title: RNA-seq, si ZEB2-2

status: Public on Jun 16 2017

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo

description: ZEB2 siRNA transfected

data_processing:
RNA-seq reads were trimmed down to 100 bases and processed by Tophat2 (version 2.0.10) and Bowtie2 (version 2.1.0) using hg19 version of index files. Parameters used are as follows: -a 6 --segment-length 25 --no-coverage-search --read-realign-edit-dist 0 -G.
FPKM calculation was performed by using Cuffdiff (cufflinks version 2.1.1, with option -u).
Genome_build: hg19
Supplementary_files_format_and_content: Expression data of the five samples were summarized into single processed file by Cuffdiff. Gene-level expressions are in genes.fpkm_tracking.txt.

growth_protocol: MDA-231-D human mammary gland triple-negative cancer cell line, a highly bone metastatic clone of MDA-MB-231, was established as described (Ehata et al., Cancer Sci 98: 127-133, 2007) and cultured in Dulbecco’s modified Eagle’s medium (DMEM: #11965, Thermo Fisher Scientific, Waltham, MA, USA).

extract_protocol:
Total RNAs were extracted as described previously (Mizutani et al., 2011, J Biol Chem).
Libraries were prepared using  Dynabeads mRNA DIRECT Purification Kit (Life Technologies) and Ion Total RNA-seq kit v2 (Thermo Scientific). Sequencing was performed as described (Sakurai et al., 2016, Oncogene).

treatment_protocol: MDA-231-D cells were transfected with siRNAs.

tag: sirna

value: ZEB1 siRNA (HSS190654, Thermo Fisher Scientific)

tag: tgf-beta treatment

value: no

tag: histology

value: basal type breast cancer


title: RNA-seq, si ZEB2-1

type: SRA

country: Japan

description: ZEB2 siRNA transfected

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

value: ZEB1 siRNA (HSS114854, Thermo Fisher Scientific)


title: Leaf wounded 24hr biological rep 2

status: Public on Jun 17 2017

city: Salt Lake City

first: Richard

middle: M

last: Clark

state: Utah

department: Department of Biology

country: USA

institute: University of Utah

description:
W24-2
13455X10

data_processing:
Following transfer of the flowcell to an Illumina HiSeq 2500 instrument (HCS v2.2.38 and RTA v1.18.61), a 125 cycle paired-end sequence run was performed using HiSeq SBS Kit v4 sequencing reagents (FC-401-4003), and the resulting reads were aligned to the Z. mays AGPv3 (Ensembl Release 31) reference genome with STAR 2.5.2b in two-pass alignment mode (alignments were independent of the existing reference annotation).
Read counts for genes (exonic features) in the AGPv3 (Ensembl Release 31) annotation were obtained using HTSeq 0.6.0 with --stranded reverse.
Genome_build: The AGPv3 genome sequence and annotation (Ensembl Release 31) were downloaded from the maize genome site at ensembl.org and used in the study.
Supplementary_files_format_and_content: Tab-delimited text file with counts of reads aligned per gene model as assessed with HTSeq (expression across all samples is included in the single processed data file).

organism: Zea mays

source_name: Leaf tissue

growth_protocol: The maize (Zea mays, B73 inbred) plants used for the experiments were germinated and grown in a greenhouse with an approximately 16h-light/8h-dark photoperiod at a temperature of about 25 degrees C. They were cultivated using SunGrow® Metro-Mix® 900 Grower Mix, watered as needed, and fertilized weekly with 200 ppm NutriCulture 16N-3P-16K.

extract_protocol:
Leaf tissue was ground to a fine powder in liquid nitrogen. Total RNA was prepared using the DirectZol RNA extraction kit (Zymo Research). Quality of the RNA extractions was assessed using a Bioanalyzer (Aligent).
The libraries were prepared at the University of Utah High Throughput Genomics facility using the Illumina TruSeq Stranded mRNA Library Preparation Kit with poly(A) selection.

treatment_protocol: The 4th leaves of 22-day-old maize plants were used for the experiment. Mite movement was restrained by barriers made of a non-toxic wax (TangleFoot). Mites were allowed to feed on both sides of a leaf section defined by TangleFoot barriers. The maize leaf sections were infested with healthy adult females, 400 mites per leaf section for 2hr-timepoints and 200 mites per leaf section for 24hr-timepoints. Wounding treatment was applied by rubbing 60 grit sand paper on both sides of the leaf. The control leaves received the TangleFoot barriers but none of the treatments. Mite infestation and wounding treatments were applied at 24hr and 2hr before sample collection. All samples were collected at the same time to limit the effects of the circadian cycle and any minor environmental differences on gene expression. Mite species used in the experiment were Tetranychus urticae, the two-spotted spider mite (TSSM), and Oligonychus pratensis, the Banks grass mite (BGM). Per treatment, a single plant (leaf) was used, and in total four biological replicates were collected per treatment.

tag: tissue

value: leaf

tag: Stage

value: V4-22 days old

tag: leaf number

value: leaf number 4

tag: cultivar

tag: mite species (treatment)


title: RNA-seq, si ZEB1-1

description: ZEB1 siRNA transfected

value: ZEB1 siRNA (HSS110548, Thermo Fisher Scientific)


title: RNA-seq, si ZEB1-2

description: ZEB1 siRNA transfected

value: ZEB1 siRNA (HSS186235, Thermo Fisher Scientific)


title: ZEB1 ChIP-seq, MCF7 cells

library_source: genomic

data_processing:
ChIP-seq reads were trimmed down to 50 bp and aligned to the hg19 genome assembly using bowtie (parameters: -a --best --strata -n 1 -m 1).
peaks were called using MACS2 (parameters: callpeak --bdg -q 0.05 or 0.0001).
Genome_build: hg19
Supplementary_files_format_and_content: bed (three files; peak regions and peak summit positions at q<0.05, and peak summit position at q<0.0001) and bw format files.

molecule: genomic DNA

growth_protocol: MCF7 human luminal type breast cancer cells were obtained from Japanese Collection of Research Bioresources (JCRB) Cell Bank (Ibaragi, Osaka, Japan) and cultured in DMEM (#11965, Thermo Fisher Scientific) with 0.01 mg/mL of insulin (12585-014, Thermo Fisher Scientific) and 10% fetal bovine serum (FBS), 100 units/ml penicillin G, and 100 μg/ml streptomycin. Cells were maintained in a 5% CO2 atmosphere at 37°C.

extract_protocol:
ChIP were performed as described (Koinuma et al, Mol Cell Biol 29: 172-186, 2009). ZEB1-DNA complexes were isolated with anti-ZEB1 antibody (NBP1-05987, Novus Biologicals, Minneapolis, MN, USA, lot number not available).
Libraries were prepared as described (Murai et al, Cell Discovery 1: 15026, 2015), using IonXpress Plus Fragment Library Kit (Thermo Fisher Scientific). Adaptor-ligated samples were amplified by 15 cycles of PCR and purified by E-Gel SizeSelect (Thermo Fisher Scientific).

treatment_protocol: Cells were treated with 1 ng/ml of TGF-beta3 for 1.5 h.

tag: zeb1 expression

value: negative

value: luminal type breast cancer

tag: ChIP


title: Leaf wounded 2hr biological rep 1

description:
W2-1
13455X7


title: RNA-seq_si ZEB1/ZEB2_TGF-beta treated

description: ZEB1/ZEB2 siRNAs transfected

data_processing:
RNA-seq reads were trimmed down to 100 bases and processed by Tophat2 (version 2.0.10) and Bowtie2 (version 2.1.0) using hg19 version of index files. Parameters used are as follows: -a 6 --segment-length 25 --no-coverage-search --read-realign-edit-dist 0 -G.
FPKM calculation was performed by using Cuffdiff (cufflinks version 2.1.1, with option -u).
Genome_build: hg19
Supplementary_files_format_and_content: Expression data of the four samples were summarized into single processed file by Cuffdiff. Gene-level expressions are in genes.fpkm_tracking.txt.

source_name: MDA-231-D_ZEB1/ZEB2 siRNAs transfected

treatment_protocol: MDA-231-D cells were transfected with siRNAs and treated with/without 1 ng/mL TGF-beta for 24 hours.

tag: cell line

tag: cell type

value: basal type breast cancer cell line

value: ZEB1, ZEB2 siRNAs (HSS110548 and HSS114854, Thermo Fisher Scientific)

value: 1 ng/ml for 24 h


title: mm10_p4

city: San Francisco

first: Aaron

last: Tward

address: 505 Parnassus AVE

institute: UCSF

description: from live organism

data_processing:
 indexed BAM file containing position-sorted reads aligned to the genome and transcriptome.
10X Genomics Cell Ranger pipeline
See their website for their proprietary steps
The web summaries for the experiments are attached as a guide to how the sequencing results turned out.
These are the web_summary.html files
Genome_build: mm10
Supplementary_files_format_and_content: The raw reads from the scRNA seq for each cell is the processed output:
E16_matrix.mtx is sparse matrix file of reads, the row and column names are attached together as E16_barcodes.tsv and E16_genes.tsv
P4_matrix.mtx is sparse matrix file of reads, the row and column names are attached together as P4_barcodes.tsv and P4_genes.tsv

molecule: total RNA

organism: Mus musculus

source_name: P4 lacrimal developmental cells

extract_protocol:
Murine LGs from timed-pregnant female mice (CD1; E16 and P4) were dissected and pooled together in PBS. A single cell suspension was created by incubating lacrimal glands in a PBS solution containing Liberase TM (Roche) and DNaseI (Roche) at 37 C for 20-40 min. The enzyme reaction was quenched by the addition of fetal calf serum and the solution was filtered through a 40 um strainer (BD Falcon) and centrifuged at 1500 rpm for 5 mins. Cell pellets were washed in PBS, centrifuged and resuspended in 0.04% BSA (ThermoFisher) at a cell density of 1000 cells/uL.
Isolate single cells for Drop seq technology to barcode.

tag: strain

value: lacrimal cells

tag: developmental stage


title: H3K4me1

city: LA TRONCHE

first: Mohamed-ali

last: HAKIMI

state: Grenoble

address: Domaine de la Merci, Campus Santé

country: France

institute: CNRS

data_processing:
Data Analysis: After the sequencing platform generated the sequencing images, the stages of image analysis and base calling were performed using Off-Line Basecaller software (OLB V1.8). After passing Solexa CHASTITY quality filter, the clean reads were aligned to Toxoplasma gondii reference genome (Tgo) using BOWTIE (V2.1.0). Aligned reads were used for peak calling of the ChIP regions using MACS V1.4.0. Statistically significant ChIP-enriched regions (peaks) were identified by comparison of two samples, using a p-value threshold of 10-5. Then the peaks in each sample were annotated by the overlapped gene using the newest Toxoplasma gondii database. The EXCEL/BED format file containing the ChIP-enriched regions was generated for each sample.
Data visualization: The mapped 100 bp reads represent enriched DNA fragments by ChIP experiment. Any region of interest in the raw ChIP-seq signal profile can be directly visualized in genome browser. We use 10-bp resolution intervals (10-bp bins) to partition the stacked reads region, and count the number of reads in each bin.  All the 10 bp resolution ChIP-seq profiles of each sample are saved as UCSC wig format files, which can be visualized in Toxoplasma gondii Genome Browser (http://protists.ensembl.org/Toxoplasma_gondii/Info/ Index).
Genome_build: Toxoplasma gondii genome (ME49 strain) file "ToxoDB-13.0_TgondiiME49_Genome.fasta" to upload at ToxoDB website : http://toxodb.org/common/downloads/release-13.0/TgondiiME49/fasta/data/
Supplementary_files_format_and_content: Statistically significant ChIP-enriched regions (peaks) were identified by comparison of two samples, using a p-value threshold of 10-5. Then the peaks in each sample were annotated by the overlapped gene using the newest Toxoplasma gondii database. The EXCEL/BED format file containing the ChIP-enriched regions was generated for each sample. We use 10-bp resolution intervals (10-bp bins) to partition the stacked reads region, and count the number of reads in each bin.  All the 10 bp resolution ChIP-seq profiles of each sample are saved as UCSC wig format files, which can be visualized in Toxoplasma gondii Genome Browser (http://protists.ensembl.org/Toxoplasma_gondii/Info/ Index).

organism: Toxoplasma gondii

source_name: intracellular parasites

growth_protocol: Toxoplasma gondii type II strain Pruku80 was maintained by serial passage Human foreskin fibroblast (HFF) monolayer under tachyzoite conditions in DMEM (Life) supplemented with 10% (vol/vol) FBS (Life) and 25 mM Hepes buffer, pH 7.2.

extract_protocol:
Crosslinked chromatin was lysed in ice-cold lysis buffer (50mM HEPES KOH pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5%NP-40, 0.125% triton X-100, protease inhibitor cocktail) and sheared in shearing buffer (1mM EDTA pH8.0, 0.5mM EGTA pH8.0, 10mM Tris pH8.0, protease inhibitor cocktail) by sonication using a Diagenode Biorupter. Samples were sonicated, for 16 cycles (30 seconds ON and 30 seconds OFF), to 200-500 base-pair average size. Immunoprecipitation was carried out using sheared chromatin, 5% BSA, protease inhibitor cocktail, 10% triton X-100, 10% deoxycholate, DiaMag Protein A-coated magnetic beads (Diagenode) and antibodies (H4K31ac, H4K31me1, pan acetyl H4, H4K20me3, H3K9me3, H3K4me3, H3K4me1, H3K14ac). A rabbit IgG antiserum was used as a control mock. After overnight incubation at 4°C on rotating wheel, chromatin-antibody complexes were washed and eluted from beads by using iDeal ChIP-seq kit for Histones (Diagenode) according to the manufacturer’s protocol. Samples were decrosslinked by heating for 4 hours at 65°C. DNA was purified by using IPure kit (Diagenode) and quantified by using Qubit Assays (Thermo Fisher Scientific) according to the manufacturer's protocol. For ChIP-seq, purified DNA was used to prepare libraries and then sequenced by Arraystar (USA, http://www.arraystar.com/ ).
ChIP-Sequencing library preparation was performed according to Illumina’s protocol Preparing Samples for ChIP Sequencing of DNA. Library Preparation: 10 ng DNA of each sample was converted to phosphorylated blunt-ended with T4 DNA polymerase, Klenow polymerase and T4 polymerase (NEB); An ‘A’ base was added to the 3' end of the blunt phosphorylated DNA fragments using the polymerase activity of Klenow (exo minus) polymerase (NEB); Illumina's genomic adapters were ligated to the A tailed DNA fragments; PCR amplification was performed to enrich ligated fragments using Phusion High Fidelity PCR Master Mix with HF Buffer (Finnzymes Oy). The enriched product of ~200-700 bp was cut out from gel and purified. Sequencing:  The library was denatured with 0.1M NaOH to generate single-stranded DNA molecules, and loaded onto channels of the flow cell at 8pM concentration, amplified in situ using TruSeq Rapid SR cluster kit (#GD-402-4001, Illumina). Sequencing was carried out by running 100 cycles on Illumina HiSeq 4000 according to the manufacturer’s instructions.

treatment_protocol: HFF cells were grown to confluence and infected with Pru∆ku80 strain. Harvested intracellular parasites were crosslinked with formaldehyde (final concentration 1%) for 8 mins at room temperature and the crosslinking was stopped by addition of glycine (final concentration 0.125M) for 5 min at room temperature.

value: Type II (Pruku80)

tag: chip antibody

value: H3K4me1 (Diagenode)

tag: dev. stage

value: tachyzoites


title: RNA-seq_si Negative control

description: control siRNA transfected

source_name: MDA-231-D_control siRNA transfected

value: Negative control siRNA (12935-112, Thermo Fisher Scientific)

value: no


title: RNA-seq_si Negative control_TGF-beta treated

description: control siRNA transfected


title: ZEB1 ChIP-seq, Hs578T cells

growth_protocol: MDA-231-D human mammary gland triple-negative cancer cell line, a highly bone metastatic clone of MDA-MB-231, was established as described (Ehata et al., Cancer Sci 98: 127-133, 2007) and cultured in Dulbecco’s modified Eagle’s medium (DMEM: #11965, Thermo Fisher Scientific, Waltham, MA, USA). Hs578T human triple-negative breast cancer cells were obtained from American Type Culture Collection (ATCC) (Manassas, VA, USA) for this research and cultured in RPMI1640 (#11875, Thermo Fisher Scientific) with 0.01 mg/mL of insulin (12585-014, Thermo Fisher Scientific).

value: basal type breast cancer

value: positive

tag: treated with

value: 1 ng/ml of TGF-beta3 for 1.5 h


title: mm10_e16

description: from live organism

source_name: E16 lacrimal developmental cells


title: NOD_pLN_DCs_3wk_4

city: St. Louis

first: Javier

middle: A

last: Carrero

state: MO

address: 660 S Euclid Ave Box 8118

department: Pathology and Immunology

description: Barcode: TGATTAC

data_processing:
We assessed average quality of sequencing reads for base pair positions in each sample using the fastqс utility from fastq-tools (Droop, 2016). Samples with a quality score less than 25 (Sanger / Illumina 1.9 encoding) across all bases were truncated with fastx_trimmer utility, removing base pairs from the end of each read in the library. All libraries were aligned to the GRCm38.p4 assembly of the mouse genome using the STAR aligner (Dobin et al., 2013) with Gencode vM7 (Harrow et al., 2012) transcripts included into the pre-generated reference. We generated raw counts of the number of tags on each gene by using htseq-count utility from HTseq package (Anders et al., 2015). Gencode vM7 (with –t exon option) was used as a reference GTF. DESeq2 package (Version 1.6.3) (Love et al., 2014) was used to detect differentially expressed genes between the analyzed conditions (output with a P<0.05, and Benjamini–Hochberg false discovery rate (FDR) of 5% was used). Variance between samples was stabilized for the purposes of hierarchical clustering and PCA to address the problem of heteroskedasticity (dependence of variance on the mean counts). Pathways analysis was done using the Broad Institute’s GSEA software (Subramanian et al., 2005). All heat maps are in log2 scale.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: Expression_table.txt

source_name: pLN dendritic cells

extract_protocol:
Islets were harvested as described previously (Calderon et al., 2015) and dispersed using Cell Dissociation Solution Non-Enzymatic (Sigma-Aldrich, St. Louis, MO) for 5 min at 37°C. Pancreatic lymph nodes and lungs were harvested, finely chopped with scissors, placed in Dulbecco’s modified Eagle’s medium (DMEM; Life Technologies, Carlsbad, CA) containing 125 ug/mL Liberase TL (Roche Life Sciences, Indianapolis, IN) and 50 ug/mL DNase I, grade II (Roche) and incubated at 37°C for 30 minutes and dispersed via gentle agitation. Single-cell suspensions incubated in PBS, pH 7.4 (Life Technologies) having 1% bovine serum albumin (BSA, Sigma), and 50% of 2.4G2 conditioned DMEM at 4°C for 15 min to block Fc receptors. Cells were stained with fluorescently labeled antibodies and sorted on a FACSAria II or analyzed on the FACSCanto II (BD Biosciences). Macrophages were sorted based on their expression of CD45, F4/80 and I-Ag7. DC were selected based on their expression of XCR1. In all cases CD3e+ and CD19+ events were eliminated from the sort (dump gated). For cell sorting experiments, approximately 500-5000 macrophages were isolated from 6-10 mice and this represented 1 biological sample in our analysis. At least 3 samples were used for each population studied by RNAseq analysis. All flow cytometry data was analyzed using FlowJo software version 10.2 (Tree Star Software, Ashland, OR).
Sorted cell RNA was isolated using the Ambion RNAqueous-Micro Kit (Life Technologies) following the manufacturer’s instructions
Library preparation was performed with 1-50 ng of total RNA, integrity was determined using an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA).  ds-cDNA was prepared using the SeqPlex RNA Amplification Kit (Sigma) per manufacturer’s protocol.  cDNA was blunt ended, had an adenosine added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-2500 using single reads extending 50 bases. All RNAseq work was performed by the Genome Technology Access Center at Washington University School of Medicine.

value: pancreatic LN

value: NOD/ShiLtJ

tag: age

value: 3 wks


title: NOD_pLN_DCs_3wk_5

institute: Washington University School of Medicine

description: Barcode: TTGCCCC


title: NOD_pLN_DCs_3wk_3

description: Barcode: TACATGG


title: NOD_Lung_3wk_1

description: Barcode: ACCATAC

source_name: lung macrophage

value: lung


title: NOD_Lung_3wk_4

description: Barcode: GATAGTT


title: NOD_Lung_3wk_3

description: Barcode: CTCAATG


title: NOD_pLN_DCs_3wk_1

description: Barcode: CACCTCC


title: NOD_Lung_3wk_2

description: Barcode: CGAAAGT


title: NOD_pLN_DCs_3wk_2

description: Barcode: CTGGTGG


title: B6g7_islet_3wk_3

description: Barcode: TCCGGGA

source_name: islet macrophage

value: pancreatic islets


title: B6g7_islet_3wk_2

description: Barcode: CTCACCC


title: B6g7_islet_3wk_1

description: Barcode: ACTGGAT


title: NODRAG_islet_3wk_3

description: Barcode: TGTTTGT


title: RNA-seq_si ZEB1/ZEB2

description: ZEB1/ZEB2 siRNAs transfected

value: basal type breast cancer cell line

tag: sirna

tag: tgf-beta treatment


title: NODRAG_islet_3wk_2

description: Barcode: GGTCCTC

tag: tissue


title: NOD_islet_3wk_3

description: Barcode: AGACTGA


title: NOD_islet_3wk_4

description: Barcode: TTCGCTG


title: NOD_islet_3wk_2

description: Barcode: ACAGATA


title: NODRAG_islet_3wk_1

description: Barcode: CCGGACC


title: NOD_islet_3wk_1

description: Barcode: GAGGCGT


title: ES_single_cell_RNA_16

city: Guangzhou

first: Lin

last: Li

address: Shatai South Road

department: Pathophysiology

country: China

institute: Southern Medical University

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
For COOL-Seq, raw reads were trimmed to remove the first 9 bases and remove the adapter-contaminated and low-quality reads using Trim Galore (v0.3.3). And for RNA-seq, reads were trimmed to remove the adapter and low quality bases with customized scripts.
For COOL-Seq, the cleaned reads were then aligned to the in silico bisulfite-converted mouse genome reference (mm9) using Bismark (v0.7.6) with paired-end and non-directional mapping parameters. After paired-end mapping, the unmapped reads were re-aligned to the same reference genome in single-end mode. Duplicated reads were excluded using SAMtools (v0.1.18) and then used for the subsequent analysis. And for RNA-seq, the cleaned reads were aligned to the mouse reference (mm9) using Tophat (v2.0.12) with default settings (Trapnell et al., 2009).
WCG and GCH methylation level of cytosines was estimated using customized scripts.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files which include the methylation level of cytosines in WCG and GCH context respectively, and txt files which include the RPKM (reads per kilobase transcriptome per million reads) values of RefSeq genes.

source_name: Embryonic stem cell

extract_protocol:
The released genomic DNA were used to construct the PBAT library, as previously described (Guo et al., 2015; Smallwood et al., 2014). Single-cell RNA-seq was performed under standard Smart-seq2 protocol. Bulk cells RNA-seq were performed under the instruction of mRNA library construction kit (NEB).
Briefly, the single-cell genomic DNA, together with unmethylated lambda DNA (New England Biolabs) spike-ins, were subjected to bisulfite conversion using a MethylCode Bisulfite Conversion Kit (Invitrogen) according to the manufacturer’s instructions. The bisulfite converted DNAs were then annealed using random nonamer primers with a 5’- biotin tag and a truncated Illumina P5 adaptor (5’-biotin- CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) supplemented with 50 units of klenow polymerase (3’ to 5’ exo-, New England Biolabs). The excess primers were removed using 40 U exonuclease I (NEB) before DNA was purified using 0.8× Agencourt Ampure XP beads (Beckman Coulter). Then, the newly synthesized DNA strands were immobilized using the Dynabeads M280 Streptavidin (Invitrogen), and the original bisulfite-treated DNA templates were removed via two rounds of 0.1 N NaOH washes. The second strands were synthesized using 50 units klenow polymerase with random nonamer primers containing a truncated P7 Illumina adaptor (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’). The beads were further collected and washed several times, and the library was generated with 13 cycles of PCR amplifications using 1 U Kapa HiFi HS DNA Polymerase (Kapa Biosystems), together with 0.4 μM Illumina Forward PE1.0 primer (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and 0.4 μM pre-indexed Illumina Reverse primer (5’-CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’; the underlined hexamer indicates the index sequences).  Amplified libraries were purified with 0.8× Agencourt Ampure XP beads twice and were assessed on the Agilent Bioanalyzer 2100 platform and quantified with a standard curve-based qPCR assay (Kapa Biosystems). The final quality- ensured libraries were pooled and sequenced on the Illumina HiSeq2500 sequencer for 150 bp paired-end sequencing.
Bisulfite-Seq and RNA-Seq

value: Embryonic stem cell

tag: passages / stage


title: ES_single_cell_RNA_15


title: ES_single_cell_RNA_14


title: RNA-seq siNC, si Negative control

description: control siRNA transfected

tag: histology


title: ZEB1 ChIP-seq, MDA-231-D cells

value: human mammary gland triple-negative cancer cell line


title: ES_bulk_cells_RNA_2


title: ES_bulk_cells_RNA_1


title: ES_1000cells_6


title: ES_1000cells_5


title: ES_1000cells_4


title: ES_single_cell_RNA_8


title: ES_single_cell_RNA_7


title: ES_1000cells_2


title: ES_single_cell_RNA_1


title: ES_single_cell_RNA_4


title: ES_single_cell_RNA_11


title: ES_single_cell_RNA_2


title: ES_single_cell_RNA_9


title: ES_single_cell_RNA_13


title: ES_1000cells_3


title: ES_single_cell_RNA_5


title: ES_single_cell_RNA_12


title: ES_100cells_5


title: ES_100cells_6


title: ES_1000cells_1


title: ES_single_cell_RNA_10


title: ES_100cells_4


title: ES_single_cell_RNA_6


title: ES_100cells_2


title: ES_bulk_cells_RNA_3


title: ES_100cells_1


title: ES_10cells_3


title: ES_single_cell_RNA_3


title: ES_10cells_2


title: ES_100cells_3


title: ES_10cells_1


title: alpha-Amanitin_Zygote_single_cell_8

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Raw reads were trimmed to remove the first 9 bases and remove the adapter-contaminated and low-quality reads using Trim Galore (v0.3.3).
The cleaned and QC-ensured reads were then aligned to the in silico bisulfite-converted mouse genome reference (mm9) using Bismark (v0.7.6) with paired-end and non-directional mapping parameters. After paired-end mapping, the unmapped reads were re-aligned to the same reference genome in single-end mode. Duplicated reads were excluded using SAMtools (v0.1.18) and then used for the subsequent analysis.
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files which include the methylation level of cytosines in WCG and GCH context respectively

source_name: Mouse zygote

extract_protocol:
The released genomic DNA were used to construct the PBAT library, as previously described (Guo et al., 2015; Smallwood et al., 2014).
Briefly, the single-cell genomic DNA, together with unmethylated lambda DNA (New England Biolabs) spike-ins, were subjected to bisulfite conversion using a MethylCode Bisulfite Conversion Kit (Invitrogen) according to the manufacturer’s instructions. The bisulfite converted DNAs were then annealed using random nonamer primers with a 5’- biotin tag and a truncated Illumina P5 adaptor (5’-biotin- CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) supplemented with 50 units of klenow polymerase (3’ to 5’ exo-, New England Biolabs). The excess primers were removed using 40 U exonuclease I (NEB) before DNA was purified using 0.8× Agencourt Ampure XP beads (Beckman Coulter). Then, the newly synthesized DNA strands were immobilized using the Dynabeads M280 Streptavidin (Invitrogen), and the original bisulfite-treated DNA templates were removed via two rounds of 0.1 N NaOH washes. The second strands were synthesized using 50 units klenow polymerase with random nonamer primers containing a truncated P7 Illumina adaptor (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’). The beads were further collected and washed several times, and the library was generated with 13 cycles of PCR amplifications using 1 U Kapa HiFi HS DNA Polymerase (Kapa Biosystems), together with 0.4 μM Illumina Forward PE1.0 primer (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and 0.4 μM pre-indexed Illumina Reverse primer (5’-CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’; the underlined hexamer indicates the index sequences).  Amplified libraries were purified with 0.8× Agencourt Ampure XP beads twice and were assessed on the Agilent Bioanalyzer 2100 platform and quantified with a standard curve-based qPCR assay (Kapa Biosystems). The final quality- ensured libraries were pooled and sequenced on the Illumina HiSeq2500 sequencer for 150 bp paired-end sequencing.

value: Zygote


title: alpha-Amanitin_Zygote_single_cell_6


title: alpha-Amanitin_Zygote_single_cell_7


title: alpha-Amanitin_Zygote_single_cell_5


title: alpha-Amanitin_Zygote_single_cell_4


title: alpha-Amanitin_Zygote_single_cell_2


title: F129sv_MB6_4-Cell_embryo1_single_cell_4

source_name: Mouse 4-cell blastomere

value: 4-cell embryo


title: F129sv_MB6_2-Cell_embryo6_single_cell_1

source_name: Mouse 2-cell blastomere

value: 2-cell embryo


title: F129sv_MB6_4-Cell_embryo2_single_cell_1


title: F129sv_MB6_4-Cell_embryo1_single_cell_3


title: F129sv_MB6_4-Cell_embryo2_single_cell_3


title: F129sv_MB6_4-Cell_embryo1_single_cell_2


title: F129sv_MB6_2-Cell_embryo5_single_cell_1


title: alpha-Amanitin_Zygote_single_cell_1


title: F129sv_MB6_4-Cell_embryo1_single_cell_1


title: F129sv_MB6_4-Cell_embryo2_single_cell_2


title: F129sv_MB6_2-Cell_embryo4_single_cell_1


title: F129sv_MB6_2-Cell_embryo4_single_cell_2


title: F129sv_MB6_2-Cell_embryo3_single_cell_1


title: ctES_single_cell_9

description: As a control, we performed in vitro DNA methylation of naked genomic DNA of individual ES cells.


title: ctES_single_cell_10


title: F129sv_MB6_2-Cell_embryo2_single_cell_1


title: F129sv_MB6_2-Cell_embryo1_single_cell_2


title: ctES_single_cell_8


title: F129sv_MB6_2-Cell_embryo1_single_cell_1


title: ctES_single_cell_7


title: alpha-Amanitin_Zygote_single_cell_3


title: ctES_single_cell_6


title: F129sv_MB6_2-Cell_embryo5_single_cell_2


title: F129sv_MB6_2-Cell_embryo3_single_cell_2


title: ctES_single_cell_4


title: ctES_single_cell_5


title: ctES_single_cell_3


title: F129sv_MB6_2-Cell_embryo2_single_cell_2


title: ctES_single_cell_1


title: TE_embryo3_single_cell_5

source_name: Mouse blastocyst

value: Trophoectoderm cells

value: Blastocyst


title: TE_embryo3_single_cell_4


title: TE_embryo3_single_cell_2


title: TE_embryo3_single_cell_3


title: TE_embryo3_single_cell_1


title: TE_embryo2_single_cell_1


title: TE_embryo1_single_cell_2


title: TE_embryo1_single_cell_1


title: TE_embryo1_single_cell_3


title: TE_single_cell_11


title: ICM_embryo3_single_cell_4

value: Inner cell mass


title: ICM_embryo2_single_cell_3


title: ICM_embryo3_single_cell_1


title: ICM_embryo3_single_cell_2


title: ICM_embryo3_single_cell_3


title: ICM_embryo1_single_cell_4


title: ICM_embryo2_single_cell_1


title: ICM_embryo2_single_cell_2


title: ICM_embryo1_single_cell_3


title: ICM_embryo1_single_cell_1


title: ICM_embryo1_single_cell_2


title: ctES_single_cell_2


title: Morula_embryo7_single_cell_2

source_name: Mouse morula blastomere

value: Morula


title: Morula_embryo7_single_cell_3


title: TE_embryo1_single_cell_4


title: Morula_embryo7_single_cell_1


title: Morula_embryo6_single_cell_1


title: Morula_embryo5_single_cell_3


title: Morula_embryo5_single_cell_2


title: Morula_embryo5_single_cell_1


title: Morula_embryo4_single_cell_1


title: 8-Cell_embryo10_single_cell_1

source_name: Mouse 8-cell blastomere

value: 8-cell embryo


title: 8-Cell_embryo8_single_cell_1


title: 8-Cell_embryo8_single_cell_2


title: 8-Cell_embryo10_single_cell_2


title: 8-Cell_embryo9_single_cell_1


title: 8-Cell_embryo7_single_cell_2


title: 8-Cell_embryo7_single_cell_3


title: 8-Cell_embryo7_single_cell_4


title: 8-Cell_embryo6_single_cell_4


title: 8-Cell_embryo7_single_cell_1


title: 8-Cell_embryo6_single_cell_3


title: 8-Cell_embryo6_single_cell_2


title: Morula_embryo6_single_cell_2


title: 8-Cell_embryo5_single_cell_4


title: 8-Cell_embryo6_single_cell_1


title: 8-Cell_embryo5_single_cell_2


title: 8-Cell_embryo5_single_cell_3


title: 8-Cell_embryo5_single_cell_1


title: 2nd-Pb_single_cell_6

source_name: Mouse 2nd polar body

value: 2nd polar body


title: 2nd-Pb_single_cell_5


title: 2nd-Pb_single_cell_4


title: 2nd-Pb_single_cell_3


title: 2nd-Pb_single_cell_2


title: 2nd-Pb_single_cell_1


title: Morula_embryo4_single_cell_2


title: 1st-Pb_single_cell_10

source_name: Mouse 1st polar body

value: 1st polar body

value: MII oocyte


title: 1st-Pb_single_cell_9


title: 1st-Pb_single_cell_11


title: 1st-Pb_single_cell_6


title: 1st-Pb_single_cell_3


title: 1st-Pb_single_cell_5


title: 1st-Pb_single_cell_4


title: 1st-Pb_single_cell_2


title: 1st-Pb_single_cell_7


title: 1st-Pb_single_cell_1


title: TE_single_cell_5

data_processing:
Illumina CASAVA version 1.8 were used to the basecalling.
Reads were trimmed to remove the adapter sequences and low quality bases.
Bisulfite-converted reads were aligned to the mouse refference genome (mm9) using Bismark software (v0.7.6)
WCG and GCH methylation level of cytosines was estimated using comstomized scripts.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files which include the methylation level of cytosines in WCG and GCH context respectively

source_name: blastocyst


title: TE_single_cell_9


title: TE_single_cell_6


title: TE_single_cell_7


title: TE_single_cell_10


title: TE_single_cell_8


title: TE_single_cell_3


title: TE_single_cell_2


title: TE_single_cell_1


title: ICM_single_cell_12


title: TE_single_cell_4


title: 1st-Pb_single_cell_8


title: ICM_single_cell_8


title: ICM_single_cell_7


title: ICM_single_cell_6


title: ICM_single_cell_9


title: ICM_single_cell_5


title: ICM_single_cell_10


title: ICM_single_cell_4


title: ICM_single_cell_3


title: ICM_single_cell_1


title: Morular_embryo2_single_cell_4

source_name: morula blastomere


title: Morular_embryo3_single_cell_1


title: Morular_embryo2_single_cell_2


title: ICM_single_cell_11


title: Morular_embryo2_single_cell_1


title: Morular_embryo1_single_cell_5


title: Morular_embryo1_single_cell_6


title: Morular_embryo1_single_cell_2


title: 8-Cell_embryo4_single_cell_3

source_name: 8-cell blastomere


title: Morular_embryo1_single_cell_1


title: Morular_embryo1_single_cell_3


title: 8-Cell_embryo4_single_cell_2


title: 8-Cell_embryo4_single_cell_1


title: 8-Cell_embryo3_single_cell_7


title: 8-Cell_embryo3_single_cell_8


title: 8-Cell_embryo3_single_cell_6


title: 8-Cell_embryo3_single_cell_5


title: 8-Cell_embryo3_single_cell_3


title: 8-Cell_embryo3_single_cell_1


title: ICM_single_cell_2


title: 8-Cell_embryo3_single_cell_4


title: 8-Cell_embryo3_single_cell_2


title: 8-Cell_embryo2_single_cell_2


title: Morular_embryo3_single_cell_2


title: 8-Cell_embryo2_single_cell_4


title: 8-Cell_embryo2_single_cell_3


title: 8-Cell_embryo1_single_cell_4


title: Morular_embryo2_single_cell_3


title: 8-Cell_embryo2_single_cell_1


title: Morular_embryo1_single_cell_4


title: 8-Cell_embryo1_single_cell_2


title: 8-Cell_embryo1_single_cell_1


title: 4-Cell_embryo8_single_cell_4

source_name: 4-cell blastomere


title: 4-Cell_embryo8_single_cell_3


title: 4-Cell_embryo8_single_cell_2


title: 4-Cell_embryo8_single_cell_1


title: 4-Cell_embryo7_single_cell_1


title: 4-Cell_embryo7_single_cell_4


title: 4-Cell_embryo6_single_cell_4


title: 4-Cell_embryo7_single_cell_3


title: 4-Cell_embryo7_single_cell_2


title: 4-Cell_embryo6_single_cell_3


title: 4-Cell_embryo6_single_cell_2


title: 4-Cell_embryo3_single_cell_3


title: 4-Cell_embryo2_single_cell_3


title: 4-Cell_embryo3_single_cell_2


title: 4-Cell_embryo3_single_cell_1


title: 4-Cell_embryo4_single_cell_1


title: 4-Cell_embryo1_single_cell_2


title: 4-Cell_embryo1_single_cell_1


title: 4-Cell_embryo1_single_cell_3


title: 2-Cell_embryo15_single_cell_1

source_name: 2-cell blastomere


title: 4-Cell_embryo5_single_cell_1


title: 4-Cell_embryo2_single_cell_2


title: 4-Cell_embryo2_single_cell_1


title: 8-Cell_embryo1_single_cell_3


title: 2-Cell_embryo13_single_cell_1


title: 2-Cell_embryo13_single_cell_2


title: 2-Cell_embryo14_single_cell_2


title: 2-Cell_embryo14_single_cell_1


title: 2-Cell_embryo12_single_cell_1


title: 2-Cell_embryo11_single_cell_2


title: 2-Cell_embryo11_single_cell_1


title: 2-Cell_embryo10_single_cell_1


title: 2-Cell_embryo10_single_cell_2


title: 4-Cell_embryo6_single_cell_1


title: 2-Cell_embryo8_single_cell_1


title: 2-Cell_embryo9_single_cell_1


title: 2-Cell_embryo9_single_cell_2


title: 2-Cell_embryo7_single_cell_1


title: 2-Cell_embryo8_single_cell_2


title: 2-Cell_embryo5_single_cell_2


title: 2-Cell_embryo3_single_cell_1


title: 2-Cell_embryo4_single_cell_2


title: 2-Cell_embryo5_single_cell_1


title: 2-Cell_embryo4_single_cell_1


title: 2-Cell_embryo12_single_cell_2


title: 2-Cell_embryo1_single_cell_1


title: 2-Cell_embryo1_single_cell_2


title: 2-Cell_embryo2_single_cell_1


title: Zygote_single_cell_18

source_name: zygote


title: Zygote_single_cell_17


title: Zygote_single_cell_16


title: Zygote_single_cell_15


title: Zygote_single_cell_13


title: Zygote_single_cell_12


title: Zygote_single_cell_11


title: 2-Cell_embryo6_single_cell_1


title: Zygote_single_cell_8


title: Zygote_single_cell_7


title: Zygote_single_cell_9


title: Zygote_single_cell_10


title: Zygote_single_cell_5


title: Zygote_single_cell_6


title: Zygote_single_cell_4


title: Zygote_single_cell_1


title: Zygote_single_cell_3


title: 2-Cell_embryo2_single_cell_2


title: Zygote_single_cell_2


title: Female-PN_single_cell_13

source_name: female pronuclei

value: Female pronuclei


title: Female-PN_single_cell_12


title: Female-PN_single_cell_11


title: Zygote_single_cell_14


title: Female-PN_single_cell_8


title: Female-PN_single_cell_9


title: Female-PN_single_cell_7


title: Female-PN_single_cell_10


title: Female-PN_single_cell_4


title: Female-PN_single_cell_6


title: Female-PN_single_cell_5


title: Male-PN_single_cell_9

source_name: male pronuclei

value: Male pronuclei


title: Female-PN_single_cell_3


title: Female-PN_single_cell_2


title: Female-PN_single_cell_1


title: Male-PN_single_cell_10


title: Male-PN_single_cell_7


title: Male-PN_single_cell_8


title: Male-PN_single_cell_6


title: Male-PN_single_cell_3


title: Male-PN_single_cell_5


title: Male-PN_single_cell_2


title: Male-PN_single_cell_1


title: Oocyte_single_cell_11

source_name: oocyte

value: Oocyte


title: Male-PN_single_cell_4


title: Oocyte_single_cell_7


title: Oocyte_single_cell_8


title: Oocyte_single_cell_9


title: Oocyte_single_cell_6


title: Oocyte_single_cell_12


title: Oocyte_single_cell_5


title: Oocyte_single_cell_4


title: Oocyte_single_cell_3


title: Sperm_bulk_cells_2_rep3

source_name: sperm

value: Sperm

value: Mature sperm


title: Oocyte_single_cell_2


title: Sperm_bulk_cells_3_rep3


title: Sperm_bulk_cells_2_rep2


title: Oocyte_single_cell_1


title: Sperm_bulk_cells_2_rep1


title: Sperm_bulk_cells_3_rep2


title: Sperm_bulk_cells_1_rep1


title: Sperm_bulk_cells_1_rep3


title: ES_single_cell_24

source_name: Embryonic stem cell

value: Embryonic stem cell


title: Oocyte_single_cell_13


title: ES_single_cell_22


title: Sperm_bulk_cells_1_rep2


title: Oocyte_single_cell_10


title: ES_single_cell_23


title: ES_single_cell_20


title: ES_single_cell_19


title: ES_single_cell_18


title: ES_single_cell_14


title: ES_single_cell_15


title: ES_single_cell_13


title: ES_single_cell_11


title: Sperm_bulk_cells_3_rep1


title: ES_single_cell_12


title: ES_single_cell_10


title: ES_single_cell_5


title: ES_single_cell_4


title: ES_single_cell_8


title: ES_single_cell_7


title: ES_single_cell_9


title: ES_single_cell_6


title: ES_bulk_cells_3


title: ES_bulk_cells_2


title: ES_bulk_cells_4


title: ES_single_cell_21


title: ES_bulk_cells_1


title: ES_single_cell_3

extract_protocol:
The released genomic DNA were used to construct the PBAT library, as previously described (Guo et al., 2015; Smallwood et al., 2014).
Briefly, the single-cell genomic DNA, together with unmethylated lambda DNA (New England Biolabs) spike-ins, were subjected to bisulfite conversion using a MethylCode Bisulfite Conversion Kit (Invitrogen) according to the manufacturer’s instructions. The bisulfite converted DNAs were then annealed using random nonamer primers with a 5’- biotin tag and a truncated Illumina P5 adaptor (5’-biotin- CTACACGACGCTCTTCCGATCTNNNNNNNNN-3’) supplemented with 50 units of klenow polymerase (3’ to 5’ exo-, New England Biolabs). The excess primers were removed using 40 U exonuclease I (NEB) before DNA was purified using 0.8× Agencourt Ampure XP beads (Beckman Coulter). Then, the newly synthesized DNA strands were immobilized using the Dynabeads M280 Streptavidin (Invitrogen), and the original bisulfite-treated DNA templates were removed via two rounds of 0.1 N NaOH washes. The second strands were synthesized using 50 units klenow polymerase with random nonamer primers containing a truncated P7 Illumina adaptor (5’-AGACGTGTGCTCTTCCGATCTNNNNNNNNN-3’). The beads were further collected and washed several times, and the library was generated with 13 cycles of PCR amplifications using 1 U Kapa HiFi HS DNA Polymerase (Kapa Biosystems), together with 0.4 μM Illumina Forward PE1.0 primer (5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3’) and 0.4 μM pre-indexed Illumina Reverse primer (5’-CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’; the underlined hexamer indicates the index sequences). Amplified libraries were purified with 0.8× Agencourt Ampure XP beads twice and were assessed on the Agilent Bioanalyzer 2100 platform and quantified with a standard curve-based qPCR assay (Kapa Biosystems). The final quality- ensured libraries were pooled and sequenced on the Illumina HiSeq2500 sequencer for 150 bp paired-end sequencing.


title: ES_single_cell_2


title: ES_single_cell_1


title: ES_single_cell_17


title: ES_single_cell_16


title: T-93 miRNA-seq

city: Vancouver

first: Daiana

middle: D.

last: Becker-Santos

state: BC

address: 675 West 10th Avenue

department: Integrative Oncology

country: Canada

institute: British Columbia Cancer Research Centreb

description: micro-dissected for >80% tumor cell content

data_processing:
Reads were filtered and aligned to NCBI GRCh37 reference genome and miRBase v18 using the BWA algorithm as previously described [TCGA: Comprehensive molecular portraits of human breast tumours. Nature 2012, 490(7418):61-70]
Genome_build: NCBI GRCh37 reference genome and miRBase v18
Supplementary_files_format_and_content: Excel file containing normalized miRNA expression values (reads per kilobase per million (RPKM)) for 77 libraries

source_name: lung adenocarcinoma tumor

extract_protocol:
Fresh-frozen NSCLC  tumor and patient matched non-malignant lung parenchymal tissues were collected from treatment naive patients; Tissue microdissection was guided by a lung pathologist to ensure >80% tumor cell or >80% non-malignant cell content. Total RNA was extracted using Trizol reagent
Full description of library construction, sequencing, read pre-processing, alignment and annotation are previously described [TCGA: Comprehensive molecular portraits of human breast tumours. Nature 2012, 490(7418):61-70]

value: lung

tag: disease

value: lung adenocarcinoma

value: IIB

value: NS

tag: gender

value: F


title: T-98 miRNA-seq

value: M


title: T-97 miRNA-seq

value: IIIB

value: EX


title: T-82 miRNA-seq

value: IIIA

value: CS


title: T-71 miRNA-seq


title: T-75 miRNA-seq

value: IIA


title: T-76 miRNA-seq


title: T-65 miRNA-seq


title: T-62 miRNA-seq


title: T-64 miRNA-seq

value: IA


title: T-53 miRNA-seq


title: T-51 miRNA-seq


title: T-59 miRNA-seq


title: T-77 miRNA-seq


title: T-119 miRNA-seq


title: T-130 miRNA-seq


title: T-132 miRNA-seq


title: T-49 miRNA-seq


title: T-48 miRNA-seq

value: IV


title: T-124 miRNA-seq


title: T-128 miRNA-seq


title: T-127 miRNA-seq


title: T-121 miRNA-seq

value: T1 N1


title: T-111 miRNA-seq

value: IB


title: T-131 miRNA-seq


title: T-72 miRNA-seq


title: T-122 miRNA-seq


title: T-74 miRNA-seq


title: T-118 miRNA-seq

value: T2b, N0


title: T-110 miRNA-seq


title: T-106 miRNA-seq


title: T-109 miRNA-seq


title: T-68 miRNA-seq


title: T-108 miRNA-seq


title: T-100 miRNA-seq


title: N-97 miRNA-seq

description: micro-dissected for >80% non-malignant cell content

source_name: non-malignant lung parenchymal tissue from lung adenocarcinoma patient


title: N-93 miRNA-seq


title: T-103 miRNA-seq


title: N-98 miRNA-seq


title: N-77 miRNA-seq


title: N-76 miRNA-seq


title: N-75 miRNA-seq


title: N-74 miRNA-seq


title: N-72 miRNA-seq


title: N-64 miRNA-seq


title: N-65 miRNA-seq


title: N-53 miRNA-seq


title: N-62 miRNA-seq


title: N-51 miRNA-seq


title: N-59 miRNA-seq


title: K36M-mRNA-Rep-1

city: Madison

first: Christine

last: Wooddell

state: WI

address: 502 S Rosa Rd

institute: Arrowhead Pharmaceuticals

description:
mRNA isolated from leaves of 21 day old plants converted to cDNA through library preparation
duplicate biological replicate 1
"M36_2_6 0" in GSE92449_K36M.final.fpkm.txt.gz

data_processing:
ChIP-seq reads were filtered for average QC score>30. Reads were mapped with Bowtie2 to the TAIR10 genome, with default parameters. Reads mapping to identical positions in the genome were collapsed into one read.
Genome_build: TAIR10
Supplementary_files_format_and_content: bed files converted to bedgraph via bedtools, bedgraph files were converted to bigwig files via the UCSC "bedGraphToBigWig" executable script

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Arabidopsis plants were grown in soil at 23 degrees C under long day light conditions (16 hrs light: 8 hrs dark) for 3 weeks .

extract_protocol:
ChIP genomic DNA protocols are similar as used in Zhong et al., Nat Struct Mol Biol, 2012, 19:870-850 , RNA was extracted from as in Du et al, Cell, 2012,  151(1): 167–180.
ChIP library was constructed  using the Ovation Ultralow Library Kit (NuGen, Part No. 0330), RNA libraries were constructed using the illumina TruSeq Stranded mRNA LT kit (ref no15032612) following manufacterers instructions

tag: ecotype/genotype

value: Columbia-0 background with transgenic H3 insertion (K36M missense mutation in AT4G40040)

value: leaf


title: WT-mRNA-Rep-1

description:
mRNA isolated from leaves of 21 day old plants converted to cDNA through library preparation
duplicate biological replicate 1
"K36_2_6 0" in GSE92449_K36M.final.fpkm.txt.gz

value: Columbia-0 background with transgenic H3 insertion (wildtype AT4G40040)


title: WT-mRNA-Rep-2

description:
mRNA isolated from leaves of 21 day old plants converted to cDNA through library preparation
duplicate biological replicate 2
"K36_2_6 1" in GSE92449_K36M.final.fpkm.txt.gz


title: N-82 miRNA-seq

value: lung

value: lung adenocarcinoma


title: N-49 miRNA-seq

value: F


title: N-132 miRNA-seq


title: Col-0-H3K36me3

description: Genomic DNA isolated from immnuoprecipitated chromatin using H3K36me3 antibody (ab9050)

value: Columbia-0 background


title: N-130 miRNA-seq


title: N-131 miRNA-seq

value: M


title: N-128 miRNA-seq


title: K36M-H3K36me3

value: Columbia-0 background with heterozygous transgenic H3 insertion (K36M missense mutation in AT4G40040)


title: K36M-hom-H3K36me3

value: Columbia-0 background with homozygous transgenic H3 insertion (K36M missense mutation in AT4G40040)


title: N-48 miRNA-seq

value: EX


title: sdg8-H3K36me3

value: Columbia-0 background with homozygous sdg8 T-DNA insertion (efs-3) Kim et al. Plant Cell, 2005


title: N-127 miRNA-seq


title: WT-H3K36me3


title: CordBlood_CD235a_RNA_m_3

city: Boston

first: Vijay

last: Sankaran

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

data_processing:
An index of length 15 k-mers was prepared from release 79 of the UCSC hg38 transcriptome using the iKallisto index. Raw paired-end reads were then pseudo-aligned to this reference using Kallisto quant with the bias correction flag enabled to account for sequence bias. Resulting counts were summed to yield transcripts per million (TPM) for each gene.
Differential gene expression in bone marrow of adult CD34 + and cord blood CD34 + recipient mice was quantified in R using limma to fit a linear model to the calculated TPM and eBayes to derive a corrected p value for each gene.
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts for RNA-seq (across the entire transcript) and for ribosome profiling (across the matching CDS exluding the first 45 nucleotides and last 15 nucleotides) are included in Counts.txt.

source_name: Cord blood CD34+ cells

growth_protocol: CD34+ cells from G-CSF mobilized peripheral blood, bone marrow, or cord blood were purified by positive magnetic selection using an Ultrapure Microbead Kit (Miltenyi Biotech) according to the manufacturer's protocol following mononuclear cell purification on a Ficoll Density Gradient. At least 95% purity was reached as assessed by post-purification flow cytometry with a PE conjugated antihuman CD34 antibody (8012-0349, eBioscience). Cells were differentiated into mature RBCs utilizing a three-phase culture protocol. In phase 1 (day 0 – 7), cells were cultured at a density of 105 - 106 cells per milliliter (mL) in IMDM supplemented with 2% human AB plasma, 3% human AB serum, 1% penicillin/streptomycin, 3 IU/mL heparin, 10 ug/mL insulin, 200 ug/mL holo-transferrin, 1 IU erythropoietin (Epo), 10 ng/mL stem cell factor (SCF) and 1 ng/mL IL-3. In phase 2 (day 7 – 12), IL-3 was omitted from the medium. In phase 3 (day 12 – 18), cells were cultured at a density of 106 cells per milliliter, with both IL-3 and SCF omitted from the medium and the holo-transferrin concentration was increased to 1 mg/mL. Cells were cultured at 37°C and 5% CO2.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy spin columns and subsequent poly(A)+ selection was performed using the NEB NEXT kit by following the manufacturers instructions. Poly(A)+ selected RNA was fragmented to ~200nt by a 3 min. incubation at 95 °C in FAST-AP buffer. Samples were quickly transferred to ice and subjected to joint Alkaline Phosphatase (FAST-AP, Thermo Scientific) and T4 Polynucleotide Kinase (PNK, NEB) treatment for end-repair. Following incubation at 37 °C for 30 min, reactions were cleaned with MyOne SILANE magnetic beads, washed twice with 70% ethanol and eluted in 6 μl H2O.
Library preparation was carried out using an Illumina TruSeq Kit, as per manufacturer’s recommendation, and samples were sequenced on the Illumina HiSeq 2500

treatment_protocol: NOD.Cg-Kit W-41J Tyr + Prkdc scid Il2rg tm1Wjl (NBSGW) mice were obtained from Jackson Laboratory (Stock 026622). Non-irradiated NBSGW mice (between 4-8 weeks of age) were tail vein injected with multiple donor-derived CB or adult CD34 + HSPCs (0.5-1x10 6 cells). NBSGW were interbred to maintain a colony of animals homozygous or hemizygous for all mutations of interest. All animal experiments were approved by the Boston Children’s Hospital Institutional Animal Care and Use Committee.

value: Cord blood

value: CD235a+ cells

tag: day


title: N-71 miRNA-seq

value: IIB


title: N-124 miRNA-seq


title: K36M-mRNA-Rep-2

description:
mRNA isolated from leaves of 21 day old plants converted to cDNA through library preparation
duplicate biological replicate 2
"M36_2_6 1" in GSE92449_K36M.final.fpkm.txt.gz


title: N-68 miRNA-seq

value: IIIA


title: CordBlood_CD235a_RNA_m_2


title: N-121 miRNA-seq

value: T1 N1


title: N-119 miRNA-seq

value: CS


title: N-111 miRNA-seq

value: IB


title: Adult_CD235a_RNA_m_3

source_name: Adult bone marrow CD34+ cells

value: Adult bone marrow


title: Adult_CD235a_RNA_m_2


title: CordBlood_CD235a_RNA_m_1


title: Adult_CD235a_RNA_m_1


title: N-118 miRNA-seq

value: lung

value: T2b, N0


title: N-110 miRNA-seq

value: lung adenocarcinoma

value: F


title: 3023-Foxo1NP-CD8-Day3

city: Seattle

first: Matthias

last: Stephan

state: WA

address: 1100 Fairview Ave. N.

department: Program in Immunology

institute: Fred Hutchinson Cancer Research Center

description:
processed data file:
Counts.txt
log2NormalizedCPM.txt

data_processing:
Filtered reads via Illumina base call filter
Aligned reads to genome using TopHat v2.1.0
Generatde gene-level counts with htseq-count v0.6.1p1, using  the "intersection-strict"   overlap mode.
Data normalization and differetial expression performed using the GLM method in edgeR.
Genome_build: Human hg38
Supplementary_files_format_and_content: Tab deliminated text files with gene level counts, log2 normalized CPM, and differential gene expression analyis for selected sample groups.

source_name: Bead isolated total CD8_Foxo1NP_Day3

extract_protocol:
Cells were lysed in Trizol reagent (Ambion) and total RNA isolate  d using DirectZol kit   (Zymo) with on-column DNA digestion according to manufacturers instr  uctions.
RNASeq libraries were prepared   using the TruSeq sample prep kit (Illiumina)
RNAseq for 50bp paired end runs on HiSeq platform. To minimize variation, libraries were multiplexed, and run as a batch on two flow cells (noted as 781 and 782, respectively). Results from the two flow cells were combined for later analysis.

tag: donor id

value: Bead isolated total CD8

value: Foxo1-3A mRNA Nanoparticle

tag: days in culture post treatment


title: N-103 miRNA-seq


title: N-108 miRNA-seq

value: M


title: N-100 miRNA-seq

value: EX


title: 882-Foxo1NP-CD8-Day3

tag: cell type


title: N-106 miRNA-seq

value: IIIB

value: NS


title: 3076-ControlNP-CD8-Day3

source_name: Bead isolated total CD8_ControlINP_Day3

value: Control eGFP mRNA Nanoparticle


title: 882-ControlNP-CD8-Day3


title: N-122 miRNA-seq


title: N-109 miRNA-seq


title: 3076-Foxo1NP-CD8-Day8

description:
processed data file:
Counts.txt
log2NormalizedCPM.txt
Foxo1NPDay8VsControlNPDay8.txt

source_name: Bead isolated total CD8_Foxo1NP_Day8


title: FL-5 Pool miRNA-seq

description: fetal lung pool (total mRNA acquired from Biocat GmbH (Heidelberg, Germany))

source_name: fetal lung


title: FL-4 miRNA-seq

description: fetal lung tissue (17 weeks gestation; derived from elective terminations for medical reasons)


title: 3023-ControlNP-CD8-Day3


title: 3023-Foxo1NP-CD8-Day8


title: FL-3 miRNA-seq

description: fetal lung tissue (24 weeks gestation; derived from elective terminations for medical reasons)


title: 3076-ControlNP-CD8-Day8

description:
processed data file:
Counts.txt
log2NormalizedCPM.txt
Foxo1NPDay8VsControlNPDay8.txt
CentralMemoryVsControlNPDay8.txt

source_name: Bead isolated total CD8_ControlINP_Day8


title: FL-2 miRNA-seq

description: fetal lung tissue (20 weeks gestation; derived from elective terminations for medical reasons)


title: 3023-ControlNP-CD8-Day8


title: FL-1 miRNA-seq

description: fetal lung tissue (21 weeks gestation; derived from elective terminations for medical reasons)


title: 3023-CM-CD8

description:
Sorted cells from cryopreserved PBMC as CD8+ CD45RA- CD62L+ CCR7+
processed data file:
Counts.txt
log2NormalizedCPM.txt
CentralMemoryVsControlNPDay8.txt

source_name: Sorted Central Memory CD8

value: Sorted Central Memory CD8


title: 3076-Foxo1NP-CD8-Day3


title: H03_RNAseq

status: Public on Jun 15 2017

city: Wanju

first: Kyung-Tai

last: Lee

state: JeonBuk

address: 1500 Kongjwipatjwi

department: Animal Genomics and Bioinformatics Division

country: South Korea

institute: National Institute of Animal Science

data_processing:
The porcine reference genome sequence and annotated transcript set were downloaded from Sscrofa 10.2.68 of Ensembl release 68
Prior to mapping reads to the reference genome, a quality check was performed using FastQC v0.10.1
Trimmomatic v0.22 (Lohse et al. 2012) was used to clip the terminal 11 bp from both the ends and quality filtration
TopHat v2.0.4 was used to map the trimmed reads to the porcine reference genome (Trapnell et al. 2009).
For more accurate mapping, mate inner distances and standard deviations for the trimmed reads were calculated using BWA v0.6.2 (Li & Durbin 2010), and adapted for mapping using TopHat.
Genome_build: Sscrofa 10.2.68
Supplementary_files_format_and_content: tab-delimited text files include count per million (CPM)  values for each Sample

organism: Sus scrofa

source_name: Longissimus muscle

extract_protocol:
Total RNA was extracted from freshly harvested longissimus dorsi muscle samples using TRIzol reagent (Life Technologies Corp., Carlsbad, CA, USA) according to the manufacturer’s instructions. Total RNA was prepared in accordance with Illumina's Truseq RNA Sample preparation guide (Illumina, San Diego, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: High_IMF (High intramuscular fat)

value: Longissimus muscle


title: 3076-CM-CD8


title: 3076-Naïve-CD8

description:
Sorted cells from cryopreserved PBMC as CD8+ CD45RA+ CD62L+ CCR7+
processed data file:
Counts.txt
log2NormalizedCPM.txt

source_name: Sorted Naïve CD8

value: Sorted Naive CD8


title: H02_RNAseq


title: 3023-Naïve-CD8


title: L03_RNAseq

value: Low_IMF (Low intramuscular fat)


title: L02_RNAseq


title: camRAS_20hpf2

city: New York

first: wei

last: wang

state: NY

address: 100 washington square east

department: Biology

institute: New York University

data_processing:
For each demultiplexed single cell RNA-seq library, sequencing reads were mapped to Ciona genome (Joined-scaffold (KH), http://ghost.zool.kyotou.ac.jp/datas/JoinedScaffold.zip) using TopHat 2.0.12 (Kim et al., 2013; Trapnell et al., 2012) with parameter: --no-coverage-search. Cufflinks 2.2.0 (Trapnell et al., 2012) was used to calculate the Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using KH gene models (ver.2013, http://ghost.zool.kyoto-u.ac.jp/datas/KH.KHGene.2013.gff3.zip) with default parameters.
Genome_build: Ciona genome (Joined-scaffold (KH), http://ghost.zool.kyotou.ac.jp/datas/JoinedScaffold.zip)
Supplementary_files_format_and_content: tab-delimited text files include raw FPKMs for each gene per cell

organism: Ciona robusta

extract_protocol:
200 to 800 cells were directly sorted in 100µl lysis buffer included in RNAqueous®-Micro Total RNA Isolation Kit (Ambion). The total RNA extraction was performed following the manufacturer’s instruction.
250-2000 pg of total RNA was loaded as template for cDNA synthesis using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) with template switching technology. RNA-Seq Libraries were prepared and barcoded using Ovation® Ultralow System V2 1–16 (NuGen).

tag: genotype/variation

value: camRAS

tag: developmental stage

value: Hatching larva

value: Trunk ventral cells

tag: cell subtype

value: Multipotent cardiopharyngeal progenitor cells


title: camRAS_18hpf1


title: L01_RNAseq


title: camRAS_20hpf1


title: camRAS_12hpf1

value: Late tailbud I


title: camRAS_15hpf1

value: Late tailbud II


title: camRAS_18hpf2


title: camRAS_12hpf2


title: dnFGFR_20hpf1

value: dnFGFR


title: dnFGFR_20hpf2


title: dnFGFR_18hpf2


title: dnFGFR_12hpf2


title: dnFGFR_15hpf1


title: handrlacz_control_20hpf2

value: Wild type


title: dnFGFR_12hpf1


title: dnFGFR_18hpf1


title: H01_RNAseq


title: handrlacz_control_20hpf1


title: handrlacz_control_18hpf1


title: handrlacz_control_18hpf2


title: handrlacz_control_15hpf2


title: foxflacz_control_20hpf1


title: foxflacz_control_20hpf2


title: handrlacz_control_12hpf2


title: handrlacz_control_15hpf1


title: handrlacz_control_12hpf1


title: foxflacz_control_18hpf1


title: foxflacz_control_18hpf2


title: camRAS_15hpf2


title: foxflacz_control_15hpf2


title: foxflacz_control_12hpf1


title: foxflacz_control_15hpf1


title: dnFGFR_15hpf2


title: hpf20-480

description:
processed data file:
hpf20.txt
wei-20-v-96

source_name: ScRNA-seq of FACS purified cardiopharyngeal progenitors_20hpf

extract_protocol:
Sample dissociation and FACS were performed essentially as described (Christiaen et al., 2009c; Razy-Krajka et al., 2014). Embryos and larvae were harvested at 12, 14, 16, 18 and 20hpf in 5ml borosilicate glass tubes (Fisher Scientific, Waltham, MA. Cat.No. 14-961-26) and washed with 2ml calcium- and magnesium-free artificial seawater (CMF-ASW: 449 mM NaCl, 33 mM Na2SO4, 9 mM KCl, 2.15 mM NaHCO3, 10 mM Tris-Cl pH 8.2, 2.5 mM EGTA). Embryos and larvae were dissociated in 2ml 0.2% trypsin (w/v, Sigma, T- 4799) ASW by pipetting with glass Pasteur pipettes. The dissociation was stopped by adding 2ml filtered ice cold 0.05% BSA CMF-ASW. The dissociated cells were passed through 40µm cell-strainer and collected in 5ml polystyrene round-bottom tube (Corning Life Sciences, Oneonta, New York. REF 352235). Cells were collected by centrifugation at 800g for 3 min at 4°C, followed by two rounds of washing with ice cold 0.05% BSA CMF-ASW. Cell suspensions were filtered again through a 40µm cell-strainer and stored on ice. Following dissociation, cell suspensions were used for sorting within 1 hour. The B7.5 lineage cells were labeled by Mesp>tagRFP reporter. Contaminating B-line mesenchyme cells were counter-selected using  MyoD905>EGFP as described (Christiaen et al., 2008; Razy-Krajka et al., 2014).  The TVC-specific Hand-r>tagBFP reporter was used in a 3-color FACS scheme for positive co-selection of TVC-derived cells, in order to minimize the effects of mosaicism. Dissociated cell were loaded in the BD FACS AriaTM cell sorter.  488 nm laser, FITC filter was used for EGFP; 407 nm laser, 561 nm laser, DsRed filter was used for tagRFP and Pacific BlueTM filter was used for tagBFP. The nozzle size was 100 µm. tagRFP +, tagBFP + and EGFP – cells were collected for downstream RNA sequencing analysis.
Reverse transcription and cDNA amplification were carried out using modified Smart-seq2 protocol (Picelli et al., 2013). Single cells were sorted by FACS as described above into 96-well plates and collected in 3.4 µl RT buffer (0.5 µl 10µM 3’ RT Primer ( 5' - AAG CAG TGG TAT CAA CGC AGA GTA C T30 VN - 3’), 0.5µl 10µM dNTP Mix, 0.5 µl 4U/µl RNase Inhibitor, 1 µl Maxima RT Buffer, 0,9 µl nuclease-free water) in each well. Plates were stored at -80°C  or processed immediately.  Plates were incubated at 72°C for 3min and chilled on the ice to denature the template RNA. 2µl  RT reaction mixture (0.5µl 10um TSO primer (5′-AGACGTGTGCTCTTCCGATCTNNNNNrGrGrG-3′), 0.925µl 5M Betaine, 0.4 100mM MgCl2, 0.125µl 40U/ RNAase inhibitor, 0.05µl 200 U/µl Maxima H Minus Reverse Transcriptase) were added to each well. Reverse transcription was carried out by incubating the plate at 42°C for 90 min, followed by 10 cycles of (50 °C for 2 min, 42 °C for 2 min) and heat inactivation at 70° for 15 min. 7µl PCR amplification mixture (0.25µl 10 μM PCR primer (5′AGACGTGTGCTCTTCCGATCT-3′), 6.25µl KAPA HIFI ReadyMix, 0.5µl nuclease-free water) were added to each well. PCR amplification was carried out with a denaturation at 98 °C for 3 min, followed by 21 cycles of (98 °C for 15 s, 67 °C for 20 s, and 72 °C for 6 min) and a final extension at 72° for 5 min. PCR products were purified by adding 10µl (0.8×) Agencourt AMPureXP SPRI beads (Beckman-Coulter) to each well, followed by 5min incubation and two rounds of wash using 100µl freshly prepared  70% Ethanol at room temperature. Purified cDNA were eluted in 20µl TE. The concentration of amplified cDNA was measured across the entire plate using Picogreen assay. The concentration of amplified cDNA was in a 0.5–2 ng/μl range.  Fragment size distribution was checked for randomly selected wells with High-Sensitivity Bioanalyzer Chip (Agilent), the expected size average should be ~2 kb. For each sample, the amplified cDNA were normalized to a working concentration ranging from 0.1 to 0.2 ng/µl with TE buffer. 1.25 µl of diluted cDNA from each well were used for library preparation. Single cell libraries were prepared using the Nextera XT DNA Sample Kit (Illumina) according to manufacturer's instructions.  After library amplification, 2.5μl from each well were pooled into a single 1.5-ml microcentrifuge tube, purified using Agencourt AMPure XP beads and eluted with 30μl TE buffer.  1μl purified library was used to measure the fragment size distribution using the Agilent HS DNA BioAnalyzer chip and another 1μl of the purified library was loaded into Qubit fluorometer to estimate library concentration according to the manufacturer's instructions.  Libraries were sequenced on an Illumina HiSeq 2500 sequencer to obtain paired-end 25bp reads.


title: hpf20-479

description:
processed data file:
hpf20.txt
wei-20-v-95


title: hpf20-478

description:
processed data file:
hpf20.txt
wei-20-v-94


title: hpf20-477

description:
processed data file:
hpf20.txt
wei-20-v-93


title: hpf20-475

description:
processed data file:
hpf20.txt
wei-20-v-91


title: hpf20-476

description:
processed data file:
hpf20.txt
wei-20-v-92


title: hpf20-473

description:
processed data file:
hpf20.txt
wei-20-v-9


title: foxflacz_control_12hpf2


title: hpf20-471

description:
processed data file:
hpf20.txt
wei-20-v-88


title: hpf20-474

description:
processed data file:
hpf20.txt
wei-20-v-90


title: hpf20-468

description:
processed data file:
hpf20.txt
wei-20-v-85


title: hpf20-467

description:
processed data file:
hpf20.txt
wei-20-v-84


title: hpf20-465

description:
processed data file:
hpf20.txt
wei-20-v-82


title: hpf20-464

description:
processed data file:
hpf20.txt
wei-20-v-81


title: hpf20-461

description:
processed data file:
hpf20.txt
wei-20-v-79


title: hpf20-460

description:
processed data file:
hpf20.txt
wei-20-v-78


title: hpf20-463

description:
processed data file:
hpf20.txt
wei-20-v-80


title: hpf20-462

description:
processed data file:
hpf20.txt
wei-20-v-8


title: hpf20-459

description:
processed data file:
hpf20.txt
wei-20-v-77


title: hpf20-458

description:
processed data file:
hpf20.txt
wei-20-v-76


title: hpf20-456

description:
processed data file:
hpf20.txt
wei-20-v-74


title: hpf20-454

description:
processed data file:
hpf20.txt
wei-20-v-72


title: hpf20-455

description:
processed data file:
hpf20.txt
wei-20-v-73


title: hpf20-457

description:
processed data file:
hpf20.txt
wei-20-v-75


title: hpf20-472

description:
processed data file:
hpf20.txt
wei-20-v-89


title: hpf20-469

description:
processed data file:
hpf20.txt
wei-20-v-86


title: hpf20-470

description:
processed data file:
hpf20.txt
wei-20-v-87


title: hpf20-450

description:
processed data file:
hpf20.txt
wei-20-v-69


title: hpf20-446

description:
processed data file:
hpf20.txt
wei-20-v-65


title: hpf20-447

description:
processed data file:
hpf20.txt
wei-20-v-66


title: hpf20-448

description:
processed data file:
hpf20.txt
wei-20-v-67


title: hpf20-451

description:
processed data file:
hpf20.txt
wei-20-v-7


title: hpf20-452

description:
processed data file:
hpf20.txt
wei-20-v-70


title: hpf20-449

description:
processed data file:
hpf20.txt
wei-20-v-68


title: hpf20-444

description:
processed data file:
hpf20.txt
wei-20-v-63


title: hpf20-466

description:
processed data file:
hpf20.txt
wei-20-v-83


title: hpf20-443

description:
processed data file:
hpf20.txt
wei-20-v-62


title: hpf20-445

description:
processed data file:
hpf20.txt
wei-20-v-64


title: hpf20-441

description:
processed data file:
hpf20.txt
wei-20-v-60


title: hpf20-442

description:
processed data file:
hpf20.txt
wei-20-v-61


title: hpf20-440

description:
processed data file:
hpf20.txt
wei-20-v-6


title: hpf20-439

description:
processed data file:
hpf20.txt
wei-20-v-59


title: hpf20-453

description:
processed data file:
hpf20.txt
wei-20-v-71


title: hpf20-432

description:
processed data file:
hpf20.txt
wei-20-v-52


title: hpf20-437

description:
processed data file:
hpf20.txt
wei-20-v-57


title: hpf20-435

description:
processed data file:
hpf20.txt
wei-20-v-55


title: hpf20-434

description:
processed data file:
hpf20.txt
wei-20-v-54


title: hpf20-436

description:
processed data file:
hpf20.txt
wei-20-v-56


title: hpf20-433

description:
processed data file:
hpf20.txt
wei-20-v-53


title: hpf20-438

description:
processed data file:
hpf20.txt
wei-20-v-58


title: hpf20-431

description:
processed data file:
hpf20.txt
wei-20-v-51


title: hpf20-429

description:
processed data file:
hpf20.txt
wei-20-v-5


title: hpf20-430

description:
processed data file:
hpf20.txt
wei-20-v-50


title: hpf20-427

description:
processed data file:
hpf20.txt
wei-20-v-48


title: hpf20-426

description:
processed data file:
hpf20.txt
wei-20-v-47


title: hpf20-425

description:
processed data file:
hpf20.txt
wei-20-v-46


title: hpf20-424

description:
processed data file:
hpf20.txt
wei-20-v-45


title: hpf20-422

description:
processed data file:
hpf20.txt
wei-20-v-43


title: hpf20-423

description:
processed data file:
hpf20.txt
wei-20-v-44


title: hpf20-421

description:
processed data file:
hpf20.txt
wei-20-v-42


title: hpf20-419

description:
processed data file:
hpf20.txt
wei-20-v-40


title: hpf20-417

description:
processed data file:
hpf20.txt
wei-20-v-39


title: hpf20-420

description:
processed data file:
hpf20.txt
wei-20-v-41


title: hpf20-416

description:
processed data file:
hpf20.txt
wei-20-v-38


title: hpf20-415

description:
processed data file:
hpf20.txt
wei-20-v-37


title: hpf20-413

description:
processed data file:
hpf20.txt
wei-20-v-35


title: hpf20-414

description:
processed data file:
hpf20.txt
wei-20-v-36


title: hpf20-411

description:
processed data file:
hpf20.txt
wei-20-v-33


title: hpf20-412

description:
processed data file:
hpf20.txt
wei-20-v-34


title: hpf20-410

description:
processed data file:
hpf20.txt
wei-20-v-32


title: hpf20-428

description:
processed data file:
hpf20.txt
wei-20-v-49


title: hpf20-409

description:
processed data file:
hpf20.txt
wei-20-v-31


title: hpf20-402

description:
processed data file:
hpf20.txt
wei-20-v-25


title: hpf20-404

description:
processed data file:
hpf20.txt
wei-20-v-27


title: hpf20-408

description:
processed data file:
hpf20.txt
wei-20-v-30


title: hpf20-405

description:
processed data file:
hpf20.txt
wei-20-v-28


title: hpf20-406

description:
processed data file:
hpf20.txt
wei-20-v-29


title: hpf20-407

description:
processed data file:
hpf20.txt
wei-20-v-3


title: hpf20-401

description:
processed data file:
hpf20.txt
wei-20-v-24


title: hpf20-399

description:
processed data file:
hpf20.txt
wei-20-v-22


title: hpf20-400

description:
processed data file:
hpf20.txt
wei-20-v-23


title: hpf20-398

description:
processed data file:
hpf20.txt
wei-20-v-21


title: hpf20-396

description:
processed data file:
hpf20.txt
wei-20-v-2


title: hpf20-397

description:
processed data file:
hpf20.txt
wei-20-v-20


title: hpf20-418

description:
processed data file:
hpf20.txt
wei-20-v-4


title: hpf20-394

description:
processed data file:
hpf20.txt
wei-20-v-18


title: hpf20-392

description:
processed data file:
hpf20.txt
wei-20-v-16


title: hpf20-391

description:
processed data file:
hpf20.txt
wei-20-v-15


title: hpf20-390

description:
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processed data file:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
processed data file:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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description:
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wei-20-ii-37


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description:
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description:
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description:
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description:
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description:
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description:
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description:
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