title: right brain, Day 10, fish 20E2

city: University Park

first: Jason

last: Keagy

address: 410 Forest Resources Bldg

department: Ecosystem Science and Management

institute: Penn State University

description: Library name: 31_20E2

data_processing:
We conducted quality control checks using fastqc (v0.11.8).
Next, reads were aligned to the Gasterosteus aculeatus Ensembl BROAD S1 draft genome (version 99) using using bowtie2 (v2.3.5.1) and the “--local” and “--very-sensitive” options. Alignment rates were 78.65±1.27%.
Mitochondrial and unmapped reads were removed with samtools (v1.9) and PCR duplicates were removed with picard (v2.10.1) (http://broadinstitute.github.io/picard).
We then used a shift-extend approach with the macs2 (v2.2.5) “callpeak” function using the parameters “--nomodel", “--extsize 200”, and “--shift -100” to model transposase cleavage sites (the start, or 5’ end, of our reads). We used the parameter “--keep-dup all” because we had already removed duplicates with picard. Additional parameters were “--nolambda”, “-f BAM”, and “-g 469e+6” (the genome size of stickleback).
We used the DiffBind package (v3.14.0) in R to generate a consensus peakset and count read peaks.
Assembly: Gasterosteus aculeatus Ensembl BROAD S1 draft genome (version 99)
Supplementary files format and content: Tab deliminated text file containing peaks on rows and columns indicating: chromosome, start, end, sample counts

organism: Gasterosteus aculeatus

source_name: right brain

extract_protocol:
Each subject was killed by rapid cervical dissection and the brain was immediately dissected under a microscope in a Sylgaard 184-lined petri-dish. Half of the brain was placed in cold PBS and Roche cOmplete Mini Protease Inhibitor Cocktail (PIC). Tissue was then cryopreserved for future use in ATACseq libraries as follows: Within 60 min of harvesting, half-brains in 350 μl of PBS with PIC kept at 4C were homogenized with a motorized pestle. They were spun down at 500x g for 5 min at 4C, then washed with 250 μl of cold PBS and spun down again at 500x g for 5 min at 4C. The pellet was gently resuspended in 300 μl of Cryostor media (Stemcell CryoStor® CS10) and frozen slowly in a Fisher Scientific Mr. Frosty isopropyl alcohol chamber at -80C.
ATAC-seq libraries were prepared in batches of 10-11 samples. Samples were first thawed at 37C for 2 minutes and mixed with a pipette. Then, 3ul (1/100) of each sample was added to 1.2 ml PBS with PIC and spun down at 500x g for 5 minutes at 4C. The supernatant was discarded and the cell pellet gently resuspended in 50 μl of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40) and spun down at 500x g for 10 minutes at 4C. The supernatant was discarded and the cell pellet gently resuspended in 50 μl of transposition reaction mix (25 μl 2x TD Buffer and 2.5 μl Tn5 Transposes from Illumina Nextera DNA Library Prep Kit and 22.5 μl Nuclease-free H2O). The samples were then incubated in a Thermomixer at 37C for 45 min with a 500 rpm mixing speed. Immediately following transposition, samples were purified using a Zymo DNA clean-up kit and eluted in 22 μl provided elution buffer. DNA fragments were amplified in a PCR reaction containing 20 μl transposed DNA, 2.5 μl Illumina Nextera i5 adapter, 2.5 μl Nextera i7 adapter, and 25 μl KAPA HiFi HotStart ReadyMix). The PCR reaction was as follows: 1) 7C for 5 min, 2) 98C for 30 sec, 3) 9°C for 10 sec, 4) 63C for 30 sec, 5) 72C for 1 min, with steps 3-5 repeated 15x. The number of PCR steps had previously been optimized for this tissue. PCR product was cleaned up using 1.8x KAPA Pure beads and eluted in 20 μl of Illumina elution buffer. Samples were quantified using Qubit fluorometry using DNA HS Assay kits and quality confirmed via Agilent 2100 Bioanalyzer using the Agilent High-Sensitivity DNA kits. One sample was determined to be of not sufficient quality. Therefore, 31 libraries were normalized using information from the Qubit and Bioanalyzer trace for a final 95.7 μl pool at 81 nM concentration submitted to Roy J. Carver Biotechnology Center at the University of Illinois Urbana-Champaign for sequencing. This pool was quality checked (using Qubit, Fragment Analyzer, and qPCR) and run on a MiSeq nano (100 nt reads) to confirm reasonably even representation of libraries. The pool was then sequenced on one lane of a NovaSeq 6000 using a NovaSeq S4 reagent kit with 2x50nt reads.

value: right brain

value: Day 10

value: female


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_271, healthy control

status: Public on Aug 18 2025

type: SRA

city: Ithaca

first: Anne

middle: E

last: Gardella

state: NY

address: 237 Tower Rd

department: Molecular Biology and Genetics

country: USA

institute: Cornell University

description:
Library name: cfs_cfrna_271
Column name in raw_counts_all.csv: cfs_cfrna_271

library_source: transcriptomic

data_processing:
Sequencing results were processed using a custom bioinformatics pipeline.
First, samples were quality filtered and trimmed using BBDuk (v38.90) and aligned to the Gencode GRCh38 human reference genome (v38, primary assembly) using STAR29 (v2.7.8a, default parameters), and features quantified using featureCounts30 (v2.0.0). Samples were also deduplicated using Picard MarkDuplicates (v2.19.2).
Ribosomal, mitochondrial ribosomal, X and Y chromosome genes were bioinformatically removed prior to analysis. Samples were filtered based on total read counts, alignment rate, total feature counts, DNA contamination, and RNA degradation
DNA contamination was determined based on the ratio of reads mapping to introns and exons. RNA degradation was estimated by calculating the 5’-3’ read alignment ratio bias using Qualimap31 (v2.2.1).
Samples which passed the quality filter all had greater than 5 million reads, greater than 100,000 feature counts, greater than 10% alignment rate, less than 1-fold intron to exon ratio, less than 3 standard deviations from the mean of the 5’-3’ bias, and less than 95% duplication rate.
Assembly: Gencode GRCh38 human reference genome (v38, primary assembly)
Supplementary files format and content: .csv file includes the gene counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Plasma, extracted cell-free RNA

extract_protocol:
Plasma was stored at -8-˚C and then thawed at room temperature. Then ~500 μL samples were aliquoted and centrifuged at 3000 x g for 8 minutes at 4˚C. cfRNA was extracted using the Norgen Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit (Norgen, 51000).  Extracted RNA was DNase treated with a combination of 10 µl DNase Turbo Buffer (Invitrogen, AM2238), 3 µl DNase Turbo (Invitrogen, AM2238), and 1 µl Baseline Zero DNase (Lucigen-Epicenter, DB0715K) for 30 minutes at 37 °C, then concentrated into 12 µl using the Zymo RNA Clean and Concentrated Kit (Zymo, R1015).
Sequencing libraries were prepared from 8 µl of concentrated RNA using the Takara SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian (Takara, 634485) and barcoded using the SMARTer RNA Unique Dual Index Kit (Takara, 634451). Library concentration was quantified using the Qubit 3.0 Fluorometer (Invitrogen, Q33216) with the dsDNA HS Assay Kit (Invitrogen, Q32854). Libraries were quality-controlled using the Agilent Fragment Analyzer 5200 (Agilent, M5310AA) with the HS NGS Fragment Kit (Agilent, DNF-474-0500) and pooled to equal concentrations. Each pool was sequenced using the Illumina NovaSeq 6000 platform (paired-end, 150 bp).

tag: tissue

value: Plasma, extracted cell-free RNA

tag: batch

tag: phenotype

value: control

tag: Sex

tag: test site

value: Ithaca, NY

tag: age bin


title: br_5555_3xTg-AD, CBD treatment group, week 8, age 6.5 mo, male

city: Loma Linda

first: Erik

middle: J

last: Behringer

state: CA

address: 11041 Campus St.

department: Basic Sciences

institute: Loma Linda University

description:
Library name: Sample 53
merged_gene_counts.txt: br_5555

data_processing:
RNAseq pipeline v2.1.0
Nextflow v21.10.6
DESeq2 v1.28.0; FDR cutoff, 0.05 & Log2FC cutoff, 0.585
gProfiler v1.0.0; FDR cutoff, 0.05
Assembly: GRCm39
Supplementary files format and content: Text file includes raw counts among all samples
Supplementary files format and content: The XLSX file contains normalized counts among all samples

organism: Mus musculus

source_name: brain

extract_protocol:
RNA was harvested and processed using Zymo's Total RNAseq Full Service Package
Zymo-Seq RiboFree Total RNA Library Kit following manufacturer's protocols

treatment_protocol: Dietary CBD was administered daily (80-100 mg/kg/day) in male 3xTg-AD mice and wild-type B6129SF2/J animals from 4.5 to 6.5 mo of age with inclusion of vehicle controls.

value: brain

tag: genotype

value: male

tag: age

tag: treatment

value: CBD, week 8


title: right brain, Day 10, fish 20E7

state: PA

description: Library name: 33_20E7

library_source: genomic

molecule: genomic DNA

tag: group


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_270, ME/CFS patient

description:
Library name: cfs_cfrna_270
Column name in raw_counts_all.csv: cfs_cfrna_270

value: case


title: br_5448_B6129SF2/J, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 44
merged_gene_counts.txt: br_5448


title: br_5444_B6129SF2/J, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 42
merged_gene_counts.txt: br_5444


title: left brain, Day 10, fish 31E3

description: Library name: 28_31E3

source_name: left brain

value: left brain


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_272, ME/CFS patient

description:
Library name: cfs_cfrna_272
Column name in raw_counts_all.csv: cfs_cfrna_272


title: right brain, Day 10, fish 31E5

description: Library name: 27_31E5


title: right brain, Day 0, fish 39E2

description: Library name: 30_39E2

value: Day 0


title: left brain, Day 0, fish 40E7

description: Library name: 26_40E7


title: br_5442_B6129SF2/J, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 41
merged_gene_counts.txt: br_5442


title: wb_5548_3xTg-AD, vehicle group, week 8, age 6.5 mo, male

description:
Library name: Sample 40
merged_gene_counts.txt: wb_5548

source_name: whole trunk blood

value: whole trunk blood

value: Vehicle, week 8


title: right brain, Day 0, fish 40E8

description: Library name: 25_40E8


title: right brain, Day 0, fish 39E3

description: Library name: 29_39E3


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_266, ME/CFS patient

description:
Library name: cfs_cfrna_266
Column name in raw_counts_all.csv: cfs_cfrna_266


title: right brain, Day 10, fish 17E3

description: Library name: 23_17E3


title: HA-PSF-TFE3_9_ChIP-seq

city: Kumamoto

first: Masaya

last: Baba

state: Kumamoto

address: 2-2-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

description: Library name: Sample2

data_processing:
Strand NGS software (Strand Life Sciences)
Peak detection was performed using the MACS algorithm.  The significant enrichment of each signal over input-DNA peaks was determined at a P cut-off value of 10-5.
Assembly: hg19
Supplementary files format and content: The processed data files are provided as BED format files (.bed). Each file represents peak summits identified using the MACS2 peak-calling algorithm applied to ChIP-seq data.

source_name: Kidney

growth_protocol: HA-PSF-TFE3-inducible HK-2 cell lines which express HA-PSF-TFE3 in a doxycycline-dependent manner were cultured with advanced DMEM/F-12 supplemented with 1.5% FCS, 100 U/ml penicillin, 100 microg/ml streptomycin.

extract_protocol:
SimpleChIP® Plus Enzymatic Chromatin IP Kit (Magnetic Beads) (#9005, Cell Signaling) was utilized for ChIP. Cell cross-linking, chromatin preparation and chromatin immunoprecipitation by anti HA Affinity Matrix (#11815016001, Roche) was performed according to the manufacturer's instructions.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

treatment_protocol: HA-PSF-TFE3-inducible HK-2 cells were cultured with 0.2 microg/ml of doxycycline for 24hr.

value: Kidney

tag: cell line

tag: cell type

value: HA-PSF-TFE3-inducible cell

value: Doxycycline +


title: right brain, Day 10, fish 17E7

description: Library name: 24_17E7

value: right brain


title: wb_5546_3xTg-AD, vehicle group, week 8, age 6.5 mo, male

description:
Library name: Sample 39
merged_gene_counts.txt: wb_5546


title: left brain, Day 10, fish 19E8

description: Library name: 22_19E8

value: Day 10


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_265, ME/CFS patient

description:
Library name: cfs_cfrna_265
Column name in raw_counts_all.csv: cfs_cfrna_265

value: female


title: wb_5554_3xTg-AD, vehicle group, week 8, age 6.5 mo, male

description:
Library name: Sample 38
merged_gene_counts.txt: wb_5554


title: left brain, Day 0, fish 22E2

description: Library name: 20_22E2


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_268, healthy control

description:
Library name: cfs_cfrna_268
Column name in raw_counts_all.csv: cfs_cfrna_268

value: Plasma, extracted cell-free RNA


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_264, healthy control

description:
Library name: cfs_cfrna_264
Column name in raw_counts_all.csv: cfs_cfrna_264

value: control


title: right brain, Day 0, fish 22E5

description: Library name: 19_22E5


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_260, healthy control

description:
Library name: cfs_cfrna_260
Column name in raw_counts_all.csv: cfs_cfrna_260

value: Ithaca, NY


title: wb_5552_3xTg-AD, vehicle group, week 8, age 6.5 mo, male

description:
Library name: Sample 37
merged_gene_counts.txt: wb_5552


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_267, healthy control

description:
Library name: cfs_cfrna_267
Column name in raw_counts_all.csv: cfs_cfrna_267


title: left brain, Day 10, fish 07E5

description: Library name: 14_07E5


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_259, ME/CFS patient

description:
Library name: cfs_cfrna_259
Column name in raw_counts_all.csv: cfs_cfrna_259


title: right brain, Day 0, fish 25E4

description: Library name: 17_25E4


title: wb_5549_3xTg-AD, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 35
merged_gene_counts.txt: wb_5549


title: right brain, Day 0, fish 25E2

description: Library name: 18_25E2


title: wb_5550_3xTg-AD, vehicle group, week 8, age 6.5 mo, male

description:
Library name: Sample 36
merged_gene_counts.txt: wb_5550


title: wb_5547_3xTg-AD, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 34
merged_gene_counts.txt: wb_5547


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_257, healthy control

description:
Library name: cfs_cfrna_257
Column name in raw_counts_all.csv: cfs_cfrna_257


title: left brain, Day 10, fish 07E3

description: Library name: 13B_07E3


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_258, ME/CFS patient

description:
Library name: cfs_cfrna_258
Column name in raw_counts_all.csv: cfs_cfrna_258


title: right brain, Day 0, fish 11E8

description: Library name: 12_11E8


title: right brain, Day 10, fish 26E7

description: Library name: 10_26E7


title: left brain, Day 0, fish 04E4

description: Library name: 16_04E4


title: left brain, Day 0, fish 11E7

description: Library name: 11_11E7


title: wb_5555_3xTg-AD, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 33
merged_gene_counts.txt: wb_5555


title: left brain, Day 10, fish 26E3

description: Library name: 09_26E3


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_256, healthy control

description:
Library name: cfs_cfrna_256
Column name in raw_counts_all.csv: cfs_cfrna_256


title: left brain, Day 10, fish 19E1

description: Library name: 21_19E1


title: right brain, Day 0, fish 32E8

description: Library name: 08_32E8


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_255, healthy control

description:
Library name: cfs_cfrna_255
Column name in raw_counts_all.csv: cfs_cfrna_255


title: wb_5553_3xTg-AD, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 32
merged_gene_counts.txt: wb_5553


title: left brain, Day 10, fish 35E1

description: Library name: 06_35E1


title: wb_5551_3xTg-AD, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 31
merged_gene_counts.txt: wb_5551


title: right brain, Day 0, fish 30E8

description: Library name: 04_30E8


title: right brain, Day 10, fish 35E8

description: Library name: 05_35E8


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_254, ME/CFS patient

description:
Library name: cfs_cfrna_254
Column name in raw_counts_all.csv: cfs_cfrna_254


title: wb_5450_B6129SF2/J, untreated, week 8, age 6.5 mo, male

description:
Library name: Sample 30
merged_gene_counts.txt: wb_5450

value: Untreated, week 8


title: left brain, Day 0, fish 30E5

description: Library name: 03_30E5

value: male


title: left brain, Day 10, fish 27E10

description: Library name: 02_27E10


title: wb_5446_B6129SF2/J, untreated, week 8, age 6.5 mo, male

description:
Library name: Sample 29
merged_gene_counts.txt: wb_5446


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_252, healthy control

description:
Library name: cfs_cfrna_252
Column name in raw_counts_all.csv: cfs_cfrna_252


title: right brain, Day 10, fish 27E11

description: Library name: 01_27E11


title: wb_5447_B6129SF2/J, vehicle group, week 8, age 6.5 mo, male

description:
Library name: Sample 28
merged_gene_counts.txt: wb_5447


title: mRNA-584 – 7day

city: Winston-Salem

first: Carl

last: Langefeld

state: NC

address: 525 Vine

institute: Wake Forest University School of Medicine

description:
Library name: KW29
column name in normalized_mRNA_counts_v1: 584 - 7day

data_processing:
The adapter for each miRNA sample was trimmed using Cutadapt (part of miRge3.0) pipeline. MiRNA sample data quality were evaluated using fastqc (html report) and the miRNA peak (at around 22 bp) was filtered for each sample. Samples with filtered miRNA peak were put into miRge3.0 pipeline to generate summary data files including miRNA read count, reads per million (RPM), etc.
Differentially expressed (DE) mRNA and miRNA were tested between 3 time points: 72hr vs. baseline, 7days vs. 72hrs and 7days vs. baseline. The DE mRNA and miRNA were tested for pathway enrichment via Ingenuity Pathway Analysis, Cytoscape, STRING and Reactome.
Principal component analysis (PCA) was computed on the differences in the expression for the timeframe.
Spearman’s correlation coefficient were computed between DE mRNA and DE miRNA for each timeframe comparison. The miRNA/mRNA with statistically significant correlation pairs were analyzed using TargetScan (version 8.0) and MirTarBase (9.0) to explore whether the pairs are reported as miRNA/mRNA targets.
Assembly: Human (Homo Sapiens) hg38
Supplementary files format and content: Normalized_miRNA_counts_v1.csv
Supplementary files format and content: Normalized_mRNA_counts_v1.csv

source_name: whole blood

extract_protocol:
miRNA: The first round of sequencing was performed on NextSeq 2000 sequencer (Illumina, San Diego, CA) to generate a few million reads to quantify the relative concentration of each library. The volume of each library was then adjusted to generate about 5M read clusters from each sample under the same PE 2x61 bp setting for the final data analysis. mRNA: Directional globin mRNA/rRNA depletion RNA-seq was performed using NEBNext Globin & rRNA Depletion Kit (NEB) with 50 to 100 ng whole blood RNA was globin mRNA/rRNA depleted according to the protocol.
miRNA: NEBNext Small RNA Sample Library Preparation kit (NEB, Ipswich, MA) was used with modified approach for precise miRNA library size selection; this makes it possible for the kit to process low input and low-quality RNA with better library recovery and miRNA reads alignment.  mRNA: NEBNext Ultra II Directional RNA Library Prep kit (NEB) was used for library preparation under PCR cycle number of 14.

value: whole blood


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_253, ME/CFS patient

description:
Library name: cfs_cfrna_253
Column name in raw_counts_all.csv: cfs_cfrna_253

value: case


title: wb_5443_B6129SF2/J, vehicle group, week 8, age 6.5 mo, male

description:
Library name: Sample 27
merged_gene_counts.txt: wb_5443


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_251, ME/CFS patient

description:
Library name: cfs_cfrna_251
Column name in raw_counts_all.csv: cfs_cfrna_251


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_248, ME/CFS patient

description:
Library name: cfs_cfrna_248
Column name in raw_counts_all.csv: cfs_cfrna_248


title: mRNA-455 – 7day

description:
Library name: KW17
column name in normalized_mRNA_counts_v1: 455 - 7day


title: mRNA-201 – 7day

description:
Library name: KW23
column name in normalized_mRNA_counts_v1: 201 - 7day


title: mRNA-380 – 7day

description:
Library name: KW20
column name in normalized_mRNA_counts_v1: 380 - 7day


title: wb_5441_B6129SF2/J, vehicle group, week 8, age 6.5 mo, male

description:
Library name: Sample 26
merged_gene_counts.txt: wb_5441


title: mRNA-387 - 7day

description:
Library name: KW14
column name in normalized_mRNA_counts_v1: 387 - 7day


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_247, ME/CFS patient

description:
Library name: cfs_cfrna_247
Column name in raw_counts_all.csv: cfs_cfrna_247


title: mRNA-523 - 7day

description:
Library name: KW5
column name in normalized_mRNA_counts_v1: 523 - 7day


title: mRNA-953 - 7day

description:
Library name: KW8
column name in normalized_mRNA_counts_v1: 953 - 7day


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_246, healthy control

description:
Library name: cfs_cfrna_246
Column name in raw_counts_all.csv: cfs_cfrna_246


title: mRNA-714 - 7day

description:
Library name: KW11
column name in normalized_mRNA_counts_v1: 714 - 7day


title: wb_5449_B6129SF2/J, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 25
merged_gene_counts.txt: wb_5449

value: CBD, week 8


title: wb_5448_B6129SF2/J, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 24
merged_gene_counts.txt: wb_5448


title: mRNA-412 - 7day

description:
Library name: KW2
column name in normalized_mRNA_counts_v1: 412 - 7day


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_245, ME/CFS patient

description:
Library name: cfs_cfrna_245
Column name in raw_counts_all.csv: cfs_cfrna_245


title: mRNA-778 - 7day

description:
Library name: CB51
column name in normalized_mRNA_counts_v1: 778 - 7day


title: mRNA-270 - 7day

description:
Library name: CB9
column name in normalized_mRNA_counts_v1: 270 - 7day


title: mRNA-327 - 7day

description:
Library name: CB42
column name in normalized_mRNA_counts_v1: 327 - 7day


title: wb_5444_B6129SF2/J, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 22
merged_gene_counts.txt: wb_5444


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_243, healthy control

description:
Library name: cfs_cfrna_243
Column name in raw_counts_all.csv: cfs_cfrna_243


title: mRNA-649 - 7day

description:
Library name: CB39
column name in normalized_mRNA_counts_v1: 649 - 7day


title: mRNA-663 – 7day

description:
Library name: KW26
column name in normalized_mRNA_counts_v1: 663 - 7day


title: wb_5442_B6129SF2/J, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 21
merged_gene_counts.txt: wb_5442


title: mRNA-729 - 7day

description:
Library name: CB33
column name in normalized_mRNA_counts_v1: 729 - 7day


title: right brain, Day 0, fish 32E1

description: Library name: 07_32E1

value: Day 0


title: tb_5548_3xTg-AD, vehicle group, week 0, age 4.5 mo, male

description:
Library name: Sample 20
merged_gene_counts.txt: tb_5548

source_name: tail blood

value: tail blood

value: Vehicle, week 0


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_241, ME/CFS patient

description:
Library name: cfs_cfrna_241
Column name in raw_counts_all.csv: cfs_cfrna_241


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_242, ME/CFS patient

description:
Library name: cfs_cfrna_242
Column name in raw_counts_all.csv: cfs_cfrna_242


title: mRNA-175 - 7day

description:
Library name: CB30
column name in normalized_mRNA_counts_v1: 175 - 7day


title: mRNA-784 - 7day

description:
Library name: CB3
column name in normalized_mRNA_counts_v1: 784 - 7day


title: mRNA-650 - 7day

description:
Library name: CB24
column name in normalized_mRNA_counts_v1: 650 - 7day


title: tb_5546_3xTg-AD, vehicle group, week 0, age 4.5 mo, male

description:
Library name: Sample 19
merged_gene_counts.txt: tb_5546


title: mRNA-914 - 7day

description:
Library name: CB15
column name in normalized_mRNA_counts_v1: 914 - 7day


title: tb_5554_3xTg-AD, vehicle group, week 0, age 4.5 mo, male

description:
Library name: Sample 18
merged_gene_counts.txt: tb_5554


title: mRNA-788 - 7day

description:
Library name: CB18
column name in normalized_mRNA_counts_v1: 788 - 7day


title: mRNA-100 - 7day

description:
Library name: CB21
column name in normalized_mRNA_counts_v1: 100 - 7day


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_236, healthy control

description:
Library name: cfs_cfrna_236
Column name in raw_counts_all.csv: cfs_cfrna_236


title: tb_5552_3xTg-AD, vehicle group, week 0, age 4.5 mo, male

description:
Library name: Sample 17
merged_gene_counts.txt: tb_5552


title: wb_5445_B6129SF2/J, CBD treatment group, week 8, age 6.5 mo, male

description:
Library name: Sample 23
merged_gene_counts.txt: wb_5445

value: whole trunk blood


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_240, ME/CFS patient

description:
Library name: cfs_cfrna_240
Column name in raw_counts_all.csv: cfs_cfrna_240


title: mRNA-159 - 7day

description:
Library name: CB48
column name in normalized_mRNA_counts_v1: 159 - 7day


title: mRNA-323 - 7day

description:
Library name: CB12
column name in normalized_mRNA_counts_v1: 323 - 7day


title: mRNA-584 – 72h

description:
Library name: KW28
column name in normalized_mRNA_counts_v1: 584 - 72hr


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_244, healthy control

description:
Library name: cfs_cfrna_244
Column name in raw_counts_all.csv: cfs_cfrna_244


title: tb_5550_3xTg-AD, vehicle group, week 0, age 4.5 mo, male

description:
Library name: Sample 16
merged_gene_counts.txt: tb_5550


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_233, ME/CFS patient

description:
Library name: cfs_cfrna_233
Column name in raw_counts_all.csv: cfs_cfrna_233


title: mRNA-454 - 7day

description:
Library name: CB27
column name in normalized_mRNA_counts_v1: 454 - 7day


title: tb_5547_3xTg-AD, CBD treatment group, week 0, age 4.5 mo, male

description:
Library name: Sample 14
merged_gene_counts.txt: tb_5547

value: CBD, week 0


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_232, healthy control

description:
Library name: cfs_cfrna_232
Column name in raw_counts_all.csv: cfs_cfrna_232


title: mRNA-201 – 72h

description:
Library name: KW22
column name in normalized_mRNA_counts_v1: 201 - 72hr


title: mRNA-714 – 72h

description:
Library name: KW10
column name in normalized_mRNA_counts_v1: 714 - 72hr


title: tb_5549_3xTg-AD, CBD treatment group, week 0, age 4.5 mo, male

description:
Library name: Sample 15
merged_gene_counts.txt: tb_5549


title: mRNA-380 – 72h

description:
Library name: KW19
column name in normalized_mRNA_counts_v1: 380 - 72hr


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_230, ME/CFS patient

description:
Library name: cfs_cfrna_230
Column name in raw_counts_all.csv: cfs_cfrna_230


title: mRNA-455 – 72h

description:
Library name: KW16
column name in normalized_mRNA_counts_v1: 455 - 72hr


title: mRNA-953 – 72h

description:
Library name: KW7
column name in normalized_mRNA_counts_v1: 953 - 72hr


title: tb_5553_3xTg-AD, CBD treatment group, week 0, age 4.5 mo, male

description:
Library name: Sample 12
merged_gene_counts.txt: tb_5553


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_226, ME/CFS patient

description:
Library name: cfs_cfrna_226
Column name in raw_counts_all.csv: cfs_cfrna_226


title: KO_Female_Day2_3

city: York

first: Fabiano

middle: Sviatopolk-Mirsky

last: Pais

state: Yorkshire

address: Wentworth Way

department: Biology

country: United Kingdom

institute: University of York

description:
ONT long read
barcode15

data_processing:
Live superaccuracy basecalling and barcode demultiplexing was performed in MinKNOW software (version 24.06.10) at the time of the run.
Demultiplexed reads were analyzed through the workflow Transcriptomes (version 1.1.1 at https://github.com/epi2me-labs/wf-transcriptomes/tree/v1.1.1) from Epi2Me(TM), specifically designed by Oxford Nanopore for ONT reads. The transcript source used fot the analysis was precomputed from the GENCODE reference transcriptome.
Assembly: GENCODE M35. May 2024 (GRCm39)
Supplementary files format and content: Count table with gene expression data provided in tab separated values (.txt) format.

source_name: spleen and lymph nodes

growth_protocol: Spleens and axillary, brachial, mesenteric, and inguinal lymph nodes of WT or Malat1-/- mice were extracted, then passed through a 70 mm filter. Resulting cell pellets were then treated with 3ml ACK lysis buffer. Naïve CD4+ T cells were then purified via MACS column isolation (Naive CD4+ T Cell Isolation Kit, mouse, catalogue number 130-104-453) normally resulting in purity of >90%. For Th2 polarisation, purified naïve CD4+ T cells (500,000 cells per well) were stimulated with 10 μg/ml plate-bound anti-CD3ε (clone 145-2C11) and 4 μg/ml soluble anti-CD28 (37.51) in RPMI 1640 in flat-bottom 96-well plates in the presence of 25 ng/ml mouse rIL-4 and 5 μg/ml anti–IFN-γ (XMG1.2). Cells were collected after isolation or at Day 2 of differentiation.

extract_protocol:
RNA (minimum of 200ng) was extracted from tissue samples or purified cell populations using QIAzol and miRNeasy RNA extraction kits (QIAGEN) according to manufacturer’s instructions.
Full length cDNA libraries were prepared using the ONT cDNA-PCR Sequencing V14 - Barcoding kit (SQK-PCB114.24). Here, cDNA RT adapters were ligated to 3' ends (polyA tails) of transcripts, prior to stand switching cDNA synthesis and a 13 cycle PCR reaction with barcoded primers, labelling each cDNA sample with a unique DNA barcode. Barcoded cDNAs were pooled at equimolar ratios before final adapter ligation and sequencing on R10.4.1 flowcells an ONT PromethION sequencer. Two Promethion flow cells in total, with 8 samples per flow cell (2 replicates per condition -Day 0, Day 2, WT, Malat1-/-).

value: spleen and lymph nodes

value: CD4+ T cells

value: CD4+ T cells 2 days after stimulation with 10 μg/ml plate-bound anti-CD3ε and 4 μg/ml soluble anti-CD28 in RPMI 1640 in flat-bottom 96-well plates in the presence of 25 ng/ml mouse rIL-4 and 5 μg/ml anti–IFN-γ.


title: tb_5555_3xTg-AD, CBD treatment group, week 0, age 4.5 mo, male

description:
Library name: Sample 13
merged_gene_counts.txt: tb_5555


title: tb_5551_3xTg-AD, CBD treatment group, week 0, age 4.5 mo, male

description:
Library name: Sample 11
merged_gene_counts.txt: tb_5551


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_235, ME/CFS patient

description:
Library name: cfs_cfrna_235
Column name in raw_counts_all.csv: cfs_cfrna_235

value: female


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_225, ME/CFS patient

description:
Library name: cfs_cfrna_225
Column name in raw_counts_all.csv: cfs_cfrna_225

value: Plasma, extracted cell-free RNA


title: tb_5450_B6129SF2/J, untreated, week 0, age 4.5 mo, male

description:
Library name: Sample 10
merged_gene_counts.txt: tb_5450

value: Untreated, week 0


title: KO_Female_Day0_4

description:
ONT long read
barcode14

value: Naïve CD4+ T cells


title: KO_Female_Day0_3

description:
ONT long read
barcode13


title: mRNA-663 – 72h

description:
Library name: KW25
column name in normalized_mRNA_counts_v1: 663 - 72hr


title: mRNA-867 - 72h

description:
Library name: CB53
column name in normalized_mRNA_counts_v1: 867 - 72hr


title: tb_5446_B6129SF2/J, untreated, week 0, age 4.5 mo, male

description:
Library name: Sample 9
merged_gene_counts.txt: tb_5446


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_224, ME/CFS patient

description:
Library name: cfs_cfrna_224
Column name in raw_counts_all.csv: cfs_cfrna_224

value: Ithaca, NY


title: mRNA-387 – 72h

description:
Library name: KW13
column name in normalized_mRNA_counts_v1: 387 - 72hr


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_231, ME/CFS patient

description:
Library name: cfs_cfrna_231
Column name in raw_counts_all.csv: cfs_cfrna_231


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_223, ME/CFS patient

description:
Library name: cfs_cfrna_223
Column name in raw_counts_all.csv: cfs_cfrna_223


title: WT_Female_Day2_4

description:
ONT long read
barcode12

value: WT


title: tb_5447_B6129SF2/J, vehicle group, week 0, age 4.5 mo, male

description:
Library name: Sample 8
merged_gene_counts.txt: tb_5447

value: male


title: WT_Female_Day2_3

description:
ONT long read
barcode11


title: KO_Female_Day2_4

description:
ONT long read
barcode16


title: mRNA-778 - 72h

description:
Library name: CB50
column name in normalized_mRNA_counts_v1: 778 - 72hr

value: whole blood


title: mRNA-159 - 72h

description:
Library name: CB47
column name in normalized_mRNA_counts_v1: 159 - 72hr


title: tb_5443_B6129SF2/J, vehicle group, week 0, age 4.5 mo, male

description:
Library name: Sample 7
merged_gene_counts.txt: tb_5443


title: WT_Female_Day0_4

description:
ONT long read
barcode10


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_221, ME/CFS patient

description:
Library name: cfs_cfrna_221
Column name in raw_counts_all.csv: cfs_cfrna_221

value: case


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_220, healthy control

description:
Library name: cfs_cfrna_220
Column name in raw_counts_all.csv: cfs_cfrna_220

value: control


title: mRNA-327 - 72h

description:
Library name: CB41
column name in normalized_mRNA_counts_v1: 327 - 72hr


title: tb_5449_B6129SF2/J, CBD treatment group, week 0, age 4.5 mo, male

description:
Library name: Sample 5
merged_gene_counts.txt: tb_5449

value: tail blood


title: WT_Female_Day0_3

description:
ONT long read
barcode09


title: tb_5441_B6129SF2/J, vehicle group, week 0, age 4.5 mo, male

description:
Library name: Sample 6
merged_gene_counts.txt: tb_5441

value: Vehicle, week 0


title: mRNA-523 – 72h

description:
Library name: KW4
column name in normalized_mRNA_counts_v1: 523 - 72hr


title: mRNA-270 - 72h

description:
Library name: CB8
column name in normalized_mRNA_counts_v1: 270 - 72hr


title: KO_Female_Day2_2

description:
ONT long read
barcode08


title: mRNA-649 - 72h

description:
Library name: CB38
column name in normalized_mRNA_counts_v1: 649 - 72hr


title: tb_5448_B6129SF2/J, CBD treatment group, week 0, age 4.5 mo, male

description:
Library name: Sample 4
merged_gene_counts.txt: tb_5448


title: KO_Female_Day2_1

description:
ONT long read
barcode07


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_219, ME/CFS patient

description:
Library name: cfs_cfrna_219
Column name in raw_counts_all.csv: cfs_cfrna_219


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_215, healthy control

description:
Library name: cfs_cfrna_215
Column name in raw_counts_all.csv: cfs_cfrna_215


title: tb_5445_B6129SF2/J, CBD treatment group, week 0, age 4.5 mo, male

description:
Library name: Sample 3
merged_gene_counts.txt: tb_5445


title: mRNA-687 - 72h

description:
Library name: CB35
column name in normalized_mRNA_counts_v1: 687 - 72hr


title: KO_Female_Day0_2

description:
ONT long read
barcode06


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_214, healthy control

description:
Library name: cfs_cfrna_214
Column name in raw_counts_all.csv: cfs_cfrna_214


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_222, ME/CFS patient

description:
Library name: cfs_cfrna_222
Column name in raw_counts_all.csv: cfs_cfrna_222


title: mRNA-729 - 72h

description:
Library name: CB32
column name in normalized_mRNA_counts_v1: 729 - 72hr


title: tb_5442_B6129SF2/J, CBD treatment group, week 0, age 4.5 mo, male

description:
Library name: Sample 1
merged_gene_counts.txt: tb_5442


title: tb_5444_B6129SF2/J, CBD treatment group, week 0, age 4.5 mo, male

description:
Library name: Sample 2
merged_gene_counts.txt: tb_5444


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_213, ME/CFS patient

description:
Library name: cfs_cfrna_213
Column name in raw_counts_all.csv: cfs_cfrna_213


title: KO_Female_Day0_1

description:
ONT long read
barcode05


title: mRNA-309 - 72h

description:
Library name: CB44
column name in normalized_mRNA_counts_v1: 309 - 72hr


title: WT_Female_Day2_2

description:
ONT long read
barcode04


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_212, healthy control

description:
Library name: cfs_cfrna_212
Column name in raw_counts_all.csv: cfs_cfrna_212


title: mRNA-454 - 72h

description:
Library name: CB26
column name in normalized_mRNA_counts_v1: 454 - 72hr


title: WT_Female_Day2_1

description:
ONT long read
barcode03


title: mRNA-650 - 72h

description:
Library name: CB23
column name in normalized_mRNA_counts_v1: 650 - 72hr


title: H3K27me3, primed NK, WT

city: SAINT LOUIS

first: Megan

last: Cooper

state: MISSOURI

address: MPRB, 6th floor, 4905 Childrens Place

department: Pediatrics

institute: Washington University in St Louis

description: Library name: H3K27me3_primed_WT

data_processing:
Trimmed the reads with cutadapt:3.2.
Trimmed reads were aligned to UCSC mm10 genome using bowtie2:2.4.1
Peaks were called using MACS2 v2.2.9.1 with the significance cut-off p-value <= 1e-6
Size factors were obtained using DEseq2. Each libraries were normalized with size factors and merged using ucsc-bigwigmerge.
Assembly: mm10
Supplementary files format and content: BigWig
Library strategy: CUT&Tag

source_name: Spleen

growth_protocol: Rosa YFP/YFP Ncr1 CRE-ERT2 or Acly fl/fl Rosa YFP/YFP Ncr1 CRE-ERT2 mice were treated with tamoxifen diet for 48 hours. 3 days after withdrawal of tamoxifen diet, YFP+ cells from splenic NK cells were sorted. Cells were cultured in RPMI + 10% fetal bovine serumn, 1x penicillin/streptomycin, 2mM glutamine. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were processed using CUTANA CUT&Tag kit (Epicypher). H3K27ac, H3K9ac, and H3K27me3 were targeted
Libraries were amplified using 16 cycles on the thermocycler. Libraries were size selected using 1.3X SPRIselect from Beckman Coulter. Post-clean libraries were valdiated using the Agilent Bioanalyzer.

treatment_protocol: Priming was induced by IL-15 (100ng/ml) for 72 hours.

value: Spleen

value: NK cell


title: H3K27me3, primed NK, KO

description: Library name: H3K27me3_primed_KO

value: KO


title: H3K9ac, primed NK, KO

description: Library name: H3K9ac_primed_KO


title: mRNA-100 - 72h

description:
Library name: CB20
column name in normalized_mRNA_counts_v1: 100 - 72hr


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_208, healthy control

description:
Library name: cfs_cfrna_208
Column name in raw_counts_all.csv: cfs_cfrna_208


title: WT_Female_Day0_1

description:
ONT long read
barcode01

value: spleen and lymph nodes

value: CD4+ T cells


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_209, healthy control

description:
Library name: cfs_cfrna_209
Column name in raw_counts_all.csv: cfs_cfrna_209

value: female

value: New York City, NY


title: mRNA-784 - 72h

description:
Library name: CB2
column name in normalized_mRNA_counts_v1: 784 - 72hr


title: H3K9ac, primed NK, WT

description: Library name: H3K9ac_primed_WT


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_207, healthy control

description:
Library name: cfs_cfrna_207
Column name in raw_counts_all.csv: cfs_cfrna_207

value: Plasma, extracted cell-free RNA


title: A673,Input for KDM6B,EWSR1-FLI1 KD

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

country: Spain

institute: Center for Genomic Regulation (CRG)

description: Library name: A673,Input for KDM6B,EWSR1-FLI1 KD

data_processing:
ChIP-seq, alignment: Sequence reads of the samples without spike-in were mapped to the human genome (hg19) using BOWTIE (PubMed ID 19261174) with the option -m 1. Sequence of the reads of the samples with spike-in were mapped to a synthetic genome containing the human and the fruit fly chromosomes (hg19+dm3).
ChIP-seq, genome profiles: SeqCode (PubMed ID 34599234) was used to generate the genome-wide profiles of each ChIP-seq experiment. Height of the profiles is normalized by the total number of reads mapped over the human genome for samples without spike/in material, and by the number of fly spike-in genome reads in the case of samples with spike-in.
ChIP-seq, peak calling: Peak detection of every sample against its corresponding Input was performed with MACS (PubMed ID: 18798982).
Assembly: hg19
Supplementary files format and content: Bedgraph format for genome-wide profiles
Supplementary files format and content: BED format for MACS and DiffBind peaks.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared using 2-5 ng of input and ChIP samples and the kit NEBNext Ultra DNA Library Prep for Illumina (New England Biolabs) following manufacturer’s protocol.

tag: chip antibody


title: H3K27ac, primed NK, KO

description: Library name: H3K27ac_primed_KO


title: mRNA-788 - 72h

description:
Library name: CB17
column name in normalized_mRNA_counts_v1: 788 - 72hr


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_206, ME/CFS patient

description:
Library name: cfs_cfrna_206
Column name in raw_counts_all.csv: cfs_cfrna_206

value: Los Angeles, CA


title: A673,KDM6B,EWSR1-FLI1 KD

description: Library name: A673,KDM6B,EWSR1-FLI1 KD

value: KDM6B (Abcam ab169197)


title: mRNA-914 - 72h

description:
Library name: CB14
column name in normalized_mRNA_counts_v1: 914 - 72hr


title: mRNA-175 - 72h

description:
Library name: CB29
column name in normalized_mRNA_counts_v1: 175 - 72hr


title: H3K27ac, primed NK, WT

description: Library name: H3K27ac_primed_WT

value: WT


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_205, ME/CFS patient

description:
Library name: cfs_cfrna_205
Column name in raw_counts_all.csv: cfs_cfrna_205

value: Ithaca, NY


title: A673,KDM6B,Control

description: Library name: A673,KDM6B,Control


title: mRNA-323 - 72h

description:
Library name: CB11
column name in normalized_mRNA_counts_v1: 323 - 72hr

value: whole blood


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_204, ME/CFS patient

description:
Library name: cfs_cfrna_204
Column name in raw_counts_all.csv: cfs_cfrna_204

value: case


title: A673,Input for KDM6B,Control

description: Library name: A673,Input for KDM6B,Control


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_211, ME/CFS patient

description:
Library name: cfs_cfrna_211
Column name in raw_counts_all.csv: cfs_cfrna_211


title: mRNA-584 – base

description:
Library name: KW27
column name in normalized_mRNA_counts_v1: 584 - base

value: baseline


title: GL261 Adherent Cell scRNAseq

city: Caldwell

first: Richard

middle: Luke

last: Daniels

state: ID

address: 2112 Cleveland Blvd

institute: The College of Idaho

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Data processing was performed by Azenta Life Sciences using the Cellranger-7.0.1 pipeline.
Assembly: Mouse mm10-2020-A (GENCODE vM23/Ensembl98).
Supplementary files format and content: Tab-separated values files and matrix files.

growth_protocol: GL261 cells were cultured in DMEM with 10% FBS, 1% Penicillin-Streptomycin at 37.0°C in 5.0% CO₂. Cells were passaged at ~80% confluency.

extract_protocol:
Adherent Cells: At ~80% confluency, cultured samples were washed in PBS, trypsinized to detach cells, and trypsin was inactivated in growth culture media (DMEM with 10% FBS and 1% Penicillin-Streptomycin). Cells were then centrifuged at 3000 RPM for 5 minutes, and resuspended in culture media (DMEM with 10% FBS and 1% Penicillin-Streptomycin) with 10% DMSO. Neurospheres: Neurosphere extraction took place 12 days following neurosphere treatment protocol. Culture media containing neurospheres was collected, centrifuged at 3000 RPM for 5 minutes, and resuspended in 2 ml trypsin. After 5 minutes, cells were triturated using a series of progressively smaller pipette tips to break up neurospheres (5 ml serological pipette, 1 ml pipette tip, 200 μl pipette tip, and finally a fire-polished glass Pasteur pipette). Cells were then centrifuged at 3000 RPM for 5 minutes, and resuspended in culture media (DMEM with 10% FBS and 1% Penicillin-Streptomycin) with 10% DMSO. A 1 ml solution of each cell sample was transferred to a cryotube, placed in a freezer (-20 C) for 1hr, then in a -80°C freezer overnight. Samples were placed on dry-ice and mailed to Azenta Life Sciences.
Library construction was performed by Azenta Life Sciences according to manufacturer's instructions (single cell 3' v3 protocol, 10x Genomics).

treatment_protocol: Adherent Cells were cultured in standard growth conditons. Neurospheres were cultured by the addition of 20 ng/ml of Epidermal Growth Factor, 20 ng/ml Fibroblast Growth Factor, and 1:50 B-27 to the cell culture media.

value: Astrocytoma

tag: strain

value: Adherent


title: WT_Female_Day0_2

description:
ONT long read
barcode02

value: Naïve CD4+ T cells


title: A673,KDM6A,EWSR1-FLI1 KD

description: Library name: A673,KDM6A,EWSR1-FLI1 KD

value: KDM6A (UTX) (Cell Signaling 33510)


title: mRNA-663 – base

description:
Library name: KW24
column name in normalized_mRNA_counts_v1: 663 - base


title: A673,Input for KDM6A,EWSR1-FLI1 KD

description: Library name: A673,Input for KDM6A,EWSR1-FLI1 KD


title: chic_VAN7201-k27me3-i9

city: Utrecht

first: Vivek

last: Bhardwaj

address: Padualaan 8

country: Netherlands

institute: Utrecht University

description:
multiplexed file from a 384-well plate, nla3/sortchic barcodes
wholecell_samples_genelevel_counts.h5ad

data_processing:
The first-in-pair reads from the T-ChIC protocol contain an RNA or ChIC barcode in the following format “RNA: 6N7X, ChIC: 3N8X”; where N=UMI nucleotide and X=Cell barcode nucleotide. We used a custom Python script to split the raw .fastq files into the ChIC and RNA fractions based on which one of the 2 barcode patterns is observed at the start. The two fractions are then independently mapped to the GRCz11/danRer11 genome.
A complete processing workflow with all parameters is available at: https://github.com/bhardwaj-lab/scChICflow
Assembly: GRCz11/danRer11
Supplementary files format and content: .h5 files (anndata object) containing gene-level raw counts for chromatin (chic) and RNA fraction per single-cell. The files can be loaded in python with scanpy (sc.read_h5ad) or in R with the LoomExperiment (import) package. The adata objects for TChIC samples contain "spliced", "unsplliced" and "chic" layers. The annotation for celltype, timepoints, and histone marks, are available as metadata columns in the same object.
Library strategy: tChIC

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish (TL strain) were maintained at 27.5°C in a 14/10 h light/dark cycle, according to standard laboratory conditions (Aleström et al., 2020). Embryos were collected and staged according to Kimmel et al. (1995). Animal experiments were approved by the Animal Experimentation Committee (DEC) of the Royal Netherlands Academy of Arts and Sciences (KNAW).

extract_protocol:
For early time points (4, 6, and 8 hpf), cells were dissociated with the addition of 200 µL of pre-warmed FACSmax cell dissociation solution (Genlantis T200100) for 5 minutes resuspending gently up and down at RT. For later time points (10, 12 and 24 hpf) cells were dissociated with the addition of 200 µL of pre-warmed Protease solution (100 µL Trypsin-EDTA (0.5%), no phenol red, Thermofisher 15400054, 20 µL 10X PBS0, 80 µL H2O) for 6 minutes on a shaker (Eppendorf Thermomixer Comfort) at 28°C and 400 rpm, resuspending vigorously every 2 minutes.
The detailed, step-by-step scT-ChIC protocol is available at: https://www.protocols.io/private/714FFF81809D11EE958A0A58A9FEAC02

treatment_protocol: Wild-type TL embryos were collected 20 minutes after fertilization in a petri dish with E3 medium (13.3 mg NaCl, 0.63 mg KCl, 2.4 mg CaCl2, 4.0 mg MgSO4, diluted in a final volume of 1 L of H2O) and kept at 28.5°C in an incubator. They were dechorionated by incubation in 5mL of 1 mg/mL of pronase solution at 28.5°C for 3 to 5 minutes, and deyolked using Ca2+-free Ringer’s solution for 5 min at RT.

value: whole embryo

value: Tupfel long-fin (TL)


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_201, ME/CFS patient

description:
Library name: cfs_cfrna_201
Column name in raw_counts_all.csv: cfs_cfrna_201

value: male


title: mRNA-201 – base

description:
Library name: KW21
column name in normalized_mRNA_counts_v1: 201 - base


title: chic_VAN7201-k27me3-i8


title: A673,KDM6A,Control

description: Library name: A673,KDM6A,Control


title: mRNA-380 – base

description:
Library name: KW18
column name in normalized_mRNA_counts_v1: 380 - base


title: chic_VAN7201-k27me3-i7


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_199, healthy control

description:
Library name: cfs_cfrna_199
Column name in raw_counts_all.csv: cfs_cfrna_199

value: control

value: female


title: mRNA-455 – base

description:
Library name: KW15
column name in normalized_mRNA_counts_v1: 455 - base


title: A673,Input for KDM6A,Control

description: Library name: A673,Input for KDM6A,Control


title: mRNA-387 – base

description:
Library name: KW12
column name in normalized_mRNA_counts_v1: 387 - base


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_198, ME/CFS patient

description:
Library name: cfs_cfrna_198
Column name in raw_counts_all.csv: cfs_cfrna_198

value: Plasma, extracted cell-free RNA


title: chic_VAN7201-k27me3-i5


title: GL261 Neurosphere scRNAseq

description: 10x Genomics

value: Neurosphere


title: A673,RNA,KDM6B-KO-2F7,R2

description:
All_2F7_A6.FPKM.txt
RNA_KDM6B-KO-2F7_R2_A673
b2F7_2

data_processing:
RNA-seq, alignment: Sequence reads were mapped against the hg19 human genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
RNA-seq, differential analysis: DeSeq2 (PubMed ID 25516281) was run to identify differentially expressed genes.
Assembly: hg19
Supplementary files format and content: *FPKM.txt: DEseq2 output columns: EnsemblGeneID,baseMean,log2FoldChange,lfcSE,stat,pvalue,padj,GeneSymbol,EntrezGeneID,RPKM

extract_protocol:
Total RNA was isolated and purified using the RNeasy Mini Kit (Qiagen) following manufacturer’s instructions
Illumina Stranded Total RNA Prep kit (Illumina) was used according to manufacturer’s instructions

value: Ewing sarcoma


title: chic_VAN7201-k27me3-i6


title: A673,RNA,KDM6B-KO-2F7,R3

description:
All_2F7_A6.FPKM.txt
RNA_KDM6B-KO-2F7_R3_A673
b2F7_3


title: chic_VAN7201-k27me3-i4


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_202, ME/CFS patient

description:
Library name: cfs_cfrna_202
Column name in raw_counts_all.csv: cfs_cfrna_202

value: Los Angeles, CA


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_196, ME/CFS patient

description:
Library name: cfs_cfrna_196
Column name in raw_counts_all.csv: cfs_cfrna_196


title: mRNA-953 – base

description:
Library name: KW6
column name in normalized_mRNA_counts_v1: 953 - base


title: chic_VAN7201-k27me3-i3


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_195, healthy control

description:
Library name: cfs_cfrna_195
Column name in raw_counts_all.csv: cfs_cfrna_195

value: New York City, NY


title: A673,RNA,KDM6B-KO-2F7,R1

description:
All_2F7_A6.FPKM.txt
RNA_KDM6B-KO-2F7_R1_A673
b2F7_1


title: A673,RNA,KDM6B-KO-2D4,R3

description:
All_2D4_A6.FPKM.txt
RNA_KDM6B-KO-2D4_R3_A673
b2D4_3


title: mRNA-523 – base

description:
Library name: KW3
column name in normalized_mRNA_counts_v1: 523 - base

value: whole blood


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_197, ME/CFS patient

description:
Library name: cfs_cfrna_197
Column name in raw_counts_all.csv: cfs_cfrna_197

value: case


title: chic_VAN7201-k27me3-i2

description:
multiplexed file from a 384-well plate, nla3/sortchic barcodes
wholecell_samples_genelevel_counts.h5ad


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_200, ME/CFS patient

description:
Library name: cfs_cfrna_200
Column name in raw_counts_all.csv: cfs_cfrna_200

value: Ithaca, NY


title: A673,RNA,KDM6B-KO-2D4,R2

description:
All_2D4_A6.FPKM.txt
RNA_KDM6B-KO-2D4_R2_A673
b2D4_2


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_194, healthy control

description:
Library name: cfs_cfrna_194
Column name in raw_counts_all.csv: cfs_cfrna_194


title: A673,RNA,KDM6B-KO-2D4,R1

description:
All_2D4_A6.FPKM.txt
RNA_KDM6B-KO-2D4_R1_A673
b2D4_1


title: mRNA-412 – base

description:
Library name: KW1
column name in normalized_mRNA_counts_v1: 412 - base

value: baseline


title: mRNA-270 - base

description:
Library name: CB7
column name in normalized_mRNA_counts_v1: 270 - base


title: chic_VAN7201-k27me3-i10


title: chic_VAN7201-k27me3-i1


title: A673,RNA,CONTROLforKDM6BKO,R3

description:
All_2D4_A6.FPKM.txt,All_2F7_A6.FPKM.txt
RNA_CTRL_for_KDM6B-KO_R3_A673
bCTRL3


title: chic_OUD6112_K27me3_i47


title: A673,RNA,CONTROLforKDM6BKO,R2

description:
All_2D4_A6.FPKM.txt,All_2F7_A6.FPKM.txt
RNA_CTRL_for_KDM6B-KO_R2_A673
bCTRL2


title: mRNA-714 – base

description:
Library name: KW9
column name in normalized_mRNA_counts_v1: 714 - base


title: mRNA-778 - base

description:
Library name: CB49
column name in normalized_mRNA_counts_v1: 778 - base


title: mRNA-867 - base

description:
Library name: CB52
column name in normalized_mRNA_counts_v1: 867 - base


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_190, healthy control

description:
Library name: cfs_cfrna_190
Column name in raw_counts_all.csv: cfs_cfrna_190


title: A673,RNA,CONTROLforKDM6BKO,R1

description:
All_2D4_A6.FPKM.txt,All_2F7_A6.FPKM.txt
RNA_CTRL_for_KDM6B-KO_R1_A673
bCTRL1


title: mRNA-159 - base

description:
Library name: CB46
column name in normalized_mRNA_counts_v1: 159 - base


title: chic_OUD6112_K27me3_i44


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_189, healthy control

description:
Library name: cfs_cfrna_189
Column name in raw_counts_all.csv: cfs_cfrna_189


title: mRNA-327 - base

description:
Library name: CB40
column name in normalized_mRNA_counts_v1: 327 - base


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_187, healthy control

description:
Library name: cfs_cfrna_187
Column name in raw_counts_all.csv: cfs_cfrna_187


title: chic_OUD6112_K27me3_i42

description:
multiplexed file from a 384-well plate, nla3/sortchic barcodes
wholecell_samples_genelevel_counts.h5ad


title: A673,RNA,KDM6A-KO-2C7,R2

description:
All_2C7_A6.FPKM.txt
RNA_KDM6A-KO-2C7_R2_A673
a2C7_2


title: chic_OUD6112_K27me3_i43


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_193, healthy control

description:
Library name: cfs_cfrna_193
Column name in raw_counts_all.csv: cfs_cfrna_193


title: chic_OUD6112_K27me3_i45


title: A673,RNA,KDM6A-KO-2C7,R1

description:
All_2C7_A6.FPKM.txt
RNA_KDM6A-KO-2C7_R1_A673
a2C7_1


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_186, ME/CFS patient

description:
Library name: cfs_cfrna_186
Column name in raw_counts_all.csv: cfs_cfrna_186


title: mRNA-649 - base

description:
Library name: CB37
column name in normalized_mRNA_counts_v1: 649 - base


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_188, healthy control

description:
Library name: cfs_cfrna_188
Column name in raw_counts_all.csv: cfs_cfrna_188


title: chic_OUD6112_K27me3_i12


title: mRNA-687 - base

description:
Library name: CB34
column name in normalized_mRNA_counts_v1: 687 - base


title: A673,RNA,KDM6A-KO-1B6,R3

description:
All_1B6_A6.FPKM.txt
RNA_KDM6A-KO-1B6_R3_A673
a1B6_3


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_184, healthy control

description:
Library name: cfs_cfrna_184
Column name in raw_counts_all.csv: cfs_cfrna_184


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_185, healthy control

description:
Library name: cfs_cfrna_185
Column name in raw_counts_all.csv: cfs_cfrna_185


title: A673,RNA,KDM6A-KO-1B6,R1

description:
All_1B6_A6.FPKM.txt
RNA_KDM6A-KO-1B6_R1_A673
a1B6_1


title: chic_OUD6112_K27me3_i11


title: A673,RNA,KDM6A-KO-2C7,R3

description:
All_2C7_A6.FPKM.txt
RNA_KDM6A-KO-2C7_R3_A673
a2C7_3


title: A673,RNA,KDM6A-KO-1B6,R2

description:
All_1B6_A6.FPKM.txt
RNA_KDM6A-KO-1B6_R2_A673
a1B6_2


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_183, healthy control

description:
Library name: cfs_cfrna_183
Column name in raw_counts_all.csv: cfs_cfrna_183


title: mRNA-729 - base

description:
Library name: CB31
column name in normalized_mRNA_counts_v1: 729 - base


title: mRNA-175 - base

description:
Library name: CB28
column name in normalized_mRNA_counts_v1: 175 - base


title: chic_OUD6106_K27me3_i6

description:
multiplexed file from a 384-well plate, nla3/sortchic barcodes
wholecell_samples_genelevel_counts.h5ad


title: chic_OUD6106_K27me3_i5


title: A673,RNA,CONTROLforKDM6AKO,R3

description:
All_1B6_A6.FPKM.txt,All_2C7_A6.FPKM.txt
RNA_CTRL_for_KDM6A-KO_R3_A673
aCTRL3


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_182, ME/CFS patient

description:
Library name: cfs_cfrna_182
Column name in raw_counts_all.csv: cfs_cfrna_182


title: mRNA-309 - base

description:
Library name: CB43
column name in normalized_mRNA_counts_v1: 309 - base


title: chic_OUD6106_K27me3_i3


title: mRNA-454 - base

description:
Library name: CB25
column name in normalized_mRNA_counts_v1: 454 - base


title: chic_OUD6106_K27me3_i4


title: A673,RNA,CONTROLforKDM6AKO,R1

description:
All_1B6_A6.FPKM.txt,All_2C7_A6.FPKM.txt
RNA_CTRL_for_KDM6A-KO_R1_A673
aCTRL1


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_179, ME/CFS patient

description:
Library name: cfs_cfrna_179
Column name in raw_counts_all.csv: cfs_cfrna_179


title: mRNA-788 - base

description:
Library name: CB16
column name in normalized_mRNA_counts_v1: 788 - base


title: A673,RNA,CONTROLforKDM6AKO,R2

description:
All_1B6_A6.FPKM.txt,All_2C7_A6.FPKM.txt
RNA_CTRL_for_KDM6A-KO_R2_A673
aCTRL2


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_181, healthy control

description:
Library name: cfs_cfrna_181
Column name in raw_counts_all.csv: cfs_cfrna_181


title: mRNA-100 - base

description:
Library name: CB19
column name in normalized_mRNA_counts_v1: 100 - base


title: TC71,RNA,KDM6B-KD6,R3

description:
All_kd6_E3.FPKM.txt
RNA_KDM6B-KD6_R3_TC71
E_3Kd6


title: mRNA-650 - base

description:
Library name: CB22
column name in normalized_mRNA_counts_v1: 650 - base


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_178, ME/CFS patient

description:
Library name: cfs_cfrna_178
Column name in raw_counts_all.csv: cfs_cfrna_178


title: chic_OUD6106_K27me3_i2


title: mRNA-914 - base

description:
Library name: CB13
column name in normalized_mRNA_counts_v1: 914 - base


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_177, ME/CFS patient

description:
Library name: cfs_cfrna_177
Column name in raw_counts_all.csv: cfs_cfrna_177


title: TC71,RNA,KDM6B-KD1,R3

description:
All_kd1_E3.FPKM.txt
RNA_KDM6B-KD1_R3_TC71
E_3Kd1


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_173, ME/CFS patient

description:
Library name: cfs_cfrna_173
Column name in raw_counts_all.csv: cfs_cfrna_173


title: TC71,RNA,KDM6B-KD6,R1

description:
All_kd6_E3.FPKM.txt
RNA_KDM6B-KD6_R1_TC71
E_1Kd6


title: TC71,RNA,KDM6B-KD6,R2

description:
All_kd6_E3.FPKM.txt
RNA_KDM6B-KD6_R2_TC71
E_2Kd6


title: mRNA-323 - base

description:
Library name: CB10
column name in normalized_mRNA_counts_v1: 323 - base


title: mRNA-784 - base

description:
Library name: CB1
column name in normalized_mRNA_counts_v1: 784 - base


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_174, ME/CFS patient

description:
Library name: cfs_cfrna_174
Column name in raw_counts_all.csv: cfs_cfrna_174


title: chic_OUD6106_K27me3_i22

description:
multiplexed file from a 384-well plate, nla3/sortchic barcodes
wholecell_samples_genelevel_counts.h5ad


title: chic_OUD6106_K27me3_i14


title: chic_OUD6106_K27me3_i13


title: chic_OUD6106_K27me3_i21


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_171, ME/CFS patient

description:
Library name: cfs_cfrna_171
Column name in raw_counts_all.csv: cfs_cfrna_171


title: TC71,RNA,KDM6B-KD1,R2

description:
All_kd1_E3.FPKM.txt
RNA_KDM6B-KD1_R2_TC71
E_2Kd1


title: miRNA-523 - 7day

description:
Library name: miKW5
column name in Normalized_miRNA_counts_v1: 523 - 7day


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_170, ME/CFS patient

description:
Library name: cfs_cfrna_170
Column name in raw_counts_all.csv: cfs_cfrna_170


title: miRNA-953 - 7day

description:
Library name: miKW8
column name in Normalized_miRNA_counts_v1: 953 - 7day


title: chic_OUD6106_K27me3_i32


title: chic_OUD6106_K27me3_i12


title: TC71,RNA,KDM6B-KD1,R1

description:
All_kd1_E3.FPKM.txt
RNA_KDM6B-KD1_R1_TC71
E_1Kd1


title: miRNA-584 - 7day

description:
Library name: miKW29
column name in Normalized_miRNA_counts_v1: 584 - 7day


title: chic_OUD6106_K27me3_i11


title: TC71,RNA,CONTROLforKDM6B,R3

description:
All_kd1_E3.FPKM.txt,All_kd6_E3.FPKM.txt
RNA_CTRL_for_KDM6B-KD_R3_TC71
E_3C


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_168, healthy control

description:
Library name: cfs_cfrna_168
Column name in raw_counts_all.csv: cfs_cfrna_168


title: miRNA-663 - 7day

description:
Library name: miKW26
column name in Normalized_miRNA_counts_v1: 663 - 7day


title: TC71,RNA,CONTROLforKDM6B,R2

description:
All_kd1_E3.FPKM.txt,All_kd6_E3.FPKM.txt
RNA_CTRL_for_KDM6B-KD_R2_TC71
E_2C


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_167, ME/CFS patient

description:
Library name: cfs_cfrna_167
Column name in raw_counts_all.csv: cfs_cfrna_167


title: chic_OUD5884_K27me3_i8


title: chic_OUD5884_K27me3_i3


title: miRNA-201 - 7day

description:
Library name: miKW23
column name in Normalized_miRNA_counts_v1: 201 - 7day


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_166, ME/CFS patient

description:
Library name: cfs_cfrna_166
Column name in raw_counts_all.csv: cfs_cfrna_166


title: TC71,RNA,KDM6A-KD7,R3

description:
All_kd7_ES.FPKM.txt
RNA_KDM6A-KD7_R3_TC71
ES_7D3


title: TC71,RNA,CONTROLforKDM6B,R1

description:
All_kd1_E3.FPKM.txt,All_kd6_E3.FPKM.txt
RNA_CTRL_for_KDM6B-KD_R1_TC71
E_1C


title: rna_VAN7201-k27me3-i9

description:
multiplexed file from a 384-well plate, celseq2 barcodes
wholecell_samples_genelevel_counts.h5ad


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_164, ME/CFS patient

description:
Library name: cfs_cfrna_164
Column name in raw_counts_all.csv: cfs_cfrna_164


title: TC71,RNA,KDM6A-KD7,R1

description:
All_kd7_ES.FPKM.txt
RNA_KDM6A-KD7_R1_TC71
ES_7D1


title: TC71,RNA,KDM6A-KD7,R2

description:
All_kd7_ES.FPKM.txt
RNA_KDM6A-KD7_R2_TC71
ES_7D2


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_165, healthy control

description:
Library name: cfs_cfrna_165
Column name in raw_counts_all.csv: cfs_cfrna_165


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_163, ME/CFS patient

description:
Library name: cfs_cfrna_163
Column name in raw_counts_all.csv: cfs_cfrna_163


title: miRNA-387 - 7day

description:
Library name: miKW14
column name in Normalized_miRNA_counts_v1: 387 - 7day


title: miRNA-412 - 7day

description:
Library name: miKW2
column name in Normalized_miRNA_counts_v1: 412 - 7day


title: rna_VAN7201-k27me3-i8


title: miRNA-455 - 7day

description:
Library name: miKW17
column name in Normalized_miRNA_counts_v1: 455 - 7day


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_169, healthy control

description:
Library name: cfs_cfrna_169
Column name in raw_counts_all.csv: cfs_cfrna_169


title: TC71,RNA,KDM6A-KD9,R2

description:
All_kd9_ES.FPKM.txt
RNA_KDM6A-KD9_R2_TC71
ES_9D2


title: miRNA-714 - 7day

description:
Library name: miKW11
column name in Normalized_miRNA_counts_v1: 714 - 7day


title: TC71,RNA,KDM6A-KD9,R3

description:
All_kd9_ES.FPKM.txt
RNA_KDM6A-KD9_R3_TC71
ES_9D3


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_161, healthy control

description:
Library name: cfs_cfrna_161
Column name in raw_counts_all.csv: cfs_cfrna_161


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_162, healthy control

description:
Library name: cfs_cfrna_162
Column name in raw_counts_all.csv: cfs_cfrna_162


title: rna_VAN7201-k27me3-i6


title: rna_VAN7201-k27me3-i7


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_160, ME/CFS patient

description:
Library name: cfs_cfrna_160
Column name in raw_counts_all.csv: cfs_cfrna_160


title: miRNA-380 - 7day

description:
Library name: miKW20
column name in Normalized_miRNA_counts_v1: 380 - 7day


title: TC71,RNA,KDM6A-KD9,R1

description:
All_kd9_ES.FPKM.txt
RNA_KDM6A-KD9_R1_TC71
ES_9D1


title: miRNA-778 - 7day

description:
Library name: miCB51
column name in Normalized_miRNA_counts_v1: 778 - 7day


title: rna_VAN7201-k27me3-i4

description:
multiplexed file from a 384-well plate, celseq2 barcodes
wholecell_samples_genelevel_counts.h5ad


title: TC71,RNA,CONTROLforKDM6A,R3

description:
All_kd7_ES.FPKM.txt,All_kd9_ES.FPKM.txt
RNA_CTRL_for_KDM6A-KD_R3_TC71
ES_MD3


title: miRNA-270 - 7day

description:
Library name: miCB9
column name in Normalized_miRNA_counts_v1: 270 - 7day


title: rna_VAN7201-k27me3-i3


title: rna_VAN7201-k27me3-i2


title: TC71,RNA,CONTROLforKDM6A,R1

description:
All_kd7_ES.FPKM.txt,All_kd9_ES.FPKM.txt
RNA_CTRL_for_KDM6A-KD_R1_TC71
ES_MD1


title: TC71,RNA,CONTROLforKDM6A,R2

description:
All_kd7_ES.FPKM.txt,All_kd9_ES.FPKM.txt
RNA_CTRL_for_KDM6A-KD_R2_TC71
ES_MD2


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_157, ME/CFS patient

description:
Library name: cfs_cfrna_157
Column name in raw_counts_all.csv: cfs_cfrna_157


title: miRNA-327 - 7day

description:
Library name: miCB42
column name in Normalized_miRNA_counts_v1: 327 - 7day


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_159, ME/CFS patient

description:
Library name: cfs_cfrna_159
Column name in raw_counts_all.csv: cfs_cfrna_159


title: miRNA-159 - 7day

description:
Library name: miCB48
column name in Normalized_miRNA_counts_v1: 159 - 7day


title: rna_VAN7201-k27me3-i1


title: miRNA-729 - 7day

description:
Library name: miCB33
column name in Normalized_miRNA_counts_v1: 729 - 7day


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_155, healthy control

description:
Library name: cfs_cfrna_155
Column name in raw_counts_all.csv: cfs_cfrna_155


title: rna_VAN6297_TnoChIC_i9

description:
multiplexed file from a 384-well plate, celseq2 barcodes
wholecell_samples_TnoChIC_genelevel_counts.h5ad


title: rna_VAN7201-k27me3-i10


title: A673,H3K27me3,CTRL for KDM6B KO,R2

value: Millipore 07-449


title: rna_VAN6297_TnoChIC_i31


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_153, ME/CFS patient

description:
Library name: cfs_cfrna_153
Column name in raw_counts_all.csv: cfs_cfrna_153


title: rna_VAN7201-k27me3-i5


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_152, healthy control

description:
Library name: cfs_cfrna_152
Column name in raw_counts_all.csv: cfs_cfrna_152


title: A673,H3K27me3 upon KDM6B KO,R2


title: miRNA-784 - 7day

description:
Library name: miCB3
column name in Normalized_miRNA_counts_v1: 784 - 7day


title: A673,H3K27me3,CTRL for KDM6B KO,R1


title: miRNA-454 - 7day

description:
Library name: miCB27
column name in Normalized_miRNA_counts_v1: 454 - 7day


title: A673,H3K27me3,CTRL for KDM6A KO,R2


title: miRNA-649 - 7day

description:
Library name: miCB39
column name in Normalized_miRNA_counts_v1: 649 - 7day


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_154, ME/CFS patient

description:
Library name: cfs_cfrna_154
Column name in raw_counts_all.csv: cfs_cfrna_154


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_156, ME/CFS patient

description:
Library name: cfs_cfrna_156
Column name in raw_counts_all.csv: cfs_cfrna_156


title: miRNA-175 - 7day

description:
Library name: miCB30
column name in Normalized_miRNA_counts_v1: 175 - 7day


title: A673,H3K27me3 upon KDM6A KO,R1


title: A673,H3K27me3 upon KDM6B KO,R1


title: A673,H3K27me3 upon KDM6A KO,R2


title: rna_VAN6297_TnoChIC_i30


title: miRNA-100 - 7day

description:
Library name: miCB21
column name in Normalized_miRNA_counts_v1: 100 - 7day


title: rna_VAN6297_TnoChIC_i29


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_151, healthy control

description:
Library name: cfs_cfrna_151
Column name in raw_counts_all.csv: cfs_cfrna_151


title: miRNA-650 - 7day

description:
Library name: miCB24
column name in Normalized_miRNA_counts_v1: 650 - 7day


title: rna_VAN6297_TnoChIC_i28


title: rna_OUD6112_TnoChIC_i9

description:
multiplexed file from a 384-well plate, celseq2 barcodes
wholecell_samples_genelevel_counts.h5ad


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_150, ME/CFS patient

description:
Library name: cfs_cfrna_150
Column name in raw_counts_all.csv: cfs_cfrna_150


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_146, healthy control

description:
Library name: cfs_cfrna_146
Column name in raw_counts_all.csv: cfs_cfrna_146


title: rna_VAN6297_TnoChIC_i27


title: miRNA-788 - 7day

description:
Library name: miCB18
column name in Normalized_miRNA_counts_v1: 788 - 7day


title: A673,H3K27me3,CTRL for KDM6A KO,R1


title: TC71,INPUT EWSR1-FLI1,R2


title: rna_VAN6297_TnoChIC_i25


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_145, healthy control

description:
Library name: cfs_cfrna_145
Column name in raw_counts_all.csv: cfs_cfrna_145


title: miRNA-953 - 72h

description:
Library name: miKW7
column name in Normalized_miRNA_counts_v1: 953 - 72h


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_192, ME/CFS patient

description:
Library name: cfs_cfrna_192
Column name in raw_counts_all.csv: cfs_cfrna_192


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_147, healthy control

description:
Library name: cfs_cfrna_147
Column name in raw_counts_all.csv: cfs_cfrna_147


title: TC71,INPUT KDM6A/FLI1,R1


title: rna_OUD6112_TnoChIC_i6


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_148, ME/CFS patient

description:
Library name: cfs_cfrna_148
Column name in raw_counts_all.csv: cfs_cfrna_148


title: rna_OUD6112_TnoChIC_i8


title: miRNA-914 - 7day

description:
Library name: miCB15
column name in Normalized_miRNA_counts_v1: 914 - 7day


title: TC71,EWSR1-FLI1,R1

value: FLI1 (Abcam ab15289)


title: miRNA-323 - 7day

description:
Library name: miCB12
column name in Normalized_miRNA_counts_v1: 323 - 7day


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_141, ME/CFS patient

description:
Library name: cfs_cfrna_141
Column name in raw_counts_all.csv: cfs_cfrna_141


title: TC71,INPUT KDM6A,R2


title: TC71,INPUT KDM6B


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_143, healthy control

description:
Library name: cfs_cfrna_143
Column name in raw_counts_all.csv: cfs_cfrna_143


title: TC71,KDM6B,R2

value: KDM6B (Abcam ab169197)


title: TC71,EWSR1-FLI1,R2


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_142, ME/CFS patient

description:
Library name: cfs_cfrna_142
Column name in raw_counts_all.csv: cfs_cfrna_142


title: TC71,KDM6B,R1


title: rna_OUD6112_K27me3_i45

value: whole embryo


title: miRNA-201 - 72h

description:
Library name: miKW22
column name in Normalized_miRNA_counts_v1: 201 - 72h


title: miRNA-584 - 72h

description:
Library name: miKW28
column name in Normalized_miRNA_counts_v1: 584 - 72h


title: miRNA-663 - 72h

description:
Library name: miKW25
column name in Normalized_miRNA_counts_v1: 663 - 72h


title: miRNA-523 - 72h

description:
Library name: miKW4
column name in Normalized_miRNA_counts_v1: 523 - 72h


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_139, ME/CFS patient

description:
Library name: cfs_cfrna_139
Column name in raw_counts_all.csv: cfs_cfrna_139


title: rna_OUD6112_TnoChIC_i5

description:
multiplexed file from a 384-well plate, celseq2 barcodes
wholecell_samples_genelevel_counts.h5ad

value: Tupfel long-fin (TL)


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_072, healthy control

description:
Library name: cfs_cfrna_072
Column name in raw_counts_all.csv: cfs_cfrna_72

value: male


title: rna_OUD6112_K27me3_i47


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_140, ME/CFS patient

description:
Library name: cfs_cfrna_140
Column name in raw_counts_all.csv: cfs_cfrna_140


title: rna_OUD6112_K27me3_i48


title: TC71,KDM6A,R2

value: KDM6A (UTX) (Cell Signaling 33510)


title: miRNA-380 - 72h

description:
Library name: miKW19
column name in Normalized_miRNA_counts_v1: 380 - 72h


title: miRNA-455 - 72h

description:
Library name: miKW16
column name in Normalized_miRNA_counts_v1: 455 - 72h


title: TC71,KDM6A,R1


title: rna_OUD6112_TnoChIC_i4


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_071, ME/CFS patient

description:
Library name: cfs_cfrna_071
Column name in raw_counts_all.csv: cfs_cfrna_71

value: female


title: A673,INPUT,BRG1 KDM6A KO

data_processing:
ChIP-seq, alignment: Sequence reads of the samples without spike-in were mapped to the human genome (hg19) using BOWTIE (PubMed ID 19261174) with the option -m 1. Sequence of the reads of the samples with spike-in were mapped to a synthetic genome containing the human and the fruit fly chromosomes (hg19+dm3).
ChIP-seq, genome profiles: SeqCode (PubMed ID 34599234) was used to generate the genome-wide profiles of each ChIP-seq experiment. Height of the profiles is normalized by the total number of reads mapped over the human genome for samples without spike/in material, and by the number of fly spike-in genome reads in the case of samples with spike-in
ChIP-seq, peak calling: Peak detection of every sample against its corresponding Input was performed with MACS (PubMed ID: 18798982).
Assembly: hg19
Supplementary files format and content: Bedgraph format for genome-wide profiles
Supplementary files format and content: BED format for MACS

growth_protocol: A673 cells were cultured in RPMI 1640 media (Gibco) and supplemented with 10% FBS, L-glutamine and penicillin/streptomycin. Cells were maintained in a humidified chamber at 37ºC and 5% CO2, and split every 2-3 days when reaching confluence.

extract_protocol:
(ChIP-seq) Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
(ChIP-seq) ChIP-seq libraries were prepared using 2-5 ng of input and ChIP samples and the kit NEBNext Ultra DNA Library Prep for Illumina (New England Biolabs) following manufacturer’s protocol. (RNA-seq) Illumina Stranded Total RNA Prep kit (Illumina) was used according to manufacturer’s instructions

treatment_protocol: EwS cell lines were seeded in 6-well plates at 0.25 x 106 cells/mL and transfected with Lipofectamine RNAiMAX (Invitrogene) using 30 pmol of siRNA in OptiMEM media (Gibco) following manufacturer’s instructions. For knock-downs, distinct target sequences for small interfering RNA and the SMARTvector inducible Tet-On shRNA system (Dharmacon) act over KDM6A or KDM6B. Empty and EWSR1-FLI1-pLIV vector was kindly provided by Dr Nicolo Riggi and published in Boulay et al., 2017. For KDM6A  knockout cells,  the Gene Knockout Kit v2 (Synthego) was used with a pool of three validated sgRNA and exogenous Cas9 following manufacturers guidelines. CRISPR-edited cell pools were isolated by limit dilution in 96-well plates. Isolated clones were expanded and cells were collected for subsequent validation by Sanger sequencing of the PCR product


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_070, ME/CFS patient

description:
Library name: cfs_cfrna_070
Column name in raw_counts_all.csv: cfs_cfrna_70

value: Plasma, extracted cell-free RNA


title: rna_OUD6112_K27me3_i43


title: rna_OUD6112_K27me3_i12


title: miRNA-387 - 72h

description:
Library name: miKW13
column name in Normalized_miRNA_counts_v1: 387 - 72h


title: rna_OUD6112_K27me3_i42


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_068, healthy control

description:
Library name: cfs_cfrna_068
Column name in raw_counts_all.csv: cfs_cfrna_68

value: control


title: miRNA-867 - 72h

description:
Library name: miCB53
column name in Normalized_miRNA_counts_v1: 867 - 72h


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_069, ME/CFS patient

description:
Library name: cfs_cfrna_069
Column name in raw_counts_all.csv: cfs_cfrna_69


title: rna_OUD6112_K27me3_i44


title: A673,INPUT,BRG1 CTRL

value: Ewing sarcoma


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_067, ME/CFS patient

description:
Library name: cfs_cfrna_067
Column name in raw_counts_all.csv: cfs_cfrna_67

value: Los Angeles, CA


title: A673,BRG1,CTRL


title: rna_OUD6112_K27me3_i11


title: miRNA-778 - 72h

description:
Library name: miCB50
column name in Normalized_miRNA_counts_v1: 778 - 72h


title: rna_OUD6106_TnoChIC_i38


title: rna_OUD6106_TnoChIC_i46


title: RNA-seq-shA1-3

city: wuhan

first: Joshua

last: Guo

address: shuiguohulu

country: China

institute: wuhan university

data_processing:
RNA-seq data were quantified with Kallisto (v0.43.1) and summarized to gene level by tximport (v1.10.1).
EdgeR (v3.24.3) was employed for data normalization and differential expression analysis of RNA-seq counts.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

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

extract_protocol:
For RNA-seq, total RNA was isolated using Trizol reagent (Thermo Fisher).
Poly (A) mRNA was subsequently purified from 1 µg total RNA using NEBNext Poly (A) mRNA Magnetic Isolation Module. NEBNext Ultra Directional RNA Library Prep Kit (NEB, #E7760) was used for library preparation.

value: HNSCC cells

value: ALKBH1 knockdown

value: transduction with indicated lentiviruses

tag: time

value: Day 4


title: miRNA-309 - 72h

description:
Library name: miCB44
column name in Normalized_miRNA_counts_v1: 309 - 72h

value: whole blood


title: miRNA-270 - 72h

description:
Library name: miCB8
column name in Normalized_miRNA_counts_v1: 270 - 72h


title: A673,BRG1,KDM6A KO


title: miRNA-327 - 72h

description:
Library name: miCB41
column name in Normalized_miRNA_counts_v1: 327 - 72h


title: shcon

value: Control


title: miRNA-714 - 72h

description:
Library name: miKW10
column name in Normalized_miRNA_counts_v1: 714 - 72h


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_065, ME/CFS patient

description:
Library name: cfs_cfrna_065
Column name in raw_counts_all.csv: cfs_cfrna_65

value: case


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_060, healthy control

description:
Library name: cfs_cfrna_060
Column name in raw_counts_all.csv: cfs_cfrna_60

value: New York City, NY


title: rna_OUD6106_TnoChIC_i37

description:
multiplexed file from a 384-well plate, celseq2 barcodes
wholecell_samples_genelevel_counts.h5ad

value: whole embryo


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_059, healthy control

description:
Library name: cfs_cfrna_059
Column name in raw_counts_all.csv: cfs_cfrna_59

value: Ithaca, NY


title: miRNA-729 - 72h

description:
Library name: miCB32
column name in Normalized_miRNA_counts_v1: 729 - 72h


title: miRNA-159 - 72h

description:
Library name: miCB47
column name in Normalized_miRNA_counts_v1: 159 - 72h


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_063, ME/CFS patient

description:
Library name: cfs_cfrna_063
Column name in raw_counts_all.csv: cfs_cfrna_63

value: male


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_064, ME/CFS patient

description:
Library name: cfs_cfrna_064
Column name in raw_counts_all.csv: cfs_cfrna_64


title: A673,RNA,KDM6B-KD6,R3

data_processing:
ChIP-seq, alignment: Sequence reads of the samples without spike-in were mapped to the human genome (hg19) using BOWTIE (PubMed ID 19261174) with the option -m 1. Sequence of the reads of the samples with spike-in were mapped to a synthetic genome containing the human and the fruit fly chromosomes (hg19+dm3).
ChIP-seq, genome profiles: SeqCode (PubMed ID 34599234) was used to generate the genome-wide profiles of each ChIP-seq experiment. Height of the profiles is normalized by the total number of reads mapped over the human genome for samples without spike/in material, and by the number of fly spike-in genome reads in the case of samples with spike-in.
ChIP-seq, peak calling: Peak detection of every sample against its corresponding Input was performed with MACS (PubMed ID: 18798982).
ChIP-seq, replicate peaks: DiffBind (PubMed ID 22217937) was used to generate a consensus set of peaks for each pair of replicates.
RNA-seq, alignment: Sequence reads were mapped against the hg19 human genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1.
RNA-seq, differential analysis: DeSeq2 (PubMed ID 25516281) was run to identify differentially expressed genes.
Assembly: hg19
Supplementary files format and content: Bedgraph format for genome-wide profiles.
Supplementary files format and content: BED format for MACS and DiffBind peaks.
Supplementary files format and content: DESeq2 format column descriptions: Ensembl gene id, baseMean, log2FC, lfcSE, stat, pvalue, padj, gene symbol id, gene entrez id, RPKMs in control, RPKMs in first KD, RPKMs in second KD. Filenames indicate which KD is performed in that comparison against the control condition.

extract_protocol:
(ChIP-seq) Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. (RNA-seq) Total RNA was isolated and purified using the RNeasy Mini Kit (Qiagen) following manufacturer’s instructions.
(ChIP-seq) ChIP-seq libraries were prepared using 2-5 ng of input and ChIP samples and the kit NEBNext Ultra DNA Library Prep for Illumina (New England Biolabs) following manufacturer’s protocol. (RNA-seq) Illumina Stranded Total RNA Prep kit (Illumina) was used according to manufacturer’s instructions.

treatment_protocol: EwS cell lines were seeded in 6-well plates at 0.25 x 10^6 cells/mL and transfected with Lipofectamine RNAiMAX (Invitrogene) using 30 pmol of siRNA in OptiMEM media (Gibco) following manufacturer’s instructions. For knock-downs, distinct target sequences for small interfering RNA and the SMARTvector inducible Tet-On shRNA system (Dharmacon) act over KDM6A or KDM6B. Empty and EWSR1-FLI1-pLIV vector was kindly provided by Dr Nicolo Riggi and published in Boulay et al., 2017. For KDM6A knockout cells, the Gene Knockout Kit v2 (Synthego) was used with a pool of three validated sgRNA and exogenous Cas9 following manufacturer's guidelines. CRISPR-edited cell pools were isolated by limit dilution in 96-well plates. Isolated clones were expanded and cells were collected for subsequent validation by Sanger sequencing of the PCR product.


title: rna_OUD6106_K27me3_i4

value: Tupfel long-fin (TL)


title: rna_OUD6106_TnoChIC_i36


title: shA1-2


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_058, ME/CFS patient

description:
Library name: cfs_cfrna_058
Column name in raw_counts_all.csv: cfs_cfrna_58

value: female


title: shA1-3


title: shmock


title: rna_OUD6106_K27me3_i6


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_066, healthy control

description:
Library name: cfs_cfrna_066
Column name in raw_counts_all.csv: cfs_cfrna_66

value: Plasma, extracted cell-free RNA


title: miRNA-175 - 72h

description:
Library name: miCB29
column name in Normalized_miRNA_counts_v1: 175 - 72h


title: rna_OUD6106_K27me3_i3


title: A673,RNA,KDM6B-KD6,R2


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_057, healthy control

description:
Library name: cfs_cfrna_057
Column name in raw_counts_all.csv: cfs_cfrna_57

value: control


title: miRNA-454 - 72h

description:
Library name: miCB26
column name in Normalized_miRNA_counts_v1: 454 - 72h


title: rna_OUD6106_K27me3_i32


title: miRNA-687 - 72h

description:
Library name: miCB35
column name in Normalized_miRNA_counts_v1: 687 - 72h


title: A673,RNA,KDM6B-KD6,R1

value: Ewing sarcoma


title: miRNA-649 - 72h

description:
Library name: miCB38
column name in Normalized_miRNA_counts_v1: 649 - 72h


title: rna_OUD6106_K27me3_i5


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_056, ME/CFS patient

description:
Library name: cfs_cfrna_056
Column name in raw_counts_all.csv: cfs_cfrna_56


title: RNA-seq-mock


title: miRNA-650 - 72h

description:
Library name: miCB23
column name in Normalized_miRNA_counts_v1: 650 - 72h


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_055, healthy control

description:
Library name: cfs_cfrna_055
Column name in raw_counts_all.csv: cfs_cfrna_55


title: A673,RNA,KDM6B-KD1,R3


title: miRNA-100 - 72h

description:
Library name: miCB20
column name in Normalized_miRNA_counts_v1: 100 - 72h


title: rna_OUD6106_K27me3_i22

description:
multiplexed file from a 384-well plate, celseq2 barcodes
wholecell_samples_genelevel_counts.h5ad


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_054, healthy control

description:
Library name: cfs_cfrna_054
Column name in raw_counts_all.csv: cfs_cfrna_54


title: miRNA-784 - 72h

description:
Library name: miCB2
column name in Normalized_miRNA_counts_v1: 784 - 72h


title: A673,RNA,KDM6B-KD1,R2


title: A673,RNA,KDM6B-KD1,R1


title: rna_OUD6106_K27me3_i21


title: A673,RNA,CONTROLforKDM6B,R3


title: rna_OUD6106_K27me3_i14


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_052, ME/CFS patient

description:
Library name: cfs_cfrna_052
Column name in raw_counts_all.csv: cfs_cfrna_52


title: miRNA-914 - 72h

description:
Library name: miCB14
column name in Normalized_miRNA_counts_v1: 914 - 72h


title: rna_OUD6106_K27me3_i13


title: miRNA-788 - 72h

description:
Library name: miCB17
column name in Normalized_miRNA_counts_v1: 788 - 72h


title: A673,RNA,CONTROLforKDM6B,R2


title: miRNA-323 - 72h

description:
Library name: miCB11
column name in Normalized_miRNA_counts_v1: 323 - 72h


title: rna_OUD6106_K27me3_i2


title: rna_OUD6106_K27me3_i12


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_051, healthy control

description:
Library name: cfs_cfrna_051
Column name in raw_counts_all.csv: cfs_cfrna_51

value: Los Angeles, CA


title: A673,RNA,CONTROLforKDM6B,R1


title: miRNA-714 - base

description:
Library name: miKW9
column name in Normalized_miRNA_counts_v1: 714 - base

value: baseline


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_047, healthy control

description:
Library name: cfs_cfrna_047
Column name in raw_counts_all.csv: cfs_cfrna_47


title: rna_OUD6106_K27me3_i11


title: rna_OUD5884_K27me3_i8


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_048, healthy control

description:
Library name: cfs_cfrna_048
Column name in raw_counts_all.csv: cfs_cfrna_48


title: A673,RNA,KDM6A-KD7,R2


title: A673,RNA,KDM6A-KD7,R3


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_053, ME/CFS patient

description:
Library name: cfs_cfrna_053
Column name in raw_counts_all.csv: cfs_cfrna_53


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_046, ME/CFS patient

description:
Library name: cfs_cfrna_046
Column name in raw_counts_all.csv: cfs_cfrna_46


title: A673,RNA,KDM6A-KD7,R1


title: A673,RNA,KDM6A-KD9,R6


title: miRNA-584 - base

description:
Library name: miKW27
column name in Normalized_miRNA_counts_v1: 584 - base


title: P7 heart

city: Oxford

first: Robin

last: Choudhury

address: Level 6 West Wing, John Radcliffe Hospital

department: Department of Cardiovascular Medicine

institute: University of Oxford

description: Library name: P7 heart

data_processing:
Raw sequence reads were aligned against the mouse mm10/GRCm38 reference transcriptome and processed using the Cell Ranger 3.1.0 pipeline (10x Genomics).
Assembly: mm10/GRCm38
Supplementary files format and content: Raw FASTQ files, matrix.mtx, barcodes.tsv, features.tsv

source_name: Heart

extract_protocol:
Hearts from P1 and P7 mice were harvested for cell dissociation and live cells FACS sorting. Briefly, for each condition, 3 hearts collected from the same litter were pooled together and finely minced with a scalpel. Tissue was then digested by gentle agitation (180 rpm shaker) in Collagenase II (Gibco,) using a solution of 500 units/ml in HBSS at 37 °C for 45 minutes (P7 hearts) or 20 minutes (P1 hearts). Cell solutions were then passed through a 70 μm filter, washed and incubated in Red Blood Cell lysis buffer (Cell Signaling Technology) for 10 minutes at RT to remove red blood cells. Finally, isolated single cardiac cells were centrifuged, resuspended in 2% FBS in PBS, passed through the filtering cap of the FACS tubes and incubated with 1% 7-AAD viability stain (Invitrogen) for 10 minutes. Approximately 100,000 live cells per sample were sorted using the BD FACSAria Fusion Sorter.
Single cell RNA-seq libraries were generated using Single Cell 3 Prime Reagent Kits v1.3 (10x Genomics) according to the manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq 6000 System operated by the Oxford Genomics Centre at the Wellcome Centre for Human Genetics.

value: Heart

tag: developmental stage


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_045, healthy control

description:
Library name: cfs_cfrna_045
Column name in raw_counts_all.csv: cfs_cfrna_45


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_044, healthy control

description:
Library name: cfs_cfrna_044
Column name in raw_counts_all.csv: cfs_cfrna_44


title: rna_OUD5884_K27me3_i3


title: A673,RNA,KDM6A-KD9,R5


title: miRNA-201 - base

description:
Library name: miKW21
column name in Normalized_miRNA_counts_v1: 201 - base


title: A673,RNA,KDM6A-KD9,R4


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_042, ME/CFS patient

description:
Library name: cfs_cfrna_042
Column name in raw_counts_all.csv: cfs_cfrna_42


title: miRNA-953 - base

description:
Library name: miKW6
column name in Normalized_miRNA_counts_v1: 953 - base


title: miRNA-380 - base

description:
Library name: miKW18
column name in Normalized_miRNA_counts_v1: 380 - base


title: P1 heart

description: Library name: P1 heart


title: miRNA-663 - base

description:
Library name: miKW24
column name in Normalized_miRNA_counts_v1: 663 - base


title: A673,RNA,KDM6A-KD9,R2


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_041, ME/CFS patient

description:
Library name: cfs_cfrna_041
Column name in raw_counts_all.csv: cfs_cfrna_41


title: Effector/Memory YFP+1

city: Philadelphia

first: Michael

last: Gonzalez

state: Pennsylvania

address: 3535 Market St

department: Translational Medicine and Human Genetics

institute: University of Pennsylvania

description: Library name: E1plus

data_processing:
Raw FASTQ sequencing reads were mapped against the mm10 reference genome using the DRAGEN genome pipeline.
BAM files were used to generate a feature/gene counts matrix using the R/Bioconductor package Rsubread.
The DESeq2 library was used for secondary analysis and differential gene expression between experimental groups
Assembly: mm10
Supplementary files format and content: tab delimited text file of gene counts per sample

source_name: GM-CSF reporter/fate reporter transgenic mice

growth_protocol: YFP+, YFP− naïve (CD62L+CD44−), and TEM (CD62L−CD44hi) CD4+ T cells from the spleens of Gr/fr mice were FACS sorted.

extract_protocol:
Then, RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions
Libraries were prepared using 200 ng of total RNA and the Illumina TruSeq Stranded Total RNA library preparation kit. Libraries’ qualities were evaluated using the PerkinElmer Labchip GX and qPCR using the Kapa Library Quantification Kit and the Life Technologies Viia7 Real-time PCR instrument. Libraries at a concentration of 2nM were sequenced on the Illumina HiSeq2500 using the High Output v4 chemistry. Raw FASTQ sequencing reads were mapped against the mm10 reference genome using the DRAGEN genome pipeline.

value: CD4+ T cell


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_038, healthy control

description:
Library name: cfs_cfrna_038
Column name in raw_counts_all.csv: cfs_cfrna_38


title: Effector/Memory YFP+3

description: Library name: E3plus

value: GM-CSF reporter/fate reporter transgenic mice


title: miRNA-455 - base

description:
Library name: miKW15
column name in Normalized_miRNA_counts_v1: 455 - base

value: whole blood


title: A673,RNA,KDM6A-KD9,R3


title: Effector/Memory YFP-3

description: Library name: E3-


title: miRNA-387 - base

description:
Library name: miKW12
column name in Normalized_miRNA_counts_v1: 387 - base


title: miRNA-523 - base

description:
Library name: miKW3
column name in Normalized_miRNA_counts_v1: 523 - base


title: A673,RNA,KDM6A-KD9,R1


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_037, healthy control

description:
Library name: cfs_cfrna_037
Column name in raw_counts_all.csv: cfs_cfrna_37


title: miRNA-412 - base

description:
Library name: miKW1
column name in Normalized_miRNA_counts_v1: 412 - base


title: Effector/Memory YFP-2

description: Library name: E2-


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_036, healthy control

description:
Library name: cfs_cfrna_036
Column name in raw_counts_all.csv: cfs_cfrna_36


title: A673,RNA,CONTROLforKDM6A,R4

value: Control


title: miRNA-867 - base

description:
Library name: miCB52
column name in Normalized_miRNA_counts_v1: 867 - base


title: Effector/Memory YFP-1

description: Library name: E1-


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_043, healthy control

description:
Library name: cfs_cfrna_043
Column name in raw_counts_all.csv: cfs_cfrna_43


title: miRNA-270 - base

description:
Library name: miCB7
column name in Normalized_miRNA_counts_v1: 270 - base


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_035, ME/CFS patient

description:
Library name: cfs_cfrna_035
Column name in raw_counts_all.csv: cfs_cfrna_35

value: case


title: Naïve YFP+3

description: Library name: N3plus


title: Effector/Memory YFP+2

description: Library name: E2plus


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_034, healthy control

description:
Library name: cfs_cfrna_034
Column name in raw_counts_all.csv: cfs_cfrna_34


title: A673,RNA,CONTROLforKDM6A,R3


title: Naïve YFP+2

description: Library name: N2plus


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_033, ME/CFS patient

description:
Library name: cfs_cfrna_033
Column name in raw_counts_all.csv: cfs_cfrna_33


title: miRNA-778 - base

description:
Library name: miCB49
column name in Normalized_miRNA_counts_v1: 778 - base


title: A673,RNA,CONTROLforKDM6A,R2


title: A673,RNA,CONTROLforKDM6A,R1


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_032, healthy control

description:
Library name: cfs_cfrna_032
Column name in raw_counts_all.csv: cfs_cfrna_32


title: miRNA-159 - base

description:
Library name: miCB46
column name in Normalized_miRNA_counts_v1: 159 - base


title: miRNA-309 - base

description:
Library name: miCB43
column name in Normalized_miRNA_counts_v1: 309 - base


title: Naïve YFP+1

description: Library name: N1plus


title: A673,INPUT EWSR1-FLI1


title: A673,RNA,CONTROLforKDM6A,R5


title: Naïve YFP-3

description: Library name: N3-


title: A673,INPUT KDM6B


title: Naïve YFP-2

description: Library name: N2-


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_028, ME/CFS patient

description:
Library name: cfs_cfrna_028
Column name in raw_counts_all.csv: cfs_cfrna_28

value: New York City, NY


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_031, ME/CFS patient

description:
Library name: cfs_cfrna_031
Column name in raw_counts_all.csv: cfs_cfrna_31


title: miRNA-327 - base

description:
Library name: miCB40
column name in Normalized_miRNA_counts_v1: 327 - base


title: A673,INPUT KDM6A,R2


title: miRNA-687 - base

description:
Library name: miCB34
column name in Normalized_miRNA_counts_v1: 687 - base


title: A673,INPUT KDM6A,R1


title: Plasma cell-free RNA, RNA seq for subject: cfs_cfrna_026, ME/CFS patient

description:
Library name: cfs_cfrna_026
Column name in raw_counts_all.csv: cfs_cfrna_26