title: MCF10A.Ca1h-3

city: Houston

first: Isabelle

last: Bedrosian

state: TX

address: 1515 Holcombe Street

department: Breast Surgical Oncology

institute: UT MD Anderson Cancer Center

description:
MCF10.CA1d and MCF10.CA1h cells, both derived from MCF10AT xenografts, form well-differentiated malignant tumors in xenograft mouse models.
Sample 18

data_processing:
Illumina small RNA adapter sequences were trimmed from the reads, and reads of length below 10nt or ending in homopolymers of length 9 nt or above were discarded.
Total usable number of reads for each sample was calculated.
The reads were mapped to the miRBase reference using BLAST; the abundance of each expressed microRNA was quantified as a fraction of the usable reads, and expressed as parts per million.
Genome_build: hg19
Supplementary_files_format_and_content: TAB-delimited text format, containing quantile normalized microRNA abundance

growth_protocol: MCF10A (P) is an immortalized human mammary epithelial cell line; MCF10.NeoT and MCF10.AT1 represent the hyperplastic/atypical hyperplastic premalignant cell lines that are generated by HRAS transformation of MCF10A (P) cells. MCF10.DCIS cells form comedo DCIS lesions in immune-deficient mice. MCF10.CA1d and MCF10.CA1h cells, both derived from MCF10AT xenografts, form well-differentiated malignant tumors in xenograft mouse models. We purchased the MCF10A (P) cell line from ATCC and obtained the MCF10.AT1, MCF10.neoT, MCF10.Ca1d, and MCF10.Ca1h cell lines from the Karmanos Cancer Center, Detroit, MI, under a Materials Transfer Agreement. MCF10.DCIS cell were bought from Wayne State University, Detroit, MI. All the cell lines used in the study were grown in the media recommended by the selling agency, and authenticated by the selling agency and used within the first 10 passages.

extract_protocol:
Total RNA, including miRNA, was extracted by using the miRNeasy Mini Kit (Qiagen, [Germantown, MD]), an extraction method that efficiently preserves the small RNA (10-200 nucleotides) fraction.
Small RNA libraries were prepared using the Illumina small RNA protocol (Illumina, Inc., San Diego, CA)

treatment_protocol: Untreated cells were used for extracting total RNA (enriched in small RNA) followed by small RNA seq

tag: passage

value: Passage 12


title: CMP_M32_Het_3

status: Public on Jan 18 2017

type: SRA

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

country: Germany

institute: Ludwig-Maximilians University Munich

description: processed data file: CMP.counts.txt

library_source: transcriptomic

data_processing:
Sequencing reads were demultiplexed from the Nextera (i5 and i7) indices using deML (Renaud 2014, Bioinformatics)
Demultiplexed reads were aligned to the mouse genome mm10 and ERCC reference using NextGenMap (Sedlazeck et al., 2013)
Count data was generated from mapped reads using featureCounts (Liao et al., 2014) on ENSEMBL gene models (GRCm38.74)
Genome_build: mm10
Supplementary_files_format_and_content: gene-wise count data in tab delimited text file, available on the series record.

molecule: total RNA

organism: Mus musculus

source_name: CMP hematopoetic stem cell

extract_protocol:
Liver single cell suspensions by homogenization of fetal liver tissue with a 1ml Eppendorf pipette and Hank ́s buffered salt solution (HBSS) with 3% foetal calf serum (FCS) were prepared. Cells were then stained with anti-CD45.2-FITC (BD Pharmingen), biotinylated lineage antibodies (anti-B220, -CD3,Gr-1, and -Ter-119; all BD), anti-Mac1/CD11b-eFluor 450 (eBioscience), anti-CD117/c-kit-Alexa Fluor®780 (eBioscience) and anti-Sca-1-PeCy7 (eBioscience). Biotinylated monoclonal antibodies were labeled by incubation with Streptavidin-PerCP/PerCP-Cy5.5 (eBioscience) and cells sorted directly into lysis buffer (0.2%TritonX supplemented with RNAse Inhibitor (Promega))
RNA was cleaned-up from the crude lysate with Agencourt RNAclean XP SPRI beads (Beckman-Coulter). cDNA was synthesized and pre-amplified from 5 μ l of lysate as described in Picelli et al 2014 (Smart-seq2). 0.7 ng of pre-amplified cDNA was used as input for tagmentation by the Nextera XT Sample Preparation Kit (Illumina), where a second amplification round was performed for 12 cycles. For each sample, 5 ng of final library was pooled.

tag: strain

tag: Sex

value: not determined

tag: developmental stage

value: fetus

tag: tissue

value: liver

tag: age

tag: genotype

value: Smarcd2 +/-

tag: cell markers


title: MCF10A.Ca1h-2

country: USA

description:
MCF10.CA1d and MCF10.CA1h cells, both derived from MCF10AT xenografts, form well-differentiated malignant tumors in xenograft mouse models.
Sample 17

organism: Homo sapiens

tag: cell type


title: CMP_M32_Het_1

description: processed data file: CMP.counts.txt


title: MCF10A.Ca1h-1

description:
MCF10.CA1d and MCF10.CA1h cells, both derived from MCF10AT xenografts, form well-differentiated malignant tumors in xenograft mouse models.
Sample 16


title: MCF10A.Ca1d-2

description:
MCF10.CA1d and MCF10.CA1h cells, both derived from MCF10AT xenografts, form well-differentiated malignant tumors in xenograft mouse models.
Sample 14


title: WT24.10

data_processing:
Sequencing reads were demultiplexed from the Nextera (i5 and i7) indices using deML (Renaud 2014, Bioinformatics)
Demultiplexed reads were aligned to the mouse genome mm10 and ERCC reference using NextGenMap (Sedlazeck et al., 2013)
Count data was generated from mapped reads using featureCounts (Liao et al., 2014) on ENSEMBL gene models (GRCm38.74)
Genome_build: mm10
Supplementary_files_format_and_content: gene-wise count data in tab delimited text file

source_name: hematopoetic stem cell

extract_protocol:
Liver single cell suspensions by homogenization of fetal liver tissue with a 1ml Eppendorf pipette and Hank ́s buffered salt solution (HBSS) with 3% foetal calf serum (FCS) were prepared. Cells were then stained with anti-CD45.2-FITC (BD Pharmingen), biotinylated lineage antibodies (anti-B220, -CD3,Gr-1, and -Ter-119; all BD), anti-Mac1/CD11b-eFluor 450 (eBioscience), anti-CD117/c-kit-Alexa Fluor®780 (eBioscience) and anti-Sca-1-PeCy7 (eBioscience). Biotinylated monoclonal antibodies were labeled by incubation with Streptavidin-PerCP/PerCP-Cy5.5 (eBioscience) and LSK cells sorted directly into lysis buffer (0.2%TritonX supplemented with RNAse Inhibitor (Promega))
RNA was cleaned-up from the crude lysate with Agencourt RNAclean XP SPRI beads (Beckman-Coulter). cDNA was synthesized and pre-amplified from 5 μ l of lysate as described in Picelli et al 2014 (Smart-seq2). 0.7 ng of pre-amplified cDNA was used as input for tagmentation by the Nextera XT Sample Preparation Kit (Illumina), where a second amplification round was performed for 12 cycles. For each sample, 5 ng of final library was pooled.

value: F

value: WT

value: CD45.2+ Lin- Mac+/low Sca1+ cKit+ (LSK)


title: WT21.5

value: M


title: WT22.8


title: CMP_M33_Het_9

description: processed data file: CMP.counts.txt


title: WT21.1


title: MCF10.DCIS-3

description:
MCF10.DCIS cells from comedo DCIS lesions in immune-deficient mice
Sample 12

value: cells comedo DCIS lesions in immune-deficient mice


title: WT19.2


title: KO24.5

value: Smarcd2 -/-


title: MCF10.DCIS-2

description:
MCF10.DCIS cells from comedo DCIS lesions in immune-deficient mice
Sample 11


title: MCF10.DCIS-1

description:
MCF10.DCIS cells from comedo DCIS lesions in immune-deficient mice
Sample 10


title: MCF10A-neoT-3

description:
MCF10.NeoT and MCF10.AT1 represent the hyperplastic/atypical hyperplastic premalignant cell lines that are generated by HRAS transformation of MCF10A (P) cells.
Sample 9


title: MCF10A-neoT-2

description:
MCF10.NeoT and MCF10.AT1 represent the hyperplastic/atypical hyperplastic premalignant cell lines that are generated by HRAS transformation of MCF10A (P) cells.
Sample 8


title: KO22.4


title: KO22.2


title: KO22.5


title: MCF10A-neoT-1

description:
MCF10.NeoT and MCF10.AT1 represent the hyperplastic/atypical hyperplastic premalignant cell lines that are generated by HRAS transformation of MCF10A (P) cells.
Sample 7


title: KO21.3


title: MCF10AT1-3

description:
MCF10.NeoT and MCF10.AT1 represent the hyperplastic/atypical hyperplastic premalignant cell lines that are generated by HRAS transformation of MCF10A (P) cells.
Sample 6


title: MCF10AT1-2

description:
MCF10.NeoT and MCF10.AT1 represent the hyperplastic/atypical hyperplastic premalignant cell lines that are generated by HRAS transformation of MCF10A (P) cells.
Sample 5


title: KO21.2


title: KO19.6


title: MCF10AT1-1

description:
MCF10.NeoT and MCF10.AT1 represent the hyperplastic/atypical hyperplastic premalignant cell lines that are generated by HRAS transformation of MCF10A (P) cells.
Sample 4


title: KO20.3


title: MCF10A(P)-3

description:
MCF10A (P) is an immortalized human mammary epithelial cell line
Sample 3

source_name: MCF10A (P)


title: MCF10A(P)-2

description:
MCF10A (P) is an immortalized human mammary epithelial cell line
Sample 2


title: KO19.5


title: MCF10A.Ca1d-1

description:
MCF10.CA1d and MCF10.CA1h cells, both derived from MCF10AT xenografts, form well-differentiated malignant tumors in xenograft mouse models.
Sample 13


title: MCF10A.Ca1d-3

description:
MCF10.CA1d and MCF10.CA1h cells, both derived from MCF10AT xenografts, form well-differentiated malignant tumors in xenograft mouse models.
Sample 15


title: MCF10A(P)-1

description:
MCF10A (P) is an immortalized human mammary epithelial cell line
Sample 1


title: HT24.2


title: HT22.6


title: HT21.6


title: Mut Carrier_3

city: Stanford

first: Marlene

last: Rabinovitch

state: CA

address: 269 Campus Drive

institute: Stanford University School of Medicine

data_processing:
1. Aligned to the human genome (GRCh37_P13) by HISAT (0.1.6 β)
2. Quantitated by the genome features based on GENCODE annotation database (GRCh37, version 19) by HT-seq (0.6.1p1).
3. Normalization and differential expressed genes (DEG) were implemented by DESeq2 (1.8.2).
Genome_build: GRCh37_P13
Supplementary_files_format_and_content: normalized expression table in text

source_name: iPS derived endothelial cells

extract_protocol:
RNA was extracted from 100,000 iPSC-ECs using RNeasy Mini Kit (Qiagen, Hilden, Germany).
Libraries were prepared using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA) and sequenced on 1–2 Illumina HiSeq 2000 lanes to obtain an average of approximately 100-150 million uniquely mapped reads for each sample

value: iPS derived endothelial cells

tag: phenotype

value: unaffected mutation carrier


title: FPAH_3

value: FPAH


title: control_3

value: wild type control from community


title: HT21.4


title: HT20.5


title: FPAH_2


title: Flag-Jmjd2c_Serum_input_rep2_DNA

city: London

first: Rute

middle: A.

last: Tomaz

state: London

address: IRDB, Imperial College, Hammersmith Campus, Du Cane Road

country: United Kingdom

institute: Imperial College London

library_source: genomic

data_processing:
Quality of the sequenced reads was assessed using the FASTQC program (Babraham Bioinformatics). Reads were aligned to the UCSC mouse reference genome (mm9) using Bowtie2 (Langmead and Salzberg, 2012), and only uniquely aligned reads were retained. Aligned reads (SAM) were converted into BED format to subsequently generate bigwig files for visualization.
Due to the high correlation between bigwig files of each pair of replicates, individual BAM files were merged and used in peak calling. List of enriched peaks were obtained using MACS2 with an FDR <0.0001 by calling peaks relative to the respective input control samples (background).
Peaks in Flag-Jmjd2c 2i+LIF replicates were called relative to 2i input replicate1 (all run on the same lane). Flag-Jmjd2c serum+LIF replicate1 peaks were called relative to input serum+LIF replicate1 (same lane), whereas Flag-Jmjd2c serum+LIF replicate2 peaks were called relative to input serum+LIF replicate2 (same lane).
Gene annotation was performed using HOMER (Heinz et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files

molecule: genomic DNA

source_name: Mouse Embryonic Stem Cells

growth_protocol: Serum+LIF: Flag-Jmjd2c mESC cell line was maintained in GMEM (Gibco) supplemented with 10% FBS, β-mercaptoethanol, L-glutamine, sodium bicarbonate, sodium pyruvate, non-essential amino acids, penicillin-streptomycin, LIF and Puromycin (1 μg/mL).

extract_protocol:
In general, Flag ChIP followed the procedure described in Frank et al., 2001. Chromatin was fixed on 1% formaldehyde for 10 minutes and was sonicated on a bioruptor (Diagenode) to produce fragments of 100-500 bp. 500 μg of protein were used per ChIP with 10 μg of anti-Flag antibody (Sigma, catalog number F1804) and protein-bound fragments were retrieved with ProteinG-coupled magnetic Dynabeads (Invitrogen).
Sequencing libraries were prepared using the NEBNext® UltraTM DNA Library Prep Kit and Multiplex Oligos (New England Biolabs) from 5 ng of DNA.

treatment_protocol: Flag-Jmjd2c mESC cell line was cultured in 2i+LIF: N2B27 with 1 μM PD0325901, 3 μM CHIR99021, LIF and Puromycin (1 μg/mL), for at least 7 days before ChIP. ChIP was preformed in either cells grown routinelly in serum+LIF or at least 7 days in 2i+LIF.

value: E14 [129 background]

tag: treatment

value: Mouse ES cells routinely cultured in serum/LIF conditions

tag: chip antibody

value: input DNA


title: Mut Carrier_2


title: HT19.4


title: Flag-Jmjd2c_Serum_ChIPseq_rep1

value: anti-FLAG (Sigma, catalog number F1804)


title: control_2


title: HT20.4

value: fetus


title: FAPH_1_3


title: HT19.3

value: liver


title: Flag-Jmjd2c_Serum_input_rep1_DNA


title: HT19.1

value: Smarcd2 +/-


title: Flag-Jmjd2c_2i_ChIPseq_rep2

value: Mouse ES cells routinely cultured in 2i/LIF conditions


title: FPAH_1_1


title: Flag-Jmjd2c_2i_input_DNA


title: control_1


title: 26% rep2

city: Claremont

first: Daniel

last: Stoebel

address: 301 Platt Blvd

department: Biology

institute: Harvey Mudd College

data_processing:
Base calls performed with RTA v1.18.5
the first ten base pairs of each read were trimmed using FASTXToolkit 0.0.13.
Reads were mapped using BWA 0.7.5a
The number read pairs mapped to each gene was counted with HTSeq 0.6.1
Supplementary_files_format_and_content: A tab deliminited file with counts for each gene.

organism: Escherichia coli

source_name: E. coli culture

growth_protocol: Cells were inoculated from frozen cultures into 5 mL of LB, and grown.  5 µL of this overnight culture was diluted into 5 mL of LB with the appropriate concentration of arabinose, and grown for 20h.

extract_protocol:
RNA was purified from 200 µL of overnight culture by pelleting and resuspeding in 500 µL of Trizol at 65°C, followed by purification on a column (Direct-Zol, Zymo Research). Samples received two 30-minute DNase treatments using TURBO DNA-free (Ambion) following the manufacturers instructions. RNA samples were then purified on a column (RNA Clean & Concentrator, Zymo Research). Three samples were prepped from each culture and pooled to generate sufficient RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: DMS2564 (K-12 derivative)

tag: rpos level


title: 0% rep2

value: DMS2545 (K-12 derivative)


title: Flag-Jmjd2c_Serum_ChIPseq_rep2


title: 26% rep1


title: 100% rep2

value: BW27786 (K-12 derivative)


title: 0% rep1


title: 100% rep1


title: G.m. anodic 2

city: Karlsruhe

first: Andreas

last: Doetsch

address: Haid-und-Neu-Str. 9

department: Physiology and Biochemistry of Nutrition

institute: Max Rubner-Institute

data_processing:
Cluster detection and base calling were performed using RTAv1.13 and quality of reads was assessed with CASAVA v1.8.1 (Illumina).
Sequence data were clipped for the samples with 2 x 100 nt to obtain a fixed read length of 51 nt in all samples and mapped to a database containing the merged genomes of Geobacter metallireducens GS-15 (NCBI GenBank accession number NC_002939.5), Geobacter sulfurreducens PCA (NC_007517.1), Shewanella oneidensis MR-1 (NC_004347.2) and its megaplasmid (NC_004349.1) using bowtie2 (Langmead and Salzberg, 2012, doi:10.1038/nmeth.1923).
Gene expression profiles were calculated for each species individually in pure cultures and the mixed culture from the mapped sequences using HTSeq (Anders et al., 2015, doi: 10.1093/bioinformatics/btu638) with the option 'intersection-nonempty'.
Genome_build: NC_002939.5 G. sulfurreducens PCA, NC_007517.1, G. metallireducens GS-15, NC_004347.2 S. oneidensis MR-1, NC_004349.1| Shewanella oneidensis MR-1 plasmid megaplasmid
Supplementary_files_format_and_content: RPG (reads per gene) files were created using HTSeq, mapping raw reads (fastq format) against the E. coli K12 genome and using a GFF file derived from the annotation of the genomes available from NCBI.

organism: Geobacter metallireducens

source_name: G.m. anodic_bacterial culture

growth_protocol: Shewanella oneidensis MR-1, Geobacter sulfurreducens PCA and Geobacter metallireducens GS-15 were routinely cultured anaerobically at 30 ᵒC on a medium that was developed following Coppi et al. (2001) and Holmes et al. (2004). The growth medium contained 0.42 g/l KH2PO4, 0.22 g/l K2HPO4, 0.2 g/l NH4Cl, 0.38 g/l KCl, 0.36 g/l NaCl, 0.21 g/l MgCl2 6H2O, 1.8 g/l NaHCO3, 0.5 g/l Na2CO3, 60 mg/l CaCl2 2H2O, 2 g/l casitone and was further complemented with 1.0 ml/l of selenite-tungstate solution (0.5 g/l NaOH, 3 mg/l Na2SeO3, 4 mg/l Na2WO4 2H2O), 10 ml NB/l trace mineral solution (Coppi et al. 2001), 10 ml/l vitamin solution (German Type Culture Collection, DSMZ, media 141), 0.2 mM sodium ascorbate, 1.0 mM cysteine, 0.2 % (w/v) yeast extract and 50 mM ferric citrate as an electron acceptor. The medium contained sodium lactate (12.5 mM), sodium acetate (6.25 mM) sodium propionate (5 mM) as electron donors. Standard anaerobic techniques were used throughout the study (Balch et al. (1976)). All anaerobic media were prepared in bottles capped with butyl rubber stoppers. To remove oxygen, the media were boiled for 10 minutes and flushed with a mixture of 80% N2/20% CO2 for 30 min. After that, the pH was adjusted to 7.2. The optical density during anaerobic growth on ferric citrate was measured at a wavelength of 655 nm to avoid an influence by ferric iron.  All experiments were carried out in at least three independent replicates. Error bars represent the standard deviation.

extract_protocol:
RNA was extracted individually from the triplicates of four experimental BES set-ups, which were inoculated either with pure cultures of Shewanella oneidensis MR-1, Geobacter sulfurreducens PCA, Geobacter metallireducens GS-15 or a mixed culture of the three strains. Prior to the extraction, all anodes with a biofilm were additionally pre-incubated in 3 ml of Bacteria Protect solution for 10 minutes at room temperature (Qiagen RNeasy Mini kit, Hilden, Germany). Total RNA was isolated from the anode-biofilms using the RNeasy kit provided by Qiagen according to the manufacturer’s instructions. Residual DNA was removed with an overnight DNAse I digestion at 37°C. Further purification of RNA from DNA was conducted using the Ambion DNA-free kit (Life Technologies, Carlsbad, CA, USA). Aliquots from treated samples were subjected to PCR amplification with specific primers (Table 1) to validate the absence of genomic DNA. The Ambion MICROBExpress bacterial mRNA enrichment kit (Life Technologies) was used for rRNA depletion.
Strand specific cDNA libraries were prepared from 50 ng of rRNA-depleted RNA following the TruSeq v2 RNA protocol (Illumina). The libraries were prepared using multiplex primers to allow simultaneous sequencing on a single lane, which was performed on a HiSeq1500 using SBS v3 kits (Illumina) generating paired end reads of 2 x 51 nt (G. sulfurreducens and S. oneidensis) or 2 x 100 nt (mixed species and G. metallireducens samples).

value: strain G.m. GS-15

tag: phase

value: anodic biofilm

tag: culture type

value: pure culture

tag: molecule subtype

value: total RNA (ribosome-depleted)


title: CROP-seq_Jurkat_TCR_unstimulated_run5

city: Vienna

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description:
Single-cell RNA-seq on Jurkat cells infected with a population of gRNAs (CROP-seq) targeting components of TCR signaling and control gRNAs; Microfluidic run number 5
processed data file: CROP-seq_Jurkat_TCR.digital_expression.csv.gz

data_processing:
Library strategy: CROP-seq
Single-cell sequencing: Data were processed using the Drop-seq Tools v1.12 software (Macosko et al, 2015). Briefly, each transcriptome Read 2 was tagged with the cell barcode (bases 1 to 12) and UMI (unique molecular identifier) barcode (bases 13 to 20) obtained from Read 1, trimmed for sequencing adapters and poly-A sequences, and aligned using STAR v2.4.0 15 to the human reference genome assembly (Ensembl GRCm38/GRCh38 release) containing artificial chromosomes that represent the CROPseq-Guide-Puro plasmid construct (250 bp common U6 promoter sequence, one gRNA sequence per artificial chromosome (20 bp), and the remaining 260 bp downstream plasmid backbone until the poly-A sequence). Cell barcodes were corrected for possible bead synthesis errors, allowing the removal of up to 4 bases using the DetectBeadSynthesisErrors tool from the Drop-seq Tools v1.12 software. Reads aligning to exons were tagged with the respective gene name, and counts of unique UMIs per gene within each cell were used to build a digital gene expression matrix for cells with counts for at least 500 genes. This matrix was converted to transcripts per million and log-transformed for further analysis. We excluded genes coding from ribosomal proteins from the analysis as we suspect their widespread detection is caused by solubilization of their mRNAs as noted previously (Macosko et al, 2015). For the assignment of gRNAs to cells, we quantified the overlap of reads to the specific gRNA sequence within the CROPseq-Guide-Puro plasmid chromosomes and assigned the most abundant gRNA to the respective cell.
Bulk RNA sequencing data: Reads were trimmed with Trimmomatic and aligned to the GRCh38 assembly of the human genome using Bowtie1 with the following parameters: -q -p 6 -a -m 100 -minins 0 maxins 5000 –fr –sam -chunkmbs 200. Duplicate reads were removed with Picard’s MarkDuplicates utility with standard parameters before transcript quantification with BitSeq 18 using the Markov chain Monte Carlo method and standard parameters. To obtain gene-level quantifications, we assigned the expression values of its highest expressed transcript to each gene.
Genome_build: hg38
Supplementary_files_format_and_content: Comma-separated values (CSV) files with genes as rows and samples/cells as columns. For the file with the single-cell expression values, we added 4 metadata header rows (stimulation condition, microfluidics run ("replicate"), cell barcode, assigned gRNA, targeted gene), which refer to the respective cells. The "replicate" field indicates the run referenced in the sample title.

molecule: polyA RNA

source_name: Jurkat cells

growth_protocol: Jurkat cells stably expressing SpCas9 (after transduction with lentiCas9-Blast, Addgene #52962) were kept in RPMI medium + 10% FCS + penicillin/streptomycin containing 25 μg/ml blasticidin. After transduction with gRNA-encoding lentiviral particles (CROPseq-Guide-Puro), cells were selected with 2 μg/ml puromycin for 10 days, while keeping up the selection for blasticidin, and then used in T cell receptor stimulation experiments followed by CROP-seq (or bulk RNA-seq on single knockout lines for validation).

extract_protocol:
CROP-seq: Adherent cells were detached using Trypsin-EDTA (Gibco #25300-054), following standard cell culture practices. Cells were collected by centrifugation at 300 rcf for 5 min, washed once with PBS-0.01% BSA (freshly prepared on the day of the run), and resuspended in 1 ml of PBS-0.01% BSA. Cells were filtered through a 40 µm cell strainer to obtain a suspension of single-cells, which were counted using a CASY device. Single cells were then co-encapsulated with barcoded beads (ChemGenes #Macosko-2011-10) using an Aquapel-coated PDMS microfluidic device (FlowJEM), connected to syringe pumps (kdScientific) via polyethylene tubing with an inner diameter of 0.38 mm (Scicominc #BB31695-PE/2). Cells were supplied in PBS-0.01% BSA at a concentration of 220 cells/µl, barcoded beads were resuspended in Drop-seq lysis buffer at a concentration of 150 beads/µl. The flow rates for cells and beads were set to 1.6 ml/hour, while Droplet Generation Oil (BioRad #1864006) was run at 8 ml/hour. During the run, the barcoded bead solution was mixed by magnetic stirring with a mixing disk set to 1 jump/s. A typical run lasted between 35 and 40 min. In case of multiple runs per day, droplets were intermittently stored at 4 °C and processed together. Our most important modification to the protocol is an alternative way to break droplets, which recovers beads much more efficiently than in the original publication of Drop-seq (Macosko et al., 2015). After removing as much oil below the droplet layer as possible, we added 30 ml of 6x SSC buffer (Promega #V4261) and 1 ml of Perfluoroctanol (Sigma Aldrich #370533-25G) and shook the tube forcefully 6 times to break the droplets. Based on their large diameter, beads were then collected by syringe-filtering the solution through a 0.22 µm filter unit (Merck #SLGV033RS), washing 2x with 20 ml of 6x SSC buffer and eluting by turning the filter upside down and rinsing it with 3x 10 ml of 6x SSC buffer. Beads were then collected by centrifugation at 1,250 rcf for 2 min, setting the brake speed to 50%. After washing a second time with 10 ml 6x SSC, the pellet was taken up in 200 µl of 5x RT buffer and transferred to a 1.5 ml tube. Bulk RNA-seq: Total RNA was extracted using the Qiagen AllPrep Kit (Qiagen #80311).
CROP-seq: Reverse transcription and Exonuclease I treatment were performed as described in the original publication, and the number of barcoded beads was estimated using a Fuchs-Rosenthal counting chamber (mixing the bead suspension with 6x DNA loading dye). Depending on the performance of the experiment, we prepared up to 24 PCR reactions per Drop-seq run, adding 4,400 beads (~220 cells) per PCR and enriching the cDNA for 4 + 10 cycles, using the already described reagents. We then prepared Drop-seq libraries using the Nextera XT kit (Illumina #15032350), starting from 1 ng of cDNA pooled in equal amounts from all PCR reactions for a given run. We typically required an additional 10 enrichment cycles, using the Illumina Nextera XT i7 primers along with the Drop-seq New-P5 SMART-PCR hybrid oligo. The slightly increased cDNA input typically results in an average size distribution of about 575 bp. After quality control, libraries were sequenced with paired-end SBS chemistry on Illumina HiSeq 3000/4000 instruments. Drop-seq Custom Read1 Primer was spiked into the HP10 primer solution, located in column 11 of the cBot Reagent Plate at 1µM final concentration. High sequence complexity needed for optimal base calling performance was achieved by adding 20-30% PhiX as spike-in. Cluster generation and Read 1 primer hybridization were completed using cBot protocol ‘HiSeq_3000_4000_HD_Exclusion_Amp_v1.0’. Alternatively, libraries were sequenced on an Illumina NextSeq 550 instrument using the 75 cycle High Output Kit. We loaded 1.8 pM library and provided Drop-seq Custom Read1 Primer at 0.3 µM in position 7 of the reagent cartridge. On NextSeq machines, we sequenced without PhiX spike-in, using a read configuration of 20 bases (Read1), 8 bases (Index) and 64 bases (Read2); Bulk RNA-seq: Bulk RNA-seq libraries were prepared using the QuantSeq 3' mRNA-Seq Library Prep Kit (Lexogen #015.96) according to the manufacturer's instructions.

treatment_protocol: Jurkat cells were serum-starved for 3 hours prior to stimulation. They were stimulated with 1 µg/ml anti-CD3 (eBioscience #16-0037) and 1 µg/ml anti-CD28 antibody (eBioscience #16-0289-81) for 4 hours while under starvation and then subjected to CROP-seq. The unstimulated (naïve) control was subjected to continued starvation.

tag: cell line

value: Jurkat

tag: library

value: CROP-seq

tag: experiment

tag: condition

value: naive

tag: knockout

value: diverse, each knockout applied on single-cell basis (see processed data file)

tag: grna

value: diverse, each gRNA applied on single-cell basis (see processed data file)


title: S.o. planktonic 1

organism: Shewanella oneidensis

source_name: S.o. planktonic_bacterial culture

tag: strain

value: strain S.o. MR-1

value: planktonic


title: S.o. planktonic 2


title: S.o. planktonic 3


title: G.m. anodic 3


title: CROP-seq_Jurkat_TCR_unstimulated_run4

description:
Single-cell RNA-seq on Jurkat cells infected with a population of gRNAs (CROP-seq) targeting components of TCR signaling and control gRNAs; Microfluidic run number 4
processed data file: CROP-seq_Jurkat_TCR.digital_expression.csv.gz


title: FPAH_1_2

tag: tissue

value: iPS derived endothelial cells

value: FPAH

tag: passage


title: Flag-Jmjd2c_2i_ChIPseq_rep1

value: E14 [129 background]

value: Mouse ES cells routinely cultured in 2i/LIF conditions

value: anti-FLAG (Sigma, catalog number F1804)


title: S.o. anodic 3

source_name: S.o. anodic_bacterial culture


title: CROP-seq_Jurkat_TCR_unstimulated_run3

description:
Single-cell RNA-seq on Jurkat cells infected with a population of gRNAs (CROP-seq) targeting components of TCR signaling and control gRNAs; Microfluidic run number 3
processed data file: CROP-seq_Jurkat_TCR.digital_expression.csv.gz


title: mixed planktonic 3

organism:
Geobacter metallireducens
Geobacter sulfurreducens
Shewanella oneidensis

source_name: mixed planktonic_bacterial culture

value: strain G.s. PCA, strain G.m. GS-15, strain S.o. MR-1

value: mixed culture, inoculated with equal OD-ratios


title: mixed planktonic 1


title: mixed planktonic 2


title: S.o. anodic 2

value: anodic biofilm


title: Mut Carrier_1

value: unaffected mutation carrier


title: mixed anodic 3

source_name: mixed anodic_bacterial culture

value: total RNA (ribosome-depleted)


title: S.o. anodic 1

value: pure culture


title: mixed anodic 2


title: CROP-seq_Jurkat_TCR_stimulated_run5

description:
Single-cell RNA-seq on Jurkat cells treated with anti-CD3/CD28 antibodies and infected with a population of gRNAs (CROP-seq) targeting components of TCR signaling and control gRNAs; Microfluidic run number 5
processed data file: CROP-seq_Jurkat_TCR.digital_expression.csv.gz

value: Jurkat

value: CROP-seq


title: G.m. anodic 1

value: strain G.m. GS-15


title: CROP-seq_Jurkat_TCR_stimulated_run4

description:
Single-cell RNA-seq on Jurkat cells treated with anti-CD3/CD28 antibodies and infected with a population of gRNAs (CROP-seq) targeting components of TCR signaling and control gRNAs; Microfluidic run number 4
processed data file: CROP-seq_Jurkat_TCR.digital_expression.csv.gz

value: diverse, each knockout applied on single-cell basis (see processed data file)

value: diverse, each gRNA applied on single-cell basis (see processed data file)


title: G.s. anodic 1

organism: Geobacter sulfurreducens

source_name: G.s. anodic_bacterial culture

value: strain G.s. PCA


title: G.s. anodic 3


title: CROP-seq_Jurkat_TCR_stimulated_run3

description:
Single-cell RNA-seq on Jurkat cells treated with anti-CD3/CD28 antibodies and infected with a population of gRNAs (CROP-seq) targeting components of TCR signaling and control gRNAs; Microfluidic run number 3
processed data file: CROP-seq_Jurkat_TCR.digital_expression.csv.gz


title: mixed anodic 1


title: TP180 supplemental far-red light cotyledon rep2

status: Public on Jan 17 2017

city: Lausanne

first: Markus

middle: Volker

last: Kohnen

state: Vaud

address: Genopode Building

department: Center for Integrative Genomics (CIG)

country: Switzerland

institute: Université de Lausanne

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.2.1)
filtered for low complexity with PrinSeq (v. 0.20.3)
Reads were aligned against Arabidopsis thaliana (version TAIR10) genome using Tophat (v2.0.9) and the parameters --bowtie1 --read-edit-dist 3 --read-realign-edit-dist 0 --library-type fr-firststrand.
The number of read counts per gene locus was summarized with htseq-count (v. 0.5.4p3; TAIR10)
Genes with low counts (< 50 counts across all samples) were filtered out
Library sizes were scaled using TMM normalization (EdgeR v 3.4.0)
data were log-transformed with limma voom function (v 3.18.2)
Differential expression was computed with limma (v 3.18.2) using a moderated t-test and a Benjamini-Hochberg corrected p-values
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text

organism: Arabidopsis thaliana

source_name: cotyledon

growth_protocol: Arabidopsis thaliana seeds (cv Columbia-0) were size selected and surface-sterilized using 70 % (v/v) ethanol and 0.05 % (v/v) Triton X-100 for 3 min followed by 10 min incubation in 100 % (v/v) ethanol. On half-strength Murashige and Skoog medium (Murashige & Skoog, 1962) containing 0.8 % (w/v) phytoagar (Agar-Agar, plant; Roth) were prepared. Seeds were sowed on plates  which were covered with a nylon mesh and subsequently stratified at 4°C for 3 day in darkness. Seedlings were grown for 5 days in long-day (16h light : 8h dark) at 21°C on one horizontal plate of c. 140 mm in diameter per sample.

extract_protocol:
All seedlings were imbibed within 75 sec in ice-cold 100 % (v/v) acetone and two times subjected to about 600 mbar below atmospheric pressure for 5min while remaining on ice. The dissection of acetone-fixed seedlings was carried out in 70 % (v/v) 4°C-cold ethanol under a binocular lens. Cotyledon and hypocotyl material of 50 seedlings per sample were collected in 100 % (v/v) ethanol. Plant materials were manually ground using pestles and total RNA was extracted using the RNeasy Kit (QIAGen) with on-column DNA digestion, according to the manufacturer’s instructions. Finally RNA samples were precipitated using 3M NAOH (pH 5.2) and 100 % (v/v) ethanol. The precipitate was visualize with glycogen and washed with 80 % (v/v) ice-cold ethanol. Stranded libraries were prepared using 400 ng high quality RNA according to the TruSeq protocol (Illumina). This included RNA purification steps using AMPure XP beads and cDNA preparation using a mix of random and polyA primer.
Truseq stranded mRNA protocoll (Illumina)

treatment_protocol: On day 6 at ZT2, seedlings were either kept in high R/FR or transferred to low R/FR.  After 0, 15, 45, 90 or 180 min in low R/FR samples of both light qualities.

tag: ecotype

tag: age

value: 5 days

tag: organ

value: cotyledon

tag: light treatment

value: low R/FR

tag: duration of treatment

value: 180 min

tag: short sample key


title: TP180 white light hypocotyl rep2

source_name: hypocotyl

value: hypocotyl

value: high R/FR


title: TP180 supplemental far-red light hypocotyl rep1


title: TP180 supplemental far-red light cotyledon rep1


title: TP180 white light hypocotyl rep3


title: TP180 white light cotyledon rep1


title: TP90 supplemental far-red light hypocotyl rep2

value: 90 min


title: TP90 supplemental far-red light hypocotyl rep1


title: CROP-seq_Jurkat_TCR_stimulated_run6

description:
Single-cell RNA-seq on Jurkat cells treated with anti-CD3/CD28 antibodies and infected with a population of gRNAs (CROP-seq) targeting components of TCR signaling and control gRNAs; Microfluidic run number 6
processed data file: CROP-seq_Jurkat_TCR.digital_expression.csv.gz


title: TP180 white light cotyledon rep2


title: TP90 white light cotyledon rep2


title: TP45 supplemental far-red light hypocotyl rep2

value: 45 min


title: TP90 white light cotyledon rep1


title: TP90 supplemental far-red light cotyledon rep2


title: TP45 supplemental far-red light hypocotyl rep1


title: TP90 supplemental far-red light cotyledon rep1


title: TP90 white light hypocotyl rep2


title: TP45 white light cotyledon rep2


title: TP45 supplemental far-red light cotyledon rep2


title: TP45 white light cotyledon rep1


title: TP15 supplemental far-red light hypocotyl rep1

value: 15 min


title: TP45 supplemental far-red light cotyledon rep1


title: TP15 supplemental far-red light hypocotyl rep3


title: TP15 supplemental far-red light cotyledon rep1


title: TP45 white light hypocotyl rep2


title: TP180 supplemental far-red light hypocotyl rep3


title: G.s. anodic 2

tag: phase

value: anodic biofilm

tag: culture type

value: total RNA (ribosome-depleted)


title: TP45 white light hypocotyl rep1


title: TP15 white light hypocotyl rep2


title: TP15 white light hypocotyl rep1


title: TP15 white light cotyledon rep2


title: TP15 white light cotyledon rep1


title: TP0 white light cotyledon rep2

value: 0 min


title: TP0 white light hypocotyl rep2


title: TP0 white light cotyledon rep1


title: TP90 white light hypocotyl rep1


title: TP0 white light hypocotyl rep1


title: ANKRD52_KO_HCT116_EGFP_miR19_Dim_LibraryB_Replicate_2

city: Dallas

first: Joshua

last: Mendell

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

description: processed data file: ankrd52ko.totalnorm.txt

data_processing:
Library strategy: Genome-scale CRISPR-Cas9 Screen (GeCKO)
Raw reads were trimmed using inhouse scripts to extract the exact sgRNA sequence
Trimmed reads were mapping to library using bowtie 1.0.1, require perfect, unique match
Summarize bowtie results to sgRNA count using inhouse script
Normalize each sample to total reads, and combine library A and library B
Call significant gene using RIGER
Genome_build: hg19
Supplementary_files_format_and_content: text file with normalized reads. A key to the sample names used in the processed data files is provided on the series record.

source_name: HCT116 cells

growth_protocol: Cell lines used in this study were obtained from ATCC and cultured under standard conditions.

extract_protocol:
gDNA was extracted from the unsorted cells using the Qiagen DNeasy Blood & Tissue Kit according to the manufacturer’s instructions.  Extractions were performed on 4x10^7 cells using 5x10^6 cells per column to ensure enough gDNA for 300X coverage of the library.  DNA was eluted by adding 125 µL of water to each column.  The same eluate was added back to the column for a second elution.  The DNA concentration in the final eluate was assessed using the Qubit dsDNA BR assay kit (Thermo Fisher).  To facilitate maximum recovery of gDNA from the sorted cells, a previously described method (Largaespada, et al., 2008) was used  with the following modifications:  Sorted cell pellets were resuspended in 500 µL of tissue lysis buffer, consisting of 460 µL of STE buffer [1 mM EDTA (pH 8.0), 10 mM Tris-HCl (pH 8.0), 100 mM NaCl] supplemented with 10 µL of 0.5 M EDTA, 10 µL of proteinase K [10 mg/mL in TE buffer containing 10 mM Tris-HCl (pH 8.0) and 1 mM EDTA], and 20 µL of 10% SDS.  Pellets were digested overnight at 55°C while shaking at 1000 rpm on a Thermomixer (Eppendorf).  The following day, 5 µL of 2 mg/mL RNase A was added to each tube and incubated at 37°C for 1 hr while shaking at 1000 rpm.  Extractions were performed with an equal volume of pH 7.9-buffer saturated phenol, followed by phenol:chloroform:isoamyl alcohol (25:24:1), followed by chloroform.  20 µg of glycogen (Roche) and 1.5 mL of 100% ethanol was added to each tube and DNA was precipitated at -80°C for 1 hr followed by centrifugation at 18,000 g for 10 min at 4°C.  Pellets were washed with 1 mL of 75% ethanol, dried, and resuspended in 21 µL of water by incubating at 37°C for a minimum of 4 hrs. DNA concentration was determined with the Qubit dsDNA BR assay kit.
Methods to prepare PCR amplicon libraries for deep sequencing were adapted from a previously published protocol (Shalem, et al., 2014).  All primer sequences are provided in Supplementary Table 8.  For unsorted cells, an initial round of PCR (PCR I) was performed using 6.6 µg of gDNA per 100 µL PCR reaction.  To maintain 300X coverage, 20 reactions were assembled for each sample.  For sorted cells, all extracted gDNA for a given sample was distributed into two 100 µL reactions.  In both cases, 18 cycles of amplification were performed using Herculase II Fusion polymerase (Agilent).  All reactions for a given sample from PCR I were then pooled together and a second round of PCR (PCR II) was performed to add the necessary adapters for Illumina sequencing.  Due to variable PCR efficiency between samples, the cycle number for PCR II was adjusted so that each library was amplified in a 50 µL reaction to a common endpoint with respect to DNA quantity (approximately 50 ng of DNA library in a 50 µL PCR sample).  DNA was purified for sequencing using AMPure XP beads (Agencourt) according to the manufacturer’s instructions with the following modifications:  Each 50 uL PCR II reaction was mixed with 25 uL of beads and incubated for 5 minutes.  Magnetic separation was used to collect the supernatant.  The supernatant was mixed with 90 µL of beads and incubated for 5 minutes.  The supernatant was collected and discarded.  Beads were washed twice with 200 µL of 70% ethanol and then dried for approximately 12 minutes.  Bound DNA was eluted from the beads using 40 µL of water.

treatment_protocol: Two days prior to sorting, ten 15 cm dishes with 1.2x10^7 cells per dish were seeded for each library-reporter pair.

tag: cell type

value: Human colorectal carcinoma

tag: cell line


title: ANKRD52_KO_HCT116_EGFP_miR19_Dim_LibraryA_Replicate_2


title: ANKRD52_KO_HCT116_EGFP_miR19_Dim_LibraryB_Replicate_1


title: TP15 supplemental far-red light cotyledon rep3


title: FH-AGO2_WT_IP_1

description: processed data file: WT.merge.bed

data_processing:
Adaptors were trimmed using cutadapt 1.9.1
Barcode in R2 were removed using inhouse script
R2 were mapped to hg38 using tophat2 with default parameter and --max-multihits 1
PCR duplicates were removed based on randomer using inhouse scripts
Peak calling was done using inhouse script based on Poisson distribution
Genome_build: hg38
Supplementary_files_format_and_content: text file with peak coordinates

extract_protocol:
Aliquots of 2.0x107 cells were then frozen at -80°C.  eCLIP was performed using the frozen samples as previously described (Van Nostrand, et al., 2016), using anti-FLAG antibody for IPs (F1804, Sigma).  For each cell line, duplicate input and IP samples were prepared and sequenced.
Libraries were constructed as described previously (Van Nostrand, et al., 2016).  The RiL19 RNA adapter was used as the 3' RNA linker for all samples.  PAGE-purified DNA oligonucleotides were obtained from Sigma for the PCR library amplification step.  PCR amplification was performed using between 11-15 cycles for all samples.  Paired-end sequencing was performed on a NextSeq 500 using the NextSeq 500/550 High Output v2 Kit, 75 cycle (Illumina).

treatment_protocol: Cells were seeded in 15 cm dishes with five dishes per cell line at 1.0x107 cells per dish.  Cells were cultured for 48 hours and subsequently UV crosslinked at 400 mJ/cm2.

tag: ip antibody

value: Anti-FLAG (F1804, Sigma)

tag: genotype


title: FH-AGO2_5xA_IP_1

description: processed data file: 5XA.merge.bed


title: AGO2_KO_IP_2


title: FH-AGO2_WT_IP_2

description: processed data file: WT.merge.bed


title: FH-AGO2_5xA_IP_2

description: processed data file: 5XA.merge.bed


title: FH-AGO2_WT_Input_2


title: FH-AGO2_5xA_Input_2


title: AGO2_KO_IP_1


title: ANKRD52_KO_HCT116_EGFP_miR19_Dim_LibraryA_Replicate_1


title: FH-AGO2_WT_Input_1


title: AGO2_KO_Input_2


title: FH-AGO2_5xA_Input_1


title: AGO2_KO_Input_1


title: FH-AGO2_5xA_Replicate_2_wholeTranscriptome

description: processed data file: wholeT.FH_5XA_vs_AGO2_KO.edgeR.txt, wholeT.FH_5XA_vs_Parental.edgeR.txt

data_processing:
High quality reads are extacted by NGSQCToolkit v2.3.3 default setting
HQ reads were mapped to hg38 using tophat v2.0.12, and only uniquely mapped reads were kept
FPKM of genes were calculated using cufflinks v2.2.1 again Ensembl annotation GRCh38.85
Gene reads count were done by featureCounts 1.4.6
Gene differential expression analysis was done using edgeR v3.8.6
Genome_build: hg38
Supplementary_files_format_and_content: text file with edgeR output

extract_protocol:
RNA was extracted using the miRNeasy Mini Kit (Qiagen) with an on-column DNase digestion.
Sequencing libraries were generated using the TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat Low-throughput (LT) kit (Illumina) and run on a NextSeq 500 using the NextSeq 500/550 High Output v2 Kit, 75 cycle (Illumina).

treatment_protocol: Biological triplicates for each cell line were seeded with 5.0x10^5 cells per well in six-well dishes.  Cells were collected 48 hours later.


title: ANKRD52_KO_HCT116_EGFP_miR19_Unsorted_LibraryB_Replicate_2


title: FH-AGO2_5xA_Replicate_3_wholeTranscriptome


title: FH-AGO2_WT_Replicate_3_wholeTranscriptome

description: processed data file: wholeT.FH_WT_vs_AGO2_KO.edgeR.txt, wholeT.FH_WT_vs_Parental.edgeR.txt


title: FH-AGO2_5xA_Replicate_1_wholeTranscriptome


title: FH-AGO2_WT_Replicate_1_wholeTranscriptome


title: ANKRD52_KO_HCT116_EGFP_miR19_Unsorted_LibraryA_Replicate_2


title: AGO2_KO_Replicate_3_wholeTranscriptome

description: processed data file: wholeT.AGO2_KO_vs_Parental.edgeR.txt


title: FH-AGO2_WT_Replicate_2_wholeTranscriptome


title: AGO2_KO_Replicate_2_wholeTranscriptome


title: ANKRD52_KO_HCT116_EGFP_miR19_Unsorted_LibraryA_Replicate_1


title: Parental_Replicate_3_wholeTranscriptome

value: parental


title: Parental_Replicate_2_wholeTranscriptome


title: ANKRD52_KO_HCT116_EGFP_miR19_Unsorted_LibraryB_Replicate_1


title: ANKRD52;CSNK1A1_KO_Replicate_3_polyA_RNA

description: processed data file: polyA_DoubleKO_vs_Parental_edgeR.xls

data_processing:
High quality reads are extacted by NGSQCToolkit v2.3.3 default setting
HQ reads were mapped to hg19 using tophat v2.0.12, and only uniquely mapped reads were kept
Gene reads count were done by featureCounts 1.4.6 against igenome annotation for hg19
Gene differential expression analysis was done using edgeR v3.8.6
Genome_build: hg19
Supplementary_files_format_and_content: text files with edgeR output

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) with an on-column DNase digestion.
Sequencing libraries were generated using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) and run on a NextSeq 500 using the NextSeq 500/550 High Output v2 Kit, 75 cycle (Illumina).

treatment_protocol: 5.0x10^5 cells were seeded per well in six-well dishes.  Cells were harvested 48 hours later,


title: Parental_Replicate_1_wholeTranscriptome


title: ANKRD52_KO_Replicate_3_polyA_RNA

description: processed data file: polyA_ANKRD52_KO_vs_Parental_edgeR.xls


title: ANKRD52;CSNK1A1_KO_Replicate_2_polyA_RNA


title: ANKRD52_KO_Replicate_1_polyA_RNA


title: ANKRD52;CSNK1A1_KO_Replicate_1_polyA_RNA


title: AGO2_KO_Replicate_3_polyA_RNA

description: processed data file: polyA_AGO2_vs_Parental_edgeR.xls


title: ANKRD52_KO_Replicate_2_polyA_RNA


title: AGO2_KO_Replicate_2_polyA_RNA


title: Parental_Replicate_3_polyA_RNA


title: AGO2_KO_Replicate_1_polyA_RNA


title: Parental_Replicate_1_polyA_RNA


title: Parental_Replicate_2_polyA_RNA


title: AGO2_KO_Replicate_1_wholeTranscriptome


title: input DNA_untreated

city: Hangzhou

first: Guoji

last: Guo

state: Zhejiang

address: Yuhangtang Road 866

department: School of Medicine

country: China

institute: Zhejiang University

data_processing:
Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.2.5
peak-calling were performed using MACS version 1.4.3
Homer software was used to annotate ChIP-seq peaks, and to find differential peaks between treated and control samples.
Genome_build: mm9

source_name: mouse embryonic fibroblasts (MEFs)

growth_protocol: MEFs from each embryo were plated onto a 15cm tissue culture dish in MEF medium containing DMEM (Life Technologies) and 10% fetal bovine serum (FBS, Gemini). Mouse adult fibroblasts were isolated from tail tip samples. Tail tips were minced into pieces, placed on culture dishes, and incubated in MEF medium for 7days. MEFs and TTF cells were seeded at a density of 20000 cells per 35mm dish. The next day, MEF medium was replaced with the iMT media containing DMEM (Life Technologies) supplemented with 15% FBS (Gemini), 2mM GlutaMax-I (Life Technologies), 1% nonessential amino acids (Life Technologies), 0.1mM β-mercaptoethanol (Sigma) and 40ng/ml basic fibroblast growth factor (bFGF, Stemgent)

extract_protocol:
Cells were fixed in 1% formaldehyde for 10 min, quenched with glycine and washed 2 times with PBS. Cells were then resuspended in lysis buffer and sonicated to shear the chromatin to an average length of 600 bp. Supernatants were precleared with Protein-A/G Dynabeads (Invitrogen) and 10% input was collected. Immunoprecipitations were performed with antibodies to H3K4me3 and H3K27me3 (Millipore). DNA-protein complexes were pulled down using Protein-A/G Dynabeads (Invitrogen) washed. DNA was recovered by overnight incubation at 65°C to reverse crosslinks and purified using QIAquick PCR purification columns (QIAGEN).
Libraries were prepared from ChIP DNA experiments with the TruSeq® DNA LT/HT Sample Prep Kit (Illumina) following manufacturer’s instructions.

treatment_protocol: experiment group treated with 6TCF chemical combinations for six days

value: mouse embryonic fibroblasts (MEFs)

tag: treatment

value: Untreated control on day 6

tag: chip antibody


title: H3K4me3_ChIPSeq_untreated

tag: strain


title: H3K27me3_ChIPSeq_untreated


title: H3K4me3_ChIPSeq_6TCF-treated

value: 6TCF treated on day 6


title: input DNA_6TCF-treated


title: S9/M8LAC+.3

city: Toronto

first: Edward

middle: Saehong

last: Oh

state: Ontario

address: 250 College st

department: Krembil Family Epigenetics Laboratory

country: Canada

institute: Centre for Addiction and Mental Health

description:
milk Segment_8 lactose-treated
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

data_processing:
library strategy: padlock BS-seq
Analysis of the padlock BS-seq data was completed using a custom pipeline based on the Bismark tool
Reads were first trimmed and residual adapter sequences removed using Trimmomatic-0.32.
Reads that did not align to phiX were aligned to the target reference genome (GRCm38/mm10).
Percent modification was estimated as the fraction of spanning reads that retained the reference “C”, and were not converted to “T” from the bisulfite treatment.
Modification estimates were only considered if 30 or more reads spanned the cytosine.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files with coverage of modified and unmodified    cytosines, with fields: chromosome, position, strand, # reads with modified    cytosine, # reads with unmodified cytosine, type of DNA modification,    sequence

source_name: Seg_8 Lactose-rep3

growth_protocol: All animal procedures were approved by the Institutional Animal Care Committee of the Toronto Centre for Phenogenomics (TCP) and compiled per the requirements of the Canadian Council on Animal Care and Province of Ontario Animals for Research Act. C57BL/6NCrl mice were bred at the TCP. Mice were housed in ventilated polycarbonate cages, and given ad libitum sterile food (Harlan 2918X) and water, unless stated otherwise. Adult mice were housed by sex in groups of 2-5 littermates. The vivarium was maintained under temperature (21°C±1°C) and humidity (50-60%), with a 12-hour diurnal cycle (lights on 0700-1900).

extract_protocol:
Enterocytes were isolated from every small intestine segment (approx. 100 mg) using a chelating method (Weiser MM (1973). J Biol Chem, 248(7):2536-41). DNA was extracted from enterocytes and the small intestinal segment lacking enterocytes using standard phenol-chloroform DNA extraction methods in combination with Phase-Lock tubes (5 Prime) after an overnight treatment in Proteinase K. DNA quantity was measured by NanoDrop ND-1000, and DNA quality was verified on a 1% agarose gel.
DNA modification state was examined with single nucleotide resolution in the Lct and Mcm6 loci of mice using the bisulfite padlock probe technique (Diep D et al (2012). Nat Methods 9(3):270-2). 314 padlock probes with 6 base pairs of degenerate sequences were targeted to unique (non-repetitive) genomic sequences (GRCm38/mm10). Probes covered 90kb of the region of interest on for both forward and reverse DNA strands. Target DNA regions were designed for bisulfite converted DNA using ppDesigner software.

treatment_protocol: To investigate the diet/environmental associated epigenetic changes, postnatal day 30 mice were supplied ad libitum sterile food with either 2% lactose-containing organic milk (Grand Pré) or 2% lactose-free milk (Natrel) in the place of water for 60 days. Approximately 500 ml of lactose-containing milk (LAC+) was supplemented with 1 tablespoon (or ~12 g) of sucrose to promote a consumption level comparable to that of mice fed lactose-free milk every 1.5~2 days.

value: Bisulfite-converted Padlock

tag: tissue

value: Small intestine

tag: subregion

value: Medial ileum

value: enterocytes

tag: developmental stage

value: Adult

value: Postnatal day 90

tag: segment

tag: milk type

value: lactose


title: S3/M8LAC+.1

source_name: Seg_8 Lactose-rep1

tag: age


title: S119/M8ctrl.5

description:
milk Segment_8 lactose-free control
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: Seg_8 ctrl-rep5

value: lactose-free


title: S15/M8LAC+.5

source_name: Seg_8 Lactose-rep5


title: S12/M8LAC+.4

source_name: Seg_8 Lactose-rep4


title: S78/M8ctrl.7

source_name: Seg_8 ctrl-rep7


title: S23/M8ctrl.6

source_name: Seg_8 ctrl-rep6


title: S117/M8ctrl.4

source_name: Seg_8 ctrl-rep4


title: S20/M8LAC+.7

source_name: Seg_8 Lactose-rep7


title: S19/M7LAC+.7

description:
milk Segment_7 lactose-treated
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: Seg_7 Lactose-rep7

value: Proximal ileum


title: S80/M8ctrl.1

source_name: Seg_8 ctrl-rep1


title: S83/M8ctrl.2

source_name: Seg_8 ctrl-rep2


title: S17/M7LAC+.6

source_name: Seg_7 Lactose-rep6


title: S11/M7LAC+.4

source_name: Seg_7 Lactose-rep4


title: S14/M7LAC+.5

source_name: Seg_7 Lactose-rep5


title: S18/M8LAC+.6

source_name: Seg_8 Lactose-rep6


title: S2/M7LAC+.1

source_name: Seg_7 Lactose-rep1


title: S5/M7LAC+.2

source_name: Seg_7 Lactose-rep2


title: S22/M7ctrl.5

description:
milk Segment_7 lactose-free control
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: Seg_7 ctrl-rep5


title: S118/M7ctrl.4

source_name: Seg_7 ctrl-rep4


title: S6/M8LAC+.2

source_name: Seg_8 Lactose-rep2


title: S77/M7ctrl.6

source_name: Seg_7 ctrl-rep6


title: S79/M7ctrl.1

source_name: Seg_7 ctrl-rep1


title: S82/M7ctrl.2

source_name: Seg_7 ctrl-rep2


title: S43/M4LAC+.7

description:
milk Segment_4 lactose-treated
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: Seg_4 Lactose-rep7

value: Proximal jejunum


title: S86/M8ctrl.3

source_name: Seg_8 ctrl-rep3


title: S41/M4LAC+.6

source_name: Seg_4 Lactose-rep6


title: S85/M7ctrl.3

source_name: Seg_7 ctrl-rep3


title: H3K27me3_ChIPSeq_6TCF-treated

source_name: mouse embryonic fibroblasts (MEFs)


title: S37/M4LAC+.4

source_name: Seg_4 Lactose-rep4


title: S39/M4LAC+.5

source_name: Seg_4 Lactose-rep5


title: S35/M4LAC+.3

source_name: Seg_4 Lactose-rep3


title: S45/M4ctrl.6

description:
milk Segment_4 lactose-free control
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: Seg_4 ctrl-rep6


title: S33/M4LAC+.2

source_name: Seg_4 Lactose-rep2


title: S31/M4LAC+.1

source_name: Seg_4 Lactose-rep1


title: S47/M4ctrl.7

source_name: Seg_4 ctrl-rep7


title: S8/M7LAC+.3

source_name: Seg_7 Lactose-rep3


title: S57/M4ctrl.5

source_name: Seg_4 ctrl-rep5


title: S55/M4ctrl.4

source_name: Seg_4 ctrl-rep4


title: S49/M4ctrl.1

source_name: Seg_4 ctrl-rep1


title: S13/M3LAC+.5

description:
milk Segment_3 lactose-treated
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: Seg_3 Lactose-rep5

value: Distal duodenum


title: S16/M3LAC+.6

source_name: Seg_3 Lactose-rep6


title: S10/M3LAC+.4

source_name: Seg_3 Lactose-rep4


title: S4/M3LAC+.2

source_name: Seg_3 Lactose-rep2


title: S116/M3ctrl.4

description:
milk Segment_3 lactose-free control
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: Seg_3 ctrl-rep4


title: S1/M3LAC+.1

source_name: Seg_3 Lactose-rep1


title: S21/M3ctrl.5

source_name: Seg_3 ctrl-rep5


title: S84/M3ctrl.3

source_name: Seg_3 ctrl-rep3


title: S76/M3ctrl.6

source_name: Seg_3 ctrl-rep6


title: S81/M3ctrl.2

source_name: Seg_3 ctrl-rep2


title: S312/M3ctrl.1

source_name: Seg_3 ctrl-rep1


title: S36/M1LAC+.5

description:
milk Segment_1 lactose-treated
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: Seg_1 Lactose-rep4

value: Proximal duodenum


title: S38/M1LAC+.6

source_name: Seg_1 Lactose-rep5


title: S42/M1LAC+.8

source_name: Seg_1 Lactose-rep7


title: S40/M1LAC+.7

source_name: Seg_1 Lactose-rep6


title: S34/M1LAC+.4

source_name: Seg_1 Lactose-rep3


title: S32/M1LAC+.3

source_name: Seg_1 Lactose-rep2


title: S30/M1LAC+.2

source_name: Seg_1 Lactose-rep1


title: S56/M1ctrl.5

description:
milk Segment_1 lactose-free control
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: Seg_1 ctrl-rep4


title: S54/M1ctrl.3

source_name: Seg_1 ctrl-rep3


title: S51/M1ctrl.2

source_name: Seg_1 ctrl-rep2


title: S46/M1ctrl.7

source_name: Seg_1 ctrl-rep6


title: S44/M1ctrl.6

source_name: Seg_1 ctrl-rep5


title: S52/M4ctrl.3

source_name: Seg_4 ctrl-rep3


title: S275/I7.4

description:
infants(P6) Segment_7
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: P6 Seg_7-rep4

value: Infant

value: Postnatal day 6


title: S29/M3LAC+.7

source_name: Seg_3 Lactose-rep7


title: S7/M3LAC+.3

source_name: Seg_3 Lactose-rep3


title: S48/M1ctrl.1

source_name: Seg_1 ctrl-rep1


title: S277/I7.1

source_name: P6 Seg_7-rep1


title: S279/I7.2

source_name: P6 Seg_7-rep2


title: S50/M4ctrl.2

source_name: Seg_4 ctrl-rep2


title: S282/I3.3

description:
infants(P6) Segment_3
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: P6 Seg_3-rep3


title: S280/I7.3

source_name: P6 Seg_7-rep3


title: S281/I1.3

description:
infants(P6) Segment_1
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: P6 Seg_1-rep3


title: S278/I3.1

source_name: P6 Seg_3-rep1


title: S276/I1.1

source_name: P6 Seg_1-rep1


title: S273/I1.2

source_name: P6 Seg_1-rep2


title: S272/A9.8

description:
adults(P60) Segment_9
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: P60 Seg_9-rep7

value: Distal ileum

value: Postnatal day 60


title: S209/A9.9

source_name: P60 Seg_9-rep8


title: S274/I3.2

source_name: P6 Seg_3-rep2


title: S254/A9.6

source_name: P60 Seg_9-rep5


title: S227/A9.2

source_name: P60 Seg_9-rep2


title: S245/A9.5

source_name: P60 Seg_9-rep4


title: S208/A8.8

description:
adults(P60) Segment_8
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: P60 Seg_8-rep8


title: S262/A8.6

source_name: P60 Seg_8-rep6


title: S271/A8.7

source_name: P60 Seg_8-rep7


title: S236/A9.3

source_name: P60 Seg_9-rep3


title: S244/A8.4

source_name: P60 Seg_8-rep4


title: S218/A9.1

source_name: P60 Seg_9-rep1


title: S226/A8.2

source_name: P60 Seg_8-rep2


title: S207/A7.7

description:
adults(P60) Segment_7
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: P60 Seg_7-rep7


title: S234/A7.3

source_name: P60 Seg_7-rep3


title: S261/A7.6

source_name: P60 Seg_7-rep6


title: S217/A8.1

source_name: P60 Seg_8-rep1


title: S225/A7.2

source_name: P60 Seg_7-rep2


title: S216/A7.1

source_name: P60 Seg_7-rep1


title: S253/A8.5

source_name: P60 Seg_8-rep5


title: S252/A7.5

source_name: P60 Seg_7-rep5


title: S251/A6.5

description:
adults(P60) Segment_6
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: P60 Seg_6-rep5

value: Distal jejunum


title: S206/A6.6

source_name: P60 Seg_6-rep6

value: Bisulfite-converted Padlock


title: S260/A6.7

source_name: P60 Seg_6-rep7

value: Small intestine


title: S242/A6.4

source_name: P60 Seg_6-rep4


title: S233/A6.3

source_name: P60 Seg_6-rep3


title: S215/A6.1

source_name: P60 Seg_6-rep1


title: S263/A9.7

source_name: P60 Seg_9-rep6


title: S235/A8.3

source_name: P60 Seg_8-rep3

value: Medial ileum


title: S259/A5.7

description:
adults(P60) Segment_5
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: P60 Seg_5-rep7

value: Medial jejunum

value: enterocytes


title: S268/A5.8

source_name: P60 Seg_5-rep8

value: Adult


title: S270/A7.8

source_name: P60 Seg_7-rep8


title: S250/A5.6

source_name: P60 Seg_5-rep6


title: S205/A5.5

source_name: P60 Seg_5-rep5


title: S214/A5.1

source_name: P60 Seg_5-rep1


title: S241/A5.4

source_name: P60 Seg_5-rep4


title: S223/A5.2

source_name: P60 Seg_5-rep2


title: S232/A5.3

source_name: P60 Seg_5-rep3


title: S258/A4.7

description:
adults(P60) Segment_4
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: P60 Seg_4-rep7


title: S249/A4.6

source_name: P60 Seg_4-rep6


title: S240/A4.5

source_name: P60 Seg_4-rep5


title: S231/A4.3

source_name: P60 Seg_4-rep3


title: S204/A4.4

source_name: P60 Seg_4-rep4


title: S222/A4.2

source_name: P60 Seg_4-rep2


title: S257/A3.7

description:
adults(P60) Segment_3
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: P60 Seg_3-rep7


title: S248/A3.6

source_name: P60 Seg_3-rep6


title: S224/A6.2

source_name: P60 Seg_6-rep2


title: S266/A3.8

source_name: P60 Seg_3-rep8


title: S239/A3.5

source_name: P60 Seg_3-rep5


title: S213/A4.1

source_name: P60 Seg_4-rep1


title: S221/A3.2

source_name: P60 Seg_3-rep2


title: S212/A3.1

source_name: P60 Seg_3-rep1


title: S230/A3.4

source_name: P60 Seg_3-rep4


title: S247/A2.6

description:
adults(P60) Segment_2
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: P60 Seg_2-rep6

value: Medial duodenum


title: S203/A3.3

source_name: P60 Seg_3-rep3


title: S265/A2.8

source_name: P60 Seg_2-rep8


title: S256/A2.7

source_name: P60 Seg_2-rep7


title: S220/A2.3

source_name: P60 Seg_2-rep3


title: S229/A2.4

source_name: P60 Seg_2-rep4


title: S202/A2.2

source_name: P60 Seg_2-rep2


title: S246/A1.6

description:
adults(P60) Segment_1
[dissection protocol] Infant mice at postnatal day 6 (P6) and adult mice at postnatal day 60 (P60) were used to investigate the segmental gradient and age-associated epigenetic changes. The small intestine was harvested and dissected into three equal parts; the duodenum, jejunum and ileum. Each of these anatomical segments was further dissected into three equal parts resulting in nine dissections of the small intestine (segments 1-9).

source_name: P60 Seg_1-rep6


title: S228/A1.5

source_name: P60 Seg_1-rep5


title: S238/A2.5

source_name: P60 Seg_2-rep5


title: S264/A1.8

source_name: P60 Seg_1-rep8


title: S255/A1.7

source_name: P60 Seg_1-rep7


title: S219/A1.3

source_name: P60 Seg_1-rep3


title: S210/A1.2

source_name: P60 Seg_1-rep2


title: S182/A1.4

source_name: P60 Seg_1-rep4


title: S267/A4.8

source_name: P60 Seg_4-rep8


title: S201/A1.1

source_name: P60 Seg_1-rep1


title: Smc1_ChIPSeq_replicate2

city: Atlanta

first: Yoonhee

last: Jung

state: Georgia

address: 615 Michael Street

department: Human Genetics

institute: Emory university

description: chormatin IP against Smc1

data_processing:
All libraries were sequenced using an Illumina Hiseq v4 sequencer and 50 bp paired-end format. Paired reads were aligned to mouse reference genome mm9 using Bowtie 0.12.7 for ChIP-seq. Duplicates were removed using Samtools.  For generating wiggle files, we combined each replicates.
Genome_build: mm9

source_name: Sperm

extract_protocol:
For ChIP-seq of crosslink samples, sperm were crosslinked with 1% formaldehyde in 1x PBS for 10 min at RT, and the reaction was quenched with 125 mM glycine for 10 min at RT. After washing with PBS, crosslinked sperm were lysed with 5 mM PIPES, 85 mM KCl, 0.5% NP40 and 1x proteinase inhibitor on ice for 10 min. Then we performed a second fixation step by directly adding 1% formaldehyde to the lysis buffer on ice. After 10 min sperm were homogenized with a glass dounce homogenizer. Following quenching and washing, sperm cells were resuspended in RIPA buffer (1x PBS; 1% NP40; 0.5% sodium deoxycholate; 0.1% SDS; 1x proteinase inhibitor) and incubated on ice for 20 min. The purified sperm chromatin was sonicated to 300-1000 bp using a Diagenode Bioruptor at 25 cycles of 30 sec on and 30 sec off and the supernatant was collected. Immunoprecipitation was performed overnight at 4°C with antibodies. For ChIP-seq of Mnase samples, lysate was digested with Mnase and histone-DNA complexes were isolated with antibody.
Libraries for Illumina sequencing were constructed using the following standard protocol. The fragment end were repaired using the NEBNext End Repair Module, and adenosine was added at the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs). Precipitated DNA and input DNA were incubated with adaptors at room temperature for 1 hr with T4 DNA ligase (New England Biolabs) and amplified with Illumina primers.

tag: strain background

value: A300-055A, Bethyl laboratories


title: H3K9me3_ChIPSeq_replicate2

description: chormatin IP against H3K9me3

value: ab8898, Abcam


title: H3K9ac_ChIPSeq_replicate2

description: chormatin IP against H3K9ac

value: 07-352, Millipore


title: Liver Basal INPUT

city: Pamplona

first: Tomas

last: Aragon

address: Avda Pio XII 55

department: Gene Therapy and Regulation of Expression

country: Spain

institute: CIMA - University of Navarra

data_processing:
Read alignment: Reads were aligned using Bowtie2 to the reference
Peak calling: Peak detection for ChIP-seq samples was performed using MACS 1.4.2 with default parameters
Peak annotation: The annotation of the obtained peaks was done using the Bioconductor package ChIPpeakAnno using as reference the annotation obtained from Mouse Gencode M1
genome build: Mus musculus genome (UCSC mm9, NCBI build 37).
processed data files format and content: MACS_peak

source_name: normal liver

growth_protocol: primary mouse liver samples

extract_protocol:
Liver tissue was washed in PBS, cut into pieces ≤ 2mm diameter and fixed for 15 min in 1% of formaldehyde (Sigma). Tissue was washed three times in PBS and stored at -80°C. Upon thawing, tissue was incubated in 125 mM glycine (Sigma) for 5 min at room temperature, washed in PBS and nuclei were prepared on ice using a dounce homogenizer. All following steps were performed on ice, if not specified otherwise. Nuclei were washed in PBS, resuspended in ChIP buffer (4 ml of buffer per 0.5 ml of tissue; 100mM NaCl, 133mM Tris pH 8.0, 5 mM EDTA, 0.2% NaN 3 ,0.67% SDS, 1.67% Triton X-100) supplemented with protease inhibitors (Complete Protease Inhibitor Cocktail Tablets, Roche, Mannheim, Germany) and phosphatase inhibitors (50 mM NaF,1 mM β-GP, 1 mM NaV). Chromatin was sonicated to an average length of 300 bp, pre-cleared once with protein A-Sepharose and once with protein G-sepharose beads, both blocked with 0.5% E. coli tRNA (Sigma) and 0.5% BSA. For immunoprecipitating XBP1 protein, we used anti-XBP1 M-186 (sc-7160-X, Santa Cruz, Heidelberg, Germany). 10 µg of antibody were incubated overnight with 2ml of chromatin. Pre-blocked proteinG-sepharose beads were added to the antibody/chromatin mix, incubated for 2-3h and washed as follows: 3 times with mixed micelle buffer (150 mM NaCl, 20 mM Tris pH 8.1, 5 mM EDTA, pH 8.0,5.2% sucrose, 0.02% NaN3 , 1% Triton X-100, 0.2% SDS), 2 times with  buffer-500 (50 mM HEPES pH 7.5, 0.1% sodium deoxycholate, 1 mM EDTA, 500 mM NaCl, 1% TritonX-100, 0.2% NaN 3 ), 2 times with  LiCl/detergent buffer (10 mM Tris pH 8.0, 0.5% sodiumdeoxycholate, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.2% NaN3 ) and once with TE. DNA was reverse-crosslinked overnight (2% SDS in TE, 65°C), purified using QiaQuickcolumns (Qiagen, Madrid, Spain) and quantified using PicoGreen (Fisher Scientific, Madrid, Spain). 2-5 ng of ChIP DNA were used for ChIPseq library preparation as described in the reference given below.
Blecher-Gonen R1, Barnett-Itzhaki Z, Jaitin D, Amann-Zalcenstein D, Lara-Astiaso D, Amit I., High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states. Nat Protoc. 2013 Mar;8(3):539-54

treatment_protocol: All the surgical procedures were performed at 8 weeks of age. Two-third partial hepatectomy was performed as described 11. Animals were operated at morning hours (10-12.00 AM) after a 2 hour fasting period. Anaesthesia was performed by isofluorane inhalation (Esteve, Barcelona, Spain). As a control of PH experiments, we performed sham operation as control surgery, which consisted on a midline abdominal skin and muscle incision until the xiphoid process, cutting the falciform ligament and exposing the median and lateral lobes by lifting them with saline-moistened cotton tips. To knock-down XBP1 expression, animals were tail vein injected with first generation adenoviruses constitutively expressing either a XBP1-specific shRNA (kindly provided by Dr. Gokhan S. Hotamisligil, Harvard T.H. Chan School of Public Health, Boston, USA) or a control shRNA targeting LacZ (Genecust, Luxembourg). Viral dose was 109 IU/100 g BW. Clodronate liposomes (ClodronateLiposomes.com, Amsterdam, NL) were injected intravenously 24h before adenovirus administration, in order to reduce the viral dose, following the instructions of manufacturer. PH hepatectomies were performed 7 days after virus delivery.

value: liver

value: wildtype


title: H3K27ac_ChIPSeq_replicate2

description: chormatin IP against H3K27ac

value: ab4729, Abcam


title: H3K4me1_ChIPSeq_replicate2

description: chormatin IP against H3K4me1

value: ab8895, Abcam


title: H3K36me3_ChIPSeq_replicate2

description: chormatin IP against H3K36me3

value: 05-801, Millipore


title: H3K27me3_ChIPSeq_replicate2

description: chormatin IP against H3K27me3

value: 07-449, Millipore


title: S211/A2.1

source_name: P60 Seg_2-rep1

value: Postnatal day 60


title: XBP1-ChIPseq Liver SHAM48h

source_name: liver: 48h after sham operation

value: anti-XBP1 M-186 (sc-7160-X, Santa Cruz, Heidelberg, Germany)


title: XBP1-ChIPseq Liver PH48h

source_name: liver: 48h after partial hepatectomy


title: XBP1-ChIPseq Liver SHAM6h

source_name: liver: 6h after sham operation


title: XBP1-ChIPseq Liver PH48h - shXBP1

source_name: liver: 7d after XBP1 silencing and 48h after partial hepatectomy

value: wildtype with shXBP1 (7 days)


title: XBP1-ChIPseq Liver PH6h

source_name: liver: 6h after partial hepatectomy


title: XBP1-ChIPseq Liver PH6h - shXBP1

source_name: liver: 7d after XBP1 silencing and 6h after partial hepatectomy


title: XBP1-ChIPseq Liver Basal - shXBP1

source_name: liver: 7d after XBP1 silencing


title: XBP1-ChIPseq Liver Basal


title: S243/A7.4

source_name: P60 Seg_7-rep4

value: Bisulfite-converted Padlock

value: Small intestine

value: Proximal ileum


title: Sperm-HiC_replicate3_biological

description: Hi-C library made using HindIII

data_processing:
For Hi-C, The paired end Hi-C reads were mapped independently using BWA mem and paired. Reads mapping to more than two genomic locations (one for each paired end or two for one paired end in agreement with its partner) were discarded. Reads were further filtered and normalized using HiFive v1.2.2 (Sauria et al., 2015) using the Express algorithm and the settings "--min-interactions 5 --min-distance 100000 --min-binsize 500 --num-bins 50 --express-iterations 5000 --min-change 0.00005 --remove-distance --express-reads cis".
Genome_build: mm9

extract_protocol:
For Hi-C, cells were crosslinked with 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with glycine and nuclear lysates were incubated with HindIII. Fragment ends were filled with biotinylated nucleotides, ligated. After reverssion of crosslinks, DNA was purified, sonicated and used to make Illumina libraries.
Libraries for Illumina sequencing were constructed using the following standard protocol. The fragment end were repaired using the NEBNext End Repair Module, and adenosine was added at the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs). Precipitated DNA and input DNA were incubated with adaptors at room temperature for 1 hr with T4 DNA ligase (New England Biolabs) and amplified with Illumina primers.


title: Sperm-HiC_replicate2_technical

description: Hi-C library made using HindIII


title: Sperm-HiC_replicate1_biological

description: Hi-C library made using HindIII


title: Sperm-HiC_replicate4_technical

description: Hi-C library made using HindIII


title: H3K4me3_ChIPSeq

description: chormatin IP against H3K4me3

value: ab8580, Abcam


title: Smc1_ChIPSeq

description: chormatin IP against Smc1


title: H3_ChIPSeq

description: chormatin IP against H3

value: ab1791, Abcam


title: Protamine1_ChIPSeq

description: chormatin IP against Protamine1

value: sc-30174, Santa Cruz


title: H3K4me1_ChIPSeq

description: chormatin IP against H3K4me1


title: H3K9me3_ChIPSeq

description: chormatin IP against H3K9me3

value: ab8898, Abcam


title: H3K9ac_ChIPSeq

description: chormatin IP against H3K9ac

value: 07-352, Millipore


title: H3K27ac_ChIPSeq

description: chormatin IP against H3K27ac


title: H3K27me3_ChIPSeq

description: chormatin IP against H3K27me3


title: CTCF_ChIPSeq_replicate3_biological

description: chormatin IP against CTCF

value: 07-729, Millipore


title: H3K36me3_ChIPSeq

description: chormatin IP against H3K36me3


title: CTCF_ChIPSeq_replicate2_technical

description: chormatin IP against CTCF


title: CTCF_ChIPSeq_replicate1

description: chormatin IP against CTCF


title: BS-seq_replicate2

description: DNA Methyl Whole Genome Bisulfite Seq

data_processing:
All libraries were sequenced using an Illumina Hiseq v4 sequencer and 50 bp paired-end format. Paired reads were aligned to mouse reference genome mm9 using Bismark for BS-seq. For generating wiggle files, we combined each replicates.
Genome_build: mm9

extract_protocol:
For BS-seq, genomic DNA (1-2 µg) spiked with 0.5% unmethylated lambda genomic DNA (Promega) were sheared with a Diagenode Bioruptor to yield DNA fragments ranging from 200 to 500 bp.  After purification of the fragmented DNA using phenol/chloroform, DNA fragments were end repaired, A-tailed, and ligated to methylated Illumina adaptors using as described for ChIP-seq. The EpiTect Bisulfite kit (QIAGEN, Cat. No. 59104) was used for bisulfite conversion and subsequent purification according to the manufacturer’s instructions.
Libraries for Illumina sequencing were constructed using the following standard protocol. The fragment end were repaired using the NEBNext End Repair Module, and adenosine was added at the 3’ ends of fragment using Klenow fragment (3’ to 5’ exo minus, New England Biolabs). Precipitated DNA and input DNA were incubated with adaptors at room temperature for 1 hr with T4 DNA ligase (New England Biolabs) and amplified with Illumina primers.


title: BS-seq_replicate1

description: DNA Methyl Whole Genome Bisulfite Seq


title: ATACseq_replicate3

description: ATAC-seq

data_processing:
All libraries were sequenced using an Illumina Hiseq v4 sequencer and 50 bp paired-end format. Paired reads were aligned to mouse reference genome mm9 using Bowtie 0.12.7 for ATAC-seq. ATAC-seq reads were aligned using default parameters except -X 2000 -m 1. Duplicates were removed using Samtools.  To adjust for fragment size, we aligned all reads as + strands offset by +4 bp and – strands offset by -5 bp (Buenrostro et al. 2013). To separate nucleosome-free (THSS)  and  mono-nucleosome (Nucleosome) fragments, we chose reads 50-115 bp 180-247 bp in length, respectively. Mono-nucleosome reads were analyzed using DANPOS2 (Chen et al. 2013). MACS2 was used for peak calling with nucleosome-free reads (Liu 2014). For generating wiggle files, we combined each replicates.
Genome_build: mm9

extract_protocol: For ATAC-seq, the purified sperm pellet was resuspended in the transposase reaction mix and incubated for 30 min at 37°C. Following incubation, sperm were lysed, incubated with Proteinase K at 55°C for 2 hr, and gDNA was isolated by phenol:chloroform:isoamyl alcohol and EtOH precipitation. Library amplification was done with 2x KAPA HiFi mix and 1.25 µM indexed primers using the following PCR conditions: 72°C for 5 min; 98°C for 30 sec; and 10-11 cycles at 98°C for 10 sec, 63°C for 30 sec, and 72°C for 1 min.


title: BS-seq_replicate3

description: DNA Methyl Whole Genome Bisulfite Seq


title: ATACseq_replicate1

description: ATAC-seq


title: Input_forChIPseq_crosslink

description: chormatin IP against IgG


title: wild-type luminal control 7

city: Santa Cruz

first: Zhu

last: Wang

address: 1156 High Street

department: MCD Biology

institute: University of California Santa Cruz

data_processing:
RTA (Illumina) was used for base calling.
bcl2fastq (v1.8.4) was used for converting BCL to fastq format, coupled with adaptor trimming.
Sequencing reads were mapped to mouse genome mm9 using TopHat (v2.0.4) by allowing up to 4 mismatches and 10 maximum multiple hits.
FPKM values were calculated using cufflinks (v2.0.2) software with default settings.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw counts

source_name: prostate

extract_protocol:
Prostate were removed, dissociated into single cells. Luminal cells were isolated by flow-sorting based on YFP fluorescence. RNA was harvested using Rneasy Micro Kit (Qiagen) and reverse-transcribed and amplified using Ovation RNA-seq System V2 kit (Nugen).
Library construction was performed by the Columbia Genome Center using standard Illumina protocols.

treatment_protocol: To lineage-mark luminal cells and delete AR gene in luminal cells, mice were administered 9 mg per 40 g tamoxifen suspended in corn oil by oral gavage once daily for 4 consecutive days

value: Nkx3.1-CreERT2/+; R26R-YFP/+

value: flow-sorted primary prostate cells

value: luminal cells


title: AR-null luminal experimental 2

value: Nkx3.1-CreERT2/+; AR flox/Y; R26R-YFP/+


title: AR-null luminal experimental 3


title: wild-type luminal control 6


title: wild-type luminal control 5


title: AR-null luminal experimental 1


title: AR-null luminal experimental 4


title: wild-type luminal control 3


title: wild-type luminal control 2


title: H3K4me3_ChIPSeq_replicate2

description: chormatin IP against H3K4me3


title: wild-type luminal control 4


title: wild-type luminal control 1


title: 72_10_DAT_Rep_3_UV

city: Ottawa

first: Sylvie

last: Cloutier

address: 960 Carling Avenue

institute: Agriculture and Agri-Food Canada

data_processing:
Adapter sequences were trimmed using a custom Perl script and quality assessment was performed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads ranging from 18 to 24 bp were filtered and exported as fasta files using Geneious (Biomatters Ltd, Auckland, New Zealand)
Redundant reads from each dataset were grouped as distinct tags and were used to query the Rfam (version 11) and wheat chloroplast (http://www.ncbi.nlm.nih.gov/nuccore/NC_002762.1) databases to remove rRNAs, tRNAs, snRNAs, snoRNAs, other long non-coding RNAs and chloroplast sequences
Distinct tags represented by ≥10 reads per million (RPM) in at least one library were mapped to miRNA coding loci previously identified from the hexaploid bread wheat assembly (International Wheat Genome Sequencing Consortium, Science 2014) using Bowtie2. These tag sequences were then matched to another set of high confidence precursor sequences (Kurtoglu et al. Funct Integr Genomics 2014). Distinct tags with 0 mismatch were extracted for hairpin structure prediction using RNAfold (Lorenz et al. Algorithms Mol Biol 2011).
The distinct tags with secondary hairpin structure with <-0.2 kcal/mol/nt were filtered for prediction of star sequence in the opposite strand with a 2bp offset on the 3’-strand of the hairpin.
The read counts of miRNAs annotated with strong evidence for biosynthesis were chossen for differential expression ananysis.
Genome_build: GCA_000818885.1 - International Wheat Genome Sequencing Consortium (IWGSC) Science 2014
Supplementary_files_format_and_content: Conserved miRNA families and their coresponding read counts.xls

organism: Triticum aestivum

source_name: Leaf tissues

growth_protocol: Wheat (Triticum aestivum L.) cv Glenlea plants, obtained from a single self-fertilized homozygous line, were grown in a PG-40 growth chamber under long-day conditions of 16h light at 18°C and 8h darkness at 16°C

extract_protocol:
Leaf tissue was collected from individual plants at six time points: 0, 1, 2, 3, 7 and 10 DAT where 0 DAT corresponded to tissue sampled immediately at the end of the 5-day stress exposure period, prior to their return to the non-stressful growth conditions. Leaf tissue pieces, approximately 2.5 cm in length, were pooled from the eight plants that represented each treatment and replicate. The harvested leaf tissue pools were flash-frozen and stored in liquid nitrogen until RNA extraction. For the latter, tissue samples were ground to a fine powder with liquid nitrogen in a mortar and pestle. Total RNA was isolated from homogenized tissue samples using TRI-reagent as per manufacturer’s instructions (Ambion, Naugatuck, CT). Total RNA quality and quantity were assessed on an Agilent 2100 Bioanalyzer with the RNA 6000 Nano chip (Agilent Technologies, Santa Clara, CA). A total of 72 high-quality total RNA samples, corresponding to three biological replicates, four treatments and six sampling time points, were produced.
Small RNA libraries were constructed for each of the 72 samples from 5 µg of total RNA using a plate-based method developed at the BC Cancer Agency Genome Sciences Centre (Vancouver, BC, Canada). Briefly, total RNA samples were mixed with oligo-dT microbeads and loaded into a 96-well MACS column (Miltenyi Biotec, Germany). The sRNA fractions were recovered from the flow-through and precipitated with ethanol. Quality was assessed for a subset of 12 samples using an Agilent Bioanalyzer RNA 6000 Nano chip (Agilent Technologies). An adenylated 3’-adapter (5’/5rApp/ ATCTCGTATGCCGTCTTCTGCTTGT /3ddC/3’) was ligated using a truncated T4 RNA ligase (New England BioLabs, Ipswich, MA) by incubating at 22°C for 1 hour. An RNA 5’-adapter (5’-GUUCAGAGUUCUACAGUCCGACGAUCUGGUCAA-3’) was then added using a T4 RNA ligase (Ambion) by incubating at 37°C for 1h. The first strand cDNA was synthesized using Superscript II reverse transcriptase (Invitrogen, Carlsbad, CA) and RT primer (5'-CAAGCAGAAGACGGCATACGAGAT-3’). The cDNA was used as template for PCR amplification where unique index sequences were introduced to enable identification of the pooled libraries. PCR cycling conditions were 98°C for 30 sec, followed by 15 cycles at 98°C for 15 sec, 62°C for 30 sec and 72°C for 15 sec and a final incubation at 72°C for 5 min. The quality of the libraries was assessed using a Caliper LabChipGX DNA chip (PerkinElmer, Waltham, MA). Three pools of randomly assigned sRNA libraries were created, resolved on a gel and, the 145-160 bp fractions were size-selected. Pooled libraries were ethanol precipitated and quality checked using an Agilent Bioanalyzer DNA1000 chip (Agilent Technologies). Each pooled library was diluted for cluster generation on a HiSeq 2000 flow cell according to manufacturer’s instructions. Small RNA sequencing was performed using a 50 cycle HiSeq SBS v4 kit

treatment_protocol: At the boot stage, three sets of 24 plants each were exposed to one of three stress conditions for five consecutive days. The first set was exposed to continuous light. The second set was exposed to UV light for two min every day of the 5-day period. The third set, called heat-stressed, was transferred to a growth chambers where the temperature was kept constant at 37°C day and night. These plants were well watered twice per day during the 5-day stress exposure to avoid a confounding drought stress. The remaining 24 control plants were kept in the growth chamber at 16h/8h day/night at 18/16°C. After the 5-day stress exposure treatment, all plants were returned to the original growth chamber under control conditions. The experiment was conducted as a completely randomized block design with three biological replicates where each treatment and replicate corresponded to a group of eight plants.

tag: stress

value: UV

tag: sampling time

value: 10 day after treatment (DAT)

tag: cultivar

value: Glenlea


title: 69_10_DAT_Rep_3_Control

value: Control


title: ATACseq_replicate2

description: ATAC-seq


title: 67_10_DAT_Rep_2_Light

value: Light


title: 71_10_DAT_Rep_3_Light


title: 70_10_DAT_Rep_3_Heat

value: Heat


title: 68_10_DAT_Rep_2_UV


title: 63_10_DAT_Rep_1_Light


title: 62_10_DAT_Rep_1_Heat


title: 61_10_DAT_Rep_1_Control


title: wild-type luminal control 8

tag: cell type


title: 59_7_DAT_Rep_3_Light

value: 7 day after treatment (DAT)


title: 58_7_DAT_Rep_3_Heat


title: 64_10_DAT_Rep_1_UV


title: 60_7_DAT_Rep_3_UV


title: 54_7_DAT_Rep_2_Heat


title: 57_7_DAT_Rep_3_Control


title: 56_7_DAT_Rep_2_UV


title: 53_7_DAT_Rep_2_Control


title: 52_7_DAT_Rep_1_UV


title: 65_10_DAT_Rep_2_Control


title: 49_7_DAT_Rep_1_Control


title: 46_3_DAT_Rep_3_Heat

value: 3 day after treatment (DAT)


title: 48_3_DAT_Rep_3_UV


title: 47_3_DAT_Rep_3_Light


title: 50_7_DAT_Rep_1_Heat


title: 45_3_DAT_Rep_3_Control


title: 44_3_DAT_Rep_2_UV


title: 42_3_DAT_Rep_2_Heat


title: 43_3_DAT_Rep_2_Light


title: 40_3_DAT_Rep_1_UV


title: 41_3_DAT_Rep_2_Control


title: 39_3_DAT_Rep_1_Light


title: 55_7_DAT_Rep_2_Light


title: 36_2_DAT_Rep_3_UV

value: 2 day after treatment (DAT)


title: 37_3_DAT_Rep_1_Control


title: 34_2_DAT_Rep_3_Heat


title: 31_2_DAT_Rep_2_Light


title: 33_2_DAT_Rep_3_Control


title: 35_2_DAT_Rep_3_Light


title: 51_7_DAT_Rep_1_Light


title: 32_2_DAT_Rep_2_UV


title: 28_2_DAT_Rep_1_UV


title: 30_2_DAT_Rep_2_Heat


title: 29_2_DAT_Rep_2_Control


title: 27_2_DAT_Rep_1_Light


title: 26_2_DAT_Rep_1_Heat


title: 25_2_DAT_Rep_1_Control


title: 24_1_DAT_Rep_3_UV

value: 1 day after treatment (DAT)


title: 20_1_DAT_Rep_2_UV


title: 23_1_DAT_Rep_3_Light


title: 22_1_DAT_Rep_3_Heat


title: 19_1_DAT_Rep_2_Light


title: 21_1_DAT_Rep_3_Control


title: 38_3_DAT_Rep_1_Heat


title: 18_1_DAT_Rep_2_Heat


title: 15_1_DAT_Rep_1_Light


title: 16_1_DAT_Rep_1_UV


title: 14_1_DAT_Rep_1_Heat


title: 13_1_DAT_Rep_1_Control


title: 11_0_DAT_Rep_3_Light

value: 0 day after treatment (DAT)


title: 12_0_DAT_Rep_3_UV


title: 8_0_DAT_Rep_2_UV


title: 9_0_DAT_Rep_3_Control


title: 4_0_DAT_Rep_1_UV


title: 10_0_DAT_Rep_3_Heat


title: 7_0_DAT_Rep_2_Light


title: 6_0_DAT_Rep_2_Heat


title: 5_0_DAT_Rep_2_Control


title: 3_0_DAT_Rep_1_Light


title: 66_10_DAT_Rep_2_Heat


title: 17_1_DAT_Rep_2_Control


title: 2_0_DAT_Rep_1_Heat