title: ATAC-seq_primed_hESC_rep2

status: Public on Apr 30 2019

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

institute: EPFL

data_processing:
Sequenced reads were de-multiplexed to attribute each read to a DNA sample and then aligned with bowtie2. Mitochondrial reads were removed.
Accessible sites were called using MACS2, only peaks with a score higher than 5 (–log10 p-value) were kept. Then differential analysis between conditions was done using unique reads (filter for MAPQ > 10)
Genome_build: hg19
Supplementary_files_format_and_content: (Peaks tabular File)  A bed file containing the output of the peak called by MACS2

growth_protocol: Conventional (primed) human ESC lines were maintained in mTSER for H1 (Male) and IPS on Matrigel, for WIBR3 (Female) on irradiated inactivated mouse embryonic fibroblast (MEF) feeders in human ESC medium (hESM) and passaged with collagenase and dispase, followed by sequential sedimentation steps in hESM to remove single cells while naïve ES cells, primed H1 and IPS were passaged by Accutase in single cells. hES media composition: DMEM/F12 supplemented with 15% fetalbovine serum, 5% KnockOut Serum Replacement, 2 mM L-glutamine, 1% nonessential amino acids, 1% penicillin-streptomycin (Lonza), 0.1 mM β-mercaptoethanol and 4 ng/ml FGF2. Naïve media composition: 500 mL of medium was generated by including: 240 mL DMEM/F12, 240 mL Neurobasal, 5 mL N2 supplement, 10 mL B27 supplement, 2 mM L-glutamine, 1% nonessential amino acids, 0.1 mM β-mercaptoethanol, 1% penicillin-streptomycin, 50 μg/ml BSA. In addition for 4i/LA:  PD0325901 (1 μM), SB590885 (0.5 μM), WH4-023 (1 μM), Activin A (10 ng/mL), 20 ng/ml hLIF, Y-27632 (10 μM) and IM-12 (0-1 μM). In addition for KN/2i media: PD0325901 (1 μM), CHIR99021 (1 μM), 20 ng/ml hLIF and Doxycycline (2 µg/ml). For conversion of primed human ESC lines (WIBR3), we seeded 2-3e105 trypsinized single cells on an MEF feeder layer in hESM supplemented with ROCK inhibitor Y-27632 (10 mM). Two days later, medium was switched to 4i/LA (+/- IM12)-containing naïve hESM (Theunissen et al., 2016). WIBR3dPE cells (OCT4 GFP knock-in depleted for its primed specific Proximal Enhancer (dPE) were converted in naïve with DOX-inducible KLF2 and NANOG transgenes and maintained in 2i/L/DOX (Theunissen et al., 2014).

extract_protocol:
ATAC-seq was performed as in (Buenrostro et al., 2013) on primed WIRB3 and WIBR3dPE; naïve WIBR3 and WIBR3dPE in 4iLA and KN/2iL media respectively; and in WIBR3dPE in KN/2iL media upon dCAS9-KRAB overexpression containing or not a guide RNA targeting SVA/LTR5Hs
Library were made using Nextera DNA Library Prep Kit (Illumina #FC-121-1030)
Libraries were ligated with Illumina adaptors
Tn5 tagmentation

treatment_protocol: ATAC-seq was performed on primed WIRB3 and WIBR3dPE; naïve WIBR3 and WIBR3dPE in 4iLA and KN/2iL media respectively; and in WIBR3dPE in KN/2iL media upon dCAS9-KRAB overexpression containing or not a guide RNA targeting SVA/LTR5Hs

tag: source

value: Early Embryo

tag: culture media

value: hESM media

tag: status

value: primed


title: ATAC-seq_primed_hESC_rep1

type: SRA

country: Switzerland

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line


title: shStag2_1_Ery_pCHiC

status: Public on Apr 09 2019

city: Mainz

first: Daniel

last: Sasca

address: Langenbeckstr 1

department: Department of Hematology and Oncology

country: Germany

institute: University Medical Center Mainz

description: processed data in file: shStag2_1_and_2_Ery_washU_text.txt

data_processing:
pCHiC pipeline: Samples were preprocessed with HiCUP. Raw HiCUP outputs were processed with the CHiCAGO pipeline (Babraham Institute).
washU browser txt files for pCHiC
Genome_build: mm10

organism: Mus musculus

source_name: shStag2 inducible shRNA in EPO_induced cells

growth_protocol: Cells were grown in standard media with addition of 20 ng/ul murine recombinant SCF and 4 U/l EPO

extract_protocol:
x-linking was performed with 1% Formaldehyde. Nuclei were homogenized with Dounce, DNA was enzymatically lysed with HindIII. Fragments were religated after 5' biotinylation.
pCHiC libraries were contructed via promoter capture with SureSelect hybridisation beads.

treatment_protocol: 72 hours knock-down induction with Doxycycline

tag: cell type

value: Hematopoietic stem and progenitors

tag: genotype


title: shStag2_2_Ery_pCHiC


title: ATAC-seq_naive_hESC_rep1

value: 4i/LA media

value: naive


title: Luc1_Myelo_Ctcf_ChIP-seq

description: ChIP antibody: Ctcf (Abcam, ab70303)

data_processing:
Chip Seq pipeline: Adapter sequences were trimmed for all reads and mapped against mm10 reference genome using Bowtie2. Uniquely mapped, deduplicated reads were retained and peaks were called using MACS2.
bedGraph files for ChIP Seq
Genome_build: mm10

source_name: Luc inducible shRNA in IL3_induced cells

growth_protocol: Cells were grown in standard media with addition of 20 ng/ul murine recombinant SCF and 50 ng/ul IL-7

extract_protocol:
x-linking was performed with 1% Formaldehyde. Lysates were clarified from sonicated nuclei and chromatin proteins were isolated with antibodies.
ChIP-Seq libraries were prepared for sequencing using a TruSeq ChIP Sample Prep Kit (Illumina) and standard Illumina protocols


title: Luc2_Myelo_Ctcf_ChIP-seq

description: ChIP antibody: Ctcf (Abcam, ab70303)

growth_protocol: Cells were grown in standard media with addition of 20 ng/ul murine recombinant SCF and 50 ng/ul IL-8


title: Luc1_Ery_Smc1_ChIP-seq

description: ChIP antibody: Smc1 (Abcam, ab9262)

source_name: Luc inducible shRNA in EPO_induced cells


title: shStag21_2_Ery_Rad21_ChIP-seq

description: ChIP antibody: Rad21 (Abcam, ab992)


title: shStag2_1_Ery_Smc1_ChIP-seq

description: ChIP antibody: Smc1 (Abcam, ab9262)


title: Luc1_Ery_Rad21_ChIP-seq

description: ChIP antibody: Rad21 (Abcam, ab992)


title: shStag2_1_Ery_Ctcf_ChIP-seq

description: ChIP antibody: Ctcf (Abcam, ab70303)


title: Luc2_Ery_Rad21_ChIP-seq

description: ChIP antibody: Rad21 (Abcam, ab992)


title: Luc2_Ery_Ctcf_ChIP-seq

description: ChIP antibody: Ctcf (Abcam, ab70303)


title: S210_MUSCLE_T460

status: Public on Apr 07 2020

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

country: USA

institute: NIA-IRP, NIH

description: Skeletal Muscle Sample from GESTALT Muscle Biopsies

library_source: transcriptomic

data_processing:
Single-read sequencing was performed for 141 cycles and Real-Time Analysis (RTA) v1.18.66.3 generated the base-call files (BCL files). BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program (v2.17.1.14)
The quality of the bases was checked using FASTQC program (v11.2) before and after adapter removal and last base trimming by cutadapt program (v1.9).
The cleaned FASTQ files were aligned, quantified and annotated to the human hg19 genome using Salmon (Patro et al., 2017) with the concept of quasi-mapping with two phase inference procedure for gene model annotations.
Genome_build: human hg19 genome
Supplementary_files_format_and_content: .quant, TPM

molecule: total RNA

source_name: Skeletal Muscle

extract_protocol:
Total RNA was prepared by lysing cell pellet (2x106) in 700ul Qiazol and extracted using Qiagen miRNeasy mini kit according to the manufacturer’s recommendation (Qiagen Inc, CA, USA)
Samples were prepared using Nugen Ovation v2 kits and the sequencing library was prepared using Illumina ChIP-Seq kits according to manufacturer’s protocol (Illumina, San Diego, CA).

tag: tissue

value: Vastus lateralis

tag: age

tag: gender

value: Male


title: shStag2_2_Ery_Smc1_ChIP-seq

description: ChIP antibody: Smc1 (Abcam, ab9262)


title: JR1830: WT-8

status: Public on Oct 03 2019

city: Boulder

first: John

last: Rinn

state: CO

address: 3415 Colorado Avenue

institute: University of Colorado Boulder

data_processing:
Read 1 was trimmed by piping cutadapt: "cutadapt -u 3 - | cutadapt -a AAAAAAAA - | cutadapt -a AAAAAAAN$ -a AAAAAAN$ -a AAAAAN$ - | cutadapt -a AGAGCACACGTCTG - "
Read 2 was trimmed by piping cutadapt: "cutadapt -g TTTTTTTT - | cutadapt -g ^NTTTTTTT -g ^NTTTTTT -g ^NTTTTT - | cutadapt -a CCCGATCGTCGG - | cutadapt -a GGGGATCGTCGG -"
The adapter-trimmed reads were mapped to the mm10 mouse reference genome using TopHat v2.1.1 with the flags: "--no-coverage-search --GTF gencode.vM9.annotation.gtf"
Uniquely-mapped reads were counted for genes by featureCounts
Transcripts per million was calculated
Genome_build: mm10
Supplementary_files_format_and_content: Comma seperated file

molecule: polyA RNA

source_name: Commom Lymphoid Projenitor

extract_protocol:
RNA was isolated using RNeasy micro columns (Qiagen) on a QIAcube (Qiagen) after TRIzol treatment.
Poly(A)+ RNA-seq libraries were constructed using CATS RNA-seq kit v2 (Diagenode, C05010041).

value: Commom Lymphoid Projenitor

tag: Sex

value: WT


title: Luc2_Ery_Smc1_ChIP-seq

description: ChIP antibody: Smc1 (Abcam, ab9262)


title: shStag2_1_Ery_Rad21_ChIP-seq

description: ChIP antibody: Rad21 (Abcam, ab992)


title: Luc1_Ery_Ctcf_ChIP-seq

description: ChIP antibody: Ctcf (Abcam, ab70303)


title: shStag2_2_Ery_H3K27ac_ChIP-seq

description: ChIP antibody: H3K27Ac (Abcam, ab4729)


title: ATAC-seq_naive_hESC_rep2

value: KN/2iL media


title: shStag2_2_HPC_Ctcf_ChIP-seq

description: ChIP antibody: Ctcf (Abcam, ab70303)

source_name: shStag2 inducible shRNA in HPC

growth_protocol: Cells were grown in standard media with addition of 100 ng/ul murine recombinant SCF


title: shStag2_1_HPC_Ctcf_ChIP-seq

description: ChIP antibody: Ctcf (Abcam, ab70303)


title: shRad21_1_HPC_Ctcf_ChIP-seq

description: ChIP antibody: Ctcf (Abcam, ab70303)

source_name: shRad21 inducible shRNA in HPC


title: Luc2_HPC_Ctcf_ChIP-seq

description: ChIP antibody: Ctcf (Abcam, ab70303)

source_name: Luc inducible shRNA in HPC


title: Luc1_HPC_Ctcf_ChIP-seq

description: ChIP antibody: Ctcf (Abcam, ab70303)


title: shSmc1a_1_HPC_SA2_ChIP-seq

description: ChIP antibody: SA2 (Abcam, ab196000)

source_name: shSmc1a inducible shRNA in HPC


title: shSmc1a_2_HPC_SA2_ChIP-seq

description: ChIP antibody: SA2 (Abcam, ab196000)


title: shRad21_2_HPC_SA2_ChIP-seq

description: ChIP antibody: SA2 (Abcam, ab196000)


title: shRad21_1_HPC_SA2_ChIP-seq

description: ChIP antibody: SA2 (Abcam, ab196000)


title: Luc2_HPC_SA2_ChIP-seq

description: ChIP antibody: SA2 (Abcam, ab196000)


title: Luc1_HPC_SA2_ChIP-seq

description: ChIP antibody: SA2 (Abcam, ab196000)


title: shRad21_2_HPC_Ctcf_ChIP-seq

description: ChIP antibody: Ctcf (Abcam, ab70303)


title: shRad21_2_HPC_Smc1_ChIP-seq

description: ChIP antibody: Smc1 (Abcam, ab9262)


title: shStag2_2_HPC_Smc1_ChIP-seq

description: ChIP antibody: Smc1 (Abcam, ab9262)


title: Luc2_HPC_Smc1_ChIP-seq

description: ChIP antibody: Smc1 (Abcam, ab9262)


title: shStag2_1_HPC_Smc1_ChIP-seq

description: ChIP antibody: Smc1 (Abcam, ab9262)


title: Luc1_HPC_Smc1_ChIP-seq

description: ChIP antibody: Smc1 (Abcam, ab9262)


title: shStag2_2_HPC_Rad21_ChIP-seq

description: ChIP antibody: Rad21 (Abcam, ab992)


title: Luc1_HPC_Rad21_ChIP-seq

description: ChIP antibody: Rad21 (Abcam, ab992)


title: shStag2_2_HPC_H3K27ac_ChIP-seq

description: ChIP antibody: H3K27Ac (Abcam, ab4729)


title: shRad21_1_HPC_Smc1_ChIP-seq

description: ChIP antibody: Smc1 (Abcam, ab9262)


title: shStag2_1_HPC_Rad21_ChIP-seq

description: ChIP antibody: Rad21 (Abcam, ab992)


title: shStag2_1_HPC_H3K27ac_ChIP-seq

description: ChIP antibody: H3K27Ac (Abcam, ab4729)


title: Luc2_HPC_Rad21_ChIP-seq

description: ChIP antibody: Rad21 (Abcam, ab992)


title: shStag2_2_Ery_RNA-seq

data_processing:
RNA Seq pipeline: Rads were trimmed for adaptor sequence. Paired end reads were aligned to mm10 genome STAR version 2.4.0. To generate the bigwig file, we first extended each read to 200 bp along 5' end and generated count files using HTSeq.
HTSeq count files for RNA Seq
Genome_build: mm10

source_name: shStag2 inducible shRNA in erythroid cells

extract_protocol:
RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) as per manufacturer’s protocol
RNA-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 72 hours knock-down induction with Doxycycline, followed by EPO-mediated differentiation (4 U/l EPO, 20 ng/ul SCF) for 48 hours


title: shStag2_1_Ery_RNA-seq


title: shSmc1a_2_HPC_Rad21_ChIP-seq

description: ChIP antibody: Rad21 (Abcam, ab992)


title: shSmc1a_1_HPC_Rad21_ChIP-seq

description: ChIP antibody: Rad21 (Abcam, ab992)


title: shRad21_3_HPC_RNA-seq (inhibitor)


title: shSmc1_2_HPC_RNA-seq (inhibitor)


title: Luc2_Ery_RNA-seq

source_name: Luc inducible shRNA in erythroid cells


title: Luc2_HPC_H3K27ac_ChIP-seq

description: ChIP antibody: H3K27Ac (Abcam, ab4729)


title: shSmc1_1_HPC_RNA-seq (inhibitor)


title: shRad21_2_HPC_RNA-seq (inhibitor)


title: control (dmso) sample 1

status: Public on Mar 28 2020

city: New York

first: Jonathan

middle: W.

last: Snow

state: New York

address: 3009 Broadway

department: Biology

institute: Barnard College

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The reads were then mapped to the A. mellifera reference genome available on NCBI using the STAR aligner.
The RNA-seq aligner is executed using a splice aligner, which detects splice junctions and incorporating them to help align the entire read sequences. BAM files were generated as a result of this step.
Gene hit counts were calculated using Feature counts from the Subread package.
After mapping and total gene hit counts calculation, the total gene hit counts table was used for downstream differential expression analysis using DESeq2 and groups were compared.
Genome_build: Amel_4.5
Supplementary_files_format_and_content: comma-separated values, normalized read ouns for paired samples

organism: Apis mellifera

source_name: honey bee midgut

extract_protocol:
Midguts were removed, stored in RNAlater, and RNA was harvested using Trizol reagent. RNA was submitted to additional quality control analysis before mRNA was enriched by polyA selectio
Llibrary preparation was performed using a NEBNext Ultra RNA library preparation kit. Sequencing was then performed using Illumina HiSeq platform.

treatment_protocol: Honey bees were fed sucose solution containning 24 uM Tunicamycin (0.5%DMSO) or 0.5% DMSO alone for 24 hours.

value: midgut

tag: treatment

value: 0.5% DMSO alone for 24 hours


title: shStag2_2_HPC_RNA-seq (inhibitor)


title: shRad21_1_HPC_RNA-seq (inhibitor)


title: shStag2_3_HPC_RNA-seq (inhibitor)


title: shStag2_1_HPC_RNA-seq (inhibitor)


title: Luc3_HPC_RNA-seq (inhibitor)


title: HeLa TUT4 Knockout TruSeq 2

status: Public on Dec 12 2018

city: Seoul

first: Haedong

last: Kim

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences

country: South Korea

institute: Seoul National University

description: small RNA-seq

data_processing:
FASTQ files were generated by base-calling using Illumina RTA (v1.18) and conversion using bcl2fastq (v1.8.4).
The TruSeq 3′ adapter sequence was removed using cutadapt. For AQ-seq data, 4 nt-long degenerate sequences at the 3′ and 5′ end were trimmed using the FASTX-Toolkit. Reads shorter than 18 nt, low-quality reads (phred quality <20 or <30 in >95% or >50% of nucleotides, respectively), and artifact reads were discarded using the FASTX-Toolkit.
Preprocessed reads were first aligned to the spike-in sequences by BWA with an option of -n 3. Reads mapped to spike-in sequences perfectly or with a single mismatch were considered as reliable spike-in reads.
Reads unmapped to spike-in sequences by BWA with an option of -n 3 were subsequently mapped to the human genome (hg38) with the same option. For multi-mapped reads, we selected the alignment results which have the best alignment score, allowing mismatches only at the 3′ end of reads using custom scripts.
Reads were classified into annotations from miRBase release 21 (from www.mirbase.org), RefSeq, RepeatMasker (from UCSC genome browser), GtRNAdb (from gtrnadb.ucsc.edu), and Rfam (from rfam.sanger.ac.uk) by intersectBed in BEDTools.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated values (tsv) files containing miRNA names and corresponding read counts.

source_name: HeLa

growth_protocol: HEK293T and HeLa cells were grown in DMEM media (Welgene) supplemented with 10% FBS (Welgene).

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen).
Total RNA was mixed with thirty synthetic miRNA-like spike-in oligos. The RNA mixture was size-fractionated by 15% urea-polyacrylamide gel electrophoresis to enrich miRNA species. Small RNA libraries were constructed using either TruSeq small RNA library preparation kit (Illumina) according to manufacturer's instructions or AQ-seq as follows: miRNA-enriched RNA was ligated to 3′ randomized adapter with 20% PEG 8000, then ligated to 5′ randomized adapter with 20% PEG 8000, reverse-transcribed, and amplified. The cDNA was sequenced using a HiSeq 2500 platform.

value: HeLa


title: Luc2_HPC_RNA-seq (inhibitor)


title: HeLa TUT4 Knockout TruSeq 1

description: small RNA-seq


title: HeLa TUT4 Knockout AQ-seq 2

description: small RNA-seq


title: bln1_t16_rep3

status: Public on May 29 2018

city: Ames

first: Roger

middle: P

last: Wise

state: IA

address: 4201 ATRB, 2213 Pammel Drive

department: Plant Pathology & Microbiology (Iowa State University)

institute: USDA-ARS, Corn Insects and Crop Genetics Research Unit

description: Barley infected first leaf (PO:0007094) of m19089 (Mla6, Rar3, bln1) at 16 HAI

data_processing:
The 100 base pair single-end reads obtained from Illumina HiSeq 2500 were preprocessed using FastQC (Andrews 2015) and Trimmomatic version 0.32 (Bolger 2014). First, quality control checks were performed on raw sequence data using FastQC (Andrews 2016). Then, the raw reads were processed using Trimmomatic (Bolger 2014). We (i) cut adapters and Illumina-specific sequences from the reads, (ii) perform a sliding window trimming, cutting once the average quality within the window of 4 base pairs fell below a threshold of 32, (iii) cut bases off the start of a read, if below a threshold quality of 36, (iv) cut bases off the end of a read, if below a threshold quality of 36, and (v) drop the read if it is below a length of 50 base pairs. We performed FastQC (Andrews 2016) check again to ensure that any data quality problems were fixed.
Bowtie2 (Langmead 2012) indices were built for the reference genome for Barley (International Barley Sequencing Consortium, 2016) and Blumeria (Ensembl Fungi Assembly EF 1, INSDC Assembly GCA_000151065.1) (Spanu 2010). The single-end reads were then aligned using the TopHat2 (Kim 2013) with the “-read-realign-edit-dist” parameter set to 0. This forces TopHat2 to map every read in all the mapping steps (transcriptome, genome, and finally splice variants detected by TopHat2), reporting the best possible alignment found in any of these mapping steps. This may greatly increase the mapping accuracy. This was followed by genome guided Cufflinks version 2.2.1 (Trapnell 2010, Trapnell 2012) with the TopHat2 BAM output file as input. Finally, transcripts sequences were extracted with the gffread utility (part of the Cufflinks software) using the GTF file from Cufflinks as input.
For each of the 90 samples, read count estimation was done using RSEM (Li 2012) with Trimmomatic (Bolger 2014) trimmed reads as input. Transcript references were built for RSEM along with Bowtie2 indices (rsem-prepare-reference) separately for Blumeria and Barley using respective reference genomes. This was done with the “--gtf” option turned on, this means RSEM assumes that reference file contains the sequence of a genome, and will extract transcript reference sequences using the gene annotations specified in that file. Gene and isoform expression was estimated using “rsem-calculate-expression” with the “--bowtie2” option.
Genome_build: Barley (Mascher 2017) and Blumeria (Ensembl Fungi Assembly EF 1, INSDC Assembly GCA_000151065.1) (Spanu 2010).
Supplementary_files_format_and_content: Read count data for barley and powdery mildew in respective csv file

organism:
Hordeum vulgare
Blumeria hordei

source_name: Barley infected first leaf (PO:0007094)

growth_protocol: CI 16151 and its derived mutant barley lines were maintained via single seed descent. Genotypes were grown in separate trays (19.5 x 27.5-cm) in a climate-controlled greenhouse using a split plot design. Each tray consisted of six rows of 16 seedlings, with rows randomly assigned to one of six harvest timepoints (0, 16, 20, 24, 32, and 48 HAI).

extract_protocol:
Total RNA was isolated from 0.5 g of each pool using a hot (60oC) phenol / guanidine thiocyanate method (Caldo et al., 2004).
RNA-sequencing (RNA-seq) libraries were prepared by the Iowa State University DNA Facility (Ames, Iowa, USA) using the Illumina TruSeq stranded RNA sample preparation kit and were subjected to single-end sequencing (100-bp reads) using the Illumina HiSeq2500 Sequencing System. A split-split-plot design was used to run the 90 samples on three Hi-Seq 2500 flow cells.  Each replication was run on a separate flow cell with each plant genotype randomly assigned to each lane and 6 barcodes randomly assigned to the 6 time points within each genotype (lane).

treatment_protocol: Seven days after sowing, seedling trays were inoculated at 16:00 with a high density of Bgh isolate 5874 (AVRa1, AVRa6, vira8, AVRa12, vira13, AVRLa) and positioned randomly in a controlled growth chamber (18°C, 8 h darkness, 16 h light). Rows of seedlings were harvested at the assigned time points, pooled, and immediately placed into liquid nitrogen. The entire procedure was replicated three times in successive weeks resulting in 90 experimental units (5 genotypes x 6 timepoints x 3 replications).

tag: pathogen

value: Blumeria graminis f. sp. hordei

tag: barley genotype

tag: fungal isolate

value: Bgh isolate 5874

tag: timepoint

value: 16 HAI

tag: replication

value: Rep 3


title: bln1_t0_rep2

description: Barley infected first leaf (PO:0007094) of m19089 (Mla6, Rar3, bln1) at 0 HAI

value: 0 HAI

value: Rep 2


title: rar3_t24_rep3

description: Barley infected first leaf (PO:0007094) of m11526 (Mla6, rar3, Bln1) at 24 HAI

value: 24 HAI


title: rar3_t24_rep2


title: rar3_t48_rep2

description: Barley infected first leaf (PO:0007094) of m11526 (Mla6, rar3, Bln1) at 48 HAI

value: 48 HAI


title: bln1_t20_rep3

description: Barley infected first leaf (PO:0007094) of m19089 (Mla6, Rar3, bln1) at 20 HAI

value: 20 HAI


title: bln1_t16_rep2


title: rar3_t20_rep3

description: Barley infected first leaf (PO:0007094) of m11526 (Mla6, rar3, Bln1) at 20 HAI


title: rar3_t20_rep2


title: bln1_t24_rep1

description: Barley infected first leaf (PO:0007094) of m19089 (Mla6, Rar3, bln1) at 24 HAI

value: Rep 1


title: HeLa TUT4 Knockout AQ-seq 1

description: small RNA-seq


title: bln1_t20_rep2


title: bln1_t16_rep1


title: bln1_t0_rep3


title: rar3_t48_rep1


title: rar3_t48_rep3


title: rar3_t32_rep3

description: Barley infected first leaf (PO:0007094) of m11526 (Mla6, rar3, Bln1) at 32 HAI

value: 32 HAI


title: rar3_t32_rep2


title: rar3_t16_rep1

description: Barley infected first leaf (PO:0007094) of m11526 (Mla6, rar3, Bln1) at 16 HAI


title: rar3_t24_rep1


title: rar3_t32_rep1


title: rar3_t16_rep3


title: rar3_t20_rep1


title: mla6_t32_rep3

description: Barley infected first leaf (PO:0007094) of m18982 (mla6, Rar3, Bln1) at 32 HAI


title: mla6_t32_rep2


title: bln1_t20_rep1


title: bln1_t0_rep1


title: rar3_t16_rep2


title: rar3_t0_rep2

description: Barley infected first leaf (PO:0007094) of m11526 (Mla6, rar3, Bln1) at 0 HAI


title: rar3_t0_rep3


title: mla6_t24_rep2

description: Barley infected first leaf (PO:0007094) of m18982 (mla6, Rar3, Bln1) at 24 HAI


title: ML226  CON

status: Public on Nov 23 2019

city: Boston

first: Annie

last: Kathuria

state: MA

address: 185 cambridge street

institute: Mass Gen Hospital

data_processing:
Analysis was performed by DNA Link USA, Inc.
Sequence quality was assessed using FASTQC
Sequences were trimmed using cutadapt v 1.18, paired-end reads mode -u 7 -u -3 -U 7 -U -3
Trimmed reads were aligned to the reference genome using TopHat v2.1.1 (--no-coverage-search, -G refseqhg38p9.gtf)
Bam files were merged using samptools v 1.9 for samples with techincal replicates.
FPKM calulcation done using cufflinks v2.2.1 using annotation from RefSeq assembly hg38 p9 which was modified according UCSC-style-name
Pairwise differential expression analysis was performed using cuffdiff v2.2.1
Genome_build: Homo sapience hg38 (UCSC tophat version as downloaded May 2017)
Supplementary_files_format_and_content: tab-delimited w/ the following columns: tracking_id, gene_id, gene_short_name, locus, FPKM for each sample

source_name: 2D cortical neurons

extract_protocol:
Tissue was dissolved in Trizol and RNA was extracted using qiagen rneasy kit
RNA libraries were prepared for sequencing using Truseq Stranded Total RNA H/M/R

value: Human iPSC derieved cerebral organoids

value: 3 months of differentiation

tag: diagnosis

value: healthy control


title: mla6_t48_rep2

description: Barley infected first leaf (PO:0007094) of m18982 (mla6, Rar3, Bln1) at 48 HAI


title: rar3_t0_rep1


title: mla6_t48_rep3


title: mla6_t16_rep2

description: Barley infected first leaf (PO:0007094) of m18982 (mla6, Rar3, Bln1) at 16 HAI


title: mla6_t48_rep1


title: mla6_t24_rep1


title: mla6_t16_rep3


title: mla6_t32_rep1


title: mla6_t16_rep1


title: mla6_t20_rep2

description: Barley infected first leaf (PO:0007094) of m18982 (mla6, Rar3, Bln1) at 20 HAI


title: mla6_t0_rep2

description: Barley infected first leaf (PO:0007094) of m18982 (mla6, Rar3, Bln1) at 0 HAI


title: mla6_t0_rep1


title: mla6_t0_rep3


title: WT_t48_rep3

description: Barley infected first leaf (PO:0007094) of CI 16151 (Mla6, Rar3, Bln1) at 48 HAI


title: mla6_t24_rep3


title: WT_t48_rep1


title: WT_t48_rep2


title: mla6_t20_rep3


title: mla6_t20_rep1


title: WT_t32_rep2

description: Barley infected first leaf (PO:0007094) of CI 16151 (Mla6, Rar3, Bln1) at 32 HAI


title: WT_t32_rep3


title: WT_t24_rep1

description: Barley infected first leaf (PO:0007094) of CI 16151 (Mla6, Rar3, Bln1) at 24 HAI


title: WT_t32_rep1


title: WT_t24_rep2


title: WT_t16_rep3

description: Barley infected first leaf (PO:0007094) of CI 16151 (Mla6, Rar3, Bln1) at 16 HAI


title: WT_t20_rep3

description: Barley infected first leaf (PO:0007094) of CI 16151 (Mla6, Rar3, Bln1) at 20 HAI


title: WT_t20_rep1


title: WT_t16_rep1


title: WT_t20_rep2


title: WT_t24_rep3


title: WT_t0_rep1

description: Barley infected first leaf (PO:0007094) of CI 16151 (Mla6, Rar3, Bln1) at 0 HAI


title: WT_t0_rep2


title: WT_t0_rep3


title: mla6_bln1_t48_rep3

description: Barley infected first leaf (PO:0007094) of m19028 (mla6, Rar3, bln1) at 48 HAI


title: WT_t16_rep2


title: mla6_bln1_t48_rep2


title: mla6_bln1_t24_rep2

description: Barley infected first leaf (PO:0007094) of m19028 (mla6, Rar3, bln1) at 24 HAI


title: mla6_bln1_t32_rep2

description: Barley infected first leaf (PO:0007094) of m19028 (mla6, Rar3, bln1) at 32 HAI


title: mla6_bln1_t32_rep1


title: mla6_bln1_t24_rep3


title: mla6_bln1_t20_rep3

description: Barley infected first leaf (PO:0007094) of m19028 (mla6, Rar3, bln1) at 20 HAI


title: bln1_t48_rep3

description: Barley infected first leaf (PO:0007094) of m19089 (Mla6, Rar3, bln1) at 48 HAI


title: mla6_bln1_t16_rep3

description: Barley infected first leaf (PO:0007094) of m19028 (mla6, Rar3, bln1) at 16 HAI


title: mla6_bln1_t16_rep2


title: mla6_bln1_t20_rep1


title: bln1_t48_rep1


title: mla6_bln1_t20_rep2


title: mla6_bln1_t0_rep1

description: Barley infected first leaf (PO:0007094) of m19028 (mla6, Rar3, bln1) at 0 HAI


title: bln1_t32_rep3

description: Barley infected first leaf (PO:0007094) of m19089 (Mla6, Rar3, bln1) at 32 HAI


title: mla6_bln1_t16_rep1


title: mla6_bln1_t0_rep3


title: bln1_t48_rep2


title: bln1_t32_rep2


title: bln1_t32_rep1


title: bln1_t24_rep3

description: Barley infected first leaf (PO:0007094) of m19089 (Mla6, Rar3, bln1) at 24 HAI


title: bln1_t24_rep2


title: Mid log_wildtype_glc minimal media_aerobic rep1

status: Public on Jun 30 2014

city: La Jolla

first: Bernhard

middle: O

last: Palsson

state: CA

address: 9500 Gilman Dr

department: Bioengineering

institute: UC San Diego

data_processing:
Illumina read were aligned to NC_000913 using Bowtie 1 with 2 mismatches allowed per read alignment
FPKM were calculated using Cufflinks v.2.0.2 with upper-quartile normalization and fr-firststrand for library type
Differential expression analysis was carried out using cuffdiff v.2.0.2 with upper-quartile normalization and fr-firststrand for library type
Genome_build: NC_000913
Supplementary_files_format_and_content: csv files, FPKM values from pairwise comparisons

organism: Escherichia coli K-12

source_name: WT

growth_protocol: E. coli cultures were grown at  37 °C in M9 minimal media with glucose as the primary carbon source and harvested at mid exponetial phase. Aerobic E. coli conditions were grown in shake flasks and anaerobic conditions were grown in anoxic serum bottles.  Condition specific media supplementation was added as described else where.

extract_protocol:
Total RNA was isolated using the Rneasy Mini Kit procedure with on column Dnase treatment (Qiagen).
Paired-end, strand-specific RNAseq libraries were generated using the dUTP method {Levin JZ et al. 2010, Nat Methods} with the following modifications. rRNA was removed with Epicentre’s Ribo-Zero rRNA Removal Kit. Subtracted RNA was fragmented for 3 min using Ambion’s RNA Fragmentation Reagents. cDNA was generated using Invitrogen’s SuperScript III First-Strand Synthesis protocol with random hexamer priming.

treatment_protocol: Mid log cultures were treated with Qiagen RNA Protect reagent following the vendor's protocol. Cells were centrifuged and stored at -80 °C for <30 days prior to use.

tag: genotype/variation

value: wild type; MG1655

tag: growth stage

value: mid exponetial phase

tag: basal media

value: M9 + 4 g/L glc (glucose minimal media)

tag: oxygen condition

value: aerobic

tag: supplementation

tag: strain


title: WT Inflorescence sRNA

status: Public on Sep 04 2014

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

data_processing:
Adapter sequences were removed from raw sequence reads using crossmatch with a minimum match parameter of 5.
siRNA sequencing frequencies for 100 base windows along all five chromosomes were calculated by summation of the per-library sequencing frequencies of 21 and 24 nt siRNAs matching with 100% identity within the window by the number of times they matched the genome as a whole. Because the results of these calculations are on different scales, on the basis of the depth of each sequence library, a layer of per-library normalization based on the sum values of all small RNAs matching the genome was implemented.
Genome_build: TAIR8
Supplementary_files_format_and_content: UCSC wiggle format coverage files

organism: Arabidopsis thaliana

source_name: Inflorescence

extract_protocol: Small RNAs of 19-28nt were size selected by denaturing 15% PAGE, and cloned as previously described (Brennecke et al., 2007). Following ligation, small RNA libraries were reverse transcribed, PCR-amplified using the forward PCR primer (5’AATGATACGGCGACCACCGAACACTCTTTCCCTACACGACG 3’) and the reverse PCR primer (5’ CAAGCAGAAGACGGCATACGATTGATGGTGCCT ACAG3’) for 22 cycles using proofreading Taq polymerase, and the products of 105 to 120bp were isolated.

tag: genotype

value: wild type

tag: tissue

value: inflorescence

tag: cultivar

value: Columbia


title: Mid log_wildtype_glc minimal media_aerobic rep2


title: Heart, MI, rep4

status: Public on May 06 2014

first: Frederic

last: Burdet

address: Quartier Sorge - Batiment Amphipole

institute: Swiss Institute of Bioinformatics

description:
11L
12 week old mice, border zone of infarct, 2 weeks after surgery

data_processing:
Base calling was with Illumina GAP Pipeline Software v1.70
Sequence reads were processed to remove the adaptor sequences and reformatted to FASTA files using the FASTX-Toolkit
Sequences were aligned to mm9 reference genome using Tophat 2.0.5 with option -g with mm9 reference GTF
Novel transcripts were predicted with Cufflinks 2.0.2 with option -G with mm9 reference GTF
Novel transcripts predictions were merged with mm9 reference genome using Cuffmerge 2.0.2 with option -G with mm9 reference GTF
Counts were generated using htseq-count v0.5.4p2
Genome_build: mm9
Supplementary_files_format_and_content: Raw count data for genes were normalized to the relative size of each library using R/Bioconductor package DESeq, estimateSizeFactors function. Count data are provided in tab-delimited format

source_name: Heart, Sham

extract_protocol:
Total RNA was isolated using Trizol (Invitrogen). RNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 BioanalyzerRNA quantities and quality were assessed using a NanoDrop ND-1000 spectrophotometer or an Agilent 2100 Bioanalyzer.
Sequencing libraries were prepared according to Illumina long RNA Seq library kit instructions with Poly(A) selection. Libraries were sequenced with the Illumina HiSeq2000 (2x100bp).

value: heart

value: infarct


title: Heart, MI, rep3

description:
7R
12 week old mice, border zone of sham infarct, 2 weeks after surgery


title: mla6_bln1_t32_rep3

value: Blumeria graminis f. sp. hordei

value: Bgh isolate 5874

value: Rep 3


title: mla6_bln1_t48_rep1

value: 48 HAI

value: Rep 1


title: mla6_bln1_t24_rep1

value: 24 HAI


title: Col_FACS_pollen

status: Public on Dec 31 2017

city: Versailles

first: Filipe

last: Borges

address: Route de St-Cyr (RD10)

country: France

institute: Institut Jean-Pierre Bourgin - INRAE

description: Small RNA

data_processing:
After de-multiplexing, 36-nt reads were pre-processed by trimming the 3’ adapter and filtering collapsed reads according to length and quality.
Filtered reads were mapped to the Arabidopsis TAIR10 genome annotation (or GFP transgene) with bowtie reporting all multi-mappers.
Only perfect match reads were used for down-stream analysis, and reads mapped to multiple genomic locations where normalized by dividing non-redundant read counts by the number of genomic hits, and subsequently calculating the number of reads per million of filtered (18-30nt) and perfectly mapped reads.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt files with 18-30nt reads and counts, and RPM of 20-24nt reads mapped to TAIR10 features

source_name: Pollen

growth_protocol: Plants were grown under long day conditions at 22 °C. Seeds were always surface sterilized with sodium hypochlorite, sowed on Murashige and Skoog (MS) medium and stratified for 3 days at 4ºC. Seedlings were transplanted to soil two weeks after germination and grown under long day conditions at 22 °C.

extract_protocol:
Pollen was collected in 1.5mL eppendorf tubes by vortexing open flowers in pollen extraction buffer (PEB, 10 mM CaCl2, 2 mM MES, 1 mM KCl, 1% H3BO3, 10%) for 3 min, followed by filtration through a 30um mesh (Partec/Sysmex) and centrifugation at 5,000g for 1 min. Purification of pollen expressing the GFP-miR845b sensor in dcl1-5/+ and dcl1/+,dcl2/dcl4 mutants was performed by vortexing open flowers in 1 mL of PEB and filtering through a 30um mesh before FACS. Pollen population was identified in SSC/FSC scatter plots, and GFP fluorescence was analyzed by excitation with a 488nm laser and detected with a 530/30 bandpass filter. Pollen total RNA was extracted using Trizol LS reagent (Life Technologies) by vortexing with glass beads for 5 minutes, and concentrated with Direct-zol columns (Zymo Research).
Small RNAs were purified by running total RNA on acrylamide gels (15% polyacrylamide, 7M urea) and performing size selection of approximately 18 to 30-nt region using a small RNA ladder (Zymo Research). The small RNA fraction was isolated from acrylamide gel plugs by grinding with a plastic pestle in Trizol LS (Life Technologies), and concentrated using Direct-zol columns (Zymo Research). Libraries were prepared using the TruSeq Small RNA Sample Preparation Kit (Illumina) following manufacturer instructions.

tag: ecotype

value: Pollen


title: Heart, MI, rep2

description:
5O
12 week old mice, border zone of sham infarct, 2 weeks after surgery

tag: treatment


title: Heart, MI, rep1

description:
2L
12 week old mice, border zone of sham infarct, 2 weeks after surgery


title: mla6_bln1_t0_rep2

tag: pathogen

value: 0 HAI

value: Rep 2


title: Heart, Sham, rep3 (reanalysis)

description:
8R
12 week old mice, border zone of sham infarct, 2 weeks after surgery

value: sham


title: Heart, Sham, rep2 (reanalysis)

description:
7LR
12 week old mice, border zone of sham infarct, 2 weeks after surgery


title: Heart, Sham, rep1 (reanalysis)

description:
3RL
12 week old mice, border zone of sham infarct, 2 weeks after surgery


title: WT Pollen sRNA

value: pollen


title: Heart, Sham, rep4 (reanalysis)

description:
12RL
12 week old mice, border zone of infarct, 2 weeks after surgery


title: LCL_untreated_rep2

status: Public on Oct 26 2010

type: RNA

city: Birmingham

last: Halsall

address: Medical School, Vincent Drive

department: Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

description: This sample is of untreated lymphoblastoid cell cell line. It is the second of three biological replicates in this experiment, each from separate cultures

hyb_protocol: Hybridization was performed by the Functional Genomics Laboratory, University of Birmingham, Birmingham, UK following the standard Nimblegen operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by the Functional Genomics Laboratory, University of Birmingham, Birmingham, UK following the standard Nimblegen operating protocol. See www.nimblegen.com.

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

source_name: Lymphoblastoid cell line

label_protocol: Labeling was performed by the Functional Genomics Laboratory, University of Birmingham, Birmingham, UK following the standard Nimblegen operating protocol. See www.nimblegen.com.

growth_protocol: Immortalized, EBV-transformed lymphoblastoid cell lines (LCL) from healthy, karyotypically normal individuals were established in house and maintained at 37oC, 5% CO2 in RPMI 1640 medium, 10% foetal bovine serum, supplemented with L-glutamine (2mM) and penicillin/streptomycin (all additives from Gibco).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

treatment_protocol: Cells were seeded at 1x106 cells/ml, cultured for 24 hours and harvested in log phase.

tag: biological replicate

tag: cell type

value: Lymphoblastoid cell line


title: LCL_untreated_rep1

description: This sample is of untreated lymphoblastoid cell cell line. It is the first of three biological replicates in this experiment, each from separate cultures


title: LCL_untreated_rep3

description: This sample is of untreated lymphoblastoid cell cell line. It is the third of three biological replicates in this experiment, each from separate cultures