title: Control, tumor 5

city: Buffalo

first: Spencer

last: Rosario

address: Elm & Carlton Sts

institute: Roswell Park Comprehensive Cancer Center

description:
Library name: RS-04402146
raw_counts.txt sample RS-04402146

data_processing:
Raw reads that passed the Illumina RTA quality filter were demultiplexed and pre-processed using FastQC for sequencing base quality control.
Assembly: GRCh38/mm10
Supplementary files format and content: tab-delimited .txt file includes raw counts for each sample

source_name: Tumor

extract_protocol:
At the time of mouse tumor harvest, a fragment was flash frozen and was later used for RNA isolation using the miRNeasy mini kit (Qiagen).
The sequencing libraries were prepared with the RNA HyperPrep Kit with RiboErase (HMR) kit (Roche Sequencing Solutions), from 500ng total RNA. Following the manufacturer’s instructions.  The first step depletes rRNA from total RNA. After ribosomal depletion, the remaining RNA is DNase-digested to remove any gDNA contamination. Samples are then purified, fragmented, and primed for cDNA synthesis. Fragmented RNA is then reverse-transcribed into first-strand cDNA using random primers. The next step removes the RNA template and synthesizes a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA. Pure Beads (KAPA BIOSYSTEMS) are used to separate the ds cDNA from the second-strand reaction mix resulting in blunt-ended cDNA. A single ‘A’ nucleotide is then added to the 3’ ends of the blunt fragments. Multiple indexing adapters containing a single ‘T’ nucleotide on the 3’ end of the adapter are ligated to the ends of the ds cDNA preparing them for hybridization onto a flow cell. Adapter-ligated libraries are amplified by PCR purified using Pure Beads and validated for appropriate size on a 4200 TapeStation D1000 Screentape (Agilent Technologies, Inc.). The DNA libraries are quantified using KAPA Biosystems qPCR kit and are pooled together in an equimolar fashion, following experimental design criteria. Each pool is denatured and diluted to 350pM with 1% PhiX control library added. The resulting pool is then loaded into the appropriate NovaSeq Reagent cartridge for 100 paired-end sequencing and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).

treatment_protocol: Mice were treated with either vehicle or Liraglutide. Tumors were allowed to grow until they reached 2000 mm3 or the end of study. They were then harvested and snap fozen.

value: Tumor

value: lung adenocarcinoma

value: PBS


title: downstream migrant lamprey multiome 2 (ATAC)

status: Public on Aug 18 2025

type: SRA

city: Saint Louis

first: Joseph

middle: C.

last: Corbo

state: MO

address: 660 S. Euclid

department: Pathology and Immunology

country: USA

institute: Washington University School of Medicine

description:
Library name: dm2_ATAC
10x Genomics

library_source: genomic single cell

data_processing:
The sequence data were processed by the Cell Ranger ARC version 2.0.0 pipeline (10x Genomics) for read filtering, alignment against the genome, and barcode counting.
Assembly: kPetMar1
Supplementary files format and content: Tab separated files

molecule: genomic DNA

organism: Petromyzon marinus

source_name: retina

extract_protocol:
The retinas of downstream-migrant lamprey were dissected and snap-frozen. The frozen nuclei were extracted using the Chromium Nuclei Isolation Kit (10x Genomics) in accordance with the manufacturer's instructions.
From a single nuclei suspension, two replicates of the multiome library were constructed using the Chromium Next GEM Single Cell Multiome Reagent Kit version 1 (10x Genomics), following the manufacturer’s instructions.

tag: tissue

value: retina

tag: developmental stage

value: downstream migrant


title: 2d post infection, dsEcR, biol rep 3

city: Boston

first: Lisa

middle: H

last: Verzier

state: MA

address: 677 Huntington Avenue

department: Department of Immunology and Infectious Diseases

institute: Harvard University

description:
Library name: SN0268067_S4
10X Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcode pre-processing, gene counting and aggregation was performed using 10X Cell Ranger software v7.0.1.
Assembly: Anopheles gambiae PEST, version 58 (Vectorbase.org); Plasmodium falciparum 3D7, version 58 (PlasmoDB.org)
Supplementary files format and content: gzip compressed archive of tab separated values and matrix files

molecule: total RNA

organism:
Plasmodium falciparum
Anopheles gambiae

source_name: midgut

extract_protocol:
Freshly dissected midguts were kept on ice in PBS and blood bolus was removed when relevant. Sinlge cell isolation was performed by enzymatic digestion (1 mg/mL elastase and collagenase IV) for 30min at 30ºC shaking as well as mechanical disruption by pipetting. Cells were filtered sequentially in 70, 40 and 20 µm cell strainer (latest filtration was not performed for 7d samples), pelleted and resuspended in PBS.
Followed manufacturer's instruction (Chromium Next GEM Single Cell 3' Reagent Kit v3.1 (Dual Index) User Guide RevC)

value: midgut

tag: timepoint

value: 2 days post infectious blood meal

tag: treatment

value: dsEcR-injected

tag: batch

value: biol rep 3


title: Fertile male, TP1, fish 3_5

type: RNA

city: Aas

first: Aleksei

last: Krasnov

address: Osloveien 1

department: Fish Health

country: Norway

institute: Nofima AS

hyb_protocol: Labeled cRNA was hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Arrays were scanned with Agilent G2565BA DNA microarray scanner at a resolution of 5 microns

data_processing: Images were processed using the standard procedures of the Agilent Feature Extraction (FE) Software version 9.5.1. After removal of flagged spots lowess normalization was performed

organism: Salmo salar

source_name: Testis

label_protocol: RNA was amplified and labeled with Low Input Quick Amp Labeling Kit (Agilent).

growth_protocol: Salmon post smolts were kept in tanks within a flow-through system.

extract_protocol: Total RNA was extracted using the RNeasy® Mini Kit (Qiagen)

treatment_protocol: Fertile fish were compared with salmon sterilized by temporal silencing of dnd gene in embryos. Part of fish were exposed to handling stress and sampled after 24 h.

value: Testis


title: Control, tumor 4

description:
Library name: RS-04402145
raw_counts.txt sample RS-04402145

library_source: transcriptomic

organism: Mus musculus

tag: cell line

tag: cell type


title: GLP-1 Treated, tumor 1

description:
Library name: RS-04402147
raw_counts.txt sample RS-04402147

value: Liraglutide


title: Control, tumor 3

description:
Library name: RS-04402144
raw_counts.txt sample RS-04402144


title: 2d post infection, dsGFP, biol rep 3

description:
Library name: SN0268067_S3
10X Genomics

value: dsGFP-injected


title: Sterile female, TP1, fish 1_1

source_name: Ovary

value: Ovary


title: Sterile male, TP1, fish 5_7


title: Sterile female, TP1, fish 1_9


title: atp-2_20hrs_3

city: Taipei

first: Chun-Liang

last: Pan

address: Taipei , Taiwan (R.O.C.)

country: Taiwan

institute: National Taiwan University

data_processing:
Illumina GA Pipeline software bcl2fastq v2.20
A sample were expected to generate 60M sequence reads.
Qualified reads were analyzed using TopHat/Cufflinks  and gene expression level was quantified as TPM (Transcripts Per Million mapped reads)
Statistical analysis of gene expression profiles was done with CummeRbund.
The reference genome (WBcel235(GCA_000002985.3)) and gene annotations were retrieved from the Ensembl genome browser.
Assembly: WBcel235(GCA_000002985.3)
Supplementary files format and content: Excel file include TPM values for two samples

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: C. elegans were cultured on nematode growth medium with HT115 E. coli strain

extract_protocol:
RNA was extracted by GENEzol RNA Isolation Kit (Geneaid)
RNA libraries for RNA-seq were prepared by using Agilent's SureSelect Strand specific RNA Library Preparation Kit.

treatment_protocol: HT115 with construct which allowed the bacterial to express atp-2 dsRNA was fed to the wroms in the experimental group.

value: whole worms

tag: strain

tag: genotype

value: WT

value: HT115 expressing atp-2 double strain RNAi


title: Fertile male, TP1, fish 3_4


title: Control, tumor 2

description:
Library name: RS-04402143
raw_counts.txt sample RS-04402143


title: 20462X1_Liver_Control_ALF_replicate1

city: Salt Lake City

first: Amandine

last: Chaix

state: Utah

department: NUIP

institute: University of Utah

data_processing:
The mouse GRCm39 genome and gene annotation files were downloaded from Ensembl release 108
Optical duplicates were removed from the paired end FASTQ files using clumpify v38.34 and reads were trimmed of adapters using cutadapt 1.16
The trimmed reads were aligned to the reference database using STAR 2.7.9a in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes using featureCounts version 1.6
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.36.0
Assembly: GRCm39
Supplementary files format and content: FeatureCount output files combined into a single tab-delimited raw count matrix

source_name: liver

extract_protocol:
Trizol Chloroform
Intact poly(A) RNA was purified from total RNA samples (10-500 ng) using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490Stranded RNA sequencing libraries were prepared as described using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L).  Purified libraries were qualified on an Agilent Technologies 4150 TapeStation using a D1000 ScreenTape assay (cat# 5067-5582 and 5067-5583).  The molarity of adapter-modified molecules was defined by quantitative PCR using the Kapa Biosystems Kapa Library Quant Kit (cat#KK4824).  Individual libraries were normalized to 5 nM in preparation for Illumina sequence analysis.

treatment_protocol: 15 week old c57bl6j male mice were placed on one of 3 diets for 9 months, a 10% fat control diet, a 60% fat high fat diet, and an 89.9% fat ketogenic diet.

value: liver


title: Fertile male, TP1, fish 2_8


title: 7d post infection, dsGFP, biol rep 3

description:
Library name: SN0268067_S7
10X Genomics

value: 7 days post infectious blood meal


title: Fertile male, TP1, fish 3_1


title: 36h post infection, dsEcR, biol rep 3

description:
Library name: SN0268067_S2
10X Genomics

value: 36 hours post infectious blood meal


title: atp-2_20hrs_2


title: Control, tumor 1

description:
Library name: RS-04402142
raw_counts.txt sample RS-04402142

value: Tumor

value: lung adenocarcinoma

value: PBS


title: Fertile male, TP1, fish 2_3


title: L4440_20hrs_3

value: HT115 with empty vector


title: downstream migrant lamprey multiome 1 (ATAC)

description:
Library name: dm1_ATAC
10x Genomics

value: retina

value: downstream migrant


title: 36h post infection, dsGFP, biol rep 3

description:
Library name: SN0268067_S1
10X Genomics

value: midgut

value: biol rep 3


title: GLP-1 Treated, tumor 5

description:
Library name: RS-04402151
raw_counts.txt sample RS-04402151

value: Liraglutide


title: 7d post infection, dsEcR, biol rep 2

description:
Library name: SN0266774_S16
10X Genomics

value: dsEcR-injected

value: biol rep 2


title: Fertile female, TP1, fish 4_9

value: Ovary


title: L4440_20hrs_1

value: whole worms

value: WT


title: 7d post infection, dsGFP, biol rep 2

description:
Library name: SN0266774_S15
10X Genomics

value: dsGFP-injected


title: L4440_20hrs_2


title: Fertile male, TP1, fish 2_7

value: Testis


title: GLP-1 Treated, tumor 4

description:
Library name: RS-04402150
raw_counts.txt sample RS-04402150


title: GLP-1 Treated, tumor 3

description:
Library name: RS-04402149
raw_counts.txt sample RS-04402149


title: 4d post infection, dsEcR, biol rep 2

description:
Library name: SN0266774_S14
10X Genomics

value: 4 days post infectious blood meal


title: 2d post infection, dsEcR, biol rep 2

description:
Library name: SN0266774_S12
10X Genomics

value: 2 days post infectious blood meal


title: atp-2_0hr_2

value: HT115 expressing atp-2 double strain RNAi


title: Fertile female, TP1, fish 2_5


title: Fertile female, TP1, fish 4_7


title: atp-2_0hr_3


title: GLP-1 Treated, tumor 2

description:
Library name: RS-04402148
raw_counts.txt sample RS-04402148

value: Tumor

value: lung adenocarcinoma


title: BMDM_M1_wildtype_rep_12

city: München

first: Chenyu

last: Li

department: Medizinische Klinik und Poliklinik IV

country: Germany

institute: LMU Klinikum

data_processing:
Sequencing reads were trimmed and filtered using Trimmomatic(V0.39) to remove adapters and low quality reads.
Reads from mouse samples were mapped to Ensembl GRCm39 transcripts annotation (release 108), using hisat2 (2.2.1), samtools (1.16.1)  and featureCounts (2.0.3) with default settings.
Assembly: Ensembl GRCm39 (release 108)
Supplementary files format and content: counts_table.csv

source_name: Bone marrow-derived macrophage

growth_protocol: After obtaining femurs and tibiae from sacrificed mice by cervical dislocation, the bones were immersed in 75% ethanol for 1 minute before being stored in PBS. Removing the residual tissue from the bones, and the tibiae were separated from the femurs by gently breaking the knee joint. Then removing the terminal caps of the bones by sterile scissors and putting marrow cavity into the cavity to flush the bone marrow with PBS until the bone appeared white. The bone marrow was centrifuged 5-minute at 1,200 rpm for. Then 0.155 M NH4Cl was used to resuspend the pellet to lyse erythrocytes for 10 minutes on ice, passed through a 70µM strainer, and centrifuged 5-minute at 1,200 rpm. L929-conditioned Dulbecco's Modified Eagle Medium was used to suspend the pellet was and cells were grown in culture dishes in an incubator with 37°C, 5% CO2, and humidity control. Every 3 day the fresh medium added to the dishes, and after 7 days the cells were harvested for further experiment.

extract_protocol:
The RNA isolation procedure was carried out by following the Qiagen mRNA extraction kit instructions.
RNA libraries were prepared for sequencing using BGI protocols.

treatment_protocol: With or without 100ng/ml LPS + 10ng/ml INFγ

value: Bone marrow-derived macrophage

value: wildtype


title: Fertile female, TP1, fish 2_4


title: 4d post infection, dsGFP, biol rep 2

description:
Library name: SN0266774_S13
10X Genomics

value: midgut


title: 2d post infection, dsGFP, biol rep 2

description:
Library name: SN0266774_S11
10X Genomics


title: L4440_0hr_3

value: HT115 with empty vector


title: HFD

city: Bonn

first: Veronika

last: Lukacs-Kornek

address: Venusberg Campus 1

department: IMMEI

institute: University of Bonn

description: 10x Genomics

data_processing:
Data processing was done using PartekFlow (Illumina, USA)
raw sequencing data was trimmed to remove tags and aligned using STAR aligner
low-quality cells and doublets were removed. The counts below 20,000, features below 2600 and the percentage of mitochondrial genes below 10 % were kept. After quality control, cells were normalized using CPM in PartekFlow (Illumina, USA).
Filtering:Cells positive for: CD45, epcam, CD31, Sftpa1, Sftpc, Aqp5, Msln and Eno2 were filtered out.
Assembly: mm39
Supplementary files format and content: tab separated values file and matrix file after filtering

source_name: lung

extract_protocol:
Cells were analyzed by Azenta Life Sciences (Burlington, MA USA) using standard RNAseq pipeline.
According to manufactural´s guidlines 10x Genomics Single Cell 3′ v3 Reagent Kit

value: lung

value: fibrobalstic stroma

value: 16 wks high fat diet


title: Fertile female, TP1, fish 2_1

value: Ovary


title: Fertile female, TP1, fish 2_2


title: BMDM_M1_wildtype_rep_11


title: 36h post infection, dsEcR, biol rep 2

description:
Library name: SN0266774_S10
10X Genomics

value: 36 hours post infectious blood meal

value: dsEcR-injected

value: biol rep 2


title: maize,PP2CKO,rep3

city: Shenzhen

first: Mei

last: Luo

state: Gangdong

address: Dapeng

country: China

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

data_processing:
The steps of data processing were as follows: (1) Discard a paired reads if either one read contains adapter contamination; (2) Discard a paired reads if more than 10% of bases are uncertain in either one read; (3) Discard a paired reads if the proportion of low quality (Phred quality
Assembly: maize B73 v4 reference genome
Supplementary files format and content: Format: txt
Supplementary files format and content: Content: The processed data file contains reads numble for each sample. Rows represent genes, and columns represent individual samples.

organism: Zea mays

source_name: leaf

extract_protocol:
The expression level were tested between maize inbred line KN5585 (WT) and  ZmPP2C45 knock-out line.  Leaves of two-week-old maize seedlings were used for RNAseq analyses
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). 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. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified.
Six gigabytes of Illumina PE150 raw reads were obtained for each sample. After filtering out adaptor and low-quality reads, the cleaned reads were mapped to the B73 v4 reference genome using the STAR 2.4.0j software
After the library construction is completed, preliminary quantification is carried out using Qubit, and the library is diluted to 1.5ng/ul. Subsequently, the inserted fragments of the library are detected. Once the inserted fragments meet expectations, the effective concentration of the library is accurately quantified using qRT PCR to ensure the quality of the library. The qualified libraries were pooled and sequenced on sequencing platforms, according to effective library concentration and data amount required.
The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQ format (Cock P. et al, 2010), which contains sequence information and corresponding sequencing quality information.
Sequence artifacts, including reads containing adapter contamination, low-quality nucleotides and unrecognizable nucleotide (N), undoubtedly set the barrier for the subsequent reliable bioinformatics analysis. Hence quality control is an essential step and applied to guarantee the meaningful downstream analysis. we used Fastp (version 0.23.1)(Chen S. et al, 2018) to perform basic statistics on the quality of the raw reads.

treatment_protocol: Maize inbred line KN5585 was used as the genetic background for genome editing of ZmPP2C45.

value: leaf

value: PP2C Knockout


title: maize,PP2CKO,rep2

growth_protocol: Leaves of two-week-old maize seedlings were used for RNAseq analyses


title: 36h post infection, dsGFP, biol rep 2

description:
Library name: SN0266774_S9
10X Genomics

value: dsGFP-injected


title: BMDM_M1_RankCre-Regnaes3cKO_rep_9


title: BMDM_M1_wildtype_rep_10


title: NC

description: 10x Genomics

value: 16 wks normal chow


title: atp-2_54hrs

value: whole worms

value: WT

value: HT115 expressing atp-2 double strain RNAi


title: L4440_0hr_1


title: maize,PP2CKO,rep1


title: L4440_0hr_2


title: atp-2_24hrs


title: maize,KN5585,rep3


title: 7d post infection, dsEcR, biol rep 1

description:
Library name: SN0266774_S8
10X Genomics

value: 7 days post infectious blood meal

value: biol rep 1


title: L4440_48hrs

value: HT115 with empty vector


title: maize,KN5585,rep2


title: 4d post infection, dsEcR, biol rep 1

description:
Library name: SN0266774_S6
10X Genomics

value: midgut

value: 4 days post infectious blood meal


title: BMDM_M0_wildtype_rep_6

value: Bone marrow-derived macrophage

value: wildtype


title: BMDM_M1_RankCre-Regnaes3cKO_rep_7


title: 4d post infection, dsGFP, biol rep 1

description:
Library name: SN0266774_S5
10X Genomics


title: L4440_36hrs


title: maize,KN5585,rep1


title: BMDM_M0_wildtype_rep_5


title: Hela, SUV39H2_KO_15

city: Shanghai

first: Yuanyong

last: Huang

state: Shanghai

address: 500 Dongchuan Road, Shanghai,China

department: School of Life Science

institute: East China Normal University

data_processing:
raw reads were mapped by STAR-2.6.0c --runMode alignReads --runThreadN 6  --readMatesLengthsIn Equal --readFilesCommand 'zcat -1' --clip5pNbases 15 --clip3pNbases 0  --outSAMtype BAM Unsorted --outSAMstrandField intronMotif --outSAMreadID Number --outFilterMultimapNmax 10 --outFilterMismatchNmax 9 --outFilterMismatchNoverLmax 0.1 --outFilterMatchNminOverLread 0.3 --outFilterScoreMinOverLread 0.3 --alignEndsType EndToEnd
reads were counted by featureCounts -T 20 -s 0 -p -M -O --fraction -t exon  -g gene_id and  by normalized by FPKM
Assembly: GRCh38
Supplementary files format and content: txt file contain the gene FPKM

organism: Homo sapiens

source_name: HeLa

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
RNA was harvested using Trizol extraction kit from TAKARA (D9108A). 2 μg of total RNAs of G2E3 KO , sgG2E3 control HeLa cells and SUV39H2 KO , sgSUV39H2 control HeLa cells were sent to Novogene Corporation for RNA-seq.Same amount of spike-in yeast RNA was added to each RNA sample for RNA-seq normalization.
RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) . RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The G2E3 KO HeLa cells and SUV39H2 KO HeLa cells lines were obtained by the CRISPR-Cas9 system essentially as described (Ran et al., 2013) with the following guide RNAs: AACCAAGCGTTCTTACAACA for G2E3 and AGAATTGCTGAAGCAGTAAC for SUV39H2.

value: HeLa

value: epithelial cell

value: SUV39H2 knockout


title: L4440_24hrs


title: atp-2_36hrs


title: BMDM_M1_RankCre-Regnaes3cKO_rep_8


title: 2d post infection, dsEcR, biol rep 1

description:
Library name: SN0266774_S4
10X Genomics

value: 2 days post infectious blood meal

value: dsEcR-injected


title: 2d post infection, dsGFP, biol rep 1

description:
Library name: SN0266774_S3
10X Genomics

value: dsGFP-injected


title: BMDM_M0_wildtype_rep_4


title: BMDM_M0_RankCre-Regnaes3cKO_rep_3


title: HeLa, G2E3_KO_11

value: G2E3 knockout


title: BMDM_M0_RankCre-Regnaes3cKO_rep_2


title: P0, chicken, snATAC-seq

description:
Library name: P0 retina
10x Genomics

data_processing:
The raw sequence data were processed by the Cell Ranger ATAC version 2.0.0 pipeline (10x Genomics) for read filtering, alignment against the genome, and barcode counting.
Assembly: galGal6
Supplementary files format and content: Tab separated file and index file

organism: Gallus gallus

extract_protocol:
Chicks were euthanized by carbon dioxide inhalation followed by manual cervical dislocation. Chicken eyes were harvested and chicken retinas were removed from the eye by dissection, transferred to calcium and magnesium-free Hank’s balanced salt solution (Thermo Fisher Scientific) and dissociated into single cells by papain digestion. A single chick retina was incubated in 800 μl of HBSS with 1.3 mg of papain (Worthington Biochemical Corporation) at 37°C for 10 min. The retina was then dissociated by gentle trituration with a pipette. The dissociated cells were washed with Dulbecco’s Modified Eagle Media (DMEM; Thermo Fisher Scientific) containing 10% fetal bovine serum (Thermo Fisher Scientific) and DNaseI (Roche) for 5 min at 37°C. The cells were then pelleted by centrifugation at 1000xg for one minute. The cells were then resuspended in Dulbecco’s phosphate-buffered saline (DPBS) with 1% BSA and filtered for nuclei isolation. For nuclei isolation, the dissociated retinal cells were subjected to centrifugation at 300xg for 5 minutes at 4°C. The cell pellet was then resuspended in 100 µl of lysis buffer (0.1% IGEPAL CA-630, 0.1% Tween-20, and 0.01% digitonin in lysis dilution buffer [10 mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 1% BSA, pH 7.4]), mixed three times by pipetting, and incubated on ice for 3 min. Subsequently, the nuclei were added to 1 ml of wash buffer (0.1% Tween-20 in lysis dilution buffer) and centrifuged at 500xg for 5 min at 4°C. Finally, the nuclei pellet was resuspended in 50 µL of 1x Diluted Nuclei Buffer (10x Genomics) and filtered through a 40 µm Flowmi™ Cell Strainer. The nuclei were enumerated on a hemocytometer. The cell nuclei (~22,000 input nuclei) were then resuspended and used for transposition, subsequently loaded into the 10x Genomics Chromium Single Cell system.
One scATAC-seq library was constructed using the Chromium Single Cell ATAC Reagent Kits v1.1 (10x Genomics), following the manufacturer’s instructions.

value: retina


title: HeLa, G2E3_KO_10


title: 7d post infection, dsGFP, biol rep 1

description:
Library name: SN0266774_S7
10X Genomics


title: Hela, sgSUV39H2

value: WT


title: Aged_meningeal_cells

city: Daejeon

first: Cheolhwa

last: Jin

address: 291 Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description: Library name: Aged_CP

data_processing:
Aligned reads were processed to generate cell-gene raw expression matrices. Then, low quality cells (expressing less than 1200 genes) and potential dead cells (>10% mitochondrial gene percentage) were removed. Also, genes that are only expressed in less than 3 cells were discarded.
Expression matrices were made after quality control. Matrices were log normalized and variables such as number of UMIs and mitochondrial gene percentage were regressed out and scaled with Seurat (v3.1.1). After removing contaminating cells, dimensionality reduction and clusterings were performed to produce processed data files.
Identification of differentially expressed genes and downstream analysis were performed by Seurat.
Assembly: mm10
Supplementary files format and content: Seurat object file of meningeal cells from each dataset after quality control,  dimensionality reduction and clustering.

molecule: polyA RNA

source_name: Meninges

extract_protocol:
FACS sorted meningeal cells were processed by 10X chromium v3.1 kit following the manufacturer's protocols.
10X v3.1 reagent kits (10X genomics) were used to generate cDNA libraries.

value: Meninges

value: CD45 depleted meningeal cells


title: 36h post infection, dsGFP, biol rep 1

description:
Library name: SN0266774_S1
10X Genomics

value: 36 hours post infectious blood meal

value: biol rep 1


title: 36h post infection, dsEcR, biol rep 1

description:
Library name: SN0266774_S2
10X Genomics

value: midgut


title: Adult_meningeal_cells

description: Library name: Adult_CP


title: HeLa, sgG2E3


title: lamprey, retina, Iso-Seq

description: Library name: lamprey_retina_Iso-Seq

data_processing:
A multiplexed Iso-Seq library was sequenced across a single PacBio Sequel II SMRT cell. Demultiplexed PacBio circular consensus sequences (CCS) generated HiFi reads, with a predicted accuracy ≥Q20, were first processed using the IsoSeq (https://isoseq.how/) lima tool (v.2.4.0) for 5’ and 3’ primer removal with parameters (--iso-seq --peek-guess). The polyA tails and artificial concatemers were trimmed and removed using the isoseq3 (v.3.4.0)  refine tool (--require-polya) resulting in Full Length Non-concatemer Reads (FLNC). Clustering was performed using the partial order alignment (POA) algorithm using the isoseq3 cluster tool (--use-qvs).
For the identification of unidentified isoforms in the lamprey retina, the resultant high-quality consensus sequences were then mapped to the genome (kPetMar1) using minimap2 with the following parameters: -ax splice -u f. We then used StringTie v2.2.1 (with the command line option –L) to assemble a new transcriptome based on the mapped Iso-Seq reads. Subsequently, StringTie was run again (with the command line option "merge -F 0 -T 0") to obtain an updated transcriptome annotation. This annotation incorporated modifications to transcript body definitions from the existing NCBI RefSeq reference (GCF_010993605.1) and novel transcripts supported by the Iso-Seq reads.
Assembly: kPetMar1
Supplementary files format and content: gff format file with all transcripts assembles from RNA-Seq data
Library strategy: Iso-Seq

extract_protocol:
The total RNA was extracted using Trizol and purified using an RNeasy Mini Kit (QIAGEN). A SMRTbell Iso-Seq library was prepared according to the manufacturer’s protocol (Pacific Biosciences).
A multiplexed Iso-Seq library was sequenced across a single PacBio Sequel II SMRT cell.

value: adult

value: single


title: Mus musculus, bone marrow macrophage, UVAB5

status: Public on Aug 17 2025

city: Hangzhou

first: Songying

last: Zhang

address: No.3 Qingchun East Road

department: Department of Obstetrics and Gynecology

institute: Sir Run Run Shaw Hospital

description:
Library name: UVAB5
Column name in gene_count.txt: UVAB5

data_processing:
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
Assembly: mm39
Supplementary files format and content: reads count values of genes for each sample

source_name: bone marrow macrophage

extract_protocol:
RNA extraction library construction and sequencing Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library. After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA).
An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol

value: bone marrow macrophage

value: UVAB


title: Mus musculus, bone marrow macrophage, STSABs5

description:
Library name: STSABs5
Column name in gene_count.txt: STSABs5

value: STSABs


title: Mus musculus, bone marrow macrophage, UVAB4

description:
Library name: UVAB4
Column name in gene_count.txt: UVAB4


title: Mus musculus, bone marrow macrophage, UVABs1

description:
Library name: UVABs1
Column name in gene_count.txt: UVABs1

value: UVABs


title: Mus musculus, bone marrow macrophage, STSABs4

description:
Library name: STSABs4
Column name in gene_count.txt: STSABs4


title: Mus musculus, bone marrow macrophage, STSABs2

description:
Library name: STSABs2
Column name in gene_count.txt: STSABs2


title: Mus musculus, bone marrow macrophage, STSABs3

description:
Library name: STSABs3
Column name in gene_count.txt: STSABs3


title: BMDM_M0_RankCre-Regnaes3cKO_rep_1

value: Bone marrow-derived macrophage


title: v15, H9c2 cells, vehicle control group

city: Charlottesville

first: Anna

last: Licznerska

state: Virginia

address: 1340 Jefferson Park Avenue, Pinn Hall 5036

department: Pharmacology

institute: University of Virginia

description:
Library name: Sample 5
Column name in gene_count.xlsx and gene_fpkm.xlsx : v15

data_processing:
Data quality was performed and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. Clean raw reads were obtained by removing reads containing ploy-N, reads containing adapter, and low-quality reads from raw data. The mapped reads of each sample were assembled by StringTie (v1.3.3b) in a reference-based approach. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. FPKM values (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene were calculated based on the length of the gene and reads count mapped to this gene.
Assembly: ncbi_rattus_norvegicus_gcf_015227675_2_mratbn7_2
Supplementary files format and content: xlsx file contain raw counts for each sample
Supplementary files format and content: xlsx file contain FPKM values for each sample

organism: Rattus norvegicus

source_name: Heart; Myocardium

growth_protocol: H9c2 cells were cultured in 4.5 g/l D-glucose Dulbecco’s Modified Eagle Medium (DMEM) (Gibco) supplemented with 10% inactivated fetal bovine serum (FBS) (R&D Systems), 1% sodium pyruvate (Gibco), 2% sodium bicarbonate (Gibco) and 1% Penicillin-Streptomycin (Gibco) and grown at 37˚ C with 5% CO2. Cells were incubated on tissue-culture coated Petri Dishes (Genesee Scientific) and passaged when reached 80% confluency using 0.25% Trypsin+EDTA (Gibco). Cells used for the experiment were used at passage 6.

extract_protocol:
Approximately 75k x 10^3 H9c2 cells were lysed using RLT buffer overnight in the freezer. Supernatants were transferred to RNeasy Mini Spin Columns with fresh 70% ethanol and RNA isolation was performed as indicated by manufacture instructions (RNeasy Mini Kit – Qiagen). Collected RNA-rich samples were quantified using Nanodrope spectrophotometer (Thermo Fisher Scientific). Their purity was assessed by the spectroscopic ratio of 260/280 and 260/230 – accepted with values between 1.8-2.3. 250ng of total RNA was sent for processing by Novogene Company (Sacramento, CA) for Bulk RNA Sequencing.
Directional and non-directional library was constructed from purified messenger RNA. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

treatment_protocol: H9c2 cells were plated at 75 x 10^3cells/well in clear-bottomed 96-well plate. Following day, oxidized phospholipids were resuspended in DMEM medium at 100µg/ml and cells were treated with OxPAPC for 6h.

value: Heart; Myocardium

value: myoblast

value: no genetic modification

value: vehicle


title: Mus musculus, bone marrow macrophage, Con1

description:
Library name: Con1
Column name in gene_count.txt: Con1

value: Con


title: Mus musculus, bone marrow macrophage, LPS4

description:
Library name: LPS4
Column name in gene_count.txt: LPS4

value: LPS


title: ox16, H9c2 cells, OxPAPC-treated group

description:
Library name: Sample 6
Column name in gene_count.xlsx and gene_fpkm.xlsx : ox16

value: 100ug/ml OxPAPC for 6h


title: Mus musculus, bone marrow macrophage, LPS1

description:
Library name: LPS1
Column name in gene_count.txt: LPS1


title: Mus musculus, bone marrow macrophage, LPS3

description:
Library name: LPS3
Column name in gene_count.txt: LPS3


title: v22, H9c2 cells, vehicle control group

description:
Library name: Sample 7
Column name in gene_count.xlsx and gene_fpkm.xlsx : v22


title: Mus musculus, bone marrow macrophage, LPS2

description:
Library name: LPS2
Column name in gene_count.txt: LPS2


title: Mus musculus, bone marrow macrophage, Con2

description:
Library name: Con2
Column name in gene_count.txt: Con2


title: ox9, H9c2 cells, OxPAPC-treated group

description:
Library name: Sample 4
Column name in gene_count.xlsx and gene_fpkm.xlsx : ox9


title: v8, H9c2 cells, vehicle control group

description:
Library name: Sample 3
Column name in gene_count.xlsx and gene_fpkm.xlsx : v8


title: Mus musculus, bone marrow macrophage, UVABs3

description:
Library name: UVABs3
Column name in gene_count.txt: UVABs3


title: Mus musculus, bone marrow macrophage, UVABs2

description:
Library name: UVABs2
Column name in gene_count.txt: UVABs2


title: ox2, H9c2 cells, OxPAPC-treated group

description:
Library name: Sample 2
Column name in gene_count.xlsx and gene_fpkm.xlsx : ox2


title: Embryo15_6_KO

city: Charlestown

first: Charles

middle: H.

last: Adelmann

address: Mass Gen Hospital, 149 13th Street

department: Cutaneous Biology Research Center

institute: Massachusetts General Hospital

description: Library name: Embryo15_6_KO

data_processing:
Data were aligned with DRAGEN (Software build 07.031.677.4.2.4-4-gfc89cfd2). Provided cram files were coordinate-sorted as bams and gene assignment was performed with featureCounts from the Subread package. Cram files were converted to paired end fastq.gz files for SRA deposition.
Assembly: GRCm39,  GCF_000001635.27
Supplementary files format and content: Counts output file from featureCounts. TPM tables include post-processing to include only autosomal and protein coding transcripts.

source_name: whole embryo

growth_protocol: Timed mating of heterozygous Mfsd12 breeders. Embryo development was refined computationally using eMOSS

extract_protocol:
Samples were stored in TRIZOL, and total RNA was prepared via phase separation and precipitation.
Samples were prepared by the Broad Clinical Labs core using the Illumina TruSeq Stranded mRNA Sample Preparation Kit with External RNA Controls Consortium (ERCC) spike-ins. A total of 325 ng of RNA was used per sample.

value: whole embryo

value: Mfsd12 Knockout


title: Embryo4_3_WT

description: Library name: Embryo4_3_WT

value: Mfsd12 Wild-type


title: Embryo4_1_WT

description: Library name: Embryo4_1_WT


title: Mus musculus, bone marrow macrophage, STSABs1

description:
Library name: STSABs1
Column name in gene_count.txt: STSABs1


title: Mus musculus, bone marrow macrophage, LPS5

description:
Library name: LPS5
Column name in gene_count.txt: LPS5


title: CPZ_cKO 9

city: Sacramento

first: Hyun Kyu

last: Kim

state: CA

address: 2425 Stockton Blvd

department: Neurology

institute: UCDAVIS

description:
Library name: Sample 9
Cuprizone-treated Olig2-Cre Serpina3n flox/flox mice

data_processing:
1. Raw reads were processed with SOAPnuke for quality filtering.
2. Alignment to the Mus musculus genome was performed using Hisat2.
3. Quantification was done with RSEM to obtain TPM values.
4. Differential expression analysis was conducted using DESeq2.
5. PCA plots were generated for sample clustering.
Assembly: Mus_musculus_10090.NCBI.GCF_000001635.27_GRCm39.v2201
Supplementary files format and content: Files are provided in .tsv format containing TPM (Transcripts Per Million) values for each gene.

source_name: brain

growth_protocol: All animals were from C57BL/6 background and maintained in 12 h light/dark cycle with water and food. Animals and procedures in this study were approved by the Institutional Animal Care and Use Committee at the University of California, Davis.

extract_protocol:
Microglia were isolated from single-cell suspensions of mouse brains using the CD11b MicroBeads and magnetic-activated cell sorting (MACS) (Miltenyi Biotec) to ensure purity. RNA extraction was performed using the RNeasy Plus Micro Kit following the manufacturer's protocol. RNA quality was assessed using the Bioanalyzer 2100 system (Agilent Technologies), and all RNA samples had a RNA integrity number (RIN) greater than 6.8.
The cDNA library was prepared using the NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs).

treatment_protocol: Two-month-old mice were either fed a standard chow diet or a 0.25% cuprizone-enriched diet for 4 weeks to induce demyelination.

value: brain

value: microglia

value: Olig2-Cre Serpina3n flox/flox

value: cuprizone diet for 4 weeks


title: Embryo18_4_KO

description: Library name: Embryo18_4_KO


title: CPZ_cKO 8

description:
Library name: Sample 8
Cuprizone-treated Olig2-Cre Serpina3n flox/flox mice


title: Embryo18_5_WT

description: Library name: Embryo18_5_WT


title: CPZ_cKO 7

description:
Library name: Sample 7
Cuprizone-treated Olig2-Cre Serpina3n flox/flox mice


title: CPZ_cKO 10

description:
Library name: Sample 10
Cuprizone-treated Olig2-Cre Serpina3n flox/flox mice


title: Mus musculus, bone marrow macrophage, Con3

description:
Library name: Con3
Column name in gene_count.txt: Con3

value: bone marrow macrophage


title: ox23, H9c2 cells, OxPAPC-treated group

description:
Library name: Sample 8
Column name in gene_count.xlsx and gene_fpkm.xlsx : ox23


title: Embryo4_4_HET

description: Library name: Embryo4_4_HET

value: Mfsd12 Het


title: CPZ_Ctrl 6

description:
Library name: Sample 6
Cuprizone-treated wild-type mice

value: wild-type


title: Embryo4.1b_7_HET

description: Library name: Embryo4.1b_7_HET


title: Embryo14_4_HET

description: Library name: Embryo14_4_HET


title: CPZ_Ctrl 5

description:
Library name: Sample 5
Cuprizone-treated wild-type mice


title: Norm_Ctrl 3

description:
Library name: Sample 3
Normal control mice


title: v1, H9c2 cells, vehicle control group

description:
Library name: Sample 1
Column name in gene_count.xlsx and gene_fpkm.xlsx : v1

value: Heart; Myocardium


title: Norm_Ctrl 2

description:
Library name: Sample 2
Normal control mice


title: Embryo18_3_HET

description: Library name: Embryo18_3_HET


title: Embryo4_5_KO

description: Library name: Embryo4_5_KO


title: CPZ_Ctrl 4

description:
Library name: Sample 4
Cuprizone-treated wild-type mice


title: MOG_Ctrl_MG_3

description:
Library name: Sample 19
Microglia from EAE mice

data_processing:
1. Raw sequencing data was processed using Hisat2 for alignment to the reference genome.
2. Read counts were generated using featureCounts.
3. Normalization and differential expression analysis were performed using DESeq2.
4. Gene ontology and pathway enrichment analysis were conducted using clusterProfiler.
5. Visualization of results was done in R using ggplot2.
Assembly: Mus_musculus_10090.NCBI.GCF_000001635.27_GRCm39.v2201
Supplementary files format and content: Processed data files include: - Raw read counts in a CSV file. - Normalized expression matrices in TPM and FPKM formats. - Differential expression analysis results in CSV format, including log2 fold change and adjusted p-values. - Gene ontology and pathway enrichment results in text and graphical formats.

source_name: brain and spinal cord

extract_protocol:
Brain and spinal cord cell suspensions were prepared, and oligodendrocytes, astrocytes, and microglia were isolated using magnetic-activated cell sorting (MACS) with cell type-specific MicroBeads: oligodendrocyte: Anti-O4 MicroBeads, astrocyte: Anti-ACSA-2 (astrocyte cell surface antigen-2) MicroBeads, and microglia: Anti-CD11b MicroBeads. RNA extraction was performed using the RNeasy Plus Micro Kit following the manufacturer's protocol. RNA quality was assessed using the Bioanalyzer 2100 system (Agilent Technologies), and all RNA samples had a RNA integrity number (RIN) greater than 6.8.
The cDNA library was prepared using the NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs).

treatment_protocol: On day 0, three-month-old mice were administrated subcutaneously of 300 µg of rodent MOG peptide (35-55) emulsified in CFA containing 5 mg/mL killed Mycobacterium tuberculosis. On day 2, mice were intraperitoneally administrated of 200 ng of pertussis toxin. CFA control mice received only CFA and pertussis toxin, without MOG peptide.

value: brain and spinal cord

value: MOG


title: Mouse PTK Transgenic kidney 7-month, biol rep 3

city: BALTIMORE

first: KAUSHAL

middle: VIJAY

last: ASRANI

state: MD

address: 1550 ORLEANS

institute: JOHNS HOPKINS MEDICINE

description: Library name: A48_PTK_245

data_processing:
Sequencing reads were mapped to the mouse genome using STAR.v2.7.3a. All subsequent analyses were performed in R. Gene level abundance was quantitated using the GenomicAlignments Bioconductor package.
Assembly: hg19
Supplementary files format and content: Tab-delimited text files with raw counts.

source_name: Kidney

extract_protocol:
Total cellular RNA was extracted using RNeasy Mini kit (#74104, Qiagen) according to manufacturer’s instructions.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using randomhexamer primers, followed by the second strand cDNA synthesis.

value: Kidney

value: Renal

value: PRCC-TFE3; KSP-Cre


title: Norm_Ctrl 1

description:
Library name: Sample 1
Normal control mice


title: Embryo14_6_KO

description: Library name: Embryo14_6_KO


title: MOG_Ctrl_MG_2

description:
Library name: Sample 18
Microglia from EAE mice


title: Mouse PTK Transgenic kidney 7-month, biol rep 2

description: Library name: A47_PTK_646


title: Mouse PTK Transgenic kidney 7-month, biol rep 1

description: Library name: A46_PTK_512


title: CFA_Ctrl_MG_3

description:
Library name: Sample 16
Microglia from CFA control mice

value: CFA


title: Embryo18_2_WT

description: Library name: Embryo18_2_WT

value: whole embryo


title: MOG_Ctrl_MG_1

description:
Library name: Sample 17
Microglia from EAE mice


title: Mouse PT Normal kidney 7-month, biol rep 3

description: Library name: A45_PT_119


title: Mouse PT Normal kidney 7-month, biol rep 2

description: Library name: A44_PT_511


title: CFA_Ctrl_MG_1

description:
Library name: Sample 14
Microglia from CFA control mice


title: Mouse PT Normal kidney 7-month, biol rep 1

description: Library name: A43_PT_510R


title: Mouse STP Transgenic kidney 4-month, biol rep 3

description: Library name: A42_STP_536

value: SFPQ-TFE3; PAX8 ERT-cre

value: Tamoxifen treated SFPQ-TFE3-Pax8 ERT CRE


title: Mouse STP Transgenic kidney 4-month, biol rep 2

description: Library name: A41_STP_442


title: MOG_Ctrl_Astro_3

description:
Library name: Sample 12
Astrocytes from EAE mice

value: astrocyte


title: Mouse STP Transgenic kidney 4-month, biol rep 1

description: Library name: A40_STP_441


title: MOG_Ctrl_Astro_2

description:
Library name: Sample 11
Astrocytes from EAE mice


title: Mouse ST Normal kidney 4-month, biol rep 3

description: Library name: A39_ST_539R

value: Tamoxifen treated SFPQ-TFE3


title: Mouse ST Normal kidney 4-month, biol rep 2

description: Library name: A38_ST_538


title: Mouse ST Normal kidney 4-month, biol rep 1

description: Library name: A37_ST_537


title: CFA_Ctrl_Astro_2

description:
Library name: Sample 8
Astrocytes from CFA control mice


title: Mouse ST Normal kidney day 15, biol rep 3

description: Library name: A33_ST_31


title: Mouse STK transgenic kidney day 15, biol rep 2

description: Library name: A35_STK_29

value: SFPQ-TFE3; KSP-Cre


title: Mouse STK transgenic kidney day 15, biol rep 3

description: Library name: A36_STK_30


title: CFA_Ctrl_Astro_1

description:
Library name: Sample 7
Astrocytes from CFA control mice


title: MOG_Ctrl_Astro_1

description:
Library name: Sample 10
Astrocytes from EAE mice


title: Mouse STK transgenic kidney day 15, biol rep 1

description: Library name: A34_STK_26


title: tong cell, shMed23_a, H3K27ac (ChIP)

first: zhang

last: yiyang

address: 2005 Songhu Road, Yangpu District, Shanghai, China

institute: Fudan

description: Library name: H3K27ac_shMed23_a

library_source: genomic

data_processing:
ChIP-seq raw reads were obtained from an Illumina X-10 sequence analyzer. We utilized Fastqc (v0.1.0) for raw data quality summary. Cutadapt was used to remove sequencing adapters and poor-quality base trimming, retaining only reads with a quality score greater than 30 and discarding reads shorter than 50 bp or 75 bp for SE100 or PE150 reads, respectively. Clean reads were aligned to the human reference genome hg19, and the mapping results were normalized to FPKM (counts per million mapped reads per kilobase) and converted to bigwig files for visualization and by bamCoverage.
Assembly: hg19
Supplementary files format and content: Wig

source_name: Tong

growth_protocol: DMEM,10% fetal bovine serum. Cells were incubated at 37oC in 5% CO2 humidified air.

extract_protocol:
Briefly, cells were crosslinked with 0.9% formaldehyde for 9 min at room temperature, and formaldehyde was quenched by glycine at a final concentration of 125 μM for 5 minutes. Cells were washed twice with ice-cold PBS and collected by a cell scraper. Cell pellets were lysed and sonicated in lysis buffer (1% SDS, 50 mM Tris-HCl (pH 7.4), 10 mM EDTA), and the chromatin was fragmented into 200-500 bp fragments using a COVARIS S220 sonicator.
ChIP-seq libraries were prepared using a commercial kit (Vazyme, Nanjing, China, ND607)  following manufacturer's protocols.

value: Tong

value: Human hepatoma cell lines


title: tong cell, shctrl, H3K27ac (ChIP)

description: Library name: H3K27ac_shCtrl


title: DPE36_3, replicate 3, scRNAseq

first: Qili

last: Qian

address: 320 Yueyang Road

institute: SINH

description: 10X Genomics

data_processing:
Alignment of 3' end counting libraries from droplet-enabled scRNAseq analyses was completed utilizing 10x Genomics Cell Ranger 7.0.1
scRNA-seq
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skin

extract_protocol:
The skin was then minced into small pieces, approximately 1mm in width, and subjected to enzymatic digestion in 0.02% collagenase type I solution at 37℃ for 1 hour and  0.05% trypsin-EDTA for 15 minutes. 37℃.
library was performed according to the manufacter's instructions (single cell 3' v2 protocol, 10x Genomics). Briefly, single cell suspension were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscipted to cDNA, which contains an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated size fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: skin

value: Epithelial cells, mescenchymal cells, immune cells, etc

value: Wild type

value: For DPE36 samples, skin was harvested from mice after 36 days expansion and about 13 weeks of age using a 10-mm punch biopsy punch.


title: Mouse ST Normal kidney day 15, biol rep 1

description: Library name: A31_ST_27


title: tong cell, shMed23_b, H3K27ac (ChIP)

description: Library name: H3K27ac_shMed23_b


title: CFA_Ctrl_MG_2

description:
Library name: Sample 15
Microglia from CFA control mice

value: brain and spinal cord

value: microglia

value: wild-type


title: DPE8_3, replicate 3, scRNAseq

description: 10X Genomics

value: For DPE8 samples, skin was harvested from mice after 8 days expansion and about 9 weeks of age using a 10-mm punch biopsy punch.


title: tong cell, shMed23_b (Input)

description: Library name: Input_shMed23_b


title: MOG_Ctrl_OL_3

description:
Library name: Sample 6
Oligodendrocytes from EAE mice

value: oligodendrocyte

value: MOG


title: MOG_Ctrl_OL_1

description:
Library name: Sample 4
Oligodendrocytes from EAE mice


title: MOG_Ctrl_OL_2

description:
Library name: Sample 5
Oligodendrocytes from EAE mice


title: MOG_Ctrl_Astro_4

description:
Library name: Sample 13
Astrocytes from EAE mice


title: DPE36_1, replicate 1, scRNAseq

description: 10X Genomics


title: CFA_Ctrl_Astro_3

description:
Library name: Sample 9
Astrocytes from CFA control mice

value: CFA


title: DPE8_2, replicate 2, scRNAseq

description: 10X Genomics


title: Mouse ST Normal kidney day 15, biol rep 2

description: Library name: A32_ST_28

value: Kidney

value: Renal


title: CFA_Ctrl_OL_2

description:
Library name: Sample 2
Oligodendrocytes from CFA control mice


title: tong cell, shMed23_a (Input)

description: Library name: Input_shMed23_a


title: DPE8_1,replicate 1, scRNAseq

description: 10X Genomics


title: tong cell, shctr (Input)

description: Library name: Input_shCtrl


title: DPE36_2, replicate 2, scRNAseq

description: 10X Genomics


title: DPE0_3, replicate 3, scRNAseq

description: 10X Genomics

value: For control samples, skin was harvested from mice at 8 weeks of age using a 10-mm punch biopsy punch.


title: CFA_Ctrl_OL_1

description:
Library name: Sample 1
Oligodendrocytes from CFA control mice


title: tong cell, shMed23_b, IgG (ChIP)

description: Library name: IgG_shMed23_b


title: CFA_Ctrl_OL_3

description:
Library name: Sample 3
Oligodendrocytes from CFA control mice


title: DPE0_2, replicate 2, scRNAseq

description: 10X Genomics


title: DPE0_1, replicate 1, scRNAseq

description: 10X Genomics


title: VDJ_D16_LN_Tet_negative

city: La Jolla

first: Vijayanand

last: Pandurangan

state: California

address: 9420 Athena Circle

institute: La Jolla Institute For Immunology

description:
processed_data_umi_counts.txt
processed_data_normalized_counts.txt
processed_data_annotations.txt

data_processing:
Processing of the Single-Cell (sc)RNA-seq Libraries: Single-cell (sc)RNA-seq reads were demultiplexed into individual libraries (n=12) using Illumina’s bcl2fastq software (v2.19.0.316). These individual libraries were then processed with 10x Genomic’s Cell Ranger software (v3.1.0), utilizing the count module to align and map the reads to the mm10 reference mouse genome (v3.0.0). This process generated unique molecular identifier (UMI) counts for each cell barcode associated with each gene. Gene expression data from the individual libraries were subsequently aggregated into a single dataset that included both tetramer-positive and tetramer-negative cells. The Seurat toolkit (v3.1.5) was employed for the analysis of the aggregated scRNA-seq dataset. Genes expressed by fewer than 0.1% of cells in the dataset were excluded from the analysis. T-cell receptor (TCR) annotations were performed as a distinct step (detailed below). To reduce the occurrence of potential doublets and low-quality transcriptomes, cell barcodes that did not meet the following criteria were filtered out: UMI counts between 500 and 15,000, gene counts between 300 and 4,500, and a mitochondrial UMI percentage not exceeding 10%. The aggregated dataset was normalized using the NormalizeData function in Seurat (default parameters). The most variable genes were identified as those with a mean UMI capture greater than 0.01, contributing to 25% and 10% of the total standardized variance in the aggregate dataset. This selection was performed using the variance-stabilizing transformation method through the FindVariableFeatures function (default parameters). Data scaling was executed using the ScaleData function, with custom variables regressed out via the vars.to.regress parameter. Cell clusters were determined within the aggregated dataset using the FindNeighbors and FindClusters functions, primarily with default parameters, except for the number of principal components (PCs; PCs=20) and the resolution parameter (res). The RunUMAP function was applied with the top 40 PCs, 15 neighboring points for local approximations of the manifold structure, and a minimum distance of 0.1 (specified as arguments dims, n.neighbors, and min.dist, respectively) to compute manifold approximation and projection (UMAP) embeddings.
Processing of the sc-T-cell Receptor (TCR)-seq Libraries: Single-cell (sc)TCR sequence libraries were processed using Cell Ranger’s VDJ software (v3.1.0). The reads were aligned and mapped to the genome using the GRCm38 reference annotations (v3.1.0). The assembly of V(D)J transcripts and their annotations were performed for each independent library. To enable integrated analysis of scRNA-seq and scTCR-seq data from the same cells, V(D)J libraries were initially aggregated using a custom script. Clonotypes, as defined by 10x Genomics as sets of productive Complementarity-Determining Region 3 (CDR3) sequences, were identified within each library. The frequencies and proportions of the clonotypes were calculated based on the aggregated results, considering only the cells present in the gene expression libraries. This procedure was independently applied to data from both Tet-negative and Tet-positive cells.
Assembly: mm10
Supplementary files format and content: processed_data_umi_counts.txt: This file contains a matrix of raw UMI counts for the aggregated dataset of tet-positive and tet-negative T cells, representing gene expression data. The matrix is formatted as tab-separated values, with each column corresponding to a single cell (identified by 10x cell barcodes) and each row corresponding to a gene (identified by Ensembl IDs).
Supplementary files format and content: processed_data_normalized_counts.txt: This file contains a matrix of non-scaled normalized UMI counts (extracted from the Seurat object's "data" slot) for the aggregated dataset of tet-positive and tet-negative T cells, representing gene expression data. The matrix is formatted as tab-separated values, with each column corresponding to a single cell (identified by 10x cell barcodes) and each row corresponding to a gene (identified by Ensembl IDs).
Supplementary files format and content: processed_data_annotations.txt: This file contains metadata, including all previously detailed annotations for the aggregated dataset of tet-positive and tet-negative T cells. The data is provided as tab-separated values, with each column representing a metadata annotation (column names are mostly self-explanatory; any questions can be addressed through our GitHub repository as mentioned in the manuscript). Each row corresponds to a cell barcode. Relevant TCR-related annotations are also included in this file.

source_name: Inguinal lymph node

growth_protocol: C3H SCC VII  cells were maintained in RPMI 1640 supplemented with 12.5% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
10x Genomics' Single Cell Immune Profiling 5'v2
All Libraries were prepared according to manufacturer's recommendations using 10x Genomics' Single Cell Immune Profiling 5'v2 (Dual Index).
Gex and and V(D)J scRNA-Seq  library preparation

treatment_protocol:
500,000 SCC VII tumor cells were injected s.c. into the left flank 17 days prior to harvest.
The inguinal lymph node was surgically removed, ground through a 70um filter, and the cells washed before staining to allow for sorting for tetramer+ and tetramer- CD4+ T cells

value: Inguinal lymph node

value: Baseline C3H murine CD4+ T cells


title: tong cell, shMed23_a, IgG (ChIP)

description: Library name: IgG_shMed23_a

value: Tong

value: Human hepatoma cell lines


title: CPZ_Ctrl_Ast_3

description:
Library name: Samples 13
cuprizone diet for 4 weeks

extract_protocol:
Brain cell suspensions were prepared, and oligodendrocytes and astrocytes were isolated using magnetic-activated cell sorting (MACS) with cell type-specific MicroBeads: oligodendrocyte: Anti-O4 MicroBeads, astrocyte: Anti-ACSA-2 (astrocyte cell surface antigen-2) MicroBeads. RNA extraction was performed using the RNeasy Plus Micro Kit following the manufacturer's protocol. RNA quality was assessed using the Bioanalyzer 2100 system (Agilent Technologies), and all RNA samples had a RNA integrity number (RIN) greater than 6.8.
The cDNA library was prepared using the NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs).

treatment_protocol: Two-month-old mice were fed either a standard chow diet or a 0.3% cuprizone-enriched diet for 4 weeks to induce demyelination.

value: brain

value: astrocyte

value: cuprizone diet for 4 weeks


title: D10_ICM_replicateMix

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

data_processing:
Read1(10bp of UMI + 9bp of barcode) was assigned to Read2(insert read) by following command "umi_tools extract -I read1.fastq --read2-in=read2.fastq --bc-pattern=NNNNNNNNNNCCCCCCCCC".
Adaptor sequence and low quality sequence were removed and read length below 20bp were discarded by using Trim Galore (ver.0.6.7).
Reads were mapped to the GRCh38 reference using HISAT2 (ver.2.2.1).
Gene count was obtaind by featureCounts(ver.2.0.1) and UMI duplication was ramoved by using UMI tools (ver.1.1.1).
Assembly: GRCm38
Supplementary files format and content: Gene count

extract_protocol:
ICM or TE was dissected from diapause embryo and lysed in 6uL of 1x direct lysis buffer(TaKaRa, #635013) including RNase Inhibitor(TaKaRa,#2313A). 3uL of lysate was used for reverse transcription.
Libraries were prepared by BRB-Seq(Alpern D, et al.) method. Individual samples were reverse transcribed using dT primer with unique cell barcodes. Then replicate were mixed and amplified by PCR. 10nt of UMI followedby 9nt of cell barcode are in read1 and 81nt of RNA insert reads are in read2.

value: Embryo from a cross between a B6D2F1 male and an ICR female

value: mouse embryo

value: WT

tag: time


title: GEX_D16_LN_Tet_positive


title: D10_TE_replicateMix


title: CPZ_Ctrl_Ast_2

description:
Library name: Samples 12
cuprizone diet for 4 weeks

value: wild-type


title: CPZ_Ctrl_Ast_1

description:
Library name: Samples 11
cuprizone diet for 4 weeks


title: GEX_D16_LN_Tet_negative


title: tong cell, shMed23_b, H3K4me1 (ChIP)

description: Library name: H3K4me1_shMed23_b


title: Naive_Ast_3

description:
Library name: Samples 10
normal diet

value: normal diet


title: tong cell, shctrl, IgG (ChIP)

description: Library name: IgG_shCtrl


title: E4_TE_replicateMix


title: hHOs, TP3

city: Nanjing

first: hao

last: sun

state: None Selected

address: longmian street

institute: nanjng medical university

data_processing:
Perl script was used to filter the original data (Raw Data).
Remove the contaminated reads for adapters (The contaminated reads for adapters was defined that the Read Bases contained more than 5bp of adapter sequences. If either one of the PE Reads was polluted, we will remove both ends of the reads)
Remove the low quality reads (The low quality reads was defined that the number of Reads Bases whose phred Quality value was less than or equal to 19 accounted for more than 15% ;Remove the reads whose N base more than 5% for total bases
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to GRCh37/hg19 using HISAT2 v2.1.0
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: heart

extract_protocol:
Total RNA was isolated and purified using GeneJET RNA Purification Kit (Thermo Fisher).
According to the operating instructions of VAHTS Universal V6 RNA-Seq Library Prepkit for Illumina (NR 604-01/02), different index tags were selected to establish the database.

value: hHOs

value: POEA


title: E4_ICM_replicateMix


title: tong cell, shMed23_a, H3K4me1 (ChIP)

description: Library name: H3K4me1_shMed23_a


title: tong cell, shctrl, H3K4me1 (ChIP)

description: Library name: H3K4me1_shCtrl


title: hHOs, TP2


title: Naive_Ast_2

description:
Library name: Samples 9
normal diet


title: CPZ_Ctrl_Ast_4

description:
Library name: Samples 14
cuprizone diet for 4 weeks


title: Naive_Ast_1

description:
Library name: Samples 8
normal diet


title: VDJ_D16_LN_Tet_positive


title: CIH-hippocampus 2-miRNA

city: Chongqing

first: Bing

address: Chongqing medical university

department: Department of ENT

institute: First Affiliated Hospital of Chongqing Medical University

description: CIH 2

data_processing:
BGISEQ-500/ MGISEQ-2000system (BGI Co., Shenzhen, China) was used to obtain raw data.
Both RNA-seq and miRNA-seq, Sequence reads were filtering for adaptor sequenc/low-quality sequence using DNBSEQ (parameter- Sequencing length: PE100+50)
Gene differential expression was compared between different samples.
For RNA-seq: Bowtie2, v2.2.5(parameters:q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200) and RSEM:v1.2.12(parameters:--forward-prob 0);
For miRNA-seq: Bowtie2, v2.2.5(parameters:-q -L 16 --phred64 -p 6), except that Rfam is compared with CMsearch(parameters --cpu 6 --noali)
Read Alignment software
For RNA-seq：：HISAT v2.2.0(parameters:--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8) and Bowtie2, v2.2.5(parameters:-q -L 16 --phred64 -p 6);
For miRNA-seq：HISAT v2.2.0(parameters:--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8)
Assembly: Rnor_6.0
Supplementary files format and content: text files include fpkm (and other) values for each sample.

source_name: hippocampus

extract_protocol:
The total RNA was harvested using TRIzol reagent (Invitrogen, Carlsbad, CA, USA)
libraries were measured using BGISEQ-500/ MGISEQ-2000system (BGI Co., Shenzhen, China).

value: hippocampus

tag: Sex

value: male

value: CIH for 4 weeks


title: EWS CAR

city: New Haven

first: Xinyan

state: CT

address: 333 Cedar St

institute: Yale University

description:
10xgenomics
Sample3-90

data_processing:
Single cell RNA-sequencing reads were processed using Cell Ranger software (10xGenomics,  version 7.2.0) with standard parameters and aligned to human reference transcriptome (GRCh38).  Gene expression comparison was performed using Loupe Browser (10xGenomics, version 7.0.0)  and cluster annotation was performed manually based on marker gene expression.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMC

extract_protocol:
In the CD19 CAR-T cancer model, mice blood was collected from  tail vein at day 43 post CAR-T cell treatment. Mice peripheral blood  mononuclear cell (mPBMC) was isolated after red blood cells were  lysed. Anti-human CD3 and CD45 antibodies were used to identify T cell population. T cells freshly sorted from mPBMC were subjected to RNA-seq library preparation by Chromium next GEM single cell 3’ reagent kits v3.1 (dual index).
Briefly, in step 1, after preparing fresh master mix, single cell suspension  (10,000 cells per sample), and gel beads, GEMs were generated by  combining the prepared master mix containing cells, gel beads and  partitioning oil onto chromium next GEM chip G in the chromium controller.  Immediately after GEM generation, GEMs were transferred to PCR tubes  to run GEM-RT incubation. In step 2, post GEM RT cleanup was performed with dynabeads, which was followed by cDNA amplification and cDNA cleanup with SPRlselect. The purified cDNA was quantified using BioAnalyser. In step 3, cDNA amplicon size was further optimized by enzymatic fragmentation and size selection. P5, P7, i7 and i5 sample indexes, and TruSeq read 2 were added via end pair, A tailing, adaptor ligation and PCR. A post-library-construction QC was run. In step 4, the chromium single cell 3’ gene expression dual index library containing standard illumina paired-end constructs which begin and end with P5 and P7 were sequenced by a Hiseq 2500 RapidRun. The 16bp 10x Barcode and 12bp UMI were encoded in read 1, and read 2 is used to sequence the cDNA fragment. I7 and i5 index sequences were incorporated as the sample index reads.

treatment_protocol: To generate liquid cancer models, 1 million of Raji B or Naml6 cells  in 100 uL of PBS were intravenously injected into the NSG (NOD. Cg-Prkdcscid Il2rgtm1Wjl/SzJ) mice (~6 weeks old) via tail vein.  Three days later, 8 million of CAR T cells in 100 uL PBS were injected by tail vein.

value: PBMC

value: Primary T cells

value: Immune cells

value: CAR engineered

value: Lentivirus transduction


title: hHOs, TP1


title: CPZ_Ctrl_OL_4

description:
Library name: Samples 7
cuprizone diet for 4 weeks

value: brain

value: oligodendrocyte


title: FUS CAR

description:
10xgenomics
Sample2-88


title: CIH-hippocampus 1-miRNA

description: CIH 1


title: CPZ_Ctrl_OL_3

description:
Library name: Samples 6
cuprizone diet for 4 weeks

value: cuprizone diet for 4 weeks


title: Control CAR

description:
10xgenomics
Sample1-848


title: Control-hippocampus 3-miRNA

description: C 3

value: normoxia for 4 weeks


title: hHOs, TGP3

value: Gly and POEA


title: Control-hippocampus 2-miRNA

description: C 2


title: liver tissues from Med23f/f mice 48 hours after DEN treatment, rep3

description: Library name: WT_3

data_processing:
Pair-ended sequencing was performed on an Illumina HiSeq 2500 using bar-coded multiplexing and a 150-bp read length, yielding a median of 34.1 M reads per sample.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: liver

growth_protocol: All animals were maintained in grouped cages in a temperature-controlled, pathogen-free facility on a 12/12-hr light/dark cycle and fed by a standard chow diet.

extract_protocol:
Total RNA was extracted from liver tissues using Trizol.
Libraries were prepared from 150 ng of total RNA (TruSeq v2, Illumina).

treatment_protocol: Mice were intraperitoneally injected with diethylnitrosamine (DEN) at a dose of 50 mg/kg body weight. Liver tissues were collected 48 hours post-injection from both Med23f/f (control) and Med23Δli mice for RNA extraction.

value: liver


title: hHOs, TGP1


title: liver tissues from Med23f/f mice 48 hours after DEN treatment, rep4

description: Library name: WT_4


title: CPZ_Ctrl_OL_2

description:
Library name: Samples 5
cuprizone diet for 4 weeks

value: wild-type


title: hHOs, TGP2

value: hHOs


title: CPZ_Ctrl_OL_1

description:
Library name: Samples 4
cuprizone diet for 4 weeks


title: hHOs, TG3

value: Gly


title: CIH-hippocampus 3-miRNA

description: CIH 3

value: hippocampus


title: hHOs, TG2


title: CIH-hippocampus 3-RNA

description: CIH 3

value: male


title: liver tissues from Med23f/f mice 48 hours after DEN treatment, rep2

description: Library name: WT_2


title: Control-hippocampus 1-miRNA

description: C 1


title: liver tissues from Med23f/f mice 48 hours after DEN treatment, rep1

description: Library name: WT_1


title: CIH-hippocampus 2-RNA

description: CIH 2

value: CIH for 4 weeks


title: Naive_OL_2

description:
Library name: Samples 2
normal diet

value: normal diet


title: hHOs, TG1


title: liver tissues from Med23Δli mice 48 hours after DEN treatment, rep4

description: Library name: KO_4


title: CIH-hippocampus 1-RNA

description: CIH 1


title: hHOs, C3

value: untreated (control)


title: Naive_OL_1

description:
Library name: Samples 1
normal diet


title: Control-hippocampus 3-RNA

description: C 3


title: hHOs, C2


title: liver tissues from Med23Δli mice 48 hours after DEN treatment, rep2

description: Library name: KO_2


title: hHOs, C1


title: Ctrl_MOG

description:
Library name: Sample 2
10x genimocs

data_processing:
1. Sequencing reads were processed using the Cell Ranger software (v6.1.2) for demultiplexing and alignment.
2. Gene expression matrices were generated and filtered for valid barcodes.
3. SCTransform normalization was applied using Seurat (v3.0.2).
4. Dimensionality reduction was performed using PCA and UMAP clustering.
5. Differential gene expression analysis was conducted using the Wilcoxon rank-sum test.
Assembly: Mus_musculus_10090.10Xgenomic.refdata-gex-mm10-2020-A.v2005
Supplementary files format and content: 1. Raw data files: FastQ format (paired-end reads, PE120).
Supplementary files format and content: 2. Processed data files: Gene expression matrices in H5 and Loom format for downstream analysis.

source_name: spinal cord

extract_protocol:
Cells were lysed, and RNA was extracted using the Qiagen RNeasy Micro Kit following the manufacturer's protocol.
Libraries were constructed using the 10x Genomics Chromium Single Cell 3' Library & Gel Bead Kit v3 according to the manufacturer's guidelines.

value: spinal cord

value: MOG


title: liver tissues from Med23Δli mice 48 hours after DEN treatment, rep3

description: Library name: KO_3


title: Ctrl_CFA

description:
Library name: Sample 1
10x genimocs

value: CFA


title: Naive_OL_3

description:
Library name: Samples 3
normal diet

value: brain


title: mice, mPFC, LINC02449-rs149707223_Ref-C OE, rep3

status: Public on Aug 16 2025

city: Guangzhou

first: 杨

last: 腾飞

address: No.1023,South Shatai Road, BaiyunDistrict

department: Medical Genetics

institute: Southern Medical University

description: Library name: mice-AAV-Lnc-Ref-C-3

data_processing:
The raw sequencing data obtained from the Illumina platform, referred to as Raw Reads, undergoes data processing to generate high-quality sequences, known as Clean Reads. This processing involves the removal of low-quality sequences and the elimination of adapter contamination. The Clean Reads are then aligned to the hg19 reference genome using the STAR aligner with default parameters. Quantification is performed using FeatureCounts, resulting in the generation of Counts and FPKM values.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM or Count values.

source_name: mPFC in brain

growth_protocol: Mice were group housed in standard housing under 12–12 hr light–dark cycle and ad libitum access to water and standard chow unless noted otherwise.  Room temperature was kept at around 22 °C and humidity between 30–80% (not controlled).  Mice were kept in an EVC cage with nesting material.

extract_protocol:
The mPFC of C57BL/6J mice were removed and the tissues were ground. And RNA was harvested by the phenol-chloroform method using TRIZOL (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
Using magnetic beads coated with Oligo(dT), mRNA with polyA tails is enriched and purified from RNA samples. Fragmentation Buffer is then added to the purified mRNA to fragment it. The resulting RNA fragments serve as templates for the reverse transcription process, utilizing random primers to synthesize the first strand of cDNA. Subsequently, a 2nd Strand Marking Buffer and a 2nd Strand/End Repair Enzyme Mix are introduced to synthesize the second strand of cDNA. Following this, end repair is performed, an adenine base is added, and sequencing adapters are ligated. The target fragments are then recovered through magnetic bead selection and subjected to PCR amplification, thereby completing the entire library preparation process.

treatment_protocol: The generated AAV were from BrainVTA (Wuhan), strains were maintained on C57BL/6J background. Male C57BL/6 mice, aged 6-8 weeks, were injected with AAV virus in bilateral mPFC for 3 weeks.

value: mPFC in brain


title: mice, mPFC, LINC02449-rs149707223_Alt-G OE, rep2

description: Library name: mice-AAV-Lnc-Alt-G-2


title: liver tissues from Med23Δli mice 48 hours after DEN treatment, rep1

description: Library name: KO_1


title: mice, mPFC, LINC02449-rs149707223_Alt-G OE, rep1

description: Library name: mice-AAV-Lnc-Alt-G-1


title: Serpina3n cKO_MOG

description:
Library name: Sample 3
10x genimocs

value: Olig2-Cre Serpina3n flox/flox


title: Control-hippocampus 1-RNA

description: C 1

value: normoxia for 4 weeks


title: Control-hippocampus 2-RNA

description: C 2


title: mice, mPFC, LINC02449-rs149707223_Ref-C OE, rep2

description: Library name: mice-AAV-Lnc-Ref-C-2


title: mice, mPFC, AAV, rep2

description: Library name: mice-AAV-2

value: WT


title: mice, mPFC, AAV, rep1

description: Library name: mice-AAV-1


title: mice, mPFC, LINC02449-rs149707223_Ref-C OE, rep1

description: Library name: mice-AAV-Lnc-Ref-C-1


title: HS294T_control biol rep 2

city: Warsaw

first: Tomasz

last: Kobiela

address: Noakowskiego 3

department: Faculty of Chemistry

country: Poland

institute: Warsaw University of Technology

description:
Library name: S8
Column name in raw_counts_All_Samples.txt: S8

data_processing:
Quality control of raw reads was performed using FastQC (v0.12.1)
Adapter trimming was performed using fastp (v0.24.0)
Cleaned reads were aligned to the human reference genome using the STAR aligner (v2.7.11b).
Aligned reads were counted together as fragments using featureCounts from the Subread package (v2.0.8).
Assembly: GRCh38 Release 47
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

growth_protocol: All melanoma cells were maintained in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 4.5 g/l glucose, 1.5 g/l NaHCO3, 2 mM glutamine, an antibiotic-antimycotic solution, and 10% fetal bovine serum. Cells were passaged using 0.25% trypsin/0.05% EDTA solution.

extract_protocol:
For RNA extraction, the culture medium was removed, and the cells were washed twice with 3 - 5 mL of PBS. After the final wash, 0.5 mL of TRIzol reagent was added, and the cells were scraped from the plate. The suspension was pipetted 12 - 15 times to ensure homogeneity and transferred to an RNase-free Eppendorf tube, which was labeled and stored at –80 °C.
RNA libraries for RNA-seq were prepared using KAPA Stranded mRNAseq Kit following manufacturer's protocols.

treatment_protocol: Resistance was induced by gradually increasing the concentrations of vemurafenib (Santa Cruz Biotechnology) and cobimetinib (Selleck Chemicals LLC) in the culture medium. The final concentrations used were 0.4 µM for both vemurafenib and cobimetinib. In parallel, the control Hs294T and WM9 cells were incubated with increasing concentra-tions of the solvent for the inhibitors - dimethyl sulfoxide (DMSO; AppliChem GmbH).

value: metastatic melanoma cell

value: BRAF; Simple; p.Val600Glu

value: control


title: HS294T_control biol rep 1

description:
Library name: S7
Column name in raw_counts_All_Samples.txt: S7


title: WM9_resistant biol rep 2

description:
Library name: S5
Column name in raw_counts_All_Samples.txt: S5

value: resistant


title: HS294T_resistant biol rep 1

description:
Library name: S10
Column name in raw_counts_All_Samples.txt: S10


title: HS294T_resistant biol rep 2

description:
Library name: S11
Column name in raw_counts_All_Samples.txt: S11


title: WM9_resistant biol rep 1

description:
Library name: S4
Column name in raw_counts_All_Samples.txt: S4


title: WM9_control biol rep 2

description:
Library name: S2
Column name in raw_counts_All_Samples.txt: S2


title: WM9_control biol rep 3

description:
Library name: S3
Column name in raw_counts_All_Samples.txt: S3


title: WM9_resistant biol rep 3

description:
Library name: S6
Column name in raw_counts_All_Samples.txt: S6


title: HS294T_control biol rep 3

description:
Library name: S9
Column name in raw_counts_All_Samples.txt: S9


title: WM9_control biol rep 1

description:
Library name: S1
Column name in raw_counts_All_Samples.txt: S1


title: HS294T_resistant biol rep 3

description:
Library name: S12
Column name in raw_counts_All_Samples.txt: S12


title: IgG_APH_rep3

first: Kun

last: Sun

state: Guangdong

address: Rm A1921, Guangming International Innovation Center,

institute: Shenzhen Bay Laboratory

description: Library name: IgG_APH_rep3

data_processing:
Raw sequencing reads were first preprocessed using Ktrim software to remove sequencing adaptors and low-quality cycles. The preprocessed reads were then aligned to NCBI GRCh38 reference human genome using Bowtie2 software. PCR duplicates (i.e., reads with identical start and end positions) were identified and removed using in house programs. Reads from mitochondrial chromosome were also removed and the remaining were kept for downstream analyses ("clean reads").
For DSMO and APH treatments, data from IgG experiments were used as controls to call peaks for Lamin A/C and B1 using MACS2 software, respectively. Peaks with adjusted p-values lower than 0.01 were considered as statistically significant. CUT&Tag signals around the peaks were visualized using deptools software.
We first stitched the peaks in the Lamin A/C or B1 that were less than 20kb in distance, and only kept those longer than 100 kb after stitching. For each kept peak after stitching, we extracted the read numbers in the CUT&Tag experiments, which were further normalized using the clean read count of the corresponding experiments. The normalized read counts were compared between DMSO and APH experiments using t-tests for Lamin A/C and B1 (each had 3 replicates), respectively. The p-values were corrected using Benjamini & Hochberg method, and peaks with adjusted p-values lower than 0.05 in both Lamin A/C and B1 were called as RESS-LAD regions. An implementation of this approach was publicly available at https://github.com/hellosunking/RESS-LADs.
Assembly: hg38
Supplementary files format and content: BED, peaks
Library strategy: CUT&Tag

growth_protocol: HCT116 cells were maintained Dulbecco's Modified Eagle Medium (DMEM)/Nutrient Mixture F-12 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin and streptomycin (Gibco)

extract_protocol:
We perform Cleavage under targets and tagging (CUT&Tag) using Hieff NGS® G-Type In-Situ DNA Binding Profiling Library Prep Kit (Yeasen, Cat#12598ES48) against lamin A/C and lamin B1 following to the manufacture’ s instruction. Briefly, for each sample, 100.000 cells were harvested after treatment with/without 0.4 μM APH for 48 hour and washed three times by PBS, resuspend  the cells with cell wash buffer gently, and incubate  with the concanavalin A coated magnetic beads previously washed by ConA bind buffer. Then concanavalin A beads coupled cells were collected and incubated with 2 μg primary antibody (mouse anti lamin A/C (Santa Cruz, Cat#sc-7292) or rabbit anti-lamin B1 (Abcam, Cat#ab16048)) and rabbit anti IgG (Thermo ) at 4 °C overnight with slow rotation. After removing primary antibodies using a magnetic stand, the secondary antibodies (goat anti-rabbit IgG (H+L) (Yeasen, Cat#34850ES60) and goat anti-mouse IgG (H+L) (Yeasen, Cat#3485ES60) were incubated with the concanavalin A beads coupled cells at room temperature for 1 h. Cells were washed three times with wash buffer to remove unbound antibodies. Then, the cells were incubated with pA/G-Transposome mix for 1 h at room temperature. To terminate tagmentation, terminate solution and proteinase K were added to the sample and incubated at 55℃ for 30 min. DNA was purified using DNA selection beads and elutes  in 21 μL ddH2O.
For library amplification, 8 µL of DNA was mixed with a uniquely barcoded i5 and a uniquely barcoded i7 primer, and amplified using 2× Ultima Amplification Mix (Yeasen). The library was then purified using DNA selection beads and washed twice with 80% ethanol and eluted in 21 μL of ddH2O. Libraries were sequenced by Genewize (Suzhou, China) on an Illumina NovaSeq platform for 10 G per sample and 150-bp paired-end reads were generated.

treatment_protocol: HCT116 cells were treated with/without 0.4 μM APH for 48 hour.

value: colon cancer cell line

value: TP53 KO

value: APH treated


title: ATCC 17978 strain, overexpressed TetR2-His-tag, rep3, 3

city: Xi'an

first: Wenbo

last: He

state: ShaanXi

address: 76 Yanta West Road

department: The First Affiliated Hospital

institute: Xi'an Jiaotong University

data_processing:
To remove technical sequences and low quality sequence, pass filter data of fastq format were processed by Cutadapt (version 1.9.1)
Bowtie2-build is used to index reference genome sequence, then trimmed sequence data were aligned to reference genome via software Bowtie2 (v2.2.6)
Using MACS(V2) to analyze peaks quality control, peaks calling and peaks annotation.
Assembly: CP012004.1
Supplementary files format and content: bigWig

organism: Acinetobacter baumannii

source_name: Acinetobacter baumannii strain ATCC 17978

growth_protocol: A. baumannii ATCC 17978 derivatives were grown at 37 °C in LB media at 37 ℃, supplemented with 15μg/ml tetracycline and 2 mM isopropyl β-D-1-thiogalactopyranoside (IPTG)

extract_protocol:
The cultures were added 1% formaldehyde for crosslinking at room temperature for 20 minutes. After quenching, bacteria were lysed using 2mg/ml lysozyme and sonicated after centrifugation. His-tagged protein-DNA complexes were isolated by nickel magnetic beads and purified by TIANquick Midi Purification Kit (Tiangen) after de-crosslinking.
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol.

value: 6×His-tag (Proteintech, #66005-1-Ig)


title: ATCC 17978 strain, input for TetR2 experiment group

value: Acinetobacter baumannii strain ATCC 17978


title: IgG_APH_rep2

description: Library name: IgG_APH_rep2


title: IgG_APH_rep1

description: Library name: IgG_APH_rep1


title: ATCC 17978 strain, overexpressed TetR2-His-tag, rep3, 2


title: ATCC 17978 strain, input for TetR1 experiment group


title: ATCC 17978 strain, overexpressed TetR1-His-tag, rep3, 3


title: IgG_DMSO_rep3

description: Library name: IgG_DMSO_rep3

value: untreated


title: ATCC 17978 strain, overexpressed TetR2-His-tag, rep3, 1


title: Replicate 3 of Lamin B1 CUT&Tag in HCT116, APH treated

description: Library name: Lamin B1 APH  3


title: Replicate 3 of Lamin B1 CUT&Tag in HCT116, untreated

description: Library name: Lamin B1 DMSO 3


title: ATCC 17978 strain, overexpressed TetR1-His-tag, rep3, 2


title: ATCC 17978 strain, overexpressed TetR1-His-tag, rep3, 1


title: IgG_DMSO_rep2

description: Library name: IgG_DMSO_rep2


title: ATCC 17978 strain, lose pAB3(LCP), supply overexpressed TetR2, rep3,3

data_processing:
To remove technical sequences and low quality sequence, pass filter data of fastq format were processed by Cutadapt (version 1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1)
Trimmed sequence data were aligned to reference genome via software Bowtie2 (v2.2.6)
HTSeq (v0.6.1p1) estimated gene expression levels from the pair-end clean data.
Assembly: ASM107767v1
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

extract_protocol:
Total RNA from each strain was extracted using RNAsimple Total RNA Kit (Tiangen,Cat#DP419), 1 μg total RNA was used for sequencing library preparations
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol.

value: Acinetobacter baumannii

value: supply TetR2


title: Replicate 3 of Lamin A/C CUT&Tag in HCT116, APH treated

description: Library name: Lamin A/C APH  3


title: ATCC 17978 strain, lose pAB3(LCP), supply overexpressed TetR1, rep3,2

value: supply TetR1


title: Replicate 1 of Lamin B1 CUT&Tag in HCT116, APH treated

description: Library name: Lamin B1 APH  1


title: ATCC 17978 strain, lose pAB3(LCP), rep3,2

value: A.baumannii with positive type VI secretion system


title: Replicate 2 of Lamin A/C CUT&Tag in HCT116, APH treated

description: Library name: Lamin A/C APH  2


title: Replicate 2 of Lamin B1 CUT&Tag in HCT116, APH treated

description: Library name: Lamin B1 APH  2


title: IgG_DMSO_rep1

description: Library name: IgG_DMSO_rep1


title: Replicate 2 of Lamin B1 CUT&Tag in HCT116, untreated

description: Library name: Lamin B1 DMSO 2


title: ATCC 17978 strain, lose pAB3(LCP), supply overexpressed TetR2, rep3,1


title: Replicate 3 of Lamin A/C CUT&Tag in HCT116, untreated

description: Library name: Lamin A/C DMSO 3


title: ATCC 17978 strain, lose pAB3(LCP), supply overexpressed TetR2, rep3,2


title: Replicate 1 of Lamin A/C CUT&Tag in HCT116, APH treated

description: Library name: Lamin A/C APH  1


title: ATCC 17978 strain, lose pAB3(LCP), rep3,1


title: Chimeric mouse diaphragm experimental dataset, Day2, multiplexing barcodes

city: Montreal

first: Qian

last: Li

state: QC

address: 845 Sherbrooke Street West

country: Canada

institute: McGill University

description:
Library name: Chimeric mouse diaphragm experimental dataset Day2 multiplexing barcodes library
Single-cell RNA-seq of macrophages from bone marrow transplant samples using 10X Genomics

data_processing:
Sequencing BCL files were converted to FASTQ using cellranger mkfastq (10x Genomics).
FASTQ files were processed with cellranger count for gene expression libraries and cellranger multi for CMO demultiplexing, using the mm10 (GRCm39) reference provided by 10x Genomics.
Output feature-barcode matrices were imported into R/Python for quality control, doublet removal, and annotation.
Filtering thresholds included mitochondrial gene percentage, UMI count, and detected gene number, optimized per dataset.
CMO barcode assignments were used to annotate donor/recipient origin in the validation dataset and to trace origins in the experimental dataset.
Assembly: Mouse reference genome mm10 (GRCm39), Ensembl gene annotation (Gencode M27), 10x Genomics reference refdata-gex-mm10-2020-A.
Supplementary files format and content: Cell Ranger–generated outputs in Matrix Market format: matrix.mtx (gene-by-cell UMI counts), features.tsv (gene IDs and symbols), barcodes.tsv (cell barcodes).
Supplementary files format and content: CMO demultiplexing results are provided as barcode annotation files with donor/recipient origin labels.

source_name: diaphragm

extract_protocol: Diaphragm macrophages were identified as CD45-positive (CD45.1 or CD45.2), CD11b-positive, and F4/80-positive cells, and negative for SiglecF and CD11c. For the Chimeric mouse diaphragm validation dataset, Cell Multiplexing Oligos (CMO, 10x Genomics) were applied to FACS-sorted CD45.1 and CD45.2 macrophages to distinguish donor and recipient origins. In Chimeric mouse diaphragm experimental datasets, CMOs were applied to unstained muscle cell suspensions prior to sorting to trace cells from different mice. All macrophage sorting was performed in PBS supplemented with 20% fetal bovine serum (FBS) to preserve viability and cell integrity. The Single Cell 3' mRNA and CMO barcode library preparation was conducted strictly following 10x Genomics protocol CG000388.

value: diaphragm

value: macrophage

value: bone marrow transplant


title: ATCC 17978 strain, lose pAB3(LCP), rep3,3


title: Replicate 2 of Lamin A/C CUT&Tag in HCT116, untreated

city: Shenzhen

description: Library name: Lamin A/C DMSO 2


title: Replicate 1 of Lamin A/C CUT&Tag in HCT116, untreated

description: Library name: Lamin A/C DMSO 1


title: RPE-1, APH treated,  Lamin B1 rep3

data_processing:
Raw sequencing reads were first preprocessed using Ktrim software to remove sequencing adaptors and low-quality cycles. The preprocessed reads were then aligned to NCBI GRCh38 reference human genome using Bowtie2 software. PCR duplicates (i.e., reads with identical start and end positions) were identified and removed using in house programs. Reads from mitochondrial chromosome were also removed and the remaining  were kept for downstream analyses ("clean reads").
For DSMO and APH treatments, data from IgG experiments were used as controls to call peaks for Lamin A/C and B1 using MACS2 software, respectively. Peaks with adjusted p-values lower than 0.01 were considered as statistically significant. CUT&Tag signals around the peaks were visualized using deptools software.
We first stitched the peaks in the Lamin A/C or B1 that were less than 20kb in distance, and only kept those longer than 100 kb after stitching. For each kept peak after stitching, we extracted the read numbers in the CUT&Tag experiments, which were further normalized using the clean read count of the corresponding experiments. The normalized read counts were compared between DMSO and APH experiments using t-tests for Lamin A/C and B1 (each had 3 replicates), respectively. The p-values were corrected using Benjamini & Hochberg method, and peaks with adjusted p-values lower than 0.05 in both Lamin A/C and B1 were called as RESS-LAD regions. An implementation of this approach was publicly available at https://github.com/hellosunking/RESS-LADs.
Assembly: hg38
Supplementary files format and content: narrowPeak for Lamin AC and B1, empty for IgG control
Supplementary files format and content: BED format for RESS-LADs regions
Library strategy: CUT&Tag

growth_protocol: RPE-1 cells were maintained Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin and streptomycin (Gibco).

extract_protocol:
We perform Cleavage under targets and tagging (CUT&Tag) using Hieff NGS® G-Type In-Situ DNA Binding Profiling Library Prep Kit (Yeasen, Cat#12598ES48) against lamin A/C and lamin B1 following to the manufacture’ s instruction. Briefly, for each sample, 105 cells were harvested after treatment with/without 0.4 μM APH for 48 hour and washed three times by PBS, resuspend  the cells with cell wash buffer gently, and incubate  with the concanavalin A coated magnetic beads previously washed by ConA bind buffer. Then concanavalin A beads coupled cells were collected and incubated with 2 μg primary antibody (mouse anti lamin A/C (Santa Cruz, Cat#sc-7292) or rabbit anti-lamin B1 (Abcam, Cat#ab16048)) and rabbit anti IgG (Thermo ) at 4 °C overnight with slow rotation. After removing primary antibodies using a magnetic stand, the secondary antibodies (goat anti-rabbit IgG (H+L) (Yeasen, Cat#34850ES60) and goat anti-mouse IgG (H+L) (Yeasen, Cat#3485ES60) were incubated with the concanavalin A beads coupled cells at room temperature for 1 h. Cells were washed three times with wash buffer to remove unbound antibodies. Then, the cells were incubated with pA/G-Transposome mix for 1 h at room temperature. To terminate tagmentation, terminate solution and proteinase K were added to the sample and incubated at 55℃ for 30 min. DNA was purified using DNA selection beads and elutes  in 21 μL ddH2O.
For library amplification, 8 µL of DNA was mixed with a uniquely barcoded i5 and a uniquely barcoded i7 primer, and amplified using 2× Ultima Amplification Mix (Yeasen). The library was then purified using DNA selection beads and washed twice with 80% ethanol and eluted in 21 μL of ddH2O. Libraries were sequenced by Berry Genomic (Beijing, China) on an Illumina NovaSeq platform for 10 G per sample and 150-bp paired-end reads were generated.

treatment_protocol: RPE-1 cells were treated with/without 0.4 μM APH for 48 hour.

value: retinal pigment epithelial cells

value: APH

tag: chip antibody

value: Abcam, Cat#ab16048


title: RPE-1, APH treated,  Lamin B1 rep2


title: ATCC 17978 strain, lose pAB3(LCP), supply overexpressed TetR1, rep3,1


title: RPE-1, APH treated,  Lamin B1 rep1


title: Chimeric mouse diaphragm experimental dataset, Day1, multiplexing barcodes

description:
Library name: Chimeric mouse diaphragm experimental dataset Day1 multiplexing barcodes library
Single-cell RNA-seq of macrophages from bone marrow transplant samples using 10X Genomics


title: Chimeric mouse diaphragm validation dataset, gene expression

description:
Library name: Chimeric mouse diaphragm validation dataset gene expression library
Single-cell RNA-seq of macrophages from bone marrow transplant samples using 10X Genomics


title: Replicate 1 of Lamin B1 CUT&Tag in HCT116, untreated

description: Library name: Lamin B1 DMSO 1


title: RPE-1, APH treated,  Lamin AC rep2

value: Santa Cruz, Cat#sc-7292


title: RPE-1, APH treated,  Lamin AC rep3


title: Chimeric mouse diaphragm validation dataset, multiplexing barcodes

description:
Library name: Chimeric mouse diaphragm validation dataset multiplexing barcodes library
Single-cell RNA-seq of macrophages from bone marrow transplant samples using 10X Genomics