title: RBG7392_KitHi_E10_G2VInt


title: RBG7380_KitHi_E10_G2VInt

status: Public on Apr 27 2020

type: SRA

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

country: China

institute: Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic

data_processing:
Raw reads were aligned to Mus musculus genome (GRCm38.81) using G-SNAP (version 2015-09-29) with the following parameters: –B 5 –n 1 –N 1 –Q. HTSeq-count (version 0.6.0) was run to assign mapped reads to Ensembl genes (GRCm38.81).
Genome_build: GRCm38.81
Supplementary_files_format_and_content: HT-Seq counts / gene counts (.txt)

molecule: total RNA

organism: Mus musculus

source_name: IAHC cells

growth_protocol: Gata2V/+ embryos were generated by timed matings of C57BL/6HsdJOla (Ly5.2) wild-type females with Gata2V/V (Kaimakis et al., 2016) males (>10 backcrosses onto C57BL/6HsdJOla).Transplantations were performed with B6.SJL-PtprcaPepcb/BoyCrl (Ly5.1/5.1, 2-4 month old) recipients and carrier spleen cells.

extract_protocol:
AGM (aorta-gonad-mesonephros) regions (including trunk portion of the vitelline and umbilical arteries) of E10/11 embryos were dissected as previously described (Medvinsky et al., 2008). Single cell suspensions were prepared by enzymatically digesting tissues at 37°C in 0.125% type 1 collagenase (C0130, Sigma-Aldrich) for 45 min, after which tissues were further mechanically disrupted with a P1000 pipette. Cells were subsequently passed over a 0.35 µm strainer, collagenase washed away with PBS+10%FBS+1%P/S (PFP), spun down (234g) and resuspended in PFP for flow cytometric antibody staining. Cells were incubated at 4°C for 30 min in PFP with directly conjugated antibodies against CD31 (CD31-BV605, 1:100, cat# 102427, Biolegend), cKit (cKit-BV421, 1:200, cat.# 562609, BD) and CD27 (CD27-APC, 1:75, cat.# 17-0271-82. eBioscience). Excess of antibodies was washed away with PFP before fluorescence activated cell sorting (FACS) on an AriaII (BD). Dead cell exclusion was by Hoechst 33342 and gates were set based on unstained WT and fluorescence-minus-one (FMO) controls. Sorted single cells were collected in 50% FBS/PBS for functional analyses (transplantation + bulk CFU-C assay). Both collagenase and FCS were batch tested for optimal AGM conditions.
Pooled libraries were run on the Illumina Hi-Seq 2500.
Libraries were prepared using the Illumina Nextera XT Libraries were prepared using the Illumina Nextera XT DNA preparation kit.

tag: condition

tag: days

tag: cell type

value: IAHC cells

tag: cluster (all cells)

tag: cluster (nocd27+ cells)

tag: clustertype (nocd27+ cells)


title: P2671_N712-S508

city: Barcelona

first: Gustavo

last: Rodriguez-Esteban

state: Catalonia

address: C. Baldiri Reixac, 4; Barcelona Science Park

department: Development

country: Spain

institute: Centro Nacional de Análisis Genómico

data_processing:
Primary data analysis and QC assessment was carried out with the standard Illumina pipeline following the manufacturer's protocol. Illumina Real-Time Analysis (RTA) 1.18.66.3 software used for basecalling.
Smart-seq2 libraries were mapped as paired-end reads using STAR 2.5.4b and RSEM 1.3.0 for the quantification.
10x RNA-Seq libraries: We processed sequencing reads with CellRanger v3.0.0 for the PBMC data and v3.0.2 for the CLL and T-cell activation data. We used the human GRCh38 assembly as reference genome. To specify the hashtag oligonucleotide (HTO) libraries, the cDNA libraries and the HTO sequences, we followed the “Feature Barcoding Analysis” pipeline, available at https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis. We set the --chemistry and --expect-cells flags of cellranger count to “SC3Pv3" and “5000”, respectively. We demultiplexed cell hashtags as described in Stoeckius et al. for each batch and donor separately. Briefly, we normalized hashtag oligonucleotide (HTO) counts using a centered log ratio (CLR), in which each count is divided by the geometric mean of a HTO across cells and log-transformed. We then clustered barcodes using k-medoids with k equal to the number of conditions (k=4 for batch 03, and k=8 for batch 04), which allowed us to identify the background distribution of each HTO. We re-clustered Male 04 with k=3, as no clear signal for the HTO “24h 4ºC” was detected. Subsequently, we considered the top 0.5% normalized HTO counts of the background distribution as outliers and excluded them. We classified barcodes to a given condition if the normalized HTO counts of that condition exceeded the 0.99 quantile. We discarded both barcodes that were assigned to more than one condition (multiplets) and barcodes that were not assigned to any condition (negatives). In subsequent datasets (CLL and T-cell activation), we demultiplexed the HTO with Seurat’s built-in functions.
10X ATAC-Seq libraries were processed with the Cell Ranger ATAC 1.1.0 pipeline
Quality control and normalization: We performed quality control (QC) and normalization separately for each dataset (PBMC, CLL, T-cell activation). Following the guidelines from Luecken et al.], we inspected the distributions of three main QC metrics: library size (total UMI), library complexity (number of detected genes) and mitochondrial expression. Importantly, we analyzed these metrics jointly to ensure that cells with high mitochondrial expression were not metabolically active. Finally, we analyzed one of the CLL donors independently as it showed markedly different distributions in QC metrics. We classified as damaged cells those barcodes with an aberrantly low number of UMI and genes, or with an abnormally high mitochondrial expression. Likewise, we classified as doublets those barcodes that possessed and aberrantly large library size and complexity. We also leveraged DoubletFinder to detect doublets that shared the same HTO and were not outliers in any qc metric. We ruled out genes that were detected in less than 10 (CLL) or 15 cells (T-cell activation). Finally, we used the Scran 1.10.2 package to normalize UMI counts with cell-based size factors.
Smart-seq2 validation: To confirm that the results obtained from 10x Genomics-derived data were technology-independent, we profiled the transcriptome of 376 CD3+ T-cells with Smart-seq2[30]. The cells originated from the same donors as in the 10x Genomics experiments, and were distributed across four 96-well plates (all time points per plate). We discarded 60 cells that either had <75,000 or >1,000,000 total counts, <435 detected genes or a mitochondrial expression >20%. Similarly, we filtered out 6,542 genes that had an average expression across cells <1. We normalized gene counts with the Scran package, which removed the batch effect between plates.
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene expression matrices:    10x Genomics and ATAC-Seq: Each matrix is stored in the Market Exchange Format (MEX) for sparse matrices. It also contains tab-separated values (TSV) files with feature and barcode sequences corresponding to row and column indices respectively. In addition, for ATAC-Seq data, a BED file with the genome coordinates for the peaks is included.      Smart-seq2: Tab-separated values (TSV) files containing gene expression values as row counts.

molecule: polyA RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
Peripheral venous blood samples were collected by venipuncture from two voluntary blood donors, one male and one female. Blood samples were collected in ACD-tubes and stored at room temperature (RT) or 4ºC. In the former condition peripheral blood mononuclear cells (PBMC) were isolated at 2, 8, 24 and 48 h. For samples stored at 4ºC, PBMC were isolated at 24 and 48hrs. PBMC separation was performed using Ficoll density gradient centrifugation. For each condition, 12 ml of blood were diluted with an equal volume of pre-warmed RPMI 1640 culture medium (Lonza). The diluted blood was then carefully layered onto a Leucosep tube (Greiner Bio‐One) prefilled with 15 ml of Ficoll-Plus (GE Healthcare Biosciences AB) and centrifuged for 15 min at 800 x g and RT (without acceleration and brake). After centrifugation, PBMC were collected with a sterile Pasteur pipette into a 50 ml tube, diluted up to 10 ml with pre-warmed RPMI medium and centrifuged for 10 min, at 400 x g and RT. Following a second washing step with 5 ml of RPMI medium and a 5 min centrifugation, PBMC were resuspended in 8 aliquots of freezing media. Freezing media consisted of RPMI 1640 with 20% heat-inactivated fetal bovine serum (Sigma-Aldrich), 10% DMSO (Sigma-Aldrich) and Penicillin-Streptomycin 1:1000 (Lonza). 1 ml aliquots, with approximately 1x10e6 cells/ml, were gradually frozen using a commercial freezing box (Mr. Frosty, Nalgene) at -80°C for 24 h and then stored in a vapor–phase liquid nitrogen tank at -150ºC.
Cryopreserved (-80ºC) PBMC samples were rapidly thawed in a 37ºC water bath. Each sample was transferred into a 15 ml Falcon using a 1000 ul cut tip without mixing by pipetting. Next, 1 ml of 37ºC pre-warmed media (Hibernate-A supplemented with 10% FCS; ThermoFisher) was added drop-wise with gentle swirling of the sample. After 1 min incubation, 2 ml of pre-warmed media were added and incubated for 1 min. Next, 5 ml pre-warmed media was gently added, inverted and incubated (1 min). This step was repeated once. Finally, the samples were centrifuged at 700 x g for 5 min (4ºC). The supernatant was removed and the pellets re-suspended in 100 ul of Cell staining buffer (BioLegend). Of note, we did not observe an increase of damaged/dead cells (cell viability staining) towards the later time points with an average viability of 95% (range: 88-98%) across time points. An increased fraction of debris could be observed at 24 and 48 hours, which, however, did not result in reduced data quality (e.g. proportion of excluded cells) during data analysis (Additional file 7: Table 6).
CLL patient samples were obtained from freshly extracted blood, stored either at RT or 4ºC. Mononuclear cells were isolated after Ficoll density gradient centrifugation, at 2, 4, 6, 8 and 24 h after patient blood extraction. The cells were directly cryopreserved with freezing media (RPMI 1640 with 20% FBS and 10% DMSO), in the concentration of 5-10x10e6 cells/ml, according to standarized protocol. The tumor cell content of all the samples was >80%, as assassed by immunostaining of CD19, CD20, CD5 and CD45 followed by flow cytometry. All patients gave informed consent for their participation in the study according to International Cancer Genome Consortium (ICGC) guidelines.
Cell hashing was performed following manufacturer’s instructions (Cell hashing and Single Cell Proteogenomics Protocol Using TotalSeq™ Antibodies; BioLegend). Therefore, samples were incubated 10 min at 4ºC with Human TruStain FcX™ Fc Blocking reagent (BioLegend). Next, sample-specific TotalSeq antibodies (anti-human Hashtag 1-8, Biolegend) were added with subsequent incubation on ice for 45 min. Cells were washed once with cold 1X PBS supplemented with 0.0005% BSA (ThermoFisher) and pelleted at 700 x g for 5 minute. A single cell solution was obtained resuspending the pellet in 1X PBS (0.0005% BSA) and filtering it through a 40 µm cell strainer. The cells were counted in an automatic cell counter (Countess v.2, ThermoFisher).
Single-cell ATAC sequencing:
For the single-cell ATAC-seq experiments, we analyzed one PBMC and one CLL sample isolated after 0 h, 8 h and 24 h of blood storage at room temperature before cryopreservation. Frozen samples were rapidly thawed in a 37°C water bath. Each sample was transferred into a 15 ml Falcon using a 1000 µl cut tip without mixing by pipetting. Next, 1 ml of 37°C pre-warmed media (Hibernate-A supplemented with 10% FCS) was added drop-wise with gentle swirling of the sample. After 1 min of RT incubation, additional 2 ml of pre-warmed media were added. The samples were again kept at RT for 1 min, before 5 ml of pre-warmed media were gently added. This step was repeated once. Then, samples were centrifuged at 700 x g for 5 min. Supernatant was removed and the pellets resuspended in 500 µl of PBS supplemented with 0.05% BSA. Cell concentration and viability were determined with a TC20™ Automated Cell Counter.
Nuclei isolation was performed following the “Nuclei Isolation for Single Cell ATAC Sequencing demonstrated protocol” (10x Genomics). Briefly, 1,000,000 cells from the CLL sample and 300,000 cells from PBMC, were transferred to a 1.5 ml microcentrifuge tube and centrifuged at 500 x g for 5 min at 4°C. The supernatant was removed without disrupting the cell pellet and 100 µl of chilled Lysis Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20; 0.1% Nonidet P40 Substitute; 0.01% Digitonin and 1% BSA) were added and pipette-mixed 10 times. Samples were then incubated on ice during 3 min. Following lysis, 1 mL of chilled Wash Buffer (10 mM Tris-HCl (pH 7.4); 10 mM NaCl; 3 MgCl2; 0.1% Tween-20 and 1% BSA) was added and pipette-mixed. Nuclei were centrifuged at 500 x g for 5 min at 4°C and the supernatant removed without disrupting the pellet. Based on the starting number of cells and assuming a 50% loss during the procedure, nuclei were resuspended into the appropriate volume of chilled Diluted Nuclei Buffer (10x Genomics) in order to achieve a nuclei concentration of 1,540-3,850 nuclei/µl, suitable for a Target Nuclei Recovery of 5000. The resulting nuclei concentration was determined using a with a TC20 Automated Cell Counter.
Single cell 3’ libraries were prepared using the 10x Genomics Single Cell 3’ Reagent Kit v2, together with the 10x Chromium Controller microfluidic platform according to manufacturer’s instructions (10x Genomics). In summary, our hashed samples (adjusted to 1000 cells/ul) were loaded into a 10x Chip A, together with the RT mix, barcoded beads and partioning oil. After 10x Chromium Controller processing, reaction was incubated 45 min at 53ºC and 5 min at 85ºC. Next, the cDNA was purified with silane magnetic beads. The cDNA amplification was performed using the cDNA amplification primer, plus a Hashtag oligonucleotide (HTO, Supplementary Table 4), and 25 PCR cycles. In order to separate the TotalSeq™ Hashtag fraction from the amplified cDNA a second purification was performed (see TotalSeq™-A Cell Hashing and TotalSeq™-A Antibodies Protocol for Simultaneous Proteomics and Transcriptomics with 10X Single Cell 3' Reagent Kit v2 protocol) and HTO specifically amplified and indexed (Supplementary Table 3. Finally, sequencing of HTO (5%) and cDNA (95%) libraries was carried out on a HSeq2500 (Illumina).
For Smart-seq2 libraries, we profiled the transcriptome of 376 PBMC. The cells originated from the same donors as in the 10x Genomics experiments, and were distributed across four 96-well plates (all conditions per plate). We discarded 60 cells that either had <75,000 or >1,000,000 total counts, <435 detected genes or a mitochondrial expression >20%. Similarly, we filtered out 6,542 genes that had an average expression across cells <1. We normalized gene counts with the Scran package, which removed the batch effect between plates.
scATAC-seq libraries were prepared according to the Chromium Single Cell ATAC Reagent Kits User Gu

value: PBMC

tag: donor

value: female

tag: time

tag: temperature

value: RT

tag: days in culture

tag: biobank

value: yes

tag: technology


title: RBG7381_KitHi_E10_G2VInt


title: RBG7368_KitHi_E10_G2VInt


title: P2671_N712-S505

value: no


title: RBG7356_KitHi_E10_G2VInt


title: P2671_N712-S507


title: P2671_N712-S506


title: RBG7331_KitHi_E10_G2VInt


title: RBG7415_KitHi_E10_G2VInt


title: P2671_N712-S502


title: P2671_N711-S511


title: P2671_N714-S505


title: RBG7403_KitHi_E10_G2VInt


title: RBG7391_KitHi_E10_G2VInt


title: P2671_N714-S506


title: P2671_N711-S510


title: P2671_N711-S507


title: P2671_N711-S508


title: P2671_N712-S510


title: RBG7355_KitHi_E10_G2VInt


title: P2671_N711-S506


title: P2671_N711-S505


title: RBG7344_KitHi_E10_G2VInt


title: RBG7402_KitHi_E10_G2VInt


title: RBG7390_KitHi_E10_G2VInt


title: P2671_N711-S502


title: RBG7366_KitHi_E10_G2VInt

value: EC


title: P2671_N712-S503


title: RBG7343_KitHi_E10_G2VInt


title: RBG7378_KitHi_E10_G2VInt


title: P2671_N710-S508


title: P2671_N710-S507


title: P2671_N710-S511


title: P2671_N710-S510


title: RBG7414_KitHi_E10_G2VInt


title: RBG7342_KitHi_E10_G2VInt


title: RBG7413_KitHi_E10_G2VInt


title: RBG7379_KitHi_E10_G2VInt


title: P2671_N710-S506


title: RBG7367_KitHi_E10_G2VInt


title: RBG7401_KitHi_E10_G2VInt


title: RBG7389_KitHi_E10_G2VInt


title: RBG7377_KitHi_E10_G2VInt


title: RBG7365_KitHi_E10_G2VInt


title: P2671_N707-S511


title: P2671_N711-S503


title: P2671_N710-S502


title: P2671_N710-S505


title: P2671_N707-S510


title: RBG7353_KitHi_E10_G2VInt


title: P2671_N707-S508


title: RBG7354_KitHi_E10_G2VInt


title: P2671_N707-S507


title: RBG7341_KitHi_E10_G2VInt


title: RBG7400_KitHi_E10_G2VInt


title: P2671_N707-S503


title: P2671_N707-S506


title: P2671_N710-S503


title: P2671_N707-S505


title: RBG7388_KitHi_E10_G2VInt


title: RBG7376_KitHi_E10_G2VInt


title: P2671_N706-S511


title: P2671_N706-S510


title: RBG7364_KitHi_E10_G2VInt


title: P2671_N706-S508


title: RBG7352_KitHi_E10_G2VInt


title: P2671_N707-S502


title: RBG7340_KitHi_E10_G2VInt


title: P2671_N706-S507


title: P2671_N706-S505


title: RBG7375_KitHi_E10_G2VInt


title: P2671_N705-S511


title: P2671_N706-S503


title: RBG7387_KitHi_E10_G2VInt


title: RBG7411_KitHi_E10_G2VInt


title: RBG7327_KitHi_E10_G2VInt


title: P2671_N706-S506


title: P2671_N705-S510


title: RBG7363_KitHi_E10_G2VInt


title: RBG7351_KitHi_E10_G2VInt


title: RBG7339_KitHi_E10_G2VInt


title: P2671_N705-S508


title: RBG7410_KitHi_E10_G2VInt


title: RBG7326_KitHi_E10_G2VInt


title: P2671_N705-S502


title: P2671_N705-S507


title: RBG7398_KitHi_E10_G2VInt


title: RBG7374_KitHi_E10_G2VInt


title: P2671_N705-S505


title: RBG7412_KitHi_E10_G2VInt


title: P2671_N705-S506


title: RBG7350_KitHi_E10_G2VInt


title: P2671_N704-S510


title: P2671_N704-S511


title: RBG7362_KitHi_E10_G2VInt


title: RBG7338_KitHi_E10_G2VInt


title: RBG8352_KitHi_E11.5_G2VInt


title: RBG8436_KitHi_E11.5_G2VInt


title: P2671_N704-S507


title: P2671_N705-S503


title: P2671_N704-S508


title: P2671_N704-S502


title: RBG7386_KitHi_E10_G2VInt


title: RBG8424_KitHi_E11.5_G2VInt


title: P2671_N704-S505


title: P2671_N704-S503


title: P2671_N704-S506


title: RBG8400_KitHi_E11.5_G2VInt


title: P2671_N703-S511


title: P2671_N703-S510


title: RBG8388_KitHi_E11.5_G2VInt


title: RBG8351_KitHi_E11.5_G2VInt


title: P2671_N703-S508


title: P2671_N703-S507


title: P2671_N703-S506


title: RBG8364_KitHi_E11.5_G2VInt


title: RBG8435_KitHi_E11.5_G2VInt


title: RBG8411_KitHi_E11.5_G2VInt


title: RBG8423_KitHi_E11.5_G2VInt


title: P2671_N703-S505


title: P2671_N703-S503


title: RBG8412_KitHi_E11.5_G2VInt


title: P2671_N703-S502


title: RBG8387_KitHi_E11.5_G2VInt


title: RBG8399_KitHi_E11.5_G2VInt


title: RBG8376_KitHi_E11.5_G2VInt


title: RBG8363_KitHi_E11.5_G2VInt


title: P2671_N702-S511


title: RBG8422_KitHi_E11.5_G2VInt


title: P2671_N702-S508


title: RBG8350_KitHi_E11.5_G2VInt


title: P2671_N702-S507


title: P2671_N702-S506


title: P2671_N702-S510


title: RBG8410_KitHi_E11.5_G2VInt


title: RBG8434_KitHi_E11.5_G2VInt


title: RBG8386_KitHi_E11.5_G2VInt


title: RBG8398_KitHi_E11.5_G2VInt


title: RBG8362_KitHi_E11.5_G2VInt


title: RBG8374_KitHi_E11.5_G2VInt


title: P2671_N701-S506


title: RBG8375_KitHi_E11.5_G2VInt


title: P2671_N702-S505


title: P2671_N702-S502


title: RBG8421_KitHi_E11.5_G2VInt


title: P2671_N702-S503


title: P2671_N701-S511


title: P2671_N701-S510


title: P2671_N701-S508


title: RBG8409_KitHi_E11.5_G2VInt


title: P2671_N701-S507


title: P2671_N701-S505


title: RBG8397_KitHi_E11.5_G2VInt


title: P2671_N701-S503


title: P2671_N701-S502


title: RBG8361_KitHi_E11.5_G2VInt


title: RBG8373_KitHi_E11.5_G2VInt


title: P2664_N715-S508

value: male


title: RBG8385_KitHi_E11.5_G2VInt


title: RBG8348_KitHi_E11.5_G2VInt


title: P2664_N715-S507


title: P2664_N715-S506


title: P2664_N715-S505


title: RBG8432_KitHi_E11.5_G2VInt


title: P2664_N715-S502


title: RBG8349_KitHi_E11.5_G2VInt


title: RBG8433_KitHi_E11.5_G2VInt


title: RBG8420_KitHi_E11.5_G2VInt


title: RBG8408_KitHi_E11.5_G2VInt


title: P2664_N714-S511


title: RBG8396_KitHi_E11.5_G2VInt


title: P2664_N714-S510


title: P2664_N714-S508


title: RBG8372_KitHi_E11.5_G2VInt


title: P2664_N714-S507


title: P2664_N714-S506


title: RBG8360_KitHi_E11.5_G2VInt


title: RBG8384_KitHi_E11.5_G2VInt


title: P2664_N714-S505


title: P2664_N714-S502


title: RBG8407_KitHi_E11.5_G2VInt


title: RBG8419_KitHi_E11.5_G2VInt


title: P2664_N714-S503


title: RBG8383_KitHi_E11.5_G2VInt


title: P2664_N712-S510


title: RBG8371_KitHi_E11.5_G2VInt


title: P2664_N712-S506


title: RBG8347_KitHi_E11.5_G2VInt


title: RBG8346_KitHi_E11.5_G2VInt


title: P2664_N712-S503


title: P2664_N711-S510


title: P2664_N712-S502


title: RBG8382_KitHi_E11.5_G2VInt


title: P2664_N711-S508


title: P2664_N711-S507


title: P2664_N712-S505


title: RBG8395_KitHi_E11.5_G2VInt


title: P2664_N712-S511


title: RBG8406_KitHi_E11.5_G2VInt


title: RBG8430_KitHi_E11.5_G2VInt


title: RBG8418_KitHi_E11.5_G2VInt


title: P2664_N712-S508


title: RBG8431_KitHi_E11.5_G2VInt


title: P2664_N711-S511


title: RBG8359_KitHi_E11.5_G2VInt


title: P2664_N715-S503


title: RBG8417_KitHi_E11.5_G2VInt


title: P2671_N706-S502


title: RBG7399_KitHi_E10_G2VInt


title: P2664_N711-S502


title: RBG8394_KitHi_E11.5_G2VInt


title: RBG8370_KitHi_E11.5_G2VInt


title: RBG8358_KitHi_E11.5_G2VInt


title: P2664_N711-S505


title: P2664_N710-S511


title: P2664_N712-S507


title: P2664_N711-S506


title: P2664_N711-S503


title: RBG8345_KitHi_E11.5_G2VInt


title: RBG8429_KitHi_E11.5_G2VInt


title: RBG8405_KitHi_E11.5_G2VInt


title: P2664_N710-S505


title: RBG8357_KitHi_E11.5_G2VInt


title: P2664_N710-S510


title: RBG8393_KitHi_E11.5_G2VInt


title: RBG8381_KitHi_E11.5_G2VInt


title: P2664_N710-S508


title: P2664_N710-S507


title: RBG8344_KitHi_E11.5_G2VInt


title: RBG8428_KitHi_E11.5_G2VInt


title: RBG8369_KitHi_E11.5_G2VInt


title: RBG8416_KitHi_E11.5_G2VInt


title: P2664_N710-S503


title: RBG8380_KitHi_E11.5_G2VInt


title: P2664_N707-S511


title: P2664_N707-S507


title: P2664_N707-S505


title: P2664_N707-S510


title: RBG8404_KitHi_E11.5_G2VInt


title: RBG8392_KitHi_E11.5_G2VInt


title: RBG8368_KitHi_E11.5_G2VInt


title: RBG8356_KitHi_E11.5_G2VInt


title: P2664_N707-S502


title: P2664_N707-S503


title: P2664_N706-S511


title: P2664_N707-S506


title: P2664_N707-S508


title: RBG8343_KitHi_E11.5_G2VInt


title: P2664_N706-S508


title: P2664_N706-S510


title: RBG8391_KitHi_E11.5_G2VInt


title: RBG8427_KitHi_E11.5_G2VInt


title: P2664_N710-S506


title: P2664_N710-S502


title: RBG8342_KitHi_E11.5_G2VInt


title: P2664_N706-S505


title: RBG8403_KitHi_E11.5_G2VInt


title: RBG8415_KitHi_E11.5_G2VInt


title: P2664_N706-S503


title: P2664_N706-S506


title: RBG8379_KitHi_E11.5_G2VInt


title: P2664_N706-S507


title: RBG8367_KitHi_E11.5_G2VInt


title: RBG8355_KitHi_E11.5_G2VInt


title: RBG8414_KitHi_E11.5_G2VInt


title: RBG8426_KitHi_E11.5_G2VInt


title: RBG8390_KitHi_E11.5_G2VInt


title: P2664_N705-S510


title: RBG8378_KitHi_E11.5_G2VInt


title: P2664_N706-S502


title: P2664_N705-S508


title: RBG8366_KitHi_E11.5_G2VInt


title: P2664_N705-S507


title: RBG8354_KitHi_E11.5_G2VInt


title: P2664_N705-S506


title: RBG8425_KitHi_E11.5_G2VInt


title: P2664_N705-S511


title: P2664_N705-S505


title: RBG8413_KitHi_E11.5_G2VInt


title: RBG8401_KitHi_E11.5_G2VInt


title: RBG8341_KitHi_E11.5_G2VInt


title: P2664_N704-S511


title: RBG8402_KitHi_E11.5_G2VInt


title: P2664_N705-S502


title: P2664_N704-S508


title: P2664_N704-S507


title: RBG8353_KitHi_E11.5_G2VInt


title: P2664_N704-S506


title: RBG8377_KitHi_E11.5_G2VInt


title: P2664_N704-S505


title: P2664_N704-S510


title: RBG8365_KitHi_E11.5_G2VInt


title: P2664_N704-S503


title: RBG8340_KitHi_E11.5_G2VInt


title: P2664_N705-S503


title: RBG8256_KitHi_E11.5_G2VInt


title: RBG8316_KitHi_E11.5_G2VInt


title: RBG8328_KitHi_E11.5_G2VInt


title: RBG8304_KitHi_E11.5_G2VInt


title: P2664_N703-S511


title: RBG8292_KitHi_E11.5_G2VInt


title: P2664_N703-S510


title: RBG8268_KitHi_E11.5_G2VInt


title: RBG8255_KitHi_E11.5_G2VInt


title: P2664_N703-S508


title: P2664_N703-S506


title: P2664_N703-S505


title: RBG8327_KitHi_E11.5_G2VInt


title: P2664_N703-S503


title: RBG8315_KitHi_E11.5_G2VInt


title: P2664_N702-S511


title: RBG8303_KitHi_E11.5_G2VInt


title: RBG8267_KitHi_E11.5_G2VInt


title: P2664_N703-S502


title: RBG8279_KitHi_E11.5_G2VInt


title: P2664_N702-S510


title: P2664_N702-S506


title: RBG8254_KitHi_E11.5_G2VInt


title: P2664_N702-S507


title: P2664_N704-S502


title: P2664_N702-S505


title: P2664_N702-S503


title: RBG8326_KitHi_E11.5_G2VInt


title: RBG8338_KitHi_E11.5_G2VInt


title: RBG8280_KitHi_E11.5_G2VInt


title: P2664_N701-S508


title: P2664_N703-S507


title: RBG8291_KitHi_E11.5_G2VInt


title: RBG8302_KitHi_E11.5_G2VInt


title: RBG8314_KitHi_E11.5_G2VInt


title: RBG8339_KitHi_E11.5_G2VInt


title: RBG8290_KitHi_E11.5_G2VInt


title: P2664_N701-S510


title: P2664_N702-S508


title: RBG8337_KitHi_E11.5_G2VInt


title: RBG8266_KitHi_E11.5_G2VInt


title: RBG8325_KitHi_E11.5_G2VInt


title: RBG8278_KitHi_E11.5_G2VInt


title: P2664_N701-S507


title: P2664_N701-S506


title: P2664_N701-S503


title: P2664_N701-S502


title: P2664_N702-S502


title: P2664_N701-S511


title: P2568_N715-S507


title: RBG8277_KitHi_E11.5_G2VInt


title: P2568_N715-S506


title: RBG8289_KitHi_E11.5_G2VInt


title: P2568_N715-S508


title: RBG8313_KitHi_E11.5_G2VInt


title: P2664_N701-S505


title: RBG8253_KitHi_E11.5_G2VInt


title: RBG8336_KitHi_E11.5_G2VInt


title: RBG8265_KitHi_E11.5_G2VInt


title: RBG8324_KitHi_E11.5_G2VInt


title: P2568_N715-S502


title: RBG8312_KitHi_E11.5_G2VInt


title: P2568_N714-S510


title: RBG8300_KitHi_E11.5_G2VInt


title: P2568_N714-S508


title: RBG8301_KitHi_E11.5_G2VInt


title: P2568_N715-S505


title: P2568_N714-S507


title: P2568_N714-S505


title: RBG8288_KitHi_E11.5_G2VInt


title: P2568_N714-S506


title: RBG8264_KitHi_E11.5_G2VInt


title: RBG8251_KitHi_E11.5_G2VInt


title: RBG8323_KitHi_E11.5_G2VInt


title: RBG8276_KitHi_E11.5_G2VInt


title: RBG8299_KitHi_E11.5_G2VInt


title: RBG8311_KitHi_E11.5_G2VInt


title: P2568_N715-S503


title: RBG8335_KitHi_E11.5_G2VInt


title: P2568_N714-S503


title: P2568_N714-S502


title: P2568_N714-S511


title: P2568_N712-S508


title: P2568_N712-S511


title: P2568_N712-S510


title: RBG8275_KitHi_E11.5_G2VInt


title: RBG8287_KitHi_E11.5_G2VInt


title: P2568_N712-S506


title: P2568_N712-S507


title: RBG8250_KitHi_E11.5_G2VInt


title: RBG8263_KitHi_E11.5_G2VInt


title: P2568_N712-S505


title: P2568_N712-S502


title: RBG8322_KitHi_E11.5_G2VInt


title: RBG8334_KitHi_E11.5_G2VInt


title: P2568_N712-S503


title: P2568_N711-S511


title: RBG8310_KitHi_E11.5_G2VInt


title: RBG8286_KitHi_E11.5_G2VInt


title: RBG8298_KitHi_E11.5_G2VInt


title: P2568_N711-S508


title: RBG8274_KitHi_E11.5_G2VInt


title: P2568_N711-S506


title: P2568_N711-S505


title: RBG8249_KitHi_E11.5_G2VInt


title: RBG8262_KitHi_E11.5_G2VInt


title: P2568_N711-S503


title: RBG8333_KitHi_E11.5_G2VInt


title: RBG8321_KitHi_E11.5_G2VInt


title: P2568_N710-S511


title: P2568_N710-S510


title: P2568_N711-S502


title: RBG8297_KitHi_E11.5_G2VInt


title: RBG8309_KitHi_E11.5_G2VInt


title: P2568_N710-S508


title: P2568_N711-S510


title: P2568_N710-S506


title: RBG8285_KitHi_E11.5_G2VInt


title: P2568_N710-S507


title: RBG8273_KitHi_E11.5_G2VInt


title: RBG8261_KitHi_E11.5_G2VInt


title: RBG8248_KitHi_E11.5_G2VInt


title: P2568_N711-S507


title: P2568_N710-S505


title: RBG8332_KitHi_E11.5_G2VInt


title: P2568_N710-S503


title: P2568_N707-S511


title: RBG8308_KitHi_E11.5_G2VInt


title: RBG8320_KitHi_E11.5_G2VInt


title: P2568_N710-S502


title: RBG8296_KitHi_E11.5_G2VInt


title: P2568_N707-S508


title: P2568_N707-S506


title: P2568_N707-S507


title: RBG8272_KitHi_E11.5_G2VInt


title: P2568_N707-S505


title: RBG8247_KitHi_E11.5_G2VInt


title: RBG8331_KitHi_E11.5_G2VInt


title: P2568_N707-S503


title: P2568_N706-S511


title: RBG8295_KitHi_E11.5_G2VInt


title: P2568_N706-S510


title: RBG8271_KitHi_E11.5_G2VInt


title: RBG8307_KitHi_E11.5_G2VInt


title: RBG8283_KitHi_E11.5_G2VInt


title: P2568_N706-S506


title: RBG8259_KitHi_E11.5_G2VInt


title: P2568_N707-S510


title: P2568_N706-S507


title: P2568_N707-S502


title: RBG8246_KitHi_E11.5_G2VInt


title: P2568_N706-S505


title: RBG8330_KitHi_E11.5_G2VInt


title: RBG8318_KitHi_E11.5_G2VInt


title: P2568_N706-S503


title: RBG8306_KitHi_E11.5_G2VInt


title: P2568_N705-S511


title: RBG8260_KitHi_E11.5_G2VInt


title: P2568_N706-S508


title: P2568_N705-S510


title: RBG8319_KitHi_E11.5_G2VInt


title: RBG8294_KitHi_E11.5_G2VInt


title: RBG8282_KitHi_E11.5_G2VInt


title: P2568_N706-S502


title: P2568_N705-S508


title: RBG8270_KitHi_E11.5_G2VInt


title: RBG8284_KitHi_E11.5_G2VInt


title: P2568_N705-S507


title: RBG8258_KitHi_E11.5_G2VInt


title: P2568_N705-S505


title: RBG8329_KitHi_E11.5_G2VInt


title: TGFB-3

city: Newark

first: Pingping

last: Hou

state: New Jersey

address: 205 South Orange Ave

department: Microbiology, Biochemistry and Molecular Genetics

country: USA

institute: Rutgers University

description: TGFbeta treatment rep3

data_processing:
BCL (raw output of Illumina HigSeq) files are processed using Illumina’s Consensus Assessment of sequence And Variation (CASAVA) tool
FASTQ files of RNA samples are processed using both STAR (Dobin et. al. 2012) following the two-step alignment procedure and TopHat (Kim and Salzberg 2011) and Cufflinks (Trapnell et. al. 2010).
data followed CBS (Olshen et. al. 2004) segmentation. Additional RNA quantification is conducted using HTSeq (Anders et. al. 2014) analyses.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include Htseq count values for each Sample

source_name: mouse PDAC cells

extract_protocol:
RNA Extraction Kits (Qiagen) were used to extract RNA from cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: mouse PDAC cells from iKPC GEMM

tag: strain


title: TGFB-2

description: TGFbeta treatment rep2


title: P2568_N704-S511


title: VEH-3

description: vehicle treatment rep3


title: TGFB-1

description: TGFbeta treatment rep1


title: P2568_N705-S502


title: RBG8317_KitHi_E11.5_G2VInt


title: RBG8305_KitHi_E11.5_G2VInt


title: P2568_N705-S503


title: VEH-2

description: vehicle treatment rep2


title: P2568_N704-S510


title: RBG8281_KitHi_E11.5_G2VInt


title: rcsBKO_3

city: Beijing

first: Jiao

last: Meng

address: 17 Tsinghua East Road

institute: CAU

data_processing:
The raw reads of the FASTQ format were processed using Perl scripts.
The clean reads were obtained by removing the reads containing the adapters, the low-quality reads and the reads containing the poly N. At the same time, the clean data were analyzed for Q20, Q30 and GC content.
The clean reads were aligned with the reference genome using the Bowtie software (http://bowtie-bio.sourceforge.net/index.shtml).
RESM software (http://deweylab.github.io/RSEM/), which comprehensively considers the sequencing depth and length for this count, was used to quantify gene expression levels, yielding transcripts per million reads (TPM).
The DEGseq (http://bioinfo.au.tsinghua.edu.cn/software/degseq) was used to analyze the differential expression between the two samples. The false discovery rate was controlled through adjusting the P values by using the Benjamini and Hochberg method. The significantly differentiated expressed genes (DEGs) were identified with the inclusion criteria of |log2FC|≥1 and P<0.05.
Genome_build: The reference genome and gene annotation files were   downloaded from the genome website (https://www.ncbi.nlm.nih.gov/genome/genomes/1041).
Supplementary_files_format_and_content: Tab-delimited text files include TPM values for each Sample .

organism: Yersinia enterocolitica

source_name: Prokaryote_ΔrcsB mutant

growth_protocol: Y. enterocolitica strains were grown at 26℃ in M63 minimal medium (100 mM of KH2PO4; 15 mM of (NH4)2SO4; 1.8 μM of FeSO4; 1.0 mM of MgSO4; 1.0 μg/ml of thiamine; pH 7.0) with glucose (0.2%).

extract_protocol:
The total RNA was extracted from Y. enterocolitica wild-type and ΔrcsB mutant strains grown to the exponential phase in M63 minimal medium with glucose (0.2%) using TRIzol (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: genotype/varition

value: rcsBKO


title: P2568_N704-S508


title: RBG8269_KitHi_E11.5_G2VInt


title: rcsBKO_2


title: P2568_N705-S506


title: RBG8257_KitHi_E11.5_G2VInt


title: KRAS-OFF-3

description: Tumor after 24-hour KRAS* extinction rep3

source_name: mouse PDAC allograft tumors


title: P2568_N704-S507


title: KRAS-OFF-2

description: Tumor after 24-hour KRAS* extinction rep2


title: RBG8245_KitHi_E11.5_G2VInt


title: P2568_N704-S506


title: rcsBKO_1


title: KRAS-OFF-1

description: Tumor after 24-hour KRAS* extinction rep1


title: RBG8160_KitHi_E11.5_G2VInt


title: WT_3

value: wild tpye


title: P2568_N704-S505


title: KRAS-ON-4

description: KRAS*-expressing tumor rep4


title: VEH-1

description: vehicle treatment rep1


title: RBG8244_KitHi_E11.5_G2VInt


title: WT_2


title: KRAS-ON-3

description: KRAS*-expressing tumor rep3


title: KRAS-ON-2

description: KRAS*-expressing tumor rep2


title: WT_1


title: RBG8232_KitHi_E11.5_G2VInt


title: KRAS-OFF-4

description: Tumor after 24-hour KRAS* extinction rep4


title: P2568_N704-S503


title: P2568_N703-S511


title: KRAS-ON-1

description: KRAS*-expressing tumor rep1


title: RBG8208_KitHi_E11.5_G2VInt


title: HDAC5-E5-shH5-2

description: shHDAC5-2 rep5

source_name: KRAS*-independent iKPC escaper cells

value: HDAC5-driven PDAC escaper cells


title: P2568_N703-S510


title: RBG8184_KitHi_E11.5_G2VInt


title: P2568_N703-S508


title: h2a_ctcf_cut_run_rep1

city: Shenzhen

first: Zengqi

last: Wen

state: Guangdong

address: No 66, Gongchang Road, Guangming District

department: School of Medicine

institute: Sun Yat-sen University

library_source: genomic

data_processing:
ChIP-seq clean reads were mapped to mm9 by Bowtie2 with default parameters.
Data were filtered by samtools with "-q 10"to retain high quality reads.
Enriched peaks were detected using MACS14 or MACS2 with input.
Genome_build: mm9
Supplementary_files_format_and_content: bed file with four tab-delimited fields, representing chromosome name, start, end and peak score.

molecule: genomic DNA

source_name: mouse embryonic stem cell

growth_protocol: Mouse ES cells were cultured in the medium with 80% DMEM (EmbryoMax, SLM-220-B), 15% FBS (Hyclone, SH30070.03), Nonessential amino acids (EmbryoMax, TMS-001-C), 2-Mercaptoethanol (EmbryoMax, ES-007-E), L-glutamine (EmbryoMax, TMS-002-C), Nucleosides (EmbryoMax, ES-008-D), Pen/Strep (EmbryoMax, TMS-AB-2C) and 1000U/ml leukemia inhibitory factor (LIF) (ESGRO, ESG1107) in standard incubator with 5% CO2 at 37 °C.

extract_protocol:
Cells were first crosslinked by formaldehyde, then digested with Mnase, then sonicated in N-lauroyl-sarcosine containing buffer to dissolve the chromatin. The clarified chromatin were immunoprecipitated with agarose conjucated with antibodies.
Libraries were prepared according to NEBNext Ultra DNA Library Prep Kit for Illumina (E7370L) and were sequenced using HiSeq2000 or Nova-seq.

value: cell line

tag: chip antibody

value: H2A (Abcam, ab18255)

tag: treatment


title: h2az_ctcf_cut_run_rep1

value: H2A.Z (Abcam, ab4174)


title: h2a_ctcf_cut_run_rep2


title: RBG8172_KitHi_E11.5_G2VInt


title: h2az_ctcf_cut_run_rep2


title: HDAC5-E4-shH5-2

description: shHDAC5-2 rep4


title: P2568_N703-S507


title: ctcf_cut_run_rep2

value: CTCF (Cell Signaling, 2899)


title: P2568_N703-S506


title: RBG8196_KitHi_E11.5_G2VInt


title: P2568_N704-S502


title: RBG8159_KitHi_E11.5_G2VInt


title: ctcf_cut_run_rep1


title: HDAC5-E5-shH5-1

description: shHDAC5-1 rep5


title: HDAC5-E4-shH5-1

description: shHDAC5-1 rep4


title: P2568_N703-S505


title: input_mnase4_no_sonication

value: input


title: RBG8220_KitHi_E11.5_G2VInt

value: IAHC cells


title: RBG8243_KitHi_E11.5_G2VInt


title: P2568_N703-S503

value: PBMC


title: RBG8231_KitHi_E11.5_G2VInt


title: input_mnase4_x_chip


title: HDAC5-E4-CTRL

description: shRNA scramble control rep4


title: HDAC5-E3-shH5-2

description: shHDAC5-2 rep3


title: P2568_N703-S502

value: female


title: RBG8219_KitHi_E11.5_G2VInt


title: HDAC5-E5-CTRL

description: shRNA scramble control rep5


title: h3_mnase4_x_chip_rep2

value: H3 (Abcam, ab1791)


title: P2568_N702-S511


title: RBG8207_KitHi_E11.5_G2VInt


title: HDAC5-E3-shH5-1

description: shHDAC5-1 rep3


title: h3_mnase4_x_chip_rep1


title: HDAC5-E3-CTRL

description: shRNA scramble control rep3


title: RBG8195_KitHi_E11.5_G2VInt


title: h2a_mnase4_x_chip_rep2


title: P2568_N702-S508

value: RT

value: yes


title: h2a_mnase4_x_chip_rep1


title: RBG8171_KitHi_E11.5_G2VInt


title: P2568_N702-S510

value: no


title: RBG8183_KitHi_E11.5_G2VInt

value: EC


title: HDAC5-E2-shH5-2

description: shHDAC5-2 rep2


title: HDAC5-E2-shH5-1

description: shHDAC5-1 rep2


title: P2568_N702-S507


title: HDAC5-E1-shH5-2

description: shHDAC5-2 rep1


title: h2az_mnase4_x_chip_rep1


title: RBG8242_KitHi_E11.5_G2VInt


title: RBG8158_KitHi_E11.5_G2VInt


title: P2568_N702-S503


title: sih2az_input_mnase32_x_chip_rep2

value: siH2A.Z (siRNA targetting H2A.Z)


title: P2568_N702-S505


title: HDAC5-E1-shH5-1

description: shHDAC5-1 rep1


title: h2az_mnase4_x_chip_rep2


title: RBG8230_KitHi_E11.5_G2VInt


title: P2568_N702-S506


title: sih2az_input_mnase32_x_chip_rep1


title: HDAC5-E1-CTRL

description: shRNA scramble control rep1


title: RBG8218_KitHi_E11.5_G2VInt


title: siNC_input_mnase32_no_sonication

value: siNC (negative control siRNA)


title: P2568_N701-S511


title: P2568_N702-S502


title: RBG8206_KitHi_E11.5_G2VInt


title: iKPC-5

description: KRAS*-expressing cells rep4

source_name: KRAS*-dependent iKPC PDAC cells

value: KRAS*-expressing iKPC PDAC cells


title: siNC_input_mnase32_x_chip_rep2


title: P2568_N701-S510


title: P2568_N701-S508


title: RBG8194_KitHi_E11.5_G2VInt


title: siNC_input_mnase32_x_chip_rep1


title: HDAC5-E2-CTRL

description: shRNA scramble control rep2

value: HDAC5-driven PDAC escaper cells


title: RBG8182_KitHi_E11.5_G2VInt


title: iKPC-3

description: KRAS*-expressing cells rep3


title: h3_mnase32_x_chip_rep2

value: cell line


title: P2568_N701-S507


title: iKPC-2

description: KRAS*-expressing cells rep2


title: iKPC-1

description: KRAS*-expressing cells rep1


title: h3_mnase32_x_chip_rep1


title: P2568_N701-S506


title: RBG8157_KitHi_E11.5_G2VInt


title: HDAC5-E5

description: HDAC5 escaper cells rep5


title: P2568_N701-S505


title: RBG8170_KitHi_E11.5_G2VInt


title: RBG8241_KitHi_E11.5_G2VInt


title: h2a_mnase32_x_chip_rep2

value: H2A (Abcam, ab18255)


title: P2568_N701-S503


title: h2a_mnase32_x_chip_rep1


title: RBG8229_KitHi_E11.5_G2VInt


title: h2az_mnase32_x_chip_rep2

description:
H2AZ_30_80bp_vs_Input_peaks.bed
H2AZ_80_168bp_vs_Input_peaks.bed
H2AZ_vs_Input_peaks.bed

value: H2A.Z (Abcam, ab4174)


title: RBG8217_KitHi_E11.5_G2VInt


title: HDAC5-E2

description: HDAC5 escaper cells rep2


title: HDAC5-E3

description: HDAC5 escaper cells rep3


title: h2az_mnase32_x_chip_rep1


title: P2568_N701-S502


title: HDAC5-E1

description: HDAC5 escaper cells rep1


title: Mycelium of 1 gram Mutant Ku70 cultured in carbon-free liquid medium for 48 hrs [NC_48hS]

city: zhengzhou

first: Li

last: Xudong

state: Henan

address: No. 1, Jianshe East Road, Erqi District

institute: The First Affiliated Hospital of Zhengzhou University

data_processing:
Remove reads with adapters;Remove reads in which unknown bases are more than 10%;Remove low quality reads (the percentage of low quality bases is over 50% in a read, we define the low quality base to be the base whose sequencing quality is no more  than 10).
The clean reads mapped onto the genome of P. oxalicum wild type strain HP7-1 to functional annotation, susing the software BWA v0.7.10-r789 and Bowtie2 v2.1.0.
FPKM, representing gene expression levels, was calculated with the software RSEM v1.2.12
DEGs were screened with NOISeq or DESeq2 tools
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

organism: Penicillium oxalicum

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in carbon-free liquid medium for 48 hours

growth_protocol: Fresh spores of the MuKu70 were statically incubated on potato-dextrose agar (PDA) plates at 28°C for 6 d, collected and resuspended in sterile water containing 0.1% Tween 80 with a final concentration of 1 × 108 per milliliter. Approximately 1.0 g of hyphae was transferred to 100 mL of basic medium with various carbon sources including 1% (w/v) AV, WB, MC, HEV and Glu, respectively, and incubated in a shaker at 180 rpm and 28°C for 4‒48 h, and basic medium without carbon source (NC) was used for a control.

extract_protocol:
Total RNA were extracted using TRIzol RNA Kit
standard RNA-seq protocol

tag: culture condition

value: carbon-free liquid medium for 48 hours

tag: tissue

value: Mycelium


title: ctcf_sih2az_xchip_rep1

value: CTCF (Cell Signaling, 2899)


title: ctcf_sih2az_xchip_rep2


title: RBG8193_KitHi_E11.5_G2VInt

tag: condition

tag: days

value: IAHC cells


title: Mycelium of 1 gram Mutant Ku70 cultured in carbon-free liquid medium for 48 hrs [NC_48hF]


title: ctcf_siNC_xchip_rep2

tag: cell type


title: AP1863

value: PBMC

value: male

value: 10X scATAC-seq


title: AP1865

value: RT


title: HDAC5-E4

description: HDAC5 escaper cells rep4


title: RBG8169_KitHi_E11.5_G2VInt

tag: cluster (all cells)

tag: cluster (nocd27+ cells)


title: AP1864

tag: donor


title: ctcf_siNC_xchip_rep1


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% glucose liquid medium for 48 hrs [Glu_48hT]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in 1% glucose liquid medium for 48 hours

value: 1% glucose liquid medium for 48 hours


title: AN6699

value: CLL

tag: time


title: AN6700

tag: temperature


title: RBG8228_KitHi_E11.5_G2VInt

tag: clustertype (nocd27+ cells)


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% glucose liquid medium for 48 hrs [Glu_48hS]


title: FLAG ChIP-seq shHDAC5

data_processing:
Basecalls performed using CASAVA version 1.7
ChIPseq reads were aligned to mm9 genome using bowtie1 with max 1 mismatch, duplicated reads were removed
peaks were called using MACS14 using pvalue cutoff of 1e-5
bigwig files were generated by deeptools bamCoverage normalized by RPKM
the pipeline used to process ChIPseq can be found at https://github.com/crazyhottommy/pyflow-ChIPseq
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated by deeptools bamCoverage normalized by RPKM; peaks were called using MACS14 using pvalue cutoff of 1e-5

source_name: PDAC escaper cells

extract_protocol:
HDAC5 escaper cells were crosslinked by 1% paraformaldehyde for 10 minutes at room temperature and then quenched by 0.125M glycine for 5 minutes. Cells were lysed on ice for 30 minutes with lysis buffer containing 10 mM Tris-HCl (pH 8.0), 1 mM EDTA (pH 8.0), 140 mM NaCl, 1% Triton X-100, 0.2% SDS, 0.1% deoxycholic acid. Chromatin DNA was fragmented to around 200-500bp by Diagenode BioruptorPico sonicator for 45 cycles of 30 seconds on and 30 second off, and then incubated overnight with anti-HDAC5 antibody and Dynabead (Life Technologies) at 4C. Next day, immune complexes were washed once with RIPA buffer with 500mM NaCl and once with LiCl wash buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA (pH 8.0), 250 mM LiCl, 0.5% NP-40, 0.5% deoxycholic acid). DNA was then reverse crosslinked and eluted overnight in elution buffer (10 mM Tris-Cl (pH 8.0), 5 mM EDTA, 300 mM NaCl, 0.5% SDS, 20 mg/ml proteinase K) at 65C. The third day, eluted DNA was purified by AMPure beads (Beckman-Coulter).
NEB Next Ultra DNA Library kit was used to prepare library

tag: chip-antibody

value: FLAG (Sigma, F1804)


title: AN6698

tag: biobank

tag: technology


title: RBG8204_KitHi_E11.5_G2VInt


title: RBG8216_KitHi_E11.5_G2VInt


title: FLAG ChIP-seq shScrmbl

tag: strain


title: Mycelium of 1 gram Mutant Ku70 cultured in carbon-free liquid medium for 48 hrs [NC_48hT]


title: RBG8205_KitHi_E11.5_G2VInt

value: EC


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% glucose liquid medium for 48 hrs [Glu_48hF]


title: RBG8156_KitHi_E11.5_G2VInt


title: HDAC5 ChIP-seq shHDAC5


title: RBG8192_KitHi_E11.5_G2VInt


title: Tcell_activation_day1_rep2_cDNA

description:
cDNA
Tcell_activation_day1_rep2_barcodes.tsv.gz
Tcell_activation_day1_rep2_features.tsv.gz
Tcell_activation_day1_rep2_matrix.mtx.gz
conditions_10X.tsv

value: T-cell

tag: days in culture

value: 10X Chromium


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 48 hrs [HEC_48hS]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in 1% methyl cellulose liquid medium for 48 hours


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 48 hrs [HEC_48hT]

value: 1% methyl cellulose liquid medium for 48 hours


title: Tcell_activation_day1_rep2_HTO

description:
HTO
Tcell_activation_day1_rep2_barcodes.tsv.gz
Tcell_activation_day1_rep2_features.tsv.gz
Tcell_activation_day1_rep2_matrix.mtx.gz
conditions_10X.tsv


title: Input-shHDAC5

value: HDAC5-driven PDAC escaper cells


title: RBG8168_KitHi_E11.5_G2VInt


title: Tcell_activation_day0_rep2_HTO

description:
HTO
Tcell_activation_day0_rep2_barcodes.tsv.gz
Tcell_activation_day0_rep2_features.tsv.gz
Tcell_activation_day0_rep2_matrix.mtx.gz
conditions_10X.tsv


title: Tcell_activation_day0_rep2_cDNA

description:
cDNA
Tcell_activation_day0_rep2_barcodes.tsv.gz
Tcell_activation_day0_rep2_features.tsv.gz
Tcell_activation_day0_rep2_matrix.mtx.gz
conditions_10X.tsv


title: Input-shScrmbl


title: RBG8227_KitHi_E11.5_G2VInt


title: Tcell_activation_day2_rep1_HTO

description:
HTO
Tcell_activation_day2_rep1_barcodes.tsv.gz
Tcell_activation_day2_rep1_features.tsv.gz
Tcell_activation_day2_rep1_matrix.mtx.gz
conditions_10X.tsv


title: RBG8239_KitHi_E11.5_G2VInt


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 48 hrs [MC_48hS]


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% wheat bran liquid medium for 48 hrs [WB_48hT]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in 1% wheat bran liquid medium for 48 hours


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 48 hrs [MC_48hF]


title: Tcell_activation_day0_rep1_cDNA

description:
cDNA
Tcell_activation_day0_rep1_barcodes.tsv.gz
Tcell_activation_day0_rep1_features.tsv.gz
Tcell_activation_day0_rep1_matrix.mtx.gz
conditions_10X.tsv


title: Tcell_activation_day0_rep1_HTO

description:
HTO
Tcell_activation_day0_rep1_barcodes.tsv.gz
Tcell_activation_day0_rep1_features.tsv.gz
Tcell_activation_day0_rep1_matrix.mtx.gz
conditions_10X.tsv


title: IP RNA replicate 2

city: Baltimore

first: John

middle: Biology

last: Kim

state: Maryland

address: 3400 N Charles St

department: Biology Department

institute: Johns Hopkins University

data_processing:
Base calling was performed using Illumina software
Reads were aligned to reference genome using Bowtie (paramters: -5 25 -3 25 -v 3 (map with up to 3 mismatches), -k 275 (map at up to 275 loci), --best, and –strata
Reads were counted and converted to RPM after adding 1 read to any feature with no reads
Genome_build: R64-1-1.93
Supplementary_files_format_and_content: tab delimited text files with RPM for each sample

organism: Saccharomyces cerevisiae

source_name: Eluted RNA from flow through of G body RIP

growth_protocol: Cells were reinocculated from overnight YPD starter cultures into 125 ml of YPD at an OD600 of 0.005 split into five 125 ml Erlenmeyer flasks. Cells were grown in hypoxia, shaking at 200 RPM for 18 h.

extract_protocol:
100 OD600 of cells were spun down at 3,000 x g for 10 min and decanted with remaining media being aspirated. Cells were resuspended in 1.5 ml of lysis buffer and lysed by glass bead lysis for 10 min alternating vortexing and ice every 30 sec. Large cell debris were removed from the supernatant by centrifugation at 500 x g for 5 min at 4°C. The supernatant was precleared once with 25 µl of Protein G Dynabeads nutating for 30 min at 4°C. G bodies were then pelleted by centrifugation at 5,000 x g for 10 min and resuspended in 1 ml of lysis buffer and incubated with Dynabeads for 2 h at 4°C. After 1 h, Dynabeads were imaged to ensure capture of G bodies. 250 µl of the flow through was saved for RNA extraction. Beads were washed 3X with 1 ml of lysis buffer and once with 1 ml of Proteinase K buffer (100 mM Tris pH 7.5, 50 m NaCL, 10 mM EDTA). Beads were resuspended in 120 µl 2 mg/ml 3X Flag peptide (Millipore F4799) in Proteinase K buffer and eluted for 30 minutes at 37°C on a thermomixer at 850 rpm. After 15 min, 1 µl of the eluate was imaged to validate elution of G bodies from Dynabeads. The eluate was mixed 1:1 with 8 mg/ml Proteinase K (Thermo Fisher 25530015) in proteinase K buffer for 1 h in a thermomixer at 37°C at 850 rpm. Eluates and flow-through RNA was extracted with Tri Reagent (Sigma-Aldrich T9424) according to the manufacturer instructions. The aqueous phase was mixed 1:1 with isopropanol with 1 µl of glycogen (Thermo Fisher R0561) and precipitated for 4 h at -80°C. RNA was pelleted by centrifugation at 4°C at 21,000 x g for 30 min. RNA was washed 3 times with 80% ethanol and re-precipitated in 80% ethanol with sodium acetate overnight at -80º C. RNA was pelleted again and washed again and dissolved in 30 µl of H2O.
Libraries were prepared with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Beverly, MA, USA) with between 5 and 25 ng of RNA. Libraries were analyzed on an Agilent 4200 TapeStation.

value: Glycolytic body

tag: growth conditions

value: hypoxic treatment of 18 h

tag: ip antibody

value: FLAG (Sigma Aldrich F1804)


title: RBG8215_KitHi_E11.5_G2VInt


title: flow through RNA replicate 2

source_name: Flow through of immunoprecipitation of G body RIP

tag: tissue


title: total RNA replicate 2

source_name: Yeast cell lysate


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% wheat bran liquid medium for 48 hrs [WB_48hS]

tag: culture condition

value: 1% wheat bran liquid medium for 48 hours

value: Mycelium


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 48 hrs [HEC_48hF]


title: RBG8180_KitHi_E11.5_G2VInt

tag: condition

tag: days

value: IAHC cells


title: 1892_4C_HTO

description:
HTO
barcodes_1892_4C.tsv.gz
features_1892_4C.tsv.gz
matrix_1892_4C.mtx.gz
conditions_10X.tsv

tag: cell type


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 48 hrs [MC_48hT]


title: RBG8203_KitHi_E11.5_G2VInt

tag: cluster (all cells)

tag: cluster (nocd27+ cells)


title: RBG8191_KitHi_E11.5_G2VInt


title: HDAC5 ChIP-seq shScrmbl


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% wheat bran liquid medium for 48 hrs [WB_48hF]


title: Tcell_activation_day2_rep1_cDNA

description:
cDNA
Tcell_activation_day2_rep1_barcodes.tsv.gz
Tcell_activation_day2_rep1_features.tsv.gz
Tcell_activation_day2_rep1_matrix.mtx.gz
conditions_10X.tsv

tag: donor

tag: time


title: 1892_4C_cDNA

description:
cDNA
barcodes_1892_4C.tsv.gz
features_1892_4C.tsv.gz
matrix_1892_4C.mtx.gz
conditions_10X.tsv

tag: temperature


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% Avicel liquid medium for 48 hrs [AV_48hT]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 48 hours

value: 1% Avicel liquid medium for 48 hours


title: RBG8238_KitHi_E11.5_G2VInt

source_name: IAHC cells

tag: clustertype (nocd27+ cells)


title: 1472_4C_HTO

description:
HTO
barcodes_1472_4C.tsv.gz
features_1472_4C.tsv.gz
matrix_1472_4C.mtx.gz
conditions_10X.tsv

source_name: blood

tag: biobank


title: total RNA replicate 1


title: 1472_4C_cDNA

description:
cDNA
barcodes_1472_4C.tsv.gz
features_1472_4C.tsv.gz
matrix_1472_4C.mtx.gz
conditions_10X.tsv

tag: technology


title: simr-1 - 25°C, 10 generation, replicate 3

city: Arlington

first: Alicia

middle: Kathryn

last: Rogers

state: Texas

address: 1225 W Mitchell Street

department: Department of Biology

institute: University of Texas at Arlington

description:
mRNA from total RNA
mRNA-seq

data_processing:
Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform.
Sequences were parsed from adapters using FASTQ/A Clipper from the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/), mapped to the C. elegans genome, WS258 using Bowtie2 {Langmead:2012jh}, and reads were assigned to genomic features using FeatureCounts which is part of the Subread package {Liao:2014cj, Liao:2013fo}. Data analysis was done using R, Excel, and custom Python scripts. Reads per million total reads were plotted along the WS258 genome using Integrative Genomics Viewer 2.3.90 {Thorvaldsdottir:2013iw, Robinson:2011gy}.
Genome_build: WS258
Supplementary_files_format_and_content: tab-delimited text files including total reads mapping to each gene

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: Synchronized L1s of wild type and simr-1(cmp36) worms were plated on enriched peptone plates and cultured at 20C and 25C.

extract_protocol:
10,000 animals per sample were harvested as adults (~68hrs at 20°C and ~48hrs at 25°C) for RNA extraction. Worms were washed off plates using water and then settled on ice to form a pellet. Water was aspirated off and worm pellets were resuspended in 1mL TRIzol reagent (Life Technologies) and freeze-thawed on dry ice followed by vortexing. Worm carcasses were pelleted using centrifugation and the supernatant containing RNA was collected. 0.2 volume chloroform was add to supernatant, vortexed, centrifuged, and then the aqueous phase was transferred to a new tube. Samples were precipitated using isopropanol and rehydrated in 50μL nuclease-free H2O.
mRNA-seq library preparation. Nuclease-free H2O was added to 7.5μg of each RNA sample, extracted from whole animals, to a final volume of 100μL. Samples were incubated at 65°C for 2 minutes then incubated on ice. The Dynabeads mRNA Purification Kit (ThermoFisher 61006) was used according to the manufacturer’s protocol. 20μL of Dynabeads was used for each sample. 100ng of each mRNA sample was used to prepare libraries with the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760S) according to the manual, using NEBNext multiplex oligos for Illumina (NEB E7335S). Library quality was assessed (Agilent BioAnalyzer Chip) and concentration was determined using the Qubit 1X dsDNA HS Assay kit (ThermoFisher Q33231). Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform. Three biological replicates were generated for wild-type (N2) and simr-1 mutants cultured at 20°C and 25°C.

tag: Stage

value: Day 1 Adult

tag: strain

value: USC863- simr-1(cmp36)

tag: experimental temp

value: Whole body


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% Avicel liquid medium for 48 hrs [AV_48hF]


title: simr-1 - 25°C, 10 generation, replicate 2

description:
mRNA from total RNA
mRNA-seq


title: Mycelium of 1 gram Mutant Ku70 cultured in carbon-free liquid medium for 4 hrs [NC_24hT]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in carbon-free liquid medium for 4 hours

value: carbon-free liquid medium for 4 hours


title: 1892_RT_HTO

description:
HTO
barcodes_1892_RT.tsv.gz
features_1892_RT.tsv.gz
matrix_1892_RT.mtx.gz
conditions_10X.tsv

value: CLL

value: RT

tag: days in culture


title: RBG8214_KitHi_E11.5_G2VInt

value: EC


title: RBG8202_KitHi_E11.5_G2VInt


title: 1892_RT_cDNA

description:
cDNA
barcodes_1892_RT.tsv.gz
features_1892_RT.tsv.gz
matrix_1892_RT.mtx.gz
conditions_10X.tsv

value: 10X Chromium


title: flow through RNA replicate 1

tag: tissue

tag: growth conditions

tag: ip antibody


title: simr-1 - 25°C, 7 generation, replicate 3

description:
mRNA from total RNA
mRNA-seq


title: RBG8190_KitHi_E11.5_G2VInt

tag: condition

tag: days


title: IP RNA replicate 1


title: RBG8167_KitHi_E11.5_G2VInt

tag: cell type

tag: cluster (all cells)


title: Mycelium of 1 gram Mutant Ku70 cultured in carbon-free liquid medium for 24 hrs [NC_24hF]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in carbon-free liquid medium for 24 hours

tag: culture condition

value: carbon-free liquid medium for 24 hours


title: 1472_RT_HTO

description:
HTO
barcodes_1472_RT.tsv.gz
features_1472_RT.tsv.gz
matrix_1472_RT.mtx.gz
conditions_10X.tsv

tag: donor

tag: time


title: Mycelium of 1 gram Mutant Ku70 cultured in carbon-free liquid medium for 24 hrs [NC_24hS]


title: 1220_RT_HTO

description:
HTO
barcodes_1220_RT.tsv.gz
features_1220_RT.tsv.gz
matrix_1220_RT.mtx.gz
conditions_10X.tsv

tag: temperature


title: 1472_RT_cDNA

description:
cDNA
barcodes_1472_RT.tsv.gz
features_1472_RT.tsv.gz
matrix_1472_RT.mtx.gz
conditions_10X.tsv

tag: biobank


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% glucose liquid medium for 24 hrs [Glu_24hT]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in 1% glucose liquid medium for 24 hours

value: 1% glucose liquid medium for 24 hours


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% Avicel liquid medium for 48 hrs [AV_48hS]


title: 1220_RT_cDNA

description:
cDNA
barcodes_1220_RT.tsv.gz
features_1220_RT.tsv.gz
matrix_1220_RT.mtx.gz
conditions_10X.tsv

tag: technology


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% glucose liquid medium for 24 hrs [Glu_24hS]


title: RBG8178_KitHi_E11.5_G2VInt

tag: cluster (nocd27+ cells)

tag: clustertype (nocd27+ cells)


title: RBG8166_KitHi_E11.5_G2VInt


title: simr-1 - 25°C, 7 generation, replicate 1

description:
mRNA from total RNA
mRNA-seq

tag: Stage

tag: strain

tag: experimental temp


title: simr-1 - 25°C, 2 generation, replicate 3

description:
mRNA from total RNA
mRNA-seq

tag: tissue


title: RBG8226_KitHi_E11.5_G2VInt


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% glucose liquid medium for 24 hrs [Glu_24hF]


title: simr-1 - 25°C, 10 generation, replicate 1

description:
mRNA from total RNA
mRNA-seq


title: simr-1 - 25°C, 2 generation, replicate 2

description:
mRNA from total RNA
mRNA-seq


title: T47D cells, Hypoxia rep 3

city: Edmonton

first: Laura

middle: Jiyoung

last: Lee

state: Alberta

address: 5-120 Katz Group Centre

department: Oncology

country: Canada

institute: University of Alberta

data_processing:
Read quality in fastq files were checked with FastQC (v0.11.5)
Fastq files were trimmed for adapter sequences using Skewer (v0.1.127)
Reads were aligned to hg19 human reference genome using STAR (v2.5.2a)
Read quantification via FeatureCounts (v1.5.1) was performed using Refseq annotations
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files show read counts with associated genomic coordinates and gene ID. These files were generated with FeatureCounts

source_name: Breast cancer

growth_protocol: T47D cells were grown in adherent culture with RPMI media supplemented with 10% FBS

extract_protocol:
Total RNA was extracted using 5Prime RNA extraction kit
Libraries were prepared using mRNA stranded library preparation from NEB

treatment_protocol: Cells were placed in a hypoxia incubation chamber set to 0.5% O2. Normoxia control cells were grown under normal tissue culture conditions.

tag: cell line

value: breast cancer cells

tag: treatment

value: Hypoxia (0.5% O2, 48 hours)


title: RBG8237_KitHi_E11.5_G2VInt

tag: condition

tag: days


title: T47D cells, Normoxia rep 3

tag: cell type

value: Control (20% O2)


title: RBG8225_KitHi_E11.5_G2VInt

tag: cluster (all cells)


title: simr-1 - 25°C, 2 generation, replicate 1

description:
mRNA from total RNA
mRNA-seq


title: simr-1 - 25°C, 7 generation, replicate 2

description:
mRNA from total RNA
mRNA-seq


title: AI0102

description:
cDNA
conditions_10X.tsv

value: PBMC

tag: donor

value: male

tag: days in culture


title: RBG8213_KitHi_E11.5_G2VInt

value: IAHC cells


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 24 hrs [HEC_24hT]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in 1% methyl cellulose liquid medium for 24 hours

tag: culture condition

value: Mycelium


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 24 hrs [HEC_24hS]

value: 1% methyl cellulose liquid medium for 24 hours


title: simr-1 - 25°C, 1 generation, replicate 2

description:
mRNA from total RNA
mRNA-seq

value: Day 1 Adult

value: USC863- simr-1(cmp36)


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 24 hrs [HEC_24hF]


title: AI0100

description:
HTO
conditions_10X.tsv

tag: time

tag: temperature

tag: biobank


title: AI0101

description:
cDNA
conditions_10X.tsv

value: female

tag: technology


title: RBG8201_KitHi_E11.5_G2VInt

tag: cluster (nocd27+ cells)

tag: clustertype (nocd27+ cells)


title: RBG8189_KitHi_E11.5_G2VInt


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 24 hrs [MC_24hT]

tag: strain


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 24 hrs [MC_24hS]

tag: tissue


title: simr-1 - 25°C, 1 generation, replicate 1

description:
mRNA from total RNA
mRNA-seq

tag: Stage

tag: experimental temp

value: Whole body


title: RBG8165_KitHi_E11.5_G2VInt

tag: condition


title: simr-1 - 20°C, replicate 3

description:
mRNA from total RNA
mRNA-seq


title: RBG8152_KitHi_E11.5_G2VInt

tag: days


title: AI0099

description:
HTO
conditions_10X.tsv

tag: cell type


title: RBG8177_KitHi_E11.5_G2VInt

tag: cluster (all cells)


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 24 hrs [MC_24hF]


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% wheat bran liquid medium for 24 hrs [WB_24hS]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in 1% wheat bran liquid medium for 24 hours


title: AH9226

description:
cDNA
conditions_10X.tsv

tag: donor


title: RBG8236_KitHi_E11.5_G2VInt


title: simr-1 - 20°C, replicate 2

description:
mRNA from total RNA
mRNA-seq


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% wheat bran liquid medium for 24 hrs [WB_24hF]

value: 1% wheat bran liquid medium for 24 hours


title: AH9223

description:
HTO
conditions_10X.tsv

tag: days in culture


title: AH9224

description:
HTO
conditions_10X.tsv


title: AH9225

description:
cDNA
conditions_10X.tsv


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% wheat bran liquid medium for 24 hrs [WB_24hT]

tag: culture condition


title: simr-1 - 20°C, replicate 1

description:
mRNA from total RNA
mRNA-seq


title: H3K9ac_Scrmbl-KD

data_processing:
Base-calling was performed with NextSeq RTA version 2.4.11.0; bcl2fastq version 2.20.0 was used to convert the bcl files into fastq files
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 1.2.2 with the following criteria: --best --chunkmbs 320
Peak-calling was performed using MACS version 1.4.2
Bigwig files were generated using deepTools version 2.7.15 by scaling the bam files to reads per kilobase per million (RPKM) using the following criteria: bamCoverage –b–normalizeUsing RPKM–smoothLength 300–binSize 30–extendReads 200 –o
Differential peaks were called using MACS2 with the following criteria: bdgdiff –g 60 –l 120
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: KRAS*-independent iKPC escaper cells

extract_protocol:
Cells were crosslinked by 1% paraformaldehyde for 10 minutes at room temperature and then quenched by 0.125M glycine for 5 minutes. Cells were lysed on ice for 30 minutes with lysis buffer containing 10 mM Tris-HCl (pH 8.0), 1 mM EDTA (pH 8.0), 140 mM NaCl, 1% Triton X-100, 0.2% SDS, 0.1% deoxycholic acid. Chromatin DNA was fragmented to around 200-500bp by Diagenode BioruptorPico sonicator for 45 cycles of 30 seconds on and 30 second off, and then incubated overnight with anti-H3K4me3 or H3K27ac or H3K9ac antibody and Dynabead (Life Technologies) at 4C. Next day, immune complexes were washed once with RIPA buffer with 500mM NaCl and once with LiCl wash buffer (10 mM Tris-HCl (pH 8.0), 1 mM EDTA (pH 8.0), 250 mM LiCl, 0.5% NP-40, 0.5% deoxycholic acid). DNA was then reverse crosslinked and eluted overnight in elution buffer (10 mM Tris-Cl (pH 8.0), 5 mM EDTA, 300 mM NaCl, 0.5% SDS, 20 mg/ml proteinase K) at 65C. The third day, eluted DNA was purified by AMPure beads (Beckman-Coulter).
NEB Next Ultra DNA Library kit was used to prepare library

value: HDAC5-driven PDAC escaper cells

tag: chip-antibody

value: H3K9ac (abcam, ab4441)


title: RBG8153_KitHi_E11.5_G2VInt


title: wild-type - 25°C, 10 generation, replicate 1

description:
mRNA from total RNA
mRNA-seq

value: N2- wild type


title: simr-1 - 25°C, 1 generation, replicate 3

description:
mRNA from total RNA
mRNA-seq


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% Avicel liquid medium for 24 hrs [AV_24hT]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 24 hours

value: 1% Avicel liquid medium for 24 hours


title: wild-type - 25°C, 10 generation, replicate 3

description:
mRNA from total RNA
mRNA-seq


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% Avicel liquid medium for 24 hrs [AV_24hF]


title: wild-type - 25°C, 10 generation, replicate 2

description:
mRNA from total RNA
mRNA-seq


title: H3K9ac_GFP-OE

source_name: KRAS*-dependent iKPC PDAC cells

value: PDAC cells


title: RBG8200_KitHi_E11.5_G2VInt

value: EC


title: wild-type - 25°C, 7 generation, replicate 2

description:
mRNA from total RNA
mRNA-seq


title: RBG8212_KitHi_E11.5_G2VInt


title: RBG8224_KitHi_E11.5_G2VInt


title: H3K9ac_HDAC5-OE


title: wild-type - 25°C, 7 generation, replicate 1

description:
mRNA from total RNA
mRNA-seq


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% Avicel liquid medium for 24 hrs [AV_24hS]


title: H3K9ac_HDAC5-KD


title: Mycelium of 1 gram Mutant Ku70 cultured in carbon-free liquid medium for 12 hrs [NC_12hS]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in carbon-free liquid medium for 12 hours

value: carbon-free liquid medium for 12 hours


title: RBG8164_KitHi_E11.5_G2VInt


title: wild-type - 25°C, 7 generation, replicate 3

description:
mRNA from total RNA
mRNA-seq


title: wild-type - 25°C, 2 generation, replicate 3

description:
mRNA from total RNA
mRNA-seq


title: H3K27ac_Scrmbl-KD

value: H3K27ac (abcam, ab4729)


title: Mycelium of 1 gram Mutant Ku70 cultured in carbon-free liquid medium for 12 hrs [NC_12hF]


title: RBG8176_KitHi_E11.5_G2VInt


title: Mycelium of 1 gram Mutant Ku70 cultured in carbon-free liquid medium for 12 hrs [NC_12hT]


title: wild-type - 25°C, 2 generation, replicate 2

description:
mRNA from total RNA
mRNA-seq


title: H3K27ac_HDAC5-KD


title: RBG8235_KitHi_E11.5_G2VInt


title: H3K27ac_GFP-OE


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% glucose liquid medium for 12 hrs [Glu_12hT]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in 1% glucose liquid medium for 12 hours

value: 1% glucose liquid medium for 12 hours


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% glucose liquid medium for 12 hrs [Glu_12hS]


title: H3K27ac_HDAC5-OE


title: wild-type - 25°C, 1 generation, replicate 3

description:
mRNA from total RNA
mRNA-seq


title: RBG8188_KitHi_E11.5_G2VInt

value: IAHC cells


title: RBG8211_KitHi_E11.5_G2VInt


title: H3K4me3_Scrmbl-KD

value: H3K4me3 (abcam, ab8580)


title: wild-type - 25°C, 1 generation, replicate 2

description:
mRNA from total RNA
mRNA-seq


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 12 hrs [HEC_12hT]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in 1% methyl cellulose liquid medium for 12 hours

value: Mycelium


title: RBG8199_KitHi_E11.5_G2VInt


title: H3K4me3_HDAC5-KD


title: wild-type - 25°C, 1 generation, replicate 1

description:
mRNA from total RNA
mRNA-seq

value: Day 1 Adult


title: H3K4me3_GFP-OE


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 12 hrs [HEC_12hS]

value: 1% methyl cellulose liquid medium for 12 hours


title: wild-type - 20°C, replicate 3

description:
mRNA from total RNA
mRNA-seq


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 12 hrs [HEC_12hF]


title: wild-type - 25°C, 2 generation, replicate 1

description:
mRNA from total RNA
mRNA-seq


title: RBG8223_KitHi_E11.5_G2VInt


title: RBG8175_KitHi_E11.5_G2VInt


title: wild-type - 20°C, replicate 2

description:
mRNA from total RNA
mRNA-seq


title: H3K4me3_HDAC5-OE


title: wild-type - 20°C, replicate 1

description:
mRNA from total RNA
mRNA-seq


title: RBG8163_KitHi_E11.5_G2VInt


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 12 hrs [MC_12hS]


title: Input_HDAC5-KD


title: Input_Scrmbl-KD


title: RBG8234_KitHi_E11.5_G2VInt


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 12 hrs [MC_12hF]


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% glucose liquid medium for 12 hrs [Glu_12hF]


title: Input_GFP-OE


title: rsd-2 rep 1

description:
size selected RNA from total RNA
Single Replicate

growth_protocol: Synchronized L1s of wild type and C06A5.6(cmp36) worms were plated on enriched peptone plates and cultured at 20C and 25C

extract_protocol:
10,000 animals per sample were harvested as adults (~68hrs at 20°C and ~48hrs at 25°C) for RNA extraction. Worms were washed off plates using water and then settled on ice to form a pellet. Water was aspirated off and worm pellets were resuspended in 1mL TRIzol reagent (Life Technologies) and freeze-thawed on dry ice followed by vortexing. Worm carcasses were pelleted using centrifugation and the supernatant containing RNA was collected. 0.2 volume chloroform was add to supernatant, vortexed, centrifuged, and then the aqueous phase was transferred to a new tube. Samples were precipitated using isopropanol and rehydrated in 50μL nuclease-free H2O.
Small RNA library preparation. Small RNAs (18 to 30-nt) were size selected on denaturing 15% polyacrylamide gels (BioRad 3450091) from total RNA samples. Small RNAs were treated with 5’ RNA polyphosphatase (Epicentre RP8092H) and ligated to 3’ pre-adenylated adapter with Truncated T4 RNA ligase (NEB M0373L). Small RNAs were then hybridized to the reverse transcription primer, ligated to the 5’ adapter with T4 RNA ligase (NEB M0204L), and reverse transcribed with Superscript III (ThermoFisher 18080-051). Small RNA libraries were amplified using Q5 High-Fidelity DNA polymerase (NEB M0491L) and size selected on a 10% polyacrylamide gel (BioRad 3450051). Library concentration was determined using the Qubit 1X dsDNA HS Assay kit and quality was assessed using the Agilent BioAnalyzer. Libraries were sequenced on the Illumina NextSeq500 (SE 75-bp reads) platform.


title: RBG8222_KitHi_E11.5_G2VInt


title: F37C4.5 rep 1


title: Input_HDAC5-OE


title: hgo-1 rep 1


title: RBG8187_KitHi_E11.5_G2VInt


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% wheat bran liquid medium for 12 hrs [WB_12hS]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in 1% wheat bran liquid medium for 12 hours


title: E14.5 FL HSC

city: San Francisco

first: Qin

last: Zhu

state: CA

address: 600 Minnesota Street

institute: UCSF

description: 10X sc-RNA-seq with cells from dissociated mouse embryos

data_processing:
Data was processed using the 10X Genomics CellRanger pipeline. Sequencing reads were mapped to mm10 reference genome.
Filtering was performed on the raw gene-barcode matrix output by the Cell Ranger cellranger count function, removing barcodes that have fewer than 1000 transcripts and 1000 expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: gene_by_cell_count_matrix.txt contains a sparse matrix where rows are genes (with gene information in the gene_annotation.csv), columns are cells (with cell information in the cell_annotation.csv), and values are background corrected UMI counts for the given gene in the given cell. cell_annotation.csv contains a data frame with annotations (i.e. 10X barcode, cell type, etc.) for each cell. gene_annotation.csv contains a data frame with gene id and gene short name.

source_name: dissociated mouse embryos

extract_protocol:
Cells were sorted into IMDM/10-20% FBS. Using the Chromium controller (10x Genomics) and reagents from the Chromium Single Cell 3′ Reagent Kit v2 (10x Genomics), cells were partitioned into nanoliter-scale Gel Beads-in-emulsion (GEMs) where each cell's trascriptome was indexed with a specific 10x BarCode. cDNA were amplified and purified for library preparation.
cDNA were used for library preparation using the Chromium Single Cell 3′ Reagent Kit v2 (10x Genomics) according to manufacturer’s protocol (CG00052, Rev D).

treatment_protocol: Females were superovulated by administering 5 IU of Pregnant Mare Serum Gonadotrophin and 5 IU human chorionic gonadotrophip at 48 and 0 hours prior to paring with males. Embryos were harvested at the appropriate embryonic day and cells were sorted on the same day as harvest.

tag: developmental stage

value: Embryonic day 14.5

tag: genotype

value: wild type

tag: marker

value: Lin- Sca1+ Kit+ CD48- CD150+

value: fetal liver


title: RBG8210_KitHi_E11.5_G2VInt

source_name: IAHC cells

tag: cluster (nocd27+ cells)


title: mut-16 rep 1


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 12 hrs [MC_12hT]


title: RBG8150_KitHi_E11.5_G2VInt

tag: clustertype (nocd27+ cells)


title: RBG8198_KitHi_E11.5_G2VInt


title: nyn-1;nyn-2 rep 1

tag: strain


title: E11.5 CD45+CD27+IAC

value: Embryonic day 11.5

tag: tissue

value: dorsal aorta plus umbilical and vitelline arteries


title: RBG8186_KitHi_E11.5_G2VInt


title: E11.5 FL LMPP


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% Avicel liquid medium for 12 hrs [AV_12hT]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 12 hours

value: 1% Avicel liquid medium for 12 hours


title: RBG8174_KitHi_E11.5_G2VInt


title: hpo40 rep 1

source_name: Whole worm

tag: Stage


title: math-33 rep 1

tag: experimental temp


title: RBG8162_KitHi_E11.5_G2VInt

tag: condition


title: RBG8149_KitHi_E11.5_G2VInt

tag: days


title: wago-1 rep 1


title: E11.5 IAC replicate 2

value: Ter119- CD41lo/- CD31+ CD144+ ESAM+ Kit+


title: Mycelium of 1 gram Mutant Ku70 cultured in carbon-free liquid medium for 4 hrs [NC_4hT]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in carbon-free liquid medium for 4 hours

value: carbon-free liquid medium for 4 hours


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% Avicel liquid medium for 12 hrs [AV_12hF]


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% Avicel liquid medium for 12 hrs [AV_12hS]


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% wheat bran liquid medium for 12 hrs [WB_12hT]

value: 1% wheat bran liquid medium for 12 hours


title: C06A5.6 rep 1

value: USC863- simr-1(cmp36)


title: E11.5 IAC replicate 1

value: CD31+ CD144+ ESAM+ Kit+


title: RBG8233_KitHi_E11.5_G2VInt

tag: cell type

value: IAHC cells

value: EC


title: RBG8221_KitHi_E11.5_G2VInt

tag: cluster (all cells)


title: Mycelium of 1 gram Mutant Ku70 cultured in carbon-free liquid medium for 4 hrs [NC_4hS]

value: Mycelium


title: Mycelium of 1 gram Mutant Ku70 cultured in carbon-free liquid medium for 4 hrs [NC_4hF]


title: E10.5 IAC

value: Embryonic day 10.5


title: N2 rep 1

value: Day 1 Adult

value: N2- wild type


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% wheat bran liquid medium for 12 hrs [WB_12hF]


title: E10.5 E+HE+IAC

value: wild type


title: C06A5.6;hpo40 rep1


title: RBG8209_KitHi_E11.5_G2VInt


title: E10.5 E replicate 2

value: Ter119- CD41- CD45- Kit- CD144+ ESAM+ Runx1:GFP-


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% glucose liquid medium for 4 hrs [Glu_4hT]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in 1% glucose liquid medium for 4 hours

value: 1% glucose liquid medium for 4 hours


title: RBG8197_KitHi_E11.5_G2VInt


title: C33G3.6 rep 1


title: Y57G11C.3 rep 1


title: E10.5 E replicate 1

value: CD41- CD45- Kit- CD31+ Runx1:GFP-


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% glucose liquid medium for 4 hrs [Glu_4hF]


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% glucose liquid medium for 4 hrs [Glu_4hS]


title: RBG8185_KitHi_E11.5_G2VInt


title: RBG8173_KitHi_E11.5_G2VInt


title: rde-8 rep 1


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 4 hrs [HEC_4hT]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in 1% methyl cellulose liquid medium for 4 hours


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 4 hrs [HEC_4hS]

value: 1% methyl cellulose liquid medium for 4 hours


title: E10.5 CD45+ IAC

value: CD31+ CD144+ ESAM+ Kit+ CD45+

value: dorsal aorta plus umbilical and vitelline arteries


title: C06A5.6 gen10 rep 2

description: size selected RNA from total RNA


title: RBG8161_KitHi_E11.5_G2VInt


title: WT 2week rep3

city: Cleveland

first: Ying

last: Ni

state: OH

address: 9500 Euclid Ave

department: Quantitative Health Science

institute: Cleveland Clinic

data_processing:
Pair-end raw fastq files ware aligned and assembled to mouse genome mm10 with STAR (v2.3.1d)
Quantified read counts from STAR were used for differential gene expression analysis using DEseq2 R package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample …

source_name: heart tissue

extract_protocol:
Mouse heart tissue were disected and RNA was harvested using RNeasy Fibrous Tissue Mini Kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Truseq Stranded Total RNA -RiboZero library was prepared

value: LMNA Wildtype

tag: timepoint


title: E9.5 HE replicate 2

value: Embryonic day 9.5

value: Ter119- CD41- CD45- Kitlo/- CD144+ ESAM+ Runx1:GFP+


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 4 hrs [HEC_4hF]


title: C06A5.6 gen10 rep 1

description: size selected RNA from total RNA

value: USC863- simr-1(cmp36)


title: E9.5 E replicate 2


title: E9.5 HE replicate 1

value: CD41- CD45- Kitlo/- CD31+ Runx1:GFP+


title: WT 2week rep2


title: WT 2week rep1


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 4 hrs [MC_4hS]


title: C06A5.6 gen7 rep 2

description: size selected RNA from total RNA


title: C06A5.6 gen7 rep 1

description: size selected RNA from total RNA


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 4 hrs [MC_4hT]


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% methyl cellulose liquid medium for 4 hrs [MC_4hF]


title: Knockout 2week rep3

value: LMNA knockout


title: C06A5.6 gen2 rep 2

description: size selected RNA from total RNA


title: E9.5 E replicate 1


title: Knockout 2week rep2


title: C06A5.6 gen2 rep 1

description: size selected RNA from total RNA


title: E9.5 E+HE+IAC

value: Ter119- CD45- CD41lo/- Kitlo/- CD31+ CD144+ ESAM+


title: E9.5 EMP

value: yolk sac


title: C06A5.6 gen1 rep 2

description: size selected RNA from total RNA

value: Day 1 Adult


title: Knockout 2week rep1


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% wheat bran liquid medium for 4 hrs [WB_4hT]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in 1% wheat bran liquid medium for 4 hours

value: 1% wheat bran liquid medium for 4 hours

value: Mycelium


title: E10.5 CD44+ E+HE+IAC (paired scATAC-Seq)

value: Embryonic day 10.5

value: wild type


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% wheat bran liquid medium for 4 hrs [WB_4hS]


title: C06A5.6 gen1 rep 1

description: size selected RNA from total RNA


title: E10.5 CD44+ E+HE+IAC (cR1 Cre-)


title: E10.5 CD44+ E+HE+IAC (cR1 Cre+)


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% wheat bran liquid medium for 4 hrs [WB_4hF]


title: WT 1month rep3


title: C06A5.6 gen0 rep 2

description: size selected RNA from total RNA


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% Avicel liquid medium for 4 hrs [AV_4hT]

source_name: Mycelium of 1 gram Mutant Ku70 were cultured in 1% Avicel liquid medium for 4 hours

value: 1% Avicel liquid medium for 4 hours


title: WT 1month rep2


title: E10.5 Runx1+/+ E+HE+IAC replicate 2

value: B6C3F1/J + Runx1tm4Dow


title: WT 1month rep1


title: C06A5.6 gen0 rep 1

description: size selected RNA from total RNA


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% Avicel liquid medium for 4 hrs [AV_4hS]


title: N2 gen10 rep 2

description: size selected RNA from total RNA

value: N2- wild type


title: E10.5 Runx1+/- E+HE+IAC replicate 1

value: dorsal aorta plus umbilical and vitelline arteries


title: Mycelium of 1 gram Mutant Ku70 cultured in 1% Avicel liquid medium for 4 hrs [AV_4hF]


title: E10.5 Runx1+/+ E+HE+IAC replicate 1


title: WT 1week rep3

value: LMNA Wildtype


title: N2 gen10 rep 1

description: size selected RNA from total RNA


title: WT 1week rep2


title: 293T138_8hpi_PAR-CLIP

city: Hangzhou

first: Dongli

last: Pan

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

description:
small RNA
Control cells, Infected with HSV-1 for 8 hours

data_processing:
Reads were trimmed to discard adapters and low-quality reads and reads less than 21 base long using fastx_clipper (http://hannonlab.cshl.edu/fastx_toolkit/).
Using the “grep” command to retain only reads that contain this sequence CACCAGC (binding site of the miR-138 seed region). These reads were aligned with the mouse (mm10 version) genome using Tophat2 (https://ccb.jhu.edu/software/tophat/index.shtml)
Counts of reads aligned to 5’ UTR, CDS and 3’ UTR of each transcript were determined by Htseq-count (https://htseq.readthedocs.io/).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts of sequencing reads for each viral or mouse/human gene

organism:
Homo sapiens
Human alphaherpesvirus 1

source_name: 293Tcontrol cells derived from 293Tcontrol cells infected

extract_protocol:
RNA crosslinked and immunoprecipitate with Agonaute was extracted according to standard PAR-CLIP protocol (Danan, C., Manickavel, S., and Hafner, M. (2016). PAR-CLIP: A Method for Transcriptome-Wide Identification of RNA Binding Protein Interaction Sites. Methods in molecular biology 1358, 153-173.)
RNA libraries were prepared for sequencing using TruSeq Small RNA Library Preparation Kit (Illumina)

treatment_protocol: For infection, cells were infected with wild-type HSV-1 (strain KOS) for 4 and 8 hpi (MOI = 1) before PAR-CLIP

value: Kidney

tag: cell line

value: control

tag: infection status

value: infected with HSV-1 for 8 hours


title: E10.5 E+HE+IAC from dorsal aortas

value: dorsal aorta


title: N2 gen7 rep 2

description: size selected RNA from total RNA


title: E10.5 E+HE+IAC from vitelline + umbilical arteries

value: umbilical and vitelline arteries


title: 293Tcontrol_8hpi_PAR-CLIP

description:
small RNA
Cells overexpressing miR-138, infected with HSV-1 for 8 hours

source_name: 293T138 cells derived from 293T cells

value: overexpressing miR-138


title: WT 1week rep1


title: E10.5 HE

value: Ter119- CD45- CD31+ CD144+ ESAM+ Kitlo/ CD41lo/mid/- Runx1:GFP+


title: Knockout 1month rep3

value: LMNA knockout


title: 293T138_4hpi_PAR-CLIP

description:
small RNA
Control cells, infected with HSV-1 for 4 hours

value: infected with HSV-1 4 hours


title: Knockout 1month rep2


title: N2 gen7 rep 1

description: size selected RNA from total RNA

value: Day 1 Adult


title: E10.5 Runx1+/- E+HE+IAC replicate 2

value: Embryonic day 10.5


title: N2 gen2 rep 2

description: size selected RNA from total RNA


title: 293Tcontrol_4hpi_PAR-CLIP

description:
small RNA
Cells overexpressing miR-138, infected with HSV-1 for 4 hours


title: Knockout 1month rep1


title: miR-138_M138_3

description: miR-138 transfected, infected with M138 virus

data_processing:
Reads were trimmed to remove adapters, low-quality reads, and reads less than 30 bases long using Trimmomatic (http://www.usadellab.org/cms/index.php?page=trimmomatic)
The trimmed reads were aligned with the HSV-1 strain KOS (GenBank accession number KT899744.1) using Tophat2 (https://ccb.jhu.edu/software/tophat/index.shtml).
Counts of reads aligned to each transcript were determined by Htseq-count (https://htseq.readthedocs.io/).
Genome_build: Herpes simplex virus 1 strain KOS (GenBank accession number KT899744.1)
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts of sequencing reads for each viral gene

organism:
Mus musculus
Human alphaherpesvirus 1

source_name: HSV-1 infected Neuro-2a cells

extract_protocol:
Total RNAs were purified using an RNeasyPlus Mini Kit following the manufacturer’s instructions (Qiagen)
mRNAs were isolated using a Takara mRNA Isolation Kit. Libraries were prepared using a PrepX RNA-seq Library Preparation Kit

treatment_protocol: Neuro-2a cells were transfected with 40 nM of a miR-138 or scrambled mimic for 24 h, and infected with WT or M138 virus (MOI = 10) for 16 h before performing RNAseq

tag: mouse cell line

tag: transfected with

value: miR-138 mimic

tag: virus genotype

value: M138 mutant


title: Knockout 1week rep3

tag: genotype


title: miR-138_M138_2


title: N2 gen2 rep 1

description: size selected RNA from total RNA


title: Knockout 1week rep2


title: N2 gen1 rep 1

description: size selected RNA from total RNA


title: N2 gen0 rep 2

description: size selected RNA from total RNA


title: miR-138_M138_1


title: Knockout 1week rep1


title: Brain, Ipsi21_3

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

description:
expressed_gene_FPKM.txt
expressed_gene_reads.txt

data_processing:
Illumina bcl2fastq software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) and low quality bases trimmed using FASTX-Toolkit (Version 0.0.13). the short reads less than 16nt were also dropped.
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 16 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
edgeR was used to the DEG analysis with FC>2, Qvalue <= 0.05.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: tab-delimited text files including gene FPKM values for each sample.

organism: Rattus norvegicus

source_name: brain

growth_protocol: Aging male Sprague Dawley rats (13- and 22-month old) were used for our experiments. These rats were obtained from Animal Center of Daping Hospital, the Army Medical University (the Third Military Medical University, Chongqing, China) and housed in specific pathogen free conditions. The rats were randomly enrolled in each experimental group. Protocols of our animal studies were approved by and conducted in accordance with the Animal Ethics Committee of the Army Medical University (Third Military Medical University, Chongqing, China).

extract_protocol:
To construct an RNA-Seq library, we first isolated total cellular RNA from brain tissue samples using TRIzol reagent (Ambion, Austin, TX, USA) according to the manufacturer’s protocol and then treated them with RQ1 DNase (Promega, Madison, WI, USA) to remove contaminated DNA and quantified them by measuring the absorbance at 260 /280 nm with the Smartspec plus (BioRad, Hercules, CA, USA). The integrity of the RNA samples was further assessed using 1.5% agarose gel electrophoresis.
Ten μg of each total RNA sample was used to construct the RNA-seq library. Specifically, polyadenylated mRNA samples were isolated, purified, and concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen, Carlsbad, CA, USA) and fragmented at 95oC and ligated by the end repair and 5' adaptor. Next, these mRNA samples were reversely transcribed into cDNA using the RT primer harboring 3'-end adaptor sequences and randomized hexamer, which was purified and amplified using PCR, leading to 200-500 bp PCR products, which was purified, quantified and stored at -80oC before DNA sequencing.

treatment_protocol: Rats were anesthetized with isoflurane at 3.5% for induction and 1.5% in maintenance and then immobilized on the stereotaxic apparatus (RWD Life Science Co., Shenzhen, China) followed by drilling of a 1-mm diameter burr hole at the location of 0.2 mm anterior and 3.5 mm lateral to the bregma. We then injected a total of 75-μL autologous blood into the striatum after attached a Hamilton needle to the micropump (RWD Life Science Co.) at 5.5 mm ventral to the skull surface.

value: Sprague Dawley

value: brain

tag: treatment

value: intracerebral hemorrhage

tag: age


title: Control_M138_3

description: Control transfected, infected with M138 virus

value: scrambled mimic (control)


title: N2 gen0 rep 1

description: size selected RNA from total RNA

tag: strain

value: N2- wild type


title: Brain, Ipsi21_2

tag: tissue


title: Control_M138_2


title: KO CD8 rep 5

city: Holl

first: Ryan

last: O'Connell

state: UT

department: Pathology

institute: University of Utah

description:
counts.txt
sample name in processed data file: 14713X20

data_processing:
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 87.
The reference database was created using STAR version 2.5.2b with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using Subread's command featureCounts (version 1.5.1).
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw gene counts (Subread's featureCounts output files combined into a single tab-delimited matrix).

source_name: CD3+ CD8+ FACS sorted splenocytes

extract_protocol:
CD4 and CD8 T cells were FACS sorted from homogenized and RBC lysed spleens of 8 week old Male MPC1fl/fl (WT) and Vav Cre MPC1fl/fl (MPC1 KO).
Illumina TruSeq Stranded Total RNA Kit with Ribo-Zero Gold

value: Spleen

value: CD8 T cell

value: Vav-Cre MPC1 fl/fl


title: Brain, Ipsi13_3


title: N2AFox3

description: pFoxc1human transfected KOS infected Neuro-2a cells

data_processing:
Reads were trimmed to remove adapters, low-quality reads, and reads less than 30 bases long using Trimmomatic (http://www.usadellab.org/cms/index.php?page=trimmomatic)
The trimmed reads were aligned with the  mouse (mm10 build) or  HSV-1 strain KOS (GenBank accession number KT899744.1) genome using Tophat2 (https://ccb.jhu.edu/software/tophat/index.shtml).
Counts of reads aligned to each transcript were determined by Htseq-count (https://htseq.readthedocs.io/).
Genome_build: mm10 (mouse), HSV1 strain KOS (GenBank KT899744.1)
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts of sequencing reads for each host gene

source_name: Neuro-2a cells

treatment_protocol: Neuro-2a cells in 24-well plates were transfected with 100 ng of plasmids for 40 hours, and then infected with KOS at an MOI of 1 for 5 hours, before being harvested by lysis buffer for RNA purification and RNAseq analysis.

value: Brain


title: Brain, Ipsi13_2


title: Brain, Ipsi21_1


title: Control_M138_1


title: N2AFox2


title: KO CD8 rep 4

description:
counts.txt
sample name in processed data file: 14713X19


title: Brain, Ipsi13_1


title: N2 gen1 rep 2

description: size selected RNA from total RNA

tag: Stage


title: KO CD8 rep 3

description:
counts.txt
sample name in processed data file: 14713X18


title: Brain, Cont21_2

value: control


title: miR-138_WT_2

description: miR-138 transfected, infected with WT virus

value: WT


title: KO CD8 rep 1

description:
counts.txt
sample name in processed data file: 14713X16


title: Brain, Cont21_3


title: N2AFox1


title: miR-138_WT_1


title: N2AC2

description: pcDNA transfected and KOS infected Neuro-2a cells


title: Brain, Cont21_1


title: N2AC3


title: Control_WT_3

description: Control transfected, infected with WT virus


title: Brain, Cont13_3


title: N2AC1


title: Brain, Cont13_2


title: WT CD8 rep 5

description:
counts.txt
sample name in processed data file: 14713X15

value: MPC1 fl/fl


title: WT CD8 rep 4

description:
counts.txt
sample name in processed data file: 14713X14


title: WT CD8 rep 3

description:
counts.txt
sample name in processed data file: 14713X13


title: Control_WT_2


title: 6 h rep2

first: Xuemei

last: Mao

address: Baishi Road

department: IAS

institute: Shenzhen University

data_processing:
Zebra process software (version 0.5.0.13875) was used for basecalling.
Data was filtered by software SOAPnuke (version v1.5.2, parameters -l 15 -q 0.5 -n 0.1) to remove reads with adaptors, unknown bases (more than 10%), and low quality reads.
HISAT (version v2.0.4) was used to do the genome mapping, and clean reads were mapped to reference genes using Bowtie2 (version v2.2.5).
Gene expression level (FPKM) was calculated with RSEM software (version v1.2.12)
Genome_build: Chromochloris zofingiensis v5.2.3.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Chromochloris zofingiensis

source_name: microalgae

growth_protocol: Chromochloris zofingiensis  were grown in 250 ml columns of photoreactor with 80 μE m-2 s-1 continuous illumination and 1.5% CO2 enriched air.

extract_protocol:
Total RNA was extracted  using the plant RNA extraction kit (TaKaRa, Japan) and poly-A  mRNA was purified using poly-T oligo-attached magnetic beads.
The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, which was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then had the addition of a single 'A' base and subsequent ligation of the adapter. The products were purified and enriched with PCR amplification. The PCR yield was quantified by Qubit, and samples were pooled together to make a single strand DNA circle (ssDNA circle), which gave the final library.

tag: time point

value: 6 h


title: miR-138_WT_3


title: WT CD8 rep 2

description:
counts.txt
sample name in processed data file: 14713X12


title: KO CD8 rep 2

description:
counts.txt
sample name in processed data file: 14713X17


title: Brain, Cont13_1


title: MiaPaCa2_KO_rep3

city: Beppu,Oita

first: Atsushi

last: Fujii

address: 4546 Tsurumibaru

department: Department of Surgery

country: Japan

institute: Kyushu University Beppu Hospital

data_processing:
The in-house pipeline Genomon 2.6.0  (https://genomon-project.github.io/GenomonPagesR)  was used for quality control and mapping.
The sequencing libraries generated from the RNA were analyzed by BGISEQ-500. The sequencing reads were trimmed for adaptor sequence, and low-complexity or low-quality reads were removed. Subsequently, the reads were aligned to the human reference sequence and the gene annotations (UCSC hg19) using Tophat2 v2.0.14 with following parameters; --runThreadN 6 --outSAMstrandField intronMotif --outSAMunmapped Within --alignMatesGapMax 500000 --alignIntronMax 500000 --alignSJstitchMismatchNmax -1 -1 -1 -1 --outSJfilterDistToOtherSJmin 0 0 0 0 --outSJfilterOverhangMin 12 12 12 12 --outSJfilterCountUniqueMin 1 1 1 1 --outSJfilterCountTotalMin 1 1 1 1 --chimSegmentMin 12 --chimJunctionOverhangMin 12.
STAR v2.5.2a was used to calculate fragments per kilobase of transcript per million fragments mapped (FPKM) values.
Genome_build: UCSC hg19 with Gencode v28 annotations
Supplementary_files_format_and_content: tab-delimited text files of read counts per gene from STAR v2.5.2a

source_name: PDAC cell line

extract_protocol:
Total RNA was extracted from the cells using ISOGEN II (Nippon Gene).
Total RNA extracted from ASAP2 knockout or wild-type Panc1 and MiaPaCa2 cells was subjected to RNA-seq analysis. The sequencing libraries generated from the RNA were analyzed by BGISEQ-500.

value: pancreatic ductal adenocarcinoma (PDAC) cells

tag: cell no

value: RIKEN BRC Cat# RCB2094

value: ASAP2 knockout


title: 6 h rep1


title: WT CD8 rep 1

description:
counts.txt
sample name in processed data file: 14713X11


title: MiaPaCa2_KO_rep2


title: Pig14_border

city: Cinicnnati

first: Katherine

middle: E

last: Yutzey

address: 240 Albert Sabin Way

department: Divison of Molecular Cardiovascular Biology

institute: Cinicnnati Children's Hospital Medical Center

data_processing:
Fastq files were trimmed to remove adapter and loq quality sequences using Trimmomatic V 0.33
Trimmed reads were mapped to the reference (Sscrofa11) using hisat2 V 2.0.5
After trimming the reads were quantified using Kallisto V 0.43.1, this gives us TPM and Counts
Genome_build: Sscrofa11
Supplementary_files_format_and_content: tab-delimited text files include TPM and COUNTS for all samples

organism: Sus scrofa

source_name: Left ventricular myocardial tissue

growth_protocol: None- tissue was extracted when pigs were 4-weeks post surgery and rapidly frozen before RNA extracted.

extract_protocol:
Myocardial tissue was harvested 4-weeks following surgery and cut into zonal sections. Tissue was washed in PBS and rapidly frozen in liquid nitrogen, before transfer to a -80C freezer for storage. RNA was then extracted using a commercially available kit (NucleoSpin RNA kit (740955, Macherey-Nagel) and eluted in RNAse free H20 prior to submission to CCHMC DNA Core for processing.
RNA libraries were prepared for sequencing using Illumina Truseq stranded mRNA protocol

treatment_protocol: Ischemia/reperfusion= 1-hour occlusion of the left anterior descending artery, just below the second diagonal branch, following by reperfusion. Sham= same procedure but no occlusion of artery.

tag: surgery

value: IR

tag: zone

value: Border

tag: Sex

value: Female


title: Pig14_scar

value: Scar