title: WRL-68_miR- 221 Treated

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: miR-221 targetted mRNA expressions in WRL - 68 cell after miR-221 inhibitor transfection

hyb_protocol: Labeled cRNA sample were fragmented at 60ºC and hybridized on to Agilent Human Gene Expression Microarray 8X60K. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Images were quantified using Feature Extraction Software (Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift normalization method. Gene based analysis was performed.

source_name: human liver cancer cell line

label_protocol: The microarray hybridization and scanning were performed at the Agilent certified microarray facility of Genotypic Technology, Bengaluru, India. The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). The total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: HepG2, Huh7 and WRL-68 human HCC lines and HEK-293 cell line were obtained from National Centre for Cell Science (NCCS), Pune, India were cultured in DMEM with 10% FBS and 1% Penicillin Streptomycin (Invitrogen, Carlsbad, CA, USA). Cells were maintained in humidified chamber with 5% CO2 at 37°C.

extract_protocol: The concentration and purity of the RNA extracted were evaluated using the Nanodrop Spectrophotometer (Thermo Scientific; 1000).  The integrity of the extracted RNA were analysed on the Bioanalyzer (Agilent; 2100). We considered RNA to be of good quality based on the 260/280 values (Nanodrop), rRNA 28S/18S ratios and RNA integrity number (RIN) (Bioanalyzer).

treatment_protocol: HCC cells were cultured in 6-well plates (1x106) and transfected with miR-221 inhibitor using Lipofectamine RNAi MAX reagents (Invitrogen, USA) in DMEM-serum- free medium.The cells were added directly to the transfection complex and replaced with a fresh medium at 48 h later. Analysis of the effects of miRNA on recipient cells were performed at 48 h after transfection.

value: WRL

value: human liver cancer cell line

tag: cell line source gender

value: Female

tag: cell line source age

tag: genotype/variation

value: miR- 221 Treated


title: Macrophages, healthy bone, JWP25

status: Public on Aug 01 2020

type: RNA

city: Edinburgh

first: Cigdem

last: Selli

address: Little France Crescent

department: Centre for Reproductive Health

country: United Kingdom

institute: Queen's Medical Research Institute

description: Gene expression data from macrophages sorted from healthy bone marrow

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array according to manufacturers recommendations.

scan_protocol: Scanning was performed according to manufacturers recommendations.

data_processing:
Data were processed and normalized using the oligo package. Annotation information was obtained from the Bioconductor MoGene 2.0 transcript cluster database and Affymetrix control probes were removed from the annotation and the transcript cluster data.
Normalized expresssion values. Mouse gene symbols are given. Mean expression was used for multiple probes.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Healthy bone from mice

label_protocol: cDNAs were labelled with biotin.

growth_protocol: MetBo2 is a selected bone homing clone of murine breast cancer cell line Met-1, which derived from Polyoma Middle T Oncoprotein (PyMT) tumour previously. Cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Gibco) and 1% penicillin-streptomycin (P/S) (Gibco). Cells were maintained at 37°C with 5% CO2 in incubator.

extract_protocol: Bone marrow macrophages and Ly6C+ inflammatory monocytes from mice bearing MetBo2 bone metastasis  and  from healthy bone marrow.  Total RNA was extracted from these sorted cells using RNeasy Mini kit (QIAGEN),  and their quality were determined using Pico Chip with a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Bone metastasis was generated through intra-cardiac injection of 1x105 tumour cells into 4-week-old female mice of respective strains described above. Mice were not treated.

tag: tissue

value: healthy bone

tag: sorted cell type

value: Macrophages


title: WRL_Control

description: miR-221 targetted mRNA expressions in WRL- 68 cell without any transfection

organism: Homo sapiens

tag: cell line

tag: cell type

value: Control


title: Huh7_miR- 221 Treated

description: miR-221 targetted mRNA expressions in Huh 7 cell after miR-221 inhibitor transfection

value: Male


title: 0806Cont

type: SRA

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

country: Germany

institute: Universitätsklinikum Tübingen

library_source: transcriptomic

data_processing:
Basecalling of raw sequencing output was performed with Illumina bcl2fast2 version 2.19.1.
For subsequent adapter sequence trimming in FASTQ files, ngs-bits SeqPurge version 2018_06 was used.
Cleaned read sequences were aligned with STAR version 2.5.4a
Read counting for exonic regions was performed with subread featureCounts version 1.6.0.
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw count data in featureCounts default output format, see description at http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf

molecule: polyA RNA

source_name: ishikawa cells

growth_protocol: A well differentiated endometrial carcinoma cell line (Ishikawa cells, ECACC #99040201, Sigma Aldrich) was cultured in a humidified atmosphere of 5% CO2 at 37 ºC in Dulbecco’s modified Eagle’s medium F-12 (DMEM: F12) phenol free supplemented with 10% (v/v) FBS, 1% antibiotic/antimycotic solution and 0.25% L-Glutamine (Invitrogen, Germany), which was replenished every 48h.   Cells were passaged when the confluency reached at 80%. When performing experiments, cells were cultured in DMEM: F12 phenol free supplemented with 2% (v/v) FBS, 0.25% L-Glutamine and 1% antibiotic/antimycotic solution overnight. .

extract_protocol:
Total RNA samples were extracted by using miRNeasy Mini kit (QIAGEN, Germany) according to the manufacturer’s protocol. RNA concentration and quality were measured by using a Nanodrop (Eppendorf µCuvette® G1.0, Microvolume measuring cell for Eppendorf BioPhotometer® and BioSpectrometer®, Eppendorf, Germany). RNA quality was assessed with an Agilent 2100 Bioanalyzer system. Samples with high RNA integrity number >8 were selected for library construction.
Sequencing libraries have been prepared with New England Biolabs NEBNext Ultra II Directional RNA Library Prep following the manufacturer's handbook.

treatment_protocol: Ishikawa cells were plated in 6-well plates at a density of 200,000 cells per well in 2% (v/v) FBS, 0.25% L-Glutamine and 1% antibiotic/antimycotic solution . Ishikawa cells were transfected with plasmid DNA (11ng/ul) encoding human NFAT5 in pcDNA6V5-HisC vector or empty vector plasmid by using VIROMER RED (#230155, Biozym, Germany) according to the manufacturer’s protocol for 24h.

tag: transfection

value: control


title: Huh7_Control

description: miR-221 targetted mRNA expressions in Huh 7 cell without any transfection


title: 0503NFA


title: 2704Cont


title: S_11

city: Davis

first: Barbara

last: Blanco-Ulate

state: CA

address: One Shields Avenue

department: Plant Sciences

country: USA

institute: University of California, Davis

data_processing:
Quality and adapter trimming was done with Trimmomatic 0.33 with the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Bowtie2 2.3.4 was used to map the reads to a combined transcriptome of Prunus persica and Monilinia laxa with the following options: --end-to-end --sensitive --no-unal -q -t -p 20
Read counts were extracted form the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Prunus persica NCBIv2, Monilinia laxa ASM293894v1
Supplementary_files_format_and_content: Monilinia_Peach_primary_transcripts.counts.csv; comma-delimited file determined by mapping trimmed sequencing reads

organism: Prunus persica

source_name: Inoculated fruit

extract_protocol: Libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2 (Illumina, CA).

tag: ripening stage

value: Immature

tag: treatment

value: Monilinia laxa Inoculated

tag: time point (hours post inoculation)


title: batch2_Control-Enza-1_S1

city: Durham

first: Jennifer

last: Freedman

address: 905 South Lasalle Street

institute: Duke Cancer Institute

data_processing:
Base-calling was done on the instrument using RTA v3.3.3.
Demultiplexing was done using bcl2fatq v2.20.0.422
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Trimmomatic v0.36
Reads were mapped to human hg38 genome using STAR v2.6.1db and quantified to features using HT-Seq built in the STAR aligner.
Genome_build: hg38
Supplementary_files_format_and_content: csv file with read counts per gene

source_name: Prostate Cancer Patient Derived Explant (PDX)

growth_protocol: All animal studies were performed under a Duke University Animal Care and Use Committee (IACUC) approved protocol. Briefly, tissues were washed with phosphate buffered saline (PBS) and then minced into pieces approximately 2mm in size and injected into the flanks of 8-10-week-old JAX NOD.CB17-PrkdcSCID-J (SCID) or NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) mice obtained from the Duke University Rodent Genetic and Breeding Core to develop subcutaneous tumors

extract_protocol: Mice were sacrificed once tumors exceeded 10 x 10 mm and tissue was harvested at 150mg/mL in PBS for serial passaging and for testing therapeutic response. To test therapeutic response, tissue was dissociated with the MACS GentleMACS Dissociater and 200μL of the suspension was injected into each new mouse with a 19-guage needle

treatment_protocol: Enzalutamide, docetaxel and cisplatin were acquired from the Duke University Pharmacy stockroom. Enzalutamide was diluted in 1:20 DMSO in ultrapure distilled water and delivered at 10mg/kg by oral gavage five times per week. Docetaxel was diluted in 1:20 DMSO and cisplatin was diluted in DPBS and administered by intraperitoneal injection twice per week at 8mg/kg and 3.5mg/kg, respectively as standard doses

value: Control-Enza


title: DMSO_H2O_exp1_rep1

city: Boulder

first: Dylan

middle: J

last: Taatjes

state: CO

address: 3415 Colorado Ave JSC Biotechnology Building Campus Box 596

department: Biochemistry

institute: University of Colorado at Boulder

description: RNA-seq from HCT116 cells

data_processing:
Read trimming using bbduk (options: ktrim=r qtrim=10 k=23 mink=11 hdist=1 maq=10 minlen=25 tpe tbo literal=AAAAAAAAAAAAAAAAAAAAAAA)
Reads were mapped to hg38 using hisat2 (options: --very-sensitive)
Reads over hg38 refseq gene annotations were counted using bedtools multibamcov and then RPKM normalized.
Highest average RPKM isoform (across replicates and treatments) was retained in cases where multiple isoform annotations existed
Batch correction performed using limma removeBatchEffect function where batch corresponded to replicate number
Genome_build: hg38

source_name: wild type HCT116 cells

growth_protocol: HCT116 cells were grown in McCoy's media (Gibco, 16600082) with Gibco 100x Antibiotic-Antimycotic (Fisher Sci, 15240062) penicillin-streptomycin and 10% fetal bovine serum (FBS) supplementation.

extract_protocol:
To isolate the nuclei, cells were resuspended in 10 mL lysis buffer (10 mM Tris-HCl, pH 7.4, 2 mM MgCl2, 3 mM CaCl2, 0.5% NP-40, 10% glycerol) and thoroughly mixed. The nuclei were then spun down at 1,000xg for 10 minutes, the lysis buffer was removed and 1 mL of TRIzol was added. The RNA was isolated as described in the TRIzol instructions, except an additional phenol/chloroform extraction and chloroform only extraction were performed to reduce contaminants that would negatively affect qPCR. RNA was precipitated and washed twice with 75% ethanol to further remove contaminants. The RNA was then converted to cDNA using the High Capacity cDNA kit from Thermo Fisher Scientific and qPCR was performed with the SYBR Select Mast Mix from Applied Biosystems.
Protocol for NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420S) was used in combination with NEBNext® rRNA Depletion Kit (Human/Mouse/Rat) (E6310L)

treatment_protocol: Cells were then trypsinized, washed with PBS and resuspended in 150 µL Neon Buffer R.  The cells were then split into three groups:  No peptide, 1 µM peptide and 10 µM peptide.  The cells were then drawn into a 10 µL Neon pipet tip, electroporated and ejected into 2 mL of McCoy’s 5A media without antibiotic.  For each peptide concentration, two cell electroporations went into media containing either 0.1% DMSO or 0.1% DMSO and 10 µM Nutlin-3a.  For wells containing cells electroporated with peptide, an additional 200 nM peptide was added to allow for peptide uptake during p53 target gene expression.  The 6-well plates of cells were then placed back at 37 °C for 3 hours.

value: colorectal carcinoma

value: 0.1% DMSO + water

tag: treatment delivery method

value: electroporation with neon transfection system invitrogen


title: 0806NFA


title: Macrophages, healthy bone, JWP23


title: Macrophages, healthy bone, JWP24


title: Macrophages, healthy bone, JWP22


title: HepG2_miR- 221 Treated

description: miR-221 targetted mRNA expressions in HepG2 cell after miR-221 inhibitor transfection


title: HepG2_Control

description: miR-221 targetted mRNA expressions in HepG2 cell without any transfection


title: mrPB microglia-like cells

status: Public on Jul 31 2020

city: Shanghai

first: Bo

last: Peng

address: 138 Yixueyuan Road

department: Institute for Translational Brain Research

country: China

institute: Fudan University

data_processing:
STAR
Cellranger
Genome_build: UCSC_mm10

source_name: Brain microglia-like cells

extract_protocol:
Cells were harvested by FACS, followed by the library preparation via 10x genomics protocol.
Followed the manufacture's protocol of 10x genomics.

tag: strain

value: Brain


title: CTRL2

city: Jerusalem

first: Oren

last: Parnas

address: Faculty of Medicine, Ein-Kerem medical center

department: Immunology

country: Israel

institute: Hebrew University

data_processing:
The Illumina bcl2fastq (v1.8.3) was used to convert Illumina base call files (bcl) to FASTQ files. Alignment of FASTQs to the mm10/hg19 reference was done by Cell Ranger  (v3.0, 10X Genomics). mm10/hg19 reference downloaded from 10x (v1.2.0, 10X Genomics) and a tdTomato sequence gene was added to mm10. Library constriction was performed according to standard  3’ 10x genomics kit and sequence using illumine Hi-Seq and Next-seq machine.
First analysis of the data was done using R package Seurat(v2.3.4). Raw transcript counts gene-cell matrices were filtered to remove cells with: (i) fewer than 200 transcripts, (ii) total UMI counts lower then 1000,(iii) cells with more than 5% or 10% mitochondrial genes for 10x chemistry v2 or v3, respectively. In addition, genes that expressed in less than 3 cells were removed. The gene-cell matrices were then normalized such that the number of UMIs in each cell was divided by the total UMI counts, multiplied by 10,000 and log transformed. Data was scaled using ScaleData Function from Seurat to remove unwanted sources of variation, so that cell-cycle heterogeneity or UMI counts does not contribute to PCA or downstream analysis.
Genome_build: mm10 and added tdTomato gene
Genome_build: hg19
Supplementary_files_format_and_content: All processed data merged are tab-delimited csv file from raw data of the Seurat object@raw.data and can be distinguish by barcode name.
Supplementary_files_format_and_content: rows are genes, columns are cell barcodes and the values are normalized and log transformed

source_name: Pancreas cells

extract_protocol:
The pancreas was removed and washed and the acinar cells were isolated using 10mg collagenase P and 0.2mg trypsin inhibitor live cells were isolated by using MACS dead cells removal kit (Miltenyi Biotech #130-090-101) with MACS MS columns. The stomach was removed and the cells isolated first with dissociation buffer containing 2mg collagenase P and then with dissociation buffer containing 5 mg Dispase II (Roche #D4693) at 37C.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: PTI, Ptf1a-CreER, LSL- tdTomato -PT mice

tag: pti

value: three months

value: Pancreas cells


title: Naive microglia

source_name: Brain microglia


title: mrBMT microglia-like cells


title: HEK-293_miR- 221 Treated

description: miR-221 targetted mRNA expressions in HEK293 cell after miR-221 inhibitor transfection

source_name: Human embryonic Kidney cell line

value: Human embryonic Kidney cell line

value: Not available


title: Macrophages, healthy bone, JWP21

value: healthy bone


title: T47D_ER_ChIP-seq_siFOXA1_IL6 rep2

city: Cambridge

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

institute: Cancer Research UK, Cambridge Institute

description:
ER ChIP-seq
sifoxa1_il6-X-sifoxa1_il6_input_peaks.narrowPeak.gz

library_source: genomic

data_processing:
Reads were mapped to hg38 genome using Bowtie2 version 2.2.6 (Langmead B and  Salzberg S., 2012).
Aligned reads with the mapping quality less than 5 were filtered out.
The read alignments from three replicates were combined into single library and peaks were called with MACS2 version 2.1.1.20160309 (Zhang Y1 at al., 2008) using sequences from MCF7 chromatin extracts as a background input control.
The peaks yielded with MACS2 q value <= 1e-4 were selected for downstream analysis.
Meme version 4.9.1 (Timothy et al., 2009) was used to detect known and discover novel binding motifs amongst tag-enriched sequences.
For visualizing tag density and signal distribution heatmap the read coverage in a window of +/- 2.5 or 5 kb region flanking the tag midpoint was generated using the bin size of 1/100 of the window length.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Genome_build: GRCh38
Supplementary_files_format_and_content: bed/text

molecule: genomic DNA

source_name: T47D cells

growth_protocol: T47D cells were grown in RPMI supplemented with 10% FBS, 2mM L-glutamine and 50 U/ml penicillin and 50 ug/ml streptomycin.  Smartpool On target plus siRNAs were used for the knockdown.

extract_protocol:
Nuclear lysates were prepared and antibody-bound chromatin was purified using appropriate antibodies. Antibodies used: ERα ab3575 and Merck Millipore 06-935 antibody mix.
DNA was prepared for Illumina sequencing on the Novaseq 6000 using the ThruPLEX DNA-seq kit according to the manufacturer's instructions.

treatment_protocol: Cells were treated with human recombinant IL6 (206-IL-200, R&D systems) for 30 min.

value: ER+  Breast Cancer Cell Line T47D

tag: passages

tag: chip antibody


title: T47D_ER_ChIP-seq_siFOXA1_IL6 rep1

value: ERα ab3575 and Merck Millipore 06-935 antibody mix


title: T47D_ER_ChIP-seq_siFOXA1_IL6 rep3


title: T47D_ER_ChIP-seq_siFOXA1_Veh rep2

description:
ER ChIP-seq
sifoxa1_veh-X-sifoxa1_veh_input_peaks.narrowPeak.gz


title: HEK-293

description: miR-221 targetted mRNA expressions in HEK293 cell without any transfection

tag: cell line source gender

value: Control


title: T47D_ER_ChIP-seq_siCont_Veh rep3

description:
ER ChIP-seq
sicont_veh-X-sicont_veh_input_peaks.narrowPeak.gz


title: T47D_ER_ChIP-seq_siCont_Veh rep1


title: T47D_ER_ChIP-seq_siFOXA1_Veh rep1


title: T47D_ER_ChIP-seq_siCont_IL6 rep2

description:
ER ChIP-seq
sicont_il6-X-sicont_il6_input_peaks.narrowPeak.gz


title: T47D_ER_ChIP-seq_siCont_IL6 rep3


title: T47D_ER_ChIP-seq_siCont_Veh rep2


title: T47D_ER_ChIP-seq_siCont_Veh_Input

description: ChIP-seq input


title: T47D_ER_ChIP-seq_siCont_IL6_Input

description: ChIP-seq input


title: T47D_ER_ChIP-seq_siFOXA1_Veh_Input

description: ChIP-seq input


title: 0503Cont

value: control


title: T47D_ER_ChIP-seq_siFOXA1_Veh rep3


title: Untreated 1

status: Public on Jul 30 2020

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

description: Patient derived breast tumor tissue injected in NSG mice

data_processing:
The Cell Ranger Single Cell Software Suite, version 3.0.2 was used for de-multiplexing, barcode ad UMI processing, and single-cell 3′ gene counting. Reads were mapped to the hg38 and mm10 genome.
Specific details and instructions to run Cell Ranger can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Genome_build: hg38 plus mm10
Supplementary_files_format_and_content: Cell Ranger output

source_name: Mammary tumor

growth_protocol: Tumor cells were orthotopically injected to the number 4 mammary gland. Tumors were allowed to grow to a diameter of 5-7 mm and then randomly assigned to treatment.

extract_protocol:
Single cell suspensions were obtained using using roto-stator homogenization and miltenyi tumor dissociation kits (130-096-730). Single cell suspensions were input to a 10x Genomics Chromium machine to establish single-cell gel beads in emulsion (GEMs) for directed retrieval of approximately 8000-10000 cells
Single-cell RNA-Seq libraries were primed using the following Single Cell 3’ Reagent Kits v3: Chromium™ Single Cell 3’ Library & Gel Bead Kit v3, PN-1000092; Protocols were performed as directed in the Single Cell 3’ Reagent Kits v3 User Guide (# CG000183 Rev B)
Libraries were sequenced on an Illumina NextSeq500 in the paired-end format 28x91x8 (R1xR2xI)

treatment_protocol: BLU9931 (0.6g of drug/Kg/day) for 18 days or BLU9931 (0.6g of drug/Kg/day) for 18 days plus drug relasead for 14 days.

value: No treatment

tag: sample type

value: Samples collected at tumor diameter of 1.5 mm.

value: Patient derived breast tumor tissue


title: BLU9931 treated and released 1

value: BLU9931 treatment and drug released

value: Therapy began at tumor diameter of 5-7mm. Samples collected after 18 days therapy and 14 days of drug released.


title: BLU9931 treated 2

value: BLU9931 treatment

value: Therapy began at tumor diameter of 5-7mm. Samples collected after 18 days therapy.


title: BLU9931 treated 1


title: BLU9931 treated and released 2


title: Untreated 2


title: RAD21-ChIP-seq-Mut-rep2

city: San Francisco

first: Nadav

last: Ahituv

address: 1550 4th Street

institute: UCSF

data_processing:
ChIP-seq:
All chipseq samples (CTCF-WT, CTCF-Mut, RAD21-WT, RAD21-Mut) were processed according to ENCODE guidelines for transcription factor ChIP-seq analysis.
Raw reads were aligned against GRCh37(hg19) using bowtie2. Duplicate reads were marked using Picard’s MarkDuplicates and multimapping, low quality, duplicated and non-properly paired reads were removed. Library complexity measures and flagstats were generated for each BAM file.
BAM files were converted to tagAlign format and two subsampled pseudoreplicates were generated for each sample with half the total reads. Peak calling, fold change and p-value signal tracks were generated using MACS2.
Irreproducible Discovery Rate (IDR) analysis was performed using self-pseudoreplicates and the main samples to obtain self-consistent sets of peaks. Final peak calls were filtered by ENCODE blacklist (Amemiya et al., 2019).
4C-seq:
Raw reads were trimmed to 50 bp with cutadapt 2.4.
Valid 4Cseq reads containing 4C reading primer were extracted from fastq file and parsed into raw .txt file aligned against the restriction-enzyme digested genome GRCh37(hg19) using 4Cseqpipe version 0.7 (van de Werken et al. 2012).
Raw files were translated into final graphical depictions of contact profiles around viewpoints, using 4Cseqpipe version 0.7 (van de Werken et al. 2012).
Genome_build: hg19
Supplementary_files_format_and_content: txt; bigwig

growth_protocol: Lymphoblastoid cells were maintained in RPMI1640 medium (Life Technologies, catalog no. 11875093) containing 15% fetal bovine serum (FBS) and penicillin-streptomycin.

extract_protocol:
ChIP-seq: Lymphoblastoid cells (1x10^7 cells) were ﬁxed in phosphate-buffered saline (PBS) with 0.96% formaldehyde for 8 minutes at room temperature. Crosslinking was quenched with 125 mM Glycine. The cells were washed with PBS and precipitated via centrifugation. The cell pellet was stored in -80°C until use.
ChIP-seq: Libraries were prepared using Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences, catalog no. 21024) according to manufacturer’s protocol.
4C-seq: 4C-seq was performed and ibraries were prepared according to standard procedures (Krijger et al. Methods 170, 17–32 (2020))

tag: condition

value: Acheiropodia patient

value: Lymphoblast cells

tag: antibody

value: RAD-21 (Abcam, catalog no. ab992)


title: COM-0048

city: New York

first: Adam

last: Price

state: NY

address: 722 West 168th St.

department: Center for Infection and Immunity

institute: Columbia University

data_processing:
Illumina adapters were trimmed from reads using Trimmomatic 0.38.
Reads were aligned to the reference genome using STAR 2.5.3
Transcript counts were quantified using rSubread-1.5.1 featureCounts utility.
Differential expression and analysis were performed using DESeq2 3.8 and DEvis 1.0.1.
Genome_build: Macaca_mulatta, refseq, Mmul_8.0.1.91
Supplementary_files_format_and_content: Files representing transcript counts and associated sample metadata are provided in tab-delimited format.  These files represent quantified expression for each associated sample anad relevant points of metadata for each sample.

organism: Macaca mulatta

source_name: Whole Blood

extract_protocol:
Whole blood was collected directly into Trizol reagent and released from BSL-4 containment. Total RNA was extracted using the manufacturer's protocol and concentrated and purified using the Qiagen RNA Cleanup Kit. RNA quantity and quality was determined using the Agilent TapeStation.
Libraries were constructed using the Illumina TruSeq version 2 reagent kit.

treatment_protocol: 8 adult rhesus macaques were infected with SARS-CoV-2 and whole blood was collected at days 0, 1, 3, 5, 7, 10, 12, 15, and 17 post-infection. We collected 30 million paired-end 150 bp reads from these samples and performed differential expression analysis.

tag: agent

tag: day post-infection

value: Day 17

tag: animal id

value: Animal 8


title: COM-0046

value: Animal 6


title: T47D_ER_ChIP-seq_siCont_IL6 rep1

tag: cell line

value: ER+  Breast Cancer Cell Line T47D


title: COM-0045

value: Animal 5


title: COM-0043

value: Day 15

value: Animal 7


title: COM-0044


title: sm_DE163_dCb_rep1

city: Moscow

first: Anton

last: Kuzmenko

email: dr.ant.kuz@gmail.com, antonk@img.ras.ru

address: Akademika Kurchatova square 2

country: Russia

institute: Institute of Molecular Genetics, Russian Academy of Sciences

data_processing:
Genome_build: NC_000913.3
All libraries were quality checked before further processing using FastQC (v. 0.11.8).
The 3’-adaptor sequence (5’-TGGAATTCTCGGGTGCCAAGGC-3’) was trimmed and reads with length less than 14 nt were removed using cutadapt (v. 2.7). Example usage: cutadapt -j 4 -a 'TGGAATTCTCGGGTGCCAAGGC' -m 14 path_to_fastq
Reads were aligned onto the reference genome allowing zero mismatches via bowtie (v. 1.2.3). Example usage: bowtie -p 4 -v 0 -m 1 -S --un path_to_the_file_with_unalligned_reads --max path_to_the_file_with_multimappers path_to_the_reference_fasta path_to_the_file_trimmed_fastq > file_name.bam
Alligned .sam files were converted to binary .bam, sorted and indexed using samtools (v. 1.9).
Genome coverage in the 1 Kb windows (RPKM) for uniquely mapped reads (total or strand-specific) were calculated using bedtools (v. 2.28.0). Example usage: bedtools coverage -counts -a path_to_the_bed -b path_to_the_sorted_bam > file_name.bedGraph
Supplementary_files_format_and_content: tsv files including depth of coverage for each nucleotide position were generated using samtools (v. 1.9). Example usage: samtools depth -a --reference path_to_the_reference_fasta path_to_the_sorted_bam "genomic region" > file_name.tsv
bedGraph files including count data for the 1kb genomic windows and tsv files including depth of coverage for each nucleotide position

molecule: other

organism: Escherichia coli

source_name: Bacterial Cell Lysates

growth_protocol: Cells were grown in LB media supplemented with 0.2% glucose, chloramphenicol, and the  inducing agent (anhydrotetracycline, 200 ng/ml)  at 24˚C until OD 600 = 1.0.

extract_protocol:
All purification steps were carried out at 4˚C. The cell pellet was resuspended in lysis buffer (50 mM Tris-HCl, 250 mM NaCl, 5% glycerol, 0.5 mM β-mercaptoethanol, pH 7.4 at 23˚C) supplemented with EDTA-free protease inhibitor cocktail (Roche) at approximately 7 ml per gram of wet weight and subjected to 3 rounds of disruption on a high-pressure homogenizer (Avestin) at 12000 psi. The cell lysate was clarified for 30 min at 35,000 g. CbAgo (dCbAgo) was pulled down on Talon metal affinity resin (Takara) charged with Co 2+ for 2 hours at 4˚C (300 ul of bead suspension per sample) with constant rocking. The beads were collected by centrifugation (300 g, 3 min) and washed one time with lysis buffer and three times with lysis buffer supplemented with 10 mM imidazole (140 ml in total). CbAgo-smDNA complexes were eluted in 500 ul of lysis buffer supplemented with 300 mM imidazole. Nucleic acids associated with CbAgo were extracted with phenol:chloroform:isoamyl alcohol (PCI) mixture (25:24:1, pH 8.0) according to a standard procedure. Briefly, the protein sample was mixed with an equal volume of PCI, vortexed intensively for 30 seconds and centrifuged at 13000 g for 3 min. The upper aqueous phase was carefully collected and treated twice with an equal volume of chloroform to eliminate any remaining traces of phenol. Nucleic acids were precipitated with three volumes of ethanol in the presence of a co-precipitating agent (PINK, Bioline) and dissolved in 20 ul of milliQ-grade water.
Libraries for high throughput sequencing of smDNAs were prepared according to the previously described bridged (splinted) ligation protocol. For the purpose of visualization, a 5 ul aliquot of the smDNA sample (1/4 of total volume) was dephosphorylated and radiolabeled as described above. Unlabeled DNA was mixed with the radiolabeled aliquot and 2x urea sample buffer (8 M urea, 20 mM EDTA, 0.005% Bromophenol Blue, 0.005% Xylene Cyanol and resolved under denaturing conditions in a 15% polyacrylamide-urea gel. Gel bands corresponding to 14-25 nt smDNAs were crashed and DNA was eluted in 0.4 M NaCl solution overnight at 21˚C with constant agitation. After ethanol precipitation, DNA was resuspended in 20 ul of milliQ-grade water. Illumina-compatible adaptors were ligated to both ends of smDNA. For this purpose, 8 ul of 5 x Rapid Ligation buffer (ThermoFisher), 2 ul of 100 uM 5’-adaptor, 2 ul of 100 uM of 3’-linker, 2 ul of 100 uM oligonucleotide bridge 1, 2 ul of 100 uM oligonucleotide bridge 2 and 2 units of T4 PNK (ThermoFisher) were added to 20 ul of the purified smDNA solution. The reaction mixture was incubated overnight at room temperature. Ligated DNA fragments were recovered by 10% denaturing PAGE. The libraries were amplified and indexed according to the standard protocol (small RNA sequencing kit, NEB), except that PCR conditions were adjusted in order to prevent library over amplification. A series of test PCR were performed to optimize the amount of adaptor-ligated smDNA to achieve the desired amplification level in 3-4 cycles. smDNA libraries were sequenced using the HiSeq2500 platform (Illumina) in the rapid run mode (50 nt single-end reads).

value: MG1655 lacZ::246pal cynX::GmR lacIq lacZc- lacZ(L8) fnr-267 ({delta}ynaJ {delta}ydaA {delta}frn {delta}ogt {delta}abgT {delta}abgB {delta}abgA {delta}abgR {delta}ydaL {delta}ydaM {delta}dboA {delta}ydaO) Z1::dCbAgo-cat


title: COM-0047


title: COM-0042


title: COM-0040

value: Day 12


title: T47D_ER_ChIP-seq_siFOXA1_IL6_Input

description: ChIP-seq input


title: sm_DE161_Cb_rep2

data_processing:
Genome_build: DL2573_draft_genome_sequence.fasta (available on the GSE107973 record)
All libraries were quality checked before further processing using FastQC (v. 0.11.8).
The 3’-adaptor sequence (5’-TGGAATTCTCGGGTGCCAAGGC-3’) was trimmed and reads with length less than 14 nt were removed using cutadapt (v. 2.7). Example usage: cutadapt -j 4 -a 'TGGAATTCTCGGGTGCCAAGGC' -m 14 path_to_fastq
Reads were aligned onto the reference genome allowing zero mismatches via bowtie (v. 1.2.3). Example usage: bowtie -p 4 -v 0 -m 1 -S --un path_to_the_file_with_unalligned_reads --max path_to_the_file_with_multimappers path_to_the_reference_fasta path_to_the_file_trimmed_fastq > file_name.bam
Alligned .sam files were converted to binary .bam, sorted and indexed using samtools (v. 1.9).
Genome coverage in the 1 Kb windows (RPKM) for uniquely mapped reads (total or strand-specific) were calculated using bedtools (v. 2.28.0). Example usage: bedtools coverage -counts -a path_to_the_bed -b path_to_the_sorted_bam > file_name.bedGraph
Supplementary_files_format_and_content: tsv files including depth of coverage for each nucleotide position were generated using samtools (v. 1.9). Example usage: samtools depth -a --reference path_to_the_reference_fasta path_to_the_sorted_bam "genomic region" > file_name.tsv
bedGraph files including count data for the 1kb genomic windows and tsv files including depth of coverage for each nucleotide position

value: BW27784 lacZ::I-SceIcsmut1 araB::PBAD-I-SceI lacIq lacZc Z1::CbAgo-cat


title: COM-0041


title: sm_DE164_dCb_rep1

value: BW27784 lacZ::I-SceIcs araB::PBAD-I-SceI lacIq lacZc- Z1::dCbAgo-cat


title: COM-0039


title: COM-0038


title: sm_DE159_Cb_rep2

value: BW27784 lacZ::I-SceIcs araB::PBAD-I-SceI lacIq lacZc- Z1::CbAgo-cat


title: sm_DE178_Cb_pET28b_rep1

value: MG1655 Z1::CbAgo-cat


title: sm_DE170_Cb_phageM13_rep1

value: F' proA+B+ lacIq {delta}lacZM15/fhuA2 {delta}(lac-proAB) glnV galK16 galE15 R(zgb-210::Tn10)TetS endA1 thi-1 {delta}(hsdS-mcrB)5 Z1::CbAgo-cat


title: sm_DE161_Cb_rep1


title: COM-0035

value: Day 10


title: COM-0036


title: sm_DE157_Cb_rep2

value: MG1655 lacIq lacZc- fnr-267 ({delta}ynaJ {delta}ydaA {delta}frn {delta}ogt {delta}abgT {delta}abgB {delta}abgA {delta}abgR {delta}ydaL {delta}ydaM {delta}dboA {delta}ydaO) Z1::CbAgo-cat


title: sm_DE159_Cb_rep1


title: sm_DE157_Cb_rep1


title: COM-0037


title: sm_DE158_Cb_rep1

value: MG1655 lacZ::246pal cynX::GmR lacIq lacZc- lacZ(L8) fnr-267 ({delta}ynaJ {delta}ydaA {delta}frn {delta}ogt {delta}abgT {delta}abgB {delta}abgA {delta}abgR {delta}ydaL {delta}ydaM {delta}dboA {delta}ydaO) Z1::CbAgo-cat


title: COM-0034


title: COM-0031

value: Day 7


title: COM-0033


title: COM-0030


title: COM-0032

value: Animal 8


title: sm_BL_Cb_pBAD_pNonChi_rep1

data_processing:
Genome_build: NC_012971.2
All libraries were quality checked before further processing using FastQC (v. 0.11.8).
The 3’-adaptor sequence (5’-TGGAATTCTCGGGTGCCAAGGC-3’) was trimmed and reads with length less than 14 nt were removed using cutadapt (v. 2.7). Example usage: cutadapt -j 4 -a 'TGGAATTCTCGGGTGCCAAGGC' -m 14 path_to_fastq
Reads were aligned onto the reference genome allowing zero mismatches via bowtie (v. 1.2.3). Example usage: bowtie -p 4 -v 0 -m 1 -S --un path_to_the_file_with_unalligned_reads --max path_to_the_file_with_multimappers path_to_the_reference_fasta path_to_the_file_trimmed_fastq > file_name.bam
Alligned .sam files were converted to binary .bam, sorted and indexed using samtools (v. 1.9).
Genome coverage in the 1 Kb windows (RPKM) for uniquely mapped reads (total or strand-specific) were calculated using bedtools (v. 2.28.0). Example usage: bedtools coverage -counts -a path_to_the_bed -b path_to_the_sorted_bam > file_name.bedGraph
Supplementary_files_format_and_content: tsv files including depth of coverage for each nucleotide position were generated using samtools (v. 1.9). Example usage: samtools depth -a --reference path_to_the_reference_fasta path_to_the_sorted_bam "genomic region" > file_name.tsv
bedGraph files including count data for the 1kb genomic windows and tsv files including depth of coverage for each nucleotide position

growth_protocol: Cells were grown in LB media supplemented with 0.2% glucose and ampicillin and aerated at 37˚C until OD 600 = 0.3-0.4. At this point, the temperature was adjusted to 30˚C and after 20 min CbAgo expression was induced by the addition of L-arabinose to 0.01% for 3 hours.

value: E. coli B F- ompT gal dcm lon hsdSB(rB-mB-) [gamma](DE3[lacI lacUV5-T7p07 ind1 sam7 nin5]) [malB+]K-12([gamma]S) pBAD_HisB_CbAgo pNonChi


title: sm_BL_Cb_pBAD_pChi_rep2

value: E. coli B F- ompT gal dcm lon hsdSB(rB-mB-) [gamma](DE3[lacI lacUV5-T7p07 ind1 sam7 nin5]) [malB+]K-12([gamma]S) pBAD_HisB_CbAgo pChi


title: sm_BLTus_Cb_pBAD_rep2

value: BL21(DE3) Tus-


title: COM-0029

value: Animal 5


title: COM-0028

value: Day 5


title: sm_BLrecC_Cb_pBAD_rep2

value: BL21(DE3) recC-


title: sm_BLTus_Cb_pBAD_rep1


title: COM-0026

value: Animal 6


title: sm_BLrecC_Cb_pBAD_rep1


title: sm_DE158_Cb_rep2


title: SPF45 siRNA treated cells #3

city: Toyoake

first: Rei

last: Yoshimoto

state: Aichi

address: 1-98 Dengakugakubo, Kutsukake

department: Institute for Comprehensive Medical Science

country: Japan

institute: Fujita Health University

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using Tophat2
bigwig files were generated using bam2wig then followed by wigToBigwig
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: HEK293 cells

growth_protocol: HEK293  cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Wako) supplemented  with 10% fetal bovine serum (FBS).

extract_protocol:
Total RNAs were prepared with NucleoSpin RNA kit (Macherey-Nagel).
rRNA depletion was performed by RiboMinus Eukaryote System v2 (Invitrogen–Thermo Fisher Scientific).  The preparation of RNA libraries were performed using NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Six independent total RNAs derived from HEK293 cells treated with three control siRNAs

tag: genotype/variation

value: SPF45 siRNA


title: sm_BLrecBD_Cb_pBAD_rep1

value: BL21(DE3) recB- recD-

value: BL21(DE3) {delta}recB::kan recD- (recD expression is abolished by a frameshift) pBAD_HisB_CbAgo


title: COM-0025


title: sm_BL_Cb_pBAD_pChi_rep1


title: SPF45 siRNA treated cells #2


title: COM-0024

value: Day 3


title: sm_BLrecA_Cb_pBAD_rep2

value: BL21(DE3) recA-


title: COM-0027

value: Animal 7


title: Control siRNA treated cells #3

value: control siRNA


title: sm_BLrecA_Cb_pBAD_rep1


title: COM-0022


title: sm_BL_dCb_pBAD_rep1

value: E. coli B F- ompT gal dcm lon hsdSB(rB-mB-) [gamma](DE3[lacI lacUV5-T7p07 ind1 sam7 nin5]) [malB+]K-12([gamma]S) pBAD_HisB_dCbAgo


title: COM-0023


title: Control siRNA treated cells #2


title: COM-0020

value: Animal 4


title: COM-0018

value: Animal 2


title: Control siRNA treated cells #1


title: COM-0021


title: COM-0019

value: Animal 3


title: sm_BL_Cb_pBAD_rep2

value: E. coli B F- ompT gal dcm lon hsdSB(rB-mB-) [gamma](DE3[lacI lacUV5-T7p07 ind1 sam7 nin5]) [malB+]K-12([gamma]S) pBAD_HisB_CbAgo


title: g_DE164_Cb_rep1

data_processing:
Genome_build: DL2573_draft_genome_sequence.fasta (available on the GSE107973 record)
All libraries were quality checked before further processing using FastQC (v. 0.11.8).
The adaptor sequence (5’-AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3’) was trimmed using cutadapt (v. 2.7). Example usage: cutadapt -j 4 -a 'TGGAATTCTCGGGTGCCAAGGC' path_to_fastq
Reads were aligned onto the reference genome allowing zero mismatches via bowtie (v. 1.2.3). Example usage: bowtie -p 4 -v 0 -m 1 -S --un path_to_the_file_with_unalligned_reads --max path_to_the_file_with_multimappers path_to_the_reference_fasta path_to_the_file_trimmed_fastq > file_name.bam
Alligned .sam files were converted to binary .bam, sorted and indexed using samtools (v. 1.9).
Genome coverage in the 1 Kb windows (RPKM) for uniquely mapped reads (total or strand-specific) were calculated using bedtools (v. 2.28.0). Example usage: bedtools coverage -counts -a path_to_the_bed -b path_to_the_sorted_bam > file_name.bedGraph
Supplementary_files_format_and_content: bedGraph files including count data for the 1kb genomic windows

extract_protocol:
Genomic DNA was extracted from exponentially grown E. coli cells harvested at OD 600 =1.0 according to the published protocol (He, F. E. coli Genomic DNA Extraction Bio-101, e97, doi:10.21769/BioProtoc.97  (2011))
Preparation of genomic DNA libraries was carried out using the NEBNext Ultra II FS DNA Library Prep Kit (NEB) according to the manufacturer’s instructions. The approximate insert size was selected to be in the range of 150-250 bp. Barcodes were introduced to both ends during library amplification step with NEBNext multiplex oligos for Illumina (NEB). Genomic DNA libraries were sequenced using HiSeq2500 platform (Illumina) in the rapid run mode (50 nt single end reads).

value: BW27784 lacZ::I-SceIcs araB::PBAD-I-SceI lacIq lacZc- Z1::dCbAgo-cat


title: g_DL2917_noAgo_rep1

value: BW27784 lacZ::I-SceIcs araB::PBAD-I-SceI lacIq lacZc-


title: COM-0017

value: Animal 1


title: COM-0015

value: Day 1


title: g_DE159_Cb_rep2

value: BW27784 lacZ::I-SceIcs araB::PBAD-I-SceI lacIq lacZc- Z1::CbAgo-cat


title: g_DE159_Cb_rep1


title: COM-0016

value: Animal 8


title: SPF45 siRNA treated cells #1

value: SPF45 siRNA


title: g_DE163_Cb_rep1

data_processing:
Genome_build: NC_000913.3
All libraries were quality checked before further processing using FastQC (v. 0.11.8).
The adaptor sequence (5’-AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC-3’) was trimmed using cutadapt (v. 2.7). Example usage: cutadapt -j 4 -a 'TGGAATTCTCGGGTGCCAAGGC' path_to_fastq
Reads were aligned onto the reference genome allowing zero mismatches via bowtie (v. 1.2.3). Example usage: bowtie -p 4 -v 0 -m 1 -S --un path_to_the_file_with_unalligned_reads --max path_to_the_file_with_multimappers path_to_the_reference_fasta path_to_the_file_trimmed_fastq > file_name.bam
Alligned .sam files were converted to binary .bam, sorted and indexed using samtools (v. 1.9).
Genome coverage in the 1 Kb windows (RPKM) for uniquely mapped reads (total or strand-specific) were calculated using bedtools (v. 2.28.0). Example usage: bedtools coverage -counts -a path_to_the_bed -b path_to_the_sorted_bam > file_name.bedGraph
Supplementary_files_format_and_content: bedGraph files including count data for the 1kb genomic windows

value: MG1655 lacZ::246pal cynX::GmR lacIq lacZc- lacZ(L8) fnr-267 ({delta}ynaJ {delta}ydaA {delta}frn {delta}ogt {delta}abgT {delta}abgB {delta}abgA {delta}abgR {delta}ydaL {delta}ydaM {delta}dboA {delta}ydaO) Z1::dCbAgo-cat


title: sm_BLrecBD_Cb_pBAD_rep2

value: BL21(DE3) recB- recD-

value: BL21(DE3) {delta}recB::kan recD- (recD expression is abolished by a frameshift) pBAD_HisB_CbAgo


title: g_DE158_Cb_rep2

value: MG1655 lacZ::246pal cynX::GmR lacIq lacZc- lacZ(L8) fnr-267 ({delta}ynaJ {delta}ydaA {delta}frn {delta}ogt {delta}abgT {delta}abgB {delta}abgA {delta}abgR {delta}ydaL {delta}ydaM {delta}dboA {delta}ydaO) Z1::CbAgo-cat


title: COM-0012


title: g_DE158_Cb_rep1


title: g_DE157_Cb_rep2

value: MG1655 lacIq lacZc- fnr-267 ({delta}ynaJ {delta}ydaA {delta}frn {delta}ogt {delta}abgT {delta}abgB {delta}abgA {delta}abgR {delta}ydaL {delta}ydaM {delta}dboA {delta}ydaO) Z1::CbAgo-cat


title: g_DE157_Cb_rep1


title: g_DL2859_noAgo_rep1

value: MG1655 lacZ::246pal cynX::GmR lacIq lacZc- lacZ(L8) fnr-267 ({delta}ynaJ {delta}ydaA {delta}frn {delta}ogt {delta}abgT {delta}abgB {delta}abgA {delta}abgR {delta}ydaL {delta}ydaM {delta}dboA {delta}ydaO)


title: COM-0014

value: Animal 6


title: COM-0009


title: COM-0006

value: Control

value: Day 0


title: COM-0007

value: Animal 7


title: COM-0001


title: COM-0002

value: Animal 2


title: COM-0003

value: Animal 3


title: COM-0005

value: Animal 5


title: COM-0008


title: MCF7_6

status: Public on Jul 29 2020

city: Mexico city

first: Aarón

last: Vázquez-Jiménez

state: Mexico city

address: Periferico Sur 4809

country: Mexico

institute: INMEGEN

description: This sample was collected at day 6th

data_processing:
Raw reads were aligned and processed to Hg19 genome assembly following ddSeeker pipeline with STAR (Romagnoli et. al. BMC Genomics, 2018)
R1 file contains molecular tags while R2 file contains the information of the mRNA sequence. Due occupied tecnology os cells encapsulation (Bio-Rad Ddseq) Moleculas label is formed by a PB+BC1+L1+BC2+L2+BC3+ACG+UMI
Barcode is conformed by BC1+BC2+BC3. Separation of cDNA from the beads can occur at different nucleotides within the PB, thus making the position of the two linkers variable See. Romagnoli et. al. BMC Genomics, 2018 for more details
Count matrix were generated by Digital Expression tool included in Drop_Seq_tools
Genome_build: Hg19
Supplementary_files_format_and_content: Comma separated values files include non-normalized UMI counts

source_name: invasive breast ductal carcinoma cell line

growth_protocol: Breast cancer cell line MCF7 was growth in DMEM containing 4 mM L-glutamine, 4500 mg/L glucose, 1 mM sodium pyruvate, and 1500 mg/L sodium. Media was supplemented with 10% v/v of FBS . Cells were incubated under a humidified atmosphere with 5% CO and 95% air at 37ºC. The generation of spheroids was carried out using a liquid overlay technique. A single cell suspension of MCF7 at a density of 1x106 cells was loaded into 12.5 cm2 suspension culture flasks containing 5 mL of L-15 media

extract_protocol:
Isolation of single cells, library preparation and sequencing were performed according to the manufacturer's reference guide (Illumina Bio-Rad SureCell WTA 3’ Library Prep Reference Guide).
Sequencing was performed with a NextSeq 500/550 High Output Kit v2.5 (150 Cycles) in the NextSeq system

tag: cell type

value: Luminal B ER+ Ephitelial breast cancer cells

tag: celll line

tag: tissue

value: Epithelium

tag: culture method

value: multicellular tumor spheroid (MCTS)

tag: day


title: MCF7_19B

description: This sample was collected at day 19th


title: COM-0010

value: Day 1


title: COM-0013


title: sm_BL_Cb_pBAD_rep1

tag: strain

tag: genotype

value: E. coli B F- ompT gal dcm lon hsdSB(rB-mB-) [gamma](DE3[lacI lacUV5-T7p07 ind1 sam7 nin5]) [malB+]K-12([gamma]S) pBAD_HisB_CbAgo


title: Palmera Restricted 3 [C8]

status: Public on Jul 24 2020

city: Lisboa

first: Andre

middle: Martinho

last: de Almeida

address: Tapada da Ajuda

department: DCEB

country: Portugal

institute: Instituto Superior de Agronomia / University of Lisbon

data_processing:
Bowtie2 v2.2.3
RSEM v1.2.17
edgeR v3.2.4
DAVID (Database for Annotation, Visualization and Integrated Discovery)  v6.7
Genome_build: CHIR_1.0
Supplementary_files_format_and_content: Raw number of reads and statistical analysis of each gene, with accession number, between Majorera (M), Palmera (P), Control and  Experiemntal as indicated in the file names

organism: Capra hircus

source_name: Palmera experimental_mammary gland

growth_protocol: Conditions for animal experimentation have been thoroughly described in Lerias et al. (2013). Body live weight and milk production parameters in the Majorera and Palmera goat breeds from the Canary Islands: influence of weight loss. Trop Anim Health Prod. 2013 Nov;45(8):1731-6. doi: 10.1007/s11250-013-0423-2.

extract_protocol:
Total RNA was extracted from the tissue using the E.Z.N.A. Total RNA Kit II (Omega Bio-Tek Inc., Norcross, Georgia, USA). About 30 mg of tissue was finely grinded in liquid nitrogen and used with the kit following manufacturer’s instruction to extract total mRNA. A DNAse digestion step was carried out after extraction to remove contaminating genomic DNA using an Ambion® TURBO™ DNase (Life Technologies, Carlsbad, CA, U.S.A.) following manufacturer´s instructions. A quantitative and qualitative assessment of the isolated RNA was performed using a NanoDrop® 2000c Spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, U.S.A.). Purity was also estimated based on the absorbance ratios of the RNA samples at 260/280 nm and 260/230 nm. For pure RNA, ratios should be of about 2.0 and 2.0-2.2, respectively (T042‐Technical Bulletin, Thermo Scientific). RNA integrity was assessed by an electrophoresis in a 2.0% agarose gel. Good quality RNA should present well defined 28S and 18S bands. RNA quality was also analysed using a RNA Nano Kit Chips from the Agilent 2100 Bioanalyzer System (Agilent Technologies, Santa Clara, CA, U.S.A.). Using this approach, a good RNA sample should present well defined peaks corresponding to 28S and 18S bands and a RNA Integrity Number (RIN) above 7. The absence of DNA in RNA treated samples was verified by standard polymerase chain reaction (PCR).
RNA Sequencing was conducted by LC-Sciences (Houston, TX, USA) following the TruSeq® Stranded mRNA  Sample Preparation Guide (Illumina)

treatment_protocol: Samples were excised from the mammary gland, preserved in RNA later following manufacturer's instructions and kept at -80ºC until further analysis

tag: breed

value: Palmera

tag: treatment

value: underfed; restricted

value: Mammary gland

tag: replicate no.

value: Biological Replicate #3


title: COM-0011


title: COM-0004

value: Animal 4


title: TC5.P2

city: Groningen

first: Steven

last: de Jong

address: Hanzeplein 1

department: Medical Oncology

country: Netherlands

institute: University Medical Center Groningen

data_processing:
Primary data analysis and quality score calculations were performed with RTA3 and Bcl2fastq v2.20 (Illumina).
Prior to alignment, the reads were trimmed for adapter sequences using Trimmomatic v0.30. Alignment of reads was done by mapping to the human reference sequence (GRCh37.75) using Tophat v2.0.14 with default settings and were quantified on gene level.
Genome_build: GRCh37.75
Supplementary_files_format_and_content: tab-delimited text files include FPKM values
tab-delimited text files include read counts for every transcript

source_name: TC PDX tumor (TC5), mouse passage 2

extract_protocol:
Subcutaneous tumors were excised and snap frozen. DNA and RNA from PDX tumours of different generations were isolated from snap frozen tumour tissue. Simultaneous isolation of DNA and RNA from the same sample was done using the AllPrep DNA/RNA mini kit (Qiagen, Hilden, Germany).
The NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs (NEB), Ipswich, MA, USA), was used to process the samples. Ribosomal RNA was depleted from total RNA using the rRNA depletion kit (NEB).

tag: tumor

value: TC PDX tumor (TC5), mouse passage 2

value: untreated

tag: tumor type

value: testicular cancer


title: TC1.P2

source_name: TC PDX tumor (TC1), mouse passage 2

value: TC PDX tumor (TC1), mouse passage 2


title: TC5.P0

source_name: TC PDX tumor (TC5), mouse passage 0

value: TC PDX tumor (TC5), mouse passage 0


title: TC1.Pt

source_name: Primary TC tumor (TC1)

value: Primary TC tumor (TC1)


title: Palmera Restricted 1 [C9]

value: Biological Replicate #1


title: TC4.P2

source_name: TC PDX tumor (TC4), mouse passage 2

value: TC PDX tumor (TC4), mouse passage 2


title: Majorera Restricted 3 [C6]

source_name: Majorera experimental_mammary gland

value: Majorera


title: Majorera Restricted 1 [C1]


title: MCF7_19A

description: This sample was collected at day 19th

value: Luminal B ER+ Ephitelial breast cancer cells

tag: passages

value: Epithelium

value: multicellular tumor spheroid (MCTS)


title: Subject_3400341

status: Public on Jul 22 2020

first: Julia

last: Rager

address: 135 Dauer Drive, CB 7431

institute: UNC

data_processing:
The counts of sequencing reads per mRNA were aligned to the GENCODE database v30 and organized using Salmon, yielding measures of 37,268 unique human RNA transcripts, including protein-coding and non-coding RNAs, representing the raw count data
Count data were normalized by median signal intensity using algorithms enabled within the DESeq2 package (v1.24.0), resulting in variance stabilized expression values.
The count data was filtered to exclude universally lowly expressed transcripts, and data were normalized by quantiles using algorithms enabled through the DESeq2 processing pipeline.
Genome_build: GENCODE database v30
Supplementary_files_format_and_content: Count data are provided as a .csv, aligned to gene symbols, and represent count values prior to normalization

source_name: Placenta of infants born at low gestational age

extract_protocol:
Recruited patients from the ELGAN cohort that were scheduled to give birth at participating institutions between 2002 to 2004. Patients involved in the study comprised of pregnancies that ended in livebirths prior to completing 28 weeks of gestation.  Maternal, demographic, and clinical assessments were taken before and after delivery. Each infant's anthropometric measures were recorded throughout hospitalization and at follow-up. Placenta samples were collected immediately after surgery and stored at -80 degrees C until further analysis.  RNA molecules with 18 nucleotides or greater were extraced with the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen) and quantified with the NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, Ma) and tested for quality based on RNA integrity scores produced by the QIiAxcel system (Qiagen).
Isolated RNA samples were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit for Illumina, and then these libraries were pooled and sequenced (single-end 50 bp) on the Illumina Hiseq 2500.

value: placenta

tag: asthma (0=absent, 1=present, 2=data not obtained)

tag: birthweight (grams)

tag: sex (0=female, 1=male)

tag: chorioamnionitis (0=absent, 1=present)

tag: fetal vessel neutrophilic infiltration (0=absent, 1=present)

tag: infarct (infarcted placenta) (0=absent, 1=present)

tag: placwt (placenta weight) (grams)

tag: mage (age of mother) (years)

tag: bmi (body mass index)

tag: smokeany (smoking or passive smoking before or during pregnancy) (0=no exposure to smoking, 1=exposure to smoking or secondhand smoking)

tag: fused2 (0=not twin, 1=twins with fused placentas, 2=twins with separate placentas)


title: Subject_3400531

tag: tissue


title: Subject_3400321


title: Subject_3400371


title: Subject_3400401


title: Subject_3400571


title: TC1.P0

source_name: TC PDX tumor (TC1), mouse passage 0

value: TC PDX tumor (TC1), mouse passage 0

tag: treatment


title: Subject_3400741


title: Subject_3400361


title: Subject_3400521


title: Subject_3400672


title: Palmera Restricted 2 [C7]

tag: breed

value: Palmera

value: underfed; restricted

value: Mammary gland

tag: replicate no.

value: Biological Replicate #2


title: Subject_3400291


title: Subject_3400301


title: Subject_3400211


title: Subject_3400661


title: Majorera Restricted 2 [C2]


title: Subject_3301321


title: Subject_3301301


title: Subject_3301331


title: Subject_3400201


title: Subject_3400362


title: Subject_3301242


title: Subject_3301202


title: Subject_3301191


title: Subject_3301081


title: Subject_3301011


title: Subject_3301021


title: Subject_3301241


title: Subject_3301201


title: Subject_3300991


title: Subject_3301001


title: Subject_3300901


title: Subject_3300841


title: Subject_3300861


title: Subject_3300732


title: Subject_3300711


title: Subject_3300611


title: Subject_3300761


title: Subject_3300641


title: Subject_3300721


title: Subject_3300601


title: Subject_3300602


title: Subject_3300592


title: Subject_3300591


title: Subject_3300501


title: Subject_3300381


title: Subject_3300531


title: Subject_3300411


title: Subject_3200612


title: Subject_3200651


title: Subject_3200611


title: Subject_3300211


title: Subject_3300371


title: Subject_3200721


title: Subject_3300981


title: Subject_3300361


title: Subject_3200531


title: Subject_3200461


title: Subject_3300911


title: Subject_3200521


title: Subject_3200541


title: Subject_3200431


title: Subject_3200342


title: Subject_3200023


title: Subject_3200021


title: Subject_3200231


title: Subject_3200022


title: Subject_3101411


title: Subject_3200241


title: Subject_3101401


title: Subject_3101341


title: Subject_3101331


title: Subject_3101471


title: Subject_3200171


title: Subject_3101241


title: Subject_3101283


title: Subject_3101163


title: Subject_3101181


title: Subject_3101141


title: Subject_3101096


title: Subject_3101051


title: Subject_3100991


title: Subject_3101131


title: Subject_3100931


title: Subject_3100863


title: Subject_3100891


title: Subject_3100862


title: Subject_3100971


title: Subject_3100981


title: Subject_3100491


title: Subject_3100573


title: Subject_3100852


title: Subject_3100972


title: Subject_3100481


title: Subject_3100461


title: Subject_3101201


title: Subject_3100861


title: Subject_3100851


title: Subject_3100371


title: Subject_3100421


title: Subject_3100351


title: Subject_3100341


title: Subject_3101161


title: Subject_3101071


title: Subject_3100261


title: Subject_3100271


title: Subject_3100041


title: Subject_2302211


title: Subject_2301671


title: Subject_2301791


title: Subject_2301891


title: Subject_2301542


title: Subject_2301521


title: Subject_2301391


title: Subject_2301281


title: Subject_2301251


title: Subject_2300921


title: Subject_2301151


title: Subject_2301061


title: Subject_2300891


title: Subject_2300901


title: Subject_2300871


title: Subject_2300861


title: Subject_2300761


title: Subject_2300692


title: Subject_2300661


title: Subject_2300701


title: Subject_2300662


title: Subject_2300741


title: Subject_2300601


title: Subject_2300651


title: Subject_2301941


title: Subject_2301631


title: Subject_2300591


title: Subject_2300522


title: Subject_2300521


title: Subject_2300551


title: Subject_2300431


title: Subject_2300481


title: Subject_2300461


title: Subject_2300441


title: Subject_2200681


title: Subject_2200811


title: Subject_2200661


title: Subject_2200582


title: Subject_2200562


title: Subject_2200511


title: Subject_2200421


title: Subject_2200171


title: Subject_2300571


title: Subject_2101531


title: Subject_2101562


title: Subject_2101561


title: Subject_2200221


title: Subject_2300491


title: Subject_2200191


title: Subject_2101521


title: Subject_2200041


title: Subject_2101501


title: Subject_2101491


title: Subject_2200821


title: Subject_2101431


title: Subject_2101461


title: Subject_2101332


title: Subject_2101391


title: Subject_2101331


title: Subject_2101321


title: Subject_2101281


title: Subject_2101282


title: Subject_2200331


title: Subject_2101221


title: Subject_2101201


title: Subject_2101182


title: Subject_2200211


title: Subject_2200301


title: Subject_2101181


title: Subject_2101171


title: Subject_2101081


title: Subject_2101101


title: Subject_2101021


title: Subject_2100961


title: Subject_2100951


title: Subject_2100941


title: Subject_2100901


title: Subject_2101111


title: Subject_2100891


title: Subject_2101301


title: Subject_2100871


title: Subject_2100911


title: Subject_2100881


title: Subject_2100712


title: Subject_2100851


title: Subject_2100711


title: Subject_2100781


title: Subject_2100841


title: Subject_2101211


title: Subject_2100691


title: Subject_2100631


title: Subject_2100621


title: Subject_2100391


title: Subject_2100381


title: Subject_2100591


title: Subject_1700671


title: Subject_2100472


title: Subject_2100301


title: Subject_1700601


title: Subject_1700731


title: Subject_1700561


title: Subject_1700551


title: Subject_1700501


title: Subject_1700443


title: Subject_1700442


title: Subject_2100783


title: Subject_1700441


title: Subject_1700412


title: Subject_1700431


title: Subject_1700343


title: Subject_2100601


title: Subject_1700411


title: Subject_1700342


title: Subject_2100571


title: Subject_1700281


title: Subject_1700331


title: Subject_1700282


title: Subject_1700341


title: Subject_1700241


title: Subject_1700242


title: Subject_1700211


title: Subject_1700221


title: Subject_1700161


title: Subject_1700181


title: Subject_1700112


title: Subject_1700141


title: Subject_1700081


title: Subject_1600891


title: Subject_2100371


title: Subject_1600902


title: Subject_1600903


title: Subject_1700011


title: Subject_1600901


title: Subject_1700102


title: Subject_1600861


title: Subject_1600752


title: Subject_1600751


title: Subject_1600721


title: Subject_1600742


title: Subject_1600732


title: Subject_1700091


title: Subject_1600722


title: Subject_1600701


title: Subject_1600692


title: Subject_1600662


title: Subject_1600651


title: Subject_1600652


title: Subject_1600641


title: Subject_1600661


title: Subject_1600611


title: Subject_1600612


title: Subject_1600561


title: Subject_1600631


title: Subject_1600511


title: Subject_1600521


title: Subject_1600491


title: Subject_1600331


title: Subject_1600351


title: Subject_1600371


title: Subject_1600381


title: Subject_1600451


title: Subject_1600151


title: Subject_1600141


title: Subject_1600111


title: Subject_1501191


title: Subject_1501261


title: Subject_1600251


title: Subject_1501301


title: Subject_1600131


title: Subject_1501171


title: Subject_1501141


title: Subject_1501021


title: Subject_1500911


title: Subject_1500931


title: Subject_1501002


title: Subject_1500981


title: Subject_1500841


title: Subject_1500821


title: Subject_1500782


title: Subject_1500681


title: Subject_1500731


title: Subject_1500781


title: Subject_1500661


title: Subject_1500391


title: Subject_1500431


title: Subject_1400061


title: Subject_1301401


title: Subject_1700061


title: Subject_1301541


title: Subject_1301101


title: Subject_1301931


title: Subject_1301031


title: Subject_1300672


title: Subject_1501121


title: Subject_1301132


title: Subject_1300651


title: Subject_1300571


title: Subject_1300441


title: Subject_1500822


title: Subject_1300391


title: Subject_1300541


title: Subject_1300361


title: Subject_1300301


title: Subject_1300232


title: Subject_1300231


title: Subject_1300221


title: Subject_1301271


title: Subject_1300201


title: Subject_1301071


title: Subject_1300161


title: Subject_1200731


title: Subject_1300113


title: Subject_1200692


title: Subject_1200671


title: Subject_1200571


title: Subject_1200522


title: Subject_1300011


title: Subject_1200741


title: Subject_1200691


title: Subject_1200521


title: Subject_1300362


title: Subject_1300542


title: Subject_1200561


title: Subject_1200441


title: Subject_1200352


title: Subject_1200321


title: Subject_1200351


title: Subject_1300412


title: Subject_1200281


title: Subject_1200261


title: Subject_1200251


title: Subject_1300171


title: Subject_1200232


title: Subject_1200182


title: Subject_1200201


title: Subject_1200192


title: Subject_1200191


title: Subject_1200181


title: Subject_1200172


title: Subject_1600702


title: Subject_1200282


title: Subject_1200031


title: Subject_1101092


title: Subject_1101131


title: Subject_1200011


title: Subject_1101142


title: Subject_1101171


title: Subject_1101042


title: Subject_1101041


title: Subject_1101081


title: Subject_1101161


title: Subject_1100881


title: Subject_1100901


title: Subject_1100853


title: Subject_1100872


title: Subject_1200171


title: Subject_1200021


title: Subject_1101091


title: Subject_1101141


title: Subject_1101001


title: Subject_1100891


title: Subject_1100852


title: Subject_1100691


title: Subject_1100551


title: Subject_1100841


title: Subject_1100601


title: Subject_1100791


title: Subject_1100751


title: Subject_1100611


title: mesc_wt_epilc_0h.rp1

city: Shenzhen

first: Andrew

middle: P

last: Hutchins

address: 1088 Xueyuan Rd

department: Bioinformatics

institute: Southern University of Science and Technology

description: Mouse ESC to EpiLC differentiation, 0hours, repeat 1

data_processing:
STAR was used to align the reads to the genocde transcriptome (mm10, m21), mouse genome and the repeatmastker transposable element (TE) database
reads mapping to genes or TEs were counted using te_counter (https://github.com/oaxiom/te_counter)
genes with more than 100 sequence tags in 2 or more timepoints were kept for further analysis
mapped tag counts were GC normalised using EDASeq v2.0.0
Genome_build: mm10
Supplementary_files_format_and_content: genes_ntc_expression.tsv: TSV containing a table of expression data, columns are samples, rows are genes or transposable elements.
Supplementary_files_format_and_content: genes_ntc_expression_escs.tsv: TSV containing a table of expression data, columns are samples, rows are genes or transposable elements, for the ESC samples.

source_name: ESC cell culture

growth_protocol: EpiLCs (epiblast-like cells) were differentiated according to the protocol described in Hayashi et al., 2011. Briefly, 1.0x105 ESCs were plated onto a well of a 6-well plate coated with human plasma fibronectin (20ug/ml) in 2iLif medium (DMEM/F12 (HyClone) and Neurobasal (Gibco) medium mixed 1:1, supplemented with N2 (Gibco), B27 (Gibco), non-essential amino acids (Gibco), GlutaMAX (Gibco), sodium pyruvate (Cellgro), penicillin/streptomycin (HyClone), 0.1 mM β-mercaptoethanol (Gibco), 1,000 U per ml leukemia inhibitory factor (LIF; Millipore), CHIR99021 (3 μM; Selleck) and PD0325901 (1 μM; Selleck)), after a 12 hour incubation, the cells would attach to the plate. We take this time point as 0h. We then changed the medium to N2B27 medium containing activin A (20ng/ml; Peprotech), bFGF (12ng/ml; Peprotrech) and Knockout Serum Replacement (1%; Gibco). The medium was changed every day. We collected cells every 12h and extracted total RNA for sequencing.

extract_protocol:
Extracted using TRIzol using the manufacturers instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At hour 0, we then changed the medium to N2B27 medium containing activin A (20ng/ml; Peprotech), bFGF (12ng/ml; Peprotrech) and Knockout Serum Replacement (1%; Gibco). The medium was changed every day. We collected cells every 12h and extracted total RNA for sequencing.

tag: cell type

value: ESC

tag: genotype

value: Wildtype

tag: time


title: NC2

status: Public on Jul 20 2020

city: Portland

first: Suzy

middle: CP

last: Renn

state: OR

address: 3203 SE Woodstock Blvd

department: Biology

institute: Reed College

data_processing:
Sequence reads were aligned to in silico bisulfite converted amplicon reference sequences (https://github.com/rose-driscoll/methylation-analysis/tree/master/reference_sequences/Bisulfite_Genome/CT_conversion) with bowtie2 using options -N 1 --dovetail -x
Samtools view -bS, samtools sort, and samtools mpileup -d 200000 were used to produce a vcf file for each sample
Custom python scripts available at https://github.com/rose-driscoll/methylation-analysis/blob/master/percent-methylation/methylation_pipeline_samtoolspythonandcat_20180605_RD.txt were employed to count the number of As, Cs, Ts, and Gs observed at each base, extract data for selected bases (CpG Cs, Ts and non-CpG Cs, and As and Gs, relative to the reference sequence), and calculate relevant statistics such as % methylation for CpG C bases and % error for A and G bases.
In a second pipeline, forward and reverse reads from each sample were combined using FLASH and aligned to in silico bisulfite converted amplicon reference sequences (https://github.com/rose-driscoll/methylation-analysis/tree/master/reference_sequences/Bisulfite_Genome/CT_conversion) with bowtie2 using options -N 1 -x in order to identify which amplicon they had come from
Reads from each of the four amplicons were extracted from the bowtie alignment, dereplicated with usearch -derep_fulllength -sizeout, and aligned with muscle along with a reference sequence.
Custom python scripts available at https://github.com/rose-driscoll/methylation-analysis/tree/master/epialleles were employed to identify CpG sites in the aligned reads.
Command line tools (cut and awk) were employed to paste together CpG bases and identify an 'epiallele' for each read, and count the number of times each unique epiallele appeared for each sample.
Supplementary_files_format_and_content: tab-delimited text files with % methylation per CpG site (all_CpGs_20180605_RD.txt), bisulfite conversion completeness per base (all_conversion_20180605_RD.txt), sequencing error per base (all_error_20180605_RD.txt), or epiallele abundance (all_haplotypes_w_AP6_20180612.tab) per sample.

organism: blank sample

extract_protocol:
Fish were euthanized with tricaine methanesulfonate and tissues were dissected out and placed in 95% EtOH. DNA was extracted by proteinase K digestion and phenol:chloroform purification. 500 ng genomic DNA was bisulfite treated using Zymo Research EZ Methylation-Gold kit.
Four regions were amplified (Bioline Immomix) from bisulfite-treated gDNA samples using primers with Illumina-compatible tails. Fragments were cleaned (Aline Biosciences PCRCLEAN DX) before a second round of PCR to attach sample-specific barcodes. Samples were pooled at equal concentrations and column purified to produce Illumina libraries.
DNA amplicon sequencing

tag: set

value: negative control (no template DNA)


title: mesc_wt_epilc_36h.rp1

description: Mouse ESC to EpiLC differentiation, 36hours, repeat 1

value: EpiLC


title: mesc_wt_epilc_48h.rp1

description: Mouse ESC to EpiLC differentiation, 48hours, repeat 1


title: mesc_wt_epilc_24h.rp1

description: Mouse ESC to EpiLC differentiation, 24hours, repeat 1


title: mesc_wt_epilc_12h.rp1

description: Mouse ESC to EpiLC differentiation, 12hours, repeat 1


title: mesc_wt_epilc_24h.rp2

description: Mouse ESC to EpiLC differentiation, 24hours, repeat 2


title: mesc_wt_epilc_12h.rp2

description: Mouse ESC to EpiLC differentiation, 12hours, repeat 2


title: mesc_wt_epilc_36h.rp2

description: Mouse ESC to EpiLC differentiation, 36hours, repeat 2


title: mesc_wt_epilc_0h.rp2

description: Mouse ESC to EpiLC differentiation, 0hours, repeat 2


title: Subject_1100111

tag: asthma (0=absent, 1=present, 2=data not obtained)

tag: birthweight (grams)

tag: sex (0=female, 1=male)


title: Subject_1100361

tag: chorioamnionitis (0=absent, 1=present)

tag: fetal vessel neutrophilic infiltration (0=absent, 1=present)

tag: infarct (infarcted placenta) (0=absent, 1=present)


title: Subject_1100381

tag: placwt (placenta weight) (grams)

tag: mage (age of mother) (years)

tag: bmi (body mass index)


title: Subject_1100461

tag: tissue

tag: smokeany (smoking or passive smoking before or during pregnancy) (0=no exposure to smoking, 1=exposure to smoking or secondhand smoking)

tag: fused2 (0=not twin, 1=twins with fused placentas, 2=twins with separate placentas)


title: Subject_1100471


title: Subject_1100391


title: Subject_1100462


title: Subject_1100511


title: Subject_1100112


title: 712

organism: Pelvicachromis pulcher

tag: timepoint

value: Adult

tag: sexual phenotype

value: B

value: M

value: gonad

value: Nicole

tag: molecule subtype

value: ampliconic DNA


title: 711

value: brain


title: 715


title: 714


title: 709

value: Y


title: 708


title: mesc_wt_epilc_48h.rp2

description: Mouse ESC to EpiLC differentiation, 48hours, repeat 2

tag: cell type

tag: genotype

tag: time


title: Subject_1100521

value: placenta

tag: asthma (0=absent, 1=present, 2=data not obtained)

tag: birthweight (grams)


title: 707

tag: set


title: 713


title: NC1


title: 706

value: R


title: 693


title: 689


title: 704


title: 703


title: 698

value: F


title: 688


title: 685


title: 694


title: 696


title: 699


title: 692


title: 697


title: 702


title: 684


title: 687


title: 683


title: 700


title: 705


title: 690


title: 701


title: 682

value: acidic

value: Oneyear

value: J


title: 681


title: 680


title: 695


title: 691


title: 686


title: 678


title: 679


title: 676


title: 672


title: 674


title: 673


title: 675


title: 677


title: 667

value: neutral


title: 670


title: 669


title: 668


title: 655

value: RD6 3


title: 661


title: 664


title: 663


title: 654


title: 658


title: 665


title: 657


title: 671


title: 662


title: 659


title: 653


title: 651


title: 652


title: 649


title: 650


title: 660


title: 666


title: 656


title: 648


title: 647


title: 643


title: 642


title: 638


title: 635


title: 636


title: 641


title: 637


title: 292

source_name: pH_acidic_Day 30_trunk

value: Day 30

value: trunk


title: 632

value: Adult


title: 629


title: 634


title: 639


title: 633


title: 290


title: 289

source_name: pH_acidic_Day 30_head

value: head


title: 291


title: 287


title: 288


title: 286


title: 285


title: 284


title: 646

value: M

value: gonad


title: 283

value: ampliconic DNA


title: 645

value: brain


title: 644


title: 640


title: 631


title: 630


title: 219


title: 215


title: 218


title: 163

source_name: pH_neutral_Day 60_head

value: Day 60


title: 217


title: 216


title: 214


title: 213


title: 159


title: 162

source_name: pH_neutral_Day 60_trunk


title: 161


title: 158


title: 220


title: 157


title: 155

source_name: pH_neutral_Day 30_head


title: 154

source_name: pH_neutral_Day 30_trunk


title: 156


title: 153


title: 149


title: 148

source_name: pH_neutral_Day 1_trunk

value: Day 1


title: 147

source_name: pH_neutral_Day 1_head


title: 151


title: 150


title: 152


title: 146


title: 145


title: Subject_1100711

value: placenta

tag: sex (0=female, 1=male)

tag: chorioamnionitis (0=absent, 1=present)

tag: fetal vessel neutrophilic infiltration (0=absent, 1=present)


title: 164


title: 160


title: 144


title: 139

source_name: pH_acidic_Day 60_head


title: 142


title: 143


title: 138

source_name: pH_acidic_Day 60_trunk


title: 137


title: 141


title: 133


title: 129


title: 130


title: 131


title: 134


title: 127


title: 136


title: 140


title: 126


title: 132


title: 128


title: 122


title: 116

source_name: pH_acidic_Day 1_trunk


title: 120


title: 123


title: 121


title: 117

source_name: pH_acidic_Day 1_head


title: 118


title: 115


title: 135


title: 65


title: 63


title: 62


title: 66


title: 19


title: 18


title: 15


title: 20


title: 11


title: 14


title: 13


title: SC-WT_S4_L004

status: Public on Jul 08 2020

city: Los Angeles

first: Shuo

last: Chen

state: California

address: 2250 Alcazar Street, Clinical Science Annex, Room 103, CLINICAL SCIENCE ANNEX ROOM 103

institute: Center for Craniofacial Molecular Biology, University of Southern California

description: genomic DNA

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome and transcriptome using STAR 2.6.1d, and normalized using Upper quartile.
Lognormal with shrinkage mean value were calculated using Gene-specific analysis by Partek flow (Partek Inc., USA). Exclude features where maximum <= 5.0.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include lognormal with shrinkage mean value for each feature in individual sample.

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol:
Dental mesenchymal cells from C57BL/6J mice were process by cell lysis, transposition, and amplification.
Transposed DNA libraries were sequenced on NextSeq500 High-Output 150 cycles (75PE). ATAC-seq reads were aligned to the UCSC mm10 reference genome with BWA-MEM. ATAC-seq peaks were called through MACS2. Peaks were annotated and known transcription factor binding motifs were further analyzed in the ATAC-seq peaks by HOMER.

tag: strain

tag: Stage

value: 4-week old

value: Wild type

value: Incisor; dental mesenchyme


title: 12

tag: tissue


title: 124

value: acidic


title: 119


title: 68

value: neutral


title: 67


title: SC-WT_S4_L002

description: genomic DNA


title: Mo17 Elicited Replicate 1

city: La Jolla

first: Alisa

last: Huffaker

address: 9500 Gilman Drive #0116

department: Cell & Developmental Biology

institute: UC San Diego

data_processing:
Trimmomatic (v0.39) was used to remove Illumina Truseq adaptor sequences and trim the first 12 bp (Bolger et al., 2014). Trimmed reads were aligned to the maize B73 V4 reference genome (ensemble 4.44) using Hisat2 (v2.0.0) (Kim et al., 2015) and sorted using Sambamba (v0.6.8) (Tarasov et al., 2015). Raw mapped reads were quantified using featureCounts (v1.6.4) (Liao et al, 2014). Counts were processed in R with DESeq2to generate normalized read counts using the default method and transform the normalized counts using the rlogTransformation method (Anders et al., 2010).
Genome_build: zea_mays.Ensemble_Zmays40.genome.fa.gz
Supplementary_files_format_and_content: excel file including CPM+0.01 values for each Sample. Note: CPM, counts per million reads

organism: Zea mays

source_name: 35-day old maize inbred Mo17 stems

growth_protocol: Zea mays Var. B73 and Mo17 seeds were germinated in MetroMix 200 (Sun Gro Horticulture Distribution, Inc.) supplemented with 14-14-14 Osmocote (Scotts Miracle-Gro) and grown in a greenhouse with a 12-h photoperiod, minimum of 300 μmol m−2 s−1 of photosynthetically active radiation supplied by supplemental lighting, 70% relative humidity, and temperature cycle of 24 °C/28 °C (night/day).

extract_protocol:
Total RNA was isolated with the NucleoSpin® RNA Plant Kit (Takara Bio USA) according to the manufacturer’s protocol. RNA quality was assessed based on RNA integrity number (RIN) using an Agilent Bioanalyzer.
3’ RNA-seq library construction and sequencing were performed at Cornell University’s Genomics Facility at the Institute of Biotechnology (Ithaca, NY, USA; http://www.biotech.cornell.edu/brc/genomics-facility/services). Approximate 500 ng of total RNA was used to construct the 3′ RNA-Seq libraries using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD (Lexogen, USA) according to the manufacturer’s instructions. All libraries, each with their own unique adapter sequences, were pooled together and sequenced on one lane of an Illumina NextSeq 500 to generate about 90 bp single-end reads.

treatment_protocol: Heat-killed F. venenatum (strain PTA-2684) hyphae was commercially obtained (Monde Nissin Corporation) and used as a non-infectious elicitor lacking known mycotoxins. Using a surgical scalpel, 35-day-old plants were slit in the centre, spanning both sides of the stem, to create a 8–10 cm long parallel longitudinal incision. The incision targeted and spanned the upper nodes, internodes and the most basal portion of unexpanded leaves. Elicited samples were treated with Heat-killed F venenatum hyphae in the slit while untreated slit plants were used as control (samples described as 'Damage')

tag: cultivar

value: stems

tag: age

value: 35 day-old

tag: treatment

value: incision and innoculated with heat killed Fusarium hyphae


title: SC-WT_S4_L003

description: genomic DNA


title: Mo17 Damage Replicate 3

value: incision with no innoculation


title: Mo17 Elicited Replicate 3


title: Mo17 Elicited Replicate 4


title: Mo17 Elicited Replicate 2


title: Mo17 Damage Replicate 4


title: Mo17 Damage Replicate 2


title: SC-WT_S4_L001

description: genomic DNA


title: B73 Elicited Replicate 4

source_name: 35-day old maize inbred B73 stems


title: Mo17 Damage Replicate 1


title: 17

tag: timepoint

value: Day 30

tag: sexual phenotype

value: head


title: B73 Elicited Replicate 3


title: B73 Elicited Replicate 2


title: B73 Damage Replicate 3


title: B73 Elicited Replicate 1


title: W22_Elicited_96h

data_processing:
Library preparations were sequenced on an Illumina platform and paired-end reads were obtained. Image analysis and base calling were performed with the standard Illumina pipeline. Raw reads were filtered to remove reads containing adapters or reads of low quality. Qualified reads were then aligned to Zea mays AGPv4 reference genome using TopHat v2.0.12 (Kim et al., 2013). Gene expression values into fragments per kilo base per million reads (FPKM) were analyzed using HTSeq v0.6.1.
Genome_build: zea_mays.Ensemble_Zmays40.genome.fa.gz
Supplementary_files_format_and_content: excel file including RPKM values for each Sample

source_name: 35-day old maize inbred W22 stems

growth_protocol: Zea mays Var. W22 seeds were germinated in MetroMix 200 (Sun Gro Horticulture Distribution, Inc.) supplemented with 14-14-14 Osmocote (Scotts Miracle-Gro) and grown in a greenhouse with a 12-h photoperiod, minimum of 300 μmol m−2 s−1 of photosynthetically active radiation supplied by supplemental lighting, 70% relative humidity, and temperature cycle of 24 °C/28 °C (night/day).

extract_protocol:
Total RNA was isolated with the NucleoSpin® RNA Plant Kit (Takara Bio USA) according to the manufacturer’s protocol. RNA quality was assessed based on RNA integrity number (RIN) using an Agilent Bioanalyzer. The mRNA was enriched from total RNA using oligo (dT) magnetic beads.
The mRNA was fragmented randomly into short sequences followed by first-strand cDNA synthesis with random hexamer-primed reverse transcription. Second-strand cDNA synthesis was done by nick-translation using RNaseH and DNA polymerase I. After adaptor end-repair and ligation, cDNA was amplified via PCR and purified to create the final cDNA library. cDNA concentration was quantified using a Qubit 2.0 fluorometer (Life Technologies) and then diluted to 1 ng/µL before assessing insert size on an Agilent Bioanalyzer 2100.

treatment_protocol: Heat-killed F. venenatum (strain PTA-2684) hyphae was commercially obtained (Monde Nissin Corporation) and used as a non-infectious elicitor lacking known mycotoxins. Using a surgical scalpel, 35-day-old plants were slit in the centre, spanning both sides of the stem, to create a 8–10 cm long parallel longitudinal incision. The incision targeted and spanned the upper nodes, internodes and the most basal portion of unexpanded leaves.

tag: treated with

value: Heat-killed F. venenatum hyphae

tag: time (hours)


title: W22_Elicited_48h


title: W22_Elicited_24h


title: B73 Damage Replicate 1


title: B73 Damage Replicate 2


title: W22_Elicited_72h


title: W22_Elicited_12h


title: W22_Elicited_120h


title: W22_Elicited_4h


title: W22_Elicited_8h


title: scRNAseq_Foxc1_1

status: Public on Jul 06 2020

city: AURORA

first: Julie

last: Siegenthaler

department: Pediatrics

institute: UNIVERSITY OF COLORADO, ANSCHUTZ MEDICAL CAMPUS

data_processing:
Generated cell feature counts for each single cell RNAseq library using cellranger count --transcriptome=mm10 --expect-cells=10000
Merged single cell RNAseq feature data for all three samples using Seurat Read10X, CreateSeuratObject and merge functions
filtered merged Seurat object to select cells with nFeatures_RNA >500 & < 8000 and percent.mitchondrial <20%
Processed filtered Seurat object using Seurat NormalizeData, FindVariableFeatures(nfeatures=2000), ScaleData, RunPCA(npcs=40),FindNeighbors(dims=1:30),FindClusters(resolution=0.4) and RunUMAP(reduction="pca",dims=1:40)
Subset Seurat object to select only fibroblast cells
Processed fibroblast only Seurat object using Seurat NormalizeData, FindVariableFeatures(nfeatures=2000), ScaleData, RunPCA(npcs=40),FindNeighbors(dims=1:40),FindClusters(resolution=0.2) and RunUMAP(reduction="pca",dims=1:40)
Subclustered each cluster by subseting cluster and using Seurat FindNeighbors(dims=1:40) and FindClusters(resolution=0.3)
Genome_build: mm10
Supplementary_files_format_and_content: gzipped csv file of matrix of normalized gene expression by cell for merged filtered fibroblasts for 3 scRNAseq samples
Supplementary_files_format_and_content: gzipped csv file of metadata for cells

source_name: E14 Col1a1-GFP forebrain meninges cells

extract_protocol:
 E14 mouse forebrain meninges were removed by dissection and digested into a single cell suspension. Live GFP+ cells (indicating Col1a1 expression) were isolated using fluorescent activated cell sorting
10x Genomics Chromium 3' GEM, Library & Gel bead v3 kit (cat#: PN-10000075) was used to add UMIs to individual transcripts on a cell-by-cell basis
Targets of 100,000 reads per cell and  >= 2,000 cells per sample in each of three biological replicates. Replicates were processed and sequenced simultaneously, avoiding the need for batch correction.

value: forebrain meninges

tag: embryo stage

value: Tg(Col1a1-EGFP)#Dab MGI:MGI:4458034


title: W22_Elicited_0h

value: not treated


title: W22_Elicited_2h


title: SP-3

status: Public on Jul 02 2020

city: Uvalde

first: Vijay

last: Joshi

state: Texas

address: 1619 Garner Field Road

department: Department of Horticultural Sciences

institute: Texas A&M AgriLife Research

data_processing:
Illumina Hiseq-4000 sequencing platform
The removal of sequence adapters, mapping to reference genome, and normalization of gene expression was performed using CLC Genomics Workbench (V4.5, CLC Bio.). The RNAseq reads were first assessed for quality with FastQC; adapters were removed with Cutadapt (Martin 2011) and trimmed the low-quality bases (q < 20) with FastX-toolkit (Gordon and Hannon 2010). Quality-filtered reads were then mapped to the reference Sinbase database (Wang et al. 2014) using TopHat2 (Kim et al. 2013) with default parameters.
The differential expressed genes (DEGs) of pooled samples from each condition was determined using Cuffdiff, using the FPKM values.
Differeantial expression analysis with DEseq2
Genome_build: Sinbase database (Wang et al. 2014) version 1.0;
Supplementary_files_format_and_content: FRKM values of differentially expressed genes in both genotypes

organism: Sesamum indicum

growth_protocol: Seeds of drought-tolerant sesame (Sesamum indicum L) ‘TEX-1’ (abbreviated S) and drought-sensitive ‘VEN-1’ (abbreviated E) proprietary experimental lines were made available by Dr. Eric Votava, Sesaco Corporation (Austin, Texas, USA) for this study. Seeds were grown in a greenhouse in a Turface® (Quick Dry Infield Conditioner) and fertilized with standard Hoagland solution (Caisson Laboratories, UT). Four-weeks-old seedlings of both genotypes were carefully transferred to a solution containing 20% polyethylene glycol (PEG)-6000. Seedlings in water were treated as control. Roots samples from three independent biological replicates for both genotypes were harvested 12 hours after initiation of treatment, immediately frozen in liquid nitrogen, and stored at −80°C for further analyses. The frozen root samples were used for transcriptomic and metabolite analysis.

extract_protocol:
The frozen root samples from the PEG-stress experiment were homogenized using a mortar and pestle, and total RNA was extracted using RNAeasy Plant mini kit (QIAGEN Sciences, Germantown, MD, USA). The purity of RNA was analyzed using a Nanodrop (DS-11+ spectrophotometer, DeNovix Inc.), and quality was verified using Agilent 2100 Bioanalyzer (Texas A&M AgriLife Genomics & Bioinformatics Service, College Station, TX) before further processing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Root

value: PEG

tag: phenotype

value: drought-tolerant


title: scRNAseq_Foxc1_3


title: DMSO_rep1

status: Public on Jul 03 2020

city: Beijing

first: Zhi

last: Zeng

address: 7 Science Park Road, ZGC life science park

institute: National Institute of Biological Sciences, Beijing

description:
DMSO
processed data file: HQ461_A549_count.txt
processed data file: HQ461_A549_CRISPR_screen_mageck.xlsx

data_processing:
Library strategy: CRISPR screen
Raw Fastq files were directly loaded into MAGeCK (v0.5.9.2) and the “count” command was used to collect read counts from Fastq files and to generate the sgRNA read count table.
Next, the “test” command was used to perform statistical test from the count table, outputting log2 fold change, p value, and false discovery rate (FDR).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: HQ461_A549_count.txt: MAGeCK file; Matrix table with raw counts.
Supplementary_files_format_and_content: HQ461_A549_CRISPR_screen_mageck.xlsx: MAGeCK file; Log2 fold change, p value, and false discovery rate (FDR) for every gene.

source_name: A549 cell line

growth_protocol: Thirty million A549 cells were infected at a multiplicity of infection (MOI) of ~0.3. Infected cells were passaged every two days in the presence of 10 μg/ml of puromycin for one week with a population size of at least 200 million. Afterwards, A549 cells transduced with the sgRNA library were passaged every two days in the presence of 4 μM HQ461 or the vehicle DMSO (0.1% v/v) for three weeks with a population size of at least 10 million.

extract_protocol:
Cells were lysed in 10 mM Tris-HCl, pH 8.0, 100 mM EDTA, 0.5% SDS, 200 μg/ml RNase A and incubated at 37 °C for 1 hour followed by the addition of 1mg/ml of proteinase K for an overnight incubation at 50 °C. The resulting lysates were extracted three times with phenol solution equilibrated with 10 mM Tris-HCl, pH 8.0, 1 mM EDTA (Sigma P4557) mixed with chloroform (1:1 v/v) using tubes with phase lock gel (Tiangen WM5-2302831). The aqueous phase was then mixed with 0.2 volume of 10 M ammonium acetate and 1 volume of isopropanol, resulting the immediate formation of cloudy DNA precipitates. Precipitated DNA was then transferred by a pipet tip to a tube containing 75% (v/v) ethanol. This process was repeated twice to ensure complete removal of residual organic solvents. Afterwards, genomic DNA was dissolved in 1 mM Tris-HCl, pH 8.0, 0.1 mM EDTA by incubation at 50 °C for three hours.
DNA fragments containing sgRNA sequences were amplified from isolated genomic DNA by two rounds of PCR using NEBNext Ultra II Q5 master mix (NEB). For the first round of PCR, forty-eight 50-μL PCR reactions (each containing 2 μg of genomic DNA template) were performed with the forward primer NGS-Lib-KO-Fwd-1 (5’- CCTACACGACGCTCTTCCGATCTNNNNNNNNNNNNNNNNNNGCTTTATATATCTTGTGGAAAGGACGAAACACC -3’) and the reverse primer NGS-Lib-KO-Rev-0 (5’- CAGACGTGTGCTCTTCCGATCTCCGACTCGGTGCCACTTTTTCAA-3’) with a thermal cycler program consisting of initial denaturation at 98°C for 5 minutes, followed by 16 cycles of (98°C denaturation for 10 seconds, 69°C annealing for 30 seconds, and 65°C extension for 45 seconds), and a final extension at 65°C for 5 minutes. Products of the firstround PCR were pooled and purified by a DNA clean and concentrator kit (Zymo) and diluted to 2 ng/μL. For the second round of PCR, six 50-μL PCR reactions (each containing 2 ng of the purified first-round PCR product) were performed for each sample with the forward primer NGS-Lib-KO-Fwd-2 (5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and one of four indexed reverse primers (NGS-Lib-KO-Rev-1, 2, 3, 4) (5’-CAAGCAGAAGACGGCATACGAGAT[8-nucleotide index]GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’). The same cycling conditions were used for second-round PCR as the first-round PCR except 18 cycles were used. Products of the second-round PCR reactions were subjected to electrophoresis on a 2% agarose gel. The expected ~300 bp amplicons were excised and extracted from the gel and sequenced by Illumina HiSeq PE150 (Novogene).

treatment_protocol: Two biological replicates were performed for both HQ461 and DMSO treatment.

tag: cell line

tag: cell type

value: adenocarcinomic human alveolar basal epithelial cells

value: DMSO


title: DMSO_rep2


title: SC-2

value: Control


title: HQ461_rep2

description:
P1F11
processed data file: HQ461_A549_count.txt
processed data file: HQ461_A549_CRISPR_screen_mageck.xlsx


title: scRNAseq_Foxc1_2


title: SP-1


title: HQ461_rep1


title: SC-3


title: SC-1


title: EP-3

value: drought-sensitive


title: EP-2


title: EC-1


title: A12CTo

status: Public on Jun 29 2020

city: London

first: Rocio Teresa

last: Martinez-Nunez

state: Greater London

address: 5th Floor Tower Wing, Guy’s Campus

department: Infectious Diseases

institute: King's College London

description: Total cytoplasmic RNA

data_processing:
Base Quality and Phred score were calculated employing the Illumina CASAVA v1.8 software with more than 92% of all reads for all samples having a Q30
Bowtie v2.2.3 was used to index the reference genome and trimmed paired-end reads were aligned using TopHat v2.0.12.
HTSeq v0.6.1 using the union mode was employed to count mapped reads and generate FPKM
Differential gene expression analysis was performed employing DESeq with Benjamini and Hochberg’s FDR correction

organism: Rattus norvegicus

source_name: Total RNA Control treated

extract_protocol: Library preparation and RNA sequencing was done by Novogene (Hong Kong). Libraries were made using polyadenylated mRNA isolation, employing NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA). Three samples had lower RNA amounts and a higher efficiency bead capture was employed for only those, maintaining the same library preparation kit otherwise. Base Quality and Phred score were calculated employing the Illumina CASAVA v1.8 software with more than 92% of all reads for all samples having a Q30. Bowtie v2.2.3 was used to index the reference genome and trimmed paired-end reads were aligned using TopHat v2.0.12.

value: Primary rat cortical neurons

value: Total RNA Control treated


title: A4CTo

description: Total cytoplasmic RNA


title: EC-2


title: A11AbTo

description: Total cytoplasmic RNA

source_name: Total RNA Ab treated

value: Total RNA Ab treated


title: A8CTo

description: Total cytoplasmic RNA


title: 61

value: neutral

tag: set

tag: molecule subtype

value: ampliconic DNA


title: EC-3


title: SP-2


title: A3AbTo

description: Total cytoplasmic RNA


title: A7AbTo

description: Total cytoplasmic RNA


title: A10CRi

description: RNA enriched in ribosome pellets

source_name: Ribosome-cushion Control treated

value: Ribosome-cushion Control treated


title: A6CRi

description: RNA enriched in ribosome pellets


title: A1AbRi

description: RNA enriched in ribosome pellets

source_name: Ribosome-cushion Ab treated

value: Ribosome-cushion Ab treated


title: A9AbRi

description: RNA enriched in ribosome pellets


title: A2CRi

description: RNA enriched in ribosome pellets


title: AcAPE1 seq_APE1shRNA HCT116 cells

status: Public on Jun 02 2020

city: Omaha

first: Shrabasti

last: Roychoudhury

state: NE

address: S 42nd &, Emile St

institute: University of Nebraska Medical Center

data_processing:
FASTQ files were generated after adaptor sequences, and low quality (Phred score < 20) ends were trimmed from the ChIP sequences using the Trim Galore software package (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/). FASTQ files were aligned to the human genome (GRCh37/hg19) using the sequence aligner Bowtie2 (version 2.2.3)
The software package Picard routine Mark Duplicates (http://broadinstitute.github.io/picard/) was used to remove sequence duplications.
Biological replicates were then merged using SAMtools.
The merged files were used to call peaks using MACS2 peak caller software (version 2.1.1). A peak from a given antibody was considered significant if it had a fold change ≥2 over IgG, ≥15 reads, and a p-value<0.001.
All bigWig files generated using the deepTools bamCoverage routine (https://deeptools.readthedocs.io/en/develop/)
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: HCT116 CELLS

growth_protocol: Cells were plated in a 150 mm cell culture dish with respective media and cultured for 24 hours.

extract_protocol:
Lysates were clarified from sonicated nuclei. ARP-tagged DNA was isolated with Streptavidin and DNA-protein complexes were isolated with antibody.
The library was made using New England Biolabs NEB Next Ultra II DNA Library Prep Kit. High-throughput sequencing was conducted at the UNMC Sequencing Core, using an Illumina HiSeq 2500 Genome Analyzer.

treatment_protocol: For mapping AP sites, 1 mM biotin-conjugated ARP (Life Technologies, #A10550) was fed to cells for 3 hours.

value: colon cancer cells

tag: passages

value: 3 to 5

tag: ip reagent

value: α-AcAPE1 (Chattopadhyay R, et al. (2008);Molecular and cellular biology 28(23):7066-7080)


title: EP-1

value: Root