title: Ctrl_1

description: Non-sorted H1 POU5F1-eGFP reporter cells, replicate 1

data_processing:
MAGeCK, a model-based analysis of genome-wide CRISPR knockout method, was applied to estimate for each dual-sgRNA the statistical significance of read count enrichment in the experimental samples versus the control samples.
Next, we partitioned the screened region (chr6:30,132,134-32,138,339) into a set of non-overlapping bins of the same length (100bp), and a bin is considered functional if many of the dual-sgRNAs cover it rank near the top of the sorted dual-sgRNAs list.
We then employed Robust Rank Aggression (RRA) (ref) algorithm to identify significant bins.
P-value is finally adjusted to FDR using Benjamini approach. A bin is predicted as significant if its FDR is smaller than given threshold.
Genome_build: hg19

extract_protocol:
For Samples 1-10, genomic DNA was extracted from H1 POU5F1-eGFP reporter cells after CREST-seq screen. For Sample 11, the plasmid DNA was extracted from E coli using Qiagen Giga prep kit.
The genomic DNA (samples 1-10) or CREST-seq plasmid DNA library (Sample 11) was PCR amplified with the following primers containing illumina TruSeq adaptor sequence. Forward primer: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCTctTGTGGAAAGGACGAAAC; Reverse Primer:  CAAGCAGAAGACGGCATACGAGATAAGGCCACGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTttttAACTTGCTATTTCTAGCTCTAAAAC. The PCR product was Gel purified, quantified and subjected to sequencing.
Other, CREST-seq

value: H1 POU5F6-eGFP reporter cells


title: High_1

status: Public on Apr 17 2017

type: SRA

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

country: USA

institute: University of California, San Diego School of Medicine

description: eGFP+/POU5F+ cells, sorted from H1 POU5F1-eGFP reporter cells after CREST-seq screen, replicate 2

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: H1 POU5F1-IRES-eGFP

growth_protocol: Cells were cultured at 37 celsius degree in 5% CO2, in Essential 8 media (Stemcell Technologies).

treatment_protocol: Regular hESC culture without any special treatment.

tag: cell type

value: H1 POU5F8-eGFP reporter cells


title: Cis_5

description: eGFP-/POU5F+ cells, sorted from H1 POU5F1-eGFP reporter cells after CREST-seq screen, replicate 6

value: H1 POU5F5-eGFP reporter cells


title: Cis_3

description: eGFP-/POU5F+ cells, sorted from H1 POU5F1-eGFP reporter cells after CREST-seq screen, replicate 4

value: H1 POU5F3-eGFP reporter cells


title: High_2

description: eGFP+/POU5F+ cells, sorted from H1 POU5F1-eGFP reporter cells after CREST-seq screen, replicate 3

value: H1 POU5F9-eGFP reporter cells


title: MCF10A_R3

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

description:
growth factor+
MCF10A_RNA-Seq_R3

library_source: transcriptomic

data_processing:
Remove adapter reads (Cutadapt v1.6). Trim low quality base calls from both ends,  Min score >= 20, window of 10 step size of 1. (FASTQ Quality Trimmer 1.0.0).
The reads were aligned to hg38 transciptome with Tophat2 (v0.6)
Reads were quantified using HTSeq-count (v0.6) with gencode annotation (v22). Genes with very low expression (<3  counts) were removed from the analysis.
Differential gene expression was calculated by using the Deseq2 version 1.8.1 package in R 3.2.0.
Genome_build: hg38
Supplementary_files_format_and_content: Tables showing the counts from the HTSeq-count quantification.

molecule: total RNA

source_name: mammary gland/breast epithelial cell

growth_protocol: MCF10a cells were grown in DMEM: F12 (Hyclone-SH30271), 5% (v/v) horse serum (Gibco #16050 lot #1075876) + 10ug/ml human insulin (Sigma I-1882)+ 20ng/ml recombinant hEGF (Peprotech AF-100-15) + 100ng/ml Cholera toxin (Sigma C-8052) + 0.5 ug/ml Hydrocortisone (Sigma H-0888) Pen/Strep (Life Technologies) and Glutamine (Life Technologies). MCF10A cells without growth factors were grown in DMEM: F12 (Hyclone-SH30271), 5% (v/v) horse serum (Gibco #16050 lot #1075876) + Pen/Strep (Life Technologies) and Glutamine (Life Technologies).

extract_protocol:
Total RNA was isolated from Trizol using Direct-zol RNA mini-prep kit (Zymo Research #R2050) with DNaseI digestion.
RNA libraries were prepared for sequencing with the TruSeq Stranded Total RNA with Ribo-Zero Gold kit using standard Illumina protocols with the exception that library amplifcation was performed using KAPA HiFi™ Real-Time PCR Library Amplification Kit (Kapa Biosystems #KK2701).
Barcoded libraries (Illumina TruSeq) were then loaded onto an Illumina HiSeq 1500 and single-end 100-base (SE100) sequencing was performed at the Advanced Genome Technologies Core Massively Parallel Sequencing Facility at UVM.

treatment_protocol: Cells were seeded at 1.5x106 cells per 100 mm dish and grown to 80% confluence. Cells were washed twice with phosphate buffered saline (PBS) and stored at -80C in TRIzol.

tag: tissue

value: breast

value: luminal ductal cells

tag: neoplasia type

value: fibrocystic disease

tag: atcc id

value: ATCC CRL-10317

tag: cell line


title: Ctrl_2

description: Non-sorted H1 POU5F1-eGFP reporter cells, replicate 2

value: H1 POU5F7-eGFP reporter cells


title: Cis_4

description: eGFP-/POU5F+ cells, sorted from H1 POU5F1-eGFP reporter cells after CREST-seq screen, replicate 5

value: H1 POU5F4-eGFP reporter cells


title: P17_2

description:
ATAC-seq using WT and mutant POU5F1-eGFP reporter hESC.
Mutant clones with PRRC2A core promoter deletion derived from POU5F1-eGFP H1 hESC reporter cells purchased from WiWell Institute.

data_processing:
Library strategy: ATAC-seq
We processed our ATAC-seq data in the following steps: 1) ATAC-seq sequencing reads were mapped to hg19 reference genome using Bowtie(61) in pair-end mode; 2) poorly mapped,  improperly paired and mitochondrial reads were filtered; 3) PCR duplications were further removed using Picards MarkDuplicates (http://broadinstitute.github.io/picard.); 4) Mapping  positions of reads were adjusted accounting for Tn5 insertion; 6) Reads were next shifted for 75bp followed by peak calling using MACS2(71) with following parameters “-q 0.01 --nomodel --shift 175 –B --SPMR --keep-dup all --call-summits”; 7) ATAC-seq signal was normalized into RPKM using deeptools(72) for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: .bw

extract_protocol:
ATAC-seq was performed by following the protocol described earlier (Buenrostro et al, Nature Method, 2013).
Briefly, each library starts with 100k cells which were permeabilized with NPB (0.2% NP-40, 5%BSA, 1Mm DTT in PBS with one complete proteinase inhibitor) at 4 degree for 10min, followed by spin down at 500g for 5min. The resulting nuclei were resuspended in 20ul 1xDMF (33mM Tris-acetate (pH=7.8), 166mM K-Acetate, 10mM Mg-Acetate, 16 % DMF). The chromatin tagmentation was done by adding 0.5ul Tn5 into 10ul solution for 30min at 37 degrees, followed by standar Illumina Tru-seq library prep protocol.

treatment_protocol:
Regular hESC culture without any special treatment.
The core promoter of MSH5 and PRRC2A was deleted by a pair of CRISPR/Cas9 targeting- 150bp to +100bp region near TSS. After picking single clones and Sanger sequencing verification of the genotype, the mutant cells and wild-type control cells were subjected to ATAC-seq analysis.


title: Cis_2

description: eGFP-/POU5F+ cells, sorted from H1 POU5F1-eGFP reporter cells after CREST-seq screen, replicate 2

value: H1 POU5F2-eGFP reporter cells


title: M3_2

description:
ATAC-seq using WT and mutant POU5F1-eGFP reporter hESC.
Mutant clones with MSH5 core promoter deletion derived from POU5F1-eGFP H1 hESC reporter cells purchased from WiWell Institute.


title: Cis_1

description: eGFP-/POU5F+ cells, sorted from H1 POU5F1-eGFP reporter cells after CREST-seq screen, replicate 1

value: H1 POU5F1-eGFP reporter cells


title: MCF10A_R1

description:
growth factor+
MCF10A_RNA-Seq_R1


title: TL27

data_processing:
Library strategy: 4C-Seq
4C-Seq data were mapped using 4Cseqpipe (van de Werken et al., 2012) with the first cutter set as DpnII and the second cutter set as NlaIII.
Genome_build: hg18

extract_protocol:
4C-Seq library was prepared following the protocol described in van de Werken et al. 2012 (PMID: 22961246). DpnII and NlaIII were used as the 4 base cutter in 4C-Seq.
Libraries were prepared according to Illumina's instructions, using TruSeq DNA Sample Preparation Kits v2, Set A (Cat# FC-121-2001). 4-12 library preps were mixed for multiplexed single-read sequencing using Illumina Hi-seq 2000 (Illumina).


title: High_3

description: eGFP+/POU5F+ cells, sorted from H1 POU5F1-eGFP reporter cells after CREST-seq screen, replicate 4

value: H1 POU5F10-eGFP reporter cells


title: MCF10A_R2

description:
growth factor+
MCF10A_RNA-Seq_R2


title: TBP ChIP-nexus (Control condtion) Rep2

city: Kansas City

first: Julia

last: Zeitlinger

state: MO

address: 1000 E 50th Street

institute: Stowers Institute for Medical Research

description:
kc167_dmso_tbp_chipnexus_normalized_and_merged_positive.bw
kc167_dmso_tbp_chipnexus_normalized_and_merged_negative.bw

data_processing:
Library strategy: ChIP-nexus
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Custom barcode sequences were removed from the first 9bp of each read and sequencing adapters were trimmed from the 3' end using cutadapt v1.3
Remaining reads with length >= 22bp were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were separated by strand and reduced to a single base at the 5' end
Genome-wide coverage counts were calculated for each strand separately and normalized to reads per million
Replicates are merged together and saved as BigWig format
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain genome coordinates and counts of the first base of aligned reads, separated by alignment strand

organism: Drosophila melanogaster

source_name: Kc167 cells

growth_protocol: grown at 25C in HyClone SFX-Insect Cell Culture Media

extract_protocol:
cells were cross-linked in 1.0% formaldehyde. Cells were then lysed by lysis buffer. Chromatin was sonicated by bioruptor to an average size of 300~500 bp. ~ 20 million cells was used for one ChIP-nexus
DNA-protein-complexes were isolated with specific antibodies when still being attached to protein A-dynabeads. DNA was end repaired using NEBNext End repair module (#E6050L). A single 3'-A overhang was added to the blunted ends using NEBNext dA-Tailing module (#E6053L). Adapters with single 3'-T overhangs and 5’ overhangs (barcode composed of 5 random nucleotides) were ligated to the adenylated fragments. Ligated fragments were blunted again by Klenow 3'-5' exo- polymerase to fill in the 5’ overhang first and then by T4 DNA polymerase to trim any possible 3’ overhang. Blunted DNA was subsequently digested by lambda exonuclease first and RecJf afterwards. Digested single strand DNA was then eluted, reverse cross-linked and purified prior to self-circularization by Circligase. An oligonucleotide was mixed with circularized single DNA for subsequent BamHI digestion to linearize the single DNA again. Linearized single strand DNA was then PCR-amplified using adaptor sequences and library was purified on 2% agarose gel to remove adaptor-adaptor ligation products. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

treatment_protocol: Cells are treated with 2% DMSO at room temperature for 1 h.

value: Kc167 cells

tag: chip antibody

value: anti-TBP rabbit polyclonal, Kadonaga lab

tag: illumina multiplex barcode

value: ATCACG


title: SOD1+/A272C rep2

city: Beijing

first: wang

middle: li

last: xia

address: 15 Datun Road, Chaoyang District

department: Institute of Biophysics

country: China

institute: University of Chinese Academy of Sciences

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were removed reads containing adapter, reads containing ploy-N and low quality reads, then mapped to GRCh37 whole genome using TopHat v2.0.12 with 2 mismatches allowed.
Expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene as described (Trapnell, Cole, et al., 2010).
Genome_build: GRCh37
Supplementary_files_format_and_content: excel files include FPKM values for each Sample ...

source_name: Human motor neurons derived from ALS iPSCs bearing SOD1+/A272C mutation

growth_protocol: SOD1+/+ iPSC and SOD1+/A272C iPSC were cultured on mitomycin C treated mouse embryonic fibroblasts (MEFs) with cDF12 medium. Motor neuron differentiation was initiated as followed. iPSCs were passaged onto MEF feeder in cDF12 medium. Then, medium 1, containing 50% Advanced DMEM/F12 (Invitrogen), 50% Neurobasal (Invitrogen), 1 x N2 (Invitrogen), 1 x B27 (Invitrogen), 1% GlutaMAX (Invitrogen), 1%NEAA (Invitrogen), 1% penicillin/streptomycin (Invitrogen), 4 mM CHIR99021 (Cellagentech), 3 mM SB431542 (Cellagentech), 1 mM dorsomorphin (Sigma), and 0.1 mM compound E (EMD Chemicals), 0.2% heparin (Sigma), was used to initiate motor neuron differentiation for 3 days. Medium 2, containing medium 1 and RA (100 nM) was used for another 3 days. At day 6, Medium 3, containing medium 2 and SAG (500 nM) without dorsomorphin, was used for next 2 days. At day 8, cells were dissociated to single cells with Accumax (Millipore) and reseeding on Matrigel-coated plates. DAPT and laminin were added on day 9 to accelerate motor neuron differentiation. At day 12, ISL1+ motor neurons were collected for subsequent analysis.

extract_protocol:
Total RNA was harvested using Trizol (Invitrogen) according to the instruction of TRIzol Reagent.
Sequencing libraries were constructed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: genotype

value: iPSC-derived motor neurons

tag: days

value: after 12 days of differentiation


title: 4C-Seq for viewpoint 6 (CTCF BS) in patient-derived RMS cells

city: Sevilla

first: Juan

middle: J.

last: Tena

address: Univ. Pablo Olavide, Ctra. Utrera km1

country: Spain

institute: CABD/CSIC

data_processing:
Library strategy: 4C-Seq
Demultiplexing: different samples were demultiplexed using the primer sequences
Mapping: reads were mapped to the Mus musculus (mm9 assembly) or Homo sapiens (hg19 assembly) genomes using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.
Filtering: only those reads that mapped withing fragments with a DpnII at one end and a Csp6I at the other end were kept.
Raw reads were converted into reads/restriction fragment end, and a running 30 fragments-window smoothing algorithm was used to smooth the data.
Data visualization: data were uploaded to UCSC Browser for visualization.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph, they contain smoothed data of 2Mb around each viewpoint that can be directly uploaded to UCSC for visualization.

source_name: RMS cell line

growth_protocol: Cells were grown in DMEM supplemented with 10% v/v FCS, 60 mg/ml Benzylpenicillin and 100 mg/ml Streptomycin sulphate at 37ºC and 5% of CO2.

extract_protocol:
Chromatin was extracted from single cells preparations from different samples. DNA was digested with DpnII and ligated. Then sample was de-crosslinked, digested with Csp6I and ligated again.
Primers with Illumina adaptors were used to amplify the library. Different samples were multiplexed for sequencing.

value: RMS


title: SOD1+/A272C rep1


title: SOD1+/+ rep2

source_name: Human motor neurons derived from SOD1 gene corrected iPSCs


title: 4C-Seq for viewpoint 8 (CTCF BS) in patient-derived RMS cells


title: 4C-Seq for viewpoint 7 (FOXO1 ECR) in patient-derived RMS cells


title: SOD1+/+ rep1


title: 4C-Seq for viewpoint 9 (CTCF BS) in patient-derived RMS cells


title: 80S_1000uM_CHX

city: Baltimore

first: Boris

last: Zinshteyn

state: Maryland

address: 725 N Wolfe St, PCTB 714

department: Molecular Biology and Genetics

institute: Johns Hopkins University School of Medicine

description: molecule type: ribosomal RNA

data_processing:
Library strategy: DMS-seq
adaptor removed with cutadapt
first 3 nt trimmed with FASTX trimmer
low quality bases trimmed (ShapeMapper)
Reads mapped to rRNA with Bowtie2 (ShapeMapper)
Coverage and mutations computed for each read (ShapeMapper)
Genome_build: SacCer3 rRNA
Supplementary_files_format_and_content: tab-separated text file of mutation rates (#mutations/coverage), a proxy for extent of DMS modification, for each nucleotide in each dataset.

organism: Saccharomyces cerevisiae

source_name: Purified ribosomes

extract_protocol:
Modified ribosomes were isopropanol precipitated, phenol extracted, reprecipitated.
rRNA was fragmented with Zinc Chloride for 5' @ 94C. 3' ends were resolved by treatment with T4 PNK, and RNA was size-selected by gel for ~60-70nt fragments.Preadenylated IDT miRNA cloning linker 2 was ligated with T4 PNK, and the ligated products gel purified. RT was performed with TGIRTIII RT @ 60C for 1 hour, and full-length RT products were gel purified. cDNA was circularized with circ ligase, and amplified by 11-13 cycles of PCR.

treatment_protocol: Ribosomes were pre-incubated with drug in vitro, then treated for 8 min with 90mM DMS, and quenched with βME buffer.

tag: dms concentration

tag: treatment time

value: 8 minutes

tag: drug

value: CHX

tag: dose


title: 4C-Seq for viewpoint 5 (FOXO1 ECR) in patient-derived RMS cells


title: 4C-Seq for viewpoint 2 (CTCF BS) in patient-derived RMS cells


title: 80S_50uM_CHX

description: molecule type: ribosomal RNA


title: 4C-Seq for viewpoint 4 (PAX3 enhancer) in patient-derived RMS cells


title: 4C-Seq for viewpoint 1 (CTCF BS) in patient-derived RMS cells


title: 80S_10uM_CHX

description: molecule type: ribosomal RNA


title: 80S_1.0mM_AglA

description: molecule type: ribosomal RNA

value: AglA


title: SPIN1_KD_RNA-Seq_rep3

city: Memphis

first: JIE

last: Lv

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
RTA software 1.18.66 used for basecalling. Illumina Casava1.8 software used for bcl conversion.
RNA-Seq reads were mapped to hg19 genome assembly using tophat v2.0.12 with parameters  --mate-std-dev 200 -p 8 -r 203
The number of fragments that originated from each gene in each sample is estimated using cuffdiff with default parameters. And then the differentially expressed genes based on read counts are inferred using edgeR R package v3.12.0
Genome_build: hg19
Supplementary_files_format_and_content: For RNA-Seq data, tab-delimited text file contains the raw counts of reads and the FPKM values for each gene of each sample.

source_name: T778 cells

growth_protocol: T778 cells were cultured in RPMI medium supplemented 10% FBS, penicillin/streptomycin and glutamine. All cells were maintained in a humidified 37° C incubator with 5% CO2.

extract_protocol:
RNeasy mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: T778 cells were transfected with 15 nM SPIN1 siRNA (Silencer® Selcet Pre-designed siRNA, Ambion/Life technologies, Cat#: 4392420) using lipofectamine RNAiMAX for 24hr

value: Liposarcoma cells

value: T778 cells


title: 80S_0.5mM_AglA

description: molecule type: ribosomal RNA


title: plasmid_lib_YD91

description: CREST-seq plasmid DNA library

organism: synthetic construct

source_name: CREST-seq plasmid DNA library

tag: sample type

value: CREST-seq plasmid DNA library


title: HeLa_X-ray_24h_H3_rep1

city: Darmstadt

first: Alexander

last: Rapp

address: Schnittspahnstr. 10

country: Germany

institute: Biology

data_processing:
Basecalls performed within the Illumina Pipeline SCS 2.8 / RTA 1.8 using CASAVA 1.8
ChIP-seq reads were aligned to the hg19 genome reference using SOAP2.21 version with the mismatches up to 2 and parameters -r 0 -v 2 -p 2
Divide genome into 10 kbp intervals, Reads Per Kilobase of intervals per Megabase of library size (RPKM) were calculated for each interval
Genome_build: NCBI Build GRCh37/UCSC Build hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

growth_protocol: HeLa cells (ATCC no. HB-8065) were cultured in DMEM (4.5 g/L glucose, Biochrom AG) supplemented with 10% fetal calf serum (Biochrom AG) and kept in a humidified environment containing 5% CO2 at 37°C.

extract_protocol:
Chromatin collection was performed as previously described (Angrisano et al., 2011), with minor adjustments. HeLa cells were fixed with 1% formaldehyde for 10 minutes at room temperature (RT) and cross-linker was quenched by the addition of 0.125 M glycine (5 minutes at RT). Nuclei were isolated after mild lysis in hypotonic buffer (10 mM Hepes pH 8, 1.5 mM MgCl2, 60 mM KCl) and 20 strokes in a tight dounce homogenizer. Chromatin was sheared in sonication buffer (0.5% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1). Fragmentation of chromatin was carried out by ultrasound treatment (Bioruptor™ UCD200) so that fragments of 200-300 bp length were produced. 60-120 µg chromatin were immunoprecipitated with anti-H2AX (A300-83A, Bethyl Laboratories, 3 g), anti-gH2AX (Clone JBW301, Upstate, 5 g) and anti-H3 (ab1791, Abcam, 3 g) antibodies. The collected chromatin (ChIP sample) was then reverse crosslinked in the presence of 200 mM NaCl at 65°C for at least five hours, followed by RNase A (50 µg/mL) treatment for 30 minutes at 37°C and proteinase K (100 µg/mL) treatment for three hours at 50°C. DNA elution was carried out in 1% SDS, 100 mM NaHCO3, in rotary shaker at RT for 15 minutes. Pure DNA was isolated using the Qiagen PCR purification kit and 15 ng of size selected DNA fragments were used to produce ChIP-seq libraries
Libraries were generated from 15 ng of immunoprecipitated DNA using the Illumina ChIP-Seq DNA sample Prep. Kit according to the suppliers information.

treatment_protocol: Treated cells were exposed to a single exposure of 10 Gy X-rays (250 kV, 16 mA, 2.5 Gy/min - GE Isovolt Titan) and postincubated under regular cell culture conditions for the times indicated; controls were treated identical except that no X-ray exposure was done.

value: HeLa

tag: x ray dose

value: 10 Gy

tag: time after exposure

value: 24 hours

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: SPIN1_KD_RNA-Seq_rep1

tag: cell type

tag: tissue


title: HeLa_input

tag: cell line

value: 0 Gy

value: 0 hours


title: Control_RNA-Seq_rep3

treatment_protocol: No treatment performed


title: 80S

description: molecule type: ribosomal RNA


title: HeLa_X-ray_0.5h_H3_rep1

value: 0.5 hours

tag: chip antibody


title: Control_RNA-Seq_rep2


title: HeLa_X-ray_unirr_H3_rep1


title: SPIN1_KD_RNA-Seq_rep2


title: 80S_no_DMS

description: molecule type: ribosomal RNA

value: 0 mM


title: Control_RNA-Seq_rep1


title: EML631_Treatment_RNA-Seq_rep3

treatment_protocol: T778 cells were treated with EML631 [10 mM] for 3days.


title: Pol II ChIP-nexus with spikein (NELF-E and NELF-B knockdown) Rep2

description:
kc167_nelfe_b_rnai_polii_chipnexus_spikein_normalized_and_merged_positive.bw
kc167_nelfe_b_rnai_polii_chipnexus_spikein_normalized_and_merged_negative.bw

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Custom barcode sequences were removed from the first 9bp of each read and sequencing adapters were trimmed from the 3' end using cutadapt v1.3
Remaining reads with length >= 22bp were aligned to the dm3-hg19 combined genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Reads aligned to dm3 genome were separated from reads aligned to hg19 genome
Reads aligned to dm3 genome were separated by strand and reduced to a single base at the 5' end
Genome-wide coverage counts on dm3 genome were calculated and normalized to genome-wide coverage counts on hg19 genome and saved in BigWig format for each strand separately
Genome_build: dm3-hg19 combined genome
Supplementary_files_format_and_content: BigWig files contain genome coordinates and counts of the first base of aligned reads, separated by alignment strand

extract_protocol:
cells were cross-linked in 1.0% formaldehyde. Cells were then lysed by lysis buffer. Chromatin was sonicated by bioruptor to an average size of 300~500 bp. ~ 20 million cells was used for one ChIP-nexus
DNA-protein-complexes were isolated with specific antibodies when still being attached to protein A-dynabeads. A fixed amount of spike-in was added to each ChIP in order to control for the loss of Pol II ChIP signal after Triptolide treatment. Human chromatin extracts from a GM12878 cell line were incubated with Dynabeads coupled to antibodies against human Pol II (N20), the entire mixture of Dynabeads and Pol II ChIP was added into each spike-in sample. DNA was end repaired using NEBNext End repair module (#E6050L). A single 3'-A overhang was added to the blunted ends using NEBNext dA-Tailing module (#E6053L). Adapters with single 3'-T overhangs and 5’ overhangs (barcode composed of 5 random nucleotides) were ligated to the adenylated fragments. Ligated fragments were blunted again by Klenow 3'-5' exo- polymerase to fill in the 5’ overhang first and then by T4 DNA polymerase to trim any possible 3’ overhang. Blunted DNA was subsequently digested by lambda exonuclease first and RecJf afterwards. Digested single strand DNA was then eluted, reverse cross-linked and purified prior to self-circularization by Circligase. An oligonucleotide was mixed with circularized single DNA for subsequent BamHI digestion to linearize the single DNA again. Linearized single strand DNA was then PCR-amplified using adaptor sequences and library was purified on 2% agarose gel to remove adaptor-adaptor ligation products. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

treatment_protocol: Cells were treated dsRNA against NELF-B and NELF-E

value: Kc167 cells

value: anti-RPB3 rabbit polyclonal, custom (GenScript)

tag: illumina multiplex barcode

value: TGACCA


title: HeLa_X-ray_3h_H2AX_repB

value: 3 hours

value: Bethyl Laboratories


title: HeLa_X-ray_3h_H2AX_repA


title: EML631_Treatment_RNA-Seq_rep2


title: Pol II ChIP-nexus with spikein(Control condtion) Rep2

description:
kc167_egfp_rnai_polii_chipnexus_spikein_normalized_and_merged_positive.bw
kc167_egfp_rnai_polii_chipnexus_spikein_normalized_and_merged_negative.bw

treatment_protocol: Cells were treated dsRNA against eGFP

value: CGATGT


title: Pol II ChIP-nexus with spikein(Control condtion) Rep1

value: ATCACG


title: HSPC day 24 rep2

city: Seattle

first: Fabiola

last: Merriam

state: WA

address: 1100 Fairview Ave N

department: Clinical Research

institute: Fred Hutchinson Cancer Research Center

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Reads not passing Illumina's base call quality filter were discarded, followed by removal of the first three bases from read 1 using fastx_toolkit v0.0.13
Reads were aligned to hg38 using TopHat v2.0.14, and counts generated using HTSeq-count v0.6.1
Genome_build: hg38

source_name: hematopoietic stem/progenitor cells

growth_protocol: HSPC were isolated from cord blood samples, resuspended in media SFEM II (StemCell Technologies) plus growth factors, and then encapsulated with the hydrogel. The cells would expand for 24 days.

extract_protocol:
Total RNA was isolated from cell pellet using RNeasy micro Kit (Qiagen, Hilden, Germany) as manufacture recommendation
Libraries were prepared using Clontech’s SMARter Stranded Total RNA-Seq Kit - Pico Mammalian

value: Cord blood


title: HSPC day 24 rep1


title: Pol II ChIP-nexus (1 h 50 uM DRB treatment) Rep2

description:
kc167_drb_50um_polii_chipnexus_normalized_and_merged_positive.bw
kc167_drb_50um_polii_chipnexus_normalized_and_merged_negative.bw

data_processing:
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Custom barcode sequences were removed from the first 9bp of each read and sequencing adapters were trimmed from the 3' end using cutadapt v1.3
Remaining reads with length >= 22bp were aligned to the reference genome using bowtie v1.0.0, retaining only uniquely aligning reads with a maximum of 2 mismatches
Aligned reads were separated by strand and reduced to a single base at the 5' end
Genome-wide coverage counts were calculated for each strand separately and normalized to reads per million
Replicates are merged together and saved as BigWig format
Genome_build: UCSC dm3
Supplementary_files_format_and_content: BigWig files contain genome coordinates and counts of the first base of aligned reads, separated by alignment strand

extract_protocol:
cells were cross-linked in 1.0% formaldehyde. Cells were then lysed by lysis buffer. Chromatin was sonicated by bioruptor to an average size of 150~500 bp. ~ 10 million cells was used for one ChIP-nexus
DNA-protein-complexes were isolated with specific antibodies when still being attached to protein A-dynabeads. DNA was end repaired using NEBNext End repair module (#E6050L). A single 3'-A overhang was added to the blunted ends using NEBNext dA-Tailing module (#E6053L). Adapters with single 3'-T overhangs and 5’ overhangs (barcode composed of 5 random nucleotides) were ligated to the adenylated fragments. Ligated fragments were blunted again by Klenow 3'-5' exo- polymerase to fill in the 5’ overhang first and then by T4 DNA polymerase to trim any possible 3’ overhang. Blunted DNA was subsequently digested by lambda exonuclease first and RecJf afterwards. Digested single strand DNA was then eluted, reverse cross-linked and purified prior to self-circularization by Circligase. An oligonucleotide was mixed with circularized single DNA for subsequent BamHI digestion to linearize the single DNA again. Linearized single strand DNA was then PCR-amplified using adaptor sequences and library was purified on 2% agarose gel to remove adaptor-adaptor ligation products. Following cluster generation on the flowcell surface, the sequencing libraries were sequenced following Illumina's protocol.

treatment_protocol: Cells were treated with 50 μM DRB (Sigma D1916 dissolved in DMSO) at room temperature for 1 h.

value: anti-RPB3 rabbit polyclonal, GenScript (custom antibody)

value: ATGTCA


title: HeLa_X-ray_3h_H3_rep1

value: HeLa

value: 10 Gy


title: 80S_DMSO

description: molecule type: ribosomal RNA

value: 8 minutes

value: DMSO


title: HSPC day 0 rep2


title: Pol II ChIP-nexus (1 h 50 uM DRB treatment) Rep1

value: GCCAAT


title: EML631_Treatment_RNA-Seq_rep1

value: Liposarcoma cells

value: T778 cells


title: HeLa_X-ray_0.5h_H2AX_rep1

value: 0.5 hours


title: HeLa_X-ray_3h_gH2AX_rep1

value: Upstate/Millipore

value: clone JBW301


title: HeLa_X-ray_24h_gH2AX_rep1

value: 24 hours


title: HeLa_X-ray_unirr_H2AX_rep1

value: 0 Gy

value: 0 hours

value: Bethyl Laboratories


title: Pol II ChIP-nexus with spikein ( (NELF-E and NELF-B knockdown) Rep1

value: Kc167 cells

value: anti-RPB3 rabbit polyclonal, custom (GenScript)

value: TTAGGC


title: HSPC day 0 rep1

value: Cord blood


title: Pol II ChIP-nexus (1 h 0.5 uM Flavopiridol treatment) Rep1

description:
kc167_flavopiridol_0.5um_polii_chipnexus_normalized_and_merged_positive.bw
kc167_flavopiridol_0.5um_polii_chipnexus_normalized_and_merged_negative.bw

treatment_protocol: Cells were treated with 0.5 μM Flavopiridol (Santa Cruz sc-202157 dissolved in DMSO) at room temperature for 1 h.

value: anti-RPB3 rabbit polyclonal, GenScript (custom antibody)

value: CAGATC


title: HeLa_X-ray_0.5h_gH2AX_rep1

value: HeLa

value: 10 Gy


title: HeLa_X-ray_unirr_gH2AX_rep1


title: HeLa_X-ray_24h_H2AX_rep1


title: Pol II ChIP-nexus (1 h 500 uM Triptolide treatment) Rep1

treatment_protocol: Cells were treated with 500 μM Triptolide (TOCRIS Bioscience Cat. No. 3253 dissolved in DMSO) at room temperature for 1 h.


title: Pol II ChIP-nexus (1 h 0.5 uM Flavopiridol treatment) Rep2

value: AGTCAA


title: UVC+photolyase replicate 2

city: Barcelona

first: Antonio

last: Torres-Mendez

address: C/ Dr. Aiguader 88

department: Systems Biology

institute: Centre for Genomic Regulation

data_processing:
Full genomic sequences for the analyzed species were downloaded from the UCSC Genome Browser database. Full transcriptomic sequences for all species were downloaded from Ensembl. For each gene, the canonical transcript was selected for gene expression analysis based on BioMart.
For each species, we assembled all canonical transcript (as defined above) sequences. In order to calculate the effective number of unique mappable positions in each transcript (i.e. the effective length) we performed the following steps. For each read length k, we extracted the L-k+1 (L being the transcript length) k-mer sequences from each canonical transcript and then aligned the full set of k-mers against the respective genome using Bowtie, allowing for a maximum of two mismatches. k-mers with no or one unique genomic alignment were then likewise aligned back to the canonical transcriptome. For each transcript, the number of such k-mers having a unique transcriptomic alignment was determined. This corresponds to the transcript’s effective number of unique mappable positions for k-mer mRNA-Seq reads. For each sample, the corresponding mRNA-Seq data were aligned against the respective genome using Bowtie, allowing for a maximum of two mismatches. Reads with one unique genomic alignment were then aligned against the canonical transcriptome and, for each transcript, the number of reads with one unique transcriptomic alignment were counted. Gene expression levels were determined as reads per thousand mappable positions of target transcript sequence per million of reads, where the reads uniquely align to the analyzed transcriptome. This procedure for estimating gene expression levels is a corrected version of the widely used RPKM (reads per kilobase of target transcript sequence per million of total reads) metric, and is referred to as “cRPKM” [Labbe RM et al. Stem Cells (2012)].
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include cRPKM values (as defined above), as well as the total read count for each gene's canonical transcript

source_name: keratinocytes

extract_protocol:
mRNA was purified using QIAGEN RNA purification kit
RNA libraries were prepared for sequencing using standard Illumina Truseq kit protocols

value: HaCaT

tag: treatment

value: UVC-treated

tag: activation

value: photolyase activated


title: HeLa_X-ray_unirr_gH2AX_rep2

value: Upstate/Millipore

value: clone JBW301


title: UVC+photolyase replicate 1


title: UVC-treated replicate 2


title: Pol II ChIP-nexus (1 h 0.5 uM Triptolide treatment) Rep1

treatment_protocol: Cells were treated with 0.5 μM Triptolide (TOCRIS Bioscience Cat. No. 3253 dissolved in DMSO) at room temperature for 1 h.

value: GCCAAT


title: DCL1 knockdown C

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

description:
sRNA
Small RNA-seq
Arab_DCL1_KD _C

data_processing:
The original fastq files were converted to fasta format and reads without Ns were kept for further analysis.
The 3' adapter and HD signatures [Sorefan et al. 2012] were trimmed and the files were converted from redundant to non-redundant format.
The reads were mapped to the reference genome, allowing 0 mis-matches and 0 gaps using PatMaN [Pruffer et al. 2008].
Reads were normalised using RPM method to the median library count.
Differential expression was calculated using the offset fold change method, where a fold change of 2 is necessary for a read to be considered DE.
Genome_build: TAIR10
Supplementary_files_format_and_content: *csv: Comma-separated text files include expression levels.

organism: Arabidopsis thaliana

source_name: Leaves, DCL1 knockdown

growth_protocol: Seeds of Arabidopsis thaliana cv. Columbia dcl1-7 (sin1-1) mutants from NASC The European Arabidopsis Stock Centre (stock ID N6953) were stratified at 4°C for 48h and germinated under long-day conditions with 16h daytime at 22°C and 8h night time at 18°C. The plants were grown under the same conditions. The seeds from wildtype and heterozygous individuals were germinated and the plants were grown under the same conditions as above.

extract_protocol:
Total RNA of both wildtype and mutant leaf tissue was extracted using TriReagent (Ambion) following the manufacturer's protocol. Small RNA (sRNA) of each sample was further enriched using the mirVana miRNA isolation kitTM (Ambion) according to the manufacturer's instructions.
The sRNA libraries were constructed using 1 μg of enriched sRNA fraction based on the previously published protocol by Xu et al., 2015.

tag: cultivar/background

value: Columbia

tag: genotype/variation

value: DCL1 knockdown

value: leaves


title: UVC-treated replicate 1


title: NELF-E ChIP-nexus (1 h Triptolide treatment) Rep1

description:
kc167_triptolide_nelfe_chipnexus_normalized_and_merged_negative.bw
kc167_triptolide_nelfe_chipnexus_normalized_and_merged_positive.bw

value: Kc167 cells

value: anti-NELF-E rabbit polyclonal, GenScript (custom antibody)

value: ATGTCA


title: Control replicate 2

value: untreated


title: DCL1 knockdown B

description:
sRNA
Small RNA-seq
Arab_DCL1_KD _B


title: NELF-E ChIP-nexus (Control condtion) Rep2

description:
kc167_dmso_nelfe_chipnexus_normalized_and_merged_positive.bw
kc167_dmso_nelfe_chipnexus_normalized_and_merged_negative.bw

treatment_protocol: Cells were treated with 2% DMSO at room temperature for 1 h.

value: ATCACG


title: 4C-Seq for Pax3 promoter in E9.5 mouse embryos

description: library strategy: 4C-seq

data_processing: Mapping: reads were mapped to the Mus musculus (mm9 assembly) or Homo sapiens (hg19 assembly) genomes using Bowtie software (http://bowtie-bio.sourceforge.net). Only uniquely mapped reads were kept.

organism: Mus musculus

source_name: E9.5 mouse embryos

growth_protocol: B6CBAF1/OlaHsd mouse embryos taken at 9.5dpc, taking the day in which the plug was found as 0.5dpc.

value: whole embryos


title: 4C-Seq for PAX3 promoter in patient-derived RMS cells

description: library strategy: 4C-seq

value: RMS


title: 4C-Seq for FoxO1 promoter in E9.5 mouse embryos

description: library strategy: 4C-seq


title: Control replicate 1


title: NELF-E ChIP-nexus (Control condtion) Rep1

value: AGTTCC


title: Pol II ChIP-nexus (Control condtion) Rep2

description:
kc167_dmso_polii_chipnexus_normalized_and_merged_positive.bw
kc167_dmso_polii_chipnexus_normalized_and_merged_negative.bw

value: anti-RPB3 rabbit polyclonal, GenScript (custom antibody)

value: ACAGTG


title: Wildtype C

description:
sRNA
Small RNA-seq
Arab_WTC

source_name: Leaves, WT

value: wildtype


title: DCL1 knockdown A

description:
sRNA
Small RNA-seq
Arab_DCL1_KD _A


title: Wildtype B

description:
sRNA
Small RNA-seq
Arab_WTB


title: Pol II ChIP-nexus (Control condtion) Rep1


title: WT_Vector_control

city: Athens

first: Ronan

middle: Kevin

last: Carroll

state: OHIO

address: 107 Irvine Hall

department: Biological Sciences

institute: Ohio University

description: rRNA-depleted

data_processing:
Raw data files (.sff) were imported into the CLC Genomics Workbench software platform for analysis
Reads corresponding to ribosomal RNA were filtered out and removed
Expression values were caculated using the "RNA-Seq Analysis" function in CLC Genomics Workbench
Expression values were exported into excel files
Genome_build: Shigella dysenteriae strain Sd197 was used as a reference for RNAseq data processing.  The accession number for the Genbank genome file used as a references was NC_007606

organism: Shigella dysenteriae

source_name: Bacterial cells, pelleted

growth_protocol: Strains were grown in LB medium at 37°C with shaking

extract_protocol:
Total bacterial RNA was isolated utilizing the Qiagen RNeasy mini kit and contaminating DNA was removed by treatment with Ambion Turbo DNAase
Library construction was performed using the Ion Total RNA-Seq v2 Kit from Life Technologies

treatment_protocol:
Strains were grown in the presence of Isopropyl β-D-1-thiogalactopyranoside (IPTG) at a concentration of 20 μM
Strains were grown in the presence of deoxycholate (DOC) at a concentration of 0.01% (v/v)
Strains were grown in the presence of ampicillin at a concentration of 50 μM
750μl of RNA preserving solution (95% EtOH, 5% phenol) was added to each tube prior to pelleting bacterial cells

tag: strain

value: vector control

tag: growth medium

value: LB broth

tag: growth conditions (time/temp/shaking)


title: NANOGNB rep 2

status: Public on Apr 16 2017

first: Thomas

last: Dunwell

address: South Parks Road

department: Zoology

description: Libraries for all samples were combined in a 15 samples multiplex which were then split across two lanes.

data_processing:
Reads for each sample were aligned to the reference hg38 genome using the STAR genome aligner with default commands with the addition of --outFilterMultimapNmax 15 --outSAMstrandField intronMotif
Raw read counts for refseq annotated genes were generated using featurecounts using gene annotations from GRCh38.p2
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file including default output from featurecounts (raw read counts)

source_name: Human Adult Fibroblasts

growth_protocol: All cells were grown at 37oC in a 5% CO2 humidified incubator on poly-l-lysine coated plastic in Fibroblast Medium (Sciencell #2301)

extract_protocol:
RNA was extracted using a RNeasy Mini Kit following the manufactures instructions with the addition of an on-column DNAse treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: transfection

value: NANOGNB


title: Empty control vector rep 3

value: empty control vector


title: Empty control vector rep 2


title: NANOGNB rep 3


title: NELF-E ChIP-nexus (1 h Triptolide treatment) Rep2

value: CGATGT


title: Wildtype A

description:
sRNA
Small RNA-seq
Arab_WTA

value: Columbia

value: leaves


title: NANOGNB rep 1


title: LkPHO4 pho2Δ replicate 2

status: Public on Apr 15 2017

city: Iowa City

first: Bin

last: He

email: emptyhb@gmail.com, bin-he@uiowa.edu

state: IA

address: 129 East Jefferson St., Biology Building 450

department: Biology

institute: the University of Iowa

data_processing:
Basecalling using bcl2fastq-1.8.3
Sequencing reads were aligned to the corresponding species reference genome using Bowtie (v1.1.1) with the option ‘-m 1 --best –strata’
The resulting SAM files were sorted using Samtools (v1.2)
The number of reads per transcript was counted using Bedtools2, with the option ‘bedtools coverage -a BAM_file -b genome_annotation.bed -S -s sorted -g Chrom.length`. Gene features for S. cerevisiae were downloaded from the Saccharomyces Genome Database (SGD), version R64-2-1.
Genome_build: S. cerevisiae genome version S288C_R64-1-1
Supplementary_files_format_and_content: text file, matrix of read counts per transcript per strain

molecule: polyA RNA

source_name: OD600=0.3~0.5 log-phase yeast culture

growth_protocol: Cells were pre-grown in 10 mM Pi Synthetic Complete (SC) medium to saturation, diluted 1:100 and regrown to saturation. The culture is then diluted to OD600 ~ 0.1 in fresh 10 mM Pi SC medium and grown to OD600 ~ 0.3-0.5 prior to extraction

extract_protocol:
20 mL of OD600=0.3-0.5 cell cultures were added directly into 30 mL cold methanol (-50 °C), mixed, and incubated in an ethanol-dry ice bath (-50 °C) for at least 20 minutes. Cells were collected by centrifugation and quickly washed with ice-cold water to remove alcohol, and resuspended in RNAlater solution (Ambion). For each sample, 5×107 cells were used to isolate total RNA with the RNase Mini kit (Qiangen),
RNA libraries were prepared using the Illumina TruSeq stranded mRNA library preparation kit (part #RS-122-2101 and #RS-122-2102) following the manufacturer’s protocol

tag: pho80 locus

tag: pho2 locus

tag: pho4 locus

value: L. kluyveri PHO4


title: Empty control vector rep 1

description: Libraries for all samples were multiplexed which were then split across two lanes.


title: NbPHO4 pho2Δ replicate 1

value: N. bacillisporus PHO4


title: CnPHO4 pho2Δ replicate 2

value: C. nivariensis PHO4


title: NdPHO4 pho2Δ replicate 2

value: N. delphensis PHO4


title: Beauveria bassiana at 48 hours post treatment of infection for Galleria mellonella

status: Public on Apr 18 2017

city: Hefei

first: Yulong

last: Wang

address: 130 West Changjiang Road

institute: Anhui Agricultural University

description:
live
The wild-type strain B. bassiana ARSEF 2860 (stocked in the Chinese Academy of Sciences)

data_processing:
Reads were mapped to the Beauveria bassiana genome from (NCBI, https://www.ncbi.nlm.nih.gov/genome/910)
Differential gene expression levelss were calculated with using the program Cufflinks software (v.2.0.1)
DAnnotations of differentially expressed genes (DEGs) including Pfam, were annotated using including Pfam database were obtained from the reference annotation of available Beauveria bassiana genome database at the NCBI website.
For each differentially expressed peach gene, up-to-datelatest Gene Ontology (GO) annotations were obtained using Blast2GOv.2.3.5 with the default parameters., Theand “GO slim” option was employedset to reduce the number of functional classes.
GO slim annotations results were then used as queries against the AgBase database to perform their classify genesication according into to the three main classes categories (molecular function, biological process and cellular component), and to be further assigned to secondary categories
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Beauveria bassiana

growth_protocol: on PDA and 28ºC

extract_protocol:
Total RNA was isolated separately from Beauveria bassiana with RNA extraction Kit
RNA samples were first treated with RNAse-free DNAse I to remove contaminatinged DNA. Then, the mRNA wais enriched by using the oligo(dT) magnetic beads. After mixed with theadding fragmentation buffer, the mRNA was fragmented into short fragments (about 200 bp). NextThen, the first strand of cDNA was synthesized by using random hexamer-primers. Buffer, dNTPs, RNase H, and DNA polymerase I were added to synthesize the second cDNA strand. The double- stranded cDNA was then purified usingwith magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition was then performed. Finally, sequencing adaptors were ligated to the fragments. The fragments were enriched by PCR amplification. During the QC step, an Agilent 2100 Bioanaylzer (Agilent Technologies, Germany) and ABI StepOnePlus Real-Time PCR System (Applied Biosystems, USA) were used to perform qualitfy-control steps  and to quantify the sample library. The library products wasere then ready for sequencing using anvia Illumina HiSeqTM 2000 (GATC Biotech, Germany), or another sequencer when if necessary


title: NbPHO4 pho2Δ replicate 2


title: NdPHO4 pho2Δ replicate 1


title: CbPHO4 pho2Δ replicate 1

value: C. bracarensis PHO4


title: WT_RyfA1_overproducing

description: rRNA-depleted

tag: genotype/variaton

value: RyfA1 overproducing


title: CgPHO4 pho2Δ replicate 1

value: C. glabrata PHO4


title: CbPHO4 pho2Δ replicate 2


title: CgPHO4 pho2Δ replicate 2


title: ScPHO4 pho2Δ replicate 1

value: S. cerevisiae PHO4


title: SpPHO4 pho2Δ replicate 2

value: S. paradoxus PHO4


title: SpPHO4 pho2Δ replicate 1


title: pho4Δ pho2Δ replicate 2


title: ScPHO4 pho2Δ replicate 2


title: pho4Δ pho2Δ replicate 1


title: LkPHO4 pho2Δ replicate 1


title: NbPHO4 ScPHO2 replicate 1

value: S. cerevisiae PHO2


title: LkPHO4 ScPHO2 replicate 1


title: LkPHO4 ScPHO2 replicate 2


title: CnPHO4 ScPHO2 replicate 1


title: CnPHO4 ScPHO2 replicate 2


title: NbPHO4 ScPHO2 replicate 2


title: NdPHO4 ScPHO2 replicate 2


title: NdPHO4 ScPHO2 replicate 1


title: CbPHO4 ScPHO2 replicate 2


title: CnPHO4 pho2Δ replicate 1


title: CgPHO4 ScPHO2 replicate 1


title: ScPHO4 ScPHO2 replicate 2


title: ScPHO4 ScPHO2 replicate 1


title: pho4Δ ScPHO2 replicate 2


title: SpPHO4 ScPHO2 replicate 1


title: pho4Δ ScPHO2 replicate 1


title: CgPho4 ChIP w/o ScPho2

data_processing:
Basecalling using bcl2fastq-1.8.3
Sequencing reads were aligned to the corresponding species reference genome using Bowtie (v1.1.1) with the option ‘-m 1 --best –strata’
The resulting SAM files were sortedand indexed using Samtools (v1.2)
Peak calling was performed using GEM v2.6 with the option '--smooth 30 --fold 1.5', using mock samples as the control, and using the default Read Distribution file downloaded from the authors' website.
To generate a visual fold enrichment profile for each ChIP experiment (including the mock samples), we used MACS2's "build signal track" feature to calculate a fold enrichment value at each position of the genome, using the input sample as the control. The resulting "BedGraph" format file was converted to "WIG" format using "bedgraph_to_wig.pl" downloaded from https://gist.github.com/svigneau/8846527. The WIG file was then imported into MochiView v1.6 for visualization.
Genome_build: S. cerevisiae genome version S288C_R64-1-1
Supplementary_files_format_and_content: Peaklist

extract_protocol:
The cross-linked cell sample was resuspended in ~1 mL of ChIP lysis buffer (50 mM HEPES, pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate), and mechanically lysed using a mini-Beadbeater-24 (BioSpec) with 0.5 mm Zirconia beads (BioSpec), using the following setting: 12 cycles of 30s bead beating, with 1 min on ice-water bath in between. The lysed sample was fragmented by sonication using Covaris E220 Adaptive Focus system (setting: Duty Factor: 10%; Peak Incident Power: 175; Cycles/Burst: 200; Time:150s). Afterwards, the sample was centrifuged to remove the unsoluable fraction. 5% of the solubalized chromatin was removed at this step to serve as input sample (not subjected to immunoprecipitation, but was reverse cross-linked and subjected to DNA extraction and library preparation). The remaining supernatant containing the solubalized chromatin was subjected to immunoprecipitation. Briefly, the supernatant was incubated with Dynabeads MyOne Streptavidin C1 (Invitrogen) with rotation at 4C overnight. The dynabeads were then washed with each of the following buffers for 2 x 2 minutes: lysis buffer, high salt wash buffer (50 mM HEPES, pH 7.5, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate), lithium wash buffer (10 mM Tris/HCl, pH 8.0, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.1% Na-Deoxycholate), and SDS wash buffer (10 mM Tris/HCl, pH 8.0, 1 mM EDTA, 3% SDS). Finally the dynabeads were washed with TE buffer (10 mM Tris/HCl, pH 8.0, 1 mM EDTA) once for 2 minutes. After washing, cross-linking was reversed by incubation of samples at 65C overnight in 10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.8% SDS. DNA was then purified using the minElute column (Qiagen).
ChIP-seq library was prepared using the NEB NextUltraII DNA library prep kit, following the manufacturer's protocol.

treatment_protocol: 300 mL of OD600=0.3-0.5 cell cultures was cross-linked by adding 8.33 mL of 37% formaldehyde (final formaldehyde concentration = 1%) and incubated with swirling for 10 minutes at room temperature. The sample was then quenched by adding 2.5 M glycine solution to a final concentration of 125 mM, and incubated with swirling for 5 minutes at room temperature. Cells were then collected by centrifugation and washed two times with ice-cold TBS.

tag: type

value: ChIP


title: input for ScPho4 ChIP with ScPho2

value: input


title: mock for CgPho4 ChIP with ScPho2

value: ChIP (mock)


title: CgPho4 ChIP with ScPho2


title: mock for ScPho4 ChIP with ScPho2


title: mock for CgPho4 ChIP w/o ScPho2


title: input for CgPho4 ChIP w/o ScPho2


title: input for CgPho4 ChIP with ScPho2


title: ScPho4 ChIP with ScPho2


title: B36M14

city: Melbourne

first: Lev

last: Kats

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

data_processing:
CASAVA 1.8.2 was used for base calling and quality control was performed using RNA-SeQC v1.1.7
Adapters were trimmed using Cutadapt v1.6
Reads were mapped to the mouse reference genome build mm10 using TopHat2
HTSeq v0.5 was used to count the number of reads per gene
Limma-Voom method was applied for noramlisation and differential gene expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes counts for each sample

growth_protocol: cKit+Mac1low AML cells were sorted from leukemic NSG mice

extract_protocol:
Cell pellets were resuspended in Trizol (Ambion) and RNA was extracted using the Direct-zol RNA kit (Zymo Research).
TruSeq RNA Library Preparation Kit v2 (Illumina)

treatment_protocol: Mice were treated with vehicle (0.5% Methyl cellulose, 0.2% Tween80), AG-221 (administered b.i.d. by oral gavage at a dose of 40mg/kg body weight) or doxy (administered ad libitum via doxycycline food and water)

tag: cells

value: IDH2R140Q/DNMT3AR882H/NRASG12D cKit+Mac1low AML cells

value: Dox


title: B36M10


title: B36M8


title: CgPHO4 ScPHO2 replicate 2


title: CbPHO4 ScPHO2 replicate 1


title: B36M13


title: B36M11


title: B36M6


title: B36M4

value: Vehicle


title: B36M1


title: TSA(0-8h)-3

city: Cambridge

first: Charles

last: Bradshaw

address: Tennis Court Road

department: Gurdon Institute

institute: University of Cambridge

description: Somatic cell nuclear transfer embryo; 28 hours after nuclear transfer

data_processing:
Alignment with tophat2
Generation of RPKM values
Genome_build: UCSC mm9
Supplementary_files_format_and_content: RPKM values

source_name: An embryo at the 2 cell stage

growth_protocol: The reconstructed SCNT oocytes were activated by the incubation for 6 hours in 5 mM SrCl2- and 2 mM EGTA-containing mKSOM medium supplemented with 0.3% dBSA and 5 µg/ml cytochalasin B at 37°C in air containing 5% CO2. After activation, SCNT embryos were cultured in mKSOM medium supplemented with 0.3% dBSA or with small molecules as indicated in the treatment protocol section.

extract_protocol:
Single embryos after the removal of zona pellucida were subjected to RNA purification using PicoPure RNA extraction kit (Thermo Scientific) according to the vendor’s instruction. At the final step of RNA extraction, 9 μl of elution buffer was used to extract RNA from the column. Two μl of RNA out of 9 μl were subjected to Ovation Single Cell RNA-seq System (NuGEN) for making a library for sequencing.
Library construction was carried out according to the vendor’s instruction (Ovation Single Cell RNA-seq System (NuGEN)). Two steps of PCR amplification (14 and 12 cycles) were needed to obtain an adequate amount of DNA for sequencing.

treatment_protocol: The reconstructed SCNT embryos were treated with 50 nM TSA for 8 hours from the commencement of activation (COA) (TSA(0-8h)), with 10 µg/ml VC for 8 hours (VC(0-8h)), with 10 µg/ml VC during the period of 8 to 15 hours after COA (VC(8-15h)) or with 50 nM TSA and 10 µg/ml VC for 8 hours (TSA(0-8h)+VC(0-8h)). The best developmental outcome was obtained by incubating the reconstructed SCNT embryos with 50 nM TSA for 8 hours after COA followed by treatment of 10 µg/ml VC for 7 hours (TSA(0-8h)+VC(8-15h)).

tag: developmental stage

value: 2-cell stage


title: SpPHO4 ScPHO2 replicate 2


title: TSA(0-8h)+VItaminC(8-15h)-3


title: B36M3


title: VitaminC(8-15h)-2


title: Control-3


title: GL_M_94

city: Nanjing

first: Shaolin

last: Shi

state: Jiangsu

address: 305 East Zhongshan Rd.

department: National Clinical Research Center for Kidney Diseases

institute: Jinling Hospital, Nanjing University School of Medicine

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mmu10090 whole genome using Tophat v2.0.12 with parameters mismatch=2
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., 2008. HTSeq v0.6.1 was used with parameters -m union
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited .txt file includes RPKM values for each Sample

source_name: Glomerular mesangial cells

extract_protocol:
We isolated mouse glomeruli with Dana-beads/magnetic concentration and dissociated them into single cells using enzymes,The cell suspension was then loaded onto a Fluidigm C1TM Single-Cell Auto Prep System, which separated the single cells and lysed them for RNA extraction in individual wells.
cDNA libraries were made automatically in the Fluidigm C1 platform.

tag: tissue

value: kindey/glomeruli

tag: cell type

value: mesangial cells

tag: age

value: 8 week

tag: genotype

value: wild type


title: GL_M_85


title: B36M2

tag: treatment


title: Control-2


title: TSA(0-8h)+VItaminC(0-8h)-2


title: GL_M_65


title: GL_M_51


title: GL_M_60


title: GL_M_47


title: GL_M_36


title: TSA(0-8h)+VItaminC(0-8h)-1


title: B36M9


title: VitaminC(8-15h)-1


title: TSA(0-8h)-1


title: GL_M_29


title: VitaminC(0-8h)-1


title: GL_M_55


title: GL_M_91


title: GL_M_11


title: TSA(0-8h)+VItaminC(8-15h)-2


title: GL_M_30


title: RNA-seq, ATF4 -/- 293T, torin 1-treated 6 h Rep2

city: New Haven

first: Carson

middle: C

last: Thoreen

state: CT

address: 333 Cedar St. SHM B 145

department: Cellular and Molecular Physiology

institute: Yale School of Medicine

data_processing:
Basecalls were perormed using CASAVA
Adapter sequences were removed using FASTX Clipper.
rRNA was filtered using Bowtie 2.2.9
Remaining reads were aligned using Tophat 2.1.1
Reads were mapped to UCSC/Gencode gene models and quantified using Cufflinks 2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: FASTQ

source_name: ATF4 -/- HEK293T cells

growth_protocol: Cells were grown in DMEM + 10% heat-inactivated FBS.

extract_protocol:
Trizol, SDS/Proteinase K
Clontech SMARTer RNA-seq or adapter ligation. Duplicate RNA-seq libraries for wild-type or ATF4-null HEK-293T cells treated with Torin 1 or tunicamycin for 6 h were prepared using the Clontech SMARTer Stranded Total RNA kit according to the manufacturer’s instructions. For ribosome profiling experiments, including both ribosome footprint (RPF) and total (RNA) libraries, HEK-293T cells were seeded in 15 cm dishes at 10 million cells/plate, incubated overnight, and then treated with vehicle (DMSO) or 250 nM Torin1 for 24 h. Cells were washed 3x in 5 ml cold PBS- and then lysed in polysome lysis buffer (15 mM Hepes pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1% Triton-X100). For RNA libraries, lysates were adjusted to 0.5% SDS, digested with proteinase K, and then extracted with acid-phenol. RNA was then fragmented by alkaline hydrolysis. RNA fragments of 40-80 nt were gel purified and used to prepare libraries as described below. For RPF libraries, lysates were digested with RNAse If for 45 min at RT, and centrifuged through 5-50% sucrose gradients to isolate monosomes. RNA was extracted from fractions containing the monosome peak by proteinase K digest, followed by acid-phenol extraction. Ribosome footprints were then isolated by excising and extracting 28-32 nt fragments from 15% polyacrylamide gels. Samples were depleted of abundant rRNA contaminants by hybridization with rRNA-specific biotinylated oligonucleotides. From this step, RNA and RPF libraries were treated identically. Samples were dephosphorylated using PNK, followed by 3’ ligation using T4 RNA ligase 1 to the 3’ linker, and ligation products were size selected by PAGE. Fragments were next 5’ phosphorylated using PNK, immediately followed by ligation to the 5’ linker using T4 RNA ligase 1. RNA was precipitated and subjected to reverse transcription using Superscript III with RT primer, after which RNA was destroyed by alkaline hydrolysis. RT products were purified by PAGE, and then amplified using the Phusion DNA polymerase. All samples were sequenced on an Illumina Hiseq system. Two biological replicates were prepared for each library.

treatment_protocol: Cells were treated with vehicle (DMSO), 250 nM Torin 1, or 1 µM tunicamycin, as indicated.

tag: source

value: cell culture

tag: library protocol

value: Clontech SMARTer RNA-seq kit


title: GL_M_6

tag: strain


title: RNA-seq, ATF4 -/- 293T, torin 1-treated 6 h Rep1


title: GL_M_75


title: CgPHO4 pho2Δ replicate 2

data_processing:
Basecalling using bcl2fastq-1.8.3
Sequencing reads were aligned to the corresponding species reference genome using Bowtie (v1.1.1) with the option ‘-m 1 --best –strata’
The resulting SAM files were sorted using Samtools (v1.2)
The number of reads per transcript was counted using Bedtools2, with the option ‘bedtools coverage -a BAM_file -b genome_annotation.bed -S -s sorted -g Chrom.length`. Gene features for C. glabrata were downloaded from the Candida Genome Database (CGD), version s02-m07-r04
Genome_build: C. glabrata genome version s02-m02-r09
Supplementary_files_format_and_content: text file, matrix of read counts per transcript per strain

organism: Nakaseomyces glabratus

value: C. glabrata PHO4


title: CgPHO4 pho2Δ replicate 1


title: TSA(0-8h)-2


title: RNA-seq, ATF4 -/- 293T, control-treated 6 h Rep2


title: RNA-seq, ATF4 -/- 293T, control-treated 6 h Rep1


title: pho4Δ pho2Δ replicate 1


title: CgPHO4 CgPHO2 replicate 2

value: C. glabrata PHO2


title: pho4Δ pho2Δ replicate 2


title: CgPHO4 CgPHO2 replicate 1


title: RNA-seq, 293T, torin 1-treated 6 h Rep2

source_name: HEK293T cells


title: RNA-seq, 293T, tunicamycin-treated 6 h Rep1


title: RNA-seq, 293T, control-treated 6 h Rep2


title: RNA-seq, 293T, torin 1-treated 6 h Rep1


title: OVE4

city: Madison

first: Ophelia

middle: S

last: Venturelli

state: WI

address: 440 Henry Mall, 3204C Biochemical Sciences Building

institute: University of Wisconsin-Madison

description: Ribosomal extracted total RNA

data_processing:
Read counts mapping using Bowtie 1 on the galaxy webserver
Reads per kilobase of transcript per million (RPKM) was computed by multiplying the number of mapped reads by 1e9 and then dividing by the gene length and median number of total reads for each sample
Genome_build: MG1655
Supplementary_files_format_and_content: Comma-delimited text files include RPKM values for each gene at each time point (RPKM_total)

organism: Escherichia coli K-12

source_name: t = 8 min after MazF-induction. Replicate #4

growth_protocol: Overnight culture of BW25113; mazF-; safesite1::TetR-pTET-mazF in LB at 37C at 225 rpm was diluted to OD of 0.05 in 10mL LB.

extract_protocol:
200 µl of the cell cultures were added to 400 µl of RNAprotect (Qiagen) to stabilize the RNA, incubated for 5 min at room temperature and then spun down for 10 min at 5000 x g. Total RNA was isolated using RNeasy purification kit and treated with DNAase I (Qiagen)
The Functional Genomics Lab (FGL), a QB3-Berkeley Core Research Facility at UC Berkeley, constructed the sequencing libraries. At the FGL, Ribo-Zero rRNA Removal Kits (Illumina) were used to remove ribosomal RNA and ERCC RNA Spike-In Control Mixes (Ambion by Life Technologies) were added to the samples. The library preparation was performed on an Apollo 324™ with PrepX™ RNAseq Library Prep Kits (WaferGen Biosystems, Fremont, CA), and 18 cycles of PCR amplification was used for index addition and library fragment enrichment.

treatment_protocol: Cultures were induced with 5 ng/mL aTc during log phase (OD600~0.5)


title: RNA-seq, 293T, control-treated 6 h Rep1


title: RNA, 293T torin 1-treated Rep2

value: adapter ligation


title: CgPho2 ChIP in no Pi media w/ CgPho4

data_processing:
Basecalling using bcl2fastq-1.8.3
Sequencing reads were aligned to the corresponding species reference genome using Bowtie (v1.1.1) with the option ‘-m 1 --best –strata’
The resulting SAM files were sortedand indexed using Samtools (v1.2)
Peak calling for CgPho4 was performed using GEM v2.6 with the option '--smooth 3 --fold 1.5', using mock samples as the control, and using the Read Distribution for ChIP-exo file downloaded from the authors' website. GEM didn't work for CgPho2 due to lack of strong sequence motif. Instead, we used MACS2 with the option "-s 50 --bw -q 0.01 --keep-dup auto --slocal 1000 -B --verbose 4 -m 2 100 --call-summits”.
To generate a visual fold enrichment profile for each ChIP experiment (including the mock samples), we used MACS2's "build signal track" feature to calculate a fold enrichment value at each position of the genome, using the input sample as the control. The resulting "BedGraph" format file was converted to "WIG" format using "bedgraph_to_wig.pl" downloaded from https://gist.github.com/svigneau/8846527. The WIG file was then imported into MochiView v1.6 for visualization.
Genome_build: C. glabrata genome version s02-m02-r09
Supplementary_files_format_and_content: Peaklist

growth_protocol: Cells were pre-grown in 10 mM Pi Synthetic Complete (SC) medium to saturation, diluted 1:100 and regrown to saturation. The culture is then diluted to OD600 ~ 0.1 in fresh 10 mM Pi SC medium and grown to OD600 ~ 0.3-0.5.

extract_protocol:
The cross-linked cell sample was resuspended in ~1 mL of ChIP lysis buffer (50 mM HEPES, pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate), and mechanically lysed using a mini-Beadbeater-24 (BioSpec) with 0.5 mm Zirconia beads (BioSpec), using the following setting: 12 cycles of 30s bead beating, with 1 min on ice-water bath in between. The lysed sample was fragmented by sonication using Covaris E220 Adaptive Focus system (setting: Duty Factor: 10%; Peak Incident Power: 175; Cycles/Burst: 200; Time:150s). Afterwards, the sample was centrifuged to remove the unsoluable fraction. The supernatant containing the solubalized chromatin was subjected to immunoprecipitation. Briefly, the supernatant was incubated with either Anti-FLAG M2 magnetic beads (Sigma-Aldrich) or Anti-V5 antibody (Abcam #15828) depending on the epitope tag that was used. After 2 hours of incubation at 4C with rotation, the V5-tagged samples were additionally incubated with Dynabeads Protein-G (Thermo-Fisher Scientific #10003D). In a traditional ChIP experiment, what follows are the washing and de-crosslinking, prior to DNA extraction. In ChIP-exo, however, the washing steps are combined with part of the library construction steps. A detailed account for the protocol can be found in (Rhee and Pugh, 2012), and is also available from Active Motif ChIP-exo vA4 manual.
As mentioned above, the ChIP washing step is combined with part of the library construction steps in ChIP-exo. A brief description of the steps is provided here: with the chromatin still bound to the beads, the DNA was end-polished and P7-exo adapters are ligated onto the blunt ends. The nicked DNA was repaired and then digested by lambda and RecJf exonulceases to excise DNA in a 5’ to 3’ direction, trimming up to the site of the cross-linking and selectively eliminating the P7 adapter at the 5 ́ end. Following cross-link reversal and elution from the beads, the DNA was made double-stranded by P7 primer extension and a P5- exo adapter was added to the exonuclease-treated ends. The DNA library was PCR amplified and size selected before it was subjected to high-throughput sequencing.

treatment_protocol:
300 mL of the culture was filtered and washed with 100 mL of synthetic media containing no inorganic phosphate, after which the cells were released into 300 mL of fresh synthetic media with no inorganic phosphate and grown for 1 hr prior to extraction.
After the sample specific treatment, 300 mL of OD600=0.3-0.5 cell cultures was cross-linked by adding 8.33 mL of 37% formaldehyde (final formaldehyde concentration = 1%) and incubated with swirling for 10 minutes at room temperature. The sample was then quenched by adding 2.5 M glycine solution to a final concentration of 125 mM, and incubated with swirling for 5 minutes at room temperature. Cells were then collected by centrifugation and washed two times with ice-cold TBS.

tag: condition

value: Synthetic media with 0 mM inorganic phosphate


title: RNA, 293T torin 1-treated Rep1


title: Control-1


title: mock for CgPho2 ChIP w/ CgPho4 in high Pi media

treatment_protocol:
300 mL of the culture was filtered and washed with 100 mL of synthetic media containing 10 mM inorganic phosphate, after which the cells were released into 300 mL of fresh synthetic media with 10 mM inorganic phosphate and grown for 1 hr prior to extraction.
After the sample specific treatment, 300 mL of OD600=0.3-0.5 cell cultures was cross-linked by adding 8.33 mL of 37% formaldehyde (final formaldehyde concentration = 1%) and incubated with swirling for 10 minutes at room temperature. The sample was then quenched by adding 2.5 M glycine solution to a final concentration of 125 mM, and incubated with swirling for 5 minutes at room temperature. Cells were then collected by centrifugation and washed two times with ice-cold TBS.

value: Synthetic media with 10 mM inorganic phosphate


title: RNA, 293T control-treated Rep2


title: pho4Δ CgPHO2 replicate 2


title: mock for CgPho2 ChIP w/ CgPho4 in no Pi media


title: OVA4

description: Ribosomal extracted total RNA

source_name: t = 0, Prior MazF induction, Replicate #4


title: OVB4

description: Ribosomal extracted total RNA

source_name: t = 2 min after MazF-induction. Replicate #4


title: OVD4

description: Ribosomal extracted total RNA

source_name: t = 6 min after MazF-induction. Replicate #4


title: mock for CgPho4 ChIP w/ CgPho2


title: RPF, 293T torin 1-treated Rep2


title: RNA-seq, 293T, tunicamycinl-treated 6 h Rep2


title: CgPho2 ChIP in high Pi media w/ CgPho4

value: ChIP


title: RPF, 293T torin 1-treated Rep1


title: RNA, 293T control-treated Rep1


title: pho4Δ CgPHO2 replicate 1


title: OVD3

description: Ribosomal extracted total RNA

source_name: t = 6 min after MazF-induction. Replicate #3


title: CgPho4 ChIP in no Pi media w/o CgPho2


title: CgPho4 ChIP in no Pi media w/ CgPho2


title: RPF, 293T control-treated Rep2


title: OVC3

description: Ribosomal extracted total RNA

source_name: t = 4 min after MazF-induction. Replicate #3


title: OVC4

description: Ribosomal extracted total RNA

source_name: t = 4 min after MazF-induction. Replicate #4


title: OVB3

description: Ribosomal extracted total RNA

source_name: t = 2 min after MazF-induction. Replicate #3


title: RPF, 293T control-treated Rep1


title: CgPho4 ChIP in high Pi media w/ CgPho2


title: OVA3

description: Ribosomal extracted total RNA

source_name: t = 0, Prior MazF induction, Replicate #3


title: OVE3

description: Ribosomal extracted total RNA

source_name: t = 8 min after MazF-induction. Replicate #3


title: OEL23_N705_S510

status: Public on Apr 14 2017

city: Berkeley

first: Diya

last: Das

state: California

address: 265 Life Sciences Addition #3200

department: Molecular & Cell Biology

institute: University of California, Berkeley

description:
oeHBCdiff_Cufflinks_eSet_counts_table.txt
oeHBCdiff_Cufflinks_eSet_fpkm_table.txt
oeHBCdiff_Cufflinks_eSet_tpm_table.txt
oeHBCdiff_RSEM_eSet_expectedCounts_table.txt
oeHBCdiff_RSEM_eSet_fpkm_table.txt
oeHBCdiff_RSEM_eSet_tpm_table.txt
oeHBCdiff_kallisto_eSet_estimatedCounts_table.txt
oeHBCdiff_kallisto_eSet_tpm_table.txt
oeHBCdiff_Cufflinks_eSet.Rda
oeHBCdiff_RSEM_eSet.Rda
oeHBCdiff_kallisto_eSet.Rda
oeHBCdiff_countsMatrix.txt

data_processing:
Illumina CASAVA bcl2fastq_v2.17 software used for basecalling.
Reads were aligned to the GRCm38.3 (mm10, patch release 3) mouse genome assembly with Tophat2 (Version 2.1.1), and low quality reads were removed with Trimmomatic (Version 0.3.2).
Gene level counts were calculated using Tophat (Version 2.1.1) alignments and featureCounts (Version 1.5.0-p3). TPMs were derived from Cufflinks (Version 2.2.1) FPKMs.
As a second strategy for getting gene level counts, we used RSEM (Version 1.2.31) to get expected counts.
As a third stategy for getting gene level counts, we used kallisto (Version 0.43.0) to obtain estimated counts and RPKMs.
Genome_build: GRCm38.3 (mm10, patch release 3)
Supplementary_files_format_and_content: tab-delimited text files include gene level count, FPKM, and TPM values for each sample derived from Cufflinks and featureCounts
Supplementary_files_format_and_content: tab-delimited text files include gene level expected count, FPKM, and TPM values for each sample derived from RSEM
Supplementary_files_format_and_content: tab-delimited text files include gene level estimated count and TPM values for each sample derived from kallisto
Supplementary_files_format_and_content: ExpressionSets that include all metadata and the appropriate count data for each of our three alignment and gene level count procedures (oeHBCdiff_Cufflnks_eSet, oeHBCdiff_RSEM_eSet, oeHBCdiff_kallisto_eSet)
Supplementary_files_format_and_content: oeHBCdiff_phenoData.txt: metadata on samples including experimental condition and batch
Supplementary_files_format_and_content: oeHBCdiff_Cufflinks_eSet_counts_table.txt: abundance measurements (featureCounts), text file
Supplementary_files_format_and_content: oeHBCdiff_Cufflinks_eSet_fpkm_table.txt: abundance measurements (Cufflinks), text file
Supplementary_files_format_and_content: oeHBCdiff_Cufflinks_eSet_tpm_table.txt: abundance measurements (derived from Cufflinks fpkms), text file
Supplementary_files_format_and_content: oeHBCdiff_Cufflinks_eSet_featureData.txt: information about the genes
Supplementary_files_format_and_content: oeHBCdiff_Cufflinks_eSet_protocolData.txt: QC metrics, text file
Supplementary_files_format_and_content: oeHBCdiff_RSEM_eSet_expectedCounts_table.txt: abundance measurements, text file
Supplementary_files_format_and_content: oeHBCdiff_RSEM_eSet_fpkm_table.txt: abundance measurements, text file
Supplementary_files_format_and_content: oeHBCdiff_RSEM_eSet_tpm_table.txt: abundance measurements, text file
Supplementary_files_format_and_content: oeHBCdiff_RSEM_eSet_featureData.txt: information about the genes
Supplementary_files_format_and_content: oeHBCdiff_RSEM_eSet_protocolData.txt: QC metrics, text file
Supplementary_files_format_and_content: oeHBCdiff_kallisto_eSet_estimatedCounts_table.txt: abundance measurements, text file
Supplementary_files_format_and_content: oeHBCdiff_kallisto_eSet_tpm_table.txt: abundance measurements, text file
Supplementary_files_format_and_content: oeHBCdiff_kallisto_eSet_featureData.txt: information about the genes
Supplementary_files_format_and_content: oeHBCdiff_Cufflinks_eSet.Rda: R data object containing expressionSet with matrices of metadata and count data
Supplementary_files_format_and_content: oeHBCdiff_RSEM_eSet.Rda: R data object containing expressionSet with matrices of metadata and count data
Supplementary_files_format_and_content: oeHBCdiff_kallisto_eSet.Rda: R data object containing expressionSet with matrices of metadata and count data
Supplementary_files_format_and_content: oeHBCdiff_countsMatrix.txt: normalized counts matrix, text file

source_name: olfactory epithelium

extract_protocol:
Olfactory epithelium was dissected from transgenic animals; the dorsal region corresponding to the sensory olfactory epithelium was isolated and dissociated with papain for 25 minutes.  Labeled cells were collected by FACS.
The Fluidigm C1 system was used for single cell capture, cell lysis, and reverse transcription to make cDNA, and amplification (C1 Single-Cell Auto Prep Reagent Kit for mRNA Seq; SMARTer Ultra Low RNA Kit for the Fluidigm C1 System). Cell capture was performed at room temperature.
The Nextera XT DNA Sample Preparation Kit (Illumina cat# FC-131-1096) and Index Kit A-D (cat# FC-131-2001-4) were used to synthesize sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
Single-cell RNA-sequencing.  scRNA-Seq was performed on Illumina HISEQ 2500 sequencer; up to 192 samples were sequenced per lane, often in Rapid Run mode.

tag: expt condition

tag: sex type

value: M

tag: number of animals

tag: visual qc

value: Yes

tag: facs selection

value: YFP+

tag: genetic background

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

value: A

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

value: medium

tag: c1 machine id

value: Frodo

tag: ercc spike-in dilution

tag: experimental condition

value: Krt5-Rosa-eYFP, p63cKO, 14 days post tamoxifen


title: OEL23_N706_S502

tag: age

tag: expt condition

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background


title: OEL23_N707_S502

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set


title: OEL23_N706_S506

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id


title: OEL23_N705_S507

tag: age

tag: expt condition

tag: sex type

tag: number of animals

tag: visual qc

tag: ercc spike-in dilution

tag: experimental condition


title: OEL23_N706_S510

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode


title: OEL23_N705_S508

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date


title: OEL23_N705_S506

tag: age

tag: expt condition

tag: sex type

tag: number of animals

tag: visual qc

tag: c1 chip size

tag: c1 machine id


title: OEL23_N706_S503

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: OEL23_N706_S507

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: OEL23_N706_S505

tag: age

tag: expt condition

tag: sex type

tag: number of animals

tag: visual qc

tag: dob

tag: facs & c1 date


title: OEL23_N706_S511

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: c1 chip size

tag: c1 machine id


title: OEL23_N705_S505

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL23_N704_S508

tag: age

tag: expt condition

tag: sex type

tag: number of animals

tag: visual qc

tag: lane

tag: cdna concentration (ng/μl)


title: OEL23_N706_S508

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: dob

tag: facs & c1 date


title: OEL23_N704_S506

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: OEL23_N704_S507

tag: age

tag: expt condition

tag: sex type

tag: number of animals

tag: visual qc

tag: ercc spike-in dilution

tag: experimental condition


title: OEL23_N705_S503

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: OEL23_N703_S511

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: OEL23_N704_S505

tag: age

tag: expt condition

tag: sex type

tag: number of animals

tag: visual qc

tag: c1 chip size

tag: c1 machine id


title: OEL23_N705_S502

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: ercc spike-in dilution

tag: experimental condition


title: OEL23_N704_S502

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: OEL23_N704_S511

tag: age

tag: expt condition

tag: sex type

tag: number of animals

tag: visual qc

tag: dob

tag: facs & c1 date


title: OEL23_N704_S510

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: c1 chip size

tag: c1 machine id


title: OEL23_N703_S510

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL23_N704_S503

tag: age

tag: expt condition

tag: sex type

tag: number of animals

tag: visual qc

tag: lane

tag: cdna concentration (ng/μl)


title: OEL23_N705_S511

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: dob

tag: facs & c1 date


title: CgPho4 ChIP in high Pi media w/o CgPho2

tag: strain

tag: condition

tag: type


title: OEL23_N703_S505

tag: age

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL23_N703_S506

tag: expt condition

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dilution plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: OEL23_N702_S507

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: dob

tag: facs & c1 date


title: OEL23_N702_S502

tag: expt condition

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL23_N702_S511

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 batch id

tag: dilution plate coordinate


title: OEL23_N702_S510

tag: age

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate

tag: lane

tag: cdna concentration (ng/μl)


title: OEL23_N703_S503

tag: expt condition

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date

tag: c1 chip size

tag: c1 machine id


title: OEL23_N701_S511

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: ercc spike-in dilution

tag: experimental condition


title: OEL23_N702_S506

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: barcode

tag: library plate coordinate


title: OEL23_N703_S508

tag: expt condition

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)

tag: dob

tag: facs & c1 date


title: OEL23_N702_S505

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 chip size

tag: c1 machine id


title: OEL23_N701_S510

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL23_N702_S508

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: OEL23_N701_S506

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: dob

tag: facs & c1 date


title: OEL23_N703_S507

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: c1 chip size

tag: c1 machine id


title: OEL23_N702_S503

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL23_N703_S502

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: lane

tag: cdna concentration (ng/μl)


title: OEL23_N701_S503

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: dob

tag: facs & c1 date


title: OEL23_N701_S502

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: OEL22_N728_S516

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

value: D

value: small

tag: ercc spike-in dilution

tag: experimental condition

value: Krt5-Rosa-eYFP, p63cKO, 7 days post tamoxifen


title: OEL23_N701_S507

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: lane

tag: cdna concentration (ng/μl)


title: OEL23_N701_S505

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: OEL23_N701_S508

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 chip size

tag: c1 machine id


title: OEL22_N728_S517

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N728_S513

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N727_S522

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: dob

tag: facs & c1 date


title: OEL22_N727_S521

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: c1 chip size

tag: c1 machine id


title: OEL22_N727_S517

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N727_S515

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N727_S516

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: dob

tag: facs & c1 date


title: OEL22_N727_S518

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: OEL22_N727_S513

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N726_S518

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N726_S521

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: OEL22_N726_S516

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 chip size

tag: c1 machine id


title: OEL22_N726_S515

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N726_S513

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N726_S517

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: dob

tag: facs & c1 date


title: OEL22_N726_S520

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: c1 chip size

tag: c1 machine id


title: OEL22_N724_S516

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N724_S518

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N724_S522

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: dob

tag: facs & c1 date


title: OEL22_N724_S521

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: OEL22_N724_S520

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N728_S515

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N724_S517

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: OEL22_N723_S522

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 chip size

tag: c1 machine id


title: OEL22_N724_S515

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N723_S521

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N723_S517

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: dob

tag: facs & c1 date


title: OEL22_N723_S520

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: c1 chip size

tag: c1 machine id


title: OEL22_N726_S522

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N727_S520

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N723_S518

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: dob

tag: facs & c1 date


title: OEL22_N723_S516

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: OEL22_N722_S521

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N722_S522

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N723_S515

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: OEL22_N722_S517

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 chip size

tag: c1 machine id


title: OEL22_N722_S518

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N722_S515

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N722_S513

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: dob

tag: facs & c1 date


title: OEL22_N721_S521

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: c1 chip size

tag: c1 machine id


title: OEL22_N721_S516

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N721_S518

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N721_S522

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: dob

tag: facs & c1 date


title: OEL22_N721_S520

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: OEL22_N720_S520

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N720_S522

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N720_S518

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: OEL22_N720_S521

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 chip size

tag: c1 machine id


title: OEL22_N720_S517

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N720_S516

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N720_S513

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: dob

tag: facs & c1 date


title: OEL22_N719_S518

tag: age

value: MF

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: c1 chip size

tag: c1 machine id


title: OEL22_N720_S515

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N724_S513

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N722_S520

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: dob

tag: facs & c1 date


title: OEL22_N723_S513

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: OEL22_N719_S517

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N722_S516

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N719_S513

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: OEL22_N719_S516

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 chip size

tag: c1 machine id


title: OEL22_N718_S522

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N718_S521

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N718_S520

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: dob

tag: facs & c1 date


title: OEL22_N721_S515

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: c1 chip size

tag: c1 machine id


title: OEL22_N718_S518

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N718_S516

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N718_S517

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: dob

tag: facs & c1 date


title: OEL22_N718_S515

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: c1 chip size

tag: c1 machine id


title: OEL22_N716_S520

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N716_S518

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N716_S522

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: dob

tag: facs & c1 date


title: OEL22_N718_S513

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: c1 chip size

tag: c1 machine id


title: OEL22_N716_S513

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: ercc spike-in dilution

tag: experimental condition


title: OEL22_N716_S516

tag: expt condition

tag: barcode

tag: library plate coordinate

tag: index set

tag: sequencing run id

tag: lane

tag: cdna concentration (ng/μl)


title: OEL22_N716_S515

tag: sex type

tag: number of animals

tag: visual qc

tag: facs selection

tag: genetic background

tag: dob

tag: facs & c1 date


title: OEL22_N719_S515

tag: age

tag: c1 batch id

tag: dilution plate coordinate

tag: c1 plate coordinate

tag: library plate id

tag: c1 chip size

tag: c1 machine id