title: 761_INPUT

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

data_processing:
Library strategy: eCLIP-seq
Takes output from raw files.  Run to trim off both 5’ and 3’ adapters on both reads. Command: quality-cutoff 6  -m 18  -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT  AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1. Run to trim off the 3’ adapters on read 2, to control for double ligation events. Command: cutadapt -f fastq --match-read-wildcards  --times 1  -e 0.1  -O 5  --quality-cutoff 6  -m 18  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2.  Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir /path/to/RepBase_human_database_file --genomeLoad LoadAndRemove  --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz --outSAMunmapped Within  --outFilterMultimapNmax 30  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam --outSAMattributes All  --readFilesCommand zcat  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam
Takes output from STAR rmRep.  Maps unique reads to the human genome.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir  /path/to/STAR_database_file --genomeLoad LoadAndRemove  --readFilesIn  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate1  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate2  --outSAMunmapped Within  --outFilterMultimapNmax 1  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --outSAMattributes All  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam
takes output from STAR genome mapping.  Custom random-mer-aware script for PCR duplicate removal. Command: barcode_collapse_pe.py  --bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --out_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  --metrics_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.metrics
Takes output from barcode collapse PE.  Sorts resulting bam file for use downstream.  Command: java  -Xmx2048m  -XX:+UseParallelOldGC  -XX:ParallelGCThreads=4  -XX:GCTimeLimit=50  -XX:GCHeapFreeLimit=10  -Djava.io.tmpdir=/full/path/to/files/.queue/tmp  -cp /path/to/gatk/dist/Queue.jar  net.sf.picard.sam.SortSam  INPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  TMP_DIR=/full/path/to/files/.queue/tmp  OUTPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  VALIDATION_STRINGENCY=SILENT  SO=coordinate  CREATE_INDEX=true
Takes output from sortSam, makes bam index for use downstream.  Command: samtools index  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam.bai
Takes inputs from multiple final bam files.  Merges the two technical replicates for further downstream analysis.  Command: samtools  merge  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.D08.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam
Takes output from sortSam, makes bam index for use downstream.  Command: samtools  index  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/CombinedID.merged.bam.bai
Takes output from sortSam.  Only outputs the second read in each pair for use with single stranded peak caller.  This is the final bam file to perform analysis on.  Command: samtools view -hb -f 128  /full/path/to/files/CombinedID.merged.bam  >  /full/path/to/files/CombinedID.merged.r2.bam
Takes results from samtools view.  Calls peaks on those files.  Command: clipper  -b /full/path/to/files/CombinedID.merged.r2.bam  -s hg19  -o /full/path/to/files/CombinedID.merged.r2.peaks.bed  --bonferroni  --superlocal  --threshold-method binomial  --save-pickle
Genome_build: hg19
Supplementary_files_format_and_content: bed format, contains clusters of predicted RBP binding

growth_protocol: HepG2 cells were grown under standard conditions (DMEM + 10% FBS + Pen/Strep (100U / mL)). K562 cells were grown in suspension in standard media (RPMI + 10% FBS + Pen/Strep (100U / mL)).

extract_protocol:
Cells were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes.
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB) (at this step, multiple replicates of the same RBP, or potentially RBPs of similar size and bound RNA amount, can be uniquely barcoded and pooled after ligation to simplify downstream steps - see Supplementary Fig. 2A). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

treatment_protocol: While plated, HepG2 cells were crosslinked with UV (254 nm, 400 mJ/cm2). HepG2 cells were then isolated with cell scrapers, pelleted at 200g, and snap frozen. K562 suspension cells were pelleted at 200g and resuspended in 1X PBS to 20 million cells per mL. 60 million cells in 3 mL were UV crosslinked (254 nm, 400 mJ/cm2) per 10 cm dish, pelleted, and snap frozen.

tag: barcodes

tag: antibody

tag: antibody catalog#

tag: antibody lot#


title: 714_INPUT

status: Public on Sep 22 2018

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line


title: pns1 (peripheral neurons)

city: Seattle

first: Jay

last: Parrish

state: Washington

department: Department of Biology

institute: University of Washington

description: Each sample isolated independently

data_processing:
Bases were called and reads were demultiplexed with Illumina CASAVA 1.8.2
Reads were filtered for the presence of adapters using Cutadapt version 1.9.1
Reads were aligned to the transcriptome using STAR version 2.5.2b with the option ‘--quantMode TranscriptomeSAM’
Transcript expression per sample, in transcripts per million (TPM), was calculated with Salmon version 0.7.2 in alignment based mode
Gene expression per sample, in transcripts per million (TPM), was calculated by summing the transcript expression for all transcripts of a given gene
Genome_build: FlyBase genome release 6.10
Supplementary_files_format_and_content: Tab delimited text files showing tpm for all isoforms for each sample
Supplementary_files_format_and_content: Tab delimited text files showing tpm for all genes for each sample

organism: Drosophila melanogaster

source_name: peripheral neurons

extract_protocol:
Cells were isolated by FACS on an AriaII and snap frozen in lysis buffer. Total RNA was isolated with the RNAqueous Micro Kit (Ambion AM1931), converted to cDNA, and pre-amplified as described in the SMARTer Ultra-low input kit (Clontech PN 634833) but with modified procedures for low cell number analysis (Fluidigm)
RNA libraries were prepared for sequencing following Illumina protocols.  cDNA libraries were diluted to 0.25ng/ul, fragmented with the Nextera XT DNA kit (Illumina PN FC-131-1024), multiplexed, and sequenced on a Hi-Seq2500

tag: developmental stage

value: third instar

tag: genotype

value: elav-Gal4 > UAS-Red Stinger

tag: tissue

value: bodywall

tag: quantity

value: 100 cells


title: epithelia4

description: Each sample isolated independently

source_name: bodywall epidermis

value: A58-Gal4 > UAS-Red Stinger


title: cns1

description: All five samples isolated together and RNA extraction performed prior to separating into five samples

source_name: central neurons

value: brain


title: 658_INPUT


title: 647_INPUT


title: 626_INPUT


title: 567_INPUT


title: 613_INPUT


title: 679_INPUT


title: 531_INPUT


title: OA-treated [qi]

type: RNA

city: Tianjin

first: long

middle: wei

last: zhong

state: Tianjin

address: Tianjin International Joint Academy of Biotechnology and Medicine,TJAB

country: China

institute: NanKai University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

source_name: PLC-PRF-5 cells were treated with OA (50 μM) for 24h

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: PLC cells (5 × 103 cells/mL) were seeded in 96-well culture plates for 20h

extract_protocol: TRIzol Reagent (Invitrogen) was then used to lyse cells and extract the total RNA

treatment_protocol: PLC-PRF-5 cells were treated with OA (50 μM) or DMSO for 24 h.

tag: cell type

value: liver hepatoma cell line

tag: treatment

value: OA (50 μM) for 24hrs


title: DMSO-treated [C1]

source_name: PLC-PRF-5 cells were treated with DMSO for 24h

value: DMSO 24hrs


title: 588_INPUT

value: custom ab from Mao lab


title: preterm 1 LPS stimulated

city: Vancouver

first: Pascal

last: Lavoie

state: BRITISH COLUMBIA

address: 950 West 28th Avenue

country: Canada

institute: BC Children's Hospital

hyb_protocol: The RNA-loaded BeadChip was hybridized in the illumina Hybridization Oven for 18 hours at 58oC and followed by wash steps and Cy3-Streptavidin bind to analytical probes step.

scan_protocol: BeadChip information from the Illumina HiScan SQ was extracted for each chip using Illumina software.

data_processing: Data were analyzed using R. Data was preprocessed by quantile normalization and log2 transformation. Probes that were non-expressed (based on their detection p-values) were removed. For differential gene analyses, linear models were fit using limma 26. Probes with FDR ≤0.05 were considered differentially expressed.

label: Biotin

source_name: preterm CD14+ LPS stimulated

label_protocol: The biotin-labeled cRNA was performed by illumina TotalPrep RNA Amplification kit.cRNA was quantified using NanoDrop 2000 sepectrophometer and the size distribution of cRNA was evaluated using Agilient 2100 Bioanalyzer.

growth_protocol: Monocytes were purified from peripheral or cord blood using CD14+ selection kit.

extract_protocol: Total RNA was extracted using the MagJET RNA purification kit. RNA was quantified using NanoDrop™ 1000 spectrophotometer, and its integrity was determined using the Agilent 2100 Bioanalyzer

treatment_protocol: CD14+ cells were cultured for 5h with or without 10ng/ml LPS in RPMI supplemented with 2 mM L-glutamine, 10% human AB serum and Pen-strep.

value: preterm

tag: tissue source

value: cord blood

tag: stimulation condition

value: 5h LPS stimulated


title: 415_INPUT


title: 529_INPUT


title: preterm 3 LPS stimulated


title: preterm 8 LPS stimulated


title: preterm 2 LPS stimulated


title: 332_INPUT


title: preterm 3

source_name: preterm CD14+ unstimulated

value: 5h unstimulated


title: preterm 5


title: preterm 4 LPS stimulated


title: 417_INPUT


title: preterm 8


title: preterm 7


title: 761_02


title: 366_INPUT


title: preterm 1


title: 761_01


title: preterm 6 LPS stimulated


title: 647_02


title: preterm 6


title: term 12 LPS stimulated

source_name: term CD14+ LPS stimulated

value: term


title: term 11 LPS stimulated


title: preterm 4


title: term 9 LPS stimulated


title: term 10 LPS stimulated


title: 714_01


title: preterm 2


title: 647_01


title: 679_02


title: 714_02


title: term 8 LPS stimulated


title: term 7 LPS stimulated


title: term 6 LPS stimulated


title: term 5 LPS stimulated


title: term 4 LPS stimulated


title: 658_01


title: term 3 LPS stimulated


title: term 2 LPS stimulated


title: Genomic DNA from twin A of pair 17

type: genomic

city: Barcelona

first: Lourdes

last: Fañanás

address: Av. Diagonal, 643, 2nd floor

department: Evolutionary Biology, Ecology and Environmental Sciences

country: Spain

institute: University of Barcelona

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Methylation Module of GenomeStudio software using HumanMethylation450 manifest v1.1

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Peripheral blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from peripheral blood using Durviz Realpure SSS Kit according to standard instructions

value: Peripheral blood

tag: pair number

value: pair 17

tag: gender

value: female

tag: age

tag: diagnosis

value: Healthy twin from discordant pair


title: 588_02

tag: barcodes


title: 588_01

tag: antibody


title: Arl13b_Rep3

city: Chapel Hill

first: Travis

last: Ptacek

state: NC

address: 5109 Neuroscience Research Building

institute: UNC Neuroscience Center Bioinformatics Core

data_processing:
Illumina Casava software used for base calling
Quality filtering was performed using FASTX v0.0.14 fastq_quality_filter for reads with 90% of bases having a quality of 20+
Reads aligned to reference genome using STAR v2.6.0
Gene expression quantified using salmon v0.9.1
Differential gene expression tested using DESeq v1.16.1
Genome_build: mm9
Supplementary_files_format_and_content: Matrix of VST normalized counts from DESeq2 for all genes and samples

molecule: polyA RNA

organism: Mus musculus

source_name: Telencephalon

extract_protocol:
RNA was extracted using RNeasy plus mini kit according to manufacturer's manual (Cat. #74134, Qiagen)
RNA samples were prepared for sequencing using standard Illumina protocols

value: Telencephalon

tag: strain


title: Genomic DNA from twin B of pair 17

value: Affected twin from discordant pair


title: 679_01

tag: antibody catalog#

tag: antibody lot#


title: term 12

source_name: term CD14+ unstimulated

tag: developmental stage


title: Genomic DNA from twin B of pair 16

value: pair 16

value: male


title: 626_02

tag: cell line


title: term 10


title: 626_01


title: term 11


title: Arl13b_Rep1

tag: tissue

tag: genotype


title: 658_02


title: term 9

tag: cell type


title: Genomic DNA from twin B of pair 13

value: pair 13

value: Affected twin from concordant pair


title: term 8


title: Ctl_Rep3

value: Wild-type


title: Genomic DNA from twin B of pair 15

value: pair 15

value: Healthy twin from healthy pair


title: term 1 LPS stimulated

value: cord blood


title: Genomic DNA from twin A of pair 14

value: pair 14


title: Genomic DNA from twin A of pair 16


title: Genomic DNA from twin B of pair 14


title: 613_02


title: Genomic DNA from twin A of pair 15


title: Ctl_Rep1


title: Genomic DNA from twin B of pair 12

value: pair 12


title: Genomic DNA from twin A of pair 13


title: Genomic DNA from twin A of pair 11

value: pair 11


title: Ctl_Rep2


title: Genomic DNA from twin A of pair 12

value: Peripheral blood


title: 613_01


title: 531_01


title: Genomic DNA from twin B of pair 09

value: pair 09


title: 529_02


title: Genomic DNA from twin B of pair 11

value: female


title: 531_02


title: Arl13b_Rep2


title: term 4

value: term

value: 5h unstimulated


title: term 5


title: 529_01


title: Genomic DNA from twin B of pair 10

value: pair 10


title: term 7


title: 567_02


title: TugelaDn5 infested leaf_48h, biological repeat 3_2

city: Stellenbosch

first: Anna-Maria

last: Botha-Oberholster

state: WP

address: Genetics, JC Smuts Building Rm 214, Stellenbosch

department: Genetics

country: South Africa

institute: Stellenbosch University

description: Diuraphid noxia (RWA) infested  TugelaDn1 wheat leaf (48h)(RWA resistant )

hyb_protocol: Hybridization was done according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

scan_protocol: Scanning was conducted following standard proceedures.

data_processing: Different quality control checks were conducted, Statstical analysis of data using Bioconductor in R were conducted as detailed in Botha et al. 2014.

organism: Triticum aestivum

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

growth_protocol: Hexaploid wheat seed were planted on pots (5 seed/pot) under greenhouse conditions in a 1:2:2:1 mixture of perlite (Chemserve, Olifantsfontein, South Africa), sifted bark compost, loam and sand at 25°C +2°C.

extract_protocol: Leaf tissue was ground in Liq N2 and incubated in PureLink Plant RNA purification Reagent (Invitrogen, USA) and RNA was then extracted usinf Qiagen Rneasy Plant Mini Kit with on-column DNAse1 digestion. Analysis was conducted at the Centre for Proteomic and Genomic Research (CPGR, Cape Town, South Africa).

treatment_protocol: Plant were infested at three leaf stage with 10 aphids/plant (no choice feeding).

tag: phenotype

value: RWA resistant

tag: host response

value: Antibiosis and antixenosis

tag: aphid response

value: Non-virulent


title: term 2

tag: tissue source

tag: stimulation condition


title: TugelaDn5 infested leaf_48h, biological repeat 3


title: Genomic DNA from twin B of pair 08

tag: pair number

value: pair 08

tag: gender

value: male

tag: age


title: Genomic DNA from twin A of pair 09

tag: diagnosis

value: Affected twin from discordant pair


title: 567_01

tag: barcodes

tag: antibody


title: 417_02

tag: antibody catalog#

tag: antibody lot#


title: 417_01

tag: cell line


title: Genomic DNA from twin A of pair 08

tag: tissue

value: Healthy twin from healthy pair


title: Genomic DNA from twin A of pair 10


title: term 6

tag: developmental stage

value: cord blood


title: Genomic DNA from twin B of pair 07

value: pair 07

value: Affected twin from concordant pair


title: Genomic DNA from twin A of pair 07


title: TugelaDn5 infested leaf_48h, biological repeat 2

tag: genotype


title: TugelaDn2 infested leaf_48h, biological repeat 3

tag: phenotype

value: Tolerance


title: adult 5 LPS stimulated

source_name: adult CD14+ LPS stimulated

value: adult

value: peripheral blood

tag: cell type

value: 5h LPS stimulated


title: adult 12 LPS stimulated


title: Genomic DNA from twin B of pair 06

value: Peripheral blood

value: pair 06

value: female


title: TugelaDn2 infested leaf_48h, biological repeat 2

value: RWA resistant

tag: host response

tag: aphid response


title: term 3

value: term

tag: tissue source

tag: stimulation condition

value: 5h unstimulated


title: 366_02


title: adult 9 LPS stimulated


title: 366_01


title: 415_02


title: Genomic DNA from twin B of pair 05

tag: pair number

value: pair 05

tag: gender


title: 415_01


title: Genomic DNA from twin A of pair 06

tag: age

tag: diagnosis

value: Healthy twin from discordant pair


title: 332_02

tag: barcodes

tag: antibody


title: TugelaDn5 infested leaf_48h, biological repeat 1

value: Antibiosis and antixenosis

value: Non-virulent


title: adult 2 LPS stimulated


title: Genomic DNA from twin A of pair 05

value: Healthy twin from healthy pair


title: term 1

value: cord blood


title: TugelaDn1 infested leaf_48h, biological repeat 3

value: Antibiosis


title: TugelaDn1 infested leaf_48h, biological repeat 2


title: TugelaDn2 infested leaf_48h, biological repeat 1

value: Tolerance


title: adult 11 LPS stimulated

value: adult


title: TugelaDn1 infested leaf_48h, biological repeat 1


title: adult 8 LPS stimulated

value: peripheral blood


title: adult 10 LPS stimulated

value: 5h LPS stimulated


title: adult 1 LPS stimulated


title: Genomic DNA from twin B of pair 04

value: Peripheral blood

value: pair 04

value: male


title: Genomic DNA from twin A of pair 04


title: P5 Xbp1 WT Matn3 MUT

city: Newcastle Upon Tyne

first: Katarzyna

last: Pirog

address: International Centre for Life

country: United Kingdom

institute: Newcastle University

description: Gene expression data

hyb_protocol: Following fragmentation,  cRNA were hybridized on Mouse 420A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 6 (MAS 6.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: P5 constochondral chondrocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Tissues were harvested at postnatal day 5 (P5).

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

treatment_protocol: Cells were harvested using standard collagenase digestion.

value: cartilage

value: postnatal day 5


title: Tugela infested leaf_48h, biological repeat 1

description: Diuraphid noxia (RWA) infested  Tugela wheat leaf (48h)(RWA susceptible )

value: RWA susceptible

value: Virulent


title: MT3

city: Granada

first: Mohammed

last: Bakkali

address: Facultad de Ciencias, Fuentenueva S/N

institute: Universidad de Granada

data_processing:
alignement using BWA+xa2multi+Samtools
read count using htseq
staistical analysis, GLM, using EdgeR
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: tab delimited text file containing the normalized read counts for each sample and locus

source_name: mutant with a reduction in the characteristics of Mitochondrial Encephalopathy due to the treatment with β-Resorcylic Acid

extract_protocol:
The RNeasy Lipid Tissue Mini Kit (Qiagen) was used to extract total RNAs from the brainstem of five animals in each experimental group. The quality and quantity of the RNAs were evaluated by gel electrophoresis and using a NanoDrop® ND-1000 Spectrophotometer. 5 mg of the total RNA of each sample were then added to a separate tube containing 100 ml of ethanol plus 10% 3 M sodium acetate, pH 5.2. The tubes were then shipped in dry ice to Macrogen Inc. (Korea) for sequencing.
The RNAs were precipitated and their quality and quantity assessed using an Agilent Bioanalyzer 2100 and an RNA 6000 chip (Agilent Technologies). The cDNA libraries were then constructed using the TruSeq RNA Sample Prep Kit v2 (Illumina, Inc.) and their quality checked using an Agilent Bioanalyzer 2100 and a DNA 1000 chip (Agilent Technologies).
The libraries were Paired End sequenced in a HiSeq 4000 system (Illumina, Inc.)

value: Beta-RA-treated Coq9R239X

value: brainstem


title: Genomic DNA from twin B of pair 02

value: pair 02

value: female

value: Affected twin from concordant pair


title: Genomic DNA from twin A of pair 02


title: MT5


title: 332_01

tag: antibody catalog#

tag: antibody lot#


title: MT4

tag: tissue


title: adult 6 LPS stimulated

tag: developmental stage


title: adult 12

source_name: adult CD14+ unstimulated

value: 5h unstimulated


title: Genomic DNA from twin B of pair 03

value: pair 03

value: Healthy twin from discordant pair


title: Genomic DNA from twin A of pair 03

value: Affected twin from discordant pair


title: adult 4 LPS stimulated

value: adult

value: peripheral blood

value: 5h LPS stimulated


title: Tugela infested leaf_48h, biological repeat 2

tag: genotype


title: MT2


title: adult 11


title: P5 Xbp1 KO Matn3 MUT

description: Gene expression data


title: M4

source_name: mutant showing Mitochondrial Encephalopathy


title: Tugela infested leaf_48h, biological repeat 3

tag: phenotype


title: P5 Xbp1 KO

description: Gene expression data


title: M5


title: M3


title: MT1


title: M2


title: Genomic DNA from twin B of pair 01

value: Peripheral blood

value: pair 01

value: male

value: Healthy twin from healthy pair


title: W4

source_name: wildtype


title: adult 8

tag: cell type


title: W5


title: adult 6


title: M1


title: W3


title: Genomic DNA from twin A of pair 01


title: adult 5


title: adult 4


title: adult 7


title: E12D008b02: urinary DNA from healthy control #2

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

country: Germany

institute: University of Tuebingen

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation450 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2, Bioconductor 'methylumi' package

source_name: DNA from urine

extract_protocol: Urine was centrifuged (1700 g, 10 min, 10°C), sediment was washed with 500 µL PBS. The sample was centrifuged again (4000 g, 10 min, 10°C) and the cells were resolved in 200 µL PBS and immediately stored at -80°C until DNA isolation with QIAmp MinElute Virus Spin Kit (Qiagen, Hilden, Germany) was used according to the recommendations of the manufacturer.

value: healthy control

value: urine

tag: ID


title: adult 3


title: adult 10


title: adult 9


title: adult 2


title: E12D008b06: urinary DNA from healthy control #6


title: CRC tissues with distant metastasis

city: Guangzhou

first: Zeng

last: zhicheng

department: Department of Pathology and Guangdong Province Key Laboratory of Molecular Tumor Pathology

institute: Southern Medical University

description: The results were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a microcirculation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics)

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).

source_name: CRC tissues with distant metastasis

label_protocol: The assay started from 2 to 5 µg total RNA sample were 3’ -extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

extract_protocol: Total RNA was extracted using the Animal Tissue RNA Purification Kit (Norgen Biotek Corporation, Thorold, Canada), following the manufacturer's recommended protocol.

value: CRC tissues with distant metastasis


title: E12D008b05: urinary DNA from healthy control #5


title: adult 1


title: E12D008b03: urinary DNA from healthy control #3


title: DLTPrc CvgrR-his

city: BeiJing

first: ChaoYing

last: Deng

state: BeiJing

address: No. 1 Beichen West Road, Chaoyang District

institute: Chinese Academy of Sciences

library_source: genomic

data_processing:
An Illumina HiSeq-2000 system (Illumina, San Diego, CA USA) was used for high-throughput sequencing, which was conducted by the Beijing Institute of Genomics genomic service.
The high-throughput sequencing reads were analysed using the Burrows–Wheeler Aligner method, and the cleaned reads were aligned to the genomic sequence database of X. campestris pv. campestris 8004.
Peak calling was conducted by MACS2
The consensus binding motif analysis was completed with MEME and FIMI tools in the MEME software suite.
Genome_build: GCA_000012105.1
Supplementary_files_format_and_content: wig files

organism: Xanthomonas campestris pv. campestris str. 8004

source_name: DLTPrc CvgrR-his

extract_protocol:
After collection by centrifugation, the samples were crossing-linked with 1% (V/V) formaldehyde for 20 min and subsequently quenched with 20% (V/V) 0.5 M glycine for 10 min. Then, the bacterial cells were recollected, washed with cold PBS (0.27 g/l KH2PO4, 1.42 g/l Na2HPO4, 8 g/l NaCl, and 0.2 g/l KCl, pH 7.4) twice, and resuspended in ChIP lysis buffer (10 mM Tris pH 8.0, 20% sucrose, 50 mM NaCl, 10 mM EDTA, pH 8.0, 10 mg/ml lysozyme, and 1 mM PMSF). Quadruple the lysis buffer volume of immuno-precipitation buffer (50 mM HEPES-KOH, pH 7.5, 150 mM NaCl, 1 mM EDTA, pH 8.0, 1% Triton X-100, 0.1% sodium deoxycholate, and 0.1% SDS) was added to the bacterial cell suspension, and the suspension was sonicated with a Diagenode Bioruptor (Diagenode, Liège, Belgium), generating 100–300-bp DNA fragments.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit

treatment_protocol: The bacterial strains grown in NYG medium until OD600 = 0.8 ± 0.05 were treated with or without 800 mM sorbitol for 5 min.

value: prc mutant

tag: treatment

value: osmostress

tag: chip antibody

value: anti-His6 antibody (Abmart, #M20001, lot:294073)


title: W1

value: brainstem


title: W2


title: WT CvgrR-his

source_name: WT CvgrR-his

value: wildtype


title: CRC tissues without metastasis

source_name: CRC tissues without metastasis

value: CRC tissues without metastasis


title: E12D008b01: urinary DNA from healthy control #1


title: adult 3 LPS stimulated

tag: tissue source

tag: stimulation condition


title: Normal mucosa

source_name: Normal mucosa

value: Normal mucosa


title: E12D008b04: urinary DNA from healthy control #4

tag: gender


title: TamCre ETP-4

status: Public on Sep 21 2018

city: Ann Arbor

first: Richard

middle: C

last: McEachin

state: United States

address: 2800 Plymouth Road

department: DCM&B

institute: University of Michigan

description:
43-44 hours post tamoxifen injection
2_genotype_repRawCounts.txt
Sample_79364

data_processing:
FastQC version 0.10.0 (http://www.bioinformatics.bbsrc.ac.uk/projects/fastqc/) was used to identify features of the raw data that may indicate quality problems
The Tuxedo Suite was used to align reads to the reference transcriptome (UCSC mm10) (http://genome.ucsc.edu/) using TopHat (version 2.0.9) and Bowtie (version 2.1.0.0). Default parameter settings were used for alignment, with the exception of: “--b2-very-sensitive” telling the software to spend extra time searching for valid alignments, as well as “--no-coverage-search” and “--no-novel-juncs” to limit the read mapping to known transcripts.
FastQC was used for a second round of quality control (post-alignment), to ensure that only high quality data would be input to expression quantitation and differential expression analysis
Cufflinks/CuffDiff (version 2.1.1) was used for expression quantitation and differential expression analysis, using UCSC mm10.fa as the reference genome sequence and UCSC mm10.gtf as the reference transcriptome annotation. Thsi analysis used parameter settings: “--multi-read-correct” to adjust expression calculations for reads that map in more than one locus, as well as “--compatible-hits-norm” and “--upper-quartile –norm” for normalization of expression values.
Locally developed scripts were used to format and annotate the differential expression data output from CuffDiff. Briefly, we identified genes and transcripts as being differentially expressed based on three criteria: test status = “OK”, FDR < 0.05 and fold change ≥ 1.5. Genes and isoforms were annotated with NCBI Entrez GeneIDs, text description, and Gene Ontology (GO) (http://david.abcc.ncifcrf.gov/) terms using NCBI annotation.
Genome_build: mm10
Supplementary_files_format_and_content: Fpkm data

source_name: TamCre ETP-4

growth_protocol: Dapi-CD44+CD25-Lineage- DN3 thymocytes and Dapi-CD44+cKit+CD25-Lineage- ETP were sorted with a BD AriaII from live mice directly into RLT-plus buffer (Qiagen)

extract_protocol:
Total RNA was extracted from 100K-400K DN3 cells and 5K-20K ETP cells using the RNeasy Plus Micro kit (Qiagen) according to the manufacturer’s protocol.
ΔMxCre, MxCre, Anti-NRR antibody, and Control IgG antibody sequencing libraries for DN3 and ETP cells were prepped from 10 ng of total RNA using the Takara RiboGone kit (634846) and the Clontech SMARTer Ultra low input RNA kit (6348493) using a modified protocol allowing for low input for anti-Notch1 and pI-pC treated cells. ΔTamCre and TamCre sequencing libraries for DN3 cells were prepped from 100 ng of total RNA using the Illumina TruSeq mRNA Sample Prep v2 kit (RS-122-2001, RS-122-2002). ΔTamCre and TamCre sequencing libraries for ETP cells were prepped from 1 ng of total RNA using the Takara SMARTer STranded Total RNA-Seq Pico Input Mammalian kit (635005, 635006, 635007). Library preparation was performed according to the manufacturer's protocol by the University of Michigan Sequencing Core. Libraries from ΔMxCre, MxCre, Anti-NRR antibody, and Control IgG antibody treated cells were amplified using 16 cycles of PCR. Libraries from tamoxifen treated cells were amplified using 12 cycles of PCR for DN3 cells and 15 cycles for ETP cells. RNA-Seq results generated from different kits were not directly compared against each other. Libraries were checked for size on the TapeStation and quantified using the Kapa Biosystems library quantification kit (KK4835) for Illumina adapters.

treatment_protocol: Rosa26CreERT2Zmiz1f/f (DeltaTamCre) mice and Rosa26CreERT2 (TamCre) control mice (4 mice per group) were injected with 0.2 mg/g tamoxifen IP. DN3 and ETP cells were sorted at 43-44 hours post-injection. MxCreZmiz1f/f mice and control MxCre mice (3 mice per group) were injected with 40 mcg pI-pC IP every 2 days for 5 times. DN3 and ETP cells were sorted at 8 weeks post-injection. Mice were injected with 10 mg/kg anti-NRR Notch1 antibody (Genentech) or the isotype control IgG antibody (Genentech) IP prior to sorting of DN3 and ETP cells at 24 hours post-injection.

tag: strain

value: ETP thymocytes

tag: time point

value: 43-44 hours

tag: agent

value: tamoxifen


title: E12D008a04: urinary DNA from urothelial cancer patient #4

tag: diagnosis

value: urothelial cancer

tag: age


title: P5 Xbp1 WT

description: Gene expression data

value: cartilage

value: postnatal day 5


title: TamCre ETP-1

description:
43-44 hours post tamoxifen injection
2_genotype_repRawCounts.txt
Sample_79361

source_name: TamCre ETP-1


title: TamCre DN3-4

description:
43-44 hours post tamoxifen injection
1_genotype_repRawCounts.txt
Sample_79356

source_name: TamCre DN3-4

value: DN3 thymocytes


title: DeltaTamCre DN3-1

description:
43-44 hours post tamoxifen injection
1_genotype_repRawCounts.txt
Sample_79357

source_name: DeltaTamCre DN3-1


title: DeltaTamCre DN3-2

description:
43-44 hours post tamoxifen injection
1_genotype_repRawCounts.txt
Sample_79358

source_name: DeltaTamCre DN3-2


title: E12D008a05: urinary DNA from urothelial cancer patient #5

value: male


title: TamCre DN3-3

description:
43-44 hours post tamoxifen injection
1_genotype_repRawCounts.txt
Sample_79355

source_name: TamCre DN3-3


title: DeltaMxCre ETP-3

description:
8 weeks post pI-pC injection
0_genotype_repRawCounts.txt
Sample_51586

source_name: DeltaMxCre ETP-3

value: 8 weeks

value: pI-pC


title: DeltaMxCre ETP-2

description:
8 weeks post pI-pC injection
0_genotype_repRawCounts.txt
Sample_51585

source_name: DeltaMxCre ETP-2


title: Control IgG antibody-treated ETP-3

description:
24 hours post antibody injection
0_genotype_repRawCounts.txt
Sample_51579

source_name: Control IgG antibody-treated ETP-3

value: 24 hours

value: antibody


title: Anti-NRR antibody-treated ETP-2

description:
24 hours post antibody injection
0_genotype_repRawCounts.txt
Sample_51581

source_name: Anti-NRR antibody-treated ETP-2


title: Anti-NRR antibody-treated ETP-1

description:
24 hours post antibody injection
0_genotype_repRawCounts.txt
Sample_51580

source_name: Anti-NRR antibody-treated ETP-1


title: E12D008a01: urinary DNA from urothelial cancer patient #1

source_name: DNA from urine

value: urine


title: DeltaTamCre DN3-4

description:
43-44 hours post tamoxifen injection
1_genotype_repRawCounts.txt
Sample_79360

source_name: DeltaTamCre DN3-4


title: DeltaTamCre DN3-3

description:
43-44 hours post tamoxifen injection
1_genotype_repRawCounts.txt
Sample_79359

source_name: DeltaTamCre DN3-3


title: Control IgG antibody-treated ETP-2

description:
24 hours post antibody injection
0_genotype_repRawCounts.txt
Sample_51578

source_name: Control IgG antibody-treated ETP-2


title: E12D008a06: urinary DNA from urothelial cancer patient #6


title: E12D008a03: urinary DNA from urothelial cancer patient #3


title: E12D008a02: urinary DNA from urothelial cancer patient #2


title: Anti-NRR antibody-treated DN3-3

description:
24 hours post antibody injection
0_genotype_repRawCounts.txt
Sample_51577

source_name: Anti-NRR antibody-treated DN3-3


title: Control IgG antibody-treated DN3-2

description:
24 hours post antibody injection
0_genotype_repRawCounts.txt
Sample_51573

source_name: Control IgG antibody-treated DN3-2


title: MxCre ETP-3

description:
8 weeks post pI-pC injection
0_genotype_repRawCounts.txt
Sample_51584

source_name: MxCre ETP-3


title: Control IgG antibody-treated DN3-3

description:
24 hours post antibody injection
0_genotype_repRawCounts.txt
Sample_51574

source_name: Control IgG antibody-treated DN3-3


title: Anti-NRR antibody-treated DN3-1

description:
24 hours post antibody injection
0_genotype_repRawCounts.txt
Sample_51575

source_name: Anti-NRR antibody-treated DN3-1


title: TamCre DN3-1

description:
43-44 hours post tamoxifen injection
1_genotype_repRawCounts.txt
Sample_79353

source_name: TamCre DN3-1


title: DeltaTamCre ETP-2

description:
43-44 hours post tamoxifen injection
2_genotype_repRawCounts.txt
Sample_79366

source_name: DeltaTamCre ETP-2


title: MxCre ETP-2

description:
8 weeks post pI-pC injection
0_genotype_repRawCounts.txt
Sample_51583

source_name: MxCre ETP-2


title: DeltaTamCre ETP-1

description:
43-44 hours post tamoxifen injection
2_genotype_repRawCounts.txt
Sample_79365

source_name: DeltaTamCre ETP-1


title: DeltaTamCre ETP-3

description:
43-44 hours post tamoxifen injection
2_genotype_repRawCounts.txt
Sample_79367

source_name: DeltaTamCre ETP-3


title: DeltaTamCre ETP-4

description:
43-44 hours post tamoxifen injection
2_genotype_repRawCounts.txt
Sample_79368

source_name: DeltaTamCre ETP-4


title: TamCre ETP-3

description:
43-44 hours post tamoxifen injection
2_genotype_repRawCounts.txt
Sample_79363

source_name: TamCre ETP-3


title: Anti-NRR antibody-treated DN3-2

description:
24 hours post antibody injection
0_genotype_repRawCounts.txt
Sample_51576

source_name: Anti-NRR antibody-treated DN3-2


title: Anti-NRR antibody-treated ETP-3

description:
24 hours post antibody injection
0_genotype_repRawCounts.txt
Sample_51582

source_name: Anti-NRR antibody-treated ETP-3


title: TamCre ETP-2

description:
43-44 hours post tamoxifen injection
2_genotype_repRawCounts.txt
Sample_79362

source_name: TamCre ETP-2


title: MxCre DN3-2

description:
8 weeks post pI-pC injection
0_genotype_repRawCounts.txt
Sample_51568

source_name: MxCre DN3-2


title: Control IgG antibody-treated DN3-1

description:
24 hours post antibody injection
0_genotype_repRawCounts.txt
Sample_51566

source_name: Control IgG antibody-treated DN3-1


title: Control IgG antibody-treated ETP-1

description:
24 hours post antibody injection
0_genotype_repRawCounts.txt
Sample_51567

source_name: Control IgG antibody-treated ETP-1


title: DeltaMxCre DN3-3

description:
8 weeks post pI-pC injection
0_genotype_repRawCounts.txt
Sample_51572

source_name: DeltaMxCre DN3-3


title: MxCre DN3-1

description:
8 weeks post pI-pC injection
0_genotype_repRawCounts.txt
Sample_51563

source_name: MxCre DN3-1


title: DeltaMxCre DN3-1

description:
8 weeks post pI-pC injection
0_genotype_repRawCounts.txt
Sample_51570

source_name: DeltaMxCre DN3-1


title: MxCre DN3-3

description:
8 weeks post pI-pC injection
0_genotype_repRawCounts.txt
Sample_51569

source_name: MxCre DN3-3


title: DeltaMxCre DN3-2

description:
8 weeks post pI-pC injection
0_genotype_repRawCounts.txt
Sample_51571

source_name: DeltaMxCre DN3-2


title: DeltaMxCre ETP-1

description:
8 weeks post pI-pC injection
0_genotype_repRawCounts.txt
Sample_51565

source_name: DeltaMxCre ETP-1


title: MxCre ETP-1

description:
8 weeks post pI-pC injection
0_genotype_repRawCounts.txt
Sample_51564

source_name: MxCre ETP-1


title: TamCre DN3-2

description:
43-44 hours post tamoxifen injection
1_genotype_repRawCounts.txt
Sample_79354

source_name: TamCre DN3-2


title: R23V_162

city: Saint-Pée-sur-Nivelle

first: Thérèse

last: Callet

country: France

institute: INRA

description: Gene expression after 5 weeks of feeding

hyb_protocol: 600ng of Cy3-cRNA was then fragmented with a specific buffer (30 minutes at 60°C) and hybridized on a sub-array. Hybridization was performed in a microarray hybridization oven (Agilent) for 17h at 65°C.

scan_protocol: After a washing step, slides were scanned (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3μm and 20bits). Data were then obtained with the Agilent Feature Extraction software (10.7.1.1).

data_processing: Data from microarray analysis were transformed with a logarithmic transformation, scale-normalized and analyzed using the package limma from R. The quality of each sample was controlled using the ArrayQualityMetrics package  and two samples (A22M_117 and R23M_146 ) were excluded from the analysis, as they did not pass the quality control.

organism: Oncorhynchus mykiss

source_name: R23, V diet

label_protocol: For each sample, 150 ng of total RNA was amplified and labelled using Cy3-CTP according to the manufacturer’s instructions (Agilent). cRNA were obtained by first reverse transcribed RNA, using a polyDT T7 primer (denaturation step: 10min at 65°C, reaction step: 2hr at 40°C, inactivation step: 5min at 70°C). cRNA were then labeled with Cy3-dye (2hr at 40°C). Excess dye was removed using a RNeasy kit (Qiagen). The level of dye incorporation was evaluated using a spectrophotometer (Nanodrop ND1000, LabTech)

extract_protocol: Total RNA was extracted from 6 individual fry per treatment, using the TRIzol reagent method (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s recommendations.T he concentration of extracted RNA was analysed using a spectrophotometer (ND-1000, NanoDrop) by measuring absorbance at 260 nm. Quality of RNAs was checked with Bioanalyzer (Agilent Technologies, Kista, Sweden).

tag: replicate

tag: line

tag: diet

value: V

tag: time

value: 5 weeks of feeding

value: Whole fry


title: AB1V_145

source_name: AB1, V diet

tag: tissue


title: R23M_153

source_name: R23, M diet

value: M


title: AB1V_143


title: R23M_148


title: AB1V_137


title: R23V_155


title: R23V_156


title: AB1M_130

source_name: AB1, M diet


title: R23V_160


title: R23V_157


title: AB1V_140


title: AB1M_131


title: AB1M_132


title: R23M_151


title: R23V_163


title: AB1M_133


title: AB1V_141


title: AB1V_144


title: AB1M_128


title: R23M_150


title: AB1M_129


title: A22V_127

source_name: A22, V diet


title: A22V_124


title: A22V_126


title: A22V_123


title: A22V_122


title: R23M_147


title: 280_INPUT

tag: barcodes

tag: antibody

value: AUH

tag: antibody catalog#

tag: antibody lot#

tag: cell line


title: 246_01


title: 280_01


title: yw_female_Repliseq_3rdinstar_wing_S_Rep1

first: Robert

middle: J

last: Duronio

address: CB #3280, Coker Hall

institute: University of North Carolina at Chapel Hill

description:
S phase DNA
Female_yw_RT_100kb

data_processing:
Library strategy: Repli-Seq
RNA reads were aligned with Tophat.
The imaginal wing disc transcriptome was assembled using Cufflinks (v2.2.1) with the following parameters: library-type fr-firsttrand, masked rRNA, and provided dm6 transcriptome obtained from Flybase release 6.04. Statistical analysis was performed with edgeR. For chromosome-wide expression analysis, read counts were normalized to the total number of reads mapping to ERCC Spike-In Mix 1.
Repli-seq reads were aligned with Bowtie2 (v2.3.2) default parameters. Two S phase replicates were generated for each genotype. Reads with a MAPQ score greater than 10 were retained using Samtools (v1.6). Bedtools coverage (v2.25.0) was used to determine the number of reads mapping to 100kb windows across the genome (10kb slide). Read counts at each 100kb window were normalized to read depth (reads per million; RPM). To generate a replication timing (RT) value for a particular window (100kb with a 10kb slide), the reads per million (RPM) value of each S phase replicate was divided by the RPM G1 value and averaged. RT profiles were generated by plotting the RT value at each window versus the genomic location. The limma statistical package was used to identify windows with significantly altered RT values between HWT and either H3K9R or H4K16R samples
Genome_build: dm6
Supplementary_files_format_and_content: text files with EdgeR output for RNA-seq, text files with replication timing (RT) value.

source_name: imaginal disc

growth_protocol: A Union Biometrica BioSorter for large particle flow cytometry equipped with a 488-nm solid state laser and accompanying FlowPilot software was used for identification and high throughput isolation of GFP-positive ΔHisC, UAS-2xEYFP/ΔHisC, twi-GAL4 mutant embryos from their GFP-negative siblings. For this purpose, three hundred to four hundred ΔHisC, twi-Gal4/CyO females and 100 ΔHisC, UAS-2xEYFP/CyO; 12xHWT/12xHWT, or 100 UAS-2xEYFP/CyO; 12xH3K9R/12xH3K9R, or 100 UAS-2xEYFP/CyO; 12xH4K16R/12xH4K16R males were placed in a large embryo collection cage (fits 100mm petri dishes) at 25°C and allowed to lay eggs on apple juice agar plates. “12xHWT” (Histone Wild  Type) refers to a control transgene containing 12 copies of the 5kb histone wild type repeat unit containing all five replication dependent histone genes. “12xH3K9R” and “12xH4K16R” are identical transgenes except with a Lys to Arg substitution mutation at the 9th residue of histone H3 and 16th residue of histone H4, respectively. Overnight collections were dechorionated in 100% bleach for two minutes and collected in embryo wash buffer (0.7% NaCl, 0.07% Triton X-100) prior to embryo sorting. Aliquots of one hundred GFP-positive embryos were transferred to vials containing standard corn medium and cultured at 25°C to obtain third instar larvae.

extract_protocol:
Third instar wing imaginal discs were dissected over a period of four hours and stored in Grace’s insect medium (supplemented with L-Glutamine, 3.33g/L Lactalbmin Hydrolysate, and 3.33g/L Yeastolate) on ice prior to nuclear isolation. Nuclear isolation was performed similarly to (Ma and Weake 2014) with the following adjustments. In brief, a 2mL dounce homogenizer was pretreated with nuclear extraction buffer (NEB; 10mM HEPES-KOH, pH 7.5; 2.5 mM MgCl2; 10mM KCl) supplemented with 5% BSA and placed on ice. Subsequently, wing imaginal discs were transferred to the empty dounce and incubated in NEB for five minutes on ice, disrupted twenty times with the loose pestle, incubated for ten minutes on ice, and disrupted 15 times with the tight pestle. Homogenate was filtered over a CellTrics 30 μm filter and isolated nuclei were stained with 1.5μg/mL DAPI prior to FACS. Nuclei were sorted into G1, S, and G2 populations based on DNA content as measured by DAPI intensity on a FACSAria II or III (using NEB-0.1% Tween sheath). Gates were chosen conservatively to prevent contamination of either fraction with nuclei from a neighboring fraction. Isolated populations of nuclei were pelleted, flash frozen, and stored at -80°C prior to DNA isolation and library preparation.
Genomic DNA libraries were prepared with the Rubicon ThruPLEX DNA-seq kit and sequencing was performed on an Illumina HiSeq 2500 in the UNC-Chapel Hill High Throughput Sequencing Facility.

tag: developmental stage

value: 3rd instar wandering larvae

value: wing disc

tag: genotype

value: yw

tag: Sex

value: female


title: H4K16R_male_Repliseq_3rdinstar_wing_G

description:
G phase DNA
Male_HWT_H4K16R_RT_100kb.txt


title: H4K16R_male_Repliseq_3rdinstar_wing_S_Rep2

description:
S phase DNA
Male_HWT_H4K16R_RT_100kb.txt


title: A22M_118

source_name: A22, M diet


title: HepG2_UVm_rep3

city: Sapporo

first: Shinichi

last: Nakagawa

state: Hokkaido

address: Kita 12-jo Nishi 6-chome, Kita-ku

department: Faculty of Pharmaceutical Sciences

country: Japan

institute: Hokkaido University

description: control RNA-Seq replicate 3

data_processing:
RNA-Seq reads are aligned to mm10 or hg38 using tophat 2.1.1.
Read counts are calculated using featureCounts allowing overlapping reads.
Genome_build: mm10 and hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts mapped to each gene.

extract_protocol:
RNAs were purified using TriZol reagents using manufacturer's protocol. Lysates were treated with 55ºC for 10 minutes before addition of chroloform.
rRNAs were removed using Ribo-Zero rRNA Removal Kit (Human/Mouse/Rat), and library was constructed using TruSeq Stranded mRNA Library Preparation Kit Set.

tag: cell type

value: Human Heptocellular Carcinoma Cells


title: HepG2_UVp_rep2

description: UPA-Seq replicate 2


title: HepG2_UVm_rep1

description: control RNA-Seq replicate 1


title: HepG2_UVp_rep1

description: UPA-Seq replicate 1


title: HepG2_UVm_rep2

description: control RNA-Seq replicate 2


title: A22V_120


title: A22M_115


title: A22M_114


title: A22M_116


title: yw_female_Repliseq_3rdinstar_wing_G

description:
G phase DNA
Female_yw_RT_100kb


title: HWT_male_Repliseq_3rdinstar_wing_G

value: HWT


title: 246_INPUT


title: yw_female_Repliseq_3rdinstar_wing_S_Rep2

description:
S phase DNA
Female_yw_RT_100kb


title: H4K16R_male_Repliseq_3rdinstar_wing_S_Rep1

value: male


title: 246_02


title: HWT_male_Repliseq_3rdinstar_wing_S_Rep1


title: HepG2_UVp_rep3

description: UPA-Seq replicate 3


title: HWT_male_Repliseq_3rdinstar_wing_S_Rep2


title: 280_02


title: A22M_113


title: H3K9R_female_Repliseq_3rdinstar_wing_G

description:
G phase DNA
Female_HWT_H3K9R_RT_100kb.txt


title: H4K16R_female_Repliseq_3rdinstar_wing_S_Rep1

description:
S phase DNA
Female_HWT_H4K16R_RT_100kb.txt


title: HWT_female_Repliseq_3rdinstar_wing_G

description:
G phase DNA
Female_HWT_H4K16R_RT_100kb.txt


title: HWT_female_Repliseq_3rdinstar_wing_S_Rep2


title: H3K9R_female_Repliseq_3rdinstar_wing_S_Rep1

description:
S phase DNA
Female_HWT_H3K9R_RT_100kb.txt


title: H4K16R_female_Repliseq_3rdinstar_wing_G


title: H4K16R_female_RNAseq_3rdinstar_wing_Rep3

data_processing:
RNA reads were aligned with Tophat.
The imaginal wing disc transcriptome was assembled using Cufflinks (v2.2.1) with the following parameters: library-type fr-firsttrand, masked rRNA, and provided dm6 transcriptome obtained from Flybase release 6.04. Statistical analysis was performed with edgeR. For chromosome-wide expression analysis, read counts were normalized to the total number of reads mapping to ERCC Spike-In Mix 1.
Repli-seq reads were aligned with Bowtie2 (v2.3.2) default parameters. Two S phase replicates were generated for each genotype. Reads with a MAPQ score greater than 10 were retained using Samtools (v1.6). Bedtools coverage (v2.25.0) was used to determine the number of reads mapping to 100kb windows across the genome (10kb slide). Read counts at each 100kb window were normalized to read depth (reads per million; RPM). To generate a replication timing (RT) value for a particular window (100kb with a 10kb slide), the reads per million (RPM) value of each S phase replicate was divided by the RPM G1 value and averaged. RT profiles were generated by plotting the RT value at each window versus the genomic location. The limma statistical package was used to identify windows with significantly altered RT values between HWT and either H3K9R or H4K16R samples
Genome_build: dm6
Supplementary_files_format_and_content: text files with EdgeR output for RNA-seq, text files with replication timing (RT) value.

growth_protocol: All stocks were maintained on standard corn media. 50 ΔHisC, twi-GAL4/CyO females and 20 ΔHisC, UAS-2xEYFP/CyO ; HWT/HWT, H4K16r/H4K16R, or H3K9R/H3K9R males were placed in a cage at 25C and allowed to lay eggs on a grape juice agar plate.~50 GFP positive larvae were moved to a corn media vial 48 hours after egg laying to separate ΔHisC, UAS-2xEYFP / ΔHisC, twi-GAL4 mutants from their siblings. Culture vials were cleared of wandering third instar larvae, and after 4-6 hours newly wandering larvae were selected.

extract_protocol:
30 wing imaginal discs per replicate were homogenized in Trizol and flash frozen in liquid nitrogen. RNA was chloroform extracted and isopropanol precipitated before column purification on Qiagen RNeasy purification with DNase digestion.
Transcriptomic libraries were prepared from cDNA from total RNA (ribo minus) with the Total RNA TruSeq Stranded Ribo Zero Gold kit. ERCC spike-in Mix 1 was included. Sequencing was performed on an Illumina HiSeq 2500 in the UNC-Chapel Hill High Throughput Sequencing Facility.


title: H4K16R_male_RNAseq_3rdinstar_wing_Rep1


title: HWT_female_Repliseq_3rdinstar_wing_S_Rep1


title: H4K16R_male_RNAseq_3rdinstar_wing_Rep3


title: HWT_female_RNAseq_3rdinstar_wing_Rep2

growth_protocol: All stocks were maintained on standard corn media. 50 ΔHisC, twi-GAL4/CyO females and 20 ΔHisC, UAS-2xEYFP/CyO ; HWT/HWT, H4K16R/H4K16R, or H3K9R/H3K9R males were placed in a cage at 25C and allowed to lay eggs on a grape juice agar plate.~50 GFP positive larvae were moved to a corn media vial 48 hours after egg laying to separate ΔHisC, UAS-2xEYFP / ΔHisC, twi-GAL4 mutants from their siblings. Culture vials were cleared of wandering third instar larvae, and after 4-6 hours newly wandering larvae were selected.


title: HWT_female_RNAseq_3rdinstar_wing_Rep1


title: H4K16R_female_RNAseq_3rdinstar_wing_Rep2


title: HWT_female_RNAseq_3rdinstar_wing_Rep3


title: H3K9R_female_Repliseq_3rdinstar_wing_S_Rep2


title: 12142017-H11-NA19130

city: Chicago

first: John

middle: D

last: Blischak

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

description:
eset.rds
scqtl-counts.txt.gz
scqtl-annotation.txt
scqtl-annotation-description.txt
quality-single-cells.txt
genes-pass-filter.txt

data_processing:
We used `umi_tools extract` (UMI-tools 0.5.3) to extract the 6 base pair unique molecular identifier (UMI) from the 5’ end of each read.
We used `subjunc` (Subread 1.5.3) to map reads to the human genome (Ensembl GRCh37.75; chromosomes 1-22, X, Y, MT) and ERCC spike-ins (http://tools.invitrogen.com/downloads/ERCC92.fa). Some samples included spike-in RNA from Drosophila melanogaster or Caenorhabditis elegans, so we also included the Ensembl genomes BDGP5.75 and WBcel235.75.
We used `featureCounts` (Subread 1.5.3) to count the number of reads for all protein-coding genes (Ensembl GRCh37 release 75) and the ERCC spike-in genes. We performed strand-specific counting (flag -s 1) because the UMI protocol preserves sequence strand information.
We used `umi_tools dedup` (UMI-tools 0.5.3) to deduplicate reads with the same UMI and start position to molecules.
We used `verifyBamID` (1.1.3) to identify the individual of origin for each sample based on the overlap of the RNA-seq reads with the known genotypes.
Genome_build: GRCh37
Supplementary_files_format_and_content: The file eset.rds is a serialized R object of the Bioconductor class ExpressionSet. It can be imported into R with `readRDS(“eset.rds”)`. It contains the gene counts, sample metadata, and feature metadata for 54,616 genes (H. sapiens, C. elegans, D. melanogaster, ERCC) and 7,584 single cells. The file scqtl-counts.txt.gz is a gzipped tab-delimited plain text file that contains the counts for 20,151 human genes for 7,584 single cells. The file scqtl-annotation.txt is a tab-delimited plain text file that contains 40 metadata columns for the 7,584 single cells.  The file scqtl-annotation-description.txt is a tab-delimited plain text file that contains descriptions of the 40 metadata columns in scqtl-annotation.txt. The file quality-single-cells.txt is a tab-delimited plain text file (no header row) that contains a logical vector denoting whether each single cell was determined to be a high-quality cell and used in the study (TRUE) or a low-quality cell that was discarded (FALSE). The file genes-pass-filter.txt is a tab-delimited plain text file (no header row) that contains a logical vector denoting whether each human gene (total of 20,151) was determined to be expressed and included in the study (TRUE) or discarded (FALSE).

source_name: LCL-derived iPSC

growth_protocol: We cultured Yoruba iPSCs (Banovich et al., 2018) in feeder-free conditions for at least ten passages in E8 medium (Life Technologies) (Chen et al., 2011).

extract_protocol:
We collected cells using the C1 Single-Cell Auto Prep IFC microfluidic chip (Fluidigm).
We performed single cell capture and library preparation as previously described using 6 bp Unique Molecular Identifiers (Tung et al., 2017). We pooled the 96 samples on each C1 chip and sequenced them on an Illumina HiSeq 2500 using the TruSeq SBS Kit v3-HS (FC-401-3002).

tag: experiment

tag: well

tag: individual

tag: batch


title: 12142017-H12-NA19102


title: 12142017-H08-NA19130


title: 12142017-H09-NA19102


title: 12142017-H07-NA19130


title: 12142017-H05-NA18517


title: H4K16R_female_Repliseq_3rdinstar_wing_S_Rep2


title: HWT_male_RNAseq_3rdinstar_wing_Rep2


title: 12142017-H04-NA18517


title: 12142017-H03-NA19130


title: H4K16R_male_RNAseq_3rdinstar_wing_Rep2


title: HWT_male_RNAseq_3rdinstar_wing_Rep1


title: 12142017-H01-NA19102


title: 12142017-G12-NA19130


title: 12142017-H06-NA19102


title: 12142017-H10-NA19130


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title: 12142017-G11-NA19143


title: 12142017-G10-NA19102


title: 12142017-G07-NA19102


title: 12142017-G03-NA19102


title: H4K16R_female_RNAseq_3rdinstar_wing_Rep1


title: 12142017-G05-NA19143


title: 12142017-G09-NA19102


title: 12142017-G06-NA19143


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title: 12142017-E09-NA19102


title: 12142017-E07-NA19130


title: 12142017-E03-NA19130


title: HWT_male_RNAseq_3rdinstar_wing_Rep3


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title: 12142017-E04-NA19143


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