title: WTPC_56A

description: RNASEQ

data_processing:
Sequencing libraries were constructed using the TruSeq RNA Sample preparation protocol (Illumina). RNA-sequencing of libraries was performed on the NextSeq 550 (Illumina) with 75 bp reads, according to the manufacturer’s instructions, by the UTSW McDermott Next Generation Sequencing Core. Read quality was assessed using the FASTQC quality control tool. Reads were mapped with STAR (with parameters:--runMode alignReads --genomeDir genomefolder --sjdbGTFfile gtf --readFilesIn sample_trim.gz --readFilesCommand zcat --outFileNamePrefix sample --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMmapqUnique 255 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --alignIntronMax 1000000 --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 10 --outFilterMismatchNmax 3 --twopassMode Basic --quantMode GeneCounts) following Cutadapt trimming (with parameters: -g AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 30) to the following genomes: PlasmoDB-31_Pchabaudichabaudi from www.PlasmoDB.org and M14 GENCODE version of mouse genome from www.gencodegenes.org. An average of 57% of the uniquely mapped reads mapped to the parasite genome. Raw reads were quantified using featureCounts tool from Rsubread package followed by RPKM calculation using in-house scripts. Downstream bioinformatic analysis after RPKM calculations was performed in R environment. Multidimensional scaling analysis was performed by plotMDS from limma package (50). Hierarchical clustering and heatmaps were obtain for each dataset by reordering of the timepoints according to gene expression using function heatmap.2 from the gplots package. Both hierarchical clustering analysis and heatmaps of Spearman correlations were performed on centered log2-transformed RPKM values. Plots were generated with ggplot2 package.
Genome_build: M14 From GENCODE; Plasmodium chabaudi chabaudi release 31 from plasmodb.org

source_name: P chabaudi infected blood

extract_protocol:
Blood was collected by cardiac puncture into 1.5mL of PBS, spin at 3,000 rpm for 2 min, added TRIzol LS and snap frozen
RNA was extracted using Trizol LS reagent according to manufactor's instructions.
mRNA-seq libraries were prepared using the TruSeq RNA Library Preparation Kit (Illumina) according to the manufacturer's instructions.

tag: mouse strain

value: P. chabaudi AS

value: WT mouse


title: 191108_HD_4_snRNA-G9

status: Public on Jul 17 2020

type: SRA

city: Cambridge

first: Myriam

last: Heiman

state: Massachusetts

address: 77 Massachusetts Ave., Bldg 46-4285

department: Brain and Cognitive Sciences

country: USA

institute: Massachusetts Institute of Technology

library_source: transcriptomic

data_processing:
Basecalls converted to FASTQ with Cellranger v3.1.
FASTQ files were aligned, demultiplexed, and sorted with Cellranger v3.1 using pre-mRNA annotated GRCh38 or mm10 reference.
Genome build: GRCm38/mm10
Supplementary_files_format_and_content: Sparse matrices (MTX) containing unique molecular identifier counts of each gene per cell.
snRNA-seq: Basecalls converted to FASTQ with Cellranger v3.1.
snRNA-seq: FASTQ files were aligned, demultiplexed, and sorted with Cellranger v3.1 using pre-mRNA annotated GRCh38 or mm10 reference.
Genome_build: snRNA-seq: GRCm38/mm10
Supplementary_files_format_and_content: snRNA-seq: Sparse matrices (MTX) containing unique molecular identifier counts of each gene per cell.
TRAP: FASTQs files were aligned to the Mus musculus genome using STAR v2.4.2a. Read counts were generated by STAR using the --quantMode GeneCounts option, along with the default options, except for  --outFilterMismatchNoverLmax, which was set to 0.04 (from 0.3), --outFilterMismatchNmax, which was set at 999 (from 10), --alignIntronMax, which was set to 1000000, and --alignMatesGapMax, which was set to 1000000.
Retro-TRAP: FASTQs files of 50-bp single-end sequencing reads were aligned using STAR 2.4 RNA-Seq aligner. As note, technical replicate data were merged for alignment. The mapped reads were processed with HTSeq to generate gene counts (GENCODE.vM9 version of mouse gene annotation).
Genome_build: TRAP: GRCm38.78, Retro-TRAP: GRCm38.p4
Supplementary_files_format_and_content: TRAP: TSV and TXT files containing raw counts and reads per kilobase mission of each gene per sample.

molecule: total RNA

organism: Homo sapiens

source_name: Putamen

extract_protocol:
Tissue was homogenized in 700 µL of homogenization buffer (320 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 0.1% NP-40, 1 mM β-mercaptoethanol, and 0.4 U/µL RNase inhibitor) with a 2 mL tissue grinder. Tissue was filtered through a 40 µm cell strainer and mixed with 450 µL solution of 50% OptiPrep density gradient medium, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], and 1 mM β-mercaptoethanol.  The mixture was then pipetted onto an OptiPrep density gradient containing 750 µL of 30% OptiPrep Solution (134 mM sucrose, 5 mM CaCl2, 3 mM Mg(CH3COO)2, 10 mM Tris HCl [pH 7.8], 0.1 mM EDTA [pH 8.0], 1 mM β-mercaptoethanol, 0.04% NP-40, and 0.17 U/µL RNase Inhibitor) on top of 300 µL of 40% OptiPrep Solution inside a microcentrifuge tube. Nuclei were pelleted at the interface of the OptiPrep density gradient by centrifugation. Nuclei were washed three times with 2% BSA and the nuclear pellet was re-suspended in 100 µL of 2% BSA.
Libraries were constructed according to the 10x Genomics Single Cell Expression v3 User Manual.

tag: tissue

value: Putamen

tag: genotype

value: HD

tag: tissue id


title: ACE2-A549-Berbamine-COV2-1

city: New York

first: Avi

last: Ma'ayan

state: NY

address: One Gustave L. Levy Place, Box 1603

department: Pharmacological Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw reads were aligned to the human genome (hg19) using the RNA-Seq Alignment App on Basespace (Illumina, CA).
Genome_build: human genome (hg19)
Supplementary_files_format_and_content: Read counts for each sample and corresponding gene

growth_protocol: Human adenocarcinomic alveolar basal epithelial (A549) cells (ATCC, CCL-185) were maintained at 37°C and 5% CO2 in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) supplemented with 10% Fetal Bovine Serum (FBS, Corning). Undifferentiated human pluripotent stem cells (hPSCs) were maintained in feeder-free conditions. Briefly, hPSCs were cultured on Matrigel-coated 6-well plates in commercial StemFlex™ Medium (ThermoFisher). The medium was changed every day, and cells were passaged every ∼4 days using ReLeSR™ (STEM Technologies). In all normal hPSC cultures, 5 μM Rho-associated protein kinase (ROCK) inhibitor Y-27632 was only added into the culture media when passaging or thawing hPSCs. For pancreatic endocrine organoid differentiation, we adapted previous published protocols (Yang et al., 2020).

extract_protocol:
Total RNA from infected and mock infected cells was extracted using TRIzol Reagent (Invitrogen) and Direct-zol RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions and treated with DNase I. RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.
RNA-seq libraries for total ribosomal RNA-depleted RNA were prepared using the TruSeq Stranded Total RNA Library Prep Gold (Illumina) according to the manufacturer’s instructions. cDNA libraries were sequenced using an Illumina NextSeq 500 platform.

treatment_protocol: Approximately 1 x 10e6 A549 cells were infected with SARS-CoV-2. Infections with IAV were performed at a multiplicity of infection of 5 for 9 h in DMEM supplemented with 0.3% BSA, 4.5 g/L D-glucose, 4 mM L-glutamine and 1 µg/ml TPCK-trypsin. Infections with SARS-CoV-2 were performed at an MOI of 0.2 for 24 h in DMEM supplemented with 2% FBS, 4.5 g/L D-glucose, 4 mM L-glutamine, 10 mM Non-Essential Amino Acids, 1 mM Sodium Pyruvate and 10 mM HEPES.

tag: cell line

value: lung alveolar (A549) transduced with vector expressing human ACE2

tag: drug

value: Berbamine

tag: sars-cov-2 infected

value: Yes


title: NCI-H660_RNA-Seq rep1

city: Seattle

first: John

middle: K

last: Lee

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology Division

institute: Fred Hutchinson Cancer Research Center

data_processing:
UC Santa Cruz Toil RNA-seq Pipeline (4.0.3)
Genome_build: hg38
Supplementary_files_format_and_content: CSV file with log-transformed FPKM+1 RSEM output for each gene and sample

source_name: Prostate cancer

growth_protocol: 22Rv1 and LNCaP95 cell lines were grown in RPMI medium supplemented with 10% FBS, 2 mM GlutaMAX, and penicillin/streptomycin. NCI-H660 and MSKCC EF1 cell lines were grown in Advanced DMEM/F12 medium supplemented with B27, 2 mM Glutamax, 10 ng/ml recombinant hEGF, 10 ng/ml recombinant hFGFb, and penicillin/streptomycin.

extract_protocol:
RNA from cell lines was extracted using the Qiagen Rneasy Mini Kit
RNA libraries were prepared for sequencing using the Illumina TruSeq Total RNA workflow

treatment_protocol: Cell lines were not treated

value: MSKCC EF1

tag: subtype

value: Neuroendocrine prostate cancer


title: 191108_HD_5_snRNA-G10

source_name: Caudate

value: Caudate

value: Control


title: ACE2-A549-Amlodipine-COV2-3

value: Amlodipine


title: 191108_HD_3_snRNA-G8


title: 191108_HD_2_snRNA-G7


title: ACE2-A549-Amlodipine-COV2-2


title: ACE2-A549-Amlodipine-COV2-1


title: MSKCC-EF1_RNA-Seq rep2


title: Organoids_Trifluoperazine-3

source_name: Pancreatic organoids

value: pancreatic organoids created from hESCs

value: Trifluoperazine


title: WTPC_52A

city: Dallas

first: Gokhul

middle: Krishna

last: Kilaru

state: TEXAS

address: 6000 Harry Hines Boulevard

department: Department of Neuroscience

institute: University of Texas Southwestern Medical Center

description: RNASEQ

molecule: polyA RNA

organism:
Plasmodium chabaudi
Mus musculus

treatment_protocol: Mice were infected with 10^6 Plasmodium chabaudi AS parasites

tag: malaria strain

value: blood

tag: knockout

tag: light condition

value: darkness

tag: feeding

value: ad libitum

tag: 1 mouse or pool of 3 mice

value: 1 mouse


title: Tumor T59

city: Minneapolis

first: Timothy

last: Starr

state: MN

address: 420 Delaware St SE

department: Department of Obstetrics

institute: University of Minnesota

data_processing:
Fastq files were analyzed  using CellRanger (v3.0.2) software which performs indexing, demultiplexing, and alignment to produce bam files and a matrix of RNA abundance (cells x genes) using the Unique Molecular Identifier (UMI) counts.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix files of UMI gene counts for every gene and every cell

source_name: tumor specimen

growth_protocol: Tumor specimens  taken from the operating room were used for clinical diagnoses and excess tissue was released to the study.

extract_protocol:
Cells were lysed and RNA was extracted and converted to cDNA and tagged with barcodes following the 10x Genomics Single Cell 3’ Protocol utilizing the ChromiumTM Single Cell 3’ v2 Library & Gel Bead Kit and ChromiumTM Single Cell A  Chip Kit (10x Genomics, Pleasanton, CA).
Barcoded cDNA was sequenced using an Illumina HiSeq 2500 flow cell with Rapid chemistry and 100 bp paired end sequencing, producing an average of 235 million reads per patient sample with an average of 11,502 cells/sample and 23,000 reads/cell

treatment_protocol: Tumor pieces were digested at  37C and gentle shaking following the Miltenyi GentleMacs Dissociation system protocol (Miltenyibiotec,  San Diego CA). This protocol uses a proprietary mix of enzymes and specially designed centrifuge tubes  to generate a single cell suspension. Cells were filtered through a 70 micron filter, washed 2x in PBS and incubated with red blood cell lysis to remove red blood cells. Cell viability was determined based on trypan blue exclusion. Cells were transported to the University of Minnesota core sequencing facility for  processing within 3 hours after excision from the patient.

value: omentum

tag: diagnosis

value: high-grade serous ovarian carcinoma

tag: tumor stage

value: IV

tag: tumor grade

tag: chemotherapy response

value: resistant


title: 191108_HD_6_snRNA-G11


title: 191108_HD_1_snRNA-G6

value: HD


title: MSKCC-EF1_RNA-Seq rep1


title: WTPC_48B

description: RNASEQ

tag: mouse strain

value: P. chabaudi AS

value: WT mouse


title: LNCaP95_RNA-Seq rep2

value: Castration-resistant adenocarcinoma


title: 190730_HD_snRNA-B1

tag: tissue

value: Putamen


title: Organoids_Trifluoperazine-2

value: Yes


title: WTPC_52B

description: RNASEQ


title: LNCaP95_RNA-Seq rep1


title: 190730_HD_snRNA-A12

value: Caudate

tag: genotype

value: Control


title: Organoids_Terfenadine-3

value: pancreatic organoids created from hESCs

value: Terfenadine


title: WTPC_44B

description: RNASEQ

value: blood

value: darkness


title: 22Rv1_RNA-Seq rep2


title: WTPC_44A

description: RNASEQ

value: ad libitum

value: 1 mouse


title: 22Rv1_RNA-Seq rep1


title: 190730_HD_snRNA-A11

tag: tissue id


title: Organoids_Terfenadine-2


title: Organoids_Terfenadine-1


title: 190730_HD_snRNA-A9


title: MSKCC_EF1_rep2

library_source: genomic

data_processing:
ENCODE ATAC-seq Pipeline (v1.6.1)
Genome_build: hg38
Supplementary_files_format_and_content: BigWig files generated for each technical replicate from the ENCODE ATAC-seq Pipeline

molecule: genomic DNA

extract_protocol:
DNA was extracted from 50,000 cells per cell line after washing, permeabilization, and transposition using the Qiagen MinElute Kit
Libraries were constructed based on a published Omni-ATAC protocol (Corces MR, et al. Nature Protocols, 2017)

tag: cell line

value: Neuroendocrine prostate cancer


title: Organoids_RS504393-3

tag: drug


title: WTPC_36B

description: RNASEQ


title: WTPC_40B

description: RNASEQ


title: 190730_HD_snRNA-A10


title: 190730_HD_snRNA-A8


title: MSKCC_EF1_rep1


title: Organoids_RS504393-2

tag: sars-cov-2 infected


title: WTPC_36A

description: RNASEQ


title: WTPC_40A

description: RNASEQ


title: 190730_HD_snRNA-A7


title: NCI-H660_rep2

tag: subtype


title: Organoids_Trifluoperazine-1

value: Trifluoperazine


title: WTPC_48A

description: RNASEQ

tag: malaria strain


title: 190730_HD_snRNA-B3


title: WTPC_32B

description: RNASEQ

tag: knockout


title: Organoids_MOCK-3

value: mock

value: No


title: NCI-H660_rep1


title: WTPC_32A

description: RNASEQ

value: P. chabaudi AS

tag: light condition


title: 190730_HD_snRNA-A5

value: HD


title: 190730_HD_snRNA-A4


title: WTPC_28A

description: RNASEQ

value: WT mouse

tag: feeding


title: LNCaP95_rep1

value: Castration-resistant adenocarcinoma


title: Organoids_MOCK-1


title: 190730_HD_snRNA-A3


title: Organoids_MOCK-2


title: 22Rv1_rep2


title: Organoids_Loperamide-3

value: Loperamide

value: Yes


title: WTPC_24B

description: RNASEQ

tag: 1 mouse or pool of 3 mice


title: 190730_HD_snRNA-A2

value: Putamen


title: WTPC_24A

description: RNASEQ


title: Organoids_Loperamide-2

value: pancreatic organoids created from hESCs


title: WTPC_20B

description: RNASEQ


title: ATAC-seq-Rep2

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

data_processing:
(RNA-seq) FastQC 0.11.4
(RNA-seq) STAR 2.5.1b
(RNA-seq) Cufflinks 2.2.1
(ChIP-seq) EDD
(ATAC-seq) Cutadapt0.5
(ATAC-seq) Bowtie2.2.6
(ATAC-seq) Sambamba0.6.5
(ATAC-seq) Samtools1.2.0
(ATAC-seq) Deeptools2.0.0
Genome_build: human reference genome (hg19)
Supplementary_files_format_and_content: (RNA-seq) tab-delimited text file (gene_exp) include gene expression and differential expression for each sample. (ChIP-seq) Bed and Bedgraphs for ChIP-seq.

source_name: H7 derived cardiomyocytes

growth_protocol: iPSC lines and hESCs were maintained in chemically defined medium Essential 8 (E8 medium) (Life Technologies) on Matrigel-coated (BD Bioscience, San Jose, CA) plates at 37°C with 5% (vol/vol) CO2.

extract_protocol:
(RNA-seq) iPSC-CMs were detached from cell culture plates and RNA was extracted using a microRNeasy kit (QIAGEN). (ChIP-seq) Lysates were clarified from sonicated nuclei and LMNA-DNA complexes were isolated with antibody. (ATAC-seq) The samples were extracted as described in previous protocol (Buenrostro J et al. Nat Methods 10: 1213-1218)
(RNA-seq) RNA libraries were prepared for sequencing using standard Illumina protocols. (ChIP-seq) ChIP-seq libraries were prepared for sequencing using The Ion Proton™ System protocols. (ATAC-seq) ATAC-seq libraries were prepared for sequencing using TruSeq Library Prep Kit (illumina).

treatment_protocol: iPSCs and hESCs were grown to 90% confluence and subsequently differentiated into beating cardiomyocytes, using a small-molecule-based monolayer method described previously. Ten days after cardiac differentiation, iPSC-CM and hESC-CM monolayers were purified using RPMI-1640 without glucose (Life Technologies) with B27 supplement (Life Technologies). Non-glucose culture medium was changed every 2 days. After 5 days, iPSC-CMs were reseeded onto Matrigel-coated plates in a culture medium containing glucose.

tag: cell-type

value: ES-derived cardiomyocyte

tag: day post-differentiation

value: day 40

value: wt/wt


title: 190726_HD_snRNA-H11


title: Organoids_Loperamide-1


title: ATAC-seq-Rep1


title: Organoids_RS504393-1


title: WTPC_20A

description: RNASEQ

value: blood

value: darkness

value: ad libitum


title: 190726_HD_snRNA-H9

value: Caudate


title: LNCaP95_rep2


title: sir3∆ H3K79me3 ChIP

city: Berkeley

first: Davis

last: Goodnight

state: CA

address: 440 Barker Hall

department: Molecular & Cell Biology

institute: UC Berkeley

data_processing:
For samples sequenced on the Illumina NovaSeq 6000, FASTQ generation was performed using Illumina Casava v2.2. For samples sequenced on the Illumina Miniseq, FASTQ generation was performed using the Generate FASTQ module of Illumina Local Run Manager
Raw reads were mapped to SacCer3 genome modified to include hml∆::HML* and mat∆ using Bowtie2 with following options: --local --soft-clipped-unmapped-tlen --no-unal --no-mixed --no-discordant
bedgraph files were generated from aligned reads and normalized to the genome-wide median (median excluded subtelomeres, chromosome III, and rDNA). For MNase samples, only reads between 130-180 bp (mononucleosome) were included in bedgraphs.
Genome_build: SacCer3 (modified)
Supplementary_files_format_and_content: bedgraph (normalized to genome-wide median)

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Yeast were cultured at 37° in YPD.

extract_protocol:
Cells were lysed by mechanical disruption in a bead beater. Chromatin was fragmented using either sonication (all H3K79me3 samples) or MNase (all Sir4-myc and Sir3-EBD samples except for a subset fragmented by sonication, noted in the sample title). DNA was purified using Qiagen spin column kit
NEB Ultra II library prep kit

treatment_protocol: For SIR3-EBD cultures, estradiol was used at 50 µM. "No estradiol" samples were grown with 0.5% ethanol (solvent control). For G1 arrests, 10 nM alpha factor was added. For G2/M arrests, 15 µg/mL nocodazole was added.

tag: strain

tag: chip antibody

tag: condition

value: Cycling

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc; sir3{delta}


title: Organoids_DMSO-3

tag: tissue

value: DMSO


title: WTPC_16B

description: RNASEQ

tag: mouse strain

value: P. chabaudi AS

value: 1 mouse


title: 190726_HD_snRNA-H8

tag: genotype

value: HD

tag: tissue id


title: Organoids_DMSO-2

tag: drug


title: WT H3K79me3 ChIP

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc


title: Organoids_DMSO-1

tag: sars-cov-2 infected

value: Yes


title: 190726_HD_snRNA-H7

value: Putamen

value: Control


title: WTPC_16A

description: RNASEQ

value: WT mouse


title: WTPC_12B

description: RNASEQ


title: 22Rv1_rep1

tag: cell line

tag: subtype

value: Castration-resistant adenocarcinoma


title: Organoids_Berbamine-3

value: pancreatic organoids created from hESCs

value: Berbamine


title: SIR3-EBD no estradiol ERalpha input

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc; SIR3-EBD78


title: 190726_HD_snRNA-H6


title: 190730_HD_snRNA-A1


title: Organoids_Berbamine-2


title: 190726_HD_snRNA-H5


title: WTPC_08B

description: RNASEQ

tag: malaria strain

value: blood

tag: knockout

value: darkness

value: ad libitum


title: SIR3-EBD no estradiol ERalpha ChIP

value: ERalpha (Santa Cruz Biotechnology cat # sc-8002, lot # H1718)

value: Cycling


title: Organoids_Berbamine-1


title: SIR3-EBD + estradiol ERalpha ChIP


title: WTPC_08A

description: RNASEQ

value: P. chabaudi AS

tag: light condition

tag: feeding


title: Organoids_Amlodipine-3

value: Amlodipine


title: Ins_100pM_3

city: Rehovot

first: Keren

last: Bahar-Halpern

address: Herzl St 234

country: Israel

institute: Weizmann Institute

data_processing:
bcl2fastq/2.15.0.4. sample demultiplexing was provided to obtain sample specific reads in two fastq files (read 1 (R1) and read 2 (R2))
To obtain the UMI counts, fastq reads were aligned to the rat reference genome (Rnor_6.0.96) using zUMI package (Parekh et al., 2018).
Genome_build: Rnor_6.0.96
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule UMI count values for each Sample

organism: Rattus norvegicus

source_name: Pancreatic acinar cells

growth_protocol: Cells were thawed and let to recover for a week before exposed to CCK or insulin. Growth medium used was low-glucose DMEM, 10% FBS, 1% Pen/strep, 1% NEAA, 1% Glutamine.

extract_protocol:
cells were lysed in TRI reagent for RNA extraction. RNA was isolated by Direct-zol RNA MiniPrep kit.
Bulk analysis, mcSCRBseq protocol was used (Bagnoli et al., 2018)

treatment_protocol: Cells were incubated in growth medium with the different 5 concentrations of CCK/insulin or with growth medium only in triplicates for 24 hours.

value: Pancreas

tag: treatment

value: 100pM Insulin


title: WTPC_04B

description: RNASEQ

tag: 1 mouse or pool of 3 mice

value: 1 mouse


title: Ins_100pM_2


title: WTPC_04A

description: RNASEQ


title: Organoids_Amlodipine-2

value: Yes


title: Ins_100pM_1


title: SIR3-EBD + estradiol ERalpha input

tag: strain


title: jc6995_T47D_ATAC-seq_siFOXA1_Veh

first: Jason

last: Carroll

address: Li Ka Shing Centre, Robinson Way

country: United Kingdom

institute: Cancer Research UK, Cambridge Institute

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.
The peaks were called with MACS2, version 2.1.1.20160309, using following parameters:  -g hs -f BAM --nomodel --shift -100 --extsize 200.
Differential binding analysis (Diffbind) was performed as described previously (Brown and Stark, 2011).
Genome_build: hg38
Supplementary_files_format_and_content: bed/text

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.  On target plus siRNAs were used for the knockdown.

extract_protocol:
Omni ATAC-seq protocol was performed from Corces et al., 2017, Nature Methods. Transposase and buffers were purchased from Illumina Nextera kits.
DNA was prepared for Illumina sequencing using Nextera indices on the Novaseq 6000 with paired end 50 bp.

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

value: T47D cells

tag: cell type

value: ER+  Breast Cancer Cell Line

tag: passages


title: jc6994_T47D_ATAC-seq_siCont_IL6


title: WTPC_00B

description: RNASEQ

tag: tissue

value: WT mouse


title: jc6996_T47D_ATAC-seq_siFOXA1_IL6


title: jc6993_T47D_ATAC-seq_siCont_Veh


title: 190726_HD_snRNA-H4

value: Caudate

value: Control


title: WTPC_00A

description: RNASEQ

tag: mouse strain


title: Organoids_Amlodipine-1

value: pancreatic organoids created from hESCs


title: jc6992_T47D_ATAC-seq_siFOXA1_IL6


title: Ins_10nM_2

value: 10nM Insulin


title: PC_72B

description: RNASEQ

value: blood

value: darkness

value: pooling 3 mice


title: RNAseq_Alisertib_rep3

city: Kiel

first: Elmar

last: Wolf

state: Schleswig-Holstein

address: Rudolf-Höber-Str. 1

department: Biochemical Institute

country: Germany

institute: Christian-Albrechts-University Kiel

data_processing:
Fastq files were generated using Illuminas base calling software GenerateFASTQ v1.1.0.64 and overall sequencing quality was analyzed using the FastQC script.
For RNA-seq, reads were aligned to the human genome (hg19) using Tophat v2.1.1 (Kim et al., 2013) and Bowtie2 v2.3.2 (Langmead et al., 2012) using the parameters  –n 1 -- and samples were normalized to the number of mapped reads in the smallest sample.
For gene expression analysis, reads per gene (Ensembl gene database) were counted with the “summarizeOverlaps” function from the R package “GenomicAlignments” using the “union”-mode and non- or weakly expressed genes were removed (mean read count over all samples <1).
Genome_build: hg19
Supplementary_files_format_and_content: Differential Expression log2FC values matrix containing all samples.

source_name: MV4-11 cells

growth_protocol: MV4-11 cells were cultured in RPMI 1640 medium, with L-Glutamine (Thermo Fisher Scientific; 21875091) supplemented with 10% Fetal Bovine Serum (Sigma; F0392) and 1% Penicillin-streptomycin solution (Sigma; P4333).

extract_protocol:
RNA extraction was performed with the miRNeasy Mini kit (Qiagen) according to manufacturer’s instruction and using in-column DNase digestion.
RNA quality was assessed employing a Fragment Analyzer (Agilent) and directional libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s instructions.
polyA_enriched_RNA_Seq

treatment_protocol: 3 ml (200k cells/ml) of MV4-11 cells were seeded and treated with either DMSO, 100 nM JB170 or 1000 nM Alisertib for 18 hours. 2 ml of cell suspension was used for RNA extraction and rest for protein extraction (to validate the effect of compounds with western blot).

tag: treatment (4-oht or etoh)

value: Alisertib

value: MV4-11 cells


title: RNAseq_Alisertib_rep1


title: jc6991_T47D_ATAC-seq_siFOXA1_Veh


title: Ins_10nM_1


title: RNAseq_JB170_rep3


title: Ins_10nM_3


title: PC_72A

description: RNASEQ

value: P. chabaudi AS

value: Light/dark

value: ad libitum


title: Ins_1µM_3

value: Pancreas

value: 1µM Insulin


title: PC_68B

description: RNASEQ


title: WTPC_12A

description: RNASEQ

value: 1 mouse


title: RNAseq_JB170_rep2


title: Ins_1µM_2


title: RNAseq_JB170_rep1


title: PC_68A

description: RNASEQ


title: jc6988_T47D_ATAC-seq_siFOXA1_IL6

value: T47D cells

value: ER+  Breast Cancer Cell Line


title: jc6989_T47D_ATAC-seq_siCont_Veh


title: PC_64B

description: RNASEQ

value: WT mouse


title: jc6987_T47D_ATAC-seq_siFOXA1_Veh


title: Ins_1µM_1


title: RNAseq_Alisertib_rep2


title: Ins_10µM_3

value: 10µM Insulin


title: RNAseq_DMSO_rep3

value: DMSO


title: PC_64A

description: RNASEQ


title: jc6986_T47D_ATAC-seq_siCont_IL6


title: PC_60B

description: RNASEQ


title: PC_60A

description: RNASEQ


title: jc6985_T47D_ATAC-seq_siCont_Veh


title: RNAseq_DMSO_rep2


title: Ins_10µM_1


title: RNAseq_DMSO_rep1


title: Non-synchronized_RNA-seq_Control_3

city: BEIJING

first: Haili

last: Qian

address: 17 South Panjiayuan Lane, Chaoyang District

country: China

institute: National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using tophat2 --read-edit-dist 4 -N 4 --b2-N 1 -a 8 -m 0 -g 2 -p 12 --microexon-search --no-coverage-search --report-secondary-alignments. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene FPKM values for each Sample

source_name: colon

growth_protocol: HCT116 were cultured in DMEM medium (Gibco) supplemented with 10% fetal bovine serum (FBS) (HyClone) and 1% penicillin/streptomycin (HyClone) at 37℃ in a humidified incubator with 5% CO2.

extract_protocol:
RNA was harvested using Trizol reagent.Total RNA was treated with RQ1 DNase (promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% Agarose gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon

tag: morphology

value: epithelial

tag: disease

value: colorectal carcinoma

tag: genotype/variation

value: control


title: Ins_100µM_3

tag: cell line

value: 100µM Insulin


title: jc6990_T47D_ATAC-seq_siCont_IL6


title: PC_56B

description: RNASEQ

value: blood

value: pooling 3 mice


title: Ins_100µM_2


title: PC_56A

description: RNASEQ

value: P. chabaudi AS

value: Light/dark


title: Non-synchronized_RNA-seq_Control_1


title: Non-synchronized_RNA-seq_Control_2


title: PC_52B

description: RNASEQ

value: ad libitum


title: Non-synchronized_RNA-seq_CrMTA1_3

value: MTA1 knockout


title: Treated by peptide 3 T3

type: RNA

city: Changsha

first: Wu

last: Qiang

address: 498 Shaoshan Road

institute: Central South University of Forestry and Technology

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60°C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: thoracic aorta in SHRs treated by G. lingzhi peptide

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: SHRs (12 weeks old, female, 220-260 g) were maintained under 12 h light and dark cycle at 23±2℃. The rats were randomly assigned to two groups, respectively administered with intravenous injection of G. lingzhi peptide SYP at a dose of 5.0 mg/kg body weight per day for 28 d, and no therapy was performed saline solution with same quantity of physiology brine as control group.

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: After administration intravenously for 28 days, 6 SHRs were selected from two group randomly, and killed to get the thoracic aorta. The collected samples were placed in liquid nitrogen quickly.

value: SHR

value: thoracic aorta

tag: Sex

value: Male

tag: age

value: 16 weeks

value: Ganoderma lingzhi oligopeptide


title: Ins_Ct3

value: Pancreas

value: No treatment


title: PC_52A

description: RNASEQ

tag: malaria strain

tag: knockout

value: WT mouse


title: Non-synchronized_RNA-seq_CrMTA1_2

value: colon

value: epithelial

value: colorectal carcinoma


title: PC_48B

description: RNASEQ

value: blood

tag: light condition

tag: feeding


title: Ins_Ct2

tag: treatment


title: Non-synchronized_RNA-seq_CrMTA1_1


title: Ins_Ct1


title: fclipseq_2nd_MTA1

data_processing:
Library strategy: fCLIP-Seq
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:TGGAATTCTCGGGTGCCAAGG;end2:GATCGTCGGACTGTAGAACT) trimmed with fastx_clipper
Reads were mapped using tophat2 -N 2. Uniq mapped reads were remained. while several mapped reads have the same start position and end position, only one is considered.
Reads with overlap region on the locus of genome were clustered. The read number (N), read length and observed max depth were then counted for each cluster. For each gene, a same number of reads with coincident lengths were generated using computational simulation. The outputting reads were further randomly placed to same genes to generate max peak height from overlapping reads. The whole process was repeated for 500 times. All the observed peaks with heights higher than those of random max peaks (p value ＜ 0.01) were selected, while the FTO peaks that have an overlap with control peaks were removed.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files include MTA1 binding peaks for each sample

extract_protocol:
Formaldehyde crosslinked cells were lysed on ice by resuspending and repeated pipetting with 10 cell pellet volumes of lysis buffer (1× PBS, 0.1% SDS, 0.5% NP-40 and 0.5% sodium deoxycholate). Then, add 1% (vol/vol) 40U/ul Recombinant RNase Inhibitor（Takara,2313A） and 2% (vol/vol) 10mg/ml PMSF to the cell lysate, mix and rotate the mixture end over end at 4 °C for 30 min. Add 10 X RQ I buffer and DNase I(Promega,M610A). Incubate the tubes at 37 °C for 3 min,shaking at 1,000rpm. Immediately afterward a Stop solution was added to the lysates to quench DNase. Then, centrifuge 10,000 rpm for 10 min at 4 °C. Carefully collect the supernatant. Prepare a 1/50000 dilution of MNase(Thermo,EN0181).
For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to illumina NextSeq 500 system for 151 nt pair-end sequencing by ABlife. Inc (Wuhan, China) and Illumina GAIIx (Illumina, San Diego, CA, USA) 150 nt paird-end sequencing .


title: PC_44B

description: RNASEQ

tag: 1 mouse or pool of 3 mice

value: pooling 3 mice


title: Treated by peptide 1 T1

tag: strain


title: no tag sonication input

tag: chip antibody

tag: condition

value: Cycling

tag: genotype

value: mat{delta} hml{delta}::HML* bar1{delta}


title: no tag sonication Sir4-myc ChIP

value: Pierce Anti-c-myc magnetic beads (Thermo Fisher Scientific 88843, lot # UF283471)


title: Cck_100pM_2

tag: tissue

value: 100pM CCK


title: chipseq_2nd_MTA1

data_processing:
Illumina Casava1.9 software used for basecalling.
3' adapter (end1:AGATCGGAAGAGC;end2:AGATCGGAAGAGC) trimmed with cutadapt
Reads were mapped using bowtie2 -N 1. Uniq mapped reads were remained.
macs14 was used to peakcalling with  default parameters
Genome_build: GRCh38
Supplementary_files_format_and_content: bed files include MTA1 binding peaks for each sample

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
To generate libraries for high-throughput sequencing, purified DNA fragments were end-repaired, adenylated, ligated to adaptors and PCR amplified for 18 cycles. The PCR products corresponding to 250-450 bps were gel purified, quantified and stored at -80℃ until used for sequencing.For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to illumina NextSeq 500 system for 151 nt pair-end sequencing

tag: morphology


title: PC_44A

description: RNASEQ

tag: mouse strain

value: P. chabaudi AS

value: Light/dark

value: ad libitum


title: SIR3-EBD G2_no_estradiol H3K79me3 ChIP rep. 2

value: G1 (alpha factor) arrest followed by release to G2/M (nocodazole) and addition of ethanol (solvent control) for 3 hours

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc; SIR3-EBD78


title: PC_48A

description: RNASEQ


title: Control 3 C3

source_name: thoracic aorta in untreated SHRs

value: SHR

value: thoracic aorta

value: Male

value: 16 weeks

value: Control


title: chipseq_2nd_input

tag: disease

value: colorectal carcinoma

value: epithelial

value: colon


title: PC_40B

description: RNASEQ

value: blood

value: WT mouse

value: pooling 3 mice


title: Control 1 C1


title: Treated by peptide 2 T2

value: Ganoderma lingzhi oligopeptide


title: Cck_1nM_3

value: Pancreas

tag: cell line

value: 1nM CCK


title: PC_40A

description: RNASEQ

value: P. chabaudi AS

value: Light/dark

value: ad libitum


title: Ins_100µM_1

value: 100µM Insulin


title: SIR3-EBD G1_no_estradiol H3K79me3 ChIP rep. 2

value: G1 (alpha factor) arrest followed by addition of ethanol (solvent control) for 3 hours

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc; SIR3-EBD78


title: chipseq_1st_MTA1


title: Cck_1nM_2


title: chipseq_1st_input


title: Cck_100pM_3

value: 100pM CCK


title: Control 2 C2

value: SHR

value: thoracic aorta

tag: Sex

value: Male

value: 16 weeks

value: Control


title: fclipseq_2nd_IgG

value: colon

value: epithelial

value: colorectal carcinoma


title: PC_36B

description: RNASEQ

value: blood

value: WT mouse

value: pooling 3 mice


title: SIR3-EBD G1_estradiol H3K79me3 ChIP rep. 2

value: G1 (alpha factor) arrest followed by addition of estradiol for 3 hours


title: Cck_1nM_1

value: Pancreas

value: 1nM CCK


title: PC_36A

description: RNASEQ

value: P. chabaudi AS

value: Light/dark

value: ad libitum


title: RNAseq_IV-1-MT

source_name: iPSC-CMs

tag: cell-type

value: iPSC-CMs

tag: day post-differentiation

value: day 40

value: isogenic line of IV-1 to insert LMNA mutation (heterozygous line)


title: PC_32B

description: RNASEQ

tag: malaria strain

tag: knockout


title: RNAseq_IV-1

value: parental line IV-1 (wt/wt)


title: Cck_10nM_3

value: 10nM CCK


title: Cck_10nM_2


title: SIR3-EBD G2_estradiol H3K79me3 ChIP rep. 2

value: G1 (alpha factor) arrest followed by release to G2/M (nocodazole) and addition of estradiol for 3 hours

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc; SIR3-EBD78


title: PC_32A

description: RNASEQ

tag: light condition

tag: feeding


title: RNAseq_III-3-KO

value: isogenic line of III-3 to knockout LMNA wild-type allele


title: Cck_10nM_1

tag: treatment


title: Cck_100nM_3

value: 100nM CCK


title: RNAseq_III-3-MT

value: isogenic line of III-3 to insert LMNA mutation (homozygous line)


title: SIR3-EBD G1_no_estradiol H3K79me3 ChIP rep. 1

tag: strain

value: G1 (alpha factor) arrest followed by addition of ethanol (solvent control) for 3 hours


title: Cck_100nM_2


title: PC_28B

description: RNASEQ

value: blood

value: WT mouse

tag: 1 mouse or pool of 3 mice

value: pooling 3 mice


title: Ins_10µM_2

value: Pancreas

value: 10µM Insulin


title: RNAseq_III-3

value: parental line III-3 (mt/wt)


title: PC_24B

description: RNASEQ

value: P. chabaudi AS

value: Light/dark

value: ad libitum


title: RNAseq_III-3-WT

value: iPSC-CMs

value: day 40

value: isogenic line to III-3 to correct LMNA mutation


title: PC_28A

description: RNASEQ


title: PC_24A

description: RNASEQ


title: SIR3-EBD pre-estradiol H3K79me3 ChIP rep. 1

tag: chip antibody

tag: condition

value: G1 (alpha factor) arrest without estradiol

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc; SIR3-EBD78


title: SIR3-EBD pre-estradiol H3K79me3 ChIP rep. 2

tag: genotype


title: ddm1 rdr6 pol V Rep B

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
Raw fast5 reads were basecalled and demultiplexed using Guppy version 3.1.5+781ed57. Reads were mapped to the Arabidopsis Araport11 genome using Minimap2 (PMID: 29750242). Only primary alignments (~95%) were retained for analysis.
Pinfish pipeline by Oxford Nanopore was used to call de novo transcripts using long reads and default parameters (except a minimum cluster size of 5 was used). Transcripts that originated within genic exons or 5’ UTRs and in the matching orientation were annotated as ‘Gene’ transcripts. Of the remaining transcripts, only those transcripts were annotated as TE transcripts if at least 25% of an exon overlapped with an annotated TE.
Genome_build: TAIR10
Supplementary_files_format_and_content: Two files are provided for each genotype sequenced. First is a transcript association file that links individual transcripts to one or more TEs. Second is a GFF transcript file with the exon structure of each transcript ID found in the transcript association file. The column headers are included in the files.

organism: Arabidopsis thaliana

growth_protocol: Plants were grown under 16-hour day conditions at 22ºC in a growth chamber. All tissues are inflorescence (stage 1-12) immature flower buds.

extract_protocol:
Total RNA was extracted from frozen inflorescence tissue using TriZOL LS protocol (Invitrogen) and enriched for poly(A) mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module.
SQK-PCS108 protocol by Oxford Nanopore was used to construct the library. 50 ng of enriched poly(A) mRNA was used for reverse transcription. 14 cycles of PCR amplification was performed with barcoding adapters as per SQK-PBK004 protocol by Oxford Nanopore. 1D sequencing adapter was added before sequencing on a SpotON flow cell in MinION sequencer. For the higher ddm1/rdr6/pol V rep B, only 13 cycles of amplification was used.
Multiplxed library of 5 genotypes was sequenced in Round 1. For round 2 with higher depth ddm1/rdr6/pol V sample, only 1 barcode was used.

tag: ecotype

value: Columbia

tag: tissue


title: Cck_100nM_1

value: 100nM CCK


title: SIR3-EBD G2_no_estradiol H3K79me3 ChIP rep. 1

value: G1 (alpha factor) arrest followed by release to G2/M (nocodazole) and addition of ethanol (solvent control) for 3 hours


title: sir3∆ sonication input rep. 2

value: Cycling

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc; sir3{delta}


title: PC_20B

description: RNASEQ

tag: mouse strain

value: blood

value: WT mouse

value: pooling 3 mice


title: sir3∆ sonication input rep. 1


title: Cck_1µM_2

value: Pancreas

tag: cell line

value: 1µM CCK


title: ddm1 rdr6 pol V Rep A

source_name: inflorescence (stage 1-12) immature flower buds


title: SIR3-EBD G2_estradiol H3K79me3 ChIP rep. 1

value: G1 (alpha factor) arrest followed by release to G2/M (nocodazole) and addition of estradiol for 3 hours


title: PC_20A

description: RNASEQ

value: P. chabaudi AS

value: Light/dark

value: ad libitum


title: WT sonication input rep. 2

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc


title: PC_16B

description: RNASEQ


title: Cck_1µM_1


title: SIR3-EBD G1_estradiol H3K79me3 ChIP rep. 1

value: G1 (alpha factor) arrest followed by addition of estradiol for 3 hours


title: ddm1 rdr6

value: inflorescence (stage 1-12) immature flower buds


title: PC_16A

description: RNASEQ


title: WT sonication input rep. 1


title: ddm1 pol V

value: Columbia


title: Cck_Ct3

value: No treatment


title: ddm1


title: sir3∆ sonication Sir4-myc ChIP rep. 2

value: Pierce Anti-c-myc magnetic beads (Thermo Fisher Scientific 88843, lot # TD260777)


title: Cck_100pM_1

value: 100pM CCK


title: Cck_Ct2


title: PC_08B

description: RNASEQ


title: sir3∆ sonication Sir4-myc ChIP rep. 1

value: Cycling

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc; sir3{delta}


title: PC_08A

description: RNASEQ

value: blood

value: WT mouse


title: wt Col

extract_protocol:
Total RNA was extracted from frozen inflorescence tissue using TriZOL protocol (Invitrogen) and enriched for poly(A) mRNA using NEBNext Poly(A) mRNA Magnetic Isolation Module.
SQK-PCS108 protocol by Oxford Nanopore was used to construct the library. 50 ng of enriched poly(A) mRNA was used for reverse transcription. 14 cycles of PCR amplification was performed with barcoding adapters as per SQK-PBK004 protocol by Oxford Nanopore. 1D sequencing adapter was added before sequencing on a SpotON flow cell in MinION sequencer. For the higher ddm1/rdr6/pol V rep B, only 13 cycles of amplification was used.
Multiplxed library of 5 genotypes was sequenced in Round 1. For round 2 with higher depth ddm1/rdr6/pol V sample, only 1 barcode was used.


title: HFD_1

city: Wuxi

first: Jun

state: Jiangsu

address: 9 Shanshi East road

institute: Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences

data_processing:
RNA-Seq :  Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) including the Q20, Q30 and GC-content of the clean data. All downstream analyses were based on clean data of high quality. De novo assembly of the transcriptome was performed with Trinity 2.4.0. Trinity groups transcripts into clusters based on shared sequence content. Such a transcript cluster is very loosely referred to as a "gene". The longest transcript in the cluster was chosen as the 'gene' sequence (aka Unigene).After splicing to obtain genes, the protein sequences in five public databases (Swiss-Prot, NR, KEGG, KOG, and Pfam) were aligned and the threshold e<=1e-10 was obtained. Functional annotation and pathway analysis were performed by sequence similarity. The measurement was united by the fragment per kilobase of exon per million fragments mapped (FPKM). The differentially expressed Unigenes were selected with log2 (fold change) ≥1 or log2 (fold change) ≤-1 and with statistical significance (p value < 0.05) and FPKM≥10.
miRNA-Seq : The raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences,Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA,snoRNA) and repeats. Subsequently, unique sequences with length in 18~ 26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3'and 5'ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (<=12); (2) number of base pairs in the stem region of the predicted hairpin (>=16); (3) cutoff of free energy (kCal/mol <=-15); (4) length of hairpin (up and down stems + terminal loop >=50); (5) length of hairpin loop (<=20); (6) number of nucleotides in one bulge in mature region (<=8); (7) number of biased errors in one bulge in mature region(<=4); (8) number of biased bulges in mature region (<=2); (9) number of errors in mature region (<=7); (10) number of base pairs in the mature region of the predicted hairpin (>=12); (11) percent of mature in stem (>=80).
Genome_build: de novo assembly; FASTA file with transcript sequences is available on the series record.
Supplementary_files_format_and_content: tab-delimited text files include gene or miRNA expression profiles for each Sample

organism: Tachysurus fulvidraco x Tachysurus vachelli

source_name: Liver

growth_protocol: The experiment was conducted in the water circulation system. The flow rate was about 5 L/min, and the feeding rate per day was 1%-3%. Moderate adjustment was made according to the feeding conditions. The feeding time were 7:30, 12:00 and 16:30. Experimental water is tap water after 3d aeration. The water were changed by 1/3 every 5 days. Continuous aeration was supplied during the entire experiment. Dissolved oxygen was >5.0 mg/L, pH 7.3-7.8, ammonia nitrogen were 0.1-0.2 mg/L, nitrate were 0.05-0.20 mg/L, water temperature were 27-28°C.

extract_protocol:
The liver tissues were taken and frozen in liquid nitrogen then placed in a refrigerator at -80°C. Total RNA was extracted from the samples according to the instructions provided in the Trizol reagent kit.About 10 µg total RNA from each mixed group was selected to construct sequencing libraries.
Libraries of RNA and miRNA were prepared for sequencing using standard Illumina protocols

treatment_protocol: The normal fat diet (NFD) and the high fat diet (HFD) were set according to experimental requirements.

value: Liver

tag: developmental stage

value: juvenile

value: High fat diet for 60 days


title: WT1

city: Chatuchak

first: Piyada

last: Juntawong

state: Bangkok

address: 50 Ngamwongwan rd.

department: Genetics

country: Thailand

institute: Kasetsart University

data_processing:
The FASTQ files were aligned to the reference transcriptome using TopHat2 software
A binary format of sequence alignment files (BAM) was generated and used to create read count tables by the HTseq python library
Differentially-expressed genes were calculated using the edgeR program with an FDR cutoff of < 0.05
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab delimited file contain raw read count values

source_name: 10 d.o whole seedlings

growth_protocol: A. thaliana seeds were surface sterilized, stratified at 4°C for 48 h and plated on 0.5x solid Murashige and Skoog (MS) medium (0.215% (w/v) MS salts containing 1% (w/v) agar, pH 5.7) in 20‐mm2 dishes. Growth was in a vertical orientation in a growth room (16 h of approximately 50 μE s−1 m−2 light and 8 h of dark at 23°C).

extract_protocol:
Total RNA samples were extracted by TriZOL and subjected to DNase treatment and RNA cleanup using an RNA-mini kit (Qiagen)
Three μg of total RNAs was used to generate a sequencing library using an Illumina® TruSeqTM RNA Sample Preparation Kit v2.

treatment_protocol: Seedlings were collected at the end of the 16-h light cycle.

tag: line

value: ecotype Col-0

value: Aerobic

tag: replicates

value: replicate 1


title: Cck_1µM_3

value: Pancreas

value: 1µM CCK


title: Cck_Ct1


title: PC_12A

description: RNASEQ

data_processing:
Sequencing libraries were constructed using the TruSeq RNA Sample preparation protocol (Illumina). RNA-sequencing of libraries was performed on the NextSeq 550 (Illumina) with 75 bp reads, according to the manufacturer’s instructions, by the UTSW McDermott Next Generation Sequencing Core. Read quality was assessed using the FASTQC quality control tool. Reads were mapped with STAR (with parameters:--runMode alignReads --genomeDir genomefolder --sjdbGTFfile gtf --readFilesIn sample_trim.gz --readFilesCommand zcat --outFileNamePrefix sample --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMmapqUnique 255 --alignSJoverhangMin 10 --alignSJDBoverhangMin 1 --alignIntronMax 1000000 --outFilterType BySJout --outFilterMultimapScoreRange 0 --outFilterMultimapNmax 10 --outFilterMismatchNmax 3 --twopassMode Basic --quantMode GeneCounts) following Cutadapt trimming (with parameters: -g AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 30) to the following genomes: PlasmoDB-31_Pchabaudichabaudi from www.PlasmoDB.org and M14 GENCODE version of mouse genome from www.gencodegenes.org. An average of 57% of the uniquely mapped reads mapped to the parasite genome. Raw reads were quantified using featureCounts tool from Rsubread package followed by RPKM calculation using in-house scripts. Downstream bioinformatic analysis after RPKM calculations was performed in R environment. Multidimensional scaling analysis was performed by plotMDS from limma package (50). Hierarchical clustering and heatmaps were obtain for each dataset by reordering of the timepoints according to gene expression using function heatmap.2 from the gplots package. Both hierarchical clustering analysis and heatmaps of Spearman correlations were performed on centered log2-transformed RPKM values. Plots were generated with ggplot2 package.
Genome_build: M14 From GENCODE; Plasmodium chabaudi chabaudi release 31 from plasmodb.org

source_name: P chabaudi infected blood

extract_protocol:
Blood was collected by cardiac puncture into 1.5mL of PBS, spin at 3,000 rpm for 2 min, added TRIzol LS and snap frozen
RNA was extracted using Trizol LS reagent according to manufactor's instructions.
mRNA-seq libraries were prepared using the TruSeq RNA Library Preparation Kit (Illumina) according to the manufacturer's instructions.

tag: malaria strain

value: P. chabaudi AS

value: Light/dark

value: ad libitum

value: pooling 3 mice


title: D4_C2

city: Bethesda

first: Megan

middle: Elizabeth

last: Roegner

state: MD

address: 10 Center Drive, RM 8N316

department: NIDDK

institute: NIH

data_processing:
Reads trimmed to 134 to 141bp using Trimmomatic.
Reads quality assessed using FASTQC and reads below phred 27 removed
Assembly by Trinity version 2.2.0
Annotation by Trinotate pipeline v3.1.1
Libraries mapped to reference transcriptome via RSEM and Bowtie2 alignment
Differential gene expression determined via Bioconductor R package DEseq2
Genome_build: De Novo assembly
Supplementary_files_format_and_content:
text file of de novo transcriptome.  All genes and sequences.
FPKM data for each gene in each sample; differential gene expression data from DEseq2

organism: Callinectes sapidus

source_name: Pre-molt Y-organ

growth_protocol: Blue crabs were collected and staged from fishing vendors in Wilmington, NC

extract_protocol:
Y-organs were dissected from crabs and preserved in RNA later.  RNA was extracted using Trizol reagent protocol and quality determined by bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: molt stage

value: Pre-molt D3

value: Y-organs


title: HFD_3


title: NFD_3

value: Normal fat diet for 60 days


title: WT2

value: replicate 2


title: HFD_2


title: WT sonication Sir4-myc ChIP rep. 1

value: Pierce Anti-c-myc magnetic beads (Thermo Fisher Scientific 88843, lot # TD260777)

value: Cycling

value: mat{delta} hml{delta}::HML* bar1{delta} SIR4-13xMyc


title: E2CL32

value: transgenics 35S:MC-JcERFVII2 line 3 (ecotype Col-0)


title: E2AL12

value: transgenics 35S:MA-JcERFVII2 line 1 (ecotype Col-0)


title: WT sonication Sir4-myc ChIP rep. 2


title: E2CL31

value: Aerobic


title: PC_00B

description: RNASEQ

value: blood

tag: knockout

value: WT mouse

tag: light condition


title: PC_00A

description: RNASEQ

tag: feeding


title: Replicate_2_24HPI

status: Public on Jul 16 2020

city: Wuerzburg

first: Thomas

last: Rudel

state: Bavaria

address: Am Hubland

department: Chair of Microbiology

institute: University of Wuerzburg

data_processing:
Fastq files were generated using Illuminas base calling software GenerateFASTQ v1.1.0.64 and overall sequencing quality was analyzed using the FastQC script.
For RNA-seq, reads were aligned to the human genome (hg19) using Tophat v2.1.1 (Kim et al., 2013) and Bowtie2 v2.3.2 (Langmead et al., 2012) using the parameters  –n 1 -- and samples were normalized to the number of mapped reads in the smallest sample.
For gene expression analysis, reads per gene (Ensembl gene database) were counted with the “summarizeOverlaps” function from the R package “GenomicAlignments” using the “union”-mode and non- or weakly expressed genes were removed (mean read count over all samples <1).
Genome_build: hg19
Supplementary_files_format_and_content: Annotated_Table_of_Counts

source_name: HUVECs

extract_protocol:
RNA extraction was performed with the miRNeasy Mini kit (Qiagen) according to manufacturer’s instruction and using in-column DNase digestion.
RNA quality was assessed employing a Fragment Analyzer (Agilent) and directional libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s instructions.

tag: treatment (4-oht or etoh)

value: 24 hour Ct infection


title: PC_12B

description: RNASEQ

value: P. chabaudi AS

tag: 1 mouse or pool of 3 mice


title: PC_04B

description: RNASEQ

value: Light/dark


title: I_C2

source_name: Intermolt Y-organ

value: Intermolt


title: Replicate_1_36HPI

value: 36 hour Ct infection


title: PC_04A

description: RNASEQ

value: ad libitum

value: pooling 3 mice


title: Replicate_2_12HPI

value: 12 hour Ct infection


title: Replicate_1_uninfected


title: Replicate_1_24HPI


title: I_C3

value: Y-organs


title: Replicate_2_uninfected


title: Replicate_1_12HPI


title: NFD_2

value: Liver

value: juvenile

tag: treatment

value: Normal fat diet for 60 days


title: NFD_1


title: HCV infected cells, replicate 2

city: Barcelona

first: Juana

last: Díez

state: Barcelona

address: Carrer del Dr. Aiguader 88

department: Department of Experimental and Health Sciences

country: Spain

institute: Universitat Pompeu Fabra

description:
replicate 2
HCV2

data_processing:
An ensemble of three published methods was used to independently detect circRNAs in every sequenced sample. The detection methods utilized were CIRI2 v2.0.6 based on BWA-MEM (v0.7.16a, parameters: -T 19), find_circ v1.2 based on Bowtie2 (v2.2.9, parameters: --score-min=C,-15,0 –very-sensitive) and CIRCexplorer v1.1.10 based on STAR (v2.5.2b, parameters: --chimSegmentMin 10). All detection programs were executed with default settings using an hg19 genome build and the RefSeq annotation obtained from UCSC Genome Browser (http://genome.ucsc.edu/). The resulting candidate lists were then merged across all samples using custom Python scripts to create a comprehensive circRNA annotation prior to quantification using SRCP v1.2.
Differential circRNA production was tested using limma-voom v3.38.3 utilizing voomWithQualityWeights() and an interaction term while accounting for possible batch effects during handling. Furthermore, as read counts for circular junctions are sparse in samples without RNAse R treatment and thus variability between replicates can be quite high, we substituted the library sizes calculated from the count matrices of circular and linear junctions with library sizes based on full mRNA quantifications performed by kallisto (v0.43.0), which better reflect the actual differences in sequencing depth between samples (lib.size parameter in DGEList). Thus, after generating an index comprising the GENCODE v24 annotation (hg38 genome build) as well as the HCV H77C/JFH1 (EU363761.1), Chikungunya virus LR2006/OPY1 (DQ443544.2) and Dengue virus type 2 (AF038403.1) genome sequences, we ran kallisto in quantification mode (parameters: --rf-stranded -b 100) and imported the resulting counts via the tximport R package (v1.10.1) prior to limma-voom testing.
Genome_build: hg19
Supplementary_files_format_and_content: The file kallisto_mRNA_hg38.tsv contains kallisto estimates for gene-level read counts, whereas raw_counts_circular_hg19.tsv and raw_counts_linear_hg19.tsv contain raw read counts for the identified putative circRNA junctions and their linear counterparts. Each column represents one sample in lexicographical order.

source_name: whole cell

growth_protocol: Huh7 cells were maintained in Dulbecco's modified Eagle's medium (DMEM, Invitrogen, Carlsbad, CA), supplemented with 10% heat inactivated fetal bovine serum (FBS) and 10% non-essential amino acids. Cells were grown in an incubator with 5% CO2 at 37 ºC.

extract_protocol:
Total RNA was extracted with TRIzol reagent. After TURBO DNAse treatment of 30 min, a new phenol:chloroform extraction was performed and the extracted RNA was subsequently used to construct the libraries.
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit  (ref. RS-122-2301) according to the manufacturer's protocol starting with 0,5 µg of total RNA for ribosomal RNA depletion. Libraries were analyzed with the Agilent Bioanalyzer using a DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior to sequencing with 2x75 cycles of High output paired-end reads on Illumina's NextSeq with v4 sequencing chemistry.

treatment_protocol: Mock infected cells were compared to cell infected with HCV for 48 hours

tag: infection status

value: HCV infection

tag: time point


title: HCV infected cells, replicate 3

description:
replicate 3
HCV3


title: D2_C1

value: Pre-molt D2


title: HCV infected cells, replicate 1

description:
replicate 1
HCV1


title: Replicate_2_36HPI


title: mock infected cells (HCV), replicate 2

description:
replicate 2
Ctl-HCV2

value: mock infection (HCV)


title: E2AL11

value: transgenics 35S:MA-JcERFVII2 line 1 (ecotype Col-0)

value: Aerobic

value: replicate 1


title: mock infected cells (DV), replicate 3

description:
replicate 3
Ctl-DV3

value: mock infection (DV)


title: mock infected cells (HCV), replicate 1

description:
replicate 1
Ctl-HCV1


title: mock infected cells (DV), replicate 1

description:
replicate 1
Ctl-DV1


title: mock infected cells (CHIKV), replicate 2

description:
replicate 2
Ctl-CHIKV2

value: mock infection (CHIKV)


title: mock infected cells (CHIKV), replicate 1

description:
replicate 1
Ctl-CHIKV1


title: mock infected cells (CHIKV), replicate 3

description:
replicate 3
Ctl-CHIKV3


title: 281M1_GFP+

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

description: GFPposi.bed

data_processing:
Basecalls performed by Illumina NextSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina NextSeq
Sequence fragments were mapped to the human reference genome using BWA mem.
HIV-1 integration sites were called using the custom script.
Genome_build: hg19
Supplementary_files_format_and_content: bed-formatted files explaining HIV-1 integration sites

source_name: Splenic human CD4-positive T cells

growth_protocol: HIV1-GFP was intraperitoneally inoculated into 13 humanized mice.

extract_protocol:
Splenic GFP-positive and GFP-negative cells were obtained from 13 infected mice and DNA was extracted by using QIAamp DNA blood mini kit (Qiagen).
Up to 150 ng genomic DNA was sheared by sonication with Picoruptor (Diagenode) instrument to a size of 300-400 bp in length. DNA end repair and addition of 3’ adenosine was performed with NEBNext Ultra II End Repair/dA-Tailing Module (New England Biolabs). Linker was then ligated to the ends using NEBNext Ultra II Ligation Module (New England Biolabs). The ligated product was amplified with primers targeting the 3’-LTR on one end and the linker on the other end. The following thermal protocol was used for both the first and second PCR: 96°C 30sec (1 cycle); 94°C 5sec, 72°C 1min (7 cycles); 94°C 5 sec, 68°C 1 min (13 cycles); 68°C 9 min (1 cycle); hold 4°C until user stops. PCR amplicons were cleaned and pooled to form a library which was then quantified using primers for Illumina P5 and P7.

treatment_protocol: The sorted GFP-negative cells were maintained in RPMI 1640 (Sigma) containing FCS and antibiotics. To induce viral activation, these cells were stimulated with with 50 ng/ml PMA (SIGMA P-8139) and 1 μM Ionomycin (SIGMA I-0634). To inhibit new viral infection, 10 nM Nelfinavir (Sigma PZ0013) was supplied. After 48 hours post-stimulation, GFP-positive and GFP-negative cells were sorted.

tag: model

value: HIV1-GFP infected humanized mouse

value: 2 weeks post-infection

tag: mouse id

tag: cell type

value: GFP+


title: 281M1_GFP-

description: GFPnega.bed

value: GFP-


title: mock infected cells (HCV), replicate 3

description:
replicate 3
Ctl-HCV3

tag: cell line


title: 272M3_GFP+

description: GFPposi.bed


title: 268F2_GFP-

description: GFPnega.bed


title: 268F2_GFP+

description: GFPposi.bed


title: 267F2_GFP-

description: GFPnega.bed


title: 357F3_GFP-_GFP-


title: 347M2_GFP-_GFP-


title: 347F4_GFP-_GFP-


title: 337F2_GFP-_GFP-


title: 337F1_GFP-_GFP-


title: 357F3_GFP-_GFP+


title: 337F3_GFP-_GFP-


title: 337F2_GFP-_GFP+


title: 347F4_GFP-_GFP+


title: 347M2_GFP-_GFP+


title: 337F3_GFP-_GFP+


title: mock infected cells (DV), replicate 2

description:
replicate 2
Ctl-DV2


title: 337F1_GFP-_GFP+


title: 337M2_GFP-

description: GFPnega.bed


title: 347M2_GFP-

description: GFPnega.bed


title: 357F3_GFP-

description: GFPnega.bed


title: 347F4_GFP-

description: GFPnega.bed


title: 337F2_GFP-

description: GFPnega.bed


title: 268F1_GFP-

description: GFPnega.bed


title: 337F1_GFP-

description: GFPnega.bed


title: 268F1_GFP+

description: GFPposi.bed


title: 337F3_GFP-

description: GFPnega.bed


title: 272M3_GFP-

description: GFPnega.bed


title: 357F3_GFP+

description: GFPposi.bed


title: 267F2_GFP+

description: GFPposi.bed


title: 337M2_GFP+

description: GFPposi.bed


title: 347M2_GFP+

description: GFPposi.bed


title: 337F4_GFP+

description: GFPposi.bed


title: 347F4_GFP+

description: GFPposi.bed


title: 337F3_GFP+

description: GFPposi.bed


title: 337F2_GFP+

description: GFPposi.bed


title: 337F1_GFP+

description: GFPposi.bed


title: 337F4_GFP-

description: GFPnega.bed


title: TB_DM_Indonesia (RSEQ533)

city: London

first: Clare

last: Eckold

state: London

address: 10 Logan Place

institute: (None)

data_processing:
Alignment - STAR, version 2.5.1b
Quantification - HTseq count, version 0.6.1, f=bam, r=name, s=rev, m=union, i=gene id
Normalization - DESeq2, version 1.12.4
Genome_build: Human_g1k_v37
Supplementary_files_format_and_content: txt - read count for each ensembl gene id, un-normalized, un-filtered

source_name: Whole Blood

extract_protocol:
Whole blood stored in PAXgene Blood RNA collection tubes and extracted using the PAXgene blood miRNA kit (Qiagen)
Bioscientific NEXTflex-Rapid-Directional mRNA-seq sample preparation (Bioscientific)

tag: patient id

tag: disease state (disease_category)

value: Indonesia

tag: tissue

value: whole blood


title: TB_IH_South_Africa (RSEQ524)


title: TB_only_Peru (RSEQ525)

value: Peru


title: TB_only_Indonesia (RSEQ531)


title: Healthy_Control_South_Africa (RSEQ513)


title: DM_only_South_Africa (RSEQ523)


title: TB_only_Romania (RSEQ521)

value: Romania


title: Healthy_Control_South_Africa (RSEQ528)


title: DM_only_Romania (RSEQ530)


title: DM_only_Romania (RSEQ527)


title: DM_only_Romania (RSEQ509)


title: TB_only_Romania (RSEQ511)


title: Healthy_Control_South_Africa (RSEQ512)


title: TB_DM_Peru (RSEQ516)


title: TB_only_Indonesia (RSEQ514)


title: Healthy_Control_South_Africa (RSEQ510)


title: IH_South_Africa (RSEQ517)

value: IH


title: DM_only_South_Africa (RSEQ508)


title: TB_only_Peru (RSEQ506)


title: TB_IH_Indonesia (RSEQ499)


title: TB_IH_South_Africa (RSEQ504)


title: TB_only_South_Africa (RSEQ494)


title: Healthy_Control_South_Africa (RSEQ490)


title: DM_only_South_Africa (RSEQ484)


title: TB_DM_Romania (RSEQ486)


title: Healthy_Control_South_Africa (RSEQ529)


title: TB_only_Peru (RSEQ520)


title: TB_only_Indonesia (RSEQ487)


title: TB_IH_South_Africa (RSEQ492)


title: TB_DM_Indonesia (RSEQ483)


title: DM_only_South_Africa (RSEQ475)


title: TB_DM_Romania (RSEQ478)


title: TB_IH_South_Africa (RSEQ476)


title: DM_only_Romania (RSEQ479)


title: TB_only_Indonesia (RSEQ465)


title: Healthy_Control_Romania (RSEQ468)


title: TB_DM_South_Africa (RSEQ473)


title: TB_DM_South_Africa (RSEQ467)


title: TB_only_South_Africa (RSEQ436)


title: TB_only_Romania (RSEQ440)


title: TB_DM_South_Africa (RSEQ446)


title: DM_only_Romania (RSEQ433)


title: DM_only_South_Africa (RSEQ439)


title: TB_DM_Indonesia (RSEQ430)


title: TB_IH_Peru (RSEQ460_p1)


title: TB_IH_Peru (RSEQ455)


title: DM_only_Romania (RSEQ459)


title: TB_DM_South_Africa (RSEQ419)


title: TB_only_Romania (RSEQ449)


title: TB_DM_Indonesia (RSEQ438)


title: TB_only_Indonesia (RSEQ464)


title: TB_DM_Indonesia (RSEQ422)


title: DM_only_South_Africa (RSEQ445)


title: TB_IH_South_Africa (RSEQ442)


title: TB_DM_Indonesia (RSEQ416)


title: TB_DM_Indonesia (RSEQ458)


title: IH_South_Africa (RSEQ421)


title: TB_only_Romania (RSEQ451)


title: TB_IH_Peru (RSEQ435)


title: TB_IH_Peru (RSEQ413)


title: Healthy_Control_South_Africa (RSEQ418)


title: TB_IH_South_Africa (RSEQ406)


title: DM_only_South_Africa (RSEQ408)


title: DM_only_Romania (RSEQ407)


title: TB_DM_Romania (RSEQ410)


title: DM_only_Romania (RSEQ403)


title: TB_IH_Romania (RSEQ401)


title: DM_only_Romania (RSEQ402)


title: Healthy_Control_South_Africa (RSEQ390)


title: TB_DM_Indonesia (RSEQ371)


title: DM_only_South_Africa (RSEQ399)


title: TB_IH_South_Africa (RSEQ389)


title: Healthy_Control_South_Africa (RSEQ378)


title: TB_only_South_Africa (RSEQ396)


title: TB_DM_Romania (RSEQ400)


title: TB_DM_Peru (RSEQ382)


title: TB_DM_Indonesia (RSEQ393)


title: TB_only_Indonesia (RSEQ370)


title: TB_IH_Peru (RSEQ367)


title: TB_only_Peru (RSEQ388)


title: TB_only_South_Africa (RSEQ385)


title: DM_only_South_Africa (RSEQ373)


title: TB_DM_Romania (RSEQ379)


title: TB_DM_Romania (RSEQ366)


title: TB_DM_Indonesia (RSEQ363)


title: IH_Romania (RSEQ362)


title: TB_IH_South_Africa (RSEQ409)


title: DM_only_South_Africa (RSEQ361)


title: TB_only_South_Africa (RSEQ353)


title: Healthy_Control_Romania (RSEQ358)


title: DM_only_South_Africa (RSEQ348)


title: Healthy_Control_South_Africa (RSEQ372)


title: Healthy_Control_Romania (RSEQ392)


title: IH_Romania (RSEQ342)


title: TB_only_Romania (RSEQ354)


title: TB_IH_South_Africa (RSEQ341_p1)


title: TB_IH_South_Africa (RSEQ368)


title: DM_only_South_Africa (RSEQ344)


title: Healthy_Control_Romania (RSEQ330)


title: DM_only_Romania (RSEQ329)


title: TB_only_Peru (RSEQ331)


title: TB_IH_South_Africa (RSEQ336)


title: DM_only_Romania (RSEQ332)


title: TB_only_Peru (RSEQ335)


title: TB_IH_South_Africa (RSEQ320)


title: Healthy_Control_South_Africa (RSEQ316)


title: DM_only_South_Africa (RSEQ340)


title: TB_DM_Peru (RSEQ327)


title: TB_only_Indonesia (RSEQ312)


title: IH_South_Africa (RSEQ317)


title: TB_only_South_Africa (RSEQ326)


title: TB_IH_Romania (RSEQ304)


title: TB_IH_South_Africa (RSEQ301)


title: DM_only_South_Africa (RSEQ302)


title: TB_DM_South_Africa (RSEQ295)


title: TB_DM_South_Africa (RSEQ300)


title: TB_only_Indonesia (RSEQ288)


title: Healthy_Control_South_Africa (RSEQ284)


title: TB_DM_South_Africa (RSEQ328)


title: TB_DM_Indonesia (RSEQ287)


title: TB_only_Indonesia (RSEQ278)


title: TB_only_South_Africa (RSEQ299)


title: TB_only_Indonesia (RSEQ285)


title: TB_DM_Peru (RSEQ276)


title: TB_DM_Romania (RSEQ265)


title: TB_IH_Peru (RSEQ356)


title: DM_only_South_Africa (RSEQ269)


title: DM_only_South_Africa (RSEQ279)


title: TB_only_Indonesia (RSEQ266)


title: DM_only_South_Africa (RSEQ283)


title: TB_DM_Romania (RSEQ264)


title: TB_DM_Romania (RSEQ259)


title: TB_IH_Romania (RSEQ268)


title: Healthy_Control_Romania (RSEQ262)


title: DM_only_South_Africa (RSEQ249)


title: DM_only_South_Africa (RSEQ250)


title: TB_DM_Peru (RSEQ247)


title: DM_only_South_Africa (RSEQ255)


title: DM_only_South_Africa (RSEQ258)


title: DM_only_Romania (RSEQ254)


title: TB_DM_Romania (RSEQ253)


title: TB_DM_Peru (RSEQ244)


title: TB_only_Romania (RSEQ238)


title: Healthy_Control_South_Africa (RSEQ236)


title: DM_only_South_Africa (RSEQ235)


title: TB_DM_Indonesia (RSEQ237)


title: DM_only_South_Africa (RSEQ232)


title: TB_IH_Romania (RSEQ228)


title: DM_only_Romania (RSEQ231)


title: TB_DM_South_Africa (RSEQ229)


title: TB_DM_Indonesia (RSEQ225)


title: TB_DM_South_Africa (RSEQ220)


title: Healthy_Control_Romania (RSEQ222)


title: Healthy_Control_Romania (RSEQ217)


title: TB_IH_Romania (RSEQ219)


title: Healthy_Control_Romania (RSEQ216)


title: TB_IH_Peru (RSEQ218)


title: IH_Romania (RSEQ203)


title: Healthy_Control_South_Africa (RSEQ215)


title: TB_DM_Indonesia (RSEQ207)


title: DM_only_Romania (RSEQ200)


title: Healthy_Control_South_Africa (RSEQ186)


title: DM_only_South_Africa (RSEQ185)


title: DM_only_Romania (RSEQ194)


title: DM_only_South_Africa (RSEQ192)


title: TB_IH_Peru (RSEQ183)


title: TB_DM_Romania (RSEQ182)


title: TB_IH_South_Africa (RSEQ180)


title: Healthy_Control_South_Africa (RSEQ230)


title: Healthy_Control_South_Africa (RSEQ240)


title: TB_only_Peru (RSEQ174)


title: IH_South_Africa (RSEQ173)


title: DM_only_South_Africa (RSEQ175)


title: TB_only_South_Africa (RSEQ176)


title: DM_only_South_Africa (RSEQ170)


title: TB_IH_South_Africa (RSEQ167)


title: TB_DM_Indonesia (RSEQ199)


title: TB_only_Peru (RSEQ158)


title: Healthy_Control_South_Africa (RSEQ161)


title: TB_DM_Indonesia (RSEQ166)


title: DM_only_Romania (RSEQ162)


title: IH_South_Africa (RSEQ163)


title: Healthy_Control_Romania (RSEQ154)


title: TB_DM_Romania (RSEQ198)


title: Healthy_Control_Romania (RSEQ152)


title: DM_only_South_Africa (RSEQ148)


title: TB_DM_Peru (RSEQ151)


title: TB_only_South_Africa (RSEQ134)


title: TB_DM_Peru (RSEQ136)


title: TB_DM_Indonesia (RSEQ145)


title: TB_IH_Peru (RSEQ143)


title: Healthy_Control_South_Africa (RSEQ149)


title: TB_DM_South_Africa (RSEQ133)


title: TB_DM_Romania (RSEQ130)


title: TB_only_Romania (RSEQ131)


title: Healthy_Control_Romania (RSEQ140)


title: TB_DM_Peru (RSEQ128)


title: TB_IH_Romania (RSEQ156)


title: IH_Romania (RSEQ153)


title: DM_only_South_Africa (RSEQ101)


title: IH_South_Africa (RSEQ106)


title: Healthy_Control_South_Africa (RSEQ116)


title: Healthy_Control_South_Africa (RSEQ090)


title: Healthy_Control_Romania (RSEQ093)


title: DM_only_Romania (RSEQ085)


title: TB_only_South_Africa (RSEQ119)


title: TB_only_Romania (RSEQ083)


title: TB_IH_Romania (RSEQ098)


title: TB_DM_South_Africa (RSEQ092)


title: TB_only_Romania (RSEQ077)


title: Healthy_Control_South_Africa (RSEQ075)


title: TB_IH_South_Africa (RSEQ074)


title: TB_IH_Indonesia (RSEQ073)


title: TB_DM_Romania (RSEQ067)


title: TB_IH_Indonesia (RSEQ066)


title: Healthy_Control_South_Africa (RSEQ065)


title: TB_DM_Indonesia (RSEQ112)


title: TB_DM_Peru (RSEQ057)


title: DM_only_South_Africa (RSEQ068)


title: TB_only_South_Africa (RSEQ060)


title: TB_IH_Romania (RSEQ071)


title: TB_IH_South_Africa (RSEQ047)


title: TB_DM_Peru (RSEQ051)


title: DM_only_Romania (RSEQ088)


title: TB_IH_South_Africa (RSEQ053)


title: Healthy_Control_South_Africa (RSEQ045)


title: TB_only_Peru (RSEQ041)


title: DM_only_South_Africa (RSEQ032)


title: TB_DM_South_Africa (RSEQ081)


title: TB_only_Indonesia (RSEQ046)


title: TB_DM_South_Africa (RSEQ038)


title: TB_only_Peru (RSEQ037)


title: DM_only_South_Africa (RSEQ033)


title: TB_IH_South_Africa (RSEQ030)


title: TB_IH_Indonesia (RSEQ029)


title: TB_IH_Indonesia (RSEQ070)


title: TB_IH_Romania (RSEQ034)


title: TB_DM_South_Africa (RSEQ020)


title: TB_IH_Romania (RSEQ017)


title: DM_only_South_Africa (RSEQ024)


title: TB_only_Indonesia (RSEQ027)


title: TB_DM_South_Africa (RSEQ015)


title: TB_DM_Peru (RSEQ012)


title: TB_IH_South_Africa (RSEQ006)


title: DM_only_Romania (RSEQ009)


title: TB_only_Indonesia (RSEQ004)


title: TB_DM_Romania (RSEQ002)


title: Tet2 knock-in ESC 5hmC-RIP Input repl 1

city: Gosselies

first: Martin

last: Bizet

address: Rue Adrienne Bolland, 8

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
The raw sequencing data were first analyzed using FastQC. Low complexity reads were removed using AfterQC tool with default parameters. Further, to get rid of reads originating from rRNA or tRNA, the reads were mapped to mouse tRNA and rRNA sequences using bowtie2. The rRNA and tRNA sequences were downloaded from https://www.ncbi.nlm.nih.gov/nuccore using "Mus musculus"[Organism] AND (biomol_rrna[PROP] OR biomol_trna[PROP] as search parameters. Reads that were unmapped to tRNA and rRNA sequences were then further processed using Trimmomatic with default parameters to remove adapter sequences. The resulting fastq data was again analyzed using FastQC to ensure no further processing is needed.
Preprocessed reads were then mapped against the mouse reference genome using STAR algorithm with RefSeq reference transcriptome (download on March 2012). 5hmC-enriched regions (peaks) were identified by applying MACS2 peak-calling tool on immunoprecipitated (IP) samples using their input counterpart for estimating background noise (q-value < 0.05). Of note, the expected genome size MACS2 parameter was set as the sum of all transcripts length including exons and introns (counting a single time regions shared by several transcripts) and the summits positions were identified using --call-summits MACS2 option. To avoid identification of extremely large enriched regions, peaks were, then, resized to 100bp from both size of the identified summit.
Genome_build: mm9
Supplementary_files_format_and_content: Peak positions (100bp around both side of the summits) in bed format

organism: Mus musculus

source_name: Embryonic Stem Cells

growth_protocol: Mouse ESCs (WT, KI or TKO) were grown under standard culture conditions. Briefly, cells were cultured on 0.1% gelatin-coated tissue culture plates in high-glucose DMEM medium containing 15% FBS, 1mM sodium pyruvate, 1% nonessential amino acids, 1% glutaMAX, 100 U/ml penicillin, 100 ug/ml streptomycin, 0.1 mM b-mercaptoethanol and 1000 unit/ml recombinant mouse leukemia inhibitory factor.

extract_protocol:
Total RNA from WT ESCs, TKO ESCs and WT EBs were extracted with either the RNeasy Mini or Maxi kit or TRIzol according to the manufacturer's instructions. Genomic DNA was eliminated by DNase treatment.
hMeRIP-seq: The procedure was performed in ESCs as described in Dominissi et al., 2012. Briefly, 1 mg of total RNA was sonicated to an average size of 200-300bp. RNA was then precipitated in ethanol, resuspended in RNase-free ddH2O and the fragmentation efficiency was checked on a Bioanalyzer RNA chip. For immunoprecipitation, RNA fragments were denatured by heating at 70  C for 5 min, chilled on ice for 5 min, then incubated overnight at 4  C with or without 12.5 ug of anti-5hmC antibody, in freshly prepared 1X IP buffer (50 mM Tris-HCl pH=7.4, 750 mM NaCl and 0.5% Igepal CA-630, RNasin 400 U/ml and RVC 2 mM) supplemented with protease inhibitors. Samples were then incubated at 4  C for 2.5h with 60 ul equilibrated Dynabeads Protein G, washed three times for 5 min with 1 ml IP buffer, and eluted by addition of 1 ml TriPure Reagent followed by RNA extraction according to the manufacturer's instructions.
Library preparation was performed as described in Delatte et al., 2016. Briefly, 5 to 10 ng dsDNA was subjected to 5' and 3' protruding end repair, followed by the addition of non-templated adenines to the 3' ends of the blunted DNA fragments, which allows ligation of Illumina multiplex adapters. The DNA fragments were then size selected so as to remove all unligated adapters and to sequence 200-300-bp fragments. 18 cycles of PCR were carried out to amplify the library. DNA was quantified by fluorometry with the Qubit 2.0 and DNA integrity was assessed with a 2100 bioanalyzer. 6 pM of DNA library spiked with 1% PhiX viral DNA was clustered on cBot and then sequenced.

treatment_protocol: (EB only) Embryoid body formation: Embryoid bodies (EBs) were formed from ESCs following the published standard protocol from Miriam Bibel et al. 2007, nature protocols. Briefly, ESCs were trypsinized, resuspend in ES medium without LIF and count the cells. Then 4 × 106 ESCs were seeded onto bacteriological Greiner Petri dishes in 15 ml ES medium without LIF. EBs were maintained in ES medium without LIF for 4 days before collection for further analysis. (KI only) Mouse ESCs (WT) producing tagged Tets were generated with the CRISPR-Cas9n nuclease system. Briefly, sgRNAs were designed to target the stop codons of Tet1 and Tet2 (for C-terminal tags) using the guidelines described in MIT’s online tool. They were cloned into the pX461 vector. Lipofectamine™ 3000 was used according to the manufacturer's instructions (Thermo Fisher Scientific, catalogue number L3000015) to co-transfect ESCs with an sgRNA-containing plasmid and a template containing triple tags (Flag+HA+Twin-Strep from the pINTO-N3 vector3, flanked by homologous arms with or without RBD for Tet2. Twenty-four hours after transfection, GFP-positive ESCs were selected by cell sorting and seeded into 96-well plates. One week later, clones were picked and analysed for the Flag tag by western blotting, and the CRISPR-Cas9n-targeted genomic regions were PCR-amplified and sequenced in clones producing tagged Tet2, or Tet2ΔRBD.

tag: sample type

tag: rip antibody

value: ESC

tag: genotype


title: Tet2deltaRBD knock-in ESC 5hmC-RIP Input repl 2


title: Tet2deltaRBD knock-in ESC 5hmC-RIP IP repl 2

value: anti-5hmC antibody


title: TB_only_Peru (RSEQ031)


title: Tet2 knock-in ESC 5hmC-RIP IP repl 2


title: Tet2deltaRBD knock-in ESC 5hmC-RIP Input repl 1


title: Tet2deltaRBD knock-in ESC 5hmC-RIP IP repl 1


title: Tet2 knock-in ESC 5hmC-RIP Input repl 2


title: WT ESC ribodepleted RNAseq amanitin-treated (4h) repl2

description: ribodepleted RNA

data_processing:
The raw sequencing data were first analyzed using FastQC. Low complexity reads were removed using AfterQC tool with default parameters. Further, to get rid of reads originating from rRNA or tRNA, the reads were mapped to mouse tRNA and rRNA sequences using bowtie2. The rRNA and tRNA sequences were downloaded from https://www.ncbi.nlm.nih.gov/nuccore using "Mus musculus"[Organism] AND (biomol_rrna[PROP] OR biomol_trna[PROP] as search parameters. Reads that were unmapped to tRNA and rRNA sequences were then further processed using Trimmomatic with default parameters to remove adapter sequences. The resulting fastq data was again analyzed using FastQC to ensure no further processing is needed.
Raw read count were obtained using HTseq tool and normalised in TPM.
Supplementary_files_format_and_content: read counts in TPM

growth_protocol: Wild type (WT) and Tet1,2,3 triple knock-out (TKO) mouse ESCs were grown under standard culture conditions. Briefly, cells were cultured on 0.1% gelatin-coated tissue culture plates in high-glucose DMEM medium containing 15% FBS, 1mM sodium pyruvate, 1% nonessential amino acids, 1% glutaMAX, 100 U/ml penicillin, 100 ug/ml streptomycin, 0.1 mM b-mercaptoethanol and 1000 unit/ml recombinant mouse leukemia inhibitory factor.

extract_protocol:
RNA from ESCs were extracted with either the RNeasy Mini or Maxi kit or TRIzol according to the manufacturer's instructions. Genomic DNA was eliminated by DNase treatment.
(WT) Poly-A enriched mRNA sequencing was performed on the Illumina Hiseq 2000 platform following library preparation using the TruSeq Stranded mRNA Library Prep Kit (which includes the polyA-enrichment step). (amanitin 0 and 4h) total RNAs from α-amanitin treated and untreated control cells were extracted and underwent ribosomal RNA depletion.100-200M strand-specific pair-end reads of 150bp were generated per sample.

treatment_protocol: (aminitin 0h and 4h) WT and TKO ESCs were treated with 10 μg/ml α-amanitin or with an equal volume of vehicle (water) as a control for 0 or 4 h, respectively.

tag: genotype/variation

value: WT

value: 10 ug/ml alpha-amanitin


title: WT ESC ribodepleted RNAseq non-treated (0h) repl1

description: ribodepleted RNA


title: TKO ESC ribodepleted RNAseq amanitin-treated (4h) repl2

description: ribodepleted RNA

value: TKO


title: WT ESC ribodepleted RNAseq amanitin-treated (4h) repl1

description: ribodepleted RNA


title: TKO ESC ribodepleted RNAseq non-treated (0h) repl2

description: ribodepleted RNA


title: TKO ESC ribodepleted RNAseq amanitin-treated (4h) repl1

description: ribodepleted RNA


title: WT ESC ribodepleted RNAseq non-treated (0h) repl2

description: ribodepleted RNA


title: TB_DM_Indonesia (RSEQ018)


title: TKO ESC ribodepleted RNAseq non-treated (0h) repl1

description: ribodepleted RNA


title: adipose_BBS_GCSi1 [B3]

city: Framingham

first: Herve

last: Husson

address: 49 New York Ave

department: Rare and Neurologic Diseases Research

institute: Sanofi Genzyme

description:
heatmap label: S11
mergedadip_B3

data_processing:
Using Array Studio version 10.0 (Omicsoft Corporation, a Qiagen Company):
adapters were stripped and reads filtered out according to the following protocol: AdapterStripping Right /AdapterSequence=AGATCGGAAGAGC /TrimReadsFirst=True;  Trimming  /Mode=Composite /LeftTrimming=0 /RightTrimming=0 /ReadTrimQuality=20 /ReadTrimSize=65536;  FilterSource IlluminaAdapters,Ercc,Mouse.rRNA,Mouse.tRNA /CustomFile="";  Options  /FileFormat=AUTO /QualityEncoding=Automatic /WriteFilterFiles=False /EnableLengthCutoff=True /LengthCutoff=25 /EnableMaxQualityCutoff=True /MaxQualityCutoff=20 /EnableAverageQualityCutoff=True /AverageQualityCutoff=10 /EnablePolyRateCutoff=True /PolyRateCutoff=80;  /CompressionMethod=Gzip /Gzip=True /PairedEnd=True /FilterPairByBothEnds=True
Mapping to Reference Mouse.B38; GeneModel OmicsoftGenCode.V19; Trimming  /Mode=TrimByQuality /ReadTrimQuality=2; Options  /ParallelJobNumber=32 /PairedEnd=True /FileFormat=AUTO /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /OutputFolder="/site/ne/data/bi/omicsoft/FtpRootCR/Users/ricbr01/Bardet_Biedl_hyp_adip_extra_WT1_samples/aligned" /ThreadNumber=4 /InsertSizeStandardDeviation=100 /ExpectedInsertSize=200 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=None /Gzip=False /SearchNovelExonJunction=True /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False; Output aligned;
counts & FPKM values were generated using the following parameters: Options  /ExpressionMeasurement=RPKM+Count /ParallelJobNumber=32 /Add1=False /CountFragments=True /ExcludeMultiReads=False /Tpm=False /Rpm=False /CountStrandedReads=False /CountReverseStrandedReads=True /AutoTrimUtr=False
Using Array Studio version 10.1.2.9:
transcripts were filtered based on counts as follows: By Variable; Filter Count if greater than or equal to>=2; Options  /Group=BatchGroup /ApplyToAllGroups=False /CountingCutoff=1 /FilterByDetection=False; Output ; End;
protein-coding genes only were normalized as follows: Mode Count; Options  /Normalization=UpperQuartile; Output Norm_FPKM_filt_meets_count_fpkm_cutoffs;End;
normalized FPKM values were transformed as follows: Options  /Transformation=Log2 /Add=1; Output Log2_Norm_FPKM
Genome_build: mm10
Supplementary_files_format_and_content: tab delimted text files include log2 normalized expression values and raw counts

extract_protocol:
RNA was isolated by TRIzol and chloroform extraction from homogenized adipose tissue followed by RNeasy purification to remove genomic DNA (Qiagen).
Libraries were prepared using the Illumina Truseq Stranded mRNA Library Prep Kit (Part Number 20020594)

treatment_protocol: Bbs2-/- mice treated with GCS inhibitor in feed (0.033% weight/weight) from 2 till 6 months of age.  Tissue collected at 6 months of age and flash frozen before RNA was extracted.

tag: strain background

value: adipose tissue


title: adipose_BBS_GCSi3 [B5]

description:
heatmap label: S9
mergedadip_B5


title: adipose_BBS3 [A12]

description:
heatmap label: S6
mergedadip_A12


title: adipose_BBS4 [B1]

description:
heatmap label: S7
mergedadip_B1


title: adipose_BBS_GCSi4 [B7]

description:
heatmap label: S10
mergedadip_B7


title: adipose_BBS_GCSi2 [B4]

description:
heatmap label: S12
mergedadip_B4


title: Tet2 knock-in ESC 5hmC-RIP IP repl 1


title: adipose_WT2 [A3]

description:
heatmap label: S3
A3_S1_001


title: adipose_WT4 [A5]

description:
heatmap label: S4
mergedadip_A5


title: adipose_WT1 [A1]

description:
heatmap label: S1
mergedadip_A1


title: adipose_BBS1 [A10]

description:
heatmap label: S5
mergedadip_A10


title: ESC_CBPKD_RNA-seq_rep2

city: Dallas

first: Laura

last: Banaszynski

address: 5323 Harry Hines Blvd

department: Green Center for Reproductive Biology Sciences

institute: University of Texas Medical Center

description: PolyA RNA

data_processing:
The RNA-seq reads were aligned to the mm10 mouse reference genome using TopHat aligner.
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks (Quinlan et al., 2010).
The sequence length was 34 for R1 and 34 for R2 for paired-end data.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig

source_name: Embryonic stem cells

growth_protocol: ESCs were cultured under standard conditions (KO-DMEM, 2 mM Glutamax, 15% ES grade fetal bovine serum, 0.1 mM 2-mercaptoethanol, and leukemia inhibitory factor (LIF)). For early passages, cells were maintained on an irradiated feeder layer. To remove feeders, cells were passaged at least two passages off of feeders onto gelatin-coated plates.

extract_protocol:
RNA was extracted using a Qiagen RNeasy kit.
Libraries were constructed according to the Illumina Tru-seq protocol.

treatment_protocol: ESCs were infected with lentivirus packaged with p300 and CBP shRNA plasmid (Dharmacon). The day after the lentivirus infection, the media was replaced with complete mESC culture media containing 1 μg/ml puromycin (for p300 plasmid) or 400 ug/ul (for CBP plasmid) of G418. After 4 days of selection, mESCs were used for downstream analysis.

tag: strain/background

value: Embryonic stem cells

value: CBP KD


title: ESC_CBPKD_ATAC-Seq_rep2

data_processing:
The ATAC-seq reads were aligned to the mm10 mouse reference genome using the BWA aligner (Li and Durbin, 2010).
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks (Quinlan et al., 2010).
The sequence length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig

extract_protocol:
Samples were prepared according to the Illumina Nextera protocol.
Libraries were constructed according to the Illumina Nextera protocol.


title: ESC_p300Ctl_RNA-seq_rep1

description: PolyA RNA

value: p300 Ctl


title: ESC_p300Ctl_RNA-seq_rep2

description: PolyA RNA


title: ESC_CBPKD_RNA-seq_rep1

description: PolyA RNA


title: ESC_CBPKD_ATAC-Seq_rep1


title: ESC_p300Ctl_ATAC-Seq_rep2


title: ESC_CBPCtl_RNA-seq_rep1

description: PolyA RNA

value: CBP Ctl


title: ESC_p300Ctl_ATAC-Seq_rep1


title: ESC_p300KD_RNA-seq_rep1

description: PolyA RNA

value: p300 KD


title: ESC_p300KD_RNA-seq_rep2

description: PolyA RNA


title: ESC_p300KD_ATAC-Seq_rep1


title: ESC_CBPCtl_H3K27ac_rep3

data_processing:
The ChIP-seq reads were aligned to the mm10 mouse reference genome using the Bowtie software package (Langmead et al., 2009).
Mapped reads were further converted to “bigWig” files counting reads in non-overlapping 200-bp windows across the genome using BEDTools for presentation as genome browser tracks (Quinlan et al., 2010).
The sequence length was 33 for R1 and 33 for R2 for paired-end data.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig

extract_protocol:
Native ChIP was performed as described (Goldberg et al. 2010). Briefly, ESCs were harvested and treated with MNase, resulting in a population consisting mainly of mono- to trinucleosomes. Crosslinking ChIP was performed as described (Goldberg et al. 2010). Briefly, cells were harvested and crosslinked in 1% PFA. Chromatin was then sheared to 200-700 bp. For both procedures, chromatin was isolated and used for ChIP according to standard procedures.
Libraries were constructed according to the Illumina Tru-seq protocol.

tag: chip type

value: Native

tag: chip antibody

value: H3K27ac (39133, Active Motif)


title: ESC_CBPCtl_ATAC-Seq_rep1


title: ESC_CBPKD_H3K27ac_rep3


title: ESC_p300KD_H3K27ac_rep3


title: ESC_p300KD_ATAC-Seq_rep2


title: adipose_BBS2 [A11]

description:
heatmap label: S8
mergedadip_A11

tag: treatment


title: adipose_WT3 [A4]

description:
heatmap label: S2
A4_S2_001


title: ESC_CBPCtl_RNA-seq_rep2

description: PolyA RNA


title: ESC_CBPKD_H3K27ac_rep2


title: ESC_CBPCtl_H3K27ac_rep2


title: ESC_p300Ctl_Input_p53

value: Crosslinked


title: ESC_p300KD_H3K27ac_rep2


title: ESC_p300Ctl_H3K27ac_rep2


title: ESC_p300Ctl_H3K27ac_rep3


title: ESC_CBPKD_H3K27ac_rep1


title: ESC_CBPCtl_ATAC-Seq_rep2


title: ESC_CBPCtl_H3K27ac_rep1


title: ESC_p300Ctl_p53

value: p53 (NCL-L-p53-CM5p, Leica)


title: ESC_p300KD_H3K27ac_rep1


title: ESC_Input


title: WT EB 5hmC-RIP Input repl 2

source_name: Embryonic Bodies

value: EB


title: WT EB 5hmC-RIP Input repl 3


title: WT EB 5hmC-RIP IP repl 1


title: WT EB 5hmC-RIP IP repl 3


title: WT EB 5hmC-RIP IP repl 2


title: TKO ESC 5hmC-RIP Input repl 3


title: TKO ESC 5hmC-RIP IP repl 3


title: TKO ESC 5hmC-RIP IP repl 2


title: TKO ESC 5hmC-RIP IP repl 1


title: TKO ESC 5hmC-RIP Input repl 1


title: WT EB 5hmC-RIP Input repl 1


title: WT ESC 5hmC-RIP Input repl 1


title: WT ESC 5hmC-RIP Input repl 3


title: WT ESC 5hmC-RIP IP repl 3


title: Tet2dRBD-KI ESC Tet2dRBD-RIP IP repl4

data_processing:
The raw sequencing data were first analyzed using FastQC. Low complexity reads were removed using AfterQC tool with default parameters. Further, to get rid of reads originating from rRNA or tRNA, the reads were mapped to mouse tRNA and rRNA sequences using bowtie2. The rRNA and tRNA sequences were downloaded from https://www.ncbi.nlm.nih.gov/nuccore using "Mus musculus"[Organism] AND (biomol_rrna[PROP] OR biomol_trna[PROP] as search parameters. Reads that were unmapped to tRNA and rRNA sequences were then further processed using Trimmomatic with default parameters to remove adapter sequences. The resulting fastq data was again analyzed using FastQC to ensure no further processing is needed.
The processed data were then mapped to mouse genome with RefSeq reference transcriptome (download on March 2012) using RSEM tool. TPM was computed from the RSEM expression counts and pseudocount of 1 TPM was added to compute fold change of IP over Input.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include TPM (with 1TPM pseudocount) values

growth_protocol: Mouse ESCs (WT) were grown under standard culture conditions. Briefly, cells were cultured on 0.1% gelatin-coated tissue culture plates in high-glucose DMEM medium containing 15% FBS, 1mM sodium pyruvate, 1% nonessential amino acids, 1% glutaMAX, 100 U/ml penicillin, 100 ug/ml streptomycin, 0.1 mM b-mercaptoethanol and 1000 unit/ml recombinant mouse leukemia inhibitory factor.

extract_protocol:
Total RNA from WT ESCs were extracted with either the RNeasy Mini or Maxi kit or TRIzol according to the manufacturer's instructions. Genomic DNA was eliminated by DNase treatment.
Library preparation was performed as described in Delatte et al., 2016. Briefly, 5 to 10 ng dsDNA was subjected to 5' and 3' protruding end repair, followed by the addition of non-templated adenines to the 3' ends of the blunted DNA fragments, which allows ligation of Illumina multiplex adapters. The DNA fragments were then size selected so as to remove all unligated adapters and to sequence 200-300-bp fragments. 18 cycles of PCR were carried out to amplify the library. DNA was quantified by fluorometry with the Qubit 2.0 and DNA integrity was assessed with a 2100 bioanalyzer. 6 pM of DNA library spiked with 1% PhiX viral DNA was clustered on cBot and then sequenced on a HiScanSQ module.

treatment_protocol: Mouse ESCs (WT) producing tagged Tets were generated with the CRISPR-Cas9n nuclease system as described previously2. Briefly, sgRNAs were designed to target the stop codons of Tet1 and Tet2 (for C-terminal tags) using the guidelines described in MIT’s online tool. They were cloned into the pX461 vector. Lipofectamine™ 3000 was used according to the manufacturer's instructions (Thermo Fisher Scientific, catalogue number L3000015) to co-transfect ESCs with an sgRNA-containing plasmid and a template containing triple tags (Flag+HA+Twin-Strep from the pINTO-N3 vector3, flanked by homologous arms for Tet1 and by homologous arms with or without RBD for Tet2. Twenty-four hours after transfection, GFP-positive ESCs were selected by cell sorting and seeded into 96-well plates. One week later, clones were picked and analysed for the Flag tag by western blotting, and the CRISPR-Cas9n-targeted genomic regions were PCR-amplified and sequenced in clones producing tagged Tet1, Tet2, or Tet2ΔRBD.

tag: experiment type

value: anti-Flag antibody


title: Tet2dRBD-KI ESC Tet2dRBD-RIP Input repl2

value: ESC


title: WT ESC 5hmC-RIP IP repl 1

value: anti-5hmC antibody


title: Tet2dRBD-KI ESC Tet2dRBD-RIP Input repl4


title: Tet2dRBD-KI ESC Tet2dRBD-RIP IP repl2


title: Tet2dRBD-KI ESC Tet2dRBD-RIP Input repl1


title: WT ESC 5hmC-RIP Input repl 2

value: WT


title: Tet2dRBD-KI ESC Tet2dRBD-RIP Input repl3


title: ESC_p300Ctl_H3K27ac_rep1


title: TKO ESC 5hmC-RIP Input repl 2


title: Tet2-KI ESC Tet2-RIP Input repl4