title: Ctr-2_ATAC

city: Copenhagen

first: Xiaochan

last: Xu

address: Blegdamsvej 17

institute: University of Copenhagen

data_processing:
sequencing datas were mapped with bowtie2.
macs2 callpeak -t sorted_K27me3_*.bam -c input.bam -n K27me3_gc --nomodel --extsize 250 --nolambda --broad --broad-cutoff 0.05 -p 0.05 -f BAM -g mm -B
coverage tracks were generated with deeptools-3.1.0 with RPKM normalization, bamCoverage -b *.bam -bs 100 --normalizeUsing RPKM -ignore chrX chrM --smoothLength 500 -o outfilename.bw
peaks were called  with MACS2, macs2 callpeak -t sorted_K4me3_*.bam -c input.bam -n K4me3_gc -nomodel --extsize 250 --nolambda -p 0.05 -f BAM -g mm -B
Genome_build: mm9
Supplementary_files_format_and_content: Excel data file, comma-separated value file, bigwig file, bed file

source_name: Chemically-induced mouse embryonic fibroblasts

growth_protocol: MEFs were cultured with high glucose Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1% GlutaMAX, 1% nonessential amino-acids (NEAAs), 0.055 mM 2-mercaptoethanol, and 1% penicillin-streptomycin.

extract_protocol:
For ChIP-seq, fix cells, nuclear extraction and sonication, immunoprecipitation with primary antibodies, elution and crosslink reversion, DNA clean up and PCR. The libraries were sequenced using an Illumina HiSeq 2500 machine. Primary antibodies used in this study included: anti-H3K4me3 (Abcam), anti-H3K27me3 (Millipore). For ATAC-seq, ATAC-seq libraries were prepared using Trueprep DNA library Prep Kit V2 for Illumina (vazyme). 50,000 cells were used for each single reaction. Cells were washed in 100 μl cold PBS and resuspended in 50 μl lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.5% NP-40_x000B_) for 10 min and nuclei were spun at 500g for 10 min using a refrigerated centrifuge. Then the pellet was re-suspended in 50μl transposase reaction mix and incubated at 37 °C for 30 min. The samples were purified and purified, then libraries were amplified by PCR for 13 cycles. The libraries were sequenced using an Illumina HiSeq 2500 machine.
For ChIP-seq, fDNA clean up and PCR. The libraries were sequenced using an Illumina HiSeq 2500 machine.  ATAC-seq libraries were prepared using Trueprep DNA library Prep Kit V2 for Illumina (vazyme). 50,000 cells were used for each single reaction. Cells were washed in 100 μl cold PBS and resuspended in 50 μl lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.5% NP-40) for 10 min and nuclei were spun at 500g for 10 min using a refrigerated centrifuge. Then the pellet was re-suspended in 50μl transposase reaction mix and incubated at 37 °C for 30 min. The samples were purified and purified, then libraries were amplified by PCR for 13 cycles. The libraries were sequenced using an Illumina HiSeq 2500 machine.

treatment_protocol:
For XEN induction, the medium was changed to
XEN reprogramming medium the next day, and it was changed every 4 days for 12 days.

value: mouse embryonic fibroblasts (MEFs)

value: Ctr

tag: time

value: day 4 of the reprogramming process


title: CFAE-2_ATAC

status: Public on Mar 17 2022

type: SRA

country: Denmark

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: treatment

value: CFAE


title: Control5

city: Bethesda

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

country: USA

institute: NIH/JHU

description: Control

library_source: transcriptomic

data_processing:
We trimmed 15 bp from 5’-end, and 10 bp from 3’-end, to remove adapter contamination as well as low quality base calls in 3’-end.  2.7.6a.
We aligned to GRCh38 reference genome using STAR, version
We counted number of reads mapped to genes using htseq, version 0.11.4.
We identified differentially expressed genes using DESeq2, version 1.30.1 with the cutoff of 0.05 on False Discovery Rate (FDR) adjusted by Independent Hypothesis Weighting. R, version 4.0.3 (2020-10-10) and Bioconductor, version 3.11 was used.
Genome_build: GRCh38
Supplementary_files_format_and_content: Text files that contain count information

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
TruSeq unstranded total RNA with Ribo-Zero globin depletion was performed
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease states

value: Control

tag: tissue

value: Blood

value: Whole blood

tag: age

tag: Sex

value: Male

tag: race

value: White/Caucasian


title: Control2

description: Control


title: Control4

description: Control


title: Control3

description: Control


title: CFAE-1_ATAC


title: N. crassa 60min [B2-3]

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

description: replicate 3

data_processing:
According to Illumina protocol, the libraries underwent 101-bp paired-end sequencing using an Illumina NovaSeq (S4).. Basecalls performed using CASAVA version 1.8.2
For each read, the first 6 and the last nucleotides were trimmed to the point where the Phred score of an examined base fell below 20 using in-house scripts. If, after trimming, the read was shorter than 45 bp, the whole read was discarded.
Trimmed reads were mapped to the Neurospora crassa OR74A reference genome (FungiDB release 43) with hisat2 v2.1.0 indicating that reads correspond to the reverse complement of the transcripts. Alignments with quality score below 20 were excluded from further analysis.
Gene counts were produced with stringtie v1.3.3b and the python script “prepde.py” provided in the package. Stringtie was limited to reads matching the reference annotation.
LOX v1.4 was applied to the tallies for each sample for each gene to estimate gene expression levels and credible intervals across developmental stages. LOX provides relative gene expression levels standardized by the lowest sample, with credible intervals
Genome_build: Neurospora crassa OR74A (FungiDB release 43)
Supplementary_files_format_and_content: CSV and tab delimited text files including raw counts and LOX output. LOX provides relative gene expression levels standardized by the lowest sample, with credible intervals

organism: Neurospora crassa

source_name: conidia germination_PDA

growth_protocol: The project was set to compare fungal conidial germination on different culture media and at different growth temperatures. For this set of expriment the N. crassa conidial germination was sampled on Bird  medium at 37C. CULTURES were performed by applying 2 ml of the suspension of  conidia in 1.5% Tween 60 (105 - 106 conidia/ml) to the surface of medium plates that were covered with cellophane membranes. Conidia germination were monitored with microscope, and roughly over 70% individual conidia showing same development stage were used to decide the sampling time points (15, 120, 240, and 360 minutes).

extract_protocol:
For transcriptomic analysis, all tissues and perithecia were immediately and rapidly frozen in liquid nitrogen as they were sampled, then stored at -80°C. RNA was isolated from homogenized mycelia with TRI REAGENT (Invitrogen) and mRNA was purified using Dynabeads oligo(dT) magnetic separation (Invitrogen)
For purified total RNA collected from samples, strand-specific sequencing libraries were produced following the Illumina TruSeq stranded protocol.

tag: strain

tag: time point

value: 120 minutes after inoculation


title: Ctr-1_ATAC


title: N. crassa 15min [B1-1]

description: replicate 1

value: 15 minutes after inoculation


title: Blast15

description: Blast

value: Blast


title: C6FAE-2_ATAC


title: Control1

description: Control


title: Blast13

description: Blast


title: C6AE-2_ATAC


title: C6FAE-1_ATAC


title: Control12

description: Control


title: C6AE-1_ATAC


title: Basal-2_ATAC

value: Basal


title: Blast11

description: Blast


title: Basal_ATAC


title: Control10

description: Control


title: Blast10

description: Blast


title: AE-2_ATAC

value: AE


title: Blast9

description: Blast


title: AE-1_ATAC


title: Blast8

description: Blast


title: Blast6

description: Blast


title: Blast14

description: Blast


title: 6FAE-1_ATAC


title: Blast7

description: Blast

value: American Indian


title: 6FAE-2_ATAC


title: Blast4

description: Blast


title: Ctrin-1a_ChIP

tag: chip antibody

value: input


title: Blast3

description: Blast

value: Asian


title: Blast5

description: Blast


title: Blast12

description: Blast


title: CFAEin-1a_ChIP

value: mouse embryonic fibroblasts (MEFs)


title: CtrK27-1a_ChIP

value: anti-H3K27me3 (Millipore)


title: CFAEK4-1a_ChIP

value: day 4 of the reprogramming process

value: anti-H3K4me3 (Abcam)


title: CtrK4-1a_ChIP


title: Blast2

description: Blast


title: C6FAEin-1a_ChIP


title: Hct116_RNAseq_R_3

city: Seattle

first: Heshani

middle: Nayanga

last: Thirimanne

state: WA

address: 1100 Fairview AV N, D2-213

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

description:
Replicate 3
Hct116_RNASeq_DGE.txt

data_processing:
STAR v2.7.1 with 2-pass mapping was used to align paired-end reads to hg19 and GENCODE gene annotation v31lift37.
FastQC 0.11.8 and RseQC 3.0.0 were used for QC.
FeatureCounts in Subread 1.6.5 was used to quantify gene-level expression.
Bioconductor package edgeR 3.26.8 was used determine differential gene expression.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Tab-delimited text file with CPM and FPKM values for each sample and differentially expressed genes.

source_name: RNA-Seq

extract_protocol:
Total RNA was isolated from three million cells per sample using the Quaigen RNAeasy Mini Kit (Cat# 74104) following the manufacturer's instructions.
Libraries for Hct116  were prepared using TruSeq RNA Samples Prep Kit v2 (Illumina Inc., San Diego CA, USA). Libraries for U5NSCs were prepared using TruSeq Stranded mRNA kit.

value: Hct116 human colorectal cancer cell line

tag: genotype


title: Blast1

description: Blast

value: Blood


title: CFAEK27-1a_ChIP

value: CFAE


title: C6FAEK4-1a_ChIP


title: Hct116_RNAseq_R_1

description:
Replicate 1
Hct116_RNASeq_DGE.txt


title: Hct116_RNAseq_R_2

description:
Replicate 2
Hct116_RNASeq_DGE.txt


title: Hct116_RNAseq_Del_2

description:
Replicate 2
Hct116_RNASeq_DGE.txt


title: Hct116_RNAseq_Del_3

description:
Replicate 3
Hct116_RNASeq_DGE.txt


title: C6FAEK27-1a_ChIP


title: Hct116_RNAseq_Del_1

description:
Replicate 1
Hct116_RNASeq_DGE.txt


title: C6AEin-1a_ChIP


title: Hct116_RNAseq_WT_2

description:
Replicate 2
Hct116_RNASeq_DGE.txt

value: wild-type


title: Hct116_RNAseq_WT_3

description:
Replicate 3
Hct116_RNASeq_DGE.txt


title: BasalK4-1a_ChIP


title: C6AEK27-1a_ChIP


title: U5NSC_Del_IgG_021820

data_processing:
Library strategy: CUT&RUN
We used Bowtie2 with options "--end-to-end --very sensitive --no-overlap --no-dovetail --nounal --no-mixed --no-discordant -q -I -10 -X 700" to map the 25bp paired-end Illumina reads to hg19 genome.
CPM normalized bigwig files were generated using bedtools genomecov. Merged bigwig files that represents all three replicates were generating by merging bam files and then converting to bw.
Merged peak set for each target was used for further analysis. FeatureCounts in Subread 1.5.6 was used to count reads mapped to merged peaks in each samples.
Bioconductor package edgeR 3.26.8 was used to detect differential peaks between conditions. The filitered count matrix was normalized by TMM method.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Bedgraph
Supplementary_files_format_and_content: Bigwig files generated using bedtools genomecov.
Supplementary_files_format_and_content: Bigwig files representing 3 replicates (bam files from 3 replicates merged and converted to bw)

source_name: AutiCUTandRUN

value: U5 neural stem cells

tag: antibody

value: Rabbit normal IgG Santa Cruz sc-2027


title: Hct116_RNAseq_WT_1

description:
Replicate 1
Hct116_RNASeq_DGE.txt


title: U5NSC_Del_Myc_3

description:
Replicate 3
U5NSC_Myc_Del_merged.bw

value: Myc Cell Signaling Tech D3N8F Cat #13987


title: AEin-1a_ChIP


title: AEK4-a1_ChIP


title: 6FAEK4-1a_ChIP


title: Basalin-1a_ChIP


title: U5NSC_WT_H3K27ac_121219

value: H3K27ac Abcam Cat #ab45173


title: AEK27-1a_ChIP


title: U5NSC_Del_Myc_2

description:
Replicate 2
U5NSC_Myc_Del_merged.bw


title: U5NSC_WT_Myc_2

description:
Replicate 2
U5NSC_Myc_WT_merged.bw


title: U5NSC_WT_Myc_3

description:
Replicate 3
U5NSC_Myc_WT_merged.bw


title: BasalK27-1a_ChIP

value: Basal


title: U5NSC_Del_Myc_1

description:
Replicate 1
U5NSC_Myc_Del_merged.bw


title: U5NSC_WT_IgG_021820


title: U5NSC_WT_Myc_1

description:
Replicate 1
U5NSC_Myc_WT_merged.bw


title: C6AEK4-1a_ChIP


title: U5NSC_Del_Jun_3

description:
Replicate 3
U5NSC_Jun_Del_merged.bw

value: cJun Santa Cruz Cat #sc-1694


title: 6FAEK27-1a_ChIP


title: K562 H3K4me2

city: Ithaca

first: Charles

middle: G

last: Danko

address: Hungerford Hill Rd

institute: Baker Institute

data_processing: Data from each experiment was aligned to genome assemblies as following:  i.) MNase ChIP-seq reads were aligned to hg19 merged to D.iulia assembly (Lewis et al., 2019). All positions with sequence similarity between the two genomes were masked using bedtools maskfasta;  ii.) ChRO-seq data was aligned to hg19 merged to the D.melanogaster dm3 genome assembly. All positions with sequence similarity between the two genomes were masked using bedtools maskfasta;  iii.) CUT&RUN was aligned to hg19 merged to S.cerevisiae SacCer1;  iv.) ATAC-seq was only aligned to hg19.   Masking hg19 was performed with BedTools maskfasta (Quinlan and Hall, 2010). All sequencing data was aligned using bowtie2 version 2.3.5.1 (Langmead and Salzberg, 2012) with parameters: --no-discordant --no-dovetail --no-unal --no-mixed. Reads mapping multiple times were removed with samtools view (Li et al., 2009), parameter: -F 256. The remaining reads were converted to paired-end BigWig files using BedTools and visualized in the WashU genome browser version 46.2 (Li et al., 2019; Zhou et al., 2011).  Supplementary_files_format_and_content: We only provide BigWig files for untreated samples due to normalization, which was performed from BAM files to preserve the identity of each read pair. In our experiments, both the human and spike-in samples were mixed and treated with MNase together, before the antibody incubation. To correct IP signals for biases in MNase cutting efficiency, handling, and other errors, we used the spike adjusted procedure (SAP) method (Bonhoure et al., 2014). We assume that ChIP-seq data reflects a linear combination of three factors: signal from the mark of interest, background which may be partially correlated with the mark, and random noise. SAP assumes that the background signals should be the same in treated and untreated samples and enforces this assumption by subtracting the expected background read count observed in the input.

source_name: Human K562 cells

extract_protocol: Library prep was performed using the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645S). The barcodes used were purchased from NEB:NEBNext Multiplex Oligos for Illumina (E6440S).

tag: assay

value: ChIP-seq

value: untreated

tag: replicate


title: U5NSC_Del_Jun_2

description:
Replicate 2
U5NSC_Jun_Del_merged.bw


title: U5NSC_WT_Jun_3

description:
Replicate 3
U5NSC_Jun_WT_merged.bw


title: U5NSC_WT_Jun_1

description:
Replicate 1
U5NSC_Jun_WT_merged.bw


title: U5NSC_Del_Jun_1

description:
Replicate 1
U5NSC_Jun_Del_merged.bw


title: U5NSC_WT_Jun_2

description:
Replicate 2
U5NSC_Jun_WT_merged.bw


title: Hct_Del_K4me2

source_name: CUTandRUN

value: H4K4me2 Cell Signaling Tech 9725


title: 6FAEin-1a_ChIP

value: mouse embryonic fibroblasts (MEFs)

value: input


title: Hct_WT_K4me1

value: H3K4me1 Abcam Cat# ab8895


title: Hct_WT_K4me2


title: Kidney Wild type Meningococci dose: 5x

type: RNA

city: Oslo

first: Ole

middle: Kristoffer

last: Olstad

address: Kirkeveien 166

department: Medical Biochemistry

country: Norway

institute: OUS

hyb_protocol: Labeled and fragmented single stranded cDNAs were hybridized to GeneChip® Clariom_S_Mouse  Arrays (Affymetrix) containing >20,000 well-annotated genes. The arrays were washed and stained using FS-450 fluidics station (Affymetrix).

scan_protocol: Signal intensities were detected by Hewlett Packard Gene Array Scanner 3000 7G (Hewlett Packard, Palo Alto, CA, USA). The scanned images were processed using AGCC (AffymetrixGeneChip Command Console) software.

data_processing: For statistical analysis the Affymetrix.CEL files (containing probe intensities) were imported into Partek Genomics Suite software (Partek, Inc. MO, USA). Robust microarray analysis (RMA) yielding normalized log2 transformed signal intensities were applied for normalization (http://bip.weizmann.ac.il/toolbox/overview/Partek_Users_Guide.pdf).

label: biotin

organism: Sus scrofa

source_name: Kidney Wild type Meningococci dose: 5x

label_protocol: 100 ng of total RNA from each sample was subjected to analysis using the GeneChip 3’ IVT Express Kit following the manufacturer's (Affymetrix , Santa Clara, CA) recommended protocol.

growth_protocol: Two groups of eight pigs each received exponentially increasing numbers of NmLPS+ or NmLPS− intravenously by doubling the infusion rate of bacteria every 30 min during 4 h.

extract_protocol: Total RNA was extracted from the supernatant after homogenization of 20 mg tissue, or from whole blood, using the TRIzol method (Invitrogen) and the RNeasy MinElute cleanup kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.

treatment_protocol: Biopsies were obtained from the lungs, liver, spleen, kidney, jejunum, colon, and muscle (vastus lateralis) immediately after euthanasia of the pigs and thereafter rapidly frozen on liquid nitrogen.

tag: breed

value: Norwegian landrace


title: Kidney Mutant Meningococci dose: 5x

source_name: Kidney Mutant Meningococci dose: 5x


title: Hct_Del_IgG_101918

source_name: AutoCUTandRUN

value: Hct116 human colorectal cancer cell line


title: Kidney Control 2

source_name: Kidney Control


title: Kidney Wild type Meningococci dose: 1x

source_name: Kidney Wild type Meningococci dose: 1x


title: Hct_R_IgG_101918


title: Hct_Del_K4me1


title: Kidney Wild type Meningococci dose: 20x

source_name: Kidney Wild type Meningococci dose: 20x


title: Hct_WT_IgG_101918


title: Kidney Control 1


title: Kidney Control 3

source_name: Kidney Cotrol


title: Hct_R_Jun_3

description:
Replicate 3
Hct116_Jun_R_merged.bw


title: Hct_R_Jun_2

description:
Replicate 2
Hct116_Jun_R_merged.bw


title: Spleen Mutant Meningococci dose: 5x

source_name: Spleen Mutant Meningococci dose: 5x


title: Spleen Wild type Meningococci dose: 5x

source_name: Spleen Wild type Meningococci dose: 5x


title: Spleen Control 3

source_name: Spleen Control


title: Spleen Control 1


title: Hct_Del_Jun_3

description:
Replicate 3
Hct116_Jun_Del_merged.bw


title: Hct_R_Jun_1

description:
Replicate 1
Hct116_Jun_R_merged.bw


title: Hct_Del_Jun_2

description:
Replicate 2
Hct116_Jun_Del_merged.bw


title: Kidney Mutant Meningococci dose: 20x

source_name: Kidney Mutant Meningococci dose: 20x


title: Kidney Mutant Meningococci dose: 1x

source_name: Kidney Mutant Meningococci dose: 1x


title: Spleen Control 2


title: Hct_WT_Jun_2

description:
Replicate 2
Hct116_Jun_WT_merged.bw


title: Spleen Mutant Meningococci dose: 20x

source_name: Spleen Mutant Meningococci dose: 20x


title: Lung Cotrol 3

source_name: Lung Cotrol


title: Hct_WT_Jun_3

description:
Replicate 3
Hct116_Jun_WT_merged.bw


title: Spleen Wild type Meningococci dose: 1x

source_name: Spleen Wild type Meningococci dose: 1x


title: Spleen Mutant Meningococci dose: 1x

source_name: Spleen Mutant Meningococci dose: 1x


title: Hct_R_Myc_2

description:
Replicate 2
Hct116_Myc_R_merged.bw


title: Lung Control 2

source_name: Lung Control


title: Hct_Del_Myc_3

description:
Replicate 3
Hct116_Myc_Del_merged.bw


title: Lung Mutant Meningococci dose: 5x

source_name: Lung Mutant Meningococci dose: 5x


title: Lung Control 1


title: Lung Wild type Meningococci dose: 5x

source_name: Lung Wild type Meningococci dose: 5x


title: Lung Wild type Meningococci dose: 20x

source_name: Lung Wild type Meningococci dose: 20x


title: Hct_Del_Jun_1

description:
Replicate 1
Hct116_Jun_Del_merged.bw

source_name: AutoCUTandRUN


title: Liver Control 3

source_name: Liver Control


title: Spleen Wild type Meningococci dose: 20x

source_name: Spleen Wild type Meningococci dose: 20x


title: Hct_WT_Myc_3

description:
Replicate 3
Hct116_Myc_WT_merged.bw


title: Hct_WT_Myc_2

description:
Replicate 2
Hct116_Myc_WT_merged.bw


title: Hct_Del_Myc_1

description:
Replicate 1
Hct116_Myc_Del_merged.bw


title: Hct_WT_Myc_1

description:
Replicate 1
Hct116_Myc_WT_merged.bw


title: Lung Mutant  Meningococci dose: 20x

source_name: Lung Mutant  Meningococci dose: 20x


title: Lung Mutant Meningococci dose: 1x

source_name: Lung Mutant Meningococci dose: 1x


title: Hct_R_IgG_111620


title: Hct_WT_Jun_1

description:
Replicate 1
Hct116_Jun_WT_merged.bw


title: Hct_Del_Myc_2

description:
Replicate 2
Hct116_Myc_Del_merged.bw


title: Lung Wild type Meningococci dose: 1x

source_name: Lung Wild type Meningococci dose: 1x


title: Hct_R_Myc_1

description:
Replicate 1
Hct116_Myc_R_merged.bw


title: Hct_WT_IgG_111620


title: Hct_Del_IgG_111620


title: Liver Wild type Meningococci dose: 1x

source_name: Liver Wild type Meningococci dose: 1x


title: Liver Control 1


title: Hct_R_Myc_3

description:
Replicate 3
Hct116_Myc_R_merged.bw


title: Hct_Del_H327me3_3

description:
Replicate 3
Hct116_H3K27me3_Del_merged.bw

value: H3K27me3 Cell Signaling Tech Cat# 9733S


title: Liver Wild type Meningococci dose: 20x

source_name: Liver Wild type Meningococci dose: 20x


title: Liver Control 2


title: Liver Mutant Meningococci dose: 5x

source_name: Liver Mutant Meningococci dose: 5x


title: Liver Mutant Meningococci dose: 1x

source_name: Liver Mutant Meningococci dose: 1x


title: Hct_R_H3K27me3_1

description:
Replicate 1
Hct116_H3K27me3_R_merged.bw


title: Hct_R_H3K27me3_3

description:
Replicate 3
Hct116_H3K27me3_R_merged.bw


title: Hct_WT_H3K27me3_3

description:
Replicate 3
Hct116_H3K27me3_WT_merged.bw


title: Hct_R_H3K27me3_2

description:
Replicate 2
Hct116_H3K27me3_R_merged.bw


title: Hct_Del_H327me3_2

description:
Replicate 2
Hct116_H3K27me3_Del_merged.bw


title: Hct_R_IgG_030118

source_name: CUTandRUN Direct Ligation


title: bovine_LKidney_MIXNTE_36_batch2

city: Lexington

first: James

middle: C

last: Matthews

state: Kentucky

address: 325 Cooper Drive

department: Animal and Food Sciences

institute: University of Kentucky

hyb_protocol: The biotinylated cRNAs were further fragmented and used as probes to hybridize the gene chips in the GeneChip Hybridization Oven 640 (Affymetrix). After hybridization, the chips were washed and stained on a GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Samples were analyzed in two batches. The reaction image and signals were read with a GeneChip Scanner (GCS 3000, 7G; Affymetrix).

data_processing: Data were collected using the GeneChip Operating Software (GCOS, version 1.2; Affymetrix). The raw expression intensity values from the GCOS were imported into Partek Genomics Suite software (PGS, version 6.6; Partek Inc., St. Louis, MO). For GeneChip background correction, the algorithm of Robust Multichip Averaging adjusted with probe length and GC oligo contents was implemented. The background-corrected data were further converted into expression values using quantile normalization across all the chips and median polish summarization of multiple probes for each probe set.

organism: Bos taurus

source_name: bovine left kidney

label_protocol: Three µg of RNA for each sample were reverse-transcribed to cDNA and then transcribed from cDNA to cRNA. cRNA samples were then labeled with biotin.

extract_protocol: Mid-cross sections of the left kidney were placed in foil packs, snap-frozen in liquid nitrogen, and stored at -80° C. Total RNA was extracted from the frozen kidney samples using TRIzol Reagent following the manufacturer's instructions. The RNA concentrations were determined using a NanoDrop ND-1000 Spectrophotometer, and the integrity of total RNA was examined by gel electrophoresis using an Agilent 2100 Bioanalyzer System.

value: MIXNTE

value: left kidney


title: bovine_LKidney_ISeTE_33_batch2

value: ISeTE


title: Hct_WT_H3K27me3_2

description:
Replicate 2
Hct116_H3K27me3_WT_merged.bw

value: wild-type


title: bovine_LKidney_ISeNTE_35_batch2

value: ISeNTE


title: Hct_WT_H3K27me3_1

description:
Replicate 1
Hct116_H3K27me3_WT_merged.bw


title: Hct_Del_H327me3_1

description:
Replicate 1
Hct116_H3K27me3_Del_merged.bw


title: Liver Mutant Meningococci dose: 20x

source_name: Liver Mutant Meningococci dose: 20x


title: Hct_WT_IgG_030118

value: Rabbit normal IgG Santa Cruz sc-2027


title: Hct_Del_IgG_030118


title: Hct_R_H3K27ac_3

description:
Replicate 3
Hct116_H3K27ac_R_merged.bw

value: H3K27ac Abcam Cat #ab45173


title: Liver Wild type Meningococci dose: 5x

source_name: Liver Wild type Meningococci dose: 5x


title: bovine_LKidney_MIXNTE_32_batch2


title: Hct_R_H3K27ac_2

description:
Replicate 2
Hct116_H3K27ac_R_merged.bw


title: bovine_LKidney_MIXNTE_26_batch1


title: bovine_LKidney_MIXNTE_25_batch1


title: bovine_LKidney_ISeNTE_28_batch1


title: bovine_LKidney_MIXTE_29_batch2

value: MIXTE


title: bovine_LKidney_MIXTE_34_batch1


title: Hct_R_H3K27ac_1

description:
Replicate 1
Hct116_H3K27ac_R_merged.bw


title: bovine_LKidney_MIXTE_23_batch1


title: Hct_Del_H3K27ac_3

description:
Replicate 3
Hct116_H3K27ac_Del_merged.bw


title: bovine_LKidney_ISeTE_22_batch1


title: bovine_LKidney_MIXNTE_19_batch1


title: Hct_WT_H3K27ac_3

description:
Replicate 3
Hct116_H3K27ac_WT_merged.bw


title: Hct_Del_H3K27ac_1

description:
Replicate 1
Hct116_H3K27ac_Del_merged.bw


title: Hct_WT_H3K27ac_1

description:
Replicate 1
Hct116_H3K27ac_WT_merged.bw


title: bovine_LKidney_ISeNTE_20_batch1


title: bovine_LKidney_MIXTE_17_batch2


title: bovine_LKidney_ISeTE_16_batch1


title: bovine_LKidney_MIXNTE_14_batch2


title: bovine_LKidney_ISeTE_18_batch1


title: bovine_LKidney_ISeTE_24_batch2


title: BRM-ATPase_mut_R2

city: Stockholm

first: Ann-Kristin

last: Östlund-Farrants

address: Svante Arrheniusväg 20 C

department: Department of Molecular Biosciences, The Wenner-Gren Institute

country: Sweden

institute: Stockholm University

description: C33A expressing exogenous ATPase defficient BRM - Replicate 2

data_processing:
Sequencing of 1ug of RNA was performed with an Illumina HiSeq 2500, with 50 million reads depth. Reads were mapped with Tophat/2.0.4 to the Human genome assembly, build GRCh37. Gene counts were generated using HTseq/0.6.1 on bam files with duplicates included.
Alternative splicing was analyzed using MISO (Katz et al. 2010), and exons with a Bayes factor >10 were considered differentially spliced. Exons showing opposite effects in the two replicates or in two different groups were discarded, as were exons with the same 5’ or 3’ and less than 50% of the length respect to the longest exon form. For our analyses we only counted a given exon once, even if it was reported more than once in the MISO output.
Differential gene expression was determined using DESeq2 with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: Tabular files generated with DESeq2 include the GeneID, Base mean, log2(FC), StdErr, Wald-Stats, P-value and P-adj
Supplementary_files_format_and_content: Txt files generated with MISO include sample1, sample2, gene, bayesF, psi1, psi2, iso1, iso2, log2-PSI, iso1up_in_s1 and iso2up_in_s2

source_name: C33A cell line

growth_protocol: Human C33A cells were cultured at 37ºC and 5% CO2 in DMEM (HyClone) medium supplemented with 10% FBS, 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol:
RNA was extracted using Tri-reagent (Ambion/ThermoFisher), treated with DNAse I (ThermoFisher) and cDNA was synthesized with SuperScript III (Invitrogen/ThermoFisher) and oligodT according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C33A cells were transiently transfected for expression of exogenous SWI/SNF ATPase subunits BRG1 and BRM using Lipofectamin 2000 (Invitrogen) according to the manufacturer’s instructions for 48 hours before harvesting.

value: C33A cell line

tag: plasmid transfected


title: bovine_LKidney_MIXTE_15_batch2


title: BRM_R2

description: C33A expressing exogenous BRM - Replicate 2

value: pCG-hBrm


title: BRG1-ATPase_mut_R2

description: C33A expressing exogenous ATPase defficient BRG1 - Replicate 2


title: BRG1_R2

description: C33A expressing exogenous BRG1 - Replicate 2


title: pOPRSVI_R2

description: C33A expressing control plasmid pOPRSVI - Replicate 2

value: pOPRSVI


title: riboRNAseq_WT3T

city: Duluth

first: Ruifeng

last: Cao

state: MN

address: 1035 University Dr

department: Biomedical Sciences

institute: University of Minnesota

description: total mRNA

data_processing:
Reads were adapter-trimmed using the FASTX toolkit.
contaminant sequences (rRNA, tRNA) removed using bowtie, and reads aligned to a reference genome  using STAR.
Cufflinks was used to quantify reads and calculate reads per kilobase of transcript per million mapped reads (RPKM) for each transcript. Translational efficiency (TE) for each transcript was calculated by dividing RPKM values of the RPF libraries by RPKM values of the total RNA libraries.
Genome_build: mm10
Supplementary_files_format_and_content: csv,xlsx;Normalized gene count, differential expressed genes

source_name: wildtype mice

growth_protocol: The breeders of Bmal1+/- mice 1 (stock No. 009100), Bmal1flx/flx mice2 (stock No. 007668) and L7-Cre3 (stock No. 004146) mice on a C57BL/6J background were purchased from the Jackson Laboratory. Animals were housed under a 12h/12h light/dark cycle with ad libitum access to mouse chow and water. The room temperature was maintained at 23 ± 1℃ and the humidity was 35-45%. Bmal1+/- mice were crossed with Bmal1+/- mice to obtain Bmal1-/-  (KO) and Bmal1+/+ (WT) littermates. Bmal1flx/flx mice were crossed with L7-Cre mice to obtain Bmal1flx/flx: L7-Cre mice and Bmal1flx/flx littermates. Mouse genotypes were confirmed by tail biopsy and polymerase chain reaction.

extract_protocol:
To prepare ribosome profiling libraries, snap-frozen cerebellar tissue (rapidly dissected on ice) was homogenized in Polysome buffer (20 mM Tris·Cl (pH 7.4), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 µg/ml Cycloheximide, 1% Triton X-100, 25 U/ml DNase I). A fraction of the lysate was digested with RNAse I (Ambion; 100U/μL) (footprints) and purified through a MicroSpin S-400 column (GE Healthcare) to size-select for monosomes, while the remaining fraction was kept as an internal mRNA control (total RNA; RNA sequencing). All samples were depleted of ribosomal RNA using the Ribo-Zero Gold (Human/Mouse/Rat) Kit (Illumina). The footprint samples were size-selected for bands running between 28 and 34 nucleotides on a 15% TBE-Urea polyacrylamide gel (ThermoFisher Scientific), while total RNA samples were heat fragmented by incubating at 95 °C in an alkaline fragmentation solution (50 mM NaCO3 pH 9.2, 2 mM EDTA) for 40 min, yielding comparably sized fragments to footprints. The quality and concentration of samples was assessed by running an Agilent Small RNA chip (Agilent Technologies).
sequencing libraries were generated using the NEXTflexTM Small RNA Sequencing Kit v3, according to the manufacturer’s instructions

tag: strain background

value: cerebellar cell

tag: kit

value: NEXTflexTM Small RNA Sequencing Kit v3


title: riboRNAseq_WT3F

description: footprint

tag: cell type


title: bovine_LKidney_MIXNTE_13_batch2

tag: treatment


title: bovine_LKidney_MIXTE_12_batch1

tag: tissue


title: bovine_LKidney_ISeNTE_11_batch2


title: Hct_Del_H3K27ac_2

description:
Replicate 2
Hct116_H3K27ac_Del_merged.bw


title: Hct_WT_H3K27ac_2

description:
Replicate 2
Hct116_H3K27ac_WT_merged.bw


title: riboRNAseq_WT2T

description: total mRNA


title: bovine_LKidney_ISeNTE_10_batch1


title: bovine_LKidney_MIXNTE_9_batch1


title: bovine_LKidney_MIXTE_7_batch1


title: bovine_LKidney_ISeNTE_8_batch2


title: riboRNAseq_WT2F

description: footprint


title: BRM_R1

description: C33A expressing exogenous BRM - Replicate 1


title: riboRNAseq_KO3T

description: total mRNA

source_name: knockout mice


title: riboRNAseq_WT1T

description: total mRNA


title: bovine_LKidney_ISeTE_6_batch2


title: riboRNAseq_KO3F

description: footprint


title: riboRNAseq_KO2T

description: total mRNA


title: BRG1-ATPase_mut_R1

description: C33A expressing exogenous ATPase defficient BRG1 - Replicate 1


title: riboRNAseq_KO1T

description: total mRNA


title: BRG1_R1

description: C33A expressing exogenous BRG1 - Replicate 1


title: bovine_LKidney_ISeNTE_5_batch2


title: pOPRSVI_R1

description: C33A expressing control plasmid pOPRSVI - Replicate 1


title: riboRNAseq_KO1F

description: footprint


title: M13 rep2

city: beijing

first: li

last: lei

address: 17 Panjiayuan Nanli

country: China

institute: Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4). Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set then expression level of gene was calculated by RSEM (v1.2.12).
Differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: KYSE150 cells

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. Total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

tag: cell line

value: KYSE150 cells

value: esophageal squamous cell carcinoma cells

value: transfected with caspase-8 M13 mutant


title: BRM-ATPase_mut_R1

description: C33A expressing exogenous ATPase defficient BRM - Replicate 1


title: bovine_LKidney_ISeTE_3_batch2


title: Sample_21

type: genomic

first: Simon

last: Merid

state: Stockholm

address: Sjukhusbacken 10

institute: Karolinska Institutet

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using an Illumina iScan bead-array reader with standard recommended Illumina scanner settings

data_processing: GenomeStudio 2011.1 with the methylation analysis module

label: Cy3 and Cy5

source_name: COPD KOLIN

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from bronchoalveolar lavage samples using Qiagen's Allprep DNA/RNA/protein mini kit according to standard instructions

tag: Sex

value: female

tag: age

tag: copd

value: Smokers with normal LF

tag: smoking

value: 2 (smoker)


title: M10 rep2

value: transfected with caspase-8 M10 mutant


title: Sample_3

value: male

value: 1 (Non-smoker)


title: bovine_LKidney_MIXTE_4_batch2

value: left kidney


title: Xdh.KO.HOMO_rep4

city: Tampa

first: Alexander

last: Starushchenko

state: FL

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

institute: University of South Florida, College of medicine

data_processing:
Genomic Sciences and Precision Medicine Center at the Medical College of Wisconsin completed sequencing on the NovaSeq6000 (Illumina) with paired-end 150 base pair reads generated at ~80 million total reads per sample.
Sequencing reads were aligned to the rat Rnor_6.0.98 (Ensemble) transcriptome and processed through the MAPR-Seq Workflow with differential expression analysis completed using Bioconductor, edgeR v 3.8.6 software.
Genes with a false discovery rate (FDR) <0.05 and an absolute fold change ≥ 1.5 were initially filtered and considered significantly differentially expressed.
Assembly: Rnor_6.0.98
Supplementary files format and content: excel tables with gene counts (GeneCount.xlsx) and differential analysis results (DEAnalyses_pairwise.xlsx)

organism: Rattus norvegicus

source_name: Kidney cortex

extract_protocol:
Flash-frozen kidney cortex tissue was used. Trizol extraction protocol was used.
RNA libraries were prepared according to the manufacturer’s protocols utilizing Illumina’s TruSeq Stranded mRNA library kit.
Final assessment, quantification, and pooling of the RNAseq libraries were completed with qPCR (Kapa Library Quantification Kit, Kapa Biosystems) and DNA high sensitivity fragment analysis (Agilent, average size 310 bp).

tag: strain

value: Homozygote

value: 6 weeks old

value: Male

value: Kidney cortex


title: Sample_20


title: Xdh.KO.HOMO_rep3

tag: genotype


title: Xdh.KO.HOMO_rep2


title: M13 rep1


title: bovine_LKidney_ISeTE_1_batch1

value: ISeTE


title: Xdh.KO.HOMO_rep1


title: M10 rep1


title: M6 rep1

value: transfected with caspase-8 M6 mutant


title: bovine_LKidney_ISeNTE_2_batch1

value: ISeNTE


title: M6 rep2

value: KYSE150 cells


title: Sample_31

value: COPD


title: Xdh.KO.HET_rep5

value: Heterozygote


title: Sample_15


title: Xdh.KO.HET_rep4


title: bovine_LAdrenal_MIXNTE_36

scan_protocol: The reaction image and signals were read with a GeneChip Scanner (GCS 3000, 7G; Affymetrix)

source_name: bovine left adrenal

extract_protocol: Mid-cross sections of the left adrenal gland were placed in foil packs, snap-frozen in liquid nitrogen, and stored at -80° C. Total RNA was extracted from the frozen adrenal samples using TRIzol Reagent following the manufacturer's instructions. The RNA concentrations were determined using a NanoDrop ND-1000 Spectrophotometer, and the integrity of total RNA was examined by gel electrophoresis using an Agilent 2100 Bioanalyzer System.

value: MIXNTE

value: left adrenal


title: M4 rep2

value: esophageal squamous cell carcinoma cells

value: transfected with caspase-8 M4 mutant


title: bovine_LAdrenal_ISeNTE_35


title: Sample_25

value: male

value: Smokers with normal LF

value: 2 (smoker)


title: bovine_LAdrenal_MIXTE_34

value: MIXTE


title: M4 rep1


title: Xdh.KO.HET_rep1

value: 6 weeks old


title: Sample_12

value: female

value: 1 (Non-smoker)


title: bovine_LAdrenal_MIXNTE_32


title: Sample_13


title: Xdh.WT_rep3

value: Wild-type

value: Male

value: Kidney cortex


title: bovine_LAdrenal_MIXTE_29


title: WT rep1

value: KYSE150 cells

value: transfected with wild-type caspase-8


title: E0771 Cells: Interferon-beta_Replicate 2

city: Boston

first: David

middle: J.

last: Waxman

state: MA

address: 5 Cummington Mall

department: Department of Biology and Bioinformatics Program

institute: Boston University

description:
polyA-selected RNA, stranded library
G180_M11

data_processing:
RNA-seq data was processed using a custom pipeline, as described in Connerney et al., 2017 (PMID: 28323953)
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) RNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene.
Differential expression analysis was performed with edgeR as described in Robinson et al., 2010 (PMID: 19910308)
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel files contain differential expression data (ratio, fold-change, FPKM for treated sample (Intensity-1), FPKM for vehicle control (Intensity-2), adjusted p-value) for 4 pairwise comparisons: 4HC vs Vehicle control, 4HC + IFNAR1 antibody vs Vehicle control, Interferon-beta vs Vehicle control, and 4HC + IFNAR1 antibody vs 4HC, respectively numbered as Experiments # 798-801.

molecule: polyA RNA

source_name: E0771_cultured-cells_total RNA fraction

growth_protocol: Cells were cultured in RPMI-1640 medium, 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C under a humidified 5% CO2 atmosphere

extract_protocol:
Trizol (cat. # 15596018, Invitrogen, Carlsbad, CA) was used to extract RNA from cells in one well of a 6-well plate. RNA was resuspended in ultrapure water and quantified.
Polyadenylated mRNA was isolated from 1 μg of total cellular RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module (cat. #E7490, New England Biolabs) and used for lllumina RNA-seq library preparation using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (cat. #E7420L, New England Biolabs), NEBNext® Multiplex Oligos for Illumina® Dual Index Primers Set 1 (cat. #E7600, New England Biolabs), and AMPure® XP Beads (cat. #A63881, Beckman Coulter Inc., Indianapolis, IN) per the manufacturer’s instructions.

treatment_protocol: Cells were treated for 4 h with 4HC (4-hydroperoxy-cyclophosphamide) at 4.2 uM (IC50-range drug concentration) using cells seeded the prior day at 50,000 cells per well of a 6-well plate (cat. #10861-696, VWR). Cells were then washed once with PBS and incubated in fresh media for an additional 68 h, i.e., a total of 72 h after the start of drug treatment, at which time total cellular RNA was isolated using Trizol. Where indicated, cells were treated with 10 µg/mL monoclonal anti-mouse IFNα/β receptor subunit 1 (IFNAR-1) antibody (clone MAR1-5A3, BioXCell, West Lebanon, NH), which was added to the cells together with 4HC for 4 h, as above. The culture media was then removed, and the cells were washed once in PBS before adding fresh media containing 10 µg/mL IFNAR-1 antibody for an additional 68 h prior to harvesting cells for RNA isolation. Where indicated, cells were treated with recombinant mouse IFNβ1 (cat. # 581302, BioLegend, San Diego, CA) at 27.8 U/mL for 4 h. Cells were then washed with PBS, fresh media was replaced, and cells were harvested 68 h later for RNA isolation.

value: Interferon-beta (27.8 U/ml) for 4 h, then collect cells 2 h later, synchronized with 72 h controls


title: Xdh.WT_rep1


title: Sample_29

value: COPD


title: Xdh.WT_rep4


title: E0771 Cells: Interferon-beta_Replicate 3

description:
polyA-selected RNA, stranded library
G180_M12


title: E0771 Cells: Interferon-beta_Replicate 1

description:
polyA-selected RNA, stranded library
G180_M10


title: Sample_2


title: E0771 Cells: 4HC+IFNAR-1 Ab_Replicate 3

description:
polyA-selected RNA, stranded library
G180_M9

value: 4.2 uM 4-HC + IFNAR1 antibody for 4 h, then collect cells 68 h later, at 72 h


title: Sample_10


title: bovine_LAdrenal_ISeTE_33

value: ISeTE

value: left adrenal


title: Sample_32

value: male


title: U2AF1 Q157R, RNA-seq, rep2

city: New Haven

first: Giulia

last: Biancon

state: Connecticut

address: 300 George Street

department: Internal Medicine - Yale Cancer Center

description:
RNA-seq from HEL cells stably expressing mutant U2AF1 (Q157R), biological replicate 2
U2AF1_RNA_counts.txt

data_processing:
eCLIP-seq (U2AF1 eCLIP-seq, U2AF2 eCLIP-seq, U2AF1 freCLIP-seq): after duplicate removal with FastUniq and adapter trimming with Cutadapt, reads were aligned to the human genome (GRCh38.p10) with STAR (v2.7.0f, --quantMode GeneCounts), using the GENCODE Release 27 for transcript annotation. Binding sites were identfied extracting the genomic position of the crosslinked nucleotide right after the end of each sequenced read. Intron-exon junctions (interval from -40 to +10 around the 3’SS) were filtered using a coverage threshold of at least 10 reads in at least two samples. Moreover, for freCLIP-seq specifically, we considered genomic positions covered by at least 5 reads in all replicates and in an interval from -4 to +2 around the 3’SS in the light fractions (U2AF1 signal) or from -20 to -5 in the heavy fractions (U2AF2 signal). Normalization with the TMM method and differential binding analysis were performed with edgeR Bioconductor package.  RNA-seq: after duplicate removal with FastUniq, reads were aligned to the human genome (GRCh38.p10) with STAR (v2.7.0f, --quantMode GeneCounts), using the GENCODE Release 27 for transcript annotation. Normalization with the TMM method and identification of differentially expressed genes were performed with edgeR. Alternative splicing analysis was performed with rMATS v4.0.2.  TL-seq: reads were trimmed with Cutadapt and aligned to GRCh38 version 26 (Ensembl 88) with HISAT2 (default parameters and --mp 4,2). Reads aligning to annotated transcripts were quantified with HTSeq htseq-count. SAMtools was used to collect only uniquely mapped read pairs (SAM flag = 83/163 or 99/147). T-to-C mutations were identified and filtered through a customized pipeline (https://bitbucket.org/mattsimon9/timelapse_pipeline/src/master/). Normalization scale factors were calculated with edgeR using calcNormFactors (method = ‘upperquartile’). Browser tracks were made using STAR v2.5.3a. Changes in expression were evaluated with DESeq2. RNA kinetic parameters were estimated using RStan software v2.19.3 as previously reported (Schofield et al., 2018).
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: U2AF1_eCLIP_counts.txt: tab-delimited text file including gene ID (column 1) and sample-specific counts of aligned eCLIP-seq reads.
Supplementary_files_format_and_content: U2AF1_freCLIP_counts.txt: tab-delimited text file including gene ID (column 1) and sample-specific counts of aligned freCLIP-seq reads.
Supplementary_files_format_and_content: U2AF1_RNA_counts.txt: tab-delimited text file including gene ID (column 1) and sample-specific counts of aligned RNA-seq reads.
Supplementary_files_format_and_content: TL-seq: bedgraph files where reads are separated by the number of T-to-C mutations (0-5+) and strandedness (min/pos).

source_name: Human Erythroleukemia Cell Line (HEL)

growth_protocol: RPMI 1640 9% tetracycline-negative FBS 1% L-glutamine 1% penicillin-streptomycin

extract_protocol:
eCLIP-seq (U2AF1 eCLIP-seq, U2AF2 eCLIP-seq, U2AF1 freCLIP-seq): Zymo RNA Clean & Concentrator-5, RNA-seq: QIAGEN RNeasy Mini kit protocol, TL-seq: ThermoFisher SCIENTIFIC TRIzol
eCLIP-seq (U2AF1 eCLIP-seq, U2AF2 eCLIP-seq, U2AF1 freCLIP-seq): cell pellets were subjected to UV-crosslinking (400 mJ/cm2 UV Stratalinker 2400, STRATAGENE), lysis and sonication. RNA was partially digested with RNase I (ThermoFisher SCIENTIFIC, Cat #AM2295). RNA-protein complexes were immunoprecipitated with 12 μg anti-FLAG M2 antibody (Sigma-Aldrich, Cat #F1804) or 8 μg anti-U2AF2 antibody (Sigma-Aldrich, Cat #U4758) and Dynabeads Protein G (ThermoFisher SCIENTIFIC, Cat #10004D), followed by RNA linker ligation and P32-labeling. U2AF-RNA complexes were isolated by SDS-PAGE and transferred to nitrocellulose membranes. Excised membranes (2 fractions for freCLIP-seq: light fraction, 37-65 kD; heavy fraction, 65-110 kD) were treated with proteinase K and the RNA was isolated. Reverse transcription and library preparation were carried out according to the published protocol (Van Nostrand et al., 2016). Libraries were deep-sequenced on Illumina HiSeq 2500 system, paired-end 75 bp and on Illumina HiSeq 4000 or NovaSeq 6000 system, paired-end 100 bp.   RNA-seq: RNA libraries after rRNA depletion were sequenced on Illumina HiSeq 4000 system, paired-end 100 bp.  TL-seq: Total RNA from 4-thiouridine(s4U)-labeled and not-labeled samples was precipitated in 50% isopropanol with 1 mM DTT. After gDNA depletion and RNA purification (Agencourt RNAClean XP beads), 5 μg of total RNA was subjected to TL chemistry for one hour at 45°C followed by reducing treatment for 30 minutes at 37°C. 10 ng of RNA was used to prepare cDNA sequencing libraries (SMARTer Stranded Total RNA-Seq kit v2 - Pico Input Mammalian, with rRNA depletion step) as previously reported (Schofield et al., 2018). Libraries were sequenced on Illumina NovaSeq 6000 system, paired-end 100 bp.

treatment_protocol: Induction with doxycycline 1µg/ml for 48 hours; TL-seq: labeling with 4-thiouridine 100 µM for 2 hours

value: Doxycycline 1ug/ml x 48 hours

tag: sequencing method

value: RNA-seq

tag: stable transfection

value: U2AF1 Q157R


title: Sample_19

value: Smokers with normal LF

value: 2 (smoker)


title: Xdh.KO.HET_rep2

value: Heterozygote

value: 6 weeks old


title: WT rep2

value: esophageal squamous cell carcinoma cells


title: bovine_LAdrenal_MIXNTE_25

value: MIXNTE


title: E0771_Cells: 4HC+IFNAR-1 Ab_Replicate 2

description:
polyA-selected RNA, stranded library
G180_M8


title: bovine_LAdrenal_MIXNTE_26


title: Sample_1

value: female

value: 1 (Non-smoker)


title: bovine_LAdrenal_ISeTE_24


title: E0771 Cells: 4HC+IFNAR-1 Ab_Replicate 1

description:
polyA-selected RNA, stranded library
G180_M7


title: bovine_LAdrenal_MIXTE_23

value: MIXTE


title: U2AF1 Q157R, RNA-seq, rep1

description:
RNA-seq from HEL cells stably expressing mutant U2AF1 (Q157R), biological replicate 1
U2AF1_RNA_counts.txt


title: U2AF1 Q157R uninduced, RNA-seq, rep1

description:
RNA-seq from uninduced U2AF1 Q157R HEL cells, biological replicate 1
U2AF1_RNA_counts.txt

value: Uninduced

value: U2AF1 Q157R uninduced


title: bovine_LAdrenal_ISeTE_22

value: ISeTE


title: Xdh.WT_rep2

value: Wild-type

value: Male

value: Kidney cortex


title: bovine_LAdrenal_ISeNTE_28

value: ISeNTE

value: left adrenal


title: Sample_16

value: male

value: COPD


title: U2AF1 S34F, RNA-seq, rep1

description:
RNA-seq from HEL cells stably expressing mutant U2AF1 (S34F), biological replicate 1
U2AF1_RNA_counts.txt

value: Doxycycline 1ug/ml x 48 hours

value: RNA-seq

value: U2AF1 S34F


title: Sample_5

value: 2 (smoker)


title: Sample_18

value: female

value: Smokers with normal LF


title: U2AF1 S34F, RNA-seq, rep2

description:
RNA-seq from HEL cells stably expressing mutant U2AF1 (S34F), biological replicate 2
U2AF1_RNA_counts.txt


title: E0771 Cells: 4HC (4-OOH-cyclophosphamide)_Replicate 2

description:
polyA-selected RNA, stranded library
G180_M5

value: 4.2 uM 4-HC for 4 h, then collect cells 68 h later, at 72 h


title: E0771 Cells: 4HC (4-OOH-cyclophosphamide)_Replicate 3

description:
polyA-selected RNA, stranded library
G180_M6


title: E0771 Cells: 4HC (4-OOH-cyclophosphamide)_Replicate 1

description:
polyA-selected RNA, stranded library
G180_M4


title: U2AF1 S34F uninduced, RNA-seq, rep1

description:
RNA-seq from uninduced U2AF1 S34F HEL cells, biological replicate 1
U2AF1_RNA_counts.txt

value: Uninduced

value: U2AF1 S34F uninduced


title: E0771 Cells: control_Replicate 3

description:
polyA-selected RNA, stranded library
G180_M3

value: Vehicle control, collect cells at 72 h


title: Sample_7


title: Sample_24


title: bovine_LAdrenal_MIXNTE_19

value: MIXNTE


title: U2AF1 WT, RNA-seq, rep2

description:
RNA-seq from HEL cells stably expressing wild-type U2AF1, biological replicate 2
U2AF1_RNA_counts.txt

value: U2AF1 wild-type


title: bovine_LAdrenal_ISeTE_18

value: ISeTE


title: bovine_LAdrenal_ISeNTE_20

value: ISeNTE


title: E0771 Cells: control_Replicate 2

description:
polyA-selected RNA, stranded library
G180_M2


title: Sample_28


title: U2AF1 WT, RNA-seq, rep1

description:
RNA-seq from HEL cells stably expressing wild-type U2AF1, biological replicate 1
U2AF1_RNA_counts.txt


title: Sample_9

value: 1 (Non-smoker)


title: Sample_27


title: 4T1 Cells: Interferon-beta_Replicate 3

description:
polyA-selected RNA, stranded library
G179_M12

data_processing:
RNA-seq data was processed using a custom pipeline, as described in Connerney et al., 2017 (PMID: 28323953)
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) RNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene.
Differential expression analysis was performed with edgeR as described in Robinson et al., 2010 (PMID: 19910308)
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel files contain differential expression data (ratio, fold-change, FPKM for treated sample (Intensity-1), FPKM for vehicle control (Intensity-2), adjusted p-value) for 4 pairwise comparisons: 4HC vs Vehicle control, 4HC + IFNAR1 antibody vs Vehicle control, 4HC + IFNAR1 antibody vs 4HC, and Interferon-beta vs Vehicle control, respectively numbered as Experiments # 882-885.

source_name: 4T1_cultured-cells_total RNA fraction

treatment_protocol: Cells were treated for 4 h with 4HC (4-hydroperoxy-cyclophosphamide) at 5 uM (IC50-range drug concentration) using cells seeded the prior day at 75,000 cells per well of a 6-well plate (cat. #10861-696, VWR). Cells were then washed once with PBS and incubated in fresh media for an additional 68 h, i.e., a total of 72 h after the start of drug treatment, at which time total cellular RNA was isolated using Trizol. Where indicated, cells were treated with 10 µg/mL monoclonal anti-mouse IFNα/β receptor subunit 1 (IFNAR-1) antibody (clone MAR1-5A3, BioXCell, West Lebanon, NH), which was added to the cells together with 4HC for 4 h, as above. The culture media was then removed, and the cells were washed once in PBS before adding fresh media containing 10 µg/mL IFNAR-1 antibody for an additional 68 h prior to harvesting cells for RNA isolation. Where indicated, cells were treated with recombinant mouse IFNβ1 (cat. # 581302, BioLegend, San Diego, CA) at 250 U/mL for 4 h. Cells were then washed with PBS, fresh media was replaced, and cells were harvested 68 h later for RNA isolation.

value: Interferon-beta (250 U/ml) for 4 h, then collect cells 2 h later, synchronized with 72 h controls


title: bovine_LAdrenal_ISeTE_16

value: left adrenal


title: Sample_33

value: male


title: bovine_LAdrenal_MIXTE_15

value: MIXTE


title: 4T1 Cells: Interferon-beta_Replicate 2

description:
polyA-selected RNA, stranded library
G179_M11


title: E0771 Cells: control_Replicate 1

description:
polyA-selected RNA, stranded library
G180_M1


title: Sample_6

value: COPD


title: Sample_4

value: 2 (smoker)


title: U2AF1 S34F, U2AF1 freCLIP-seq heavy fraction, rep2

description:
U2AF1 freCLIP-seq from HEL cells stably expressing mutant U2AF1 (S34F), heavy fraction, biological replicate 2
U2AF1_freCLIP_counts.txt

value: Doxycycline 1ug/ml x 48 hours

value: freCLIP-seq

value: U2AF1 S34F


title: U2AF1 S34F, U2AF1 freCLIP-seq heavy fraction, rep1

description:
U2AF1 freCLIP-seq from HEL cells stably expressing mutant U2AF1 (S34F), heavy fraction, biological replicate 1
U2AF1_freCLIP_counts.txt


title: 4T1 Cells: Interferon-beta_Replicate 1

description:
polyA-selected RNA, stranded library
G179_M10


title: bovine_LAdrenal_MIXNTE_13


title: bovine_LAdrenal_MIXTE_17


title: U2AF1 WT uninduced, RNA-seq, rep1

description:
RNA-seq from uninduced U2AF1 WT HEL cells, biological replicate 1
U2AF1_RNA_counts.txt

value: Uninduced

value: RNA-seq

value: U2AF1 wild-type uninduced


title: 4T1 Cells: 4HC+IFNAR-1 Ab_Replicate 2

description:
polyA-selected RNA, stranded library
G179_M8

value: 5 uM 4-HC + IFNAR1 antibody for 4 h, then collect cells 68 h later, at 72 h


title: Sample_11


title: U2AF1 WT, U2AF1 freCLIP-seq heavy fraction, rep2

description:
U2AF1 freCLIP-seq from HEL cells stably expressing wild-type U2AF1, heavy fraction, biological replicate 2
U2AF1_freCLIP_counts.txt

value: U2AF1 wild-type


title: 4T1 Cells: 4HC+IFNAR-1 Ab_Replicate 3

description:
polyA-selected RNA, stranded library
G179_M9


title: 4T1 Cells: 4HC+IFNAR-1 Ab_Replicate 1

description:
polyA-selected RNA, stranded library
G179_M7


title: U2AF1 WT uninduced, RNA-seq, rep2

description:
RNA-seq from uninduced U2AF1 WT HEL cells, biological replicate 2
U2AF1_RNA_counts.txt


title: bovine_LAdrenal_MIXTE_12


title: U2AF1 WT, U2AF1 freCLIP-seq heavy fraction, rep1

description:
U2AF1 freCLIP-seq from HEL cells stably expressing wild-type U2AF1, heavy fraction, biological replicate 1
U2AF1_freCLIP_counts.txt


title: bovine_LAdrenal_ISeNTE_11


title: Sample_23

value: female


title: Sample_14


title: 4T1 Cells: 4HC (4-OOH-cyclophosphamide)_Replicate 3

description:
polyA-selected RNA, stranded library
G179_M6

value: 5 uM 4-HC for 4 h, then collect cells 68 h later, at 72 h


title: bovine_LAdrenal_ISeNTE_10

value: ISeNTE


title: U2AF1 Q157R, U2AF1 freCLIP-seq light fraction, rep2

description:
U2AF1 freCLIP-seq from HEL cells stably expressing mutant U2AF1 (Q157R), light fraction, biological replicate 2
U2AF1_freCLIP_counts.txt

value: U2AF1 Q157R


title: U2AF1 Q157R, U2AF1 freCLIP-seq heavy fraction, rep2

description:
U2AF1 freCLIP-seq from HEL cells stably expressing mutant U2AF1 (Q157R), heavy fraction, biological replicate 2
U2AF1_freCLIP_counts.txt


title: U2AF1 S34F, U2AF1 freCLIP-seq light fraction, rep2

description:
U2AF1 freCLIP-seq from HEL cells stably expressing mutant U2AF1 (S34F), light fraction, biological replicate 2
U2AF1_freCLIP_counts.txt


title: 4T1 Cells: 4HC (4-OOH-cyclophosphamide)_Replicate 2

description:
polyA-selected RNA, stranded library
G179_M5


title: bovine_LAdrenal_MIXNTE_9

value: MIXNTE

value: left adrenal


title: bovine_LAdrenal_MIXTE_7

value: MIXTE


title: 4T1 Cells: 4HC (4-OOH-cyclophosphamide)_Replicate 1

description:
polyA-selected RNA, stranded library
G179_M4


title: bovine_LAdrenal_ISeTE_6

value: ISeTE


title: U2AF1 S34F, U2AF1 freCLIP-seq light fraction, rep1

description:
U2AF1 freCLIP-seq from HEL cells stably expressing mutant U2AF1 (S34F), light fraction, biological replicate 1
U2AF1_freCLIP_counts.txt


title: 4T1 Cells: control_Replicate 2

description:
polyA-selected RNA, stranded library
G179_M3

value: Vehicle control, collect cells at 72 h


title: bovine_LAdrenal_MIXNTE_14


title: Sample_26

value: Smokers with normal LF

value: 2 (smoker)


title: Sample_17

value: male

value: COPD

value: 1 (Non-smoker)


title: bovine_LAdrenal_ISeNTE_8


title: U2AF1 WT, U2AF1 freCLIP-seq light fraction, rep2

description:
U2AF1 freCLIP-seq from HEL cells stably expressing wild-type U2AF1, light fraction, biological replicate 2
U2AF1_freCLIP_counts.txt

value: Doxycycline 1ug/ml x 48 hours

value: freCLIP-seq


title: 4T1 Cells: control_Replicate 1

description:
polyA-selected RNA, stranded library
G179_M1


title: bovine_LAdrenal_ISeNTE_5


title: AB85

city: Crawley, Perth

first: Emma

last: de Jong

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

data_processing:
Image analysis was performed in real time by the NovaSeq Control Software (NCS) v1.6.0  and Real Time Analysis (RTA) v3.4.4, running on the instrument computer.
RTA performs  real-time base calling on the NovaSeq instrument computer
Then the Illumina bcl2fastq  2.20.0.422 pipeline was used to generate the sequence data.
Read libraries were mapped to the mouse genome using HISAT2 (v2.0.4)
Gene-level quantitation (counts) of aligned reads was performed using SummerizeOverlaps
Genome_build: mm11
Supplementary_files_format_and_content: genecounts.txt file contains a matrix of raw gene counts (unfiltered and un-normalised data)

source_name: AB1-HA tumour

growth_protocol: Subcutaneous AB1-HA murine mesothelioma tumors growth in BALB/c mice.

extract_protocol:
Frozen tumours were dissociated in TRIzol (Life Technologies) using a TissueRuptor (QIAGEN). RNA was extracted using chloroform and purified on RNeasy MinElute columns (QIAGEN) and RNA integrity was confirmed using a Bioanalyzer (Agilent Technologies)
Library preparation and sequencing  with Illumina NovaSeq standard protocols were performed by Australian Genome Research Facility.

treatment_protocol: PBS, Tretinoin (given daily for 5 days from day 4, 5 mg/kg), Immune checkpoint therapy (100 ug aCTLA-4 + 100ug anti-PD-L1 day 7)

value: BALB/c

value: ICT

tag: response


title: U2AF1 WT, U2AF2 eCLIP-seq, rep2

description:
U2AF2 eCLIP-seq from HEL cells stably expressing wild-type U2AF1, biological replicate 2
U2AF1_eCLIP_counts.txt

value: eCLIP-seq

value: U2AF1 wild-type


title: Sample_30


title: U2AF1 WT, U2AF1 eCLIP-seq, rep2

description:
U2AF1 eCLIP-seq from HEL cells stably expressing wild-type U2AF1, biological replicate 2
U2AF1_eCLIP_counts.txt


title: Sample_22


title: AB83


title: AB84


title: U2AF1 WT, U2AF1 eCLIP-seq, rep1

description:
U2AF1 eCLIP-seq from HEL cells stably expressing wild-type U2AF1, biological replicate 1
U2AF1_eCLIP_counts.txt


title: bovine_LAdrenal_ISeNTE_2

value: ISeNTE


title: bovine_LAdrenal_ISeTE_3


title: Sample_8


title: bovine_LAdrenal_ISeTE_1


title: HCT116_shTRF2_Rep11

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

description:
technical replicate of sh-TRF2-N2_1
technical replicate of sh-TRF2-N2_1

hyb_protocol: For miRNA microarray, 100 ng of RNA was labeled (Cy3) and hybridized using the miRNA complete labeling and hyb kit (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays.

scan_protocol: Scanning and image analysis were performed using the Agilent DNA Microarray Scanner (P/N G2565BA) equipped with extended dynamic range (XDR) software, according to the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit Protocol manual. Feature Extraction Software (Version 10.5) was used for data extraction from raw microarray image files using the miRNA_105_Dec08 FE protocol

data_processing: signal intensities were extracted by Agilent Feature Extraction 10.7.3.1 software. The arrays were quantile normalized. All values lower than 1 were considered below detection and thresholded to 1 and  log2-trasformed. miRNAs not expressed were excluded

growth_protocol: Colorectal cancer cells (HCT116) were infected with the indicated lentiviral vectors (Control, shTRF2). Four days after cells selection with puromycin cells were seeded (350.000 cells in T25 flask) and, three days after, were processed to RNA extraction. Three independent infection were performed to infect HCT116 cells.

extract_protocol: Total RNA extraction was performed using the RNeasy kit (Qiagen) following the manufacturer's instructions.

tag: genotype/variation


title: bovine_LAdrenal_MIXTE_4


title: AB82


title: Thy5W

city: Shenzhen

first: Lisha

last: Mou

state: Guangdong

address: Room 604, Building 1, Yinxingzhijie 1 Qi Guanlan, Longhua District

institute: Shenzhen Second People's Hospital

description: Thymus

data_processing:
We used fastp v0.19.4 to perform basic statistics on the quality of the raw reads to remove low-quality reads and adapters.
We used Cell Ranger 3.1.1 pipeline provided by 10X Genomics to do quality control.
We performed principal component analysis (PCA) using the Seurat R Package (v.3.1) on a matrix composed of cells and gene expression values.
Assembly: mm10-1.2.0
Supplementary files format and content: Raw_gene_counts_matrix.xls
Supplementary files format and content: *.h5 files

source_name: non-hematopoietic thymic cells

extract_protocol:
After dissection, the adhering non-thymus tissue were carefully cleared off with sharp tweezers. Thymi were chopped into small pieces and disintegrated with 0.01% (w/v) Liberase TH and 100 U/ml DNase I in RPMI 1640. Cells were then filtered through a 40-μm Falcon cell strainer and washed with 5 ml MACS buffer (1 X PBS with 2 mM EDTA and 0.5% BSA), followed by centrifugation at 200g for 5 min. Cells (from newborn and 5-week-old thymus) were resuspended with 5 ml ACK lysis buffer, holding on ice for 5 min. Wash the cells with 10 ml MACS buffer twice. Cells were then subjected to MACS negative separation (mouse CD45 microbeads) according to the manufacturer’s instructions to deplete the CD45+ lymphocytes. The stromal cells were then suspended at the concentration of 1x10^6 cells/ml in RPMI 1640-10% FBS, holding on ice.
Library construction was performed with the 10X Genomics Chromium Single Cell 3’ Reagent Kit v2 following the manufacturer’s instructions. Libraries were sequenced on Illumina Hiseq PE150 platform at an average read depth of about 84,000 reads per cell.

value: non-hematopoietic thymic cells

tag: developmental stage

value: 5 weeks


title: Control_Injured

city: Livermore

first: Stephen

middle: Patrick

last: Wilson

state: CA

address: 7000 East Ave

department: BBTD

institute: LLNL

data_processing:
Cellranger mkfastq to generate FASTQ
Cellranger count to generate count matrix
Assembly: mm10
Supplementary files format and content: gene list (features.tsv) and cell barcodes (barcodes.tsv) as well as gene/barcode matrices (matrix.mtx) are provided for each experimental group.

source_name: Immune cells from the knee joints

extract_protocol:
Single-cell preparation of joint-derived cells were obtained from freshly dissected six weeks post-injury and contralateral knee joints from control and T1DM mice; 4-5 mice per group. Briefly, the tissue around the joint was removed without disrupting the joint or fracture the bone and then washed in PBS to further remove superficial cells. Connective tissue was next severed into digestion media 7.5 mL of 3mg/ml Collagenase type I; (Worthington, Lakewood, NJ) with 100 µg/mL Dnase I (Roche, Basel, Switzerland) in DMEM/F12 for 2 sequential 1h digests at 37°C with shaking at 150 rpm. Following each digest, cells were washed in 5 mL PBS with 1% FBS, supernatants were collected and centrifuged at 500 x g. Red blood cell removal was next performed using ACK lysing buffer (ThermoFisher Scientific, Waltham, MA) followed by immune cell depletion using anti-CD45 magnetic microbeads (Miltenyi Biotec) in combination with LS columns (Miltenyi Biotec).
Cells were resuspended in PBS with 0.04% non-acetylated BSA prior to the single-cell sequencing step using Chromium Single-cell 3ʹ GEM, Library & Gel Bead Kit v3 (10× Genomics) on a 10x Genomics Chromium Controller following manufacturers protocol. Single-cell library preparation was performed using Chromium Single Cell 3′ GEM, Library & Gel Bead Kit v3 (10x Genomics, Pleasanton, CA, USA; Catalog no. 1000075) following the manufacturer’s protocol.

treatment_protocol: Knee injury: 10-week-old C57Bl/6J (BL6) and T1DM mice (purchased from Jackson Laboratory Bar Harbor, ME, USA) were subjected to anterior cruciate ligament injury using a non-invasive single dynamic tibial compressive overload model

tag: injury status

value: Injured joints

value: CD45- cells


title: Control_Uninjured

value: Uninjured joints


title: U2AF1 WT, U2AF2 eCLIP-seq, rep1

description:
U2AF2 eCLIP-seq from HEL cells stably expressing wild-type U2AF1, biological replicate 1
U2AF1_eCLIP_counts.txt


title: AB81

tag: strain background


title: T1DM 4

data_processing:
Sequence reads were aligned against Mus musculus reference genome (mm10) using STAR (version 2.6).  After read alignment, the number of read counts per gene locus was summarized with ‘featureCounts’ from Rsubread package (version 1.30.5), using mm10 gene annotation. Read counts were subsequently normalized  using TMM normalization (edgeR version 3.31.7).
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include TMM normalized CPM values for each Sample .

source_name: Cells from knee joints

extract_protocol:
Control and T1DM mice were euthanized at 16 weeks old. Knee joints were collected, dissected and cut at the edges of the joint region with small traces of soft tissue to preserve the articular integrity. Joints were then homogenized in Qiazol (79306, Qiagen, Valencia, CA, USA) using a PRO tissue homogenizer (Bio-Gen PRO 200, PRO Scientific Inc.). Total RNA was purified using Rneasy Mini Kit (QIAGEN Inc., Germantown, MD, USA) according to the manufacturer’s protocol and the RNA integrity was assessed using a bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Poly(A)+-enriched cDNA libraries were generated using the Illumina TruSeq RNA Library Prep kit v2 (Illumina Inc., Hayward, CA, USA).

treatment_protocol: Eight week old buffer-injected control mice (C57BL/6J, Stock No: 000664) and STZ injected C57BL/6J (Stock No: 33853) male mice were purchased from Jackson Laboratory (Jackson Laboratory, Bar Harbor, ME, USA). Diabetes status was confirmed by cutting off the tip of the tail and using a blood glucose meter (O’WELL Blood Glucose Monitoring System). Readings of ≥300 mg/dL were used to assign animals to the T1DM groups.

tag: background strain

value: 16 weeks

tag: condition

value: STZ injected

value: knee joint


title: Newborn

description: Thymus

tag: cell type

value: newborn


title: AB75

tag: treatment

value: Tretinoin


title: AB74


title: HCT116_shTRF2_Rep3

description: shTRF2 vector contains a sequence targeting the coding sequence of the telomeric protein TRF2, N2571, TRCN0000004811 OpenBiosystems

label_protocol: For miRNA microarray, 100 ng of RNA was labeled (Cy3) and hybridized using the miRNA complete labeling and hyb kit (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays.

tag: cell line


title: T1DM_Uninjured

value: STZ injected C57BL/6J

tag: age


title: E16

description: Thymus


title: T1DM_Injured


title: HCT116_shTRF2_Rep1


title: T1DM 3

tag: Sex

value: male

tag: tissue


title: HCT116_shTRF2_Rep2


title: HCT116_shControl_Rep11

description:
technical replicate of sh-cntrl1
technical replicate of sh-cntrl1

value: shControl


title: AB71

value: BALB/c


title: AB72


title: HCT116_shControl_Rep2

description: shControl vector contains a seguence targeting the E.coli DNA polymerase, N2040, OpenBiosystems


title: T1DM 2


title: E13

description: Thymus

tag: strain


title: E15

description: Thymus


title: E14

description: Thymus


title: E12

description: Thymus


title: AB65

value: ICT


title: AB64


title: T1DM 1


title: Control 4

value: Control


title: E11

description: Thymus


title: U2AF1 Q157R, TL-seq, rep2

description: TL-seq from HEL cells stably expressing mutant U2AF1 (Q157R), biological replicate 2

data_processing:
Library strategy: TL-seq
eCLIP-seq (U2AF1 eCLIP-seq, U2AF2 eCLIP-seq, U2AF1 freCLIP-seq): after duplicate removal with FastUniq and adapter trimming with Cutadapt, reads were aligned to the human genome (GRCh38.p10) with STAR (v2.7.0f, --quantMode GeneCounts), using the GENCODE Release 27 for transcript annotation. Binding sites were identfied extracting the genomic position of the crosslinked nucleotide right after the end of each sequenced read. Intron-exon junctions (interval from -40 to +10 around the 3’SS) were filtered using a coverage threshold of at least 10 reads in at least two samples. Moreover, for freCLIP-seq specifically, we considered genomic positions covered by at least 5 reads in all replicates and in an interval from -4 to +2 around the 3’SS in the light fractions (U2AF1 signal) or from -20 to -5 in the heavy fractions (U2AF2 signal). Normalization with the TMM method and differential binding analysis were performed with edgeR Bioconductor package.  RNA-seq: after duplicate removal with FastUniq, reads were aligned to the human genome (GRCh38.p10) with STAR (v2.7.0f, --quantMode GeneCounts), using the GENCODE Release 27 for transcript annotation. Normalization with the TMM method and identification of differentially expressed genes were performed with edgeR. Alternative splicing analysis was performed with rMATS v4.0.2.  TL-seq: reads were trimmed with Cutadapt and aligned to GRCh38 version 26 (Ensembl 88) with HISAT2 (default parameters and --mp 4,2). Reads aligning to annotated transcripts were quantified with HTSeq htseq-count. SAMtools was used to collect only uniquely mapped read pairs (SAM flag = 83/163 or 99/147). T-to-C mutations were identified and filtered through a customized pipeline (https://bitbucket.org/mattsimon9/timelapse_pipeline/src/master/). Normalization scale factors were calculated with edgeR using calcNormFactors (method = ‘upperquartile’). Browser tracks were made using STAR v2.5.3a. Changes in expression were evaluated with DESeq2. RNA kinetic parameters were estimated using RStan software v2.19.3 as previously reported (Schofield et al., 2018).
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: U2AF1_eCLIP_counts.txt: tab-delimited text file including gene ID (column 1) and sample-specific counts of aligned eCLIP-seq reads.
Supplementary_files_format_and_content: U2AF1_freCLIP_counts.txt: tab-delimited text file including gene ID (column 1) and sample-specific counts of aligned freCLIP-seq reads.
Supplementary_files_format_and_content: U2AF1_RNA_counts.txt: tab-delimited text file including gene ID (column 1) and sample-specific counts of aligned RNA-seq reads.
Supplementary_files_format_and_content: TL-seq: bedgraph files where reads are separated by the number of T-to-C mutations (0-5+) and strandedness (min/pos).

value: Doxycycline 1ug/ml x 48 hours, 4-thiouridine 100 uM x 2 hours

value: TL-seq

value: U2AF1 Q157R


title: U2AF1 Q157R, TL-seq, rep1

description: TL-seq from HEL cells stably expressing mutant U2AF1 (Q157R), biological replicate 1


title: HCT116_shControl_Rep1


title: AB63


title: Control 3


title: Control 2


title: AB62


title: HCT116_shControl_Rep3


title: U2AF1 S34F, TL-seq, rep2

description: TL-seq from HEL cells stably expressing mutant U2AF1 (S34F), biological replicate 2

value: U2AF1 S34F


title: AB61


title: NSC 40 hr 2

city: Rochester

first: Ryan

last: Watkins

address: 200 First St SW

department: Surgery

institute: Mayo Clinic

data_processing:
We aligned the reads to the human reference genome (hg38) using MAPRSeq 3.1.4 which utilizes the aligner STAR-2.6.1
Gene counts were generated using featureCounts from subread package 1.5.1
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Raw counts and FPKM values for each gene per sample

source_name: Liver

extract_protocol:
Livers were lysed in Trizol followed by chloroform precipitation. RNA was then applied to Qiagen RNAeasy column and processed according to manufacturer protocol
Illumina TruSeq Stranded mRNA library prep protocol

treatment_protocol: Mice were treated with vehicle or NSC87877 7.5 mg/kg/dose twice daily starting 12 hours prior to 70% partial hepatectomy and continued until euthanasia at 40 hours.

value: 12 weeks


title: U2AF1 S34F, TL-seq, rep1

description: TL-seq from HEL cells stably expressing mutant U2AF1 (S34F), biological replicate 1


title: NSC 40 hr 3


title: Control 1


title: U2AF1 WT, TL-seq, rep2

description: TL-seq from HEL cells stably expressing wild-type U2AF1, biological replicate 2

value: U2AF1 wild-type


title: NSC 40 hr 1


title: AB55

value: PBS


title: U2AF1 WT, TL-seq, rep1

description: TL-seq from HEL cells stably expressing wild-type U2AF1, biological replicate 1


title: vehicle 40hr 3

value: vehicle


title: AB53


title: AB92

city: Copenhagen

first: Josh

middle: M

last: Brickman

address: 3B Blegdamsvej

department: reNEW

institute: Copenhagen University

description: read2 concatenated to R1 header separated to plate barcode - cell barcode - UMI

data_processing:
library strategy: MARS-seq
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: [AB*.txt] single cell expression matrix include mRNA molecule count values for each Sample
Supplementary_files_format_and_content: [metadata_s.txt] Meta data file associating each single cell with its amplification batch and index sorting readouts

source_name: ESC differentiation

extract_protocol:
Embryos were dissociated with Accutase (Sigma) into singlet cells immediately after collection, the in vitro differentiated cells were dissociated by 0.1% trypsin.
Samples were flow sorted using AriaIII (BD Biosciences, BD Diva Software) cell sorter.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)

tag: Stage

value: in vitro ESC-derived endoderm organoids


title: AB91


title: U2AF1 WT uninduced, TL-seq, rep2

institute: Yale University

description: TL-seq from uninduced U2AF1 WT HEL cells, biological replicate 2

value: Uninduced, 4-thiouridine 100 uM x 2 hours

tag: sequencing method

value: U2AF1 wild-type uninduced


title: AB90


title: vehicle 40hr 2


title: AB54


title: AB52


title: Vehicle 0 hr 3


title: AB89


title: U2AF1 WT, TL-seq, unlabeled

description: TL-seq from HEL cells stably expressing wild-type U2AF1, no 4-thiouridine labeling

value: Doxycycline 1ug/ml x 48 hours, unlabeled

tag: stable transfection


title: AB51

tag: response


title: AB88


title: Vehicle 0hr 2


title: U2AF1 Q157R, U2AF1 freCLIP-seq heavy fraction, rep3

description:
U2AF1 freCLIP-seq from HEL cells stably expressing mutant U2AF1 (Q157R), heavy fraction, biological replicate 3
U2AF1_freCLIP_counts.txt

value: Doxycycline 1ug/ml x 48 hours

value: freCLIP-seq


title: AB45

value: BALB/c

value: Tretinoin+ICT

value: Responder


title: Vehicle 0hr 1


title: AB87


title: AB85

value: nEnd

value: in vitro ESC-derived naive endoderm


title: U2AF1 S34F, U2AF1 freCLIP-seq heavy fraction, rep3

description:
U2AF1 freCLIP-seq from HEL cells stably expressing mutant U2AF1 (S34F), heavy fraction, biological replicate 3
U2AF1_freCLIP_counts.txt


title: AB86


title: AB83

data_processing:
library strategy: MARS-seq
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (respectively) and concatenated to the fastq header, delimited by a underscore i.e. POOL_BARCODE_WELL_BARCODE_RMT while "NNNNNN" was used as a place holders if plate barcode was not used.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: mm9
Supplementary_files_format_and_content: [AB*.txt]  single cell expression matrix include mRNA molecule count values for each Sample
[metadata_s.txt]  Meta data file associating each single cell with its amplification batch and index sorting readouts

extract_protocol:
Embryos were dissociated with Accutase (Sigma) into singlet cells immediately after collection, the in vitro differentiated cells were dissociated by 0.1% trypsin.
Samples were flow sorted using AriaIII (BD Biosciences, BD Diva Software) cell sorter.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single cell RNA-seq for gene expression quantitation

value: in vitro ESC-derived primitive streak


title: AB44

value: Non-responder


title: AB35

value: Tretinoin


title: U2AF1 WT, U2AF1 freCLIP-seq heavy fraction, rep4

description:
U2AF1 freCLIP-seq from HEL cells stably expressing wild-type U2AF1, heavy fraction, biological replicate 4
U2AF1_freCLIP_counts.txt

value: U2AF1 wild-type


title: 3T3 TC ATA 2

city: Cleveland

first: Brian

middle: P

last: Rubin

state: OH

address: 9620 Carnegie Ave NE2-215

department: Cancer Biology

institute: Cleveland Clinic

data_processing:
Gapped aligment was performed to the mm10 genome with HISAT2 v2.2.1
Raw counts were created with Featurescounts v2.0.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: NIH3T3 Cells

extract_protocol:
Cells were washed with cold PBS and total RNA was extracted with the RNeasy Mini (Qiagen) kit.
Generation of a cDNA library was performed with polyA tail selection using the NEBNext Ultra II RNA Library Prep kit (NEB E7770).

treatment_protocol: NIH3T3 cells were seeded for 16 hours without treatment. Media was then removed and replaced with either DMSO or ATA treated cells at a concentration of 10uM for 48 hours.

value: NIH3T3 Cells

value: ATA


title: 3T3 TC ATA 1


title: 3T3 TC ATA 3


title: vehicle 40hr 1

value: vehicle

value: 12 weeks


title: U2AF1 WT, U2AF1 freCLIP-seq heavy fraction, rep3

description:
U2AF1 freCLIP-seq from HEL cells stably expressing wild-type U2AF1, heavy fraction, biological replicate 3
U2AF1_freCLIP_counts.txt


title: AB76


title: AB43


title: AB84

value: in vitro ESC-derived definitive endoderm


title: AB42


title: U2AF1 Q157R, U2AF1 freCLIP-seq light fraction, rep3

description:
U2AF1 freCLIP-seq from HEL cells stably expressing mutant U2AF1 (Q157R), light fraction, biological replicate 3
U2AF1_freCLIP_counts.txt

value: U2AF1 Q157R


title: HC_4

city: Beijing

first: Wenjie

last: Zheng

address: No1 ShuaiFuYuan，Dong Cheng District ，Beijing, Beijing, CN

institute: Peking Union Medical College Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.  We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: hg38
Supplementary_files_format_and_content: combined csv file of matrix table with raw gene counts and fpkm for every gene and every sample

source_name: human monocyte derived macrophage

growth_protocol: Monocytes were isolated from HC peripheral blood mononuclear cells (PBMCs) with CD14+ MicroBeads (Miltenyi Biotec) and were incubated in DMEM (Gibco) supplemented with 20ng/ml M-CSF (Sigma) and 10% heat-inactivated fetal bovine serum (Gibco) for 7 days to differentiate into human monocyte derived macrophages (HMDM).

extract_protocol:
RNA was harvested using Trizol reagent.A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HMDMs were treated with 10% BD or HC serum in DMEM for 48 hours.

value: HC serum


title: U2AF1 WT uninduced, TL-seq, rep1

description: TL-seq from uninduced U2AF1 WT HEL cells, biological replicate 1

value: Uninduced, 4-thiouridine 100 uM x 2 hours

value: TL-seq

value: U2AF1 wild-type uninduced


title: AB41

value: BALB/c

value: Tretinoin+ICT

value: Responder


title: AB75

value: nEnd

value: in vitro ESC-derived naive endoderm


title: U2AF1 S34F, U2AF1 freCLIP-seq light fraction, rep3

description:
U2AF1 freCLIP-seq from HEL cells stably expressing mutant U2AF1 (S34F), light fraction, biological replicate 3
U2AF1_freCLIP_counts.txt

value: Doxycycline 1ug/ml x 48 hours

value: freCLIP-seq

value: U2AF1 S34F


title: 3T3 TC DMSO 1

value: NIH3T3 Cells

value: DMSO


title: AB82


title: HC_3


title: AB32

value: Tretinoin


title: U2AF1 WT, U2AF1 freCLIP-seq light fraction, rep4

description:
U2AF1 freCLIP-seq from HEL cells stably expressing wild-type U2AF1, light fraction, biological replicate 4
U2AF1_freCLIP_counts.txt

value: U2AF1 wild-type


title: AB31


title: Cyclophosphamide_day6_OneCycle_pool2

description:
polyA-selected RNA, stranded library
G170_M29

data_processing:
RNA-seq data was processed using a custom pipeline, as described in Connerney et al., 2017 (PMID: 28323953)
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) RNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene.
Differential expression analysis was performed with edgeR as described in Robinson et al., 2010 (PMID: 19910308)
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel files contain differential expression data (ratio, fold-change, FPKM for treated sample (Intensity-1), FPKM for vehicle control (Intensity-2), adjusted p-value) for pairwise comparisons between Cyclophosphamide-treatment and Vehicle control at each of the 5 time points, respectively numbered as Experiments # 704-708.

source_name: E0771 tumor tissue_total RNA fraction

growth_protocol: 7-week-old female C57/BL6N mice (Taconic Farms, Germantown, NY) were were implanted with E0771 tumor cells (approx. 200,000/mouse) resuspended in 0.1 ml PBS were inoculated into the fourth mammary fat pad. Tumor growth was monitored every 3 d using a vernier caliper, and tumor volumes were calculated: Volume = (π/6) x (L x W)3/2.

extract_protocol:
Tumors were excised, washed with PBS and flash-frozen in liquid nitrogen after placing ~1/3 piece of fresh tumor in 1 mL TRIzol for immediate downstream extraction of tumor RNA.
Polyadenylated mRNA was isolated from 1 μg of total tumor RNA using NEBNext® Poly(A) mRNA Magnetic Isolation Module (cat. #E7490, New England Biolabs) and used for lllumina RNA-seq library preparation using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (cat. #E7420L, New England Biolabs), NEBNext® Multiplex Oligos for Illumina® Dual Index Primers Set 1 (cat. #E7600, New England Biolabs), and AMPure® XP Beads (cat. #A63881, Beckman Coulter Inc., Indianapolis, IN) per the manufacturer’s instructions.

treatment_protocol: Mice were randomized into two groups, cyclophosphamide (treatment) and PBS vehicle (control) groups, when average tumor volumes reached 200-250 mm3. Cyclophosphamide (cat. # C0768, Sigma-Aldrich, St. Louis, MO) dissolved in sterile PBS and passed through a 0.2 µm filter was then injected i.p. at 0 (vehicle control) or 130 mg/kg. Tumor tissue was collected and used for RNAseq analysis at the following time points: day 1, day 2, day 3, day 6, and day 12, where cyclophosphamide treatments were given on day 0, and then again on day 6 in the case of the day 12 time point.

value: Female

value: 11 weeks

value: Cyclophosphamide_130 mg/kg on day 0


title: AB34


title: AB73

value: in vitro ESC-derived definitive endoderm


title: AB81

value: in vitro ESC-derived primitive streak


title: HC_2

value: HC serum


title: 3T3 EV DMSO 1

value: Empty vector


title: HC_1


title: AB24

value: BALB/c

value: Tretinoin+ICT

value: Responder


title: U2AF1 WT, U2AF1 freCLIP-seq light fraction, rep3

description:
U2AF1 freCLIP-seq from HEL cells stably expressing wild-type U2AF1, light fraction, biological replicate 3
U2AF1_freCLIP_counts.txt

value: Doxycycline 1ug/ml x 48 hours


title: BD_4

value: BD serum


title: Cyclophosphamide_day12_TwoCycles_pool2

description:
polyA-selected RNA, stranded library
G170_M31

value: 12 weeks

value: Cyclophosphamide_130 mg/kg on day 0 and on day 6


title: Cyclophosphamide_day12_TwoCycles_pool1

description:
polyA-selected RNA, stranded library
G170_M30


title: AB74


title: 3T3 EV DMSO 2

value: NIH3T3 Cells

value: DMSO


title: AB70


title: AB22


title: BD_2


title: AB69


title: Cyclophosphamide_day1_pool2

description:
polyA-selected RNA, stranded library
G170_M23

value: 9-10 weeks


title: BD_1


title: AB25

value: Non-responder


title: AB15

value: PBS


title: AB67

source_name: Foxa2-Venus mouse embryos

value: Foxa2-Venus positive populations - primitive streak, visceral endoderm


title: AB33

value: Tretinoin


title: Cyclophosphamide_day3_pool2

description:
polyA-selected RNA, stranded library
G170_M27

value: Female

value: Cyclophosphamide_130 mg/kg on day 0


title: AB23


title: AB72

value: in vitro ESC-derived definitive endoderm


title: AB13

value: BALB/c


title: BD_3


title: Cyclophosphamide_day3_pool1

description:
polyA-selected RNA, stranded library
G170_M26


title: CA2_shRNA_1

city: St. Louis

last: DeBosch

state: Missouri

address: 660 South Euclid Avenue

department: Pediatrics and Cell Biology & Physiology

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.5.1a
Gene counts quantitated with Subread:featureCount 1.4.6-p5 with CPM and RPKM transformations added with custom Rscripting.
Genome_build: Ensembl GRCh38.101
Supplementary_files_format_and_content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: C28/I2 cells

extract_protocol:
Total RNA was extracted with the use of RNeasy Mini Kit (QIAGEN)
Qiagen FastSelect

value: C28/I2 cells

value: chondrocyte

value: CA2 shRNA


title: Vehicle_pool1

description:
polyA-selected RNA, stranded library
G170_M20

value: Vehicle


title: CA2_scrambled_3

value: Scrambled


title: Cyclophosphamide_day2_pool2

description:
polyA-selected RNA, stranded library
G170_M25


title: AB21

value: Tretinoin+ICT


title: Cyclophosphamide_day2_pool1

description:
polyA-selected RNA, stranded library
G170_M24


title: AB63


title: Control TFH, rep3

city: Chiciago

first: Prabhakaran

last: Kumar

state: Illinois

address: 835 S Wolcott Ave.

department: Microbiology and Immunology

institute: UIC

data_processing:
Raw reads were aligned to the reference genome using STAR.
ENSEMBL gene expression was quantified using FeatureCounts.
Genome_build: mm10
Supplementary_files_format_and_content: quant_counts.txt

source_name: TFH cells sorted from control mice

growth_protocol: 23 weeks old female NZBWF1/j mice were used in this study.

extract_protocol:
Total RNA was purified from Tconv, Treg, TFH and TFR cells sorted from control and OX40L-JAG1 treated mice using Qiagen RNeasy kit with inclusion of on-column DNase treatment step.
CORALL prep kit (Lexogen) with RiboCop rRNA depletion kit (Lexogen)
Total RNA-seq

treatment_protocol: Mice were injected (i.p.) with recombinant mouse OX40L (2mg/kg body weight) and mouse JAG1 (2mg/kg body weight)  once a week for three consecutive weeks. Age and sex-matched control mice received PBS.

value: female

value: 23 weeks old

value: control

value: TFH cells


title: CA2_shRNA_3


title: AB60


title: AB66


title: AB68


title: Control TFH, rep2


title: Cyclophosphamide_day6_OneCycle_pool1

description:
polyA-selected RNA, stranded library
G170_M28

value: 11 weeks


title: Cyclophosphamide_day1_pool1

description:
polyA-selected RNA, stranded library
G170_M22

value: 9-10 weeks


title: AB14

value: PBS


title: CA2_shRNA_2


title: Control TFH, rep1


title: AB58

value: Foxa2-Venus positive populations - primitive streak, visceral endoderm


title: Control TFR, rep3

source_name: TFR cells sorted from control mice

value: TFR cells


title: AB71

value: in vitro ESC-derived definitive endoderm


title: Vehicle_pool2

description:
polyA-selected RNA, stranded library
G170_M21

value: Female


title: CA2_control_1

value: C28/I2 cells

value: Control


title: AB12

value: BALB/c


title: AB65

value: Foxa2-Venus positive populations - notochord, gut, liver


title: AB57

value: Foxa2-Venus positive populations - notochord, gut, floor plate, visceral endoderm


title: AB64


title: AB55


title: Cyclophosphamide_7-cycles_pool2

description:
polyA-selected RNA, stranded library
G170_M17

data_processing:
RNA-seq data was processed using a custom pipeline, as described in Connerney et al., 2017 (PMID: 28323953)
Sequence reads were mapped to the mouse genome (mm9) using TopHat2 (Trapnell et al, Nat. Biotechnol, 2010)
FeatureCounts (Liao, 2014, Bioinformatics) was used to obtain read counts for RefSeq genes. Mature (spliced) RNAs were quantified by counting sequence reads that map to a concatenated sequence comprised of the union of the exonic regions for all isoforms of a given gene.
Differential expression analysis was performed with edgeR as described in Robinson et al., 2010 (PMID: 19910308)
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel files contain differential expression data (ratio, fold-change, FPKM for treated sample (Intensity-1), FPKM for vehicle control (Intensity-2), adjusted p-value) for 4 pairwise comparisons: Cyclophosphamide_2-cycles vs Vehicle control, Cyclophosphamide_4-cycles vs Vehicle control, Cyclophosphamide_7-cycles vs Vehicle control, and Cyclophosphamide_4-cycles-then-regrowth vs Vehicle control, respectively numbered as Experiments # 700, 701, 702 and 703.

source_name: 4T1 tumor tissue_total RNA fraction

growth_protocol: 7-week-old female BALB/c mice (Taconic Farms, Germantown, NY) were were implanted with 4T1 tumor cells (approx. 100,000/mouse) resuspended in 0.1 ml PBS were inoculated into the fourth mammary fat pad. Tumor growth was monitored every 3 d using a vernier caliper, and tumor volumes were calculated: Volume = (π/6) x (L x W)3/2.

treatment_protocol: Mice were randomized into two groups, cyclophosphamide (treatment) and PBS vehicle (control), when average tumor volumes reached 100-150 mm3. Cyclophosphamide (cat. # C0768, Sigma-Aldrich, St. Louis, MO) dissolved in sterile PBS and passed through a 0.2 µm filter was then injected i.p. at 0 (vehicle control) or 130 mg/kg. CPA injections were repeated every 6 days for a total of 2, 4 or 7 treatment cycles, at which point the mice were euthanized and tumors were excised. Where indicated, treatment was halted after 4 treatment cycles, and the tumor were allowed to grow for a further 18 days, during which time substantial tumor regrowth was observed.

value: 14-15 weeks

value: Cyclophosphamide_7-cycles at 130 mg/kg each cycle


title: U5NSC_RNAseq_Del_2

city: Seattle

first: Heshani

last: Thirimanne

address: 1100 Fairview AV N, D2-213

institute: Fred Hutchinson Cancer Research Center

description:
Replicate 2
U5NSC_RNASeq_DGE.txt

data_processing:
STAR v2.7.1 with 2-pass mapping was used to align paired-end reads to hg19 and GENCODE gene annotation v31lift37.
FastQC 0.11.8 and RseQC 3.0.0 were used for QC.
FeatureCounts in Subread 1.6.5 was used to quantify gene-level expression.
Bioconductor package edgeR 3.26.8 was used determine differential gene expression.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Tab-delimited text file with CPM and FPKM values for each sample and differentially expressed genes.

source_name: RNA-Seq

extract_protocol:
Total RNA was isolated from three million cells per sample using the Quaigen RNAeasy Mini Kit (Cat# 74104) following the manufacturer's instructions.
Libraries for Hct116  were prepared using TruSeq RNA Samples Prep Kit v2 (Illumina Inc., San Diego CA, USA). Libraries for U5NSCs were prepared using TruSeq Stranded mRNA kit.

value: U5 neural stem cells

tag: genotype


title: AB56

tag: developmental stage


title: Cyclophosphamide_2-cycles_pool3

description:
polyA-selected RNA, stranded library
G170_M12

value: 10-11 weeks

value: Cyclophosphamide_2-cycles at 130 mg/kg each cycle


title: AB59


title: AB11


title: AB53

value: Foxa2-Venus positive populations - primitive streak, node, definitive endoderm, visceral endoderm


title: OX40L-JAG1 TFR, rep1

source_name: TFR cells sorted from OX40L-Jagged-1 treated mice

value: female

value: 23 weeks old

value: OX40L-Jagged-1 treated


title: Cyclophosphamide_4-cycles-then-regrowth_pool2

description:
polyA-selected RNA, stranded library
G170_M19

value: Cyclophosphamide_4-cycles at 130 mg/kg each cycle, then continued growth without further treatment for 18 days


title: CA2_scrambled_2

value: chondrocyte

value: Scrambled


title: Cyclophosphamide_2-cycles_pool1

description:
polyA-selected RNA, stranded library
G170_M10

value: Female


title: Cyclophosphamide_4-cycles-then-regrowth_pool1

description:
polyA-selected RNA, stranded library
G170_M18


title: CA2_scrambled_1

value: C28/I2 cells


title: CA2_control_3

value: Control


title: CA2_control_2


title: Cyclophosphamide_4-cycles_pool3

description:
polyA-selected RNA, stranded library
G170_M15

value: BALB/c

value: 12-13 weeks

value: Cyclophosphamide_4-cycles at 130 mg/kg each cycle


title: Vehicle pool2

description:
polyA-selected RNA, stranded library
G170_M8

value: Vehicle


title: U5NSC_RNAseq_WT_3

description:
Replicate 3
U5NSC_RNASeq_DGE.txt

value: U5 neural stem cells


title: AB50

value: in vitro ESC-derived primitive streak


title: Vehicle pool1

description:
polyA-selected RNA, stranded library
G170_M7

value: 10-11 weeks


title: U5NSC_RNAseq_Del_3

description:
Replicate 3
U5NSC_RNASeq_DGE.txt