title: Banf1 KO RNA-seq

city: Columbus

first: Patrick

middle: Leonard

last: Collins

state: OH

address: 770 BRT,  460 W 12th Ave

department: Microbial Infection and Immunity

institute: Ohio State University

description:
processed data file: all.transcript_RPKM.xls
RNAseq_Banf1KO

data_processing:
For RNA-seq, The reads were aligned to the mm9 build using Bowtie2 to map clean reads to reference gene. RPKM values were determined using STAR aligner. For ChIP-seq reads were aligned ot the mm9 genome assemply using NovaAlign with the following options:-r None -l 30 -e 100 -i 230 140.
duplicates were removed using Picard markDuplicates
peaks were called using MACS2 findpeaks --broad
The reads were aligned to the mm9 build using Bowtie2 to map clean reads to reference gene
Genome_build: mm9
Supplementary_files_format_and_content: . RPKM values were determined using STAR aligner.

source_name: BV1 Cells Banf1 KO

extract_protocol:
For RNA-Seq, total RNA from 10^6 control BV2 cells, Banf1 gene-edited cells, and Banf1-complemented cells were extracted using RNeasy Mini Kit (Qiagen).   For native ChIP-Seq, aliquots of 10^5 cells were suspended in 20 µl of EZ nuclei isolation buffer (Sigma) and digested using 20 µl MNase (NEB MNase buffer, 1 µl MNase, and 3 mM DTT) for 5 min at 37°C, which was quenched by addition of 4.4 µl of 100 mM EDTA, and 4.4 µl of 1% Triton X-100 and 1% deoxycholate. Digested nucleosomes were diluted in complete ChIP immunoprecipitation buffer (20 mM Tris-HCL pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1% Triton X-100, 5 mM sodium butyrate, and protease inhibitors (Roche)), precleared using Dynabeads (Invitrogen) for 1 h at 4°C, and subjected to immunoprecipitation overnight at 4°C (0.1 µg H3K27ac, Abcam, ab4729). Bead chromatin complexes were washed sequentially using low-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.0, 150 mM NaCl) and high-salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris pH 8.0, 500 mM NaCl) and then eluted with 1% SDS and 100 mM NaHCO3 for 1 h at 65°C. DNA was purified using Maxtract tubes (QIAGEN) and precipitated overnight.
The quality of the RNA samples was evaluated using Bioanalyzer 2100 (Agilent) and prepared using mRNA ribo-deplete.
Libraries were sequenced on Illumina HiSeq2500 platforms (Genome Technology Access Center, Washington University).

value: Banf1 Knock Out

tag: molecule subtype

value: ribosome depleted


title: Banf1 WT ChIP-seq

status: Public on Dec 31 2020

type: SRA

country: USA

description:
processed data file: all.transcript_RPKM.xls
RNAseq_WT

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: BV1 Cells Banf1 WT

tag: genotype/variation

value: Banf1 Wild Type


title: ZIP13

city: Essen

first: Laura

last: Steenpass

address: Hufelandstrasse 55

department: Institute of Human Genetics

country: Germany

institute: University Hospital Essen, University Duisburg-Essen

data_processing:
Basecalling with Illumina CASAVA 1.8.1
Trimming of Fastq reads with Trim Galore! version 0.4.3.1 (Galaxy server, use.galaxy.eu)
Mapping to GRCh38.p10 (GCA_000001405.25; retrieved from ENSEMBL archive 89) using RNA STAR version 2.7.2b (Galaxy server, use.galaxy.eu)
Read counting was performed with HTseq-count version 0.9.1, (Galaxy server, use.galaxy.eu)
DEseq2 (version 2.11.40.5; Galaxy server, use.galaxy.eu) was used to identify differentially expressed genes using an adjusted p-value < 0.05 and a fold change of at least 2 as cut-off (log2(FC)>1)
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: text files; DESeq2_results; DESeq2_normalized_counts

organism: Homo sapiens

source_name: iPSC differentiated neurons d50

growth_protocol: Cultivation on Vitronectin XF-coated 6-well plates in respective culture medium at 37°C, 5% CO2; splitting ratio 1:5 to 1:10 with Gentle Cell Dissociation Reagent or ReLeSR; daily medium change

extract_protocol:
RNeasy mini kit (Qiagen)
NuGEN Trio RNAseq kit; non-stranded; HiSeq Rapid SBS kit v2 kit (Illumina); 100 bp paired-end reads

treatment_protocol: Neuronal differentiation with protocol after Qi et al.: Combined small-molecule inhibition accelerates the derivation of functional cortical neurons from human pluripotent stem cells. Nat Biotechnol 35(2): 154-163, 2017.Differentiation medium d8 to d50: Neurobasal, 2% B27+RA, 1% GlutaMAX, 20 ng/ml BDNF, 0.5 mM dbcAMP, 0.2 mM Acorbic Acid, 8mM PD0325901, 10mM SU5402, 10mM DAPT, 3mM CHIR99021

tag: disease

value: healthy control

tag: molecular cause

value: wt

tag: reprogramming method

value: episomal

tag: culture medium


title: D257A ooycte rep2

city: Beijing

first: Wenjie

last: Shu

address: Taiping Road 27

country: China

institute: Beijing Institute of Radiation Medicine

library_source: genomic

data_processing:
sequence data were process by trim-galore
Clean data were mapped  to mm10 using Bismark
Methylation levels of CpG sites were extracted using Bismark suite
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph, the forth column contains the methylation level

molecule: genomic DNA

source_name: D257A treated oocyte

growth_protocol: Briefly, MII oocytes without granulosa cells attachment (20 oocytes from five mice) were collected.

extract_protocol:
The oocytes were lysed in buffer containing 0.5 µl proteinase K for 1 h at 37°C. DNA was converted by the EZ DNA Methylation-Gold kit (Zymo Reserch) according to the instructions.
Then the converted DNA was subjected to library construction. The purified libraries were assessed for quality using High-Sensitivity DNA chips on the Agilent Bioanalyzer 2100 and StepOnePlus RealTime PCR System.
The libraries were sequenced on one lane of an Illumina HiSeq 2500 for 140-bp paired-end sequencing.

value: D257A treated


title: Ctrl_42

value: lentivirus


title: Input

description: Input

value: whole gneomic DNA


title: Banf1 TC RNA-seq

description:
processed data file: all.transcript_RPKM.xls
RNAseq_Banf1TC

source_name: BV1 Cells Banf1 TC

value: Banf1 Trans-Complement


title: D257A ooycte rep1


title: Banf1 TC H3K27ac ChIP-seq

tag: chip antibody

value: H3K27ac ab Ab4729

value: DNA - chromatin Immunoprecipiation


title: Banf1 WT H3K27ac ChIP-seq


title: Banf1 KO H3K27ac ChIP-seq


title: Tumor T15 total mRNA

city: Stockholm

first: Ola

last: Larsson

department: Department of oncology-pathology

country: Sweden

institute: Karolinska Institutet

data_processing:
RNA sequencing reads were aligned to mm10 using HISAT2 (D. Kim, B. Langmead, S. L. Salzberg, HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12, 357-360 (2015)) and reads mapping to multiple locations in the genome were discarded.
Gene expression was quantified as described using default settings (D. Ramskold, E. T. Wang, C. B. Burge, R. Sandberg, An abundance of ubiquitously expressed genes revealed by tissue transcriptome sequence data. PLoS Comput Biol 5, e1000598 (2009).) and RefSeq gene definitions (N. R. Coordinators, Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 46, D8-D13 (2018).).
Only genes with <4 missing data points were included.
Raw counts were TMM normalized (M. D. Robinson, A. Oshlack, A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11, R25 (2010)) and log2 transformed using Voom (M. E. Ritchie et al., limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res 43, e47 (2015).) in R 3.5.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RNA sequencing counts and TMM-log2 normalized data

source_name: CD11b+F4/80+Ly6G- macrophages

growth_protocol: PyMT cells were injected into the fourth inguinal mammary gland of anesthetized female FVB mice (5-7 weeks old). Mice with tumors of different sizes were sacrificed by cervical dislocation and the excised tumor was weighed prior to dissociation. Animals were purchased from Charles River Laboratory.

extract_protocol:
Polysome-profiling was performed  using macrophages isolated from 13 tumors ranging in size. Sorting of Møs from tumors was performed on a FACSJazz (BD Biosciences) flow sorter and gating the CD11b positive, F4/80 positive and Ly6G negative cell population. Sorted cells were kept in ice-cold PBS supplemented with 2% FBS and 100 μg/mL cycloheximide. For sorted TAMs, a fraction (~10%) of the obtained cell population was lysed in TRIzol reagent (ThermoFisher Scientific) and used for RNA sequencing with total RNA as input. Remaining cells were lysed in a hypotonic lysis buffer, as described and and lysates were  applied onto a 5%-50% (w/v) sucrose gradient, fractionated, and fractions corresponding to mRNA associated with 3 or more ribosomes were collected in TRIzol reagent for subsequent RNA extraction. Such pooled samples were used for RNA sequencing of efficiently translated polysome-associated mRNA.
SmartSeq2 sequencing libraries were prepared

tag: rna source

value: total mRNA

tag: tumor weight

tag: cell type

value: Tumor-associated macrophages (TAMs)

tag: experimental batch


title: Tumor T2 total mRNA

treatment_protocol: Mice with tumors of different sizes were sacrificed by cervical dislocation and the excised tumor was weighed prior to dissociation.


title: MCH2-10

value: retrovirus


title: CD54-18-3

city: Paris

first: Francisca

last: Soares da Silva

address: 25 Rue du Dr Roux

country: France

institute: Institut Pasteur

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11.Only sequences at least 25 nt in length were considered for further analysis
STAR version 2.5.0a, with default parameters, was used for alignment on the reference genome
Genes were counted using featureCounts version 1.4.6-p3  from Subreads package (parameters: -t gene -g ID).
Count data were analyzed using R version 3.5.1 and the Bioconductor packageDE Seq2 version 1.20.0f. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between all conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: mm10 GRCm38 from Ensembl version 87
Supplementary_files_format_and_content: tab-delimited text files include counts and normalized counts for each sample

source_name: embryonic mouse liver

extract_protocol:
fetal livers were removed and digested with liberase to obtain single cells. Cells were sorted according to phenotype, RNA was extracted with RNeasy micro kit (QIAGEN). Quality and integrity of RNA were analyzed for RNA integrity and ribosomal ratio. rRNA sequences were eliminated by enzymatic treatment (Zap R, Clontech).
libraries were prepared according to SMARTer Stranded Total RNA- Seq Kit - Pico Input Mammalian (ref 635005, Clontech) protocol

tag: tissue

value: embryonic mouse liver

tag: age

value: embryonic day 18.5

tag: strain

tag: surface phenotype


title: AS_D3

value: Angelman syndrome

value: 3bp deletion in maternal UBE3A


title: AGI-0

value: large deletion chr15q11q13


title: CD54-18-2


title: AS_ID

value: imprinting defect

value: StemMACS iPS-Brew XF, human


title: kit-14-3

value: embryonic day 14.5


title: CD54-18-1


title: kit-14-2


title: kit-14-1


title: CD31-14-3


title: CD31-14-2


title: CD54-14-3


title: CD54-14-1


title: BAHD1-V5_R3 (ChIP-seq)

city: Memphis

first: Mitch

last: Weiss

state: Tennessee

address: 262 Danny Thomas Place

department: Hematology

institute: st jude children's research hospital

data_processing:
Basecalls performed using CASAVA
BWA (default parameter) was used to align reads to human genome hg19. Duplicated reads were marked by Picard, and uniquely mapped reads were retained by samtools (parameter “-q 1 -F 1024”).
We confirmed quality control results were good following the ENCODE guideline for CHIPSEQ, reads were then extend to the estimated fragment size(by SPP) and converted to bigwig files.  We observed clear peaks observed by inspection on Integrated Genomics Viewer (Broad Institute) and there was high consistency among replicates.
Free pipeline to run with DNAnexus available at https://www.stjude.cloud/tools.html. Source code of ChIP-Seq pipeline to deposit on DNAnexus were also available at https://github.com/stjude/ChIP-Seq
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

growth_protocol: Cells were expanded in StemSpan serum-free expansion medium (SFEM; Stem Cell Technologies) supplemented with 1 µM dexamethasone, 1 µg/mL doxycycline, 50 ng/mL human stem cell factor (SCF), 3 units/mL erythropoietin (EPO), and 1% penicillin–streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

value: erythroblast cells

tag: passage

value: V5 (ThermoFisher #R960-25)


title: CD31-14-1


title: [alpha]PD-1 CD4+ T cells GEX seq

city: Seoul

first: Kyungsoo

last: Kim

address: 50 Yonsei-ro, Seodaemun-gu

department: Biotechnoloty

country: South Korea

institute: Yonsei University

description: Single-cell RNA-seq with 10x Genomics 5' v1 paired-end

data_processing:
mkfastq (Cell Ranger 3.1.0) was used to generate FASTQ files with default parameters
count (Cell Ranger 3.1.0) was used to generate the filtered UMI matrix with default parameters
Seurat (3.2.1) was used to filter (cutoffs as follows: 1. number of genes per cell, at least 200 and 6000 at most; 2. percentage of mitochondrial counts per cell, 5% at most), normalize (LogNormalize function with default parameters) and scale the UMI matrix (ScaleData function regressing the variables mitochondrial gene percentage and number of UMIs per cell).
Genome_build: mm10-3.0.0
Supplementary_files_format_and_content: Whole_Processed_annotations.tsv : meta data
Supplementary_files_format_and_content: Whole_Processed_normalized_counts.tsv : log-normalized counts
Supplementary_files_format_and_content: Whole_Processed_umi_counts.tsv : UMI count data matrix

source_name: Tumor infiltrating CD4+ T cells

extract_protocol:
For single cell RNA sequencing, Lungs from TC-1 tumor bearing Pdcd1fl/fl × Foxp3eGFP-Cre-ERT2(+/-) mice were digested with type IV collagenase and DNaseI mixture. Digested lung samples were stained with CD4 antibody and the LIVE/DEAD fixable dead cell stain kit for sorting of live CD4+ T cells. Tumor infiltrating CD4+ T cells were sorted from isotype control or anti-PD-1 antibody treated Pdcd1fl/fl × Foxp3eGFP-Cre-ERT2(+/-) mice. Single-cell sequencing libraries were prepared by using Chromium 10X Genomics platform with a VDJ Enrichment Kit and 5’ Library & Gel Bead Kit according to the manufacturer’s instructions.
Libraries were constructed using Chromium™ Single Cell 5' v1 Reagent Kits following the manufacturer’s protocol

treatment_protocol: PD-1 hetero conditional KO mice were treated with tamoxifen on days 0-4. TC-1 tumor cells were intravenously injected on day 12 into PD-1 hetero conditional KO mice. Isotype control or anti-PD-1 antibody were injected into tamoxifen treated PD-1 hetero conditional KO mice on every 3 days after day 13. TC-1 bearing PD-1 hetero conditional KO mice were euthanized at 14 days after TC-1 tumor injection.

value: Tumor infiltrating CD4+ T cells

tag: genotype

value: PD-1fl/fl X Foxp3eGFP-Cre-ERT2(+/-)

tag: treatment

value: [alpha]PD-1 antibody (RMP1-14)


title: WT_INPUT (ChIP-seq)


title: GAR0965: Raw264.7_wt_DexLPS_aGR_rep1

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

institute: TU München

data_processing:
Reads were aligned to the mouse mm10 (GRCm38.6) or Drosophila melanogaster dm6 (BDGP6 release 78) reference genome using BWA-MEM version 0.7.13 with default parameter settings.
PCR duplicates were removed using Picard Tools version 2.0.1.
Peaks  were  called  using  MACS2 version  2.1.1.20160309 in paired-end mode with a FDR threshold of 0.05.
Blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse/mm10.blacklist.bed.gz) were removed from the called peaks.
Peaks were annotated to the closest TSS using the ChiPpeakAnno R package v3.18.2. (doi: 10.1186/1471-2105-11-237)
Genome_build: mm10, dm6
Supplementary_files_format_and_content: The .txt files containing the annotated peak positions called with MACS2. The .bw files contain coverage data for visualization in the genome browser.

growth_protocol: Raw264.7 cells were kept at subconfluent conditions in DMEM (Gibco) supplemented with 10% FBS (heat inactivated, Sigma) and 1% penicillin/streptomycin (Gibco). Cells were cultured at 5% CO2 at 37°C in humified incubators. Medium was changed every other day.

extract_protocol: For ChIP-Seq, 40 mio cells per sample or 20 mio cells in case of H3K4me1/me2/me3 were fixed as mentioned in the sample section either for 30 min in 2 mM DSG (#C1104 ProteoChem) and 10 min 1% MeOH-free formaldehye (#2890, ThermoFisher) or 10 min 1% formaldehyde at room temperature. Remaining formaldehyde was quenched with 150 uM glycin, cells collected and washed 2x in ice-cold D-PBS. Pellets were stored at -80°C until ChIP was performed. For ChIP-Seq nuclei were extracted in Fast-IP buffer (150 mM NaCl, 5 mM EDTA (pH=7.5), 5 mM Tris (pH=7.5), 1% Triton X-100, 0.5% NP40), chromatin sonicated in shearing buffer (1% SDS, 10 uM EDTA (pH=8),50 mM Tris (pH=8)) using the Bioruptor Pico (Diagenode) for 10-15 cycles (30s on/off) at high settings. Sonicated chromatin was diluted 1:10 in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 uM EDTA (pH= 8), 16.7 uM Tris (pH=8), 167 mM NaCl) and the immunoprecipitation against the protein of interest was performed over night at 4°C. Antigen-antibody complexes were captured with protein A/G Dynabeads (Life Techn. #11202D or #11204D), 5x washed in Fast-IP buffer. Reverse crosslink was performed overnight at 65°C and proteins degraded with 100 uM proteinase K. The DNA was puriefied using Quiagen PCR purification kit according to manufacture?s manual (#28006).

treatment_protocol: Raw264.7 cells were either treated with 1 uM dexamethason (Dex, Sigma #D4902) or 0.1% EtOH (=vehicle) for 16 h followed by 3h treatment with 100 ng/ul LPS (Sigma #L2630).

value: Balb/c

tag: Sex

value: male

value: wt

tag: spike-in

value: no

value: 16h 1uM Dex, 3h 100ng/ul LPS

tag: fixation

value: 30min 2mM DSG/10min 1% FA

tag: antibody

value: rabbit polyclonal a-GR (24050-1-AP, ProteinTech)


title: BAHD1-V5_R2 (ChIP-seq)

tag: chip antibody


title: Iso CD4+ T cells GEX seq

value: Isotype control antibody


title: F11KO_INPUT (ChIP-seq)


title: BAHD1-V5_R1 (ChIP-seq)


title: CD54-14-2

value: embryonic mouse liver


title: Iso CD4+ T cells VDJ seq

description: Single-cell RNA-seq with 10x Genomics 5' v1 V(D)J


title: [alpha]PD-1 CD4+ T cells VDJ seq


title: WT Clonorchis sinensis-infected + antibiotics  rep4

city: Xuzhou

first: Bo

last: Zhang

state: Jiangsu Province

address: 209 tongshan road, yunlong district.

department: Jiangsu Key Laboratory of Immunity and Metabolism

institute: Xuzhou Medical University

data_processing:
Illumina HiSeq X-TEN software used for basecalling
The raw reads were filtered by removing reads containing adapter, ploy-N and low quality reads for subsequent analysis.1) removing reads containing adapter;2) removing reads containing ploy-N (i.e., unrecognized bases), reads with a ratio greater than 5%;3) removing low-quality reads (the number of base which is Q≤10 is more than 50% of the entire read)
Cuffdiff (v1.3.0) was used to calculate FPKMs for coding genes in each sample. Gene FPKMs were computed by summing the FPKMs of the transcripts in each gene group. FPKM stands for “fragments per kilobase of exon per million fragments mapped”, and it is calculated based on the length of the fragments and the reads count mapped to each fragment.
Supplementary_files_format_and_content: FPKM

source_name: Liver

extract_protocol:
Liver were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 1μg qualified RNA per sample was used as input material for the library preparation. The sequencing libraries were generated using the VAHTS mRNA-seq v2 Library Prep Kit for Illumina®(Vazyme, NR601) following manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: BALB/c

value: liver

value: wild type


title: WT Clonorchis sinensis-infected  rep1


title: WT Clonorchis sinensis-infected  rep2


title: IL-33KO Clonorchis sinensis-infected + antibiotics  rep3


title: WT Clonorchis sinensis-infected + antibiotics  rep3


title: WT Clonorchis sinensis-infected + antibiotics  rep1


title: WT Clonorchis sinensis-infected + antibiotics  rep2


title: WT Clonorchis sinensis-infected  rep3


title: IL-33KO Clonorchis sinensis-infected + antibiotics  rep1


title: WT Clonorchis sinensis-infected  rep4


title: IL-33KO Clonorchis sinensis-infected  rep2


title: IL-33KO Clonorchis sinensis-infected  rep1


title: scRNA_Retina_VSX2SEKO_Rep2

first: Michael

middle: A

last: Dyer

address: 262 Danny Thomas

department: DNB

institute: St. Jude Children's Research Hospital

description:
1657572_VSX2SEKO_Rep_2_S18_L004
processed data file:
scRNA_WT_VSX2-SEKO_barcodes.tsv.gz
scRNA_WT_VSX2-SEKO_features.tsv.gz
scRNA_WT_VSX2-SEKO_matrix.mtx.gz

data_processing:
scRNA-sequencing data was processed individually then aggregated using cellranger v3.0.2
scATAC-sequencing data was processed using cellranger-atac v1.0.1
Genome_build: mm10
Supplementary_files_format_and_content: For scRNA-seq tab delimited features(genes) and barcodes file and matrix file.
Supplementary_files_format_and_content: For scATAC-seq tab delimited fragments and barcodes file, matrix file, peaks bed file, and tab delimited peak_annotation

source_name: Vsx2SE Δ/Δ_retina

extract_protocol:
Retinas were removed, dissociated with papain, and run through a 4% BSA cushion. Cells were processed using the 10x genomics protocols.
Library construction was completed using the 10x RNA(v3) and ATAC-seq(v1) single cell kits

tag: strain background

value: Vsx2SE {delta}/{delta}

tag: tissue/cell type

value: retina

tag: molecule subtype

value: 3’ RNA


title: scATAC_Retina_WT

source_name: wild type_retina


title: scRNA_Retina_VSX2SEKO_Rep1

description:
1657571_VSX2SEKO_Rep_1_S17_L004
processed data file:
scRNA_WT_VSX2-SEKO_barcodes.tsv.gz
scRNA_WT_VSX2-SEKO_features.tsv.gz
scRNA_WT_VSX2-SEKO_matrix.mtx.gz


title: scRNA_Retina_WT_Rep1

description:
1657569_WT_Rep_1_S15_L004
processed data file:
scRNA_WT_barcodes.tsv.gz
scRNA_WT_features.tsv.gz
scRNA_WT_matrix.mtx.gz
scRNA_WT_VSX2-SEKO_barcodes.tsv.gz
scRNA_WT_VSX2-SEKO_features.tsv.gz
scRNA_WT_VSX2-SEKO_matrix.mtx.gz


title: SP-R210(KO) Cells 2

city: Hershey

first: Zissis

last: Chroneos

state: PA

address: 500 University Drive

department: Pediatrics

institute: Penn State College of Medicine

description:
processed data file:
DNvKO_p05.csv
KOvWT_p05.csv

data_processing:
De-multiplexed and adapter-trimmed sequencing reads were aligned to the mm10 reference genome using hisat2. Abundance for each gene was obtained using featureCounts function available in Rsubread R package. The raw count data from 3 independent replicates were analyzed using DESeq2 to obtain differentially expressed genes with p-value <0.05
Genome_build: mm10
Supplementary_files_format_and_content: Procesed Deseq results providing differentially expressed genes with p-value <0.05 between cell type  are in the correspondingly labeled CSV file. Deseq results comparing infected samples without filtereing are in the correspondingly labeled CSV file.

source_name: Modified RAW264.7 RAW Cell Line

growth_protocol: RAW264.7 cells were stably transfected with empty for SP-R210ct pTriex-2-Neo vectors and selected using 600ug/mL neomycin sulfate to generate WT and SP-R210L(DN) RAW264.7 cells, respectively. SP-R210KO cells were generated using CRISPR/Cas9.  Guide RNA sequences targeting exons 5, 6, 12, and 14 were designed using crispr.mit.edu and gRNA oligonucleotides were ligated into the LRG hU6-sgRNA- EFS-GFP-P2A vector.  RAW 264.7 macrophages were transduced with a Cas9 containing lentivirus and selected using blasticidin to generate a stable Cas9 expressing cell line. Stable Cas9 RAW264.7 cells were transfected with a pooled library of ligated gRNA vectors. Transfected GFP+ cells were isolated by flow activated cell sorting into 96-well plates to culture individual clones.  SP-R210-deficient cells were identified by Western blot analysis. 1E6 cells of each of WT, SP-R210L(DN) and SP-R210KO cells were plated for each sample.

extract_protocol:
RNA was isolated from 1,000,000 cells per sample using the RNA-Bee protocol. Briefly, plated cells were washed with PBS and 0.5 mL of RNA-Bee Isolation Reagent was added to the cells, lysed with repeated pipetting, and transferred to a microcentrifuge tube followed by the addition of 0.1 mL of chloroform was added and mixed by shaking for 15-30 seconds. Homogenate was centrifuged at 12,000xg for 15 minutes at 4oC. The aqueous phase was retained and mixed with 0.5 mL ice-cold isopropanol and placed at -20oC for 3 hours. Samples were then centrifuged at 12,000 x g for 15 minutes at 4oC and supernatant was discarded. Precipitated RNA was washed with 1 mL ice-cold 75% ethanol twice, and then allowed to air dry for 15-30 minutes at 4oC. RNA was dissolved in 25 uL RNAse, DNAse-free deionized water.
The cDNA libraries were prepared using the NEXTflex™ Illumina Rapid Directional RNA-Seq Library Prep Kit (BioO Scientific) as per the manufacturer’s instructions. Briefly, polyA RNA was purified from 200 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique index sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). .
Pooled libraries were diluted and then denatured using the Illumina protocol. The denatured libraries were loaded onto a TruSeq v2 Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe or onto a S1 flow cell on an Illumina NovaSeq 6000 and run for 2X50 cycles according to the manufacturer's instructions.

treatment_protocol: Infected cells were infected with MOI 2 of PR8 influenza A virus for 2 hours in infection media (1:1 DMEM/PBS), after which virus-containing media was removed and replaced with DMEM with 10% FBS. Infection was allowed to porceed for 22 hour for a total 24 hour infection period. Control cells had media replaced with infection media for 2 hours, after which 10% FBS containing DMEM was replaced for the remainder of the time.

tag: sp-r210 isoform expression

value: RAW264.7 cells Cas9-mediated SP-R210 deletion

tag: iav infection

value: Uninfected


title: scRNA_Retina_WT_Rep2

description:
1657570_WT_Rep_2_S16_L004
processed data file:
scRNA_WT_barcodes.tsv.gz
scRNA_WT_features.tsv.gz
scRNA_WT_matrix.mtx.gz
scRNA_WT_VSX2-SEKO_barcodes.tsv.gz
scRNA_WT_VSX2-SEKO_features.tsv.gz
scRNA_WT_VSX2-SEKO_matrix.mtx.gz


title: SP-R210(KO) Cells 3


title: SP-R210L(DN) Cells 3

description:
processed data file:
DNvKO_p05.csv
DNvWT_p05.csv

value: RAW264.7 cells with SP-R210ct pTriex-2-Neo vector


title: SP-R210L(DN) Cells 1


title: SP-R210L(DN) Cells 2


title: WT RAW Cells 2

description:
processed data file:
KOvWT_p05.csv
DNvWT_p05.csv

value: WT RAW 264.7 cells with empty pTriex-2-Neo vector


title: SP-R210(KO) Cells 1


title: WT RAW Cells 1


title: WT RAW Cells 3


title: Raw264.7_wt_DexLPS_aCxxc1_rep2

extract_protocol:
For ChIP-Seq, 40 mio cells per sample or 20 mio cells in case of H3K4me1/me2/me3 were fixed as mentioned in the sample section either for 30 min in 2 mM DSG (#C1104 ProteoChem) and 10 min 1% MeOH-free formaldehye (#2890, ThermoFisher) or 10 min 1% formaldehyde at room temperature. Remaining formaldehyde was quenched with 150 uM glycin, cells collected and washed 2x in ice-cold D-PBS. Pellets were stored at -80°C until ChIP was performed. For ChIP-Seq nuclei were extracted in Fast-IP buffer (150 mM NaCl, 5 mM EDTA (pH=7.5), 5 mM Tris (pH=7.5), 1% Triton X-100, 0.5% NP40), chromatin sonicated in shearing buffer (1% SDS, 10 uM EDTA (pH=8),50 mM Tris (pH=8)) using the Bioruptor Pico (Diagenode) for 10-15 cycles (30s on/off) at high settings. Sonicated chromatin was diluted 1:10 in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 uM EDTA (pH= 8), 16.7 uM Tris (pH=8), 167 mM NaCl) and the immunoprecipitation against the protein of interest was performed over night at 4°C. Antigen-antibody complexes were captured with protein A/G Dynabeads (Life Techn. #11202D or #11204D), 5x washed in Fast-IP buffer. Reverse crosslink was performed overnight at 65°C and proteins degraded with 100 uM proteinase K. The DNA was puriefied using Quiagen PCR purification kit according to manufacture‘s manual (#28006).
Library preperation was performed from 2 ng of ChIP DNA using the Kapa Hyper Prep Kit with PCR library amplification (#KK8504, KapaBiosystems) according to the manufactur's protocol. Shortly, ChIP DNA was end-repaired and A-tailed before adapter ligation. After adapter ligation, the ChIP DNA was purified with Agencourt AMPure XP beads (#A63880, Beckman Coulter) and size-selected for 360-600 bp using the Pippin Prep System from Saga Science. The size-selected library is amplified by PCR using the Kapa Hyper Prep Kit (#KK8504,KapaBiosystems) and purified terminally with Agencourt AMPure XP beads (#A63880, Beckman Coulter).

tag: cell type

value: Balb/c

value: male

value: wt

value: 10min 1% FA

value: rabbit polyclonal a-CGBP Abcam #ab56035


title: IL-33KO Clonorchis sinensis-infected + antibiotics  rep4

tag: strain

tag: tissue

tag: age


title: IL-33KO Clonorchis sinensis-infected + antibiotics  rep2


title: Raw264.7_wt_LPS_aSetd1a_rep2

value: no

value: 16h 0.1% EtOH, 3h 100ng/ul LPS

value: rabbit polyclonal a-hSet1 Bethyl Laboratories #A300-289A


title: IL-33KO Clonorchis sinensis-infected  rep3

value: BALB/c

value: liver


title: Raw264.7_Setd1aDel/+_DexLPS_aH3K4me1_rep3

value: Drosophila melanogaster

value: 16h 1uM Dex, 3h 100ng/ul LPS

value: rabbit polyclonal a-H3K4me1 Diagenode #C15410194


title: Raw264.7_wt_LPS_aSetd1a_rep1


title: Raw264.7_wt_DexLPS_aSetd1a_rep2


title: Raw264.7_wt_DexLPS_aSetd1a_rep1


title: Raw264.7_Setd1aDel/+_LPS_aH3K4me1_rep3


title: Raw264.7_wt_LPS_aH3K4me1_rep3


title: Raw264.7_Setd1aDel/+_DexLPS_aH3K4me1_rep2


title: Raw264.7_Setd1aDel/+_DexLPS_aH3K4me1_rep1


title: Raw264.7_Setd1aDel/+_LPS_aH3K4me1_rep2


title: Raw264.7_Setd1aDel/+_LPS_aH3K4me1_rep1


title: Raw264.7_wt_DexLPS_aH3K4me1_rep1


title: Raw264.7_wt_DexLPS_aH3K4me1_rep2


title: Raw264.7_wt_LPS_aCxxc1_rep1


title: Raw264.7_wt_LPS_aCxxc1_rep2


title: Raw264.7_wt_DexLPS_aCxxc1_rep1


title: RING_H3K4me3_1

city: Cologne

first: Giuliano

last: Crispatzu

address: Joseph-Stelzmann-Straße 26

department: CECAD

institute: University of Cologne (UoC), Germany

description: biological replicate 1

data_processing:
Library strategy: HiChIP
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools 1.2
Reads were mapped to the human (hg19), mouse (mm10) or chicken (galgal6) genome reference assembly using Bowtie2 within the HiC-Pro 2.10 framework.
Normalized bedGraph files were generated using hichipper 0.7.3 and DeepTools 2.5.7
Peaks were called using MACS2.1.1.20160309 and used  as input for loop calling by FitHiChIP 7.0
Valid pairs were converted using cooler 0.8.7 and the custom scripts within HiC-Pro 2.10, then loops were visualized with coolpup.py 0.9.2, hicexplorer 3.0 and HiCPlotter 0.8.1.
Genome_build: hg19, galGa6, mm10

source_name: RINGko/fl E14 mESC

growth_protocol: 10cm plates were coated in 0.1% gelatine generally overnight. Cells (E14 WT, EED−/− and RING1a−/−RING1bfl/fl mESC) were thawed and resuspended in 10ml of medium (serum + LIF). Standard serum + LIF medium contained 500 mL Knock-out DMEM (Gibco 10829-018), 95 mL of filtered ES FBS (Gibco 16141-061), 5.9 mL of antibiotics (Hyclone SV30079.01), 5.9 mL Glutamax (Gibco 35050-038), 5.9 mL MEM NEAA (Gibco 11140-035), 4.7 mL titrated LIF (Miltenyi Biotec 130-095-777), and 1.3 mL Beta-mercaptoethanol 55 mM (Gibco 21985-023). Cells were split once (1/3 or 1/4) every two days. When they reached 80-100% confluence protein was extracted using the abcam cell nuclear protein preparation protocol for western blot. RNA was was extracted with 400ul (for 6wp) or 1 mL (for 10cm plates) of Lysis Solution RL (Guanidinium Thiocyanate; analytik jena), stored at -80°C or then purified using the innuPREP DNA/RNA Mini Kit (analytik jena) according to the manufacturer’s instructions, and reverse transcribed with ProtoScript II First Strand cDNA Synthesis Kit (E6560L, NEB). For RING1a−/−RING1bfl/fl mESC cells we added 1000x Tamoxifen (OHT) for 72h right after first passage. Floxed deletion was assessed after ChIP / HiChIP lysis in electrophoresis gel using flanking primers. Deleted protein was assessed via standard Western blot (using plate reader).

extract_protocol:
Fertilized chicken eggs (white leghorn; Gallus gallus domesticus) were obtained from a local breeder (LSL Rhein-Main) and incubated at 37°C and 80% humidity in a normal poultry egg incubator (Typenreihe Thermo-de-Lux). Following microsurgical procedures, the eggs were re-incubated until the embryos reached the desired developmental stages. The developmental progress was determined according to the staging system of HH (Hamburger and Hamilton, 1992). Mice were housed and bred under standard conditions in the CECAD ivRF. The breedings described were approved by the Landesamt für Natur, Umwelt, und Verbraucherschutz Nordrhein-Westfalen (LANUV), Germany (animal application 84-02.04.2015.A405). Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibodies againts the specific proteins of interest in each case.
HiChIP was performed as described by Mumbach et al. 2016 Nat Methods with some modifications. We generally replaced the ChIP protocol with the one described above, we cut and ligated overnight (NEB T4 Ligase, instead of Invitrogen T4) and DNA was extracted with phenol-chlorophorm not a kit. For low cell numbers, we increased the centrifugation time to 30 minutes and 15 minutes after lysis, as well as 30 minutes after ligation to see a pellet more accurately. Generally 12 cycles were used for Tn5 Nextera PCR amplification (Illumina Nextera DNA UD Indexes Kit). We aimed for 100M read pairs for each run on a NovaSeq 6000 sequencer (Illumina).

treatment_protocol: A full E14 WT 10cmp vial was thawed and resuspended in 10 mL of serum + LIF. The next day, cells were washed with PBS and medium was changed and the day after cells were split ¼. We began the differentiation the day after (d0). First, we trypsinized cells with 2mL TrypLE Express (Life technologies). After 5 minutes, Trypsin was quenched using 4 mL of serum + LIF. We then took 400ul for RNA extraction and the residual cells for differentiation. Both vials were centrifugated (750 and 1000 RPM respectively). Supernatant was discarded and cell pellet for RNA extraction was resuspended in Lysis Solution RL. The other vial was heavily resuspended in 5 mL of N2B27 with 0.1% of BSA (Life Technologies) and 0.1% of bFgf (Life Technologies) to get single cells. Cell resuspension and count was assessed using the BioRad TC20. We placed droplets of 15000 cells / cm2 in 10 mL of N2B27 with 0.1% of BSA and 10 ng/mL of bFgf. On d1 of differentiation, we changed medium (10 mL of N2B27 with 0.004% of BSA and 10 ng/mL bFgf) without PBS washing. On d2 of differentiation, we changed medium (10 mL of N2B27 with 0.004% of BSA, 10 ng/mL bFgf and 5 μM Xav939/Wnt inhibitor) without PBS washing. On d3 of differentiation, we changed medium (10 mL of N2B27 with 0.004% of BSA and 5 μM Xav939/Wnt inhibitor) without PBS washing. On d4 of differentiation, we changed medium (10 mL of N2B27 with 0.004% of BSA and 5 μM Xav939/Wnt inhibitor) without PBS washing. On the last day of differentiation (d5), we washed 1-2 with PBS (depending on amount of dead cells), resuspended plate in 5 mL of N2B27, scratched off cells, then extracted RNA and crosslinked these. Differentiation was assessed using RT-qPCR on a Light Cycler 480II comparing AntNPC d5 vs. E14 WT d0 relative gene expression levels (using the 2ΔCt method) with house keeping gene (Eef1a1), pluripotency markers (Pou5f1/Oct4 and Nanog), mesoderm marker (T) and ectoderm markers (Six3 and Lhx5). Standard deviations were calculated from technical triplicate reactions and were represented as error bars. Primers used can be found in the Supplemental Table.

value: WT E14 mESC

value: E14 RING1a-/- mESC were treated for 72 hours with Tamoxifen to flox RING1b

value: H3K4me3 (39159, Active Motif)


title: RING_H3K4me3_2

description: biological replicate 2


title: Raw264.7_wt_DexLPS_aH3K4me1_rep3


title: mE10.5_H3K27ac_2

description: biological replicate 2

source_name: Whole brain from E10.5 mice

value: Whole brain from E10.5 mice

value: WT

value: H3K27ac (39133, Active Motif)


title: E14_H3K4me3_2

description: biological replicate 2

source_name: WT E14 mESC


title: EED_H3K4me3_1

description: biological replicate 1

source_name: EEDko E14 mESC


title: mE10.5_H3K27ac_1

description: biological replicate 1


title: EED_H3K4me3_2

description: biological replicate 2


title: Interferon lambda plus poly(I:C) treatment, biological replicate 1

type: RNA

city: Washington

first: Karima

last: Abutaleb

state: District of Columbia

address: 111 Michigan Ave NW

department: Center for Genetic Medicine Research

institute: Children's National Hospital

description: Gene expression data from infant nasal airway epithelial cells treated with interferon lambda and poly(I:C)

hyb_protocol: Fragmented and labeled cDNA were hybridized to Gene Chip cartridge array in the Affymetrix GeneChip Hybridization oven for 16 hours at 45°C and 60 rpm.

scan_protocol: The Affymetrix Gene Chip scanner was used to scan chips per manufacturer's protocol. CEL files were generated and used for analysis in Transcriptomic Analysis Console (TAC) software.

data_processing: The total RNA isolated from harvested cells was used for transcriptome profiling via Clariom S Human microarrays (ThermoFisher). Normalizations, quality checks, and data analysis were done using the Transcriptome Analysis Console (TAC) software 4.0.

label: Biotin

source_name: Nasal airway epithelial cells (infant), treated with interferon-lambda and poly(I:C)

label_protocol: Fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the proprietary DNA Labeling Reagent that is covalently linked to biotin according to Affymetrix fragmenting and labeling protocols.

growth_protocol: Primary cells were grown at 37 degrees Celsius and 5% CO2. They were maintained using a growth media consisting of conditionally reprogrammed cells and bronchial epithelial growth medium (Lonza).

extract_protocol: Total RNA was extracted from cells using TriZol reagents and purified using phenol:chloroform extraction. RNA quality was assesed using the Agilent 2100 Bioanalyzer.

treatment_protocol: 3.5x10^5 cells were seeded onto collagen-coated 6-well plates.  Cells were serum-starved for 24 hours prior to exposure to IFN-lambda (100 ng/mL). Sixteen hours after exposure to IFNλ, cells were exposed to poly(I:C) (10 ng/μL) for an additional 20 hours prior to harvesting.

value: Nasal airway epithelium

value: 14 months

tag: age group

value: Infant


title: Interferon lambda treatment, biological replicate 3

source_name: Nasal airway epithelial cells (infant), treated with interferon-lambda

value: 10 months


title: GFP-ddc_H3K4me3

first: Qikun

last: Liu

state: Beijing

address: Haidian District, 5 Yiheyuan Rd., Zonghekeyan BLDG, Rm 502

department: School of Advanced Agricultural Sciences

institute: Peking University

data_processing:
ChIP-seq fastq reads were aligned to the TAIR10 reference genome with Bowtie using default settings and allowing only uniquely mapping reads.
ChIP-Seq peaks were called using callpeak function in MACS2 (v2.1.1.)
ChIP-seq data metaplots were generated by  NGSPLOT.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig

organism: Arabidopsis thaliana

source_name: rosette leaf

growth_protocol: long data condition. Plants were grown on soil.

extract_protocol:
Following in-vivo fixation, isolated nuclei were sonicate, cell lysates were cleared and  histone-DNA complexes were isolated with  antibody.
Libraries were generated with NuGEN Ovation Ultra Low System V2 kit, according to manufacturer’s instructions

treatment_protocol: no treatment

tag: developmental stage

value: 3-week old

tag: genotype/variation

value: GFP-ddc

value: rosette leaf

value: H3K4me3 (Millipore 04-745)


title: MED12-YFP-FLAG_R1

source_name: inflorescence

value: 6-week old

value: cct-2 mutant expressing MED12-YFP-FLAG transgene

value: inflorescence

value: anti-FLAG (SIGMA-A8592-1MG)


title: GFP-morc1_H3K4me3


title: MED12-YFP-FLAG_R2


title: columbia-0_FLAG


title: GFP-ddc_H3


title: Poly(I:C) treatment, biological replicate 3

source_name: Nasal airway epithelial cells (infant), treated with poly(I:C)


title: GFP-morc1_H3


title: Interferon lambda plus poly(I:C) treatment, biological replicate 3


title: Poly(I:C) treatment, biological replicate 2

value: 8 months


title: Interferon lambda plus poly(I:C) treatment, biological replicate 2


title: Poly(I:C) treatment, biological replicate 1


title: GFP-wt_H3

value: GFP-wt


title: Interferon lambda treatment, biological replicate 1


title: GFP-wt_H3K4me3


title: WGBS Dnmt3a-/-

city: Gainesville

first: Rene

last: Opavsky

state: FL

address: 2033 Mowry rd, CGRC r..265

department: Anatomy and cell biology

institute: University of FLORIDA

data_processing:
Quality check, trimming, filtering, and alignment of reads to the Mus musculus UCSC mm10 reference genome was performed at the ICBR Bioinformatics Core (UF, Florida). Methylation calling was performed with Methyldackel (v 0.3.0.1) using the mm10-CG index. Only CpG sites with a minimum sequencing depth 5x were included in analysis. Differentially methylated regions (DMRs) were determined by Metilene and defined based on average of minimum three consecutive differentially methylated cytosines (DMCs) with methylation change of ≥30% in the same direction with p values < 0.05 (as determined by MWU test). Maximal base pair cut-off for a distance between consecutive DMCs in DMR was set to 50 bp.
For RNA-seq, trimmed sequencing data were first aligned to mm10 reference genome using STAR aligner. RNA-seq data with minimum mapped quality 50 were quantitated using the RNA-seq quantitation pipeline in SeqMonk software. For differentially expressed genes, only genes with a fold change ≥ 2 and a p-value < 0.05 (by DeSeq2) were considered to be significant.
Genome_build: mm10 - Mus musculus GRCm38 (08/06/2012)
Supplementary_files_format_and_content: Processed data files are bigwig files, they contain methylation value for CpG sites whith coverage ≥ 5x

source_name: peripheral T-cell lymphoma

extract_protocol:
For WGBS, genomic DNA was isolated from two independent Dnmt3b+/- PTCL samples using phenol/chloroform. For RNA-seq, total RNA was isolated by trizol from three independent  Dnmt3b+/- PTCL samples.
The WGBS libraries were prepared and sequenced on an Illumina NovaSeq6000 sequencer using 150 bp long paired-end reads. The RNAseq libraries were generated and sequenced on Illumina HiSeq 2500 platform using paired-end 150 bp runs.

value: lymph node

tag: genotype

value: FVB


title: WGBS Dnmt3b+/- 1


title: Control, biological replicate 1

source_name: Nasal airway epithelial cells (infant), untreated


title: Interferon lambda treatment, biological replicate 2


title: Control, biological replicate 3


title: Control, biological replicate 2


title: 5xFAD mouse B

city: Daegu

first: Jae-Yeol

last: Joo

address: 61, cheomdan-ro, Dong-gu,

institute: Korea Brain Research Institute

data_processing:
Base-calling was performed by the BGISEQ-500 software version 0.3.8.1111
The quality of the RNA-seq libraries was first evaluated using the FastQC v0.11.5 software.
(1) trimming and cleaning reads that aligned to primers and/or adaptors, (2) reads with over 50% of low-quality bases (quality value ≤5) in one read, and (3) reads with over 10% unknown bases (N bases)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Cufflinks 2.2.1
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Blood

extract_protocol:
Total RNA was extracted from mouse cortex or whole blood using TRIzol method. cDNA synthesis using High-Capacity reverse transcription kit (Applied Biosystems) according to the manufacturer protocols
TruSeq Stranded Total RNA Library Prep kit (Illumina,Inc)

value: Blood

value: 5~6 month


title: Single DAPI+ nuclei (mixed samples)_scTHS-seq

city: La Jolla

first: Thu

last: Duong

address: 9500 Gilman Dr.

institute: University of California San Diego

description:
scTHS-seq data
Mutiple instruments (Illumina Hiseq 2500 and Illumina MiSeq)

data_processing:
Library strategy: scTHS-seq
Basecalls performed using bcl2fastq v2.17.1.14
Sequencing data from the same samples was concatenated together and then as input to deindexder (https://github.com/ws6/deindexer) with 0 mismatch barcode demultiplexing.
Barcode combinations associated with each read were appended to each reads header with in house perl scripts and all fastqs were combined and mapped to a hg38 no alternative loci plus decoy reference genome (GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set) and mm10 no alternative loci reference genome (GCA_000001635.5_GRCm38.p3_no_alt_analysis_set) using BWA 0.7.12-r1039. Mapped sam outputs were redemultiplexed by barcodes, converted to bam files and clonal reads removed with samtools 1.3.1
Multimapping reads MAPQ<5 were removed from each single cell dataset to remove reads in repeat regions
Peak calling using combined reads from each raw cluster generated using SnapATAC v2 was run using MACS2 v2.1.1.20160309 with the command "--nomodel --shift 37 --ext 73 --qvalue 5e-2 -B --SPMR --call-summits".  Peaks from all clusters were merged to generate a consensus list of peaks, and a binary chromosomal peak locations by cell barcodes matrix was generated.  Peak locations were filtered to keep only chromosomes 1-22, X for human and 1-19, X for mouse, and only peaks belonging to a minimum of 25 cells and cells with at least 200 accessible sites were kept.
Genome_build: GENCODE GRCh38, GENCODE GRCm38
Supplementary_files_format_and_content: accessible peaks bed file for human and mouse
binary count matrices for human and mouse. Matrices (columns = cell names, rows = peaks with accessible reads) have been subsetted to ~10k columns for each tsv file exported from R.  For cell names, part 1-3 are barcodes, part 4 are processed plate numbers and species (H=human, M=mouse), and part 5 is sample age and L=lung. Each processed file contains information from all samples from the same species.

organism:
Homo sapiens
Mus musculus

source_name: lung - right middle lobe, left lower lobe

extract_protocol:
Samples were thawed in 1-1.5mL 10% DMSO in FBS on ice for 5-10 minutes.  For nuclei isolation, contents were transferred into Miltenyi GentleMACS C tubes and ice-cold nuclei extraction buffer was added (0.32M sucrose, 5 mM CaCl, 3mM MgAc2, 0.1 mM EDTA, 10 mM Tris-HCl, 0.1% TritonX-100).  GentleMACS dissociation was completed using preset programs A through E and placed on ice in between programs.  Samples and 1 mL of NEB buffer used to rinse C tubes were passed through 30-um filters into 15 mL tubes.  Total volume was brought up to 10 mL with PBS + 2 mM EGTA (PBSE, pH ~7.4), centrifuged for 10 mins x 900g at 4C, and pellets resuspended in 1 mL PBSE + 2% fatty-acid-free BSA (Gemini) containing 4’,6-diamidino-2-phenylindole (DAPI).  Subsequent DAPI+ flow cytometry sorting was completed as described previously (Lake et al., 2018).
scTHS-seq library generation was completed as described previously (Lake et al., 2018).
scTHS-seq and Nextera, sequencing using Illumina Miseq and Hiseq 2500
All 8 samples were barcoded and mixed for sequencing.  They were later de-multiplexed.

tag: experiment

tag: disease state

value: no known lung disease

value: 1 day old-9 year old (human), postnatal day 1-28 (mouse)

tag: lung developmental stage

value: alveolar, saccular


title: WT mouse B

value: wild type


title: 5xFAD mouse CTX

source_name: Brain(CTX)

value: Brain(CTX)


title: WT mouse CTX


title: Sucrose_wild-type_PFC

city: Tokyo

first: Shinobu

last: Hirai

address: Setagaya Kamikitazawa 2-1-6

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

description: 70 days sucrose diet fed wild-type mice from postnatal day 21

hyb_protocol: 0.6 µg of Cy3-labeled cRNA was fragmented and hybridized to Agilent SurePrint G3 Mouse Gene Expression v2 Microarray (G4852B) using Agilent Gene Expression Hybridization Kit. Hybridization was performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 3µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: pre frontal cortex, sucrose diet, wild-type

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng of total RNA using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Three independent total RNA samples from each group were mixed and purified using the RNeasy Mini Kit (Qiagen). RNA quality was assessed using a 2100 bioanalyzer (Agilent Technologies).

treatment_protocol: We investigated four groups of mice that were fed two kinds of diets for about 70 days immediately after weaning (from postnatal day 21): wild-type, starch-fed mice (control, CTL); wild-type, sucrose-fed mice; Glo1 heterozygous, starch-fed mice; and Glo1 heterozygous, sucrose-fed mice. The prefrontal cortex was removed immediately after cervical dislocation and decapitation.

value: pre frontal cortex

value: 3 month-old

tag: diet

value: sucrose diet


title: WGBS Dnmt3b+/- 2


title: Sucrose_glo1 heterozygote_PFC

description: 70 days sucrose diet fed glo1 heterozygote mice from postnatal day 21

source_name: pre frontal cortex, sucrose diet, glo1 heterozygote

value: glo1 heterozygote


title: Starch_glo1 heterozygote_PFC

description: 70 days starch diet fed glo1 heterozygote mice from postnatal day 21

source_name: pre frontal cortex, starch diet, glo1 heterozygote

value: starch diet


title: salt_Botrytis_t_7d_rep2

city: Tuebingen

first: Andrea

middle: A.

last: Gust

state: BW

address: Auf der Morgenstelle 32

department: Center for Plant Molecular Biology (ZMBP)

institute: University of Tuebingen

description: This sample is of wild-type Arabidopsis thaliana, watered with 150 mM NaCl for 4 days and then infected with Botrytis cinerea for an additional 3 days (total of 7 days). It is the second of three biological replicates used in this experiment, each from separate leaves.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: salt-treatment + Botrytis-infection, day 4+3, replicate 2

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Arabidopsis thaliana ecotype Columbia-0 (Col-0) was sown on steam-sterilized GS90 soil (Gebr. Patzer), stratified for 2 days at 4°C, and cultivated in short day conditions with  8 h light, 22 °C, 150 μmol/m2s light intensity and 40-60 % humidity.

extract_protocol: Total RNA was isolated from 200 mg of leaf tissue according to Chomczynski and Sacchi (Analytical biochemistry 162:156-159), using Phase Lock GelTM Heavy reaction tubes (5Prime, Hamburg). DNA contaminations were removed with Deoxyribonuclease I (Thermo Fisher Scientific) and total RNA was reverse transcribed into double stranded cDNA using the SuperScript® Double-Stranded cDNA Synthesis Kit (Invitrogen). Concentration of nucleic acids was done with the NanoDrop 2000 photometer and the NanoDrop Software (both Thermo Scientific).

treatment_protocol: 5 weeks old Arabidopsis plants were either normally watered or watered with 25 ml 150 mM NaCl per pot for 4 days, For subsequent Botrytis cinerea (isolate BO5-10) infection, normally or salt-watered plants were  infected by placing 5 μl drops of a spore suspension (5*105 spores/ml in ¾ potato dextrose broth) on each 2 leaves of 3 plants per pre-treatment (pooled samples are one biological replicate out of three). Plant were afterwards kept for 3 days under a clear cover to obtain high humidity, then leaves were harvested, snap frozen in liquid N2 and stored at -80°C until RNA extraction.

value: Wild-type

tag: ecotype


title: UMUC-14 - lipo#2

city: paris

first: Elodie

last: chapeaublanc

address: 26 rue d'ulm

department: UMR 144

institute: Institut Curie

description: UMUC-14 treated with LipofectaminRNAimax

hyb_protocol: Affymetrix microarrays were hybridized with 10µg of biotinylated cRNA according the supplier recommendations. Microarrays were washed and stained using FS450 fluidics upon a protocol provided by Affymetrix, corresponding to the U133plus 2.0 arrays

scan_protocol: Microarrays were scanned using a 7G, Affymetrix GCS3000 scanner, raw data were acquired with Affymetrix Genechip Command Console.

data_processing: Signal reconstruction was performed with the RMA algorithm as implemented in Bioconductor affy package on R statistical software using the Dai custom CDF package: HGU133Plus2_Hs_ENTREZG Brainarray Custom CDF EntrezG version 20

label: biotin

source_name: human bladder cancer cell line, UMUC-14

label_protocol: 100ng of total RNA were amplified to produced biotinylated complementary RNAs, as recommended by Affymetrix.

growth_protocol: The bladder cancer cells, UMUC-14, have been cultured in DMEM 10% fetal bobine serum

extract_protocol: mRNAs were extracted and purified using RNeasy Mini kits (Qiagen).

treatment_protocol: UMUC-14 cells were transfected for 40h either with siRNA FGFR3 (1.siFGFR3#35, Ambion, 144467; 2.siFGFR3#36, Ambion, 144468; 3.siFGFR3#3, Ambion, s5167) or using LipofectaminRNAimax (Invitrogen) according to the manufacturer's instructions (reverse protocol)

tag: cell line

tag: sirna

value: LipofectaminRNAimax


title: UMUC-14 - siFGFR3#36_1_

description: UMUC-14 treated with siFGFR3#36, Ambion, 144468

value: siFGFR3#36, Ambion, 144468


title: normal_ watering_t_4d_rep3

description: This sample is of wild-type Arabidopsis thaliana,  normally watered at time point 4 days. It is the third of three biological replicates used in this experiment, each from separate leaves.

source_name: water-control day 4, replicate 3


title: salt_t_4d_rep1

description: This sample is of wild-type Arabidopsis thaliana, watered with 150 mM NaCl at time point 4 days. It is the first of three biological replicates used in this experiment, each from separate leaves.

source_name: salt-treatment day 4, replicate 1


title: AS fs_2

city: Dummerstorf

first: Siriluck

last: Ponsuksili

address: Wilhelm-stahl-allee 2

institute: FBN

description:
SMSCs derived from porcine synovial membrane
Gene expression data from mesenchymal stem cells derived from fibrous synovium of AS pig

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 42 C on Affymetrix Porcine Snowball Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning using the GeneChip scanner 3000 were performed according to Affymetrix protocols

data_processing: Data were analysed with Affymetrix GCOS 1.1.1 software using global scaling to a target signal of 500.

organism: Sus scrofa

source_name: mesenchymal stem cells

label_protocol: biotin-labeled cRNAs were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated using TRI Reagent (Sigma, Taufkirchen, Germany) according to the manufacturer’s protocol. After DNaseI treatment the RNA was cleaned up using the RNeasy Kit (Qiagen, Hilden, Germany).

tag: breed

value: Angeln Saddleback

value: fibrous synovium


title: salt_Botrytis_t_7d_rep1

description: This sample is of wild-type Arabidopsis thaliana, watered with 150 mM NaCl for 4 days and then infected with Botrytis cinerea for an additional 3 days (total of 7 days). It is the  first of three biological replicates used in this experiment, each from separate leaves.

source_name: salt-treatment + Botrytis-infection, day 4+3, replicate 1


title: Starch_wild-type_PFC

description: 70 days starch diet fed wild-type mice from postnatal day 21

source_name: pre frontal cortex, starch diet, wild-type


title: normal_ watering_t_4d_rep2

description: This sample is of wild-type Arabidopsis thaliana, normally watered at time point 4 days. It is the second of three biological replicates used in this experiment, each from separate leaves.

source_name: water-control day 4, replicate 2


title: UMUC-14 - siFGFR3#35_2_

description: UMUC-14 treated with siFGFR3#35, Ambion, 144467

value: siFGFR3#35, Ambion, 144467


title: AS fp_1

description:
SMSCs derived from porcine synovial membrane
Gene expression data from mesenchymal stem cells derived from adipose synovium of AS pig

value: adipose synovium


title: intestine_normal_rep2 [NX-3C]

city: Lanzhou

first: Jie

last: Meng

state: Gansu

address: 35 Dingxi dong lu, Chengguan district, Lanzhou city, Gansu province, China

institute: Gansu University of Chinese Medicene

hyb_protocol: DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray. Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: Agilent chip scanner (G2565CA) was used to scan the cleaned chip and obtain hybrid images.

data_processing: The lncRNA+mRNA array data were analyzed for data summarization, normalization and quality control by using the GeneSpring software V13.0 (Agilent). To select the differentially expressed genes, we used threshold values of ≥2 and ≤−2-fold change and a Benjamini-Hochberg corrected p vlaue of 0.05. The data was Log2 transformed and median centered by genes using the Adjust Data function of CLUSTER 3.0 software then further analyzed with hierarchical clustering with average linkage (Eisen et al., 1998).

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been previously described,  2 and the procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

growth_protocol: Gastric and intestinal tissues were removed from euthanized mice and stored at -80 ° c in a refrigerator

extract_protocol: Total RNA containing small RNA was extracted from stomach and intestine by using the Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin,TX, USA) according to manufacter’s protocol. The purity and concentration of RNA were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000). RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

treatment_protocol: The tissue blocks were ground into a tissue homogenate to extract RNA

value: Kunming (KM)

tag: gender

value: male

tag: sample group

value: normal mice

value: intestine


title: intestine_normal_rep3 [NC-1C]

tag: strain

value: female


title: UMUC-14 - lipo#3


title: AS fs_1

tag: tissue


title: normal_watering_Botrytis_t_7d_rep3

description: This sample is of wild-type Arabidopsis thaliana, normally watered for 4 days and then infected with Botrytis cinerea for an additional 3 days (total of 7 days). It is the  third of three biological replicates used in this experiment, each from separate leaves.

source_name: Botrytis-infection, day 3, replicate 3


title: salt_t_4d_rep2

description: This sample is of wild-type Arabidopsis thaliana, watered with 150 mM NaCl at time point 4 days. It is the second of three biological replicates used in this experiment, each from separate leaves.

source_name: salt-treatment day 4, replicate 2


title: stomach_normal_rep3 [NC-3W]

tag: age

value: stomach


title: normal_watering_Botrytis_t_7d_rep1

description: This sample is of wild-type Arabidopsis thaliana, normally watered for 4 days and then infected with Botrytis cinerea for an additional 3 days (total of 7 days). It is the  first of three biological replicates used in this experiment, each from separate leaves.

source_name: Botrytis-infection, day 3, replicate 1


title: salt_Botrytis_t_7d_rep3

description: This sample is of wild-type Arabidopsis thaliana, watered with 150 mM NaCl for 4 days and then infected with Botrytis cinerea for an additional 3 days (total of 7 days). It is the  third of three biological replicates used in this experiment, each from separate leaves.

source_name: salt-treatment + Botrytis-infection, day 4+3, replicate 3


title: control_ t_0_rep3

description: This sample is of wild-type Arabidopsis thaliana, untreated at time point zero. It is the third of three biological replicates used in this experiment, each from separate leaves.

source_name: untreated control replicate 3


title: salt_t_4d_rep3

description: This sample is of wild-type Arabidopsis thaliana,  watered with 150 mM NaCl at time point 4 days. It is the third of three biological replicates used in this experiment, each from separate leaves.

source_name: salt-treatment day 4, replicate 3


title: UMUC-14 - siFGFR3#3_1_

description: UMUC-14 treated with siFGFR3#3, Ambion, s5167

value: siFGFR3#3, Ambion, s5167


title: DL fs_2

description:
SMSCs derived from porcine synovial membrane
Gene expression data from mesenchymal stem cells derived from fibrous synovium of DL pig

value: German Landrace


title: control_ t_0_rep2

description: This sample is of wild-type Arabidopsis thaliana, untreated at time point zero. It is the second of three biological replicates used in this experiment, each from separate leaves.

source_name: untreated control replicate 2


title: AS fp_2


title: normal_ watering_t_4d_rep1

description: This sample is of wild-type Arabidopsis thaliana, normal watering at time point 4 days. It is the first of three biological replicates used in this experiment, each from separate leaves.

source_name: water-control day 4, replicate 1


title: intestine_normal_rep1 [NX-2C]


title: UMUC-14 - lipo#1

description: UMUC-14 treated with LipofectaminRNAimax


title: normal_watering_Botrytis_t_7d_rep2

description: This sample is of wild-type Arabidopsis thaliana, normally watered for 4 days and then infected with Botrytis cinerea for an additional 3 days (total of 7 days). It is the second of three biological replicates used in this experiment, each from separate leaves.

source_name: Botrytis-infection, day 3, replicate 2


title: vriΔ679 ZT14 rep2

city: College Station

first: Paul

last: Hardin

state: Texas

address: 3258 TAMU Dept of Biology Buttler Hall room 100H

institute: Texas A&M University

data_processing:
Basecalls performed using RTA v2 software
Reads were mapped to the Drosophila melanogaster genome (dm6 – UCSC) with STAR aligner version 2.6.1d using the following parameters STAR --runThreadN 8
mapped reads were assembled and expression levels were quantified using Strigtie v1.3.5 following parameters described in Pertea et al., Nature Protocols. 2016. Ballgown input table files were generated in StringTie using -B option
Ballgown input table files were used to estimate to identify differentially expressed genes, transcripts and exons. The Ballgown object generated was filtered to remove low expressed transcripts with variance across samples less than one as suggested in Pertea et al., Nature Protocols. 2016.
The Ballgown_filtered object was used to estimate the different genes, transcritps and exons using the function stattest with the following arguments: genes and transcripts (meas="fpkm"). Exon (meas="rcount")
Genome_build: Drosophila melanogaster genome (dm6 – UCSC)
Supplementary_files_format_and_content: Matrix table with gene-level expression values (FPKM) combined for all samples.
Supplementary_files_format_and_content: Ballgown input tables for each sample with transcript-level expression values (FPKM) saved as a text file.

organism: Drosophila melanogaster

source_name: Heads

growth_protocol: Flies were reared on standard cornmeal/agar medium supplemented with yeast and kept in 12 hr light/12 hr dark (LD) cycles at 25oC.

extract_protocol:
Total RNA from heads was extracted using TRIzol, treated with TURBO™ DNase (Thermo Fisher Scientific), precipitated and then purified with Lithium Chloride (Thermo Fisher Scientific) following manufacturer’s instructions.
A total of 1ug of RNA was used to isolate mRNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). RNA library construction was conducted using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s instructions. Libraries quality and size distribution was verified on a Bioanalyzer, libraries were quantified by real-time quantitative PCR, and 4 multiplexed libraries were mixed in equimolar ratios and sequenced on Illumina Next Seq 500, 75 nt, single end sequencing run

treatment_protocol: Flies were entrained  under a condition of 12 hr light/12 hr dark (LD) cycles at 25oC for 3 days prior the collection at ZT2 and ZT14 on the fourth day.

value: mutant


title: vriΔ679 ZT2 rep2


title: vriΔ679 ZT2 rep1


title: wild type ZT14 rep2

value: wild-type


title: wild type ZT14 rep1


title: wild type ZT2 rep2


title: wild type ZT2 rep1


title: vriΔ679 ZT14 rep1


title: control_ t_0_rep1

description: This sample is of wild-type Arabidopsis thaliana, untreated at time point zero. It is the first of three biological replicates used in this experiment, each from separate leaves.

source_name: untreated control replicate 1

value: Wild-type


title: DL fs_1


title: stomach_normal_rep2 [NC-1W]


title: stomach_normal_rep1 [NX-2W]


title: AJ15_JAL055-3_01

city: Montreal

first: Jack

last: Antel

state: Quebec

address: 3801 University, Montreal Neurological Institut

country: Canada

institute: Montreal Neurological Institute

hyb_protocol: RNAs were hybridized to the GeneChip Human Transcriptome 2.0 Arrays, hybridized target cRNAs were stained with streptavidin phycoerythrin

scan_protocol: Arrays were scanned using GeneArray Scanner at excitation wavelength of 488nm

data_processing: The CEL data files were analyzed with R using the oligo (version 1.34.0) Bioconductor R package.

source_name: brain, 2 days N1 control treatment

label_protocol: Biotin-labeled cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Tissues from the surgical corridor from the adult samples were collected into CUSA bags. Tissue derived from the CUSA bags was subjected to trypsin digestion followed by Percoll gradient centrifugation in order to obtain a myelin-depleted whole cell fraction comprised mainly of OLs and microglia with few if any astrocytes or neurons.We derived an enriched OL population by adhering the total cell population overnight to remove adherent microglia.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The cells were treated in N1 medium or low glucose (0.25g/L glucose) medium for two days.

value: adult

tag: donor

value: donor 3

value: brain


title: AJ12_JAL052-3_01

source_name: brain, 2 days low glucose treatment

value: donor 2


title: WT_H3K4me3_R2 (ChIP-seq)

city: Memphis

first: Mitch

last: Weiss

address: 262 Danny Thomas Place

institute: st jude children's research hospital

data_processing:
Basecalls performed using CASAVA
BWA (default parameter) was used to align reads to human genome hg19. Duplicated reads were marked by Picard, and uniquely mapped reads were retained by samtools (parameter “-q 1 -F 1024”).
We confirmed quality control results were good following the ENCODE guideline for CHIPSEQ, reads were then extend to the estimated fragment size(by SPP) and converted to bigwig files.  We observed clear peaks observed by inspection on Integrated Genomics Viewer (Broad Institute) and there was high consistency among replicates.
Free pipeline to run with DNAnexus available at https://www.stjude.cloud/tools.html. Source code of ChIP-Seq pipeline to deposit on DNAnexus were also available at https://github.com/stjude/ChIP-Seq
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell type

value: erythroblast cells

tag: passage

tag: chip antibody

value: H3K4me3(Cell Signaling Technology, CST#9751)


title: WT_H3K4me3_R1 replicate (ChIP-seq)


title: AJ16_JAL056-3_01


title: DL fp_2

description:
SMSCs derived from porcine synovial membrane
Gene expression data from mesenchymal stem cells derived from adipose synovium of DL pig

source_name: mesenchymal stem cells

value: adipose synovium


title: WT_H3K27me3_R2 replicate (ChIP-seq)

value: H3K27me3(Cell Signaling Technology, CST#9733)


title: AJ11_JAL051-3_01


title: AJ4_JAL048-3_01

value: donor 1


title: Aj3_JAL047-3_01


title: securinine treatment_biological rep1

city: Copenhagen

first: Dennis

last: Özcelik

address: Universitetsparken 2

country: Denmark

institute: University of Copenhagen

hyb_protocol: 5.5 ug of cDNA were hybridized for 16 hr at 45C on Human Gene 2.0 ST microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450_0002.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: Data sets were analyzed in an R environment and pre-processed by robust multi-array averaging (RMA) of the R package “oligo”. The R packages “genefilter” and “limma” were used to further analyze and filter the data set

source_name: SH-SY5Y treated with securinine for 24 h

label_protocol: Biotinylated cDNA were prepared from 400 ng RNA using the Affymetrix WT Plus Kit.

growth_protocol: The human neuroblastoma cell line SH-SY5Y was maintained in Dulbecco’s modified Eagle medium supplemented with 100 nmol/L non-essential amino acids and 10 % fetal bovine serum. All cell were cultured at 37 °C in a humidified atmosphere of 95 % air and 5 % CO2.

extract_protocol: Total RNA was prepared using the RNeasy© Mini kit (Qiagen, Mississauga, Ontario) according to manufacturer's protocol.

treatment_protocol: Inhibitor (30 uM for securinine; 4 uM for 16F16) or solvent (methanol) was added and cells were incubated for 24 h at standard culturing conditions

value: neuroblastoma cells

tag: treatment

value: securinine for 24 h


title: securinine treatment_biological rep2


title: DL fp_1


title: intestine_high-dose Codonopsis Pilosula_rep2 [GX-3C]

source_name: intestine_high-dose Codonopsis Pilosula

value: Kunming (KM)

value: male

value: high-dose Codonopsis Pilosula treatment

value: intestine


title: intestine_aging_rep3 [PC-3C]

value: female

value: aging


title: stomach_aging_rep3 [PC-2W]

value: stomach


title: intestine_high-dose Codonopsis Pilosula_rep1 [GX-1C]


title: 16F16 treatment_biological rep2

source_name: SH-SY5Y treated with 16F16 for 24 h


title: stomach_high-dose Codonopsis Pilosula_rep3 [GC-3W]

source_name: stomach_high-dose Codonopsis Pilosula


title: 16F16 treatment_biological rep1


title: stomach_high-dose Codonopsis Pilosula_rep2 [GC-1W]


title: intestine_aging_rep1 [PC-1C]


title: stomach_aging_rep2 [PC-1W]


title: Rha1-GOF_S2

city: London

first: Vanessa

last: Dumeaux

state: Ontario

address: Elgin Dr

department: Anatomy and Cell Biology

institute: Western University

data_processing:
RNA sequencing reads were pre-processed with the sequence-grooming tool cutadapt version 0.4.1(MARTIN 2011) with the following quality trimming and filtering parameters (`--phred33 --length 36 -q 5 --stringency 1 -e 0.1`). Each set of paired-end reads was mapped against the C. albicans SC5314 haplotype A, version A22 downloaded from the Candida Genome Database (CGD) (www.candidagenome.org) using HISAT2 version 2.0.4. SAMtools was then used to sort and convert SAM files. The read alignments and C. albicans SC5314 genome annotation were provided as input into StringTie v1.3.3 (PERTEA et al. 2015) which returned gene abundances for each sample. We imported gene abundances into R and conducted differential analysis of gene count data using the DESeq2 R package (Love et al. 2014).
Genome_build: C. albicans SC5314 haplotype A, version A22
Supplementary_files_format_and_content: Tab-delimited gene abundances files

molecule: polyA RNA

organism: Candida albicans

source_name: yeast cells

extract_protocol:
Total RNA isolation was performed using Qiagen RNeasy plus Minikit
Libraries were prepared according to Illumina's mRNASeq stranded library preparation kit

treatment_protocol: YPD medium at 30°C

tag: genotype

value: Rha1-Gofum6 delta/delta deletion strain


title: stomach_aging_rep1 [PX-1W]


title: F11KO_H3K4me3_R2 (ChIP-seq)


title: intestine_aging_rep2 [PC-2C]


title: Rha1-GOF_S1


title: intestine_high-dose Codonopsis Pilosula_rep3 [GC-2C]


title: WT_S2

extract_protocol:
Total RNA isolation was performed as previously described (Tebbji et al, PloSGenetics 2014)
Libraries were prepared according to Illumina's mRNASeq stranded library preparation kit

value: wild type yeast cells


title: F11KO_H3K4me3_R1 (ChIP-seq)


title: WT_H3K27me3_R1 (ChIP-seq)


title: F11KO_H3K27me3_R2 replicate (ChIP-seq)


title: F11KO_H3K27me3_R1 (ChIP-seq)


title: WT_S1


title: rd9Iin110: input from IBRD9 rep1

status: Public on Dec 28 2020

city: West Lafayette

first: Emily

last: Dykhuizen

state: IN

address: 201 S. University

department: medicinal chemistry and molecular pharmacology

institute: Purdue University

data_processing:
Data quality control and filtering was performed with Trim Galore.
Read-mapping against the human (hg19) genome was performed with bowtie2.
Alignment were filtered using SAMtools to keep only the reads with MAPQ < 10.
Filtered alignment (BAM) files were conveted to bigwig format using deeptools bamCoverage.
peaks were called using EPIC2.
Genome_build: Hg19
Supplementary_files_format_and_content: BigWig file are in an indexed binary format and contain genome-wide coverage information.
Supplementary_files_format_and_content: BED files are TAB delimited text files and contains peaks locations and other relevant information.

source_name: prostate cancer

growth_protocol: LNCaP prostate cancer cell lines were grown under normal conditions: RPMI with 10% FBS

extract_protocol:
Cells were fixed, washed, and lysed. The chromatin was sheared using a probe sonicator and protein/DNA complexes were isolated with antibody. Fragments were further sheared using a Covaris sonicator.
Libraries were constructed using Ovation® Ultralow V2 DNA-Seq Library Preparation Kit from Tecan, according the manufacturer's instructions

treatment_protocol: knockouts were generated using lentiviral mediated CRISPR-Cas9. DMSO and IBRD9 (10µM) were added 24h prior to harvest

value: prostate cancer cell line

value: LNCaP

value: 10 uM IBRD9 for 24 h

tag: antibody

value: none (input)


title: so2in110: input from DMSO rep1

value: DMSO for 24h


title: mock treatment_biological rep1

source_name: SH-SY5Y treated with methanol for 24 h

value: methanol for 24 h


title: origamicin treatment, biological rep2

source_name: SH-SY5Y treated with origamicin for 24 h

treatment_protocol: Inhibitor (30 uM) or solvent was added and cells were incubated for 24 h at standard culturing conditions

value: neuroblastoma cells

tag: treatmnet

value: origamicin for 24 h


title: mso2BRD4: BRD4 ChIP DMSO rep1

value: BRD4 (Bethyl A301-985A)


title: mock treatment, biological rep2


title: RD9IBRD9: BRD9 ChIP IBRD9 rep1

value: BRD9 (active motif AB_2614970)


title: 6x_pfd_C

status: Public on Dec 22 2020

city: Valencia

first: Javier

last: Forment

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: Biotecnología

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (UPV-CSIC)

data_processing:
read trimming with cutadapt
read mapping to TAIR10 with HISAT2
read counting with htseq-count
differential expression analysis with DESeq2
Genome_build: TAIR10 (Araport11 anotation)
Supplementary_files_format_and_content: Excel and tab-separated text files with differentially expressed genes and their corresponding statistics (log2FoldChange, pvalue, padj, etc.)

source_name: 6x_pfd seedlings under standard conditions

extract_protocol:
QIAGEN rneasy plant mini kit
Truseq stranded mRNA kit (Illumina)

tag: genotype/variation

tag: organ

value: whole seedlings

tag: ecotype

tag: growth conditions

value: in vitro, 7 days, LL


title: 6x_pfd_A


title: MX-1_80nM_doxorubicin_1

status: Public on Dec 30 2020

city: Vilnius

first: Raimonda

last: Kubiliūtė

state: Saulėtekis

address: Sauletekio al., 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

description:
MX-1/D_1
Gene expression in doxorubicin (80 nM) treated MX-1/D cells

hyb_protocol: All amount of labeled cRNA was prepared for hybridization using Gene Expression Hybridization Kit following manufacturer's protocol (Agilent technologies). Samples were hybridized onto Human Gene Expression (v2) 8×60K microarrays for 17 hours at 65°C in a rotating hybridization oven (Agilent Technologies)

scan_protocol: Microarrays were scanned immediately after washing using SureScan microarray scanner (Agilent Technologies).

data_processing: Scanned images were analyzed with Feature Extraction software v10.7 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09, grid 039494_D_F_20140228 for MX-1(1) and MX-1/D(1) and protocol GE1_1105_Oct12, grid 039494_D_F_20150330 for MX-1(2), MX-1/D(2), MX-1/T, and MX-1/TD). Background subtracted and spatially detrended signals were obtained.

source_name: Breast cancer cell line MX-1 cultured with 80 nM of doxorubicin

label_protocol: Cyanine-3 labeled cRNA was prepared from 200 ng of purified RNA using Low Input Quick Amp Labeling Kit, One Color and RNA Spike-In Kit, One Color acording to manufacturer's protocol (Agilent Technologies), followed by purification with RNeasy Mini Kit (Qiagen). Dye incorporation and cRNA yield was measured with NanoDrop 2000.

growth_protocol: The MX-1 cell line was maintained as an attached monolayer culture in RPMI 1640 medium, supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS), 100 U/mL and 100 μg/mL penicillin-streptomycin (all from Biochrom AG, Germany). The cells were grown in cell culture bottles (growth surface 75 cm2) with filter screw caps (Carl Roth, Germany) at 37 °C in an atmosphere with  90% humidity and 5% CO2.

extract_protocol: The total RNA was extracted from about 2 mln cells with mirVana Kit according to the manufacturer’s protocol (Ambion, Thermo Fisher Scientific, Foster City, CA, USA). Extracted RNA was quantified using NanoDrop-2000 spectrophotometer (Thermo Fisher Scientific). The RNA integrity number (RIN) was ≥9.4, as evaluated with 2100 Bioanalyzer system using RNA 6000 Nano Kit (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: Chemoresistant cell sublines were obtained by a stepwise selection method. Initially DOX-sensitive MX-1 cells were incubated with 10 nM DOX (Teva, UK), and doubling of the drug concentration was performed until the final concentration of 80 nM DOX was applied. These MX-1/D cell sublines were cultured in the indicated concentrations to maintain the resistance. For generation of ABCB1-active MX-1 cells, increasing concentrations (from 2 μM to 128 μM) of TPP+ (chloride salt, Fluka, St. Gallen, Switzerland), as a model substrate of ABC transporters, were used and cells resistant up to 128 μM of TPP+ were generated (MX-1/T). Finally, ABCB1-active cells were exposed to high concentrations (up to 1280 nM) of DOX for a week in order to generate MX-1/TD cell sublines.

tag: cell line background

value: Breast cancer cell line

value: chemoresistant

value: Doxorubicin (80 nM)


title: 6x_pfd_B


title: stomach_high-dose Codonopsis Pilosula_rep1 [GX-3W]

value: Kunming (KM)

tag: gender

value: male

tag: sample group

value: high-dose Codonopsis Pilosula treatment

value: stomach


title: MX-1_Control_2

description:
MX-1_2
Gene expression in parental MX-1 cells

source_name: Breast cancer cell line MX-1

value: parental

value: No


title: WT_C

source_name: WT Col-0 seedlings under standard conditions

value: WT


title: WT_A


title: mock treatment, biological rep1

tag: cell line

value: methanol for 24 h


title: MX-1_80nM_doxorubicin_2

description:
MX-1/D_2
Gene expression in doxorubicin (80 nM) treated MX-1/D cells


title: mso2BRD9: BRD9 ChIP DMSO rep1

tag: tissue

value: prostate cancer cell line

value: LNCaP

value: DMSO for 24h


title: pfd4_mock_B

source_name: pfd4 seedlings under standard conditions

value: in vitro, 14 days, LD, ZT1


title: MX-1_128nM_tetraphenylphosphonium_cation_1280nM_doxorubicin_1

description:
MX-1/TD_3
Gene expression in tetraphenylphosphonium cation (TPP+) (128 nM) and doxorubicin (1280 nM) treated MX-1/TD cells

source_name: Breast cancer cell line MX-1 cultured with 128 nM of TPP+ followed by the exposure to 1280 nM of doxorubicin for a week

value: Tetraphenylphosphonium cation (TPP+) (128 nM) and doxorubicin (1280 nM)


title: WT_B

value: whole seedlings

value: in vitro, 7 days, LL


title: MX-1_128nM_tetraphenylphosphonium_cation_1280nM_doxorubicin_2

description:
MX-1/TD_4
Gene expression in tetraphenylphosphonium cation (TPP+) (128 nM) and doxorubicin (1280 nM) treated MX-1/TD cells

value: Breast cancer cell line

value: chemoresistant


title: MX-1_128nM_tetraphenylphosphonium_cation_1

description:
MX-1/T_1
Gene expression in tetraphenylphosphonium cation (TPP+) (128 nM) treated MX-1/T cells

source_name: Breast cancer cell line MX-1 cultured with 128 nM of TPP+

value: Tetraphenylphosphonium cation (TPP+) (128 nM)


title: MX-1_128nM_tetraphenylphosphonium_cation_2

description:
MX-1/T_2
Gene expression in tetraphenylphosphonium cation (TPP+) (128 nM) treated MX-1/T cells


title: MX-1_128nM_tetraphenylphosphonium_cation_80nM_doxorubicin_2

description:
MX-1/TD_2
Gene expression in tetraphenylphosphonium cation (TPP+) (128 nM) and doxorubicin (80 nM) treated MX-1/TD cells

source_name: Breast cancer cell line MX-1 cultured with 128 nM of TPP+ followed by the exposure to 80 nM of doxorubicin for a week

value: Tetraphenylphosphonium cation (TPP+) (128 nM) and doxorubicin (80 nM)


title: MX-1_128nM_tetraphenylphosphonium_cation_80nM_doxorubicin_1

description:
MX-1/TD_1
Gene expression in tetraphenylphosphonium cation (TPP+) (128 nM) and doxorubicin (80 nM) treated MX-1/TD cells


title: pfd4_mock_C


title: Col_mock_B


title: Col_mock_C


title: Col_mock_A


title: mock treatment_biological rep2

value: neuroblastoma cells


title: sRNA K562i ZSWIM8 knockdown gRNA A rep2

city: Cambridge

first: Charlie

middle: Y.

last: Shi

state: MA

address: 455 Main St.

department: Biology

institute: Whitehead Institute / MIT

description: Lentiviral transduction of gRNA

data_processing:
Standard base calls were made using the Illumina HiSeq platform protocol.
Adapter sequences were trimmed using cutadapt (Martin, 2011) and filtered using fastq_quality_filter (FastX Toolkit; http://hannonlab.cshl.edu/fastx_toolkit/) with the parameters ‘-q 30 –p 100’ to ensure that all bases had an accuracy of 99.9%.
Counting of miRNAs was performed by string-matching the first 19 nt of each read to a dictionary derived from mature miRNA sequences.  These dictionaries were generated from sets of mature miRNA sequences downloaded from TargetScan7 (Agarwal et. al, 2015) in the case of human, mouse, and fly miRNAs, or as reported (Jan et. al, 2011) in the case of worm miRNAs.  These sequences were filtered to retain only those for which the first 19 nt were distinct. This matching method had the advantage of reducing the ambiguity in assigning miRNA isoforms, which exhibited heterogeneity at their 3′ ends, to a single mature miRNA.
Count files were merged to generate tables of counts for each cell line, organized by the gRNA expressed for knockdown/knockout.
Differential expression and significance levels were determined using DESeq2 (1.18.1) (Love et. al, 2014) without the lfcShrink() function.
Genome_build: TargetScanHuman release 7.2 or TargetScanMouse release 7.2
Supplementary_files_format_and_content: Tab-delimited text files generated by DESeq2 contain normalized counts for each library, log2-fold changes, adjusted p-values, and other output.

extract_protocol:
Cells were pelleted by centrifugation and washed with PBS.  RNA was harvested using TRI-Reagent.
Small-RNA sequencing libraries were prepared as described (Kingston and Bartel, 2019).  A step-by-step protocol is available at http://bartellab.wi.mit.edu/protocols.html. Libraries were prepared from 5 ug total RNA extracted from K562i cells.

value: K562 expressing inducible KRAB-dCas9 (K562i)

tag: grna

value: ZSWIM8 gRNA A


title: sRNA K562i ZSWIM8 knockdown gRNA A rep1

description: Lentiviral transduction of gRNA

tag: cell type


title: sRNA K562i ZSWIM8 knockdown gRNA A rep3

description: Lentiviral transduction of gRNA


title: sRNA K562i CYRANO knockdown rep2

description: Lentiviral transduction of gRNA

value: CYRANO gRNA


title: sRNA K562i CYRANO knockdown rep3

description: Lentiviral transduction of gRNA


title: sRNA K562i Control knockdown rep3

description: Lentiviral transduction of gRNA

value: Non-targeting control gRNA


title: sRNA K562i ZSWIM8 knockdown gRNA B rep3

description: Lentiviral transduction of gRNA

value: ZSWIM8 gRNA B


title: sRNA K562i ZSWIM8 knockdown gRNA B rep2

description: Lentiviral transduction of gRNA


title: sRNA K562i ZSWIM8 knockdown gRNA B rep1

description: Lentiviral transduction of gRNA


title: sRNA K562i Control knockdown rep1

description: Lentiviral transduction of gRNA


title: RPE_Dam_CRISPRa_Combo_Rep2

status: Public on Dec 17 2020

city: Amsterdam

first: Anna

last: Gonzalez Manjon

email: a.gonzalez@nki.nl, li.koob@nki.nl

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description:
DamID RPE-1 CRISPRa ABCB4 and RUNDC3B Dam-control Replicate 2
pADamID-RPE_CRISPRa-combo_Lmnb1-10kb-combined.bw

data_processing:
Library strategy: DamID-seq
Sequences were generated by the Illumina Hiseq 2500 genome analyzer (using 65bp reads) and were processed by the Illumina pipeline.
RNA-seq: For RNA sequencing data was aligned to hg38 using TopHat and Differential expression (DE) was performed using optimized DESeq2 pipeline.
DAMID: The constant sequence of the DamID adapter was removed using cutadapt 1.11 and custom scripts. Remaining sequences were mapped to the human genome (hg19) using bwa mem 0.7.17. Reads were counted in GATC fragments, summed in genomic bins and normalized over Dam-only control using custom R scripts.
TLA data was processed as described before by (de Vree et al Nat Gen 2014).
Supplementary_files_format_and_content: DamID: BigWig files of normalized LMNB1 DamID scores for 10kb genomic bins
Genome_build: RNA seq: Hg38
Genome_build: DAMID, ChIP-seq & TLA: Hg19

source_name: RPE-1 cells

growth_protocol: RPE-1 cells were grown in DMEMF12 with 6% FCS and 1%Pen/Strep

extract_protocol:
Genomic DNA was isolated using the Bioline Isolate II Genomic DNA Kit.
The full protocol is described in Leemans, 2019, with the addition of a dephosphase step to prevent amplification of apoptotic fragments. 500 ng of genomic DNA was first dephosphorylated with rSAP (NEB), before digested at Dam-methylated GATC sequences with DpnI and ligated to adapters. Following DpnII digestion of intact GATC sequences, DNA fragments were amplified with 22-26 PCR cycles. Amplified fragments were further processed with end-repair, 3A-overhang tailing and Y-shaped adapter ligation, before a final round of 9-12 PCR cycles with illumina index adapters.

treatment_protocol: 200.000 cells were plated in a 6-well plate in 2mL full medium, supplemented with 8 μg/mL polybrene to enhance viral transduction efficiency. Cells were transduced with either Dam-only lentivirus or Dam-LMNB1lentivirus. The following day, medium was refreshed. Three days after transduction, cells were harvested and genomic DNA was isolated.

tag: technique

value: DAMID

value: CRISPRa_ABCB4 and RUNDC3B


title: RPE_Dam_CRISPRa_ABCB1_Rep2

description:
DamID RPE-1 CRISPRa ABCB1 Dam-control Replicate 2
pADamID-RPE_CRISPRa-ABCB1_Lmnb1-10kb-combined.bw

tag: chip antibody


title: sRNA K562i CYRANO knockdown rep1

description: Lentiviral transduction of gRNA


title: RPE_LMNB1_CRISPRa_Combo_Rep1

description:
DamID RPE-1 CRISPRa ABCB4 and RUNDC3B Dam-LMNB1 Replicate 1
pADamID-RPE_CRISPRa-combo_Lmnb1-10kb-combined.bw


title: RPE_LMNB1_CRISPRa_ABCB1_Rep1

description:
DamID RPE-1 CRISPRa ABCB1 Dam-LMNB1 Replicate 1
pADamID-RPE_CRISPRa-ABCB1_Lmnb1-10kb-combined.bw


title: Control 2

status: Public on Nov 24 2020

city: Newark

first: Gopal

middle: J.

last: Babu

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers NJMS

data_processing:
bases were trimmed to a minimum phred quality score of 25 and Partek Filter contaminans was used to filter rDNA and mtrDNA
reads were aligned to STAR 2.6.1 mm10 genome build
reads were normalized to a 1+ log(TMM ) format and all transcripts with an abundance of less than 1 were removed
Partek remove batch effect was used to mitigate the statistical effect of total reads present on sampleheterogeneity
PARTEK GSEA, a version of LIMMA, was used to identify differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: txt files

growth_protocol: mice were reared until the age of 6 months old

extract_protocol: RNA extraction from mouse LV was done with standard kit

treatment_protocol: wt, mdx, and mdx sln+/-  mice were examined

value: WT

value: Left ventricle

tag: age

value: 6 month old

tag: strain

value: C57 genetic background


title: TRT2 3

tag: genotype

value: mdx sln +/-


title: DMD2 3

value: mdx


title: TRT2 1


title: DMD2 2


title: TRT2 2


title: MX-1_Control_1

description:
MX-1_1
Gene expression in parental MX-1 cells

value: Breast cancer cell line

value: parental

tag: treatment

value: No


title: Control 1


title: TL_control

status: Public on Nov 01 2020

city: Berkeley

first: Amy

middle: Moreda

last: Tresenrider

state: CA

address: 628 Barker Hall

department: Molecular and Cell Biology

institute: UC Berkeley

data_processing:
Library strategy: TL-seq
The processing steps for each type of data is outlined in our methods section.
Genome_build: SK1 budding yeast genome published in PMID 28416820 (SK1.cds.fa, SK1.all_feature.gff).
Supplementary_files_format_and_content: bigWig, narrowPeak, txt, csv

organism: Saccharomyces cerevisiae

source_name: SPO 2h

growth_protocol: Yeast cells were prepared for meiosis as described in our methods section.

extract_protocol:
Cells were collected by filtration and then flash frozen in liquid nitrogen. RNA was extracted by AcidPhenol:Chloroform:Isoamyl alcohol isolation. PolyA selection was performed with 100 ug of RNA and oligo-dT DynaBeads.
The 5’ end sequencing approach was performed as in (Wu et al., 2018). See methods for details.

treatment_protocol: To induce entry into meiosis, after 2 hours in SPO, cells were treated with 50 𝜇M CuSO4.

tag: ploidy

value: diploid

tag: stage of meiosis

value: premeiotic (2h in SPO)


title: origamicin treatment, biological rep1

value: neuroblastoma cells

tag: treatmnet

value: origamicin for 24 h


title: sRNA K562i Control knockdown rep2

description: Lentiviral transduction of gRNA

value: K562 expressing inducible KRAB-dCas9 (K562i)

value: Non-targeting control gRNA


title: TL_2h_R5

description:
processed data file: 181130TL_de_counts_all_genes.csv
processed data file: 181130_luti_and_orf_peaks_with_counts.csv
processed data file: 190408TL_de_counts_all_genes.csv
processed data file: 190408_luti_and_orf_peaks_with_counts.csv


title: TL_4h_R3

description:
processed data file: 181130TL_de_counts_all_genes.csv
processed data file: 181130_luti_and_orf_peaks_with_counts.csv

source_name: SPO 4h

value: meiotic prophase (4h in SPO)


title: TL_2h_R3


title: TL_4h_R1


title: TL_2h_R1

extract_protocol:
Cells were collected by filtration and then flash frozen in liquid nitrogen. RNA was extracted by AcidPhenol:Chloroform:Isoamyl alcohol isolation.
The 5’ end sequencing approach was performed as in (Wu et al., 2018). See methods for details.


title: Nanopore_4h

description: Nanopore direct RNA-seq

data_processing:
The processing steps for each type of data is outlined in our methods section.
Genome_build: SK1 budding yeast genome published in PMID 28416820 (SK1.cds.fa, SK1.all_feature.gff).
Supplementary_files_format_and_content: bigWig, narrowPeak, txt, csv

extract_protocol:
Cells were collected by filtration and then flash frozen in liquid nitrogen. RNA was extracted by AcidPhenol:Chloroform:Isoamyl alcohol isolation. PolyA selection was performed with 100 ug of RNA and oligo-dT DynaBeads.
Using 500 ng of polyA RNA, libraries were prepared with the Direct RNA Sequencing Kit (SQK-RNA001) from Oxford Nanopore Technologies.


title: Ume6_IP_r2

description:
processed data file: Ume6-IP-R2_rand_diffbind_narrow_0.001_FE.bw
processed data file: Ume6-IP-R2_rand_diffbind_narrow_0.001_peaks.narrowPeak

source_name: BYTA

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes at RT with mild shaking. Crosslinking was halted with 125 mM Glycine for 5 minutes. Cells were washed with PBS and the pellet was flash frozen in liquid nitrogen. Cells were lysed by bead beating, the chromatin was sheared by sonication, and protein-DNA fragments of interest were isolated with a specific antibody and magnetic protein A Dynabeads.
Libraries were prepared as instructed by the ThruPLEX DNA-seq Kit (R400427, Takara). 0.5-1 ng of starting material was used with 11 rounds of PCR. AMPure XP beads (A63881, Beckman Coulter) were used to select fragments between 200-500 bp.


title: Ume6_in_r3

description:
processed data file: Ume6-IP-R3_rand_diffbind-narrow_0.001_FE.bw
processed data file: Ume6-IP-R3_rand_diffbind-narrow_0.001_peaks.narrowPeak

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes at RT with mild shaking. Crosslinking was halted with 125 mM Glycine for 5 minutes. Cells were washed with PBS and the pellet was flash frozen in liquid nitrogen. Cells were lysed by bead beating, the chromatin was sheared by sonication, and protein-DNA fragments of interest were isolated with a specific antibody and magnetic protein A Dynabeads.
Libraries were prepared as instructed by the ThruPLEX DNA-seq Kit (R400427, Takara). 15 ng of starting material was used with 7 rounds of PCR. AMPure XP beads (A63881, Beckman Coulter) were used to select fragments between 200-500 bp.


title: Ume6_in_r1

description:
processed data file: Ume6-IP-R1_rand_diffbind_narrow_0.001_FE.bw
processed data file: Ume6-IP-R1_rand_diffbind_narrow_0.001_peaks.narrowPeak