - mm10 genome to obtain gene expression matrices
Assembly: GRCm38 - mm10
Supplementary files format and content: _filtered_feature_bc_matrix.h5: Feature barcode matrices file in the HDF5 format

molecule: polyA RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
Livers were digested with Collagenase and Dnase and passed through a 33% Percoll gradient to retain non-parenchymal cells
Manufacturer's instructions (10x Visium) were followed to prepare sequencing libraries

value: Liver

tag: genotype

value: C57BL/6J wild type

value: L. donovani infected


title: siMETTL3 HEK293T (1h) rep2

city: Beijing

first: Yuan

last: Zhou

address: 38 Xueyuan Rd, Haidian District

department: Department of Biomedical Informatics and Department of Physiology and Pathophysiology, School of Basic Medical Sciences

country: China

institute: Peking University

library_source: transcriptomic

data_processing:
The quality control, adapter cutting and low quality sequence removal were performed by FastQC, fastp and FASTX toolkits.
The clean reads were mapped to human genome (hg38) by HISAT2 software (v2.2.1) and the expression values were calculated by featureCounts command with suggested parameter of the software.
The mRNA half-life was estimated following the method modified from (Wang et al., Nature, 2014, 505: s117–120).
The alternative splicing events were analyzed by rMATS turbo software (v4.1.0, default parameter), focusing on exon skipping and intron retention events.
Assembly: hg38
Supplementary files format and content:
Matrix table with raw gene counts for every gene and every sample
*exonskipping.txt: detected exon skipping event
*intronretention.txt: detected intron retention event
*estimatedhalflife.txt: estimated transcript half-life

growth_protocol: HEK293T and A549 cells were maintained in high-glucose Dulbecco's modified Eagle's medium (DMEM, Gibco, Cat# C11995500BT) supplemented with 10% fetal bovine serum (FBS, Gemini, Cat# 900-108). JURKAT cells were cultured in RPMI 1640 medium (Gibco, Cat# C22400500BT). H9 cells were maintained in TeSR-E8 Kit for hESC/hiPSC Maintenance (StemCell, Cat# 05990). HUVEC cells were cultured in ECM (HARVEYBIO, Cat# 1001).

extract_protocol:
Cells from each group and time points were collected and total RNA was harvested with Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB #E7770)and NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB #E7760) were used with 400 ng of total RNA for the construction of sequencing libraries.
ERCC spike-in were added to total RNA before library construction, following the protocol recommended by ERCC spike-in kit manufacturer. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: shRNA targeting sequences against METTL3 and control were designed, synthesized and subcloned into the GV307 vector. Then lentivirus was made by co-transfection of every GV307 shRNA vector with pHelper 1.0 and pHelper 2.0 in a 5:3:2 ratio into HEK293T cells. And each cell line was infected with siControl and siMETTL3 concentrated lentivirus supernatant.

tag: cell line


title: L. donovani infected non-parenchymal liver cells, SI5 [scRNA-seq]

description:
Library name: SI5
10x Genomics


title: Control_replicate_11

description: Sample name: K37

value: M


title: 8018, plasma sample, IFNβ-1a_placebo, 6days

description: Library name: F11639284


title: naïve liver section, N4

description:
Library name: 345-N4
10x Visium spatial transcriptomics

data_processing:
Raw sequencing data was used to generate FASTQ files using default settings
Spatial 3' v1 chemistry using spaceranger-1.3.0 was used to align reads to GRCm38 - mm10 genome to obtain gene expression matrices
Assembly: GRCm38 - mm10
Supplementary files format and content: .h5: Feature barcode matrices file in the HDF5 format
Supplementary files format and content: _detected_tissue_image.jpg: Image showing spots over tissue section
Supplementary files format and content: _scalefactors_json.json: Json file for scalefactors
Supplementary files format and content: _tissue_hires_image.png: tissue section image in high resolution
Supplementary files format and content: _tissue_lowres_image.png: tissue section image in low resolution
Supplementary files format and content: _tissue_positions_list.csv: spatial barcodes and their xy co-ordinates on tissue
Library strategy: Spatial Transcriptomics

extract_protocol:
Livers were flash frozen in liquid nitrogen. 7μm sections were cut with a Leica cryostat and placed on 10x Visium spatial transcriptomics slide
Manufacturer's instructions (10x Visium) were followed to prepare sequencing libraries

value: no treatment


title: 8018, plasma sample, IFNβ-1a_placebo, 5days

description: Library name: F11639107


title: siMETTL3 HEK293T (0h) rep2


title: T1D_replicate_10

description: Sample name: D42


title: Control_replicate_9

description: Sample name: K24


title: Control_replicate_8

description: Sample name: K50


title: 8018, plasma sample, IFNβ-1a_placebo, 4days

description: Library name: F11638992


title: naïve liver section, N3

description:
Library name: 334-N3
10x Visium spatial transcriptomics


title: T1D_replicate_8

description: Sample name: D39


title: siMETTL3 HEK293T (0h) rep1


title: 8018, plasma sample, IFNβ-1a_placebo, 2days

description: Library name: F11638746


title: siMETTL3 HEK293T (1h) rep1


title: L. donovani infected liver section, I5

description:
Library name: 345-I5
10x Visium spatial transcriptomics


title: siControl HEK293T (6h) rep2


title: 8018, plasma sample, IFNβ-1a_placebo, 1.33days

description: Library name: F11638709


title: L. donovani infected liver & naïve section, N2-I4

description:
Library name: 334-N2-I4
10x Visium spatial transcriptomics


title: T1D_replicate_9

description: Sample name: D40


title: L. donovani infected liver section, I3

description:
Library name: 345-I3
10x Visium spatial transcriptomics


title: naïve liver section, N1

description:
Library name: 345-N1
10x Visium spatial transcriptomics


title: T1D_replicate_7

description: Sample name: D34


title: siControl HEK293T (6h) rep1

value: siControl


title: siControl HEK293T (3h) rep2


title: Control_replicate_7

description: Sample name: K30


title: L. donovani infected liver section, I2

description:
Library name: 334-I2
10x Visium spatial transcriptomics


title: 8018, plasma sample, IFNβ-1a_placebo, 0.67days

description: Library name: F11638559


title: siControl HEK293T (3h) rep1


title: TG, CON, day3, rep3

city: GuangZhou

first: Jia

last: Shilin

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: Institute of Stomatological Research, Sun Yat-sen University

description:
Library name: Sample6
N3

data_processing:
Agilent 2100 Bioanalyzer
Assembly: GRCm38
Supplementary files format and content: FPKM values for each sample

source_name: TG

extract_protocol:
RNA was enriched by NEB Next poly(A) mRNA Magnetic Isolation Module
KAPA stranded RNA-seq Library Prep kit (Illumina)

value: TG

tag: cell type

value: Neuron, Glia cells

value: WT

value: Saline


title: 8018, plasma sample, IFNβ-1a_placebo, 0.33days

description: Library name: F11638478


title: Control_replicate_6

description: Sample name: K36


title: 8018, plasma sample, IFNβ-1a_placebo, 0.25days

description: Library name: F11638462


title: TG, CON, day3, rep2

description:
Library name: Sample5
N2


title: siControl HEK293T (1h) rep2


title: 8018, plasma sample, IFNβ-1a_placebo, Baseline

description: Library name: F11638260


title: T1D_replicate_6

description: Sample name: D29


title: TG, CON, day3, rep1

description:
Library name: Sample4
N1


title: 8018, plasma sample, IFNβ-1a_placebo, 0.125days

description: Library name: F11638384


title: Control_replicate_5

description: Sample name: K29


title: siControl HEK293T (0h) rep2


title: T1D_replicate_5

description: Sample name: D32


title: 8017, plasma sample, IFNβ-1a, 6days

description: Library name: F11637370


title: Control_replicate_4

description: Sample name: K49


title: TG, CFA, day3, rep2

description:
Library name: Sample2
C2

value: CFA


title: T1D_replicate_4

description: Sample name: D36


title: 8017, plasma sample, IFNβ-1a, 4days

description: Library name: F11637080


title: TG, CFA, day3, rep1

description:
Library name: Sample1
C1


title: Control_replicate_3

description: Sample name: K26


title: siControl HEK293T (1h) rep1


title: siControl HEK293T (0h) rep1


title: TG, CFA, day3, rep3

description:
Library name: Sample3
C3


title: siMETTL3 H9 (6h) rep2


title: 8017, plasma sample, IFNβ-1a, 2days

description: Library name: F11636834


title: T1D_replicate_3

description: Sample name: D41


title: siMETTL3 H9 (6h) rep1


title: Induced, induced Tet-opsin-VEGFA mice (ChIP)

city: Chengdu

first: feipeng

last: jiang

address: #37 Guoxue Alley, Wuhou District, Chengdu, Sichuan Province, P.R.China

institute: west china hospital

description: Library name: Induced-IP

library_source: genomic

data_processing:
After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8).
Sequence quality was examined using the FastQC software.
After passing Solexa CHASTITY quality filter, the clean reads were aligned to mouse genome (UCSC MM10) using BOWTIE software (V2.2.7). Aligned reads were used for peak calling of the ChIP regions using MACS V1.4.2. Statistically significant ChIP-enriched regions (peaks) were identified by comparison of IP vs Input or comparison to a Poisson background model, using a p-value threshold of 10-4.
The peaks in samples were annotated by the nearest gene using the newest UCSC RefSeq database. The annotation of the peaks which were located within -2Kb to +2Kb around the corresponding gene TSS in samples.
Assembly: GRCm38
Supplementary files format and content: Fastqc, Alignment Result, Peak Calling,

molecule: genomic DNA

source_name: Retina

extract_protocol:
The tissue was first crosslinked with methanol before being lysed, and the DNA was fragmented via sonication. A transketolase antibody (Santa Cruz, sc-390179) was used to immunoprecipitate the DNA-protein complexes. The cross-links were reversed, and the DNA was purified and quantified before sequencing.
The libraries were prepared following Illumina’s protocol. Briefly, 10 ng of DNA was blunt-ended, A-tailed, and ligated to Illumina adapters. The fragments (~200-1500 bp) were enriched via PCR and purified with AMPure XP beads. The library was denatured to single strands, loaded onto a flow cell at 8 pM, and sequenced on an Illumina NovaSeq 6000 (2×150 cycles).

value: Retina

value: Retinal cell

value: induced Tet-opsin-VEGFA


title: 8017, plasma sample, IFNβ-1a, 1.33days

description: Library name: F11636797

value: plasma


title: 8017, plasma sample, IFNβ-1a, 5days

description: Library name: F11637195


title: Induced, induced Tet-opsin-VEGFA mice (Input)

description: Library name: Induced-input


title: siMETTL3 H9 (3h) rep2


title: 8017, plasma sample, IFNβ-1a, 0.67days

description: Library name: F11636647


title: siMETTL3 H9 (3h) rep1


title: Control_replicate_2

description: Sample name: K40

value: Control


title: Control, noninduced Tet-opsin-VEGFA mice (Input)

description: Library name: Control-input

value: noninduced Tet-opsin-VEGFA


title: Control, noninduced Tet-opsin-VEGFA mice (ChIP)

description: Library name: Control-IP


title: T1D_replicate_2

description: Sample name: D50

value: F


title: T1D_replicate_1

description: Sample name: D24


title: 8017, plasma sample, IFNβ-1a, 0.33days

description: Library name: F11636566

value: Healthy


title: 8017, plasma sample, IFNβ-1a, 0.25days

description: Library name: F11636550


title: siMETTL3 H9 (1h) rep1


title: siMETTL3 H9 (0h) rep2


title: Pooled mesenchymal cell samples [CMO_SC_S4]

city: Bethesda

first: Ryo

last: Sato

state: MD

address: 10 Center Dr

department: NHLBI

institute: National Institutes of Health

data_processing:
Sequencing reads were aligned to the mouse reference genome (mm10) using Cell Ranger (v7.1.0). Sample demultiplexing was performed using the "cellranger multi" pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Pooled mesenchymal cell samples

extract_protocol:
Mouse lungs were harvested following perfusion with 5 mL of PBS through the right ventricle. The tissue was mechanically dissociated using scissors and digested in an enzyme solution containing 0.25% Collagenase A, 1 U/mL Dispase II, and 2,000 U/mL DNase I in Hanks' Balanced Salt Solution. The tissue suspension was incubated at 37°C for 60 min with gentle trituration using a micropipette every 20 min. Following digestion, the cell suspension was filtered through a 100-μm cell strainer, washed with PBS, and resuspended in PBS containing 0.5% BSA. For whole cell samples, erythrocytes were removed by magnetic negative selection using rat anti-mouse TER-119 antibody followed by sheep anti-rat Dynabeads. For mesenchymal cell samples, cells were enriched by magnetic negative selection using rat anti-mouse antibodies against CD31, CD45, EpCAM, and TER-19, followed by sheep anti-rat Dynabeads. Following negative selection, both whole cell and mesenchymal cell samples from two biological replicates per genotype were multiplexed using the 10x Genomics 3' CellPlex Kit Set A. Sample tags were assigned as follows: whole cell samples (WT_1: CMO301, WT_2: CMO302, Tubb3-/-_1: CMO303, Tubb3-/-_2: CMO304) and mesenchymal cell samples (WT_1: CMO305, WT_2: CMO306, Tubb3-/-_1: CMO307, Tubb3-/-_2: CMO308). The labeled samples were then pooled according to sample type (whole cell or mesenchymal cell) and stained with DAPI (0.1 μg/mL) prior to cell sorting. For the pooled whole cell sample, live cells were sorted. For the pooled mesenchymal cell sample, MCAM+ PDGFRα- (mural cells) and MCAM- (non-mural cells) populations were sorted and mixed at a 1:1 ratio to achieve mural cell enrichment.
Single-cell isolation, RNA capture, cDNA preparation, and library preparation were performed according to the manufacturer's protocol (Chromium Next GEM Single Cell 3' Reagent Kit, v3.1 chemistry, 10x Genomics).

treatment_protocol: For fibrosis induction, a dose of 0.8 U/kg bleomycin was intratracheally administered into mice.

value: Lung

value: Mural cell-enriched mesenchymal cells

value: Bleomycin


title: siMETTL3 H9 (1h) rep2


title: 8017, plasma sample, IFNβ-1a, 0.125days

description: Library name: F11636472


title: Pooled whole cell samples [CMO_WL_S3]

source_name: Pooled whole cell samples

value: Whole cells


title: Pooled mesenchymal cell samples [GEX_SC_S2]


title: 8017, plasma sample, IFNβ-1a, Baseline

description: Library name: F11636348


title: Control_replicate_1

description: Sample name: K44

value: M


title: Sim_minus_2-8_S10, Control

city: Tallahassee

first: Michelle

middle: N

last: Arbeitman

state: Florida

address: 1115 W. Call Street

department: Department of Biomedical Sciences

institute: Florida State University

description:
Library name: Sim_minus_2-8_S10
CUT&Tag

data_processing:
The CUT&Tag sequencing reads were pre-processed to remove Illumina adaptor sequences using BBduk (ktrim=r k=23 mink=11 hdist=1 tpe tbo (https://sourceforge.net/projects/bbmap/).
The adaptor trimmed reads were aligned to the D. melanogaster genome (BDGP6) genome assembly, using Bowtie2 (--local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700 -p 8 -x /; v. 2.2.5)
The mapped reads then underwent a series of file format conversion steps to prepare for SEACR peak calling. The mapped read files, in the .sam format, were converted to .bam files using Samtools view command (view -bS -F 0x04). These .bam files were sorted using the Samtools sort command (sort -n -O bam -@ 12). The sorted .bam files were converted to .bed files using bedtools bamtobed command (bamtobed -bedpe -i). These files were filtered to keep read pairs on the same chromosome with a fragment length <1000bp (awk '$1==$4 && $6-$2 < 1000 {print $0}) and the fragment related columns were extracted using ‘cut -f 1,2,6’.
The .bed files were converted to .bedgraph files for peak calling using bedtools (genomecov -bg -i).
Assembly: D. melamogaster BDGP6
Supplementary files format and content: .bedgraph files for SEACR peak calling.
Library strategy: CUT&Tag

organism: Drosophila simulans

source_name: Brain

growth_protocol: Males used in CUT&Tag were 15-24 hours old. To collect these males, bottles with D. melanogaster and D. simulans were cleared at 10:00 AM, flies were collected at 5:00 PM, and aged overnight to allow for recovery from CO2 anesthesia. The male flies were stored individually in small vials with food, in a 25°C incubator. The next day, brain dissections started at 8:00 AM and ended at 10:00 AM.

extract_protocol:
Ten brains were used for each CUT&Tag sequencing library. The CUT&Tag procedure and sequencing library preparation protocol was previously described, with some modifications (Ahmad 2020). After dissection, brains were fixed in 1% paraformaldehyde/1X PBS for 1 minute, then transferred to 1X PBS. Brains were washed two additional times for 5 minutes per wash. The rat polyclonal anti-FruM antibody was used at a 1:50 dilution (Sanders and Arbeitman 2008). The secondary rabbit anti-rat IgG (abcam ab6703) was used at 1:100 dilution. For control libraries, the brains were only incubated in secondary antibody. DNA recovery was performed as previously described (Kaya-Okur et al. 2019). Samples underwent 21 cycles of PCR and were purified by agencourt bead purification before sequencing (Ahmad 2020).
CUT&Tag

value: Brain

value: Male


title: Sim_plus_2_9_S5, FruM

description:
Library name: Sim_plus_2_9_S5
CUT&Tag


title: 8014, plasma sample, pegIFNβ-1a, 13days

description: Library name: F11632201


title: siMETTL3 H9 (0h) rep1


title: Pooled whole cell samples [GEX_WL_S1]


title: TDP-43cKO-TDP-43mNLS 3

city: Nagoya

first: Jiayi

last: Li

state: Aichi

address: 65 Tsurumai-cho, Showa-ku

department: Department of Neurology

country: Japan

institute: Nagoya University Graduate School of Medicine

data_processing:
DRAGEN Bio-IT Platform version 3.6.3
Sequence reads were mapped to GRCm38/mm10 using DRAGEN Bio-IT Platform
Read count extraction and normalization to TPM values were performed using DRAGEN Bio-IT Platform
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
Total RNA was extracted from the sorted cells using miRNeasy Micro Kit (Qiagen, 217084). The RNA purity was tested with a Nanodrop spectrophotometer (Thermo Scientific).
RNA-seq libraries were prepared with SMART-Seq Stranded Kit (Takara, 634442) and SMARTer RNA Unique Dual Index Kit (Takara, 634451) using 1ng purified total RNA according to the manufacturer’s instructions.

treatment_protocol: AAV-FLEX-GFP was injected to the dentate gyrus of TDP-43flox/flox::CamKIICre/- or CamKIICre/- mice or AAV-FLEX-TDP-43mNLS-GFP was injected to TDP-43flox/flox::CamKIICre/- mouse. One month after AAV injection GFP positive cells were screened from mouse brain cell homogenates by FACS.

value: AAV-FLEX-TDP-43mNLS-GFP  injection


title: siControl H9 (3h) rep2

value: siControl


title: siControl H9 (6h) rep2


title: TNAPi

city: San Francisco

first: Yasuhiro

last: Fuseya

state: CA

address: 513 Parnassus Ave Bldg S1364, Medical Science

department: Anatomy

institute: University of California, San Franc

description:
Library name: Sample 4
10x Genomics

data_processing:
Raw FASTQ files were processed and aligned to mm10 using the Cell Ranger software package (10x Genomics) for the RNA expression matrix, including introns for single nucleus analysis.
Assembly: Mus Musculus
Supplementary files format and content: matrix.h5 files with filtered features generated from CellRanger

source_name: hippocampus

growth_protocol: aged mice

extract_protocol:
Single cell RNA sequencing for endothelial cells Single cell analysis was performed on endothelial cells from eight mice per group (Young, Aged, Gpld1, TNAPi). Briefly, mice were sedated with ketamine followed by perfusion with 30 mL of ice-cold PBS. The entire brain was removed, then the hippocampus was sub-dissected. Single-cell suspensions were generated by enzyme-mediated (papain) and mechanical dissociation using Miltenyi Neural Dissociation Kits (P) (Miltenyi, 130-092-628) according to the manufacturer’s instructions. The papain dissociation was done at 37°C for 10 minutes with three trituration steps. All other processing steps were performed at 4°C. Myelin was depleted from the suspensions using 22% Percoll solution (Cytiva, 17089101). Cell Fc receptors were blocked using a purified anti-mouse CD16/32 antibody (BD Biosciences, 553142) and then and then stained for 30 minutes at 4°C in the dark with CD45-PE (BD Biosciences, 553081), CD41-PE (BD Biosciences, 558040) and CD31-APC (BD Biosciences, 551262) and DAPI (Thermo Scientific, 62248 1:1000). Cells were sorted on a BD FACSAria Fusion with a 100 μm nozzle and with a flow rate of 1–2.5. Cells were first gated by forward and side scatter, then gated for doublets with area and height. Cells per sample that were DAPI-, CD45-,CD41-, CD31+ were collected for sequencing analysis.
Isolated cells were given to the UCSF-CoLab Genomics Core for analysis with the 10x Genomics Chromium Single Cell Expression Solution 3′ kit. The Genomics Core prepared cells for 10x Genomics Chromium single-cell capture. 20,000 cells were loaded per sample. cDNA libraries were prepared according to the standard 10x Genomics protocols. The final library pool was sequenced on the NovaSeq 6000 or the NovaSeq X 10B system at the UCSF CAT Core. The raw base sequence calls were demultiplexed into sample-specific cDNA files with bcl2fastq/mkfastq and converted to count matrices using Cell Ranger 7.1 (10x Genomics).

treatment_protocol: liver expression of GPLD1 or TNAP inhibitor compared to control mice

value: hippocampus

value: sorted endothelial cells


title: TDP-43cKO-TDP-43mNLS 4


title: siControl H9 (6h) rep1


title: 8014, plasma sample, pegIFNβ-1a, 6days

description: Library name: F11631636


title: siControl H9 (3h) rep1


title: Gpld1

description:
Library name: Sample 3
10x Genomics


title: TDP-43cKO-TDP-43mNLS 1


title: Sim_plus_2_8_S9, FruM

description:
Library name: Sim_plus_2_8_S9
CUT&Tag


title: TDP-43cKO-TDP-43mNLS 2


title: siControl H9 (1h) rep2


title: 8014, plasma sample, pegIFNβ-1a, 9days

description: Library name: F11632099


title: Aged

description:
Library name: Sample 2
10x Genomics


title: Young

description:
Library name: Sample 1
10x Genomics


title: siControl H9 (1h) rep1


title: 8014, plasma sample, pegIFNβ-1a, 5days

description: Library name: F11631459


title: TDP-43cKO-GFP 3

value: AAV-FLEX-GFP injection


title: 8014, plasma sample, pegIFNβ-1a, 2days

description: Library name: F11631098

value: plasma


title: 8014, plasma sample, pegIFNβ-1a, 4days

description: Library name: F11631344


title: 8014, plasma sample, pegIFNβ-1a, 1.33days

description: Library name: F11631061


title: siControl H9 (0h) rep2


title: VSV_control_cortex

city: Freiburg

first: Chintan

last: Chhatbar

address: Breisacher strasse 64

department: Department of Neuropathology

country: Germany

institute: Uniklinikum Freiburg

description: Library name: VSV_control_cortex

data_processing:
Fastq files were further processed using the Cell Ranger v7.1.0 pipeline (10x Genomics) for read alignment to generate counts data.
Assembly: GRCm38, Gencode v33
Supplementary files format and content: filtered counts matrices

source_name: CNS

extract_protocol:
snRNA-seq using 10x was conducted on nuclei extracted from frozen brain specimen
cDNA amplification and library preparation were conducted following the manufacturer’s instructions (Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics))

value: CNS


title: NC-GFP 3

value: CamKIIcre/-


title: TDP-43cKO-GFP 1


title: TDP-43cKO-GFP 2


title: siControl H9 (0h) rep1


title: 8014, plasma sample, pegIFNβ-1a, 0.33days

description: Library name: F11630830


title: siMETTL3 A549 (6h) rep2


title: NC-GFP 2


title: 8014, plasma sample, pegIFNβ-1a, 0.25days

description: Library name: F11630814


title: VSV_control_OB

description: Library name: VSV_control_OB


title: VSV_7d_OB

description: Library name: VSV_7d_OB


title: 8014, plasma sample, pegIFNβ-1a, 0.67days

description: Library name: F11630911


title: NC-GFP 1


title: siMETTL3 A549 (6h) rep1


title: VSV_15d_OB

description: Library name: VSV_15d_OB


title: 8014, plasma sample, pegIFNβ-1a, 0.125days

description: Library name: F11630736


title: siMETTL3 A549 (3h) rep2


title: P7_rep3

city: Guangzhou

first: Ming

last: Yuan

state: Guangdong

address: 26 Yuancun Erheng Rd

institute: The sixth affiliated hostpital, sun yat-sen university

description:
Library name: P7_rep3
P7_rep3

data_processing:
Clean reads were obtained from BGItech and mapped to hg38 human genome by Bowtie2. Then the bam file were processed by HTSeq software to obtain gene counts.
Assembly: hg38
Supplementary files format and content: csv file include fpkm for each sample

source_name: ADSCs

growth_protocol: ADSCs were maintained in DMEM with 1 g/L glucose containing 1% streptomycin–penicillin and 10% FBS in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was isolated using Trizol (Thermo Fisher). 2μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared by BGItech (Shenzhen, China).

value: ADSCs

value: Adipose-derived Stem Cells

value: WT

tag: batch

value: Passage 7


title: VSV_15d_cortex

description: Library name: VSV_15d_cortex


title: siMETTL3 A549 (1h) rep2


title: VSV_7d_cortex

description: Library name: VSV_7d_cortex


title: P7_rep1

description:
Library name: P7_rep1
P7_rep1


title: siMETTL3 A549 (3h) rep1


title: Vehicle_only_cortex_7d

description: Library name: Vehicle_only_cortex_7d


title: P7_rep2

description:
Library name: P7_rep2
P7_rep2


title: 8011, plasma sample, IFNβ-1a, 6days

description: Library name: F11625898

value: Healthy


title: siMETTL3 A549 (1h) rep1


title: 8011, plasma sample, IFNβ-1a, 5days

description: Library name: F11625723


title: siMETTL3 A549 (0h) rep2


title: SOD1_Tg_spinal_cord

description: Library name: SOD1_Tg_spinal_cord


title: P3_rep3

description:
Library name: P3_rep3
P3_rep3

value: Passage 3


title: P3_rep2

description:
Library name: P3_rep2
P3_rep2


title: 8014, plasma sample, pegIFNβ-1a, Baseline

description: Library name: F11630612


title: SOD1_Tg_cortex

description: Library name: SOD1_Tg_cortex


title: 8011, plasma sample, IFNβ-1a, 4days

description: Library name: F11625608


title: 8011, plasma sample, IFNβ-1a, 2days

description: Library name: F11625362


title: P3_rep1

description:
Library name: P3_rep1
P3_rep1


title: SOD1_control_spinal_cord

description: Library name: SOD1_control_spinal_cord


title: siMETTL3 A549 (0h) rep1


title: SOD1_control_cortex

description: Library name: SOD1_control_cortex


title: siControl A549 (6h) rep2


title: 8011, plasma sample, IFNβ-1a, 1.33days

description: Library name: F11625325


title: 8011, plasma sample, IFNβ-1a, 0.67days

description: Library name: F11625175


city: Davis

first: Satoshi

middle: H

last: Namekawa

address: One Shields Ave

institute: University of California, Davis

description: Library name: DMRT1_CUTTag_P8_Aundiff_Smarca5_cKO_rep2

data_processing:
Raw paired-end CUT&Tag reads after trimming by Trim-galore were aligned to either the mouse (GRCm38/mm10) genomes using Bowtie2 (version 2.3.3.1) with options: –end-to-end –very-sensitive –no-mixed –no-discordant –phred33 -I 10 -X 700. All unmapped and non-uniquely mapped reads were filtered out by samtools (version 1.9) before being subjected to downstream analyses. PCR duplicates were removed using the ‘MarkDuplicates’ command in Picard tools (version 2.23.8) (https://broadinstitute.github.io/picard/, Broad Institute). For CUT&Tag on DMRT1, D. melanogaster DNA delivered by Drosophila S2 cells was used as spike-in DNA described . For mapping D. melanogaster spike-in fragments, we also aligned to either the D. melanogaster (dm6) genome using Bowtie2 and use the '–no-overlap –no-dovetail' options to avoid cross-mapping using Bowtie2. PCR duplicates were removed using the ‘MarkDuplicates’ command in Picard tools. Spike-in normalization was implemented using the exogenous scaling factor computed from the dm6 mapping files (scale factors = 10000/spike-in reads for DMRT1 CUT&Tag).
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: testis

extract_protocol:
To prepare single cell suspensions for cell sorting, detangled seminiferous tubules were incubated in 1× Krebs–Ringer Bicarbonate Buffer (Sigma, K4002) supplemented with 1.5 mg/ml collagenase Type 1 and 0.04 mg/ml DNase I at 37°C for 15 min with gentle agitation and dissociated using vigorous pipetting, and then add 0.75 mg/ml hyaluronidase (Sigma, H3506) and incubated at 37°C for 10 min with gentle agitation and dissociated using vigorous pipetting. The cell suspension was centrifuged at 300 × g, the cells resuspended in 10 ml FACS buffer (PBS containing 2% FBS) and then centrifuged again at 300 × g for 5 min, and this step was repeated one more time. The pelleted cells were resuspended 1 ml FACS buffer and then filtered through a 70 μm nylon cell strainer (Falcon, 352350). The resultant single cells were stained with cocktails of antibodies diluted with FACS buffer listed as follows: PE-conjugated anti-mouse/human CD324 (E-cadherin) antibody (1:500, Biolegend, 147303), PE/Cy7-conjugated anti-mouse CD117 (c-Kit) antibody (1:200, Biolegend, 105814) and FITC-conjugated anti-mouse CD9 antibody (1:500, Biolegend, 124808). After a 50 min incubation on ice, cells were washed with 10 ml FACS buffer three times by centrifugation at 300 × g for 5 min and filtered into a 1 ml FACS tube through a 35 μm nylon mesh cap (Falcon, 352235). 7-AAD Viability Stain (Invitrogen, 00-6993-50) was added to cell suspension for the exclusion of dead cells. Samples were kept on ice until sorting. Cell sorting was performed using SH800S (SONY). Cells were analyzed after removing small and large debris in FSC-A versus SSC-A gating, doublets in FSC-W versus FSC-H gating, and 7AAD+ dead cells. Then the desired cell population was collected in gates determined based on antibody staining.
CUT&Tag libraries of ctrl Aundiff and ProSG for SMARCA5 were prepared as previously described (a step-by-step protocol https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3) using CUTANA™ pAG-Tn5 (Epicypher, 15-1017). Quantitative spike-in CUT&Tag for DMRT1 of Smarca5-ctrl and cKO Aundiff was performed by adding Drosophila S2 cells at a 1:5 ratio to mouse spermatogonial cells (5,000 S2 cells to 25,000 mouse cells) in each reaction. The antibodies used were rabbit anti-SMARCA5 (1/100) or rabbit anti-DMRT1 antibody (1/50). CUT&Tag libraries were sequenced on the Novaseq X Plus system with 150-bp paired-end reads.

value: testis

value: primary cell

value: Undifferentiated spermatogonia


description: Library name: DMRT1_CUTTag_P8_Aundiff_Smarca5_cKO_rep1


title: 8011, plasma sample, IFNβ-1a, 0.33days

description: Library name: F11625094


title: Rnaset2_KO_cortex

description: Library name: Rnaset2_KO_cortex


title: siControl A549 (6h) rep1


title: siControl A549 (3h) rep2


title: PBS_24_hr_cortex

description: Library name: PBS_24_hr_cortex


title: 8011, plasma sample, IFNβ-1a, 0.25days

description: Library name: F11625078


title: siControl A549 (3h) rep1


description: Library name: DMRT1_CUTTag_P8_Aundiff_Smarca5_ctrl_rep1


title: MuMT_cortex

description: Library name: MuMT_cortex


description: Library name: DMRT1_CUTTag_P8_Aundiff_Smarca5_ctrl_rep2


title: 8011, plasma sample, IFNβ-1a, 0.125days

description: Library name: F11625000


title: MuMT_control_cortex

description: Library name: MuMT_control_cortex


title: Rnaset2_control_cortex

description: Library name: Rnaset2_control_cortex


title: siControl A549 (1h) rep2


description: Library name: SMARCA5_CUTTag_P0_ProSG_Smarca5_ctrl_rep2

value: Prospermatogonia


title: MCAO_control_7d_cortex

description: Library name: MCAO_control_7d_cortex


title: siControl A549 (0h) rep2

value: siControl


title: siControl A549 (1h) rep1


title: 8011, plasma sample, IFNβ-1a, Baseline

description: Library name: F11624876


description: Library name: SMARCA5_CUTTag_P0_ProSG_Smarca5_ctrl_rep1


title: 8010, plasma sample, pegIFNβ-1a _placebo, 13days

description: Library name: F11624553

value: pegIFNβ-1a _placebo


description: Library name: SMARCA5_CUTTag_P8_Aundiff_Smarca5_ctrl_rep1


title: siControl A549 (0h) rep1


title: 8010, plasma sample, pegIFNβ-1a _placebo, 9days

description: Library name: F11624451


title: MCAO_7d_cortex

description: Library name: MCAO_7d_cortex


title: MCAO_control_14d_cortex

description: Library name: MCAO_control_14d_cortex


title: RNA-seq of Homo sapiens: IsoCtrl hiPSC neuron sample6

city: Chapel Hill

first: Hyejung

last: Won

state: North Carolina

address: 116 Manning Dr

department: Genetics

institute: University of North Carolina at Chapel Hill

description: Library name: Ctrl_hiPSC_Neu_RNA-seq_rep6

data_processing:
Hi-C and Micro-C processing: Read quality of fastq files was first assessed using FastQC (v0.12.1). Sequencing reads were then aligned to the GRCh38 reference genome using bwa mem (v0.7.17). Duplicate reads were removed with Pairtools (v1.1.3). Resulting BAM files were converted to multi-resolution contact matrices using cooler (v0.10.4) for downstream analysis.
CHART procossing: CHART reads were aligned to the GRCh38 reference genome using bwa mem (v0.7.17). Duplicate reads were removed with Picard (v3.1.1), and replicates were merged using Samtools (v1.6). Peaks were called using MACS2 (v2.2.9.1) with the following parameters: -t STR_nodups_sorted.bam -f BAMPE -q 0.05 -g hs --keep-dup all -B –SPMR. Read counts per peak were quantified using bedtools multicov (v2.31.0) on the merged BAM files for each control and STR replicate. C9-STR gained CHART peaks were defined if the mean CPM-normalized read count in C9-STR samples was at least two-fold higher than that in control samples.
CUT&RUN processing: CHART reads were aligned to the GRCh38 reference genome using bwa mem (v0.7.17). Duplicate reads were removed with Picard (v3.1.1), and replicates were merged using Samtools (v1.6). Replicates were merged separately for C9-STR and isogenic control conditions. Peaks were called using MACS2 (v2.2.9.1) with the following parameters: -t CTCF_STR_isoCtrl.bam -c input_nodups_sorted.bam -f BAM -q 0.01 -g hs --nomodel --shift 0 --extsize 200 --keep-dup all -B –SPMR. Differential peaks were identified using DESeq2 (v1.44.0) with an LRT comparing a full model that adjusts for replication and condition against a reduced model that includes replication only. Log fold change shrinkage was performed using the apeglm method. C9-STR gained CTCF peaks were defined as those with padj < 0.05 and LFC > log₂(1.5), while C9-STR lost CTCF peaks were defined as padj < 0.05 and LFC < −log₂(1.5).
RNA-seq processing: RNA-seq reads were aligned to the reference genome using STAR (v2.7.11b), and gene-level quantification was performed using HTSeq (v2.0.5). Differential expression analysis was conducted using DESeq2 (v1.44.0), with a model that included replication and condition as design factors. A likelihood ratio test (LRT) was used to assess the effect of condition by comparing the full model (replication + condition) against a reduced model containing only replication. We defined upregulated DEGs as an adjusted p-value (padj) < 0.05 and log2 fold change (LFC) > 0, whereas downregulated DEGs were identified using padj < 0.05 and LFC < 0.
Assembly: GRCh38
Supplementary files format and content: 10kb cooler files of Hi-C and Micro-C data, along with bigwig files of CUT&RUN, CHART, and RNA-seq data.

source_name: iPSC derived neurons

extract_protocol:
Hi-C libraries: Nuclei were isolated from the visual cortex of three individuals with C9-ALS and three neurotypical controls. Neuronal (NeuN-positive) and glial (NeuN-negative) nuclei were separated using fluorescence-activated nuclei sorting (FANS).
Micro-C libraries: Micro-C was performed using the Dovetail Genomics Cantata Bio Micro-C kit (Dovetail Proximity Ligation Core Box 1, PN DG-REF-001; Dovetail Micro-C Module Box 2, PN DG-NUC-001), following the manufacturer’s user guide (version 1.0).
CHART libraries: Cells were first fixed with 1% PFA for 10 minutes at room temperature to preserve chromatin architecture, followed by nuclei isolation. A second crosslinking step was performed on isolated nuclei using 3% formaldehyde for 10 minutes at room temperature. After washing, nuclei were resuspended in sonication buffer (50 mM HEPES-OH pH 7.5, 75 mM NaCl, 0.5% N-lauroylsarcosine, 0.1% sodium deoxycholate, 0.1 mM EGTA) and sonicated using a Covaris M220 Focused-ultrasonicator (75 Peak Incident Power, 10% Duty Factor, 200 Cycles per Burst, 3 minutes) to obtain 2-10 kb chromatin fragments. Crosslinks were then reversed, and the DNA was purified and assessed for fragmentation.
CUT&RUN libraries: CUT&RUN was performed using the CUTANA CUT&RUN Kit (Epicypher, 14-1048) using 4 replicates per condition (C9-STR neurons and isogenic control neurons, totaling 8 samples).
RNA-seq libraries: RNA was extracted from 1 million hiPSC-derived neurons per sample for each of 6 biological replicates per condition (C9-STR neurons and isogenic control neurons, n=12 samples total) using the Zymo Quick-RNA Miniprep Kit (R10564).
Hi-C libraries: Sorted nuclei were fixed in 1% formaldehyde to preserve chromatin interactions. Crosslinked chromatin was then digested with MboI (NEB, R0147S), followed by end repair, biotin labeling, and proximity-based ligation. The resulting DNA was sheared to 300-600 base-pair (bp) fragments, and biotinylated fragments were selectively captured via streptavidin pulldown. Illumina sequencing adapters were ligated to the recovered fragments, which were then amplified by PCR.
Micro-C libraries: Micro-C was performed using the Dovetail Library Module, PN DG-LIB-001, following the manufacturer’s user guide (version 1.0).
CHART libraries: DNA libraries were prepared using the CUTANA CUT&RUN Library Prep Kit (EpiCypher, 14-1001).
CUT&RUN libraries: DNA (calculated with the Qubit dsDNA HS Assay Kit) using the CUTANA CUT&RUN Library Prep Kit (EpiCypher 14-1001) according to the manufacturer’s recommendations.
RNA-seq libraries: Library preparation was performed by the UNC Integrated Genomics Core High-Throughput Sequencing Facility (RRID: SCR_022620) using the KAPA Stranded mRNA-Seq Kit (Roche Diagnostics, 07962193001), following the manufacturer’s protocol.

value: iPSC derived neurons

tag: condition

value: Neuron


title: 8010, plasma sample, pegIFNβ-1a _placebo, 6days

description: Library name: F11623988

value: plasma


title: MCAO_14d_cortex

description: Library name: MCAO_14d_cortex

value: CNS


title: 8010, plasma sample, pegIFNβ-1a _placebo, 5days

description: Library name: F11623811


title: RNA-seq of Homo sapiens: IsoCtrl hiPSC neuron sample4

description: Library name: Ctrl_hiPSC_Neu_RNA-seq_rep4


title: 8010, plasma sample, pegIFNβ-1a _placebo, 4days

description: Library name: F11623696


title: RNA-seq of Homo sapiens: IsoCtrl hiPSC neuron sample5

description: Library name: Ctrl_hiPSC_Neu_RNA-seq_rep5


description: Library name: SMARCA5_CUTTag_P8_Aundiff_Smarca5_ctrl_rep2


title: HFD_siNampt_1

city: Kyoto

first: Shinnosuke

last: Honda

address: Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto-shi

institute: Kyoto University

description: Library name: Sample11

data_processing:
The sequencing reads were mapped to the mouse genome (mm10) using STAR aligner software (v2.7.10.b). Gene expression levels were calculated using RSEM (ver. 1.2.28).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample generated by RSEM (v1.2.28).

source_name: Embryo

growth_protocol: Superovulated mouse oocytes were in vitro fertilized and resulting embryos were cultured in KSOM up to the blastocyst stage (96 hpi).

extract_protocol:
RNA-seq library was generated from ten blastocysts (control, non-targeting siRNA or Nampt-targeting siRNA groups), by using SMART-Seq v4 PLUS Kit (Takara Bio USA) according to the manufacturer’s manual.
SMART-Seq v4 PLUS Kit (Takara Bio USA) was used according to the manufacturer’s manual.

treatment_protocol: One-cell stage embryos at 3–6 hpi were electroporated with non-targeting or Nampt-targeting siRNAs and further cultured up to the blastocyst stage (96 hpi).

value: Embryo


title: LPS_Cx3cr1_cre_ER_pos_IFNgRfl_cortex

description: Library name: LPS_Cx3cr1_cre_ER_pos_IFNgRfl_cortex


title: 8010, plasma sample, pegIFNβ-1a _placebo, 2days

description: Library name: F11623450


title: HFD_siNT_1

description: Library name: Sample9


title: LPS_Cx3cr1_cre_ER_pos_IFNARfl_cortex

description: Library name: LPS_Cx3cr1_cre_ER_pos_IFNARfl_cortex


title: RNA-seq of Homo sapiens: IsoCtrl hiPSC neuron sample3

description: Library name: Ctrl_hiPSC_Neu_RNA-seq_rep3


title: 8010, plasma sample, pegIFNβ-1a _placebo, 0.33days

description: Library name: F11623182


title: LPS_Cx3cr1_cre_ER_neg_IFNgRfl_cortex

description: Library name: LPS_Cx3cr1_cre_ER_neg_IFNgRfl_cortex


title: RNA-seq of Homo sapiens: IsoCtrl hiPSC neuron sample2

description: Library name: Ctrl_hiPSC_Neu_RNA-seq_rep2


title: HFD_siNampt_2

description: Library name: Sample12


title: 8010, plasma sample, pegIFNβ-1a _placebo, 0.25days

description: Library name: F11623166


title: LPS_24h_vehicle

description: Library name: LPS_24h_vehicle


title: LPS_Cx3cr1_cre_ER_neg_IFNARfl_cortex

description: Library name: LPS_Cx3cr1_cre_ER_neg_IFNARfl_cortex


title: HFD_C_1

description: Library name: Sample7


title: LPS_24h_inhibitor

description: Library name: LPS_24h_inhibitor


title: ND_siNampt_2

description: Library name: Sample6


title: RNA-seq of Homo sapiens: C9STR hiPSC neuron sample5

description: Library name: STR_hiPSC_Neu_RNA-seq_rep5


title: RNA-seq of Homo sapiens: IsoCtrl hiPSC neuron sample1

description: Library name: Ctrl_hiPSC_Neu_RNA-seq_rep1


title: ND_siNampt_1

description: Library name: Sample5


title: 8010, plasma sample, pegIFNβ-1a _placebo, 0.125days

description: Library name: F11623088


title: 8010, plasma sample, pegIFNβ-1a _placebo, Baseline

description: Library name: F11622964


title: HFD_C_2

description: Library name: Sample8


title: 8006, plasma sample, IFNβ-1a_placebo, 9days

description: Library name: F11616803


title: LPS_24_hr_cortex

description: Library name: LPS_24_hr_cortex


title: 8006, plasma sample, IFNβ-1a_placebo, 13days

description: Library name: F11616905


title: ND_siNT_2

description: Library name: Sample4


title: RNA-seq of Homo sapiens: C9STR hiPSC neuron sample3

description: Library name: STR_hiPSC_Neu_RNA-seq_rep3


title: RNA-seq of Homo sapiens: C9STR hiPSC neuron sample6

description: Library name: STR_hiPSC_Neu_RNA-seq_rep6


title: Huntingtons_model_striatum

description: Library name: Huntingtons_model_striatum


title: ND_siNT_1

description: Library name: Sample3


title: 8006, plasma sample, IFNβ-1a_placebo, 6days

description: Library name: F11616340


title: RNA-seq of Homo sapiens: C9STR hiPSC neuron sample2

description: Library name: STR_hiPSC_Neu_RNA-seq_rep2


title: Inhibitor_only_cortex_7d

description: Library name: Inhibitor_only_cortex_7d


title: RNA-seq of Homo sapiens: C9STR hiPSC neuron sample4

description: Library name: STR_hiPSC_Neu_RNA-seq_rep4


title: ND_C_2

description: Library name: Sample2


title: ND_C_1

description: Library name: Sample1


title: 8006, plasma sample, IFNβ-1a_placebo, 5days

description: Library name: F11616163


title: RNA-seq of Homo sapiens: C9STR hiPSC neuron sample1

description: Library name: STR_hiPSC_Neu_RNA-seq_rep1


title: Huntingtons_model_control_striatum

description: Library name: Huntingtons_model_control_striatum


title: 8006, plasma sample, IFNβ-1a_placebo, 4days

description: Library name: F11616048


title: GvHD_cortex

description: Library name: GvHD_cortex


title: GvHD_control_cortex

description: Library name: GvHD_control_cortex


title: RSV/SARS-CoV2_4

city: Galveston

first: Haiping

last: Hao

state: Texas

address: 301 University Blvd

institute: UTMB NGS Core

description:
Library name: Sample_15
AA16

data_processing:
Adapter and Quality trimmed using Trimmomatic-0.39
STAR alignment using ENCODE parameter
Differrential expression analyzed using DESeq2
Assembly: GRCm39 with gencode vM34 annotation
Supplementary files format and content: raw counts matrix file in txt format

source_name: Lung

extract_protocol:
RNA was extracted using the Trizol method.
NEBNext Ribo Depletion and Ultra II Direction RNA Library preparation

value: Lung

value: Infected with RSV then SARS-COV-3


title: RSV/SARS-CoV2_3

description:
Library name: Sample_14
AA15

value: Infected with RSV then SARS-COV-2


title: 8006, plasma sample, IFNβ-1a_placebo, 2days

description: Library name: F11615802


title: Patient 4 Area 8

first: Ayushi

last: Agrawal

address: 1650 Owens St

institute: Gladstone Institutes

description:
Library name: V13B16-356_D1
Spatial gene expression for FFPE tissue microarray using 10x Genomics Visium v1 platform. (slide no: V13B16-356 ; capture area: D1)

data_processing:
Demultiplexed FASTQ files and histology images were processed using 10x Genomics Space Ranger v2.1.1 count pipeline.
Sequences were aligned to the GRCh38 human reference genome (refdata-gex-GRCh38-2020-A) using default parameters.
Gene expression was quantified using the Visium Human Transcriptome Probe Set v1.0 to generate filtered feature-spot matrices.
Assembly: 10x Genomics pre-built human reference package GRCh38 2020-A
Supplementary files format and content: aligned_fiducials.jpg:  aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg:  image of tissue and spots
Supplementary files format and content: scalefactors_json.json:  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_positions.csv:  list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: filtered_barcodes.tsv.gz:  list of spatial barcodes for filtered spots
Supplementary files format and content: filtered_features.tsv.gz:  list of detected genes in filtered matrix
Supplementary files format and content: filtered_matrix.mtx.gz:  filtered gene expression count matrix in Matrix Market Exchange Format
Library strategy: Spatial Transcriptomics

source_name: Small intestinal neuroendocrine tumor

extract_protocol:
Formalin-fixed, paraffin-embedded (FFPE) tissue blocks were retrieved from the archive. Tissue microarray cores of non-tumoral tissues (mucosal layers, submucosal layers, muscularis propria, mesenteric stroma) and tumoral tissues in different locations of different primary tumors (the mucosa, the submucosa, the muscularis propria for each primary tumors) or of metastatic tumors (lymphatic metastasis and perineural and non-perineural sites of mesenteric metastasis) were collected from the blocks (72 cores, ⌀ 1 mm).
Visium Spatial for FFPE Gene Expression Kit, Human Transcriptome, (10× Genomics, CA, USA, PN-1000338, RRID:SCR_023571) was used according to the manufacturer’s instructions to generate cDNA with spatial barcode information

value: Small intestinal neuroendocrine tumor


title: RSV/SARS-CoV2_2

description:
Library name: Sample_13
AA14


title: Grem_free_cortex

description: Library name: Grem_free_cortex


title: Patient 4 Area 7

description:
Library name: V13B16-356_C1
Spatial gene expression for FFPE tissue microarray using 10x Genomics Visium v1 platform. (slide no: V13B16-356 ; capture area: C1)


title: 8006, plasma sample, IFNβ-1a_placebo, 1.33days

description: Library name: F11615765

data_processing:
CLC Genomics Workbench v21.0.1
Samples were processed using Toolbox "Ready to use workflow" for "Small RNA sequencing" and "Qiaseq miRNAquantification"
Sequence reads were trimmed for adapters and size, UMI reads are generated from grouping greads with the same or similar UMI and similar sequence.
Mature miRNA reads are considered as expression counts.
Raw data was normalized using Deseq2 R package
Assembly: mirBase v22
Supplementary files format and content: csv file includes raw counts for each sample

extract_protocol:
EDTA plasma from whole blood. RNA was extracted using miRNeasy® Serum/Plasma Kit (Cat. 217184, Qiagen LLC).
Library preparations were carried out using the QIAseq miRNA Library Kit [96] (# 331505) together with QIAseq miRNA [96] Index IL (#331565), and an automated liquid handling method developed for preparation of 96 cDNA using the Biomek i7 Automated Liquid Handler (Beckman).

value: Healthy


title: Patient 3 Area 6

description:
Library name: V13B16-356_B1
Spatial gene expression for FFPE tissue microarray using 10x Genomics Visium v1 platform. (slide no: V13B16-356 ; capture area: B1)


title: RSV/SARS-CoV2_1

description:
Library name: Sample_12
AA13


title: 8006, plasma sample, IFNβ-1a_placebo, 0.67days

description: Library name: F11615615


title: GL261_IDH_WT

description: Library name: GL261_IDH_WT


title: Patient 3 Area 5

description:
Library name: V13B16-356_A1
Spatial gene expression for FFPE tissue microarray using 10x Genomics Visium v1 platform. (slide no: V13B16-356 ; capture area: A1)


title: Germ_free_2_years_cortex

description: Library name: Germ_free_2_years_cortex


title: Patient 2 Area 4

description:
Library name: V13B16-367_D1
Spatial gene expression for FFPE tissue microarray using 10x Genomics Visium v1 platform. (slide no: V13B16-367 ; capture area: D1)


title: Mock/ SARS-CoV2_3

description:
Library name: Sample_11
AA11

value: infected with SARS-COV-2


title: Patient 2 Area 3

description:
Library name: V13B16-367_C1
Spatial gene expression for FFPE tissue microarray using 10x Genomics Visium v1 platform. (slide no: V13B16-367 ; capture area: C1)


title: Mock/ SARS-CoV2_2

description:
Library name: Sample_10
AA10


title: FnX_7d_FN

description: Library name: FnX_7d_FN


title: 8006, plasma sample, IFNβ-1a_placebo, 0.125days

description: Library name: F11615440


title: Patient 1 Area 2

description:
Library name: V13B16-367_B1
Spatial gene expression for FFPE tissue microarray using 10x Genomics Visium v1 platform. (slide no: V13B16-367 ; capture area: B1)


title: Mock/ SARS-CoV2_1

description:
Library name: Sample_9
AA9


title: HFD_siNT_2

description: Library name: Sample10


title: 8006, plasma sample, IFNβ-1a_placebo, Baseline

description: Library name: F11615316


title: Patient 1 Area 1

description:
Library name: V13B16-367_A1
Spatial gene expression for FFPE tissue microarray using 10x Genomics Visium v1 platform. (slide no: V13B16-367 ; capture area: A1)


title: 8006, plasma sample, IFNβ-1a_placebo, 0.33days

description: Library name: F11615534


title: 8006, plasma sample, IFNβ-1a_placebo, 0.25days

description: Library name: F11615518


title: RSV4

description:
Library name: Sample_8
AA8

value: infected with RSV


title: FMF_disease_cortex

description: Library name: FMF_disease_cortex


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 2 uptake, SLAM-seq 24h, replicate 3

city: Rehovot

first: Igor

last: Ulitsky

address: Hertzl St.

country: Israel

institute: Weizmann Institute of Science

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA2_24h_3

data_processing:
RNA-seq: RNA-seq reads were mapped to the human genome (hg19 or hg38 assembly) using STAR (Dobin et al., 2013) to generate read coverage tracks visualized using the UCSC genome browser. RSEM (Li and Dewey, 2011) or STAR -quant with RefSeq annotations were used to call differential expression between samples.
CUT&RUN: CUT&RUN reads were mapped to the human genome using Bowtie2 (Langmead and Salzberg, 2012) and peaks were called using all the samples together using MACS2 (Zhang et al., 2008) or epic2 (Stovner and Sætrom, 2019). HOMER (Heinz et al., 2011) was used to call differential expression between samples.
SLAM-seq: estimation of half-lives and synthesis rates was performed using GRAND-SLAM/grandR (Jürges et al., 2018).
Assembly: hg19 and hg38
Supplementary files format and content: bigWig read coverage files are provided for all samples. RSEM/STAR quantification is provided for the RNA-seq samples, MACS2/epic2-called peaks are provided for the CUT&RUN data, and GRAND-SLAM kinetics parameters are provided for the SLAM-seq data.

source_name: MCF-7 cells

growth_protocol: MCF-7 cells were cultured in DMEM supplemented with 4.5 g/L of glucose, 4 mM L-Glutamine, 10% FBS, 1% PenStrep solution, grown in incubators maintained at 37°C with 5% CO2, and were routinely passaged by gentle dissociation using a Trypsin (0.05%) – EDTA (0.02%) solution. DNA plasmid, siRNAs (final concentration 25 µM) and GapmeRs (50 µM) transfections were performed by using Lipofectamine 3000 (ThermoFisher Scientific), according to the respective protocols. For each transfection, the optimal DNA/siRNAs/GapmeRs concentration and amount of transfection reagents were empirically determined to minimize cellular stress and maximize efficiency, to eventually ensure clean readouts. In all cases, cells were plated the day before the transfection in an antibiotic-free medium which was subsequently changed prior to adding the transfection mix, and again after 24h to minimize cell death. Finally, transfections were carried out for 72h, unless stated otherwise.

extract_protocol:
Metabolic labeling and SLAM-seq were then performed as previously described (Herzog et al., 2017; Zuckerman et al., 2020), with minor modifications. All steps were performed in the dark until the chemical conversion with iodoacetamide (IAA). After 48h hours, the growth medium was replaced with fresh media supplemented with 500 µM 4-Thiouridine (4sU, Sigma), and replaced again with fresh 4sU after every time point. In total, we collected RNA from cells at time 0 (unlabeled), and after 4, 8 and 24h hours post-4sU addition. RNA extraction was carried out as described above with the addition of DTT (0.1 mM final concentration) to keep the samples under reducing conditions, and IAA conversion was performed as described previously (Zuckerman et al., 2020).
UMI-4C was performed as previously described (Schwartzman et al., 2016)
CUT&RUN reactions were performed as previously described (Meers et al., 2019).
RNA-seq libraries were prepared using the CORALL mRNA-Seq Kit V2 (Lexogen), following the manufacturer’s instructions. SLAM-seq libraries were prepared using the NEBNext Ultra II Directional Library Kit (NEB), according to the manufacturer's protocol. SLAM-seq libraries were generated as described before (Schwartzman et al., 2016). CUT&RUN libraries were prepared as described previously (Meers et al., 2019).

value: MCF-7 cells


title: RSV3

description:
Library name: Sample_7
AA7


title: FnX_control_FN

description: Library name: FnX_control_FN


title: FMF_control_cortex

description: Library name: FMF_control_cortex


title: FnX_30d_FN

description: Library name: FnX_30d_FN


title: 8002, plasma sample, IFNβ-1a, 5days

first: Lakshmi Manasa

last: Chekka

address: 10903 New Hampshire Avenue

institute: U.S. FDA

description: Library name: F11608515


title: RSV1

description:
Library name: Sample_5
AA5


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 2 uptake, SLAM-seq 24h, replicate 2

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA2_24h_2


title: 8002, plasma sample, IFNβ-1a, 4days

description: Library name: F11608400


title: FAD_control_16_week_hip

description: Library name: FAD_control_16_week_hip


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 2 uptake, SLAM-seq 24h, replicate 1

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA2_24h_1


title: RSV2

description:
Library name: Sample_6
AA6


title: FAD_control_40_week_hip

description: Library name: FAD_control_40_week_hip


title: 8002, plasma sample, IFNβ-1a, 2days

description: Library name: F11608154


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 2 uptake, SLAM-seq 8h, replicate 3

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA2_8h_3


title: Mock_3

description:
Library name: Sample_3
AA3

value: injected with PBS


title: 8002, plasma sample, IFNβ-1a, 1.33days

description: Library name: F11608117


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 2 uptake, SLAM-seq 8h, replicate 2

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA2_8h_2


title: FAD_16_week_hip

description: Library name: FAD_16_week_hip


title: 8002, plasma sample, IFNβ-1a, 0.67days

description: Library name: F11607967


title: Mock_4

description:
Library name: Sample_4
AA4


title: EAE_peak_SPC

description: Library name: EAE_peak_SPC


title: FAD_40_week_hip

description: Library name: FAD_40_week_hip


title: 8002, plasma sample, IFNβ-1a, 6days

description: Library name: F11608690


title: Mock_1

description:
Library name: Sample_1
AA1


title: Mock_2

description:
Library name: Sample_2
AA2


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 2 uptake, SLAM-seq 4h, replicate 2

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA2_4h_2


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 2 uptake, SLAM-seq 4h, replicate 3

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA2_4h_3


title: EAE_peak_cerebellum

description: Library name: EAE_peak_cerebellum


title: 8002, plasma sample, IFNβ-1a, 0.33days

description: Library name: F11607886


title: Arabidopsis_shoot_Col-0_Repeat2

city: Wuhan

first: Wenying

last: Zhong

address: Lion Rock Street

institute: Huazhong Agricultural University

description: Library name: Arabidopsis_shoot_Col-0_Repeat2

data_processing:
BatMeth2-pipel (v1.1)60 with the '-fastp' parameter was used to call the DNA methylation levels from the sequencing data, using the Arabidopsis genome (TAIR10)61 as the reference. For visualization, BedGraph files were converted to BigWig format using BatMeth2-bedGraphToBigWig (v1.1)
Assembly: Arabidopsis thaliana : TAIR10
Supplementary files format and content: bigwig

organism: Arabidopsis thaliana

source_name: shoot

growth_protocol: Plants were grown at 22 °C under a 16 h light/8 h dark photoperiod. Shoots and roots of two-week-old plants and stems of four-week-old plants were collected for the indicated genotypes.

extract_protocol:
Genomic DNA was extracted using the DNeasy Plant Mini Kit (QIAGEN, 69104). Bisulfite conversion of DNA was performed using the EpiTect Plus Bisulfite Kit (Qiagen, 59124), and bisulfite-treated DNA libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, E7645), following the manufacturer’s instructions.
Llibraries were sequenced on an Illumina NovaSeq X Plus platform

value: shoot


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 2 uptake, SLAM-seq 8h, replicate 1

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA2_8h_1


title: EAE_peak_brainstem

description: Library name: EAE_peak_brainstem


title: 8002, plasma sample, IFNβ-1a, 0.125days

city: Silver Spring

description: Library name: F11607792

source_name: plasma


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 2 uptake, SLAM-seq 4h, replicate 1

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA2_4h_1


title: 8002, plasma sample, IFNβ-1a, Baseline

description: Library name: F11607668


title: EAE_Cx3cr1_cre_ER_pos_IFNgRfl

description: Library name: EAE_Cx3cr1_cre_ER_pos_IFNgRfl


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 2 uptake, SLAM-seq 0h, replicate 3

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA2_0h_3

value: untreated


title: ROS1_Flag_ros1-4_line3_Repeat_2

description: Library name: ROS1_Flag_ros1-4_line3_Repeat_2

data_processing:
Evaluated the quality of sequencing data using FastQC.
Fastp with “-l 15 -f 0 -t 0” parameters to was used to filter out adaptors and low-quality reads from raw reads, resulting in clean reads.
bwa mem algorithm43 with “-k 19 -T 30” parameters to map trimmed reads to the corresponding reference genomes.
SAMtools  with parameters “-q 30 -f 2” to remove low-quality mapping and removed PCR-duplicated reads and redundant reads using the GATK MarkDuplicates.
Narrow peaks were called by MACS2, with parameters “-B -q 1e-5 -f BAMPE”
Assembly: Brassica napus : westar.v0, Arabidopsis thaliana : TAIR10
Supplementary files format and content: Narrowpeak

extract_protocol:
Tissues were evenly cut into small pieces, crosslinked with 1% formaldehyde in vacuum for 10 min, and then quenched with 0.2 M glycine for 5 min at room temperature.
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs, E7645) and sequenced on an Illumina NovaSeq X Plus platform (paired-end 150 bp reads, Annoroad Gene Technology).

value: ROS1-Flag_ros1-4 line3

tag: chip antibody

value: Flag


title: EAE_onset_SPC

description: Library name: EAE_onset_SPC


title: 8002, plasma sample, IFNβ-1a, 0.25days

description: Library name: F11607870


title: 8001, plasma sample, pegIFNβ-1a, 13days

description: Library name: F11607345


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 2 uptake, SLAM-seq 0h, replicate 1

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA2_0h_1


title: ROS1_Flag_ros1-4_line2_Repeat_2

description: Library name: ROS1_Flag_ros1-4_line2_Repeat_2

value: ROS1-Flag_ros1-4 line2


title: ROS1_Flag_ros1-4_line3_Repeat_1

description: Library name: ROS1_Flag_ros1-4_line3_Repeat_1


title: 8001, plasma sample, pegIFNβ-1a, 9days

description: Library name: F11607243

value: plasma


title: Arabidopsis_shoot_ros1-4_Repeat2

description: Library name: Arabidopsis_shoot_ros1-4_Repeat2


title: EAE_Cx3cr1_cre_ER_neg_IFNgRfl

description: Library name: EAE_Cx3cr1_cre_ER_neg_IFNgRfl

value: CNS


title: 8001, plasma sample, pegIFNβ-1a, 6days

description: Library name: F11606780


title: EAE_Cx3cr1_cre_ER_pos_IFNARfl

description: Library name: EAE_Cx3cr1_cre_ER_pos_IFNARfl


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 2 uptake, SLAM-seq 0h, replicate 2

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA2_0h_2


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 1 uptake, SLAM-seq 24h, replicate 3

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA1_24h_3


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 1 uptake, SLAM-seq 24h, replicate 1

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA1_24h_1


title: EAE_control_SPC

description: Library name: EAE_control_SPC


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 1 uptake, SLAM-seq 24h, replicate 2

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA1_24h_2


title: 8001, plasma sample, pegIFNβ-1a, 4days

description: Library name: F11606488


title: 241127_Yumeng2

city: Uppsala

first: Yumeng

last: Mao

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: Fov 1:67 is mice with NEDD8 KO tumor treated with IgG2a isotype  Fov 68:161 is mice with WT tumor treated with anti-PD1

hyb_protocol: Tissues underwent fixation, dehydration, and heat-induced epitope retrieval, followed by digestion with Proteinase K. Fiducials were applied for spatial alignment, and blocking was performed before in-situ hybridization (ISH) using NanoString probes. After overnight hybridization at 37 °C, excess probes were washed off, and the tissues were stained with DAPI and a 4-fluorophore-conjugated antibody cocktail, namely segmentation markers (CD298/B2M, PanCK, CD45, and CD3).

scan_protocol: Tissue sections were then prepared for imaging by affixing a custom flow cell for analysis on the CosMX SMI instrument. RNA target readout was performed by loading the flow cell and selecting a total of 330 fields of view (FOVs) (169 Slide 1 and 161 Slide 2) based on H&E staining. RNA detection was achieved through sequential hybridization and imaging of 16 reporter pools, with UV cleavage and washing cycles to improve sensitivity.

data_processing: Spatial data preprocessing was performed on NanonString AtoMX platform and R

label: Xenium probe set

source_name: Tumor

label_protocol: Xenium probe set

growth_protocol: Tumor cells were cultured in Iscove’s Modified Dulbecco’s Medium (IMDM) (Thermo Fisher Scientific) supplemented with 10% heat-inactivated fetal bovine serum (FBS) and 1% penicillin-streptomycin (Thermo Fisher Scientific) at 37°C in a humidified incubator with 5% CO₂

extract_protocol: tissue preparation protocol: Tumor tissues were harvested and placed in 4% paraformaldehyde overnight, followed by dehydration with 70% ethanol.  To prepare formalin-fixed paraffin-embedded (FFPE) tumor blocks, tumors were embedded and block with paraffin using the standard procedure for tissues paraffin embedding. Next, FFPE blocks were sectioned at 5 μm thickness and mounted on VWR Premium Superfrost Plus Micro slides (48311-703) using a standard rotary microtome (UC7, Leica). Slides with the largest area which best represent the tumors were selected. After sectioning, slides were baked at 37 °C overnight to improve tissue adherence

treatment_protocol: Mice were treated intraperitoneally (i.p.) with either an anti-PD-1 antibody (clone RMP1-14, BioXcell), or a Rat isotype IgG2a control (clone 2A3, BioXCell), 50 μg per mouse every 3 days

value: Tumor

tag: tissue preservation method

value: FFPE


title: EAE_control_cerebellum

description: Library name: EAE_control_cerebellum


title: 241127_Yumeng1

description: Fov 1:66 is mice with NEDD8 KO tumor treated with anti-PD1  Fov 67:161 is mice with WT tumor treated with IgG2a isotype


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 1 uptake, SLAM-seq 8h, replicate 3

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA1_8h_3


title: EAE_Cx3cr1_cre_ER_neg_IFNARfl

description: Library name: EAE_Cx3cr1_cre_ER_neg_IFNARfl


title: ROS1_Flag_ros1-4_line2_Repeat_1

description: Library name: ROS1_Flag_ros1-4_line2_Repeat_1


title: Taf1_1 heterozygous mutant

city: Luebeck

first: Melissa

last: Vos

address: Ratzeburger Allee 160, building 67

department: Institute of Neurogenetics

institute: University of Luebeck, UKSH

description: Library name: GC051717

data_processing:
Raw sequencing data was pseudo-aligned against the D. melanogaster transcriptome (Ensembl BDGP6). Assembly: Ensembl drosophila melanogaster Release 91 Gene expression was summarized from the scaledTPM values of the transcripts
Assembly: Assembly: Ensembl drosophila melanogaster Release 91
Supplementary files format and content: scaled TPM values summarized to gene expression using tximport

organism: Drosophila melanogaster

source_name: whole body

extract_protocol:
Total high-purity RNA of 10 flies per genotype was isolated using the Qiagen RNA isolation kit.
Input total RNA was quantified and RIN scores were determined and All RIN scores were > 8. 2 µg input total RNA were processed using the Illumina stranded mRNA kit (Illumina, San Diego, USA).

value: whole body

value: Taf1_1 heterozygous mutant


title: EAE_control_brainstem

description: Library name: EAE_control_brainstem


title: 8001, plasma sample, pegIFNβ-1a, 2days

description: Library name: F11606242


title: 8001, plasma sample, pegIFNβ-1a, 1.33days

description: Library name: F11606205


title: 8001, plasma sample, pegIFNβ-1a, 0.67days

description: Library name: F11606055


title: 8001, plasma sample, pegIFNβ-1a, 5days

description: Library name: F11606603


title: w1118_control

description: Library name: GC051712


title: Glial cells from injured optic lobes 48h AI_3

city: Sant Joan d'Alacant

first: Marta

last: Neto

state: Alicante

address: Av. Ramon y Cajal, s/n

country: Spain

institute: Instituto de Neurociencias - CSIC/UMH

description: Library name: INJ3

data_processing:
Clean reads were mapped to the Drosophila melanogaster reference genome (release 6 plus ISO1 MT) using STAR 2.7.0a.
Assembly: dm6
Supplementary files format and content: csv file includes normalized counts for each sample

source_name: optic lobes from adult brain

extract_protocol:
CDNAs for RNA-seq were prepared using SMART-SEQ2 protocol following manufacturer's protocol.
RNA libraries for RNA-seq were prepared using Pico Nextera protocol following manufacturer's protocol.

value: optic lobes from adult brain

value: glial cells


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 1 uptake, SLAM-seq 4h, replicate 3

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA1_4h_3


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 1 uptake, SLAM-seq 8h, replicate 1

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA1_8h_1


title: E16_brain

description: Library name: E16_brain


title: Cup_Vehicle

description: Library name: Cup_Vehicle


title: 8001, plasma sample, pegIFNβ-1a, 0.25days

description: Library name: F11605958

value: Healthy


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 1 uptake, SLAM-seq 8h, replicate 2

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA1_8h_2


title: 8001, plasma sample, pegIFNβ-1a, 0.125days

description: Library name: F11605880


title: EAE_chronic_SPC

description: Library name: EAE_chronic_SPC


title: Glial cells from intact optic lobes_2

description: Library name: NI2


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 1 uptake, SLAM-seq 4h, replicate 1

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA1_4h_1


title: Cup_inhibitor

description: Library name: Cup_inhibitor


title: Glial cells from intact optic lobes_3

description: Library name: NI3


title: 8001, plasma sample, pegIFNβ-1a, Baseline

description: Library name: F11605756


title: Cup_RE_CC

description: Library name: Cup_RE_CC


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 1 uptake, SLAM-seq 0h, replicate 2

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA1_0h_2


title: 8001, plasma sample, pegIFNβ-1a, 0.33days

description: Library name: F11605974


title: RNAseq_P8_Adiff_Smarca5_ctrl_rep1

description:
Library name: RNAseq_P8_Adiff_Smarca5_ctrl_rep1
Diff_Ctrl_1

data_processing:
Raw paired-end RNA-seq reads after trimming by Trim-galore (https://github.com/FelixKrueger/TrimGalore) (version 0.6.7) were aligned to the mouse (GRCm38/mm10) genome using STAR (version STAR_2.5.4b) with following options: --outSAMtype BAM SortedByCoordinate; --twopassMode Basic; --outFilterType BySJout; --outFilterMultimapNmax 1; --winAnchorMultimapNmax 50; --alignSJoverhangMin 8; --alignSJDBoverhangMin 1; --outFilterMismatchNmax 999; --outFilterMismatchNoverReadLmax 0.04; --alignIntronMin 20; --alignIntronMax 1000000; --alignMatesGapMax 1000000 for unique alignments. To quantify aligned reads in RNA-seq, aligned read counts for each gene were generated using featureCounts (v2.0.1), which is part of the Subread package based on annotated genes (gencode.vM25.annotation.gtf). The transcripts per million (TPM) values of each gene were for comparative expression analyses and computing the Pearson correlation coefficient between biological replicates using corrplot.
Assembly: mm10
Supplementary files format and content: TPM

extract_protocol:
To prepare single cell suspensions for cell sorting, detangled seminiferous tubules were incubated in 1× Krebs–Ringer Bicarbonate Buffer (Sigma, K4002) supplemented with 1.5 mg/ml collagenase Type 1 and 0.04 mg/ml DNase I at 37°C for 15 min with gentle agitation and dissociated using vigorous pipetting, and then add 0.75 mg/ml hyaluronidase (Sigma, H3506) and incubated at 37°C for 10 min with gentle agitation and dissociated using vigorous pipetting. The cell suspension was centrifuged at 300 × g, the cells resuspended in 10 ml FACS buffer (PBS containing 2% FBS) and then centrifuged again at 300 × g for 5 min, and this step was repeated one more time. The pelleted cells were resuspended 1 ml FACS buffer and then filtered through a 70 μm nylon cell strainer (Falcon, 352350). The resultant single cells were stained with cocktails of antibodies diluted with FACS buffer listed as follows: PE-conjugated anti-mouse/human CD324 (E-cadherin) antibody (1:500, Biolegend, 147303), PE/Cy7-conjugated anti-mouse CD117 (c-Kit) antibody (1:200, Biolegend, 105814) and FITC-conjugated anti-mouse CD9 antibody (1:500, Biolegend, 124808). After a 50 min incubation on ice, cells were washed with 10 ml FACS buffer three times by centrifugation at 300 × g for 5 min and filtered into a 1 ml FACS tube through a 35 μm nylon mesh cap (Falcon, 352235). 7-AAD Viability Stain (Invitrogen, 00-6993-50) was added to cell suspension for the exclusion of dead cells. Samples were kept on ice until sorting. Cell sorting was performed using SH800S (SONY). Cells were analyzed after removing small and large debris in FSC-A versus SSC-A gating, doublets in FSC-W versus FSC-H gating, and 7AAD+ dead cells. Then the desired cell population was collected in gates determined based on antibody staining.
10,000 Aundiff or Adiff cells were pooled from two independent mice as one replicate, and two independent biological replicates were used for RNA-seq library generation. Total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN, Cat # 74034) according to the manufacturer’s instructions. Library preparation was performed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB, E6420S) according to the manufacturer’s instructions. Prepared RNA-seq libraries were sequenced on the HiSeq X Ten system (Illumina) with paired-ended 150-bp reads.

value: testis

value: primary cell

value: Differentiating spermatogonia


title: Glial cells from injured optic lobes 48h AI_1

description: Library name: INJ1


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 1 uptake, SLAM-seq 4h, replicate 2

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA1_4h_2

value: MCF-7 cells


title: Cup_DE_CC

description: Library name: Cup_DE_CC


title: RNAseq_P8_Adiff_Smarca5_ctrl_rep2

description:
Library name: RNAseq_P8_Adiff_Smarca5_ctrl_rep2
Diff_Ctrl_2


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake, SLAM-seq 24h, replicate 3

description: Library name: SLAMseq_MCF7_NT_24h_3


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 1 uptake, SLAM-seq 0h, replicate 3

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA1_0h_3

value: untreated


title: P13, scRNAseq

city: Fukuoka

first: Yuichiro

last: Semba

address: 3-1-1 Maidashi

institute: Kyushu University

description: 10x Genomics

data_processing:
Sequencing data was aligned to the hg38 genome, and single cell features were counted by 10x Genomics CellRanger (v7.2.0).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Bone marrow

extract_protocol:
Bone marrow mononuclear cells were isolated from two AML patients.
BMMNC were processed for scRNA-seq with a Chromium Next GEM Single Cell 5' Reagent Kit v2 (10x Genomics), following the manufacturer’s instructions.

value: Bone marrow

value: BMMNC


title: RNAseq_P8_Aundiff_Smarca5_cKO_rep1

description:
Library name: RNAseq_P8_Aundiff_Smarca5_cKO_rep1
Undiff_cKO_1

value: Undifferentiated spermatogonia


title: P12, scRNAseq

description: 10x Genomics


title: CSF1R_EAE_9_SPC

description: Library name: CSF1R_EAE_9_SPC


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake, SLAM-seq 24h, replicate 2

description: Library name: SLAMseq_MCF7_NT_24h_2


title: RNAseq_P8_Aundiff_Smarca5_cKO_rep2

description:
Library name: RNAseq_P8_Aundiff_Smarca5_cKO_rep2
Undiff_cKO_2


title: Cup_control_CC

description: Library name: Cup_control_CC


title: CSF1R_EAE_8_SPC

description: Library name: CSF1R_EAE_8_SPC


title: CSF1R_EAE_7_SPC

description: Library name: CSF1R_EAE_7_SPC


title: RNAseq_P8_Aundiff_Smarca5_ctrl_rep2

description:
Library name: RNAseq_P8_Aundiff_Smarca5_ctrl_rep2
Undiff_Ctrl_2


title: Ribodepleted RNA-seq in MCF-7 cells after EPB41L4A-AS1 GapmeR 1 uptake, SLAM-seq 0h, replicate 1

description: Library name: SLAMseq_MCF7_EPB41L4A-AS1_LNA1_0h_1


title: high-fat diet mice, treated with NM-FGF19, replicate 3

city: Pamplona

first: David

last: Ruiz Guillamón

state: Navarra

address: Av. de Pío XII, 55

department: Programa de Inmunología e Inmunoterapia

institute: Centro de Investigación de Medicina Aplicada (CIMA) - Clínica Universidad de Navarra

data_processing:
Trimming of sequences using Trimmomatic.
Alignment to reference genome mm39 (Mus musculus) using STAR software.
Uniquely mapped reads were counted using featureCounts.
Assembly: mm39
Supplementary files format and content: Raw counts matrix for all the samples in a txt file. Genes described with the Mus musculus ensembl references.

source_name: liver

growth_protocol: Mice fed during 28 weeks with normal chow diet (lean mice) or high-fat diet (control mice or FGF19 mice).

extract_protocol:
Liver sections were mechanically disrupted with a pellet pestle cordless motor in homogenization solution and RNA was inmediately extracted after using the simplyRNA Tissue kit.
Preparation using 100 ng of total RNA using the Illumina Stranded mRNA Prep Ligation kit following the manufacturer's protocol. Libraries were then sequenced using a NextSeq2000 sequencer (Illumina) with 30 - 40 million pair-end reads (200bp;Rd1:101;Rd2:101) for each sample, and demultiplexed.

treatment_protocol: Six week treatment, with weekly injections of mRNA-LNPs. Control mRNA-LNPs used for the lean and control mice groups, while FGF19 mice were treated with mRNA-LNPs containing NM-FGF19 mRNA.

value: liver

value: male

value: high-fat diet, NM-FGF19-mRNA


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake, SLAM-seq 24h, replicate 1

description: Library name: SLAMseq_MCF7_NT_24h_1


title: high-fat diet mice, treated with NM-FGF19, replicate 4


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake, SLAM-seq 8h, replicate 3

description: Library name: SLAMseq_MCF7_NT_8h_3


title: high-fat diet mice, treated with NM-FGF19, replicate 2


title: ATACseq_P0_ProSG_Smarca5_ctrl_rep2

description: Library name: ATACseq_P0_ProSG_Smarca5_ctrl_rep2

data_processing:
Raw paired-end ATAC-seq reads after trimming by Trim-galore were aligned to either the mouse (GRCm38/mm10) genomes using bowtie2 (version 2.3.3.1) with default arguments. All unmapped and non-uniquely mapped reads were filtered out by samtools (version 1.9) before being subjected to downstream analyses. PCR duplicates were removed using the ‘MarkDuplicates’ command in Picard tools (version 2.23.8) (https://broadinstitute.github.io/picard/, Broad Institute).
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
To prepare single cell suspensions for cell sorting, detangled seminiferous tubules were incubated in 1× Krebs–Ringer Bicarbonate Buffer (Sigma, K4002) supplemented with 1.5 mg/ml collagenase Type 1 and 0.04 mg/ml DNase I at 37°C for 15 min with gentle agitation and dissociated using vigorous pipetting, and then add 0.75 mg/ml hyaluronidase (Sigma, H3506) and incubated at 37°C for 10 min with gentle agitation and dissociated using vigorous pipetting. The cell suspension was centrifuged at 300 × g, the cells resuspended in 10 ml FACS buffer (PBS containing 2% FBS) and then centrifuged again at 300 × g for 5 min, and this step was repeated one more time. The pelleted cells were resuspended 1 ml FACS buffer and then filtered through a 70 μm nylon cell strainer (Falcon, 352350). The resultant single cells were stained with cocktails of antibodies diluted with FACS buffer listed as follows: PE-conjugated anti-mouse/human CD324 (E-cadherin) antibody (1:500, Biolegend, 147303), PE/Cy7-conjugated anti-mouse CD117 (c-Kit) antibody (1:200, Biolegend, 105814) and FITC-conjugated anti-mouse CD9 antibody (1:500, Biolegend, 124808). After a 50 min incubation on ice, cells were washed with 10 ml FACS buffer three times by centrifugation at 300 × g for 5 min and filtered into a 1 ml FACS tube through a 35 μm nylon mesh cap (Falcon, 352235). 7-AAD Viability Stain (Invitrogen, 00-6993-50) was added to cell suspension for the exclusion of dead cells. Samples were kept on ice until sorting. Cell sorting was performed using SH800S (SONY). Cells were analyzed after removing small and large debris in FSC-A versus SSC-A gating, doublets in FSC-W versus FSC-H gating, and 7AAD+ dead cells. Then the desired cell population was collected in gates determined based on antibody staining.
ATAC-seq libraries of germ cells were prepared as described; briefly, 10,000 Aundiff, Adiff or P0 prospermatogonia (ProSG) were pooled from two independent mice as one replicate. Samples were lysed in 50 μl of lysis buffer (10 mM Tris–HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2 and 0.1% NP-40, 0.1% Tween-20, and 0.01% Digitonin) on ice for 5 min. Immediately after lysis, the samples were spun at 500 × g for 10 min at 4°C and the supernatant was removed. The sedimented nuclei were then incubated in 10 μl of transposition mix (0.5 μl homemade Tn5 transposase (∼1 μg/μl), 5 μl 2× tagment DNA buffer (10 mM Tris–HCl (pH 7.6), 10 mM MgCl2 and 20% dimethyl formamide), 3.3 μl PBS, 0.1 μl 1% digitonin, 0.1 μl 10% Tween-20 and 1 μl water) at 37°C for 30 min in a thermomixer with shaking at 500 rpm. After tagmentation, the transposed DNA was purified with a MinElute kit (Qiagen). Polymerase chain reaction (PCR) was performed to amplify the library using the following conditions: 72°C for 3 min; 98°C for 30 s; thermocycling at 98°C for 10 s, 60°C for 30 s and 72°C for 1 min. Quantitative PCR was used to estimate the number of additional cycles needed to generate products at 25% saturation. Seven to eight additional PCR cycles were added to the initial set of five cycles. Amplified DNA was purified by 1.0x SPRIselect beads (Beckman Coulter). ATAC-seq libraries were sequenced on the HiSeq X Ten system with 150-bp paired-end reads.

value: Prospermatogonia


title: high-fat diet mice, treated with NM-FGF19, replicate 1


title: CSF1R_EAE_6_SPC

description: Library name: CSF1R_EAE_6_SPC

data_processing:
Fastq files were further processed using the Cell Ranger v7.1.0 pipeline (10x Genomics) for read alignment to generate counts data.
Assembly: GRCm38, Gencode v33
Supplementary files format and content: filtered counts matrices

extract_protocol:
snRNA-seq using 10x was conducted on nuclei extracted from frozen brain specimen
cDNA amplification and library preparation were conducted following the manufacturer’s instructions (Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics))

value: CNS


title: high-fat diet mice, replicate 4

value: high-fat diet, Control-mRNA


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake, SLAM-seq 8h, replicate 2

description: Library name: SLAMseq_MCF7_NT_8h_2


title: ATACseq_P0_ProSG_Smarca5_ctrl_rep1

description: Library name: ATACseq_P0_ProSG_Smarca5_ctrl_rep1


title: CSF1R_EAE_5_SPC

description: Library name: CSF1R_EAE_5_SPC


title: CSF1R_EAE_4_SPC

description: Library name: CSF1R_EAE_4_SPC


title: high-fat diet mice, replicate 2


title: ATACseq_P8_Adiff_Smarca5_ctrl_rep2

description: Library name: ATACseq_P8_Adiff_Smarca5_ctrl_rep2


title: RNAseq_P8_Aundiff_Smarca5_ctrl_rep1

description:
Library name: RNAseq_P8_Aundiff_Smarca5_ctrl_rep1
Undiff_Ctrl_1


title: CSF1R_EAE_3_SPC

description: Library name: CSF1R_EAE_3_SPC


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake, SLAM-seq 4h, replicate 3

description: Library name: SLAMseq_MCF7_NT_4h_3


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake, SLAM-seq 8h, replicate 1

description: Library name: SLAMseq_MCF7_NT_8h_1


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake, SLAM-seq 4h, replicate 2

description: Library name: SLAMseq_MCF7_NT_4h_2


title: high-fat diet mice, replicate 3


title: ATACseq_P8_Adiff_Smarca5_ctrl_rep1

description: Library name: ATACseq_P8_Adiff_Smarca5_ctrl_rep1


title: CSF1R_EAE_1_SPC

description: Library name: CSF1R_EAE_1_SPC


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake, SLAM-seq 4h, replicate 1

description: Library name: SLAMseq_MCF7_NT_4h_1


title: ATACseq_P8_Aundiff_Smarca5_cKO_rep2

description: Library name: ATACseq_P8_Aundiff_Smarca5_cKO_rep2


title: high-fat diet mice, replicate 1


title: normal chow diet mice, replicate 4

value: normal chow diet, Control-mRNA


title: APP_23_hip

description: Library name: APP_23_hip


title: ATACseq_P8_Aundiff_Smarca5_ctrl_rep2

description: Library name: ATACseq_P8_Aundiff_Smarca5_ctrl_rep2


title: normal chow diet mice, replicate 3


title: normal chow diet mice, replicate 2


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake, SLAM-seq 0h, replicate 2

description: Library name: SLAMseq_MCF7_NT_0h_2


title: Aging_control

description: Library name: Aging_control


title: CSF1R_EAE_2_SPC

description: Library name: CSF1R_EAE_2_SPC


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake, SLAM-seq 0h, replicate 3

description: Library name: SLAMseq_MCF7_NT_0h_3


title: Ribodepleted RNA-seq in MCF-7 cells after control GapmeR uptake, SLAM-seq 0h, replicate 1

description: Library name: SLAMseq_MCF7_NT_0h_1


title: T72Z3

status: Public on Feb 08 2026

city: Hohhot

first: Zhenyu

last: Cao

state: Inner Mongolia

address: No. 306, Zhaowuda Road

institute: Inner MongoliaAgricultural University

description: Library name: Sample12

data_processing:
Raw data (raw reads) of fastq format were firstly processed using Trimmomatic . The reads   containing ploy-N and the low quality reads were removed to obtain the clean reads. After removing adaptor and low quality sequences, the clean reads were assembled into expressed sequence tag clusters (contigs) and de novo assembled into transcripts by Trinity  (vesion: 2.4) with paired-end method. The longest transcript was choose as a unigene based on the similarity and length for subsequent analyse
Assembly: unaligned
Supplementary files format and content: xls file includes the raw counts for each sample

organism: Allium mongolicum

source_name: Root

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s protocol. RNA purity and quantification were evaluated NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina according to the manufacturer’s instructions. The libraries were finally sequenced using the Illumina Novaseq 6000 platform. 150 bp paired-end reads were generated. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Root


title: ATACseq_P8_Aundiff_Smarca5_cKO_rep1

description: Library name: ATACseq_P8_Aundiff_Smarca5_cKO_rep1


title: T72Z2

description: Library name: Sample11


title: ATACseq_P8_Aundiff_Smarca5_ctrl_rep1

description: Library name: ATACseq_P8_Aundiff_Smarca5_ctrl_rep1


title: normal chow diet mice, replicate 1


title: T48Z1

description: Library name: Sample7


title: T48Z3

description: Library name: Sample9


title: T48Z2

description: Library name: Sample8


title: T24Z2

description: Library name: Sample5


title: Aging_2_years

description: Library name: Aging_2_years


title: CKZ3

description: Library name: Sample3


title: CKZ2

description: Library name: Sample2


title: T72Z1

description: Library name: Sample10


title: T24Z1

description: Library name: Sample4


title: CKZ1

description: Library name: Sample1


title: Sham HIPPO rep2

first: Chen

last: Yanglin

address: Xilin road

institute: Inner Mongolia University

description: Library name: Sham_HIPPO_rep2

data_processing:
Adaptor sequences and low-quality base calls were trimmed using fastp with default parameters.
Trimmed reads were aligned to the rat reference genome (Rattus norvegicus.mRatBN7.2.109) or human reference genome (GRCh38) using STAR v2.7.7a in paired-end mode with default parameters
Gene level counts were generated using FeatureCounts from Subread v2.0.
Assembly: Rattus norvegicus.mRatBN7.2.109, GRCh38
Supplementary files format and content: comma-separated csv file include count value of each sample

organism: Rattus

source_name: hippocampus

extract_protocol:
Total RNA was extracted from cultured cells using Rneasy mini kit (Qiagen). 1.5 ug of total RNA was used for the construction of sequencing libraries.
Library for RNA-seq were prepared using Illumina TruseqTM RNA sample prep Kit.

value: hippocampus

value: tissue

value: Nerve cell

value: wildtype

value: Drepressed+normal saline


title: Con HIPPO rep2

description: Library name: Con_HIPPO_rep2

value: No treatment


title: Depressed HIPPO rep2

description: Library name: Depressed_HIPPO_rep2

value: Drepressed


title: Sham HIPPO rep1

description: Library name: Sham_HIPPO_rep1


title: Depressed HIPPO rep1

description: Library name: Depressed_HIPPO_rep1


title: Con HIPPO rep1

description: Library name: Con_HIPPO_rep1


title: T24Z3

description: Library name: Sample6


title: NSC HIPPO rep1

description: Library name: NSC_HIPPO_rep1

value: Drepressed+NSC


title: NSC HIPPO rep2

description: Library name: NSC_HIPPO_rep2


title: cornus4

city: Nanjing

first: po

last: hu

state: jiangsu

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

institute: 南京中医药大学

description:
Library name: sample12
cornus4_FPKM

data_processing:
Sequencing data contains a number of connectors, low-quality Reads, so we use fastp(0.22.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis .
The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2 (v2.1.0).
Use HTSeq (v0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Assembly: Ensembl
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: xls file includes FPKM values for each Sample

source_name: bone narrow cells

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies. Three micrograms of RNA were used as input material for the RNA sample preparations.
Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First strand cDNA was synthesized using random oligonucleotides and Super Script II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare forhybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA).DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

value: bone narrow cells

value: WT

value: cornus officinalis


title: ANSC HIPPO rep1

description: Library name: ANSC_HIPPO_rep1

value: Drepressed+ANSC


title: cornus3

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample11
cornus3_FPKM


title: ANSC HIPPO rep2

description: Library name: ANSC_HIPPO_rep2


title: cornus2

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample10
cornus2_FPKM


title: model4

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample8
model4_FPKM

value: CTX


title: cornus1

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample9
cornus1_FPKM


title: model2

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample6
model2_FPKM


title: model3

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample7
model3_FPKM


title: model1

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample5
model1_FPKM


title: control2

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample2
control2_FPKM


title: control4

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample4
control4_FPKM


title: control3

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample3
control3_FPKM


title: control1

address: 栖霞区 南京中医药大学 B3-F106（栖霞仙林校区）

description:
Library name: sample1
control1_FPKM