title: CA80758F-02

type: RNA

city: Portland

first: Julie

middle: A

last: Saugstad

state: Oregon

address: 3181 SW Sam Jackson Park Road

department: Anesthesiology & Perioperative Medicine

institute: Oregon Health & Science University

scan_protocol: Each card was assayed on a QuantStudio 7K Flex (TFS) by automatic loading of the cards using an Orbitor R2 robot to increase throughput.

data_processing:
For each RT-qPCR well, we examined a variety of quality control (QC) metrics exported by ExpressionSuite software. Cq values for miRNA amplifications were included in statistical analysis if they had an AmpScore ≥1.0 with CqConf ≥0.8. MiRNA amplifications (e.g., let-7b-5p) that showed performance slightly below those thresholds (either AmpScore ≥0.9 with CqConf ≥0.8, or CqConf ≥0.75 with AmpScore ≥1.0) had Cq values accepted for statistical analysis conditional on meeting other criteria for good amplification (strong consistency of Cq values across triplicate wells). For accepted amplifications we examined the appropriateness of the baseline separation from the recorded Cq value and compared our QC assessments with other quality flags exported by QuantStudio, finding nothing unusual. Amplifications with acceptable QC but Cq >35 were considered censored values and given special handling using censoring-aware methods in the analysis. Amplifications that did not meet the QC standards for accepted or censored amplifications were considered missing measurements, regardless of Cq value. Amplifications labeled "Undetermined" by QuantStudio were also considered missing measurements. As a final fidelity check we 1) examined the amplifications for the two negative control miRNAs (miR-1293 and miR-647) to verify that no sample had a Cq value recorded for either of those with acceptable QC, and 2) verified that the spike-in positive control (cel-miR-39-3p) and primary endogenous normalization control (miR-16-5p) were both completely observed with acceptable QC in all replicates for all samples. The other endogenous normalizer control miRNAs (miR-24-3p, miR-92a-3p, miR-204-5p) showed good performance, with expression of miR-24-3p and miR-92a-3p in 100% of samples and miR-204-5p in 77% of samples. Given our built-in redundancy of normalizer control miRNAs and model-based methods of normalization that can handle noninformative missing data, we considered this amount of normalizer measurement dropout acceptable.
For technical calibration, all raw Cq values were adjusted for RNA isolation differences via median-alignment of the cel‑miR‑39‑3p spike‑in control reactions as an exogenous calibration factor. This adjustment represented the largest contribution to the overall normalization, with 57% of the technical variance explained by differences in spike-in control values (Note that we define technical variance as the variance in average Cq values across samples.) After technical calibration, all Cq values for the cel‑miR‑39‑3p spike-in (being exactly aligned by median) were removed from the dataset and did not contribute to later normalization steps. Next, these technical calibrated Cq values were batch calibrated to remove residual artifacts attributed to processing order. We fit a linear mixed-effects regression model including the same 5-knot restricted cubic spline of the RT-qPCR run order as above, plus indicators for known abnormal sample or processing events (e.g., visible hemolysis), with PCR run batches entered as random intercepts. Fitted values from this regression were subtracted from the corresponding Cq values for all miRNAs as the adjustment for batch and order-related effects. Batch calibration adjustments were relatively minor for our dataset, accounting for 10% of the technical variance.
Calibrated Cq values were normalized using a mixed-effects model on the endogenous miRNA normalizer Cq values only. The model included quadratic effects of age (interaction effect of age with itself, to model the effect of age at differing ages rather than assuming the effect is linear for all ages), fully-interacted indicators for sex and diagnosis group to adjust out study factors (because we wish to retain these factors for analysis), and crossed random effects of miRNA and sample to model the miRNA-sample interaction. We used this model to estimate the residual differences between samples as BLUPs (best linear unbiased predictions). The BLUP values were subtracted from the fully calibrated Cq values as endogenous normalizer level effects across samples. The resulting normalized Cq values were recentered to the global median of the input Cq value distribution. This final normalization step accounted for 26% of the technical variance in the data. The remaining 7% of technical variance was unexplained. After normalization, 83% of the total Cq variance (expected between-miRNA variance plus signal and residual technical and noise variance) was attributable to differences in mean expression across miRNAs (expected variance), 9% was attributable to sample-miRNA interactions (the biological signal), and <1% to differences in mean expression across samples (the residual technical variance, meaning the normalization was highly successful); the remainder of ~7% is residual variance (the measurement noise). We verified that the normalized Cq values of the normalizer miRNAs themselves had essentially flat profiles and noted that the normalization achieved substantial variance reduction.
Censored Cq values are quantitatively unreliable because their measurement falls outside the linear range of the assay. These were treated as interval observations, defined as an unobserved value falling between an upper and a lower limit. For the purposes of regression on the Cq values as an outcome predicted by diagnosis status these can be handled as interval observations directly via modeling. However, when the Cq values are used as predictors of diagnosis status the interval observation must be collapsed to a single most-likely value falling within the interval. To accomplish this, we used a Bayesian multilevel interval regression model that considers all replicate wells for the sample jointly and naturally accounts for the different character of censored values in the context of non-censored values for the same miRNA. For the Bayesian prior distribution on the mean level for the miRNA, we used a Student's t distribution with 4 degrees of freedom and a (wide and uninformative) scale of 10, and for the log of the root mean square error we used a (similarly uninformative) half-Cauchy distribution with the same scale of 10. Random effects for individual samples were assigned a zero-centered prior normal distribution with default conjugate inverse-gamma hyperprior (shape and scale parameters both 1/100) for the random-effect variance. The imputed value for a censored observation was taken as the posterior grand mean for the miRNA plus the posterior mean of the random effect, based on 10000 Markov chain Monte Carlo draws from the posterior distribution, following a burn-in run of 2500 draws. Note that the rank correlation between the predictions from this model and the naïve means of the corresponding replicate wells was 0.98, reflecting almost complete preservation of rank ordering among samples, but the model prediction is less biased because it accounts for censoring, which prevents it from overestimating the expression level. (The mean overestimate was 0.95 Cq.)
Prior to imputation the normalized Cq values, both censored and uncensored, are converted to an expression scale using inverted Cq units so that positive values mark higher expression. Non-censored Cq values with acceptable QC were used as exact measurements (both bounds of the interval are the same normalized Cq value). Censored Cq values with acceptable QC were treated as falling between the censoring threshold of 35 (lower bound) and the average (upper bound) of the normalized Cq value and the maximum normalized Cq value across all observations on all miRNAs (the "observed maximum", a value that will be strictly less than the maximum cycle number of 40, specified as a machine setting). Missing Cq values were treated as falling between the observed maximum (lower bound) and the maximum cycle number (upper bound of 40). Non-missing Cq values with unacceptable QC were treated as missing measurements for most purposes, but in this context the recorded Cq (with all normalization adjustments) was used as the lower bound and the maximum cycle number (40) as the upper bound. Finally, all the interval bounds were subtracted from the maximum cycle number of 40 to invert the scale.

label: FAM

source_name: total cell-free biofluid RNA

label_protocol: MiRNA was converted to cDNA as previously described using the TaqMan Advanced miRNA cDNA Synthesis kit (TFS). Briefly, 3 μL of total RNA was 3’ poly-adenylated, followed by a 5’ adaptor ligation step and reverse transcription. The resulting cDNA (5 μL) was added to a 14-cycle universal miR-amplification step. The miR-amplification reaction was diluted 1:10 with nuclease free water, 220 µL of the diluted cDNA was mixed with 220 µL of nuclease free water and 440 µL of TaqMan Fast Advanced master mix (TFS). The RT-qPCR mix (100 µL) was loaded into custom TaqMan Advanced Human miRNA Custom Cards.

extract_protocol: Total RNA was isolated from 100 μL of plasma using the MagMax Mirvana Total RNA Isolation Kit (Thermo Fisher Scientific, TFS) using a KingFisher Apex System (TFS) automated purification instrument following the manufacturer’s protocol. For the RNA isolation, the 289 plasma samples were processed in a total of 4 batches (3 plates x 80 samples = 240, 1 plate x 49 samples). On the first day, plasma samples were mixed with 5 µL of proteinase K and 45 µL of digestion buffer and incubated for 30 minutes at 65°C. 100 µL of lysis buffer containing 1% β-mercaptoethanol was added to each well, mixed and stored at -20°C overnight. The following day, the plate was thawed to room temperature and an exogenous cel-miR-39-3p spike-in control (TFS) was added at a final concentration of 3 pM, followed by the addition of 20 µL of magnetic isolation beads. Samples were mixed for 5 minutes using a plate shaker followed by the addition of 270 µL of isopropanol and brief mix. The sample plate as well as 4 wash plates (each containing 150 µL of wash buffer), a DNase plate containing 45 µL of Turbo DNase buffer and 2 µL of DNase, and an elution plate containing 50 µL of nuclease free water were all processed using the KingFisher Apex instrument. Following the DNase step, 50 µL re-binding buffer and 100 µL of isopropanol was added to each well and automation was resumed for the washing and elution steps. All isolations were completed within two consecutive days. Following the elution step, the miRNA concentration of a subset of samples from each batch (minimum of 30% of samples per batch across each plate) was measured using the Qubit miRNA Assay kit (TFS) and read using a Qubit 4.0 fluorometer (TFS) to ensure the isolation was consistent across the batch. Prior to the eluted RNA being frozen at -80°C until RT-qPCR, each plate of 80 RNA samples was divided into 2 plates of 40 RNA samples, as 40 is the maximum number of miRNA RT-qPCR assays that can be processed in a day, and the plate with 49 RNA samples was divided into 1 plate of 40 samples and 1 plate of 9 samples. Thus, the RT-qPCR was performed with the 289 eluted RNA samples in a total of 8 batches (7 x 40 RNA = 280, 1 x 9 RNA), with one batch being completed per day in unbroken succession to mitigate time drift in measurements.

tag: donor id

value: Plasma

tag: disease

value: NC

value: Male

tag: mmse

tag: anatomical location

value: Circulating blood

tag: sample collection method

value: Venous

tag: starting amount

tag: holding temperature


title: WGDL_F14_2N_FH_C73

status: Public on Jul 09 2026

type: SRA

city: Nanjing

first: Xuan

last: Li

address: No. 666, Binjiang Avenue, Jiangbei New Area

country: China

institute: Nanjing Agricultural University

description:
Library name: C73
WGDL_F14_2N_FH_C73

library_source: transcriptomic

data_processing:
Alignment was performed with STAR (v2.7.11a) against the reference genome using a pre-built STAR genome index. STAR was run with “--outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts” to generate sorted alignment files and gene-level count profiles. Gene-level expression quantification was carried out using RSEM (v1.3.1) with STAR-generated transcriptome BAM files as input (--paired-end --no-bam-output --alignments).
Assembly: Nasonia vitripennis reference genome (RefSeq No. GCF_009193385.2, NCBI GenBank)
Supplementary files format and content: Tab-delimited text file includes raw counts and tpm value for each sample

molecule: polyA RNA

organism: Nasonia vitripennis

source_name: Head

extract_protocol:
RNA extraction was performed using Quick-RNATM Tissue/Insect Microprep (Catalogue No. R2030 Zymo Research, Germany) (without DNase treatment). For sequencing, RNA was resuspended in 10 µL DNase/RNase-free water and the RNA concentration and purity was measured using a fluorometer (Qubit 2.0, Life Technologies); poor quality samples judged by A260/A280 and A260/A230 ratios were discarded. The extracted RNA was sent to Novogene (UK) Company Limited for sequencing. Novogene Hongkong prepared the sample library.
Unique index codes were added to each sample using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, USA). mRNA was purified from total RNA using poly-T magnetic beads, and libraries were prepared according to the manufacturer's instructions (Illumina).

tag: tissue

value: Head

tag: Sex

value: female

tag: age

value: 1 day after emergence

tag: genotype

tag: strain

value: WGDL


title: control siRNA 25nM 48 h_1

city: Urbana

first: Ruiying

last: Cheng

state: IL

address: B520 Chemical & Life Sciences Laboratory

department: School of Molecular & Cellular Biology

country: USA

institute: The University of Illinois Urbana-Champaign

description: Library name: siPOLR3GL_control_1

data_processing:
FASTQ files were generated and demultiplexed using Illumina bcl2fastq v2.20 conversion software. Reads were subsequently trimmed with TrimGalore, mapped to the hg38 transcriptome, and quantified using Salmon. Differentially expressed genes were identified using DESeq2.
Assembly: hg38
Supplementary files format and content: Supplementary files format and content: raw counts, and Transcribe per milion in CSV format

organism: Homo sapiens

growth_protocol: HEK293Tcells were obtained from ATCC (CRL-3216, Batch#70049877) and grown in 10 cm BioLite™   Cell Culture   Treated   Dishes   (Catalog# 12-556-002 Thermo   Scientific)   in Dulbecco’s Modified Eagle Medium, high glucose (Catalog# 11965092, Gibco). HEK293T experiments were conducted on cells between passage 10-25. THP-1 monocytes were obtained from ATCC (TIB-202 Batch# 62454382) and propagated in T-75 flasks between 0.2 and 1 × 10e6 cells/mL in an RPMI-1640 (Catalog# 11875093, Gibco, Billings, MT, USA) growth medium. THP-1 experiments were conducted on cells between passage 10 and 15.

extract_protocol:
E.Z.N.A.® Total RNA Kit I (Catalog# R6834-01, Omega), with 100% ethanol instead of 70% at the binding step to enrich small RNA.
Libraries were prepared with the Kapa Hyper Stranded mRNA library kit (Roche) and sequenced on two 10B lanes for 151 cycles from both ends of the fragments on a NovaSeq X Plus with V1.0 sequencing kits.

treatment_protocol: siRNA and ASO transfected using Lipofectamine® RNAiMax (cat # 13778150) with standard protocol, Overexpression sample are transfected using Lipofectamine 3000 (cat #L3000015)

tag: cell line

tag: cell type

value: Kidney

tag: treatment

value: control siRNA 25nM 48 h_1


title: A673_NChIP-H3K27ac_SW39_rep1

city: Dallas

first: Laura

last: Banaszynski

state: TX

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: UT Southwestern Medical Center

description: Library name: A673_NChIP-H3K27ac_SW39_rep1

library_source: genomic

data_processing:
The ChIP-seq reads were aligned to the hg38 human reference genome using the Bowtie2 aligner (Langmead and Salzberg, 2012) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 5-bp windows across the genome using deepTools for presentation as genome browser tracks  (Ramirez et al, 2016).
The seqeunce length was 50 for R1 and 50 for R2 for paired-end data from NextSeq 500. The sequence length was 150 for R1 and 150 for R2 for paired-end data from NovaSeq 6000.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

growth_protocol: Ewing sarcoma cell lines were cultured in RPMI (sigma R7256) + 5-10% FBS + 2mM L-glutamine with pen/strep antibiotics.

extract_protocol:
Native ChIP was performed as described (Martire et al. 2019). Briefly, A673 cells were harvested and treated with Mnase, resulting in a population consisting mainly of mono- to trinucleosomes. Chromatin was isolated and used for ChIP according to standard procedures. Cross-linked ChIP was performed as described (Martire et al. 2019). Briefly, A673 cells were cross-linked with 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures.
ChIP-seq libraries were constructed according to the NEBNext protocol.

treatment_protocol: For inhibitor studies, cells were treated for 24 hours with small molecule inhibitors of CDK8 at the described concentrations (100nM for SW393109), or vehicle DMSO at the same final concentration.   For Ewing’s sarcoma cell lines engineered with the auxin inducible degron in the EWSR1-FLI1 fusion, cells were treated with 5-Ph-IAA for 24 hours at a final concentration of 300nM.

value: Ewing sarcoma cell line

tag: chip antibody

value: H3K27ac (Active Motif #39133)


title: POLR3G_siRNA_200nM_48_h_3

description: Library name: siPOLR3G_si3G_3


title: WGDL_F14_2N_FH_C74

description:
Library name: C74
WGDL_F14_2N_FH_C74


title: POLR3G_siRNA_200nM_48_h_2

description: Library name: siPOLR3G_si3G_2


title: A673_NChIP-H3K27ac_DMSO_rep2

description: Library name: A673_NChIP-H3K27ac_DMSO_rep2

value: DMSO


title: WGDL_F2_2N_FA_C28

description:
Library name: C28
WGDL_F2_2N_FA_C28

source_name: Abdomen

value: Abdomen


title: control_siRNA_200nM_48_h_3

description: Library name: siPOLR3G_control_3


title: A673_NChIP-H3K27ac_DMSO_rep1

description: Library name: A673_NChIP-H3K27ac_DMSO_rep1


title: control_siRNA_200nM_48_h_2

description: Library name: siPOLR3G_control_2


title: control_siRNA_200nM_48_h_1

description: Library name: siPOLR3G_control_1


title: WGDL_F14_2N_FA_C76

description:
Library name: C76
WGDL_F14_2N_FA_C76


title: A673_CnR-FLI_SW39_rep2

description: Library name: A673_CnR-FLI_SW39_rep2

data_processing:
The CUT&RUN reads were aligned to the hg38 human reference genome using the Bowtie2 aligner (Langmead and Salzberg, 2012) .
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 5-bp windows across the genome using deepTools for presentation as genome browser tracks  (Ramirez et al, 2016).
The seqeunce length was 50 for R1 and 50 for R2 for paired-end data from NextSeq 500. The sequence length was 150 for R1 and 150 for R2 for paired-end data from NovaSeq 6000.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Run

extract_protocol:
Samples were prepared according to the Epicypher CUT&RUN protocol.
CUT&RUN libraries were constructed according to the NEBNext protocol.

tag: antibody

value: FLI (Santa Cruz sc-53826)


title: Scramble_ASO_200nM_ 48h_2

description: Library name: ASOPOLR3G_control_2

value: Scramble_ASO_200nM_ 48h_2


title: A673_CnR-FLI_DMSO_rep2

description: Library name: A673_CnR-FLI_DMSO_rep2


title: WES, patient 60

city: Boston

first: Sarah

middle: J.

last: Hill

state: MA

address: 450 Brookline Ave., Dana Building, Room 1410C

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Library name: Patient 60 DNA

data_processing:
WES data were processed through the nf-core sarek pipeline version 3.6.1 in WES mode using the Twist Exome 2.0 bed file from Twist Bioscience.
Read quality control and preprocessing was performed using FastQC version 0.12.1 (RRID: SCR_014583) and FastP version 0.24.0 (RRID:SCR_016962).
Sequences were aligned to GRCh38 using BWA-MEM version 0.7.18 (RRID: SCR_022192). Only WES samples with average coverage > 20X were assessed for variants.
Single nucleotide variants (SNVs) were called using Mutect2 from GATK version 4.6.1.0 and annotated using the Ensembl Variant Effect Predictor (VEP) version 115.2.
SnpSift version 5.4 was used to select somatic variants that were annotated to the RB1 or TP53 gene.
Assembly: GRCh38
Supplementary files format and content: Somatic variants annotated to the RB1 gene in VCF format.
Supplementary files format and content: Somatic variants annotated to the TP53 gene in VCF format.

source_name: Endometrial cancer

growth_protocol: There was no growth or treatment. Tissue was scraped from FFPE slides and used to prepare genomic DNA.

extract_protocol:
Methods are provided directly from the linked manuscript. For additional details, please see the linked manuscript.
For each patient, tumor was identified and circled on an H&E stained slide. Matched unstained slides for that patient were then held up to the circled H&E stained slide, and the tumor-containing region was circled on the unstained slide. Tissue within the circled area on the unstained slide or slides for each individual patient was scraped from the slide and collected into one mL of xylene (Fisher Cat. #447240010) in a microcentrifuge tube for each patient sample. Depending on the size of the tumor section, one to four slides were processed for each patient. The sample collected was vortexed vigorously for 10 seconds and spun at 13,500 rpm for two minutes in a tabletop microcentrifuge. The supernatant was removed, followed by the addition of one mL of ≥99.45% ethanol (Sigma-Aldrich Cat. #E7023-500mL). The tube was vortexed and spun again at 13,500 rpm for two minutes in a tabletop microcentrifuge, the supernatant was removed, and residual ethanol was evaporated completely by allowing the tube to stand open at room temperature. The resulting pellet was then processed for DNA extraction. DNA extraction was performed using the QIAamp DNA FFPE Tissue Kit (Qiagen, Cat. #56404) following the manufacturer's protocol, with RNase A digestion performed to remove RNA. DNA samples were stored at -20°C until all samples were ready for whole exome sequencing analysis, for which methods are described below.
Standard hybridization and capture and whole exome sequencing were performed by the Molecular Biology Core Facilities (MBCF) at Dana-Farber Cancer Institute, and the methodological details were provided by the MBCF as described below. Genomic DNA was fragmented  to 200bp on a Covaris R230 instrument according to the manufacturer’s protocol. Libraries were prepared using IDT xGEN 2S Plus DNA reagents on a Beckman Coulter Biomek i7 liquid handling platform from approximately 200ng of DNA according to the manufacturer’s protocol with 14 cycles of PCR amplification. Finished libraries were quantified by Qubit fluorometer and fragment size distribution was evaluated by Agilent TapeStation 4200. Libraries were pooled together for target enrichment using Twist Exome v2.0 reagents and hybrid capture was performed with a 16-hour hybridization incubation using Twist Exome v2.0 probes according to the manufacturer’s protocol. Post-capture library pool was quantified by Qubit fluorometer and Agilent TapeStation 4200. Library pool was further evaluated for quality and pool balance with shallow sequencing on an Illumina MiSeq. Subsequently, libraries were sequenced on an Illumina NovaSeqX+ with paired-end 150bp reads by the MBCF at Dana-Farber Cancer Institute.

value: Endometrial cancer


title: WGDL_F14_2N_FA_C78

description:
Library name: C78
WGDL_F14_2N_FA_C78


title: WES, patient 58

description: Library name: SH-58


title: Human TS cells (CT27), control shRNA treated, replicate 3

city: Kansas City

first: Esteban

middle: Mauricio

last: Dominguez

state: Kansas

address: 3901 Rainbow Blvd.

department: Pathology

institute: University of Kansas Medical Center

description: Library name: SCR_3

data_processing:
Raw data obtained from the sequencing facility was converted to fastq format using bcl2fastq (v2.20.0.422) and data quality was inspected using FastQC (v0.11.9)
Read mapping was performed by using the STAR’s (v2.7.10b) alignReads subcommand and was optimized for short reads with the options --outFilterScoreMinOverLread 0.3 and --outFilterMatchNminOverLread 0.3
featureCounts from the subread package to generate a combined count file
The raw count files were imported into R (v4.2.2) and analyzed to obtain differentially expressed genes by using DESeq2 (v1.38.3)
rawCounts_EXPNAME.tsv.gz
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files include raw counts values for each Sample (each column represent the condition and each row represents the gene)

molecule: total RNA

source_name: human trophoblast stem cells- CT27 (Okae et.al)

growth_protocol: Human Triophoblast Stem cells  were grown and differentiated in the dish for 8 days into extravillous trophoblast cells

extract_protocol:
Total RNA was isolated using the Trizol reagent according to the manufacturer’s instructions (Thermo-Fisher)
Extracted RNA was used as template for cDNA isolation with the High Capacity cDNA Reverse Transcription kit (Applied Biosystems). cDNA libraries were prepared and sequenced using a NovaSeq 6000 by the KUMC Genomics Core

treatment_protocol: Human Triophoblast Stem cells  were treated with control shRNA or PPARG shRNA before differentiation into extravillous trophoblast cells

value: extravilloustrophoblast

value: Control shRNA


title: WES, patient 57

description: Library name: Patient 57 DNA


title: WES, patient 50

description: Library name: Patient 50 DNA


title: WGDL_F14_2N_FA_C79

description:
Library name: C79
WGDL_F14_2N_FA_C79


title: Human TS cells (CT27), control shRNA treated, replicate 2

description: Library name: SCR_2

value: human trophoblast stem cells- CT27 (Okae et.al)


title: WGDL_F15_1N_MH_C81

description:
Library name: C81
WGDL_F15_1N_MH_C81

value: male


title: Human TS cells (CT27), control shRNA  treated, replicate 1

description: Library name: SCR_1


title: WES, patient 42

description: Library name: SH-42


title: WES, patient 48

description: Library name: Patient 48 DNA


title: WES, patient 35

description: Library name: Patient 35 DNA


title: WES, patient 34

description: Library name: Patient 34 DNA


title: WGDL_F15_1N_MH_C82

description:
Library name: C82
WGDL_F15_1N_MH_C82

value: Head


title: Human TS cells (CT27), PPARG shRNA treated, replicate 3

description: Library name: PPARG_3

value: PPARG shRNA


title: WGDL_F15_1N_MH_C83

description:
Library name: C83
WGDL_F15_1N_MH_C83

value: 1 day after emergence


title: WES, patient 29

description: Library name: SH-29


title: WES, patient 25

description: Library name: Patient 25 DNA


title: WES, patient 30

description: Library name: SH-30


title: Human TS cells (CT27), PPARG shRNA treated, replicate 1

description: Library name: PPARG_1


title: WES, patient 15

description: Library name: SH-15


title: Human TS cells (CT27), Input, replicate 3

description: Library name: INPUT_3

data_processing:
The sequence quality of the raw FASTQ files was evaluated by fastqc (version 0.11.9). Quality control for the FASTQ files was performed by HTStream (version 1.3.3).
For each biological replicate, peaks were independently identified using  MACS3 (version 3.0.0b1) with fold enrichment >1.5 and q-value <0.01.
Bigwig files were created by deeptools (version 3.5.1) to visualize peaks in the UCSC genome browser (https://genome.ucsc.edu/s/kchen7/hg38_p14_Pparg_ChIPseq).
Genomic features of the peak regions and motif analysis were performed using HOMER (version 5.1) scripts annotatePeaks.pl and findMotifsGenome.pl
Assembly: GRCh38.p14
Supplementary files format and content: Bigwig files

growth_protocol: Human Triophoblast Stem cells  were grown and differentiated in the dish for 8 days into extravillous trophoblast cells media

extract_protocol:
EVT cells were fixed with 1% Formaldehyde for 10 minutes at RT, following Simple ChIP Enzymatic Chromatin IP Kit (9003, Cell Signaling Technology) protocol.
ChIP-seq library was constructed using the Tecan Ovation Ultralow DNA System V2 (NuGEN Technologies, Redwood City, CA)


title: WES, patient 10

description: Library name: Patient 10 DNA


title: WGDL_F15_1N_MA_C87

description:
Library name: C87
WGDL_F15_1N_MA_C87

value: WGDL


title: WES, patient 7

description: Library name: Patient 7 DNA


title: Human TS cells (CT27), Input, replicate 2

description: Library name: INPUT_2


title: WES, patient 6

description: Library name: Patient 6 DNA


title: WGDL_F2_2N_FA_C29

description:
Library name: C29
WGDL_F2_2N_FA_C29

value: female


title: RNAseq, Patient 60

description: Library name: Patient 60

data_processing:
Exome-capture RNA sequencing data were processed through the nf-core rnaseq pipeline version 3.14.0.
Quality control of raw reads was performed using FastQC version 0.12.1 (RRID: SCR_014583) and adapter and quality trimming was performed using cutadapt version 3.4 (RRID: SCR_011841) and Trim Galore version 0.6.7 (RRID: SCR_011847).
Trimmed reads were aligned to human genome (GRCh38.p14) using STAR version 2.7.9a (RRID:SCR_004463) and quantified using Salmon version 1.10.1 (RRID:SCR_017036).
Alignments were checked for evenness of coverage, rRNA content, genomic content of alignments, complexity, and other quality checks using a combination of FastQC (RRID:SCR_014583), Qualimap version 2.3 (RRID:SCR_001209), Samtools version 1.17 (RRID:SCR_002105), MultiQC version 1.19 (RRID:SCR_014982), and bcbioR version 0.4.5.
Lowly expressed genes (total counts ≤10 or expressed in <80% of samples) were filtered out.
Assembly: GRCh38.p14
Supplementary files format and content: Raw counts for non-lowly-expressed genes in CSV format.

growth_protocol: There was no growth or treatment. Tissue was scraped from FFPE slides and used to prepare RNA

extract_protocol:
Methods are provided directly from the linked manuscript. For additional details, please see the linked manuscript.
For each patient, tumor was identified and circled on an H&E stained slide. Matched unstained slides for that patient were then held up to the circled H&E stained slide, and the tumor-containing region was circled on the unstained slide. Tissue within the circled area on the unstained slide or slides for each individual patient was scraped from the slide and collected into one mL of xylene (Fisher Cat. #447240010) in a microcentrifuge tube for each patient sample. Depending on the size of the tumor section, one to four slides were processed for each patient. The sample collected was vortexed vigorously for 10 seconds and spun at 13,500 rpm for two minutes in a tabletop microcentrifuge. The supernatant was removed, followed by the addition of one mL of ≥99.45% ethanol (Sigma-Aldrich Cat. #E7023-500mL). The tube was vortexed and spun again at 13,500 rpm for two minutes in a tabletop microcentrifuge, the supernatant was removed, and residual ethanol was evaporated completely by allowing the tube to stand open at room temperature. The resulting pellet was then processed for RNA extraction. Total RNA extraction was performed using the RNeasy FFPE Kit (Qiagen, Cat. #73504) following the manufacturer’s protocol, with DNase I digestion performed to remove genomic DNA. RNA samples were snap frozen and stored at -80°C until all samples were ready for sequencing as described below.
The exome-capture RNA sequencing was performed by the Molecular Biology Core Facilities (MBCF) at Dana-Farber Cancer Institute, and the methodological details were provided by the MBCF as described below. Purified total RNA was evaluated for quality and quantity using the Agilent Fragment Analyzer RNA assay. Samples were prepared from 200ng of RNA using Roche Kapa RNA Hyper reagents without any prior enrichment or depletion according to the manufacturer’s protocol on a Beckman Coulter Biomek i7. Following library preparation, samples were characterized by Qubit fluorometer and Agilent TapeStation 4200. Libraries were pooled in 10 or 11 plex reactions based on available material. Pools were then hybridized to Twist Exome 2.0 probes for target enrichment. Post capture library pools were quantified by Qubit fluorometer and Agilent TapeStation 4200. Pre-pooled, uniquely dual indexed libraries were shallowly sequenced on an Illumina MiSeq to further evaluate overall library quality and pool balance. Final library pools were sequenced on an Illumina NovaSeqX+ targeting 35 million reads per library with 150bp paired-end reads at the Dana-Farber Cancer Institute Molecular Biology Core Facilities.


title: RNAseq, Patient 59

description: Library name: Patient 59


title: WGDL_F15_1N_MA_C88

description:
Library name: C88
WGDL_F15_1N_MA_C88


title: Human TS cells (CT27), Input, replicate 1

description: Library name: INPUT_1


title: Human TS cells (CT27), IP PPARG, replicate 3

description: Library name: IP_PPARG_3

value: PPARG (2435S, Cell Signaling Technology)


title: RNAseq, Patient 58

description: Library name: Patient 58


title: RNAseq, Patient 57

description: Library name: Patient 57


title: WGDL_F15_1N_MA_C89

description:
Library name: C89
WGDL_F15_1N_MA_C89


title: RNAseq, Patient 56

description: Library name: Patient 56


title: Human TS cells (CT27), IP PPARG, replicate 2

description: Library name: IP_PPARG_2


title: RNAseq, Patient 55

description: Library name: Patient 55


title: WGDL_F15_2N_MH_C91

description:
Library name: C91
WGDL_F15_2N_MH_C91


title: RNAseq, Patient 49

description: Library name: Patient 49


title: WGDL_F15_2N_MH_C92

description:
Library name: C92
WGDL_F15_2N_MH_C92


title: hRPE-19 cells, AMnp3, day 7

city: Chongqing

first: BINGLIN

last: ZHU

address: 313 Jinyue Road

institute: Jinfeng Laboratory

description: Library name: SAMPLES 6

data_processing:
Sequencing was performed at the Jinfeng Laboratory Single-Cell Sequencing Center. Raw sequencing data were processed through a standardized bioinformatics pipeline. Clean reads were aligned to the human reference genome (hg38) using HISAT2, and gene-level counts were obtained with featureCounts.
Assembly: human reference genome (hg38)
Supplementary files format and content: txt files include FPKM values for each sample

source_name: hRPE-19 cells

growth_protocol: Human retinal pigment epithelial cells (hRPE-19) were maintained in DMEM/F12 supplemented with 10% fetal bovine serum, NEAA, L-glutamine and antibiotics in humidified atmosphere with 5% CO₂ at 37°C

extract_protocol:
Total RNA was extracted from control and AMnp-reprogrammed hRPE-19 cells using TRIzol Reagent, following the manufacturer’s protocol.
RNA libraries were prepared with the TruSeq Stranded RNA Library Prep Kit (Illumina) and sequenced using the NovaSeq 6000 SP Reagent Kit on the Illumina NovaSeq 6000 platform, generating 50 bp paired-end reads.

treatment_protocol: hRPE-19 cells were transduced with lentiviral AMnp reprogramming factors (ASCL1 + miR-9/9-124 + PTBP2/p53 shRNA) and cultured in neural induction medium under hypoxia (5% O₂) for 7 days, with untreated cells as controls.

value: hRPE-19 cells

value: human retinal pigment epithelial cells


title: RNAseq, Patient 48

description: Library name: Patient 48


title: WGDL_F15_2N_MH_C93

description:
Library name: C93
WGDL_F15_2N_MH_C93


title: RNAseq, Patient 47

description: Library name: Patient 47


title: hRPE-19 cells, AMnp2, day 7

description: Library name: SAMPLES 5


title: WGDL_F15_2N_MH_C94

description:
Library name: C94
WGDL_F15_2N_MH_C94


title: RNAseq, Patient 44

description: Library name: Patient 44


title: hRPE-19 cells, AMnp1, day 7

description: Library name: SAMPLES 4


title: WGDL_F15_2N_MA_C96

description:
Library name: C96
WGDL_F15_2N_MA_C96


title: RNAseq, Patient 43

description: Library name: Patient 43


title: hRPE-19 cells, Ctrl3, day 7

description: Library name: SAMPLES 3


title: RNAseq, Patient 41

description: Library name: Patient 41


title: WGDL_F15_2N_MA_C97

description:
Library name: C97
WGDL_F15_2N_MA_C97


title: RNAseq, Patient 38

description: Library name: Patient 38


title: LN-229 cells, SMSM74 316 nM, 24 h, biol rep 1

city: Chicago

first: Jingxin

last: Wang

address: Abbott Memorial Hall 210A, 947 E 58th St.

department: Section of Genetic Medicine

institute: University of Chicago

description:
Library name: Exp1_LN229_polyA_SMSM74_316_1
Column 'Exp1_LN229_polyA_SMSM74_316_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.

data_processing:
Reads were aligned to the human reference genome GRCh38 with STAR using two-pass mode per sample, using the Gencode v44 comprehensive gene annotation.
Gene-level read counts were generated with featureCounts (Subread) against Gencode v44 comprehensive gene models, in unstranded mode.
Intron-junction-level counts were generated with leafcutter (extract junctions from STAR-aligned BAMs; leafcutter_cluster.py to define junction clusters); the per-cluster numerator count matrix (`*_perind_numers.counts.gz`) is provided as a processed data file.
Assembly: GRCh38 (Gencode Release 44 comprehensive annotation)
Supplementary files format and content: Two file types are provided. (1) Gzipped tab-separated featureCounts gene-by-sample raw read-count tables (`Exp1_GeneCounts.tsv.gz`, `Exp2_GeneCounts.tsv.gz`): first 6 columns are Geneid/Chr/Start/End/Strand/Length followed by one column of integer counts per sample. (2) Gzipped space-separated leafcutter junction-cluster-by-sample numerator count tables (`Exp1_leafcutter_perind_numers.counts.gz`, `Exp2_leafcutter_perind_numers.counts.gz`): header row lists sample names; each data row has `chrom:start:end:cluster_id` followed by one integer per sample (junction-supporting reads).

growth_protocol: LN-229 glioblastoma cells were cultured in DMEM supplemented with 5% FBS, 1x ThermoFisher anti(biotic)-anti(mycotic), at 37 °C, 5% CO2. GM12878 lymphoblastoid cells were cultured in RPMI 1640 supplemented with 15% FBS, 1x ThermoFisher anti-anti, at 37 °C, 5% CO2.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy column-based purification kit following the manufacturer's protocol.
Strand-specific polyA-enriched RNA-seq libraries were prepared with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, following the manufacturer's protocol.

treatment_protocol: Cells were treated with the indicated splicing-modulator compound (or DMSO vehicle) at the specified dose for 24 hours prior to harvest.

value: glioblastoma

value: SMSM74 at 316 nM (24 h)

tag: batch


title: hRPE-19 cells, Ctrl2, day 7

description: Library name: SAMPLES 2


title: RNAseq, Patient 37

description: Library name: Patient 37


title: WGDL_F15_2N_MA_C98

description:
Library name: C98
WGDL_F15_2N_MA_C98

value: Abdomen


title: RNAseq, Patient 36

description: Library name: Patient 36


title: hRPE-19 cells, Ctrl1, day 7

description: Library name: SAMPLES 1


title: RNAseq, Patient 35

description: Library name: Patient 35


title: WGDL_F15_2N_MA_C99

description:
Library name: C99
WGDL_F15_2N_MA_C99


title: RNAseq, Patient 34

description: Library name: Patient 34


title: SF_AGI_2

city: Ann Arbor

first: Maria

middle: G

last: Castro

state: MI

address: 1150 East Medical Center Drive

department: Neurosurgery

institute: University of Michigan Medical School

library_source: transcriptomic single cell

data_processing:
fastq files were created using Illumina NovaSeq 6000 and Cellranger v7.0. Cellranger v7.0 was also used to create the matrices of features (UMI counts linked to a gene and barcode)
Assembly: hg38
Supplementary files format and content: Processed data is filtered and presented as a matrix for input into data analysis programs

source_name: glioma neurospheres

growth_protocol: Human SF10602 cells were grown in NeuroCult NS-A Basal Medium supplemented with 100units/mL antibiotic-antimycotic, 10mL B-27 without vitamin A, 5mL N-2, 100µg/ml Normocin, 20ng/mL FGF, 20ng/mL EGF, and 20ng/mL PDGF-AA.

extract_protocol:
SF10602 cells were collected and suspended in NeuroCult NS-A Basal Medium. Libraries were prepared according to the manufacturer's instructions (10X Genomics) using the Chromium Single Cell 3' Reagent Kits
10X Genomics Cellranger v7.0 was used to process the raw sequencing data. First, CellRanger mkfastq demultiplexed libraries that are based on sample indices, converted the barcodes and read data to fastq files. Then CellRanger count aligned the reads to hg38 reference genome, filtered and counted unique molecular indentifiers (UMIs). Finally, CellRanger took multiple run outputs of CellRanger count and normalized them to same sequencing depth and recalculated the matrices and analyses of the gene-barcodes on the combined data.

treatment_protocol: SF10602 cells were treated with mIDH1 inhibitor (AGI-5198) for 1 week.

value: glioma neurospheres

value: radioresistant patient-derived glioma cell culture

value: IDH1 mutant


title: RNAseq, Patient 33

description: Library name: Patient 33

value: Endometrial cancer


title: WGDL_F2_2N_FA_C30

description:
Library name: C30
WGDL_F2_2N_FA_C30


title: SF_AGI_1


title: RNAseq, Patient 31

description: Library name: Patient 31


title: RNAseq, Patient 42

description: Library name: Patient 42


title: WGDL_F2_3N_FH_C31

description:
Library name: C31
WGDL_F2_3N_FH_C31


title: LN-229 cells, CP3 316 nM, 24 h, biol rep 1

description:
Library name: Exp1_LN229_polyA_CP3_316_1
Column 'Exp1_LN229_polyA_CP3_316_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.


title: LN-229 cells, Risdiplam 31600 nM, 24 h, biol rep 1

description:
Library name: Exp1_LN229_polyA_Risdiplam_31600_1
Column 'Exp1_LN229_polyA_Risdiplam_31600_1' in Exp1_GeneCounts.tsv.gz and Exp1_leafcutter_perind_numers.counts.gz.

value: Risdiplam at 31600 nM (24 h)


title: RNAseq, Patient 30

description: Library name: Patient 30


title: SF_DMSO_2

value: untreated


title: WGDL_F2_3N_FH_C32

description:
Library name: C32
WGDL_F2_3N_FH_C32

value: Head


title: RNAseq, Patient 29

description: Library name: Patient 29


title: RNAseq, Patient 28

description: Library name: Patient 28


title: SF_DMSO_1


title: RNAseq, Patient 27

description: Library name: Patient 27


title: TRA_F3_1N_MH_A1A

description:
Library name: A1A
TRA_F3_1N_MH_A1A

value: male

value: TRA


title: RNAseq, Patient 25

description: Library name: Patient 25


title: PPWM3 cells, Input (ChIP)

city: Ann Abor

first: Carl

last: Koschmann

address: 100 Washtenaw Ave.

institute: University of Michigan

description: Library name: PPWM3_Input_ChIP

data_processing:
Reads were trimmed, aligned to mm10 using Bowtie2, and indexed. Duplicated reads were removed and peaks were called using MACS2.
Assembly: mm10
Supplementary files format and content: bigWig

organism: Mus musculus

source_name: cell line

extract_protocol:
10 million cells per cell line were fixed with 1% formaldehyde for 15 min, then quenched with 1X glycine and snap frozen for shipment to Active Motif.
Samples underwent library preparation at Active Motif using a standard dual indexing protocol, including adapter ligation, adapter ligated DNA purification, and library purification.

value: cell line

value: murine glioma cells


title: POLR3G_siRNA_200nM_48_h_1

description: Library name: siPOLR3G_si3G_1

value: Kidney


title: TRA_F3_1N_MH_A2A

description:
Library name: A2A
TRA_F3_1N_MH_A2A

value: 1 day after emergence


title: Scramble_ASO_200nM_ 48h_1

description: Library name: ASOPOLR3G_control_1

value: Scramble_ASO_200nM_ 48h_1


title: WGDL_F14_2N_FA_C77

description:
Library name: C77
WGDL_F14_2N_FA_C77

value: female

value: WGDL


title: RNAseq, Patient 23

description: Library name: Patient 23


title: PPGM1 cells, Input (ChIP)

description: Library name: PPGM1_Input_ChIP


title: RNAseq, Patient 22

description: Library name: Patient 22


title: RNAseq, Patient 15

description: Library name: Patient 15


title: TRA_F3_2N_MH_A11

description:
Library name: A11
TRA_F3_2N_MH_A11


title: GM12878 cells, DMSO vehicle, 24 h, biol rep 2

description:
Library name: Exp2_GM12878_polyA_DMSO_NA_2
Column 'Exp2_GM12878_polyA_DMSO_NA_2' in Exp2_GeneCounts.tsv.gz and Exp2_leafcutter_perind_numers.counts.gz.

value: B-lymphocyte (lymphoblastoid)

value: DMSO vehicle (24 h)


title: RNAseq, Patient 14

description: Library name: Patient 14


title: PPKM1 cells, Input (ChIP)

description: Library name: PPKM1_Input_ChIP


title: RNAseq, Patient 13

description: Library name: Patient 13


title: RNAseq, Patient 12

description: Library name: Patient 12


title: TRA_F3_2N_MH_A12

description:
Library name: A12
TRA_F3_2N_MH_A12


title: PPWM3 cells, H3K4me3 (ChIP)

description: Library name: PPWM3_H3K4me3_ChIP


title: RNAseq, Patient 10

description: Library name: Patient 10


title: WES, patient 32

description: Library name: SH-32


title: TRA_F3_2N_MH_A13

description:
Library name: A13
TRA_F3_2N_MH_A13


title: 2658297_JW_001

city: Memphis

first: Rashid

last: Mehmood

state: Tennessee

address: 324 NIGHT SAIL DR N APT 112, UNIT # 04-112

department: Hematology

institute: St Jude Children's Research Hospital

description: Library name: 2658297_JW_001

data_processing:
Single-cell RNA libraries, sequenced by 10x Genomics, were processed using CellRanger software (v7.0.0) with default parameters. The count function mapped the raw reads to the human reference genome GRCh38 and generated a gene expression count matrix. The filtered_feature_bc_matrix were used for downstream analysis in Seurat (V. 5.3.0) using R (V. 4.2.3). Seurat tutorial(https://satijalab.org/seurat/articles/seurat5_integration) was followed for downstream analysis, where batch effects were corrected using harmony integration method.
Assembly: hg38
Supplementary files format and content: filterd_featured_bc_matrix.h5

source_name: hCD34 cells

growth_protocol: CD34⁺ hematopoietic stem and progenitor cells (HSPCs) mobilized with G-CSF from healthy donors were expanded 7 days in StemSpan™ SFEM II with CD34⁺ Expansion Supplement, human LDL, and Penicillin-Streptomycin. Cells were then cultured with thrombopoietin (50 ng/mL, increased to 100 ng/mL after 3 days) to induce megakaryocyte differentiation. On day 14, cells were harvested.

extract_protocol:
Cells were processed for single cell RNA-seq via the 10X Genomics 3' v3.1 kit
Libraries were constructed via the 10X Genomics 3' v3.1 kit

treatment_protocol: For each experimental condition (DMSO vs. treatment; non-targeting vs. sgRNA), equal number of cells were allocated per group when thrombopoietin was added to the cells. The cells were cultured with thrombopoietin for 7 days and at the end of the 7 days, the cells were harvested.

value: hCD34 cells

value: Wild type

value: DMSO


title: PPGM1 cells, H3K4me3 (ChIP)

description: Library name: PPGM1_H3K4me3_ChIP


title: RNAseq, Patient 11

description: Library name: Patient 11

value: Endometrial cancer


title: RNAseq, Patient 7

description: Library name: Patient 7


title: Control, 0 h, RNA-seq, r1

city: Badalona

first: José

middle: Luis

last: Sardina

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukaemia Research Institute

description: Library name: CTRL_0h_r1

data_processing:
Reads were aligned using STAR, default mode for paired-end data
Aligned reads were quantified using featureCounts
Differential expression analysis was performed using the R package DESeq2
Assembly: GRCh38
Supplementary files format and content: Raw counts are provided as .txt file

source_name: B-ALL cell line

growth_protocol: BlaER cells and subclones were grown in suspension in RPMI 1640 supplemented with 10% heat-inactivated FBS, 1X Penicillin-Streptomycin, 1X L-glutamine and 0,1X β-mercaptoethanol.

extract_protocol:
Total RNA was extracted using Rneasy Mini Kit (Qiagen).
RNA-seq libraries were prepared by an external sequencing service provider. Briefly, mRNA enrichment was performed on total RNA using the RNase H to remove ribosomal RNA. The enriched mRNA was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double -stranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control. Sequencing was performed on DNBSEQ platform with PE100 (read length).

treatment_protocol: BlaER cells with shTET2 and shCTRL were first pre-treated with doxycycline (1 µg/ml) for 48 hours. Next, to induce transdifferentiation cells were supplemented with 100 nM of 17-beta estradiol (E2), human IL-3 (10 ng/ml), and human M-CSF (10 ng/ml) during 7 days. Doxycycline (1 µg/ml) was re-added every 48 hours during the process. Cells were collected at 0, 72 and 144 hours post induction.

value: B-ALL cell line

value: B-ALL cell line with shCTRL

value: B cell

value: Doxycycline (1 µg/ml)


title: WGDL_F15_1N_MH_C84

description:
Library name: C84
WGDL_F15_1N_MH_C84

value: Head

value: male


title: TRA_F3_2N_MH_A14

description:
Library name: A14
TRA_F3_2N_MH_A14

value: TRA


title: RNAseq, Patient 6

description: Library name: Patient 6


title: Human TS cells (CT27),PPARG shRNA treated, replicate 2

description: Library name: PPARG_2

value: human trophoblast stem cells- CT27 (Okae et.al)

value: extravilloustrophoblast

value: PPARG shRNA


title: PPKM1 cells, H3K4me3 (ChIP)

description: Library name: PPKM1_H3K4me3_ChIP

value: cell line

value: murine glioma cells


title: shNrf24_3

city: Nantong,Jiangsu,China

first: Xiaorong

last: Zhou

state: Jiangsu province

address: 19 Qixiu Road

institute: Nantong University

description:
Library name: Sample 12
Column name in gene_fpkm.xls:  shNrf24_3

data_processing:
Differential expression analysis was performed using the DESeq2 R package, and the genes with adjusted p values < 0.05 and log fold change (logFC) > 1 or < -1 were designated as differentially expressed genes (DEGs).
Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of DEGs were performed using the clusterProfiler package (version 4.8.3) in R.
Enriched GO terms and KEGG pathways were filtered with adjusted P-value < 0.05 and q-value < 0.5. Gene Set Enrichment Analysis (GSEA) was performed using the clusterProfiler package
Assembly: GRCh38
Supplementary files format and content: csv

growth_protocol: A549/DDP shNC and shNRF2 cells were cultured in Ham's F-12K (Kaighn's) medium supplemented with 10% fetal bovine serum, 5 mg/mL penicillin-streptomycin, and 1µg/ml DDP specific for them at 37 °C under 5% CO2.

extract_protocol:
Cells were collected after 24h DMSO or 4 µM GNA treatment, washed with PBS, and submitted for RNA isolation, quality check, and subsequent RNA sequencing by the Novogene (Beijing, China) on the Illumina platform.
Cells were collected after 24h DMSO or 4 µM GNA treatment, washed with PBS, and submitted for RNA isolation, quality check, and subsequent RNA sequencing by the Novogene (Beijing, China) on the Illumina platform.

treatment_protocol: A549/DDP shNC and shNRF2 cells were cultured to reach 70% confluence，then treated with DMSO or 4 µM GNA for 24 h. After that, cells were harvested for bulk RNA sequencing and scRNA-seq.

value: A549/DDP shNRF2


title: RNAseq, Patient 32

description: Library name: Patient 32


title: WES, patient 23

description: Library name: Patient 23 DNA


title: WGDL_F15_1N_MA_C86

description:
Library name: C86
WGDL_F15_1N_MA_C86

value: Abdomen

value: 1 day after emergence

value: WGDL


title: TRA_F3_2N_MH_A15A

description:
Library name: A15A
TRA_F3_2N_MH_A15A


title: shNrf24_2

description:
Library name: Sample 11
Column name in gene_fpkm.xls:  shNrf24_2


title: PPWM3 cells, H3K36me3 (ChIP)

description: Library name: PPWM3_H3K36me3_ChIP


title: shNrf24_1

description:
Library name: Sample 10
Column name in gene_fpkm.xls:  shNrf24_1


title: shNrf20_3

description:
Library name: Sample 9
Column name in gene_fpkm.xls:  shNrf20_3

value: DMSO


title: TRA_F3_2N_MA_A16

description:
Library name: A16
TRA_F3_2N_MA_A16


title: PPGM1 cells, H3K36me3 (ChIP)

description: Library name: PPGM1_H3K36me3_ChIP


title: TRA_F3_2N_MA_A18

description:
Library name: A18
TRA_F3_2N_MA_A18


title: shNrf20_1

description:
Library name: Sample 7
Column name in gene_fpkm.xls:  shNrf20_1


title: PPWM3 cells, H3K27me3 (ChIP)

description: Library name: PPWM3_H3K27me3_ChIP


title: NC4_3

description:
Library name: Sample 6
Column name in gene_fpkm.xls: NC4_3

value: A549/DDP shNC


title: TRA_F3_2N_MA_A20

description:
Library name: A20
TRA_F3_2N_MA_A20


title: shNrf20_2

description:
Library name: Sample 8
Column name in gene_fpkm.xls:  shNrf20_2


title: NC4_2

description:
Library name: Sample 5
Column name in gene_fpkm.xls: NC4_2


title: TRA_F2_2N_FH_A21

description:
Library name: A21
TRA_F2_2N_FH_A21

value: female


title: NC4_1

description:
Library name: Sample 4
Column name in gene_fpkm.xls: NC4_1


title: PPGM1 cells, H3K27me3 (ChIP)

description: Library name: PPGM1_H3K27me3_ChIP


title: NC0_3

description:
Library name: Sample 3
Column name in gene_fpkm.xls: NC0_3


title: PPKM1 cells, H3K27me3 (ChIP)

description: Library name: PPKM1_H3K27me3_ChIP


title: TRA_F2_2N_FH_A22

description:
Library name: A22
TRA_F2_2N_FH_A22


title: Control, 0 h, r2

description: Library name: CTRL_0h_r2

extract_protocol:
Total RNA was extracted using Rneasy Mini Kit (Qiagen).
RNA-seq libraries were prepared by an external sequencing service provider. Briefly, mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized double -stranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3' end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control. Sequencing was performed on DNBSEQ platform with PE150 (read length).

treatment_protocol: To induce transdifferentiation, the BlaER cells with shAGO2.1, shAGO2.2 and shCTRL were supplemented with 100 nM of 17-beta estradiol (E2), human IL-3 (10 ng/ml), and human M-CSF (10 ng/ml) during 7 days. Cells were collected at 0, 72 and 144 hours post induction.

value: B-ALL cell line

value: B-ALL cell line with shCTRL

value: B cell


title: NC0_1

description:
Library name: Sample 1
Column name in gene_fpkm.xls: NC0_1


title: PPWM3 cells, H3K27Ac (ChIP)

description: Library name: PPWM3_H3K27Ac_ChIP


title: TRA_F3_1N_MH_A3

description:
Library name: A3
TRA_F3_1N_MH_A3

value: Head

value: male


title: RNA-seq in HEK Blue hTLR7 cells: IRF7 RE Haplotype R848 Stimulated Replicate 2

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

description: Library name: RNA-seq_HEK-Blue-hTLR7_RE32_E005624

data_processing:
RNA-seq reads were mapped to the hg19 genome using the nf-core RNA-seq pipeline with the default alignment options (STAR and Salmon).
Transcription abundance estimates generated by Salmon
Assembly: hg19
Supplementary files format and content: Aligned reads in bigWig format. Reads were normalized using deepTools bamCoverage with the parameters --normalizeUsing CPM --binSize 10. The reads aligned to the forward strand were processed separately from the reads aligned to the reverse strand. The parameter --scaleFactor -1 was used when generating the reads on the reverse strand.

source_name: HEK Blue hTLR7

growth_protocol: THP-1 IRF7 deficient and HEK Blue hTLR7 cells were purchased from InvivoGen. THP-1 cells were grown in RPMI 1640 medium supplemented with 10% FBS, 10,000 units/mL of penicillin, 10,000 ug/mL of streptomycin, and Normocin. Following transduction, THP-1 cell lines stably expressing IRF7 variants were also cultured in 1 ug/mL puromycin. HEK Blue hTLR7 cells were grown in DMEM medium supplemented with 10% FBS, 10,000 units/mL of penicillin, and 10,000 ug/mL of streptomycin. All cells were kept at 37°C and 5% CO2 and were determined to be mycoplasma free.

extract_protocol:
Total RNA was isolated using the mirVana RNA extraction kit
rRNA depleted, stranded libraries were generated by and sequenced at the Cincinnati Children’s Hospital Medical Center Genomics Sequencing Facility (CCHMC)

treatment_protocol: THP-1 cells were stimulated using 2.5ug/mL of low molecular weight Poly(I:C) transfected using Lipofectamine 2000. HEK Blue hTLR7 cells were stimulated using 1ug/mL of Resiquimod (R848).

value: HEK Blue hTLR7

tag: irf7 genotype

value: Protective

tag: stimulation


title: NC0_2

description:
Library name: Sample 2
Column name in gene_fpkm.xls: NC0_2


title: RNA-seq in HEK Blue hTLR7 cells: IRF7 RE Haplotype R848 Stimulated Replicate 1

description: Library name: RNA-seq_HEK-Blue-hTLR7_RE31_E005623


title: RNA-seq in HEK Blue hTLR7 cells: IRF7 RE Haplotype R848 Stimulated Replicate 3

description: Library name: RNA-seq_HEK-Blue-hTLR7_RE33_E005621


title: RNA-seq in HEK Blue hTLR7 cells: IRF7 QK Haplotype R848 Stimulated Replicate 3

description: Library name: RNA-seq_HEK-Blue-hTLR7_QK33_E005613

value: Risk


title: PPGM1 cells, H3K27Ac (ChIP)

description: Library name: PPGM1_H3K27Ac_ChIP

value: cell line


title: TRA_F2_2N_FH_A23

description:
Library name: A23
TRA_F2_2N_FH_A23

extract_protocol:
RNA extraction was performed using Quick-RNATM Tissue/Insect Microprep (Catalogue No. R2030 Zymo Research, Germany) (without DNase treatment). For sequencing, RNA was resuspended in 10 µL DNase/RNase-free water and the RNA concentration and purity was measured using a fluorometer (Qubit 2.0, Life Technologies); poor quality samples judged by A260/A280 and A260/A230 ratios were discarded. The extracted RNA was sent to Novogene (UK) Company Limited for sequencing. Novogene Hongkong prepared the sample library.
Unique index codes were added to each sample using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, USA). mRNA was purified from total RNA using poly-T magnetic beads, and libraries were prepared according to the manufacturer's instructions (Illumina).

value: TRA


title: Control, 72 h, r2

description: Library name: CTRL_72h_r2

value: B cell intermediate to iMac


title: PPKM1 cells, H3K27Ac (ChIP)

description: Library name: PPKM1_H3K27Ac_ChIP

value: murine glioma cells


title: RNA-seq in HEK Blue hTLR7 cells: IRF7 QK Haplotype R848 Stimulated Replicate 2

description: Library name: RNA-seq_HEK-Blue-hTLR7_QK32_E005620


title: TRA_F2_2N_FH_A24

description:
Library name: A24
TRA_F2_2N_FH_A24

value: 1 day after emergence


title: ATAC-seq in control (empty vector) wild-type BMDMs (rep2)

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

description: Library name: mm_BMDM_C57_ATAC_lenti_empty_vector_rep2.fastq.gz

data_processing:
[mm_RNA_Lung_*.bw, mm_BMDM_RNA_*.bw]
alignment to mm10 reference genome with HISAT2 (v2.1.0) using default parameters
transcript assembly with StringTie (v1.3.4d)
BAM file indexing with SAMtools (v1.7)
coverage (bigwig) file generation with bamCoverage program of deepTools (v3.0.2)
[mm_ATAC_AM_*.bedgraph.gz]
alignment to mm10 reference genome with BWA v0.7.10 using default parameters
bam generation with SAMtools v1.7 using default parameters
tag directory generation with HOMER's makeTagDirectory using -checkGC parameter
generation of coverage (bedgraph) files with HOMER's makeUCSCfile using -fsize 1e50 -norm parameters
peak prediction with callpeak function of MACS2
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: bedgraph
[mm_BMDM_C57_ATAC_*.bw]
alignment to mm10 reference genome with BWA v0.7.10 using default parameters
bam generation with SAMtools v1.7 using default parameters
tag directory generation with HOMER's makeTagDirectory using -checkGC parameter
generation of coverage (bedgraph) files with HOMER's makeUCSCfile followed by conversation to bigwig using UCSC bedGraphToBigWig
peak prediction with callpeak function of MACS2

source_name: bone marrow-derived macrophage

growth_protocol:
For the alveolar macrophages (AMs) profiling experiment, tissue-derived CD45.1⁺ WT and CD45.2⁺ Bach1 fl/flLyz2-Cre alveolar macrophages (AMs) were FAC-Sorted from Bone Marrow chimeric mice (lethally irradiated recipients ≥8 weeks after transfer of a 1:1 mixture of donor BM cells).
For the alveolar macrophages (AMs) profiling experiment, WT and Bach1 fl/flLyz2-Cre alveolar macrophages (AMs) were FAC-Sorted and were lysed with the following lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL). After lysis, nuclei were subjected to tagmentation. Nextera DNA Library Prep Kit was used for library generation according to manufacturer's protocol.
For the Lentiviral transduction of BMDMs, a high titer (>1x108 TU/ml) lentiviral vector containing the full-length cDNA of mouse BACH1 was designed and ordered as packaged virus from VectorBuilder (pLV[Exp]-Neo-CMV>3xFLAG/mBach1). Transduction efficiency was tested with control virus: pLV[Exp]-EGFP/Puro-EF1A>mCherry. 5x105 BMDMs were transduced at Day 3 of differentiation at MOI:5 and used for RNA-seq after 48-72 hours in the presence of 10ug/ml doxycycline.
For the Lentiviral transduction of BMDMs, a high titer (>1x108 TU/ml) lentiviral vector containing the full-length cDNA of mouse BACH1 was designed and ordered as packaged virus from VectorBuilder (pLV[Exp]-Neo-CMV>3xFLAG/mBach1). Transduction efficiency was tested with control virus: pLV[Exp]-EGFP/Puro-EF1A>mCherry. 5x105 BMDMs were transduced at Day 3 of differentiation at MOI:5 and used for ATAC-seq after 48-72 hours in the presence of 10ug/ml doxycycline.

extract_protocol:
AMs were sorted directly to 500μl Tri Reagent (MRC) and total RNA was isolated according to the manufacturer’s protocol.
Indexed cDNA libraries were prepared following the TruSeq™ RNA Sample Preparation Kit (Illumina, Inc.) protocol.
WT and Bach1 fl/flLyz2-Cre alveolar macrophages (AMs) were FAC-Sorted and were lysed with the following lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL).
Nextera DNA Library Prep Kit was used for library generation according to manufacturer's protocol.
Total RNA was extracted from transduced BMDMs 48–72 hours post-transduction.
Indexed cDNA libraries were prepared following the TruSeq™ RNA Sample Preparation Kit (Illumina, Inc.) protocol.

value: bone marrow-derived macrophage

value: wild-type

value: vehicle


title: RNA-seq in THP1 cells: IRF7 RE Haplotype PolyIC Transfected Replicate 2

description: Library name: RNA-seq_THP1_REP32_E007064

value: PolyIC


title: RNA-seq in THP1 cells: IRF7 RE Haplotype PolyIC Transfected Replicate 3

description: Library name: RNA-seq_THP1_REP33_E007065


title: ATAC-seq in control (empty vector) wild-type BMDMs (rep3)

description: Library name: mm_BMDM_C57_ATAC_lenti_empty_vector_rep3.fastq.gz


title: RNA-seq in THP1 cells: IRF7 RE Haplotype PolyIC Transfected Replicate 1

description: Library name: RNA-seq_THP1_REP31_E007063


title: TRA_F2_2N_FA_A26

description:
Library name: A26
TRA_F2_2N_FA_A26

data_processing:
Alignment was performed with STAR (v2.7.11a) against the reference genome using a pre-built STAR genome index. STAR was run with “--outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts” to generate sorted alignment files and gene-level count profiles. Gene-level expression quantification was carried out using RSEM (v1.3.1) with STAR-generated transcriptome BAM files as input (--paired-end --no-bam-output --alignments).
Assembly: Nasonia vitripennis reference genome (RefSeq No. GCF_009193385.2, NCBI GenBank)
Supplementary files format and content: Tab-delimited text file includes raw counts and tpm value for each sample

value: Abdomen

value: female


title: TRA_F2_2N_FH_A25

description:
Library name: A25
TRA_F2_2N_FH_A25


title: RNAseq, Patient 53

description: Library name: Patient 53

value: Endometrial cancer


title: RNA-seq in THP1 cells: IRF7 RE Haplotype Unstimulated Replicate 3

description: Library name: RNA-seq_THP1_RE03_E007062


title: AGO2 KD, Region 2, 144 h, r2

description: Library name: AGO2_KD2_144h_r2

value: B-ALL cell line

value: B-ALL cell line with shAGO2-KD2

value: iMac


title: TRA_F2_2N_FA_A27

description:
Library name: A27
TRA_F2_2N_FA_A27


title: RNA-seq in THP1 cells: IRF7 QK Haplotype PolyIC Transfected Replicate 3

description: Library name: RNA-seq_THP1_QKP33_E007056


title: RNA-seq in HEK Blue hTLR7 cells: IRF7 QK Haplotype R848 Stimulated Replicate 1

description: Library name: RNA-seq_HEK-Blue-hTLR7_QK31_E005600

value: HEK Blue hTLR7


title: TRA_F2_2N_FA_A28

description:
Library name: A28
TRA_F2_2N_FA_A28


title: ATAC-seq in BACH1-overexpressing wild-type BMDMs (rep2)

description: Library name: mm_BMDM_C57_ATAC_lenti_BACH1_vector_rep2.fastq.gz


title: TRA_F2_3N_FH_A31

description:
Library name: A31
TRA_F2_3N_FH_A31

value: Head


title: RNA-seq in THP1 cells: IRF7 QK Haplotype PolyIC Transfected Replicate 2

description: Library name: RNA-seq_THP1_QKP32_E007055

value: Risk


title: TRA_F2_3N_FH_A32

description:
Library name: A32
TRA_F2_3N_FH_A32

value: TRA


title: RNA-seq in control (empty vector) wild-type BMDMs treated with LPS (4h) (rep3)

description: Library name: mm_BMDM_RNA_WT_EMPTY_VECTOR_DOX_LPS4h_rep3.fastq.gz

value: doxycycline, LPS (4h)


title: TRA_F2_3N_FH_A33

description:
Library name: A33
TRA_F2_3N_FH_A33


title: RNA-seq in THP1 cells: IRF7 KO PolyIC Transfected Replicate 3

description: Library name: RNA-seq_THP1_KOP33_E007047

value: KO


title: RNA-seq in THP1 cells: IRF7 QK Haplotype Unstimulated Replicate 3

description: Library name: RNA-seq_THP1_QK03_E007053


title: RNA-seq in THP1 cells: IRF7 QK Haplotype Unstimulated Replicate 2

description: Library name: RNA-seq_THP1_QK02_E007052


title: RNA-seq in THP1 cells: IRF7 QK Haplotype Unstimulated Replicate 1

description: Library name: RNA-seq_THP1_QK01_E007051


title: RNA-seq in control (empty vector) wild-type BMDMs treated with LPS (4h) (rep2)

description: Library name: mm_BMDM_RNA_WT_EMPTY_VECTOR_DOX_LPS4h_rep2.fastq.gz


title: TRA_F2_3N_FH_A34

description:
Library name: A34
TRA_F2_3N_FH_A34

value: 1 day after emergence


title: RNA-seq in control (empty vector) wild-type BMDMs treated with LPS (4h) (rep1)

description: Library name: mm_BMDM_RNA_WT_EMPTY_VECTOR_DOX_LPS4h_rep1.fastq.gz

value: bone marrow-derived macrophage


title: RNA-seq in THP1 cells: IRF7 KO Unstimulated Replicate 2

description: Library name: RNA-seq_THP1_KO02_E007043


title: RNA-seq in THP1 cells: IRF7 KO Unstimulated Replicate 3

description: Library name: RNA-seq_THP1_KO03_E007044


title: TRA_F3_1N_MH_A4

description:
Library name: A4
TRA_F3_1N_MH_A4

value: male


title: RNA-seq in THP1 cells: IRF7 KO Unstimulated Replicate 1

description: Library name: RNA-seq_THP1_KO01_E007042


title: RNA-seq in control (empty vector) wild-type BMDMs untreated (rep2)

description: Library name: mm_BMDM_RNA_WT_EMPTY_VECTOR_DOX_veh_rep1.fastq.gz

value: wild-type

value: doxycycline, vehicle


title: A6_mock_ML6_3

description: Library name: A6_mock_ML6_3_CTTGTA_L007_R1_001.fastq.gz

data_processing:
Reads were processed using a standardized pipeline. Raw single-end reads were trimmed with Trim_Galore to remove adapter sequences and low-quality bases, and read quality was assessed using FastQC. Trimmed reads were aligned to the custom THP1_active_PolIIIgenes_100exp index using Bowtie2/2.3.5.1, and resulting SAM files were converted, sorted, and indexed as BAM files using SAMtools/1.9-IGB-gcc-4.9.4. Genome-normalized coverage tracks were generated using deepTools/3.2.1.  Reads counts at RNA central noncoding genes (gene body +- 50bp) were obtained with BEDTools/2.28.0 (coverage function, -counts mode).
Assembly: GRCh38.109
Supplementary files format and content: Bigwig

molecule: nuclear RNA

growth_protocol: THP−1 cells were propagated in T-75 flasks between 0.2 and 1 × 106 cells/mL in an RPMI-1640 (Catalog# 11875093, Gibco, Billings, MT, USA) growth medium. THP−1 experiments were conducted on cells between passage 10 and 15.

extract_protocol:
FastGro sequencing experiment are performed following https://doi.org/10.17504/protocols.io.bbmgik3w
The small RNA were treated with Antartic Phosphatase and PNK and libraries were constructed with the NEBNext Small RNA Sample Prep kit (NEB).The libraries were sequenced on one 10B lane for 101 cycles from one end of the fragments on a NovaSeq X Plus with V1.0 sequencing kits.

treatment_protocol: 10 million THP1 nuclei are used per experiment; freshly isolated nuclei are pretreated with 50nM final concentration ML-60218 (Catalog# 557403-10MG, SigmaAldrich) or DMSO for 10 min and in vitro run-on is carried out with 25nM ML-60218 or DMSO.


title: RNA-seq in BACH1-overexpressing (BACH1 cDNA vector) wild-type BMDMs untreated  (rep1)

description: Library name: mm_BMDM_RNA_WT_BACH1_VECTOR_veh_rep1.fastq.gz

value: vehicle


title: A5_mock_ML6_2

description: Library name: A5_mock_ML6_2_GGCTAC_L007_R1_001.fastq.gz


title: TRA_F2_3N_FH_A35

description:
Library name: A35
TRA_F2_3N_FH_A35

value: female


title: TRA_F2_3N_FA_A36

description:
Library name: A36
TRA_F2_3N_FA_A36

value: Abdomen


title: A4_mock_ML6_1

description: Library name: A4_mock_ML6_1_TAGCTT_L007_R1_001.fastq.gz


title: A3_mock_DMSO_3

description: Library name: A3_mock_DMSO_3_GATCAG_L007_R1_001.fastq.gz

value: DMSO


title: A2_mock_DMSO_2

description: Library name: A2_mock_DMSO_2_ACTTGA_L007_R1_001.fastq.gz


title: RNA-seq in BACH1-overexpressing (BACH1 cDNA vector) wild-type BMDMs untreated  (rep2)

description: Library name: mm_BMDM_RNA_WT_BACH1_VECTOR_DOX_veh_rep1.fastq.gz


title: TRA_F2_3N_FA_A37

description:
Library name: A37
TRA_F2_3N_FA_A37


title: A1_mock_DMSO_1

description: Library name: A1_mock_DMSO_1_CAGATC_L007_R1_001.fastq.gz


title: HemECs, sh-EPAS1, independent run 3

city: Jinan

first: Zheren

last: Su

address: No. 324, Jingwu Road

department: Plastic and Cosmetic Surgery

institute: Shandong Provincial Hospital

description:
Library name: Sample 6
L1EIJ1000726-sh_30_3

data_processing:
Sequencing was performed on the Illumina NovaSeq X Plus platform using paired-end 150 bp reads (PE150) with the NovaSeq Reagent Kit.
The raw paired end reads were trimmed and quality controlled by fastp (Version 0.23.4) with default parameters.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 (Version 2.2.1) software.
The mapped reads of each sample were assembled by StringTie (Version 2.2.1) in a reference-based approach.
Gene-level expression was quantified using RSEM (Version 1.3.3) to calculate TPM (transcripts per million) values.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes TPM values for all samples

source_name: infantile hemangioma endothelial cells (HemECs)

growth_protocol: HemECs were cultured in complete Endothelial Cell Medium (ECM; ScienCell, 1001), supplemented with 5% fetal bovine serum (FBS), 1% endothelial cell growth supplement (ECGS), and 1% penicillin-streptomycin (P/S). Cells were cultured under normoxic (21% O₂, 5% CO₂) conditions in CO₂ incubators (Thermo Fisher).

extract_protocol:
Total RNA was extracted from cultured HemECs using TRIzol® Reagent according the manufacturer’s instructions.
RNA-seq transcriptome library was prepared following Illumina® Stranded mRNA Prep, Ligation (San Diego, CA).

treatment_protocol: EPAS1 knockdown lentiviruses were constructed using the GV493 vector by Shanghai GeneChem (China), with the target sequence CAGTACCCAGACGGATTTCAA for sh-EPAS1. The negative control lentivirus (sh-NC) contained a non-targeting shRNA sequence (TTCTCCGAACGTGTCACGT). HemECs were infected with sh-NC or sh-EPAS1 lentivirus, followed by puromycin selection.


title: RNA-seq in BACH1-overexpressing (BACH1 cDNA vector) wild-type BMDMs treated with LPS (4h) (rep3)

description: Library name: mm_BMDM_RNA_WT_BACH1_VECTOR_DOX_LPS4h_rep3.fastq.gz


title: TRA_F2_3N_FA_A38

description:
Library name: A38
TRA_F2_3N_FA_A38


title: RNA-seq in BACH1-overexpressing (BACH1 cDNA vector) wild-type BMDMs treated with LPS (4h) (rep2)

description: Library name: mm_BMDM_RNA_WT_BACH1_VECTOR_DOX_LPS4h_rep2.fastq.gz


title: HemECs, sh-EPAS1, independent run 2

description:
Library name: Sample 5
L1EIJ1000725-sh_30_2

value: infantile hemangioma endothelial cells (HemECs)


title: HemECs, sh-EPAS1, independent run 1

description:
Library name: Sample 4
L1EIJ1000724-sh_30_1


title: TRA_F2_3N_FA_A39

description:
Library name: A39
TRA_F2_3N_FA_A39


title: HemECs, sh-NC, independent run 2

description:
Library name: Sample 2
L1EIJ1000722-sh_nc_2

value: sh-NC


title: HemECs, sh-NC, independent run 1

description:
Library name: Sample 1
L1EIJ1000721-sh_nc_1


title: RNA-seq in control (empty vector) wild-type bone marrow-derived macrophages untreated (rep1)

description: Library name: mm_BMDM_RNA_WT_EMPTY_VECTOR_veh_rep1.fastq.gz


title: sperm, 699_sperm, sperm

city: Madison

first: Hasan

last: Khatib

state: Wisconsin

address: 1675 Observatory Drive

department: Animal and Dairy Sciences

institute: University of Wisconsin Madison

description:
Library name: 699_sperm
699_sperm

data_processing:
Alignment (STAR)
Read counts (Rsubread)
Differential expression analysis (DEseq2 R package)
Annotation
Assembly: ARS-UI_Ramb_v3.0
Supplementary files format and content: read counts

organism: Ovis aries

source_name: Sperm

extract_protocol:
RNA were extracted with either TRIzol reagent  (for sheep samples) or  Zymo Quick-RNA miniprep plus extraction kit (rat samples) followed by DNase I treatment before RNA sequencing.
RNA sequencing was performed for all samples using the NovaSeq X Plus platform with two 25B lanes, using V1.0 sequencing kits, and as 150 bp paired-end reads. Sheep RNA-Seq libraries were prepared with the Kapa Hyper Stranded mRNA library kit. Rat RNA-Seq libraries were prepared with the Watchmaker Stranded mRNA library kit. The libraries were pooled, quantified by qPCR, and sequenced on one 25B lane for 151 cycles from both ends of the fragments.

treatment_protocol: No specific treatment was applied.

value: Sperm


title: TRA_F2_3N_FA_A40

description:
Library name: A40
TRA_F2_3N_FA_A40


title: TRA_F14_3N_FH_A51

description:
Library name: A51
TRA_F14_3N_FH_A51

value: Head


title: brain, 699_VC, visual cortex

description:
Library name: 699_VC
699_VC

source_name: Brain

value: Brain


title: ATAC-seq in Bach1 cKO alveolar macrophages (rep3)

description: Library name: mm_ATAC_AM_BACH1KO_rep3.fastq.gz

source_name: alveolar macrophage

value: alveolar macrophage

value: Bach1 cKO

value: untreated


title: brain, 699_Pons, pons

description:
Library name: 699_Pons
699_Pons


title: ATAC-seq in Bach1 cKO alveolar macrophages (rep2)

description: Library name: mm_ATAC_AM_BACH1KO_rep2.fastq.gz


title: brain, 699_PPC, posterior parietal cortex

description:
Library name: 699_PPC
699_PPC


title: brain, 699_PC, prefrontal cortex

description:
Library name: 699_PC
699_PC


title: brain, 699_MC, motor cortex

description:
Library name: 699_MC
699_MC


title: ATAC-seq in Bach1 cKO alveolar macrophages (rep1)

description: Library name: mm_ATAC_AM_BACH1KO_rep1.fastq.gz


title: TRA_F14_3N_FH_A54

description:
Library name: A54
TRA_F14_3N_FH_A54

value: 1 day after emergence

value: TRA


title: brain, 699_FC, frontal cortex

description:
Library name: 699_FC
699_FC


title: brain, 699_EC, entorhinal cortex

description:
Library name: 699_EC
699_EC


title: ATAC-seq in wild-type alveolar macrophages (rep3)

description: Library name: mm_ATAC_AM_WT_rep3.fastq.gz


title: brain, 699_CB, cerebellum

description:
Library name: 699_CB
699_CB


title: TRA_F3_1N_MH_A5

description:
Library name: A5
TRA_F3_1N_MH_A5

value: male


title: ATAC-seq in wild-type alveolar macrophages (rep2)

description: Library name: mm_ATAC_AM_WT_rep2.fastq.gz

value: wild-type


title: brain, 699_BG, basal ganglia

description:
Library name: 699_BG
699_BG


title: TRA_F14_3N_FH_A55

description:
Library name: A55
TRA_F14_3N_FH_A55


title: sperm, 694_sperm, sperm

description:
Library name: 694_sperm
694_sperm


title: ATAC-seq in wild-type alveolar macrophages (rep1)

description: Library name: mm_ATAC_AM_WT_rep1.fastq.gz


title: brain, 694_VC, visual cortex

description:
Library name: 694_VC
694_VC


title: brain, 694_PPC, posterior parietal cortex

description:
Library name: 694_PPC
694_PPC


title: RNA-seq in Bach1 cKO alveolar macrophages from bone marrow-chimeric mice (rep3)

description: Library name: mm_RNA_Lung_AM_Bach1LysMCre_CD45_2_rep3


title: TRA_F14_3N_FA_A57

description:
Library name: A57
TRA_F14_3N_FA_A57


title: brain, 694_PC, prefrontal cortex

description:
Library name: 694_PC
694_PC


title: RNA-seq in Bach1 cKO alveolar macrophages from bone marrow-chimeric mice (rep2)

description: Library name: mm_RNA_Lung_AM_Bach1LysMCre_CD45_2_rep2


title: brain, 694_MC, motor cortex

description:
Library name: 694_MC
694_MC


title: TRA_F14_3N_FA_A58

description:
Library name: A58
TRA_F14_3N_FA_A58


title: brain, 694_Hip, hippocampus

description:
Library name: 694_Hip
694_Hip


title: RNA-seq in Bach1 cKO alveolar macrophages from bone marrow-chimeric mice (rep1)

description: Library name: mm_RNA_Lung_AM_Bach1LysMCre_CD45_2_rep1


title: TRA_F14_3N_FA_A59

description:
Library name: A59
TRA_F14_3N_FA_A59


title: brain, 694_EC, entorhinal cortex

description:
Library name: 694_EC
694_EC


title: brain, 694_CB, cerebellum

description:
Library name: 694_CB
694_CB


title: TRA_F14_3N_FA_A60

description:
Library name: A60
TRA_F14_3N_FA_A60


title: RNA-seq in wild-type alveolar macrophages from bone marrow-chimeric mice (rep2)

description: Library name: mm_RNA_Lung_AM_WT_CD45_1_rep2


title: sperm, 690_sperm, sperm

description:
Library name: 690_sperm
690_sperm


title: brain, 690_VC, visual cortex

description:
Library name: 690_VC
690_VC


title: brain, 690_PPC, posterior parietal cortex

description:
Library name: 690_PPC
690_PPC


title: RNA-seq in wild-type alveolar macrophages from bone marrow-chimeric mice (rep1)

description: Library name: mm_RNA_Lung_AM_WT_CD45_1_rep1


title: TRA_F14_2N_FH_A62

description:
Library name: A62
TRA_F14_2N_FH_A62


title: brain, 690_Pons, pons

description:
Library name: 690_Pons
690_Pons


title: brain, 690_PC, prefrontal cortex

description:
Library name: 690_PC
690_PC


title: TRA_F14_2N_FH_A63

description:
Library name: A63
TRA_F14_2N_FH_A63


title: brain, 690_MC, motor cortex

description:
Library name: 690_MC
690_MC


title: midbrain and hindbrain 13hpf DMSO treated, snATAC-seq

city: Aurora

first: rebecca

middle: L

last: orourke

state: CO

institute: University of Colorado Anschutz SOM

description:
Library name: MBHB13hpf_DMSO_ATAC
10x Genomics multiomic, ATAC-seq

library_source: genomic single cell

data_processing:
Generated cell feature counts for each single cell RNAseq library using cellranger arc  count --reference=GRCz11
single cell RNAseq feature and ATACseq feature data generated using Signac/Seurat Read10X_h5 and SeuratFromMatrixh5 functions using GRCz11.v99.EnsDb annotation
filtered Seurat object to select cells with nCount_ATAC>1000 & nCount_RNA >500  & percent.mitchondrial <5% & nucleosome_signal<2 & TSS.enrichment>1
generated ATAC peaks with Signac CallPeaks function using macs2 and used in CreateChromatinAssay with name "peaks"
processed filtered Seurat object using Seurat SCTransform, RunPCA, FindTopFeatures, RunTFIDF, RunSVD, FindMultiModalNeighbors(reduction.list=list("pca","lsi"),dims.list=list(1:50,2:50),FindClusters(various resolutions) and RunUMAP(reduction="pca",dims=1:50)
Assembly: GRCz11
Supplementary files format and content: h5 files are Hierarchical Data Formats files of cellranger_arc count matrix output
Supplementary files format and content: tsv.gz files are gzipped tab delimited bed files of atac fragments
Supplementary files format and content: rds files are R file containing SeuratObject

organism: Danio rerio

source_name: dissected forebrain, midbrain and hindbrain region

growth_protocol: Zebrafish embryos were generated by natural spawnings and grown under standard conditions

extract_protocol:
Tissue was collected in 1XPBS, dissociated by repeated pipetting through a p1000 tip, and centrifuged at 4℃ at 400G for 5 minutes followed by resuspension of the pellet in 500 μl of protease (10 mg/ml BI protease (Sigma, P5380), 125 U/ml DNase, 2.5 mM EDTA in PBS) for 15minutes on ice. Samples were centrifuged at 4℃ at 400G for 5 minutes, resuspended in 1ml HBSS + FBS (2%), filtered through a 20 μm cell strainer (pluriSelect, KL-071912), recentrifuged at 4℃ at 400G for 5 minutes, resuspended in 500 μl of HBSS + FBS (2%) and again filtered through a 20 μm cell strainer. Following centrifugation at 4℃ at 400G for 5 minutes, the cells were resuspended in 200 μl PBS. For nuclei isolation, we followed the 10X Genomics recommended protocol with minor modifications. The dissociated cells were centrifuged at 900G at 4℃ for 5 minutes, resuspended in 100 μl of 0.1X lysis buffer (1 mM Tris-HCl pH7.4, 1 mM NaCl, 0.3 mM MgCl2, 0.1% BSA, 0.01 % Tween-20, 0.01 % NP40, 0.001 % Digitonin (Invitrogen, BN2006), 0.1 mM DTT, 0.1 U/μl RNase inhibitor, in nuclease-free water) and incubated on ice for 5 min. Samples were then washed three times by centrifugation at 4℃ at 900G for 10 min and resuspension in 1 ml of chilled wash buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1 % Tween-20, 1 mM DTT, 1 U/μl RNase inhibitor in nuclease-free water). Finally, nuclei were counted and resuspended in 1X nuclei buffer (provided in the 10x Genomics Single Cell Multiome ATAC Kit A; 1 mM DTT, 1 U/μl RNase inhibitor in nuclease free water) at a final concentration of approximately 2,000-3,000 nuclei/μl for sequencing on the 10X scMultiome platform.
10x Genomics Single Cell Multiome ATAC Kit A was used with the standard protocol

treatment_protocol: SU5402 (Abcam, ab141368) was used to inhibit Fgf signaling. SU5402 was dissolved in DMSO and diluted to a final concentration of 10 µM. Embryos were randomly assigned to DMSO control or SU5402 treatment groups and treated beginning at 7hpf until collection at the indicated developmental stage. Embryos were dissected to include the forebrain, midbrain, and hindbrain using forceps (Fine Science Tools Dumont #5 Forceps, Cat #NC9889584) and yolk and posterior tissues were excluded. DMSO-treated embryos were used as controls. Dead embryos were manually removed and excluded from our analyses.

value: wildtype(TU line obtained from ZIRC stockcenter)


title: ATAC-seq in control (empty vector) wild-type BMDMs (rep1)

description: Library name: mm_BMDM_C57_ATAC_lenti_empty_vector_rep1.fastq.gz

value: bone marrow-derived macrophage

value: vehicle


title: brain, 690_Hip, hippocampus

description:
Library name: 690_Hip
690_Hip


title: MLLAF9_chemo_resistant_rep1

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

data_processing:
Sequencing reads were aligned to mouse mm9 version of the genome using Tophat2.
The raw read counts for genes were computed using RSEM.
Assembly: mm9
Supplementary files format and content: tab-delimited text file containing raw counts for each samples.

source_name: Bone Marrow

extract_protocol:
Total RNA was extracted using Qiagen RNeasy kit.
Libraries were prepared using Illumina TruSeq RNAseq kit.

value: Bone Marrow

value: Myeloid Leukemic Blasts

value: Cytarabin+Doxorubicin


title: midbrain and hindbrain 13hpf DMSO treated, snRNA-seq

description:
Library name: MBHB13hpf_DMSO_GEX
10x Genomics multiomic, RNA-seq

value: dissected forebrain, midbrain and hindbrain region

value: DMSO


title: TRA_F3_1N_MA_A6

city: Nanjing

first: Xuan

last: Li

address: No. 666, Binjiang Avenue, Jiangbei New Area

institute: Nanjing Agricultural University

description:
Library name: A6
TRA_F3_1N_MA_A6

value: Abdomen


title: TRA_F14_3N_FA_A56

description:
Library name: A56
TRA_F14_3N_FA_A56

value: female


title: brain, 694_Pons, pons

description:
Library name: 694_Pons
694_Pons

value: Brain


title: MLLAF9_chemo_sensitive_rep3

value: vehicule


title: brain, 694_FC, frontal cortex

description:
Library name: 694_FC
694_FC


title: TRA_F14_2N_FH_A65

description:
Library name: A65
TRA_F14_2N_FH_A65

source_name: Head

value: Head


title: brain, 690_EC, entorhinal cortex

description:
Library name: 690_EC
690_EC


title: MLLAF9_chemo_sensitive_rep2


title: TRA_F14_2N_FH_A61

description:
Library name: A61
TRA_F14_2N_FH_A61

value: 1 day after emergence


title: midbrain and hindbrain 13hpf SU5402 treated, snRNA-seq

description:
Library name: MBHB13hpf_SU5402_GEX
10x Genomics multiomic, RNA-seq

value: 10 µM SU5402 dissolved in DMSO


title: TRA_F14_2N_FA_A66

description:
Library name: A66
TRA_F14_2N_FA_A66

source_name: Abdomen

value: TRA


title: brain, 690_CB, cerebellum

description:
Library name: 690_CB
690_CB


title: brain, 690_FC, frontal cortex

description:
Library name: 690_FC
690_FC


title: MLLAF9_chemo_sensitive_rep1


title: MLLAF9_chemo_resistant_rep3


title: TRA_F14_2N_FA_A67

description:
Library name: A67
TRA_F14_2N_FA_A67


title: Htr2b,Ms4a3

city: shanghai

first: Yong

middle: hui

last: Chen

address: 160, Pujian Road

institute: Renji hospital

description: Library name: 25110151_number_2_expression_S01_L000

data_processing:
Raw sequencing data (FASTQ files) were processed using SeekSpace™ Tools (version [1.0.3], SeekGene). The RNA sequencing reads were aligned to the [Human GRCh38 / Mouse mm10] reference genome using the internal SeekSoul Tools module to perform cell calling and UMI counting.
For spatial positioning, spatial barcodes were extracted from the spatial library and HDMI library. SeekSpace™ Tools was utilized to decode the mapping relationship between cell barcodes and spatial barcodes, project the single cells onto the physical coordinates of the chip, and segment the valid tissue regions from the background image, generating the final spatial gene expression matrix.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of cell barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_DAPI.png: The high-resolution DAPI-stained tissue image that has been aligned and registered to the spatial transcriptomics coordinate system, used for identifying cell nuclei positions.
Supplementary files format and content: aligned_HE.png: The corresponding H&E (Hematoxylin and Eosin) stained tissue image, aligned to the spatial coordinate system, providing histological context and tissue morphology.
Supplementary files format and content: cell_locations.tsv.gz: A table containing the spatial metadata for each barcode, including the corresponding physical X and Y coordinates in-tissue status.
Library strategy: Spatial Transcriptomics

source_name: brain

extract_protocol:
Fresh frozen tissue were OCT embedded, and 20μm frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with SeekSpace® Single Cell Spatial Transcriptome-seq Kit(K02501-08) according to manufacturer's construction.

value: brain


title: TET2 KD, 144 h, r3

type: genomic

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium MethylationEPIC Bead-Chip arrays using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Methylation data were analyzed using the minfi package in R. Data was imported into R and normalized (noob and quantile normalization). Probes were removed if they did not pass the detection cut-off (p < 0.01), and if were associated with known SNPs or with the X and Y chromosomes
Normalized (preprocessNoob and preprocessQuantile) Beta-values

label: Cy3 and Cy5

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated using Blood & Cell Culture DNA Mini Kit (QIAGEN).

value: B-ALL cell line

value: B-ALL cell line with shTET2

value: iMac

value: TET2 KD

tag: time point

value: Doxycycline (1 µg/ml)


title: brain, 690_BG, basal ganglia

description:
Library name: 690_BG
690_BG


title: KO2

city: Kyoto

first: Wooseok

last: Seo

address: Yoshida-Konoe-cho, Sakyo-ku

country: Japan

institute: Kyoto University Graduate School of Medicine

description: Library name: KO2

data_processing:
Sequencing results were aligned to the mouse reference genome (mm10) using the HISAT2 (version 2.1.0) with standard parameters. Read counts were obtained by HTSeq (version 0.11.0).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Tumor

extract_protocol:
Tumor tissue was treated by BD Horizon Dri Tissue & Tumor Dissociation Reagent (BD Biosciences) and CD45.2+CD8+ cells were sorted (BD Symphony S6).
Purified mRNAs were used for the library construction with the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s protocol.

value: Tumor


title: TRA_F14_2N_FA_A68

description:
Library name: A68
TRA_F14_2N_FA_A68


title: sperm, 688_sperm, sperm

description:
Library name: 688_sperm
688_sperm

value: Sperm


title: KO1

description: Library name: KO1


title: TET2 KD, 144 h, r2


title: midbrain and hindbrain 13hpf SU5402 treated, snATAC-seq

description:
Library name: MBHB13hpf_SU5402_ATAC
10x Genomics multiomic, ATAC-seq

value: dissected forebrain, midbrain and hindbrain region

value: wildtype(TU line obtained from ZIRC stockcenter)


title: MLLAF9_chemo_resistant_rep2

value: Bone Marrow

value: Myeloid Leukemic Blasts

value: Cytarabin+Doxorubicin


title: TRA_F14_2N_FA_A69

description:
Library name: A69
TRA_F14_2N_FA_A69

value: Abdomen

value: female


title: TET2 KD, 144 h, r1


title: brain, 688_VC, visual cortex

description:
Library name: 688_VC
688_VC

value: Brain


title: TRA_F14_2N_FA_A70

description:
Library name: A70
TRA_F14_2N_FA_A70

value: 1 day after emergence

value: TRA


title: WT2

description: Library name: WT2


title: brain, 688_PPC, posterior parietal cortex

description:
Library name: 688_PPC
688_PPC


title: TET2 KD, 72 h, r3

value: B-ALL cell line

value: B cell intermediate to iMac


title: WT1

description: Library name: WT1


title: TRA_F15_1N_MH_A71

description:
Library name: A71
TRA_F15_1N_MH_A71

value: Head

value: male


title: brain, 688_Pons, pons

description:
Library name: 688_Pons
688_Pons


title: TRA_F14_2N_FH_A64

description:
Library name: A64
TRA_F14_2N_FH_A64


title: TET2 KD, 72 h, r2

value: B-ALL cell line with shTET2

value: TET2 KD

value: Doxycycline (1 µg/ml)


title: S1(WT), S2(Satb1 F/F; ThPOK-Cre), S3((Satb1 F/F; E8I-Cre)

description: Library name: TIL scRNA-seq

data_processing:
Sequence was read by HiSeq 4000 and aligned to the mm10 mouse genome using cellranger using Chromium Mouse Transcriptome Probe Set v1.0.1.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Tumor tissue was treated by BD Horizon Dri Tissue & Tumor Dissociation Reagent (BD Biosciences) and CD45+ cells were sorted (BD Symphony S6). Sorted cells were fixed by Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10x Genomics) and frozen at -80°C until ready.
1,000,000 cells were loaded onto Chromium X and 12,000-14,000 cells per sample were captured for the library preparation by Chromium Fixed RNA Kit - Mouse Transcriptome (10x Genomics).

value: Tumor


title: TRA_F15_1N_MH_A72

description:
Library name: A72
TRA_F15_1N_MH_A72


title: brain, 688_PC, prefrontal cortex

description:
Library name: 688_PC
688_PC


title: TET2 KD, 72 h, r1


title: TRA_F15_1N_MH_A73

description:
Library name: A73
TRA_F15_1N_MH_A73


title: STC5

city: Suzhou

first: Shuai

last: Yan

state: Jiangsu

address: 18 Yangsu Road

institute: Suzhou TCM Hospital Affiliated to Nanjing University of Chinese Medicine

data_processing:
Quality control: The quality of raw reads was first assessed using the FastQC. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Genomic alignment and quantification: Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters. HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz. The CIRCexplorer program (v2.3.8) was used to identify both the circularizing junction and the spliced sequence of circRNAs. All circRNA candidates with junction reads less than 2 were discarded. The remaining circRNA candidates were considered bonafide circRNAs.
DESeq2 (v2) was applied for the detection of differentially expressed mRNAs/lncRNAs between two groups, the limma R package (3.40.6) was used for differentially expressed circRNAs.
Assembly: GRCh38
Supplementary files format and content: FileincludeFPKM/TPMvaluesforeachsample

source_name: colon

growth_protocol: This study comprised a total of 10 participants: 5 individuals diagnosed with STC who underwent subtotal colectomy, and 5 control subjects who underwent radical surgery for colon cancer. We chose patients with STC in strict accordance with international and national guidelines: (1) Meet the Rome IV STC diagnostic criteria; (2) Constipation symptoms are severe, defecation frequency is less than twice per week, there is no urge to defecate or there is no obvious desire to defecate, there is a high incidence of abdominal distension, laxatives must be used to maintain defecation or laxatives cannot maintain defecation; (3) Constipation sensations have been present for more than 5 years, substantially hurting quality of life, and medical treatment has been ineffective for more than two years, with a strong desire for surgery; (4) Colorectal organic lesions are excluded; (5) There was no evident stomach or intestinal motility impairment based on three colonic transit tests; (6) Hamilton anxiet scale < 14 points, no visible mental symptoms such as depression; (7) Excluding the constipation kind of irritable bowel syndrome.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Firstly,ribosomal RNA was removed by Epicentre Ribo-zero™ rRNA Removal Kit (Epicentre, USA), and rRNA free residue was cleaned up by ethanol precipitation. Subsequently, sequencing libraries were generated using the rRNA-depleted RNA by NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

treatment_protocol: Before the operation, all patients had a gastrointestinal transit test. The running track of the opaque marker was used to locate the intestinal segment of colonic transit dysfunction, and the normal intestinal segment of colon cancer patients was chosen as the control. Each sample was collected from the colon tissue within 3 min after surgery, and was divided into 1 cm3 samples, and then cryopreserved in liquid nitrogen at -80°C.

value: colon

value: Human

value: STC


title: brain, 688_MC, motor cortex

description:
Library name: 688_MC
688_MC


title: TET2 KD, 0 h, r3

value: B cell

value: 0 h


title: STC4


title: TRA_F15_1N_MH_A74

description:
Library name: A74
TRA_F15_1N_MH_A74


title: brain, 688_Hip, hippocampus

description:
Library name: 688_Hip
688_Hip


title: TET2 KD, 0 h, r2


title: TRA_F3_1N_MA_A7

description:
Library name: A7
TRA_F3_1N_MA_A7

value: Abdomen


title: STC3


title: brain, 688_FC, frontal cortex

description:
Library name: 688_FC
688_FC

value: Brain


title: TET2 KD, 0 h, r1


title: STC2


title: TRA_F15_1N_MH_A75

description:
Library name: A75
TRA_F15_1N_MH_A75

value: 1 day after emergence


title: brain, 688_EC, entorhinal cortex

description:
Library name: 688_EC
688_EC


title: Control, 144 h, r3

value: B-ALL cell line with shCTRL

value: iMac

value: Control


title: STC1


title: TRA_F15_1N_MA_A76

description:
Library name: A76
TRA_F15_1N_MA_A76

value: TRA


title: brain, 688_CB, cerebellum

description:
Library name: 688_CB
688_CB


title: NP5

value: control


title: TRA_F15_1N_MA_A77

description:
Library name: A77
TRA_F15_1N_MA_A77

value: male


title: Control, 144 h, r2

value: B-ALL cell line


title: brain, 688_BG, basal ganglia

description:
Library name: 688_BG
688_BG


title: Control, 144 h, r1

value: Doxycycline (1 µg/ml)


title: NP4


title: TRA_F15_1N_MA_A78

description:
Library name: A78
TRA_F15_1N_MA_A78


title: sperm, 687_sperm, sperm

description:
Library name: 687_sperm
687_sperm

value: Sperm


title: TRA_F15_1N_MA_A79

description:
Library name: A79
TRA_F15_1N_MA_A79


title: Control, 72 h, r3

value: B cell intermediate to iMac


title: NP3

value: colon

value: Human


title: Control, 72 h, r2


title: brain, 687_VC, visual cortex

description:
Library name: 687_VC
687_VC


title: NP2