title: Fibroblast:DicerWT mix2, 30:70

description: Library name: MIX-2-5


title: Healthy_004

status: Public on Jul 27 2026

type: SRA

city: Miami

first: Qin

last: Yang

state: FL

address: 1501 NW 10th Avenue

department: Sylvester Comprehensive Cancer Center

country: USA

institute: University of Miami Miller School of Medicine

library_source: genomic

data_processing:
Reads were trimmed using Trim Galore (version 0.6.2) and aligned to a bisulfite-converted human genome (hg19) using Bowtie2 and Bismark (versions 2.4.1 and 0.23.1, respectively).
After strand collapsing and filtering by coverage (keep loci with reads between 10-400), methylation loci were tiled by window (25bp) and a methylDiff object was created using MethylSig (version 1.5.0) for regions that were present in at least 3 samples per group.
Significant differentially methylated regions (DMRs) were identified as those with an absolute mean methylation difference of ≥ 25 and a DMR q-value of ≤ 0.05.
Assembly: hg19
Supplementary files format and content: genome-wide cytosine report output from bismark
Supplementary files format and content: tab-delimited text files include base-pair resolution information of the read strand and coverage of the methylated and unmethylated Cs in the sequenced DNA for each Sample

molecule: genomic DNA

organism: Homo sapiens

source_name: Bone marrow

extract_protocol:
For the isolation of CD34+ cells from human bone marrow samples, we utilized the Miltenyi MACS magnetic bead purification kit. In a nutshell, 2 mL frozen vials of human mononuclear cells (MNC) were thawed at 37°C, followed by treatment with 200 µL of DNase-I (Roche) at a concentration of 1 mg/mL for 90 seconds. Subsequently, the cells were gently resuspended in Iscove's Modified Dulbecco's Medium (IMDM) containing 40% fetal bovine serum (FBS) to minimize primary human cell mortality. All centrifugation steps were performed at 1500 rpm. After an 8-minute centrifugation, the cells were resuspended in 15 mL of MACS buffer and then incubated with magnetic beads for 50 minutes at 4°C. Following three consecutive washes with MACS buffer (each for 10 minutes at 4°C), the cells were resuspended in 6 mL of MACS buffer and passed through an AUTOMACS instrument using the Posseld program. After another 8-minute centrifugation at 4°C, the cells were resuspended in RTL buffer with beta-mercaptoethanol. DNA and RNA were extracted from the CD34+ fraction using the AllPrep Micro kit (QIAGEN), while the CD34+ depleted fraction was processed with the AllPrep Mini kit.
Prior to adapter ligation, the methylated adapters were diluted to a concentration of 150 nmol/L. During the gel size selection step, fragments falling within the range of 150 to 450 base pairs were excised from the gel.

tag: tissue

value: Bone marrow

tag: cell line

tag: individual

value: Healthy


title: Pure fibroblast, Rep2

city: Houston

first: George

last: Calin

state: TX

address: 1515 Bertner Ave

institute: The University of Texas MD Anderson Cancer Center

description: Library name: MIX-2-1

library_source: other

data_processing:
Raw single-end miRNA-seq reads were generated as FASTQ files and assessed for base quality, GC content, and adapter contamination using FastQC.
Adapter sequences and low-quality bases were trimmed, and very short reads removed, using Trim Galore (default settings); only trimmed reads passing quality control were retained for downstream analysis.
Trimmed reads were processed with mapper.pl from the miRDeep2 package to remove reads with ambiguous bases,  collapse identical reads to unique sequences, and align reads to the human reference genome assembly38
Reads were analyzed with miRDeep2.pl using mature miRNA reference sequences mirbase v22, hairpin precursor sequences, and species code hsa to identify and quantify known and candidate novel miRNAs.
Per-miRNA read counts were extracted from the miRDeep2 output for each sample
Assembly: GRCh38
Supplementary files format and content: Comma separated values with samples as columns and miRNAs as rows

molecule: other

growth_protocol: HCT116 colon cancer cells and HS-5 stromal cells were cultured at 37°C in a humidified incubator with 5% CO2. HS-5 cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM; Corning) supplemented with 10% fetal bovine serum (FBS; Corning) and 1% Antibiotic-Antimycotic (Gibco), while HCT116 cells were maintained in McCoy’s 5A medium (Corning) with the same supplements. The Dicer1 knockout (KO) HCT116 cells were cultured under the same conditions with the addition of G-418 selective antibiotic solution (neomycin resistance) to preserve the homogenous KO population.

extract_protocol:
Total RNA was extracted from 1 x 106 cells using the Zymo RNA Isolation Mini Kit (Zymo Research). Small RNA concentrations (ng/µL) were quantified using a Qubit 4 Fluorometer (Invitrogen) with the Qubit microRNA Assay Kit (Invitrogen). Sample quality was validated using an Agilent Bioanalyzer (Agilent).
MiRNA sequencing libraries were prepared using the QIAseq miRNA Library Kit (Qiagen) and sequenced on an Illumina platform by SeqMatic LLC.

tag: cell type

value: Fibroblast


title: Fibroblast:DicerWT mix2, 50:50

description: Library name: MIX-2-3

source_name: Mix

value: Mix


title: NF54_33hpi_minCHO_IP

city: Barcelona

first: Elisabet

last: Tinto-Font

address: c/Rossello 153

department: Malaria

country: Spain

institute: ISGlobal

description: Library name: NF54_33hpi_minCHO_IP

data_processing:
ChIP-seq data analysis was carried out using custom scripts written in Python (v3.7.16), as previously described (Michel-Todó, L., 2023. PMID: 36515553). ChIP-seq reads were trimmed using the bbduk command from BBmap (v36.99) software. The 3' end was trimmed if it had a quality score < 6 and reads shorter than 10 bp after trimming were discarded. Quality control of raw reads was performed using FastQC (v0.11.9) and contamination with non-P. falciparum reads was checked with FastqScreen (v0.14.0).  Bowtie2 (v2.4.5) was used to align reads to the Plasmodium falciparum 3D7 reference genome (PlasmoDB v67) using the parameters: --very-sensitive --local -5 4 -3 4 -I 50 -X 2000, which are different from the default ones. SAMtools (v1.15) was used for compressing, sorting and filtering-out < 5 mapping quality reads, from the alignment files. PCR duplicates were removed using GATK (v4.4.0.0) MarkDuplicates command. Normalized coverage (log₂-transformed enrichment of IP over input) was calculated at 10-bp resolution using the bamCompare function from DeepTools (v3.5.1), with the parameters: --normalizeUsing RPKM -bs 10 --smoothLength 200 --pseudocount 10. Negative values were set to -1 to avoid the detection of apparent differential coverage in non-heterochromatic regions. Normalized log₂(IP/input) coverage values were used to generate bedgraph tracks.
Assembly: Plasmodium falciparum 3D7 reference genome (PlasmoDB v67)
Supplementary files format and content: Bedgraph tracks (.bdg): normalized log₂(IP/input) coverage values

organism: Plasmodium falciparum

growth_protocol: Parasites were cultured in B+ or O+ erythrocytes at a 3% hematocrit under standard conditions in RPMI-1640-based media, supplemented with 0.5% Albumax II (Gibco, 11021037) and 2 mM choline chloride (Sigma-Aldrich, C7527), and maintained in a shaking incubator with a 5% CO₂, 3% O₂, and balance N₂ atmosphere. All cultures were kept at 37ºC, except for parasite lines in which pfap2-hs was disrupted and control cultures grown in parallel , which were maintained at 35ºC because at 37ºC they show reduced growth (Tintó-Font, E., et al., 2021; PMID:34400833). Tight synchronization to a 5 h age window was achieved by purification of late stages in 63% Percoll gradients (GE Healthcare, 17-0891-01) followed by sorbitol lysis 5 h later (Sigma-Aldrich, S3889). For ChIP-seq experiments, erythrocyte were filtered with Plasmodipur (R-Biopharm Nederland B.V., 8011FILTER) to remove leukocytes before using them for parasite cultures.

extract_protocol:
ChIP-seq was performed using tightly synchronized cultures at the mid-trophozoite stage: 33–38 hpi, or 37–42 hpi for the ap2-hs KO line, to account for their slower IDC progression (Tintó-Font, E., et al., 2021; PMID:34400833), unless otherwise stated. Chromatin was extracted from ~30–45 ml at ~2% parasitemia and immunoprecipitated as previously described (Llorà-Batlle, O., 2020. PMID: 32577509). Briefly, after saponin lysis and formaldehyde cross-linking, chromatin was extracted using the MAGnify Chromatin Immunoprecipitation System (Life Technologies, 492024). Sonication was performed with a Covaris M220 sonicator to generate ~150–200 bp fragments. For immunoprecipitation, 2 μg of chromatin and 4 μg of anti-H3K9me3 antibody (Diagenode, C15410193) were used. An equal sample was processed in parallel as input, with no immunoprecipitation. The resulting DNA was quantified using Qubit HS before library preparation.
Library preparation was performed using 5 ng of DNA, as previously described (Llorà-Batlle, O., 2020. PMID: 32577509). NEBNext multiplex oligonucleotides for Illumina (NEB, E7335, E7500 and E7710) were used, and 9 cycles of amplification were performed with the Kapa HiFi HotStart PCR kit (Roche, 7958889001). All purification steps were carried out using AMPure XP beads (Beckman Coulter, 082A63881). Quality and concentration of all libraries was determined using a Tapestation 4200 (Agilent). We obtained ~8-19 million 150 bp paired-end reads per sample using a NextSeq500 System (Illumina).

treatment_protocol: Sexual conversion was induced by three different methods: choline depletion, dihydroartemisinin (DHA; Sigma-Aldrich, D7439) treatment or heat shock (HS). For induction by choline depletion, the regular RPMI medium with Albumax II and a 2 mM choline supplement was replaced by the same medium without the choline supplement in cultures at the early ring stage (0-5 h post-invasion, hpi) and cultures were placed in static conditions in a hypoxia chamber for the rest of the experiment. For induction of sexual conversion by DHA or HS, tightly synchronized cultures (0-5 hpi) were placed in static conditions in a hypoxia chamber, and left undisturbed until the early trophozoite stage (25-30 hpi for most experiments; 30-35 hpi for proteomics experiments; 29-34 hpi for experiments with transgenic lines in which ap2hs was disrupted, to account for their slower growth), when they were exposed to a 3 h of 10 nM DHA pulse or maintained for 3 h at 41.5 ºC (placing the full hypoxia chamber in an incubator at 41.5 ºC), respectively. After exposure, DHA was removed from the medium by centrifugation or cultures were placed back in an incubator at the normal growth temperature. Medium  was refreshed at ~33 hpi to all conditions. A control condition was always kept in parallel until the end of the experiment

tag: genotype

value: WT

tag: treatment

value: choline depletion

tag: biological replicate

tag: chip antibody

value: H3K9me3 (Diagenode, C15410193)

tag: time


title: NF54_33hpi_plusCHO_IP

description: Library name: NF54_33hpi_plusCHO_IP

value: control choline


title: NF54_10hpi_minCHO_IP

description: Library name: NF54_10hpi_minCHO_IP


title: MDS_AZA_006

value: MDS patient

tag: Sex

value: Female

tag: responder

value: Responder


title: NF54_23hpi_minCHO_IP

description: Library name: NF54_23hpi_minCHO_IP


title: NF54_10hpi_plusCHO_IP

description: Library name: NF54_10hpi_plusCHO_IP


title: Pure DicerWT, Rep1

description: Library name: MIX-1-7

value: Colorectal cancer


title: NF54_HS_rep2_in

description: Library name: NF54_HS_rep2_in

value: heat shock exposure


title: MDS_AZA_003

tag: age

value: Male

value: NonResp


title: NF54_HS_rep2_IP

description: Library name: NF54_HS_rep2_IP


title: NF54_ctrl_rep2_in

description: Library name: NF54_ctrl_rep2_in

value: control heat shock


title: MDS_AZA_094


title: NF54_ctrl_rep2_IP

description: Library name: NF54_ctrl_rep2_IP


title: Fibroblast:DicerWT mix1, 30:70

description: Library name: MIX-1-5


title: Fibroblast:DicerWT mix1, 15:85

description: Library name: MIX-1-6


title: MDS_AZA_093


title: Fibroblast:DicerWT mix1, 40:60

description: Library name: MIX-1-4


title: NF54 ctrl_rep1_in

description: Library name: NF54 ctrl_rep1_in


title: NF54_HS_rep1_IP

description: Library name: NF54_HS_rep1_IP


title: MDS_AZA_091


title: NF54_HS_rep1_in

description: Library name: NF54_HS_rep1_in


title: NF54 ctrl_rep1_IP

description: Library name: NF54 ctrl_rep1_IP


title: Fibroblast:DicerWT mix1, 50:50

description: Library name: MIX-1-3


title: NF54_plusDHA_rep3_in

description: Library name: NF54_plusDHA_rep3_in

value: DHA treatment


title: MDS_AZA_092

value: Bone marrow


title: Fibroblast:DicerWT mix1, 70:30

description: Library name: MIX-1-2


title: MDS_AZA_090


title: Pure fibroblast, Rep1

description: Library name: MIX-1-1


title: NF54_plusDHA_rep2_IP

description: Library name: NF54_plusDHA_rep2_IP


title: NF54_plusDHA_rep2_in

description: Library name: NF54_plusDHA_rep2_in


title: NF54_plusDHA_rep3_IP

description: Library name: NF54_plusDHA_rep3_IP


title: MDS_AZA_089


title: NF54_minDHA_rep2_in

description: Library name: NF54_minDHA_rep2_in

value: control DHA


title: MDS_AZA_088


title: RPL41 KO HEK293T SLAM-seq 12 h replicate 2

city: Chikusa-ku, Nagoya, Aichi

first: Kazuya

last: Ichihara

address: Furo-cho

country: Japan

institute: Nagoya University

description: Library name: Sample 44

library_source: transcriptomic

data_processing:
Adaptor sequences were trimmed from raw reads with the use of cutadapt. Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit. Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCh38.p13) and human genome (hg38) also with the use of STAR. Multiple mappings were allowed. Metagene analysis was performed with custom Python script and with the use of Numpy (v1.17.3) and Pysam (v0.15.3). Reads of Ribo-seq and RNA-seq mapped to human coding transcripts were counted with the use of featureCounts (Subread package).
Assembly: hg38 / mm10
Supplementary files format and content: Excel file includes raw counts for each sample

molecule: polyA RNA

growth_protocol: HEK293T cells were obtained from American Type Culture Collection and were checked for mycoplasma contamination with the use of MycoAlert (Lonza). The cells were cultured under an atmosphere of 5% CO2 at 37°C in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (Life Technologies) and antibiotics.

extract_protocol:
Extract protocol for RNA-seq Total RNA was extracted from cell lysates with the use of a PureLink RNA Mini Kit (Thermo Fisher Scientific), and the quality of the purified RNA was assessed with a 2100 Bioanalyzer (Agilent). Extract protocol for Ribo-seq, Disome-seq, and harringtonine run-off assay For the harringtonine run-off assay, cells were treated with 2 μg/ml harringtonine (MedChemExpress) at 37 °C for 60, 120, or 180 s, followed by treatment with 100 μg/ml cycloheximide for 1 minute to halt translation. Cells were then immediately harvested. Cell and tissue lysate supernatants were assayed for RNA concentration with a Qubit RNA BR Assay Kit (Thermo Fisher Scientific), incubated with RNase I (20 U per 10 μg of RNA, Epicentre) for 45 min at 25°C, and placed on ice before the addition of SUPERase•In RNase inhibitor (Invitrogen) to a concentration of 20 U/ml. The samples were then loaded on a 1 M sucrose cushion (containing 20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 5 mM MgCl2, SUPERase•In (10 U/ml), 1 mM dithiothreitol, and cycloheximide (100 μg/ml)), and the gradients were centrifuged at 100,000 rpm (417,200 × g) for 1 h at 4°C in a Beckman TLA110 rotor. Ribosome footprints were purified using ISOGEN (Fujifilm). The recovered RNA was size-selected by electrophoresis on a 15% polyacrylamide TBE–urea gel (SuperSep RNA, Fujifilm), isolating fragments of 17–34 nucleotides for Ribo-seq and 50–80 nucleotides for Disome-seq. Extract protocol for SLAM-seq To label newly synthesized RNA, cells were incubated for 24 h in culture medium containing 50 μM 4-thiouridine (4sU, Merck). The medium was then replaced with fresh medium containing 50 μM uridine, and cells were harvested at 0, 3, 6, 12, and 24 h after the switch. Total RNA was extracted using ISOGEN (NIPPON GENE) according to the manufacturer’s instructions.
Library construction protocol for RNA-seq For RNA-seq, after mRNA selection via the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs), libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs), and the libraries were sequenced with a NovaSeq (Illumina). Library construction protocol for Ribo-seq, Disome-seq, and harringtonine run-off assay The footprint fragments were treated with T4 polynucleotide kinase (New England Biolabs) to repair the 2'-3' cyclic phosphates, a DNA linker including barcode sequences (NI-810 to NI-817) was ligated with the use of T4 RNA ligase 2, truncated K227Q (New England Biolabs), and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. Ribosomal RNAs were further depleted with the use of RiboZero Gold (Illumina). Reverse transcription (RT) was performed with the NI-802 primer, and the resulting products were purified on a 15% polyacrylamide and TBE-urea gel. The purified cDNAs were circularized with circLigase II (Lucigen), and index sequences were then added by amplification with the polymerase chain reaction (PCR) as performed with the common primer (NI-798) and primers including index sequences (NI-799 and NI-822 to NI-826). Products of the desired size were purified on a 15% polyacrylamide nondenaturing gel (SuperSep DNA, Fujifilm), and the libraries were sequenced with a NovaSeq 6000 system (Illumina). Library construction protocol for SLAM-seq The purified RNA was alkylated by adding iodoacetamide (IAA) to a final concentration of 10 mM, followed by incubation at 50 °C for 15 min. The reaction was quenched by adding DTT to a final concentration of 20 mM. RNA was then purified, and libraries were prepared using the QuantSeq 3' mRNA-Seq V2 Library Prep Kit (Forward) with Unique Dual Indices (12 nt) (Lexogen). Sequencing was performed on a NovaSeq platform (Illumina).


title: NF54_minDHA_rep2_IP

description: Library name: NF54_minDHA_rep2_IP


title: NF54_plusDHA_rep1_in

description: Library name: NF54_plusDHA_rep1_in


title: NF54_plusDHA_rep1_IP

description: Library name: NF54_plusDHA_rep1_IP


title: RPL41 KO HEK293T SLAM-seq 6 h replicate 2

description: Library name: Sample 43


title: NF54_minDHA_rep1_in

description: Library name: NF54_minDHA_rep1_in


title: MDS_AZA_087


title: RPL41 KO HEK293T SLAM-seq 3 h replicate 2

description: Library name: Sample 42


title: A7_minCHO_rep2_in

description: Library name: A7_minCHO_rep2_in


title: MDS_AZA_086


title: A7_minCHO_rep2_IP

description: Library name: A7_minCHO_rep2_IP


title: RPL41 KO HEK293T SLAM-seq 0 h replicate 2

description: Library name: Sample 41


title: A7_plusCHO_rep2_in

description: Library name: A7_plusCHO_rep2_in


title: MDS_AZA_085


title: RPL41 KO HEK293T SLAM-seq 12 h replicate 1

description: Library name: Sample 40


title: A7_plusCHO_rep2_IP

description: Library name: A7_plusCHO_rep2_IP


title: MDS_AZA_083


title: A7_minCHO_rep1_IP

description: Library name: A7_minCHO_rep1_IP


title: NF54_minDHA_rep1_IP

description: Library name: NF54_minDHA_rep1_IP


title: A7_minCHO_rep1_in

description: Library name: A7_minCHO_rep1_in


title: RPL41 KO HEK293T SLAM-seq 6 h replicate 1

description: Library name: Sample 39


title: A7_plusCHO_rep1_in

description: Library name: A7_plusCHO_rep1_in


title: RPL41 KO HEK293T SLAM-seq 3 h replicate 1

description: Library name: Sample 38


title: A7_plusCHO_rep1_IP

description: Library name: A7_plusCHO_rep1_IP


title: E5_minCHO_rep2_in

description: Library name: E5_minCHO_rep2_in


title: MDS_AZA_082


title: E5_minCHO_rep2_IP

description: Library name: E5_minCHO_rep2_IP


title: RPL41 KO HEK293T SLAM-seq 0 h replicate 1

description: Library name: Sample 37


title: E5_plusCHO_rep2_in

description: Library name: E5_plusCHO_rep2_in


title: MDS_AZA_081


title: E5_plusCHO_rep2_IP

description: Library name: E5_plusCHO_rep2_IP


title: E5_minCHO_rep1_in

description: Library name: E5_minCHO_rep1_in


title: MDS_AZA_074


title: WT HEK293T SLAM-seq 12 h replicate 2

description: Library name: Sample 36


title: MDS_AZA_080


title: E5_minCHO_rep1_IP

description: Library name: E5_minCHO_rep1_IP


title: WT HEK293T SLAM-seq 6 h replicate 2

description: Library name: Sample 35


title: E5_plusCHO_rep1_in

description: Library name: E5_plusCHO_rep1_in


title: MDS_AZA_079


title: E5_plusCHO_rep1_IP

description: Library name: E5_plusCHO_rep1_IP


title: WT HEK293T SLAM-seq 3 h replicate 2

description: Library name: Sample 34


title: NF54_minCHO_rep3_in

description: Library name: NF54_minCHO_rep3_in


title: MDS_AZA_078


title: NF54_minCHO_rep3_IP

description: Library name: NF54_minCHO_rep3_IP


title: MDS_AZA_077


title: NF54_plusCHO_minDHA_rep3_in

description: Library name: NF54_plusCHO_minDHA_rep3_in

value: control choline, control DHA


title: WT HEK293T SLAM-seq 0 h replicate 2

description: Library name: Sample 33


title: WT HEK293T SLAM-seq 12 h replicate 1

description: Library name: Sample 32


title: NF54_plusCHO_minDHA_rep3_IP

description: Library name: NF54_plusCHO_minDHA_rep3_IP


title: NF54_minCHO_rep2_in

description: Library name: NF54_minCHO_rep2_in


title: MDS_AZA_075


title: WT HEK293T SLAM-seq 6 h replicate 1

description: Library name: Sample 31


title: NF54_minCHO_rep2_IP

description: Library name: NF54_minCHO_rep2_IP


title: NF54_plusCHO_rep2_in

description: Library name: NF54_plusCHO_rep2_in


title: MDS_AZA_073


title: NF54_plusCHO_rep2_IP

description: Library name: NF54_plusCHO_rep2_IP


title: WT HEK293T SLAM-seq 3 h replicate 1

description: Library name: Sample 30


title: NF54_minCHO_rep1_in

description: Library name: NF54_minCHO_rep1_in


title: MDS_AZA_072


title: NF54_plusCHO_rep1_in

description: Library name: NF54_plusCHO_rep1_in


title: WT HEK293T SLAM-seq 0 h replicate 1

description: Library name: Sample 29


title: NF54_minCHO_rep1_IP

description: Library name: NF54_minCHO_rep1_IP


title: MDS_AZA_071


title: NF54_plusCHO_rep1_IP

description: Library name: NF54_plusCHO_rep1_IP


title: MDS_AZA_070


title: RPL41 KO HEK293T disome-seq replicate 2

description: Library name: Sample 28

data_processing:
Adaptor sequences were trimmed from raw reads with the use of cutadapt. Reads of low quality were discarded with the use of fastq_quality_trimmer and fastq_quality_filter of the FASTX-Toolkit. Ribosomal RNA reads were removed by alignment with human rRNA sequences with the use of STAR, and the remaining reads were aligned with the human transcriptome (GRCh38.p13) and human genome (hg38) also with the use of STAR. Multiple mappings were allowed. Metagene analysis was performed with custom Python script and with the use of Numpy (v1.17.3) and Pysam (v0.15.3). Reads of Ribo-seq and RNA-seq mapped to human coding transcripts were counted with the use of featureCounts (Subread package).
Assembly: hg38 / mm10
Supplementary files format and content: Excel file includes raw counts for each sample
Library strategy: Ribo-Seq

molecule: total RNA


title: Vehicle 16 hpt, biological replicate 3

city: Baltimore

first: Daniel

middle: John

last: Kelpsch

email: dkelpsc1@jh.edu, kelpschd@gmail.com

state: MD

address: 3400 N. Charles Street

institute: Johns Hopkins University

description:
Library name: 3V16_TCTCGCGC_GTCAGTAC
Pool of five whole larvae, treated from 3 dpf for 16 h. Sequencing indices i7 TCTCGCGC, i5 GTCAGTAC. Demultiplex ID S9; sequenced across 4 lanes (L001-L004).

data_processing:
Reads were processed using the nf-core/rnaseq v3.11.1 pipeline (Ewels et al., 2020, Nat Biotechnol; doi:10.1038/s41587-020-0439-x).
Adapter sequences were trimmed from the reads and ribosomal RNA reads were filtered.
Remaining reads were mapped to the GRCz11 genome using Ensembl release 110 annotation.
Differential expression was assessed using DESeq2 v1.42 in R. Each treatment duration was analyzed as an independent experiment comparing enoxolone-treated to time-matched vehicle-treated samples. Samples from 8 hours post-treatment were batch corrected using the sva package.
Differentially expressed genes were defined as those with a log2 fold change beyond 1.5 (0.9 for the 4 and 8 hour timepoints) and an adjusted p-value below 0.05. Gene ontology analysis was performed using the topGO package.
Assembly: GRCz11 (Ensembl release 110)
Supplementary files format and content: salmon.merged.gene_counts.tsv: tab-delimited text file of gene-level estimated counts produced by Salmon and aggregated to gene level by tximport within the nf-core/rnaseq v3.11.1 pipeline. Columns are gene_id, gene_name, and one column per library; rows are Ensembl gene IDs from the GRCz11 Ensembl release 110 annotation. This matrix was the input to the DESeq2 differential expression analysis.
Supplementary files format and content: salmon.merged.gene_tpm.tsv: tab-delimited text file of gene-level transcripts per million (TPM) for the same genes and libraries, produced by the same pipeline. Used for expression-level comparisons between samples.

organism: Danio rerio

source_name: whole larva

growth_protocol: Fus(ApoBb.1-NanoLuciferase); Tg(ubi:mCherry-2A-Firefly Luciferase) embryos were obtained by pair-wise natural spawning, raised in E2 embryo medium at 28.5 C on a 14:10 h light:dark cycle, and cleaned manually each day. Animals remained within the yolk-dependent (lecithotrophic) period throughout and were not fed. All zebrafish protocols were approved by the Carnegie Institution Department of Embryology Animal Care and Use Committee (Protocol #139).

extract_protocol:
Pooled larvae were homogenized with 0.5 mm zirconium oxide beads (Next Advance ZrOB05) using a Bullet Blender (Next Advance) in TRIzol reagent (Thermo Fisher 15596026). Homogenates were mixed 1:1 with 100% ethanol and RNA was extracted using the Direct-zol RNA Microprep Kit (Zymo Research R2060). RNA concentration and quality were assessed using a Thermo Scientific NanoDrop One and an Agilent 2100 Bioanalyzer.
RNA-seq libraries were prepared from approximately 500 ng total RNA using the TruSeq Stranded mRNA Library Prep kit (Illumina 20020595) with the TruSeq RNA CD Index plate (Illumina 20019792), according to the manufacturer's protocol. Sequencing was performed on an Illumina NextSeq 500 using a 75 bp run with 8x8 indexing, yielding between 23 and 45 million reads per sample.

treatment_protocol: At 3 days post fertilization, individual larvae were incubated in either vehicle (0.1% DMSO / 50 ppm Tween-20 / E2) or 8 uM enoxolone (Cayman Chemical 11845) in the same vehicle. After 4, 8, 12, 16, or 24 hours, five larvae per condition were collected and pooled for RNA extraction. Samples were prepared from three independent clutches. After 48 hours, total lipoprotein levels were measured in the remaining animals from each treatment duration to confirm efficacy of enoxolone treatment.

value: whole larva

value: vehicle (0.1% DMSO), 16 h

tag: batch


title: Vehicle 24 hpt, biological replicate 3

description:
Library name: 3V24_AGCGATAG_AGGCTATA
Pool of five whole larvae, treated from 3 dpf for 24 h. Sequencing indices i7 AGCGATAG, i5 AGGCTATA. Demultiplex ID S10; sequenced across 4 lanes (L001-L004).

value: vehicle (0.1% DMSO), 24 h


title: RPL41 KO HEK293T disome-seq replicate 1

description: Library name: Sample 27


title: Vehicle 12 hpt, biological replicate 3

description:
Library name: 3V12_TCTCGCGC_ACGTCCTG
Pool of five whole larvae, treated from 3 dpf for 12 h. Sequencing indices i7 TCTCGCGC, i5 ACGTCCTG. Demultiplex ID S8; sequenced across 4 lanes (L001-L004).

value: vehicle (0.1% DMSO), 12 h


title: Vehicle 8 hpt, biological replicate 3

description:
Library name: 3V8_TCTCGCGC_TAAGATTA
Pool of five whole larvae, treated from 3 dpf for 8 h. Sequencing indices i7 TCTCGCGC, i5 TAAGATTA. Demultiplex ID S7; sequenced across 4 lanes (L001-L004).

value: vehicle (0.1% DMSO), 8 h


title: MDS_AZA_069

value: MDS patient


title: WT HEK293T disome-seq replicate 2

description: Library name: Sample 26


title: Vehicle 4 hpt, biological replicate 3

description:
Library name: 3V4_TCTCGCGC_CTTCGCCT
Pool of five whole larvae, treated from 3 dpf for 4 h. Sequencing indices i7 TCTCGCGC, i5 CTTCGCCT. Demultiplex ID S6; sequenced across 4 lanes (L001-L004).

value: vehicle (0.1% DMSO), 4 h


title: MDS_AZA_068

value: Responder


title: Enoxolone 16 hpt, biological replicate 3

description:
Library name: 3E16_AGCGATAG_CTTCGCCT
Pool of five whole larvae, treated from 3 dpf for 16 h. Sequencing indices i7 AGCGATAG, i5 CTTCGCCT. Demultiplex ID S14; sequenced across 4 lanes (L001-L004).

value: 8 uM enoxolone, 16 h


title: Enoxolone 12 hpt, biological replicate 3

description:
Library name: 3E12_AGCGATAG_TCAGAGCC
Pool of five whole larvae, treated from 3 dpf for 12 h. Sequencing indices i7 AGCGATAG, i5 TCAGAGCC. Demultiplex ID S13; sequenced across 4 lanes (L001-L004).

value: 8 uM enoxolone, 12 h


title: WT HEK293T disome-seq replicate 1

description: Library name: Sample 25


title: MDS_AZA_067

value: Male


title: Enoxolone 8 hpt, biological replicate 3

description:
Library name: 3E8_AGCGATAG_AGGATAGG
Pool of five whole larvae, treated from 3 dpf for 8 h. Sequencing indices i7 AGCGATAG, i5 AGGATAGG. Demultiplex ID S12; sequenced across 4 lanes (L001-L004).

value: 8 uM enoxolone, 8 h


title: Enoxolone 4 hpt, biological replicate 3

description:
Library name: 3E4_AGCGATAG_GCCTCTAT
Pool of five whole larvae, treated from 3 dpf for 4 h. Sequencing indices i7 AGCGATAG, i5 GCCTCTAT. Demultiplex ID S11; sequenced across 4 lanes (L001-L004).

value: 8 uM enoxolone, 4 h


title: RPL41 KO HEK293T harringtonine 3 min Ribo-seq replicate 2

description: Library name: Sample 24


title: MDS_AZA_066

value: NonResp


title: Vehicle 24 hpt, biological replicate 2

description:
Library name: 2V24_TCCGCGAA_ACGTCCTG
Pool of five whole larvae, treated from 3 dpf for 24 h. Sequencing indices i7 TCCGCGAA, i5 ACGTCCTG. Demultiplex ID S15; sequenced across 4 lanes (L001-L004).


title: RPL41 KO HEK293T harringtonine 3 min Ribo-seq replicate 1

description: Library name: Sample 23


title: Vehicle 16 hpt, biological replicate 2

description:
Library name: 2V16_TCCGCGAA_TAAGATTA
Pool of five whole larvae, treated from 3 dpf for 16 h. Sequencing indices i7 TCCGCGAA, i5 TAAGATTA. Demultiplex ID S14; sequenced across 4 lanes (L001-L004).


title: MDS_AZA_065

value: Bone marrow

value: Female


title: Vehicle 12 hpt, biological replicate 2

description:
Library name: 2V12_TCCGCGAA_CTTCGCCT
Pool of five whole larvae, treated from 3 dpf for 12 h. Sequencing indices i7 TCCGCGAA, i5 CTTCGCCT. Demultiplex ID S13; sequenced across 4 lanes (L001-L004).


title: WT HEK293T harringtonine 3 min Ribo-seq replicate 2

description: Library name: Sample 22


title: MDS_AZA_064


title: Vehicle 8 hpt, biological replicate 2

description:
Library name: 2V8_TCCGCGAA_TCAGAGCC
Pool of five whole larvae, treated from 3 dpf for 8 h. Sequencing indices i7 TCCGCGAA, i5 TCAGAGCC. Demultiplex ID S12; sequenced across 4 lanes (L001-L004).


title: Vehicle 4 hpt, biological replicate 2

description:
Library name: 2V4_TCCGCGAA_AGGATAGG
Pool of five whole larvae, treated from 3 dpf for 4 h. Sequencing indices i7 TCCGCGAA, i5 AGGATAGG. Demultiplex ID S11; sequenced across 4 lanes (L001-L004).


title: WT HEK293T harringtonine 3 min Ribo-seq replicate 1

description: Library name: Sample 21


title: MDS_AZA_063


title: Enoxolone 24 hpt, biological replicate 2

description:
Library name: 2E24_TCTCGCGC_TCAGAGCC
Pool of five whole larvae, treated from 3 dpf for 24 h. Sequencing indices i7 TCTCGCGC, i5 TCAGAGCC. Demultiplex ID S5; sequenced across 4 lanes (L001-L004).

value: 8 uM enoxolone, 24 h


title: MDS_AZA_062


title: Enoxolone 8 hpt, biological replicate 2

description:
Library name: 2E8_TCTCGCGC_AGGCTATA
Pool of five whole larvae, treated from 3 dpf for 8 h. Sequencing indices i7 TCTCGCGC, i5 AGGCTATA. Demultiplex ID S2; sequenced across 4 lanes (L001-L004).

value: whole larva


title: Enoxolone 12 hpt, biological replicate 2

description:
Library name: 2E12_TCTCGCGC_GCCTCTAT
Pool of five whole larvae, treated from 3 dpf for 12 h. Sequencing indices i7 TCTCGCGC, i5 GCCTCTAT. Demultiplex ID S3; sequenced across 4 lanes (L001-L004).


title: RPL41 KO HEK293T harringtonine 2 min Ribo-seq replicate 2

description: Library name: Sample 20


title: Enoxolone 4 hpt, biological replicate 2

description:
Library name: 2E4_TCCGCGAA_GTCAGTAC
Pool of five whole larvae, treated from 3 dpf for 4 h. Sequencing indices i7 TCCGCGAA, i5 GTCAGTAC. Demultiplex ID S1; sequenced across 4 lanes (L001-L004).


title: MDS_AZA_061


title: Vehicle 24 hpt, biological replicate 1

description:
Library name: 1V24_CGGCTATG_CTTCGCCT
Pool of five whole larvae, treated from 3 dpf for 24 h. Sequencing indices i7 CGGCTATG, i5 CTTCGCCT. Demultiplex ID S5; sequenced across 4 lanes (L001-L004).


title: Enoxolone 16 hpt, biological replicate 2

description:
Library name: 2E16_TCTCGCGC_AGGATAGG
Pool of five whole larvae, treated from 3 dpf for 16 h. Sequencing indices i7 TCTCGCGC, i5 AGGATAGG. Demultiplex ID S4; sequenced across 4 lanes (L001-L004).


title: WT HEK293T harringtonine 2 min Ribo-seq replicate 2

description: Library name: Sample 18


title: Vehicle 16 hpt, biological replicate 1

description:
Library name: 1V16_CGGCTATG_TCAGAGCC
Pool of five whole larvae, treated from 3 dpf for 16 h. Sequencing indices i7 CGGCTATG, i5 TCAGAGCC. Demultiplex ID S4; sequenced across 4 lanes (L001-L004).

value: vehicle (0.1% DMSO), 16 h


title: MDS_AZA_060


title: Vehicle 12 hpt, biological replicate 1

description:
Library name: 1V12_CGGCTATG_AGGATAGG
Pool of five whole larvae, treated from 3 dpf for 12 h. Sequencing indices i7 CGGCTATG, i5 AGGATAGG. Demultiplex ID S3; sequenced across 4 lanes (L001-L004).


title: WT HEK293T harringtonine 2 min Ribo-seq replicate 1

description: Library name: Sample 17


title: MDS_AZA_059


title: Vehicle 8 hpt, biological replicate 1

description:
Library name: 1V8_CGGCTATG_GCCTCTAT
Pool of five whole larvae, treated from 3 dpf for 8 h. Sequencing indices i7 CGGCTATG, i5 GCCTCTAT. Demultiplex ID S2; sequenced across 4 lanes (L001-L004).


title: Vehicle 4 hpt, biological replicate 1

description:
Library name: 1V4_CGGCTATG_AGGCTATA
Pool of five whole larvae, treated from 3 dpf for 4 h. Sequencing indices i7 CGGCTATG, i5 AGGCTATA. Demultiplex ID S1; sequenced across 4 lanes (L001-L004).


title: RPL41 KO HEK293T harringtonine 1 min Ribo-seq replicate 2

description: Library name: Sample 16


title: Enoxolone 24 hpt, biological replicate 1

description:
Library name: 1E24_TCCGCGAA_GCCTCTAT
Pool of five whole larvae, treated from 3 dpf for 24 h. Sequencing indices i7 TCCGCGAA, i5 GCCTCTAT. Demultiplex ID S10; sequenced across 4 lanes (L001-L004).


title: MDS_AZA_058


title: Enoxolone 16 hpt, biological replicate 1

description:
Library name: 1E16_TCCGCGAA_AGGCTATA
Pool of five whole larvae, treated from 3 dpf for 16 h. Sequencing indices i7 TCCGCGAA, i5 AGGCTATA. Demultiplex ID S9; sequenced across 4 lanes (L001-L004).


title: RPL41 KO HEK293T harringtonine 1 min Ribo-seq replicate 1

description: Library name: Sample 15


title: Enoxolone 12 hpt, biological replicate 1

description:
Library name: 1E12_CGGCTATG_GTCAGTAC
Pool of five whole larvae, treated from 3 dpf for 12 h. Sequencing indices i7 CGGCTATG, i5 GTCAGTAC. Demultiplex ID S8; sequenced across 4 lanes (L001-L004).


title: MDS_AZA_056


title: Enoxolone 8 hpt, biological replicate 1

description:
Library name: 1E8_CGGCTATG_ACGTCCTG
Pool of five whole larvae, treated from 3 dpf for 8 h. Sequencing indices i7 CGGCTATG, i5 ACGTCCTG. Demultiplex ID S7; sequenced across 4 lanes (L001-L004).


title: MDS_AZA_055


title: GDT4-FB

city: Daejeon

first: Bae-Hyeon

last: Moon

address: 193, Munji-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description: Library name: GDT4-FB

data_processing:
Raw sequencing data were processed with Cell Ranger software (v7.0.1). The mkfastq pipeline was used for demultiplexing, and the multi pipeline aligned reads to the GRCh38 human reference genome (refdata-gex-GRCh38-2020-A). Standard Seurat clustering and UMAP-based dimensional reduction were employed. Differentially expressed genes and cell-type-specific markers were identified using the FindMarkers function, applying thresholds of minimum percentage (min.pct) > 0.1 and log2 fold change ≥ 0.5. Batch effects were corrected using Harmony integration. Filtered gene expression matrices were analyzed using R (v4.2.2) and the Seurat package (v4.1.1). Donor identity was confirmed using TotalSeq™-C anti-human hashtag ADT expression and cellsnp-lite for single nucleotide polymorphism (SNP)-based demultiplexing. Cells with mitochondrial gene expression ≥5% or fewer than 200 detected features were excluded. Doublets were filtered using DoubletFinder (v2.0.3). Dying cells were excluded by removing clusters showing elevated stress or apoptosis-associated genes.
Assembly: Human GRCh38 (GENCODE v32/Ensembl98)
Supplementary files format and content: SeuratObject, RDS format.
Library strategy: CITE-seq

molecule: protein

source_name: Liver perfusate

extract_protocol:
Sorted gd T cells were subjected to library preparation using the Chromium Next GEM Single Cell 5' Kit v2 and the 5' Feature Barcode Kit (10X Genomics). Libraries for transcriptome and ADTs profiling were generated according to the manufacturer’s protocols.
Sorted gd T cells were subjected to library preparation using the Chromium Next GEM Single Cell 5' Kit v2 and the 5' Feature Barcode Kit (10X Genomics). Libraries for transcriptome and ADTs profiling were generated according to the manufacturer’s protocols.

value: Liver perfusate

value: Primary cell

value: gammadelta T cell


title: WT HEK293T harringtonine 1 min Ribo-seq replicate 1

description: Library name: Sample 13


title: GDT4-Expr

description: Library name: GDT4-Expr

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed with Cell Ranger software (v7.0.1). The mkfastq pipeline was used for demultiplexing, and the multi pipeline aligned reads to the GRCh38 human reference genome (refdata-gex-GRCh38-2020-A). Standard Seurat clustering and UMAP-based dimensional reduction were employed. Differentially expressed genes and cell-type-specific markers were identified using the FindMarkers function, applying thresholds of minimum percentage (min.pct) > 0.1 and log2 fold change ≥ 0.5. Batch effects were corrected using Harmony integration. Filtered gene expression matrices were analyzed using R (v4.2.2) and the Seurat package (v4.1.1). Donor identity was confirmed using TotalSeq™-C anti-human hashtag ADT expression and cellsnp-lite for single nucleotide polymorphism (SNP)-based demultiplexing. Cells with mitochondrial gene expression ≥5% or fewer than 200 detected features were excluded. Doublets were filtered using DoubletFinder (v2.0.3). Dying cells were excluded by removing clusters showing elevated stress or apoptosis-associated genes.
Assembly: Human GRCh38 (GENCODE v32/Ensembl98)
Supplementary files format and content: SeuratObject, RDS format.


title: GDT3-FB

description: Library name: GDT3-FB


title: MDS_AZA_054

value: MDS patient


title: RPL41 KO HEK293T harringtonine 0 min Ribo-seq replicate 2

description: Library name: Sample 12


title: GDT3-Expr

description: Library name: GDT3-Expr


title: MDS_AZA_053


title: Enoxolone 4 hpt, biological replicate 1

description:
Library name: 1E4_CGGCTATG_TAAGATTA
Pool of five whole larvae, treated from 3 dpf for 4 h. Sequencing indices i7 CGGCTATG, i5 TAAGATTA. Demultiplex ID S6; sequenced across 4 lanes (L001-L004).


title: GDT2-FB

description: Library name: GDT2-FB


title: RPL41 KO HEK293T harringtonine 0 min Ribo-seq replicate 1

description: Library name: Sample 11


title: WT HEK293T harringtonine 1 min Ribo-seq replicate 2

description: Library name: Sample 14


title: RPL41 KO HEK293T harringtonine 2 min Ribo-seq replicate 1

description: Library name: Sample 19


title: GDT2-Expr

description: Library name: GDT2-Expr


title: GDT1-FB

description: Library name: GDT1-FB


title: MDS_AZA_052


title: GDT1-Expr

description: Library name: GDT1-Expr


title: RNA-seq, whole cortex, P70, Saline, rep6

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description: Library name: S_W10_K_03_

data_processing:
RNA-seq: Read quality was assessed using FastQC (Andrews, 2010). STAR (2.5.1b; Dobin et al., 2013) was used to map sequence reads and RSEM (version 1.2.31; Li and Dewey, 2011) was used to quantify gene expression.
MethylC-seq: MethylC-seq reads were processed as previously described using the methylpy pipeline (v1.3.2, https://github.com/yupenghe/methylpy and Lister et al., 2013) for alignment and mC calling. Briefly, computationally bisulfite-converted genome index was built using the a substituted genome file that masked SNPs called in the two mouse strains (see genomic DNA sequencing data processing and SNP calling),  appended with the lambda phage genomic sequence. MethylC-seq raw reads were first trimmed to remove sequencing adapters and low-quality sequences (minimum Phred score 10) using Cutadapt in paired-end mode. To acquire higher mappability, we treated the two ends of the clean reads as they were sequenced in single-end mode, and mapped them to the converted genome index with bowtie (v2.3.0) as aligner in the single-end pipeline of methylpy. Only reads uniquely mapped were kept, and clonal reads were removed. The bisulfite non-conversion rate was estimated using the spiked-in unmethylated lambda phage DNA. For each cytosine, a binomial test was performed to test whether the methylation levels are significantly greater than 0 with an FDR threshold of 0.01.
RNA-seq: Batch correction in P0 samples was performed using ComBat-seq (Zhang et al., 2020). Mitochondrial and lowly expressed genes with fewer than 10 raw counts in all but one sample were removed before differential gene expression analysis. Differential expression analysis was conducted using DESeq2 (Love et al., 2014) with a false discovery rate 0.1. Enrichment analysis was performed by inputting differentially expressed genes into EnrichR (Kuleshov et al., 2016; Chen et al., 2013).
MethylC-seq: CG differentially methylated regions (DMRs) were identified using a previously reported method (Lister et al. 2013), which is implemented in the DMRfind function in methylpy. We required at least 3 differentially methylated sites within a particular DMR, and the maximum distance two significant sites can be to be included in the same DMR to be 500 nucleotides. DMRs were further filtered with an FDR cutoff of 0.01 and a post-filtering cutoff of methylation levels change greater than 30%.
Assembly: mm10
Supplementary files format and content: Tab-delimited file contains transcripts per million counts for each RNA-seq sample
Supplementary files format and content: Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosine Context, 5. methylated base call, 6. total mapped base call, 7. indicator of significant methylation (0: unmethylated; 1, methylated)

organism: Mus musculus

source_name: brain (frontal cortex)

extract_protocol:
Cortex dissecxtion and nuclei isolation: The frontal cortex tissue was rapidly dissected from perinatal mice on ice. The INTACT method was used to label excitatory neurons and fluoreescence-activated nuclei sorting (FANS) was used to affinity purify GFP+ nuclei. RNA-seq: RNA was extracted by using the RNeasy Mini kit with DNAse I treatment (Qiagen, 74104) for whole frontal cortex, or by using Single-Cell RNA Purification Kit (Norgen, 51800) for nuclei. Bisulfite-Seq (MethylC-seq):  Isolated nuclei were resuspended in PBS for DNA purification using the DNeasy Blood and Tissue kit (Qiagen 69504) following the standard kit protocol.
RNA-seq: For whole tissue RNA, strand-specific cDNA libraries were constructed by selecting poly-adenylated mRNA transcripts using Truseq Stranded mRNA High Throughput Library Prep kit (Illumina, 20015963) with TruSeq RNA CD Indexes (Illumina, 20015949). Libraries were sequenced using Illumina NextSeq500, generating 20 million reads (75 bp, paired-end sequencing, whole cortex). INTACT-purified nuclear RNA (Norgen, 51800) was converted to cDNA and amplified with the Ovation RNA-seq System V2 (Nugen, 7102-A01) and libraries prepared with Kapa LTP library preparation kit (Illumina, KK8232) with TruSeq DNA Single Indexes (Illumina, 20015960), generating 40 million reads (150 bp, paired-end sequencing using Illumina HiSeq 4000 or NovaSeq 6000).
Bisulfite-Seq (MethylC-seq):  MethylC-seq libraries were constructed using the snmC-seq2 adapted for Bulk samples (https://dx.doi.org/10.17504/protocols.io.pjvdkn6). 40ng of DNA samples  were subjected to sodium bisulfite conversion using Zymo EZ DNA Methylation-Direct Kit (D5020, D5021), 0.5% of Lambda was added to each sample, resuspended in 9ul of EB buffer, 1ul of random primer was added to each of the samples, denature for 3 min at 95°C, put in ice for 3 min, then 10ul of Random primer was added and mixed, put in thermocycler with at 4°C 5 min,  25°C 5 min, 37°C 60 min. Exonuclease/SAP mix was added next put at 37°C 30min. Samples were subjected to one round of 0.8x SPRI beads clean up. Samples were resuspended in 10ul of EB and denature once again. Adaptase mix was added next, and put at 37°C 30min and 95°C 2min. The bisulfite-converted, adapter-ligated DNA molecules were enriched by 8 cycles of PCR with the following reaction composition: 25 µL of Kapa HiFi Hotstart, 1ul of P5 index primer (30uM), and 5ul of P7 index primer (10uM), for a final vol of 50ul. The reaction products were purified using SPRI beads. MethylC-seq libraries were sequenced on Illumina HiSeq 4000 or Novaseq 6000.

treatment_protocol: Dams received IP injection of 0.9% saline or 20 mg/kg polyriboinosinic–polyribocytidylic acid potassium salt (P9582, Lot number 095M4085V, Sigma-Aldrich, St. Louis, MO) in 0.9% saline on embryonic day 12.5.

value: brain (frontal cortex)

value: whole tissue

tag: strain

value: WT

value: Saline

value: Postnatal day 70

value: male


title: WT HEK293T harringtonine 0 min Ribo-seq replicate 1

description: Library name: Sample 9


title: MDS_AZA_051

value: Male

value: Responder


title: MDS_AZA_050

value: Bone marrow


title: RNA-seq, whole cortex, P70, Saline, rep5

description: Library name: S_W10_K_01_


title: WT HEK293T harringtonine 0 min Ribo-seq replicate 2

description: Library name: Sample 10


title: RNA-seq, whole cortex, P70, Saline, rep4

description: Library name: S_W10_AF_02


title: RNA-seq, whole cortex, P70, Saline, rep3

description: Library name: S_W10_AF_01


title: RPL41 KO HEK293T RNA-seq replicate 2

description: Library name: Sample 8


title: RPL41 KO HEK293T RNA-seq replicate 1

description: Library name: Sample 7


title: RNA-seq, whole cortex, P70, Saline, rep2

description: Library name: S_W10_AE_04


title: MDS_AZA_049

value: Female


title: MDS_AZA_048

value: NonResp


title: RNA-seq, whole cortex, P70, Saline, rep1

description: Library name: S_W10_AE_02


title: WT HEK293T RNA-seq replicate 2

description: Library name: Sample 6


title: RNA-seq, whole cortex, P70, Poly IC, rep5

description: Library name: P_W10_L_01_

value: Poly IC


title: RNA-seq, whole cortex, P70, Poly IC, rep4

description: Library name: P_W10_AG_02


title: MDS_AZA_047


title: RNA-seq, whole cortex, P70, Poly IC, rep2

description: Library name: P_W10_AD_02


title: MDS_AZA_046


title: RNA-seq, whole cortex, P70, Poly IC, rep3

description: Library name: P_W10_AG_01


title: WT HEK293T RNA-seq replicate 1

description: Library name: Sample 5


title: RNA-seq, whole cortex, P70, Poly IC, rep1

description: Library name: P_W10_AD_01


title: RPL41 KO HEK293T Ribo-seq replicate 2

description: Library name: Sample 4


title: RNA-seq, whole cortex, P0, Saline, rep4

description: Library name: S_P0_J_04

value: Postnatal day 0


title: MDS_AZA_045


title: RNA-seq, whole cortex, P0, Saline, rep3

description: Library name: S_P0_J_03


title: RNA-seq, whole cortex, P0, Saline, rep2

description: Library name: S_P0_I_03


title: MDS_AZA_043


title: RPL41 KO HEK293T Ribo-seq replicate 1

description: Library name: Sample 3


title: RNA-seq, whole cortex, P0, Saline, rep1

description: Library name: S_P0_I_01


title: RNA-seq, whole cortex, P0, Poly IC, rep4

description: Library name: P_P0_F_11


title: MDS_AZA_042


title: WT HEK293T Ribo-seq replicate 2

description: Library name: Sample 2


title: RNA-seq, whole cortex, P0, Poly IC, rep3

description: Library name: P_P0_F_10


title: MDS_AZA_041


title: WT HEK293T Ribo-seq replicate 1

description: Library name: Sample 1


title: RNA-seq, whole cortex, P0, Poly IC, rep2

description: Library name: P_P0_E_09


title: RNA-seq, whole cortex, P0, Poly IC, rep1

description: Library name: P_P0_E_08


title: hiPSC-CMs, LMNAH222P, rep6

city: Paris

first: Jean-Sébastien

last: Hulot

address: Rue Leblanc

country: France

institute: Paris Centre de Recherche Cardiovasculaire

description: Library name: CM_LMNA_H222P_DC75

data_processing:
Sequencing quality was assessed with FastQC (version 0.11.4). Analyses were performed with Galileo v1.0 by Integragen. STAR was used to obtain the number of reads associated to each gene in the Gencode v31 annotation (restricted to protein-coding genes, antisense and lincRNAs).
Raw counts for each sample were imported into R statistical software using the Bioconductor DESeq2 package.
Extracted count matrix was normalized for library size and coding length of genes to compute FPKM expression levels.
The Bioconductor edgeR package was used to import raw counts into R statistical software, and compute normalized log2 CPM (counts per millions of mapped reads) using the TMM (weighted trimmed mean of M-values) as normalization procedure.
Assembly: GRCh38
Supplementary files format and content: csv file contains the raw counts for all samples

growth_protocol: hiPSCs were kept on stem cell-qualified Matrigel-coated with mTeSR Plus medium at 5% CO2, 37°C. Cardiac differentiation was carried out with 6 um CHIR-99021 and 5 um IWR-1. Cardiomyocytes were enriched by two rounds of glucose starvation and kept in RPMI-1640 medium with B27 supplement until day 30 post-differentiation.

extract_protocol:
Total RNA was extracted with a NucleoSpin RNA mini Kit (Macherey-Nagel).
Library was constructed with the 'NEBNext® UltraTM II mRNA-Seq' kit.

treatment_protocol: The hiPSC line LMNAH222P was derived by Sendai virus infection from PBMCs of a 23-year-old male patient with the LMNA p.H222P mutation. The corrected isogenic control cell line was generated by CRISPR-Cas9 homology-directed repair using the vector (BB)-2A-Puro (PX459) V2.0 (Addgene plasmid #62988, Addgene). The plasmid and single-stranded guide RNA were delivered into the cells by electroporation, followed by puromycin selection. Correction of the desired mutation was confirmed by sequencing.

value: Human induced pluripotent stem cell-derived cardiomyocytes


title: RNA-seq, whole cortex, E15, Saline, rep4

description: Library name: S_E14_H_06

value: Embryonic day 15


title: RNA-seq, whole cortex, E15, Saline, rep3

description: Library name: S_E14_H_05


title: MDS_AZA_040


title: hiPSC-CMs, LMNAH222P, rep5

description: Library name: CM_LMNA_H222P_DC74


title: RNA-seq, whole cortex, E15, Saline, rep1

description: Library name: S_E14_G_02


title: RNA-seq, whole cortex, E15, Poly IC, rep4

description: Library name: P_E14_B_07


title: RNA-seq, whole cortex, E15, Saline, rep2

description: Library name: S_E14_G_04


title: hiPSC-CMs, LMNAH222P, rep4

description: Library name: CM_LMNA_H222P_DC40


title: MDS_AZA_038


title: RNA-seq, whole cortex, E15, Poly IC, rep3

description: Library name: P_E14_B_05


title: MDS_AZA_039


title: hiPSC-CMs, LMNAH222P, rep3

description: Library name: CM_LMNA_H222P_DC38


title: MDS_AZA_037


title: hiPSC-CMs, LMNAH222P, rep2

description: Library name: CM_LMNA_H222P_DC31


title: RNA-seq, whole cortex, E15, Poly IC, rep2

description: Library name: P_E14_A_02


title: RNA-seq, whole cortex, E15, Poly IC, rep1

description: Library name: P_E14_A_01


title: MDS_AZA_036


title: mouse lung adenocarcinoma cell line, KP-H3K36M-Setd2KO, ATAC, biol rep 3

city: Philadelphia

first: Sharan

last: Venkatesh

state: PA

address: 421 Curie blvd

institute: University of Pennsylvania

description: Library name: KP-H3K36M-Setd2KO-ATAC-S3

data_processing:
For the RNA-Seq Samples, reads were trimmed using atria and were then mapped to GRCm39 using salmon with libType A and validateMapping options.
For the ChIP-Seq and ATAC seq samples, reads were trimmed using Atria and then were aligned to GRCm39 using bowite with local, discordant and no-mixed options. Deeptools was then used to generate the bigwig files. ChIP-Seq samples were also aligned to dm6 and a scaling factor was calculated based on drosophila read counts
Assembly: GRCm39
Supplementary files format and content: Quant files from Salmon containing TPM values
Supplementary files format and content: Bigwig files of mapped ChIP and ATAC seq reads

source_name: Lung

extract_protocol:
RNA was extracted from 3 cell lines per group (KP-Ctrl, KP-Setd2KO, KP-H3K36M-Ctrl, KP-H3K36M-Setd2KO) and subjected to paired-end sequencing. ChIP was peformed for H3K36me2, H3K36me3, and H3K27me3 on lung adenocarcinoma cell lines (2 per group: KP-Ctrl, KP-Setd2KO, KP-H3K36M-Ctrl, KP-H3K36M-Setd2KO). ChIP-seq libraries were generated and sequenced by Genewiz/Azenta Life Sciences. ATAC-seq libraries were generated and sequenced by Genewiz/Azenta Life Sciences from cyropreserved cell lines (3 per group: KP-Ctrl, KP-Setd2KO, KP-H3K36M-Ctrl, KP-H3K36M-Setd2KO).
RNA was extracted from 3 cell lines per group (KP-Ctrl, KP-Setd2KO, KP-H3K36M-Ctrl, KP-H3K36M-Setd2KO) and subjected to paired-end sequencing. ChIP was peformed for H3K36me2, H3K36me3, and H3K27me3 on lung adenocarcinoma cell lines (2 per group: KP-Ctrl, KP-Setd2KO, KP-H3K36M-Ctrl, KP-H3K36M-Setd2KO). ChIP-seq libraries were generated and sequenced by Genewiz/Azenta Life Sciences. ATAC-seq libraries were generated and sequenced by Genewiz/Azenta Life Sciences from cyropreserved cell lines (3 per group: KP-Ctrl, KP-Setd2KO, KP-H3K36M-Ctrl, KP-H3K36M-Setd2KO).

value: Lung

value: mouse lung adenocarcinoma cell line


title: mouse lung adenocarcinoma cell line, KP-H3K36M-Setd2KO, ATAC, biol rep 2

description: Library name: KP-H3K36M-Setd2KO-ATAC-S2


title: hiPSC-CMs, LMNAH222P, rep1

description: Library name: CM_LMNA_H222P_DC27


title: MDS_AZA_035

value: MDS patient


title: mouse lung adenocarcinoma cell line, KP-H3K36M-Ctrl, ATAC, biol rep 3

description: Library name: KP-H3K36M-Ctrl-ATAC-S3


title: hiPSC-CMs, Corrected Isogenic control, rep6

description: Library name: CM_C1-3_DC145

source_name: Corrected Isogenic control

value: Corrected Isogenic control


title: mouse lung adenocarcinoma cell line, KP-H3K36M-Setd2KO, ATAC, biol rep 1

description: Library name: KP-H3K36M-Setd2KO-ATAC-S1


title: mouse lung adenocarcinoma cell line, KP-H3K36M-Ctrl, ATAC, biol rep 1

description: Library name: KP-H3K36M-Ctrl-ATAC-S1


title: mouse lung adenocarcinoma cell line, KP-H3K36M-Ctrl, ATAC, biol rep 2

description: Library name: KP-H3K36M-Ctrl-ATAC-S2


title: mouse lung adenocarcinoma cell line, KP-Setd2KO, ATAC, biol rep 3

description: Library name: KP-Setd2KO-ATAC-S3


title: MDS_AZA_034


title: hiPSC-CMs, Corrected Isogenic control, rep5

description: Library name: CM_C1-3_DC143


title: MDS_AZA_033


title: mouse lung adenocarcinoma cell line, KP-Setd2KO, ATAC, biol rep 2

description: Library name: KP-Setd2KO-ATAC-S2


title: mouse lung adenocarcinoma cell line, KP-Setd2KO, ATAC, biol rep 1

description: Library name: KP-Setd2KO-ATAC-S1


title: MDS_AZA_032


title: hiPSC-CMs, Corrected Isogenic control, rep4

description: Library name: CM_C1-3_DC142


title: hiPSC-CMs, Corrected Isogenic control, rep3

description: Library name: CM_C1-3_DC133


title: mouse lung adenocarcinoma cell line, KP-Ctrl, ATAC, biol rep 3

description: Library name: KP-Ctrl-ATAC-S3

value: KP-Ctrl


title: mouse lung adenocarcinoma cell line, KP-Ctrl, ATAC,biol rep 2

description: Library name: KP-Ctrl-ATAC-S2


title: MDS_AZA_027


title: hiPSC-CMs, Corrected Isogenic control, rep2

description: Library name: CM_C1-3_DC130


title: mouse lung adenocarcinoma cell line, KP-Ctrl, ATAC,biol rep 1

description: Library name: KP-Ctrl-ATAC-S1


title: IgG Control

description: Library name: KP-IgG

tag: antibody

value: IgG Control


title: KP-H3K36M-Setd2KO, H3K27me3, biol rep 2

description: Library name: KP-H3K36M-Setd2KO-H3K27me3-S2


title: MDS_AZA_031


title: KP-H3K36M-Setd2KO, H3K27me3, biol rep 1

description: Library name: KP-H3K36M-Setd2KO-H3K27me3-S1


title: hiPSC-CMs, Corrected Isogenic control, rep1

description: Library name: CM_C1-3_DC126


title: Input DNA

description: Library name: KP-Input

value: Input DNA


title: MDS_AZA_030


title: KP-H3K36M-Ctrl, H3K27me3, biol rep 2

description: Library name: KP-H3K36M-Ctrl-H3K27me3-S2


title: KP-H3K36M-Ctrl, H3K27me3, biol rep 1

description: Library name: KP-H3K36M-Ctrl-H3K27me3-S1


title: 114, CON, CD154

city: Doha

first: Asmma

last: Doudin

address: Al Gharrafa Street, Ar Rayyan

department: Research

country: Qatar

institute: Sidra Medicine

description: Library name: 200902061

data_processing:
Raw sequencing data were demultiplexed using bcl2fastq v2.20 to generate FASTQ files for each sample. Downstream processing of RNA-seq data was carried out using the bcbio-nextgen v1.2.0 pipeline.Reads were aligned to the reference genome using STAR v2.6.1d, and gene-level quantification was performed using featureCounts v2.0.0.
Assembly: GRCh38
Supplementary files format and content: CPM_ComBat_seq_geo.csv
Supplementary files format and content: a gene expression matrix that contains normalized CPM (Counts Per Million) values — after batch correction using ComBat-seq.

growth_protocol: Cells revived in RPMI 1640 GlutaMAX medium  and 10% human serum

extract_protocol:
Cells were sorted based on the surface staining of CD154+CD137- for TconCM+ cells and CD137+CD154- for TregCM+ cells and RNA was extracted using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing based on manufacturer's instructions.
Isolated RNA was used to create double-stranded cDNA fragments using SMARTer® Pico PCR cDNA Synthesis Kit (Takara) according to the manufacturer’s protocol. SeqAmp DNA Polymerase (Takara) was used to amplify purified first-strand cDNA into RNA-seq libraries based on the manufacturer’s instructions. Nextera XT Index Kit v2 (Illumina, USA) was used for library indexing.

treatment_protocol: Cells stimulated in RPMI 1640 GlutaMAX medium and 10% human serum, for 6 hours (5% CO2, 37oC) with 100μg CM,  1 μg/ml CD40 and 1μg/ml CD28 functional grade antibodies.

tag: sample group

value: CON


title: 113, CON, CD137

description: Library name: 200902051


title: MDS_AZA_029

value: Male


title: KP-Setd2KO, H3K27me3, biol rep 2

description: Library name: KP-Setd2KO-H3K27me3-S2


title: KP-Setd2KO, H3K27me3, biol rep 1

description: Library name: KP-Setd2KO-H3K27me3-S1


title: MDS_AZA_028


title: KP-Ctrl, H3K27me3, biol rep 2

description: Library name: KP-Ctrl-H3K27me3-S2


title: 111, AD, CD137

description: Library name: 200902031

value: AD


title: 112, AD, CD154

description: Library name: 200902041


title: CTL_USNT_003

status: Public on Jul 28 2026

city: Montreal

first: Michel

last: Tremblay

state: Quebec

address: 1160 Pine Avenue West

country: Canada

institute: Goodman Cancer Research Centre

description:
Library name: A_003
Data2/A003_quant

data_processing:
Salmon
Assembly: MM_grch38_ens94
Supplementary files format and content: .csv

growth_protocol: DMEM 10% FBS + 1X Pen Strep. Cell were kept at

extract_protocol:
Quiiagen Plus mini kit
NEBNext_dual_i7

value: sgCTL

value: NT


title: CTL_IFNb_001

description:
Library name: A_004
Data2/A004_quant

value: IFN-beta, 6h, 20ng/mL


title: CTL_USNT_001

description:
Library name: A_001
Data2/A001_quant


title: KP-Ctrl, H3K27me3, biol rep 1

description: Library name: KP-Ctrl-H3K27me3-S1


title: KP-H3K36M-Setd2KO, H3K36me3, biol rep 1

description: Library name: KP-H3K36M-Setd2KO-H3K36me3-S1


title: MDS_AZA_026

value: Bone marrow

value: NonResp


title: SW1990, NC-3

city: Changchun

first: Ziyu

last: Liu

address: 1 Xinmin Street

country: China

institute: Jilin University

description: Library name: Sample 3

data_processing:
Clean reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2 (v2.2.1) with default parameters.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: SW1990 pancreatic ductal adenocarcinoma cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) according to the manufacturer’s instructions. RNA quality and integrity were assessed using the Agilent 2100 Bioanalyzer, and RNA concentration was measured with a Qubit Fluorometer.
mRNA was enriched from total RNA using oligo(dT) magnetic beads. After fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis using dUTP. The cDNA fragments then underwent end repair, A-tailing, adapter ligation, USER enzyme digestion, PCR amplification, and purification. Libraries were quantified using Qubit and real-time PCR and size-checked with a Bioanalyzer.

treatment_protocol: Cells in the treatment group were exposed to 5 µM EPZ-5676 (MedChemExpress), a selective DOT1L inhibitor. Cells in the control group were treated with equal volumes of DMSO.

value: pancreatic ductal adenocarcinoma (PDAC) cell line

value: none; untreated


title: MDS_AZA_025


title: 110, CON, CD154

description: Library name: 200902021


title: KP-H3K36M-Setd2KO, H3K36me3, biol rep 2

description: Library name: KP-H3K36M-Setd2KO-H3K36me3-S2

value: Lung


title: MDS_AZA_024


title: KP-H3K36M-Ctrl, H3K36me3, biol rep 1

description: Library name: KP-H3K36M-Ctrl-H3K36me3-S1


title: KP-H3K36M-Ctrl, H3K36me3, biol rep 2

description: Library name: KP-H3K36M-Ctrl-H3K36me3-S2


title: KP-Setd2KO, H3K36me3, biol rep 2

description: Library name: KP-Setd2KO-H3K36me3-S2


title: 109, CON, CD137

description: Library name: 200902011


title: KP-Setd2KO, H3K36me3, biol rep 1

description: Library name: KP-Setd2KO-H3K36me3-S1


title: KP-Ctrl, H3K36me3, biol rep 1

description: Library name: KP-Ctrl-H3K36me3-S1


title: 107, AD, CD137

description: Library name: 200901991


title: MDS_AZA_023

value: Female


title: MDS_AZA_021

value: MDS patient

value: Responder


title: MDS_AZA_022


title: 106, AD, CD154

description: Library name: 200901981


title: KP-Ctrl, H3K36me3, biol rep 2

description: Library name: KP-Ctrl-H3K36me3-S2

value: KP-Ctrl


title: 108, AD, CD154

description: Library name: 200902001


title: MDS_AZA_020


title: KP-H3K36M-Setd2KO, H3K36me2, biol rep 2

description: Library name: KP-H3K36M-Setd2KO-H3K36me2-S2


title: KP-H3K36M-Setd2KO, H3K36me2, biol rep 1

description: Library name: KP-H3K36M-Setd2KO-H3K36me2-S1


title: KP-H3K36M-Ctrl, H3K36me2, biol rep 2

description: Library name: KP-H3K36M-Ctrl-H3K36me2-S2


title: 105, AD, CD137

description: Library name: 200901971


title: KP-H3K36M-Ctrl, H3K36me2, biol rep 1

description: Library name: KP-H3K36M-Ctrl-H3K36me2-S1


title: MDS_AZA_019


title: KP-Setd2KO, H3K36me2, biol rep 2

description: Library name: KP-Setd2KO-H3K36me2-S2


title: KP-Setd2KO, H3K36me2, biol rep 1

description: Library name: KP-Setd2KO-H3K36me2-S1


title: KP-Ctrl, H3K36me2, biol rep 2

description: Library name: KP-Ctrl-H3K36me2-S2


title: 104, ALL, CD154

description: Library name: 200901961

value: ALL


title: 103, ALL, CD137

description: Library name: 200901951


title: KP-Ctrl, H3K36me2, biol rep 1

description: Library name: KP-Ctrl-H3K36me2-S1


title: MDS_AZA_018


title: mouse lung adenocarcinoma cell line, KP-H3K36M-Setd2KO, biol rep 3

description: Library name: KP-H3K36M-Setd2KO-S3

value: mouse lung adenocarcinoma cell line


title: MDS_AZA_008


title: 102, CON, CD137

description: Library name: 200901891

value: CON


title: mouse lung adenocarcinoma cell line, KP-H3K36M-Setd2KO, biol rep 1

description: Library name: KP-H3K36M-Setd2KO-S1


title: mouse lung adenocarcinoma cell line, KP-H3K36M-Ctrl, biol rep 3

description: Library name: KP-H3K36M-Ctrl-S3


title: mouse lung adenocarcinoma cell line, KP-H3K36M-Ctrl, biol rep 2

description: Library name: KP-H3K36M-Ctrl-S2


title: MDS_AZA_004

value: Male


title: 100, AD, CD137

description: Library name: 200901871

value: AD


title: mouse lung adenocarcinoma cell line, KP-H3K36M-Setd2KO, biol rep 2

description: Library name: KP-H3K36M-Setd2KO-S2


title: mouse lung adenocarcinoma cell line, KP-Setd2KO, biol rep 2

description: Library name: KP-Setd2KO-S2


title: mouse lung adenocarcinoma cell line, KP-H3K36M-Ctrl, biol rep 1

description: Library name: KP-H3K36M-Ctrl-S1


title: A22LP036Z1

city: Shanghai

first: Xiaojie

address: No. 639 Zaozhiju Rd., Huangpu District

department: Department of Oral Medicine

institute: Shanghai Ninth People's Hospital

description:
Library name: Sample15
one sample from oral mucosa tissue from oral lichen planus

data_processing:
Raw sequence reads were processed using CLC Genomics Workbench v11.0.1. Adapter sequences and low-quality bases were trimmed with a quality limit of 0.05. Trimmed reads were mapped to the human reference genome (GRCh38/hg38) using the following alignment parameters: mismatch cost = 2, insertion cost = 3, deletion cost = 3, length fraction = 0.8, and similarity fraction = 0.8. Gene-level read counts were extracted, and normalization was performed using the default settings in CLC Genomics Workbench.
Assembly: GRCh38
Supplementary files format and content: txt,gene counts expression

source_name: oral mucosa

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: oral mucosa

value: oral mucosal cell

tag: disease state

value: Oral lichen planus


title: mouse lung adenocarcinoma cell line, KP-Setd2KO, biol rep 3

description: Library name: KP-Setd2KO-S3

tag: tissue


title: MDS_AZA_013

value: Bone marrow

tag: cell line


title: MDS_AZA_010

tag: individual


title: SPIRIT, Sun Yat-sen University Cancer Center, M2319466a

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

data_processing:
The protocol of high-throughput sequencing was fully according to the manufacturer's instructions (Illumina).
The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4).
The fragments of genes were counted using stringtie (v1.3.3b) followed by TMM (trimmed mean of M values) normalization.
Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q< 0.05) and fold-change >2 using edgeR software
Supplementary files format and content: "standard processed data.xlsx" represents TMM-normalized data

source_name: lymph node/skin tissue

extract_protocol:
Total RNA was extracted from FFPE tissues followed by library preparation according to Illumina standard instruction (SMARTer Stranded Total RNA-Seq Kit v2).
Agilent 4200 bioanalyzer was employed to evaluate the concentration and size distribution of cDNA library before sequencing with an Illumina NovaSeq6000.

value: previously untreated advanced ENKTL

value: lymph node/skin tissue

value: Sintilimab with P-GEMOX chemotherapy

tag: medical center

value: Sun Yat-sen University Cancer Center

value: male

tag: Stage

value: IV


title: 101, AD, CD154

description: Library name: 200901881

tag: cell type


title: 98, ALL, CD154

description: Library name: 200901841


title: mouse lung adenocarcinoma cell line, KP-Ctrl, biol rep 2

description: Library name: KP-Ctrl-S2

value: Lung

tag: genotype


title: mouse lung adenocarcinoma cell line, KP-Ctrl, biol rep 1

description: Library name: KP-Ctrl-S1

value: KP-Ctrl


title: mouse lung adenocarcinoma cell line, KP-Setd2KO, biol rep 1

description: Library name: KP-Setd2KO-S1


title: 99, AD, CD137

description: Library name: 200901851


title: Long-chase Pax7 lineage (2mo)1

first: Takuto

last: HAYASHI

address: 160 Rue de Vaugirard

institute: Institut Necker Enfants Malades

description:
Library name: Sample8-1/2
The same sample was sequenced twice and treated as a single dataset.

data_processing:
feature-barcode matrices were generated by aligning the reads to the mouse genome (mm10 Ensemble: version 92) with CellRanger v8.0.1.
Assembly: mm10
Supplementary files format and content: The Cell Ranger output includes three files: features.tsv, barcodes.tsv, and matrix.mtx, which together represent the gene expression count matrix. The matrix contains UMI counts for each gene (features) in each cell (barcodes)., For 10X genomics: data processing pipeline Cell Ranger version 8.0.1 Data analysis for 10X genomics using Seurat version 5.2.2

molecule: nuclear RNA

source_name: Skeletal muscle

extract_protocol:
Approximately 10,000 cells were processed using the Chromium Next GEN Single Cell 3’Reagent Kits v3.1
RNA libraries were prepared using a chromium controller from10X Genomics, according to the manufacturer’s instructions.

value: Skeletal muscle

value: Pax7 progeny

value: Pax7CreERT2; Rosa26HTB::GFP

tag: treatment

value: Four administrations of tamoxifen were performed at P1-P4 (postnatal days 1 to 4).


title: MDS_AZA_002

data_processing:
Reads were trimmed using Trim Galore (version 0.6.2) and aligned to a bisulfite-converted human genome (hg19) using Bowtie2 and Bismark (versions 2.4.1 and 0.23.1, respectively).
After strand collapsing and filtering by coverage (keep loci with reads between 10-400), methylation loci were tiled by window (25bp) and a methylDiff object was created using MethylSig (version 1.5.0) for regions that were present in at least 3 samples per group.
Significant differentially methylated regions (DMRs) were identified as those with an absolute mean methylation difference of ≥ 25 and a DMR q-value of ≤ 0.05.
Assembly: hg19
Supplementary files format and content: genome-wide cytosine report output from bismark
Supplementary files format and content: tab-delimited text files include base-pair resolution information of the read strand and coverage of the methylated and unmethylated Cs in the sequenced DNA for each Sample

value: MDS patient

value: Male

value: NonResp


title: Postnatal Day22-1, Pax7 Progeny cells3

description: Library name: Smaple4-3/4

value: Two administrations of tamoxifen were performed starting two days prior to sampling.


title: MDS_AZA_005

value: Bone marrow


title: mouse lung adenocarcinoma cell line, KP-Ctrl, biol rep 3

description: Library name: KP-Ctrl-S3

value: mouse lung adenocarcinoma cell line


title: MDS_AZA_001

value: Female


title: 96, AD, CD154

description: Library name: 200901821

value: AD


title: Postnatal Day22-1, Pax7 Progeny cells4

description: Library name: Smaple4-4/4


title: MDS_AZA_014

value: Responder


title: 93, CON, CD137

description: Library name: 200901791

value: CON


title: Long-chase Pax7 lineage (2mo)2

description: Library name: Sample8-2/2


title: MDS_AZA_011


title: MDS_AZA_017


title: MDS_AZA_009


title: Postnatal Day22-1, Pax7 Progeny cells1

description:
Library name: Smaple4-1/4
Each sample was sequenced across 4lanes of the flow cell.


title: Postnatal day 22 bio replicate 1 (Female)

city: Bethesda

first: Whitney

last: Heavner

address: 35 Convent Drive

department: NINDS

institute: National Institutes of Health

description:
Library name: p22_F
10x Genomics

data_processing:
The demultiplexing, barcoded processing, and gene counting were made using the Cell Ranger software v9.0.1 (https://www.10xgenomics.com/support/software/cell-ranger/latest).
Assembly: mm10
Supplementary files format and content: tab separated values files and matrix files

source_name: main olfactory epithelium

growth_protocol: Olfactory epithelium (OE) was dissected from the nasal cavity of wild-type (C57Bl/6) mice at P1, P3, P5, P8, P15, or P22

extract_protocol:
The sensory OE was microdissected from the mouse nasal cavity at P1, P3, P5, P8, P15, and P22, dissociated in 2-3 mL pre-warmed dissociation medium (Worthington) (150 units papain, 100 units DNAse I, 2.5 mM cysteine, and 2.5 mM EDTA in 5 mL Neurobasal), and kept at 37°C for 25 min in a CO2 incubator. Samples were washed 3 times with 10% fetal bovine serum in phosphate-buffered saline (FBS-PBS), gently triturated 5-10 times using a fire-polished glass Pasteur pipette, and strained through a 35 μm nylon filter into a 5 mL polypropylene tube. DAPI, used to identify dead cells, was added at a final concentration of 0.1-1 μg/mL, and live cells (DAPI-low) were collected using a Sony LE-SH-800G cell sorter. At least two biological replicates and at least one female and one male per time point were used for all time points except P5, which only contained males.
Cells were pelleted in a swinging bucket centrifuge at 400g for 5 minutes at 4°C. The cell pellet was resuspended in 43.2 μl FBS-PBS, then 31.8 μl RT master mix was added to the cell pellet before loading the cells onto a Next GEM Chip G. A Chromium Next GEM Single Cell 3′ Kit v3.1 (10x Genomics, PN-1000268) and Dual Index Kit TT Set A (10x Genomics, PN-1000215) were used to generate single-cell whole-transcriptome libraries according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 Dual Index User Guide Rev E).

value: main olfactory epithelium

value: postnatal day 22

tag: cell types

value: multipotent progenitors and their progeny

value: wild-type

tag: sequencing batch


title: 94, CON, CD154

description: Library name: 200901801


title: 97, ALL, CD137

description: Library name: 200901831

value: ALL


title: Postnatal Day22-2, Pax7 Progeny cells

description: Library name: Sample5

value: Skeletal muscle

value: Pax7 progeny

value: Pax7CreERT2; Rosa26HTB::GFP


title: 92, ALL, CD137

description: Library name: 200901771


title: MDS_AZA_016

value: MDS patient

tag: Sex

value: Male

tag: responder


title: 91, ENP, CD154

description: Library name: 200901761

value: ENP

tag: batch


title: Postnatal Day10, Pax7 Progeny cells1

description:
Library name: Sample3-1/4
Each sample was sequenced across 4lanes of the flow cell.

value: Two administrations of tamoxifen were performed starting two days prior to sampling.


title: 90, ENP, CD137

description: Library name: 200901751


title: Postnatal Day3, Pax7 Progeny cells3

description: Library name: Sample2-3/4


title: Postnatal Day10, Pax7 Progeny cells2

description: Library name: Sample3-2/4


title: Postnatal Day10, Pax7 Progeny cells4

description: Library name: Sample3-4/4


title: Postnatal Day3, Pax7 Progeny cells4

description: Library name: Sample2-4/4


title: 89, AD, CD154

description: Library name: 200901741


title: Postnatal Day3, whole muscle Tibialis Anterior4

description: Library name: Sample1-4/4


title: 88, AD, CD137

description: Library name: 200901731


title: 87, ENP, CD154

description: Library name: 200901721


title: MDS_AZA_015

value: Bone marrow

tag: age


title: HCR voluntary-running aged soleus RNA-seq Le5

city: Budapest

first: Zsolt

last: Radák

address: Budapest, Alkotás u. 42-48, 1123

department: Research Center for Molecular Exercise Science

country: Hungary

institute: University of sports science, Hungary

description:
Library name: UPL26-002517
Aged female rat soleus muscle; group=LCR + Exercise; original sample name=Le 5; count matrix column=UPL26-002517.

data_processing:
Raw reads were assessed using FastQC and MultiQC.
The first six nucleotides of each read were extracted as unique molecular identifiers using UMI-tools.
Reads were trimmed using Cutadapt to remove library-derived bases, Illumina adapters, poly(A) tails, ambiguous bases, and low-quality sequences.
Trimmed reads were aligned to the rat mRatBN7.2 reference genome using STAR, and coordinate-sorted BAM files were generated.
PCR duplicates were removed using UMI-tools, and gene-level counts were obtained from deduplicated BAM files using featureCounts in stranded mode.
Assembly: mRatBN7.2 (Rattus norvegicus; rn7)
Supplementary files format and content: gene_count_matrix_clean.tsv is a tab-delimited text file containing raw gene-level counts generated by featureCounts from UMI-deduplicated BAM files. Rows correspond to genes (Geneid) and columns correspond to RNA-seq libraries UPL26-002492 through UPL26-002517.

organism: Rattus norvegicus

source_name: soleus muscle

growth_protocol: Selectively bred low- and high-running-capacity rats (LCR and HCR; 44th generation) were used. Female rats were housed in temperature-controlled rooms under a 12:12 h light-dark cycle with ad libitum access to standard chow and water.

extract_protocol:
Rats were deeply anesthetized, and soleus muscle samples were rapidly excised, snap-frozen, and stored at -80 C. Total RNA was extracted from soleus muscle using the Quick-RNA Miniprep Plus Kit (Zymo Research) according to the manufacturer's instructions.
RNA-seq libraries were generated using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD v2 for Illumina (Lexogen). Briefly, 100 ng of total RNA was used for first-strand cDNA synthesis using an oligo(dT) primer, followed by RNA removal. Second-strand synthesis was initiated by random priming, and products were purified using magnetic beads. Libraries were amplified and barcoded by PCR, quality assessed using an Agilent 4200 TapeStation, and sequenced to generate single-end reads.

treatment_protocol: Sedentary LCR and HCR animals were maintained without wheel access. For the voluntary exercise cohort, female rats were pair-housed in cages equipped with a running wheel for more than five months.

value: soleus muscle

value: selectively bred LCR rat

value: voluntary wheel running


title: HCR voluntary-running aged soleus RNA-seq He1

description:
Library name: UPL26-002513
Aged female rat soleus muscle; group=HCR + Exercise; original sample name=He 1; count matrix column=UPL26-002513.

value: selectively bred HCR rat


title: Postnatal Day3, Pax7 Progeny cells2

description: Library name: Sample2-2/4


title: 2_HKM7VBGXT.2.CGATCAGT_TATGCAGT

city: Helsinki

first: Olli

last: Pietilainen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
Library name: 2_SM-NBW8B_plate1
DHMT_48hr_LDLR_A_b

data_processing:
To identify cell-type-specific gene expression profiles, the fastq files of the bulk RNA-seq data were aligned to a mixed human-mouse reference genome (GRCh37/hg19 and GRCm38/mm10, GSE63269) using STAR65 (v.2.5). As quality control, Illumina adapters and low-quality base bares were trimmed using Trimmomatic66 (v.0.36) and short reads (< 36 base pairs) were removed. Next the reads were annotated with GENCODE GTF annotation version 19 and a custom GTF file for the mixed genome (GSE63269) for the mixed genome. A raw counts matrix was generated using featureCounts67 by Rsubread (v.1.32). Genes with a total read count less than 10 were filtered using filterByExpr function in edgeR68 (v. 4.2.0). Read counts were then normalized for library size (method = TMM) and transformed to log2 counts-per-million (logCPM) estimates using the voom function by limma69 (v. 3.60.3) package. The normalized logCPM gene expression matrices were used as input for all the following analyses.
Assembly: GRCh37/hg19 and GRCm38/mm10, GSE63269
Supplementary files format and content: counts_raw_all.txt contain raw counts for each sample (link: barcode).
Supplementary files format and content: counts_logCPM_human.txt contain logCPM values for all iPCS WT samples.
Supplementary files format and content: counts_logCPM_mouse.txt contain logCPM values for all astrocyte samples that have not been co-cultured CRISPRi-neurons.
Supplementary files format and content: counts_logCPM_CRISPRi_human.txt contain logCPM values for all CRISPRi-edited iPCS  samples.
Supplementary files format and content: counts_logCPM_CRISPRi_mouse.txt contain logCPM values for all astrocyte samples that have been co-cultured with CRISPRi-neurons.

extract_protocol:
The neuronal mono-cultures and co-cultures underwent bulk RNA sequencing at the Broad Genomics Platform according to the Smartseq2 workflow
The neuronal mono-cultures and co-cultures underwent bulk RNA sequencing at the Broad Genomics Platform according to the Smartseq2 workflow

value: iPSC-derived excitatory neuron, astrocyte

value: LDLR knockdown

tag: day

tag: guide rna

tag: barcode


title: MDS_AZA_012

city: Miami

first: Qin

last: Yang

address: 1501 NW 10th Avenue

institute: University of Miami Miller School of Medicine

extract_protocol:
For the isolation of CD34+ cells from human bone marrow samples, we utilized the Miltenyi MACS magnetic bead purification kit. In a nutshell, 2 mL frozen vials of human mononuclear cells (MNC) were thawed at 37°C, followed by treatment with 200 µL of DNase-I (Roche) at a concentration of 1 mg/mL for 90 seconds. Subsequently, the cells were gently resuspended in Iscove's Modified Dulbecco's Medium (IMDM) containing 40% fetal bovine serum (FBS) to minimize primary human cell mortality. All centrifugation steps were performed at 1500 rpm. After an 8-minute centrifugation, the cells were resuspended in 15 mL of MACS buffer and then incubated with magnetic beads for 50 minutes at 4°C. Following three consecutive washes with MACS buffer (each for 10 minutes at 4°C), the cells were resuspended in 6 mL of MACS buffer and passed through an AUTOMACS instrument using the Posseld program. After another 8-minute centrifugation at 4°C, the cells were resuspended in RTL buffer with beta-mercaptoethanol. DNA and RNA were extracted from the CD34+ fraction using the AllPrep Micro kit (QIAGEN), while the CD34+ depleted fraction was processed with the AllPrep Mini kit.
Prior to adapter ligation, the methylated adapters were diluted to a concentration of 150 nmol/L. During the gel size selection step, fragments falling within the range of 150 to 450 base pairs were excised from the gel.

tag: tissue

value: NonResp


title: Postnatal Day3, Pax7 Progeny cells1

description:
Library name: Sample2-1/4
Each sample was sequenced across 4lanes of the flow cell.


title: Postnatal Day3, whole muscle Tibialis Anterior1

description:
Library name: Sample1-1/4
Each sample was sequenced across 4lanes of the flow cell.


title: MDS_AZA_094

data_processing:
The quality of the resulting reads was assessed using FastQC (v0.11.8) and multiQC (1.11). Then all reads were processed using Trim Galore (version 0.6.2) to trim to paired end 50 basepairs and remove adapters.
The resulting reads were aligned to the hg19 Gencode v19 reference genome using the STAR aligner (version 2.7.6a) with specific parameters: outFilterType=BySJout, outFilterMultimapNmax=20, alignSJoverhangMin=8, alignSJDBoverhangMin=1, outFilterMismatchNmax=999, alignIntronMin=20, alignIntronMax=1000000, alignMatesGapMax=1000000, and alignEndsType=EndToEnd.
Gene expression was quantified using featureCounts (v2.0.1), which was run in paired-end mode with the hg19 gencode annotation file (excluding entries for ribosomal RNA).
Differential expression analysis was performed using DESeq2 (v1.32.0) with a multifactor design that accounted for both the donor's condition and any batch effects. Genes with an absolute fold change of at least 1.5 and a p-value adjusted for multiple comparisons of less than or equal to 0.05 were considered significant.
Assembly: hg19
Supplementary files format and content: featureCounts  files

extract_protocol:
RNA extracted from the CD34+ fraction was employed for RNA-seq. To guarantee RNA quality, Tapestation was utilized prior to library preparation. The RNA was treated with Illumina Ribo-Zero
For library preparation, we used the Nugen Ovation Solo RNA-seq ultra-low input kit, following the manufacturer's instructions. Subsequently, the prepared libraries were sequenced on an Illumina NextSeq platform. These libraries were paired-end and they were strand-specific.

tag: cell line

value: Responder


title: Postnatal Day3, whole muscle Tibialis Anterior3

description: Library name: Sample1-3/4


title: 85, AD, CD154

description: Library name: 200901701

tag: sample group

value: AD


title: Nur77_2_1h

city: Amsterdam

first: Claudia

last: van Tiel

address: Meibergdreef 15

department: Medical Biochemistry

country: Netherlands

institute: Amsterdam UMC

data_processing:
Bases were called using Illumina CASAVA 1.8.2
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Skewer 0.2.2
Reads were aligned to the mouse genome mm10 by HISAT2 2.1.0
BAM files were indexed and filitered on MAPQ > 15 with SAM Tools 1.16.1
Raw tag counts per gene were counted using HOMER2's analyzeRepeats.pl script
Assembly: mm10
Supplementary files format and content: tab-delimited text file with raw read counts for each sample

growth_protocol: The RAW264.7 macrophage stable cell lines with doxycyclin-inducible expression of Nur77 or GFP were seeded at a density of 3x10^5 cells/ml and the next day Nur77 or GFP expression was induced by incubation with 50ng/ml doxycyclin for 18 h

extract_protocol:
Cells were lysed in RLT buffer and total RNA was isolated using the RNeasy mini kit with on-column DNase treatment (Qiagen)
RNA seq libraries were generated using the KAPA mRNA Hyperprep kit protocol

treatment_protocol: Cells were stimulated with 500 ng/ml LPS for 0, 1 and 5h

value: macrophages

value: 1h 500 ng/ml LPS


title: HCR voluntary-running aged soleus RNA-seq He4

description:
Library name: UPL26-002516
Aged female rat soleus muscle; group=HCR + Exercise; original sample name=He 4; count matrix column=UPL26-002516.


title: MDS_AZA_092

tag: individual

value: Female


title: Postnatal Day3, whole muscle Tibialis Anterior2

description: Library name: Sample1-2/4

value: Skeletal muscle

value: Pax7 progeny

value: Pax7CreERT2; Rosa26HTB::GFP


title: HCR voluntary-running aged soleus RNA-seq He3

description:
Library name: UPL26-002515
Aged female rat soleus muscle; group=HCR + Exercise; original sample name=He 3; count matrix column=UPL26-002515.


title: MDS_AZA_091

value: MDS patient

value: Male


title: Postnatal day 1 bio replicate 2 (Male)

description:
Library name: p1_M
10x Genomics

value: main olfactory epithelium

value: postnatal  day 1

value: multipotent progenitors and their progeny

value: wild-type


title: LCR voluntary-running aged soleus RNA-seq He5

description:
Library name: UPL26-002512
Aged female rat soleus muscle; group=HCR + Exercise; original sample name=He 5; count matrix column=UPL26-002512.

value: soleus muscle

value: selectively bred HCR rat

value: voluntary wheel running


title: 84, AD, CD137

description: Library name: 200901691


title: LCR voluntary-running aged soleus RNA-seq Le2

description:
Library name: UPL26-002509
Aged female rat soleus muscle; group=LCR + Exercise; original sample name=Le 2; count matrix column=UPL26-002509.

value: selectively bred LCR rat


title: 83, CON, CD154

description: Library name: 200901681

value: CON


title: HCR sedentary aged soleus RNA-seq H6

description:
Library name: UPL26-002505
Aged female rat soleus muscle; group=HCR; original sample name=H 6; count matrix column=UPL26-002505.

value: sedentary


title: 81, AD, CD154

description: Library name: 200901661

value: AD


title: MDS_AZA_085

value: Bone marrow

value: Responder


title: 1_HKM7VBGXT.1.CGATCAGT_TATGCAGT

description:
Library name: 1_SM-NBW8B_plate1
DHMT_48hr_LDLR_A_b

value: iPSC-derived excitatory neuron, astrocyte

value: LDLR knockdown


title: HCR sedentary aged soleus RNA-seq H5

description:
Library name: UPL26-002504
Aged female rat soleus muscle; group=HCR; original sample name=H 5; count matrix column=UPL26-002504.


title: HCR sedentary aged soleus RNA-seq H8

description:
Library name: UPL26-002507
Aged female rat soleus muscle; group=HCR; original sample name=H 8; count matrix column=UPL26-002507.


title: HCR sedentary aged soleus RNA-seq H7

description:
Library name: UPL26-002506
Aged female rat soleus muscle; group=HCR; original sample name=H 7; count matrix column=UPL26-002506.


title: 82, CON, CD137

description: Library name: 200901671


title: MDS_AZA_087

value: MDS patient


title: LCR voluntary-running aged soleus RNA-seq Le4

description:
Library name: UPL26-002511
Aged female rat soleus muscle; group=LCR + Exercise; original sample name=Le 4; count matrix column=UPL26-002511.


title: LCR voluntary-running aged soleus RNA-seq Le1

description:
Library name: UPL26-002508
Aged female rat soleus muscle; group=LCR + Exercise; original sample name=Le 1; count matrix column=UPL26-002508.


title: LCR voluntary-running aged soleus RNA-seq Le3

description:
Library name: UPL26-002510
Aged female rat soleus muscle; group=LCR + Exercise; original sample name=Le 3; count matrix column=UPL26-002510.


title: HCR sedentary aged soleus RNA-seq H4

description:
Library name: UPL26-002503
Aged female rat soleus muscle; group=HCR; original sample name=H 4; count matrix column=UPL26-002503.


title: 80, AD, CD137

description: Library name: 200901651


title: HCR sedentary aged soleus RNA-seq H3

description:
Library name: UPL26-002502
Aged female rat soleus muscle; group=HCR; original sample name=H 3; count matrix column=UPL26-002502.


title: HCR sedentary aged soleus RNA-seq H2

description:
Library name: UPL26-002501
Aged female rat soleus muscle; group=HCR; original sample name=H 2; count matrix column=UPL26-002501.


title: MDS_AZA_084

value: Male

value: NonResp


title: 78, ALL, CD137

description: Library name: 200901631

value: ALL


title: LCR sedentary aged soleus RNA-seq L7

description:
Library name: UPL26-002498
Aged female rat soleus muscle; group=LCR; original sample name=L7; count matrix column=UPL26-002498.


title: MDS_AZA_083

value: Female


title: MDS_AZA_074


title: LCR sedentary aged soleus RNA-seq L6

description:
Library name: UPL26-002497
Aged female rat soleus muscle; group=LCR; original sample name=L6; count matrix column=UPL26-002497.


title: 95, AD, CD137

description: Library name: 200901811


title: 77, CON, CD154

description: Library name: 200901621


title: LCR sedentary aged soleus RNA-seq L4

description:
Library name: UPL26-002495
Aged female rat soleus muscle; group=LCR; original sample name=L4; count matrix column=UPL26-002495.


title: Postnatal Day22-1, Pax7 Progeny cells2

description: Library name: Smaple4-2/4

value: Skeletal muscle

value: Pax7 progeny

value: Pax7CreERT2; Rosa26HTB::GFP

value: Two administrations of tamoxifen were performed starting two days prior to sampling.


title: LCR sedentary aged soleus RNA-seq L5

description:
Library name: UPL26-002496
Aged female rat soleus muscle; group=LCR; original sample name=L5; count matrix column=UPL26-002496.

value: soleus muscle

value: selectively bred LCR rat


title: 79, ALL, CD154

description: Library name: 200901641


title: HCR sedentary aged soleus RNA-seq H1

description:
Library name: UPL26-002500
Aged female rat soleus muscle; group=HCR; original sample name=H 1; count matrix column=UPL26-002500.

value: selectively bred HCR rat

value: sedentary


title: MDS_AZA_081

value: Bone marrow


title: LCR sedentary aged soleus RNA-seq L8

description:
Library name: UPL26-002499
Aged female rat soleus muscle; group=LCR; original sample name=L8; count matrix column=UPL26-002499.


title: 76, CON, CD137

description: Library name: 200901611

value: CON


title: LCR sedentary aged soleus RNA-seq L2

description:
Library name: UPL26-002493
Aged female rat soleus muscle; group=LCR; original sample name=L2; count matrix column=UPL26-002493.


title: 73, ALL, CD154

description: Library name: 200901581


title: LCR sedentary aged soleus RNA-seq L1

description:
Library name: UPL26-002492
Aged female rat soleus muscle; group=LCR; original sample name=L1; count matrix column=UPL26-002492.


title: MDS_AZA_078

value: Responder


title: 75, ALL, CD154

description: Library name: 200901601


title: NC_3

first: Yaodi

last: Shao

address: 2699 West Gaoke Road

institute: Shanghai First Maternity and Infant Hospital

description: Library name: NC_3

data_processing:
Raw sequencing fastq files stored in Rawdata folder were quality-controlled using FastQC, and low-quality reads/adapters were trimmed by Trim Galore. BigWig coverage signal files normalized by RPM were generated from BAM files and deposited in Bigwig folder for genome browser visualization.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Raw data: gzipped FASTQ paired-end files, deposited under Rawdata directory, containing original sequencing reads for NC and shCHI3L1 replicate samples. Processed data: normalized BigWig files in Bigwig directory, presenting genome-wide read density signal for each sample.

extract_protocol:
Total RNA was extracted from NC (negative control shRNA) and shCHI3L1 knockdown SKOV-3 human ovarian cancer cell lines using TRIzol reagent (Invitrogen) following the manufacturer’s instructions. RNA integrity was assessed using Agilent 2100 Bioanalyzer (RIN value ≥7.0 for all samples), and RNA concentration was quantified by Qubit fluorometer. Genomic DNA contamination was removed by DNase I digestion before subsequent library construction.
mRNA was enriched from qualified total RNA using oligo (dT) magnetic beads. Fragmentation buffer was added to interrupt mRNA into short fragments. First-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. After end repair, A-tailing and adapter ligation, fragments with suitable size were purified, PCR amplified to construct the final cDNA library. Paired-end sequencing was performed on Illumina sequencing platform.

value: human ovarian cancer cells


title: 74, ALL, CD137

description: Library name: 200901591


title: shCHI3L1_2

description: Library name: shCHI3L1_2


title: shCHI3L1_3

description: Library name: shCHI3L1_3


title: MDS_AZA_080

value: MDS patient


title: MDS_AZA_079

value: Male


title: shCHI3L1_1

description: Library name: shCHI3L1_1


title: NC_2

description: Library name: NC_2


title: 72, ALL, CD137

description: Library name: 200901571


title: MDA-MB-231 siBYSL biological replicate 3

city: DaLian

first: Luo

last: Kai

state: Liaoning Province

address: No. 467, Zhongshan Road, Shahekou District, Dalian 116011, China

institute: The Second Hospital of Dalian Medical University

description:
Library name: MDA_MB_231_siBYSL_3
MDA-MB-231 cells transfected with SI-BYSL-Homo-838; biological replicate 3.

data_processing:
Adapters, random bases introduced for library balancing, and low-quality sequence were removed from raw reads to generate clean reads.
Clean paired-end reads were aligned to the Homo sapiens GRCh38.p13 reference genome with HISAT2 using Gencode release 38 comprehensive gene annotation.
Gene-level unnormalized read counts and FPKM expression values were generated for annotated genes. The submitted processed matrix contains complete gene-level raw read counts for all six libraries.
Differential expression analysis between siBYSL and siNC groups was performed using DESeq2.
Assembly: GRCh38.p13; Gencode release 38
Supplementary files format and content: Tab-delimited matrix containing gene-level unnormalized raw read counts for all six RNA-seq libraries.
Supplementary files format and content: Rows are identified by Gencode v38 gene accessions and include gene symbol, chromosome, gene type, and description. Sample column headers exactly match the corresponding sample library names.

growth_protocol: MDA-MB-231 human breast cancer cells (Procell, CL-0150A; STR authenticated) were maintained in high-glucose DMEM (Procell, PM150210) supplemented with 10% fetal bovine serum, 100 U/mL penicillin, and 100 micrograms/mL streptomycin at 37 degrees C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIZOL (Ambion, 15596-018), further purified by phenol-chloroform extraction, and treated with RQ1 DNase (Promega, M6101) to remove DNA. RNA purity and quantity were assessed spectrophotometrically, and integrity was verified by 1% agarose gel electrophoresis.
For each sample, 1 microgram total RNA was treated with RQ1 DNase. Poly(A)+ mRNA was captured using VAHTS mRNA Capture Beads (Vazyme, N401). Directional libraries were prepared using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme, NR605) and VAHTS RNA Multiplex Oligos Set 1 for Illumina (Vazyme, N323). The dUTP-marked second cDNA strand was not amplified, enabling strand-specific sequencing. Libraries were sequenced as 150-nt paired-end reads on an Illumina NovaSeq X Plus system.

treatment_protocol: Cells were seeded at 1.8 x 10^5 cells per well in 12-well plates. Negative-control siRNA or SI-BYSL-Homo-838 (sense 5'-GAGAUGACGUUGCUGAAUATT-3'; antisense 5'-UAUUCAGCAACGUCAUCUCTT-3') was transfected at 160 pmol per well using 4 microliters Lipofectamine RNAiMAX Transfection Reagent (Invitrogen, 13778030). Medium was replaced 6 h after transfection and cells were harvested 48 h after transfection.

value: siRNA-mediated BYSL knockdown using SI-BYSL-Homo-838


title: 71, ENP, CD154

description: Library name: 200901561

value: ENP


title: Nur77_4_0h

value: macrophages

value: untreated


title: MDA-MB-231 siNC biological replicate 3

description:
Library name: MDA_MB_231_siNC_3
MDA-MB-231 cells transfected with negative-control siRNA; biological replicate 3.

value: Negative-control siRNA


title: 70, ENP, CD137

description: Library name: 200901551


title: MDS_AZA_076


title: MDS_AZA_075


title: 69, ALL, CD154

description: Library name: 200901541

value: ALL


title: MDS_AZA_073

value: Female

value: NonResp


title: 68, ALL, CD137

description: Library name: 200901531