title: PBMC_Donor_0037_biological_replicate_2_LPS

city: San Francisco

first: Kord

last: Kober

address: 521 Parnassus Avenue, 3229, Box 0638

institute: University of California San Francisco

description: Library name: 0037_A4

data_processing:
Post-sequencing basecall files (bclfiles) were demultiplexed and converted into a FASTQ file format using the bcl2fastq v2.17 software (Illumina Inc., San Diego, CA).
Briefly, individual samples were inspected with FASTQC and in aggregate with MultiQC.  Reads were filtered and trimmed using Trimmomatic. The reference genome was prepared using the GRCh38.p14 assembly and transcriptome annotations were obtained from the Gencode v46 primary assembly. Trimmed reads were aligned to the annotated reference genome using the STAR aligner. Alignments were created for all RNA samples individually for gene level analysis (n=12) as well as combined across biological replicates of a donor for alternative splicing analysis (n=6).
Abundance of RNA at the gene level were estimated from the aligned reads as estimated counts using featureCounts and as transcripts per million (TPM) using TPMcalculator. Ensembl gene and transcripts were annotated with Entrez gene ID and symbol. Splicing events were evaluated using RMATs.
Assembly: GRCh38.p14 assembly, transcriptome annotations were obtained from the Gencode v46 primary assembly
Supplementary files format and content: fcnt.all.csv is a comma-deliminted text file that contains count estimates from feature counts for each biological replicate separately
Supplementary files format and content: tpm.all.csv is a comma -delimited text file that contains transcript count estimates as transcripts per million for each biological replicate separately
Supplementary files format and content: A3SS.MATS.JC.txt contains the RMATs analsysis output including only reads that span junctions defined by rmats (Junction Counts) for A3SS events. Sample_1 includes the LPS treated specimens. Sample_2 includes the PBS treated samples.
Supplementary files format and content: A5SS.MATS.JC.txt contains the RMATs analsysis output including only reads that span junctions defined by rmats (Junction Counts) for A5SS events. Sample_1 includes the LPS treated specimens. Sample_2 includes the PBS treated samples.
Supplementary files format and content: MXE.MATS.JC.txt contains the RMATs analsysis output including only reads that span junctions defined by rmats (Junction Counts) for MXE events. Sample_1 includes the LPS treated specimens. Sample_2 includes the PBS treated samples.
Supplementary files format and content: RI.MATS.JC.txt contains the RMATs analsysis output including only reads that span junctions defined by rmats (Junction Counts) for RI events. Sample_1 includes the LPS treated specimens. Sample_2 includes the PBS treated samples.
Supplementary files format and content: SE.MATS.JC.txt contains the RMATs analsysis output including only reads that span junctions defined by rmats (Junction Counts) for SE events. Sample_1 includes the LPS treated specimens. Sample_2 includes the PBS treated samples.

extract_protocol:
The PBMC pellets were retrieved from the -80°C freezer and thawed on a cool rack for approximately 15 minutes. Prior to RNA isolation, cell counts and cell viability were assessed for each sample on the Countess 3 FL. Each measurement was performed in duplicate, and the averages of the duplicate values were calculated to determine the total number of viable cells in each PBMC pellet. This information was used to assess the appropriate amount of lysis buffer required for RNA isolation. RNA was isolated from the PBMC pellets using the RNeasy mini kit (Qiagen, Catalog 74104) in accordance with the manufacturer's instructions, which included a DNAse digestion step in the isolation protocol. Subsequently, the concentration, integrity, and purity of the isolated RNA were quantified using the ND 8000 spectrophotometer. The purified RNA, was stored at 80°C. The RNA Clean & Concentrator-5 kit (Zymo Research, Catalog R1015) was later used for purification of the extracted RNA. The same technician performed all of the RNA extractions and purifications in one laboratory.
Total RNA from the 3 donors (12 total samples) was sent to the UC Davis Genomics Core Facility for library preparation and for sequencing. Prior to library preparation, 200 nanograms (ng) of total RNA was treated and the QIAseq FastSelect–5S/16S/23S ribodepletion reagent (Qiagen, Hilden Germany) following the instructions of the manufacturer.  Dual-barcode indexed RNA-seq libraries were generated from 200 ng total RNA each using the Watchmaker RNA Library Prep Kit (Watchmaker Genomics, Boulder, Colorado).  Eleven cycles of PCR amplification were used for double six base pair index addition and library fragment enrichment.  The fragment size distribution of the libraries was verified via micro-capillary gel electrophoresis on TapeStation (Agilent, Santa Clara, CA). Prepared libraries were quantified on a Qubit fluorometer (LifeTechnologies, Carlsbad, CA) and pooled in equimolar ratios. Final pool was quantified using KAPA Illumina library quantitative PCR reagents (Roche Diagnostics Corp., Indianapolis, IN). Sequencing of the 12 samples was done on an Illumina NovaSeqX (Illumina Inc., San Diego, CA). All 12 samples were multiplexed into a single pool, with each sample labeled with a dual-indexed adapter. The sample pool was sequenced on four lanes for 150 cycles of paired-end reads with a 1% PhiX v3 control library spike (Illumina Inc., San Diego, CA).

treatment_protocol: Donor samples (1 × 10E8 cells) were thawed in a water bath set to 37°C and subsequently washed twice with pre-warmed complete RPMI 1640 medium (STEMCELL Technologies, Catalog 36750), which was supplemented with GlutaMAX (Fisher Scientific, Catalog A4192301) and 5% FBS (Fisher Scientific, Catalog A5669401). Cell viability and cell counts were measured immediately following the initial thaw and again after the final wash using the Countess 3 FL (Fisher Scientific, Catalog AMQAF2000). Thawed PBMCs were resuspended in complete RPMI 1640, and additional cell viability and cell counts were performed on the resuspended cells. The PBMC cell suspension was divided into two primary aliquots. Cell viability and cell counts were measured for each primary aliquot. Primary aliquots were further subdivided into four sub-aliquots, each containing approximately 1 x 10E7 cells, which were plated into individual wells of a 12-well cell culture plate. Two sub-aliquots served as duplicate controls and were treated with PBS, while the other two sub-aliquots were treated with 100 ng/mL of LPS (from E. coli 026:B6; eBioscience LPS, Catalog 00-4976, Invitrogen, Carlsbad, CA). All the cells were then incubated in a 37°C environment with 5% CO2 for 24 hours. Following the 24-hour treatment period, cells were washed twice with warm RPMI 1640. Cell viability and cell counts were then measured. The cell suspensions were centrifuged at 1000g for 10 minutes, after which the cell supernatants and cell pellets were collected and stored at -80°C. The same technician performed all of the experiments in one laboratory.  All experiments were conducted in duplicate.

value: PBMC

tag: age

tag: race

value: Black

tag: Sex

value: Female

tag: smoker

value: No

value: LPS

tag: weight

tag: height


title: MZCS002_R2

status: Public on Nov 09 2025

type: SRA

city: Cologne

first: David

last: Willemsen

address: Joseph-Stelzmann-Str 9b

department: Valenzano

country: Germany

institute: Max Planck Institute for Biology of Ageing

library_source: transcriptomic

data_processing:
Reads were trimmed with trimmomatic  (Bolger et al., 2014)
Reads were mapped with STAR (Dobin et al., 2013, v.2.7.8a) and the following parameters: --outSAMmapqUnique 200, --outFilterIntronMotifs RemoveNoncanonicalUnannotated, --outFilterType BySJout , --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --alignIntronMax 1000000, --alignMatesGapMax 1000000.
Raw reads were counted with featureCounts (Liao et al., 2014, v.1.6.2) using a minimum mapping quality of 30.
Differential gene expression analyses were performed using DESeq2 (Love et al., 2014)
Genome_build: NFZv2.0 genome assembly (Willemsen et al., 2020)

molecule: total RNA

organism: Nothobranchius furzeri

source_name: tail fin

extract_protocol:
For each sample, the pigmented region (or the corresponding region in females) of the tailfin was excised and stored at -20°C in RNAlater. We then extracted total RNA using QIAzol (Qiagen) according to the manufacturer’s protocol with modifications. Briefly, tissue taken out of the RNA later was rinsed with 1xPBS buffer and then dipped on a clean paper towel. After transferring the tissue into a 1.5ml Eppendorf tube containing 200µl Qiazol solution, we homogenized the tissue with a micro pestle. After 5 min incubation on ice, 80 µl chloroform was added and the tube was vigorously shaken for 20 s. The tube was incubated at RT for 3 min and then centrifuged at 12,000 x g for 15 min at 4°C. The aqueous phase was transferred into a fresh tube and 100 µl isopropanol was added. The tube was inverted 4-5 times for mixing and then incubated at RT for 10 min. To precipitate RNA, we centrifuged the tube at 21,130 x g for 30 min at 4°C. The supernatant was removed and the pellet was washed with 200µl of 75% EtOH. The aspirated pellet was resuspended in 26 µl nuclease-free water and treated with DNase using DNA-free Kit (Ambion). After measurements of concentration with Qubit-BR RNA Assay Kit (Invitrogen), samples were stored at -80°C.
For first-strand cDNA synthesis, 125ng of total RNA purified with 1.2X SeraSure beads (2.5M NaCl (Roth), 20 mM PEG8000 (Sigma), 10mM Tris-HCl pH 8.0  (Sigma), 1mM EDTA (Sigma), 1 ml SeraMag GE Healthcare, 65152105050250 beads in 100mL solution) was added to 1 µl of 3’ SfiI Oligo T primer (10µM) and 1µl of dNTP mix (10mM, Invitrogen) and incubated at 72°C for 3 min. Then, a first-strand mix containing 0.5 µl superscript II (200U/µl, Invitrogen), 0.25 µl RNAse inhibitor (40U/µl, Thermo Scientific), 2 µl Superscript II buffer (5X, Invitrogen), 0.25 µl DTT (100mM), 2 µl Betaine (5M, Sigma), 0.9 µl MgCl2 (100mM, Sigma), 1 µl 5’ sfiI plug oligo (10mM), and 0.1 µl water was mixed into a tube and then incubated in a thermocycler with the following program: 90 min at 42°C, 10 cycles of 2 min at 50°C and 2 min at 42°C, and 15 min at 72°C. For preamplification, 12.5 µl 2X KAPA HiFi HotStart ReadyMix, 1 µl of cDNA universal primer (10uM), 2 µl of 1st strand cDNA, and 9.5 µl of water were mixed and incubated in a thermocycler with the following program: 3 min at 98°C, 16 cycles of 15 s at 98°C, 20 s at 67°C, and 6 min at 72°C, and 5 min at 72°C. 2 µl NEB CutSmart buffer (10X) and 1 µl SfiI (10U/µl, NEB) were added into the PCR mix and incubated overnight at 50°C. The resulting PCR product was purified with 1X SeraSure beads. For library preparation, a maximum of 250ng of cDNA was added for a 10 µl reaction mix containing 1µl of dsDNA fragmentase (NEB), 1µl fragmentase buffer (10X, NEB), and water and then incubated for 22.5 min at 37°C. The reaction was stopped with 5 µl of EDTA (0.5 M, Sigma). 5 µl of nuclease-free water (Qiagen) was added to the reaction mixture, which was followed by a purification with 1.2X SeraSure beads and resuspension in 5µl of Tris buffer. 1 µl of end repair reaction buffer (10X, NEB), 0.5 µl of Klenow (NEB), 0.5 µl of Taq polymerase (Invitrogen), 0.2 µl of T4 polynucleotide kinase (10U/µl, NEB) was added to 5 µl of fragmented DNA and incubated in a thermocycler for end-repair reaction with the following program: 30 min at 25°C and 30 min at 75°C. Then, cDNA was ligated with adaptors containing 8-bp barcodes using Quick Ligase (NEB). The resulting cDNA was enriched with 7-9 cycles of PCR.  After amplification, we performed size selection using 0.55X SeraSure beads. The quality of libraries was assessed with an Agilent 4200 TapeStation. Libraries were pooled and sequenced across one lane of Illumina HiSeq X at NGX bio (US).

tag: strain


title: PBMC_Donor_0037_biological_replicate_1_LPS

state: CA

country: USA

description: Library name: 0037_A3

organism: Homo sapiens

source_name: PBMC

tag: tissue

tag: treatment


title: OPC-Con-6

city: Kyoto

first: Kazuto

last: Tsukita

state: Kyoto

address: 54 Shogoin-Kawaharacho

country: Japan

institute: Kyoto university

data_processing:
or the processing of RNAseq data, adapter sequences were first removed, and reads were quality-trimmed using Trimmomatic (version 0.36). The trimming process involved removing Nextera adapter sequences, trimming low-quality bases from both the leading and trailing ends, and applying a sliding window trimming approach. The minimum length threshold for reads after trimming was set to 50 bases. Post-trimming, the quality of the reads was assessed using FastQC (version 0.11.9). The reference genome for Rattus norvegicus (mRatBN7.2) was downloaded from the Ensembl database and used for subsequent alignment and gene expression quantification. Trimmed reads were aligned to the reference genome using STAR (version 2.7.9a) with the aligner configured to run in paired-end mode utilizing 10 threads. The output files included sorted BAM files and transcriptome alignments for downstream analysis. Gene expression levels were quantified using RSEM (version 1.3.3), with quantification performed in paired-end mode, specifying reverse strandedness.
Assembly: mRatBN7.2
Supplementary files format and content: comma-delimited file includes the raw counts for each sample.

organism: Rattus norvegicus

source_name: Brain

extract_protocol:
RNA was harvested using RNeasy Mini Kit (QIAGEN).
The cDNA libraries were prepared using the Agilent Sure Select Strand Specific RNA prep kit (Catalog no.G9691A) with 200 ng of total RNA, following the manufacturer's guidelines.

value: Brain

tag: cell type

value: OPCs

tag: genotype

value: WT

value: Room air


title: PBMC_Donor_0036_biological_replicate_2_LPS

description: Library name: 0036_A4

value: Caucasian


title: OPC-Con-5


title: PBMC_Donor_0036_biological_replicate_1_LPS

description: Library name: 0036_A3


title: OPC-Con-4


title: OE_3

city: Yinchuan

first: ruijuan

last: Xin

state: Ningxia

address: Zhengyuan South Street

country: China

institute: People's Hospital of Ningxia

description: Library name: Sample 9

data_processing:
The raw data format of Nanopore sequencing offmachine data is POD5 format, which contains all raw sequencing signals, through dorado (version: 0.8.2) software performs (Base Calling) analysis and converts POD5 format data into FASTQ format, which contains the base information of sequencing sequences (reads) and their corresponding sequencing quality information, and Pychopper (version 2.7.9) is used to prune ONT reads and recognize full-length tools. Only reads with sequence quality value less than 10 and sequences with length less than 50bp screened by chopper (version 0.7.0) were retained for subsequent analysis.
The ONT reads were aligned to ensembl reference genome mRatBN7.2 using minimap2 (version 2.27-r1193) (Li 2018) in spliced alignment mode with the command ‘mnimap2 -ax splice -uf -k14’. The detection of alternatively spliced isoforms and is implemented using the Pinfish package (github.com/nanoporetech/pinfish). The output of polished transcripts is provided in the GTF format，and transcripts assembled by long-read assembly were merged using StringTie (version 2.1.6) (Pertea et al. 2015) merge to obtain a non-redundant pool of transcripts across samples. Then, gffcompare (version 0.12.6; Parameters: -G,-R) (Pertea & Pertea 2020) were used to compare non-redundant transcripts with known transcripts of the genome to find new transcripts and new genes. Finally, we identified the transcripts as new and known by classcode's [uxijo] and [c=], and finally merged them together for subsequent analysis.
We used DESeq2 (version 1.30.1) (Love et al. 2014) to analyze the differences in transcripts and genes between the two groups. A statistical cutoff of Fold change ≥ 2 and FDR ≤ 0.05 was used to find differentially expressed genes (DEGs) and differential transcript expression (DTEs). Differential transcript usage (DTU) was performed using DEXSeq (Li et al. 2015) as implemented within IsoformSwitchAnalyzeR (version 2.2.0) (Vitting-Seerup & Sandelin 2019). We use gffcompare (version 0.12.6) (Pertea & Pertea 2020) identification of transcripts as input, A difference in isoform fraction (dlF) value between the two conditions and an FDR adjusted p-value were calculated for Each isoform. We considered isoforms with an adjusted P value lower than 0.05 as exhibiting DTU, regardless of dIF. At the gene level, the lowest adjusted p-value of any isoform was considered to be the p-value for the gene, therefore genes with at least one significant isoform were considered significant.
SUPPA2 (version 2.3) (Trincado et al. 2018) was used for calling AS differences. For each identified AS event, the splicing level was defined by Percentage of Spliced-In (PSI) while the mean difference of splicing levels between two groups was measured by ΔPSI (dPSI) and by the P-value from independent T-tests against PSIs in the two groups. We screened out the difference AS with dPSI ≥ 0.05 and P value ≤ 0.05 for analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: AGS cells

growth_protocol: The lentivirus packaging plasmids overexpressing (OE) or suppressing miR-214-3p (KD), and control plasmids (Con) were obtained from Ningxia Saisi Juxin Biotechnology Co.,Ltd. (Ningxia, China). In brief, the antisense sequences (GATCCGACAGCAGGCACAGACAGGCAGTCTCGAGACTGCCTGTCTGTGCCTGCTGTTTTTT) and mature sequences (GATCCGACTGCCTGTCTGTGCCTGCTGTCTCGAGACAGCAGGCACAGACAGGCAGTTTTTT) of miR-214-3p were obtain through PCR amplification. Then, these sequences were inserted into lentivirus expression vectors (pLVX-shRNA2-puro) by enzyme digestion and ligation. The correctness of the inserted sequence were verified through PCR and sequencing.

extract_protocol:
For each sample, 500 ng total RNA was transferred to 0.2 ml PCR tubes and adjusted to a final volume of 9 μl with nuclease free water. Reactions were prepared (9 μl total RNA, 1 μl 10 μM VNP primer, 1 μl 10 mM dNTPs) and incubated for 5 min at 65°C, then snap cooled on a pre-chilled freezer block. Strand-switching buffer (4 μl 5x RT buffer, 1 μl RNaseOUT, 1 μl nuclease-free water, and 2 μl 10 μM strand-switching primer) was then added to the snap-cooled, annealed mRNA, and incubated at 42°C for 2 min. 1 μl of Maxima H Minus Reverse Transcriptase was added, and reactions were incubated at 42°C for 90 min, 85°C for 5 min, then held at 4°C. DNA library were set up for each cDNA (2 μl PR1 Primer, 2 μl PR2 Primer, 20 μl first-strand cDNA, 25 μl LongAmp Taq 2x master mix, 1 μl nuclease free water), and cycled for [3 min at 94°C] ×1 cycle, [15 s at 94°C, 15 s at 50°C, 2 min at 65°C] ×12 cycles, [10 min at 65°C] ×1 cycle, then held at 4°C. cDNA were added barcodes using the Native Barcode Kit 96 V14 (SQK-NBD114.96) following manufacturer’s guidelines. Each barcoded DNA was purified in 1× Ampure XP Beads, eluted in 20 μl of nuclease free water and quantified using Qubit. Finally, 300 fmol of adapter ligated library was loaded onto a PromethION flow cell.
For Long‑read sequencing, the libraries were prepared for following the manufacturer's instructions and applied to MinION system sequencing.

treatment_protocol: The human gastric cancer cell line AGS was purchased from Procell Life Science & Technology Co., Ltd. (Wuhan, China). AGS cells line were cultured at 37℃ with 5% CO2 in MEM with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, 100 U/mL penicillin. AGS cells were transfected with those plasmids using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) and then incubated for 48 hours.

tag: cell line

value: AGS cells

value: miR-214-3p overexpression in AGS cell


title: OPC-Con-3


title: PBMC_Donor_0035_biological_replicate_2_LPS

description: Library name: 0035_A4

value: Asian


title: OE_2

description: Library name: Sample 8


title: PBMC_Donor_0035_biological_replicate_1_LPS

description: Library name: 0035_A3


title: Oral wild-type tumor 1

city: East Lansing

first: Bin

last: Gu

state: MI

address: 755 Woodlot Drive

department: OBGYN

institute: Michigan State University

description: Library name: Oral wild-type tumor 1

data_processing:
Raw reads were trimmed with TrimGalore (v0.6.10) with the default parameters. FastQC (v0.12.1) was used to ensure the quality of data.
Trimmed reads were quantified with Kallisto (v0.50.0) using the GENCODE mouse transcriptome (GRCm38, release M23) with settings --rf-stranded -b 100.
Differential gene expression analysis was conducted using DESeq2.
Gene set enrichment analysis (GSEA) [28] was performed using clusterProfiler.
Assembly: GENCODE mouse transcriptome (GRCm38, release M23)
Supplementary files format and content: csv file containing raw count for each sample

organism: Mus musculus

source_name: mNC tumor

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol.
One microgram of RNA per sample was subjected to ribosomal RNA (rRNA) depletion and library preparation using the Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit, following the manufacturer’s instructions

value: mNC tumor

value: KRT14-Cre; NCT+/-


title: GRZ_BELL_Y2

value: GRZ-BELL


title: OPC-Con-1


title: PBMC_Donor_0037_biological_replicate_2_PBS

description: Library name: 0037_A2

value: PBS


title: OPC-5per-6

value: 5% FiO2 for 6 hours


title: KD_2

description: Library name: Sample 5

value: miR-214-3p knockdown in AGS cell


title: MZCS002_F3


title: KD_3

description: Library name: Sample 6


title: MZCS002_R1


title: Hm2 G-

type: RNA

city: Toronto

first: Norman

middle: David

last: Rosenblum

state: Ontario

address: 686 Bay St

department: Developmental and Stem Cell Biology

country: Canada

institute: Hospital for Sick Children

description: Gene expression data from mouse E15.5 embryonic kidney non-ureteric cells expressing IlkT173I

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip™ Mouse Gene 2.0 ST Array. GeneChips were washed and stained in a Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with the Applie Biosystems Transcriptome Analysis Console software.

label: biotin

source_name: Mouse E15.5 embryonic kidney sorted non-ureteric cells

label_protocol: Biotin-labeled cRNA was produced using a Affymetrix RNA Transcript Labeling Kit as per manufacturer's instructions.

growth_protocol: IlkT173I was knocked-in by CRISPR gene editing to create a IlkT173I mouse line, which was then crossed with Hoxb7-myrVenus mouse line in which ureteric cells were labeled with GFP. Offsprings were then inbred to generate IlkT173I homozygous or IlkWT mice with ureteric GFP labeling.

extract_protocol: Total RNA was extracted using a Qiagen RNeasy kit as per manufacturer's instructions.

treatment_protocol: Ureteric cells and non-ureteric cells were FAC-sorted from  IlkT173I homozygous or IlkWT mouse E15.5 kidneys by GFP expression.

value: IlkT173I homozygous

tag: lineage

value: Non-ureteric


title: PBMC_Donor_0037_biological_replicate_1_PBS

description: Library name: 0037_A1

value: PBMC

value: Black

value: Female

value: No


title: MZCS002_F2


title: OPC-5per-5

value: Brain

value: OPCs

value: WT


title: KD_1

description: Library name: Sample 4

value: AGS cells


title: PBMC_Donor_0036_biological_replicate_2_PBS

description: Library name: 0036_A2

value: Caucasian


title: PBMC_Donor_0036_biological_replicate_1_PBS

description: Library name: 0036_A1


title: OPC-5per-4


title: Con_3

description: Library name: Sample 3

value: AGS cells(control plasmid)


title: OPC-5per-3


title: OE_1

description: Library name: Sample 7

value: miR-214-3p overexpression in AGS cell


title: PBMC_Donor_0035_biological_replicate_2_PBS

description: Library name: 0035_A2

value: Asian


title: Con_2

description: Library name: Sample 2


title: Con_1

description: Library name: Sample 1


title: OPC-5per-2


title: Hm3 G-


title: Hm3 G+

description: Gene expression data from mouse E15.5 embryonic kidney ureteric cells expressing IlkT173I

source_name: Mouse E15.5 embryonic kidney sorted ureteric cells

value: Ureteric


title: OPC-5per-1

value: 5% FiO2 for 6 hours


title: PBMC_Donor_0035_biological_replicate_1_PBS

description: Library name: 0035_A1

value: PBS


title: Hm1 G-

value: IlkT173I homozygous


title: WT3 G-

description: Gene expression data from mouse E15.5 embryonic kidney non-ureteric cells expressing IlkWT

value: IlkWT

value: Non-ureteric


title: Hm1 G+


title: WT2 G-


title: Amplicon sequencing, intron-less, no UV, G518 200 µg/ml

status: Public on Nov 08 2025

city: Worcester

first: Leonard

last: Schärfen

state: MA

address: 368 Plantation Street

department: RNA Therapeutics Institute

institute: UMass Chan Medical School

description:
Library name: kan_intronless_nouv_200
amplicon sequencing

library_source: other

data_processing:
The modular data analysis pipeline, implemented including all custom sub modules in Snakemake, is available at https://github.com/lschaerfen/intron_sortseq. Reads for all bins and for the input library were first processed with fastp, merging read pairs into a single read.The resulting fastq files were parsed directly and reads were counted if the sequence was matching a variant in the library perfectly.
Assembly: sacCer3
Supplementary files format and content: _counts.pkl files contain variant counts that can be loaded using the "pickle" Python package. Each file includes a dictionary where keys are the intron variant sequences, and values are the number of reads assigned to that variant.
Supplementary files format and content: .vcf files are standard Variant Call Format files produced by lofreq call --call-indels

molecule: other

organism: Saccharomyces cerevisiae

growth_protocol: Liquid cultures from individual colonies of Saccharomyces cerevisiae BY4741 were grown in liquid YPAD medium to an OD600 around 0.6 at 30 ºC with 200 rpm shaking.

extract_protocol:
Yeast cells were harvested and resuspended at low density in H2O. Cell walls were digested in 20 µl reactions with 1 µl Zymolase (Zymo Research) in 25 mM sodium phosphate pH 7.5 for 20 min at room temperature, then 5 min at 37 ºC. Samples were diluted with 60 µl H2O and 2 µl of the resulting crude gDNA was used as template for amplicon sequencing.
the variable region was amplified by PCR with 15 cycles using KAPA HiFi HotStart polymerase (Roche) with primers adding Illumina flowcell binding sequences. Reactions were purified using AMPure XP beads (Beckman) and used as template for a second round of PCR with Illumina TruSeq i5 and i7 index primers for 15 cycles. Final libraries were again purified with AMPure XP beads, pooled and sequenced on Illumina NovaSeq machines in 2x150 paired-end mode.

treatment_protocol: Yeast libraries were harvested and washed with ice cold 100 mM potassium phosphate buffer (PPB), then resuspended in 100 mM ice cold PPB for subsequent sorting. Cells were sorted into approximately evenly spaced bins of mNeongreen over mScarletI fluorescence emission ratio (488 nm and 635 nm excitation, respectively) using a BD FACS Aria III sorter. Fresh YPAD cultures were started from the sorted populations, grown over night, and each population was again sorted into four bins, yielding 16 cultures in total. Sorted populations were grown overnight and then subjected to gDNA isolation.

value: Saccharomyces cerevisiae

value: a his3DELTA1 leu2DELTA0 met15DELTA0 ura3DELTA0 his3::mScarletI met17::land71

value: no UV, G418 200 µg/ml


title: WT3 G+

description: Gene expression data from mouse E15.5 embryonic kidney ureteric cells expressing IlkWT


title: WT1 G-


title: Amplicon sequencing, intron-less, UV, G518 1500 µg/ml

description:
Library name: kan_intronless_uv_1500
amplicon sequencing


title: Amplicon sequencing, intron-less, no UV, G518 1500 µg/ml

description:
Library name: kan_intronless_nouv_1500
amplicon sequencing

value: no UV, G418 1500 µg/ml


title: Amplicon sequencing, stem loop, no UV, G518 200 µg/ml

description:
Library name: kan_stem_nouv_200
amplicon sequencing


title: WT2 G+


title: Sort-seq, 5SS stem loop library, MYC exon 1, bin 7

description:
Library name: 5ss_stem_MYC_bin07
Sort-seq

value: 5SS stem loop library #2 (MYC)


title: Amplicon sequencing, stem loop, UV, G518 1500 µg/ml

description:
Library name: kan_stem_uv_1500
amplicon sequencing


title: Sort-seq, 5SS stem loop library, MYC exon 1, bin 4

description:
Library name: 5ss_stem_MYC_bin04
Sort-seq


title: Sort-seq, 5SS stem loop library, MYC exon 1, bin 6

description:
Library name: 5ss_stem_MYC_bin06
Sort-seq


title: Sort-seq, 5SS stem loop library, MYC exon 1, bin 8

description:
Library name: 5ss_stem_MYC_bin08
Sort-seq


title: Sort-seq, 5SS stem loop library, MYC exon 1, bin 5

description:
Library name: 5ss_stem_MYC_bin05
Sort-seq


title: Sort-seq, 5SS stem loop library, MYC exon 1, bin 2

description:
Library name: 5ss_stem_MYC_bin02
Sort-seq


title: Sort-seq, 5SS stem loop library, MYC exon 1, bin 1

description:
Library name: 5ss_stem_MYC_bin01
Sort-seq


title: Sort-seq, 5SS stem loop library, MYC exon 1, bin 3

description:
Library name: 5ss_stem_MYC_bin03
Sort-seq


title: Amplicon sequencing, intron-less, UV, G518 200 µg/ml

description:
Library name: kan_intronless_uv_200
amplicon sequencing


title: Sort-seq, 5SS stem loop library, MYC exon 1, input

description:
Library name: 5ss_stem_MYC_input
Sort-seq


title: Sort-seq, 5SS stem loop library, HA exon 1, bin 14

description:
Library name: 5ss_stem_HA_bin14
Sort-seq

value: 5SS stem loop library #2 (HA)


title: Sort-seq, 5SS stem loop library, HA exon 1, bin 13

description:
Library name: 5ss_stem_HA_bin13
Sort-seq


title: Sort-seq, 5SS stem loop library, HA exon 1, bin 11

description:
Library name: 5ss_stem_HA_bin11
Sort-seq


title: Sort-seq, 5SS stem loop library, HA exon 1, bin 8

description:
Library name: 5ss_stem_HA_bin08
Sort-seq


title: Sort-seq, 5SS stem loop library, HA exon 1, bin 16

description:
Library name: 5ss_stem_HA_bin16
Sort-seq


title: Sort-seq, 5SS stem loop library, HA exon 1, bin 7

description:
Library name: 5ss_stem_HA_bin07
Sort-seq


title: Sort-seq, 5SS stem loop library, HA exon 1, bin 3

description:
Library name: 5ss_stem_HA_bin03
Sort-seq


title: Amplicon sequencing, stem loop, UV, G518 200 µg/ml

description:
Library name: kan_stem_uv_200
amplicon sequencing


title: Sort-seq, 5SS stem loop library, HA exon 1, bin 10

description:
Library name: 5ss_stem_HA_bin10
Sort-seq


title: WT1 G+

description: Gene expression data from mouse E15.5 embryonic kidney ureteric cells expressing IlkWT


title: Sort-seq, 5SS stem loop library, HA exon 1, bin 15

description:
Library name: 5ss_stem_HA_bin15
Sort-seq


title: Sort-seq, 5SS stem loop library, HA exon 1, bin 6

description:
Library name: 5ss_stem_HA_bin06
Sort-seq


title: Sort-seq, 5SS stem loop library, HA exon 1, bin 12

description:
Library name: 5ss_stem_HA_bin12
Sort-seq


title: Sort-seq, 5SS stem loop library, HA exon 1, bin 2

description:
Library name: 5ss_stem_HA_bin02
Sort-seq


title: Sort-seq, 5SS stem loop library, HA exon 1, input

description:
Library name: 5ss_stem_HA_input
Sort-seq


title: Sort-seq, walking stem loop library, bin 16

description:
Library name: walking_stem_bin16
Sort-seq

value: walking stem loop library


title: Sort-seq, 5SS stem loop library, HA exon 1, bin 9

description:
Library name: 5ss_stem_HA_bin09
Sort-seq


title: Sort-seq, 5SS stem loop library, HA exon 1, bin 5

description:
Library name: 5ss_stem_HA_bin05
Sort-seq


title: Sort-seq, 5SS stem loop library, HA exon 1, bin 4

description:
Library name: 5ss_stem_HA_bin04
Sort-seq


title: Sort-seq, walking stem loop library, bin 13

description:
Library name: walking_stem_bin13
Sort-seq


title: Sort-seq, walking stem loop library, bin 14

description:
Library name: walking_stem_bin14
Sort-seq


title: Sort-seq, walking stem loop library, bin 15

description:
Library name: walking_stem_bin15
Sort-seq


title: Sort-seq, walking stem loop library, bin 10

description:
Library name: walking_stem_bin10
Sort-seq


title: Sort-seq, walking stem loop library, bin 8

description:
Library name: walking_stem_bin08
Sort-seq


title: Sort-seq, walking stem loop library, bin 12

description:
Library name: walking_stem_bin12
Sort-seq


title: Sort-seq, walking stem loop library, bin 11

description:
Library name: walking_stem_bin11
Sort-seq


title: Sort-seq, walking stem loop library, bin 7

description:
Library name: walking_stem_bin07
Sort-seq


title: Sort-seq, walking stem loop library, bin 9

description:
Library name: walking_stem_bin09
Sort-seq


title: Sort-seq, walking stem loop library, bin 5

description:
Library name: walking_stem_bin05
Sort-seq


title: Sort-seq, walking stem loop library, bin 3

description:
Library name: walking_stem_bin03
Sort-seq


title: Sort-seq, walking stem loop library, bin 6

description:
Library name: walking_stem_bin06
Sort-seq


title: Sort-seq, walking stem loop library, bin 2

description:
Library name: walking_stem_bin02
Sort-seq


title: Sort-seq, walking stem loop library, bin 4

description:
Library name: walking_stem_bin04
Sort-seq


title: Sort-seq, walking stem loop library, bin 1

description:
Library name: walking_stem_bin01
Sort-seq


title: Sort-seq, 5SS stem loop library, HA exon 1, bin 1

description:
Library name: 5ss_stem_HA_bin01
Sort-seq


title: Sort-seq, walking stem loop library, input

description:
Library name: walking_stem_input
Sort-seq


title: Sort-seq, 3SS and branch site stem loop library, bin 15

description:
Library name: 3ss_bs_stem_bin15
Sort-seq

value: 3SS and branch site stem loop library


title: Sort-seq, 3SS and branch site stem loop library, bin 14

description:
Library name: 3ss_bs_stem_bin14
Sort-seq


title: Sort-seq, 3SS and branch site stem loop library, bin 13

description:
Library name: 3ss_bs_stem_bin13
Sort-seq


title: Sort-seq, 3SS and branch site stem loop library, bin 10

description:
Library name: 3ss_bs_stem_bin10
Sort-seq


title: Sort-seq, 3SS and branch site stem loop library, bin 12

description:
Library name: 3ss_bs_stem_bin12
Sort-seq


title: Sort-seq, 3SS and branch site stem loop library, bin 11

description:
Library name: 3ss_bs_stem_bin11
Sort-seq


title: Sort-seq, 3SS and branch site stem loop library, bin 9

description:
Library name: 3ss_bs_stem_bin09
Sort-seq


title: Sort-seq, 3SS and branch site stem loop library, bin 6

description:
Library name: 3ss_bs_stem_bin06
Sort-seq


title: Sort-seq, 3SS and branch site stem loop library, bin 7

description:
Library name: 3ss_bs_stem_bin07
Sort-seq


title: Sort-seq, 3SS and branch site stem loop library, bin 8

description:
Library name: 3ss_bs_stem_bin08
Sort-seq


title: Sort-seq, 3SS and branch site stem loop library, bin 4

description:
Library name: 3ss_bs_stem_bin04
Sort-seq


title: Sort-seq, 3SS and branch site stem loop library, bin 3

description:
Library name: 3ss_bs_stem_bin03
Sort-seq


title: Sort-seq, 3SS and branch site stem loop library, bin 5

description:
Library name: 3ss_bs_stem_bin05
Sort-seq


title: Sort-seq, 3SS and branch site stem loop library, bin 1

description:
Library name: 3ss_bs_stem_bin01
Sort-seq


title: Sort-seq, 3SS and branch site stem loop library, input

description:
Library name: 3ss_bs_stem_input
Sort-seq


title: Sort-seq, 5SS stem loop library, bin 16

description:
Library name: 5ss_stem_bin16
Sort-seq

value: 5SS stem loop library


title: Sort-seq, 5SS stem loop library, bin 14

description:
Library name: 5ss_stem_bin14
Sort-seq


title: Sort-seq, 5SS stem loop library, bin 13

description:
Library name: 5ss_stem_bin13
Sort-seq


title: Sort-seq, 5SS stem loop library, bin 15

description:
Library name: 5ss_stem_bin15
Sort-seq


title: Sort-seq, 5SS stem loop library, bin 11

description:
Library name: 5ss_stem_bin11
Sort-seq


title: Sort-seq, 5SS stem loop library, bin 10

description:
Library name: 5ss_stem_bin10
Sort-seq


title: Sort-seq, 5SS stem loop library, bin 12

description:
Library name: 5ss_stem_bin12
Sort-seq


title: Sort-seq, 5SS stem loop library, bin 8

description:
Library name: 5ss_stem_bin08
Sort-seq


title: Sort-seq, 5SS stem loop library, bin 7

description:
Library name: 5ss_stem_bin07
Sort-seq


title: Sort-seq, 5SS stem loop library, bin 9

description:
Library name: 5ss_stem_bin09
Sort-seq


title: Sort-seq, 5SS stem loop library, bin 6

description:
Library name: 5ss_stem_bin06
Sort-seq


title: Sort-seq, 5SS stem loop library, bin 5

description:
Library name: 5ss_stem_bin05
Sort-seq


title: Cardiac, Heart Failure, DCM, s20

city: Leuven

first: Hywel

middle: Llewelyn

last: Roderick

address: Herestraat 49

department: Cardiovascular Sciences

country: Belgium

institute: Katholieke Universiteit Leuven

description:
Library name: GC123830
10x genomics

library_source: transcriptomic single cell

data_processing:
All processing steps were performed using Cell Ranger softwar (v6.01)
Assembly: hg38
Supplementary files format and content: TSV,rds, and matrix files

molecule: nuclear RNA

source_name: Cardiac

extract_protocol:
70-100 mg of Snap frozen mid-myocardium tissues samples were mechanically homogenized gently using Miltenyi gentleMACS™ Tissue Dissociator with gentleMACS M tubes using the protocol “protein_01_01” in 5 ml lysis buffer solution (5 mM CaCL2, 3mM MgAc, 2mM EDTA, 0.5mM EGTA, 10mM Tris-HCL in water supplemented with 2mg/ml Actinomycin D, 1:1000 protease inhibitor cocktail, and 40 U/µl RNase OUT), then incubated on ice for 15 min with extra 5 ml of the same solution supplemented with 0.1% NP-40. Lysate was then gently filtered through a 30 μm filter into 15 ml conical tube, followed by rinsing the filter once with 2 ml lysis buffer supplemented with 0.1% NP-40. Nuclei were then centrifuged at 1000g for 5 min at 4 °C. Nuclei pellet was then resuspended in 2 ml of sucrose buffer solution (1 M sucrose, 3mM MgAc, and 10 mM Tris-HCL supplemented with 2mg/ml Actinomycin D, 1:1000 protease inhibitor cocktail, 40 U/µl RNase OUT, and 2µl/ml WGA) and layed over another 2 ml sucrose solution in 5 ml canonical tube. Centrifugation was repeated according to the above parameters. Supernatant was then removed and nuclei were resuspended in 400 μl nuclei wash buffer (PBS with 40 U/µl RNase OUT, 15 µl/ml UltraPure BSA,and 2µl/ml WGA) and centrifuged at 650g for 6 min at 4 °C. Another washing step repeated similar to the previous step with centrifugation speed of 500g, and a third wash was performed with 1 µl/ml DAPI and incubated for 10 min in 1.5 ml Eppendorf tube before centrifuging again at 500g speed. The pellet was then resuspended in 300 µl of PBS and filtered in FACS tubes with 35 µl strained. Nuclei were sorted based on size and DAPI positive staining into 40 µl PBS + 15 µl/ml UltraPure BSA using 100-µM nozzle, and collected in 1.5 ml tubes.
Single sorted nuclei were counted by LUNA automated counter in duplicates, then nuclei were centrifuged again and were gently resuspended to a target concentration of 1,000 nuclei/µl and loaded on the Chromium Controller (10X Genomics) with a targeted cell or nuclei recovery of 6,000–10,000 per reaction. 3′ gene expression libraries were prepared according to the manufacturer’s instructions of the v3 Chromium Single Cell Reagent Kits (10X Genomics). Quality control of cDNA and final libraries was done using Bioanalyzer High Sensitivity DNA Analysis (Agilent) and libraries were sequenced using NovaSeq 6000 (Illumina) at Genomics Core facility at KU Leuven targeting 80,000 read pairs nucleus. Nuclei were aligned to the human GRCh38-3.0.0 transcriptome with “Include-introns= TRUE” using the CellRanger- 6.0.1 software (10X Genomics) according to the 10X Genomics’ instructions.

value: Cardiac

value: M

tag: type

value: tissue

tag: batch


title: Cardiac, Heart Failure, ICM-scar, s19

description:
Library name: GC123829
10x genomics


title: Sort-seq, 5SS stem loop library, bin 3

description:
Library name: 5ss_stem_bin03
Sort-seq


title: Sort-seq, 5SS stem loop library, bin 4

description:
Library name: 5ss_stem_bin04
Sort-seq


title: Sort-seq, 5SS stem loop library, bin 1

description:
Library name: 5ss_stem_bin01
Sort-seq


title: Cardiac, Heart Failure, ICM-scar, s18

description:
Library name: GC123828
10x genomics


title: Cardiac, non-Failure , Donor, s16

description:
Library name: GC108600
10x genomics

value: M/F


title: Sort-seq, 3SS and branch site stem loop library, bin 2

description:
Library name: 3ss_bs_stem_bin02
Sort-seq


title: Sort-seq, N47 random library, bin 16

description:
Library name: random_bin16
Sort-seq

value: N47 random library


title: Sort-seq, N47 random library, bin 15

description:
Library name: random_bin15
Sort-seq


title: Cardiac, Heart Failure, DCM, s14

description:
Library name: GC108598
10x genomics


title: Cardiac, Heart Failure, DCM, s13

description:
Library name: GC108597
10x genomics

value: F


title: Cardiac, non-Failure , Donor, s15

description:
Library name: GC108599
10x genomics


title: Sort-seq, N47 random library, bin 14

description:
Library name: random_bin14
Sort-seq


title: Sort-seq, 5SS stem loop library, input

description:
Library name: 5ss_stem_input
Sort-seq


title: Cardiac, Heart Failure, DCM, s12

description:
Library name: GC108596
10x genomics


title: Cardiac, Heart Failure, ICM, s11

description:
Library name: GC108595
10x genomics


title: Inoculated, 44 dpi, rep4

city: Pretoria

first: Dave

middle: Kenneth

last: Berger

state: Gauteng

address: Lynnwood  road

department: Dept. Plant and Soil Sciences

country: South Africa

institute: University of Pretoria

description: Library name: Zm_Cz_44dpi_rep4

data_processing:
Galaxy V24.1
Raw RNA-seq reads were assed using FastQC to evaluate the quality of data. Trimmomatic was used to process the data to remove adapter sequences, low quality reads (AVGQUAL > 20) and short reads (MINLEN  > 35).  High quality reads were then mapped to the concatenated maize-C. zeina genome using HiSAT2 with default settings. The number of reads mapped to each gene was then computed by htseq-count using the union mode with a minimum alignment quality of 10. Data normalisation and differential expression analyses were computed using DEseq2 with a single factor (group) and three factor levels (early (23 dpi), mid (30dpi) and late (44 dpi)). Pre-filtering (N > 38) was used to remove low expressed genes from the dataset.
Assembly: GCA_002844615.2 (Cercospora zeina) and GCA_902167145.1 (Maize)
Supplementary files format and content: Tab-delimited text file with normalized count values for each sample

organism:
Zea mays
Cercospora zeina

source_name: Leaf

extract_protocol:
Total RNA was isolated from each sample using the QIAzol lysis reagent (Qiagen, Hilden, USA) followed by purification using the NucleoSpin RNA purification kit (Machery-Nagel, Duren, Germany). 1 µg of each sample was used for library preparation
library preparation was done using a P3 PE100 kit (Illumina Inc. San Diego, USA) following manufacturer instructions

value: Leaf

value: Inoculated, 44 dpi


title: Sort-seq, N47 random library, bin 11

description:
Library name: random_bin11
Sort-seq

value: Saccharomyces cerevisiae


title: Inoculated, 44 dpi, rep3

description: Library name: Zm_Cz_44dpi_rep3


title: Sort-seq, N47 random library, bin 10

description:
Library name: random_bin10
Sort-seq

value: a his3DELTA1 leu2DELTA0 met15DELTA0 ura3DELTA0 his3::mScarletI met17::land71


title: Cardiac, Heart Failure, ICM, s10

description:
Library name: GC108594
10x genomics


title: Sort-seq, N47 random library, bin 12

description:
Library name: random_bin12
Sort-seq


title: Inoculated, 44 dpi, rep2

description: Library name: Zm_Cz_44dpi_rep2


title: Sort-seq, N47 random library, bin 9

description:
Library name: random_bin09
Sort-seq


title: Sort-seq, N47 random library, bin 8

description:
Library name: random_bin08
Sort-seq


title: Sort-seq, 5SS stem loop library, bin 2

description:
Library name: 5ss_stem_bin02
Sort-seq


title: Inoculated, 44 dpi, rep1

description: Library name: Zm_Cz_44dpi_rep1


title: Cardiac, Heart Failure, ICM-scar, s9

description:
Library name: GC108593
10x genomics


title: Sort-seq, N47 random library, bin 6

description:
Library name: random_bin06
Sort-seq


title: Sort-seq, N47 random library, bin 5

description:
Library name: random_bin05
Sort-seq


title: Cardiac, Heart Failure, DCM, s8

description:
Library name: GC1003523
10x genomics


title: Inoculated, 30 dpi, rep4

description: Library name: Zm_Cz_30dpi_rep4

value: Inoculated, 30 dpi


title: Sort-seq, N47 random library, bin 4

description:
Library name: random_bin04
Sort-seq


title: Inoculated, 30 dpi, rep3

description: Library name: Zm_Cz_30dpi_rep3


title: Cardiac, Heart Failure, DCM, s6

description:
Library name: GC1003521
10x genomics


title: Sort-seq, N47 random library, bin 3

description:
Library name: random_bin03
Sort-seq


title: Sort-seq, N47 random library, bin 13

description:
Library name: random_bin13
Sort-seq


title: Sort-seq, N47 random library, bin 2

description:
Library name: random_bin02
Sort-seq


title: Cardiac, Heart Failure, ICM, s5

description:
Library name: GC1003520
10x genomics


title: Sort-seq, N47 random library, bin 1

description:
Library name: random_bin01
Sort-seq


title: Inoculated, 30 dpi, rep2

description: Library name: Zm_Cz_30dpi_rep2


title: Sort-seq, N47 random library, input

description:
Library name: random_input
Sort-seq


title: Cardiac, Heart Failure, ICM-scar, s4

description:
Library name: GC1003519
10x genomics


title: Old male KO bio rep 1

city: Philadelphia

first: Sean

last: Louzon

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

description: Library name: Sample 9

data_processing:
Paired-end sequencing reads using publicly available Drop-seq Tools software
each mRNA read was tagged with its nucleus barcode and unique molecular identifier and aligned using STAR
digital expression matrices were assembled using a list of UMIs in each gene and within each cell
Raw digital expression matrices were combined and loaded into the R package Seurat
QC, filtering and DE analysis was done using the Seurat R package
Assembly: mm10
Supplementary files format and content: txt file containing raw digital expression matrices

source_name: Cortex

extract_protocol:
Cortical tissue was mechanically homogenized in a sucrose solution and nuclei were isolated through a sucrose gradient and ultracentrifugation
Nuclei were captured and libraries were prepared for sequencing using the sNucDrop-seq protocol described in Hu et al. 2017

value: Cortex

value: old

value: male


title: Inoculated, 30 dpi, rep1

description: Library name: Zm_Cz_30dpi_rep1


title: Cardiac, Heart Failure, ICM, s3

description:
Library name: GC1003518
10x genomics


title: Old male KO bio rep 2

description: Library name: Sample 10


title: Inoculated, 23 dpi, rep4

description: Library name: Zm_Cz_23dpi_rep4

value: Inoculated, 23 dpi


title: Old male WT bio rep 1

description: Library name: Sample 7

value: WT


title: Cardiac, Heart Failure, ICM-scar, s2

description:
Library name: GC1003517
10x genomics


title: Young male KO bio rep 3

description: Library name: Sample 6

value: young


title: Old male WT bio rep 2

description: Library name: Sample 8


title: Inoculated, 23 dpi, rep3

description: Library name: Zm_Cz_23dpi_rep3


title: Sort-seq, N47 random library, bin 7

description:
Library name: random_bin07
Sort-seq


title: Young male KO bio rep 2

description: Library name: Sample 5


title: Cardiac, Heart Failure, ICM, s1

description:
Library name: GC1003516
10x genomics

value: Cardiac


title: Young male KO bio rep 1

description: Library name: Sample 4


title: Inoculated, 23 dpi, rep2

description: Library name: Zm_Cz_23dpi_rep2


title: Young male WT bio rep 3

description: Library name: Sample 3


title: U87-ART-3

city: beijing

first: Li

last: tao

state: beijing

address: dongchen

institute: China Academy of Chinese Medical Sciences

data_processing:
Use fastp software to clean and filter the original offline data to obtain high-quality sequences (Clean Reads)
Use Hisat2 2.1.0 software to compare Clean Reads with reference genes (the reference genome version is GRCh 38.91)
Stringtie 1.3.3b software was used to compare the results and quantify the transcriptome expression; Normalize with TMM (trimmed mean of M values) algorithm, and finally calculate FPKM (Fragments PerKilobase Million) value of each gene
Differential analysis of gene expression between samples/groups using edgeR 3.30.3 software package
Assembly: GRCh 38.91
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

source_name: U87 cell,ART,Day9

extract_protocol:
Before and after 24h treatment with artemisinin, U87 and U251 glioma cell lysates were centrifuged at 3000 rpm for 15 min, and total RNA was extracted according to conventional procedures
After the total RNA passes the quality inspection, it is further purified and reverse transcribed to obtain double stranded cDNA, which is used as a template for PCR amplification to construct a cDNA library

value: brain

value: Glioma


title: Young male WT bio rep 2

description: Library name: Sample 2


title: Inoculated, 23 dpi, rep1

description: Library name: Zm_Cz_23dpi_rep1


title: Young male WT bio rep 1

description: Library name: Sample 1


title: IgG bio rep 3

description: Library name: Sample 6

library_source: genomic

data_processing:
Fastq files were aligned with Bowtie2
NGS plot was used to generate metaplots
deepTools was used to generate bigwig files
MACS3 was used for peak-calling
Assembly: mm10
Supplementary files format and content: bigwig files generated by deepTools from bam files aligned by Bowtie2
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: cortex

extract_protocol:
At 7 DIV, primary cortical astrocytes were collected in wash buffer (Kaya-Okue et al. 2019) and CUT&Tag was performed with anti-H2BE antibody (Millipore ABE1384) or Normal Rabbit Control IgG antibody (SInoBiological CR1).
Transposition reaction mix from Nextera Library Prep kit was used (Tagment DNA Enzyme 1 and Tagment DNA Buffer).

value: cortex

value: primary cortical astrocytes

tag: antibody


title: IgG bio rep 2

description: Library name: Sample 5

value: Normal Rabbit Control IgG antibody (SInoBiological CR1)


title: U87-ART-1


title: OPC-Con-2

value: Brain

value: OPCs

value: Room air


title: IgG bio rep 1

description: Library name: Sample 4


title: H2BE bio rep 3

description: Library name: Sample 3

value: anti-H2BE antibody (Millipore ABE1384)


title: Slc2a5 KO Microglia,OGD 6 hours and recovery for 1 day,rep2

city: Beijing

first: Daosheng

last: Ai

address: Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District

institute: Chinese Institute for Brain Research

description: Library name: KO_recovery_rep2

data_processing:
Raw RNA-seq reads were aligned to the mouse reference genome (GRCm38, UCSC) using HISAT2 and the GENCODE (mouse v32) gene annotation file. The count matrix was generated using FeatureCounts.
Assembly: GRCm38
Supplementary files format and content: OGD_RNAseq.csv

source_name: brain

extract_protocol:
Mice at an age of postnatal day (P)30–45 were anesthetized with isoflurane. They were perfused with cold PBS(Corning) through the heart. Brains were isolated and immediately immersed into cold hibernation medium (5mM KCl, 5mM NaOH, 5mM NaH2PO4, 0.5mM MgCl2, 20mM Na Pyruvate, 5.5mM Glucose, 200mM Sorbitol, pH 7.2-7.4, filtered with 0.22μm filters). Dissected brain hemispheres were cut into small pieces and incubated in cold hibernation medium (BrainBits, USA) containing papain (2mg /ml, Sigma) and DNase I (100 units, Sigma) at 37˚C for 30 min with intermittent flicking. The tissue was triturated into individual cell suspension by a siliconized Pasteur pipette with a fire-polished tip (BrainBits). Cell suspensions were added into Optiprep gradient (Brewer and Torricelli, 2007b) and centrifuged at 900 g for 15min at 4℃. We then removed most upper 5ml debris and collected specific Optiprep layers (neurons and astrocytes were enriched in upper layers while microglia were enriched in pellets). Cells from different layers were washed with cold hibernation medium without Ca2+ and Mg2+(BrainBits) and centrifuged at 600 g for 10 min at 4℃. Cell pellets were resuspended with a 500µl cold hibernation medium for sorting.
The RNA sequencing library was prepared according to the protocol for the SMARTer Stranded Total RNA-Seq Kit v2.

value: microglia

value: Male

value: OGD for 6 hours with 24hours recovery


title: Hm2 G+

description: Gene expression data from mouse E15.5 embryonic kidney ureteric cells expressing IlkT173I

value: IlkT173I homozygous

value: Ureteric


title: Slc2a5 KO Microglia,OGD 6 hours and recovery for 1 day,rep1

description: Library name: KO_recovery_rep1


title: Microglia,OGD 6 hours and recovery for 1 day,rep3

description: Library name: WT_recovery_rep3


title: U87-2

source_name: U87 cell,Control,Day9


title: WT P1 bio rep merged

data_processing:
Fastq files were aligned by Bowtie2
Assembly: mm10
Supplementary files format and content: deepTools was used to generate raw counts files

extract_protocol:
Cells were collected in cell lysis buffer (10mM TrisHCl ph7.5, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween20, 0.1% Digitonin)
Transposition reaction mix from Nextera Library Prep kit was used (Tagment DNA Enzyme 1 and Tagment DNA Buffer). Nextera primer sets with NEBNext Master Mix was used to generate libraries with AMPure beads used for cleanup.

value: astrocytes

value: WT


title: H2BE bio rep 1

description: Library name: Sample 1


title: WT P1 bio rep 3

data_processing:
Fastq files were aligned by Star
DESeq2 was used to obtain normalized counts
Assembly: mm10
Supplementary files format and content: normalized counts

extract_protocol:
Zymo Quick-RNA Miniprep kits were used to isolate RNA
RNA libraries were prepared for sequencing using TruSeq stranded mRNA library prep kit


title: WT P1 bio rep 2


title: U87-1


title: Microglia,OGD 6 hours and recovery for 1 day,rep1

description: Library name: WT_recovery_rep1

value: OGD for 6 hours without 24hours recovery


title: Microglia,OGD 6 hours and recovery for 1 day,rep2

description: Library name: WT_recovery_rep2

value: brain


title: Male P28 bio rep 3

source_name: male forebrain cortical nuclei

value: male forebrain cortical nuclei

value: CAG-Sun1/sfGFP +/-; NEX-Cre +/-


title: U251-ART-3

source_name: U251 cell,ART,Day9

value: Glioma


title: Slc2a5 KO Microglia,OGD 6 hours and recovery for 1 day,rep3

description: Library name: KO_recovery_rep3


title: Male P28 bio rep 4


title: Slc2a5 KO Microglia,OGD 6 hours,rep3

description: Library name: KO_rep3


title: U251-ART-2


title: WT P1 bio rep 1

value: cortex


title: U251-ART-1


title: Male P28 bio rep 1


title: Male P28 bio rep 2


title: Male P14 bio rep 4


title: U87-3


title: Slc2a5 KO Microglia,OGD 6 hours,rep2

description: Library name: KO_rep2


title: U87-ART-2


title: Male P14 bio rep 2


title: U251-3

source_name: U251 cell,Control,Day9


title: Male P14 bio rep 3


title: H2BE bio rep 2

description: Library name: Sample 2

value: primary cortical astrocytes


title: Slc2a5 KO Microglia,OGD 6 hours,rep1

description: Library name: KO_rep1


title: Male P14 bio rep 1


title: Microglia,OGD 6 hours,rep3

description: Library name: WT_rep3


title: Male P0 bio rep 2


title: U251-2


title: Male P0 bio rep 3


title: U251-1


title: Microglia,OGD 6 hours,rep2

description: Library name: WT_rep2


title: Male P0 bio rep 1


title: patient 2.02

type: genomic

city: Oslo

first: Gunhild

last: Trøen

address: Ullernchausseen 70

department: Pathology

country: Norway

institute: Oslo University Hospital

hyb_protocol: Analysis was performed using cytogenetic microarrays, OncoScan CNV Plus Assay (Thermo Fisher Scientific), following the manufacturer recommendations.

scan_protocol: Arrays were scanned on the GeneChip Scanner 300 7G and array fluorescence intensity (CEL) files were automatically generated by the Affymetrix GeneChip Command Console (AGCC) Software.

data_processing:
The CEL-files were further processed using the Chromosome Analysis Suite (ChAS 4.0) software using human genome version hg38 to produce OSCHP files.
Primary data description: Copy number data

source_name: clonal B-cells

label_protocol: As per manufacturer (Thermo Fisher Scientific).

extract_protocol: Clonal B cells were acquired using fluorescence-activated cell sorting from mononuclear cell, obtained from cryopreserved bone marrow or peripheral blood. Genomic DNA was extracted using the Qiagen AllPrep DNA/RNA Micro Kit. DNA quality and quantity were assessed using a Nanodrop Spectrophotometer and Qubit Fluorometer.

tag: diagnosis

value: Cold agglutinin disease (CAD)

value: Sorted clonal B-cells


title: patient 1.37


title: Mouse testis_valine_rep4

city: Jingzhou

first: Fang

last: Wang

state: Hubei

address: West Campus of Yangtze University, Jingzhou District

institute: Yangtze University

data_processing:
Illumina Casava1.7 software used for basecalling.
Clean Data were mapped to the reference genome using HISAT2. HISAT2 is a specialized software for transcriptome sequencing reads mapping, can identify exon-exon junctions by splitting the mapped reads and mapping them to the reference genome again--rna-strandness RF --dta–t–p 4.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample .

source_name: testis

extract_protocol:
Mouse testis were extracted and placed in liquid nitrogen,and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: testis

value: valine


title: patient 1.34


title: Mouse testis_valine_rep3


title: Mouse testis_valine_rep2


title: patient 1.32


title: patient 1.31


title: patient 1.30


title: Mouse testis_valine_rep1


title: patient 1.26


title: Mouse testis_control_rep4

value: control


title: patient 1.23


title: Wild type, hemispheres ipsilateral to infarction

description: Library name: WT_ispi

data_processing:
Raw scRNA-seq and snRNA-seq reads were preprocessed using CellRanger and subsequently aligned to the mouse reference genome (GRCm38, UCSC) with gene annotations from GENCODE (mouse v32)
Assembly: GRCm38
Supplementary files format and content: OGD_RNAseq.csv

extract_protocol:
After samples harvested, tissues were washed in ice-cold RPMI1640 and dissociated using Multi-tissue dissociation kit 2(Miltenyi Catalog No.130-110-204) from Miltenyi Biotec as instructions. DNase treatment was optional according to the viscosity of the homogenate. Cell count and viability was estimated using fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after removal erythrocytes (Miltenyi Catalog No.130-094-183) and then debris and dead cells removal was decided to be performed or not (Miltenyi Catalog No.130-109-398/130-090-101). Finally fresh cells were washed twice in the RPMI1640 and then resuspended at 1×106 cells per ml in 1×PBS and 0.04% bovine serum albuminat.
For single-cell RNA sequencing, the library was constructed following the SeekOne® MM Single Cell 3' Library Preparation Kit protocol. For single-nucleus RNA sequencing, the library preparation adhered to the protocol for the SeekOne® Digital Droplet Single Cell 3' Library Preparation Kit.

value: Wild Type

tag: age

value: Male

value: tMCAO for 1 hours with 24hours reperfusion


title: patient 1.25


title: Male P0 bio rep 4


title: Mouse testis_control_rep3


title: patient 1.07


title: Mouse testis_control_rep2


title: patient 1.06


title: Wild type, cortex

description: Library name: WT_cortex

source_name: brain,cortex

value: brain,cortex


title: Microglia,OGD 6 hours,rep1

description: Library name: WT_rep1

value: microglia


title: Slc2a5 KO, hemispheres contralateral to infarction

description: Library name: KO_contra


title: Fracture+PDX-Female-DRG-3

status: Public on Nov 07 2025

city: Durham

first: Sharat

last: Chandra

state: NC

address: 3 Genome Court

department: Department of Anesthesiology

institute: Duke University

description: Library name: sample18

data_processing:
Cutadapt (v1.10) and in-house Perl scripts were used to remove reads containing adaptors, low-quality bases, or undetermined bases
sequence quality was verified using FastQC (V:0.10.1)
We used HISAT2(V: 2.0) to map reads to the genome. The mapped reads of each sample were assembled using StringTie(V:1.3.4).
All transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare
The ﬁnal transcriptome was generated, StringTie and ballgown was used to estimate the expression levels of all transcripts.
Assembly: mm10
Supplementary files format and content: tab-deliminited text file including raw counts and RPKM value for each Sample

source_name: DRG

extract_protocol:
RNA was harvested using a Qiagen mini prep kit. Approximately 6–7 µg of total RNA was used for the construction of sequencing libraries.
A poly(A) RNA sequencing library was prepared following Illumina’s TruSeq Stranded mRNA sample preparation protocol. RNA integrity was first checked on an Agilent Technologies 2100 Bioanalyzer. Poly(A)-containing mRNAs were purified using oligo(dT)-magnetic beads over two rounds. Following purification, the enriched RNA was fragmented in a divalent cation buffer at an elevated temperature.

value: DRG

value: Fracture+PDX

value: Female


title: Fracture+PDX-Female-DRG-1

description: Library name: sample16


title: Fracture+PDX-Female-DRG-2

description: Library name: sample17


title: Slc2a5 KO, hemispheres ipsilateral to infarction

description: Library name: KO_ispi

value: brain


title: Fracture+PDX-Male-DRG-3

description: Library name: sample15


title: Fracture-Female-DRG-3

description: Library name: sample12

value: Fracture


title: Fracture+PDX-Male-DRG-1

description: Library name: sample13


title: Fracture+PDX-Male-DRG-2

description: Library name: sample14


title: Wild type, hemispheres contralateral to infarction

description: Library name: WT_contra


title: Untreated microglial cells

city: Lucknow

first: Shailendra K

last: Saxena

state: UP

address: Chowk

department: Centre for Advanced Research

country: India

institute: King George's Medical University

data_processing:
Stringent quality control of paired-end sequence reads of all the samples was done using NGS QC Tool kit, then mapped to hg38 whole genome using TopHat pipeline .
Cufflink and Cuffdiff pipeline was used for identification of transcript coding regions followed by quantitation and annotation using default parameters
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: Cell culture

growth_protocol: CHME3 human microglia cells were cultured at 37 °C, as per the standard protocol.

extract_protocol:
Total RNA was isolated from control and treated human microglia by SV total RNA isolation system (Promega) and quality control was performed with the Agilent 2100 bioanalyzer
Sequencing libraries were generated using TruSeq RNA Library Prep Kits for Illumina® (NEB, USA)

treatment_protocol: Cells were treated with 5µg/ml (EC50) of drug

tag: passages

value: 4 to 6

value: untreated


title: Treated microglial cells

value: muscarinic receptor antagonists


title: Fracture-Female-DRG-1

description: Library name: sample10

tag: Sex


title: Fracture-Male-DRG-3

description: Library name: sample9


title: Fracture-Male-DRG-2

description: Library name: sample8


title: Fracture-Female-DRG-2

description: Library name: sample11


title: patient 1.24

value: Cold agglutinin disease (CAD)

value: Sorted clonal B-cells


title: patient 1.22


title: Sham-Female-DRG-2

description: Library name: sample5

value: Sham


title: Slc2a5 KO, cortex

description: Library name: KO_cortex


title: Sham-Female-DRG-3

description: Library name: sample6


title: Fracture-Male-DRG-1

description: Library name: sample7


title: Sham-Female-DRG-1

description: Library name: sample4


title: Sham-Male-DRG-3

description: Library name: sample3


title: Sham-Male-DRG-2

description: Library name: sample2


title: Sham-Male-DRG-1

description: Library name: sample1


title: Mouse testis_control_rep1

value: testis

value: control


title: Mouse tumor, EZH2wildtype, biol rep5

city: Montreal

first: William

last: Muller

state: Quebec

address: 1160 Av des Pins O

department: Biochemistry

institute: McGill University

description:
Library name: WTEIC_4432
WTEIC_4432

data_processing:
Adaptor sequences and low quality score bases (Phred score < 30) were first trimmed using Trimmomatic (Bolger et al., 2014).
The resulting reads were aligned to the GRCm38 mouse reference genome assembly, using STAR (Dobin et al., 2012).
Read counts were obtained using HTSeq (Anders et al 2015) with parameters -m intersection-nonempty -stranded=reverse.
For all downstream analyses, we excluded lowly-expressed genes with an average read count lower than 10 across all samples.
Raw counts were normalized using edgeR’s TMM algorithm (Robinson et al., 2010) and were then transformed to log2-counts per million (logCPM) using the voom function implemented in the limma R package (Ritchie et al., 2015).
To assess differences in gene expression levels, we fitted a linear model using limma’s lmfit function. Nominal p-values were corrected for multiple testing using the Benjamini-Hochberg method.
Assembly: GRCm38-mm10 mouse reference genome
Supplementary files format and content: tsv file containing raw counts for each sample

source_name: Mouse mammary gland tumors

growth_protocol: Tumors were harvested from genetically engineered mice that had been treated with doxycycline (doxycycline inducible breast cancer model) until they reached the experimental endpoint.

extract_protocol:
Total RNA from flash-frozen tumor pieces or cell pellets was extracted and purified using the FavorPrep Tissue Total RNA Mini Kit (Favorgen, FATRK001) according to manufacturer’s protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Doxycycline water supplied

value: Mouse mammary gland tumors

value: Doxycycline induced at age 8-12weeks until tumor reach endpoint


title: Mouse tumor, EZH2wildtype, biol rep4

description:
Library name: WTEIC_434
WTEIC_434


title: P8

city: Guangzhou

first: Yage

last: Nie

address: No.74 Zhongshan Rd.2, Guangzhou

institute: Sun Yat-sen University

data_processing:
Cell Ranger V1.2.0
‘cellranger-atac count’ was used to perform read filtering, alignment, peak calling, and count matrix generation from fastq files per sample
Assembly: mm10
Supplementary files format and content: tsv file include barcode, peak position and peak signal for each sample

source_name: heart

extract_protocol:
Isolated hearts were washed with DPBS twice, and then collected in 1.5 mL EP tubes. Tissues were minced into pieces (~1 mm) on ice using scissors, and digested into single-cell suspensions with 1 mg/ml type II collagenase (17101015, GIBCO) and 1 mg/ml type IV collagenase (17104019, GIBCO) for 30min at 37 ℃ with intermittent shaking. The dissociated cells were separated and remaining undigested tissue were digested again with fresh digestion buffer. Digested suspension was passed through 70um strainer (Biologix).Dissociated cells were centrifuged at 300 g for 5 min at 4 °C, then re-suspended in 1 mL of cold DPBS with 0.1% BSA. After passing through a 40um cell strainer (Biologix), cells were washed twice, centrifuged at 300 g for 5 min at 4 °C.To isolate nuclei, 500,000 cell pellets were re-suspended in 100 uL chilled lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin - from (Corces, Trevino et al. 2017) supplemented with 1% BSA), and pipette mix 10X. After incubation for 5 min on ice, add 1 ml chilled Wash Buffer ((10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA) to the lysed cells. Pipette mix 5x, then centrifuged at 300 g for 5 min at 4 °C. Based on number of cells used for isolation and assuming ~50% nuclei loss during cell lysis, resuspend in chilled Diluted Nuclei Buffer (PN-2000153, 10x Genomics). If cell debris and large clumps are observed, pass through a cell strainer. For low volume, use a 40µm Flowmi Cell Strainer (H13680-0040, Bel-Art) to minimize volume loss.
The scATAC library was prepared using the 10x Genomics platform with the Chromium Single Cell ATAC Library & Gel Bead Kit (10x Genomics, Pleasanton, California) as instructed by the manufacturer. A total of 15,000 nuclei per sample were used as input for single-cell ATAC-seq following the manufacturer’s instructions. Briefly, after tagmentation, the cells were loaded on a Chromium Controller Single-Cell instrument to generate single-cell Gel Bead-In-Emulsions (GEMs) followed by linear PCR as described in the 10X scATAC-seq protocol using a Veriti 96-well thermal cycler (BioRad, 1851197). After breaking the GEMs, the barcoded tagmented DNA was purified with SPRIselect Reagent Kit (Beckman Coulter, Pasadena, CA) and further amplified to enable sample indexing and enrichment of scATAC-seq libraries. The final libraries were quantified using Bioanalyzer (Agilent) and QuBit (Thermofisher) analysis and then sequenced in MGISeq-2000FCL (MGI Tech Co., Ltd., China) with 100-bp paired-end read length targeting a depth of 30,000–50,000 reads per cell.
single cell ATACseq

value: heart

value: sham


title: Mouse tumor, EZH2wildtype, biol rep3

description:
Library name: WTEIC_3321
WTEIC_3321


title: Mouse tumor, EZH2wildtype, biol rep1

description:
Library name: WTEIC_2883
WTEIC_2883


title: NAR14

value: apex resection


title: NAR7


title: Mouse tumor, EZH2wildtype, biol rep2

description:
Library name: WTEIC_2943
WTEIC_2943


title: P15


title: AR7


title: Mouse tumor, EZH2knockout, biol rep5

description:
Library name: KOEIC_4970
KOEIC_4970


title: Mouse tumor, EZH2knockout, biol rep2

description:
Library name: KOEIC_0729
KOEIC_0729


title: KH2235, Day 6 Red, Repeat 6

city: Boston

middle: B

last: Mair

address: 677 Huntington Avenue

department: Molecular Metabolism

institute: Harvard TH Chan School of Public Health

description:
Library name: 20180510_CH36_CH5502_S12
Column name in NormalizedCounts_LLvsSLRNA-Seq.xlsx: CH36

data_processing:
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/). Raw reads were examined for quality issues using FastQC (v0.11.8) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing were suitable for further analysis. To perform additional quality checks of the data, all reads were aligned to Wormbase assembly WBcel235, release WS272 of the C. elegans genome (Project PRJNA13578 (N2 strain)) using STAR (v. 101 2.6.1d) (Dobin et al., 2013). Alignments were checked for evenness of coverage, rRNA content, genomic context of alignments (for example, alignments in known transcripts and introns), complexity and other quality checks using a combination of FastQC, Qualimap (García-Alcalde et al., 2012), (http://doi.org/10.1093/bioinformatics/bts503), MultiQC (https://github.com/ewels/MultiQC) and custom tools.
To quantitate the reads corresponding to each transcript, quasi alignment was performed using Salmon (v. 0.14.2) (Patro et al., 2017), outputting the transcripts Per Million (TPM) measurements per isoform. Differential expression at the gene level was called with DESeq2 (Love et al., 2014), using counts per gene estimated from the Salmon quasi alignments by tximport.
Assembly: Wormbase assembly WBcel235, release WS272 of the C. elegans genome (Project PRJNA13578 (N2 strain)) using STAR (v. 101 2.6.1d)
Supplementary files format and content: NormalizedCounts_LLvsSLRNA-Seq.xlsx: Excel file that contains in each column each sample and the normalized count for each gene.

organism: Caenorhabditis elegans

source_name: Whole-body

extract_protocol:
RNA was extracted using Qiagen miRNeasy kit. Submitted 300 ng of each sample for sequencing.
RNA libraries for RNA seq were prepared using Roche Kapa stranded mRNA HyperPrep, following manufacter's protocol.

value: Whole-body

tag: group

value: Red

value: Day 6


title: Mouse tumor, EZH2knockout, biol rep4

description:
Library name: KOEIC_4331
KOEIC_4331


title: KH2235, Day 6 Red, Repeat 5

description:
Library name: 20180510_CH34_CH5502_S10
Column name in NormalizedCounts_LLvsSLRNA-Seq.xlsx: CH34


title: KH2235, Day 6, Green, Repeat 6

description:
Library name: 20180510_CH35_CH5502_S11
Column name in NormalizedCounts_LLvsSLRNA-Seq.xlsx: CH35

value: Green


title: Mouse tumor, EZH2knockout, biol rep1

description:
Library name: KOEIC_0384
KOEIC_0384


title: KH2235, Day 6, Green, Repeat 4

description:
Library name: 20180510_CH31_CH5502_S7
Column name in NormalizedCounts_LLvsSLRNA-Seq.xlsx: CH31


title: LysMCre 5-8 4h Carrageenan

city: Stony Brook

first: Martin

last: Kaczocha

address: Health Sciences Center

institute: Stony Brook University

description:
Library name: Sample 11
Column name in normalized_counts_carrageenan_LysMVSFlox.tsv: 301270_RNA_11
normalized_counts_carrageenan_LysMVSFlox.tsv

data_processing:
Raw paired-end reads were trimmed using cutadapt to remove adapter seqeunces and low-quality bases. R2 reads were used to collapse PCR duplicates using Lexogen LUTHOR pipeline. Collasped reads were aligned with the Mus Musculus reference genome using STAR aligner.
Assembly: Reads were aligned to the Mus musculus reference genome GRCm38 using Ensembl release 101 annotations. ERCC and SIRV spike-in controls were included in the reference during alignment.
Supplementary files format and content: tab-separated values normalized_counts file includes normalized counts for each sample
Supplementary files format and content: tab-separated values DEresults file include differential expression for all samples

source_name: paw

growth_protocol: Adult mice were bred and maintained under Stony Brook University Institutional Animal Care and Use Committee protocol with ad libitum access to food and water in temperature-controlled environment.

extract_protocol:
Four-hours post injection, hind paws were dissociated into single cell suspension. Ly6G- myeloid cell populations were sorted by flow cytometry. Total RNA was extracted from the sorted cells using PureLink Micro RNA Kit.
Library preparation was prepared by Lexogen NGS services with LUTHOR 3' mRNA seq kit with integrated Unique Molecular Identifiers (UMIs). Libraries were seqenced on the Illumina NovaSeq platform using paired-end reads.

treatment_protocol: Mice were injected in the hind paw with either sterile saline or 1% carrageenan.

value: paw

value: sorted cells

value: Ly6G- sorted myeloid cells

value: LysMCre-cKO

value: Carrageenan


title: KH2235, Day 6 Red, Repeat 4

description:
Library name: 20180510_CH32_CH5502_S8
Column name in NormalizedCounts_LLvsSLRNA-Seq.xlsx: CH32


title: LysMCre 9-12 4h Carrageenan

description:
Library name: Sample 12
Column name in normalized_counts_carrageenan_LysMVSFlox.tsv: 301270_RNA_12
normalized_counts_carrageenan_LysMVSFlox.tsv


title: Mouse tumor, EZH2knockout, biol rep3

description:
Library name: KOEIC_0794
KOEIC_0794


title: AR14


title: LysMCre 9-12 4h Saline

description:
Library name: Sample 9
Column name in normalized_counts_saline_LysMCreVsFlox.tsv: 301270_RNA_9
normalized_counts_saline_LysMCreVsFlox.tsv

value: Saline


title: KH2235, Day 6, Green, Repeat 5

description:
Library name: 20180510_CH33_CH5502_S9
Column name in NormalizedCounts_LLvsSLRNA-Seq.xlsx: CH33


title: LysMCre 5-8 4h Saline

description:
Library name: Sample 8
Column name in normalized_counts_saline_LysMCreVsFlox.tsv: 301270_RNA_8
normalized_counts_saline_LysMCreVsFlox.tsv


title: LysMCre 1-4 4h Saline

description:
Library name: Sample 7
Column name in normalized_counts_saline_LysMCreVsFlox.tsv: 301270_RNA_7
normalized_counts_saline_LysMCreVsFlox.tsv


title: Flox 8-10 4h Carrageenan

description:
Library name: Sample 6
Column name in normalized_counts_carrageenan_LysMVSFlox.tsv: 301270_RNA_6
normalized_counts_carrageenan_LysMVSFlox.tsv

value: Flox


title: KH2235, Day 6, Green, Repeat 2

description:
Library name: 20180510_CH27_CH5502_S3
Column name in NormalizedCounts_LLvsSLRNA-Seq.xlsx: CH27


title: KH2235, Day 6 Red, Repeat 2

description:
Library name: 20180510_CH28_CH5502_S4
Column name in NormalizedCounts_LLvsSLRNA-Seq.xlsx: CH28


title: Flox 4-7 4h Carrageenan

description:
Library name: Sample 5
Column name in normalized_counts_carrageenan_LysMVSFlox.tsv: 301270_RNA_5
normalized_counts_carrageenan_LysMVSFlox.tsv


title: Flox 8-10 4h Saline

description:
Library name: Sample 3
Column name in normalized_counts_saline_LysMCreVsFlox.tsv: 301270_RNA_3
normalized_counts_saline_LysMCreVsFlox.tsv


title: TJ1052, repo-1 RNAi, Day 1, Repeat 4

description:
Library name: 20180929_D10_TJ1052_repo-1_RNAi_SD6021-2_S20
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:age1_repo1_D10

data_processing:
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/). Raw reads were examined for quality issues using FastQC (v0.11.8) (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing were suitable for further analysis. To perform additional quality checks of the data, all reads were aligned to Wormbase assembly WBcel235, release WS272 of the C. elegans genome (Project PRJNA13578 (N2 strain)) using STAR (v. 101 2.6.1d) (Dobin et al., 2013). Alignments were checked for evenness of coverage, rRNA content, genomic context of alignments (for example, alignments in known transcripts and introns), complexity and other quality checks using a combination of FastQC, Qualimap (García-Alcalde et al., 2012), (http://doi.org/10.1093/bioinformatics/bts503), MultiQC (https://github.com/ewels/MultiQC) and custom tools.
To quantitate the reads corresponding to each transcript, quasi alignment was performed using Salmon (v. 0.14.2) (Patro et al., 2017), outputting the transcripts Per Million (TPM) measurements per isoform. Differential expression at the gene level was called with DESeq2 (Love et al., 2014), using counts per gene estimated from the Salmon quasi alignments by tximport.
Assembly: Wormbase assembly WBcel235, release WS272 of the C. elegans genome (Project PRJNA13578 (N2 strain)) using STAR (v. 101 2.6.1d)
Supplementary files format and content: NormalizedCounts_REPO-1RNA-Seq.xlsx: Excel file that contains in each column each sample and the normalized count for each gene.

source_name: Whole body

value: Whole body

value: repo-1 RNAi


title: Flox 1-3 4h Carrageenan

description:
Library name: Sample 4
Column name in normalized_counts_carrageenan_LysMVSFlox.tsv: 301270_RNA_4
normalized_counts_carrageenan_LysMVSFlox.tsv


title: KH2235, Day 6, Green, Repeat 1

description:
Library name: 20180510_CH25_CH5502_S1
Column name in NormalizedCounts_LLvsSLRNA-Seq.xlsx: CH25


title: KH2235, Day 6 Red, Repeat 1

description:
Library name: 20180510_CH26_CH5502_S2
Column name in NormalizedCounts_LLvsSLRNA-Seq.xlsx: CH26


title: TJ1052, Empty Vector, Day 1, Repeat 4

description:
Library name: 20180929_D9_TJ1052_ev_SD6021-2_S19
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:age1_ctrl_D9

value: Empty vector


title: MQ130, repo-1 RNAi, Day 1, Repeat 4

description:
Library name: 20180929_D8_MQ130_repo-1_RNAi_SD6021-2_S18
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:clk1_repo1_D8


title: LysMCre 1-4 4h Carrageenan

description:
Library name: Sample 10
Column name in normalized_counts_carrageenan_LysMVSFlox.tsv: 301270_RNA_10
normalized_counts_carrageenan_LysMVSFlox.tsv


title: RAW_WT_mock_3_R1_001

city: Montpellier

first: Nadine

last: LAGUETTE

address: 1919 Rte de Mende

country: France

institute: Institut de Génétique Moléculaire de Montpellier

description:
Library name: Sample18
Colum_name_in_raw_mecp2_counts_all: RAW_WT_mock-3

data_processing:
MinION: MinKNOW24.02.8, Bream7.9.8, Configuration5.9.18, Dorado base-calling 7.3.11, MinKNOW Core5.9.12.
Illumina base-calling: RTA3 sofware
trimed sequence reads were mapped to gemone mm9  using minimap2 (v.2.28)
Read count extraction were performed using telescope (v.1.0.3)
Assembly: mm9
Supplementary files format and content: fastq file, RNA or DNA sequence

extract_protocol:
WT-RAW264.7 and RAW Mecp2 KO : extraction ARN kit RTN350. MEF cyDNA extraction: STAR Protocol, Isolation of endogenous cytosolic DNA from cultured cells
RNAseq: kit stranded mRNA Prep Ligation d’Illumina. CyDNAseq: MinION Barcoding Kit 24 V14 (SQK-NBD114.24)

value: WT

value: mock


title: MQ130, Empty Vector, Day 1, Repeat 4

description:
Library name: 20180929_D7_MQ130_ev_SD6021-2_S17
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:clk1_ctrl_D7


title: RAW_WT_mock_2_R1_001

description:
Library name: Sample17
Colum_name_in_raw_mecp2_counts_all: RAW_WT_mock-2


title: KH2235, Day 6 Red, Repeat 3

description:
Library name: 20180510_CH30_CH5502_S6
Column name in NormalizedCounts_LLvsSLRNA-Seq.xlsx: CH30


title: Da1116, repo-1 RNAi, Day 1, Repeat 4

description:
Library name: 20180929_D4_DA1116_repo-1_RNAi_SD6021-2_S14
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:eat2_repo1_D4


title: VC222, Empty Vector, Day 1, Repeat 4

description:
Library name: 20180929_D5_VC222_ev_SD6021-2_S15
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:raga1_ctrl_D5


title: RAW_Mecp2KO_mock_2_R1_001

description:
Library name: Sample14
Colum_name_in_raw_mecp2_counts_all: RAW_Mecp2KO_mock-2

value: MECP2 KO


title: RAW_WT_mock_1_R1_001

description:
Library name: Sample16
Colum_name_in_raw_mecp2_counts_all: RAW_WT_mock-1


title: RAW_Mecp2KO_mock_3_R1_001

description:
Library name: Sample15
Colum_name_in_raw_mecp2_counts_all: RAW_Mecp2KO_mock-3


title: RAW_Mecp2KO_mock_1_R1_001

description:
Library name: Sample13
Colum_name_in_raw_mecp2_counts_all: RAW_Mecp2KO_mock-1


title: KH2235, Day 6, Green, Repeat 3

description:
Library name: 20180510_CH29_CH5502_S5
Column name in NormalizedCounts_LLvsSLRNA-Seq.xlsx: CH29

value: Whole-body


title: DA1116, Empty Vector, Day 1, Repeat 4

description:
Library name: 20180929_D3_DA1116_ev_SD6021-2_S13
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:eat2_ctrl_D3


title: 6-Raw_wt_ds_S6_R1_001_val1

description:
Library name: Sample12
Colum_name_in_raw_counts_all: Raw_wt_ds_S6

value: dsDNA


title: Wild type N2, repo-1 RNAi, Day 1, Repeat 4

description:
Library name: 20180929_D2_N2_repo-1_RNAi_SD6021-2_S12
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:WT_repo1_D2

value: Wild type


title: 5-Raw_wt_ds_S5_R1_001_val1

description:
Library name: Sample11
Colum_name_in_raw_counts_all: Raw_wt_ds_S5


title: Wild type N2, Empty Vector, Day 1, Repeat 4

description:
Library name: 20180929_D1_N2_ev_SD6021-2_S11
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:WT_ctrl_D1


title: 4-Raw_wt_ds_S4_R1_001_val1

description:
Library name: Sample10
Colum_name_in_raw_counts_all: Raw_wt_ds_S4


title: TJ1052, repo-1 RNAi, Day 1, Repeat 3

description:
Library name: 20180929_C10_TJ1052_repo-1_RNAi_SD6021-2_S10
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:age1_repo1_C10


title: TJ1052, Empty Vector, Day 1, Repeat 3

description:
Library name: 20180929_C9_TJ1052_ev_SD6021-2_S9
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:age1_ctrl_C9


title: Flox 4-7 4h Saline

description:
Library name: Sample 2
Column name in normalized_counts_saline_LysMCreVsFlox.tsv: 301270_RNA_2
normalized_counts_saline_LysMCreVsFlox.tsv


title: MQ130, repo-1 RNAi, Day 1, Repeat 3

description:
Library name: 20180929_C8_MQ130_repo-1_RNAi_SD6021-2_S8
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:clk1_repo1_C8


title: 2-Raw_wt_mock_S2_R1_001_val1

description:
Library name: Sample08
Colum_name_in_raw_counts_all: Raw_wt_mock_S2


title: 1-Raw_wt_mock_S1_R1_001_val1

description:
Library name: Sample07
Colum_name_in_raw_counts_all: Raw_wt_mock_S1


title: VC222, repo-1 RNAi, Day 1, Repeat 3

description:
Library name: 20181004_C6_VC222_repo-1_RNAi_SD6021-26_S1
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:raga1_repo1_C6


title: Flox 1-3 4h Saline

description:
Library name: Sample 1
Column name in normalized_counts_saline_LysMCreVsFlox.tsv: 301270_RNA_1
normalized_counts_saline_LysMCreVsFlox.tsv


title: VC222, repo-1 RNAi, Day 1, Repeat 4

description:
Library name: 20180929_D6_VC222_repo-1_RNAi_SD6021-2_S16
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:raga1_repo1_D6


title: VC222, Empty Vector, Day 1, Repeat 3

description:
Library name: 20180929_C5_VC222_ev_SD6021-2_S5
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:raga1_ctrl_C5


title: Hashtags of samples pooled across conditions

first: Qiu Chang

last: Wu

address: 220 Longwood Ave

department: Systems Biology

institute: Harvard University

description: MULTI-seq (McGinnis et al. 2019)

data_processing:
The sequencing libraries were demultiplexed using Bcl2fastq (Illumina) and concatenated across multiple sequencing runs. The demultiplexed Fastq files were merged for the same libraries and individually processed using Cellranger (v6.1.2) Gene Expression Pipeline. Cellranger aggr function (see attached aggregation.csv file for input) was used for integrating multiple samples. Alignments were performed using M. musculus Ensembl release 84 mm10 v1.2.0 cDNA reference. The MULTI-seq library Fastq files were processed using CITE-seq-Count tool (v1.4.5) to determine sample identity of pooled cells. Sample barcode identity assignments to cells were performed using a custom python-based adaption inspired by the deMULTIplex R package.
Assembly: M. musculus Ensembl release 84 mm10
Supplementary files format and content: Gene expression output: gex_barcode.tsv.gz, gex_features.tsv.gz, gex_matrix.mtx.gz, gex_cell_metadata.tsv.gz
Supplementary files format and content: Hashtag  output: ht_barcode.tsv.gz, ht_features.tsv.gz, ht_matrix.mtx.gz
Library strategy: MULTI-seq Hashing

source_name: spleen and bone marrow

extract_protocol:
Tissue Harvesting Femur, tibiae, and spleen were harvested following euthanasia and submerged in SB5 buffer (phosphate-buffered saline (PBS) supplemented with 0.2% (w/v) bovine serum albumin (BSA), 0.08% (w/v) glucose, and 5 mM of Ethylenediaminetetraacetic acid (EDTA)). Tissue harvest methods are described in detail in Swaminathan et al.3. In brief, for bone marrow samples, the ends of the bones were cut and flushed with SB5 using a 26-gauge needle and 5 mL syringe. Harvested bone marrow was filtered through a 100 µM cell strainer. For spleen samples, spleens were placed onto a staining buffer-wetted 100 µM cell strainer and macerated through using the rubber side of a syringe plunger. The samples were washed with more SB5 and pelleted at 2000rpm for 10 minutes. Bone marrow and spleen samples were then processed into single-cell suspensions by adding 2 mL of SB5 and triturating cell pellet using a P1000 pipette and a large orifice pipet tip.  Singe cell RNA sequencing (scRNAseq) of bone marrow and spleen cells CD117 positive cell enrichment Harvested tissue samples were first enriched for CD117+ cells. Bone marrow and spleen cell samples were washed using Easy Sep buffer (PBS, 2% fetal bovine serum (FBS), and 1 mM EDTA) and enriched for CD117 expressing cells using EasySepTM Mouse CD117 Positive Selection Kit. The enrichment was performed largely following the manufacturer’s protocol; however, all room temperature steps were instead performed at 4oC in a walk-in cold room.  Live cell enrichment using density centrifugation Following CD117 enrichment, dead cell and debris were removed using gradient centrifugation in OptiPrep. Solutions of 40%, 18%, 12%, and 5% OptiPrep were prepared using weight by volume (w/v) and pre-chilled. Cells were resuspended in 0.5 mL PBS and mixed with 1 mL of 40% OptiPrep in a 5 mL FACS tube. 18%, 12%, and 5% OptiPrep were sequentially and carefully overlay on-top of the cell sample. The samples were then spun at 800g for 15 minutes with the centrifuge break off to prevent disruption of gradient. The live cell layer, which formed between the 40% and 18% interface, was collected, and washed using cold PBS.  MULTIseq labeling of cell samples To reduce technical variability from sample processing, we performed MULTIseq labelling to multiplex samples for 10X Chromium-based encapsulation. Samples were labeled with MULTI-Seq Lipid-Modified Oligos and unique sample barcode oligos following the MULTI-Seq protocol (see "Sample_hashing_barcodes.csv" for MULTI-Seq barcodes per sample). Antibody-based hashing methods were tested for these cell samples but ultimately not used due to poor labeling of reticulocytes which lack of the hashing epitope.
Single cell encapsulation and library prep Following MULTI-seq sample labeling, samples were pooled in equal ratios and cells were resuspended in PBS and 0.04% BSA at 1000 cells/uL prior to cell encapsulation. To help with demultiplexing, single injection condition pools were run individually, and an all-sample pool was run in another, for a total of five unique pools (see "Library_barcodes.csv") and a target total cell number of 48,000 loaded separately onto a 10X Genomics Chromium Next GEM Chip G. Samples were encapsulated using a Chromium X Instrument based on manufacturer’s instructions.

treatment_protocol: Mice were injected with cytokines subcutaneously, in a total volume of 4 microliters/g body weight.  Recombinant IL-17A (made in Chinese Hamster Ovary (CHO) cells) was freshly resuspended in phosphate buffered saline (PBS) up to 12 hours prior to use and injected at 200 ng/g body weight every 12 hours. Epo (Procrit) was injected at 0.25 IU/g every 24 hours. Vehicle- treated mice were injected with an equal volume of PBS.

value: spleen and bone marrow

value: Mixed

value: Wild type Balb/C

value: Pooled Across all treatemnts

tag: library type

value: Hashtag


title: Da1116, repo-1 RNAi, Day 1, Repeat 3

description:
Library name: 20180929_C4_DA1116_repo-1_RNAi_SD6021-2_S4
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:eat2_repo1_C4


title: Hashtags of samples from IL-17A treated mice

description: MULTI-seq (McGinnis et al. 2019)

value: 200ng/g IL-17A injections


title: DA1116, Empty Vector, Day 1, Repeat 3

description:
Library name: 20180929_C3_DA1116_ev_SD6021-2_S3
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:eat2_ctrl_C3


title: Wild type N2, Empty Vector, Day 1, Repeat 3

description:
Library name: 20180929_C1_N2_ev_SD6021-2_S1
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:WT_ctrl_C1


title: Wild type N2, repo-1 RNAi, Day 1, Repeat 3

description:
Library name: 20180929_C2_N2_repo-1_RNAi_SD6021-2_S2
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:WT_repo1_C2


title: Gene expression of samples pooled across conditions

description: 10X Genomics

data_processing:
The sequencing libraries were demultiplexed using Bcl2fastq (Illumina) and concatenated across multiple sequencing runs. The demultiplexed Fastq files were merged for the same libraries and individually processed using Cellranger (v6.1.2) Gene Expression Pipeline. Cellranger aggr function (see attached aggregation.csv file for input) was used for integrating multiple samples. Alignments were performed using M. musculus Ensembl release 84 mm10 v1.2.0 cDNA reference. The MULTI-seq library Fastq files were processed using CITE-seq-Count tool (v1.4.5) to determine sample identity of pooled cells. Sample barcode identity assignments to cells were performed using a custom python-based adaption inspired by the deMULTIplex R package.
Assembly: M. musculus Ensembl release 84 mm10
Supplementary files format and content: Gene expression output: gex_barcode.tsv.gz, gex_features.tsv.gz, gex_matrix.mtx.gz, gex_cell_metadata.tsv.gz
Supplementary files format and content: Hashtag  output: ht_barcode.tsv.gz, ht_features.tsv.gz, ht_matrix.mtx.gz

value: Gene Expression


title: Hashtags of samples from vehicle treated mice

description: MULTI-seq (McGinnis et al. 2019)

value: Vehicle


title: TJ1052, Empty Vector, Day 1, Repeat 2

description:
Library name: 20180929_B9_TJ1052_ev_SD6021-1_S19
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:age1_ctrl_B9

value: Whole body


title: TJ1052, repo-1 RNAi, Day 1, Repeat 2

description:
Library name: 20180929_B10_TJ1052_repo-1_RNAi_SD6021-1_S20
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:age1_repo1_B10

value: repo-1 RNAi


title: VC222, repo-1 RNAi, Day 1, Repeat 2

description:
Library name: 20180929_B6_VC222_repo-1_RNAi_SD6021-1_S16
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:raga1_repo1_B6


title: MQ130, Empty Vector, Day 1, Repeat 2

description:
Library name: 20180929_B7_MQ130_ev_SD6021-1_S17
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:clk1_ctrl_B7

value: Empty vector


title: Hashtags of samples from Epo treated mice

description: MULTI-seq (McGinnis et al. 2019)

value: 0.25 U/g Procrit Injections


title: Gene expression of samples from vehicle treated mice

description: 10X Genomics


title: Jimpy Brain Perk Cre Plus 04

city: Chicago

first: Brian

last: Popko

state: IL

address: 7601 Morton Medical Research Building, 320 East Superior Street

department: Neurology

institute: Northwestern Feinberg School of Medicine

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: Brain

extract_protocol:
The Aurum™ Total RNA Fatty and Fibrous Tissue Module kit (from Bio Rad #7326870) was used for RNA extractions.
Directional mRNA libraries were prepared using Illumina UDI Kits per the manufacturer’s instructions

value: Brain

value: Jimpy Perk fl/fl Cre+

value: P19, olig2-Cre pos.


title: MQ130, Empty Vector, Day 1, Repeat 3

description:
Library name: 20180929_C7_MQ130_ev_SD6021-2_S7
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:clk1_ctrl_C7


title: VC222, Empty Vector, Day 1, Repeat 2

description:
Library name: 20180929_B5_VC222_ev_SD6021-1_S15
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:raga1_ctrl_B5


title: 3-Raw_wt_mock_S3_R1_001_val1

description:
Library name: Sample09
Colum_name_in_raw_counts_all: Raw_wt_mock_S3

value: WT

value: mock


title: Gene expression of samples from Epo and IL-17A treated mice

description: 10X Genomics

value: spleen and bone marrow

value: 200ng/g IL-17A and 0.25U/g Epo injections


title: Jimpy Brain Perk Cre Plus 02


title: Hashtags of samples from Epo and IL-17A treated mice

description: MULTI-seq (McGinnis et al. 2019)

value: Mixed

value: Wild type Balb/C


title: Jimpy Brain Perk Cre Plus 01


title: DA1116, Empty Vector, Day 1, Repeat 2

description:
Library name: 20180929_B3_DA1116_ev_SD6021-1_S13
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:eat2_ctrl_B3


title: Da1116, repo-1 RNAi, Day 1, Repeat 2

description:
Library name: 20180929_B4_DA1116_repo-1_RNAi_SD6021-1_S14
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:eat2_repo1_B4


title: MQ130, repo-1 RNAi, Day 1, Repeat 2

description:
Library name: 20180929_B8_MQ130_repo-1_RNAi_SD6021-1_S18
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:clk1_repo1_B8


title: Wild type N2, repo-1 RNAi, Day 1, Repeat 2

description:
Library name: 20180929_B2_N2_repo-1_RNAi_SD6021-1_S12
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:WT_repo1_B2

value: Wild type


title: Jimpy Brain Perk Cre minus 04

value: Jimpy Perk fl/fl Cre-

value: P19, olig2-Cre neg.


title: Wild type N2, Empty Vector, Day 1, Repeat 2

description:
Library name: 20180929_B1_N2_ev_SD6021-1_S11
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:WT_ctrl_B1


title: TJ1052, repo-1 RNAi, Day 1, Repeat 1

description:
Library name: 20180929_A10_TJ1052_repo-1_RNAi_SD6021-1_S10
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:age1_repo1_A10


title: Jimpy Brain Perk Cre minus 03


title: Jimpy Brain Perk Cre minus 02


title: Gene expression of samples from Epo treated mice

description: 10X Genomics

value: Gene Expression


title: TJ1052, Empty Vector, Day 1, Repeat 1

description:
Library name: 20180929_A9_TJ1052_ev_SD6021-1_S9
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:age1_ctrl_A9

value: Whole body


title: V3_Nil_HD_05

city: Washington, DC

first: Max

last: Stevenson

state: DC

address: 3970 Reservoir Rd. NW

institute: Georgetown University

data_processing:
miRNA expression profiles at the baseline and 3 months were quantified in UMI counts., Longitudinal differentially expressed miRNA (DEMs) were determined via DESeq2 with ratio of means normalization and followed by Wald test [65] to compute the longitudinal measurement at baseline and 3 months.
Assembly: hg38
Supplementary files format and content: Excel

source_name: CSF

extract_protocol:
Cell-free total RNA was isolated from 200 μl of CSF using the Qiagen miRNAeasy extraction kit
Samples were normalized to an input volume of 5 μl RNA eluate to prepare miRNAseq libraries using Qiagen QiaSeq miRNA-seq library preparation kit

treatment_protocol: HD patients had CSF samples collected at baseline and after 3 months treatment with nilotinib, 150mg.

value: CSF

tag: disease

value: HD

tag: time point

value: Nilotinib


title: MQ130, repo-1 RNAi, Day 1, Repeat 1

description:
Library name: 20180929_A8_MQ130_repo-1_RNAi_SD6021-1_S8
Column name in NormalizedCounts_REPO-1RNA-Seq.xlsb:clk1_repo1_A8

tag: tissue

value: repo-1 RNAi