title: T2063-09-02; 35 mg


title: T2063-09-01; 32 mg

status: Public on Mar 19 2025

type: SRA

city: Nashville

first: Qi

last: Liu

state: Tennessee

address: 2525 WEST END AVE

country: USA

institute: Vanderbilt University Medical Center

library_source: transcriptomic

data_processing:
Quality control and adapter trimming were performed using FastQC.
Reads were aligned to hg38 using STAR
Gene counts were quantified using featureCounts.
Assembly: hg38
Supplementary files format and content: Tab-delimited file containing read counts for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: Thymus

extract_protocol:
Human thymusd was obtained from anonymous patients undergoing corrective cardiac surgery where a portion of the thymus was removed in order to expose the operative field. Portions of thymi were immediately placed in RNALater, incubated at 4C overnight, and stored in liquid nitrogen until processed.
Frozen tissues were homogenized in a Precelly's soft tissue lysing tube and RNA was extracted using Rneasy Kit according to manufacturer's protocol. RNA was cleaned and concentrated using Turbo DNA-free and Rneasy MiniElute.
Libraries were prepared using a KAPA Stranded mRNA-seq kit.

tag: tissue

value: Thymus

tag: age (years)

tag: Sex

value: Female


title: T2060-06-01; 44 mg

value: Male


title: DUPLICATE T2059-07-01; 41 mg


title: T2059-07-01; 41 mg


title: DUPLICATE T2057-07-01; 53 mg


title: T2057-07-01; 53 mg


title: T2056-09-02; 43 mg


title: T2056-09-01; 34 mg


title: T2055-12-02; 35 mg


title: T2055-12-01; 45 mg


title: T2046-07-02; 45 mg


title: T2046-07-01; 34 mg


title: T2044-12-02; 43 mg


title: T2035-12-03; 39 mg


title: T2035-12-02; 46 mg


title: T2067-12-02; 45 mg


title: T2067-12-01; 47 mg


title: DUPLICATE T2039-08-01; 35 mg


title: T2039-08-01; 35 mg


title: DUPLICATE T2038-15-01; 29 mg


title: T2038-15-01; 29 mg


title: T2036-13-01; 54 mg


title: T2033-12-03; 29 mg


title: T2033-12-02; 40 mg


title: T2027-08-03; 35 mg


title: T2025-06-01; 52 mg


title: T2024-09-03; 38 mg


title: T2018-08-03; 31 mg


title: Organoids_ISC_3d_aKG_1

status: Public on Apr 02 2025

city: New York

first: Yu-Jui

last: Ho

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

description: Library name: ISC_3d_aKG_1

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.6.1a), and quantified transcript counts using featureCounts (2.0.6).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

organism: Mus musculus

source_name: Organoids

growth_protocol: All animal experiments in this study were performed in accordance with protocols approved by the Memorial Sloan Kettering Institutional Animal Care and Use Committee (approval number: 11-06-012). The mice were housed with a 12 h light/dark cycle between 8:00 and 20:00 in a temperature-controlled room (22 ± 1°C) with free access to water and food. Both male and female mice were used in equal proportions for all experiments. .

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

treatment_protocol: Crypts were isolated from mice with the described phenotype and cultured in ENR-CV media for six days before adding DM-αKG or doxycycline. Organoids were then maintained under the indicated treatment for three days.

tag: mouse strain

value: Mix

tag: cell type

value: Organoids

tag: time

tag: genotype

value: TetO. shRen; Cag-rtTA

tag: treatment

value: 600 mg/ Kg DM-aKG


title: T2018-08-01; 26 mg


title: T2016-07-04; 36 mg


title: T2015-06-01; 35 mg


title: T2015-06-04; 39 mg


title: Organoids_ISC_3d_346_1

description: Library name: ISC_3d_346_1

value: TetO. shOgdh; Cag-rtTA

value: doxycycline


title: IntestCrypts_aKG_Day10_R1_Mouse_4

description: Library name: IntestCrypts_aKG_Day10_R1_Mouse_4

source_name: Murine crypts

treatment_protocol: DM-aKG supplementation, mice were injected (intraperitoneally) once daily with 600 mg/kg of DM-aKG (349631-5G, Sigma-Aldrich) dissolved in PBS. For the vehicle control, mice were injected with PBS.

value: Murine crypts


title: T2013-12-04; 30 mg


title: T2036-13-04; 34 mg


title: T2012-12-03; 20 mg


title: T2010-11-03; 32 mg


title: T2012-13-04; 20 mg


title: T2010-12-02; 27 mg


title: T2050-12-01; 30 mg


title: T2012-13-01; 27 mg


title: IntestCrypts_Control_R1_Mouse_2

description: Library name: IntestCrypts_Control_R1_Mouse_2

value: PBS


title: DUPLICATE T2048-11-03;75 mg


title: DUPLICATE T2057-8 (T.N.S)


title: T2048-11-03;75 mg


title: DUPLICATE T2052-10 (T.N.S)


title: scRNASeq Mouse Thymus: Wild type, P28, Bio Rep 2, Batch E

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed with Cellranger v 6.0.1 to derive filtered feature count matrices. Reads were aligned against mm10 and filtered feature matrices were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: Default outputs from Cellranger: barcodes, features, and count matrices

extract_protocol:
Thymus cells were extracted from perinatal mice (days 0, 3, 7, 10, 15, and 28) and FACS sorted to isolate TEC populations.
Single cell suspensions were processed in the University of Texas Genomic Sequencing and Analysis Facility. Briefly, cell suspensions were loaded on the Chromium Controller (10X Genomics) and processed for cDNA library generation following the manufacturer’s instructions for the Chromium NextGEM Single Cell 3’ Reagent Kit v3.1 (10X Genomics).

value: Thymic Epithelial Cells

value: WT

tag: age (days)


title: T2052-10 (T.N.S)


title: scRNASeq Mouse Thymus: Wild type, P28, Bio Rep 1, Batch C


title: T2060-06-04; 26 mg


title: scRNASeq Mouse Thymus: Wild type, P15, Bio Rep 1, Batch F


title: scRNASeq Mouse Thymus: Wild type, P10, Bio Rep 1, Batch C


title: scRNASeq Mouse Thymus: Wild type, P10, Bio Rep 2, Batch F


title: scRNASeq Mouse Thymus: Wild type, P07, Bio Rep 2, Batch D


title: scRNASeq Mouse Thymus: Wild type, P07, Bio Rep 1, Batch D


title: scRNASeq Mouse Thymus: Wild type, P03, Bio Rep 2, Batch F


title: scRNASeq Mouse Thymus: Wild type, P03, Bio Rep 1, Batch D


title: scRNASeq Mouse Thymus: Wild type, P00, Bio Rep 2, Batch E


title: CornOil_WT3

status: Public on Feb 17 2025

city: London

first: Probir

last: Chakravarty

address: 1Midland Road

country: United Kingdom

institute: Francis Crick

description:
Lexogen QuantSeq protocol
47

data_processing:
FASTQC version 11.7 was used to assess FASTQ file quality. Trimmomatic version 36 was used to trim adapter sequences from fastq files
Alignment to Ensembl Mus_musculus.GRCm38.89 using STAR 2.5.2 and RSEM version 1.3
Raw counts were normlaised using DESeq2 verion 1.32 using R version 4.10
Differential analysis was done using DESEQ2 Wald’s test
Assembly: GRCm38.89
Supplementary files format and content: tab delimted text files, where columns are samples and rows are ensembl geneIDs

source_name: Liver

extract_protocol:
Trizol
Lexogen QuantSeq™ 3’ mRNA-Seq Library Prep Kit for Ion Torrent (#012)

treatment_protocol: Mice were treated with corn oil (CO), CITCO (10mg/kg)  intraperitoneal (IP), daily, 4d and sacrificed on day 5 for blood and tissue collection.

value: Liver

value: wt

value: Corn Oil


title: CITCO_CarKO3

description:
Lexogen QuantSeq protocol
46

value: CarKO/hPXR

value: CITCO


title: CITCO_hCAR3

description:
Lexogen QuantSeq protocol
45

value: hCAR/hPXR


title: scRNASeq Mouse Thymus: Wild type, P00, Bio Rep 1, Batch D

value: Thymus


title: CornOil_WT2

description:
Lexogen QuantSeq protocol
43


title: CITTO_WT3

description:
Lexogen QuantSeq protocol
44


title: CITCO_CarKO2

description:
Lexogen QuantSeq protocol
42


title: CITCO_hCAR2

description:
Lexogen QuantSeq protocol
41


title: CITTO_WT2

description:
Lexogen QuantSeq protocol
40


title: CITCO_hCAR1

description:
Lexogen QuantSeq protocol
37


title: CornOil_WT1

description:
Lexogen QuantSeq protocol
39


title: CITTO_WT1

description:
Lexogen QuantSeq protocol
36


title: A431, 60min EGF, Rep 2

status: Public on Jan 28 2025

city: Stanford

first: Luca

last: Ducoli

state: California

address: 269 Campus Drive CCSR 2150

institute: Stanford University

description: EGF timecourse analysis

data_processing:
FASTQs were quantified at the transcript level using Salmon and GENCODE Human Release 39
Assembly: GENCODE Human Release 39
Supplementary files format and content: Salmon quantification output

growth_protocol: A431 cells were grown in DMEM 10% FBS supplemented with 1xPS.

extract_protocol:
Total RNA was extracted using the RNeasy Plus mini kit (QIAGEN).
Libraries for mRNA splicing and stability analyses were prepared at Novogene. Libraries of EGF timecourse analysis were prepared using QuantSeq 30 mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen).

treatment_protocol: Cells were treated with 50ng/mL recombinant human EGF and, where specified, also with 5µg/mL actinomycin D. Samples were collected in RLT plus buffer at the specified time points.

tag: cell line

value: human epidermoid carcinoma cell line


title: CITCO_CarKO1

description:
Lexogen QuantSeq protocol
38


title: A431, 60min EGF, Rep 1

description: EGF timecourse analysis


title: A431, 30min EGF, Rep 2

description: EGF timecourse analysis


title: A431, 15min EGF, Rep 1

description: EGF timecourse analysis


title: A431, 15min EGF, Rep 2

description: EGF timecourse analysis


title: A431, 0min EGF, Rep 2

description: EGF timecourse analysis


title: A431, 30min EGF, Rep 1

description: EGF timecourse analysis


title: A431, 0min EGF, Rep 1

description: EGF timecourse analysis


title: siUPF1, A431 , 1h EGF, 4h actinomycinD,  Rep 2

description: mRNA stability analysis


title: siUPF1, A431 , 1h EGF, 4h actinomycinD,  Rep 1

description: mRNA stability analysis


title: siHNRNPC, A431 , 1h EGF, 4h actinomycinD,  Rep 2

description: mRNA stability analysis


title: siHNRNPC, A431 , 1h EGF, 4h actinomycinD,  Rep 1

description: mRNA stability analysis


title: Control siRNA, A431 , 1h EGF, 4h actinomycinD,  Rep 2

description: mRNA stability analysis


title: Lung-Smad4OFF_m2

status: Public on May 14 2025

description: paired-end sequencing

library_source: genomic

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
FASTQ files were trimmed with trimGalore and cutadapt (PMID: 28715235), and the filtered, pair-ended reads were aligned to mm10 with Bowtie2 (PMID: 22388286).
Peaks were called over input using MACS2 (PMID: 18798982), and only peaks with ap-value of ≤ 0.001 and outside the ENCODE blacklist region were kept. All peaks from all samples were merged by combining peaks within 500 bp of each.
featureCounts (PMID: 24227677)was used to count the mapped reads for each sample. The resulting peak atlas was normalized using DESeq2 (PMID: 25516281). For comparison to DepthNorm, samples were normalized to 10 million mapped reads. Normalized bigWig files were created using the normalization factors from DESeq2 as previously described (PMID: 30429377)and BEDTools genomeCoverageBed (PMID: 20110278). Dynamic ATAC peaks were called if they had an absolute log2-transformed fold change≥0.58 and FDR≤0.1.
Assembly: Reads were aligned to the mouse genome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

molecule: genomic DNA

source_name: PDAC Lung Metastasis

growth_protocol: For pancreatic tumors, mouse hosts were placed on doxycycline chow 5-7 days before transplantation. Mice were anesthetized and a survival surgery was performed to expose the pancreas. 1 x 10^5 tumor-derived cells were resuspended in 25 uL 1:1 DMEM (Gibco) : Matrigel (Corning) mix and injected in the tail of the pancreas of each mouse. For liver metastasis assays, mice were anesthetized and a survival surgery was performed to expose the spleen. 4 x 10^5 tumor-derived cells resuspended in 20 uL PBS were injected in the splenic parenchyma of each mouse, followed by removal of the spleen and cauterization (splenectomy). For lung metastasis assays, mice were restrained, and 2.5 x 10^5 tumor-derived cells resuspended in 250 uL PBS were injected in the tail vein of each mouse.

extract_protocol:
A total of 60,000 mKate2+cells were isolated by FACS, washed once with 50 μl cold PBS and resuspended in 50 μl cold lysis buffer. Cells were then centrifuged immediately for 10 min at 500gat 4°C, and the pellet of nuclei was subjected to transposition with Nextera Tn5 transposase (Illumina #FC-121–1030) for 30 min at 37°C, according to the manufacturer’s instructions. DNA was eluted using a DNA Clean & Concentrator Kit in 21 μl elution buffer (Zymo Research #D4013).
ATAC-seq libraries were prepared using the NEBNext High-Fidelity 2X PCR Master Mix (NEB M0541) as previously described (PMID: 25559105). Purified libraries were assessed using a Bioanalyzer High-Sensitivity DNA Analysis kit (Agilent).
Approximately 50 million paired-end 150-bp reads (25 million each side) were sequenced per replicate on a HiSeq instrument (Illumina).

treatment_protocol: Mouse hosts were fed Doxycycline chow. Where applicable, doxycycline withdrawal was done at 4 (pancreas), 5 (liver) or 6 weeks (lungs) post-injection by switching the food source to regular chow.

value: PDAC lung metastasis cells


title: Control siRNA, A431 , 1h EGF, 4h actinomycinD,  Rep 1

description: mRNA stability analysis


title: siUPF1, A431 , 1h EGF, 3h actinomycinD,  Rep 2

description: mRNA stability analysis


title: siHNRNPC, A431 , 1h EGF, 3h actinomycinD,  Rep 2

description: mRNA stability analysis


title: siUPF1, A431 , 1h EGF, 3h actinomycinD,  Rep 1

description: mRNA stability analysis


title: siHNRNPC, A431 , 1h EGF, 3h actinomycinD,  Rep 1

description: mRNA stability analysis


title: Control siRNA, A431 , 1h EGF, 3h actinomycinD,  Rep 2

description: mRNA stability analysis


title: Control siRNA, A431 , 1h EGF, 3h actinomycinD,  Rep 1

description: mRNA stability analysis


title: siUPF1, A431 , 1h EGF, A431 , 1h actinomycinD,  Rep 1

description: mRNA stability analysis


title: siUPF1, A431 , 1h EGF, A431 , 1h actinomycinD,  Rep 2

description: mRNA stability analysis


title: siHNRNPC, A431 , 1h EGF, A431 , 1h actinomycinD,  Rep 2

description: mRNA stability analysis


title: siHNRNPC, A431 , 1h EGF, A431 , 1h actinomycinD,  Rep 1

description: mRNA stability analysis


title: Control siRNA, A431 , 1h EGF, A431 , 1h actinomycinD,  Rep 2

description: mRNA stability analysis


title: CRISPR library from Cal27 derived tumor 2 from mouse replicate 1

status: Public on Apr 28 2025

description: Library name: LD_Cal27_T_1_2

library_source: other

data_processing:
In each screen, UMI was compressed using umi_tools extract, and adaptor sequences were removed using cutadapt. Subsequently, the remaining reads were aligned on the guide sequences using bowtie (maximum error: 1, minimum length: 16). The count for each guide was collected using umi_tools count, then transformed into scc format. For in vitro screen analysis, MaGeCK MLE was performed based on the guide counts with the design matrix of comparing the timepoint of the initial collection and the post-screen collection as described in (W. Li et al. 2015). In vivo and in vitro CRISPR screens were integrated by first determining the ß scores of each sample against plasmid DNA determined by miSeq (Illumina) using the MaGeCK MLE algorithm (W. Li et al. 2015). ß scores were normalized and visualized using the MaGeCKFlute R package (B. Wang et al. 2019) following the authors’ guidelines.
Assembly: hg38
Supplementary files format and content: tab separated txt file containing unnormalized feature (guide) counts
Library strategy: CRISPR Screen

molecule: other

growth_protocol: The human A431 and Cal27 cell lines were cultured in DMEM media with 10% FBS and 1% PS in 5% CO2 at 36°C

extract_protocol:
Three mice (a total of six tumors) were performed on each cell line. Based on the visual observation of subcutaneous tumor growths, the mice injected with the same cell lines were sacrificed on the same days after 3-4 weeks. (A431: 3.5 weeks, Cal27: 4.5 weeks) The tumors were surgically harvested, minced, and homogenized in an MP Biomedical lysing matrix A tube. Genomic DNA was isolated using QIAGEN DNeasy Blood and Tissue Kit
Sequencing library was made as described in (Mathiowetz et al. 2023, PMID: 37000620) with an adjustment of using <10g of gDNA in PCR1 reaction and a pair of primers matching with our sequences and manually determining PCR2 cycles based on a trial run to prevent overamplification.

treatment_protocol: The pooled oligo Lenti virus was made and transfected on dCas9-KRAB expressing A431 and Cal27 with MOI of 0.3.. After the 3 days of selection in puromycin, the transfection rates were chekced with Cell Titer Blue. Four million cells in 100ul were gently mixed with 50ul Matrigel (Corning) until it turned into a homogenous mixture and injected with 28G insulin syringe into both sides of rear flanks of SCID Hairless Outbred (SHO®) mice (Charles River). Triplicate of cells (with +1000x coverage) were collected, flash frozen, and stored at -80C for each replicate as the initial screen time point.

value: Lentivirus-mediated CRISPR library infection and a tumor grown in mouse


title: Control siRNA, A431 , 1h EGF, A431 , 1h actinomycinD,  Rep 1

description: mRNA stability analysis


title: siUPF1, A431 , 1h EGF, 0h actinomycinD,  Rep 2

description: mRNA stability analysis


title: siUPF1, A431 , 1h EGF, 0h actinomycinD,  Rep 1

description: mRNA stability analysis


title: siHNRNPC, A431 , 1h EGF, 0h actinomycinD,  Rep 2

description: mRNA stability analysis


title: Control siRNA, A431 , 1h EGF, 0h actinomycinD,  Rep 2

description: mRNA splicing analysis


title: siHNRNPC, A431 , 1h EGF, 0h actinomycinD,  Rep 1

description: mRNA stability analysis


title: Control siRNA, A431 , 1h EGF, 0h actinomycinD,  Rep 1

description: mRNA splicing analysis


title: siUPF1, A431 , 1h EGF, Rep 2

description: mRNA splicing analysis


title: siUPF1, A431 , 1h EGF, Rep 1

description: mRNA splicing analysis


title: siHNRNPC, A431 , 1h EGF, Rep 2

description: mRNA splicing analysis


title: siHNRNPC, A431 , 1h EGF, Rep 1

description: mRNA splicing analysis


title: CRISPR library from_Normal Keratinocyte cells, TSK library, Week 0, replicate 2

description: Library name: LD_Kerat_W0_TSK2

source_name: Human Keratinocyte

growth_protocol: The human A431 and Cal27 cell line was cultured in DMEM media with 10% FBS and 1% PS in 5% CO2 at 36°C. Primary human keratinocytes were obtained from fresh, surgically discarded neonatal foreskin, cultured in Keratinocyte-SFM and Medium 154 with Keratinocyte supplement, and subcultured regularly before reaching high confluency for a few cycles.

extract_protocol:
DNA was isolated from the cell pellet using QIAGEN DNeasy Blood and Tissue Kit
The sequencing library was made as described in (Ji et al. 2020) [PMID: 32579974]

treatment_protocol: Lentivirus has been produced in Lenti-X cells seeded higher than 70% in 10cm (or 15cm) dish. Cells in each 10cm dish were transfected with 7.5ug CMV, 3.5ug MDG, 7.5ug Plasmid in 625ul OptiMEM mixed with another tube containing 25ul Lipofectamine in 625ul OptiMEM. (The volume or amount were doubled for cells in 15cm dish). The media was replaced after the overnight incubation, collected after every 24h with media replacement for two times, filtered through a 0.45um PES membrane, and concentrated with Lenti-X concentrator (Takara). Cas9 transfection was performed on A431, Cal27, and Primary Keratinocytes and selected with blasticidin. Pooled guide lentivirus was titrated in each of dCas9-KRAB expressing cell lines to achieve an MOI of 0.3. Following selection with puromycin for two to three days, the transfection rates were checked with Cell Titer Blue, and triplicate of cells (with +1000x coverage) were collected, flash frozen, and stored at -80°C for each replicate as the initial screen time point. Cells were cultured by maintaining at least 1000x coverage with regular basis of subculturing for three weeks (Primary Keratinocyte for 1.5 week due to inherently limited proliferation capacity).

value: Human Keratinocyte

value: Lentivirus-mediated CRISPR library infection


title: Control siRNA 1h EGF, Rep 2

description: mRNA splicing analysis


title: Control siRNA, A431 , 1h EGF, Rep 1

description: mRNA splicing analysis


title: siCSDE1, A431 , 1h EGF, Rep 2

description: mRNA splicing analysis


title: UPF1, siHNRNPC, irCLIPv2, A431, 60min EGF, Rep 2

description: irCLIPv2 protocol

data_processing:
Custom processing scripts available at https://github.com/lducoli/irCLIP-RNP/.
Assembly: Human GRCh38 Gencode release 39 and a custom chromosome made of repetitive elements
Supplementary files format and content: Tab separated text file of RT stops counts at genomic windows as determined by htseq-clip. Scaled bigwig files using scale factors estimated from window counts using DEWSeq.
Library strategy: CLIP-seq

growth_protocol: HEK293T and A431 cells were grown in DMEM 10% FBS supplemented with 1xPS.

extract_protocol:
For irCLIPv2, immunoprecipitation (IP) followed by 3'ligation. For Re-CLIP, 1st IP, 3' ligation, IP destruction and reconstitution, 2nd IP. Then, ligated RNPs were resolved on SDS-page, transferred to nitrocellulose, and RNA was recovered after protein K digestion using streptavidin beads.
On-beads 1st strand cDNA synthesis, 3’ cDNA-tailing, 2nd strand synthesis, and amplification.

treatment_protocol: UV cross-linked at 253nm on plates. Where specified, cells were treated with 50ng/mL recombinant human EGF for the given time.


title: siCSDE1, A431 , 1h EGF, Rep 1

description: mRNA splicing analysis


title: UPF1, siHNRNPC,  irCLIPv2, A431, 0min EGF, Rep 2

description: irCLIPv2 protocol


title: UPF1, siHNRNPC, irCLIPv2, A431, 60min EGF, Rep 1

description: irCLIPv2 protocol


title: UPF1, siHNRNPC,  irCLIPv2, A431, 0min EGF, Rep 1

description: irCLIPv2 protocol


title: UPF1, siRNA control, irCLIPv2, A431, 60min EGF, Rep 2

description: irCLIPv2 protocol


title: UPF1, siRNA control, irCLIPv2, A431, 60min EGF, Rep 1

description: irCLIPv2 protocol


title: UPF1, siRNA control, irCLIPv2, A431, 0min EGF, Rep 2

description: irCLIPv2 protocol


title: HNRNPC, UPF1, Re-CLIP, A431, 60min EGF, Rep 2

description: Re-CLIP protocol


title: UPF1, siRNA control, irCLIPv2, A431, 0min EGF, Rep 1

description: irCLIPv2 protocol


title: HNRNPC, UPF1, Re-CLIP, A431, 60min EGF, Rep 1

description: Re-CLIP protocol


title: HNRNPC, UPF1, Re-CLIP, A431, 30min EGF, Rep 1

description: Re-CLIP protocol


title: HNRNPC, UPF1, Re-CLIP, A431, 30min EGF, Rep 2

description: Re-CLIP protocol


title: HNRNPC, UPF1, Re-CLIP, A431, 0min EGF, Rep 2

description: Re-CLIP protocol


title: UPF1, irCLIPv2, A431, 60min EGF, Rep 2

description: irCLIPv2 protocol


title: HNRNPC, UPF1, Re-CLIP, A431, 0min EGF, Rep 1

description: Re-CLIP protocol


title: UPF1, irCLIPv2, A431, 60min EGF, Rep 1

description: irCLIPv2 protocol


title: UPF1, irCLIPv2, A431, 30min EGF, Rep 2

description: irCLIPv2 protocol


title: UPF1, irCLIPv2, A431, 15min EGF, Rep 1

description: irCLIPv2 protocol


title: UPF1, irCLIPv2, A431, 15min EGF, Rep 2

description: irCLIPv2 protocol


title: UPF1, irCLIPv2, A431, 30min EGF, Rep 1

description: irCLIPv2 protocol


title: CRISPR library from_A431 cells, TSK library, Week 0, replicate 3

description: Library name: LD_A431_W0_TSK3


title: UPF1, irCLIPv2, A431, 0min EGF, Rep 2

description: irCLIPv2 protocol


title: UPF1, irCLIPv2, A431, 0min EGF, Rep 1

description: irCLIPv2 protocol


title: HNRNPC, KHSRP, Re-CLIP, HEK293T, Rep 2

description: Re-CLIP protocol

value: Human embryonic kidney cell line


title: HNRNPC, KHSRP, Re-CLIP, HEK293T, Rep 1

description: Re-CLIP protocol


title: HNRNPC,  IgG, Re-CLIP, A431, 60min EGF, Rep 2

description: Re-CLIP protocol


title: HNRNPC,  IgG, Re-CLIP, A431, 60min EGF, Rep 1

description: Re-CLIP protocol


title: HNRNPC,  IgG, Re-CLIP, A431, 30min EGF, Rep 2

description: Re-CLIP protocol


title: CRISPR library from_A431 cells, KC library, Week 0, replicate 2

description: Library name: LD_A431_W0_KC2


title: HNRNPC,  IgG, Re-CLIP, A431, 30min EGF, Rep 1

description: Re-CLIP protocol


title: HNRNPC, HuR, Re-CLIP, HEK293T, Rep 2

description: Re-CLIP protocol


title: HNRNPC,  IgG, Re-CLIP, A431, 0min EGF, Rep 2

description: Re-CLIP protocol


title: Bulk RNA-seq in A431 LINC01116-ASO Knockdown (ASO #1). Replicate 1

description: Library name: S13_1116_1_1

data_processing:
For analyzing differentially expressed genes compared to the control, raw reads were first quantified with Salmon (ver. 0.12.0) (Patro et al. 2017) using the gencode release v39 basic annotation with the following settings: -l A -p 8 --gcBias --numGibbsSamples 20 --validateMappings.
Assembly: hg38
Supplementary files format and content: Salmon count output files

molecule: polyA RNA

growth_protocol: The human A431 cell line was cultured in DMEM media with 10% FBS and 1% PS in 5% CO2 at 36°C

extract_protocol:
After 48h of ASO transfection, cells were lysed in LRT plus lysis buffer (Qiagen), and RNA isolation was performed using an RNeasy mini kit (Qiagen) following the manufacturer’s instructions.
From each sample, 500ng of RNA was used for the library preparation using the kit (QuantSeq 3’ mRNA-Seq V2 Library Prep Kit FWD with UDI, Lexogen), pooled together with an equal concentration, and then sequenced on a NovaSeq X+, paired-end, 150 bp length, with ~30 M reads for each sample.

treatment_protocol: For each ASO, we performed a reverse transfection using Lipofectamine RNAiMAX (Thermo Fisher Scientific). In 10cm dishes, 2mL Opti-MEM, 20nM of scrambled control ASO or two ASOs targeting LINC00704 and LINC01116, and 25µL Lipofectamine RNAiMAX (Thermo) were mixed and incubated for 20min. Then, 1x106 A431 cells per dish were seeded into each 10cm dish and cultured for 48h in a 5% CO2 incubator.

value: LINC01116-ASO transfection with Lipofectamine reagents


title: HNRNPC,  IgG, Re-CLIP, A431, 0min EGF, Rep 1

description: Re-CLIP protocol


title: HNRNPC, HuR, Re-CLIP, HEK293T, Rep 1

description: Re-CLIP protocol


title: HNRNPC, HNRNPM, Re-CLIP, HEK293T, Rep 2

description: Re-CLIP protocol


title: HNRNPC, HNRNPM, Re-CLIP, HEK293T, Rep 1

description: Re-CLIP protocol


title: HNRNPC, siUPF1, irCLIPv2, A431, 60min EGF, Rep 2

description: irCLIPv2 protocol


title: Bulk RNA-seq in A431 LINC00704-ASO Knockdown (ASO #1). Replicate 2

description: Library name: S08_704_1_2

value: LINC00704-ASO transfection with Lipofectamine reagents


title: HNRNPC, siUPF1, irCLIPv2, A431, 60min EGF, Rep 1

description: irCLIPv2 protocol


title: HNRNPC, siUPF1, irCLIPv2, A431, 0min EGF, Rep 2

description: irCLIPv2 protocol


title: HNRNPC, siRNA control,  irCLIPv2, A431, 60min EGF, Rep 2

description: irCLIPv2 protocol


title: HNRNPC, siUPF1, irCLIPv2, A431, 0min EGF, Rep 1

description: irCLIPv2 protocol


title: HNRNPC, siRNA control, irCLIPv2, A431, 60min EGF, Rep 1

description: irCLIPv2 protocol


title: HNRNPC, siRNA control, irCLIPv2, A431, 0min EGF, Rep 1

description: irCLIPv2 protocol


title: HNRNPC, siRNA control, irCLIPv2, A431, 0min EGF, Rep 2

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, A431, 60min EGF, Rep 2

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, A431, 60min EGF, Rep 1

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, A431, 30min EGF, Rep 2

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, A431, 30min EGF, Rep 1

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, A431, 15min EGF, Rep 2

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, A431, 15min EGF, Rep 1

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, A431, 0min EGF, Rep 2

description: irCLIPv2 protocol


title: HNRNPC, HNRNPC, Re-CLIP, HEK293T, Rep 1

description: Re-CLIP protocol


title: THOC4, irCLIPv2, HEK293T, Rep 2, Section 3

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, A431, 0min EGF, Rep 1

description: irCLIPv2 protocol


title: THOC4, irCLIPv2, HEK293T, Rep 2, Section 1

description: irCLIPv2 protocol


title: THOC4, irCLIPv2, HEK293T, Rep 2, Section 2

description: irCLIPv2 protocol


title: THOC4, irCLIPv2, HEK293T, Rep 1, Section 3

description: irCLIPv2 protocol


title: THOC4, irCLIPv2, HEK293T, Rep 1, Section 2

description: irCLIPv2 protocol


title: THOC4, irCLIPv2, HEK293T, Rep 1, Section 1

description: irCLIPv2 protocol


title: KHSRP, irCLIPv2, HEK293T, Rep 2, Section 3

description: irCLIPv2 protocol


title: THOC4, irCLIPv2, HEK293T, Rep 1, noUV

description: irCLIPv2 protocol


title: KHSRP, irCLIPv2, HEK293T, Rep 2, Section 2

description: irCLIPv2 protocol


title: KHSRP, irCLIPv2, HEK293T, Rep 2, Section 1

description: irCLIPv2 protocol


title: KHSRP, irCLIPv2, HEK293T, Rep 1, Section 3

description: irCLIPv2 protocol


title: KHSRP, irCLIPv2, HEK293T, Rep 1, Section 2

description: irCLIPv2 protocol


title: KHSRP, irCLIPv2, HEK293T, Rep 1, Section 1

description: irCLIPv2 protocol


title: THOC4, irCLIPv2, HEK293T, Rep 2, noUV

description: irCLIPv2 protocol


title: KHSRP, irCLIPv2, HEK293T, Rep 2, noUV

description: irCLIPv2 protocol


title: KHSRP, irCLIPv2, HEK293T, Rep 1, noUV

description: irCLIPv2 protocol


title: HuR, irCLIPv2, HEK293T, Rep 2, Section 3

description: irCLIPv2 protocol


title: HuR, irCLIPv2, HEK293T, Rep 2, Section 1

description: irCLIPv2 protocol


title: HuR, irCLIPv2, HEK293T, Rep 1, Section 3

description: irCLIPv2 protocol


title: HuR, irCLIPv2, HEK293T, Rep 1, Section 2

description: irCLIPv2 protocol


title: HuR, irCLIPv2, HEK293T, Rep 2, Section 2

description: irCLIPv2 protocol


title: HuR, irCLIPv2, HEK293T, Rep 1, Section 1

description: irCLIPv2 protocol


title: HuR, irCLIPv2, HEK293T, Rep 2, noUV

description: irCLIPv2 protocol


title: HuR, irCLIPv2, HEK293T, Rep 1, noUV

description: irCLIPv2 protocol


title: HNRNPU, irCLIPv2, HEK293T, Rep 2, Section 3

description: irCLIPv2 protocol


title: HNRNPU, irCLIPv2, HEK293T, Rep 2, Section 2

description: irCLIPv2 protocol


title: HNRNPU, irCLIPv2, HEK293T, Rep 1, Section 3

description: irCLIPv2 protocol


title: HNRNPU, irCLIPv2, HEK293T, Rep 2, Section 1

description: irCLIPv2 protocol


title: HNRNPU, irCLIPv2, HEK293T, Rep 2, noUV

description: irCLIPv2 protocol


title: HNRNPU, irCLIPv2, HEK293T, Rep 1, noUV

description: irCLIPv2 protocol


title: HNRNPU, irCLIPv2, HEK293T, Rep 1, Section 1

description: irCLIPv2 protocol


title: HNRNPM, irCLIPv2, HEK293T, Rep 2, Section 3

description: irCLIPv2 protocol


title: HNRNPM, irCLIPv2, HEK293T, Rep 2, Section 2

description: irCLIPv2 protocol


title: HNRNPM, irCLIPv2, HEK293T, Rep 1, Section 3

description: irCLIPv2 protocol


title: HNRNPM, irCLIPv2, HEK293T, Rep 2, Section 1

description: irCLIPv2 protocol


title: HNRNPM, irCLIPv2, HEK293T, Rep 1, Section 1

description: irCLIPv2 protocol


title: HNRNPM, irCLIPv2, HEK293T, Rep 1, Section 2

description: irCLIPv2 protocol


title: HNRNPM, irCLIPv2, HEK293T, Rep 2, noUV

description: irCLIPv2 protocol


title: HNRNPM, irCLIPv2, HEK293T, Rep 1, noUV

description: irCLIPv2 protocol


title: HNRNPFH, irCLIPv2, HEK293T, Rep 2, Section 2

description: irCLIPv2 protocol


title: HNRNPFH, irCLIPv2, HEK293T, Rep 2, Section 3

description: irCLIPv2 protocol


title: HNRNPFH, irCLIPv2, HEK293T, Rep 2, Section 1

description: irCLIPv2 protocol


title: HNRNPFH, irCLIPv2, HEK293T, Rep 1, Section 1

description: irCLIPv2 protocol


title: HNRNPFH, irCLIPv2, HEK293T, Rep 1, Section 3

description: irCLIPv2 protocol


title: HNRNPFH, irCLIPv2, HEK293T, Rep 2, noUV

description: irCLIPv2 protocol


title: HNRNPFH, irCLIPv2, HEK293T, Rep 1, noUV

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, HEK293T, Rep 2, Section 3

description: irCLIPv2 protocol


title: HNRNPFH, irCLIPv2, HEK293T, Rep 1, Section 2

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, HEK293T, Rep 2, Section 2

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, HEK293T, Rep 2, Section 1

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, HEK293T, Rep 1, Section 3

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, HEK293T, Rep 1, Section 2

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, HEK293T, Rep 1, Section 1

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, HEK293T, Rep 2, noUV

description: irCLIPv2 protocol


title: HNRNPC, irCLIPv2, HEK293T, Rep 1, noUV

description: irCLIPv2 protocol


title: FUS, irCLIPv2, HEK293T, Rep 2, Section 2

description: irCLIPv2 protocol


title: FUS, irCLIPv2, HEK293T, Rep 2, Section 3

description: irCLIPv2 protocol


title: FUS, irCLIPv2, HEK293T, Rep 2, Section 1

description: irCLIPv2 protocol


title: FUS, irCLIPv2, HEK293T, Rep 1, Section 3

description: irCLIPv2 protocol


title: FUS, irCLIPv2, HEK293T, Rep 1, Section 2

description: irCLIPv2 protocol


title: HNRNPU, irCLIPv2, HEK293T, Rep 1, Section 2

description: irCLIPv2 protocol


title: FUS, irCLIPv2, HEK293T, Rep 1, Section 1

description: irCLIPv2 protocol


title: FUS, irCLIPv2, HEK293T, Rep 2, noUV

description: irCLIPv2 protocol


title: FUS, irCLIPv2, HEK293T, Rep 1, noUV

description: irCLIPv2 protocol


title: mESC_R7

status: Public on Jan 19 2025

city: München

first: Marlies

middle: E

last: Oomen

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

description:
2x150bp reads
This sample did not pass quality control as described in the methods of our accompanying paper. Therefore it was not included in the count table.

data_processing:
Reads were mapped to the appropriate reference genome using STAR
Internal fragments and 5' transcript ends were distinguished using a custom python script available on github. For smart-seq2 and smart-seq2-polyA libraries, reads were not seperated by 5' or internal fragments and all reads were processed together
BigWig files were generated from unique mapping reads, rRNA removed and rpm normalized, using bedtools and ucsc bedGraphToBigWig
TEs and genes were quantified from unique and multimapping reads from 5' fragments using TEtranscript
For more information see (gitlab link)
Assembly: GRCm38 (Mus musculus), Sscrofa11.1 (Sus scrofa), Btau_5.0.1 (Bos taurus), OryCun2.0 (Oryctolagus cuniculus), Mmul_8.0.1 (Macaca mulatta)
Supplementary files format and content: merged bigWig files, 2 files per species/stage seperated for 5' fragments ("FivePrime") and internal fragments ("Else")
Supplementary files format and content: table txt file containing gene and TE counts for each species using 5' fragments (Smart-seq+5') or all fragments (Smart-seq2)

source_name: mouse embryonic stem cells

growth_protocol:
Oocyte and preimplantation stages were collected from mouse, pig, cow, rabbit and rhesus.
Stem cells were cultured in appropriate medium and collected at least 48hr since last cell split. rbESC were seperated from feeder cells by FACS using the Oct4-GFP marker. For more information see methods of accompaning paper

extract_protocol:
For each library a single embryo from was used originating from the listed species and developmental stage. For stem cells, RNA was extracted using the ReliaPrep kit. 250pg was used as input for the Smart-seq+5 protocol. For more information see methods of accompaning paper
An adapted version of Smart-seq2 (called Smart-seq+5') was used to capture both 5' transcript information as well as internal transcript fragments. For Smart-seq2 libraries (SS2), embryos were processed as described in published protocol (Picelli et. al. 2014). For Smart-seq2-polyA libraries (SS2-PA), an additional polyadenylation step was preformed at the start of the protocol. See methods of accompaning paper for more information
Smart-seq+5'

treatment_protocol: Mouse and rabbit embryos were collected after natural mating. Pig, cow and rhesus embryos were harvested by IVF. For more information see methods of accompaning paper

value: mouse embryonic stem cells


title: KO6_S22

status: Public on Jan 03 2025

first: Coen

last: van Solingen

state: NY

address: 435 E30th street SB 704

department: Medicine/Cardiology

institute: NYU Grossman School of Medicine

data_processing:
Quality control of sequencing reads was assessed using FastQC (v.0.11.7)
Reads were mapped to mouse reference genome mm39 using STAR (v2.6.1d).
Genomic features were then assigned using Subread featureCounts (v.1.6.3)
Assembly: mm39
Supplementary files format and content: space-delimited text file includes raw counts per sample per gene

source_name: lung

growth_protocol: Mice were inoculated with influenza strain PR8 and were euthanized 4 days later. Lungs were harvested and snapfrozen. Four mice of each groups were used.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) and Direct-zol RNA MiniPrep columns (Zymo Research).
Illumina TruSeq RNA sample preparation kit. Illumina HiSeq, 2x150bp configuration, single index, per lane

treatment_protocol: Lungs were isolated at Day=4 after inoculation with influenza.Lungs were homogenized and RNA was isolated using trizol.

value: lung

value: bone marrow derived macrophages

value: KO

value: flu


title: KO4_S20


title: KO3_S19


title: KO1_S18


title: WT5_S17

value: WT


title: WT3_S15


title: WT2_S14


title: WT1_S13


title: WT-veh sample 3

source_name: bone marrow derived macrophages

growth_protocol: Bone marrow derived macrophages (BMDMs) were prepared by flushing the marrow from the tibiae and femorae of 6- to 8-week-old mice. Cells were differentiated into macrophages in DMEM supplemented with 10% FBS, 1% P/, and 15% L929-conditioned media for 7 days.

extract_protocol:
Total RNA was isolated using TRIzol reagent (Invitrogen) and Direct-zol RNA MiniPrep columns (Zymo Research).
Illumina TruSeq RNA sample preparation kit. Illumina HiSeq, 2x50bp configuration, single index, per lane

treatment_protocol: BMDM were treated with IFNBeta (1000 U/mL) or vehicle control for 8 hours

value: Vehicle


title: WT-veh sample 1


title: WT-veh sample 2


title: WT-IFN sample 3

value: IFN


title: WT-IFN sample 2


title: WT-IFN sample 1


title: KO-veh sample 2


title: KO-veh sample 1


title: KO-veh sample 3


title: KO-IFN sample 3


title: KO-IFN sample 2


title: KO-IFN sample 1


title: R513H/WT forebrain organoids, scRNA-seq, library 1

status: Public on Dec 25 2024

city: San Francisco

first: Kelsey

last: Hennick

state: CA

address: 1651 4th St room 521A

institute: UCSF

description:
Library name: R513H-scRNAseq-rep1
het3 in metadata, labeled R514H (same residue, different isoform), one pool of cells split into two technical replicates for library prep
FOXP1R513H_scRNAseq_metadata.csv

data_processing:
scRNA-seq data was first processed using PIPseeker for quality control, and then following the Seurat pipeline.
Assembly: hg38
Supplementary files format and content: scRNA-seq: csv file with cell metadata

source_name: hiPSC-derived forebrain organoid

extract_protocol:
RNA was extracted following the Fluent PIP-seq protocol (PMID: 36879006)
Libraries were constructed using the Fluent PIP-seq reagents (PMID: 36879006)

value: hiPSC-derived forebrain organoid

value: CRISPR isogenic 13234 clone

value: hiPSC

value: forebrain organoid differentiation


title: WT forebrain organoids, scRNA-seq, library 2

description:
Library name: WT-scRNAseq-rep2
wt7 in metadata, one pool of cells split into two technical replicates for library prep
FOXP1R513H_scRNAseq_metadata.csv

value: WT/WT


title: R513H/WT forebrain organoids, scRNA-seq, library 2

description:
Library name: R513H-scRNAseq-rep2
het3 in metadata, labeled R514H (same residue, different isoform), one pool of cells split into two technical replicates for library prep
FOXP1R513H_scRNAseq_metadata.csv


title: WT forebrain organoids, scRNA-seq, library 1

description:
Library name: WT-scRNAseq-rep1
wt7 in metadata, one pool of cells split into two technical replicates for library prep
FOXP1R513H_scRNAseq_metadata.csv


title: GCB_S5

status: Public on Dec 19 2024

type: genomic

city: Ulm

first: Selina

last: Glaser

address: Albert-Einstein-Allee 11

institute: Ulm University and Ulm University Medical Center

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation 450 Beadchip using standard Illumina protocol

scan_protocol: The arrays were scanned using a iScan device or NextSeq 550.

data_processing:
Raw idat files were read into the statistical program R (version 4.3.0) using the minfi package (version 1.46.0). Normalization was performed with the preprocessIllumina() function against the intrinsic controls and without background correction. For normalization, we placed the here the normalization sample within the first row of the sample sheet. For downstream analysis, beta values were calculated, rs loci, loci on gonosomes and loci with a detection p value > 0.01 were excluded.
processed_data: normalized (minfi, preprocessIllumina(), against instrinisc controls, without background correction) average Beta

label: Cy3, Cy5

source_name: Non-neoplastic, genomic DNA, cryo preserved

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified according to commercially available kits form Qiagen according to standard instructions

tag: gender

value: Male

tag: disease state

value: non neoplastic DNA from patient with Burkitt lymphoma


title: GCB_S4


title: GCB_S3


title: GCB_S1


title: GCB_S2


title: Cryo_S6

source_name: Burkitt lymphoma, genomic DNA, cryo preserved

value: DNA from Burkitt lymphoma


title: Cryo_S5


title: Cryo_S2


title: Cryo_S3

value: Female


title: Cryo_S4


title: Cryo_S1


title: FFPE_S6

source_name: Burkitt lymphoma, genomic DNA, FFPE


title: FFPE_S5


title: FFPE_S4


title: FFPE_S3


title: FFPE_S2


title: FFPE_S1


title: Normalization_sample 1

source_name: peripheral blood

value: normal DNA from healthy donor


title: P17

status: Public on Dec 02 2024

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each MeDIP sample were mapped to the Rnor 6.0 rat genome using Bowtie2.
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 1000 bp windows. The edgeR p-value was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR p-value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR p-value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
Assembly: Rnor_6.0
Supplementary files format and content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.

organism: Rattus norvegicus

source_name: Sperm

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley SD (Harlan) were fed ad lib with a standard rat diet and ad lib tap water. All animal cages were housed in the same room and environment with gestating females and females with litters being housed individually within cages. Conditions were designed to minimize differences that would cause maternal effects. The breeding of unrelated males and females at 70 to 100 days of age within specific exposure lineages (interbreeding) was used to optimize the maternal and paternal lineage contributions to the phenotypes observed. No inbreeding within the colonies was performed. Sixteen unrelated breeding pairs made up the treated lineage F0 generation, so that offspring of subsequent generations could be bred at the F1, F2 F3 and F4 generations without inbreeding.

extract_protocol:
The epididymis was dissected free of fat and connective tissue, then, after cutting open the cauda, placed into 6 ml of phosphate buffer saline (PBS) for 20 minutes at room temperature. The tissue was then minced, the released sperm pelleted at 4ºC by centrifuging at 3,000 x g for 10 min, then resuspended in 250 µL NIM buffer and stored at -80ºC. For molecular analysis, an appropriate amount of rat sperm suspension (approximately 50 µL) was used for DNA extraction. Previous studies have shown mammalian sperm heads are resistant to sonication unlike somatic cells. Somatic cell contamination and debris were removed by brief sonication (Fisher Sonic Dismembrator, model 300, power level 25), which destroys the somatic cells, then centrifugation and washing 1-2 times in 1X PBS. The resulting purified sperm pellet was resuspended in 820 µL DNA extraction buffer and 80 µl 0.1M DTT added, then incubated at 65°C for 15 minutes. Proteinase K (80 µl of 20 mg/ml) was added and the sample was incubated at 55°C for 2-3 hours under constant rotation. Protein was removed by addition of protein precipitation solution (300 µl, Promega A795A), incubation for 15 min on ice, then centrifugation at 13,500  g for 30 minutes at 4°C. One ml of the supernatant was precipitated with 2 µl of GlycoBlue (Invitrogen, AM9516) and 1 ml of cold 100% isopropanol at -20° overnight. After incubation, the sample was spun at 13,500  g for 30 min at 4°C, then washed with 70% cold ethanol. The pellet was air-dried for about 5 minutes then resuspended in 100 µl of nuclease free water.  For all generations equal amounts of DNA from each individual’s sample was used to produce 6 different DNA pools per lineage and the pooled DNA used for methylated DNA immunoprecipitation (MeDIP).  Each pool containted 10-11 individual rat samples for each treatment group, with the exception of one control pool that only contained 5 individual samples. For the MeDIP procedure, genomic DNA was sonicated and run on 1.5% agarose gel for fragment size verification. The sonicated DNA was then diluted with 1X TE buffer to 400 μl, then heat-denatured for 10 min at 95˚C, and immediately cooled on ice for 10 min to create single-stranded DNA fragments. Then 100 μl of 5X IP buffer and 5μg of antibody (monoclonal mouse anti 5-methyl cytidine; Diagenode #C15200006) were added, and the mixture was incubated overnight with rotation at 4˚C. The following day magnetic beads (Dynabeads M280 Sheep anti-Mouse IgG; Life Technologies 11201D) were pre-washed per manufacturer’s instructions, and for each sample 50 μl of beads were added to the 500 μl of DNA-antibody mixture from the overnight incubation, then incubated for 2h with rotation at 4˚C. After this incubation, the samples were washed three times with 1X IP buffer using a magnetic rack. The washed samples were then resuspended in 250 μl digestion buffer (5mM Tris PH 8, 10.mM EDTA, 0.5% SDS) with 3.5 μl Proteinase K (20 mg/ml), and incubated for 2-3 hours on a rotator at 55˚C. DNA clean-up was performed using a Phenol-Chloroform-Isoamyl-Alcohol extraction, and the supernatant precipitated with 2 μl of GlycoBlue (20 mg/ml), 20 μl of 5M NaCl and 500 μl ethanol at -20˚C for one to several hours. The DNA precipitate was pelleted at 13,500  g for 30 minutes at 4°C, washed twice with 70% ethanol, then dried and resuspended in 20 μl H2O. DNA concentration was measured in a Qubit apparatus (Life Technologies) with the ssDNA analysis kit (Molecular Probes Q10212).
MeDIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext Ultra II RNA Library Prep Kit for Illumina (E770L, New England Biolabs, San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA from the single-stranded DNA resulting from MeDIP. After this step, the manufacturer’s protocol was followed indexing each sample individually with NEBNext Multiplex Oligos for Illumina.

treatment_protocol: Timed-pregnant F0 generation females were mated and on embryonic days 8 through 14 (E8-E14) of gestation were administered daily intraperitoneal injections of the treatment compound (vinclozolin 100mg/kg). Similarly, pregnant F1 females were treated with jet fuel hydrocarbons (250mg/kg JP8), and F2 females were treated with 25 mg/kg DDT (dichlorodiphenyltrichloroethane, Sigma-Aldrich). The F3 and F4 generations were bred without additional treatments during gestation. The F5 generation animals are considered transgenerational, as neither they nor the germ cells that produced them were directly exposed to these toxicants. For control lineage animals, F0 generation pregnant females were treated with vehicle dimethyl sulfoxide (DMSO, Sigma-Aldrich) from E8-E14, the F1 and F2 generations were not treated during pregnancy, and the F3 generation rats were considered to be the control lineage transgenerational generation. No sibling or cousin breeding was used to avoid any inbreeding artifacts. All animals were aged to 1 year for pathology and epigenetic analysis.

value: Sperm

tag: generation

tag: lineage

value: control


title: P15


title: P14


title: P18


title: P16


title: GIA3857A20

status: Public on Nov 29 2024

description: High VitD3 biovailability

data_processing:
Trimmomatic v0.36 was used to remove the adapters and filter raw reads below 36 bases long. The filtered reads were aligned to the Mus musculus genome Ensembl GRCm38 (release 86) using RSEM v1.3.0  and STAR v2.5.2 with the “--forward-prob” parameter was set to “0.5” and all other parameters were kept as default.
Raw counts were processed using the bioconductor package DESeq2 v1.18.1 in R v3.4.3, and normalized using the DESeq method to remove the library-specific artefacts. Variance stabilizing transformation was applied to obtain normalized log2 gene expression values.
Assembly: Ensembl GRCm38 (release 86)
Supplementary files format and content: VST log2 normalised expression values. Rows = genes; Columns = samples.

source_name: colon

extract_protocol:
RNA extraction kit (QIAGEN) - mouse colon
Biological replicate libraries were prepared using the polyA KAPA mRNA HyperPrep Kit and sequenced on Illumina Novaseq 6000 platform

treatment_protocol: Male mice (8 ½ weeks old) were fed with the following diets 3 ½ weeks :1)C57BL/6J/WT mice that were fed with standard VitD3 diet (2 IU/g) for 3 ½ weeks, 2) C57BL/6J/WT mice that were fed with high VitD3 diet (10 IU/g) for 3 ½ weeks, 3) Gc KO mice that were fed with standard VitD3 diet (2 IU/g) for 3 ½ weeks, 4) Gc KO mice that were fed with VitD3 deficient diet (10 IU/g) for 3 ½ weeks

tag: strain

value: colon

value: GCKO

value: standard VitD3 diet (2 IU/g)


title: P13


title: GIA3857A19

description: High VitD3 biovailability


title: GIA3857A17

description: High VitD3 biovailability


title: GIA3857A18

description: High VitD3 biovailability


title: GIA3857A16

description: High VitD3 biovailability


title: GIA3857A15

description: Low VitD3 biovailability

value: deficient VitD3 diet (0 IU/g)


title: GIA3857A13

description: Low VitD3 biovailability


title: GIA3857A14

description: Low VitD3 biovailability


title: GIA3857A12

description: Low VitD3 biovailability


title: GIA3857A10

description: High VitD3 biovailability

value: wildtype

value: high VitD3 diet (10 IU/g)


title: GIA3857A8

description: High VitD3 biovailability


title: GIA3857A11

description: Low VitD3 biovailability


title: GIA3857A7

description: High VitD3 biovailability


title: GIA3857A6

description: High VitD3 biovailability


title: GIA3857A5

description: Low VitD3 biovailability


title: GIA3857A4

description: Low VitD3 biovailability


title: GIA3857A3

description: Low VitD3 biovailability


title: GIA3857A2

description: Low VitD3 biovailability


title: GIA3857A1

description: Low VitD3 biovailability


title: BxPC3,plusIFNγ, Replicate5, H3K27ac HiChIP

status: Public on Nov 28 2024

city: NEW YORK

first: Xinhe

last: Xue

state: New York

address: 101 Avenue of the Americas

institute: New York Genome Center/New York University

data_processing:
We mapped HiChIP paired end reads to hg38 using HiC-Pro (Servant, 2015). Default settings were using to remove duplicate reads, identify valid interactions, and generate contact maps.
Valid pair files were binned to 5kb resolutions and filtered for loops that had 3 or more contacts.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

growth_protocol: BxPC-3 cells were cultured in RPMI-1640 (Thermo Fisher Scientific) supplemented with 10% Serum Plus-II (Thermo Fisher)

extract_protocol:
We prepared HiChIP cell libraries using H3K27ac AQuA-HiChIP method (Gryder, Khan and Stanton, 2020). We cultured BxPC-3 cells in RPMI media supplemented with 10% Serum Plus-II (Thermo Fisher) only or in RPMI media supplemented with 10% Serum Plus-II (Thermo Fisher) and 100 IU/mL IFNγ (BioLegend) for 2 days. For absolute quantification (AQuA-HiChIP), we grew 3T3 mouse fibroblasts in DMEM media (supplemented with 10% Serum Plus-II (Thermo Fisher Scientific) with no IFNγ. Then, we fixed cells in 1% formaldehyde (Sigma-Aldrich) for 10 mins and quenched to a final concentration of 125nM glycine (Sigma-Aldrich). We spiked in 2 million fixed mouse cells (with no IFNγ treatment) with 10 million of fixed treated-BxPC-3 cells or non-treated cells. The cells were lysed in 0.5% SDS (Sigma-Aldrich), quenched with 10% Triton X-100 (Sigma-Aldrich), and digested with MboI (NEB R0147M). Next, the DNA overhangs were blunted, biotinylated (ThermoFisher 19524016), and ligated. Nuclei were spun down, resuspended in nuclear lysis buffer and sonicated using a Covaris LE220 program: Fill level 10, PIP 450, Duty factor 30, CPB 200. We incubated the sheared DNA with Dynabeads Protein A (ThermoFisher 10001D) for 2 hours at 4 °C to preclear the samples. We then placed the tubes on a magnet and the supernatant was kept. We performed immunoprecipitation with a cross-species reactive H3K27ac antibody (Active Motif 39133). The samples were incubated with the antibody and Dynabeads Protein A overnight at 4 °C. We then washed, eluted and treated the samples with Proteinase K (New England Biolabs). We purified the samples using Zymo DNA Clean & Concentrator.
Biotin capture was performed with Dynabeads M-280 Streptavidin (ThermoFisher 11205D), followed by library preparation as previously described (Gryder, Khan and Stanton, 2020). We purified the amplified libraries with Illumina Sample Purification Beads. We sequenced the libraries using paired-end reads with NovaSeq 6000 S1 2x100 kit to generate 100-200 million read pairs per sample.
H3K27ac HiChIP

treatment_protocol: For IFNγ-stimulated conditions, cells were cultured in medium supplemented with 100 IU/mL human IFNγ (BioLegend) for 48 hours.

value: PDAC

value: IFNg treatment


title: BxPC3,plusIFNγ, Replicate6, H3K27ac HiChIP


title: BxPC3,plusIFNγ, Replicate4, H3K27ac HiChIP


title: BxPC3,plusIFNγ, Replicate2, H3K27ac HiChIP


title: BxPC3,plusIFNγ, Replicate1, H3K27ac HiChIP


title: BxPC3,noIFNγ, Replicate6, H3K27ac HiChIP

value: no treatment


title: BxPC3,noIFNγ, Replicate5, H3K27ac HiChIP


title: BxPC3,noIFNγ, Replicate4, H3K27ac HiChIP


title: BxPC3,noIFNγ, Replicate3, H3K27ac HiChIP


title: BxPC3,plusIFNγ, Replicate3, H3K27ac HiChIP


title: BxPC3,noIFNγ, Replicate2, H3K27ac HiChIP


title: BxPC3,noIFNγ, Replicate1, H3K27ac HiChIP


title: Murine AML, OGDH shRNA2, clone 5, D4, rep2

status: Public on Nov 27 2024

description:
Library name: SH24_Ogdh2081c5
SH24_IGO_09521_34_S34

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.6.1a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

growth_protocol: Murine AML cells were maintained in culture in RPMI + 10% FBS + 1% penicillin-streptomycin and stimulated with doxycycline for the indicated durations. Approximately 5x105-1x106  cells were harvested for RNA extraction for each condition.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.

treatment_protocol: Prior to doxycycline induction, cells were transduced with retroviral vectors expressing the indicated doxycycline-inducible shRNAs

value: Murine AML

value: Mll-Af9; NrasG12D

value: doxycycline


title: GIA3857A9

description: High VitD3 biovailability


title: Murine AML, OGDH shRNA2, clone 5, D4, rep1

description:
Library name: SH23_Ogdh2081c5
SH23_IGO_09521_33_S33


title: Murine AML, OGDH shRNA2, clone 3, D4, rep2

description:
Library name: SH22_Ogdh2081c3
SH22_IGO_09521_32_S32


title: Murine AML, OGDH shRNA2, clone 3, D4, rep1

description:
Library name: SH21_Ogdh2081c3
SH21_IGO_09521_31_S31


title: Murine AML, OGDH shRNA1, clone 5, D4, rep1

description:
Library name: SH19_Ogdh346c5
SH19_IGO_09521_29_S29


title: Murine AML, OGDH shRNA1, clone 5, D4, rep2

description:
Library name: SH20_Ogdh346c5
SH20_IGO_09521_30_S30


title: Murine AML, OGDH shRNA1, clone 1, D4, rep2

description:
Library name: SH18_Ogdh346c1
SH18_IGO_09521_28_S28


title: Murine AML, control shRNA, clone 7, D4, rep2

description:
Library name: SH16_Ren713c7
SH16_IGO_09521_26_S26


title: Murine AML, OGDH shRNA1, clone 1, D4, rep1

description:
Library name: SH17_Ogdh346c1
SH17_IGO_09521_27_S27


title: Murine AML, control shRNA, clone 2, D4, rep1

description:
Library name: SH13_Ren713c2
SH13_IGO_09521_23_S23


title: Murine AML, control shRNA, clone 7, D4, rep1

description:
Library name: SH15_Ren713c7
SH15_IGO_09521_25_S25


title: Murine AML, control shRNA, clone 2, D4, rep2

description:
Library name: SH14_Ren713c2
SH14_IGO_09521_24_S24


title: Murine AML, OGDH shRNA2, clone 5, D0, rep2

description:
Library name: SH12_Ogdh2081c5
SH12_IGO_09521_22_S22

value: untreated


title: Murine AML, OGDH shRNA2, clone 3, D0, rep2

description:
Library name: SH10_Ogdh2081c3
SH10_IGO_09521_20_S20


title: Murine AML, OGDH shRNA2, clone 3, D0, rep1

description:
Library name: SH9_Ogdh2081c3
SH9_IGO_09521_19_S19


title: Murine AML, OGDH shRNA1, clone 5, D0, rep2

description:
Library name: SH8_Ogdh346c5
SH8_IGO_09521_18_S18


title: Murine AML, OGDH shRNA1, clone 5, D0, rep1

description:
Library name: SH7_Ogdh346c5
SH7_IGO_09521_17_S17


title: Murine AML, OGDH shRNA1, clone 1, D0, rep2

description:
Library name: SH6_Ogdh346c1
SH6_IGO_09521_16_S16


title: Murine AML, OGDH shRNA1, clone 1, D0, rep1

description:
Library name: SH5_Ogdh346c1
SH5_IGO_09521_15_S15


title: Murine AML, control shRNA, clone 2, D0, rep2

description:
Library name: SH2_Ren713c2
SH2_IGO_09521_12_S12


title: Murine AML, control shRNA, clone 7, D0, rep2

description:
Library name: SH4_Ren713c7
SH4_IGO_09521_14_S14


title: Murine AML, control shRNA, clone 2, D0, rep1

description:
Library name: SH1_Ren713c2
SH1_IGO_09521_11_S11


title: Murine AML, OGDH shRNA2, D4, induced sorted, rep2

description: Library name: KL30_E06_shOgdh2081_D4BFPplus

growth_protocol: Murine AML cells were maintained in culture in RPMI + 10% FBS + 1% penicillin-streptomycin + murine IL3/IL6/SCF and stimulated with doxycycline for the indicated durations. BFP negative (min; uninduced) and BFP positive (plus;induced) cells were isolated by FACS. Approximately 5x105-1x106  cells were harvested for RNA extraction for each condition.

treatment_protocol: Prior to doxycycline induction, cells were transduced with lentiviral vectors expressing the indicated BFP-linked, doxycycline-inducible shRNAs


title: Murine AML, OGDH shRNA2, D4, induced sorted, rep1

description: Library name: KL15_D03_shOgdh2081_D4BFPplus


title: Murine AML, control shRNA, clone 7, D0, rep1

description:
Library name: SH3_Ren713c7
SH3_IGO_09521_13_S13


title: Murine AML, OGDH shRNA1, D4, induced sorted, rep2

description: Library name: KL10_C10_shOgdh346_D4BFPplus


title: Murine AML, OGDH shRNA2, clone 5, D0, rep1

description:
Library name: SH11_Ogdh2081c5
SH11_IGO_09521_21_S21


title: Murine AML, OGDH shRNA1, D4, induced sorted, rep1

description: Library name: KL25_E01_shOgdh346_D4BFPplus


title: Murine AML, control shRNA, D4, uninduced sorted, rep2

description: Library name: KL19_D07_shRen713_D4BFPmin


title: Murine AML, control shRNA, D4, induced sorted, rep2

description: Library name: KL20_E07_shRen713_D4BFPplus


title: Murine AML, control shRNA, D2, induced sorted, rep2

description: Library name: KL18_D06_shRen713_D2BFPplus


title: Murine AML, control shRNA, D2, uninduced sorted, rep2

description: Library name: KL17_D05_shRen713_D2BFPmin


title: Murine AML, control shRNA, D0, rep2

description: Library name: KL16_D04_shRen713_D0


title: Murine AML, control shRNA, D4, uninduced sorted, rep1

description: Library name: KL4_C04_shRen713_D4BFPmin


title: Murine AML, control shRNA, D4, induced sorted, rep1

description: Library name: KL5_C05_shRen713_D4BFPplus


title: Murine AML, control shRNA, D2, induced sorted, rep1

description: Library name: KL3_C03_shRen713_D2BFPplus


title: Murine AML, control shRNA, D0, rep1

description: Library name: KL1_C01_shRen713_D0


title: Murine AML, control shRNA, D2, uninduced sorted, rep1

description: Library name: KL2_C02_shRen713_D2BFPmin


title: cMyc-GFP+ LZ GC-B cells, KO4

status: Public on Nov 01 2024

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
KO4

data_processing:
The RSEM package (version 1.3.0) and STAR (2.5.2a) were used to align reads to the mouse Ensembl GRCm38 transcriptome.
Raw counts were normalised and differential expression analysis was performed with the DESeq2 package (version 1.18.1) within the R programming (version 3.4.3)
Assembly: Mouse Ensembl GRCm38
Supplementary files format and content: VSD normalised expression values, where rows represent mouse Ensembl genes and columns represent individual samples.

source_name: Spleen

extract_protocol:
Spleens were crushed and filtered with a 70µM mesh strainer. Harvested splenic B-cells were enriched by CD43, Ter119 and CD4 negative selection using MACS LS Columns (Miltenyi Biotec). Single-cell suspensions were stained with antibodies and sorted by flow cytometry. RNA was extracted from the sorted samples by TRIzol coupled to RNAeasy Mini Kit (#74104, QIAGEN, for cMyc+ GC-B cells).
Libraries were prepared with TruSeq Standard mRNA Sample Prep Kit (Illumina) following the manufacturer's protocols.

treatment_protocol: B cells from 8-15 week old HEL-specific BCR expressing B cells from male and female mice were adoptively transferred into congenic mice and immunized with 2x10^8 HEL3x-SRBC. Splenic GC-B cells from these mice were sorted by flow cytometry after five days. B cells from females and males from miR-155-sufficient and -deficient, respectively, were mainly used for adoptive transfer.

value: Spleen

value: Primary

value: GC-B cells

value: miR-155 KO

value: 5 days after HEL3x-SRBC immunization


title: cMyc-GFP+ LZ GC-B cells, KO5

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
KO5


title: cMyc-GFP+ LZ GC-B cells, KO3

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
KO3


title: cMyc-GFP+ LZ GC-B cells, KO2

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
KO2


title: cMyc-GFP+ LZ GC-B cells, KO1

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
KO1


title: cMyc-GFP+ LZ GC-B cells, WT5

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
WT5

value: WT


title: cMyc-GFP+ LZ GC-B cells, WT4

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
WT4


title: cMyc-GFP+ LZ GC-B cells, WT3

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
WT3


title: cMyc-GFP+ LZ GC-B cells, WT2

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
WT2


title: cMyc-GFP+ LZ GC-B cells, WT1

description:
CD45.1- CD45.2+ HEL+ B220+ CD38+ CD95+ CXCR4lo CD86hi cMyc-GFP+
WT1


title: ChIP-Seq WT arthroconidia arthroconidia Replicate 3 Figure4 WCE

status: Public on Oct 21 2024

first: Christina

middle: M.

last: Homer

department: Biochemistry & Biophysics

data_processing:
For ChIP-Seq: Reads were aligned to the Silveira genome22 using BWA version 0.7.17-r1188. Peaks were called using IP samples compared to control input samples with macs2 version 2.2.7.1, --mfold 5-60, with option –keep-dup set to all, and with the nomodel option selected and a manually set extension size of 197 for all samples based on estimated fragment size from bioanalyzer traces.
Assembly: Silveira genome (de Melo Teixeira et al 2022, PMID 35137016)
Supplementary files format and content: For ChIP-Seq: Processed data are MACS peaks output files.

organism: Coccidioides posadasii str. Silveira

source_name: liquid culture

growth_protocol: The wildtype Coccidioides posadasii strain Silveira (NR-48944) was used for growth experiments and as the background for the generation of the ryp1∆ mutant. All manipulation of live Coccidioides strains were performed in a biosafety level 3 facility. Standard spherulation conditions: polypropylene flasks containing Converse media were inoculated with 1 x 10^6/mL arthroconidia (unless otherwise stated) and placed at 39˚C, 10 % CO2, shaking at 120 rpm.  Where noted, spherulation was induced under the same conditions with different media: DMEM (UCSF Media Core) containing 20 % FBS (Corning) or RPMI (UCSF Media Core) containing 10 % FBS. For hyphal growth, polypropylene flasks containing Converse media were inoculated with 1 x 10^6 arthroconidia/mL and grown at 25˚C (Figures 2, S2) or room temperature (RT) (Figure 4, S4) shaking at 120 rpm. Experiments were performed in 1 L flasks with 330 mL Converse for wildtype and 500 mL flasks with 100 mL Converse for ryp1∆ mutant.Arthroconidia were generated on 2x GYE agar (2% Dextrose (Fisher), 1% Yeast extract (Gibco), 1.5% Bacto-Agar (BD)) + Penicillin/Streptomycin (100 U/ml penicillin and 100 g/ml streptomycin, UCSF Media Core) in T225 tissue culture flasks for 4-6 weeks at 30˚C, 25˚C, or 37˚C. Arthroconidia were then collected through scraping and washing as previously described (Mead et al 2020, PMID 32894648) and stocks were stored in PBS until use.

extract_protocol:
For ChIP-Seq: 50 mL of cultures were collected at start of the experiment (arthroconidia), and 8h, day 1, day2, and day 4 timepoints from spherule or hyphal growth induced as described above. Paired samples for RNA-seq (50mL initial culture for arthroconidia and 8h spherules/hyphae timepoints, then 10 mL of day 1, 2, and 4 spherules/hyphae) were also collected and processed as above. Cells were immediately crosslinked with 1 % formaldehyde (Neta Scientific) and incubated at RT for 20 min, mixing every 4 min. Crosslinking was then quenched with 125mM glycine (Fisher) and incubated for 5 min at RT, then frozen at -80˚C. Frozen samples were collected for all timepoints in the experiment prior to downstream processing. All following buffers were made using autoclaved ddH2O in baked glassware/DNA-free plastic tubes. Samples were thawed, pelleted, and washed twice with 25mL of TBS (20 mM Tris-HCl pH 7.5 (Fisher), 150mM NaCl (EMD)), centrifuging at 3000 x g for 5 min at 4˚C at each step. Pellets were resuspended in 700 µL of 4˚C lysis buffer (50mM HEPES (Fisher) / KOH (Fisher), 140 mM NaCl, 1 mM EDTA (Fisher), 1 % Triton X-100 (Acros Organics), 0.1 % sodium deoxycholate (Sigma), 2X Halt Protease Inhibitor Cocktail (ThermoFisher), 0.2X Halt Phosphatase Inhibitor Cocktail (ThermoFisher)). Cells were lysed by 8 x 1 min cycles of bead beating (0.5mm Zirconia/silica beads Biospec) at RT with 2 min rests on ice in between each cycle. Insoluble chromatin was pelleted by centrifugation at 8000rpm for 10 min, 4˚C and resuspended in 350 µL cold lysis buffer then sonicated (Diagenode Biorupter) for 15 cycles (30 seconds on, 30 seconds off). Cell debris was removed by centrifuged at 14000 rpm at 4˚C, yielding soluble chromatin fraction. 10 µL of input DNA was removed from the sample and placed in TE (10 mM Tris HCl pH 8.0, 1 mM EDTA) + 1 % SDS (Fisher). The remaining chromatin was immunoprecipitated (IP) with 5 µg of a polyclonal rabbit antibody against an epitope of Ryp1 (ID: 3878, Epitope: VYRELDKPFPPGEKKRAMKK, Bethyl laboratories) with rotation overnight at 4˚C. 50 µL of a 50% slurry of protein A dynabeads (Life technologies, washed 2x with cold TBS and 3x with cold lysis buffer) were added to each protein/antibody mixture and incubated an additional 3h at 4˚C with rotation. Beads were then pelleted on a magnetic rack and washed 2x with cold lysis buffer (without protease or phosphatase inhibitors), 2x with cold lysis buffer with 500 mM NaCl instead of 140 mM NaCl, 2x with cold wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl (Sigma), 0.5 % NP-40 (Fluka), 0.5 % sodium deoxycholate, 1 mM EDTA), 1x with cold TE. Bound protein/DNA complexes were eluted by adding 110 µL of elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1 % SDS), vortexing, and incubating 10 min at 65˚C, mixing every 2 min. Samples placed on a magnet and 100 µL eluate was moved to a new tube. Then 150 µL TE + 0.65 % SDS was added to same beads, vortexed and placed back on the magnet, allowing 150 µL to be removed and combined with previous eluate for 250 µL for each sample. 1 µL of proteinase K (20 mg/mL, Qiagen) was added to these IP samples and previously-collected input samples and incubated at 65˚C overnight (approximately 16h). 2 ug of RNase A (Qiagen) was added to each sample, which was incubated at 37˚C for 1h. Samples were then purified using the Zymo ChIP DNA Clean and Concentrator kit.
For ChIP-Seq: . Libraries were prepared using NEBNext Ultra II DNA Library Prep kit, with an additional round of higher and lower size selection (calibrated to select for 150-350 bp fragment sizes) using homemade Serapure size selection beads. Library quality and adaptor dimer contamination was analyzed using Agilent High Sensitivity DNA Chip. Final library concentrations were measured using the Qubit High Sensitivity or Broad Range reagents depending on estimated library concentration by Agilent analysis of libraries. Libraries were pooled and final pool subjected to another round of size selection with homemade Serapure beads to remove remaining adaptor dimers.

treatment_protocol: No additional treatments aside from the differing growth conditions above.

value: fungal cell

tag: morphology

value: arthroconidia

tag: timepoint

tag: media

value: PBS

tag: figure of related microscopy data

tag: replicate


title: ChIP-Seq WT arthroconidia arthroconidia Replicate 1 Figure4 WCE


title: ChIP-Seq WT arthroconidia arthroconidia Replicate 2 Figure4 WCE


title: ChIP-Seq WT spherules 8h Replicate 1 Figure4 WCE

value: spherules

value: Converse


title: ChIP-Seq WT spherules 8h Replicate 2 Figure4 WCE


title: ChIP-Seq WT spherules 8h Replicate 3 Figure4 WCE


title: ChIP-Seq WT hyphae 8h Replicate 2 Figure4 WCE

value: hyphae


title: ChIP-Seq WT hyphae 8h Replicate 1 Figure4 WCE


title: ChIP-Seq WT hyphae 8h Replicate 3 Figure4 WCE


title: ChIP-Seq Ryp1 spherules D1 Replicate 3 Figure4 WCE


title: ChIP-Seq Ryp1 spherules D1 Replicate 1 Figure4 WCE


title: ChIP-Seq Ryp1 hyphae D1 Replicate 1 Figure4 WCE


title: ChIP-Seq Ryp1 spherules D1 Replicate 2 Figure4 WCE


title: ChIP-Seq Ryp1 hyphae D1 Replicate 2 Figure4 WCE


title: ChIP-Seq Ryp1 hyphae D1 Replicate 3 Figure4 WCE


title: ChIP-Seq Ryp1 arthroconidia arthroconidia Replicate 1 Figure4 WCE


title: ChIP-Seq Ryp1 arthroconidia arthroconidia Replicate 2 Figure4 WCE


title: ChIP-Seq Ryp1 arthroconidia arthroconidia Replicate 3 Figure4 WCE


title: ChIP-Seq WT spherules D4 Replicate 3 Figure4 WCE


title: ChIP-Seq WT spherules D4 Replicate 2 Figure4 WCE


title: ChIP-Seq WT spherules D4 Replicate 1 Figure4 WCE


title: ChIP-Seq WT hyphae D4 Replicate 3 Figure4 WCE


title: ChIP-Seq WT hyphae D4 Replicate 2 Figure4 WCE


title: ChIP-Seq WT hyphae D4 Replicate 1 Figure4 WCE


title: ChIP-Seq WT spherules D2 Replicate 2 Figure4 WCE


title: ChIP-Seq WT spherules D2 Replicate 1 Figure4 WCE


title: ChIP-Seq WT spherules D2 Replicate 3 Figure4 WCE


title: ChIP-Seq WT hyphae D2 Replicate 1 Figure4 WCE


title: ChIP-Seq WT spherules D1 Replicate 3 Figure4 WCE


title: ChIP-Seq WT hyphae D2 Replicate 3 Figure4 WCE


title: ChIP-Seq WT hyphae D2 Replicate 2 Figure4 WCE


title: ChIP-Seq WT spherules D1 Replicate 1 Figure4 WCE


title: ChIP-Seq WT spherules D1 Replicate 2 Figure4 WCE


title: ChIP-Seq WT hyphae D1 Replicate 2 Figure4 WCE


title: ChIP-Seq WT hyphae D1 Replicate 3 Figure4 WCE


title: ChIP-Seq WT hyphae D1 Replicate 1 Figure4 WCE


title: ChIP-Seq WT arthroconidia arthroconidia Replicate 1 Figure4


title: ChIP-Seq WT arthroconidia arthroconidia Replicate 3 Figure4


title: ChIP-Seq WT arthroconidia arthroconidia Replicate 2 Figure4


title: ChIP-Seq WT spherules 8h Replicate 2 Figure4


title: ChIP-Seq WT spherules 8h Replicate 1 Figure4


title: ChIP-Seq WT spherules 8h Replicate 3 Figure4


title: ChIP-Seq WT hyphae 8h Replicate 2 Figure4


title: ChIP-Seq WT hyphae 8h Replicate 1 Figure4


title: ChIP-Seq Ryp1 spherules D1 Replicate 1 Figure4


title: ChIP-Seq WT hyphae 8h Replicate 3 Figure4


title: ChIP-Seq Ryp1 spherules D1 Replicate 3 Figure4


title: ChIP-Seq Ryp1 hyphae D1 Replicate 2 Figure4


title: ChIP-Seq Ryp1 spherules D1 Replicate 2 Figure4


title: ChIP-Seq Ryp1 hyphae D1 Replicate 1 Figure4


title: ChIP-Seq Ryp1 hyphae D1 Replicate 3 Figure4


title: ChIP-Seq Ryp1 arthroconidia arthroconidia Replicate 1 Figure4


title: ChIP-Seq Ryp1 arthroconidia arthroconidia Replicate 3 Figure4


title: ChIP-Seq Ryp1 arthroconidia arthroconidia Replicate 2 Figure4


title: ChIP-Seq WT spherules D4 Replicate 2 Figure4


title: ChIP-Seq WT spherules D4 Replicate 3 Figure4


title: ChIP-Seq WT spherules D4 Replicate 1 Figure4


title: ChIP-Seq WT hyphae D4 Replicate 3 Figure4


title: ChIP-Seq WT hyphae D4 Replicate 1 Figure4


title: ChIP-Seq WT spherules D2 Replicate 2 Figure4


title: ChIP-Seq WT spherules D2 Replicate 3 Figure4


title: ChIP-Seq WT hyphae D2 Replicate 1 Figure4


title: ChIP-Seq WT spherules D2 Replicate 1 Figure4


title: ChIP-Seq WT hyphae D4 Replicate 2 Figure4


title: ChIP-Seq WT hyphae D2 Replicate 3 Figure4


title: ChIP-Seq WT hyphae D2 Replicate 2 Figure4


title: ChIP-Seq WT spherules D1 Replicate 3 Figure4


title: ChIP-Seq WT spherules D1 Replicate 1 Figure4


title: ChIP-Seq WT spherules D1 Replicate 2 Figure4


title: ChIP-Seq WT hyphae D1 Replicate 2 Figure4


title: ChIP-Seq WT hyphae D1 Replicate 1 Figure4


title: ChIP-Seq WT hyphae D1 Replicate 3 Figure4


title: RNA-seq WT arthroconidia arthroconidia Replicate 3 Figure2

data_processing:
For RNA-Seq: Estimated counts of each transcript were calculated for each sample by alignment-free comparison against the predicted mRNA for the published Silveira genome (de Melo Teixeira et al 2022, PMID 35137016) using KALLISTO version 0.46.2 (Bray et al 2016, PMID 27043002).
Assembly: Silveira genome (de Melo Teixeira et al 2022, PMID 35137016)
Supplementary files format and content: For RNA-Seq: Processed data are Kallisto output files with estimated counts per gene.

growth_protocol: The wildtype Coccidioides posadasii strain Silveira (NR-48944) was used for growth experiments and as the background for the generation of the ryp1∆ mutant. All manipulation of live Coccidioides strains were performed in a biosafety level 3 facility. Standard spherulation conditions: polypropylene flasks containing Converse media were inoculated with 1 x 10^6/mL arthroconidia (unless otherwise stated) and placed at 39˚C, 10 % CO2, shaking at 120 rpm.  Where noted, spherulation was induced under the same conditions with different media: DMEM (UCSF Media Core) containing 20 % FBS (Corning) or RPMI (UCSF Media Core) containing 10 % FBS. For hyphal growth, polypropylene flasks containing Converse media were inoculated with 1 x 10^6 arthroconidia/mL and grown at 25˚C (Figures 2, S2) or room temperature (RT) (Figure 4, S4) shaking at 120 rpm. All growth experiments were performed in 125 mL polypropylene flasks with 50 mL of media except for experiments in Figures 2, S2, which were performed in 1 L flasks with 350 mL of media (except for replicate 3 of ryp1∆ mutant in spherulation conditions, which was placed in 300 mL of media given limited arthroconidia stock, to maintain the same concentration across all samples) and Figures 4, S4, which were performed in 1 L flasks with 330 mL Converse for wildtype and 500 mL flasks with 100 mL Converse for ryp1∆ mutant.Arthroconidia were generated on 2x GYE agar (2% Dextrose (Fisher), 1% Yeast extract (Gibco), 1.5% Bacto-Agar (BD)) + Penicillin/Streptomycin (100 U/ml penicillin and 100 g/ml streptomycin, UCSF Media Core) in T225 tissue culture flasks for 4-6 weeks at 30˚C, 25˚C, or 37˚C. Arthroconidia were then collected through scraping and washing as previously described (Mead et al 2020, PMID 32894648) and stocks were stored in PBS until use.

extract_protocol:
For RNA-Seq: RNA from arthroconidia were collected from the same arthroconidia stock in triplicate by placing 5x10^7 arthroconidia into Trizol LS (Ambion) and bead beating for 2 minutes. For all other samples, at indicated timepoints, RNA was extracted by pelleting cells by centrifugation at 1200 x g for 5 minutes at RT, removing supernatants, and flash freezing cell pellets in liquid nitrogen. Cell pellets were resuspended in Trizol, thawed, and bead beat for 2 minutes. Samples were stored at -80˚C until all samples at all timepoints in an individual experiment had been collected. RNA was extracted using the Direct-zol RNA Miniprep Plus isolation kit (Zymo) with on-column DNAse digestion step extended for 15-30 minutes.
For RNA-Seq: Sequencing libraries were prepared using the Ultra II Directional RNA Library Prep kit with dual-indexed multiplexing barcodes with polyA selection. Library quality and adaptor dimer contamination were analyzed using Agilent High Sensitivity DNA Chip. An additional round of library size selection was performed using homemade Serapure size selection beads (Rohland et al 2012, PMID 22267522) for libraries containing significant adaptor dimers.


title: RNA-seq Ryp1 arthroconidia arthroconidia Replicate 3 Figure2


title: RNA-seq Ryp1 arthroconidia arthroconidia Replicate 2 Figure2


title: RNA-seq Ryp1 arthroconidia arthroconidia Replicate 1 Figure2


title: RNA-seq WT arthroconidia arthroconidia Replicate 1 Figure2


title: RNA-seq WT spherules D3 RPMI Replicate 3 FigureS5

value: RPMI


title: RNA-seq WT spherules D3 RPMI Replicate 2 FigureS5


title: RNA-seq WT spherules D3 RPMI Replicate 1 FigureS5


title: RNA-seq Ryp1 spherules 8Hour Replicate 3 Figure2


title: RNA-seq WT arthroconidia arthroconidia Replicate 2 Figure2


title: RNA-seq WT arthroconidia arthroconidia Replicate 3 FigureS4


title: RNA-seq WT arthroconidia arthroconidia Replicate 2 FigureS4


title: RNA-seq WT arthroconidia arthroconidia Replicate 1 FigureS4


title: RNA-seq Ryp1 spherules 8Hour Replicate 2 Figure2


title: RNA-seq Ryp1 spherules 8Hour Replicate 1 Figure2


title: RNA-seq WT spherules 8h Replicate 2 FigureS4


title: RNA-seq WT spherules 8Hour Replicate 3 Figure2


title: RNA-seq WT spherules 8h Replicate 1 FigureS4


title: RNA-seq WT spherules 8h Replicate 3 FigureS4


title: RNA-seq WT hyphae 8h Replicate 2 FigureS4


title: RNA-seq WT spherules 8Hour Replicate 2 Figure2


title: RNA-seq WT hyphae 8h Replicate 1 FigureS4


title: RNA-seq WT hyphae 8h Replicate 3 FigureS4


title: RNA-seq WT spherules 8Hour Replicate 1 Figure2


title: RNA-seq Ryp1 spherules D1 Replicate 3 FigureS4


title: RNA-seq Ryp1 spherules D1 Replicate 1 FigureS4


title: RNA-seq WT hyphae 8Hour Replicate 3 Figure2


title: RNA-seq Ryp1 spherules D1 Replicate 2 FigureS4


title: RNA-seq Ryp1 hyphae D1 Replicate 1 FigureS4


title: RNA-seq WT hyphae 8Hour Replicate 2 Figure2


title: RNA-seq Ryp1 hyphae D1 Replicate 2 FigureS4


title: RNA-seq Ryp1 hyphae D1 Replicate 3 FigureS4


title: RNA-seq WT hyphae 8Hour Replicate 1 Figure2


title: RNA-seq Ryp1 arthroconidia arthroconidia Replicate 2 FigureS4


title: RNA-seq Ryp1 arthroconidia arthroconidia Replicate 1 FigureS4


title: RNA-seq Ryp1 hyphae 8Hour Replicate 3 Figure2


title: RNA-seq Ryp1 arthroconidia arthroconidia Replicate 3 FigureS4


title: RNA-seq WT spherules D4 Replicate 2 FigureS4


title: RNA-seq Ryp1 hyphae 8Hour Replicate 2 Figure2


title: RNA-seq WT spherules D4 Replicate 3 FigureS4


title: RNA-seq WT spherules D4 Replicate 1 FigureS4


title: RNA-seq Ryp1 hyphae 8Hour Replicate 1 Figure2


title: RNA-seq WT hyphae D4 Replicate 3 FigureS4


title: RNA-seq WT hyphae D4 Replicate 2 FigureS4


title: RNA-seq WT hyphae D4 Replicate 1 FigureS4


title: RNA-seq WT spherules D3 DMEM Replicate 3 FigureS5

value: DMEM


title: RNA-seq WT spherules D2 Replicate 2 FigureS4


title: RNA-seq WT spherules D3 DMEM Replicate 2 FigureS5


title: RNA-seq WT spherules D2 Replicate 1 FigureS4


title: RNA-seq WT spherules D3 DMEM Replicate 1 FigureS5


title: RNA-seq WT spherules D2 Replicate 3 FigureS4


title: RNA-seq WT hyphae D2 Replicate 1 FigureS4


title: RNA-seq WT hyphae D2 Replicate 3 FigureS4


title: RNA-seq WT hyphae D2 Replicate 2 FigureS4


title: RNA-seq WT spherules D6 Replicate 3 Figure2


title: RNA-seq WT spherules D1 Replicate 3 FigureS4


title: RNA-seq WT spherules D6 Replicate 2 Figure2


title: RNA-seq WT spherules D1 Replicate 1 FigureS4


title: RNA-seq WT spherules D6 Replicate 1 Figure2


title: RNA-seq WT hyphae D1 Replicate 2 FigureS4


title: RNA-seq WT spherules D1 Replicate 2 FigureS4


title: RNA-seq WT hyphae D1 Replicate 3 FigureS4


title: RNA-seq Ryp1 spherules D6 Replicate 3 Figure2


title: RNA-seq WT hyphae D1 Replicate 1 FigureS4


title: RNA-seq Ryp1 spherules D6 Replicate 2 Figure2


title: RNA-seq Ryp1 spherules D6 Replicate 1 Figure2


title: RNA-seq WT hyphae D6 Replicate 3 Figure2


title: RNA-seq WT hyphae D6 Replicate 1 Figure2


title: RNA-seq WT hyphae D6 Replicate 2 Figure2


title: RNA-seq Ryp1 hyphae D6 Replicate 2 Figure2


title: RNA-seq Ryp1 hyphae D6 Replicate 3 Figure2


title: RNA-seq Ryp1 hyphae D6 Replicate 1 Figure2


title: RNA-seq WT spherules D5 Replicate 3 Figure2


title: RNA-seq WT spherules D5 Replicate 2 Figure2


title: RNA-seq WT spherules D5 Replicate 1 Figure2


title: RNA-seq Ryp1 spherules D5 Replicate 3 Figure2


title: RNA-seq Ryp1 spherules D5 Replicate 2 Figure2


title: RNA-seq WT spherules D4 Replicate 3 Figure2


title: RNA-seq Ryp1 spherules D5 Replicate 1 Figure2


title: RNA-seq WT spherules D4 Replicate 2 Figure2


title: RNA-seq WT spherules D4 Replicate 1 Figure2


title: RNA-seq WT spherules D3 Replicate 3 Figure2


title: RNA-seq Ryp1 spherules D4 Replicate 2 Figure2


title: RNA-seq Ryp1 spherules D4 Replicate 1 Figure2


title: RNA-seq WT spherules D3 Replicate 1 Figure2


title: RNA-seq WT spherules D3 Replicate 2 Figure2


title: RNA-seq Ryp1 spherules D4 Replicate 3 Figure2


title: RNA-seq Ryp1 spherules D3 Replicate 2 Figure2


title: RNA-seq Ryp1 spherules D3 Replicate 3 Figure2


title: RNA-seq Ryp1 spherules D3 Replicate 1 Figure2


title: RNA-seq WT hyphae D3 Replicate 3 Figure2


title: RNA-seq WT hyphae D3 Replicate 1 Figure2


title: RNA-seq WT hyphae D3 Replicate 2 Figure2


title: RNA-seq Ryp1 hyphae D3 Replicate 3 Figure2


title: RNA-seq Ryp1 hyphae D3 Replicate 2 Figure2


title: RNA-seq Ryp1 hyphae D3 Replicate 1 Figure2


title: RNA-seq WT spherules D2 Replicate 3 Figure2


title: RNA-seq WT spherules D2 Replicate 2 Figure2


title: RNA-seq Ryp1 spherules D2 Replicate 3 Figure2


title: RNA-seq WT spherules D2 Replicate 1 Figure2


title: RNA-seq Ryp1 spherules D2 Replicate 1 Figure2


title: RNA-seq Ryp1 spherules D2 Replicate 2 Figure2


title: RNA-seq WT hyphae D2 Replicate 3 Figure2


title: RNA-seq WT hyphae D2 Replicate 2 Figure2


title: RNA-seq WT hyphae D2 Replicate 1 Figure2


title: RNA-seq Ryp1 hyphae D2 Replicate 1 Figure2


title: RNA-seq Ryp1 hyphae D2 Replicate 2 Figure2


title: RNA-seq WT spherules D1 Replicate 3 Figure2


title: RNA-seq WT spherules D1 Replicate 2 Figure2


title: RNA-seq WT spherules D1 Replicate 1 Figure2


title: RNA-seq Ryp1 spherules D1 Replicate 3 Figure2


title: RNA-seq Ryp1 spherules D1 Replicate 2 Figure2


title: RNA-seq WT hyphae D1 Replicate 1 Figure2


title: RNA-seq Ryp1 spherules D1 Replicate 1 Figure2


title: RNA-seq WT hyphae D1 Replicate 2 Figure2


title: RNA-seq WT hyphae D1 Replicate 3 Figure2


title: RNA-seq Ryp1 hyphae D1 Replicate 3 Figure2


title: RNA-seq Ryp1 hyphae D1 Replicate 2 Figure2


title: RNA-seq Ryp1 hyphae D1 Replicate 1 Figure2


title: RNA-seq WT arthroconidia arthroconidia Replicate 2 Figure1


title: RNA-seq WT arthroconidia arthroconidia Replicate 1 Figure1


title: RNA-seq WT arthroconidia arthroconidia Replicate 3 Figure1


title: RNA-seq Ryp1 hyphae D2 Replicate 3 Figure2


title: RNA-seq WT spherules D6 Replicate 1 Figure1


title: RNA-seq WT spherules D6 Replicate 2 Figure1


title: RNA-seq WT spherules D5 Replicate 3 Figure1


title: RNA-seq WT spherules D6 Replicate 3 Figure1


title: RNA-seq WT spherules D5 Replicate 2 Figure1


title: RNA-seq WT spherules D5 Replicate 1 Figure1


title: RNA-seq WT spherules D4 Replicate 1 Figure1


title: RNA-seq WT spherules D4 Replicate 3 Figure1


title: RNA-seq WT spherules D4 Replicate 2 Figure1


title: RNA-seq WT spherules D3 Replicate 1 Figure1


title: RNA-seq WT spherules D3 Replicate 3 Figure1


title: RNA-seq WT spherules D3 Replicate 2 Figure1


title: RNA-seq WT spherules D2 Replicate 3 Figure1


title: RNA-seq WT spherules D2 Replicate 2 Figure1


title: RNA-seq WT spherules D2 Replicate 1 Figure1


title: RNA-seq WT spherules D1 Replicate 2 Figure1


title: RNA-seq WT spherules D1 Replicate 1 Figure1


title: RNA-seq WT spherules D1 Replicate 3 Figure1


title: RNA-seq WT spherules 8Hour Replicate 2 Figure1


title: RNA-seq WT spherules 8Hour Replicate 3 Figure1


title: RNA-seq WT spherules 8Hour Replicate 1 Figure1


title: 2153L GEMM TNBC Combo, J2-RIP, biol rep 2

status: Public on Oct 16 2024

city: Houston

first: FEI

last: YUAN

state: TX

address: 1 Baylor Plaza

department: Pathology & Immunology

institute: Baylor College of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastp v.0.23.2 (Chen et al. 2018) with default parameters and duplicated reads with the --dup option enabled.
The trimmed reads were aligned to the reference genome mm10 using STAR aligner v.2.7.3a (Dobin et al. 2013) and gene-specific read counts (on reverse strand) were obtained with the --quantMode GeneCounts option enabled
The Transposable Elements (TE) annotation, including their classification in classes and families, was based on GTF file curated by the Hammell Lab: (http://labshare.cshl.edu/shares/mhammelllab/wwwdata/TEtranscripts/TE_GTF/mm10_rmsk_TE.gtf.gz). The reads mapped to TE classes were quantified using featureCounts v.2.0.3 (Liao et al. 2014) with option "-p -M -s 2".
Assembly: mm10
Supplementary files format and content: CSV (comma-separated values) gzip text file include gene level feature counts for each Sample
Supplementary files format and content: CSV (comma-separated values) gzip text file include Transposible Elements class level feature counts for each Sample

source_name: 2153L GEMM TNBC tumor

growth_protocol: Fresh tumor fragments were transplanted into the cleared mammary fat pads of 6- to 8-week-old female BALB/c mice.

extract_protocol:
Input and dsRIP RNAs were extracted using Direct-zol RNA Microprep Kit (ZYMO Research, R2060). The antibodies used in the study were manufactured by Exalpha Biologicals, Inc. with catalog number 10010500.
RNA libraries for RNA-seq were prepared using Illumina Stranded Total RNA Prep with Ribo-Zero Kit (Illumina, 20040525) following Illumina’s recommended protocol. First stranded cDNA synthesis was performed using SuperScript III (ThermoFisher, 18080044) with the following modifications: RNA was heated to 70°C for 3 minutes to reduce secondary structure, followed by reverse transcription for 10 minutes at 25°C, 50 minutes at 50°C, and 15 minutes at 70°C. Amplified libraries were purified and quantified using the KAPA quantification kit (Roche).

treatment_protocol: When tumors reached a volume of approximately 100 mm3, mice were randomized and treated with drugs. Tumor volume was monitored using calipers and calculated as length × width2 / 2. The IRE1α RNase inhibitor ORIN1001 formulated in 1% microcrystalline cellulose and 50% sucrose solution was administered by daily oral gavage (150 mg/kg). Docetaxel (MilliporeSigma) was dissolved in 25% Tween 80 and 12% ethanol and administered through weekly i.p. injections at 10 mg/kg dose. Mice undergoing mono-therapy also received vehicle as in the combination treatment study.

tag: tissue

value: 2153L GEMM TNBC tumor

value: Bulk Tumor cells

value: p53 knocckout

tag: rip antibody

value: anti double-stranded RNA (J2) [Exalpha, catalog number 10010500)

value: ORIN1001 plus Docetasel


title: 2153L GEMM TNBC Combo, J2-RIP, biol rep 1

tag: cell type


title: 2153L GEMM TNBC Combo, J2-RIP, biol rep 3

tag: genotype


title: 2153L GEMM TNBC Docetaxel, J2-RIP, biol rep 3

tag: treatment

value: Docetaxel


title: 2153L GEMM TNBC Docetaxel, J2-RIP, biol rep 2


title: 2153L GEMM TNBC Docetaxel, J2-RIP, biol rep 1


title: 2153L GEMM TNBC ORIN1001, J2-RIP, biol rep 3

value: ORIN1001 (IRE1a RNase inhibitor)


title: 2153L GEMM TNBC ORIN1001, J2-RIP, biol rep 2


title: 2153L GEMM TNBC ORIN1001, J2-RIP, biol rep 1


title: 2153L GEMM TNBC Vehicle, J2-RIP, biol rep 3

value: Vehicle


title: 2153L GEMM TNBC Vehicle, J2-RIP, biol rep 2


title: 2153L GEMM TNBC Combo, Input, biol rep 3

value: none (input)


title: 2153L GEMM TNBC Combo, Input, biol rep 2


title: 2153L GEMM TNBC Docetaxel, Input, biol rep 2


title: 2153L GEMM TNBC Vehicle, J2-RIP, biol rep 1


title: 2153L GEMM TNBC Docetaxel, Input, biol rep 1


title: 2153L GEMM TNBC Combo, Input, biol rep 1


title: 2153L GEMM TNBC Docetaxel, Input, biol rep 3


title: Panc-d7-Smad4OFF_m2

description: single-end sequencing

data_processing:
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.5.3a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample

source_name: PDAC Primary Tumor

extract_protocol:
Total RNA was extracted using Trizol Total RNA was isolated using TRIzol LS (Thermo Fisher Scientific # 10296028) followed by column clean-up using an RNeasy kit (Qiagen #74106). the RNeasy Mini Kit (Qiagen)
100-500 ng of total RNA underwent polyA selection and TruSeq library preparation according to instructions provided by Illumina (TruSeq Stranded mRNA HT Kit, Illumina #20020595), with 15 cycles of PCR.
Samples were barcoded and run on a HiSeq (Illumina) in a 75-bp SE run, with an average of 50 million reads per sample.

value: PDAC primary tumor cells

tag: time

value: day 7


title: 2153L GEMM TNBC ORIN1001, Input, biol rep 3


title: 2153L GEMM TNBC ORIN1001, Input, biol rep 2


title: Liv-d7-Smad4ON_m1

description: single-end sequencing

source_name: PDAC Liver Metastasis

value: PDAC liver metastasis cells


title: 2153L GEMM TNBC Vehicle, Input, biol rep 3


title: 2153L GEMM TNBC ORIN1001, Input, biol rep 1


title: 2153L GEMM TNBC Vehicle, Input, biol rep 1


title: 2153L GEMM TNBC Vehicle, Input, biol rep 2


title: Sox9iresGFP PND3  XX

status: Public on Sep 10 2024

description: 10X Genomics

data_processing:
All subsequent analyses were performed in R v.3.6.0 using the Seurat (v3) package.  Genes were considered to be ‘expressed’ if the estimated (log10) count was at least 0.1. Primary filtering was then performed by removing from consideration: cells expressing fewer than 50 genes and cells for which mitochondrial genes made up greater than 10% of all expressed genes.
All further analyses done using Seurat v4 R package. Genes were deemed “expressed” if their estimated (log10) count was at least 0.1. Initial filtering excluded cells expressing fewer than 50 genes and cells with mitochondrial gene expression greater than 3 standard deviations from the mean.
Assembly: mm10
Supplementary files format and content: tab delimited text containing raw counts

source_name: Pituitary

growth_protocol: Harvested from PND3 animal

extract_protocol:
Chromium Controller and Chromium10x 3 prime v2.0, Chromium Single Cell 30 Reagent Kits UserGuide (v3 Chemistry)
Chromium Next GEM Single Cell

value: Pituitary

tag: Sex

value: F

value: Stem cell


title: Sox9iresGFP PND3  XY

description: 10X Genomics

value: M


title: CD4 T cells_Ctrl-7

status: Public on Aug 31 2024

type: RNA

city: Bern

first: Ramin

last: Radpour

address: Murtenstrasse 35

department: Medical Oncology

country: Switzerland

institute: Bern University Hospital

description: Gene expression data

hyb_protocol: The labelled products were hybridized using GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix Inc.) for 48 hours at 45°C and 60rpm.

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G (Affymetrix Inc.).

data_processing: The expression signals were acquired using the Affymetrix GeneChip Command Console Software (AGCC). The system was used to generate the numerical values of the probe intensity (Signal). The differentially expressed mRNAs were defined using Partek Genomics Suite software (Partek Incorporated, Missouri, USA) and and RMA normalization.

label: biotin

source_name: healthy control

label_protocol: Biotinylated mRNAs were prepared according to the GeneChip® Human Transcriptome Pico Assay 2.0  protocol (Affymetrix Inc.) using 50ng total RNA.

extract_protocol:
CD4+ T cells were FACS-purified from BM of newly diagnosed AML patients and also control subjects.
Total RNA was extracted using RNeasiy micro kit (QIAGEN AG) according to the manufacturer's instructions.

tag: patient id

tag: disease

value: healthy control

value: CD4 T cells


title: CD4 T cells_Ctrl-6

description: Gene expression data


title: CD4 T cells_Ctrl-5

description: Gene expression data


title: CD4 T cells_Ctrl-4

description: Gene expression data


title: CD4 T cells_Ctrl-2

description: Gene expression data


title: CD4 T cells_Ctrl-3

description: Gene expression data


title: CD4 T cells_AML-30

description: Gene expression data

source_name: acute myeloid leukemia

value: acute myeloid leukemia


title: CD4 T cells_Ctrl-1

description: Gene expression data


title: CD4 T cells_AML-29

description: Gene expression data


title: CD4 T cells_AML-28

description: Gene expression data


title: CD4 T cells_AML-26

description: Gene expression data


title: CD4 T cells_AML-25

description: Gene expression data


title: CD4 T cells_AML-27

description: Gene expression data


title: CD4 T cells_AML-22

description: Gene expression data


title: CD4 T cells_AML-23

description: Gene expression data


title: CD4 T cells_AML-24

description: Gene expression data