title: CUTAC_Control_TSM_Rep1

status: Public on Jul 10 2026

city: Oxford

first: Alan

last: Jiao

address: Old Road Campus Research Building

country: United Kingdom

institute: Ludwig Institute for Cancer Research, Oxford University

data_processing:
*library strategy: CUTAC
Reads were aligned to the human hg38 genome using Bowtie2 v2.3.5.1, with settings --no-unal --local --very-sensitive-local --no-mixed --no-discordant --phred33 -I 10 -X 700
Bigwig track files were created using bamCoverage from deepTools v3.3.1, with settings --binSize=20 --smoothLength=60 --normalizeUsing BPM
Assembly: hg38
Supplementary files format and content: bigWig

source_name: DIPG-XIII

growth_protocol: DIPG-XIII cells were maintained in tumor stem medium as gliomaspheres in low attachment culture flasks in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
CUTAC was performed with anti-H3K4me2 (Sigma-Aldrich 07-030). Tagmented genomic DNA was extracted using 1%SDS/Proteinase K
Released, tagmented DNA from ~50,000 starting cells was amplified using non-hot-start polymerase (NEB M0541S) using the following program: 58oC, 5 mins; 72oC, 5mins; 98oC 30s; (98oC 10s, 63oC 30s) x 12 cycles total, 72oC, 1min.

treatment_protocol: Differentiation was induced by treatment with DMEM/F-12 medium containing 10% FBS

value: DIPG-XIII

value: Glioma

value: Control

value: Serum differentiation

tag: time

tag: cutac antibody

value: anti-H3K4me2 (Sigma Aldrich 07-030)


title: Sample 2; Knockout Group, Replicate 1

status: Public on Jul 09 2026

type: SRA

city: Huntington

first: Yen On

last: Chan

state: WV

address: Arthur Weisberg Family Applied Engineering Complex, Suite # 4103, 1676 Third Avenue

department: Department of Biomedical Sciences

country: USA

institute: Marshall University

description: Library name: T1_Pos

library_source: transcriptomic single cell

data_processing:
The snRNA-seq bioinformatics analysis was performed on six datasets corresponding to three KO and three CO conditions. The reads were then aligned to the mouse reference genome (GRCm38) and quantified using Cell Ranger v3.0.2 to generate six filtered feature-barcode matrices suitable for analysis with the Seurat v5.2.1 package in the R programming language. The Read10X function in the Seurat package was employed to import the matrices, followed by the Seurat CreateSeuratObject function to generate individual Seurat objects for each sample. The Seurat objects were then normalized and variance-stabilized using the SCTransform function and subsequently integrated across all samples using the Harmony algorithm to correct for batch effects and inter-sample variability. Following integration, a shared nearest neighbor (SNN) graph was constructed using the FindNeighbors function, and clusters were identified with the FindClusters function to facilitate unsupervised cell-type identification. Dimensionality reduction was performed using both the RunTSNE and RunUMAP functions to enable visualization of cellular heterogeneity and clustering in two-dimensional space.
Assembly: Mus Musculus GRCm38
Supplementary files format and content: Feature Barcode Matrices

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
Frozen mouse tumor tissues were processed for nuclei isolation. Approximately 200 mg tissue per sample was homogenized on ice using a Dounce homogenizer in RNase-free lysis buffer, lysed at 4°C for 5 min, filtered through a 40 μm nylon filter, rinsed with wash buffer ± RNase inhibitor, and centrifuged at 500g for 5 min at 4°C. Nuclear pellets were resuspended in PBS with 0.02% BSA ± RNase inhibitor. Selected samples received 1–3 additional PBS/BSA washes to reduce ambient RNA contamination. Nuclei were counted using a Countess II Automated Cell Counter.
Single-nucleus libraries were generated using the Chromium Next GEM Single Cell 3′ Kit v3.1 with Chip G. Approximately 4,000 nuclei per sample were loaded into the Chromium Controller to generate GEMs. cDNA synthesis and library construction followed the manufacturer’s 10x Genomics protocol. Final libraries were sequenced on an Illumina NextSeq platform targeting approximately 25,000 reads per cell.

tag: tissue

value: Lung

tag: treatment

value: MCT2 Knockout


title: TE_WT1

city: Hangzhou

first: Fan

last: Zhao

state: Zhejiang Province

address: 866 Yuhangtang Road, Xihu District

country: China

institute: Zhejiang University

description:
Library name: Sample 7
WT effector CD8+ T cell

library_source: transcriptomic

data_processing:
Raw sequencing reads were quality-controlled and adapter-trimmed using fastp to generate clean data. These clean reads were aligned to the mouse referenceG genome (GRCm39) using HISAT2 (v2.2.1), and gene expression levels were quantified using featureCounts (v2.0.6). Differential expression analysis was performed with DESeq2 (v1.42.0), applying a significance threshold of adjusted p-value < 0.05 and |log2(fold change)| > 1.
Assembly: GRCm39
Supplementary files format and content: excel file includes RPKM values for each Sample

source_name: lymph nodes and spleen

extract_protocol:
WT and cKO naive CD8⁺ T cells, along with their in-vitro-differentiated effector and memory subsets, were lysed in TRIzol reagent (Invitrogen). Total RNA was extracted from the lysates using the Direct-zol RNA MiniPrep kit (Zymo Research) according to the manufacturer's protocol.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: lymph nodes and spleen

tag: cell type

value: effector CD8+ T cell

tag: genotype

value: WT

value: no treatment


title: Sample 1; Control Group, Replicate 1

description: Library name: T1_NG

value: MCT2 Control


title: Clc-k2-/-/Wnk4D561A/+_3

city: Iowa City

first: Chih-Jen

last: Cheng

address: 285 Newton Rd, 3270B CBRB

department: Department of Internal Medicine

institute: The University of Iowa

description: Library name: Sample 9

data_processing:
Parteck flow 12.8.0
Assembly: mm10
Supplementary files format and content: total counts_all.csv

source_name: Kidney

extract_protocol:
Total RNA extraction using the RNeasy Plus Mini Kit (Qiagen, Venlo, Netherlands). Total RNA was eluted in 10 μl of RNase-free water. For RNA-Seq, cDNA was synthesized using a SMART-Seq mRNA LP (Takara Bio, San Jose, CA, USA) according to the manufacturer’s protocol. The cDNA was then amplified for 15 PCR cycles, purified by AmPure XP magnetic beads (Beckman Coulter Genomics), and eluted with 15 μl of Elution Buffer. The purified cDNA was quantified fluorometrically using a Qubit 2.0 Fluorometer.
Library size distribution was determined using the Agilent 2100 bioanalyzer using High-Sensitive DNA kit (Agilent Genomics). The SMART-Seq Library Prep Kit (Takara) was used to generate the libraries, with an input of 1 ng of cDNA. Libraries were pooled and sequenced to obtain 75-base-pair paired-end reads on the Illumina NextSeq550 platform to a depth of >20 million reads per sample.

value: Kidney


title: TN_cKO3

description:
Library name: Sample 6
Hspa9 cKO naive CD8+ T cell

value: naive CD8+ T cell

value: cKO


title: JA80B644-01

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

organism: Homo sapiens

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: AD

tag: Sex

value: Male

tag: age

tag: mmse

tag: anatomical location

value: Circulating blood

tag: sample collection method

value: Venous

tag: starting amount

tag: holding temperature


title: Clc-k2-/-/Wnk4D561A/+_2

description: Library name: Sample 8


title: Clc-k2-/-/Wnk4D561A/+_1

description: Library name: Sample 7


title: Clc-k2-/-_3

description: Library name: Sample 6


title: DLBC-03-010

value: DLB


title: Clc-k2-/-_2

description: Library name: Sample 5


title: TN_cKO1

description:
Library name: Sample 4
Hspa9 cKO naive CD8+ T cell


title: PWA12-0525

value: PD


title: TN_WT3

description:
Library name: Sample 3
WT naive CD8+ T cell


title: AA807Q87-03

value: Female


title: Wild type_3

description: Library name: Sample 3

value: Wild type


title: Clc-k2-/-_1

description: Library name: Sample 4


title: Wild type_2

description: Library name: Sample 2


title: Wild type_1

description: Library name: Sample 1


title: DLBC-03-012


title: TN_WT2

description:
Library name: Sample 2
WT naive CD8+ T cell

value: lymph nodes and spleen


title: 662_SPF

city: Newark

first: Dahui

last: Wang

state: NJ

address: 73 Warren st

department: Biological Science

institute: Rutgers University, Newark

description: Library name: SPF_2

library_source: genomic

data_processing:
ATAC-seq fastq file was quality checked using fastQC. Nextera transpose adapter reverse complement was removed from the 3′ end of the ATAC-Seq reads using CutAdapt, version 1.9.1. Trimmed reads were aligned to the mouse genome build mm9 using Bowtie2. Picard (v2.18.27) was used to determine the median alignment size of each alignment bam file.
Peak region bed files were called from each alignment bam file using MACS2 (v2.1.0). MACS2 was run with a “shift” distance of −0.5 times the median alignment size and an “extsize” distance equal to the median alignment size for each alignment bed file.
.  Peak files were filtered against the ENCODE blacklist and BEDtools was used to subtract the sites on the ENCODE blacklist. The Integrative Genomics Viewer (IGV 2.4.13) was used to visualize ATAC-seq bigwig tracks. DiffBind (v2.4.7) FDR < 0.01 as the cutoff for significance
Assembly: mm9
Supplementary files format and content: Bigwig File

molecule: genomic DNA

source_name: Duodenum

extract_protocol:
For ATAC-seq, freshly FACS-isolated tdTomato+ live Paneth cells from GF or SPF Paneth cell reporter mice were processed according to the OMNI-ATAC-Seq protocol
Samples were then purified with the Zymo DNA Clean and Concentrator-5 kit and pre-amplified using the NEBnext 2X Master Mix for 5 cycles. 5 μL of the pre-amplified sample was subjected to qRT-PCR amplification for additional 20 cycles to determine the optimal additional cycles of the remaining 45 μL of sample. The PCR-amplified libraries were purified; fragment size was selected using Pippin Prep and sequenced on Illumina NextSeq 150 cycle mid output

value: Duodenum

value: Paneth

value: SPF


title: AD_Quinn_9


title: C140

city: Nantong,Jiangsu,China

first: Xiaorong

last: Zhou

state: Jiangsu province

address: 19 Qixiu Road

institute: Nantong University

description: Library name: Sample 3

data_processing:
raw gene expression matrices (from the filtered_cell_gene_matrix directory) were imported via the Read10X function, and Seurat objects for each group were constructed using CreateSeuratObject with filtering criteria: each gene must be expressed in at least 3 cells and each cell must have at least 200 detected genes, to exclude low-quality cells and rarely expressed genes. The DoubletFinder package (version 2.0.4) was used for doublet removal to eliminate cell co-capture artifacts. A final quality control step was applied to the dataset: cells with < 200 detected genes or mitochondrial gene percentage > 10% were excluded to remove low-quality cells affected by mitochondrial contamination.
For dimensionality reduction, visualization and clustering, log-normalization was first performed on the Seurat object. Principal component analysis (PCA) was then conducted based on the highly variable genes, and the first 10 principal components were ultimately selected for subsequent analyses. The Harmony algorithm was applied to the PCA results for batch effect correction, aiming to eliminate technical biases among different sample batches. T-distributed stochastic neighbor embedding (t-SNE) was adopted for two-dimensional visualization of single-cell data. To identify cell types, a graph-based clustering method implemented in Seurat was employed. Specifically, a K-nearest neighbor (KNN) graph among cells was constructed using the FindNeighbors() function, followed by clustering analysis with the FindClusters() function. The clustering resolution was set within a range of 0.1 to 1.0 with an increment of 0.1. Based on the number of detectable cell clusters, a resolution of 0.6 was determined as the optimal clustering granularity parameter. The selection of this optimal parameter was evaluated via visual inspection and the Clustree package.
Assembly: mm10
Supplementary files format and content: rds

source_name: tumor

growth_protocol: All animal-related procedures were performed following the ethical guidelines of the Animal Experimentation Institution of Nantong University, and all animal experiments were approved by the Ethics Committee.

extract_protocol:
Tumors were dissociated to generate the single cell suspension, and the sequencing was performed with NovaSeqTM 6000 Illumina® sequencer.
Tumors were dissociated to generate the single cell suspension, and the sequencing was performed with NovaSeqTM 6000 Illumina® sequencer.

treatment_protocol: In the subcutaneous tumor formation experiment, 4T1 cells resuspended in 100 μL PBS buffer were inoculated into the subcutaneous mammary gland area of each mice (1×10⁶ cells). Nine days later, when the tumor volume reached approximately 100 mm³, the mice were randomly divided into three groups according to the experimental grouping designing. The control group was intraperitoneally injected with 100 μL PBS, and the experimental groups were intraperitoneally injected with 100 or 140 mg/kg CTX in 100 μL PBS, respectively. All groups were injected once every 6 days. On the third day after the third treatment cycle, the mice were euthanized, and the tumor tissues were harvested for bulk RNA sequencing and scRNA-seq.

value: tumor

tag: cell line

value: TNBC cell

value: 140mg/kg CTX


title: 22859_GF

description: Library name: GF_3

value: Germ Free


title: 55869_GF

description: Library name: GF_2


title: AA8097FQ-02

value: Plasma


title: 68993_GF

description: Library name: GF_1


title: Capture Hi-C in Bach1-deficient mouse bone marrow derived macrophages (rep2)

city: Debrecen

first: Laszlo

last: Nagy

address: Egyetem ter 1.

country: Hungary

institute: University of Debrecen

data_processing:
library strategy: cHi-C
Reads were aligned and quality controlled using Hicup (v0.6.1). Interactions between virtual restriction fragments were detected using Chicago (v1.6.0) using custom weights calculated from high confidence interactions in the data.
Assembly: mm10

source_name: mouse bone marrow derived macrophages

growth_protocol: Isolation and differentiation were completed as described earlier (Daniel et al., 2014). Isolated bone marrow-derived cells were differentiated for 6 days in the presence of L929 supernatant.

extract_protocol:
Mouse bone marrow-derived macrophages were cross-linked using formaldehyde-based cross-linking method and processed to Hi-C using the Arima Hi-C kit. A capture enrichment step was applied to the generated Hi-C libraries using sustom-designed probes (SureSelect, Agilent Tier 2 -2,9Mb ). Our design has two components combined in the same probe set : a. The Hmox1 genomic locus (tiled probescovering a 500kb area). The coordinates of this area arechr8:74850001-75350000. b.9127 sites covering the top BACH1’s ChIP-seqsites (in untreated BMDMs) sorted based on the RPKM.
Hi-C and cHi-C libraries were prepared with the Arima Hi-C kit and Agilent SureSelect library systems according to the manufacturer protocol.

treatment_protocol: Treatments of mouse bone marrow-derived macrophages occurred at Day7 of differentiation after an overnight incubation in fresh medium.

value: bone marrow derived macrophages

tag: strain

value: Bach1 fl/fl;LysM Cre+ (Myeloid specific conditional KO)

tag: cell treatment

value: Vehicle

tag: duration of_treatment_(hours)

tag: capture selection_probes

value: Custom-designed selection probes (SureSelect- Agilent) against BACH1-bound genomic sites


title: Capture Hi-C in Bach1-deficient mouse bone marrow derived macrophages (rep1)


title: NC

description: Library name: Sample 1

tag: tissue

tag: treatment

value: PBS


title: PWA10-0201

value: PD

value: Male

value: Circulating blood

value: Venous


title: Capture Hi-C in wild type mouse bone marrow derived macrophages treated with 100 uM heme (rep2)

tag: cell type

tag: genotype

value: Bach1 fl/fl (Control)

value: 100μΜ Hemin (Sigma 51280)


title: C140_5

description:
Library name: Sample 14
Column name in gene_fpkm.txt: C140_5

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: mm10
Supplementary files format and content: csv

extract_protocol:
Tumors were collected three days after the third cycle of CTX treatment, washed with PBS, and submitted for RNA isolation, quality check, and subsequent RNA sequencing by the Novogene (Beijing, China) on the Illumina platform.
Tumors were collected three days after the third cycle of CTX treatment, washed with PBS, and submitted for RNA isolation, quality check, and subsequent RNA sequencing by the Novogene (Beijing, China) on the Illumina platform.


title: FA808BM7-08

tag: donor id

tag: disease

value: NC


title: Capture Hi-C in wild type mouse bone marrow derived macrophages (rep2)


title: C140_4

description:
Library name: Sample 13
Column name in gene_fpkm.txt: C140_4

value: tumor


title: HEK293T, mCherry targeting, biol rep 3

city: Melbourne

first: Honglin

last: Chen

state: VIC

address: 305 Grattan St, North Melbourne VIC

country: Australia

institute: PeterMacCallum Cancer Centre

description:
Library name: TAR3
Matrix column: TAR3

data_processing:
cutadapt 4.4: paired-end reads processed with quality trimming (quality-cutoff 20) and minimum-length filtering (minimum-length 20, pair-filter any); error rate 0.1, times 1, overlap 3. No adapter sequence specified (quality and length trimming only).
STAR 2.7.4a: trimmed reads aligned to hg19 (GRCh37) with --quantMode GeneCounts, --sjdbGTFfile gencode.v19.annotation.gtf, --sjdbOverhang 36
Gene-level counts taken from STAR ReadsPerGene.out.tab, Counts_secondStrand column (reverse-stranded library)
Per-sample count columns joined on gene ID into a single matrix; STAR summary rows (N_unmapped, N_multimapping, N_noFeature, N_ambiguous) removed
Assembly: hg19 (GRCh37) + mCherry and RfxCas13d
Supplementary files format and content: Tab-delimited text (transcriptomic_count_matrix.tsv); rows = GENCODE v19 gene IDs, columns = raw read counts per sample (NT1-3, TAR1-3)

growth_protocol: 37 degree and 10% CO2 in DMEM media with 10% heat-inactivated fetal bovine serum (Thermo Fisher, 10100147), 100 mg/mL Penicillin/-Streptomycin (Thermo Fisher, 151401220), and 2 mM GlutaMAX (Thermo Fisher, A1286001).

extract_protocol:
Total RNA was isolated by standard Trizol-chloroform extraction according to manufacturer’s instruction (Thermo Fisher, 15596026), followed by DNase treatment with RQ1 RNase-Free DNase according to manufacturer’s instruction (Promega, M6101). RNA integrity was analysed by Agilent 2200 Tapestation (Agilent, G2964AA) with RNA ScreenTape (Agilent, 5067- 5576) according to the manufacturer’s instructions
Poly(A)+ mRNA was enriched from total RNA, then chemically fragmented. First-strand cDNA was synthesised by random priming, followed by second-strand synthesis incorporating dUTP for strand marking. Libraries were prepared using the Illumina Stranded mRNA Prep protocol with adapter ligation and sample indexing, then amplified by PCR with a uracil-sensitive polymerase (yielding reverse-stranded libraries). Library preparation and sequencing were performed by the Australian Genome Research Facility (AGRF), Melbourne.

treatment_protocol: RfxCas13d paired with either non-targeting crRNA (negative control) or mCherry-targeting crRNA

value: mCherry


title: C140_3

description:
Library name: Sample 12
Column name in gene_fpkm.txt: C140_3

value: TNBC cell

value: 140mg/kg CTX


title: HEK293T, mCherry targeting, biol rep 2

description:
Library name: TAR2
Matrix column: TAR2


title: HA807XR3-06

value: Plasma

tag: Sex

value: Female

tag: age


title: HA809BZF-01

tag: mmse

tag: anatomical location


title: HEK293T, non-targeting control, biol rep 2

description:
Library name: NT2
Matrix column: NT2

value: non-targeting


title: C140_1

description:
Library name: Sample 10
Column name in gene_fpkm.txt: C140_1


title: HEK293T, non-targeting control, biol rep 1

description:
Library name: NT1
Matrix column: NT1


title: AA808J1S-04

value: AD

tag: sample collection method

tag: starting amount


title: D01-48h_R1

city: Kagoshima

first: Ayako

last: Nagat

state: Kagoshima

address: 8-35-1 Sakuragaoka

department: Department of Digestive Surgery, Breast and Thyroid Surgery

country: Japan

institute: Kagoshima University

description: Library name: Sample 4

data_processing:
bcl2fastq version 2.15.0 was used for base calling.
Sequence reads were trimmed to remove adapter sequences and low-quality sequences using FastQC version 0.11.9 and MultiQC version 1.14.
Alignment of RNA-seq reads was performed using the GeneGlobe Data Analysis Center (QIAGEN).
Normalization was performed using StrandNGS version 4.0. Annotations were added to reads using miRBase.
The expression levels of miRNAs among samples and groups were compared using CLC Genomics Workbench version 23.0.2.
Assembly: Human hg38
Supplementary files format and content: Processed data files are provided in Microsoft Excel format. The files contain normalized miRNA expression data and comparative expression data between sample 1 and each sample.

source_name: pancreas

growth_protocol: MIA PaCa-2 cells were maintained in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) in a humidified atmosphere containing 5% CO₂ at 37°C.

extract_protocol:
RNA was harvested using TRIzol reagent. One microgram of total RNA was used for the construction of sequencing libraries.
miRNA libraries for miRNA-seq were prepared using the QIAseq miRNA Library Kit according to the manufacturer’s protocol.

treatment_protocol: MIA PaCa-2 cells were treated with 1 μM sotorasib for 0, 6, 24, and 48 hours.

value: pancreas

tag: cell line

value: MIA PaCa-2

value: pancreatic cancer cell

value: sotorasib

tag: time point


title: D01-24h_R1

description: Library name: Sample 3


title: DUP207_Poly_Rep1

city: BAR HARBOR

first: CGDS

last: Data

state: ME

address: 159 OLD BAR HARBOR RD

institute: MDI Biological Laboratory

description: Library name: DUP207_Poly_Rep1

data_processing:
fastq files were run through the nextflow nf-core/rnaseq version 3.14.0 with default parameters and "remove_ribo_rna = true"
Raw counts were run through the CombatSeq R package to remove replicate batch effect
Batch-corrected counts file was uploaded into NIH SEQUIN app and analyzed using DEseq2
Assembly: Ensembl Release 111
Supplementary files format and content: Tab-separated file containing Salmon gene counts
Supplementary files format and content: Comma-separated file containing batch-corrected, non-normalized counts for NIH SEQUIN app
Supplementary files format and content: Comma-separated file containing metadata for NIH SEQUIN app
Library strategy: Polysome-seq

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: C. elegans strains were maintained according to standard procedures on OP50-seeded NGM plates at 20 C. Synchronized populations were generated by bleaching 500-1,000 gravid adults in a solution of 8 mL M9 buffer, 1 mL 6.25 M NaOH, and 1 mL 5% NaOCl for 5-10 minutes. Embryos were pelleted at 1,200 x g for 1 minute, washed three times in 10 mL M9 buffer, and approximately 3,000-3,500 eggs per plate were cultured at 20 C to day 1 of adulthood.

extract_protocol:
Trizol RNA extraction
Roche Kapa stranded mRNASeq kit

treatment_protocol: No treatment was applied. Synchronized worms were grown to day 1 of adulthood, harvested (100-150 uL packed volume), and washed three times in M9 buffer to remove residual bacteria prior to lysis and fractionation.

tag: fraction

value: Polysome

tag: developmental stage

value: synchronized young adults

tag: strain

value: lotr-1(sam117[3xFLAG::gfp::lotr-1]) I

value: whole animal


title: 849_SPF

description: Library name: SPF_4

tag: tissue

value: Duodenum

value: Paneth

value: SPF


title: KA8081GK-06

value: NC

value: Circulating blood

value: Venous

tag: holding temperature


title: D01-6h_R1

description: Library name: Sample 2

tag: cell type

tag: treatment


title: TN_WT1

description:
Library name: Sample 1
WT naive CD8+ T cell

value: lymph nodes and spleen

value: naive CD8+ T cell

tag: genotype

value: WT

value: no treatment


title: DA80C2YS-01

tag: donor id

value: Plasma

tag: disease

value: AD

value: Male


title: 598_SPF

description: Library name: SPF_1


title: C100

description: Library name: Sample 2

value: tumor

value: TNBC cell

value: 100mg/kg CTX


title: D01-0h_R1

description: Library name: Sample 1

value: pancreas

value: MIA PaCa-2

value: pancreatic cancer cell

value: sotorasib


title: PC9 mycoplasma-positive rep 2

city: Amsterdam

first: Elisa

last: Giovannetti

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam University Medical Center

description: Library name: Sample 8

data_processing:
STAR alignment tool (version 2.5.3a) was used for data processing
Assembly: Sequences were mapped to the human reference genome assembly GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for eah Sample

extract_protocol:
Total RNA was extracted using TRIzol reagent following manufacturer's protocol. RNA concentration measured by NanoDrop, quality assessed by Bioanalyzer.
RNA libraries for RNA-seq were preparewd using Illumina NextSeq 500  following manufacturer's instructions.


title: Control, 144 h, r3

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_144h_r3

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 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: iMac


title: C100_3

description:
Library name: Sample 7
Column name in gene_fpkm.txt: C100_3


title: PC9 mycoplasma-positive rep 1

description: Library name: Sample 7


title: PWA15-0611

value: PD

tag: Sex

tag: age

value: Circulating blood

value: Venous


title: PC9 mycoplasma-negative rep 2

description: Library name: Sample 6


title: C100_2

description:
Library name: Sample 6
Column name in gene_fpkm.txt: C100_2


title: Capture Hi-C in wild type mouse bone marrow derived macrophages (rep1)

value: bone marrow derived macrophages

value: Bach1 fl/fl (Control)

tag: cell treatment

value: Vehicle

tag: duration of_treatment_(hours)

tag: capture selection_probes

value: Custom-designed selection probes (SureSelect- Agilent) against BACH1-bound genomic sites


title: PC9 mycoplasma-negative rep 1

description: Library name: Sample 5

tag: cell line


title: AD_Quinn_8

value: Plasma

value: AD

value: Female

tag: mmse

tag: anatomical location

tag: sample collection method

tag: starting amount


title: H1975 mycoplasma-positive rep 2

description: Library name: Sample 4


title: C100_1

description:
Library name: Sample 5
Column name in gene_fpkm.txt: C100_1

tag: tissue

value: tumor

value: TNBC cell

value: 100mg/kg CTX


title: H1975 mycoplasma-positive rep 1

description: Library name: Sample 3


title: H1975 mycoplasma-negative rep 2

description: Library name: Sample 2


title: AA807815-04

value: NC

tag: holding temperature


title: HEK293T, mCherry targeting, biol rep 1

description:
Library name: TAR1
Matrix column: TAR1

value: mCherry


title: NC_4

description:
Library name: Sample 4
Column name in gene_fpkm.txt: NC_4

tag: cell type

value: PBS


title: A_740_Pericardial_fluid

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

description: 10X Genomics Single Cell RNAseq v3.1 NEXT GEM

data_processing:
All raw FASTQs reads were aligned to GRCh38 human reference using the STAR algorithm and quantified through the 10X Genomics cellranger v3.0.0 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat R toolkit for quality control and all downstream analysis. All functions were run with default or recommended parameters, unless specified otherwise. Low quality cells (<300 genes/cell and <20 cells/gene) were excluded from the overall experiment. Gene expression was log normalized to a scale factor of 10,000. To begin unsupervised clustering of cells, a selection of highly variable genes was obtained and used to calculate up to 50 principle components. Significance of principle components was determined using JackStraw analysis and by creating a PCElbowPlot. PCs 1 to 25 were used to run and plot a UMAP plot for all cells.
Assembly: Homo_sapiens : GRCh38
Supplementary files format and content: Filtered feature - barcode HDF5 file output from CellRanger pipeline

source_name: pericardial fluid

extract_protocol:
PF was collected from patients undergoing elective cardiac surgery. Cells were spun at 300g for 5min. Cells were resuspended in 2% BSA in PBS at a final concentration of 30,000 cells/100uL and run through a 40µm cell strainer, before loading into the 10X controller.
The sample was prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v3 Chemistry. Briefly, single cells were partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed using Illumina NovaSeq S2 flow cell at the Center for Health Genomics and Informatics at the University of Calgary.

tag: treatment

value: cardiac surgery


title: NC_3

description:
Library name: Sample 3
Column name in gene_fpkm.txt: NC_3


title: SPF_ileum

description: Library name: SPF_ileum

data_processing:
sequencing data were basecalled and modified bases were identified using Dorado with the model dna_r10.4.1_e8.2_400bps_hac@v4.3.0_5mC_5hmC@v1.
aligned BAM files containing base modification information were processed using the DSS R package to identify differentially modified regions/sites (DMRs/DMSs)
Visualization was performed using the NanoMethViz
Assembly: mm10
Supplementary files format and content: .tsv.gz, DSS based differential modified region result for 5mC and 5hmC

source_name: Small intestine

extract_protocol:
Paneth cells were isolated from the small intestine of GF and SPF PC reporter mice using fluorescence-activated cell sorting (FACS). Genomic DNA was extracted from the sorted Paneth cells using the Qiagen AllPrep DNA/RNA Kit,
No library construction needed for Nanopore based direct DNA sequencing

value: Small intestine

value: Paneth


title: NC_2

description:
Library name: Sample 2
Column name in gene_fpkm.txt: NC_2


title: A_490_Pericardial_fluid

data_processing:
All raw FASTQs reads were aligned to GRCh38 human reference using the STAR algorithm and quantified through the 10X Genomics cellranger v3.0.0 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat R toolkit for quality control and all downstream analysis. All functions were run with default or recommended parameters, unless specified otherwise. Low quality cells (<300 genes/cell and <20 cells/gene) were excluded from the overall experiment. Gene expression was log normalized to a scale factor of 10,000. To begin unsupervised clustering of cells, a selection of highly variable genes was obtained and used to calculate up to 50 principle components. Significance of principle components was determined using JackStraw analysis and by creating a PCElbowPlot. PCs 1 to 25 were used to run and plot a UMAP plot for all cells.
Genome_build: Homo_sapiens : GRCh38
Supplementary_files_format_and_content: Filtered feature - barcode HDF5 file output from CellRanger pipeline


title: A_547_Pericardial_fluid


title: NC_1

description:
Library name: Sample 1
Column name in gene_fpkm.txt: NC_1


title: A_555_Pericardial_fluid


title: EXP1365RNA46

city: TAmpa

first: Yonghong

last: Zhang

state: FL

address: 12902 USF Magnolia Drive

department: Biomedical Informatics

institute: Moffitt Cancer Center

description: Library name: 06S21071075

data_processing:
Illumina NextSeq 500 pair-end reads from RNA-Seq libraries were first adaptor trimmed
STAR v2.5.3a was used for alignment to the reference genome.
RSEM v1.3.0 was used for reads counting to estimate expression level of genes
Library size normalization was performed using DESeq2
No batch correction was performed.
Assembly: GRCh37/GENCODE Release 30
Supplementary files format and content: tab-delimited text file including read counts of each gene (in rows) for each sample (in columns)

source_name: Lymphoma tumor biopsy

extract_protocol: Total RNA-seq libraries were generated from 100 ng of RNA using the Nugen Ovation Human FFPE RNA-Seq kit according to the manufacturer’s instructions

treatment_protocol: Total RNA was extracted using the Allprep Qiagen Kit according to the manufacturer’s instructions

value: Lymphoma tumor biopsy

tag: tissue type

value: Fresh Frozen

tag: pfs days

tag: pfs months

tag: pfs event

tag: age range_at_apheresis


title: A_500_Pericardial_fluid


title: WPL_LSL_1N_MH_B1A

city: Nanjing

first: Xuan

last: Li

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

institute: Nanjing Agricultural University

description:
Library name: B1A
WPL_LSL_1N_MH_B1A

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

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).

value: Head

tag: Sex

value: male

tag: age

value: 1 day after emergence

tag: genotype

tag: strain

value: WPL


title: A_575_Pericardial_fluid


title: EXP1365RNA29

description: Library name: 06S21071074

value: Male


title: A_565_Pericardial_fluid


title: WPL_LSL_1N_MH_B2A

description:
Library name: B2A
WPL_LSL_1N_MH_B2A


title: Sample 6; Knockout Group, Replicate 3

description: Library name: T5

data_processing:
A total of six raw RNA-seq datasets consisting of the KO and CO conditions with three replicates each were analyzed. All RNA-seq datasets were screened for quality control using the FastQC tool v0.12.0 and the MultiQC tool v1.28. For alignment, the raw reads were aligned to the mouse reference genome (GRCm38) using the STAR tool v2.7.11b. Next, the count matrix was generated by the Subread featureCounts v2.1.1, and the differential expression analysis was completed using the DESeq2 tool v1.18.1 to output the differential expression gene list. The genes in the differential expression gene list were filtered using q-value ≤ 0.05 and absolute log2 fold change ≥ 0.58 to obtain significant differentially expressed genes (DEGs).
Assembly: Mus Musculus GRCm38
Supplementary files format and content: Count Matrix

extract_protocol:
Total RNA was isolated from TAMs using the RNeasy Lipid Tissue Mini Kit with on-column DNase digestion according to the manufacturer’s instructions. RNA integrity and quality were assessed using the Eukaryote Total RNA Nano 6000 LabChip assay on an Agilent 2100 Bioanalyzer. RNA concentration was measured by absorbance at 260 nm using a NanoDrop ND-1000 spectrophotometer.
Poly-A enriched mRNA-seq libraries were prepared from 0.5 µg total RNA using Illumina’s TruSeq Stranded mRNA LT library preparation protocol. Poly-A RNA was isolated and converted into cDNA libraries suitable for sequencing. Libraries were sequenced on an Illumina HiSeq 2500 platform.

value: Lung

value: Purified Macrophage

value: MCT2 Knockout


title: EXP1365RNA24

description: Library name: 06S21071002


title: Sample 5; Knockout Group, Replicate 2

description: Library name: T3


title: WPL_LSL_2N_MH_B11

description:
Library name: B11
WPL_LSL_2N_MH_B11


title: Sample 4; Knockout Group, Replicate 1

description: Library name: T2


title: EXP1365RNA22

description: Library name: 06S21071000


title: Sample 3; Control Group, Replicate 3

description: Library name: C3

value: MCT2 Control


title: Sample 1; Control Group, Replicate 1

description: Library name: C1


title: WPL_LSL_2N_MH_B13

description:
Library name: B13
WPL_LSL_2N_MH_B13


title: Epidermis, Mice, DMBA/TPA, Sample 2

city: Boston

first: Vladimir

last: Botchkarev

state: MA

address: 609 Albany Street

institute: Boston University

description:
Library name: Sample 8
Column names in raw Counts Mice Epidermis DMBA TPA Sample 2.xlsx

data_processing:
The bioinformatics analysis of the RNAseq data was performed by the LC Sciences (Houston, TX). Firstly, Cutadapt (Martin, 2011) and Perl scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then, sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Bowtie2 (Langmead and Salzberg, 2012) and Tophat2 (Kim et al., 2013) were used to map reads to the genome of Heterocephalus glaber (https://useast.ensembl.org/Heterocephalus_glaber_female/Info/Index). The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with parametric F-test comparing nested linear models (p value < 0.05) by R package Ballgown. Ballgown was used to generate a list and heatmaps of differentially expressed genes, and in-house generated Perl scripts (LC Science, Houston, TX) were used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses.
Assembly: mm10
Supplementary files format and content: Excel files include FPKM values for each Sample

source_name: Skin epidermis

extract_protocol:
For RNA-Seq analysis of epidermis, skin was collected and cleaned thoroughly to remove any fat or muscle tissue and washed in PBS. Skin was then digested overnight in Dispase II (5mg/ml) in HBSS in +40C. After overnight digestion, epidermis was carefully separated from the dermis, homogenized in TRI Reagent and RNA was isolated using Direct-Zol Miniprep Kit following manufacturer’s protocol.
Libraries were prepared using Next Generation Sequencing Library Preparation kit from NEBNext® according to manufacturer protocol. Ribosomal RNAs (rRNAs) were depleted using NEBNext® rRNA Depletion Kit v2 and libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®. After purifications, quality of the libraries was assessed on 5200 Fragment Analyzer with DNA Chip. For RNA-sequencing library preparation, concentration, quality and integrity of RNA was checked, and RNA with RIN>7 was used for the libraries.

treatment_protocol: Two-stage chemically induced carcinogenesis was performed as described previously (PMID: 19713956). 7,12-dimethylbenz[a]-anthracene (DMBA, 1mg/ml) and 12-O-tetra-decanoylphorbol-13-acetate (TPA, 0.1 mg/ml) were dissolved in acetone. In animals treated with DMBA only, single dose of DMBA (100µl) was applied on the back skin, and skin was harvested on day 10 of experiment. In DMBA/TPA treated animals, after single DMBA application, TPA was applied to the back skin twice a week, and skin was harvested on day 52 after beginning of experiment. Skin of the control animals was treated by aceton.

value: Skin epidermis

value: Epidermis

value: WT

value: DMBA/TPA


title: EXP1365RNA3

description: Library name: 06S21070997

value: Female


title: WPL_LSL_2N_MH_B14

description:
Library name: B14
WPL_LSL_2N_MH_B14


title: Epidermis, Mice, DMBA/TPA, Sample 1

description:
Library name: Sample 7
Column names in raw Counts Mice Epidermis DMBA TPA Sample 1.xlsx


title: EXP1365RNA16

description: Library name: 06S21070996


title: DLBC-03-015

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.

tag: donor id

value: Plasma

tag: disease

value: DLB

tag: mmse

value: Circulating blood

value: Venous


title: WPL_LSL_2N_MH_B15

description:
Library name: B15
WPL_LSL_2N_MH_B15

value: Head

value: male


title: H1975 mycoplasma-negative rep 1

description: Library name: Sample 1

tag: cell line


title: PWA11-0373

tag: tissue

value: PD

tag: anatomical location

tag: sample collection method

tag: starting amount


title: Epidermis, Mice, Control, DMBA/TPA, Sample 1

description:
Library name: Sample 5
Column names in raw Counts Mice Epidermis Control DMBA TPA Sample 1.xlsx

tag: cell type

tag: treatment

value: Aceton


title: A_630_Pericardial_fluid

source_name: Pericardial fluid

tag: transgenic strain

value: cardiac surgery


title: A_477_Pericardial_fluid


title: GF_ileum

description: Library name: GF_ileum

value: Small intestine

value: Paneth


title: Epidermis, Mice, DMBA, Sample 1

description:
Library name: Sample 3
Column names in raw Counts Mice Epidermis DMBA Sample 1.xlsx

value: DMBA


title: EXP1365RNA18

description: Library name: 06S21070993

value: Lymphoma tumor biopsy

tag: tissue type

value: Fresh Frozen

tag: pfs days

tag: pfs months

tag: pfs event

value: Male


title: WPL_LSL_2N_MA_B16

description:
Library name: B16
WPL_LSL_2N_MA_B16

source_name: Abdomen

value: Abdomen

tag: Sex

tag: age

value: 1 day after emergence

tag: genotype

value: WPL


title: EXP1365RNA14

description: Library name: 06S21070991

value: Female

tag: age range_at_apheresis


title: Epidermis, Mice, Control DMBA Sample 2

description:
Library name: Sample 2
Column names in raw Counts Mice Epidermis Control DMBA Sample 2.xlsx

value: Skin epidermis

value: Epidermis

value: WT


title: WPL_LSL_2N_MA_B17

description:
Library name: B17
WPL_LSL_2N_MA_B17

value: male

tag: strain


title: EXP1365RNA10

description: Library name: 06S21070987


title: Epidermis, Mice, Control DMBA Sample 1

description:
Library name: Sample 1
Column names in raw Counts Mice Epidermis Control DMBA Sample 1.xlsx


title: Epidermal keratinocytes, Mice Sample 3

description:
Library name: Sample 6
Column name in raw Counts_Mice_Epid_KCs 485 Sample3.xlsx

data_processing:
The bioinformatics analysis of the RNAseq data was performed by the LC Sciences (Houston, TX). Firstly, Cutadapt (Martin, 2011) and Perl scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then, sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Bowtie2 (Langmead and Salzberg, 2012) and Tophat2 (Kim et al., 2013) were used to map reads to the genome of Heterocephalus glaber (https://useast.ensembl.org/Heterocephalus_glaber_female/Info/Index). The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with parametric F-test comparing nested linear models (p value < 0.05) by R package Ballgown. Ballgown was used to generate a list and heatmaps of differentially expressed genes, and in-house generated Perl scripts (LC Science, Houston, TX) were used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses.
Assembly: Naked Mole-Rat genome (version Ensemble 104.1)
Assembly: mm10
Supplementary files format and content: Excel files include FPKM values for each Sample

extract_protocol:
For RNA-Seq analysis of epidermal keratinocytes, NMR and mouse skin was digested overnight with Dispase II (5mg/ml) and separated epidermis was then digested with TrypLE Express. Detached keratinocytes were washed, labelled with anti-CD49f antibody and FACS-sorted. Keratinocytes were lysed in TRI Reagent and RNA was isolated using Direct-Zol Microprep Kit.
Libraries were prepared using Next Generation Sequencing Library Preparation kit from NEBNext® according to manufacturer protocol. Ribosomal RNAs (rRNAs) were depleted using NEBNext® rRNA Depletion Kit v2 and libraries were prepared using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®. After purifications, quality of the libraries was assessed on 5200 Fragment Analyzer with DNA Chip. For RNA-sequencing library preparation, concentration, quality and integrity of RNA was checked, and RNA with RIN>7 was used for the libraries.

value: Keratinocytes

value: 7-8 week-old FVB mice


title: Epidermal keratinocytes, Mice Sample 2

description:
Library name: Sample 5
Column name in raw Counts_Mice_Epid_KCs 484 Sample2.xlsx


title: WPL_LSL_2N_MA_B18

description:
Library name: B18
WPL_LSL_2N_MA_B18


title: Epidermis, Mice, DMBA, Sample 2

description:
Library name: Sample 4
Column names in raw Counts Mice Epidermis DMBA Sample 2.xlsx


title: Epidermal keratinocytes, Mice Sample 1

description:
Library name: Sample 4
Column name in raw Counts_Mice_Epid_KCs 483 Sample1.xlsx


title: EXP1365RNA6

description: Library name: 06S21070983


title: RNA-seq of day 4 Ly6C low cell populations after CTX injury in Bach1 LysMCre muscle samples (rep3)

data_processing:
alignment to mm10 reference genome with HISAT2 (v2.1.0) using default parameters
transcript assembly with StringTie (v1.3.4d)
generation of coverage (bigWig) files with bamCoverage2 (v3.1.3) of deepTools using -binsize 1 --normalizeUsing RPKM parameters
Assembly: mm10
Supplementary files format and content: bigWig

source_name: tibialis anterior (TA) muscle

growth_protocol: Tiisue extraction,digestion and FACS-based purification of Ly6C+ and Ly6C- macrophages from CTX-injured TA muscles

extract_protocol:
Mice were anaesthetized with isoflurane (adjusted flow rate or concentration to 1.5%) and 50 µl of cardiotoxin (10x10-6 M in PBS) (Latoxan) was injected in the tibialis anterior (TA) muscle. Muscles were recovered for flow cytometry analysis at day 1,2 and 4 post-injury and were dissociated in RPMI containing 0.2% collagenase B (Roche Diagnostics GmbH) at 37°C for 1 hour and filtered through a 100 µm and a 40 µm filter. CD45+ cells were isolated using magnetic sorting (Miltenyi Biotec). For FACS, macrophages were treated with Fcγ receptor blocking antibodies and with 10% normal rat serum: normal mouse serum 1:1 mix, then stained with a combination of PE-conjugated anti-Ly6C antibody (HK1.4, eBioscience), APC-conjugated F4/80 antibody (BM8, eBioscience) and FITC-conjugated Ly6G antibody (1A8, Biolegend). Ly6Chigh F4/80low macrophages, Ly6Clow F4/80high macrophages and Ly6Ghigh Ly6Cint F4/80- neutrophils were quantified and sorted. For RNA extraction, we added Trizol to sorted cell populations and extracted total RNA accrording to manufacturer's protocol.
Indexed cDNA libraries were prepared from 1 µg of total RNA following the TruSeq™ RNA Sample Preparation Kit (Illumina, Inc.) protocol. Briefly, the mRNA Poly-A was selected on oligo (dT) magnetic beads and fragmented by divalent cations at 94°C for 5 min. Reverse transcription was performed using SuperScript II reverse transcriptase (Life Technologies, Inc.) and random primers. After second strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. cDNA libraries were purified and size selected after PCR with AMPure XP beads (Beckman Coulter, Inc, Fullerton, C.A USA).

treatment_protocol: Intramuscular injection of 50 µl of 12 µM cardiotoxin (CTX, L8102-1MG, Latoxan) for 1,2 or 4 days.

value: tibialis anterior (TA) muscle

value: Bach1 fl/fl;LysM Cre+ (Myeloid specific conditional KO)

value: Ly6C- monocytes from TA muscle

tag: duration of treatment (days)


title: WPL_LSL_2N_MA_B19

description:
Library name: B19
WPL_LSL_2N_MA_B19

tag: tissue


title: RNA-seq of day 4 Ly6C low cell populations after CTX injury in Bach1 LysMCre muscle samples (rep2)

value: Intramuscular injection of 50 µl of 12 µM cardiotoxin (CTX, L8102-1MG, Latoxan)


title: EXP1132RNA17

description: Library name: 06S19129601

value: Lymphoma tumor biopsy


title: RNA-seq of day 4 Ly6C low cell populations after CTX injury in Bach1 LysMCre muscle samples (rep1)


title: WPL_LSL_2N_MA_B20

description:
Library name: B20
WPL_LSL_2N_MA_B20


title: EXP1132RNA16

description: Library name: 06S19113734

value: Fresh Frozen


title: RNA-seq of day 1 Ly6C high cell populations after CTX injury in Bach1 LysMCre muscle samples (rep3)

value: Ly6C+ monocytes from TA muscle


title: RNA-seq of day 1 Ly6C high cell populations after CTX injury in Bach1 LysMCre TA muscle samples (rep2)


title: WPL_LSL_1N_MH_B3

description:
Library name: B3
WPL_LSL_1N_MH_B3

value: Head


title: WPL_LSL_2N_MH_B12A

description:
Library name: B12A
WPL_LSL_2N_MH_B12A

value: 1 day after emergence


title: RNA-seq of day 1 Ly6C high cell populations after CTX injury in Bach1 LysMCre TA muscle samples (rep1)


title: EXP1132RNA11

description: Library name: 06S19092856


title: RNA-seq of day 4 Ly6C low cell populations after CTX injury in control TA muscle samples (rep2)

value: Bach1 fl/fl (Control)


title: Sample 2; Control Group, Replicate 2

description: Library name: C2

source_name: Lung

value: Lung

value: Purified Macrophage

value: MCT2 Control


title: EXP1365RNA20

description: Library name: 06S21070999

value: Male


title: WPL_LSL_2N_FH_B21

description:
Library name: B21
WPL_LSL_2N_FH_B21

value: female

value: WPL


title: RNA-seq of day 4 Ly6C low cell populations after CTX injury in control TA muscle samples (rep1)


title: EXP1132RNA9

description: Library name: 06S19087497


title: RNA-seq of day 1 Ly6C high cell populations after CTX injury in control TA muscle samples (rep3)


title: WPL_LSL_2N_FH_B22

description:
Library name: B22
WPL_LSL_2N_FH_B22


title: RNA-seq of day 1 Ly6C high cell populations after CTX injury in control TA muscle samples (rep2)


title: EXP1132RNA8

description: Library name: 06S19085606


title: WPL_LSL_2N_FH_B23

description:
Library name: B23
WPL_LSL_2N_FH_B23


title: RNA-seq in Bach1-deficient mouse bone marrow derived macrophages (LPS, 24h, rep3)

source_name: bone marrow derived macrophages

extract_protocol:
Total RNA was isolated from cells using Tri Reagent (MRC) according to the manufacturer’s protocol.
Indexed cDNA libraries were prepared from 1 µg of total RNA following the TruSeq™ RNA Sample Preparation Kit (Illumina, Inc.) protocol. Briefly, the mRNA Poly-A was selected on oligo (dT) magnetic beads and fragmented by divalent cations at 94°C for 5 min. Reverse transcription was performed using SuperScript II reverse transcriptase (Life Technologies, Inc.) and random primers. After second strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. cDNA libraries were purified and size selected after PCR with AMPure XP beads (Beckman Coulter, Inc, Fullerton, C.A USA).

treatment_protocol: Treatments with 10ng/ml LPS (0,1,4,24h) of mouse bone marrow-derived macrophages occurred at Day7 of differentiation after an overnight incubation in fresh medium.

value: bone marrow derived macrophages

tag: genotype wt wt bach1-/- (exon 3+4 deletion) bach1-/- (exon 3+4 deletion)

value: Bach1-/- (exon 3+4 deletion)

value: 10ng/ml LPS-SM Ultrapure (Invivogen-LPS from S. minnesota R595)

tag: duration of treatment (hours)


title: EXP1132RNA4

description: Library name: 06S19069559


title: RNA-seq in Bach1-deficient mouse bone marrow derived macrophages (LPS, 24h, rep2)


title: RNA-seq of day 1 Ly6C high cell populations after CTX injury in control TA muscle samples (rep1)

value: tibialis anterior (TA) muscle


title: WPL_LSL_2N_FH_B24

description:
Library name: B24
WPL_LSL_2N_FH_B24


title: RNA-seq in Bach1-deficient mouse bone marrow derived macrophages (LPS, 24h, rep1)


title: EXP1132RNA3

description: Library name: 06S19065942


title: RNA-seq in Bach1-deficient mouse bone marrow derived macrophages (LPS, 4h, rep3)


title: WPL_LSL_2N_FH_B25

description:
Library name: B25
WPL_LSL_2N_FH_B25


title: WPL_LSL_2N_FA_B26A

description:
Library name: B26A
WPL_LSL_2N_FA_B26A

value: Abdomen


title: EXP1132RNA2

description: Library name: 06S19065123

value: Lymphoma tumor biopsy

value: Female


title: RNA-seq in Bach1-deficient mouse bone marrow derived macrophages (LPS, 4h, rep1)


title: RNA-seq in Bach1-deficient mouse bone marrow derived macrophages (LPS, 4h, rep2)


title: RNA-seq in Bach1-deficient mouse bone marrow derived macrophages (LPS, 1h, rep3)


title: V_3

city: Beijing

first: zhiyang

last: xie

address: No. 33, Badachu Road, Shijingshan District

department: Plastic Surgery Hospital

institute: Chinese Academy of Medical Sciences / Peking Union Medical College

description:
Library name: V_3
Empty-vector lentivirus group

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to hg38  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text files include gene count and FPKM value for each Sample

source_name: cell culture

extract_protocol:
RNA was extracted from cell culture using TRIzol reagent. Briefly, culture samples were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA is enriched for small RNAs, followed by 3' and 5' adapter ligation. Reverse transcription generates cDNA, which is then PCR amplified with indexed primers. The final library is size-selected (typically ~150 bp) and validated by Bioanalyzer before sequencing on an DNBSEQ flow cell.

value: cell culture

tag: cell line

value: Human Umbilical Vein Endothelial Cells (HUVECs)

value: Empty-vector lentivirus group


title: RNA-seq in Bach1-deficient mouse bone marrow derived macrophages (LPS, 1h, rep2)

tag: cell type


title: WPL_LSL_2N_FA_B27

description:
Library name: B27
WPL_LSL_2N_FA_B27

value: 1 day after emergence


title: RNA-seq in Bach1-deficient mouse bone marrow derived macrophages (LPS, 1h, rep1)

tag: treatment


title: V_2

description:
Library name: V_2
Empty-vector lentivirus group


title: WPL_LSL_2N_FA_B28A

description:
Library name: B28A
WPL_LSL_2N_FA_B28A


title: V_1

description:
Library name: V_1
Empty-vector lentivirus group


title: RNA-seq in Bach1-deficient mouse bone marrow derived macrophages (LPS, 0h, rep1)


title: WPL_LSL_2N_FA_B30

description:
Library name: B30
WPL_LSL_2N_FA_B30


title: RNA-seq in Bach1-deficient mouse bone marrow derived macrophages (LPS, 0h, rep3)


title: RNA-seq in Bach1-deficient mouse bone marrow derived macrophages (LPS, 0h, rep2)


title: Epidermis, Mice, Control, DMBA/TPA, Sample 2

description:
Library name: Sample 6
Column names in raw Counts Mice Epidermis Control DMBA TPA Sample 2.xlsx

value: Skin epidermis

value: Epidermis

value: WT

value: Aceton


title: RNA-seq in wild type mouse bone marrow derived macrophages (LPS, 24h, rep3)


title: WPL_LSL_3N_FH_B31

description:
Library name: B31
WPL_LSL_3N_FH_B31

value: Head

value: female


title: O_3

description:
Library name: O_3
OASL-overexpressing lentivirus group

value: OASL-overexpressing lentivirus group


title: RNA-seq in wild type mouse bone marrow derived macrophages (LPS, 24h, rep2)

value: bone marrow derived macrophages


title: RNA-seq in wild type mouse bone marrow derived macrophages (LPS, 24h, rep1)

value: 10ng/ml LPS-SM Ultrapure (Invivogen-LPS from S. minnesota R595)


title: O_2

description:
Library name: O_2
OASL-overexpressing lentivirus group


title: WPL_LSL_1N_MH_B4A

description:
Library name: B4A
WPL_LSL_1N_MH_B4A

value: male

value: WPL


title: RNA-seq in wild type mouse bone marrow derived macrophages (LPS, 4h, rep2)


title: O_1

description:
Library name: O_1
OASL-overexpressing lentivirus group


title: RNA-seq in wild type mouse bone marrow derived macrophages (LPS, 4h, rep3)


title: RNA-seq in wild type mouse bone marrow derived macrophages (LPS, 4h, rep1)


title: WPL_LSL_3N_FH_B32

description:
Library name: B32
WPL_LSL_3N_FH_B32


title: RNA-seq in wild type mouse bone marrow derived macrophages (LPS, 1h, rep3)


title: RNA-seq in wild type mouse bone marrow derived macrophages (LPS, 1h, rep2)


title: RNA-seq in wild type mouse bone marrow derived macrophages (LPS, 1h, rep1)


title: WPL_LSL_3N_FH_B33

description:
Library name: B33
WPL_LSL_3N_FH_B33


title: WPL_LSL_3N_FH_B34A

description:
Library name: B34A
WPL_LSL_3N_FH_B34A


title: HEK293T with RNASET2 KD, Palmitate treated, replicate 3

city: Austin

first: Alan

last: Lambowitz

state: TX

address: 2500 Speedway

institute: University of Texas at Austin

description: Library name: KD_PA_3

data_processing:
Illumina TruSeq adapters and PCR primer sequences were trimmed from the reads with Cutadapt v2.8 (https://github.com/marcelm/cutadapt) (sequencing quality score cut-off at 20; p- value <0.01) and reads <15-nt after trimming were discarded. To minimize mismapping, we used a sequential mapping strategy. First, reads were mapped to the human mitochondrial genome (Ensembl GRCh38 Release 93) and the Escherichia coli genome (GeneBank: NC_000913) using HISAT2 v2.1.0 (https://github.com/DaehwanKimLab/hisat2) with customized settings (-k 10 --rfg 1,3 --rdg 1,3 --mp 4,2 --no-mixed --no-discordant -- no-spliced- alignment) to identify reads derived from mitochondrial and E. coli RNAs (denoted Pass 1). Unmapped reads from Pass1 were then mapped to a collection of customized references sequences for human sncRNAs (miRNA, tRNA, Y RNA, Vault RNA, 7SL RNA, 7SK RNA) and rRNAs (2.2-kb 5S rRNA repeats from the 5S rRNA cluster on chromosome 1 (1q42, Gene- Bank: X12811) and 43-kb 45S rRNA containing 5.8S, 18S and 28S rRNAs from clusters on chromosomes 13,14,15, 21, and 22 (GeneBank: U13369), using HISAT2 with the following settings -k 20 --rdg 1,3 --rfg 1,3 --mp 2,1 --no-mixed --no-discordant --no-spliced-alignment -- norc (denoted Pass 2). Unmapped reads from Pass 2 were then mapped to the human genome reference sequence (Ensembl GRCh38 Release 93) using HISAT2 with settings optimized for nonspliced mapping (-k 10 --rdg 1,3 --rfg 1,3 --mp 4,2 --no-mixed --no-discordant --no-spliced- alignment) (denoted Pass 3) followed by splice aware mapping (-k 10 --rdg 1,3 --rfg 1,3 --mp 4,2 --no-mixed --no-discordant --dta) (denoted Pass 4). For reads that mapped to multiple genomic loci with the same mapping score in passes 3 to 4, the alignment with the shortest distance between the two paired ends (i.e., the shortest read span) was selected. In the case of ties (i.e., reads with the same mapping score and read span), reads mapping to a chromosome were selected over reads mapping to scaffold sequences, and in other cases, the read was assigned randomly to one of the tied choices. The filtered multiply mapped reads were then combined with the uniquely mapped reads from Passes 3-4 by using SAMtools v1.10 (https://github.com/samtools/samtools).
To generate counts for different genomic features, the mapped reads were intersected with Ensembl GRCh38 Release 93 gene annotations plus the RNY5 gene and its 10 pseudogenes, which were not annotated in this release. Annotations for repeat elements were from RepBase (https://www.girinst.org/repbase/), and annotations for hairpin miRNA and mature miRNA were from miRBase (https://www.mirbase.org/). Coverage of each feature was calculated by BEDTools v2.29.2 (https://bedtools.readthedocs.io/en/latest/content/bedtools-suite.html). To avoid miscounting reads with embedded sncRNAs that were not filtered out in Pass 2 (e.g., snoRNAs), reads were first intersected with sncRNA annotations, and the remaining reads were then intersected with the annotations for protein-coding gene RNAs, lincRNAs, antisense RNAs, and other lncRNAs to get the read count for each annotated feature.
Read counts were normalized by using DESeq2 (https://github.com/thelovelab/DESeq2) with sample size factors estimated based on counts from nuclear protein-coding genes. Likelihood ratio test (LRT) was then used to identify any genes that show change in expression across datasets with different treatments in different cells.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Embryonic kidney

growth_protocol: HEK 293T cells were cultured in Dulbecco’s Modified Eagle Medium containing 4500 mg/L glucose and 110 mg/L pyruvate supplemented with 10% heat-inactivated FBS and 2 mM glutamine at 37 °C with 5% CO₂.

extract_protocol:
RNA was extracted using TRIzol and the Direct-zol RNA Miniprep kit (Zymo Research R2050).
Total RNA was prepared for TGIRT-seq library preparation using a two-fraction method. Briefly, following treatment with DNase I, rRNA was depleted (Ribocop depletion kit, Lexogen 144.24), and size fractionated into short (<200 nt) and long RNAs fractions according to RCC5 protocol. Long RNAs were fragmented to ~200 nucleotides (NEB Next RNA Fragmentation Module, New England Biolabs E6150S). Small and fragmented large RNAs were pooled prior to treatment with T4 Polynucleotide Kinase (Lucigen P0503K). Each step of RNA processing was evaluated and quantitated using an RNA 6000 Pico Chip mRNA assay on an Agilent 2100 Bioanalyzer. TGIRT-seq library construction was as previously described using the low salt template switching reaction buffer.

treatment_protocol: Actively growing cells (~60-65% confluency) were treated by supplementing growth media with 1 mM palmitic acid freshly complexed with 0.5 mM fatty acid-free BSA as a carrier or with 0.5 mM fatty acid-free BSA as vehicle control, for 8 hours.

value: Embryonic kidney

value: kidney epithelial cells

value: RNASET2 KD

value: Palmitate

tag: batch

tag: treatment time

value: 8 hours treatment


title: HEK293T with RNASET2 KD, Palmitate treated, replicate 4

description: Library name: KD_PA_4


title: RNA-seq in wild type mouse bone marrow derived macrophages (LPS, 0h, rep2)


title: RNA-seq in wild type mouse bone marrow derived macrophages (LPS, 0h, rep3)


title: RNA-seq in wild type mouse bone marrow derived macrophages (LPS, 0h, rep1)


title: WPL_LSL_3N_FH_B35A

description:
Library name: B35A
WPL_LSL_3N_FH_B35A

value: 1 day after emergence


title: HEK293T with RNASET2 KD, Palmitate treated, replicate 1

description: Library name: KD_PA_1


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages, untreated (rep2)

data_processing:
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
Assembly: mm10
Supplementary files format and content: bedgraph

extract_protocol:
Mouse bone marrow-derived macrophages were cross-linked using DSG and formaldehyde-based double cross-linking method and processed for ChIP.
Libraries were prepared with the TruSeq ChIP library systems (Illumina) according to the manufacturer protocol.

tag: chip antibody

value: Rabbit polyclonal to RNA polymerase II CTD repeat YSPTSPS (phospho S2) (Abcam - ab5095)

tag: cell treatment

value: No treatment

tag: duration of_treatment_(hours)


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages, untreated (rep1)


title: WPL_LSL_3N_FA_B36A

description:
Library name: B36A
WPL_LSL_3N_FA_B36A

value: Abdomen

tag: Sex


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 20 uM heme (rep2)

value: 20μΜ Hemin (Sigma 51280)


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 20 uM heme (rep1)


title: TN_cKO2

city: Hangzhou

first: Fan

last: Zhao

address: 866 Yuhangtang Road, Xihu District

institute: Zhejiang University

description:
Library name: Sample 5
Hspa9 cKO naive CD8+ T cell

data_processing:
Raw sequencing reads were quality-controlled and adapter-trimmed using fastp to generate clean data. These clean reads were aligned to the mouse referenceG genome (GRCm39) using HISAT2 (v2.2.1), and gene expression levels were quantified using featureCounts (v2.0.6). Differential expression analysis was performed with DESeq2 (v1.42.0), applying a significance threshold of adjusted p-value < 0.05 and |log2(fold change)| > 1.
Assembly: GRCm39
Supplementary files format and content: excel file includes RPKM values for each Sample

source_name: lymph nodes and spleen

extract_protocol:
WT and cKO naive CD8⁺ T cells, along with their in-vitro-differentiated effector and memory subsets, were lysed in TRIzol reagent (Invitrogen). Total RNA was extracted from the lysates using the Direct-zol RNA MiniPrep kit (Zymo Research) according to the manufacturer's protocol.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained.

value: lymph nodes and spleen

value: naive CD8+ T cell

value: cKO

value: no treatment


title: WPL_LSL_3N_FA_B37A

description:
Library name: B37A
WPL_LSL_3N_FA_B37A

value: female

tag: age


title: HEK293T with RNASET2 KD, BSA treated, replicate 4

description: Library name: KD_BSA_4

tag: genotype

value: BSA


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 20 uM heme and 100 ng LPS (rep2)

description: mm_BMDM_Bach1KO_PolII_20uM_heme_100ng_LPS_rep2

source_name: mouse bone marrow derived macrophages

value: bone marrow derived macrophages


title: 846_SPF

description: Library name: SPF_3

data_processing:
ATAC-seq fastq file was quality checked using fastQC. Nextera transpose adapter reverse complement was removed from the 3′ end of the ATAC-Seq reads using CutAdapt, version 1.9.1. Trimmed reads were aligned to the mouse genome build mm9 using Bowtie2. Picard (v2.18.27) was used to determine the median alignment size of each alignment bam file.
Peak region bed files were called from each alignment bam file using MACS2 (v2.1.0). MACS2 was run with a “shift” distance of −0.5 times the median alignment size and an “extsize” distance equal to the median alignment size for each alignment bed file.
.  Peak files were filtered against the ENCODE blacklist and BEDtools was used to subtract the sites on the ENCODE blacklist. The Integrative Genomics Viewer (IGV 2.4.13) was used to visualize ATAC-seq bigwig tracks. DiffBind (v2.4.7) FDR < 0.01 as the cutoff for significance
Assembly: mm9
Supplementary files format and content: Bigwig File

source_name: Duodenum

extract_protocol:
For ATAC-seq, freshly FACS-isolated tdTomato+ live Paneth cells from GF or SPF Paneth cell reporter mice were processed according to the OMNI-ATAC-Seq protocol
Samples were then purified with the Zymo DNA Clean and Concentrator-5 kit and pre-amplified using the NEBnext 2X Master Mix for 5 cycles. 5 μL of the pre-amplified sample was subjected to qRT-PCR amplification for additional 20 cycles to determine the optimal additional cycles of the remaining 45 μL of sample. The PCR-amplified libraries were purified; fragment size was selected using Pippin Prep and sequenced on Illumina NextSeq 150 cycle mid output

value: Duodenum

value: Paneth

value: SPF


title: HEK293T with RNASET2 KD, BSA treated, replicate 3

description: Library name: KD_BSA_3

value: Embryonic kidney

value: kidney epithelial cells

value: RNASET2 KD


title: WPL_LSL_3N_FA_B38

description:
Library name: B38
WPL_LSL_3N_FA_B38

value: 1 day after emergence

value: WPL


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 20 ng/ml IL-4 (rep2)

value: Rabbit polyclonal to RNA polymerase II CTD repeat YSPTSPS (phospho S2) (Abcam - ab5095)

value: 20ng/mL IL-4 (Peprotech 214-14)


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 20 uM heme and 100 ng LPS (rep1)

description: mm_BMDM_Bach1KO_PolII_20uM_heme_100ng_LPS_rep1

value: 20μΜ Hemin (Sigma 51280)


title: HEK293T with RNASET2 KD, BSA treated, replicate 2

description: Library name: KD_BSA_2

value: 8 hours treatment


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 20 ng/ml IFNg (rep2)

value: 20ng/mL IFNgamma (Biotechne 485-MI-100)


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 20 ng/ml IL-4 (rep1)


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 20 ng/ml IFNg (rep1)


title: HEK293T with RNASET2 KD, BSA treated, replicate 1

description: Library name: KD_BSA_1


title: WPL_LSL_3N_FA_B39A

description:
Library name: B39A
WPL_LSL_3N_FA_B39A

value: Abdomen


title: WPL_LSL_3N_FA_B40A

description:
Library name: B40A
WPL_LSL_3N_FA_B40A

value: female


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 1 uM ODN1286 (rep2)

value: 1μΜ ODN1826 (Invivogen tlrl-1826-1)


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 1 uM ODN1286 (rep1)

value: bone marrow derived macrophages


title: HEK293T with control shRNA, Palmitate treated, replicate 4

description: Library name: SCR_PA_4

value: WT

value: Palmitate


title: WPL_LSL_1N_MH_B5D

description:
Library name: B5D
WPL_LSL_1N_MH_B5D

value: Head

value: male


title: HEK293T with control shRNA, Palmitate treated, replicate 3

description: Library name: SCR_PA_3

value: Embryonic kidney

value: kidney epithelial cells


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 1 ug/ml R848 (rep2)

value: 1μg/mL (Invivogen tlrl-r848-5)


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 1 ug/ml R848 (rep1)


title: WPL_LSL_1N_MA_B6A

description:
Library name: B6A
WPL_LSL_1N_MA_B6A

value: 1 day after emergence

value: WPL


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 10 ug/ml HMW:PIC (rep2)

description: mm_BMDM_Bach1KO_PolII_10_ug_HMW_PIC_rep2

value: Rabbit polyclonal to RNA polymerase II CTD repeat YSPTSPS (phospho S2) (Abcam - ab5095)

value: 10μg/mL (Invivogen tlrl-pic)


title: HEK293T with control shRNA, Palmitate treated, replicate 2

description: Library name: SCR_PA_2

value: 8 hours treatment


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 10 ug/ml HMW:PIC (rep1)

description: mm_BMDM_Bach1KO_PolII_10_ug_HMW_PIC_rep1


title: WPL_LSL_1N_MA_B7

description:
Library name: B7
WPL_LSL_1N_MA_B7


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 10 ng/ml IFNb (rep2)

value: 10ng/mL IFNbeta (Biotechne 8234-MB)


title: HEK293T with control shRNA, Palmitate treated, replicate 1

description: Library name: SCR_PA_1


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 10 ng/ml IFNb (rep1)


title: WPL_LSL_1N_MA_B8

description:
Library name: B8
WPL_LSL_1N_MA_B8

value: Abdomen


title: HEK293T with control shRNA, BSA treated, replicate 4

description: Library name: SCR_BSA_4

value: BSA


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 100 uM heme (rep2)

value: 100μΜ Hemin (Sigma 51280)


title: WPL_LSL_1N_MA_B9

description:
Library name: B9
WPL_LSL_1N_MA_B9


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 100 uM heme (rep1)

value: bone marrow derived macrophages


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 100 ng/ml LPS (rep1)

value: 100ng/ml LPS-SM Ultrapure (Invivogen-LPS from S. minnesota R595)


title: HEK293T with control shRNA, BSA treated, replicate 3

description: Library name: SCR_BSA_3

value: WT


title: PolII ChIP-seq in Bach1-deficient mouse bone marrow derived macrophages treated with 100 ng/ml LPS (rep2)


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages, untreated (rep2)

value: No treatment


title: HEK293T with control shRNA, BSA treated, replicate 2

description: Library name: SCR_BSA_2


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages, untreated (rep1)


title: HEK293T with control shRNA, BSA treated, replicate 1

description: Library name: SCR_BSA_1


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 uM heme (rep1)

value: 20μΜ Hemin (Sigma 51280)


title: PolII ChIP-seq in wild type mouse bone marrow derived macrophages treated with 20 uM heme (rep2)