title: MB468.FOXR2_rep2

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
ChIP-seq reads were aligned to the hg19 genome using Bowtie version 0.12.7
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq wig files were generated using MACS; Scores represent the ChIP-seq tag numbers

growth_protocol: MDA-MB-468 cells were cultured in Dulbecco's modified Eagle's medium, supplemented with 10% fetal bovine serum.

extract_protocol:
Cells were rinsed with cold PBS, harvested in 200 μl of SDS lysis buffer supplemented with protease inhibitor mixture (Roche Applied Science) and 1 mM phenylmethylsulfonylfluoride (PMSF) per 1 × 106 cells, and sonicated to shear the DNA to yield fragments of 500 bp or less. Samples were then diluted with 9 volumes of ChIP dilution buffer before being precleared for 1 hour with 40 μl of a mixture of protein A/G agarose and salmon sperm DNA. Approximately 5 μg of FOXR2, MYC or MAX antibody or mouse normal immunoglobulin (IgG) were added to the precleared supernatant and incubated for 1 hour at 4°C. Forty μl of protein A/G agarose were added, and the mixture was incubated overnight at 4°C. Washes were sequentially performed with low-salt buffer, high-salt buffer, LiCl buffer, and twice with TE buffer. Immunoprecipitates were eluted in 500 μl of elution buffer (1% SDS, 0.1 M NaHCO3), followed by the addition of NaCl (20 μl). Crosslinking was reversed by overnight incubation of samples at 65°C and treatment with protease K (Sigma) for 2 hours at 45°C. The recovered DNA was extracted with phenol-chloroform and precipitated with ethanol. Quantification was performed by real-time PCR with the My IQ real-time PCR detection system and an IQ SYBR Green Supermix (Bio-Rad). Control IgG and input DNA values were used to normalize values from ChIP recovery.
Library was contracted by the MD Anderson DNA sequencing Core facility following standard protocol.

treatment_protocol: 1 × 10^7 MDA-MB-468 cells were cross-linked with 1% formaldehyde in growth medium for 10 min. Cross-linking was terminated by the addition of glycine to a final concentration of 125 mM and incubation at 37°C for 10 min.

tag: cell line

value: breast cancer cell line MDA-MB-468

value: anti-FOXR2 (Rabbit polyclonal antibody against human FOXR2 (residues 1311) was generated and affinity purified in house)


title: MB468.MAX_rep1

status: Public on Feb 17 2017

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: chip antibody

value: anti-MAX(S20) (Cell signaling, catalog# 4739)


title: 1703-CB-0014

status: Public on Feb 16 2017

city: New Brunswick

first: Caroll

last: Bagnell

state: New Jersey

address: 59 Dudley Road

department: Animal Sciences

institute: Rutgers University

library_source: transcriptomic

data_processing:
Quality control checks on raw sequence data from each sample were performed using FastQC (Babraham Bioinformatics, London, UK). Raw reads were imported on a commercial data analysis platform Avadis NGS (Strand Scientifics, CA, USA). Adapter trimming was done to remove ligated adapters from the 3' end of the sequenced reads with only one mismatch allowed; poorly aligned 3' ends were also trimmed. Sequences shorter than 15 nucleotides in length were excluded from further analysis. Trimmed reads with low qualities (base quality score less than 30, alignment score less than 95, mapping quality less than 40) were removed. Filtered reads were used to extract and count miRNAs which were annotated with miRBase release 18 database. Reads were grouped according to their respective identifiers followed by quantification of miRNA abundance. Differentially expressed miRNAs, based on fold change (≥ ± 2.0), were identified with respect to effects of neonatal age (PND 2N versus PND 0 and PND 2R versus PND 0) and nursing (PND 2N versus PND 2R). Probability values for each differentially expressed miRNA were estimated by z-score calculations using a false discovery rate of 0.05.
Genome_build: NCBI Sscrofa10.2
Supplementary_files_format_and_content: Excel file with normalized expression values for each sample

molecule: total RNA

organism: Sus scrofa

source_name: uterus

extract_protocol:
Total RNA was isolated using Rneasy kit (Qiagen) following the manufacturer's protocol.  RNA quality was assessed using Agilent Bioanalyzer and Qbit Fluorometer.
smRNA-Seq was performed at the Genomic Services Laboratory, HudsonAlpha Institute for Biotechnology. Total RNA (500 ng) from each uterine sample was used for small RNA library preparation using the NEBNext® Small RNA Library Prep Set for Illumina (New England Biolabs Inc., Ipswich, MA, USA) according to the manufacturer’s protocol. Briefly, adapters were ligated to total RNA, multiplex primers were hybridized, and reverse transcription was accomplished using SuperScript III RT (Life Technologies, Grand Island, NY, USA) for 1 hour at 50°C. Bar codes with uniquely indexed primers were attached to each cDNA library and amplified through six PCR cycles. Following PCR amplification, purification was done using the QIAquick PCR purification kit (Qiagen Inc., Valencia, CA, USA). Size selection of the libraries was then performed using a 3% dye-free agarose gel on the Pipin prep instrument (Sage Science, Beverly, MA, USA). Post size-selected miRNA library concentration was assessed using a Qubit® 2.0 Fluorometer and library quality was determined using a DNA High Sense (HS) chip on Agilent 2100 Bioanalyzer. Further library quantification was performed using the qPCR-based KAPA Biosystem Library Quantification kit (Kapa Biosystems Inc., Woburn, MA, USA). Individual sample libraries were diluted to a final concentration of 1.25 nM, equimolar amounts of each sample and were pooled prior to sequencing.  MicroRNA sequencing was performed using an Illumina HiSeq 2500 instrument (Illumina Inc., San Diego, CA, USA) at 50bp Single End (SE) condition.

treatment_protocol: Pigs were euthanized within 1 h of birth (PND 0) or at 50 h of age (PND 2N and PND 2R).  Uteri were trimmed of connective tissue, immersed in RNALater and stored at -80C until RNA extraction.

tag: breed

value: Crossbred (Landrace, Yorkshire, Duroc, Hampshire)

tag: feeding

value: no nursing

tag: age (days)

value: PND 0


title: MB468.MYC_rep1

value: anti-MYC(D84C12) (Cell signaling, catalog# 5605S, lot# 6)


title: 1703-CB-0016


title: WT rep3

city: Taipei

first: Cheng-Yen

last: Kao

state: Taiwan

address: Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming University, No.155, Sec. 2, Linong St., Beitou Dist

country: Taiwan

institute: National Yang Ming University

description:
J5
Processed data file: RNA-seq_Summary.xls

data_processing:
The 50-base short read sequences produced by the 5500XL SOLiD™ sequencer were first run through SOLiD Accuracy Enhancement Tool (SAET) to improve color call accuracy.
Mapped in color space using SOLiD™ LifeScope™ software version 2.5 using default parameters against the H. pylori J99 reference genome (NCBI RefSeq accession number, NC_000921.1).
The BAM file from LifeScope was performed the analysis of gene expression with Partek software package.
The gene expression from each sample was then tested separately for statistical differences using one-way ANOVA at 5% confidence level.
Gene expression of the csrA mutant compared to wild-type J99 with a fold change > 1.5-fold was selected and confirmed by RT-qPCR.
Genome_build: H. pylori J99 reference genome (NC_000921.1)
Supplementary_files_format_and_content: RNA-seq_Summary.xls

organism: Helicobacter pylori J99

source_name: WT

growth_protocol: H. pylori cells were grown on CDC plates in microaerophilic conditions for 36 h, then transferred to 100 ml Brucella broth containing 10% (v/v) horse serum at an optical density of 0.2 and incubated with shaking (180 rpm, reduce cell aggregation) for 18 h in microaerophilic conditions.

extract_protocol:
Mini Qiagen columns and a Qiagen RNeasy mini kit (Qiagen, Valencia, CA) were used for RNA extraction. Ribosomal RNA was depleted according to the manufacturer's instruction using Bacteria MinusTM Transcriptome Isolation Kit (Invitrogen Life Technologies).
The Applied Biosystems SOLiD™ Total RNA-Seq kit was used to generate the cDNA template library.

tag: strain/background

tag: genotype/variation

value: wild-type


title: MB468.FOXR2_rep1


title: 1703-CB-0004

value: nursed

value: PND 2


title: 1703-CB-0001


title: 1703-CB-0003


title: 1703-CB-0007

value: replacer-fed


title: NEB_1_0.1_10

city: Seattle

first: Kai

last: Wang

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

data_processing:
Remove both 3’-end adapter sequence (AGATCGGAAGAGCACACGTCT) and 5’-end adapter sequence (GTTCAGAGTTCTACAGTCCGACGATC) using Cutadapt v1.6.
First align trimmed reads against miRNA precursor sequences in miRBase 21 using Bowtie 1.0.1, instead of mapping to mature miRNA sequences directly. Then assign a mapped read either to one of the corresponding mature miRNAs (-5p or -3p), or to the precursor itself, based on which part of the precursor sequence it is aligned with.
For miRNA mapping, our default parameters count a perfect match (zero mismatch) as 1, one mismatch as 0.8, two mismatches count as 0.6, and three mismatches count as 0.4.
Both single assignment and multiple assignment results are provided.
Genome_build: miRBase 21
Supplementary_files_format_and_content: single assignment and multiple assignment results

source_name: synthetic miRNA pool

extract_protocol: The sequencing libraries were constructed using commercial small RNA library preperation kit (NEB NEBNext® Small RNA Library Prep library kit),  and were analyzed on Illumina HiSeq 2000 platform with single end 50 nucleotide read length.

tag: component

value: 1 ng Plate 1, 0.1 ng Plate 2, 10 ng Plate 3


title: NEB_0.1_1_10

value: 0.1 ng Plate 1, 1 ng Plate 2, 10 ng Plate 3


title: H39236/TMD-8_+_1uM_ID_clone_1E6C5_L3.D711

city: Foster City

first: Li

last: Li

address: 333 Lakeside Drive

institute: Gilead Sciences

data_processing:
Clipping adapters and low-quality bases.
BWA
RSEM
edgeR
limma
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2(CPM) values for each Sample

growth_protocol: Idela-sensitive TMD8 clones were cultured in RPMI-1640 medium supplemented with 20% FBS, 100 U/mL penicillin, and 100 pg/mL  streptomycin (Life Technologies). Idela-resistant TMD8 clones were cultured in the same growth media but supplemented with 1 µM idelalisib.  Cultures were grown in a humidified atmosphere of 5% CO2 and 95% air at 37°C.

extract_protocol:
1 x 10^7 cells were harvested by centrifugation.  Pellets were resuspended in 1 mL of PBS, transferred to eppendorf tubes and pelleted again.  Pellets were resuspended in 150 uL of QIAGEN RLT buffer and frozen (-80'C).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: Idela 1uM

tag: cell type

value: Diffuse Large B Cell Lymphoma


title: NEB_10_0.1_1

value: 10 ng Plate 1, 0.1 ng Plate 2, 1 ng Plate 3


title: 1703-CB-0008


title: MB468.MAX_rep2


title: 1703-CB-0005


title: NEB_10_1_0.1

value: 10 ng Plate 1, 1 ng Plate 2, 0.1 ng Plate 3


title: 1703-CB-0002


title: 16_BeWo_input

city: Urbana

first: Lisa

middle: J

last: Stubbs

state: IL

address: 1206 West Gregory Drive | MC-195

department: IGB

institute: University of Illinois Urbana-Champaign

data_processing:
Fastq files were generated with the software Casava 1.8.2 (Illumina).
ChIP-Seq reads were aligned to the hg19 genome using Bowtie2 (using version 2.1.0) with the following options: -N  1 -L 32 --solexa-quals
Data was filtered to remove alignments with more than one mismatch and those mapping to multiple locations.
Peaks were called with MACS 1.4.2 with the MFLOD option (-m) set to 3,50 and the wiggle file option (-w) set to single-profile: (-m '3,50' -w --single-profile)
For the above MACS processing samples titled 19_HEK_ZSCAN5B_SC and 20_HEK_ZSCAN5B_SC were pooled together as the treatment and sample 22_HEK_input was used as the control.
For the above MACS processing samples titled 7_BeWo_ZSCAN5A and 84_BeWo_ZSCAN5A were pooled together as the treatment and sample 16_BeWo_input was used as the control.
For the above MACS processing samples titled 10_BeWo_ZSCAN5B_SC and 11_BeWo_ZSCAN5B_SC were pooled together as the treatment and sample 16_BeWo_input was used as the control.
For the above MACS processing samples titled 11_BeWo_ZSCAN5D and 28_BeWo_ZSCAN5D were pooled together as the treatment and sample 4_BeWo_input was used as the control.
Genome_build: hg19
Supplementary_files_format_and_content: The processed file are in wiggle (wig) format created by MACS 1.4.2.  19_20_HEK_ZSCAN5B_SC_pooled_22_HEK_input_control_MACS142_control_all.wig.gz Scores represent the read depth of control sample 22_HEK_input.  19_20_HEK_ZSCAN5B_SC_pooled_22_HEK_input_control_MACS142_treat_all.wig.gz Scores represent the pooled read depth of samples 19_HEK_ZSCAN5B_SC and 20_HEK_ZSCAN5B_SC.  10_11_BeWo_ZSCAN5B_SC_pooled_16_BeWo_input_control_MACS142_control_all.wig.gz Scores represent the read depth of control sample 16_BeWo_input.  10_11_BeWo_ZSCAN5B_SC_pooled_16_BeWo_input_control_MACS142_treat_all.wig.gz Scores represent the pooled read depth of samples 10_BeWo_ZSCAN5B_SC and 11_BeWo_ZSCAN5B_SC.  ZSCAN5A-BeWo-wiggle_MACS142_control_all.wig.gz Scores represent the read depth of control sample 4_BeWo_input.  ZSCAN5A-BeWo-wiggle_MACS142_treat_all.wig.gz Scores represent the read depth of sample 7_BeWo_ZSCAN5A.  pooled_11-BeWo-ZSCAN5D_28-BeWo-ZSCAN5D_MACS142_control_all.wig.gz Scores represent the read depth of control sample 4_BeWo_input.  pooled_11-BeWo-ZSCAN5D_28-BeWo-ZSCAN5D_MACS142_treat_all.wig.gz Scores represent the pooled read depth of samples 11_BeWo_ZSCAN5D and 28_BeWo_ZSCAN5D. The wiggle file 84_BeWo_ZSCAN5A.wig.gz was not create by MACS 1.4.2, rather by converting single maps reads with 1 or fewer mismatches to a wiggle file using bedtools' genomecov and bedgraph_to_wig.pl written by Sebastien Vigneau.

source_name: Human BeWo cell line

growth_protocol: HEK-293 cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM) containing 2 mM L-glutamine, 10% fetal bovine serum (FBS), 1X Pen Strep, and BeWo cells in DMEM/F12K containing 2 mM L-glutamine, 10% FBS, 1X NEAA, 1X Pen Strep, incubated at 37 °C in 5% CO2.

extract_protocol:
Cross-linked chromatin was prepared and sonicated using Bioruptor UCD-200 in ice water bath to generate DNA fragments 200-300 bp in size. Twenty micrograms of each antibody preparation, or 20 µg IgG for mock pulldown controls, were incubated with chromatin prepared from nuclei of approximately 5 million cells.
ChIP-seq libraries were generated using KAPA LTP Library Preparation Kits (Kapa Biosystems, KK8232) to yield two independent ChIP replicates for the antibody. We also generated libraries from sonicated genomic input DNA from the same chromatin preparations as controls. Libraries were bar-coded with Bioo Scientific index adapters and sequenced to generate 15-23 million reads per duplicate sample using the Illumina Hi-Seq 2000 instrument at the University of Illinois W.M. Keck Center for Comparative and Functional Genomics according to manufacturer’s instructions.

treatment_protocol: Cells were counted using hemocytometer and crosslinked with 4% paraformaldehyde (Electron Microscopy Sciences, PA) for 10 minutes at room temperature before nuclear isolation.

value: Human BeWo

tag: antibody

tag: treatment or control

value: control


title: 84_BeWo_ZSCAN5A

value: treatment


title: C2C12_Diff_Input

city: Illkirch

first: Shilpy

last: Joshi

address: 1 Rue laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2.
Sequence reads were mapped to reference genome mm9/NCBI37 using Bowtie -m 1 --strata --best -y -S -l  40 -p 2.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)

organism: Mus musculus

source_name: C2C12 cells

extract_protocol: ChIP-seq libraries were prepared using NEXTflex ChIP-Seq Kit (#5143-02, Bioo Scientific) following the manufacturer's protocol (V12.10) with some modifications. Briefly, 10 ng of ChIP enriched DNA or INPUT DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK, then size selected and cleaned-up using Agencourt AMPure XP beads (#A63881, Beckman). A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded barcoded DNA adapters (NEXTflex ChIP-Seq Barcodes - 6, #514120, Bioo Scientific) using T4 DNA Ligase. The ligated products were enriched by PCR (2 min at 98°C; [30 sec at 98°C, 30 sec at 65°C, 60 sec at 72°C] x 14 cycles; 4 min at 72°C) and cleaned-up using Agencourt AMPure XP beads.

treatment_protocol: C2C12 cells were harvested either in non-differentiated or differentiated state and resuspended in sonication buffer for 10 mins and then sonicated using covarys sonicator. Muscle from hind limbs of three wil-type B6 were minced and homogenised, fixed in 1% formaldehyde and incubated for 10 min at room temperature. Cross-linking was stopped by the addition of glycine to final concentration 0.125 M. Tissue fragments were washed with cold PBS supplemented with protease inhibitors. The tissues were then homogenized in hypotonic buffer inorder to obtain nuclei, the nuclear pellet was resuspended in sonication buffer and were sonicated to obtain DNA fragments <500 bp and centrifuged. The soluble chromatin fraction was pretreated with blocked protein G sepharose beads. Subsequently, samples were incubated overnight at 4°C with antibodies to AcH3K27 (Abcam, ab4729) or 7C2 RNAPII antibody. Blocked beads were then added and the mixture was incubated for 2 h at 4°C. Prot G beads were washed, protein-DNA complexes were eluted from the beads and decrosslinked, and DNA recovered by phenol chloroform extraction and ethanol precipitation after treatment with ribonuclease A (Abcam) and proteinase K.

tag: tissue

value: myotubes

tag: strain

value: No antibody


title: 4_BeWo_input


title: MB468.MYC_rep2

value: breast cancer cell line MDA-MB-468


title: 10_BeWo_ZSCAN5B_SC

description: 10_11_BeWo_ZSCAN5B_SC_pooled_16_BeWo_input_control_MACS142_treat_all.wig.gz

value: ZSCAN5B (Santa Cruz)


title: 22_HEK_input

source_name: Human HEK 293 cell line

value: Human HEK 293


title: ZSCAN5B Si1

data_processing:
Fastq files were generated with Casava 1.8.2 (Illumina)
Illumina adapters including barcodes were trimmed using Trimmomatic v0.30
read alignment: Tophat 2.1.0, default parameters
differential expression: Cufflinks 2.2.1, default parameters
none
Genome_build: human version hg19
Supplementary_files_format_and_content: [SiRNA_fpkm_matrix.txt] FPKM values for each gene in each sample in a tab-delimited table in .txt format

source_name: ZSCAN5B Si1, HEK 293 cell line

growth_protocol: HEK-293 cells were maintained in DMEM containing 2 mM L-glutamine, 10% FBS, 1x PenStrep and incubated at 37C, 5% CO2

extract_protocol:
Total RNA was isolated from siRNA-treated cells using TRIzol (Invitrogen) followed by 30 minutes of RNase-free DNaseI treatment (NEB) at 37C and RNA Clean & ConcentratorTM-5 (Zymo Research). 2 µg of total RNA was used to generate cDNA using Superscript III Reverse Transcriptase (Invitrogen) with random hexamers (Invitrogen) according to manufacturer’s instructions.
The RNAseq libraries were constructed with the TruSeq® Stranded mRNA HT (Illumina) using an epMotion 5075 robot (Eppendorf). The libraries were pooled in equimolar concentration as instructed and each pool was quantitated by qPCR and sequenced  for 101 cycles on a HiSeq2000 using a TruSeq SBS sequencing kit version 3.

treatment_protocol: 10 nM of each siRNA was transfected using Lipofectamine RNAi MAX for 48 hours

value: HEK 293

value: ZSCAN5B SiRNA #1 knockdown


title: 11_BeWo_ZSCAN5D

description: pooled_11-BeWo-ZSCAN5D_28-BeWo-ZSCAN5D_MACS142_treat_all.wig.gz

value: ZSCAND


title: 20_HEK_ZSCAN5B_SC

description: 19_20_HEK_ZSCAN5B_SC_pooled_22_HEK_input_control_MACS142_treat_all.wig.gz


title: 11_BeWo_ZSCAN5B_SC


title: 19_HEK_ZSCAN5B_SC


title: ZSCAN5A Si4

source_name: ZSCAN5A Si4, HEK 293 cell line

value: ZSCAN5A SiRNA #4 knockdown


title: patient 2 [SLX-8969.N711_N508]

city: Cambridge

first: Anthony

last: Green

state: Cambridgeshire

address: Hills Road

department: Department of heamatology

country: United Kingdom

institute: University of Cambridge

description: processed data file: patient2.txt

data_processing:
Illumina basecalling
Sequenced reads were trimmed for Nextera Transposase Sequence,
Trimmed reads were mapped to Human GRCh38-77 reference genome from ENSEMBL plus ERCC92 spike-in controls with tophat 2.0.13 and bowtie 2.2.3
Quality control of the cells were performed by looking at the  number of detected genes. Cells expressing low counts were removed for the following step
Gene expression count matrix were calculated with seqmonk
Genome_build: GRCh38-77
Supplementary_files_format_and_content: Space separated raw counts. Rows are genes, columns are cells.

source_name: patient 2 single cell RNA-Seq

extract_protocol:
CD90+, CD34+, CD38-, CD45RA- cells were flow sorted and subjected to Smart-Seq 2
Smart-Seq2 and Nextera XP

tag: subject id

value: patient 2

tag: disease state

value: myeloprolifertive disease

value: hameatopoietic stemand progenitor cells

tag: protocol


title: patient 2 [SLX-8969.N707_N508]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N701_N508]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N703_N506]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N708_N508]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N701_N505]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N704_N501]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N705_N507]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N710_N506]

description: processed data file: patient2.txt


title: NEB_10_10_10

value: 10 ng Plate 1, 10 ng Plate 2, 10 ng Plate 3


title: Control

source_name: Control, HEK 293 cell line

tag: cell line

value: scrambled negative control knockdown


title: patient 2 [SLX-8969.N711_N502]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N705_N501]

description: processed data file: patient2.txt


title: 28_BeWo_ZSCAN5D

value: Human BeWo


title: patient 2 [SLX-8969.N702_N503]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N703_N501]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N704_N504]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N705_N506]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N707_N503]

description: processed data file: patient2.txt


title: ZSCAN5A Si5

source_name: ZSCAN5A Si5, HEK 293 cell line

value: ZSCAN5A SiRNA #5 knockdown


title: patient 2 [SLX-8969.N708_N503]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N712_N505]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N708_N505]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N702_N505]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N703_N507]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N701_N501]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N709_N508]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N703_N503]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N704_N508]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N710_N504]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N708_N507]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N712_N501]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N709_N506]

description: processed data file: patient2.txt


title: NEB_10_10_1

value: 10 ng Plate 1, 10 ng Plate 2, 1 ng Plate 3


title: patient 2 [SLX-8969.N707_N501]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N703_N508]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N705_N504]

description: processed data file: patient2.txt


title: Mutant rep1

department: Department of Biotechnology and Laboratory Science in Medicine

description:
delta_1
Processed data file: RNA-seq_Summary.xls

source_name: csrA mutant

value: csrA mutant


title: patient 2 [SLX-8969.N705_N505]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N709_N501]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N708_N502]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N702_N506]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N701_N506]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N703_N505]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N710_N501]

description: processed data file: patient2.txt


title: 1703-CB-0009

value: Crossbred (Landrace, Yorkshire, Duroc, Hampshire)

value: replacer-fed

value: PND 2


title: patient 2 [SLX-8969.N701_N502]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N706_N504]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N706_N507]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N710_N507]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N709_N502]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N712_N503]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N712_N508]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N706_N501]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N704_N502]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N711_N503]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N704_N503]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N706_N505]

description: processed data file: patient2.txt


title: 7_BeWo_ZSCAN5A

value: treatment


title: patient 2 [SLX-8969.N712_N506]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N710_N502]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N702_N504]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N704_N506]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N702_N501]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N711_N507]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N702_N502]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N709_N504]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N707_N504]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N705_N503]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N704_N505]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N708_N506]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N703_N502]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N702_N507]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N701_N503]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N710_N505]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N709_N503]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N707_N505]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N708_N504]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N707_N507]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N706_N508]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N706_N506]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N702_N508]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N703_N504]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N705_N502]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N709_N507]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N705_N508]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N712_N507]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N701_N507]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N707_N502]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N709_N505]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N710_N503]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N701_N504]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N711_N504]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N710_N508]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N711_N505]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N711_N501]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N706_N502]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N708_N501]

description: processed data file: patient2.txt


title: patient 1 [SLX-8966.N706_N502]

description: processed data file: patient1.txt

source_name: patient 1 single cell RNA-Seq

value: patient 1


title: patient 1 [SLX-8966.N704_N503]

description: processed data file: patient1.txt


title: patient 2 [SLX-8969.N707_N506]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N704_N507]

description: processed data file: patient2.txt


title: patient 2 [SLX-8969.N712_N504]

description: processed data file: patient2.txt


title: patient 1 [SLX-8966.N705_N508]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N702_N505]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N708_N502]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N711_N502]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N711_N507]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N701_N505]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N709_N501]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N708_N508]

description: processed data file: patient1.txt


title: patient 2 [SLX-8969.N711_N506]

description: processed data file: patient2.txt


title: patient 1 [SLX-8966.N709_N503]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N706_N505]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N710_N504]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N710_N501]

description: processed data file: patient1.txt


title: patient 2 [SLX-8969.N706_N503]

description: processed data file: patient2.txt


title: patient 1 [SLX-8966.N701_N506]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N706_N503]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N711_N504]

description: processed data file: patient1.txt


title: patient 2 [SLX-8969.N712_N502]

description: processed data file: patient2.txt


title: patient 1 [SLX-8966.N702_N501]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N704_N505]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N707_N508]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N704_N507]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N701_N502]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N706_N508]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N705_N503]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N708_N506]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N706_N507]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N705_N507]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N703_N504]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N708_N503]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N703_N502]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N702_N503]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N710_N503]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N707_N505]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N707_N506]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N709_N504]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N712_N506]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N709_N508]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N704_N502]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N709_N507]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N707_N504]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N710_N502]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N704_N508]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N712_N504]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N708_N505]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N709_N506]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N701_N504]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N709_N502]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N704_N504]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N706_N501]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N710_N506]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N701_N507]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N710_N507]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N702_N508]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N702_N502]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N711_N501]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N707_N503]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N708_N501]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N711_N503]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N712_N507]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N703_N506]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N703_N508]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N705_N505]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N701_N508]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N712_N502]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N707_N501]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N706_N506]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N704_N506]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N709_N505]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N705_N502]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N705_N504]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N702_N504]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N707_N507]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N705_N501]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N703_N501]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N712_N503]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N707_N502]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N712_N505]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N708_N504]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N701_N501]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N703_N507]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N710_N508]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N712_N508]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N702_N506]

description: processed data file: patient1.txt


title: patient 1 [SLX-8966.N703_N505]

description: processed data file: patient1.txt


title: 2-PS6-NHBV3_S244-1.PS4

city: Chicago

first: Mark

last: Maienschein-Cline

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description: Amplicon sequencing – fixed size based on amplicon. All pairs should overlap in their ends.

data_processing:
paired-end read merging: Raw paired-end sequence data were merged without trimming using the software package PEAR
amplicon reference sequence: A single sequence was generated to serve as a reference for mapping purposes. This hybrid reference sequence was derived from “top” strand and “bottom” strand sequences (derived from the bisulfite treatment, which generates DNA strands which are no longer inverse complements of each other), and merged according to allow for the mapping of the product PCR amplicons. Potential methylation sites were changed to “N” in the reference sequence to more easily identify methylation counts in the final data. See attached document. The region of interest is an approximately 4 kb viral genome integrated into the mouse genome; repetitive sequences of approximately 1 kb bound the fragment, leaving approximately 3 kb of unique sequence. Based on the known sequence, there are 99 CpG sites in the viral DNA sequence, and these were targeted using PCR amplification from bisulfite-treated DNA, followed by sequencing of the amplicons on an Illumina MiSeq instrument. Eleven primer sets were used to cover the viral genome, and 95 of the 99 sites were targeted; suitable primers could not be designed to cover the remaining CpG sites. For some positions, the protocol is unable to distinguish between CpG sites in the repetitive regions of the full 4 kb viral genome since the location of integration into host genome is not known.
genome alignment and genome reference construction: Merged, trimmed reads were sub-sampled to 2,500 sequences per sample, and mapped to the HBV reference DNA sequence in the CLC genomics workbench.
methylation quantification: Overall methylation per CpG site was obtained from the nucleotide composition at each potential methylation position. In addition, the methylation status of each read was assessed individually by counting the number of methylated CpG sites observed within that read. The distribution of methylation levels per read allows for the characterization of the cellular heterogeneity in the methylation status at each amplicon.
Supplementary_files_format_and_content: Processed data files are one file per sample per amplicon, plus one additional file for each sample for reads that were unmatched to any amplicon. Each file is a table, with one row per read, giving: Amplicon name assigned, number and percent of methylated, unmethylated, or ambiguous bases, the overall percent methylation, and the coordinates of the methylated CpGs (relative to the reference sequence used). This table was used to obtain overall methylation levels per amplicon, and the distribution of methylation levels per read across a sample.

source_name: HBV transgenic mouse lineage 1.3.32

growth_protocol: HBV transgenic mice contain a single copy of the terminally redundant, 1.3-genome length copy of the HBVayw genome integrated into the mouse chromosomal DNA.  High levels of HBV replication occur in the livers of these mice.  The mice used in the breeding experiments were homozygous for the HBV transgene and were maintained on the SV129 genetic background.

extract_protocol:
Bisulfite treatment of protein-free genomic DNA for methylation analysis was performed using the EZ DNA Methylation-Lightning™ Kit (D5030; Zymo Research, Inc., Irvine, CA, USA) according to the manufacturer’s instructions.  The 99 CpG sequences in the HBV DNA genome were targeted using PCR amplification of the bisulfite-treated DNA, followed by sequencing of the amplicons on an Illumina MiSeq instrument.  Preparation of DNA for high-throughput amplicon sequencing was performed in two PCR steps in a protocol termed “targeted amplicon sequencing (TAS)” as described previously (50,51). Thirteen HBV primer pairs targeting 95 of the 99 CpG sites were used.   The primer pairs targeting the bisulfite converted HBV DNA were (i) 5’-ACACTGACGACATGGTTCTACACAATACCTAAACCTTTACCC-3’ (oligo CS1FP1; HBV nucleotide coordinates 1131-1150) and 5’-TACGGTAGCAGAGACTTGGTCTGTTTTAGTTAGTGGGGGT-3’ (oligo CS2RP1; HBV coordinates 1214-1197), (ii) 5’-ACACTGACGACATGGTTCTACACAAACTTTCACTTTCTC-3’ (oligo CS1FP1a; HBV coordinates 1086-1102) and 5’-TACGGTAGCAGAGACTTGGTCTGTTGATGGTTTATGATTAA (oligo CS2RP1a; HBV coordinates 1233-1215), (iii) 5’-ACACTGACGACATGGTTCTACACCCCCACTAACTAAAAC-3’ (oligo CS1FP2; HBV nucleotide coordinates 1198-1214) and 5’- TACGGTAGCAGAGACTTGGTCTGGGTAATATTTGGTGG-3’ (oligo CS2RP2; HBV nucleotide coordinates 1645-1630), (iv) 5’-  ACACTGACGACATGGTTCTACATTAAACTCTCAACAATATCA-3’ (oligo CS1FP3; HBV nucleotide coordinates 1668-1687) and 5’-TACGGTAGCAGAGACTTGGTCTAAGTTATTTAAGGTATAGTTTG-3’  (oligoCS2RP3;  HBV nucleotide coordinates 1896-1875), (v) 5’-ACACTGACGACATGGTTCTACAGTGGTTTTGGGGTATGG-3’ (oligo CS1FP4; HBV nucleotide coordinates 1890-1906) and 5’- TACGGTAGCAGAGACTTGGTCTCAAATTAACACCCACCC-3’ (oligo CS2RP4; HBV nucleotide coordinates 2130-2114), (vi) 5’-ACACTGACGACATGGTTCTACAGGGTGGGTGTTAATTTG-3’ (oligo CS1FP5; HBV nucleotide coordinates 2114-2130) and 5’-TACGGTAGCAGAGACTTGGTCTCCAAAAAATACTAACATTAAAAT-3’ (oligo CS2RP5; HBV nucleotide coordinates 2464-2442), (vii) 5’-  ACACTGACGACATGGTTCTACAAGTTATAGAGTATTTGGTGT-3’  (oligo CS1FP5a;  HBV nucleotide coordinates 2244-2263) and 5’-TACGGTAGCAGAGACTTGGTCTCCCAATAAAATTCCCCA-3’ (oligo CS2RP5a; HBV nucleotide coordinates 2491-2475), (viii) 5’- ACACTGACGACATGGTTCTACAGATTGTAATTGATTATGTTTG -3’ (oligo  CS1FP6;  HBV nucleotide coordinates 2625-2645) and 5’-  TACGGTAGCAGAGACTTGGTCTCCATACTATAAATCTTATTCCC-3’ (oligo CS2RP6; HBV nucleotide coordinates 2832-2853), (ix) 5’-  ACACTGACGACATGGTTCTACAGGGAATAAGATTTATAGTATGG (oligo  CS1FP7;  HBV  nucleotide coordinates 2832-2853) and 5’-TACGGTAGCAGAGACTTGGTCTTAAACCTAAAAACTCCACC-3’ (oligo CS2RP7; HBV  nucleotide coordinates 3061-3043, (x) 5’-ACACTGACGACATGGTTCTACAAATCAAAAAAACAACCTACC-3’ (oligo CS1FP8; HBV  nucleotide coordinates 3115-3134) and 5’-TACGGTAGCAGAGACTTGGTCTGTGAGTGATTGGAGGT-3’ (oligo CS2RP8; HBV  nucleotide coordinates 340-325), (xi) 5’-ACACTGACGACATGGTTCTACAACCTCCAATCACTCAC-3’ (oligo  CS1FP9; HBV  nucleotide coordinates 325-340) and 5’-TACGGTAGCAGAGACTTGGTCTGTTAAATAGTGGGGGAAAG-3’ (oligo CS2RP9; HBV  nucleotide coordinates 730-712), (xii) 5’-ACACTGACGACATGGTTCTACAGGATGATGTGGTATTGG-3’ (oligo CS1FP10; HBV  nucleotide coordinates 743-759) and 5’-TACGGTAGCAGAGACTTGGTCTCAAAACCCAAAAAACCCAC-3’ (oligo CS2RP10; HBV  nucleotide coordinates 1020-1002), and (xiii) 5’-  ACACTGACGACATGGTTCTACATTGATGTTTTTGTATGTA-3’ (oligo  CS1FP11;  HBV nucleotide coordinates 1053-1070) and 5’-TACGGTAGCAGAGACTTGGTCTATAACCAAACCCCAACC-3’ (oligo CS2RP11; HBV nucleotide coordinates 1222-1206).  These primers contained linker sequences (underlined) at the 5’ ends of the oligonucleotides, termed common sequences (CS1 and CS2). These PCR reactions were performed using ZymoTaq PreMix according to the manufacturer’s instructions (Zymo Research). PCR amplification involved 10 minutes denaturation at 95°C, followed by 40 cycles of 95°C for 30 s, 50°C for 40 s, 72°C for 60 s.  Finally, a seven 7 minute incubation at 72°C was performed.  The HBV amplicons were subsequently subjected to a second stage PCR reaction (AccuPrime SuperMix II, Life Technologies), used to incorporate unique barcodes and sequencing adapters. The PCR primers used were 5’-  AATGATACGGCGACCACCGAGATCTACACTGACGACATGGTTCTACA-3’ (oligo PE1CS1) and 5’-CAAGCAGAAGACGGCATACGAGATNNNNNNNNNNTACGGTAGCAGAGACTTGGTCT-3’ (oligo PE2BCCS2).  The unique 10 base sample-specific barcodes are indicated with bold Ns and represent a subset of 384 unique sequences (Fluidigm).  PCR amplification involved 5 minutes denaturation at 95°C, followed by 8 cycles of 95°C for 30 s, 60°C for 30 s, 68°C for 30 s.  Finally, a seven minute incubation at 68°C was performed.
Pooled libraries were sequenced using an Illumina MiSeq instrument and data were analyzed using the Casava1.8 pipeline. Sequencing was performed using MiSeq V2 chemistry, with paired-end 2x300 base reads, employing Fluidigm custom sequencing primers. Sequence data were demultiplexed on instrument.

treatment_protocol: HBV transgenic mice (lineage 1.3.32) were bred with mice carrying the floxed FoxA1 (FoxA1fl/fl), floxed FoxA2 (FoxA2fl/fl), FoxA3-null (FoxA3-/-) alleles and the albumin Cre (lineage B6.Cg-Tg(Alb-cre)21Mgn/J, Jackson Laboratory) transgene (AlbCre) to generate HBVFoxA2fl/flAlbCre, HBVFoxA1fl/flFoxA2fl/flAlbCre and HBVFoxA1fl/flFoxA2fl/flFoxA3+/-AlbCre transgenic mice.  Littermate HBVFoxA2fl/fl, HBVFoxA1fl/flFoxA2fl/fl and HBVFoxA1fl/flFoxA2fl/flFoxA3+/- transgenic mice without the AlbCre transgene were used as controls. Mice were screened for the HBV transgene, the FoxA1fl/fl, FoxA2fl/fl, FoxA3-null alleles and the AlbCre transgene by polymerase chain reaction (PCR) analysis of tail DNA.  Tail DNA was prepared by incubating 1 cm of tail in 500 μl of 100 mM Tris hydrochloride (pH 8.0), 200 mM NaCl, 5 mM EDTA, 0.2% (wt/vol) SDS containing 100 μg/ml Proteinase K for 16 to 20 hours at 55°C.  Samples were centrifuged at 14,000 rpm in an Eppendorf 5417C microcentrifuge for 10 minutes and the supernatant was precipitated with 500 μl of isopropanol.  DNA was pelleted by centrifugation at 14,000 rpm in an Eppendorf 5417C microcentrifuge for 10 minutes and subsequently dissolved in 100 μl of 5 mM Tris hydrochloride (pH 8.0), 1 mM EDTA.  The HBV transgene was identified by PCR analysis using the oligonucleotides, 5’-TCGATACCTGAACCTTTACCCCGTTGCCCG-3’ (oligo XpHNF4-1, HBV coordinates 1133 to 1159) and 5’-TCGAATTGCTGAGAGTCCAAGAGTCCTCTT-3’ (oligo CpHNF4-2, HBV coordinates 1683 to 1658), and 1 μl of tail DNA.  A PCR product of 551 bp indicated the presence of the HBV transgene.  The FoxA1 wild type and floxed alleles were identified by PCR analysis using the oligonucleotides, 5’-CTGTGGATTATGTTCCTGATC-3’ (oligo FoxA1F) and 5’-GTGTCAGGATG CCTATCTGGT-3’ (oligo FoxA1R), and 1 μl of tail DNA.  A PCR product of 290 bp indicated the wild type FoxA1 allele whereas a PCR product of 480 bp indicated the floxed FoxA1 allele.  The FoxA2 wild type and floxed alleles were identified by PCR analysis using the oligonucleotides, 5’-CCCCTGAGTTGGCGGTGGT-3’ (oligo FoxA2F) and 5’-TTGCTCACGGAAGAGTAGCC-3’ (oligo FoxA2R), and 1 μl of tail DNA.  A PCR product of 290 bp indicated the wild type FoxA2 allele whereas a PCR product of 450 bp indicated the floxed FoxA2 allele.  The FoxA3 wild type and null alleles were identified by PCR analysis using the oligonucleotides, 5’-GGCAGTGCTTCCGGGTATGTA-3’ (oligo FoxA3F), 5’-GGGAAGAGGTCCATGATCCAT-3’ (oligo FoxA3R), and 5’-CAAAGCGCCATTCGCCATTCA-3’ (oligo FoxA3LacZ-3), and 1 μl of tail DNA.  A PCR product of 196 bp indicated the wild type FoxA3 allele whereas a PCR product of 290 bp indicated the null FoxA3 allele.  The AlbCre transgene was identified by PCR analysis using the oligonucleotides, 5’-CCAGCTAAACATGCTTCATCGTCG-3’ (oligo CRE-1) and 5’-ATTCTCCCACCGTCAGTACGTGAG-3’ (oligo CRE-2), and 1 μl of tail DNA.  A PCR product of 300 base pairs indicated the presence of the Cre transgene.  The samples were subjected to 42 amplification cycles involving denaturation at 94°C for 1 minute, annealing at 55°C for 1 minute, and extension from the primers at 72°C for 2 minutes.  The 20 μl reaction conditions used were as described by the manufacturer (Gene Choice) and contained 2 units of Taq DNA polymerase.   HBV transgenic mice were fed normal rodent chow and water was available ad libitum.  Mice were sacrificed and liver tissue was frozen in liquid nitrogen and stored at –70oC prior to DNA and RNA extraction.

tag: genetic background

tag: genotype

value: HBV (wild type)

tag: Sex

tag: age

value: Neonate

tag: organ

value: Liver


title: 2-PS6-NHBV3_S244-1.PS11


title: 2-PS6-NHBV3_S244-1.PS5


title: 2-PS6-NHBV3_S244-1.PS3


title: 2-PS6-NHBV3_S244-1.PS9


title: 2-PS6-NHBV3_S244-1.PS8


title: 2-PS6-NHBV3_S244-1.PS6


title: 2-PS6-NHBV3_S244-1.PS1


title: 2-PS6-NHBV3_S244-1.PS7


title: PS11-NHBV2_S46-1.PS10


title: PS11-NHBV2_S46-1.PS11


title: PS11-NHBV2_S46-1.PS4


title: PS11-NHBV2_S46-1.PS6


title: PS11-NHBV2_S46-1.PS7


title: PS11-NHBV2_S46-1.PS9


title: PS11-NHBV2_S46-1.PS2


title: PS11-NHBV2_S46-1.PS5


title: PS11-NHBV2_S46-1.PS1


title: PS10-NHBV1_S221-1.PS11


title: patient 1 [SLX-8966.N705_N506]

description: processed data file: patient1.txt


title: PS10-NHBV1_S221-1.PS9


title: PS10-NHBV1_S221-1.PS8


title: 2-PS6-NHBV3_S244-1.PS10


title: PS10-NHBV1_S221-1.PS10


title: PS10-NHBV1_S221-1.PS7


title: PS10-NHBV1_S221-1.PS5


title: 2-PS6-NHBV3_S244-1.PS2


title: PS11-NHBV2_S46-1.PS8


title: PS10-NHBV1_S221-1.PS4


title: PS11-NHBV2_S46-1.PS3


title: PS10-NHBV1_S221-1.PS1


title: PS9-FHBVBrn_S220-1.PS9

value: F

value: Adult

value: Brain


title: PS10-NHBV1_S221-1.PS3


title: PS10-NHBV1_S221-1.PS2


title: PS9-FHBVBrn_S220-1.PS8


title: PS9-FHBVBrn_S220-1.PS10


title: PS9-FHBVBrn_S220-1.PS11


title: PS9-FHBVBrn_S220-1.PS6


title: PS9-FHBVBrn_S220-1.PS4


title: PS9-FHBVBrn_S220-1.PS7


title: PS9-FHBVBrn_S220-1.PS2


title: PS9-FHBVBrn_S220-1.PS5


title: PS9-FHBVLng_S219-1.PS9

value: Lung


title: PS9-FHBVLng_S219-1.PS10


title: PS9-FHBVBrn_S220-1.PS3


title: PS9-FHBVBrn_S220-1.PS1


title: PS10-NHBV1_S221-1.PS6


title: PS9-FHBVLng_S219-1.PS8


title: PS9-FHBVLng_S219-1.PS5


title: PS9-FHBVLng_S219-1.PS4


title: PS9-FHBVLng_S219-1.PS2


title: PS9-FHBVLng_S219-1.PS3


title: PS9-FHBVLng_S219-1.PS6


title: PS9-FHBVLng_S219-1.PS1


title: PS9-FHBVSpl_S218-1.PS11

value: Spleen


title: PS9-FHBVSpl_S218-1.PS9


title: PS9-FHBVSpl_S218-1.PS6


title: PS9-FHBVSpl_S218-1.PS8


title: PS9-FHBVSpl_S218-1.PS10


title: PS9-FHBVSpl_S218-1.PS7


title: PS9-FHBVLng_S219-1.PS11


title: PS9-FHBVSpl_S218-1.PS5


title: PS7-FHBVMus_S173.PS11

value: Muscle


title: PS9-FHBVSpl_S218-1.PS2


title: PS9-FHBVLng_S219-1.PS7


title: PS9-FHBVSpl_S218-1.PS3


title: PS9-FHBVSpl_S218-1.PS1


title: PS7-FHBVMus_S173.PS10


title: PS7-FHBVMus_S173.PS7


title: PS7-FHBVMus_S173.PS8


title: PS7-FHBVMus_S173.PS6


title: PS7-FHBVMus_S173.PS4


title: PS7-FHBVMus_S173.PS3


title: PS7-FHBVMus_S173.PS2


title: PS7-FHBVMus_S173.PS1


title: PS9-FHBVSpl_S218-1.PS4


title: PS9-FHBVKid_S216-1.PS11

value: Kidney


title: PS9-FHBVKid_S216-1.PS8


title: PS9-FHBVKid_S216-1.PS9


title: PS9-FHBVKid_S216-1.PS7


title: PS9-FHBVKid_S216-1.PS10


title: PS9-FHBVKid_S216-1.PS6


title: PS9-FHBVKid_S216-1.PS5


title: PS7-FHBVMus_S173.PS9


title: PS9-FHBVKid_S216-1.PS3


title: PS9-FHBVKid_S216-1.PS4


title: PS9-FHBVKid_S216-1.PS2


title: PS9-FHBVLiv_S215-1.PS11


title: PS9-FHBVKid_S216-1.PS1


title: PS7-FHBVMus_S173.PS5


title: PS9-FHBVLiv_S215-1.PS9


title: PS9-FHBVLiv_S215-1.PS5


title: PS9-FHBVLiv_S215-1.PS7


title: PS9-FHBVLiv_S215-1.PS8


title: PS9-FHBVLiv_S215-1.PS6


title: PS9-FHBVLiv_S215-1.PS10


title: PS9-FHBVLiv_S215-1.PS4


title: PS9-FHBVLiv_S215-1.PS3


title: PS9-FHBVLiv_S215-1.PS1


title: PS9-FHBVLiv_S215-1.PS2


title: PS10-MHBVBrn_S236-1.PS11

value: M


title: PS10-MHBVBrn_S236-1.PS7


title: PS10-MHBVBrn_S236-1.PS8


title: PS9-MHBVLng_S213-1.PS11


title: PS10-MHBVBrn_S236-1.PS5


title: PS10-MHBVBrn_S236-1.PS3


title: PS10-MHBVBrn_S236-1.PS4


title: PS10-MHBVBrn_S236-1.PS6


title: PS10-MHBVBrn_S236-1.PS1


title: PS9-MHBVLng_S213-1.PS10


title: PS9-MHBVLng_S213-1.PS6


title: PS9-MHBVLng_S213-1.PS9


title: PS9-MHBVLng_S213-1.PS7


title: PS9-MHBVLng_S213-1.PS5


title: PS9-MHBVLng_S213-1.PS3


title: PS9-MHBVLng_S213-1.PS4


title: PS9-MHBVLng_S213-1.PS2


title: PS9-MHBVLng_S213-1.PS1


title: PS10-MHBVBrn_S236-1.PS10


title: PS9-MHBVSpl_S212-1.PS8


title: PS10-MHBVBrn_S236-1.PS2


title: PS9-MHBVSpl_S212-1.PS7


title: PS9-MHBVSpl_S212-1.PS11


title: PS10-MHBVBrn_S236-1.PS9


title: PS9-MHBVSpl_S212-1.PS10


title: PS9-MHBVSpl_S212-1.PS6


title: PS9-MHBVSpl_S212-1.PS5


title: PS9-MHBVSpl_S212-1.PS4


title: PS9-MHBVSpl_S212-1.PS2


title: PS9-MHBVLng_S213-1.PS8


title: PS9-MHBVSpl_S212-1.PS3


title: PS9-MHBVSpl_S212-1.PS1


title: PS9-MHBVSpl_S212-1.PS9


title: PS9-MHBVMus_S211-1.PS11


title: PS9-MHBVMus_S211-1.PS8


title: PS9-MHBVMus_S211-1.PS9


title: PS9-MHBVMus_S211-1.PS7


title: PS9-MHBVMus_S211-1.PS2


title: PS9-MHBVMus_S211-1.PS3


title: PS9-MHBVMus_S211-1.PS5


title: PS9-MHBVMus_S211-1.PS6


title: PS9-MHBVMus_S211-1.PS4


title: PS9-MHBVMus_S211-1.PS1


title: PS6-MHBVKid_S144-1.PS11


title: PS6-MHBVKid_S144-1.PS9


title: PS6-MHBVKid_S144-1.PS7


title: PS6-MHBVKid_S144-1.PS6


title: PS6-MHBVKid_S144-1.PS8


title: PS6-MHBVKid_S144-1.PS5


title: PS6-MHBVKid_S144-1.PS2


title: PS6-MHBVKid_S144-1.PS1


title: PS9-MHBVMus_S211-1.PS10


title: PS6-MHBVKid_S144-1.PS3


title: PS4-MHBVLiv_S121-1.PS9


title: PS6-MHBVKid_S144-1.PS4


title: PS4-MHBVLiv_S121-1.PS10


title: PS4-MHBVLiv_S121-1.PS5


title: PS4-MHBVLiv_S121-1.PS6


title: PS4-MHBVLiv_S121-1.PS7


title: FHBVA1A2A3Cre_plus_2.PS11


title: PS4-MHBVLiv_S121-1.PS4


title: PS4-MHBVLiv_S121-1.PS3


title: FHBVA1A2A3Cre_plus_2.PS8


title: FHBVA1A2A3Cre_plus_2.PS7


title: FHBVA1A2A3Cre_plus_2.PS6


title: FHBVA1A2A3Cre_plus_2.PS10


title: FHBVA1A2A3Cre_plus_2.PS5


title: FHBVA1A2A3Cre_plus_2.PS9


title: PS4-MHBVLiv_S121-1.PS1


title: FHBVA1A2A3Cre_plus_2.PS4


title: FHBVA1A2A3Cre_plus_2.PS3


title: PS4-MHBVLiv_S121-1.PS8


title: FHBVA1A2A3Cre_plus_2.PS2


title: PS6-MHBVKid_S144-1.PS10


title: PS4-MHBVLiv_S121-1.PS2


title: FHBVA1A2A3Cre_plus_2.PS1


title: FHBVA1A2A3Cre_plus_1.PS11


title: FHBVA1A2A3Cre_plus_1.PS10


title: FHBVA1A2A3Cre_plus_1.PS7


title: FHBVA1A2A3Cre_plus_1.PS8


title: FHBVA1A2A3Cre_plus_1.PS6


title: PS4-MHBVLiv_S121-1.PS11


title: FHBVA1A2A3Cre_plus_1.PS5


title: FHBVA1A2A3Cre_plus_1.PS4


title: FHBVA1A2A3Cre_plus_1.PS2


title: FHBVA1A2A3Cre_plus_1.PS3


title: FHBVA1A2A3Cre_minus_2.PS11


title: FHBVA1A2A3Cre_minus_2.PS10


title: FHBVA1A2A3Cre_minus_2.PS6


title: FHBVA1A2A3Cre_minus_2.PS5


title: FHBVA1A2A3Cre_minus_2.PS9


title: FHBVA1A2A3Cre_minus_2.PS8


title: FHBVA1A2A3Cre_minus_2.PS7


title: FHBVA1A2A3Cre_minus_2.PS3


title: FHBVA1A2A3Cre_minus_2.PS2


title: FHBVA1A2A3Cre_minus_2.PS4


title: FHBVA1A2A3Cre_minus_2.PS1


title: FHBVA1A2A3Cre_minus_1.PS11


title: FHBVA1A2A3Cre_minus_1.PS10


title: FHBVA1A2A3Cre_minus_1.PS9


title: FHBVA1A2A3Cre_minus_1.PS8


title: FHBVA1A2A3Cre_minus_1.PS4


title: FHBVA1A2A3Cre_minus_1.PS5


title: FHBVA1A2A3Cre_minus_1.PS3


title: FHBVA1A2A3Cre_minus_1.PS7


title: FHBVA1A2A3Cre_minus_1.PS1


title: FHBVA1A2A3Cre_minus_1.PS2


title: FHBVA1A2Cre_plus.PS11


title: FHBVA1A2Cre_plus.PS10


title: FHBVA1A2Cre_plus.PS8


title: FHBVA1A2A3Cre_plus_1.PS1


title: FHBVA1A2Cre_plus.PS7


title: FHBVA1A2Cre_plus.PS9


title: FHBVA1A2Cre_plus.PS6


title: FHBVA1A2Cre_plus.PS5


title: FHBVA1A2Cre_plus.PS4


title: FHBVA1A2Cre_plus.PS3


title: FHBVA1A2Cre_plus.PS2


title: FHBVA1A2A3Cre_minus_1.PS6


title: FHBVA1A2Cre_minus.PS11


title: FHBVA1A2Cre_plus.PS1


title: FHBVA1A2Cre_minus.PS6


title: FHBVA1A2Cre_minus.PS8


title: FHBVA1A2Cre_minus.PS10


title: FHBVA1A2Cre_minus.PS9


title: FHBVA1A2Cre_minus.PS4


title: FHBVA1A2Cre_minus.PS5


title: FHBVA1A2Cre_minus.PS1


title: FHBVA1A2Cre_minus.PS3


title: FHBVA1A2Cre_minus.PS2


title: FHBVA2Cre_plus.PS10


title: FHBVA2Cre_plus.PS11


title: FHBVA2Cre_plus.PS9


title: FHBVA2Cre_plus.PS6


title: FHBVA2Cre_plus.PS5


title: FHBVA2Cre_plus.PS7


title: FHBVA2Cre_plus.PS8


title: FHBVA2Cre_plus.PS4


title: FHBVA2Cre_plus.PS2


title: FHBVA1A2Cre_minus.PS7


title: FHBVA2Cre_plus.PS1


title: FHBVA2Cre_minus.PS10


title: HC125 #4 RNA-seq

first: Olga

last: Minkina

state: MA

address: 16 Divinity Ave.

department: Molecular and Cellular Biology

institute: Harvard University

description:
N2_HC125_RNA-seq_SingleEnd_gene_exp_diff.xlsx
Single end, stranded

data_processing:
Align to WS235 with Tophat v. 2.0.1;  -i 20, -I 10000 and all other parameters set to default
Identify differentially expressed genes with Cufflinks v. 2.2.1; default parameters; FDR < .05
Genome_build: C. elegans WS235

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: C. elegans

growth_protocol: Synchronized to young adults by timed egg lay

extract_protocol:
Trizol/chroloroform, isopropanol precipitation, DNaseI treatment, purification and concentration
Apollo 324™ NGS Library Prep System
(In SAMPLES section)
(In SAMPLES section)

tag: developmental stage

value: Young adult


title: FHBVA2Cre_plus.PS3


title: FHBVA2Cre_minus.PS8


title: FHBVA2Cre_minus.PS9


title: FHBVA2Cre_minus.PS6


title: FHBVA2Cre_minus.PS5


title: FHBVA2Cre_minus.PS4


title: FHBVA2Cre_minus.PS3


title: FHBVA2Cre_minus.PS2


title: N2 #4 RNA-seq


title: N2 #3 RNA-seq


title: MHBVA1A2A3Cre_plus_2.PS11


title: MHBVA1A2A3Cre_plus_2.PS10


title: HC125 #2 RNA-seq

description:
N2_HC125_RNA-seq_PairedEnd_gene_exp_diff.xlsx
Paired end, no strand information

extract_protocol:
Trizol/chroloroform, isopropanol precipitation, DNaseI treatment, purification and concentration
Illumina TruSeq RNA Library Preparation Kit v2
(In SAMPLES section)
(In SAMPLES section)


title: MHBVA1A2A3Cre_plus_2.PS9


title: HC125 #1 RNA-seq


title: MHBVA1A2A3Cre_plus_2.PS8


title: FHBVA2Cre_minus.PS11


title: MHBVA1A2A3Cre_plus_2.PS7


title: MHBVA1A2A3Cre_plus_2.PS5


title: HC125 5' dependent #1 Small RNA-seq

data_processing:
Filter 21-26nt reads (custom script)
Align to C. elegans genome WS235 using Bowtie2, allowing 0 mismatches (--score-min L,0,0) and up to four alignments per read (-k 4)
Generate small RNA counts per gene using HTseq
Genome_build: C. elegans WS235

extract_protocol:
Trizol/chroloroform, isopropanol precipitation, DNaseI treatment, purification and concentration
(In SAMPLES section)
Small RNA libraries made with Apollo 324 NGS Library Prep System (Small RNA 8 Protocol), amplified for 12 cycles, size selected on Pippin Prep, purified and concentrated.


title: HC125 5' dependent #2 Small RNA-seq


title: FHBVA2Cre_minus.PS1


title: NonArrayF21 #2 Small RNA-seq

extract_protocol:
Trizol/chroloroform, isopropanol precipitation, DNaseI treatment, 5' polyphosphatase treatment, purification and concentration
(In SAMPLES section)
Small RNA libraries made with Apollo 324 NGS Library Prep System (Small RNA 8 Protocol), amplified for 12 cycles, size selected on Pippin Prep, purified and concentrated.

value: HC83 non-array F21


title: HC125 #3 RNA-seq


title: MHBVA1A2A3Cre_plus_2.PS3


title: NonArrayF21 #1 Small RNA-seq


title: MHBVA1A2A3Cre_plus_2.PS2


title: NonArrayF6 #1 Small RNA-seq

value: HC83 non-array F6


title: MHBVA1A2A3Cre_plus_2.PS1


title: MHBVA1A2A3Cre_plus_1.PS11


title: MHBVA1A2A3Cre_plus_1.PS10


title: HC125 #4 Small RNA-seq


title: MHBVA1A2A3Cre_plus_1.PS9


title: N2 #1 RNA-seq


title: MHBVA1A2A3Cre_plus_2.PS6


title: hrde-1;HC125 #1 Small RNA-seq


title: MHBVA1A2A3Cre_plus_1.PS8


title: N2 #2 RNA-seq


title: MHBVA1A2A3Cre_plus_1.PS6


title: MHBVA1A2A3Cre_plus_1.PS7


title: HC125 #3 Small RNA-seq


title: MHBVA1A2A3Cre_plus_2.PS4


title: HC125 #2 Small RNA-seq


title: N2 #2 Small RNA-seq


title: MHBVA1A2A3Cre_plus_1.PS4


title: HC125 #1 Small RNA-seq


title: MHBVA1A2A3Cre_plus_1.PS3


title: NonArrayF6 #2 Small RNA-seq


title: N2 #1 Small RNA-seq


title: hrde-1;HC125 #2 Small RNA-seq


title: MHBVA1A2A3Cre_plus_1.PS2


title: MHBVA1A2A3Cre_plus_1.PS1


title: MHBVA1A2A3Cre_minus_2.PS10


title: MHBVA1A2A3Cre_minus_2.PS11


title: MHBVA1A2A3Cre_minus_2.PS7


title: MHBVA1A2A3Cre_minus_2.PS8


title: MHBVA1A2A3Cre_minus_2.PS5


title: MHBVA1A2A3Cre_minus_2.PS4


title: MHBVA1A2A3Cre_plus_1.PS5


title: MHBVA1A2A3Cre_minus_2.PS6


title: MHBVA1A2A3Cre_minus_2.PS3


title: MHBVA1A2A3Cre_minus_2.PS2


title: MHBVA1A2A3Cre_minus_2.PS1


title: MHBVA1A2A3Cre_minus_1.PS11


title: MHBVA1A2A3Cre_minus_1.PS8


title: MHBVA1A2A3Cre_minus_1.PS10


title: MHBVA1A2A3Cre_minus_1.PS6


title: MHBVA1A2A3Cre_minus_1.PS7


title: MHBVA1A2A3Cre_minus_1.PS9


title: MHBVA1A2A3Cre_minus_1.PS5


title: MHBVA1A2A3Cre_minus_1.PS4


title: MHBVA1A2A3Cre_minus_1.PS3


title: MHBVA1A2A3Cre_minus_2.PS9


title: MHBVA1A2Cre_plus.PS10


title: MHBVA1A2Cre_plus.PS11


title: MHBVA1A2A3Cre_minus_1.PS1


title: MHBVA1A2Cre_plus.PS8


title: MHBVA1A2A3Cre_minus_1.PS2


title: MHBVA1A2Cre_plus.PS9


title: MHBVA1A2Cre_plus.PS5


title: MHBVA1A2Cre_plus.PS3


title: MHBVA1A2Cre_plus.PS4


title: MHBVA1A2Cre_minus.PS10


title: MHBVA1A2Cre_minus.PS9


title: MHBVA1A2Cre_plus.PS1


title: MHBVA1A2Cre_minus.PS11


title: MHBVA1A2Cre_minus.PS6


title: MHBVA1A2Cre_minus.PS8


title: MHBVA1A2Cre_minus.PS7


title: MHBVA1A2Cre_minus.PS5


title: MHBVA1A2Cre_minus.PS2


title: MHBVA1A2Cre_plus.PS2


title: MHBVA1A2Cre_minus.PS4


title: MHBVA1A2Cre_minus.PS3


title: MHBVA1A2Cre_plus.PS7


title: MHBVA2Cre_plus.PS11


title: MHBVA1A2Cre_minus.PS1


title: MHBVA2Cre_plus.PS9


title: FHBVA1A2A3Cre_plus_1.PS9


title: MHBVA2Cre_plus.PS8


title: MHBVA2Cre_plus.PS6


title: MHBVA1A2Cre_plus.PS6


title: MHBVA2Cre_plus.PS7


title: MHBVA2Cre_plus.PS1


title: MHBVA2Cre_minus.PS11


title: MHBVA2Cre_plus.PS5


title: MHBVA2Cre_plus.PS3


title: MHBVA2Cre_plus.PS4


title: MHBVA2Cre_minus.PS9


title: MHBVA2Cre_minus.PS8


title: MHBVA2Cre_minus.PS6


title: MHBVA2Cre_minus.PS7


title: MHBVA2Cre_plus.PS2


title: MHBVA2Cre_minus.PS10


title: MHBVA2Cre_minus.PS4


title: MHBVA2Cre_minus.PS5


title: FHBVA2Cre_minus.PS7


title: MHBVA2Cre_minus.PS1


title: MHBVA2Cre_minus.PS2


title: WTY Rep2 – Ames Prop1 Het – 2 month

city: Glasgow

first: Neil

middle: A

last: Robertson

state: Scotland

address: Switchback Road

department: Beatson Institute for Cancer Research

institute: University of Glasgow

description:
Cole.14L_N_young.RNA-seq
RNA sequencing of young (2 month) mice
DESeq2.WTO-WTY.csv
DESeq2.DY-WTY.csv
FPKM_Matrix.csv

data_processing:
Basecalls performed in phred64 (solexa1.3-quals).
Sequenced reads were mapped to mm9 whole genome using Tophat with default settings
FPKM matrix was derived using Cufflinks suite using default settings
Differential expression quantified using DESeq2 (Bioconductor) following non-normalised read counting with Htseq (intersection-nonempty)
Genome_build: mm9
Supplementary_files_format_and_content: Summary files describe the results of DESeq2 differential expression analysis for core comparisons as well as FPKM matrix for all replicate created using Cufflinks suite.

source_name: Hepatocytes

growth_protocol: Ames dwarf mice were derived from a closed colony with a heterogeneous background (over 25 years) at the University of North Dakota. Dwarf mice were generated by mating either homozygous (df/df) or heterozygous (df/+) dwarf males with carrier females (df/+).

extract_protocol:
RNA was extracted by Rneasy Mini Kit  (Quiagen)
Samples were sequenced in house on a single flow cell on the illumina NextSeq

treatment_protocol: All mice were bred and maintained at the University of North Dakota Center for Biomedical Research under controlled conditions of photoperiod (12:12 h light/dark cycle) and temperature (22 -/+1 °C) and ad libitum access to food (Teklad #8640) and water.  Animal procedures were reviewed and approved by the UND Institutional Animal Care and Use Committee. Liver tissue from male WT and Ames dwarf mice was collected at 2 and 22 months of age (n=4/genotype/age).

value: Ames Dwarf

value: Prop1 Het


title: MHBVA2Cre_plus.PS10


title: WTY Rep4 – Ames Prop1 Het – 2 month

description:
Cole.16L_N_young.RNA-seq
RNA sequencing of young (2 month) mice
DESeq2.WTO-WTY.csv
DESeq2.DY-WTY.csv
FPKM_Matrix.csv


title: DY Rep4 – Ames Prop1 Hom – 2 month

description:
Cole.35L_df_young.RNA-seq
RNA sequencing of young (2 month) mice
DESeq2.DY-WTY.csv
DESeq2.DO-DY.csv
FPKM_Matrix.csv

value: Prop1 Hom


title: WTY Rep3 – Ames Prop1 Het – 2 month

description:
Cole.15L_N_young.RNA-seq
RNA sequencing of young (2 month) mice
DESeq2.WTO-WTY.csv
DESeq2.DY-WTY.csv
FPKM_Matrix.csv


title: DY Rep1 – Ames Prop1 Hom – 2 month

description:
Cole.9L_df_young.RNA-seq
RNA sequencing of young (2 month) mice
DESeq2.DY-WTY.csv
DESeq2.DO-DY.csv
FPKM_Matrix.csv


title: WTO Rep1 – Ames Prop1 Het – 22 month

description:
Cole.5L_N_old.RNA-seq
RNA sequencing of old (22 month) mice
DESeq2.WTO-WTY.csv
DESeq2.DO-WTO.csv
FPKM_Matrix.csv


title: WTO Rep4 – Ames Prop1 Het – 22 month

description:
Cole.8L_N_old.RNA-seq
RNA sequencing of old (22 month) mice
DESeq2.WTO-WTY.csv
DESeq2.DO-WTO.csv
FPKM_Matrix.csv


title: WTO Rep2 – Ames Prop1 Het – 22 month

description:
Cole.6L_N_old.RNA-seq
RNA sequencing of old (22 month) mice
DESeq2.WTO-WTY.csv
DESeq2.DO-WTO.csv
FPKM_Matrix.csv


title: WTO Rep3 – Ames Prop1 Het – 22 month

description:
Cole.7L_N_old.RNA-seq
RNA sequencing of old (22 month) mice
DESeq2.WTO-WTY.csv
DESeq2.DO-WTO.csv
FPKM_Matrix.csv


title: WTY Rep1 – Ames Prop1 Het – 2 month

description:
Cole.13L_N_young.RNA-seq
RNA sequencing of young (2 month) mice
DESeq2.WTO-WTY.csv
DESeq2.DY-WTY.csv
FPKM_Matrix.csv


title: DY Rep2 – Ames Prop1 Hom – 2 month

description:
Cole.10L_df_young.RNA-seq
RNA sequencing of young (2 month) mice
DESeq2.DY-WTY.csv
DESeq2.DO-DY.csv
FPKM_Matrix.csv


title: DO Rep3 - Ames Prop1 Hom – 22 month

description:
Cole.3L_df_old.RNA-seq
RNA sequencing of old (22 month) mice
DESeq2.DO-WTO.csv
DESeq2.DO-DY.csv
FPKM_Matrix.csv


title: DO Rep1 - Ames Prop1 Hom – 22 month

description:
Cole.1L_df_old.RNA-seq
RNA sequencing of old (22 month) mice
DESeq2.DO-WTO.csv
DESeq2.DO-DY.csv
FPKM_Matrix.csv


title: mouse_YFPpos_12w_cell182

city: Stanford

first: Martin

last: Enge

state: CA

address: James H. Clark Center, 318 Campus Drive,

department: Bioengineering

institute: Stanford University

description:
Single cell from mouse pancreas
C10.1000200104

data_processing:
Sequencing reads were trimmed, adapter sequences removed and the reads aligned using STAR with default parameters.
Duplicate reads were removed using picard. Transcript counts were obtained using HT-Seq and mm10 UCSC exon/transcript annotations.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample

source_name: Single cell from pancreas, YFPpos_12w_cell182

extract_protocol:
Isolated mouse islets were dissociated into single cells by enzymatic digestion using 0.05% Trypsin (25300-120; Life Technologies). 7-aminoactinomycin D (7-AAD, eBiosciences) was used at 1:500 dilution as Live/Dead stain to exclude dead cells. Sort gates were adjusted with reference to negative controls (wild-type islets without YFP labeling). We collected cells from YFP+, lineage-traced population and also YFPNeg, non-labeled population. Cells were sorted on a special order 5-laser FACS Aria II (BD Biosciences) using a 100 µm nozzle at a flow rate of 1 following doublet removal. Sorted single-cells were collected directly into 96-well plates (Bio-Rad cat #: HSP9601) containing 4 µL of lysis buffer with dNTPs37 for downstream single-cell RNA-Seq assays.
Single-cells were collected  in lysis buffer in 96-well plates, followed by reverse transcription with template-switch using an LNA-modified template switch oligo to generate cDNA. After 21 cycles of pre-amplification, DNA was purified and analyzed on an automated Fragment Analyzer (Advanced Analytical). Each cell’s cDNA fragment profile was individually inspected and only wells with successful amplification products (concentration higher than 0.06 ng/ul) and with no detectable RNA degradation were selected for final library preparation. Tagmentation assays and barcoded sequencing libraries were prepared using Nextera XT kit (FC-131-1024; Illumina) according to the manufacturer’s instructions. Barcoded libraries were pooled and subjected to 75 bp paired-end sequencing on the Illumina NextSeq instrument.

value: YFPpos

tag: time (weeks after arx and dnmt1 depletion)

value: endocrine pancreatic islet cell

tag: inferred cell type

value: beta-like


title: DO Rep2 - Ames Prop1 Hom – 22 month

description:
Cole.2L_df_old.RNA-seq
RNA sequencing of old (22 month) mice
DESeq2.DO-WTO.csv
DESeq2.DO-DY.csv
FPKM_Matrix.csv


title: mouse_control_contr_cell180

description:
Single cell from mouse pancreas
A8.1000200106

source_name: Single cell from pancreas, control_contr_cell180

value: control

tag: cell type


title: MHBVA2Cre_minus.PS3

description: Amplicon sequencing – fixed size based on amplicon. All pairs should overlap in their ends.

value: Adult

value: Liver


title: DY Rep3 – Ames Prop1 Hom – 2 month

description:
Cole.34L_df_young.RNA-seq
RNA sequencing of young (2 month) mice
DESeq2.DY-WTY.csv
DESeq2.DO-DY.csv
FPKM_Matrix.csv


title: mouse_YFPpos_12w_cell179

description:
Single cell from mouse pancreas
B3.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell179


title: mouse_YFPpos_12w_cell178

description:
Single cell from mouse pancreas
B5.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell178

value: delta-like


title: mouse_YFPpos_12w_cell177

description:
Single cell from mouse pancreas
A5.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell177


title: mouse_YFPpos_12w_cell175

description:
Single cell from mouse pancreas
A5.10001000005

source_name: Single cell from pancreas, YFPpos_12w_cell175


title: mouse_YFPpos_12w_cell174

description:
Single cell from mouse pancreas
D5.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell174


title: mouse_YFPpos_12w_cell172

description:
Single cell from mouse pancreas
A10.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell172


title: mouse_YFPpos_12w_cell171

description:
Single cell from mouse pancreas
D7.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell171


title: mouse_YFPpos_12w_cell170

description:
Single cell from mouse pancreas
D9.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell170


title: mouse_YFPpos_12w_cell169

description:
Single cell from mouse pancreas
B2.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell169


title: mouse_YFPpos_12w_cell167

description:
Single cell from mouse pancreas
A6.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell167


title: mouse_YFPpos_12w_cell166

description:
Single cell from mouse pancreas
A3.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell166


title: DO Rep4 - Ames Prop1 Hom – 22 month

description:
Cole.4L_df_old.RNA-seq
RNA sequencing of old (22 month) mice
DESeq2.DO-WTO.csv
DESeq2.DO-DY.csv
FPKM_Matrix.csv


title: mouse_YFPpos_12w_cell165

description:
Single cell from mouse pancreas
A7.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell165


title: mouse_YFPpos_12w_cell164

description:
Single cell from mouse pancreas
D3.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell164


title: mouse_YFPpos_12w_cell173

description:
Single cell from mouse pancreas
C8.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell173


title: mouse_YFPpos_12w_cell181

description:
Single cell from mouse pancreas
A8.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell181


title: mouse_YFPpos_12w_cell163

description:
Single cell from mouse pancreas
A9.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell163


title: mouse_YFPpos_12w_cell162

description:
Single cell from mouse pancreas
C4.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell162


title: mouse_control_contr_cell176

description:
Single cell from mouse pancreas
E1.1000200107

source_name: Single cell from pancreas, control_contr_cell176


title: mouse_YFPpos_12w_cell160

description:
Single cell from mouse pancreas
A2.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell160


title: mouse_YFPpos_12w_cell159

description:
Single cell from mouse pancreas
A2.10001000005

source_name: Single cell from pancreas, YFPpos_12w_cell159


title: mouse_YFPpos_12w_cell161

description:
Single cell from mouse pancreas
A4.10001000005

source_name: Single cell from pancreas, YFPpos_12w_cell161


title: mouse_YFPpos_12w_cell157

description:
Single cell from mouse pancreas
B6.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell157

value: alpha-like


title: mouse_YFPpos_12w_cell158

description:
Single cell from mouse pancreas
D10.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell158


title: mouse_YFPpos_12w_cell154

description:
Single cell from mouse pancreas
C11.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell154


title: mouse_YFPpos_12w_cell152

description:
Single cell from mouse pancreas
C2.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell152


title: mouse_YFPpos_12w_cell156

description:
Single cell from mouse pancreas
D11.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell156


title: mouse_YFPpos_12w_cell148

description:
Single cell from mouse pancreas
B7.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell148


title: mouse_YFPpos_12w_cell168

description:
Single cell from mouse pancreas
C3.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell168


title: mouse_YFPpos_12w_cell146

description:
Single cell from mouse pancreas
A1.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell146


title: mouse_YFPpos_12w_cell149

description:
Single cell from mouse pancreas
C1.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell149


title: mouse_YFPpos_12w_cell151

description:
Single cell from mouse pancreas
A4.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell151


title: mouse_YFPpos_12w_cell144

description:
Single cell from mouse pancreas
B1.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell144


title: mouse_YFPpos_12w_cell141

description:
Single cell from mouse pancreas
A6.10001000005

source_name: Single cell from pancreas, YFPpos_12w_cell141


title: mouse_YFPpos_12w_cell143

description:
Single cell from mouse pancreas
B4.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell143


title: mouse_control_contr_cell137

description:
Single cell from mouse pancreas
C3.1000200107

source_name: Single cell from pancreas, control_contr_cell137


title: mouse_YFPpos_12w_cell139

description:
Single cell from mouse pancreas
A1.10001000005

source_name: Single cell from pancreas, YFPpos_12w_cell139


title: mouse_YFPpos_12w_cell138

description:
Single cell from mouse pancreas
B10.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell138


title: mouse_YFPpos_low_12w_cell136

description:
Single cell from mouse pancreas
G9.1000200104

source_name: Single cell from pancreas, YFPpos_low_12w_cell136


title: mouse_YFPpos_8w_cell133

description:
Single cell from mouse pancreas
A6.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell133


title: mouse_YFPpos_8w_cell132

description:
Single cell from mouse pancreas
A6.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell132


title: mouse_YFPpos_12w_cell150

description:
Single cell from mouse pancreas
A8.10001000005

source_name: Single cell from pancreas, YFPpos_12w_cell150


title: mouse_YFPpos_8w_cell129

description:
Single cell from mouse pancreas
D5.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell129


title: mouse_YFPpos_8w_cell134

description:
Single cell from mouse pancreas
C11.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell134


title: mouse_YFPpos_8w_cell130

description:
Single cell from mouse pancreas
C9.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell130


title: mouse_YFPpos_8w_cell128

description:
Single cell from mouse pancreas
B3.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell128


title: mouse_YFPpos_8w_cell124

description:
Single cell from mouse pancreas
B8.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell124


title: mouse_YFPpos_8w_cell120

description:
Single cell from mouse pancreas
D11.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell120


title: mouse_YFPpos_8w_cell121

description:
Single cell from mouse pancreas
D10.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell121


title: mouse_YFPpos_12w_cell145

description:
Single cell from mouse pancreas
A3.10001000005

source_name: Single cell from pancreas, YFPpos_12w_cell145


title: mouse_YFPpos_8w_cell126

description:
Single cell from mouse pancreas
C6.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell126


title: mouse_YFPpos_8w_cell125

description:
Single cell from mouse pancreas
A11.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell125


title: mouse_YFPpos_12w_cell155

description:
Single cell from mouse pancreas
D4.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell155


title: mouse_YFPpos_12w_cell153

description:
Single cell from mouse pancreas
C5.1000200104

source_name: Single cell from pancreas, YFPpos_12w_cell153


title: mouse_YFPpos_8w_cell123

description:
Single cell from mouse pancreas
C8.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell123


title: mouse_YFPpos_8w_cell118

description:
Single cell from mouse pancreas
B12.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell118


title: mouse_YFPpos_8w_cell119

description:
Single cell from mouse pancreas
C6.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell119


title: mouse_YFPpos_8w_cell131

description:
Single cell from mouse pancreas
D5.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell131


title: mouse_YFPpos_8w_cell115

description:
Single cell from mouse pancreas
A4.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell115


title: mouse_YFPpos_8w_cell127

description:
Single cell from mouse pancreas
C7.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell127


title: mouse_YFPpos_8w_cell112

description:
Single cell from mouse pancreas
B3.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell112


title: mouse_YFPpos_8w_cell108

description:
Single cell from mouse pancreas
A10.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell108


title: mouse_YFPpos_8w_cell111

description:
Single cell from mouse pancreas
B10.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell111


title: mouse_YFPpos_8w_cell117

description:
Single cell from mouse pancreas
D3.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell117


title: mouse_YFPpos_8w_cell107

description:
Single cell from mouse pancreas
A9.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell107


title: mouse_YFPpos_8w_cell109

description:
Single cell from mouse pancreas
B2.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell109


title: mouse_YFPpos_8w_cell106

description:
Single cell from mouse pancreas
D6.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell106


title: mouse_YFPpos_8w_cell122

description:
Single cell from mouse pancreas
D7.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell122


title: mouse_YFPpos_8w_cell105

description:
Single cell from mouse pancreas
C12.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell105


title: mouse_YFPpos_8w_cell116

description:
Single cell from mouse pancreas
A8.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell116


title: mouse_YFPpos_8w_cell101

description:
Single cell from mouse pancreas
D12.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell101


title: mouse_YFPpos_8w_cell102

description:
Single cell from mouse pancreas
C11.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell102


title: mouse_YFPpos_8w_cell103

description:
Single cell from mouse pancreas
D6.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell103


title: mouse_YFPpos_8w_cell100

description:
Single cell from mouse pancreas
D3.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell100


title: mouse_YFPpos_8w_cell98

description:
Single cell from mouse pancreas
B5.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell98


title: mouse_YFPpos_8w_cell104

description:
Single cell from mouse pancreas
A11.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell104


title: mouse_YFPpos_8w_cell99

description:
Single cell from mouse pancreas
B7.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell99


title: mouse_YFPpos_8w_cell113

description:
Single cell from mouse pancreas
D11.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell113


title: mouse_YFPneg_8w_cell96

description:
Single cell from mouse pancreas
F2.1000200102

source_name: Single cell from pancreas, YFPneg_8w_cell96

value: YFPneg


title: mouse_YFPpos_8w_cell95

description:
Single cell from mouse pancreas
B4.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell95


title: mouse_YFPpos_8w_cell93

description:
Single cell from mouse pancreas
B5.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell93


title: mouse_YFPpos_8w_cell97

description:
Single cell from mouse pancreas
A9.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell97


title: mouse_YFPpos_8w_cell94

description:
Single cell from mouse pancreas
C1.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell94


title: mouse_YFPpos_8w_cell90

description:
Single cell from mouse pancreas
A2.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell90


title: mouse_YFPpos_8w_cell110

description:
Single cell from mouse pancreas
D1.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell110


title: mouse_YFPpos_8w_cell88

description:
Single cell from mouse pancreas
B3.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell88


title: mouse_YFPpos_8w_cell84

description:
Single cell from mouse pancreas
A12.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell84


title: mouse_YFPpos_8w_cell87

description:
Single cell from mouse pancreas
B1.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell87


title: mouse_YFPpos_8w_cell92

description:
Single cell from mouse pancreas
B6.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell92


title: mouse_YFPneg_8w_cell86

description:
Single cell from mouse pancreas
E11.1000200102

source_name: Single cell from pancreas, YFPneg_8w_cell86


title: mouse_YFPpos_8w_cell89

description:
Single cell from mouse pancreas
C5.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell89


title: mouse_YFPpos_8w_cell91

description:
Single cell from mouse pancreas
B10.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell91


title: mouse_YFPpos_8w_cell83

description:
Single cell from mouse pancreas
B8.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell83


title: mouse_YFPpos_8w_cell81

description:
Single cell from mouse pancreas
B1.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell81


title: mouse_YFPpos_8w_cell82

description:
Single cell from mouse pancreas
B2.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell82


title: mouse_YFPpos_8w_cell80

description:
Single cell from mouse pancreas
C5.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell80


title: mouse_YFPpos_8w_cell77

description:
Single cell from mouse pancreas
C6.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell77


title: mouse_YFPpos_8w_cell79

description:
Single cell from mouse pancreas
C4.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell79


title: mouse_YFPpos_8w_cell78

description:
Single cell from mouse pancreas
C8.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell78


title: mouse_YFPpos_8w_cell76

description:
Single cell from mouse pancreas
D2.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell76


title: mouse_YFPneg_8w_cell71

description:
Single cell from mouse pancreas
F4.1000200101

source_name: Single cell from pancreas, YFPneg_8w_cell71


title: mouse_YFPpos_8w_cell74

description:
Single cell from mouse pancreas
A3.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell74


title: mouse_YFPpos_8w_cell69

description:
Single cell from mouse pancreas
C8.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell69


title: mouse_YFPpos_8w_cell85

description:
Single cell from mouse pancreas
A10.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell85


title: mouse_YFPpos_8w_cell72

description:
Single cell from mouse pancreas
B8.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell72


title: mouse_YFPpos_8w_cell73

description:
Single cell from mouse pancreas
D6.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell73


title: mouse_YFPpos_8w_cell70

description:
Single cell from mouse pancreas
B11.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell70


title: mouse_YFPpos_8w_cell75

description:
Single cell from mouse pancreas
C3.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell75


title: mouse_YFPpos_8w_cell66

description:
Single cell from mouse pancreas
B9.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell66


title: mouse_YFPpos_8w_cell65

description:
Single cell from mouse pancreas
B6.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell65


title: mouse_YFPpos_8w_cell62

description:
Single cell from mouse pancreas
C12.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell62


title: mouse_YFPpos_8w_cell67

description:
Single cell from mouse pancreas
D7.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell67


title: mouse_YFPpos_8w_cell68

description:
Single cell from mouse pancreas
A2.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell68


title: mouse_YFPpos_8w_cell61

description:
Single cell from mouse pancreas
D5.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell61


title: mouse_YFPpos_8w_cell63

description:
Single cell from mouse pancreas
A7.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell63


title: mouse_YFPpos_8w_cell64

description:
Single cell from mouse pancreas
A6.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell64


title: mouse_YFPneg_8w_cell58

description:
Single cell from mouse pancreas
F1.1000200101

source_name: Single cell from pancreas, YFPneg_8w_cell58


title: mouse_YFPpos_8w_cell57

description:
Single cell from mouse pancreas
A5.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell57


title: mouse_YFPpos_8w_cell55

description:
Single cell from mouse pancreas
C1.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell55


title: mouse_YFPpos_8w_cell59

description:
Single cell from mouse pancreas
B10.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell59


title: mouse_YFPpos_8w_cell54

description:
Single cell from mouse pancreas
D10.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell54


title: mouse_YFPpos_8w_cell56

description:
Single cell from mouse pancreas
A2.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell56


title: mouse_YFPpos_8w_cell60

description:
Single cell from mouse pancreas
D9.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell60


title: mouse_YFPpos_8w_cell52

description:
Single cell from mouse pancreas
D7.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell52


title: mouse_YFPpos_8w_cell53

description:
Single cell from mouse pancreas
C10.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell53


title: mouse_YFPpos_8w_cell51

description:
Single cell from mouse pancreas
A1.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell51


title: mouse_YFPpos_8w_cell48

description:
Single cell from mouse pancreas
A11.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell48


title: mouse_YFPpos_8w_cell47

description:
Single cell from mouse pancreas
C3.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell47


title: mouse_YFPpos_8w_cell49

description:
Single cell from mouse pancreas
D8.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell49


title: mouse_YFPpos_8w_cell50

description:
Single cell from mouse pancreas
A1.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell50


title: mouse_YFPpos_8w_cell46

description:
Single cell from mouse pancreas
A5.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell46


title: mouse_YFPpos_8w_cell44

description:
Single cell from mouse pancreas
A3.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell44


title: mouse_YFPpos_8w_cell45

description:
Single cell from mouse pancreas
D1.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell45


title: mouse_YFPneg_8w_cell43

description:
Single cell from mouse pancreas
E9.1000200102

source_name: Single cell from pancreas, YFPneg_8w_cell43


title: 77_FP_E17_5d_mZscan5B

description: processed data file: 77+78_FP_E17_5d_mZscan5B.ucsc.bigWig

data_processing:
Fastq files were generated with the software Casava 1.8.2 (Illumina).
Sequence data were aligned with Bowtie2 (Langmead et al 2009) to the Mus musculus mm9 genome, allowing 1 mismatch per read but otherwise using default settings.
Bowtie files were used to identify peaks using MACS software (version 14.2), with default settings.
The Bowtie files were also analyzed using the more sensitive HOMER software package (http://homer.salk.edu/homer/ngs/index.html) using default conditions for the TF setting and false discovery rate cutoffs of 0.1  After comparison of the individual files, sequence reads from the treatment samples were pooled and a final peak set determined in comparison to the genomic-input control.
Genome_build: mm9
Supplementary_files_format_and_content: BigWig files were generated using HOMER's makeBigWig.pl script with default settings.  Scores represent read depth.  BigWig files for the input represents the single sample.  The treatment BigWig file represents the pooled read depth for the two samples.

source_name: Mouse Fetal Placenta

growth_protocol: To obtain chromatin samples from mouse fetal placenta, pregnancies were identified in C57BL/6J females by detection vaginal plugs (day of plug detection is E0.5)

extract_protocol:
Viable cells were counted using hemocytometer and crosslinked with 4% paraformaldehyde (Electron Microscopy Sciences, PA) for 10 minutes at room temperature before nuclear isolation. Cross-linked chromatin was prepared and sonicated using Bioruptor UCD-200 in ice water bath to generate DNA fragments 200-300 bp in size. Twenty micrograms of each antibody preparation, or 20 µg IgG for mock pulldown controls, were incubated with chromatin prepared from nuclei of approximately 5 million cells.
DNA was released and quantitated using Qubit 2.0 (Life Technologies) with dsDNA HS Assay kit (Life Technologies, Q32854), and 15 ng of DNA was used to generate libraries for Illumina sequencing. ChIP-seq libraries were generated using KAPA LTP Library Preparation Kits (Kapa Biosystems, KK8232) to yield two independent ChIP replicates for the antibody. We also generated libraries from sonicated genomic input DNA from the same chromatin preparations as controls. Libraries were bar-coded with Bioo Scientific index adapters and sequenced to generate 15-23 million reads per duplicate sample using the Illumina Hi-Seq 2000 instrument at the University of Illinois W.M. Keck Center for Comparative and Functional Genomics according to manufacturer’s instructions.

treatment_protocol: Placentas were dissected at E17.5. After removing maternal decidua, samples were homogenized in cold PBS containing PIC using a loose-fitting Dounce homogenizer. Debris was removed using cell strainer (Fisher Scientific), and single cell suspension was washed twice with cold PBS.

tag: embryonic stage

value: Embryo at day 17.5

tag: background strain

tag: control or treatment

value: Treatment

tag: chip antibody


title: mouse_YFPpos_8w_cell41

description:
Single cell from mouse pancreas
D2.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell41


title: 78_FP_E17_5d_mZscan5B


title: 81_FP_E17_5d_input

value: Control


title: MeDIP_input_9

first: Gavin

last: Kelsey

address: Babraham Research Campus

institute: The Babraham Institute

description:
TruSeq9
processed data file: MeDIP_Input_1kb_tiles_readcount.txt

data_processing:
Libraries were sequenced on an Illumina HiSeq using the default RTA analysis software.
Raw Bisulfite-Seq reads were trimmed to remove both poor quality calls and adapters using Trim Galore version 0.2.5 (default parameters; www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Remaining Bisulfite-Seq reads were mapped using Bismark version 0.13.1 (default parameters), and CpG methylation calls were extracted using the Bismark methylation extractor (Krueger and Andrews, 2011).
MeDIP-Seq: Trimmed sequences were mapped to the mouse NCBIM37 genome using Bowtie 2 with default parameters.
Genome_build: NCBIM37
Supplementary_files_format_and_content: The Bismark CpG coverage report is tab-delimited, uses 1-based genomic coordinates for every covered cytosine position in the experiment and is in the following format: <chromosome>  <start position>  <end position>  <methylation percentage>  <count methylated>  <count non-methylated>
Supplementary_files_format_and_content: Quantitated MeDIP Input data file is tab delimited and contains read count over 1kb tiles within the following 12 columns: (1) Chromosome; (2) Start; (3) End; (4-12) log2 readcount for each sample

source_name: ES cells_non-bisulfute converted genomic DNA control

growth_protocol: ESCs were cultured without feeders in standard serum-containing media (DMEM 4500 mg/L glucose, 4 mM L-glutamine and 110 mg/L sodium pyruvate, 15% fetal bovine serum, 1 U/ml penicillin, 1 μg/ml streptomycin, 0.1mM nonessential amino acids, 50 uM beta-mercaptoethanol, 103 U/ml LIF ESGRO).

extract_protocol:
Genomic DNA was extracted with DNeasy Blood and Tissue Kit (Qiagen) following manufacturer’s instructions.
Full details can be found in Olova et al. (2016). BS-seq: DNA samples were fragmented by sonication (Covaris) and adaptor ligated (using Illumina supplied methylated adaptors and NEB Next library preparation kit). Subsequently, DNA was bisulfite-treated using the Imprint kit (Sigma), EpiTect kit (Qiagen), EZ DNA Methylation Kit (Zymo). Final library amplification (15 cycles) was done using Pfu Turbo Cx (Agilent) and iPCRtag primers, after which the libraries were purified with AMPure XP beads (Agencourt).
MeDIP-seq: DNA samples were fragmented by sonication (Covaris) and adaptor ligated (using Illumina TruSeq indexed adaptors and NEB Next library preparation kit). Subsequently, DNA samples were pooled, denatured and the input sample was sequenced directly without immuno-precipitation, after 6 cycles of amplification with NEB Next 2x Phusion mix and purification with AMPure XP beads (Agencourt).

treatment_protocol: In vitro DNA methylation with M.CviPI (NEB) was performed on 0.5 – 1.0 µg of TKO mESC genomic DNA, incubated for 2 hours at 37°C, purified with GeneJet PCR Purification kit (Thermo).

tag: strain background

value: 129/Ola derived

tag: genotype/variation

value: ES cells


title: mouse_YFPpos_8w_cell40

description:
Single cell from mouse pancreas
D3.1000200101

source_name: Single cell from pancreas, YFPpos_8w_cell40


title: mouse_YFPpos_8w_cell39

description:
Single cell from mouse pancreas
B5.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell39


title: MeDIP_input_6

description:
TruSeq6
processed data file: MeDIP_Input_1kb_tiles_readcount.txt

value: 129S4/SvJae derived


title: MeDIP_input_8

description:
TruSeq8
processed data file: MeDIP_Input_1kb_tiles_readcount.txt

value: 129/terSv derived


title: mouse_YFPpos_8w_cell36

description:
Single cell from mouse pancreas
A12.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell36


title: MeDIP_input_7

description:
TruSeq7
processed data file: MeDIP_Input_1kb_tiles_readcount.txt

value: Dnmt1,Dnmt3a,Dnmt3b-KO (triple KO)


title: mouse_YFPpos_8w_cell37

description:
Single cell from mouse pancreas
D12.1000200103

source_name: Single cell from pancreas, YFPpos_8w_cell37

value: YFPpos


title: mouse_YFPpos_8w_cell38

description:
Single cell from mouse pancreas
D11.1000200102

source_name: Single cell from pancreas, YFPpos_8w_cell38

value: endocrine pancreatic islet cell


title: MeDIP_input_4

description:
TruSeq4
processed data file: MeDIP_Input_1kb_tiles_readcount.txt


title: MeDIP_input_5

description:
TruSeq5
processed data file: MeDIP_Input_1kb_tiles_readcount.txt