title: Astrocyte ECM LPS 3


title: STIM_24h_CAR_PacBio

status: Public on Mar 18 2022

type: SRA

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

country: USA

institute: NCI, NIH

library_source: transcriptomic

data_processing:
CITE-seq including cell surfae protein and gene expression
fastq generation: Illumina bcl2fastq 2.20
sample demultiplexing: popscle demuxlet (https://github.com/statgen/popscle)
mapping, CellRanger 3.1.0 (10x Genomics)
secondary analysis: Seurat 3.1.0 or 4.0.0 (R package)
Genome_build: GRCh38-3.0.0
CAR detection
Whitelist generation: Umi-tools  was used to create a whitelist from the scRNA-seq combined read1 fastq file with parameters --set-cell-number=5000 and --set-cell-number=15000 for cell hashed triplicates in addition to --error-correct-threshold=1.
UMI and barcodes extraction: umi-tools extract function, for PacBio the 26 bp preceding the Template Switch Oligo (TSO) sequence, for MiSeq and Illumina-Seq first 26 bp in read1.
mapping: blastn
A custom script was written to deal with multimapping by selecting best hit for each read if read maps to more than one CAR with same accuracy level it gets disregarded.
Supplementary_files_format_and_content: 14 CAR sequences

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral Blood Mononuclear Cells(PBMCs)

extract_protocol: Eight anti-GPC2 and six anti-CD276 CAR T- cells were first thawed separately and recover for overnight. Then they were pooled the same way according to its counterpart experiment co-cultured with tumor cells using an E:T ratio of 1:1 for individual anti-GPC2 CAR T- cells expect G27; and 1:4 for each anti-CD276 and G27 CAR T- cells. Pooled CAR T-cells were evenly divided into seven fractions for multimodal single cell assay. One of the 7 fractions were taken as CTRL_0h and remaining 6 fractions were split into two groups: one group of 3 fractions cultured without target tumor cells for 24 hours (CTRL_24h) and other group of 3 fractions co-cultured with target tumor cells for 24 hours (STIM_24h). To improve the cell viability to >85%, dead cells were removed by magnetic negative selection (Dead Cell Removal Kit, Miltenyi Biotec, Cat# 130-090-101). For 2 groups of pooled CAR T-cells at 24 hours, Totalseq-C human ‘hashtag’ antibodies were used for each of CAR T-cell triplicates in 2 groups allowing identification of different samples in the analysis, and then triplicates in each group were combined. Next, three CAR T- cell pools (CTRL_0h, CTRL_24h, and STIM_24h) were stained with a cocktail of TotalSeq-C human lyophilized panel (BioLegend) of 31 surface proteins. After washed three times, CAR-T cells were resuspended in PBS, and counted before proceeding immediately to the single cell immune profiling using a 10X Genomics Chromium system (10x Genomics, Pleasanton, CA). Briefly, CAR T-cells were mixed with the reverse transcription (RT) mix and partitioned into single cell Gel-Bead in Emulsion (GEM) using 10x 5’ Chromium Single Cell Immune Profiling Next GEM v1.1 chemistry. For detection of 14 CAR binders, a fraction of amplified full-length cDNA was used for PCR with CAR binder specific reverse primers, then size selected products (>600bp) were sequenced by PacBio Sequel II for full-length of binder sequences.

tag: cell type

value: PBMCs transduced individually with 14 different CAR constructs

tag: treatment

value: 14 pooled CAR T-cells exposured to target neuroblastoma cells for 24 hours

tag: molecule

value: mRNA


title: Astrocyte ECM PBS 3

type: RNA

city: Indianapolis

first: Cristian

last: Lasagna-Reeves

state: IN

address: 320 West 15th Street

department: Anatomy & Cell Biology

institute: Indiana University School of Medicine

hyb_protocol: NanoString Technologies protocol

scan_protocol: NanoString Technologies protocol

data_processing: Counts for target genes were normalized to the best fitting house-keeping genes as determined by nSolver software to account for variability in RNA content. Background signal was calculated as a mean value of the negative hybridization control probes.

organism: Mus musculus

source_name: Primary Astrocyte

growth_protocol: Cells were plated at a density of 1x10^6 and incubated until 90% confluent, changing media every 2 days.

extract_protocol: Total RNA was isolated from primary cultures with Rneasy Plus Universal Mini Kit

treatment_protocol: Cells were treated with 50ug of total protein from conditioned media

tag: tissue

value: Brain

value: Primary Astrocyte

tag: medium

value: ECM

value: PBS


title: S37

city: Parma

first: Marco

last: Morselli

state: Parma

address: Parco Area delle Scienze, 23/A

country: Italy

institute: University of Parma

library_source: genomic

data_processing:
data demultiplexing using Illumina's bcl2fastq
adapter removal using cutadapt (v2.10)
alignment using BSBolt Align (v1.3.0)
PCR duplicate removal using samtools markdup (samtools v. 1.9)
CpG methylation calling using BSBolt CallMethylation
CGmatrix creation with BSBolt AggreagateMatrix (CpG sites covered by at least 20 reads)
Genome_build: GRCh38
Supplementary_files_format_and_content: CGmap for each sample: text file containing CpG position and methylation values. Please refer to https://doi.org/10.1093/gigascience/giab033 for additional information.
Supplementary_files_format_and_content: CGmatrix: matrix of  sites common to all the samples. Common position and methylation levels for each sample

molecule: genomic DNA

source_name: peripheral blood

extract_protocol:
Genomic DNA was isolated from the individuals by standard phenol-chloroform extraction method (Guha et al. 2018). 500 ng of extracted DNA were used for Targeted BS-seq library preparation as described in Chang et al., with minor modifications (Chang et al. 2021).
500 ng of extracted DNA were used for TBS-seq library preparation as described in Chang et al., with minor modifications (Chang et al. 2021). Briefly, fragmented DNA was subject to end repair, dA-tailing and adapter ligation using the NEBNext Ultra II Library prep kit using custom pre-methylated adapters (IDT) (Morselli et al. 2020). Purified libraries were hybridized to the biotinylated probes according to the manufacturer’s protocol. Captured DNA was treated with bisulfite prior to PCR amplification using KAPA HiFi Uracil+ with the following conditions: 2 min at 98°C; 14 cycles of (98°C for 20 sec; 60°C for 30 sec; 72°C for 30 sec); 72°C for 5 minutes; hold at 4°C. Library QC was performed using the High-Sensitivity D1000 Assay on a 2200 Agilent TapeStation. Libraries were sequenced on a NovaSeq6000 (S1 lane) as paired-end 150 bases.
Custom protocol based off the NEBNext Ultra II library prep kit, IDT xGen Hybridization Capture, Zymo Lightning bisulfite conversion kit
Illumina NovaSeq 6000 (S1 flowcell)

value: peripheral blood

tag: age

tag: disease state

tag: pcr positivity

value: PCRpos


title: Astrocyte ECM LPS 1

value: LPS


title: CTRL_24h_CAR_PacBio

value: 14 pooled CAR T-cells without exposure to target neuroblastoma cells at 24 hours


title: CTRL_0h_CAR_PacBio

value: 14 pooled CAR T-cells without exposure to target neuroblastoma cells at time 0


title: S36

value: ATYPICALpneumonia

value: PCRneg


title: S47


title: S35


title: WT_rep2

city: Beijing

first: xiaofeng

last: Liu

address: No.2 Yuanmingyuan Xi Lu

country: China

institute: China Agricultural University

data_processing:
HISAT2 software used to compare the sequenced Reads to the reference genome (Kim D, Langmead B, Salzberg S L. HISAT: a fast spliced aligner with low memory requirements[J]. Nature methods, 2015, 12(4): 357-360.).
Differentially expressed genes (DEGs) were calculated using DESeq2 (Love MI, Huber W and Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, pp. 550. doi:10.1186/s13059-014-0550-8.). The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate. The false discovery rate (FDR) less than 0.05 and the fold change larger than 1.0 as were set as the threshold.
Genome_build: ChineseLong_v3
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample

organism: Cucumis sativus

source_name: female bud

extract_protocol:
The RNA of the sample was harvested using Trizol reagent. Illumina NEBNext® Ultra™ RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Fruits

tag: developmental stage

value: at anthesis

tag: genotype

value: wild type


title: S34


title: WT_rep1


title: Ci_rep2

value: CsCRC-RNAi lines


title: S33


title: S2


title: Ci_rep1


title: Astrocyte MCM PBS 1

value: MCM


title: S32


title: Irf1_t0d_R2

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
Reads were aligned with bowtie2 to the mouse genome (UCSC version mm10). The output was sorted and indexed with samtools.
Duplicated reads were marked with picard. Coverage tracks per sample were generated by tiling the genome in 20bp windows and counting 5'end of reads per window using the function bamCount from the bioconductor package bamsignals.
These window counts were exported in bigWig format using the bioconductor package rtracklayer.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: BigWig file with FPKM counts per bin (20bp).

source_name: normal mammary gland cells

growth_protocol: NMuMG/E9 cells were grown in DMEM supplemented with 10% FBS, 2mM GlutaMax and 100mg/ml penicillin-streptomycin.

extract_protocol: Cells were fixed in 1% formaldehyde/PBS and cell pellets lyzed before sonication with the Bioruptor sonicator. 150mg of sonicated DNA was used as input per ChIP and Irf1 was precipitated with proteinA sepharose beads and 5mg Irf1 antibody. RNA and protein were digested and DNA purified by phenol/chloroform extraction.

treatment_protocol: One day after plating NMuMG/E9 cells, the medium was replaced with medium +/- 2ng/ml rhTGFbeta1. The assay was terminated on day 3 (2d TGFbeta treatment).

tag: cell line

value: NMuMG

tag: subclone

value: Subclone 9

tag: treatment time

value: Irf1 ChIP

tag: chip antibody

value: Irf1 antibody (M20, St Cruz sc-640)

tag: replicate


title: S27


title: Irf1_t0d_R1


title: S29


title: S31


title: S32R


title: E167 rhlR- rep2

city: Seattle

first: Kyle

middle: Lowe

last: Asfahl

state: Washington

address: 1705 NE Pacific St

department: Microbiology

institute: University of Washington

data_processing:
Illumina bcl2fastq2 Conversion Software v2.18 for fastq file generation
Quality filtering and adapter removal using Trim Galore!
Alignment to reference using subread-align
Count matrix generation using featureCounts
Assembly: E167 complete genome: PRJNA814703, SAMN26565253, JGI-IMG#2870695665
Supplementary files format and content: Raw count data in a tab-delimited text file with genes as rows and samples as columns

organism: Pseudomonas aeruginosa

source_name: bacterial cells

growth_protocol: All cells were grown in 25 ml LB+MOPS broth in a 250 ml baffled flask incubated at 37C with 250 rpm shaking from a starting OD600 of 0.001.

extract_protocol:
mRNA was preserved immediately upon cell harvest using Qiagen RNAprotect. Cells were lysed using a bead-beating protocol and mRNA was extracted using Qiagen RNEasy miniprep columns, followed by DNAse I treatment and cleanup using another round of RNEasy-based purification. rRNA was removed using Illumina RiboZero protocol.
150bp PE Illumina TruSeq; Sequencing performed on Illumina HiSeq 4000

treatment_protocol: 10 uM C4-HSL and 2 uM 3oxoC12-HSL synthetic signals were added to WT samples (samples E167sig1-3)

tag: growth phase

tag: growth medium

value: LB+MOPS liquid culture

tag: isolate

value: rhlR-


title: E167 rhlR- rep1


title: Irf1_t2d_R1

tag: treatment

value: TGFbeta


title: E167 rhlR- rep3


title: input_t0d_R2

value: Input


title: Irf1_t2d_R2


title: input_t0d_R1


title: E167 WT rep3

value: WT


title: S24

value: peripheral blood


title: E167 WT rep2


title: shhnRNPK

city: Zhengzhou

first: Zhuoyu

last: Gu

address: Jianshe East Road

institute: The First Affiliated Hospital, Zhengzhou University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

source_name: normal colonic epithelial

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: FHC

value: normal colonic epithelial

value: Fifth generation

value: hnRNPK knockdown


title: R3

first: yongpan

last: an

address: xueyuanlu

institute: Peking University

data_processing:
Illumina Casava software used for basecalling.
Read quality was checked for each sample using fastx_toolkit_0.0.14.
High-quality reads were then imported into HISAT2 to get mapped reads.
Mapped Reads are spliced using StringTie software, based on the selected reference genome sequence.
The functional annotations of gene/transcript in NR, Swiss-PROt, Pfam, EggNOG, GO and KEGG were summarized.
RSEM software conducts quantitative analysis of gene and transcript expression levels respectively. The quantitative index is TPM, which refers to the number of transcripts as the unit of calculation.
After obtaining the Read Counts of genes/transcripts, DESeq2, DEGseq or edgeR can be used to conduct sample or intergroup gene/transcript differential expression analysis for multiple (≥2) items to identify the differentially expressed genes/transcripts.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: WI-38 cells were provided by the National Institutes for Food and Drug Control. The cells were counted and inoculated for each passage at the same density, and incubated in MEM (Gibco) supplemented with 10% FBS (Gibco) in an incubator at 37°C and 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WI-38 cells were first induced with 1μM doxorubicin for 12 hours, and then treated with oridonin or DMSO-containing medium for 48 hours.

tag: dox treatment

value: doxorubicin

tag: medium treatment

value: oridonin


title: shNC control for shhnRNPK

tag: tissue

tag: age

value: hnRNPK shNC


title: S23

tag: disease state

value: ATYPICALpneumonia

tag: pcr positivity

value: PCRneg


title: R2


title: R1


title: S21


title: E167 WT rep1

tag: genotype


title: M3

tag: cell line

value: DMSO


title: S22

value: PCRpos


title: S19


title: E131 rhlR- rep3

data_processing:
Illumina bcl2fastq2 Conversion Software v2.18 for fastq file generation
Quality filtering and adapter removal using Trim Galore!
Alignment to reference using subread-align
Count matrix generation using featureCounts
Assembly: E131 complete genome: PRJNA814694, SAMN26565131, JGI-IMG#2913685979
Supplementary files format and content: Raw count data in a tab-delimited text file with genes as rows and samples as columns

treatment_protocol: 10 uM C4-HSL and 2 uM 3oxoC12-HSL synthetic signals were added to WT samples (samples 1-3)

value: LB+MOPS liquid culture


title: C3


title: C2


title: E131 rhlR- rep1

value: rhlR-


title: S25


title: S18

value: BRONCHOpneumonia


title: E131 rhlR- rep2


title: S28


title: S30


title: C1


title: 1713-uRNA_3

city: London

first: Olivier

middle: Emmanuel

last: Pardo

address: Hammersmith Hospital, Du Cane Road

department: Surgery and Cancer

country: United Kingdom

institute: Imperial College

description: Human Universal RNA Control

data_processing:
Illumina bcl2fastq is used for generation of FASQ files
HTG EdgeSeq Parser software (version 5.1) is used for alignment to a priori defined target sequences.  Requirements include %Q30 >= 85%, %PF >= 75%, and 180 < CD < 290
Post-sequencing quality control using three quality control metrics: 1) Percent of reads allocated to the Positive control probe must not exceed 15%, 2) Total aligned reads must exceed 1,500,000, and 3) Relative Standard Deviaion (CV) of counts within a sample must exceed 0.1 (CV is calculated after removal of counts from ANT and POS control probes and log2 transformation after addition of 2 to avoid taking the log of 0).
Assembly: hg19
Supplementary files format and content: Two processed files are provided as comma separated values: "VLP00614_Median normalised.csv" contains the median normalised expression data while "VLP00614_CPM.csv" contains the CPM values.

source_name: Human Universal RNA Control

extract_protocol:
HTG EdgeSeq Oncology Biomarker Panel (Tucson, Arizona)
Tumor samples were processed by adding HTG Lysis Buffer to lyse and/or permeabilize the RNA available to subsequently bind to corresponding target-specific Nuclease Protection Probes (NPPs). The lysed samples was transferred to a 96-well micro-titer plate. Target capture was done by adding NPPs to the lysed samples to hybridize to the target mRNA. Then S1 nuclease was added to digest non-hybridized miRNA and excess NPPs, leaving target mRNA/NPP duplexes. S1 digestion was terminated by heat denaturation of S1 enzyme. The processed samples were used as template to set up PCR reactions with primer tags. These tags share common sequences that are complementary to 5’-end and 3’-end “wing” sequences of the probes and common adaptors required for cluster generation for deep sequencing. The library was prepared using HTG EdgeSeq PCR processing. Following library preparation, it was quantified using HTG EdgeSeq KAPA Library Quantification for Illumina Sequencing. All samples and controls were quantified in triplicate.
HTG EdgeSeq KAPA Library Quantification/Calculator

tag: progression status


title: 1713-uRNA_2

description: Human Universal RNA Control


title: S17


title: 1713-uRNA_1

description: Human Universal RNA Control


title: E131 WT rep2


title: S16


title: 1713-A031940

description: Microdissected from FFPE slide of tumour at presentation

source_name: Breast cancer sample

value: Stable disease (SD)

tag: disease

value: metastatic breast cancer


title: E131 WT rep1

value: WT


title: 1713-A031939


title: S15

value: peripheral blood


title: 1713-A031937


title: M1


title: M2


title: E125 rhlR- rep3

data_processing:
Illumina bcl2fastq2 Conversion Software v2.18 for fastq file generation
Quality filtering and adapter removal using Trim Galore!
Alignment to reference using subread-align
Count matrix generation using featureCounts
Assembly: E125 complete genome: PRJNA814691, SAMN26565087, JGI-IMG#2870682680
Supplementary files format and content: Raw count data in a tab-delimited text file with genes as rows and samples as columns

treatment_protocol: 10 uM C4-HSL and 2 uM 3oxoC12-HSL synthetic signals were added to WT samples (samples E125sig1-3)


title: S13


title: E125 rhlR- rep2


title: E125 rhlR- rep1


title: 1713-A031936


title: 1713-A031925


title: S12


title: 1713-A031932


title: 1713-A031934


title: E125 WT rep3


title: 1713-A031923


title: S12R


title: E125 WT rep2


title: E131 WT rep3


title: 1713-A031935


title: 1713-A031941


title: S11


title: 1713-A031931

value: Progressive disease (PD)


title: E125 WT rep1


title: S100


title: 1713-A031927


title: 1713-A031930


title: E113 rhlR- rep3

data_processing:
Illumina bcl2fastq2 Conversion Software v2.18 for fastq file generation
Quality filtering and adapter removal using Trim Galore!
Alignment to reference using subread-align
Count matrix generation using featureCounts
Assembly: E113 complete genome: PRJNA814681, SAMN26564916, JGI-IMG#2913673089
Supplementary files format and content: Raw count data in a tab-delimited text file with genes as rows and samples as columns

treatment_protocol: 10 uM C4-HSL and 2 uM 3oxoC12-HSL synthetic signals were added to WT samples (samples E113sig1-3)


title: 1713-A031926


title: S239

value: CTRL


title: 1713-A031938


title: 1713-A031924


title: 1713-A031922


title: E113 rhlR- rep2


title: S238


title: h3k9me3_input_suv2_u937

city: Copenhagen

first: Bo

last: Porse

address: Ole Maaløes Vej 5, 4

department: Finsen Laboratory and BRIC

country: Denmark

institute: University of Copenhagen

data_processing:
H3K9me3 ChIP-seq reads were mapped to combined genome assembly of human (hg19) and drosophila melanogaster (dm6) using bowtie2 (Langmead and Salzberg, 2012), and reads mapping to multiple regions in the human genome were kept to account for expression of repeat regions in the genome. Total reads mapping to drosophila genome were used to determine the scaling factor, which was later employed for spike-in normalization. PCR-duplicates were identified using samtools markdup (Li et al., 2009), and were collapsed as one read. H3K9me2 enrichment at gene bodies (ensembl annotated, hg19 release 87, N=55774) and transposons (TEtranscripts annotated, hg19, N=992) was computed using featureCounts (--countMultimapping=T, --fraction=T), and were spike-in normalized (Jin et al., 2015; Liao et al., 2014; Yates et al., 2020).
Genome_build: hg19

growth_protocol: U937 cells grown in RPMI 10 % FBS 1 % P/S

extract_protocol:
The IP was performed with H3K9me3 (C15500003, Diagenode)
NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1)

treatment_protocol: U937 cells were transduced with lentiviral shRNA against SUV39H1 and selected 3 days in puromycin. UNC0638 treated cells were harvest after 3 days

value: SUV39H1 shRNA #1


title: h3k9me3_input_suv4_u937

value: SUV39H1 shRNA #2


title: S237


title: h3k9me3_input_scr_u937

value: Scrambled shRNA


title: E113 WT rep3


title: S236


title: E113 rhlR- rep1


title: SUV_4_rep2_H3K9me3


title: S10


title: SUV_2_rep2_H3K9me3


title: S235


title: 1713-A031933


title: S232


title: SUV_2_rep1_H3K9me3


title: SCR_rep2_H3K9me3


title: E113 WT rep1


title: 1713-A031929


title: SCR_rep1_H3K9me3


title: S230


title: SUV39H1 shRNA treatment (replicate 3)

description: noinfo-S2_rep_3-Tumor_Tissue_RNAlater-RNA_v1_CustomSI_X-210625_A00559_AH2HKHDMXY-EXT_LABKA_PR104-noinfo

data_processing:
Paired-end (150bp) reads were randomly subsampled to 100 million reads using seqtk package (-s100 parameter) (https://github.com/lh3/seqtk), and are aligned to human genome (hg19 assembly) using bwa-meth (v0.2.2, default parameters) (https://arxiv.org/abs/1401.1129). PCR Duplicate reads were marked using markdup function of sambamba package (v0.6.8) (https://lomereiter.github.io/sambamba/).
DNA methylation levels were analyzed using MethylDackel (v0.3.0). First, we used mbias function of MethylDackel to compute the 5' and 3' end position of reads that show disproportionate levels of methylated CpGs. These positions were excluded in the downstream analysis using extract function of MethyDackel (--OT and --OB parameters).
The bedGraph files from MethyDackel were used to compute the DNA methylation fraction at CpG dinucleotides using methrix package (v1.4.7; pipeline=”MethyDackel”, stranded=F, zero_based=F, collapse_strands=F parameters) (https://pubmed.ncbi.nlm.nih.gov/33346800/).
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files from MethylDackel

source_name: U937 cells

growth_protocol: RPMI-1640 medium with 10% FBS and 1% penicillin/streptomycin

extract_protocol: EZ DNA Methylation-GoldTM Kit (Zymo Research, D5005) + Pico Methyl-Seq Library Prep Kit (Zymo Research, D5455)

treatment_protocol: Lentiviral transduction with p.LKO.1 shRNA puromycin resistant

tag: genotype/variation

value: SUV39H1 knockdown


title: E104 rhlR- rep3

data_processing:
Illumina bcl2fastq2 Conversion Software v2.18 for fastq file generation
Quality filtering and adapter removal using Trim Galore!
Alignment to reference using subread-align
Count matrix generation using featureCounts
Assembly: E104 complete genome: PRJNA784987, SAMN26565086, JGI-IMG#2913679597
Supplementary files format and content: Raw count data in a tab-delimited text file with genes as rows and samples as columns

extract_protocol:
mRNA was preserved immediately upon cell harvest using Qiagen RNAprotect. Cells were lysed using a bead-beating protocol and mRNA was extracted using Qiagen RNEasy miniprep columns, followed by DNAse I treatment and cleanup using another round of RNEasy-based purification. rRNA was removed using Illumina RiboZero protocol.
150bp PE Illumina TruSeq

treatment_protocol: 10 uM C4-HSL and 2 uM 3oxoC12-HSL synthetic signals were added to WT samples (samples E104sig1-3)

value: rhlR-deletion


title: SUV39H1 shRNA treatment (replicate 2)

description: noinfo-S2_rep_2-Tumor_Tissue_RNAlater-RNA_v1_CustomSI_X-210625_A00559_AH2HKHDMXY-EXT_LABKA_PR104-noinfo


title: E104 rhlR- rep2


title: S229


title: Scrambled (replicate 3)

description: noinfo-Scr_rep_3-Tumor_Tissue_RNAlater-RNA_v1_CustomSI_X-210625_A00559_AH2HKHDMXY-EXT_LABKA_PR104-noinfo

value: Scrambled


title: SUV39H1 shRNA treatment (replicate 1)

description: noinfo-S2_rep_1-Tumor_Tissue_RNAlater-RNA_v1_CustomSI_X-210625_A00559_AH2HKHDMXY-EXT_LABKA_PR104-noinfo


title: Scrambled (replicate 2)

description: noinfo-Scr_rep_2-Tumor_Tissue_RNAlater-RNA_v1_CustomSI_X-210625_A00559_AH2HKHDMXY-EXT_LABKA_PR104-noinfo


title: S228


title: STIM_24h_CAR_Nextseq

extract_protocol: Eight anti-GPC2 and six anti-CD276 CAR T- cells were first thawed separately and recover for overnight. Then they were pooled the same way according to its counterpart experiment co-cultured with tumor cells using an E:T ratio of 1:1 for individual anti-GPC2 CAR T- cells expect G27; and 1:4 for each anti-CD276 and G27 CAR T- cells. Pooled CAR T-cells were evenly divided into seven fractions for multimodal single cell assay. One of the 7 fractions were taken as CTRL_0h and remaining 6 fractions were split into two groups: one group of 3 fractions cultured without target tumor cells for 24 hours (CTRL_24h) and other group of 3 fractions co-cultured with target tumor cells for 24 hours (STIM_24h). To improve the cell viability to >85%, dead cells were removed by magnetic negative selection (Dead Cell Removal Kit, Miltenyi Biotec, Cat# 130-090-101). For 2 groups of pooled CAR T-cells at 24 hours, Totalseq-C human ‘hashtag’ antibodies were used for each of CAR T-cell triplicates in 2 groups allowing identification of different samples in the analysis, and then triplicates in each group were combined. Next, three CAR T- cell pools (CTRL_0h, CTRL_24h, and STIM_24h) were stained with a cocktail of TotalSeq-C human lyophilized panel (BioLegend) of 31 surface proteins. After washed three times, CAR-T cells were resuspended in PBS, and counted before proceeding immediately to the single cell immune profiling using a 10X Genomics Chromium system (10x Genomics, Pleasanton, CA). Briefly, CAR T-cells were mixed with the reverse transcription (RT) mix and partitioned into single cell Gel-Bead in Emulsion (GEM) using 10x 5’ Chromium Single Cell Immune Profiling Next GEM v1.1 chemistry. For detection of 14 CAR binders, a fraction of amplified full-length cDNA was used for PCR with CAR specific reverse primers using a similar approach as T cell receptor (TCR-VDJ) sequencing libraries per 10x Genomics user guide (https://www.10xgenomics. com/resources/user-guides/). CAR binder libraries were prepared as instructed by 10x Genomics user guides and sequenced on Illumina Nextseq500.

tag: cell type

value: PBMCs transduced individually with 14 different CAR constructs

value: 14 pooled CAR T-cells exposured to target neuroblastoma cells for 24 hours

tag: molecule

value: mRNA


title: S227


title: E104 WT rep3

tag: growth phase

tag: growth medium

value: LB+MOPS liquid culture

value: wild type


title: CTRL_0h_CAR_Nextseq

tag: treatment

value: 14 pooled CAR T-cells without exposure to target neuroblastoma cells at time 0


title: CTRL_24h_CAR_Nextseq

value: 14 pooled CAR T-cells without exposure to target neuroblastoma cells at 24 hours


title: E113 WT rep2

tag: isolate

value: WT


title: S226

value: peripheral blood


title: SUV_4_rep1_H3K9me3


title: S225


title: E104 WT rep1


title: STIM_24h_RNA

data_processing:
Library strategy: CITE-seq
CITE-seq including cell surfae protein and gene expression
fastq generation: Illumina bcl2fastq 2.20
sample demultiplexing: popscle demuxlet (https://github.com/statgen/popscle)
mapping, CellRanger 3.1.0 (10x Genomics)
secondary analysis: Seurat 3.1.0 or 4.0.0 (R package)
Genome_build: GRCh38-3.0.0
CAR detection
Whitelist generation: Umi-tools  was used to create a whitelist from the scRNA-seq combined read1 fastq file with parameters --set-cell-number=5000 and --set-cell-number=15000 for cell hashed triplicates in addition to --error-correct-threshold=1.
UMI and barcodes extraction: umi-tools extract function, for PacBio the 26 bp preceding the Template Switch Oligo (TSO) sequence, for MiSeq and Illumina-Seq first 26 bp in read1.
mapping: blastn
A custom script was written to deal with multimapping by selecting best hit for each read if read maps to more than one CAR with same accuracy level it gets disregarded.
Supplementary_files_format_and_content: 14 CAR sequences

extract_protocol: Eight anti-GPC2 and six anti-CD276 CAR T- cells were first thawed separately and recover for overnight. Then they were pooled the same way according to its counterpart experiment co-cultured with tumor cells using an E:T ratio of 1:1 for individual anti-GPC2 CAR T- cells expect G27; and 1:4 for each anti-CD276 and G27 CAR T- cells. Pooled CAR T-cells were evenly divided into seven fractions for multimodal single cell assay. One of the 7 fractions were taken as CTRL_0h and remaining 6 fractions were split into two groups: one group of 3 fractions cultured without target tumor cells for 24 hours (CTRL_24h) and other group of 3 fractions co-cultured with target tumor cells for 24 hours (STIM_24h). To improve the cell viability to >85%, dead cells were removed by magnetic negative selection (Dead Cell Removal Kit, Miltenyi Biotec, Cat# 130-090-101). For 2 groups of pooled CAR T-cells at 24 hours, Totalseq-C human ‘hashtag’ antibodies were used for each of CAR T-cell triplicates in 2 groups allowing identification of different samples in the analysis, and then triplicates in each group were combined. Next, three CAR T- cell pools (CTRL_0h, CTRL_24h, and STIM_24h) were stained with a cocktail of TotalSeq-C human lyophilized panel (BioLegend) of 31 surface proteins. After washed three times, CAR-T cells were resuspended in PBS, and counted before proceeding immediately to the single cell immune profiling using a 10X Genomics Chromium system (10x Genomics, Pleasanton, CA). Briefly, CAR T-cells were mixed with the reverse transcription (RT) mix and partitioned into single cell Gel-Bead in Emulsion (GEM) using 10x 5’ Chromium Single Cell Immune Profiling Next GEM v1.1 chemistry. Single cell gene expression libraries were prepared as instructed by 10x Genomics user guides and sequenced on Illumina Nextseq500.


title: CTRL_24h_RNA


title: CTRL_24h_CSP

extract_protocol: Eight anti-GPC2 and six anti-CD276 CAR T- cells were first thawed separately and recover for overnight. Then they were pooled the same way according to its counterpart experiment co-cultured with tumor cells using an E:T ratio of 1:1 for individual anti-GPC2 CAR T- cells expect G27; and 1:4 for each anti-CD276 and G27 CAR T- cells. Pooled CAR T-cells were evenly divided into seven fractions for multimodal single cell assay. One of the 7 fractions were taken as CTRL_0h and remaining 6 fractions were split into two groups: one group of 3 fractions cultured without target tumor cells for 24 hours (CTRL_24h) and other group of 3 fractions co-cultured with target tumor cells for 24 hours (STIM_24h). To improve the cell viability to >85%, dead cells were removed by magnetic negative selection (Dead Cell Removal Kit, Miltenyi Biotec, Cat# 130-090-101). For 2 groups of pooled CAR T-cells at 24 hours, Totalseq-C human ‘hashtag’ antibodies were used for each of CAR T-cell triplicates in 2 groups allowing identification of different samples in the analysis, and then triplicates in each group were combined. Next, three CAR T- cell pools (CTRL_0h, CTRL_24h, and STIM_24h) were stained with a cocktail of TotalSeq-C human lyophilized panel (BioLegend) of 31 surface proteins. After washed three times, CAR-T cells were resuspended in PBS, and counted before proceeding immediately to the single cell immune profiling using a 10X Genomics Chromium system (10x Genomics, Pleasanton, CA). Briefly, CAR T-cells were mixed with the reverse transcription (RT) mix and partitioned into single cell Gel-Bead in Emulsion (GEM) using 10x 5’ Chromium Single Cell Immune Profiling Next GEM v1.1 chemistry. Cell surface protein feature libraries were prepared as instructed by 10x Genomics user guides and sequenced on Illumina Nextseq500.

value: cell surface Protein (CSP)


title: STIM_24h_CSP


title: S222

value: CTRL


title: nTg, 6 month mouse 3

city: Gainesville

first: Benoit

last: Giasson

state: FL

address: 1275 Center Drive, BMS J427

institute: University of Florida

data_processing:
Partek Flow Genomic Analysis software was used for data analysis for alignment (using STAR method), filtering, and normalization of reads. It also generated differential expression analysis outputs using the GSA algorithm by comparing nontransgenic to tau SPAM mice at 6 months
Assembly: mm10
Supplementary files format and content: Differential expression analysis of nontransgenic and transgenic tau SPAM mice at 6 months is organized as a table of gene lists and values on a .txt file.

source_name: Brain cortex

extract_protocol:
Brain cortex from different mice lines were extracted as a service by BGI Genomics using standard RNA extraction kits.  RNA quality was validated using an Agilent Technologies 2100 bioanalyzer.
RNA-seq library was constructed using BGISEQ-500 plateform and was performed as a service by BGI Genomics.

value: Brain cortex

value: nontransgenic mice

value: 6 month


title: S224


title: CTRL_0h_RNA

value: 14 pooled CAR T- cells without exposure to target neuroblastoma cells at time 0


title: nTg, 6 month mouse 2


title: CTRL_0h_CSP


title: RPE, ZIKV 96h 2

city: Atlanta

first: Manoj

last: Bhasin

state: GA

address: Woodruff Memorial Research Building, Room 4107, 101 Woodruff Circle, 4th Floor East

institute: Emory

data_processing:
quality of the reads with checked using FastQC program
high quality clean reads were aligned against human genome using Tophat2 algorithm that uses bowtie2 aligner
HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: count

source_name: RPE

growth_protocol: RPE cells were grown in 35mm Petri-dish in RtEGM™Bulletkit® media at 37°C with 5% CO2.

extract_protocol:
RNA Extraction by Qiagen RNAeasy Mini kit as per manufactor's protocol
Sequencing libraries of Poly(A)-selected mRNA were generated from the double-stranded cDNA using the Illumina TruSeq kit, as per the manufacturer’s protocol
Single end

treatment_protocol: RPE cells were infected with ZIKV (PRVABC59, NR-50240) for 48 and 96h at MOI 1

value: RPE

tag: infection

value: ZIKV infected 96h


title: nTg, 6 month mouse 1


title: RPE, ZIKV 96h 1


title: S221


title: Scrambled (replicate 1)

description: noinfo-Scr_rep_1-Tumor_Tissue_RNAlater-RNA_v1_CustomSI_X-210625_A00559_AH2HKHDMXY-EXT_LABKA_PR104-noinfo

value: Scrambled


title: E104 rhlR- rep1

value: rhlR-deletion


title: nTg, 4 month mouse 3

value: 4 month


title: RPE, ZIKV 48h 1

value: ZIKV infected 48h


title: S220


title: RPE, Control 2

value: Uninfected control


title: E104 WT rep2

value: LB+MOPS liquid culture

value: wild type


title: RPE, Control 1


title: S218


title: nTg, 4 month mouse 1


title: CRISPR_2nd_ERX-41_rep3

city: Dallas

first: Ganesh

middle: V.

last: Raj

state: TX

address: 5323 Harry Hines Blvd., JA5.150

department: Urology

institute: UT Southwestern Medical Center

description:
CRISPR Screen
Screen2.pdf

data_processing:
Library strategy: DNA-Seq
The mRNAseq sequencing reads were mapped to Human GRCh38 genome using HiSAT2 (Kim et al. 2015).
Abundances of transcripts, FPKMs, are calculated using ballgown (Frazee et al. 2014).
CRISPR screen sequencing data were analyzed using MAGeCK-VISPR (Li et al. 2014).
Genome_build: GRCh38
Supplementary_files_format_and_content: fpkm

source_name: MDA-MB-231 cells

growth_protocol: MDA-MB-231 and BT-549 cells were cultured in RPMI1640 (Gibco) supplemented with 10% FBS, 0.2% Normocin and 1% penicillin-streptomycin. SUM-159 cells were cultured in F-12 (Gibco) supplemented with 10% FBS, 0.2% Normocin and 1% penicillin-streptomycin.

extract_protocol:
For mRNA-seq samples, RNA was extracted using RNease Mini Kit (Qiagen) according to the manufacturer protocols. For CRISPR screen samples, genomic DNA was extracted using Quick-DNA Midiprep Plus kit (Zymo Research).
mRNA-seq libraries were prepared using the TruSeq RNA Library Preparation Kit (Illumina) according to the manufacturer's instructions. CRISPR screen libraries were prepared uing PCR primers with barcode which can amplify sgRNA sequences.

treatment_protocol: Cells were treated with DMSO or ERX-41. For mRNAseq samples, ERX-41 treated cells were treated with 1 uM of ERX-41 for 2 or 4 hours. For CRISPR screen samples, ERX-41 treated cells were treated with 0.25 uM (1st screen) or 0.5 uM (2nd screen) for 2 weeks.

value: TNBC cells

tag: agent

value: ERX-41 treatment


title: YhgF plus crosslink biorep 3

city: Uppsala

first: Erik

last: Holmqvist

state: Uppland

address: Husargatan 3, Box 596, Uppsala University, Dept. of Cell and Molecular Biology

country: Sweden

institute: Uppsala University

data_processing:
All rRNA operons +/- 50 nt except rrnH were masked from genome sequence prior to mapping.
Adapter removal and read pair merging performed with SeqPrep (https://github.com/jstjohn/SeqPrep)
Read mapping performed with bowtie 1.2.2 allowing for 1 mismatch.
Mapped reads were converted to strand separated bedgraph files with samtools and bedtools genomecov.
Bedgraph files converted to bigWig file format (www.encodeproject.org/software/bedgraphtobigwig/)
Assembly: NC_000913.3
Supplementary files format and content: Strand separated bigWig files for viewing mapping coverage in genome browsers.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli cultured in M9 minimal media

growth_protocol: The strain EHS-2291 carrying a 3x-FLAG tagged YhgF was grown in M9 minimal media supplemented with 0.2 % glycerol and 0.1 % casamino acids until an OD600 of ~1.7. The experiment was done using biological independent tripicates.

extract_protocol:
The YhgF protein was purified using anti-FLAG beads and bound RNA was partly digested and labeled with P32. The samples were separated on polyacrylamide gels andtransferred to nitrocellulose membranes. The RNA was prepared from the membrane by cutting out the pieces cotaining protein. Co-purifying RNA was identified by deep sequencing
Libraries were prepared using the NEBNext multiplex small RNA library prep set for Illumina (New England Biolabs) according to the manufacturer’s directions, except that 20 cycles of PCR was done after the reverse transcription. MinElute PCR purification kit (Qiagen) was used to purify and up-concentrate PCR samples. The amplified libraries were size separated on a 6 % polyacrylamide gel, stained with SYBR gold (Thermo Fisher) and fragments in the size of 140-250 bp excised from the gel. The DNA was purified using the elution buffer supplied with the kit and overnight incubation at 16 °C while shaking at 1200 rpm. To remove gel fragments from the samples, they were centrifuged through a Costar Spin-X column (0.45 µl cellulose membrane, Corning) and ethanol precipitated using linear acrylamide (from kit) as coprecipitant. To amplify the DNA library, another nine rounds of PCR was done followed again by purification and up-concentration using MinElute PCR purification kit

treatment_protocol: Half of each culture was crosslinked by applying UV-light the other half was not treated.

tag: strain

tag: condition

value: plus crosslink

tag: tagged protein

value: 3x-FLAG tagged YhgF

tag: protocol

value: CLIP-seq


title: CRISPR_2nd_ERX-41_rep2

description:
CRISPR Screen
Screen2.pdf


title: nTg, 2 month mouse 3

tag: tissue

value: Brain cortex

tag: genotype

value: nontransgenic mice

tag: age

value: 2 month


title: S216

data_processing:
data demultiplexing using Illumina's bcl2fastq
adapter removal using cutadapt (v2.10)
alignment using BSBolt Align (v1.3.0)
PCR duplicate removal using samtools markdup (samtools v. 1.9)
CpG methylation calling using BSBolt CallMethylation
CGmatrix creation with BSBolt AggreagateMatrix (CpG sites covered by at least 20 reads)
Genome_build: GRCh38
Supplementary_files_format_and_content: CGmap for each sample: text file containing CpG position and methylation values. Please refer to https://doi.org/10.1093/gigascience/giab033 for additional information.
Supplementary_files_format_and_content: CGmatrix: matrix of  sites common to all the samples. Common position and methylation levels for each sample

extract_protocol:
Genomic DNA was isolated from the individuals by standard phenol-chloroform extraction method (Guha et al. 2018). 500 ng of extracted DNA were used for Targeted BS-seq library preparation as described in Chang et al., with minor modifications (Chang et al. 2021).
500 ng of extracted DNA were used for TBS-seq library preparation as described in Chang et al., with minor modifications (Chang et al. 2021). Briefly, fragmented DNA was subject to end repair, dA-tailing and adapter ligation using the NEBNext Ultra II Library prep kit using custom pre-methylated adapters (IDT) (Morselli et al. 2020). Purified libraries were hybridized to the biotinylated probes according to the manufacturer’s protocol. Captured DNA was treated with bisulfite prior to PCR amplification using KAPA HiFi Uracil+ with the following conditions: 2 min at 98°C; 14 cycles of (98°C for 20 sec; 60°C for 30 sec; 72°C for 30 sec); 72°C for 5 minutes; hold at 4°C. Library QC was performed using the High-Sensitivity D1000 Assay on a 2200 Agilent TapeStation. Libraries were sequenced on a NovaSeq6000 (S1 lane) as paired-end 150 bases.
Custom protocol based off the NEBNext Ultra II library prep kit, IDT xGen Hybridization Capture, Zymo Lightning bisulfite conversion kit
Illumina NovaSeq 6000 (S1 flowcell)

value: peripheral blood

tag: disease state

value: CTRL

tag: pcr positivity


title: YhgF minus crosslink biorep 3

value: minus crosslink


title: CRISPR_2nd_ERX-41_rep1

description:
CRISPR Screen
Screen2.pdf

tag: cell type

tag: cell line


title: S215


title: nTg, 2 month mouse 2


title: S214


title: YhgF plus crosslink biorep 2


title: CRISPR_2nd_Control_rep3

description:
CRISPR Screen
Screen2.pdf

value: Vehicle DMSO


title: nTg, 2 month mouse 1


title: YhgF minus crosslink biorep 2


title: RPE, ZIKV 48h 2

value: RPE


title: CRISPR_2nd_Control_rep2

description:
CRISPR Screen
Screen2.pdf


title: YhgF plus crosslink biorep 1


title: CRISPR_2nd_Control_rep1

description:
CRISPR Screen
Screen2.pdf


title: By tau SPAM, 6 month mouse 4

value: By line of tau SPAM transgenic mice

value: 6 month


title: By tau SPAM, 6 month mouse 5


title: S212


title: nTg, 4 month mouse 2

value: 4 month


title: CRISPR_1st_ERX-41_rep2

description:
CRISPR Screen
Screen1.pdf


title: YhgF minus crosslink biorep 1


title: S209


title: By tau SPAM, 6 month mouse 3


title: By tau SPAM, 6 month mouse 2


title: CRISPR_1st_ERX-41_rep1

description:
CRISPR Screen
Screen1.pdf


title: nhr-8(ok186)_OP50_3

city: Worcester

first: Read

last: Pukkila-Worley

state: Massachusetts

address: 55 N Lake Ave

department: Medicine

institute: University of Massachusetts Medical School

data_processing:
Raw fastq reads were evaluated by FastQC (version 0.11.5), clean reads were aligned to the C. elegans reference genome (WBcel235) and quantified using Kallisto (version 0.45.0). Differentially expressed genes were identified using Sleuth (version 0.30.0).
Genome_build: WBcel235
Supplementary_files_format_and_content: tsv files include TPM transcript abundance values for each sample

organism: Caenorhabditis elegans

source_name: Whole animal

extract_protocol:
RNA was isolated using TriReagent (Molecular Research Center, Inc.) and purified with RNeasy columns (Qiagen)
Oligo (dT) magnetic beads are used to select mRNA with polyA tail. Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. End repair the dscDNA with phosphate at 5' end and stickiness 'A' at 3' end, then ligate and adaptor with stickiness 'T' at 3' end to the dscDNA. Two specific primers were used to amplify the ligation product. Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.

treatment_protocol: Synchronized L1 staged C. elegans wild-type and nhr-8 loss of function animals were grown to L4, transferred to P. aeruginosa or E. coli and incubated at 25°C for 4 hours..

tag: developmental stage

tag: exposure


title: S206


title: nhr-8(ok186)_OP50_2


title: CRISPR_1st_Control_rep2

description:
CRISPR Screen
Screen1.pdf


title: By tau SPAM, 6 month mouse 1


title: nhr-8(ok186)_OP50_1


title: S205


title: S213


title: By tau SPAM, 4 month mouse 3


title: nhr-8(hd117)_PA14_3


title: S204


title: By tau SPAM, 4 month mouse 2


title: mRNA_159_KO_ERX-41_rep2

description:
159_countTable.fpkm.txt
159KO-ERX41-rep2

data_processing:
The mRNAseq sequencing reads were mapped to Human GRCh38 genome using HiSAT2 (Kim et al. 2015).
Abundances of transcripts, FPKMs, are calculated using ballgown (Frazee et al. 2014).
CRISPR screen sequencing data were analyzed using MAGeCK-VISPR (Li et al. 2014).
Genome_build: GRCh38
Supplementary_files_format_and_content: fpkm

molecule: polyA RNA

source_name: SUM-159 cells

value: ERX-41 4h treatment

value: LIPA KO


title: mRNA_159_KO_ERX-41_rep1

description:
159_countTable.fpkm.txt
159KO-ERX41-rep1

value: TNBC cells


title: By tau SPAM, 4 month mouse 1


title: nhr-8(hd117)_PA14_2


title: S203


title: nhr-8(hd117)_PA14_1


title: mRNA_159_KO_Veh_rep2

description:
159_countTable.fpkm.txt
159KO-Veh-rep2


title: S202


title: mRNA_159_KO_Veh_rep1

description:
159_countTable.fpkm.txt
159KO_Veh-rep1


title: S201


title: S207


title: nhr-8(hd117)_OP50_3


title: By tau SPAM, 2 month mouse 2


title: By tau SPAM, 2 month mouse 3


title: mRNA_159_WT_ERX-41_rep2

description:
159_countTable.fpkm.txt
159WT-ERX41-rep2

value: WT


title: N2_PA14_3


title: nhr-8(hd117)_OP50_2


title: mRNA_159_WT_Veh_rep2

description:
159_countTable.fpkm.txt
159WT-Veh-rep2


title: Patient PF_02_49

city: Poznań

first: Tomasz

middle: P.

last: Lehmann

address: Święcickiego 6

department: Biochemistry and Molecular Biology

country: Poland

institute: Poznan University of Medical Sciences

description: Group 2

data_processing:
Analysis of data was performed with GENEGLOBE online software (https://geneglobe.qiagen.com/pl/analyze). Missing raw Ct values have been replaced by 35 in matrix for normalized Ct values. Fold change/regulation have been calculated using delta-delta Ct method, in which delta Ct is calculated between miRNA of interest and an average of reference miRNAs, followed by delta-delta Ct calculations (delta Ct (Test Group)-delta Ct (Control Group)). Fold Change is then calculated using 2^ (-delta-delta Ct ) formula.
Raw Ct values for target miRNA, matrix normalized worksheet reports normalized signal, fold change worksheet reports test/control ratios.

label: SYBR Green

source_name: plasma

label_protocol:
4 µl of each total RNA was reversely transcribed with miRCURY LNA RT Kit (Cat. no. 339340, Qiagen). The UniSp6 RNA spike-in from the miRCURY LNA RT Kit and cel-miR-39-3p RNA from miRCURY LNA RT Kit were applied as controls. RT temperature protocol: reverse transcription step 60 min. 42°C, inactivation of reaction 5 min. 95°C.
20 µl cDNA product of miRCURY LNA RT Kit was applied for each quantitative PCR (qPCR). qPCR was performed using miRCURY LNA SYBR Green PCR Kit (Cat. no. 339345, 339346, 339347, Qiagen) on miRCURY LNA Serum/Plasma Focus PCR Panels (Cat. no. YAHS – 106YF-8, Qiagen) and LightCycler 480 (Roche, Basel, Switzerland).

extract_protocol: The miRNAs were isolated from individual 200 μl frozen plasmas using miRNeasy Serum/Plasma Advanced Kit (Cat. no. 217204, Qiagen, Dusseldorf, Germany) manufacturer's instructions.

treatment_protocol: EDTA-blood samples (10 ml) were collected from all patients on the first day after the cardiac catheterization procedure. Samples were processed within 30 minutes of collection. Samples were centrifuged at 1300 g for 15 min at room temperature. The supernatant was transferred to RNase-free tubes and then stored at -80 °C.

value: coronary artery disease

value: plasma


title: nhr-8(hd117)_OP50_1


title: mRNA_159_WT_ERX-41_rep1

description:
159_countTable.fpkm.txt
159WT-ERX41-rep1


title: Patient PF_02_121

description: Group 2


title: N2_PA14_2


title: mRNA_159_WT_Veh_rep1

description:
159_countTable.fpkm.txt
159WT-Veh-rep1


title: Patient PF_02_111

description: Group 2


title: Patient PF_02_25

description: Group 2


title: By tau SPAM, 2 month mouse 1

value: Brain cortex


title: mRNA_549_4h_rep_2

description:
549_countTable.fpkm.txt
549_4H_REP2

source_name: BT-549 cells


title: N2_PA14_1


title: CRISPR_1st_Control_rep1

description:
CRISPR Screen
Screen1.pdf


title: N2_OP50_3


title: mRNA_549_4h_rep_1

description:
549_countTable.fpkm.txt
549_4H_REP1


title: N2_OP50_2


title: mRNA_549_2h_rep_2

description:
549_countTable.fpkm.txt
549_2H_REP2

value: ERX-41 2h treatment


title: Patient PF_02_44

description: Group 2


title: N2_OP50_1


title: Patient PF_02_63

description: Group 2


title: Patient PF_02_42

description: Group 2


title: mRNA_549_Veh_rep_2

description:
549_countTable.fpkm.txt
549_VEH_REP2


title: mRNA_549_Veh_rep_1

description:
549_countTable.fpkm.txt
549_VEH_REP1


title: mRNA_231_4h_rep_2

description:
231_countTable.fpkm.txt
231_4H_REP2


title: Rat_oil4

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

data_processing:
Illumina bcl2fastq software used for basecalling.
We first discarded raw reads with unknown N bases. Sequencing adaptors and low-quality bases were then trimmed following the first step by FASTX-Toolkit (Version 0.0.13). Too short reads (less than 16nt) were also removed.
Quality filtered reads were then aligned onto the mRatBN7.2 genome using HISAT2 (Kim D et al. 2015) with no more than four mismatches.
Uniquely aligned reads were used to count the number of gene reads and to calculate FPKM
The R Bioconductor package DESeq2 was used to identify the differentially expressed genes (DEGs). The P value after correction <0.05 and fold change > 2 or < 0.5 were set as the threshold for the identification of DEGs.
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified using the ABLas pipeline.
Genome_build: mRatBN7.2
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

organism: Rattus norvegicus

source_name: ileum tissues

growth_protocol: We used a well-established protocol to generate the rat model of SAP. SD rats, 6–8 weeks of age, were anesthetized, and a median incision was made to locate the duodenal opening.  A No. 5 puncture needle was used to retrogradely puncture the pancreaticobiliary duct near the duodenal opening.  The puncture needle at the duodenal opening and the hilar opening of the common bile duct was fixed in place with two non-invasive artery clamps.  A micropump was used to inject 3% sodium taurocholate solution into the pancreatic duct at a uniform rate of 0.1 ml/min (at a dose of 0.1 ml/100 g). The needle was maintained in place for 5 min after injection, and after visually observing that the color of the pancreas turned dark red, the puncture needle was pulled out,  the vascular clamp was loosened, and the duodenal wall puncture was sutured to avoid intestinal fluid leakage into the abdominal cavity.  After confirming that there was no active bleeding in the abdominal cavity, the abdominal cavity was closed layer by layer.

extract_protocol:
Total RNAs were extracted from ileal tissue of rats with TRIzol Reagent (Invitrogen, NO 15596026) adopting the methods by Chomczynski et al,1987.
About 2 μg RNAs per sample were used for stranded transcriptome library preparation using KCTM Stranded mRNA Library Prep Kit for Illumina (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) under the instruction. PCR products with 200-500 bps were enriched, quantified and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.

treatment_protocol: SD rats were randomly divided into the following three groups 24 hours after the surgery: Control group, SAP group and SAP treated with JZL184 group.  The JZL184 group received intraperitoneal injection of the selective MAGL inhibitor JZL184 (Cayman Europe, Talin, Estonia), which was prepared in a mixture of saline/ethanol/Tween-80 and administered at a dosage of 10 mg/kg.  The rats were injected intraperitoneally with the same volume of vehicle in the Control and SAP groups.  After 24 h of intervention, the rats were killed for further analysis.

tag: cell

value: intestinal epithelial cell

tag: treatment

value: SAP


title: Rat_oil2


title: Patient PF_02_65

description: Group 2


title: Patient PF_02_52

description: Group 2


title: Rat_JZL4

value: SAP treated with JZL184


title: Rat_oil1


title: Patient PF_02_48

description: Group 2


title: mRNA_231_4h_rep_1

description:
231_countTable.fpkm.txt
231_4H_REP1


title: Patient PF_02_47

description: Group 2


title: Rat_JZL2


title: Patient PF_02_56

description: Group 2


title: mRNA_231_2h_rep_2

description:
231_countTable.fpkm.txt
231_2H_REP2


title: Patient PF_02_29

description: Group 2


title: Patient PF_02_35

description: Group 2


title: Rat_con3

value: control plasmid


title: U937_SUV4_rep3  [RNA-seq]

data_processing:
Reads were mapped to human genome assembly (hg19) using STAR (Dobin et al., 2013) with parameters (--outFilterMultimapNmax 10000 --winAnchorMultimapNmax 10000 --outSAMmultNmax 1 --alignTranscriptsPerReadNmax 15000) optimized to account for reads mapping to repeat regions in the genome. Number of reads mapping to ensembl annotated genes (release 87, N=55,774) were quantified using featureCounts (--countMultimapping=T, --fraction=T) (Liao et al., 2014; Yates et al., 2020). Similarly, number of reads mapping to transposable elements (TEtranscripts annotated (Jin et al., 2015)) in human genome (hg19, N=992) were quantified using featureCounts (--countMultimapping=T, --fraction=T).
Genome_build: hg19
Supplementary_files_format_and_content: MATRIX*xls

source_name: U937_SUV39H1 shRNA #4

extract_protocol:
Qiagen RNeasy
TruSeq RNA Library Preparation Kit v2, Set A (48 samples, 12 indexes)

treatment_protocol: U937 cells were transduced with lentiviral shRNA against SUV39H1 or G9a and selected 3 days in puromycin. UNC0638 treated cells were harvest after 3 days

value: SUV39H1 shRNA #4


title: mRNA_231_Veh_rep_2

description:
231_countTable.fpkm.txt
231_VEH_REP2

value: Vehicle DMSO


title: Rat_JZL1


title: Patient PF_02_71

description: Group 2


title: mRNA_549_2h_rep_1

description:
549_countTable.fpkm.txt
549_2H_REP1


title: mRNA_231_Veh_rep_1

description:
231_countTable.fpkm.txt
231_VEH_REP1


title: Patient PF_02_53

description: Group 2


title: U937_SUV_4_rep2  [RNA-seq]


title: Rat_oil3


title: Rat_con2


title: Rat_con1


title: Patient PF_01_143

description: Group 1

value: coronary artery aneurysm


title: Patient PF_02_76

description: Group 2


title: Patient PF_01_17

description: Group 1


title: U937_SUV_2_rep2  [RNA-seq]

source_name: U937_SUV39H1 shRNA #2

value: SUV39H1 shRNA #2


title: U937_SUV_4_rep1  [RNA-seq]


title: Patient PF_02_22

description: Group 2


title: U937_SUV_2_rep1  [RNA-seq]


title: Rat_JZL3


title: mRNA_231_2h_rep_1

description:
231_countTable.fpkm.txt
231_2H_REP1


title: Patient PF_01_122

description: Group 1


title: U937_SCR_rep3  [RNA-seq]

source_name: U937_Scrambled shRNA

value: Scrambled shRNA


title: MCF7 LCN2-/- rep 1

city: New York

first: Jorge

last: Morales-Valencia

state: NY

address: 430 East 29th st.

institute: NYU Langone

data_processing:
The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. DESeq2 package was used to normalize the sample for sequencing depth.
Assembly: hg10
Supplementary files format and content: counts.normalized.csv
Supplementary files format and content: counts.raw.csv

source_name: breast cancer cells

extract_protocol:
cells were washed with PBS and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: MCF7 LCN2+/+ rep 1


title: MCF7 LCN2-/- rep 2


title: MCF7 LCN2+/+ rep 2


title: MCF7 Sen rep 2

data_processing:
The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. DESeq2 package was used to normalize the sample for sequencing depth.
Assembly: hg10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

value: wildtype

tag: media

value: conditioned media from senescent fibroblasts


title: Patient PF_01_20

description: Group 1


title: U937_SCR_rep2  [RNA-seq]


title: U937_SCR_rep1  [RNA-seq]


title: Patient PF_01_14

description: Group 1


title: MCF7 Sen rep 1


title: U937_Mock_rep3  [RNA-seq]

source_name: U937_Mock DMSO

value: Mock DMSO


title: Patient PF_01_146

description: Group 1


title: U937_Mock_rep2  [RNA-seq]


title: Patient PF_01_2

description: Group 1


title: MCF7 Grow rep 3

value: conditioned media from growing fibroblasts


title: Patient PF_01_12

description: Group 1


title: U937_Mock_rep1  [RNA-seq]


title: U937_SUV2_rep3  [RNA-seq]


title: MCF7 Grow rep 2


title: U937_G9a3_rep3  [RNA-seq]

source_name: U937_G9a shRNA #3

value: G9a shRNA #3


title: Patient PF_01_10

description: Group 1

value: plasma


title: Patient PF_01_91

description: Group 1


title: U937_G9a_3_rep2  [RNA-seq]


title: Patient PF_01_19

description: Group 1


title: ChIP_Input_C_rep2

city: Barcelona

first: Debayan

last: Datta

address: Carrer del Rosselló, 132

country: Spain

institute: ISGlobal

data_processing:
ChIP-seq : Single-end 50 bp reads were adaptor trimmed using TrimGalore (version 0.6.5). Trimmed reads were aligned to the hg19 genome (UCSC) using the BowTie 2 Aligner (version 2.4.2). Aligned reads were filtered using SAMtools (version 1.11) to retain reads with MapQ value >= 30. Duplicate read pairs were removed with Picard (version 2.23.8). Peaks were called using MACS2 (version 2.2.7.1) 74 with FDR < 0.01. Normalized read coverage values were obtained using deepTools (version 3.5.0).
genome_build: hg19

extract_protocol:
10x106 MDA-MB-231 cells infected with shControl (C) or shLOXL2 (KD) were crosslinked in suspension using 1% formaldehyde for 10 min at 37 °C. Crosslinking was stopped by adding glycine to a final concentration of 0.125 M for 5 min at room temperature. Cells were collected by centrifugation at 300g for 5min at 4ºC. Cell pellets were resuspended in SDS sonication lysis buffer (1M Tris-HCl pH 8, 10% SDS, 0.5M EDTA) supplemented with protease inhibitors. Extracts were sonicated to generate 200-600 bp DNA fragments, diluted 1:1,5 with equilibration buffer (10mM Tris, 233mM NaCl, 1.66% TritonX-100, 0.166% DOX, 1mM EDTA) supplemented with protease inhibitors and centrifuged at 14,000g for 10min at 4ºC to pellet insoluble material. The primary antibody or an irrelevant antibody (IgG) was added to the sample, and the mixture was incubated overnight with rotation at 4 °C  (a 10% fraction was taken before adding the antibodies as an Input).  Chromatin bound to the antibody was then immunoprecipitated using 25ul of protein A Dynabeads (Thermo Scientific; 10002D) for 2 h with rotation at 4 °C. Precipitated samples were then washed two times with RIPA-LS (10mM Tris-HCl pH 8.0, 140mM NaCl, 1mM EDTA, 0.1% SDS, 0.1% DOX, 1% TritonX-100), two times with RIPA-HS (10mM Tris-HCl pH 8.0, 0.5M EDTA, 5M NaCl, 10% TritonX-100, 10% SDS, 10% DOX) and two times with RIPA-LiCl (10mM Tris-HCl pH 8.0, 1mM EDTA, 250mM LiCl, 0.5% NP-40, 0.5% DOX). Beads were resuspended in 48µl of ChIP elution buffer (10mM Tris-HCl pH 8.0, 5mM EDTA, 300mM NaCl, 0.4% SDS) and 2µl of Proteinase K and incubated at 55ºC for 1h and 65ºC O/N for de-crosslinking (inputs were also incubated for de-crosslinking).   DNA was purified with MinElute PCR purification kit (Qiagen) and eluted in nuclease-free water.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

value: Triple-negative breast cancer derived cell line

value: shControl


title: Patient PF_01_5

description: Group 1


title: MCF7 Sen rep 3


title: U937_G9a_3_rep1  [RNA-seq]


title: Patient PF_01_9

description: Group 1


title: ChIP_BB_KD


title: U937_G9a2_rep3  [RNA-seq]

source_name: U937_G9a shRNA #2

value: G9a shRNA #2


title: U937_G9a_2_rep2  [RNA-seq]


title: ChIP_BB_C


title: Patient PF_01_38

description: Group 1


title: ChIP_Input_KD_rep1


title: Patient PF_01_39

description: Group 1


title: Patient PF_01_32

description: Group 1


title: Patient PF_01_13

description: Group 1


title: U937_4uM_rep3  [RNA-seq]

value: UNC0638 4 uM


title: ChIP_Input_C_rep1


title: U937_4uM_rep2  [RNA-seq]


title: MCF7 Grow rep 1


title: ChIP_AB_KD_rep1


title: ChIP_AB_KD_rep2


title: Patient PF_01_16

description: Group 1


title: U937_2uM_rep3  [RNA-seq]

value: UNC0638 2 uM


title: ChIP_AB_C_rep2


title: Patient PF_01_45

description: Group 1


title: ChIP_Input_KD_rep2


title: ChIP_AB_C_rep1


title: U937_2uM_rep2 [RNA-seq]


title: Patient PF_03_116

description: Group 3

value: normal


title: Patient PF_03_126

description: Group 3


title: U937_2uM_rep1  [RNA-seq]


title: ATAC_KD_rep2

data_processing:
ATAC-seq : Paired-end 50 bp reads were adaptor trimmed using TrimGalore (version 0.6.5). Trimmed reads were aligned to the hg19 genome (UCSC) using the BowTie 2 Aligner (version 2.4.2) with parameters --very-sensitive -X 2000. Aligned reads were filtered using SAMtools (version 1.11) to retain proper pairs with MapQ value >= 30. Read pairs aligning to ChrM were also discarded. Duplicate read pairs were removed with Picard (version 2.23.8). Read alignment was offset as previously described in Buenrostro et al. Nat. Methods 2013. Peaks were called using MACS2 (version 2.2.7.1) with FDR < 0.01. Differentially accessible regions were determined using the DiffBind package (version 3.0.7) in R (version 4.0.2) with FDR < 0.005. Normalized read coverage values were obtained using deepTools (version 3.5.0).
genome_build: hg19

extract_protocol:
For ATAC-seq, 50.000 MDA-MB-231 cells infected with shControl (C) or shLOXL2 (KD) were collected and treated with transposase Tn5 (Nextera Tn5 Transposase, Illumina Cat #FC-121-1030). DNA was purified using AMPure XP beads to remove big fragments (0.5x beads; >1kb) and small fragments (1.5x beads; <100bp). Samples were then amplified using NEBNexthigh-Fidelity 2x PCR Master Mix (New England Labs Cat #M0541) with primers containing a barcode to generate the libraries. DNA was again purified using MinElute PCR Purification Kit (Qiagen) and samples were sequenced with Illumina HiSeq 2500.
ATAC-seq libraries were prepared for sequencing using standard Illumina protocols


title: mock_rep2_h3k9me3

data_processing:
H3K9me2 ChIP-seq reads were mapped to combined genome assembly of human (hg19) and drosophila melanogaster (dm6) using bowtie2 (Langmead and Salzberg, 2012), and reads mapping to multiple regions in the human genome were kept to account for expression of repeat regions in the genome. Total reads mapping to drosophila genome were used to determine the scaling factor, which was later employed for spike-in normalization. PCR-duplicates were identified using samtools markdup (Li et al., 2009), and were collapsed as one read. H3K9me2 enrichment at gene bodies (ensembl annotated, hg19 release 87, N=55774) and transposons (TEtranscripts annotated, hg19, N=992) was computed using featureCounts (--countMultimapping=T, --fraction=T), and were spike-in normalized (Jin et al., 2015; Liao et al., 2014; Yates et al., 2020).
H3K9me3 ChIP-seq reads were mapped to hg19 genome assembly using bowtie2 (Langmead and Salzberg, 2012), and reads mapping to multiple regions in the human genome were kept to account for expression of repeat regions in the genome. PCR-duplicates were identified using samtools markdup (Li et al., 2009), and were collapsed as one read. H3K9me3 enrichment at gene bodies and transposons was computed as is done for aforementioned H3K9me2 enrichment analysis, except were not spike-in normalized due to lack of spike-in normalization data.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

extract_protocol:
The IP was performed with 2ug H3K9me2 antibody (ab1220, abcam) and H3K9me3 (C15500003, Diagenode)
NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1)

tag: antibody

value: H3K9me3 (C15500003, Diagenode)


title: ATAC_KD_rep3


title: Patient PF_03_163

description: Group 3


title: U937_G9a_2_rep1  [RNA-seq]


title: Patient PF_03_128

description: Group 3


title: ATAC_KD_rep1


title: mock_rep1_h3k9me3


title: ATAC_C_rep3


title: Patient PF_03_27

description: Group 3


title: shRNA2_rep2_h3k9me3

source_name: U937_SUV39H1 shRNA


title: ATAC_C_rep2


title: shRNA2_rep1_h3k9me3


title: Patient PF_03_117

description: Group 3


title: U937_4uM_rep1  [RNA-seq]


title: ATAC_C_rep1


title: Patient PF_03_118

description: Group 3


title: Patient PF_03_164

description: Group 3


title: shRNA1_rep1_h3k9me3

value: SUV39H1 shRNA #1


title: RNA_KD_rep3

data_processing:
RNA-seq : 50 bp single-end reads were aligned to the GRCh37.p13 Homo Sapiens reference genome using the STAR Aligner (version 2.7.6a) . Gene level counts were obtained by STAR using the --quantMode GeneCounts option, using gene annotations downloaded from Gencode (Release 19 GRCh37.p13). Differential expression analysis was performed in R (version 4.0.2) using the DESeq2 package (version 1.30.0).
genome_build: GRCh37.p13

extract_protocol:
RNA from MDA-MB-231 was extracted using the PureLink RNA mini kit (Invitrogen) and converted into cDNA using the High Capacity RNA-to-DNA kit (Applied Biosystems) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: RNA_KD_rep2


title: Patient PF_03_108

description: Group 3


title: Mock_rep2_H3K9me2

value: H3K9me2 antibody (ab1220, abcam)


title: Patient PF_03_95

description: Group 3


title: Mock_rep1_H3K9me2


title: RNA_KD_rep1


title: RNA_C_rep3


title: Patient PF_03_68

description: Group 3


title: Patient PF_03_81

description: Group 3


title: Input_Mock_H3K9me2


title: RNA_C_rep2


title: RNA_C_rep1


title: Input_4uM_H3K9me2


title: Input_2uM_H3K9me2


title: Patient PF_03_28

description: Group 3


title: Pregnant peri-blood

city: Guangzhou

first: Ji-Long

address: 483 Wushan Rd

institute: South China Agricultural University

data_processing:
Raw data of fastq files were aligned to the Sscrofa11.1 pig reference genome by using the CellRanger software v3.0.1 (10x Genomics).
The resulting gene counts matrix was processed by R package Seurat.
Assembly: Sscrofa11.1
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample in RDS format.

organism: Sus scrofa

source_name: Peri-blood

extract_protocol:
Endometrial tissues were minced with a blade and then incubated in dissociation buffer containing 2 mg/ml Collagenase II (#C6885, Sigma-Aldrich), 10 mg/ml Dispase II (#354235, Corning) and 50000 U/ml DNase I (#DN25, Sigma-Aldrich) for up to 30 min at 37 °C in a shaking incubator.To remove undigested tissues, the single-cell suspension was then passed through a 40-μm cell strainer and cells were spun down at 250 g at 4°C for 4 min. Red blood cells (RBC) were removed by using RBC Lysis Buffer (#00-4333, Invitrogen). In order Cell viability was measured by AO/PI solution (#CS2-0106, Nexcelom Bioscience). The quality control criteria for single-cell suspension were cell viability > 80% and the percentage of cell clumps < 10%.
The final concentration of single-cell suspension was adjusted to 1000 cells/μl. In order to recover 8000-10000 cells, a volume of 15 µl was loaded into one channel of the ChromiumTM Single Cell B Chip (#1000073, 10x Genomics). Single-cell bar-coding, cDNA synthesis and library preparation were performed by using the Chromium Single Cell 3' Library & Gel Bead Kit v3 (#1000075, 10x Genomics). DNA libraries were then sequenced on an Illumina novaseq 6000 system configured with the paired-end 150-bp protocol for a sequencing depth of approximately 400 million reads per library.

value: Peri-blood


title: 4uM_rep1_H3K9me2


title: 4uM_rep2_H3K9me2


title: Patient PF_03_46

description: Group 3


title: Pregnant tissue

source_name: Endometrium and fetal tissue

value: Endometrium and fetal tissue


title: Patient PF_03_57

description: Group 3


title: Patient PF_03_24

description: Group 3


title: shRNA1_rep2_h3k9me3


title: Patient PF_03_60

description: Group 3


title: 2uM_rep1_H3K9me2


title: ASTRO-HD-JAK2ca6 [C001CIC]

city: Evry

first: Eric

last: Bonnet

address: 2 rue Gaston Crémieux

country: France

institute: CNRGH

description:
C001CIC
replicate 5-astrocyte-HD-JAK2ca-group

data_processing:
paired-end reads were mapped on the mouse genome using Hisat v2.2.1.
reads were counted by gene with featureCounts v2.0.0, using the ensembl annotation.
differentially expressed genes were determined using R v4.0.2 and the DESeq2 v1.28.1 package.
Genome_build: GRCm38
Supplementary_files_format_and_content: count files

extract_protocol:
RNA was extracted from sorted cells with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy micro kit in accordance with the prescribed protocol provided by the supplier.
Full length double strand cDNA librairies were constructed with the Smarter Ultra Low Input RNA kit v4 (Takara-Clontech, Mountain View, CA) with 16 LD-PCR cycles. Libraries were normalized to 750 pg in 5µl as starting materiel to Nextera XT sample preparation kit (Illumina Incorporated, San Diego, CA). Ligation products were amplified with 12 PCR cycles.

tag: strain background

value: knock-in Hdh140

value: striatum

value: astrocytes


title: Patient PF_03_23

description: Group 3


title: ASTRO-HD-GFP5 [C001CIB]

description:
C001CIB
replicate 5-astrocyte-HD-GFP-group

value: AAV-GFP


title: ASTRO-HD-JAK2ca5 [C001CI9]

description:
C001CI9
replicate 5-astrocyte-HD-JAK2ca-group


title: ASTRO-HD-JAK2ca4 [C001CI6]

description:
C001CI6
replicate 4-astrocyte-HD-JAK2ca-group


title: Patient PF_03_61

description: Group 3


title: ASTRO-HD-GFP4 [C001CI5]

description:
C001CI5
replicate 4-astrocyte-HD-GFP-group


title: ASTRO-HD-JAK2ca3 [C001CI4]

description:
C001CI4
replicate 3-astrocyte-HD-JAK2ca-group


title: Patient PF_03_87

description: Group 3


title: ASTRO-HD-GFP3 [C001CI3]

description:
C001CI3
replicate 3-astrocyte-HD-GFP-group


title: ccr4∆ pbp1∆ mutant, stationary phase in YPD

city: Tsukuba

first: Kenji

last: Irie

state: JAPAN

address: 1-1-1 Tennoudai

country: Japan

institute: University of Tsukuba

hyb_protocol: The procedure of labeling is followed by Agilent Yeast Oligo MicrOarray Kit(V2). 100ng Total RNA was used for this assay.

scan_protocol: Agilent Technologies Microarray Scanner System(G2600D)

data_processing: Data normalization were performed using Subio Platform(ver.1.24.5849) and CLC Main Workbench(version 22.0) software. Normalization was done by the quantile method.

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cells were grown at 28° in YPD

extract_protocol: Total RNAs were prepared from yeast cells using ISOGEN reagent (Nippon Gene) and the RNeasy Mini kit (Qiagen), following the instructions of the manufacturer.

value: ccr4delta pbp1delta mutant

tag: growth phase

value: stationary phase in YPD


title: ASTRO-HD-JAK2ca1 [C001CHZ]

description:
C001CHZ
replicate 1-astrocyte-HD-JAK2ca-group


title: Non-pregnant tissue

last: Liu

source_name: Endometrium

value: Endometrium


title: ASTRO-HD-GFP2 [C001CHY]

description:
C001CHY
replicate 2-astrocyte-HD-GFP-group


title: ccr4∆ pbp1∆ mutant, log phase in YPD

source_name: ccr4∆ pbp1∆ mutant, log phase in YPD

label_protocol: The procedure of labeling is followed by Agilent Yeast Oligo MicrOarray Kit(V2). 100ng Total RNA was used for this assay.

value: log phase in YPD


title: 2uM_rep2_H3K9me2


title: ASTRO-HD-GFP1 [C001CHV]

description:
C001CHV
replicate 1-astrocyte-HD-GFP-group


title: MCM_LPS_3

city: Indianapolis

first: Cristian

last: Lasagna-Reeves

address: 320 West 15th Street

institute: Indiana University School of Medicine

description: analysis.xlsx

data_processing:
QC and preprocessing of the data: QC of the raw sequence data with FASTQC (version 0.11.5). no trimming required
Sequencing Quality and Alignment: The sequence reads were mapped to the designated reference genome using STAR (version 2.5) (Spliced Transcripts Alignment to a Reference) (Dobin et al. 2012). To evaluate the quality of the RNA-seq data, number of reads that fall into different annotated regions (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) of the reference genes were determined with bamUtils (version 0.5.9) (Breese and Liu 2013)
Differential gene expression analysis: Low quality mapped reads (including reads mapped to multiple positions) were excluded and featureCounts (version 1.5.1) (Liao, Smyth, and Shi 2013) was used to quantify the gene level expression. Differential gene expression analysis was performed with edgeR (version 3.28.1) (Robinson, Mccarthy, and Smyth 2010). In this workflow, the statistical methodology applied uses negative binomial generalized linear models with likelihood ratio tests.
Genome_build: mm10
Supplementary_files_format_and_content: raw & normalized counts, differential expression, common & unique genes, DAVID functional annotation

source_name: Astrocyte

extract_protocol:
Astrocytes were lysed and RNA was isolated using RNA mini kit
KAPA mRNA Hyperprep Kit (KK8581)

treatment_protocol: Astrocytes were treated with 50ug of total protein from Conditioned Media.

tag: strain

value: Brain

value: Activated MCM


title: MCM_LPS_2

description: analysis.xlsx


title: wild-type, log phase in YPD

source_name: wild-type, log phase in YPD

value: wild-type


title: ccr4∆ mutant, stationary phase in YPD

source_name: ccr4∆ mutant, stationary phase in YPD

value: ccr4delta mutant


title: 2d2_e3__siIrf1_t2d_R2

city: Basel

first: DBM Bioinformatics

last: Core Facility

address: Hebelstrasse 20

institute: University of Basel

description:
Sample 10
processed data file: counts.txt

data_processing:
All reads were trimmed to the same length (51b) to avoid any mapping bias.
Obtained single-end RNA-seq reads were mapped to the mouse genome assembly, version mm10, with RNA-STAR (Dobin et al., Bioinformatics 2013), with default parameters except for reporting only one hit for multimapping reads (outFilterMultimapNmax=10, outSAMmultNmax=1) and filtering reads without evidence in spliced junction table (outFilterType="BySJout").
All subsequent gene expression data analysis was done within the R software (R Foundation for Statistical Computing, Vienna, Austria). Raw reads and mapping quality were assessed by the qQCreport function from the R/Bioconductor software package QuasR (Gaidatzis et al., 2015).
Using RefSeq mRNA coordinates from UCSC (genome.ucsc.edu, downloaded in December 2015) and the qCount function from QuasR package, we quantified gene expression as the number of reads that started within any annotated exon of a gene.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: counts.txt: TSV file (tab separated values) with raw counts for Entrez Genes. Column 1 is Entrez GeneID, Column 2 is length of all exons in nt, and Column 3 and remaining columns contain raw counts.

source_name: normal mammary gland cells

extract_protocol:
Total RNA was extracted using miRNeasy kit (Qiagen) with on column DNase digestion.
200ng RNA was used to generate sequencing libraries with the TruSeq Stranded RNA LT kit (Illumina). Sequencing was performed on an Illumina HiSeq 2500 with the HiSeq SBS kit v4 from Illumina.

treatment_protocol: NMuMG/E9 cells were transfected with 20nM siRNA. One day after transfection, 2ng/ml rhTGFbeta1 was added and cells harvested on day 3 (2d TGFbeta). 0d TGFbeta cells were transfected for three days in the absence of TGFbeta.

value: NMuMG

tag: subclone

value: Subclone 9

tag: sirna

value: TGFbeta

tag: treatment time

tag: replicate


title: Teg49_mutant_3H_R2

city: Hanover

first: Liviu

last: Cengher

state: NH

address: 45 Dewey Field Rd

department: Microbiology and Immunology

institute: Geisel School of Medicine

description: Teg49 mutant empty vector replicate at 3h

data_processing:
Basecalling using Illumina Native App
Reads were mapped to the S. aureus NCTC8325 genome (NC_007795.1) using CLC Genomics Workbench 11
Reads were filtered for reads properly paired and sorted by pairs
Read pairs were mapped using CLC workbench 11
Gene expression counted using CLC workbench 11
Assembly: Staphylococcus aureus subps, aureus  SH1000
Supplementary files format and content: CSV file include raw counting

organism: Staphylococcus aureus

source_name: RNA cell extract

growth_protocol: After an overnight growth in TSB medium, OD measurement have been made and culture was grown 3h in TSB Cm 5 ug/mL

extract_protocol:
Cells were lyzed with glass beads in a Fast Prep instrument and RNAs extract with Phenol/Chloroform (Trizol). Ribosomal RNAs were depleted using the Ribo-zero rRNA remmoval kit (bacteria).
NEBNext ultra directional RNA library prep kit (E7420)

treatment_protocol: no treatment

tag: timepoint

value: transcriptome at 3h growth

tag: genotype/variation

value: Teg49 mutant empty vector


title: 2d1_e3__siCtr_t2d_R2

description:
Sample 9
processed data file: counts.txt

value: siCtr


title: Teg49_mutant_3H_R1


title: MCM_LPS_1

description: analysis.xlsx

tag: tissue


title: MCM_PBS_3

description: analysis.xlsx

value: Contorl MCM


title: pEPSA_Teg49_Comp_3H_R2

description: Teg49 pEPSA complement at 3h

value: Teg49 pEPSA complement at 3h


title: MCM_PBS_2

description: analysis.xlsx


title: pEPSA_Teg49_Comp_3H_R1

description: Teg49 pEPSA complement at 3h


title: MCM_PBS_1

description: analysis.xlsx


title: WT_3H_R2

description: wild type empty vector replicate at 3h

value: wild type empty vector


title: 2d1_e4__siCtr_t2d_R3

description:
Sample 6
processed data file: counts.txt

tag: cell line


title: WT_3H_R1

description: wild type empty vector replicate at 3h


title: ASTRO-HD-JAK2ca2 [C001CI2]

description:
C001CI2
replicate 2-astrocyte-HD-JAK2ca-group

value: knock-in Hdh140

value: striatum

tag: cell type

value: astrocytes


title: ECM_LPS_3

description: analysis.xlsx

value: Activated ECM


title: wild-type, stationary phase in YPD

source_name: wild-type, stationary phase in YPD

tag: genotype

value: stationary phase in YPD


title: 0d2_e4__siIrf1_t0d_R3

description:
Sample 5
processed data file: counts.txt


title: ECM_LPS_2

description: analysis.xlsx

value: Brain


title: ccr4∆ mutant, log phase in YPD

source_name: ccr4∆ mutant, log phase in YPD

value: log phase in YPD


title: 0d1_e4__siCtr_t0d_R3

description:
Sample 4
processed data file: counts.txt


title: ECM_LPS_1

description: analysis.xlsx


title: 0d2_e2__siIrf1_t0d_R1

description:
Sample 2
processed data file: counts.txt


title: ECM_PBS_3

description: analysis.xlsx

value: Control ECM


title: ECM_PBS_2

description: analysis.xlsx


title: ECM_PBS_1

description: analysis.xlsx


title: N. crassa 360min [P4-2]

status: Public on Mar 17 2022

city: West Haven

first: Francesc

last: Lopez

state: CT

department: Department of Genetics

institute: Yale University

description:
P4-2
replicate 2

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 and times. For this experiment, the N. crassa conidial germination was sampled on PDA medium at 25C. 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)
Standard Illumina protocal

tag: time point

value: 360 minutes after inoculation


title: 0d2_e3__siIrf1_t0d_R2

description:
Sample 8
processed data file: counts.txt

value: NMuMG

value: Subclone 9

tag: treatment


title: 0d1_e2__siCtr_t0d_R1

description:
Sample 1
processed data file: counts.txt


title: N. crassa 240min [P3-3]

description:
P3-3
replicate 3

value: 240 minutes after inoculation


title: N. crassa 360min [P4-3]

description:
P4-3
replicate 3


title: N. crassa 240min [P3-2]

description:
P3-2
replicate 2


title: N. crassa 360min [P4-1]

description:
P4-1
replicate 1


title: N. crassa 240min [P3-1]

description:
P3-1
replicate 1


title: 2d2_e4__siIrf1_t2d_R3

description:
Sample 7
processed data file: counts.txt

value: TGFbeta


title: N. crassa 120min [P2-3]

description:
P2-3
replicate 3

value: 120 minutes after inoculation


title: GCT-B 2D

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

description: Gene expression data from GCT-B cultured in 2D condition

hyb_protocol: Following fragmentation, 4 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip (Human Clariom S Array). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software (build.1.2.1.20) using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

label: biotin

source_name: GCT-B cultured in 2D condition

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

growth_protocol: GCT PDCs were maintained in 3D culture condition in STEMPRO hESC SFM medium supplemented with 8 ng/mL basic fibroblast growth factor, 100 unit/mL penicillin, 100 microg/mL streptomycin, 20 mmol/L ROCK inhibitor Y-27632, and 0.1 mmol/L 2-mercaptoethanol using ultra-low-attachment culture dish.

extract_protocol: Total RNA was extracted using ISOGEN reagent (Nippon Gene, Japan).

treatment_protocol: For 2D culture, GCT PDCs were plated on cell culture-treated dish with the 3D culture medium containing 10% fetal bovine serum.

value: GCT-B

value: testicular germ cell tumor

tag: culture method


title: N. crassa 120min [P2-2]

description:
P2-2
replicate 2


title: GCT-A 3D

description: Gene expression data from GCT-A cultured in 3D condition

source_name: GCT-A cultured in 3D condition

value: GCT-A


title: N. crassa 120min [P2-1]

description:
P2-1
replicate 1


title: N. crassa 240min [B4-2]

description: replicate 2

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.


title: GCT-A 2D

description: Gene expression data from GCT-A cultured in 2D condition

source_name: GCT-A cultured in 2D condition


title: GCT-B 3D

description: Gene expression data from GCT-B cultured in 3D condition

source_name: GCT-B cultured in 3D condition


title: N. crassa 240min [B4-3]

description: replicate 3


title: N. crassa 15min [P1-2]

description:
P1-2
replicate 2

value: 15 minutes after inoculation


title: N. crassa 15min [P1-3]

description:
P1-3
replicate 3


title: N. crassa 240min [B4-1]

description: replicate 1


title: N. crassa 15min [P1-1]

description:
P1-1
replicate 1


title: 2d2_e2__siIrf1_t2d_R1

description:
Sample 3
processed data file: counts.txt


title: N. crassa 120min [B3-2]

description: replicate 2


title: N. crassa 120min [B3-1]

description: replicate 1


title: N. crassa 120min [B3-3]

description: replicate 3


title: N. crassa 60min [B2-2]

description: replicate 2


title: N. crassa 60min [B2-1]

description: replicate 1


title: N. crassa 15min [B1-3]

description: replicate 3


title: N. crassa 15min [B1-2]

description: replicate 2


title: U2AF1 WT, U2AF2 eCLIP-seq, rep2a

city: New Haven

first: Giulia

last: Biancon

state: Connecticut

address: 300 George Street

department: Internal Medicine - Yale Cancer Center

description:
U2AF2 eCLIP-seq from HEL cells stably expressing wild-type U2AF1, technical replicate 2a
U2AF1_eCLIP_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: eCLIP-seq

tag: stable transfection

value: U2AF1 wild-type


title: U2AF1 WT, U2AF1 eCLIP-seq, rep1a

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


title: U2AF1 WT, U2AF2 eCLIP-seq, rep1a

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


title: Control13

city: Bethesda

first: Sijung

last: Yun

state: Maryland

address: 8908 Ewing Drive

institute: NIH/JHU

description: Control

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

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

value: Blood

value: Whole blood

tag: age

tag: Sex

value: Male

tag: race

value: Asian


title: Control11

description: Control

value: not collected


title: Control14

description: Control

value: White/Caucasian


title: Control9

description: Control


title: Control8

description: Control


title: Control7

description: Control


title: Control6

description: Control

value: African American