title: HiC-A549-24h-rep2

description: HiC

data_processing:
Hi-C data was processed as described in (Heinz et al., 2018). Briefly, Hi-C reads were trimmed at MboI/DpnII recognition sites (GATC) and aligned to the human genome (GRCh38/hg38) using STAR (Dobin et al., 2013), keeping only read pairs that both map to unique genomic locations for further analysis (MAPQ > 10). All PCR duplicates were also removed. PCA analysis of Hi-C experiments used to define chromatin compartments were performed with HOMER(Lin et al., 2012). For each chromosome, a balanced and distance normalized contact matrix was generated using window size of 50 kb sampled every 25 kb, reporting the ratios of observed to expected contact frequencies for any two regions. The correlation coefficient of the interaction profiles for any two regions across the entire chromosome were then calculated to generate a correlation matrix (also visualized in Figure 1A). This matrix was then analyzed using Principal Component Analysis (PCA) from the prcomp function in R (https://www.r-project.org), and the eigenvector loadings for each 25 kb region along the first principal component were assigned to each region (PC1 values). The PC1 values from each chromosome were scaled by their standard deviation to make them more comparable across chromosomes and analysis parameters. For each chromosome, PC1 values are multiplied by −1 if negative PC1 regions are more strongly enriched for active chromatin regions defined by H3K27ac peaks to ensure the positive PC1 values align with the A/permissive compartment (as opposed to the B/inert compartment). chrY was excluded from the PCA analysis due to its small size and high repeat content. Balanced, normalized Hi-C contact maps were generated at 25 kb resolution for visualization (Figure 1A). Assignment of PC1 values to Gencode gene promoters and other features was performed using HOMER’s annotatePeaks.pl function using the results from the PCA analysis.
Genome_build: Hg38
Supplementary_files_format_and_content: HiC table

extract_protocol:
Twenty-four hours post infection, media was removed from the well, and replaced with Fixation buffer (PBS, 2% FBS, 1% Methanol-Free Formaldehyde). Cells were fixed at room temperature for 10 min. 2M Glycine was then added to a final concentration of 0.125M, and cells were incubated at room temperature for 5min to quench the reaction. Supernatants were then removed wells, and each well was washed 2 times with cold PBS. Cells were then lysed in the well using 250 µl of Lysis Buffer [0.5% SDS + Halt Protease and Phosphatase Inhibitors (Thermo Scientific)]. Cell lysates were collected in a 1.5ml tube. 1.5 mU RNAseA (Thermo Scientific) was added to each lysate, and lysates were then incubated at 37oC for 1h. RNAseA treated lysates were then snap frozen and stored in -80°C.
After thawing, nuclei were collected at 1500 g for 5 minutes at room temperature. Most of the supernatant was discarded, leaving the nuclei in 10 µl liquid. Samples were resuspended in reaction buffer (25 µl 10% Triton X-100, 25 µl 10x Dpn II buffer, 188 µl water) and rotated at 37°C, 8 RPM for 15 minutes. Chromatin was digested overnight (ON) with either 2 µl (100 U) Dpn II (NEB) (later experiments) at 37°C, rotating overhead with 8 RPM. Nuclei were collected by centrifugation at 1500 g for 5 minutes at room temperature, 225 µl of the supernatant were discarded, leaving the nuclei in 25 µl liquid, and overhangs were filled in with Biotin-14-dATP by adding 75 µl Klenow Master Mix (54.45 µl water, 7.5 µl NEBuffer 2, 0.35 µl 10 mM dCTP, 0.35 µl 10 mM dTTP, 0.35 µl 10 mM dGTP, 7.5 µl 0.4 mM Biotin-14-dATP (Invitrogen), 2 µl 10% Triton X-100, 2.5 µl (12.5 U) Klenow fragment (Enzymatics)) and rotating overhead at RT, 8 RPM for 40 minutes. Reactions were stopped by adding 2.5 µl 0.5 M EDTA and placed on ice. Proximity ligation was performed by transferring the entire reaction into 1.5 ml Eppendorf tubes containing 400 µl ligase mix (322.5 µl water, 40 µl 10x T4 DNA ligase buffer (Enzymatics), 36 µl 10% Triton X-100, 0.5 µl 10 % BSA, 1 µl (600 U) T4 DNA ligase (HC, Enzymatics) and rotating ON at 16°C, 8 RPM. Reactions were stopped with 20 µl 0.5 M EDTA, treated with 1 µl 10 mg/ml DNase-free RNAse A for 15 minutes at 42°C, then 31 µl 5 M NaCl, 29 µl 10 % SDS and 5 µl 20 mg/ml DNase-free proteinase K (Thermo) were added, proteins digested for 1 h at 55°C while shaking at 800 RPM, then crosslinks reversed ON at 65°C. After extraction with 600 µl pH 8-buffered phenol/chloroform/isoamyl alcohol (Ambion) followed by extraction with 600 µl chloroform, DNA was precipitated with 1.5 µl (22.5 µg) Glycoblue (Ambion) and 1400 µl 100% ethanol ON at -20°C. After centrifugation for 20’ at 16000g, 4°C, the DNA pellet was washed twice with 80% ethanol, and the pellet air-dried and dissolved in 131 µl TT (0.05% Tween 20/Tris pH 8). DNA (200 ng) was sheared to 300 bp in 130 µl TT on a Covaris E220 sonicator using the manufacturer’s protocol. Biotinylated DNA was captured on Dynabeads MyOne Streptavidin T1 (Thermo) by combining the sonicated DNA sample (130 µl) with 20 µl Dynabeads that had previously been washed with 1x B&W buffer (2X B&W: 10 mM Tris-HCl pH=7.5, 1 mM EDTA, 2 M NaCl) and had been resuspended in 130 µl 2x B&W containing 0.2% Tween 20. The binding reaction was rotated at RT for 45 minutes, and DNA-bound beads were vigorously washed twice with 150 µl 1x B&W/0.1% Triton-X 100, once with 180 µl TET (0.05% Tween 20, 10 mM Tris pH 8, 1 mM EDTA). Libraries were prepared on-beads using an NEBnext Ultra II DNA library prep kit using half the reagent/reaction volumes given in NEB’s instruction manual and 1.6 pmol Bioo DNA sequencing adapters (Illumina TruSeq-compatible) per reaction. Reactions were stopped by adding 5 µl 0.5 M EDTA, beads collected on a magnet and washed twice with 150 µl 1x B&W/0.1% Triton-X 100, twice with 180 µl TET and resuspended in 20 µl TT (0.05% Tween 20, 10 mM Tris pH 8.0). Libraries were amplified by PCR for 10 cycles (98°C, 30s; 10x [98°C, 10s; 63°C, 20s; 72°C, 30s]; 72°C, 2 min; 4°C, ∞), using 10 µl of the bead suspension in a 50 µl reaction with NEBNext Ultra II Q5 2x master mix (NEB) and 0.5 µM each Solexa 1GA/1GB primers (Solexa 1GA: AATGATACGGCGACCACCGA, Solexa 1GB: CAAGCAGAAGACGGCATACGA). Libraries were precipitated onto magnetic beads by adding 40 µl 20% PEG8000/2.5 M NaCl and 2 µl SpeedBeads (8.9 % PEG final) to 48 µl PCR reaction, thorough mixing by vortexing followed by 10-minute incubation at RT. Beads were collected using a magnet and the supernatant discarded. After washing beads twice by adding 180 µl 80% EtOH, moving the tube strip 6x from side to side of the magnet, collecting beads and discarding the supernatant, beads were air-dried, and DNA eluted by adding 20 µl TT. Libraries were sequenced paired-end for 42 cycles each to a depth of approximately 250 million reads per experiment on an Illumina NextSeq 500 sequencer.

treatment_protocol: The day before infection, 200k A549-ACE2 cells were plated in a 12 well dishes. Cells were either mock-infected (PBS only) or infected with SARS-CoV-2 virus at MOI 2

tag: time point


title: Infected_no_siRNA_rep3

status: Public on Mar 30 2021

type: SRA

city: New York

first: Sook Yuin Jessica

last: Ho

state: New York

address: 1468 Madison Avenue

department: Microbiology

country: USA

institute: Icahn School of Medicine at Mount Sinai

description:
RNAseq
J6_S6_CAT.genes.both.count

library_source: transcriptomic

data_processing:
After adaptor removal with cutadapt (Martin, 2011) and base-quality trimming to remove 3′read sequences if more than 20 bases with Q <20 were present, paired-end reads were mapped to the SARS-CoV-2 and human (hg38) reference genomes with STAR . Gene-count summaries were generated with featureCounts (Liao et al., 2014). A numeric matrix of raw read counts was generated, with genes in rows and samples in columns, and used for differential gene expression analysis with the Bioconductor Limma package.
Genome_build: Hg38 and Sars_cov_2.ASM985889v3
Supplementary_files_format_and_content: tab delimited table of raw counts for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: Generation of A549-ACE2 cells was performed as previously described (Blanco-Melo et al., 2020; Daniloski et al., 2020). Briefly, A549 cells were transduced with lentiviral vector pHR-PGK expressing human ACE2 coding sequence. A549 cells were then transduced with the lentivirus in the presence of polybrene (8 μg/ml). Cells were used for downstream assays after 48h post transduction.

extract_protocol:
RNA extracted using the Purelink RNA Minikit (Invitrogen) with DNAseI treatment, according to the manufacturer’s recommendations. RNA quality was determined using the RNA 6000 Nano kit and the Eukaryote Total RNA Nano assay on the Agilent 2100 Bioanalyzer System. RNA quantity was determined by Qubit™ RNA HS Assay Kit.
To  prepare RNA-sequencing libraries, 300 ng of RNA was depleted of ribosomal RNA using NEBNext® rRNA Depletion Kit (Human/Mouse/Rat), according to the manusfacturer’s instructions. Libraries were then prepared from rRNA depleted RNA using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina®, following the manufacturer’s instructions. Final libraries were quantified and sizing was determined using the High Sensitivity DNA Assay reagents and chip in the Agilent 2100 Bioanalyzer System and the Qubit 1X dsDNA HS Assay Kit respectively. Individual libraries were then pooled and sequenced using 75bp paired end on the NextSeq 550 using the NextSeq 500/550 High Output Kit

treatment_protocol: 7.5E4 A549-ACE2 cells were plated in a 24 well dishes. 16 hours post plating, cells were transfected with control, scrambled (siSCR), Top1-targeting (siTOP1) or no siRNA (no siRNA) using Lipofectamine RNAiMax to a final concentration of 50nM. 48hours post transfection, the media was replaced, and fresh media was added to each well. Cells were then mock infected (PBS only) or infected with SARS-CoV-2 at MOI 0.5. 24 hours post infection, media was removed, and cells were lysed in 250ul of Trizol reagent (Thermo Scientific).

tag: cell line

tag: infection

value: Infected

tag: sirna


title: SSE mimetic rep2

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

institute: UCSF

description: RNA-seq

data_processing:
FASTQ reads were mapped to the human genome (hg38) while allowing junction mapping using STAR (v2.7)
Reads from biological replicates were combined prior to alternative splicing analysis.
MISO (v0.5) was used to estimate PSI (percent spliced-in) for alternatively spliced (cassette) exons annotated in the human transcriptome (RefSeq)
Genome_build: hg38
Supplementary_files_format_and_content: misopy summarized files (miso_summary) and delta-psi (miso_bf) values comparing decoy mimetic to scrambled controls.

growth_protocol: Cells were grown in DMEM-based media supplemented with 10% FBS, 1% L-glutamine, 1% Sodium Pyruvate, and 1% Pen/Strep

extract_protocol:
Total RNA was extracted using Norgen total RNA extraction kit (included the on-column DNase treatment step).
ScriptSeq v2 (Expicentre) was used to generate sequencing libraries.

treatment_protocol: Cells were transfected with mimetic RNA or scrambled controls (using Lipofectamin)

tag: rep

tag: transfected with

value: SSE mimetic


title: HiC-A549-24h-rep1

description: HiC

library_source: genomic

molecule: genomic DNA


title: Mock_no_siRNA_rep3

description:
RNAseq
J3_S3_CAT.genes.both.count

value: Uninfected


title: HiC-A549-8h-rep2

description: HiC


title: Infected_siTOP1_rep1

description:
RNAseq
J16_S16_CAT.genes.both.count

value: TOP1 siRNA


title: SSE mimetic rep1

description: RNA-seq


title: Scrambled oligo rep1

description: RNA-seq

value: scrambled oligo


title: HiC-A549-8h-rep1

description: HiC


title: HiC-A549-0h-rep2

description: HiC


title: MDA-LM2 rep2

data_processing:
FASTQ reads were mapped to the human genome (hg38) while allowing junction mapping using STAR (v2.7)
Reads from biological replicates were combined prior to alternative splicing analysis.
MISO (v0.5) was used to estimate PSI (percent spliced-in) for alternatively spliced (cassette) exons annotated in the human transcriptome (RefSeq)
Genome_build: hg38
Supplementary_files_format_and_content: misopy summarized files (miso_summary) and delta-psi (miso_bf) values comparing MDA-LM2 to MDA-Par.


title: Scrambled oligo rep2

description: RNA-seq


title: MDA-231 Parental rep2


title: MDA-LM2 rep1


title: MDA-231 Parental rep1


title: Mock_siSCR_rep3

description:
RNAseq
J9_S9_CAT.genes.both.count

value: Scrambled siRNA


title: 1268 myo primary HOXA13 RNA-seq

city: Urbana

first: Jun

middle: S

last: Song

state: IL

address: 1110 West Green Street, MC 704

department: Department of Physics

institute: University of Illinois, Urbana-Champaign

description: Primary cells

data_processing:
Basecalls were performed using RTA v.2.4.11 on Nextseq instrument.
Reads were adapter trimmed using TrimGalore v0.4.4 with parameters --illumina --stringency 13 --paired
After adapter trimming reads were aligned to the hg19 genome with the UCSC knownGene annotation with STAR options --quantmode
The fourth column of the quantmode output was extracted to obtain reads aligning to features in the correct orientation
Genome_build: hg19
Supplementary_files_format_and_content: Tab deliminated files containing the first and fourth columns of the output from STAR quantmode. The first column is the gene name and the second is the number of reads aligning to the gene in the correct strand specific orientation.

molecule: polyA RNA

source_name: Uterine myometrium

growth_protocol: Normal myometrial tissues were enzymatically digested to obtain primary cells. Primary cells were then plated and grown at 37°C in a humidified cell culture incubator conatining 5% CO2. Cells were used in expreiment after two passages.

extract_protocol:
Cells were harvested for RNA using RNeasy mini kit (Qiagen, 74104).
TruSeq stranded mRNA (Illumina, 20020594) kit was used for the preparation of libraries for RNA-seq. From 100ng of the total RNA, mRNA was purified and fragmented using the reagents provided with the kit. Blunt ends of cDNA were adenylated at 3’ end, adapters ligated, and library amplified. 2nM libraries were pooled, quantified and sequenced as paired end using Nextseq 500/550 high output kit (v2, 75 cycles).

treatment_protocol: Primary myometrial cells were transduced with lentivirus containing either empty or V5-tagged HOXA13 construct in the presence of 6ug/ml polybrene for 18 hours. Fresh SmGM complete media was added then after 24 hours, cells were selected in 2ug/ml puromycin.

tag: patient id


title: 1268 myo primary control RNA-seq

description: Primary cells


title: 1263 myo primary control RNA-seq

description: Primary cells


title: 1165 myo primary HOXA13 RNA-seq

description: Primary cells


title: 1165 myo primary control RNA-seq

description: Primary cells


title: 1263 myo primary HOXA13 RNA-seq

description: Primary cells


title: SC175IPFUP

city: Pittsburgh

first: Tracy

last: Tabib

state: PA

address: 200 Lothrop Street

department: Department of Medicine

institute: University of Pittsburgh

data_processing:
10X Genomics' Cell Ranger 3.0.2 software's mkfastq command was used for basecalling.  It is a wrapper for Illumina's bcl2fastq
Sequenced reads were then mapped to GRCh38 whole genome using 10X Genomics' Cell Ranger 3.0.2 software's cellranger count function
Cell Ranger output of raw_feature_bc_matrix.h5 files were utilized for further downstream analysis in R v3.6.0 with the package Seurat v3.1.1, only cells expressing at least 200 genes were kept for downstream analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_feature_bc_matrix.h5 files contain the cell barcode and gene UMI count matrix for each sample

source_name: upper whole lung

extract_protocol:
Explanted lungs were finely diced and digested for 1 hour in a mix of collagenase A/DNAse I.  A single cell suspension was generated by filtering lungs through 70 micron filters and resuspending cells in PBS containing 0.04% BSA.  Cells were loaded into the 10X Genomics Chromium instrument per manufacturer's directions.
Libraries were constructed according to 10X Genomics' Single Cell 3’ Reagent Kits v2 User Guide

tag: disease

value: Idiopathic pulmonary fibrosis (IPF)

tag: tissue

value: Lung

tag: tissue/cell type

value: whole upper lung lobe, single cell suspension


title: HiC-A549-0h-rep1

description: HiC


title: ptC leio primary control RNAseq

description: Primary cells

source_name: Uterine leiomyoma

growth_protocol: Leiomyoma tissues were enzymatically digested to obtain primary cells. Then, primary cells were plated and grown at 37°C in a humidified cell culture incubator containing 5% CO2. Cells were used in experiment after two passages.

treatment_protocol: 2 x 10(5) primary leiomyoma cells (Passage 2 or 3) were transduced in a 6-well plate with either control or HOXA13 gene silencing lentiviral particles in the presence of 6ug/ml polybrene for 18 hours. Fresh SmGM complete media was added and then after 24 hours, cells were selected in 2ug/ml puromycin for 3 days.

value: C

tag: disease condition

value: leiomyoma

tag: knock down status

value: control


title: ptC leio primary HOXA13kd RNAseq

description: Primary cells

value: HOXA13 knock down


title: SC174IPFLOW

source_name: lower whole lung

value: whole lower lung lobe, single cell suspension


title: pt20 leio primary control RNAseq

description: Primary cells


title: pt20 leio primary HOXA13kd RNAseq

description: Primary cells


title: pt8 leio ATACseq

data_processing:
Basecalls were performed using RTA v.2.4.11 on Nextseq instrument.
Sequenced reads were adapter trimmed using TrimGalore v0.4.4 with parameters --illumina --stringency 13 --paired
Trimmed reads were aligned to the hg19 genome using bowtie2 v2.3.2 with parameters --end-to-end --sensitive --score-min L,-1.5,-0.3 --no-unal
Aligned reads were filtered using samtools v1.7 view with parameters -b -f 2 -F 2828 -F 1024 -q13
Peaks were called from the filtered alignment files using MACS2 v2.1.1 with parameters -f BAMPE -g hs -B --keep-dup 1
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak files containing peak calls returned from MACS2

growth_protocol: Tissues were dissected, snap-frozen in liquid nitrogen and immediately stored at -80°C in small aliquots (about 1g) until further processing

extract_protocol:
The frozen tissues were pulverized in a Covaris CP02 cryoPREP dry pulverizer. About 30mg of powdered tissue was transferred to 1.5ml tubes and resuspended in ice cold Nuclei Lysis Buffer (NIB) (20mM Tris-HCl, 50mM EDTA, 5mM Spermidine, 0.15mM Spermidine, 0.1% mercaptoethanol, 40% glycerol, pH 7.5).  Samples were agitated for 5 minutes on ice, filtered through Miracloth (EMD Millipore Corp), and then centrifuged at 1,100 x g for 10 minutes at 40C. The resulting nuclear pellet was then subjected to transposition as per Buenrostro et al., 2013 with no modifications.
Following transposition the library traces were analyzed on Bioanalyzer and then paired end sequencing was performed on an Illumina Nextseq 500/550.

tag: condition


title: pt11 myo ATACseq

value: myometrium


title: pt12 leio ATACseq


title: pt12 myo ATACseq


title: pt8 myo ATACseq


title: pt6 myo ATACseq


title: pt11 leio ATACseq


title: pt5 myo ATACseq


title: pt6 leio ATACseq


title: pt7 myo ATACseq


title: pt4 leio ATACseq


title: pt7 leio ATACseq


title: pt3 myo ATACseq


title: pt21 leio RNAseq

data_processing:
Basecalls were performed using RTA v.2.4.11 on Nextseq instrument.
Reads were adapter trimmed using TrimGalore v0.4.4 with parameters --illumina --stringency 13 --paired
After adapter trimming reads were aligned to the hg19 genome with the UCSC knownGene annotation with STAR options --quantmode
The fourth column of the quantmode output was extracted to obtain reads aligning to features in the correct orientation
The principal components are obtained using DESeq2 plotPCA modified to return the first 10 PCs. Prior to PCA, a regularized log transform is applied to the count data (DESeq2 rlog option blind=False).
Genome_build: hg19
Supplementary_files_format_and_content: Tab deliminated files containing the first and fourth columns of the output from STAR quantmode. The first column is the gene name and the second is the number of reads aligning to the gene in the correct strand specific orientation.
The first 10 principal components returned by the DESeq2 plotPCA function. The first 10 comma separated values correspond to the ordered PCs. The next four comma separated values correspond to the condition-patient pair, condition, patient, and corresponding feature count file.

extract_protocol:
RNA was isolated from approximately 30mg of the frozen tissue using RNeasy Fibrous tissue kit (Qiagen, 74704). Frozen tissue was finely grounded in mortar-pestle in liquid nitrogen. Tissue lysate prepared by addition of Buffer RLT (guanidine isothiocyanate, along with 10µl β-mercaptoethanol/ml of RLT buffer) was homogenized by spinning down through QIAshredder (Qiagen, 79656). Following the manufacturer’s instructions, RNA was isolated from the homogenized tissue lysates. RNA obtained was analyzed on Bioanalyzer eukaryote total RNA 6000 nano assay (Agilent technologies, 5067) for RNA Integrity. Samples with RNA Integrity Number (RIN) values 8 or above were processed further for next generation sequencing.
TruSeq stranded mRNA (Illumina, 20020594) kit was used for the preparation of libraries for RNA-seq. From 1ug of the total RNA, mRNA was purified and fragmented using the reagents provided with the kit. Blunt ends of cDNA were adenylated at 3’ end, adapters ligated, and library amplified. 2nM libraries were pooled, quantified and sequenced as paired end using Nextseq 500/550 high output kit (v2, 75 cycles).


title: pt21 myo RNAseq


title: pt20 myo RNAseq


title: pt20 leio RNAseq


title: pt18 leio RNAseq


title: pt19 leio RNAseq


title: pt18 myo RNAseq


title: pt5 leio ATACseq


title: pt15 myo RNAseq


title: pt15 leio RNAseq


title: pt14 myo RNAseq


title: pt3 leio ATACseq


title: pt13 leio RNAseq


title: pt12 leio RNAseq


title: pt11 myo RNAseq


title: pt9 myo RNAseq


title: pt12 myo RNAseq


title: pt11 leio RNAseq


title: pt10 myo RNAseq


title: pt13 myo RNAseq


title: pt17 myo RNAseq


title: pt10_1 leio RNAseq

description:
pt10_1 and p10_2 are two different tumors obtained from the same patient. pt10_1 was 7cm and pt10_2 was 5cm in diameter.
leiomyoma_RNAseq_DESeq2_10PCA.csv


title: pt8 myo RNAseq


title: pt9 leio RNAseq


title: pt7 myo RNAseq


title: pt14 leio RNAseq


title: pt17 leio RNAseq


title: pt8 leio RNAseq


title: pt4 myo ATACseq


title: pt7 leio RNAseq


title: pt19 myo RNAseq


title: pt6 myo RNAseq


title: pt6 leio RNAseq


title: pt4 myo RNAseq


title: pt5 leio RNAseq


title: pt5 myo RNAseq


title: pt4 leio RNAseq


title: pt3 leio RNAseq


title: pt2 myo RNAseq


title: pt1 myo RNAseq


title: pt1 leio RNAseq


title: pt3 myo RNAseq


title: pt26 leio H3K4me1

description:
leiomyoma_HOSVD_final_additional_pt_tensor.pt
leiomyoma_additional_tensor_index.txt
leiomyoma_HOSVD_final_additional_pt_projections.txt

data_processing:
Basecalls were performed using RTA v.2.4.11 on Nextseq instrument.
Reads were adapter trimmed using TrimGalore v0.4.4 with parameters --illumina --stringency 13
After adapter trimming reads were aligned to the hg19 genome using Bowtie2 v2.3.2 with parameters --end-to-end --sensitive --score-min L,-1.5,-0.3 --no-unal
Aligned reads were filtered for PCR duplicates using Picard v2.10.1 and then further filtered using samtools v1.7 with parameters -b -F 3588 -q 13
The filtered reads were sorted and converted to bed format. Lastly reads overlapping repeat regions identified by RepeatMaser or segmental duplication regions identified by Variant Tools were removed using bedtools v2.26.0 subtract -A
The code for generating the processed files from the filtered bed files can be found at https://github.com/jssong-lab/DeCET
Genome_build: hg19
Supplementary_files_format_and_content: leiomyoma_HOSVD_final_scaled_tensor.pt is a PyTorch double tensor. The tensor contains ChIP-seq signal at 2 kb binned genomic locations for the hg19 genome for matched leiomyoma and myometrium data from 21 patients. The four indices of the tensor correspond to condition, patient, assay, and genomic location respectively.
leiomyoma_tensor_index.txt is a tab delimited text file that specifies for each condition, patient, and assay the corresponding three indices in leiomyoma_HOSVD_final_scaled_tensor.pt that specify the subtensor corresponding to that sample's data.
leiomyoma_HOSVD_final_projections.txt is a text file that contains the projections onto each HOSVD location vector for each sample in leiomyoma_HOSVD_final_scaled_tensor.pt. A colon separates the tensor index (on the left) from the corresponding projections (on the right) which are comma separated and sorted by the HOSVD order.
leiomyoma_HOSVD_final_core_tensor.pt is a PyTorch double tensor. This is the core tensor from the HOSVD of leiomyoma_HOSVD_final_scaled_tensor.pt
leiomyoma_HOSVD_final_factor_matrix_condition.pt is a PyTorch double tensor. It is the condition space factor matrix from the HOSVD of leiomyoma_HOSVD_final_scaled_tensor.pt
leiomyoma_HOSVD_final_factor_matrix_patient.pt is a PyTorch double tensor. It is the patient space factor matrix from the HOSVD of leiomyoma_HOSVD_final_scaled_tensor.pt
leiomyoma_HOSVD_final_factor_matrix_assay.pt is a PyTorch double tensor. It is the assay space factor matrix from the HOSVD of leiomyoma_HOSVD_final_scaled_tensor.pt
leiomyoma_HOSVD_final_factor_matrix_location.pt is a PyTorch double tensor. It is the location space factor matrix from the HOSVD of leiomyoma_HOSVD_final_scaled_tensor.pt
location_vector_4_differential_regions_pos.txt is a tab delimited text file containing the regions (in 0-start half-open convention) with an observed decrease in histone modifications (H3K27ac, H3K4me3, H3K4me1) in leiomyoma compared to healthy myometrium. These are the regions with significant positive value for the corresponding component of the fourth HOSVD location vector. The first line of the file is a header. Each subsequent line corresponds to one of the differential genomic bins. The first three columns specify the genomic location of the 2kb bin, the fourth  column gives the corresponding vector component value for the fourth HOSVD location vector, and the fifth column gives the characterization of the region as an enhancer or promoter based on the profile of histone modifications.
location_vector_4_differential_regions_neg.txt is a tab delimited text file containing the regions (in 0-start half-open convention) with an observed increase in histone modifications (H3K27ac, H3K4me3, H3K4me1) in leiomyoma compared to healthy myometrium. These are the regions with significant negative value for the corresponding component of the fourth HOSVD location vector. The first line of the file is a header. Each subsequent line corresponds to one of the differential genomic bins. The first three columns specify the genomic location of the 2kb bin, the fourth  column gives the corresponding vector component value for the fourth HOSVD location vector, and the fifth column gives the characterization of the region as an enhancer or promoter based on the profile of histone modifications.
location_vector_7_differential_regions_pos.txt is a tab delimited text file containing the regions (in 0-start half-open convention) with observed higher histone modifications (H3K27ac, H3K4me3, H3K4me1) in leiomyomas with mutations in exon 1 or 2 of MED12 compared to MED12 wild-type leiomyomas. These are the regions with significant positive value for the corresponding component of the seventh HOSVD location vector. The first line of the file is a header. Each subsequent line corresponds to one of the differential genomic bins. The first three columns specify the genomic location of the 2kb bin, the fourth  column gives the corresponding vector component value for the seventh HOSVD location vector, and the fifth column gives the characterization of the region as an enhancer or promoter based on the profile of histone modifications.
location_vector_7_differential_regions_neg.txt is a tab delimited text file containing the regions (in 0-start half-open convention) with observed higher histone modifications (H3K27ac, H3K4me3, H3K4me1) in MED12 wild-type leiomyomas compared to leiomyomas with mutations in exon 1 or 2 of MED12. These are the regions with significant negative value for the corresponding component of the seventh HOSVD location vector. The first line of the file is a header. Each subsequent line corresponds to one of the differential genomic bins. The first three columns specify the genomic location of the 2kb bin, the fourth  column gives the corresponding vector component value for the seventh HOSVD location vector, and the fifth column gives the characterization of the region as an enhancer or promoter based on the profile of histone modifications.
leiomyoma_HOSVD_final_additional_pt_tensor.pt is a PyTorch double tensor. The tensor contains ChIP-seq signal at 2kb binned genomic locations for the hg19 genome for 7 leiomyoma samples. The three indices correspond to patient, assay, and genomic location respectively
leiomyoma_additional_tensor_index.txt is a tab delimited text file specifying for each additional patient and assay the two indices of leiomyoma_HOSVD_final_additional_pt_tensor.pt that specify the subtensor corresponding to that sample's data.
leiomyoma_HOSVD_final_additional_pt_projections.txt is a text file that contains the projections onto each HOSVD location vector for each additional leiomyoma patient and assay in leiomyoma_HOSVD_final_additional_pt_tensor.pt. A colon separates the tensor index (on the left) from the corresponding projections (on the right) which are comma separated and sorted by the HOSVD order.

extract_protocol:
About 1g of frozen tissues for each case were pulverized in a Covaris CP02 cryoPREP dry pulverizer (setting 5, 4 strikes) making sure to rechill the tissue in liquid nitrogen between strikes. Further, tissue was finely powdered with mortar-pestle in liquid nitrogen, followed by fixation with 1% paraformaldehyde for 15 minutes at room temperature. To stop cross-linking 1X glycine (Cell Signaling Technology, 9003) was added for 5 minutes. Cross-linked tissues were either stored at -80°C or used immediately for ChIP. The cross-linked tissues were processed for ChIP using the SimpleChIP Kit (Cell Signaling Technology, 9003).
Library preparation of the purified DNA from ChIP was performed by following the Kapa hyper prep protocol (Kapa Biosystems, KK8502). 1-5ng of the DNA was end-repaired and A-tailed according to the kit instructions. Adapters were ligated at 20°C for 15 minutes with post-ligation cleanup and libraries were size selected for 250-450 bp fragments using 0.6X- 0.8X ratio of AMPure beads (Beckman Coulter, A63881). The size selected libraries were amplified and checked for size by Agilent Bioanalyzer for high sensitivity DNA (Agilent technologies, 5067). Libraries were diluted to 2nM, pooled and quantified with Kapa quantification kit (Kapa biosystems, KK4835) before single end sequencing with Nextseq 500/550 high output kit (v2, 75 cycles).

tag: chip antibody

value: Diagenode, C15410194


title: pt10_2 leio H3K27ac

value: Active motif, 39133


title: pt25 leio H3K4me3

value: Diagenode, C15410003


title: pt25 leio H3K27ac


title: pt25 leio H3K4me1


title: pt2 leio RNAseq


title: pt10_2 leio H3K4me3


title: pt25 leio input


title: pt10_2 leio input


title: pt26 leio H3K27ac


title: pt24_2 leio H3K27ac


title: pt24_2 leio H3K4me3


title: pt24_1 leio H3K4me1


title: pt24_1 leio H3K4me3


title: pt26 leio input


title: pt24_2 leio input


title: pt24_2 leio H3K4me1


title: pt23 leio H3K4me1


title: pt23 leio H3K27ac


title: pt10_2 leio H3K4me1


title: pt24_1 leio H3K27ac


title: pt23 leio H3K4me3


title: pt26 leio H3K4me3


title: pt22 leio H3K4me3


title: pt22 leio H3K4me1


title: pt22 leio H3K27ac


title: pt22 leio input


title: pt21 leio input

description:
leiomyoma_HOSVD_final_scaled_tensor.pt
leiomyoma_tensor_index.txt
leiomyoma_HOSVD_final_projections.txt
leiomyoma_HOSVD_final_core_tensor.pt
leiomyoma_HOSVD_final_factor_matrix_condition.pt
leiomyoma_HOSVD_final_factor_matrix_patient.pt
leiomyoma_HOSVD_final_factor_matrix_assay.pt
leiomyoma_HOSVD_final_factor_matrix_location.pt
location_vector_4_differential_regions_pos.txt
location_vector_4_differential_regions_neg.txt
location_vector_7_differential_regions_pos.txt
location_vector_7_differential_regions_neg.txt


title: pt21 leio H3K4me1


title: pt21 leio H3K27ac


title: pt21 myo H3K27ac


title: pt21 leio H3K4me3


title: pt21 myo H3K4me3


title: pt21 myo H3K4me1


title: pt20 leio H3K4me1


title: pt21 myo input


title: pt20 leio H3K4me3


title: pt20 leio H3K27ac


title: pt20 myo H3K4me1


title: pt20 myo H3K4me3


title: pt24_1 leio input

description:
pt24_1 and p24_2 are two different tumors obtained from the same patient. pt24_1 was 7cm and pt24_2 was 3.5cm in diameter.
leiomyoma_HOSVD_final_additional_pt_tensor.pt
leiomyoma_additional_tensor_index.txt
leiomyoma_HOSVD_final_additional_pt_projections.txt


title: pt23 leio input


title: pt20 myo input


title: pt19 leio H3K4me3


title: pt19 leio H3K4me1


title: pt19 leio input


title: pt20 myo H3K27ac


title: pt19 leio H3K27ac


title: pt19 myo H3K4me3


title: pt19 myo input


title: pt19 myo H3K4me1


title: pt19 myo H3K27ac


title: pt20 leio input


title: pt18 leio input


title: pt18 myo H3K4me1


title: pt18 myo H3K4me3


title: pt18 myo input


title: pt18 leio H3K4me3


title: pt17 leio H3K4me1


title: pt17 myo H3K4me3


title: pt17 myo input


title: pt17 myo H3K27ac


title: pt17 leio input


title: pt17 myo H3K4me1


title: pt17 leio H3K27ac


title: pt17 leio H3K4me3


title: pt16 leio H3K27ac


title: pt16 leio H3K4me3


title: pt16 leio input


title: Acesulfame potassium_3

city: Brisbane

first: Jianhua

last: Guo

address: Research Road, Level 4 Gehrmann Building

department: Australian Centre for Water and Environmental Biotechnology

country: Australia

institute: University of Queensland

data_processing:
Base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18).
The NGS QC toolkit (version 2.3.3) was used to treat the raw sequence reads to trim the 3’-end residual adaptors and primers, and the ambiguous characters in the reads were removed. Then, the sequence reads consisting of at least 85% bases were progressively trimmed at the 3’-ends until a quality value ≥ 20 were kept. Downstream analyses were performed using the generated clean reads of no shorter than 75 bp.
The clean reads of each sample were aligned to the E. coli reference genome (NC_000913), P.putida reference genome (NC_002947), and IncPα plasmid reference genome (L27758) using SeqAlto (version 0.5). Cufflinks (version 2.2.1) was used to calculate the strand-specific coverage for each gene, and to analyze the differential expression in triplicate bacterial cell cultures. The statistical analyses and visualization were conducted using CummeRbund package in R (http://compbio.mit.edu/cummeRbund/).
Gene expression was calculated as fragments per kilobase of a gene per million mapped reads (FPKM), a normalized value generated from the frequency of detection and the length of a given gene.
Genome_build: NC_000913.3, NC_002947.4, L27758.1
Supplementary_files_format_and_content: Excel files include log2(Fold Change) values for each sample

organism:
Plasmid RP4
Escherichia coli K-12
Pseudomonas putida KT2440

source_name: E. coli K-12 LE392, P. putida KT2440, and IncPα RP4 plasmid

growth_protocol: Liquid LB culture at 30℃

extract_protocol:
Bacterial cells were then harvested by centrifugation at 8000 × g for 10 min. Total RNA was extracted from the mutants using the QIAGEN miRNeasy Mini Kit (QIAGEN, Germany) manufacturer’s protocol with one extra bead-beating step to completely lyse the bacterial cells.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mixed wild-type strains E. coli K-12 LE392, P. putida KT2440 and IncPα RP4 plasmid were cultured in triplicate in 10 mL 0 and 3 mg/L artificial sweeteners (SAC, SUC, ASP, and ACE-K), at 25 °C, without shaking

tag: strain

value: E. coli K-12 LE392, P. putida KT2440, IncP[alpha] RP4 plasmid

tag: treatment

value: 3 mg/L Acesulfame potassium


title: pt16 myo H3K4me1


title: Acesulfame potassium_2


title: pt16 myo input


title: pt16 myo H3K4me3


title: pt18 myo H3K27ac


title: pt16 myo H3K27ac


title: Acesulfame potassium_1


title: pt15 leio H3K4me1


title: Aspartame_3

value: 3 mg/L aspartame


title: pt18 leio H3K27ac


title: pt18 leio H3K4me1


title: Aspartame_2


title: pt15 leio H3K4me3


title: pt16 leio H3K4me1


title: pt15 leio H3K27ac


title: Sucralose_2

value: 3 mg/L sucralose


title: Sucralose_3


title: Sucralose_1


title: ControlZG_3


title: pt15 leio input


title: Saccharin_3

value: 3 mg/L saccharin


title: Saccharin_2


title: 2D2-WT 2

city: Vienna

first: Wilfried

last: Ellmeier

address: Lazarettgase 19

department: Institute of Immunology

country: Austria

institute: Medical University of Vienna

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.4.0.38 was used for the data acquisition on the sequencing instrument.
On-instrument base-calling performed by the Illumina Real-Time Analysis (RTA) software 2.7.7.
BCL to BAM file conversion and demultiplexing with custom programmes (https://github.com/DanieleBarreca/picard/) based on Picard tools 2.19.2 (https://broadinstitute.github.io/picard/)
Spliced genome alignments to GRCm38 (UCSC Genome Browser mm10) and Ensembl reference transcriptome e96 (April 2019) with STAR 2.5.2b and options recommended by the ENCODE project (--alignIntronMax 1000000 --alignIntronMin 20 --alignMatesGapMax 1000000 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 20 --outFilterType BySJout)
Differential expression modelling with Bioconductor 3.9 package DESeq2 1.24.0, running under R 3.6.1.
Genome_build: UCSC hg38 based on GRCh38
Supplementary_files_format_and_content: Per gene and sample raw (integer) counts and DESeq2-calculated FPKMs in tab-separated value (TSV) format

organism: Mus musculus

source_name: popliteal lymph node

extract_protocol:
500 FACS-purified 2D2+ CD4+ T cells were sorted into 96 wells filled with 3.8 μl 0.2 % (vol/vol) Triton X-100 solution and 0.2 μl RNase inhibitor (2313A, Clontech).
For the generation of full-length cDNA, the Smart-seq2 protocol (Picelli, S. et al, Nat Protoc. 2014 Jan;9(1):171-81. doi:10.1038/nprot.2014.006) was used.
The subsequent library preparation from the amplified cDNA was performed using the Nextera XT DNA library prep kit (Illumina).
For sequencing, libraries were pooled, diluted and sequenced on Illumina HiSeq 3000/4000 using 50 bp single-read chemistry.

value: popliteal lymph node

tag: cell type

value: CD4+ T cell

tag: genotype


title: 2D2-WT 3


title: 2D2-WT 1


title: ControlZG_1


title: ControlZG_2


title: 2D2-HDAC1-cKO 1


title: pt15 myo H3K27ac


title: 2D2-HDAC1-cKO 2


title: 2D2-HDAC1-cKO 3


title: pt15 myo H3K4me1


title: pt14 leio H3K4me1


title: Saccharin_1


title: C. crescentus, GroESL depletion, 4h, 30C

city: Stockholm

first: Kristina

last: Jonas

address: Svante Arrheniusväg 20 C

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

country: Sweden

institute: Stockholm University

data_processing:
Data processing was performed by Genewiz.
Sequence reads were trimmed to remove low quality bases at ends, mapped to the reference genome (C. crescentus NA1000), hit counts were calculated and RPKM values for genes determined
Samples were compared to determine relative changes in gene expression (fold changes)
Supplementary_files_format_and_content: Excel files containing differentially expressed genes (fold-change of original RPKM values and the normalized RPKM values)

organism: Caulobacter vibrioides NA1000

source_name: Caulobacter crescentus

growth_protocol: Cultures were grown in mid-log phase in rich medium (PYE) while shaking.

extract_protocol:
Total RNA was extracted using the RNAeasy kit (Qiagen) according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols (done by Genewiz)

tag: synonym

value: Caulobacter crescentus

value: SG300 (Pxyl-groES-groEL)

tag: growth and treatment protocol

value: Cells were grown to mid-log phase in PYE supplemented with the inducer xylose. Cells were then washed two times with PYE by centrifugation (6000 g, 4 min) before resuspension in PYE medium devoid of xylose. Cells were grown for four hours in PYE without xylose before sampling.


title: C. crescentus, wt, 30C

value: Cells were grown in mid-log phase in PYE.


title: pt14 leio H3K4me3

value: leiomyoma


title: pt15 myo input


title: pt14 leio H3K27ac


title: pt14 leio input


title: LN95 ARCC-32 48hr rep2

city: Boston

first: Steven

last: Balk

state: MA

address: 330 Brookline Avenue

institute: Beth Israel Deaconess Medical Center

data_processing:
pair-end 150bp sequence tags from DNBSEQ G400 sequencer were subjected to data cleaning by SOAPnuke
Hisat and Bowtie2 were then used to align the clean data after filtering to reference genome (hg19) and gene respectively
Genome_build: hg19
Supplementary_files_format_and_content: fpkm

source_name: LN95 ARCC-32 48hr

growth_protocol: Cells were maintained in phenol red-free RPMI1640 medium with 5% charcoal dextran stripped FBS

extract_protocol:
RNA was extracted from cells using the RNeasy Mini kit (#74104, Qiagen)
For the RNA-seq analysis, quality control (QC) and sequencing were performed by BGI (North America). Total RNA of each sample was qualified by Agilent 2100 Bioanalyzer, BGI in-house kit was used for library prep, and the sequencing platform is DNBSEQ G400.
oligo-dT primed BGI in-house kit

treatment_protocol: Cells were treated with DMSO vehicle control or ARCC-32 at 100 nM for 16, 24, or 48 hours

tag: cell line

value: prostate cancer cell line

value: ARCC-32 48hr


title: LN95 ARCC-32 48hr rep1


title: LN95 ARCC-32 24hr rep2

source_name: LN95 ARCC-32 24hr

value: ARCC-32 24hr


title: pt15 myo H3K4me3

value: myometrium


title: LN95 ARCC-32 24hr rep1


title: LN95 ARCC-32 16hr rep2

source_name: LN95 ARCC-32 16hr

value: ARCC-32 16hr


title: LN95 ARCC-32 16hr rep1


title: LN95 vehicle control rep2

source_name: LN95 vehicle control

value: vehicle control


title: LN95 vehicle control rep1


title: pt14 myo H3K4me1

value: Diagenode, C15410194


title: pt14 myo H3K27ac

value: Active motif, 39133


title: pt14 myo input


title: pt13 leio H3K4me3

value: Diagenode, C15410003


title: pt13 leio H3K4me1


title: pt13 leio H3K27ac


title: pt13 leio input


title: Aspartame_1

value: E. coli K-12 LE392, P. putida KT2440, IncP[alpha] RP4 plasmid

value: 3 mg/L aspartame


title: pt13 myo H3K4me1


title: Rnase H treated DRIP-seq

city: San Antonio

first: Rong

last: Li

state: TX

address: 7703 Floyd Curl Drive

department: Molecular Medicine

institute: University of Texas Health Science Center at San Antonio

description:
Library strategy: DRIP-seq
RNase treatment overnight was performed before immunoprecipitation.

data_processing:
Reads in FASTQ file were aligned to mouse genome by BWA, a software package for mapping low-divergent sequences against reference genome, and only unique mapped reads were selected for analysis.
BELT, a peak-calling program, was used to identify the peaks for uniquely mapped reads. The peak calling parameter is window size 250 bp and p-value 0.05
Genome_build: mm9

source_name: primary mouse mammary epithelial cells

extract_protocol:
primary mammary epithelial isolation protocol: Thoracic and inguinal mammary glands were isolated from 6-8 week virgin mice. Lymph nodes were removed from the inguinal glands. Tissues were quickly minced with scissors and digested with Collagenase and Hyaluronidase for 45 min with gentle shaking. Samples were vortexed vigorously for 15 sec every 15 min during the digestion.  After tissue digestion mammary organoids were collected and red blood cells were lysed. Organoids were further digested by Trypsin and Dispase, and single mammary epithelial cells were obtained after passing through cell strainer.
Sonicated (ChIP-seq) or digested (DRIP-seq) genomic DNA was immunoprecipitated by specific antibodies.
ChIP-seq and DRIP-seq libraries were built following the instruction of MicroPlex library preparation kit (Diagenode, C05010011).  For RNAPII ChIP-seq, 1 ng of ChIP DNA was used for a total of 15 cycles of PCR amplification.  For NELF-A/B ChIP-seq, 0.2 ng ChIP DNA were used for a total of 18 cycles of PCR amplification.  For DRIP-seq, a total of 15 cycles of PCR amplification was performed. After amplification, libraries were purified using Agencourt AMPure XP system (Beckman Coulter, A63880) following the product manual.  Quantity of the libraries was measured with Qubit dsDNA HS Assay Kit (Life Technologies, Q32851), and quality of the libraries was verified using Bioanalyzer 2100.

value: mammary gland

value: mixed

value: R-loop (Kerafast, ENH001)


title: pt14 myo H3K4me3


title: DRIP-seq rep 1 and 2

description: Library strategy: DRIP-seq


title: pt13 myo H3K27ac


title: RNA Pol II ChIP-seq rep 1 and 2

value: RNA Pol II (Abcam, ab5408)


title: pt13 myo input


title: pt12 leio H3K4me1


title: cap LEC, biological rep3

type: RNA

city: Uppsala

first: Ying

last: Sun

address: Dag Hammarskjölds väg 20

institute: Uppsala University

description: cap LEC, biological rep3

hyb_protocol: GeneChip® ST Arrays (GeneChip® Mouse Transcriptome Array 1.0) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm, according to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 3, Affymetrix Inc., Santa Clara, CA).

scan_protocol: The arrays were then washed and stained using the Fluidics Station 450 and finally scanned using the GeneChip® Scanner 3000 7G.

data_processing: The raw data was normalized to gene level  using the robust multi-array average (RMA) method (Irizarry et al, 2003; Li & Wong, 2001) and data was logarithm based 2 transformed.

label: biotin

source_name: cap LEC

label_protocol: RNA concentration and quality were evaluated using the Agilent 2100 Bioanalyzer system (Agilent Technologies Inc, Palo Alto, CA). 500 pg of total RNA was estimated from each sample and this starting amount was used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChip® WT Pico Reagent Kit User Manual (P/N 703262 Rev 1 Affymetrix Inc., Santa Clara, CA).

extract_protocol: Extraction of RNA was performed using RNeasy Micro Kit, Qiagen

value: ear skin

tag: age

value: adult


title: BEC biological rep1

description: BEC biological rep1

source_name: BEC


title: cap LEC, biological rep2

description: cap LEC, biological rep2


title: BEC biological rep2

description: BEC biological rep2


title: pt13 myo H3K4me3


title: pre-col LEC biological rep2

description: pre-col LEC biological rep2

source_name: pre-col LEC


title: pre-col LEC biological rep1

description: pre-col LEC biological rep1


title: pt12 leio H3K27ac

value: leiomyoma


title: NELF-B ChIP-seq

value: NELF-B homemade


title: col LEC biological rep2

description: col LEC biological rep2

source_name: col LEC


title: col LEC biological rep1

description: col LEC biological rep1


title: BEC biological rep3

description: BEC biological rep3


title: cap LEC biological rep1

description: cap LEC biological rep1


title: NELF-A ChIP-seq

value: NELF-A homemade


title: col LEC biological rep3

description: col LEC biological rep3


title: pre-col LEC biological rep3

description: pre-col LEC biological rep3


title: pt12 leio H3K4me3


title: pt12 myo H3K4me1

value: myometrium


title: pt12 myo H3K4me3


title: pt12 myo H3K27ac


title: MDA231_AbemaDocetax_rep2

first: Eugen

last: Dhimolea

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description:
MDAMB231 3D culture docetaxel persister treated with abemaciclib followed by abemaciclib and docetaxel
processed data file:
GSE162285_upload2__readcount.HGNCSYMBOL.GCHR38.txt

data_processing:
RNA sequencing using NovaSeq PE150 at the Novogene Corporation Inc
Differential gene expression analysis for the RNA-seq data using the bioconductor DEseq2 package
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Breast cancer cell line

growth_protocol: Cancer cells were grown in  in matrigel  in  DMEM/10% FBS and treated as indicated

extract_protocol:
The gels collected at the end of treatment and were mechanicaly and enzymatically disintegrated.  Next, the RNA was extracted from the tumor cells using RNA extraction kit (Qiagen), The lysates from in vitro samples were also supplemented with ERCC RNA spike-in mix to adjust for the cell number. RNA was sequenced using NovaSeq 150PE
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DMSO, docetaxel (100nM), afatinib (100nM), abemaciclib (250nM), NVP2 (1uM)

tag: culture setting

value: MDA231 organoids cell-cycle arrested (with abema) docetaxel-persister


title: MDA231_AbemaDocetax_rep3


title: MDA231_AbemaDocetax_rep1


title: Non-pregnant rep1

city: London

first: Ruben

last: Esse

address: Guy's Hospital, Great Maze Pond

department: Department of Medical and Molecular Genetics

country: United Kingdom

institute: King’s College London

description: SAMPLE 5

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were quantile normalised and processed with variance stabilizing transformation using the Lumi package in R/Bioconductor.

label: Biotin

source_name: Non-pregnant dam pituitary

label_protocol: Labelled targets were generated from the total RNA and hybridised to the MouseWG-6 v2.0 Expression BeadChip (Genomics Centre, KCL).

extract_protocol: RNA for microarray analysis was extracted using a Qiagen RNA extraction kit, in-cluding the DNase step. The total RNA quality was verified using an Agilent 2200 TapeS-tation and concentrations were measured by the Qubit fluorometer.

tag: group

value: Non-pregnant

value: Pituitary gland


title: Non-pregnant rep4

description: SAMPLE 8


title: Non-pregnant rep2

description: SAMPLE 6


title: pt12 myo input

source_name: Uterine myometrium

tag: patient id


title: Pregnant rep8

description: SAMPLE 12

source_name: Pregnant dam pituitary

value: Pregnant

tag: tissue


title: MDA231_AbemaOnly_rep2

description:
MDAMB231 3D culture docetaxel persister treated with abemaciclib
processed data file:
GSE162285_upload2__readcount.HGNCSYMBOL.GCHR38.txt

value: MDA231 organoids cell-cycle arrested (with abema)


title: MDA231_AbemaOnly_rep3


title: Pregnant rep6

description: SAMPLE 10


title: Pregnant rep7

description: SAMPLE 11


title: Pregnant rep3

description: SAMPLE 3


title: MDA231_Vehicle_rep2

description:
MDAMB231 3D culture from control samples (same experiment with abemaciclib +/- docetaxel)
processed data file:
GSE162285_upload2__readcount.HGNCSYMBOL.GCHR38.txt

value: MDA231 organoids control


title: Non-pregnant rep3

description: SAMPLE 7


title: Pregnant rep1

description: SAMPLE 1


title: Pregnant rep5

description: SAMPLE 9


title: MDA231_AbemaOnly_rep1


title: pt11 leio H3K4me1

source_name: Uterine leiomyoma

value: Diagenode, C15410194


title: pt11 leio H3K4me3

value: Diagenode, C15410003


title: Pregnant rep4

description: SAMPLE 4


title: Pregnant rep2

description: SAMPLE 2


title: MDA231_PersistCDK9i_rep2

description:
MDAMB231 3D culture docetaxel persister treated with NVP2
processed data file:
GSE162285_upload2__readcount.HGNCSYMBOL.GCHR38.txt

value: MDA231 organoids docetaxel-persister treated with CDK9 inhibitor


title: pt11 leio H3K27ac

value: Active motif, 39133


title: MDA231_Persist_rep3

description:
MDAMB231 3D culture docetaxel persister (same experiment with NVP2 +/- docetaxel)
processed data file:
GSE162285_upload2__readcount.HGNCSYMBOL.GCHR38.txt

value: MDA231 organoids docetaxel-persister


title: MDA231_Persist_rep1


title: pt11 leio input


title: MDA231_Persist_rep2


title: MDA231_PersistCDK9i_rep3


title: pt11 myo H3K4me1


title: MDA231_Naive_rep3

description:
MDAMB231 3D culture from control samples (same experiment with NVP2 +/- docetaxel)
processed data file:
GSE162285_upload2__readcount.HGNCSYMBOL.GCHR38.txt


title: MDA231_Naive_rep2


title: pt11 myo H3K4me3


title: MDA231_Vehicle_rep1


title: HSC-sh-EPO-3

city: Beijing

first: Yiming

last: Lu

address: Taiping Road

country: China

institute: State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine

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 quantifying abundances of transcripts by using kallisto program.
log2(count) and TPM were calculated using a protocol from DESeq2 package.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with log2(counts) and TPM for every gene and every sample.

source_name: CD34+ HPCs

growth_protocol: hypoxia (1% O2) following 2 days of EPO stimulation

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: genotype/variation


title: MDA231_PersistCDK9i_rep1


title: pt11 myo H3K27ac

tag: disease condition


title: MDA231_Naive_rep1


title: MDA231_Vehicle_rep3


title: HSC-sh-EPO-2

value: hypoxia (1% O2) following 2 days of EPO stimulation


title: HSC-NC-EPO-1

value: NC


title: pt10_1 leio H3K4me1

value: leiomyoma


title: pt10_1 leio H3K4me3


title: HSC-NC-EPO-3


title: HSC-NC-EPO-2


title: pt11 myo input


title: siRNA against hnRNP K, replicate 1

first: Pietro

last: Fratta

address: Queen Square House

institute: University College London

data_processing:
Each sample was aligned to the human genome (build hg38) using STAR  (v 2.7.2) using GENCODE v30 as the transcript reference.
Splice junction reads were extracted from each alignment file using Regtools (v0.5.1)
Gene abundance was estimated using RSEM v1.3.1 (cite) using the GENCODE v30 transcript set.
Genome_build: hg38
Supplementary_files_format_and_content: Summed transcript abundances with expected counts, FPKM and TPM.
Supplementary_files_format_and_content: Counts of junction spanning reads in BED12 format.

source_name: SH-SY5Y cells

extract_protocol:
After 48 hours, cells were collected and subjected to further analysis. Three replicates were taken for each condition.
Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads and then fragmented randomly by addition of fragmentation buffer. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA was purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA are converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library was prepared by PCR amplification and purification of PCR products by AMPure XP beads.  Paired-end 150bp reads were sequenced on an Illumina NovaSeq and base-called with CASAVA.

treatment_protocol: SH-SY5Y cells (80X104) were seeded in 6-well plates and transfected with a mix composed of 150 μl Opti-MEM (Life-Technologies), 3 μl of 40 μM siRNA and 9 μl Lipofectamine RNAiMAX (Invitrogen, ThermoFisher) for a final siRNA concentration of 80 nM. Gene knockdown was performed according to the manufacturer’s instructions. The siRNA sense sequences used for transfections were fire-fly luciferase (control) 5’-uaaggcuaugaagagauac-3’; TDP-43 5’-gcaaagccaagaugagccu-3’; and hnRNP K 5’-aauauuaaggcucuccguaca-3’.

value: siRNA against hnRNP K


title: siRNA against hnRNP K, replicate 2


title: siRNA against firefly luciferase, replicate 2

value: siRNA against firefly luciferase


title: siRNA against hnRNP K, replicate 3


title: pt10_1 leio input

description:
pt10_1 and p10_2 are two different tumors obtained from the same patient. pt10_1 was 7cm and pt10_2 was 5cm in diameter.
leiomyoma_HOSVD_final_scaled_tensor.pt
leiomyoma_tensor_index.txt
leiomyoma_HOSVD_final_projections.txt
leiomyoma_HOSVD_final_core_tensor.pt
leiomyoma_HOSVD_final_factor_matrix_condition.pt
leiomyoma_HOSVD_final_factor_matrix_patient.pt
leiomyoma_HOSVD_final_factor_matrix_assay.pt
leiomyoma_HOSVD_final_factor_matrix_location.pt
location_vector_4_differential_regions_pos.txt
location_vector_4_differential_regions_neg.txt
location_vector_7_differential_regions_pos.txt
location_vector_7_differential_regions_neg.txt


title: siRNA against firefly luciferase, replicate 1


title: siRNA against firefly luciferase, replicate 3


title: pt10 myo H3K4me1

value: myometrium


title: HSC-sh-EPO-1


title: pt10 myo input


title: pt9 leio H3K4me1


title: pt9 leio H3K4me3


title: pt9 leio H3K27ac


title: pt10 myo H3K27ac


title: pt9 leio input


title: pt10_1 leio H3K27ac


title: pt9 myo H3K4me3


title: pt9 myo H3K4me1


title: pt9 myo input


title: pt9 myo H3K27ac


title: pt8 leio input


title: pt8 myo input


title: pt8 myo H3K4me1


title: pt8 myo H3K4me3


title: pt8 leio H3K27ac


title: pt8 leio H3K4me1


title: pt7 leio H3K4me1


title: pt8 leio H3K4me3


title: pt8 myo H3K27ac


title: pt10 myo H3K4me3


title: pt7 leio H3K4me3


title: pt7 myo H3K4me1


title: pt7 myo H3K4me3


title: pt7 myo input


title: pt7 myo H3K27ac


title: pt7 leio H3K27ac


title: pt7 leio input


title: pt6 leio H3K4me1


title: pt6 leio H3K4me3


title: pt6 leio H3K27ac


title: pt6 leio input


title: pt6 myo H3K4me1


title: pt6 myo H3K4me3


title: pt6 myo input


title: pt5 leio H3K4me1


title: pt5 leio input


title: pt5 leio H3K4me3


title: pt6 myo H3K27ac


title: pt5 leio H3K27ac


title: pt5 myo input


title: pt5 myo H3K4me1


title: pt4 leio H3K4me3


title: pt4 leio H3K4me1


title: pt4 leio H3K27ac


title: pt4 leio input


title: pt5 myo H3K27ac


title: pt4 myo H3K4me3


title: pt4 myo H3K27ac


title: pt4 myo input


title: pt3 myo H3K4me1


title: pt3 leio H3K27ac


title: pt3 leio H3K4me3


title: pt3 leio H3K4me1


title: pt3 leio input


title: pt3 myo input


title: pt3 myo H3K27ac


title: pt2 leio H3K27ac


title: pt2 leio H3K4me3


title: pt2 leio input


title: pt2 leio H3K4me1


title: pt5 myo H3K4me3


title: pt4 myo H3K4me1


title: pt2 myo H3K4me3


title: pt2 myo H3K27ac


title: pt2 myo H3K4me1


title: pt2 myo input


title: pt1 leio H3K4me1


title: pt1 myo H3K4me1


title: pt1 leio H3K4me3


title: pt1 myo input


title: pt1 leio input


title: pt3 myo H3K4me3


title: pt1 myo H3K27ac


title: Pyraclostrobin 10-6M

city: Lyon

first: Yanis

last: ZEKRI

address: 32-34 Avenue Tony Garnier

country: France

institute: IGFL-ENS

data_processing:
Reads were mapped on mouse mm10 genome using Bowtie Galaxy version 2.3.2.2 with default parameters
Read were counted using htseqcount Galaxy version 0.6.1galaxy3 using these parameters // Mode : Union / Stranded : Reverse / Minimul alignement quality : 10 / Feature type : exon / ID Attribute : gene name
Heatmap were made using Clustvis web tool (https://biit.cs.ut.ee/clustvis/)
Genome_build: mm10
Supplementary_files_format_and_content: Count files

source_name: C17.2 neural cells

growth_protocol: Cells were cultivated in GlutaMAX Dulbecco modified Eagle medium (GlutaMAX DMEM, Thermo Fisher Scientific) 12% of newborn calf serum (Thermo Fisher Scientific). Endogenous TH were depleted from the serum by stripping with activated charcoal (Sigma Aldrich, St Louis MI USA) to prevent background thyroid hormone signaling

extract_protocol:
Cells were lysed 24h after chemical exposure and RNA extracted using a Macherey-Nagel NucleoSpin RNA II kit. RNA concentrations were measured with a Nanodrop spectrophotometer (Thermo Fisher Scientific).
cDNA libraries were prepared using the total RNA SENSE kit (Lexogen, Vienna Austria) and deep sequencing was performed on a NextSeq500 (Illumina) sequencer

treatment_protocol: C17.2α neural cells, expressing TRα1 were seeded in 6-wells plates (3.10^5 cells/well). T3 and the tested compounds were added in the medium on the next day. DMSO was used in control cells to keep solvent concentration constant. Cells were lysed 24h after chemical exposure

value: C17.2 neural cells (from mouse cerebellum)

value: Pyraclostrobin 10-6M


title: Trifloxystrobin 3.10-7M

value: Trifloxystrobin 3 x 10-7M


title: Pyraclostrobin 3.10-8M

value: Pyraclostrobin 3 x 10-8M


title: Trifloxystrobin 10-7M

value: Trifloxystrobin 10-7M


title: Pyraclostrobin 10-7M

value: Pyraclostrobin 10-7M


title: Trifloxystrobin 10-6M

value: Trifloxystrobin 10-6M


title: Azoxystrobin 10-7M

value: Azoxystrobin 10-7M


title: Picoxystrobin 10-7M

value: Picoxystrobin 10-7M


title: Picoxystrobin 10-6M

value: Picoxystrobin 10-6M


title: Picoxystrobin 3.10-8M

value: Picoxystrobin 3 x 10-8M


title: Azoxystrobin 10-6M

value: Azoxystrobin 10-6M


title: pt12 leio input


title: DMSO ctrl strobin, rep2

value: Untreated


title: Pyraclostrobin 3.10-7M

value: Pyraclostrobin 3 x 10-7M


title: Picoxystrobin 3.10-7M

value: Picoxystrobin 3 x 10-7M


title: pt1 myo H3K4me3

value: Diagenode, C15410003


title: NK cells, antiIFNAR_rep3

city: San Diego

first: John

middle: R

last: Teijaro

address: 10550 North Torrey Pines Rd

department: Immunology and Microbial Science

institute: The Scripps Research Institute

data_processing:
Illumina’s bcl2fastq Conversion Software (version 2.17.1.14) was used to de-multiplex reads and convert BCL files generated by the Illumina NextSeq 500 to FASTQ.
Quality of raw RNA-sequencing reads was checked using FastQC version 0.11.9 (Barbaham Institute, Cambridge, UK; http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were mapped to the mouse genome (GRCm38 assembly with Ensembl v95 transcriptome annotations) and gene counts calculated using STAR version 2.7.1a (Dobin et al., 2013) using the following parameters: --quantMode GeneCounts –outSAMtype None –sjdbGTfile /Ensembl/Mus_musculus.GRCm38.95.gtf –sjdbOverhang 74
Genome_build: GRCm38
Supplementary_files_format_and_content: raw gene counts

source_name: NK cells

growth_protocol: C57BL/6J mice were maintained in specific pathogen free conditions.

extract_protocol:
RNA was isolated using Rneasy Mini kit (Qiagen)
Amplified cDNA was prepared using SMART-Seq v4 Ultra Low Input RNA Kit (Clontech, Mountain View, CA), sheared using Covaris tubes (Covaris, Woburn, MA) and Illumina libraries constructed using the NEBNext Ultra DNA Library Prep Kit (NEB, Ipswich, MA) and sequenced using the NextSeq 500 system (Illumina, San Diego, CA) at a depth of 20-25 million single-end 75 bp reads per sample.

treatment_protocol: Mice received intravenous dose of LCMV Clone 13 (2x10^6 pfu).

tag: infection

value: LCMV Clone 13

tag: agent

value: spleen

value: NK cells


title: NK cells, antiIFNAR_rep4


title: NK cells, isotype_rep1

value: isotype control antibody


title: NK cells, isotype_rep2


title: NK cells, antiIFNAR_rep2


title: Trifloxystrobin 3.10-8M

value: C17.2 neural cells (from mouse cerebellum)

value: Trifloxystrobin 3 x 10-8M


title: NK cells, isotype_rep4


title: DMSO ctrl strobin, rep1


title: NK cells, isotype_rep3


title: pt1 leio H3K27ac

value: leiomyoma

tag: chip antibody

value: Active motif, 39133


title: 2W_ATP5MD

city: Guangzhou

first: Zhongju

last: Wang

state: Guangdong

address: No. 1023-1063, South Sha-tai Road, Baiyun District

institute: Southern Medical University

description: 2 week neurons derived from commercial iPSC

data_processing:
Library strategy: 4C-seq
Data analysis protocol were established in python scripts and followed previously established protocol(van de Werken, H. J. G. et al. 4C technology: protocols and data analysis. Methods in enzymology 513, (Elsevier Inc., 2012).)
In breif, reads containing first enzyme sequence were extracted and followed by quality control with fastp.
Reads were then trimmed and merged according to 4C construction progress, followed by mapping to NCBI37/hg19 using bowtie2, and tranforming to bed format with bedtools.
After removing self-ligation reads, reads coverage were normalized.
R package 4c-ker were then used to identify significant chromatin interactions with bait regions.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph

source_name: iPSC-derived 2 week neuron

growth_protocol: Differentiation of iPS cellls into neurons were performed following previously established protocol (Wen, et al. Synaptic dysregulation in a human iPS cell model of mental disorders.(10.1038/nature13716)). In brief, iPS cell colonies were detached from the feeder layer collagenase treatment for 1h and suspended in embryoid body (EB) medium in non-treated polystyrene plates for 4 days, followed by replacement with neural induction medium (hNPC medium). The floating EBs were then transferred to matrigel-coated 6-well plates at day 7 to form neural tube-like rosettes. The attached rosettes were kept for 15 days with hNPC medium change every other day. On day 22, the rosettes were picked mechanically and transferred to low attachment plates in hNPC medium containing B27. For neuronal differentiation, resuspended neural progenitor spheres were dissociated with Accutase at 37⁰C for 10 min and placed onto Poly-D-Lysine/laminin-coated coverslips in the neuronal culture medium, consisting of Neurobasal medium.

extract_protocol:
4C assay libraries were generated according to previously established protocols (van de Werken, H. J. G. et al. 4C technology: protocols and data analysis. Methods in enzymology 513, (Elsevier Inc., 2012).). In brief, the chromatin was cross-linked with formaldehyde, followed by two rounds of degestion-ligation using two different 4-bp cutters, MboI and NlaIII. The quality of 4C products was assessed on agarose gels.
4C templates were then amplified with specific 4C-primers, which were designed for correponding bait regions. Primers pairs were pooled according to primer efficiency and PCR products were purified. Thereafter, 4C products with primers contained sequencing adaptor sequences.

value: iPSC-derived neurons

tag: differentiation time

value: 2 weeks


title: 6W_rs1926032

description: 6 week neurons derived from commercial iPSC

source_name: iPSC-derived 6 week neuron

value: 6 weeks


title: 6W_ATP5MD


title: mock rep 2

data_processing:
FASTQ reads were mapped to the human genome (hg38) while allowing junction mapping using STAR (v2.7)
Reads from biological replicates were combined prior to alternative splicing analysis.
MISO (v0.5) was used to estimate PSI (percent spliced-in) for alternatively spliced (cassette) exons annotated in the human transcriptome (RefSeq)
Genome_build: hg38
Supplementary_files_format_and_content: misopy summarized files

growth_protocol: 48 hours before transfection MDA-LM2 cancer cells were seeded at 1x10^5 per well in 6-well plates. Cells were grown in a 37degC 5% CO2 humidified incubator. Cells were grown in DMEM media supplemented with 10% FBS, glucose (4.5g/L), L-glutamine (4mM), sodium pyruvate (1mM), penicillin (100 units/mL), streptomycin (100 ug/mL) and amphotericin (1ug/mL).

extract_protocol:
48 hours after transfection, total RNA was harvested using the zymo research RNA quick prep kit, including an on-column DNase-treatment step.
The Takara SMARTer stranded total RNA-seq V2-pico input mammalian kit (634411) was used to prepare libraries from the total RNA.

treatment_protocol: Each well of cells was transfected with 100pmol of the indicated RNA using lipofectamine 2000 (thermo) per the manufacturer's protocol. Mock transfected cells were treated identically except RNA was excluded from the transfection mix.

tag: rep

tag: synthetic rna oligo

value: mock


title: loopNunstructured rep pool rep 2

description: loopNunstructured_hg38_se_miso.miso_summary

value: loopN+unstructured


title: mock rep 1


title: unstructured rep pool rep 2

value: unstructured


title: structured rep pool rep 2

value: structured


title: unstructured rep pool rep 1


title: wt rep 1

value: WT


title: siSNRPA1_rep2

data_processing:
FASTQ reads were mapped to the human genome (hg38) while allowing junction mapping using STAR (v2.7)
Reads from biological replicates were combined prior to alternative splicing analysis.
MISO (v0.5) was used to estimate PSI (percent spliced-in) for alternatively spliced (cassette) exons annotated in the human transcriptome (RefSeq)
Genome_build: hg38
Supplementary_files_format_and_content: misopy summarized files (miso_summary) and delta-psi (miso_bf) values comparing siCtrl to siSNRPA1 samples

extract_protocol:
48-hours post-transfection, total RNA was extracted using Norgen total RNA extraction kit (included the on-column DNase treatment step).
ScriptSeq v2 (Expicentre) was used to generate sequencing libraries.

treatment_protocol: Cells transfected with siRNAs (IDT) with Lipofectamin as the transfection reagent. Knockdown was confirmed using qPCR.

tag: knockdown


title: SiCtrl_rep2

value: siCtrl


title: loopNonly rep 2

value: loopN


title: wt rep 2


title: NK cells, antiIFNAR_rep1

tag: strain

value: LCMV Clone 13

value: spleen

tag: cell type


title: siSNRPA1_rep1

tag: cell line


title: loopNonly rep 1


title: SiCtrl_rep1


title: siSNRPB2-rep1

data_processing:
FASTQ reads were mapped to the human genome (hg38) while allowing junction mapping using STAR (v2.7)
Reads from biological replicates were combined prior to alternative splicing analysis.
MISO (v0.5) was used to estimate PSI (percent spliced-in) for alternatively spliced (cassette) exons annotated in the human transcriptome (RefSeq)
Genome_build: hg38
Supplementary_files_format_and_content: misopy summarized files (miso_summary) and delta-psi (miso_bf  ) values comparing siCtrl and siSNRPB2 samples

extract_protocol:
48-hours post-transfection, total RNA was extracted using Zymo RNA micoprep kit (included the on-column DNase treatment step).
SMARTer stranded total RNA-seq kit v2- pico input mammalian (Takara #634411) was used to generate sequencing libraries.

treatment_protocol: Cells transfected with siRNAs (IDT) with Lipofectamin as the transfection reagent. Knockdown was confirmed to be higher than 95% for the two selected siRNAs using qPCR.


title: PT9_Eff_1

first: Sagar

last: Chhangawala

state: NY

address: 1300 York Ave.

department: PBSB

institute: Weill Cornell Medical College

data_processing:
fastq files were aligned using STAR (v2.5.0b, default parameters)
Read counting was performed using htseq-count (v0.9.1, parameters: --stranded=no -t exon)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited file that contains gene IDs and read counts for each sample

source_name: PDAC EpCAM- primary tumor

extract_protocol:
DNA and RNA were extracted from same samples of each of the EpCAM+ and EpCAM- subpopulations using Qiagen All-prep DNA/RNA micro kit (Qiagen Cat # 80284) following manufacturer’s standard guidelines.
Library was constructed using QuantSeq FWD HT Kit (015.384) based on manufacturer's protocol
Quant-seq

tag: tumor differentiation

value: moderately diff

tag: margin status

value: Positive

tag: tumor stage

value: T3 N0

tag: adjuvant therapy

value: Yes

tag: radiotherapy

value: No

tag: recurrence status


title: loopNunstructured rep pool rep 1

first: Hani

last: Goodarzi

institute: UCSF


title: SiControl-rep2


title: SiControl-rep1


title: siSNRPB-rep1

data_processing:
FASTQ reads were mapped to the human genome (hg38) while allowing junction mapping using STAR (v2.7)
Reads from biological replicates were combined prior to alternative splicing analysis.
MISO (v0.5) was used to estimate PSI (percent spliced-in) for alternatively spliced (cassette) exons annotated in the human transcriptome (RefSeq)
Genome_build: hg38
Supplementary_files_format_and_content: misopy summarized files (miso_summary) and delta-psi (miso_bf) values comparing siCtrl to siSNRPA1 and siSNRPB samples

treatment_protocol: Cells transfected with siRNAs (IDT) with Lipofectamin as the transfection reagent. Knockdown was confirmed using qPCR: 86%, 83%, and 75% for SNRPA1 (1, 2, and 3) and 86% for SNRPB.

value: siSNRPB


title: siSNRPB2-rep2


title: PT9_Ep_1

source_name: PDAC EpCAM+ primary tumor


title: siSNRPA1-rep3


title: PT65_Ep_1

value: Free

value: T3 N1


title: PT65_Eff_1


title: 2W_rs1926032

value: iPSC-derived neurons

value: 2 weeks


title: structured rep pool rep 1


title: PT64_Ep_1

value: poorly diff


title: PT64_Eff_1


title: siSNRPA1-rep1


title: siSNRPA1-rep2


title: PT63_Ep_1


title: SiCtrl-rep2


title: PT62_Ep_1


title: PT63_Eff_1


title: SNRPA1 CLIP-seq rep2

data_processing:
Linkers were removed and reads were quality trimmed using cutadapt (v1.10)
Reads were mapped to the genome (hg19) using BWA (v0.7)
Duplicated reads were removed based on UMIs using CTK
Peaks were then called using both CTK and clipper
Genome_build: hg19
Supplementary_files_format_and_content: bed (peak calls)

growth_protocol: MDA-231-LM2 cancer cells were  grown in a 37degC 5% CO2 humidified incubator. Cells were grown in DMEM media supplemented with 10% FBS, glucose (4.5g/L), L-glutamine (4mM), sodium pyruvate (1mM), penicillin (100 units/mL), streptomycin (100 ug/mL) and amphotericin (1ug/mL).

extract_protocol:
irCLIP was performed for SNRPA1 in MDA-231-LM2 cells using an antibody targeting the endogenous protein.
Performed as in the irCLIP protocol: a linker was ligated to the RNA-protein complexes, and after RNA isolation and cDNA synthesis circligase was used to circularize the cDNA. This was then used as the template for PCR to construct the library.

tag: rip antibody

value: Anti-SNRPA1, 1ug/ul (Bethyl A303-948A)


title: PT61_Ep_1


title: PT62_Eff_1


title: SF3B1 HITS-CLIP rep 1

description: CLIP-seq

data_processing:
Linkers were removed and reads were quality trimmed using cutadapt (v2.3)
Reads were mapped to the genome (hg38) using BWA (v0.7.17)
Duplicated reads were removed based on UMIs using CTK  (v1.1)
Peaks were then called using CTK (v1.1)
Genome_build: hg38
Supplementary_files_format_and_content: bed (peak calls)

extract_protocol:
HITS-CLIP was performed for SNRBP2 in MDA-231-LM2 cells using an antibody targeting the endogenous protein.
Performed as in the HITS-CLIP protocol, sequential linker ligation was performed, then cDNA synthesis and PCR

value: Anti-SF3B1 (bethyl A300-997A)


title: SF3B1 HITS-CLIP rep 2

description: CLIP-seq


title: PT7_Eff_1


title: SNRPA1 CLIP-seq rep1


title: PT60_Ep_1


title: PT60_Eff_1


title: PT7_Ep_1


title: PT61_Eff_1


title: mCherry over-expresison rep2

description: RNA-seq

data_processing:
FASTQ reads were mapped to the human genome (hg38) while allowing junction mapping using STAR (v2.7)
Reads from biological replicates were combined prior to alternative splicing analysis.
MISO (v0.5) was used to estimate PSI (percent spliced-in) for alternatively spliced (cassette) exons annotated in the human transcriptome (RefSeq)
Genome_build: hg38
Supplementary_files_format_and_content: misopy summarized files (miso_summary) and delta-psi (miso_bf) values comparing mCherry Ctrl to SNRPA1 over-expression samples

treatment_protocol: Cells were transduced with SNRPA1 lentiviral construct (pLX-SNRPA1) or with mCherry controls (pLX-mCherry).

tag: overexpression

value: mCherry


title: PT6_Ep_1


title: SNRPA1 over-expresison rep2

description: RNA-seq


title: CPC RAB5CKO Day 28 Rep3

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

data_processing:
Basecalling and demultiplexing was done using bcl2fastq verion 2.20.0.422
STAR version 2.5.2a was used to align the reads to the reference genome
featureCounts version 1.5.0-p1 was used to quantify reads for genes
Genome_build: Hg38 gene version 89
Supplementary_files_format_and_content: Tab-delimited gene counts

source_name: Chondrogenic Progenitor Cells

growth_protocol: CPCs were grown in T75 flask using standard medium containing DMEM + 10% FCS and 50µg/mL Gentamycin until cells reached 80% confluency. Either cells were collected as day 0 samples or coated with 20µL of a 0.15 M NaCl solution containing 1.2% alginate. Beads were cultivated in chondrogenic medium containing standard medium supplemented with 3.9 µg/100 mL Dexamethasone,  10 µg/100 mL Na-Pyruvate,  4 µg/100 mL L-Proline,  10 µg/100 mL Ascorbat and 5µL ITS+Premium/mL medium. Samples were then collected on days 3 and 28. Alginate beads were dissolved in a HEPES-EDTA-Buffer (55 mM EDTA, 10 mmHEPES, pH 7.4)

extract_protocol: non stranded mRNA Seq TruSeq standard according to the illimina protocol

value: Chondrogenic Progenitor Cells

tag: cell state

value: Immortalized

tag: genotype

tag: culture

value: 3D in alginate, chondrogenic Medium

tag: time

value: day 28


title: SNRPA1 over-expresison rep1

description: RNA-seq

tag: rep


title: mCherry over-expresison rep1

description: RNA-seq


title: PT6_Eff_1

value: Positive


title: PT59_Ep_1

value: moderately diff

value: T3 N0


title: PT59_Eff_1

value: Yes

value: No


title: CPC RAB5CKO Day 28 Rep2


title: SiCtrl-rep1

tag: knockdown

value: siCtrl


title: PT58_Eff_1

value: T3 N1


title: PT58_Ep_1


title: CPC RAB5CKO Day 3 Rep3

value: day 3


title: PT57_Ep_1


title: CPC RAB5CKO Day 3 Rep2


title: PT57_Eff_1


title: CPC RAB5CKO Day 3 Rep1


title: PT56_Ep_1

value: Free


title: CPC RAB5CKO Day 0 Rep2

value: 2D in Flask, standard Medium

value: day 0


title: PT56_Eff_1


title: PT55_Ep_1


title: CPC RAB5CKO Day 0 Rep1


title: PT55_Eff_1


title: CPC Control Day 28 Rep2

value: Control


title: CPC Control Day 28 Rep3


title: PT53_Ep_1


title: CPC Control Day 28 Rep1


title: CPC RAB5CKO Day 28 Rep1


title: PT53_Eff_1


title: untreated replicate 7

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

description:
Untreated.7
CD22_counts.gct

data_processing:
Basecalling and sample de-multiplexing were performed with CASAVA-1.8.4 and default parameters.
Reads were quality check with fastqc v0.11.9 and multiqc v1.8.
Reads were mapped to the amplicon sequences of the panel using Bowtie2 v2.3.5 with the mapping parameters --no-mixed, --no-discordant and --sensitive
multiBamCov from bedtools v2.29.2 was used to count reads mapped onto amplicons.
Genome_build: Human RefSeq transcripts for amplicons.
Supplementary_files_format_and_content: CD22_counts.gct: GCT format, with amplicon counts for pathway reporter genes in each sample.

source_name: iPSC-derived macrophages

growth_protocol: Growth protocol according to Gutbier et al. 2020 (PMID: 32645954).

extract_protocol:
After treatment, cells were lysed in MagNA Pure LC RNA Buffer (Roche Diagnostics) and purified using the MagNA Pure 96 System (Roche Diagnostics).
10 ng of total RNA from each biological replicate were reverse transcribed to cDNA using Super Script IV Vilo (Thermo Fisher, 11766500, user guide MAN0015862). Libraries were generated with the AmpliSeq Library Plus Kit (Illumina Catalog number 20019103) according to the Reference Guide. Pipetting Steps for target amplification, primer digestion and adapter ligation were done with the mosquito automatic pipettor (ttp labtech) in a miniaturisation fashion. For the purifications before and after final library amplification, SPRI magnetic bead purification was chosen (Clean NGS, LABGENE Scientific SA) semi automated on multidrop (Thermo Fisher). Amplicon size and DNA concentration were measured using an Agilent High Sensitivity DNA Kit (Agilent Technologies, Waldbronn, Germany) according to the manufacturer’s recommendation. Prior sequencing samples have to be normalized and pooled to 2nM final concentration on Biomek FXP workstation.
Amplicon sequencing. Pooled libraries were sequenced on the Illumina NovaSeq 6000 Instrument, SBS (sequencing by synthesis) technology. 75 cycles end up with a minimum of 2 Mio SR per sample for analysing.

treatment_protocol: Cells were treated with respective antibody at a concentration of 5 ug/ml or left untreated for 4 hours.

value: iPSC-derived macrophages

tag: treatment

value: untreated


title: untreated replicate 3

description:
Untreated.3
CD22_counts.gct

tag: cell type


title: untreated replicate 5

description:
Untreated.5
CD22_counts.gct


title: anti-CD22 antibody replicate 3

description:
CD22_MAB.3
CD22_counts.gct

value: anti-CD22 antibody


title: IgG isotype control antibody replicate 2

description:
IgG1_cont.2
CD22_counts.gct

value: IgG isotype control antibody


title: untreated replicate 4

description:
Untreated.4
CD22_counts.gct


title: IgG isotype control antibody replicate 0

description:
IgG1_cont
CD22_counts.gct


title: IgG isotype control antibody replicate 3

description:
IgG1_cont.3
CD22_counts.gct


title: CPC Control Day 3 Rep3

tag: cell line

value: Chondrogenic Progenitor Cells

value: Immortalized

value: 3D in alginate, chondrogenic Medium


title: untreated replicate 6

description:
Untreated.6
CD22_counts.gct


title: CPC RAB5CKO Day 0 Rep3


title: anti-CD22 antibody replicate 2

description:
CD22_MAB.2
CD22_counts.gct


title: untreated replicate 2

description:
Untreated.2
CD22_counts.gct


title: CPC Control Day 3 Rep2


title: PT52_Ep_1

city: New York

tag: tumor differentiation

value: poorly diff


title: PT52_Eff_1

tag: margin status

value: Yes


title: CPC Control Day 3 Rep1


title: IgG isotype control antibody replicate 1

description:
IgG1_cont.1
CD22_counts.gct


title: PT51_Ep_1

value: moderately diff

value: Positive

tag: tumor stage

value: No


title: anti-CD22 antibody replicate 1

description:
CD22_MAB.1
CD22_counts.gct


title: CPC Control Day 0 Rep3


title: untreated replicate 1

description:
Untreated.1
CD22_counts.gct


title: PT51_Eff_1

value: T3 N1

tag: adjuvant therapy


title: CPC Control Day 0 Rep2


title: PT50_Ep_1

tag: radiotherapy


title: anti-CD22 antibody replicate 0

description:
CD22_MAB
CD22_counts.gct


title: PT50_Eff_1

tag: recurrence status


title: CPC Control Day 0 Rep1


title: PT5_Ep_1

value: Free


title: HCT116-5-FU for 24 hours rep 1

city: Rochester

first: Julia

last: Freewoman

address: 1 Lomb Memorial Dr

department: Thomas H. Gosnell School of Life Sciences

institute: Rochester Institute of Technology

data_processing:
University of Rochester Genomics Research Center (URGRC) sequenced the samples and the resulting raw reads were cleaned using Trimmomatic-0.32 with a cutoff 25 bp for the read size
The filtered fastq were further cleaned by FASTX-toolkit (version 0.0.13) with a quality score cutoff of 28. Then, cutadapt (version 1.10) was used to filter out all reads greater than 50bp.
Reads in the FASTQ files were aligned to the human genome assembly hg19 using TopHat (version 2.1.1) with the default setting.
The resulting BAM files were sorted by SAM-tools (version 1.3.1) for visualization in the UCSC Genome Browser.
Following the Cufflinks (version 2.2.1) pipleline for version 2.0 and greater CuffDiff2 was used for differential expression analysis.
For DESeq2 (version 2_1.24.0, ref. 33), read counts for each gene were calculated using htseq-count (version 0.10.0, ref. 32) using the bam files produced by TopHat and sorted by Samtools (version 1.9) by position. Following the tutorial of the Bioconductor package DESeq2 was used for differential expression analysis.
Genome_build: HG19
Supplementary_files_format_and_content: matrix_deseq2.txt.   Matrix of the normalized count values from DESeq2 from the counts command with the first column as the name of gene and following columns the normalized count values for each replicate
Supplementary_files_format_and_content: matrix_cuffdiff2.txt.   Matrix of the FPKM values from CuffDiff2 from the repFpkmMatrix call along with the featureNames with the first column as the name of gene and following columns the normalized count values for each replicate.

source_name: Colon Cancer Cells

growth_protocol: HCT116 p53 cells were grown in recommended McCoy’s 5a modified media with 10% FBS and 1X antibiotic mix. Cells were grown in the media at 37º C with 5% CO2 in a 35 mm plates until 70-80% confluence

extract_protocol:
RNA was extracted following the instruction of the QUIAGEN RNeasy Mini Kit and the QIAshredder (QIAGEN) was used during the RNeasy Kit’s lyse and homogenization stage. The RNA concentration was determined using NanoDrop (Thermo Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At 6, 12 or 24 hours prior to RNA extraction, the media was changed and 2 ml of fresh media, along with fluorouracil (5-FU) (with final concentration of 375 µM) or 2uL dimethyl sulphoxide (DMSO) were added to the cells. The DMSO-treated samples were used as controls because DMSO is the solvent of 5-FU. Non-treatment controls were also set up. For each treatment and each time point, two biological replicates were performed.

value: Colon

tag: disease state

value: colorectal carcinoma

tag: p53 genotype

value: wildtype

value: 24 hours


title: PT5_Eff_1


title: ConA treated rabbit, biological rep3

city: STONY BROOK

first: Adam

last: Master

state: NEW YORK

address: 101 Nicolls Road, Sciences Center

department: Department of Preventive Medicine

institute: The State University of New York in Stony Brook

description: Gene expression data

hyb_protocol: RNA quality was evaluated with a 2100 Bioanalyzer (Agilent Technologies) that assessed the relative abundance of the 18S and 28S ribosomal bands and the presence of baseline rise.  150 ng of total RNA was labeled for hybridization to Affymetrix GeneChip™ Rabbit Gene 1.0 ST Array (ThermoFisher Scientific) containing 496,321 probes to assess 23,364 transcripts, transcript variants and alternative splicing events. The total RNA was labeled using the Affymetrix GeneChip® WT PLUS Kit according to the manufacturer’s protocol.

scan_protocol: Once the hybridization was completed, the arrays were washed and stained in a GeneChip Fluidics 450 station.  These arrays were then scanned in a GeneChip Scanner 3000 G7 controlled by Affymetrix GeneChip Command Console v 4.3.3.1616.

data_processing: Microarray results were analyzed with the Transcriptome Analysis Console (TAC) Software (ThermoFisher Scientific). Each transcript was measured with a median of 22 probes. Of these 23,364 transcripts, 14,713 (63%) are fully annotated, with known homology to human genes (HomoGene NCBI database) while 8,651 (37%) are partially annotated without clear homology to human genes.

organism: Oryctolagus cuniculus

source_name: Rabbit conjunctiva, Concanavalin A (ConA), dry eye disease (DED) model, 18 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Male Dutch-Belted rabbits, 1.8-2 kg (Covance Research Products, Somerset, NJ) were housed singly under strict temperature (70 +/- 5 ̊F) and humidity (45+/-5%) control and acclimated for at least 2 weeks before the induction of DED. They had unlimited access to water and standard rabbit chow without dietary enrichment. The nictitating membranes were removed surgically during the early acclimation period. All animal studies were approved by the Institutional Review Board of Stony Brook University and performed in accordance with the Association for Research in Vision and Ophthalmology Statement for the Use of Animals in Ophthalmic and Vision Research.

extract_protocol: After each rabbit was euthanized, a 4x4 mm sample of full-thickness conjunctiva tissue that included Tenon's capsule was immediately placed in 1 mL of TRIzol Reagent (ThermoFisher Scientific, CA), frozen in liquid nitrogen and stored at -80 °C until analyzed. Samples were homogenized in TRIzol, mixed with 0.2 mL of chloroform, vortexed 20 s and centrifuged at 12,000 × g at 4°C for 10 min. Pre-cleaned RNA, present in the upper aqueous phase, was transferred to a new tube on ice and processed using the RNeasy® Mini column kit (Qiagen, Valencia, CA) with DNase digestion during RNA purification.

treatment_protocol: The periorbital lacrimal glands of rabbits were injected with ConA on days 1, 8 and 14 to induce DED. Tear osmolarity, tear break-up time, tear production and corneal sensitivity were measured at baseline and at the conclusion of the study.  Tears were both collected (at the junction of the palpebral and bulbar conjunctivas along the lower fornix) and tear osmolarity was measured with the same instrument, a TearLab Osmometer (TearLab Corporation, San Diego, CA). Tear break-up time (TBUT) was determined after application of a drop of 0.2% fluorescein over the ocular surface. The pre-corneal tear film was observed and the time until the development of black dots, lines or obvious disruption of the fluorescein film was measured up to a maximum of 60 sec. Tear production was determined using the Schirmer tear test (STT). The STT was performed in triplicate by inserting the appropriate strips (EagleVision, Denville, NJ) at the midpoint of the lower lid.  The average of the length of the moistened strip at 5 min was recorded. Corneal sensitivity (CS) was measured with the Cochet-Bonnet aesthesiometer (Luneau, France). The aesthesiometer contains a thin nylon filament that is applied perpendicularly to the central cornea, initially at its full length of 6 cm.  If a positive response (full blink and retraction of the eye into the ocular orbit) is not noted on 3-5 attempts, the filament is incrementally retracted in 5 mm steps until a clear stimulus is evoked.  The length of filament simulating a positive response was recorded.

tag: tissue

value: conjunctiva

tag: breed

value: Dutch Belted rabbits

tag: developmental stage

value: adult

tag: Sex

value: male

tag: disease model

value: Dry Eye Disease (DED)


title: CTL_5

city: St Louis

first: David

last: Gutmann

state: MO

address: 660 S Euclid Ave

department: Neurology

institute: Washington University in St Louis

data_processing:
STAR 2.7.3a aligner
Ensembl Transcripts release 100 annotations
Genome_build: hg38
Supplementary_files_format_and_content: Matrix with raw gene counts before normalization

source_name: Human control tissue

extract_protocol:
RNAs were isolated using the Qiagen RNeasy Mini Kit per manufacturer’s instructions.
the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® was used and mRNA enriched using oligo(dT) beads.
Constructed cDNA libraries that pass a library quality control test (consists of Qubit, LabChip fragment analysis, and qPCR steps) are sequenced on an Illumina NovaSeq 6000 PE150 platform.

value: Female

value: CTL

tag: tumor

tag: age


title: untreated replicate 0

description:
Untreated
CD22_counts.gct

tag: cell type

value: iPSC-derived macrophages

tag: treatment

value: untreated


title: HCT116-5-FU for 24 hours rep 2

tag: cell line

tag: time


title: CTL_6

value: Male


title: CTL_4


title: CTL_7


title: PT49_Ep_1

tag: tumor differentiation

value: moderately diff

tag: margin status

tag: tumor stage


title: HCT116-5-FU for 12 hours rep 1

value: 12 hours


title: PT47_Ep_1

value: Free

value: T3 N1

tag: adjuvant therapy

value: Yes

tag: radiotherapy

value: No

tag: recurrence status


title: ConA treated rabbit, biological rep2

description: Gene expression data

tag: tissue


title: CTL_3


title: HCT116-5-FU for 6 hours rep 2

value: Colon

tag: disease state

value: colorectal carcinoma

tag: p53 genotype

value: wildtype

value: 6 hours


title: ConA treated rabbit, biological rep1

description: Gene expression data

value: conjunctiva

tag: breed

value: Dutch Belted rabbits

tag: developmental stage

value: adult

tag: Sex

value: male


title: HCT116-5-FU for 6 hours rep 1


title: RVKM-Ascl2

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

data_processing:
For RNA-seq, low quality reads and adaptor sequences were removed by Trim Galore,then clean reads were aligned to mm10 by bowtie2 with default parameter.
Differentially expressed genes were identified by at least 1.5fold change and fdr adjusted p-value 0.05
For ChIP-seq, all sequencing reads were mapped to the mouse genome mm10 by bowtie2, then PCR duplicates were removed using picard MarkDuplicates
For ChIP-seq, the uniquely mapped reads were used to call peak with MACS2 using a p value cutoff 0.01
Genome_build: mm10
Supplementary_files_format_and_content: expression data, bigwig file

source_name: RVKM-Ascl2 transfected and in vitro cultured  activated B cells

growth_protocol: For RNA-seq, Naïve B cells were isolated from C57BL/6 mice, infected with RVKM-Empty/Ascl2 retrovirus and in vitro cultured with anti-IgM&anti-CD40. For ChIP-seq, GC B cells were isolated from draining LN after KLH immunization at 7 days.

extract_protocol:
The total RNA was extracted with Trizol (Life Technologies) according to manufacturer’s instructions. The ChIP assay was performed using ChIP-IT Express Chromatin Immunoprecipitation Kits (Active Motif) according to manufacturer’s instructions with slight modifications.
RNA-seq library was constructed for deep sequencing by BGI Genomics. ChIP-seq DNA library was constructed for deep sequencing by BGI Genomics.

value: Naive B cells

tag: strain


title: GC B cells, input

source_name: GC B cells

tag: cell type

value: GC B cells

tag: tag


title: RVKM-Empty

source_name: RVKM-Empty transfected and in vitro cultured  activated B cells


title: CTL_2

value: Male

value: CTL

tag: tumor

tag: age


title: HCT116-5-FU for 12 hours rep 2

tag: cell line

tag: treatment

tag: time

value: 12 hours


title: GC B cells, Ascl2

value: Ascl2 (Millipore, MAB4418)


title: CTL_1


title: PT47_Eff_1

tag: tumor differentiation

value: moderately diff

tag: margin status

value: Free

tag: tumor stage

value: T3 N1

tag: adjuvant therapy


title: ANTHER-csaLD04:00_rep2

city: Shanghai

first: Jingbin

last: Li

address: 800 Dongchuan Road

institute: Shanghai Jiao Tong University

description: ANTHER_All counts.txt

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to rice  genome using Mapsplice v2.1.8 with  parameters -s 22 -p 15 --ins 6 --del 6 --non-canonical --bam -o
count counting
Genome_build: Tigr7
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Oryza sativa Japonica Group

source_name: Stage 12 anther

growth_protocol: Oryza sativa L. ssp. japonica 9522 curtiva was grown in paddy fields of Shanghai (China) from June–August).

extract_protocol:
Total RNA, excluding miRNAs, was extracted using TRIzol (Life Technologies) for RNA sequencing according to the manufacturer’s protocol. C
DNA libraries were prepared with the FastQuant RT Kit with DNase (Tiangen), according to manufacturer’s instructions.

treatment_protocol: By the middle of August (initiation of reproductive development), the daylength is ~14.5 h (LD photoperiod). Rice plots (WT and csa) were divided into two groups, and SD photoperiod (12 h light) was simulated by covering plants in one group with lightproof plastic film from 18:00 to 6:00 of next day.

tag: genotype

value: csa

tag: tissue

value: Anther

tag: development stage

value: Stage 12

value: long day photoperiod

tag: collection time


title: PT46_Ep_1

value: Positive

value: Yes

tag: radiotherapy

value: No

tag: recurrence status


title: PT49_Eff_1


title: HCT116-DMSO for 24 hours rep 1

tag: cell type

value: Colon

tag: disease state

value: colorectal carcinoma

tag: p53 genotype

value: wildtype

value: DMSO

value: 24 hours


title: PA_33

tag: Sex

value: Male

value: CTL

tag: tumor

tag: age


title: Naive rabbit (control), biological rep3

description: Gene expression data

source_name: Rabbit conjunctiva, naive

value: conjunctiva

tag: breed

value: Dutch Belted rabbits

tag: developmental stage

value: adult

value: male

tag: disease model

value: Healthy, normal


title: Naive rabbit (control), biological rep1

description: Gene expression data


title: HCT116-DMSO for 12 hours rep 2

tag: cell line

tag: treatment

tag: time

value: 12 hours


title: PT46_Eff_1

tag: tumor differentiation

value: moderately diff

tag: margin status

tag: tumor stage

value: T3 N1

tag: adjuvant therapy


title: Naive rabbit (control), biological rep2

description: Gene expression data

tag: tissue


title: ANTHER-csaLD16:00_rep1

description: ANTHER_All counts.txt

tag: genotype

value: csa

value: Anther

tag: development stage

value: Stage 12

value: long day photoperiod

tag: collection time


title: HCT116-DMSO for 6 hours rep 2

tag: cell type

value: Colon

tag: disease state

value: colorectal carcinoma

tag: p53 genotype

value: wildtype

value: 6 hours


title: PA_32

source_name: Human tumor tissue

tag: Sex

value: Female

value: No

tag: tumor

value: PA

tag: age


title: PT45_Eff_1

value: Positive

value: Yes

tag: radiotherapy

tag: recurrence status


title: PA_31


title: ANTHER-WTLD04:00_rep2

description: ANTHER_All counts.txt

value: WT

tag: treatment


title: HCT116-DMSO for 12 hours rep 1

tag: cell line

value: DMSO

tag: time

value: 12 hours


title: ANTHER-WTLD04:00_rep1

description: ANTHER_All counts.txt


title: PA_30


title: HCT116-DMSO for 6 hours rep 1


title: PT44_Ep_1

tag: tumor differentiation

value: moderately diff

tag: margin status

value: Free

tag: tumor stage

value: T3 N1


title: HCT116-DMSO for 24 hours rep 2

value: 24 hours


title: PT44_Eff_1

tag: adjuvant therapy


title: PA_29


title: ANTHER-WTLD16:00_rep2

description: ANTHER_All counts.txt

tag: genotype

tag: tissue

value: Anther

tag: development stage

value: Stage 12

value: long day photoperiod


title: ANTHER-csaLD04:00_rep1

description: ANTHER_All counts.txt

value: csa

tag: collection time