title: corrected clone 1-B10-E2 0.5%

city: Uppsala

first: L.

last: He

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description: corrected clone 1-B10-E2 0.5%

data_processing:
The reads were aligned to the human genome hg19 assembly (https://genome.ucsc.edu) using Tophat2 software (version 2.0.4)
The FPKM summary and statistical tests were performed using the Cufflinks tool (version 2.2.1)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files with RPKM values for each Sample.

source_name: colorectal cancer cell line HCT116

extract_protocol: Total RNA was extracted using an RNeasy Plus Mini kit (Qiagen). The RNA integrity and concentration was determined on a Bioanalyzer instrument (Agilent) using an RNA 6000 Nano kit.

tag: tissue

value: colon


title: control sample HCT116_2 0.5%

status: Public on Feb 22 2018

type: SRA

description: control sample HCT116_2 0.5%

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line


title: control sample HCT116_3 0.5%

description: control sample HCT116_3 0.5%


title: control sample HCT116_1 0.5%

description: control sample HCT116_1 0.5%


title: corrected clone 2-E6-A4 0.5%

description: corrected clone 2-E6-A4 0.5%


title: corrected clone 2-B6-1F 0.5%

description: corrected clone 2-B6-1F 0.5%


title: corrected clone 2-E6-A4 10%

description: corrected clone 2-E6-A4 10%


title: control sample HCT116_2 10%

description: control sample HCT116_2 10%


title: control sample HCT116_1 10%

description: control sample HCT116_1 10%


title: corrected clone 1-B10-E2 10%

description: corrected clone 1-B10-E2 10%


title: control sample HCT116_3 10%

description: control sample HCT116_3 10%


title: MCF-7 G11 TamR E2

city: Ithaca

first: Charles

middle: G

last: Danko

state: NY

address: Hungerford Hill Rd

department: Baker Institute

country: USA

institute: Cornell University

description:
nascent RNA
Herein

data_processing:
Library strategy: PRO-Seq
We trimmed adapter sequences and mapped PRO-seq data using BWA.
Data was converted into bigWig format.
Genome_build: hg19
Supplementary_files_format_and_content: PRO-seq data are provided in standard bigWig and raw fastq formats.
Supplementary_files_format_and_content: dREG/dREG-HD interpretation of TREs based on PRO-seq data are provided in bigWig and BED formats
Supplementary_files_format_and_content: MCF-7 TamS/ TamR combined data
Supplementary_files_format_and_content: Combined data from MCF-7 subclones
Supplementary_files_format_and_content: mcf7.bedgraph.gz.bed.gz_imputedDnase.bw
Supplementary_files_format_and_content: mcf7_tamSR_dREG.bw
Supplementary_files_format_and_content: mcf7.bedgraph.gz.bed.gz_dREG_HD_stringent.bed
Supplementary_files_format_and_content: MCF-7 TamS/ TamR GDNF timecourse combined data
Supplementary_files_format_and_content: Combined data from MCF-7 subclones across the GDNF timecourse
Supplementary_files_format_and_content: GDNF, 0h, 1h, 24h
Supplementary_files_format_and_content: mcf7.gdnf.bedgraph.gz.bed.gz_imputedDnase.bw
Supplementary_files_format_and_content: mcf7_gdnf_dREG.bw
Supplementary_files_format_and_content: mcf7.gdnf.bedgraph.gz.bed.gz_dREG_HD_stringent.bed

source_name: MCF-7 cells subclone

growth_protocol: Tamoxifen sensitive (TamS; B7TamS and C11TamS) and resistant (TamR; G11TamR and H9TamR) MCF-7 cells (Gonzalez-Malerva et al., 2011) were a gift from Dr. Joshua LaBaer. TamS cells were grown in Dulbecco's Modified Eagle Medium supplemented with 5% fetal bovine serum and 1% Penicillin Streptomycin, and TamR cells were grown in the same media supplemented with 1 μM tamoxifen. TamS and TamR lines were grown in 150mm TC-treated culture dish in their respective normal culture media. Cells were rinsed with PBS for at least three times 24 hours after plating. Both the TamS and TamR cells were grown in Dulbecco's Modified Eagle Medium supplemented with 5% fetal bovine serum and 1% Penicillin Streptomycin for an additional three days until ~80% confluency in the absence of tamoxifen, in order to measure the difference between TamS and TamR cells pre-treatment. For estrogen (E2) and tamoxifen treated TamS and TamR cells, cells were instead grown in phenol-red free Dulbecco's Modified Eagle Medium supplemented with 5% charcoal-stripped fetal bovine serum and 1% Penicillin Streptomycin for three days. The cells were then treated with either EtOH (vehicle control), 100 nM E2, or with 1 M tamoxifen for 40 min. For GDNF treated TamS and TamR cells, the same experimental set up as the pre-treatment was performed. In addition, the cells were treated with 10 ng/mL GDNF for 0, 1, or 24 hours.

extract_protocol:
Nuclei were isolated as described in previously (Core et al., 2008). Briefly, cells were rinsed three times with ice-cold PBS and lysed using lysis buffer (10 mM Tris-HCl pH 7.4, 2 mM MgCl2, 3 mM CaCl2, 0.5% NP-40, 10% Glycerol, 1 mM DTT, 1X PIC (Roche; Cat# 11836153001), and 1 ml/10 mL SUPERase-In (ThermoFisher; Cat# AM2694) dissolved in DEPC water). Cells were homogenized by gently pipetting at least 30 times and the nuclei were harvested by centrifugation at 1000g for five minutes at 4°C. The isolated nuclei were washed twice with lysis buffer and were resuspended in 100 mL freezing buffer (50 mM Tris HCl pH 8.3, 5 mM MgCl2, 40% Glycerol, 0.1 mM EDTA pH 8.0, and 4 U/mL SUPERase-In). The isolated nuclei were used for nuclear run-on and precision nuclear run-on sequencing (PRO-seq) library preparation.
We prepared PRO-seq libraries as described in Kwak et. al. (2013) Science.

treatment_protocol: Ligand treatments were applied for the indicated time as described in our paper.

tag: clone

tag: resistance

value: TamR

tag: treatment


title: corrected clone 2-B6-1F 10%

description: corrected clone 2-B6-1F 10%


title: TRIM28 ChIP

city: Beijing

first: Huiping

last: Lu

address: Tsinghua university

country: China

institute: Tsinghua university

library_source: genomic

data_processing:
Basecalls performed using bcl2fastq Conversion Software v1.8.4
RNA-seq reads were aligned to the mm10 genome using SOAP2.
Reads count were calculated using htseq-count.
ChIP-seq reads were aligned to the mm10 genome using bowtie.
peaks were called using SICER version 1.1.
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using SICER version 1.1; tdf files were converted using igvtools.

molecule: genomic DNA

organism: Mus musculus

source_name: Th17 cells

growth_protocol: RPMI-1640 medium with 10% FBS, 0.5ng/ml TGFβ and 20ng/ml IL-6

extract_protocol:
RNA was extracted from cells by Trizol. ChIP-seq was performed from crosslinked and MNase digested nuclear lysates; protein-DNA complexes were pulled down by indicated antibodies; after reverse-crosslinking, DNA was purified by phenol-chloroform.
RNA libraries were prepared by the BerryGenomics company and only mRNA was used. ChIP libraries were constructed following the protocol of NEXTflex ChIP-Seq DNA Sequencing Kit(Bioo Scientific, 5143) described in the paper.

treatment_protocol: Naive CD4+ T cells were cultured under Th17 differentiation conditions for 3 days

tag: strain

value: Th17 differentiated in vitro for 24h

tag: genotype

value: wild type

tag: chip antibody

value: TRIM28 antibody(Active Motif, 61173)


title: WT Input for TRIM28


title: TRIM28KO Input for p300

value: Th17 differentiated in vitro for 3 days


title: MCF-7 B7 TamS DMSO

description:
nascent RNA
Herein

value: TamS

value: DMSO, 40m


title: WT Input for p300


title: TRIM28KO p300

value: p300 antibody(santa-cruz, sc-585)


title: TRIM28KO Th17


title: WT p300


title: WT Th17


title: MCF-7 B7 TamS None

description:
nascent RNA
Herein


title: BMT722-combo-B26

city: New York

first: Barbara

last: Spitzer

address: 411 E 67th St

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Raw reads from FASTQ files were aligned to mm10 using STAR v 2.5.1a using default parameters.
Counts were generated using the ensembl gene model and STAR v 2.5.1a with the —quantMode parameter.
Differential expression analysis was performed using the R Bioconductor DESeq2 v.1.6.3 package using default parameters.
Genome_build: mm10, ENSEMBL Mus_musculus.GRCm38.75
Supplementary_files_format_and_content: Raw and normalized count tables as computed by DESeq2

source_name: bone marrow

extract_protocol:
CD45.2+ LSK cells were sorted into ice cold FACS Buffer, pelleted, and stored in Trizol.  RNA was extracted from Trizol using phenol-chloroform.
The library was produced using SMARTer amplification (Clontech) to amplify and create the library

treatment_protocol: Drugs were administered BID by gavage for 21-28 days, except where otherwise indicated. Ruxolitinib (James Bradner, Dana Farber Cancer Institute) was administered 60 mg per kg; AG221 (Agios Pharmaceuticals) was administered at 40 mg per kg. Final doses were administered approximately 1.5 hours before sacrifice.

tag: cell type

value: CD45.2+ LSK

value: Combined Therapy


title: BMT722-WT-B30

value: Wild Type


title: BMT722-WT-B28


title: BMT722-WT-B31


title: BMT722-combo-B24


title: BMT722-combo-B25


title: BMT722-Rux-A17

value: Ruxolitinib Monotherapy


title: BMT722-AG221-A8

value: AG221 Monotherapy


title: BMT722-AG221-A9


title: BMT722-vehicle-A4

value: Vehicle


title: BMT722-Rux-A16


title: BMT722-AG221-A10


title: BMT722-vehicle-A3


title: BMT722-Rux-A14


title: 1HR_LTP_ANIMAL_3 (3' READS)

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

description: library strategy: 3'READS

data_processing:
Alligned to mm9 using bowtie-2
identifying pA site supporting reads and clustering of pA site
calculating RPM for normalized genes and analysing the changes between treatment
Genome_build: mm9

source_name: hippocampus

extract_protocol: All libraries were prepared from 1ug of RNA as described in Hoque M., et al 2013.

treatment_protocol: To induce LTP in acute hippocampal slices we used a chemical LTP protocol: 50uM forskolin for 5 minutes followed by 5 minutes of 50uM forskolin, 30mM KCl and 10mM Ca2+ ACSF. Control samples were treated for 10 minutes with ACSF containing 0.2% DMSO. Hippocampal slices were collected directly on dry ice either 1 hour or 3 hours after the treatment. (Makhinson M., 1999; Chotiner JK., 2003)

value: hippocampus

tag: condition

value: LTP

tag: age

value: 3 month old


title: Input_SOX2_Mouse_Cortex

city: Dallas

first: Derek

middle: K

last: Smith

state: Texas

address: 5323 Harry Hines Blvd, NA5.202

department: Molecular Biology

institute: The University of Texas Southwestern Medical Center

data_processing:
Genome_build: mm10
Reads were aligned to the mouse reference sequence mm10 with the Bowtie algorithm (version 1.0.0). Peak calling, peak‑gene annotation, motif discovery (parameter: 200 nucleotide window from peak center), and generation of heatmap matrices were performed using HOMER (version 4.7). Gene ontology classification was performed using HOMER and Genomic Regions Enrichment of Annotations Tool (version 2.0.2). The UCSC Genome Browser was used to visualize tag densities and multi-experiment datasets.
Supplementary_files_format_and_content: Alignment files (.bam) were generated using Bowtie (version 1.0.0). UCSC.bedGraph and peak files (.txt) were generated using HOMER (version 4.7)

source_name: Mouse Cortex

extract_protocol:
Two-month old male wide-type mouse cortex tissue (0.3 g) was dissected on ice and cut into small pieces. Then the tissues were incubated 10 ml 1.5 mM ethylene glycolbis (succinimidyl succinate, EGTA) in a long-arm cross-linker buffer (15 mM Hepes-Cl 7.6, 60 mM KCl, 15 mM NaCl, 0.34 M sucrose, 2 mM MgCl2, 1 tab/10 mL EDTA free Protease inhibitor tablet) for 20 min at room temperature. The tissue was then crosslinked with at least ﬁve volumes of freshly prepared solution (1% formaldehyde, 50 mM Hepes-KOH, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 12 min. The reaction was quenched with 1/20 volume of 2.5 M glycine and the tissue was washed twice with ice-cold PBS. The tissue was dounced in ice-cold PBS ﬁrst with the loose and later with the tight pestle and then ﬁltered through a 100 um cell strainer to remove connective tissue. The tissue was collected by centrifuge at 4 ℃ at 2000 rcf for 5 min. Resuspend each pellet of cross linked tissue in 10 ml of lysis buffer 1 (50 mM Hepes-KOH, pH 7.5; 140 mM NaCl; 1 mM EDTA;10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100, Proteinase inhibitor). Rock at 4 ℃ for 10 min. Spin at 2000 rcf for 4 min at 4 ℃. Resuspend each pellet in 10 ml of lysis buffer 2 (10 mM Tris-HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA, Proteinase inhibitor). Rock gently at 4 ℃ for 5 min. Collected nuclei pellet by spinning at 2000 rcf for 5 min at 4 ℃. Resuspended nuclei pellet in shearing buffer (50 mM HEPES [pH 8.0], 10 mM EDTA [pH 8.0], 1% SDS, EDTA-free complete protease inhibitor), and chromatin sheared for 45 min of 30 s ON and 30 s OFF until DNA fragments were 200-600 bp. Sheared chromatin (50 mg) was diluted 10-fold in immunoprecipitation buffer (50 mM HEPES (pH 8.0], 20 mM NaCl, 1 mM EDTA [pH 8.0], 0.1% Triton X-100, EDTA-free complete protease inhibitor) and immunoprecipitated with anti-SOX2 (AB5603, rabbit, 5 mg, Millipore) at 4℃ for 14 hr. Protein G magnetic Dynabeads (100 ml, Life Technologies) were used to isolate immunoprecipitated chromatin at 4℃ for 2 hr. The immunoprecipitated fraction was washed twice with immunoprecipitation buffer, twice with wash buffer (100 mM Tris-HCl [pH 9.0], 500 mM LiCl, 1% IGEPAL CA-630, 1% deoxycholic acid, and EDTA-free complete protease inhibitor) and one time with high salt wash buffer (wash buffer containing 150 mM NaCl). Chromatin was eluted in 100 ml elution buffer (1% SDS, 50 mM sodium bicarbonate) at 25℃ for 30 min with shaking. Eluted chromatin was treated with 1 ml RNase A (10 mg/ml) and 2 ml Proteinase K (40 mg/ml) at 37℃ for 1 hr, and then then crosslinking was reversed with NaCl (333 mM ﬁnal concentration) at 67℃ for 14 hr. Immunoprecipitated DNA was puriﬁed using the QIAquick PCR Puriﬁcation Kit (QIAGEN) according to the manufacturer’s speciﬁcations. Quantitative real-time PCR was performed to determine the foldenrichment of SOX2 immunoprecitated DNA relative to background in Input samples. ChIP experiments were repeated for three times, and three mice were used for each Immunoprecipitated.
Libraries were synthesized from 5 ng purified input chromatin and 5 ng purified immunoprecipitated chromatin using a NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina (New England Biolabs, E6240S) with NEBNext Multiplex Oligos for Illumina (New England Biolabs, E7335S). Replicate libraries were prepared from independent immunoprecipitations.
ChIP-seq: single end 50-base length sequencing reads were generated on an Illumina HiSeq 2500 System.

tag: transduced with <factor>

tag: antibody

value: two-month old

tag: Sex

value: male


title: IP1_SOX2_Mouse_Cortex

value: Rabbit anti-SOX2 polyclonal antibody (Millipore, AB5603)


title: 1HR_LTP_ANIMAL_2 (3' READS)

description: library strategy: 3'READS


title: 1HR_LTP_ANIMAL_1 (3' READS)

description: library strategy: 3'READS


title: IP2_SOX2_Mouse_Cortex


title: IP3_SOX2_Mouse_Cortex


title: 3HR_LTP_ANIMAL_1 (3' READS)

description: library strategy: 3'READS


title: 1HR_CTRL_ANIMAL_3 (3' READS)

description: library strategy: 3'READS

value: control


title: 1HR_CTRL_ANIMAL_2 (3' READS)

description: library strategy: 3'READS


title: 1HR_CTRL_ANIMAL_1 (3' READS)

description: library strategy: 3'READS


title: 3HR_LTP_ANIMAL_3 (3' READS)

description: library strategy: 3'READS


title: 3HR_CTRL_ANIMAL_3 (3' READS)

description: library strategy: 3'READS


title: 3HR_CTRL_ANIMAL_1 (3' READS)

description: library strategy: 3'READS


title: 3HR_CTRL_ANIMAL_2 (3' READS)

description: library strategy: 3'READS


title: 3HR_LTP_ANIMAL_2 (3' READS)

description: library strategy: 3'READS


title: 1HR_LTP_ANIMAL_2

data_processing:
Basecalls/demultiplexing performed using Illumina BaseSpace FastQ V 1.0.0
Aligned to mm10 using STAR2.4.0
Count read using HT-seq0.6.1 using Gencode Release M3 as reference
Normalization of raw counts and differential expression analysis using DESEQ2 for each timepoint separately using a multifactor analysis including both animal and treatment as factors.
Genome_build: mm10
Supplementary_files_format_and_content: bam alignment files generated using STAR2.4.0, tab-delimited text file of raw read-count files generated using HT-seq0.6.1

extract_protocol:
RNA was purified using microRNAeasy kit (Qiagen). Integrity of the eluted RNA was analyzed by a 4200 Tapestation (Agilent). RNA concentration determined by SYBR green (Qiagen).
All libraries were prepared using the TruSeq Stranded Total RNA kit with Ribo-Zero (Illumina) according to manufacturer specifications.

value: Wild type

value: 2-3 month old


title: 1HR_LTP_ANIMAL_1


title: 3HR_LTP_ANIMAL_1


title: 3HR_LTP_ANIMAL_2


title: 1HR_LTP_ANIMAL_3


title: 3HR_LTP_ANIMAL_3


title: 1HR_CTRL_ANIMAL_3


title: 3HR_CTRL_ANIMAL_3


title: 3HR_CTRL_ANIMAL_2


title: 1HR_CTRL_ANIMAL_1


title: 3HR_CTRL_ANIMAL_1


title: 1HR_CTRL_ANIMAL_2


title: anti-A9, colorectal adenocarcinoma, biological rep 3

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110  Xiangya  Road

department: Cancer  Research Institute

institute: Central South University

description: mouse treated with AOM/DSS, with anti-S100A9 antibody treament, at the end of 18 wk

data_processing:
Raw data (raw reads) were processed using NGS QC Toolkit. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to reference human genome using Tophat.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count. DEGs were identified using the DESeq functions estimate Size Factors and nbinomTest. P value < 0.05 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of DEGs was performed to explore genes expression pattern. GO enrichment and KEGG pathway enrichment analysis of DEGs were respectively performed using R based on the hypergeometric distribution.
Genome_build: mouse genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each samples

source_name: colorectum

growth_protocol: Mice were maintained in Central Sourth University Animal Facility according to the Institutional Animal Care Guidelines. All animals were housed in plastic cages (5 mice/cage) with free access to distilled water and a standard diet under specific-pathogen free (SPF) conditions of humidity (50±10%), lightning (12-h light/dark cycle) and temperature (24±0.5℃).

extract_protocol:
mirVana miRNA ISOlation Kit (Ambion#1561) extraction of RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Solexa protocols.

treatment_protocol: 5-week-old male ICR mice were randomized divided into three groups: control (i.e. no AOM/DSS and antibody treatment), AOM/DSS+IgG Ab (1.5 mg/kg), and AOM/DSS+anti-S100a9 Ab (1.5 mg/kg). Mice were intraperitoneal injected with a single dose of 10 mg/kg azoxymethane (AOM) (A5486; Sigma, MO, USA) on day 1. One week after the AOM injection, mice were given three cycles of DSS (cycle 1: 2%, 7 days; cycle 2: 1.5%, 5 days; and cycle 3: 1.5%, 5 days) in their drinking water, and then distilled water until the end of the experiment. Antibodies were administrated intravenously every two days during the three cycles of DSS treatment. Mice were sequentially killed at the end of the 18th week, and at least five mice were killed for each group at each time point.

value: ICR

value: colorectal adenocarcinoma


title: BMT722-vehicle-A1

value: CD45.2+ LSK


title: anti-A9, colorectal adenocarcinoma, biological rep 2

value: AOM/DSS, with anti-S100A9 antibody treament


title: IgG, colorectal adenocarcinoma, biological rep 2

description: mouse treated with AOM/DSS, with negative control IgG antibody treatment, at the end of 18 wk


title: Control, normal colorectal mucosa, biological rep 3

description: mouse under normal condition, no AOM/DSS, no antibody treatment

value: no AOM/DSS, no antibody treatment

value: normal colorectal mucosa


title: anti-A9, colorectal adenocarcinoma, biological rep 1


title: IgG, colorectal adenocarcinoma, biological rep 3

value: AOM/DSS, with negative control IgG antibody treatment


title: Control, normal colorectal mucosa, biological rep 2


title: Control, normal colorectal mucosa, biological rep 1


title: IgG, colorectal adenocarcinoma, biological rep 1


title: MDH-3 (miRNA)

first: Lihong

last: Xiao

address: No.105 North Road of West 3rd-ring Road.Haidian District

institute: Capital Normal University

data_processing:
Basecalls performed using the Illumina GA Pipeline.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity (unknown bases are less than 10%) or low-quality sequence (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read), then mapped to Bhy_V1.0 (unpublished) whole genome using SOAPaligner/soap2.
The transcript abundance of each gene were normalized by TPM.
Genome_build: miRBase
Supplementary_files_format_and_content: tab-delimited text files include read number and annotations for each Sample.

organism: Physcomitrium patens

source_name: Gametophores

extract_protocol:
Total RNA extracted from  hydrated (HD), mild dehydrated (MDH), severe dehydrated (SDH), partially rehydrated (PRE) and fully rehydrated (FRE) gametophores of moss P. patens.
Enrich 18-30nt RNA fragments; add 5' and 3' adaptors; cDNA sysnthesis by reverse trancription; PCR amplification using 5' and 3' adaptor primers. Qualified library for sequencing.

treatment_protocol: Plants growing in BCD mediums were subjected to hydrated (HD), mild dehydrated (MDH), severe dehydrated (SDH), partially rehydrated (PRE) and fully rehydrated (FRE) treatments.

value: moderate dehydrated tissues


title: HD-2 (miRNA)

value: hydrated tissues


title: FRE-2 (miRNA)

value: severe dehydrated tissues


title: MDH-2 (miRNA)


title: PRE-3 (miRNA)


title: PRE-2 (miRNA)


title: PRE

data_processing:
Basecalls performed using the Illumina GA Pipeline.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity (unknown bases are less than 10%) or low-quality sequence (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read), then mapped to Bhy_V1.0 (unpublished) whole genome using SOAPaligner/soap2.
The conversion rate would be calculated when we got the alignment information of whole-genome base (qmap).
Clean data were mapped to reference genome when we made sure the data quantity of clean data was qualified. After quality test, the uniquely mapped data were used to get methylation information of cytosine in whole genome after we made sure that the alignment result was qualified. Later, we used the cytosine information for standard bioinformatics analysis and personalized bioinformatics analysis.
Genome_build: phytozome V1.6
Supplementary_files_format_and_content: excel files include annotation, methylation level and methylation changes of each differentially methylated genes.

extract_protocol:
DNA extracted from  hydrated (HD), mild dehydrated (MDH), severe dehydrated (SDH), partially rehydrated (PRE) and fully rehydrated (FRE) gametophores of moss P. patens.
Fragment genome DNA to 100-300bp by Sonication, and then DNA-end repair , 3’-dA overhang and ligation of methylated sequencing adaptors are conducted. Bisulfite treatment by ZYMO EZ DNA Methylation-Gold kit. Desalting, size selection, PCR amplification and size selection again. Qualified library for sequencing.

value: partially rehydrated tissues


title: FRE

value: fully rehydrated tissues


title: FRE-3 (miRNA)


title: SDH


title: MDH


title: HD-3 (miRNA)


title: PRE-3

data_processing:
Basecalls performed using the Illumina GA Pipeline.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity (unknown bases are less than 10%) or low-quality sequence (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read), then mapped to Bhy_V1.0 (unpublished) whole genome using SOAPaligner/soap2.
The transcript abundance of each gene were normalized by RPKM.
Genome_build: phytozome V1.6
Supplementary_files_format_and_content: tab-delimited text files include read number and annotations for each Sample.

extract_protocol:
Total extracted from  hydrated (HD), mild dehydrated (MDH), severe dehydrated (SDH), partially rehydrated (PRE) and fully rehydrated (FRE) gametophores of moss P. patens.
Illumina standard protocol for HiSeq 2000 platform


title: FRE-1


title: PRE-2


title: FRE-3


title: SDH-3


title: HD


title: SDH-3 (miRNA)


title: SDH-2 (miRNA)


title: SDH-2


title: MDH-2


title: MDH-3


title: HD-3


title: SDH-1


title: HD-1


title: FRE-2


title: HD-2


title: PRE-1


title: KO6

city: Worcester

first: Javier

middle: Elbio

last: Irazoqui

state: MA

address: 368 Plantation street

department: Microbiology

institute: University of Massachusetts Chan Medical School

description: Murano_DSS_d11_(Cuffdiff_gene_differential_expression_testing).txt

data_processing:
FASTQ Groomer, V1.0.4, ASCII Quality Score encoding, summarize input
TopHat, V2.0.14, paired-end; 400 mean distance between mate pairs; 200 St Dev distance between mate pairs; report discordant alignments; mm10; preSet settings
Cuffdiff, V2.1.1., 2 replicates; classic-fpkm library normalization; pooled dispersion estimation; FDR = 0.05; Min. alignment count = 1; Bias correction using mm10
Genome_build: mm10
Supplementary_files_format_and_content: txt; contain expression values by condition, fold change, test statistic, p value, q value, significance

source_name: KO, isolated epithelial cell

extract_protocol:
number of cells: 1.3M
total volume: 600ul
collection buffer: RLT
EDTA treatment
SmartSeq2
full length cDNA libraries were prepared using template switching and whole transcriptome amplification in a slight variation of the SmartSeq2 protocol described in PMID: 24056875

tag: genotype/variation

value: KO

value: colon

value: epithelial cells

value: 10 wks

value: DSS on day11


title: WT4

description: Murano_DSS_d4__(Cuffdiff_gene_differential_expression_testing).txt

source_name: WT, isolated epithelial cell

extract_protocol:
number of cells: 900K
total volume: 600ul
collection buffer: RLT
EDTA treatment
SmartSeq2
full length cDNA libraries were prepared using template switching and whole transcriptome amplification in a slight variation of the SmartSeq2 protocol described in PMID: 24056875

value: WT

value: 12 wks

value: DSS on day4


title: WT2

description: Murano_DSS_d0_(Cuffdiff_gene_differential_expression_testing).txt

extract_protocol:
number of cells: 1.5M
total volume: 600ul
collection buffer: RLT
EDTA treatment
SmartSeq2
full length cDNA libraries were prepared using template switching and whole transcriptome amplification in a slight variation of the SmartSeq2 protocol described in PMID: 24056875

value: DSS on day0


title: WT1

extract_protocol:
number of cells: 2M
total volume: 600ul
collection buffer: RLT
EDTA treatment
SmartSeq2
full length cDNA libraries were prepared using template switching and whole transcriptome amplification in a slight variation of the SmartSeq2 protocol described in PMID: 24056875


title: KO5

extract_protocol:
number of cells: 1.2M
total volume: 600ul
collection buffer: RLT
EDTA treatment
SmartSeq2
full length cDNA libraries were prepared using template switching and whole transcriptome amplification in a slight variation of the SmartSeq2 protocol described in PMID: 24056875


title: KO3

extract_protocol:
number of cells: 2.4M
total volume: 600ul
collection buffer: RLT
EDTA treatment
SmartSeq2
full length cDNA libraries were prepared using template switching and whole transcriptome amplification in a slight variation of the SmartSeq2 protocol described in PMID: 24056875


title: KO1

extract_protocol:
number of cells: 3.2M
total volume: 600ul
collection buffer: RLT
EDTA treatment
SmartSeq2
full length cDNA libraries were prepared using template switching and whole transcriptome amplification in a slight variation of the SmartSeq2 protocol described in PMID: 24056875


title: CARDIAC-CDL4

city: Philadelphia

first: Jason

middle: Adam

last: Mills

state: PA

address: 422 Curie Blvd

department: Ophthalmology

institute: The University of Pennsylvania

data_processing:
Align pair-ended reads to reference genome using STAR (version 2.5.1b),  in a 2-pass mode.
The first pass mapped reads to known splice junctions in reference transcriptome (Illumina iGenome) during alignment while allowing for detection of novel junction sites.
Junction sites detected from multiple samples by the first pass were collected, combined and filtered.
The second pass re-aligned reads to the reference genome and transcriptome, plus the novel junction sites detected by the first pass.
Aligned reads were mapped to known genes. Only reads with both ends uniquely mapped to a gene were assigned to that gene to get its read count. Read counts of 3 technical replicates were combined.
Genome_build: NCBI GRCh38

source_name: Cardiomyocytes

growth_protocol: iPSC samples were maintained in HES media containing 5ng/mL of bFGF

extract_protocol:
Samples were collected and total RNA was isolated using Trizol reagent then collected on Purelink RNA isolation column with DNASE treatment
RNA-seq libraries were prepared with Illumina TruSeq RiboZero Sample Prep kits.  Samples sequenced on a HiSeq 2500 (Illumina), using the paired end protocol with 100 bp read length to obtain three technical sequencing replicates per sample, each individual had three techincal replicates

value: iPSC-derived cardiomyocytes

tag: Stage

value: Day 18 post-induction


title: CARDIAC-WT3


title: KO2

extract_protocol:
number of cells: 1.6M
total volume: 600ul
collection buffer: RLT
EDTA treatment
SmartSeq2
full length cDNA libraries were prepared using template switching and whole transcriptome amplification in a slight variation of the SmartSeq2 protocol described in PMID: 24056875


title: CARDIAC-CDL1


title: WT6


title: WT3

extract_protocol:
number of cells: 1.9M
total volume: 600ul
collection buffer: RLT
EDTA treatment
SmartSeq2
full length cDNA libraries were prepared using template switching and whole transcriptome amplification in a slight variation of the SmartSeq2 protocol described in PMID: 24056875


title: WT5

extract_protocol:
number of cells: 2.1M
total volume: 600ul
collection buffer: RLT
EDTA treatment
SmartSeq2
full length cDNA libraries were prepared using template switching and whole transcriptome amplification in a slight variation of the SmartSeq2 protocol described in PMID: 24056875


title: CDLS2

source_name: iPSC

value: Human derived -iPSCs

tag: passage

value: NIPBL+/-


title: MDH-1

value: moderate dehydrated tissues


title: CDLS3


title: WT4

value: CTRL


title: CARDIAC-CDL2


title: WT1


title: WT2


title: CARDIAC-WT2


title: CHD6

city: Shanghai

first: Shengli

last: Li

address: 270 Dong An Road

institute: Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences

description: Coronary Heart Disease sample6

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat
mRNA and lncRNA annotated in GENCODEv25 were quantified using featureCounts, and circular RNA were identified and quantified by ACFS
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Blood exosome

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using ribosome minus RNAseq protocols

tag: tissue

value: Blood exosome

tag: disease state

value: Coronary Heart Disease


title: CHD5

description: Coronary Heart Disease sample5


title: CHD4

description: Coronary Heart Disease sample4


title: CDLS1


title: KO4

value: KO


title: WT3


title: CHD3

description: Coronary Heart Disease sample3


title: CHD1

description: Coronary Heart Disease sample1


title: CHD2

description: Coronary Heart Disease sample2


title: CARDIAC-WT4


title: Day 0

city: San Antonio

first: Yidong

last: Chen

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

description: small RNA

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed, mapped to contamination library, and then unmapped reads mapped to matured miRNA library, and measured miRNA read counts by using Illumina Flicker v3.0
Genome_build: hg19
Supplementary_files_format_and_content: After using Flicker, the processed data files are in tabular format. The first column contains the miRNA name, the second column contains the read counts, and the third column contains the normalized read counts (Normalized count = (Column2/total count)*1 million))

source_name: hiPSCs differentiation at day 0

growth_protocol: Three oriP/EBNA—based episomal vectors (obtained from Addgene), pEP4EO2SEN2K, pEP4EO2SET2K, and pCEP4-M2L were co-transfected into 2X10^6 human newborn fibroblasts (ATCC CRL-2703) via nucleofection using Amaxa 4D-nucleofector system. The transfected fibroblasts were placed on Matrigel-coated dishes in human fibroblast medium (DMEM, 10% FBS, 2mM L-glutamine, 50U/ml penicillin + 50 mg/ml streptomycin). On day one post-transfection, the fibroblast medium was replaced with human embryonic stem cell (hESC) medium (GlobalStem, Molecular Transfer, Inc.), supplemented with 20% KnockOut™ serum (Invitrogen) and 0.5mM sodium butyrate (Invitrogen). Culture medium was refreshed every other day. Around 18 days, the visible ESC-like morphology colonies were picked and transferred to MEF feeder layers in hESC medium supplemented with 20ng/ml of basic fibroblast growth factor

extract_protocol:
1 ug of total RNAs collected each at different time point during the differentiation and maturation process of human iPSC were also used in the small RNA protocol with the TruSeq™ Small RNA sample prep kit v2 (Illumina) according to the instructions of the manufacturer.
Illumina TruSeq small RNA library protocol

value: hiPSCs differentiation at day 0

tag: days of differentiation


title: Day 95

description: small RNA

source_name: hiPSCs differentiation at day 95

value: hiPSCs differentiation at day 95


title: Day 115

description: small RNA

source_name: hiPSCs differentiation at day 115

value: hiPSCs differentiation at day 115


title: Oxstress total RNA control replicate 2

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

data_processing:
Raw reads from sequencing were aligned on hg19 reference genome using STAR aligner with default parameters.
Aligned reads have been used with FeatureCounts software to summarize counts on the genomic features listed on hg19 annotation
Genome_build: hg19
Supplementary_files_format_and_content: Tab-deliminted text file containing raw counts for each gene in annotation

source_name: HUVEC cell line

extract_protocol:
Extraction was performed following manufacturer instructions for Nugen OVATION RNA-Seq System V2
Library preparation was performed following manufacturer instructions for Nugen OVATION Ultralow Library Systems

tag: cell line

value: HUVEC

value: control


title: Day 55

description: small RNA

source_name: hiPSCs differentiation at day 55

value: hiPSCs differentiation at day 55


title: Day 35

description: small RNA

source_name: hiPSCs differentiation at day 35

value: hiPSCs differentiation at day 35


title: Oxstress total RNA control replicate 3

tag: treatment


title: Oxstress total RNA h2o2 36h replicate 3


title: Oxstress total RNA h2o2 36h replicate 2


title: Day 75

description: small RNA

source_name: hiPSCs differentiation at day 75

value: hiPSCs differentiation at day 75


title: Day 25

description: small RNA

source_name: hiPSCs differentiation at day 25

value: hiPSCs differentiation at day 25


title: Oxstress total RNA h2o2 36h replicate 1


title: Oxstress total RNA h2o2 16h replicate 2


title: oxstress small RNA control replicate 3 sequencing 1

description: small RNA

data_processing:
Raw reads from sequencing were trimmed from adapter using Trimmomatic software and aligned on hg19 reference genome using BWA aligner with default parameters.
Aligned reads have been used with FeatureCounts software to summarize counts on the miRBase v21 annotation of microRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-deliminted text file containing raw counts for each miRNA in annotation

extract_protocol:
Extraction was performed following manufacturer instructions for TruSeq Small RNA Library Preparation Kit
Library preparation was performed following manufacturer instructions for TruSeq Small RNA Library Preparation Kit


title: Oxstress total RNA h2o2 16h replicate 1


title: Day 10

description: small RNA

source_name: hiPSCs differentiation at day 10

value: hiPSCs differentiation at day 10


title: Oxstress total RNA control replicate 1


title: oxstress small RNA control replicate 2 sequencing 1

description: small RNA


title: oxstress small RNA control replicate 1 sequencing 2

description: small RNA


title: d130_non-adherent_us1_infected.CTTGGAA

city: Silver Spring

first: Mangala

last: Rao

state: MD

address: 503 Robert Grant Avenue

institute: WRAIR

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with custom demultiplexer written in python
Alignments performed with STAR 2.0.4b
Gene counts dervied with Subread:featureCount 1.45 and normalized with CPM and RPKM transformations
Genome_build: Ensembl GRCh38.76
Supplementary_files_format_and_content: Gene Counts

source_name: monocyte-derived macrophage

growth_protocol: PBMCs from healthy HIV-1 seronegative donors were isolated by Ficoll density gradient centrifugation and monocytes were enriched from the PBMCs by plastic adherence in 24-well plates, and differentiated into monocyte-derived macrophages (MDM) in 1ml M-CSF media  The non-adherent MDM were isolated from their adherent counterparts by repeated gentle washes with monocyte media. The non-adherent MDM were gently aspirated, and collected in 50ml tubes. Accutase (500μl) was added to the remaining adherent MDM, and the cultures were incubated at 37oC/5%CO2 for 20 minutes, to detach the cells. The detached MDM were transferred into 50ml tubes, and washed with monocyte media.

extract_protocol:
RNA was isolated from uninfected and HIV-1 infected MDM using the Qiagen RNeasy Mini Kit
Clontech Smarter

treatment_protocol: For HIV-1 infection, polybrene  (2mg/ml) was added to the MDM cultures during the last 30 minutes of the in vitro culture, before subsequent exposure to HIV-1.

value: monocyte-derived macrophage

tag: phenotype

value: Siglec-1 hi CD4+

tag: hiv-1 infection status

value: Infected


title: oxstress small RNA control replicate 3 sequencing 2

description: small RNA


title: oxstress small RNA control replicate 2 sequencing 2

description: small RNA


title: d130_adherent_us1_infected.TTTTCGG

value: Siglec-1 low CD4-


title: HFC

description: small RNA

source_name: human fibroblast cells

value: human fibroblast cells


title: Day 45

description: small RNA

source_name: hiPSCs differentiation at day 45

value: hiPSCs differentiation at day 45


title: d130_adherent_uninfected.TTCGCTG

value: Uninfected


title: d124_non-adherent_us1_infected.TATCTTA


title: Oxstress total RNA h2o2 16h replicate 3


title: d124_adherent_us1_infected.TCCGGGA


title: d124_adherent_uninfected.CCAGGCA


title: d002_non-adherent_us1_infected.TTTCAGA


title: d124_non-adherent_uninfected.ACAGATA


title: oxstress small RNA h2o2 16h replicate 1 sequencing 2

description: small RNA


title: oxstress small RNA h2o2 16h replicate 1 sequencing 1

description: small RNA


title: oxstress small RNA h2o2 16h replicate 3 sequencing 1

description: small RNA


title: oxstress small RNA h2o2 16h replicate 3 sequencing 2

description: small RNA


title: d002_adherent_us1_infected.AACGGAG


title: d002_non-adherent_uninfected.AGACTGA


title: oxstress small RNA h2o2 16h replicate 2 sequencing 2

description: small RNA


title: oxstress small RNA h2o2 16h replicate 2 sequencing 1

description: small RNA


title: d002_adherent_uninfected.AGGACCT


title: d130_non-adherent_uninfected.AAACCTT


title: Input for RING1B replicate 2

city: Boston

first: Mitzi

last: Kuroda

address: 77 Ave. Louis Pasteur

institute: Brigham & Women's Hospital

data_processing:
Raw FASTQ files were quality filtered using the FASTX-toolkit ‘fastq_quality_filter’ tool (http://hannonlab.cshl.edu/fastx_toolkit/) so that only reads containing a Qual score of ≥ 20 at least 80% of base positions were kept.
Filtered reads were aligned to the hg19 human genome annotation using Bowtie2 with default parameters (Langmead et al. 2009). Reads with a MAPQ ≥ 20 were kept and extended to an estimated fragment length of 150 bp using deepTools (Ramirez et al. 2014).
Peaks were called for each IP replicate using HOMER ‘findPeaks’ tool with a matched input as control. Considering the broad nature of peaks upon visual inspection, we set peak parameters so that the minimum peak size was 1000 bp and the minimum allowable distance between peaks was 2500 bp.
Common peaks from two biological replicates were identified using DiffBind (R Bioconductor) for each IP and these common peaks sets were used for downstream analyses.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files showing RPM normalized tag density

source_name: hES HUES64

growth_protocol: HUES64 cells were cultured at 37° C in mTeSR 1 media (STEMCELL Technologies) on plates coated with Matrigel (Corning). Media was replaced daily and cells were passaged with 0.05 M EDTA/PBS.

extract_protocol:
ChIP was performed in HUES64 cells using the Myers lab ChIP-seq protocol (http://myers.hudsonalpha.org/documents/Myers%20Lab%20ChIP-seq%20Protocol%20v041610.pdf) with the following modifications. Nuclei were sonicated using a BioRuptor (Diagenode) for 20 cycles (30 sec on/30 sec off) on high power. After centrifugation at 4°C for 15 min at 20,000 rcf., 5% of total chromatin was set aside for input and the remainder was incubated with 10 ug of anti-BRD1 (Abcam, ab71877) or anti-RING1B (Abcam, ab3832) overnight at 4° C. Chromatin/antibody complexes were captured by incubation with Protein A Dynabeads (Invitrogen) for 2 hr at 4° with rotation. After cross-link reversal, DNA was purified by phenol-chloroform exctraction and ethanol precipitation. Illumina ChIP-seq libraries were prepared using the NEBNext ChIP-seq library preparation kit (New England Biolabs) and sequenced as described above.
ChIP

tag: chip antibody

value: No antibody


title: IP for BRD1 replicate 1

value: anti-BRD1 (Abcam, ab71877)


title: IP for BRD1 replicate 2


title: Input for BRD1 replicate 1


title: Input for BRD1 replicate 2


title: IP for RING1B replicate 2

value: anti-RING1B (Abcam, ab3832)


title: T-PLL_10

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

data_processing:
Alignment was performed with TopHat2.
For quantification and analysis of variants Avadis NGS was used.

source_name: Peripheral blood mononuclear cells

extract_protocol:
After density gradient centrifugation, peripheral blood mononuclear were stained with anti CD3 FITC and CD4 PE antibodies and sorted by FACS. RNA was extracted with TRIzol and purified with the RNeasy Mini Kit.
Libraries were prepared using the TruSeq platform according to manufacturer´s giudelines

tag: cell type

value: sorted CD3 pos CD4 pos T cells

tag: rna library preparation

value: TruSeq RNA Library Preparation Kit v2

value: T-cell prolymphocytic leukemia


title: T-PLL_38


title: T-PLL_8


title: oxstress small RNA control replicate 1 sequencing 1

description: small RNA

value: HUVEC


title: T-PLL_7


title: T-PLL_6


title: IP for RING1B replicate 1


title: T-PLL_11


title: T-PLL_5


title: T-PLL_4


title: T-PLL_2


title: Input for RING1B replicate 1


title: Donor_7

value: MACS enriched CD3 pos T cells

value: healthy


title: Donor_6


title: Donor_5


title: Donor_2


title: T-PLL_1


title: input_yw_wing

data_processing:
To trim adaptor sequences, Cutadapt ver. 1.2.1 (Martin 2011) was used. For the alignment, the trimmed reads were mapped to the Drosophila genome (dm3 assembly) using Bowtie ver. 12.0 (Langmead et al. 2009) with a parameter (-m 1).
Consistency of replicates was checked by genome-wide correlation analysis and by visual inspection.
Only uniquely aligned reads were used for the entire analyses. To obtain input normalized profiles, callpeak function was used with parameters (-B --nomodel --extsize 75 --SPMR) and bgdcmp function (-m FE) using MACS. Ver.2 (Zhang et al. 2008).
Genome_build: dm3
Supplementary_files_format_and_content: tdf (wig) and IP fold enrichment profile compared to input

organism: Drosophila melanogaster

source_name: Developmental Stage Imaginal Disc wing disc

extract_protocol:
We followed the BioTAP-XL protocol as described in (Alekseyenko et al. 2015). In brief, 12-24 hr old embryos from transgenic fly lines expressing BioTAP-N-Br140 were collected and stored for up to 3 days at 4°C. Embryos were cross-linked with 3% formaldehyde, extracts were prepared as described, and snap-frozen in liquid nitrogen for storage at -80°C. 20 grams of embryos were used for each experiment. S2 cell lines stably expressing BioTAP-N-Br140, BioTAP-N-dBRD4, and dBRD4-C-BioTAP were grown at 26.5°C to a density of ∼1 × 107 cells per milliliter using 500 mL of HyClone CCM3 serum-free medium in 2.8-L Fernbach glass flasks with shaking at 90 rpm. Cross-linked nuclear extracts from S2 cells were prepared from a total of 5 × 109 cells. After sonication, tandem affinity purification was performed to purify the BioTAP-tagged bait along with its protein interaction partners and associated genomic DNA. Genomic localization was determined by high-throughput sequencing of libraries generated from the tandem affinity-purified material using the NEBNext ChIP-seq library preparation master mix set for Illumina (New England Biolabs, catalog no. E6240S) and TruSeq adaptors (Illumina). Imaginal disc ChIP-seq was performed as described in Langlais et al (Langlais et al. 2012) with some modifications. 50~100 wing discs or haltere and 3rd leg discs were collected from dissection of 3rd instar larvae, crosslinked in 2% formaldehyde and sonicated using a BioRuptor (Diagenode) for 15 cycles (30 sec on/30 sec off) on high power. 5% of the total volume of sonicated chromatin was saved for input. ChIP was performed with 1:200 dilutions of anti-H3K27me3 (Cell Signaling), anti-H3K27ac (Active Motif). DNA was purified from immunoprecipitated samples. Illumina ChIP-seq libraries for H3K27me3 and H3K27ac were prepared using the library preparation kit (New England Biolabs) and sequenced as described above.
Libraries for sequencing were prepared using standard Illumina protocols.

tag: developmental stage

value: Third instar larvae

tag: genotype

value: wildtype


title: H3K27ac_IP_wing_replicate2

value: Developmental Stage Imaginal Disc wing disc

tag: antibody


title: H3K27me3_IP_wing_replicate2


title: input_wing


title: Donor_1


title: H3K27ac_IP_wing_replicate1


title: input_yw_haltere

source_name: Developmental Stage Imaginal Disc haltere and third leg disc


title: H3K27me3_IP_haltere_replicate1

value: Developmental Stage Imaginal Disc haltere and third leg disc


title: BioTAP-N-Br140_input_S2_replicate1

source_name: Embryo-derived cell-line

value: Embryo-derived cell-line

value: Late embryonic stage


title: BioTAP-C-Fs(1)h_IP_S2_replicate1


title: BioTAP-C-Fs(1)h_input_S2_replicate1


title: BioTAP-N-Fs(1)h_IP_S2_replicate1


title: H3K27ac_IP_haltere_replicate2


title: BioTAP-N-Br140_IP_S2_replicate1


title: input_haltere


title: BioTAP-N-Fs(1)h_input_S2_replicate1


title: Fs(1)h_IP_emb_replicate3

source_name: Developmental Stage Embryo 12-24h

value: Developmental Stage Embryo 12-24h

value: Embryo 12-24h


title: Fs(1)h_input_emb_replicate3


title: Fs(1)h_input_emb_replicate2


title: H3K27me3_IP_wing_replicate1


title: Fs(1)h_input_emb_replicate1


title: Fs(1)h_IP_emb_replicate1


title: BioTAP-N-Br140_input_emb_replicate12


title: BioTAP-N-Br140_input_emb_replicate1


title: BioTAP-N-Br140_IP_emb_replicate1


title: H3K27me3_IP_haltere_replicate2


title: H3K27ac_IP_haltere_replicate1


title: BioTAP-N-Br140_IP_emb_replicate2


title: M27H4 empty vector empty vector control, biological rep2, technical replicate 2

city: Heidelberg

first: Reka

last: Toth

address: Im Neuenheimer Feld 280

institute: DKFZ

description:
M27-vec2b
processed data column: AS-145087-LR-20283

data_processing:
adapter trimming with cutadapt
alignment with HISAT2 --rna-strandness RF, --max-intronlen 20000, --no-unal, --dta
transcript assembly with Stringtie -eB
calculate raw counts with Stringtie prepDE
calculate logcpm values with edgeR
Genome_build: mm10, GRCm38 assembly (release 85)
Supplementary_files_format_and_content: Raw count data in a comma-separated .csv file and cpm data in .txt file

source_name: murine cell line derived from a mammary gland tumor of the C3(1)SV40 TAg mouse model

growth_protocol: DMEM +10% FCS in a humidified atmosphere at 5% CO2 and 37°C

extract_protocol:
Total RNA isolation with RNeasy Mini Kit (Qiagen), ribodepletion with Ribo-Zero® Gold rRNA Removal Kit, purification with RNAeasy MinElute Kit (Qiagen)
SureSelect Strand-Specific Library Preparation Kit

treatment_protocol: LNA antisense Gapmer-mediated knockdown of Esrp2-as in the M6 cell line, and overexpression of Esrp2-as in M27H4 and 3T3-L1 cell lines

value: empty vector control


title: 3T3-L1 empty vector empty vector control, biological replicate 1, technical replicate 2

description:
3T3-vec2b
processed data column: AS-145089-LR-20283

source_name: murine preadipocyte cell line


title: 3T3-L1 empty vector empty vector control, biological replicate 1, technical replicate 1

description:
3T3-vec2a
processed data column: AS-145089-LR-20282


title: 3T3-L1 Esrp2-as overexpression, biological replicate 2

description:
3T3-oe3
processed data column: AS-145097-LR-20998

value: Esrp2-as overexpression


title: 3T3-L1  Esrp2-as overexpression, biological replicate 1, technical replicate 2

description:
3T3-oe2b
processed data column: AS-145093-LR-20283


title: 3T3-L1 empty vector empty vector control, biological replicate 2

description:
3T3-vec3
processed data column: AS-145096-LR-20998


title: M27H4 empty vector empty vector control, biological rep1

description:
M27-vec1
processed data column: AS-145034-LR-20284


title: M27H4 empty vector empty vector control, biological rep3

description:
M27-vec3
processed data column: AS-145095-LR-20998


title: M27H4  Esrp2-as overexpression, biological rep3

description:
M27-oe3
processed data column: AS-143065-LR-20998


title: 3T3-L1  Esrp2-as overexpression, biological replicate 1, technical replicate 1

description:
3T3-oe2a
processed data column: AS-145093-LR-20282


title: M6 empty vector control, biological rep1

description:
M6-ctrl1
processed data column: AS-143700-LR-20281


title: M27H4  Esrp2-as overexpression, biological rep2, techical replicate 1

description:
M27-oe2a
processed data column: AS-145092-LR-20282


title: M27H4  Esrp2-as overexpression, biological rep1

description:
M27-oe1
processed data column: AS-143051-LR-20284


title: M6 empty vector control, biological rep2, technical replicate 3

description:
M6-ctrl2c
processed data column: AS-145094-LR-20283


title: M27H4  Esrp2-as overexpression, biological rep2, techical replicate 2

description:
M27-oe2b
processed data column: AS-145092-LR-20283


title: M6 Esrp2-as knockdown, biological rep2, technical replicate 2

description:
M6-kd2b
processed data column: AS-143062-LR-20998

value: Esrp2-as knockdown


title: M6 empty vector control, biological rep2, technical replicate 1

description:
M6-ctrl2a
processed data column: AS-145090-LR-20281


title: M6 Esrp2-as knockdown, biological rep2, technical replicate 1

description:
M6-kd2a
processed data column: AS-145091-LR-20281


title: Fs(1)h_IP_emb_replicate2


title: M6 Esrp2-as knockdown, biological rep1

description:
M6-kd1
processed data column: AS-143702-LR-20281


title: wt_2

city: Liège

first: Elise

last: PEYRE

address: Quartier Hopital Avenue Hippocrate 15, Tour B36

department: Giga neuroscience

country: Belgium

institute: University of Liège

description:
total RNA ribosome depleted
Isoform processed data.xlsx
Processed data.xlsx

data_processing:
Illumina RTA V2 software used for basecalling.
Trimming was done with the bcl2fastq2 Conversion Software v2.19  using defaut settings
Mapping and differential expression was done using the Tuxedo workfow, using Bowtie2
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include on FPKM values and stastistical analysis of differences between Wt and cKO samples

source_name: wt, FACS sorted Interneurons from ganglionic eminences

extract_protocol:
Ganglionic eminences were dissected from E13.5 embryos and cells were dissociated with Papain and FACS sorted thanks to the Dlx5,6 CRE GFP transgene. RNA was extracted from fesh FACS sorted cells and  purified on columns (Quiagen RNeasy mini kit).
RNA libraries were prepared for sequencing using standard Illumina protocols with the TruSeq® Stranded Total RNA kit

tag: strain

value: CCP1 Wt/Wt; Dlx5,6 CRE GFP

tag: age

value: FACS sorted interneurons from ganglionic eminences


title: cko_3

source_name: cko, FACS sorted Interneurons from ganglionic eminences

value: CCP1 lox/lox; Dlx5,6 CRE GFP


title: wt_3


title: cko_1


title: cko_2


title: M27H4 empty vector empty vector control, biological rep2, technical replicate 1

description:
M27-vec2a
processed data column: AS-145087-LR-20282

tag: genotype/variation


title: FVB/N_WT_24w_#3

first: Katharina

last: Heilmann

institute: German Cancer Research Centre

data_processing:
Basecalling was performed with Illumina Real-Time Analysis (RTA) Software 1.13.48
Sequencing reads were trimmed for adapter sequence (SeqPrep v0.4 ) and then aligned to the mm10 reference assembly with BWA (bwa-0.6.1-tpx) with default parameters
Reads were filtered to remove duplicates with Picard (version 1.61) and to remove reads of alignment quality smaller than 1 with samtools (version 1.3) (MAPQ <1)
For calling of differentially methylated regions (DMRs), reads of three animals (matched for age and genotype) were combined in one tag directory and processed with HOMER findPeaks (FDR<0.001, p-value<0.0001, size 150bp, minDist 300bp)
DMRs overlapping between age groups were identified with HOMER mergePeaks (-d 300 -venn)
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph files were produced with HOMER software suite (Heinz et al. , Mol Cell, 2010) applying make UCSCfile

source_name: FVB/N_WT_24w_mammary gland

extract_protocol:
genomic DNA was isolated with AllPrep DNA&RNA kit (Qiagen, Germany) and fragmented to ≈ 150bp with Covaris S2 sonicator. Enrichment for highly methylated fragments was performed with Methyl CpG immunoprecipitation (MCIp) according to Sonnet et al, (Methods Mol Biol, 2013) with 5µg of genomic DNA as input and 60µg of MBD2 fusion protein
10ng MCIP-enriched DNA was used as input for library preparation according to the manufacturer's protocol  for the Illumina ChIP Sample Prep Kit with minor modifications.

tag: strain background

value: FVB/N

value: 24 weeks

value: wild type

value: mammary gland


title: FVB/N_WT_24w_#2

tag: tissue


title: M6 empty vector control, biological rep2, technical replicate 2

description:
M6-ctrl2b
processed data column: AS-145094-LR-20282


title: C3(1)SV40TAg _24w_#2

source_name: C3(1)SV40TAg_24w_mammary gland tumor

value: mammary gland tumor


title: C3(1)SV40TAg _20w_#2

source_name: C3(1)SV40TAg_20w_mammary gland tumor

value: 20 weeks


title: C3(1)SV40TAg _24w_#1


title: FVB/N_WT_20w_#2

source_name: FVB/N_WT_20w_mammary gland


title: C3(1)SV40TAg _24w_#3


title: FVB/N_WT_20w_#1


title: C3(1)SV40TAg _20w_#3


title: tatcre-sample-replicate-2-female

city: Edmonton

first: Guanxiang

last: Liang

state: Alberta

address: 410 Agriculture/Forestry Centre

country: Canada

institute: University of Alberta

data_processing:
Reads were QC by trimmomatic following dwfault parameters for single end reads
Good qulaity reads mapped to mm10 genome by tophat2 using default parameters
BAM files were processed by samtools and gene reads number were counted by htseq-count.txt
Genome_build: mm10
Supplementary_files_format_and_content: genes reads number

source_name: female_splenic B cell_TAT-CRE

growth_protocol: cells from each mouse were treated with TAT-CRE in OptiMEM to delete the yy1 gene and then grown in RPMI medium along with anti-IgM and 20% FBS for 48 hours

extract_protocol:
Follicular B cells were purified from spleen by positive selection using anti-CD23 antibody and Streptavidin coated microbeads (Milteny Biotech) according to the manufacturer’s instructions
Following the protocal from Illumina Truseq-Stranded RNA library kit

treatment_protocol: Treated with TAT-CRE in OptiMEM to delete the yy1 gene

tag: mouse strain

value: C57BL/6 yy1 f/f

tag: gender

value: female

value: splenic B cell

tag: treated with

value: TAT-CRE in OptiMEM (to delete the yy1 gene)


title: tatcre-sample-replicate-1-male

source_name: male_splenic B cell_TAT-CRE

value: male


title: tatcre-sample-replicate-3-male


title: tatcre-sample-replicate-3-female


title: tatcre-sample-replicate-2-male


title: wt_1


title: naive-sample-replicate-2-female

source_name: female_splenic B cell_naïve

value: none (naïve cells)


title: naive-sample-replicate-3-male

source_name: male_splenic B cell_naïve


title: naive-sample-replicate-3-female


title: naive-sample-replicate-2-male


title: tatcre-sample-replicate-1-female


title: C3(1)SV40TAg _20w_#1


title: naive-sample-replicate-1-male


title: mock-sample-replicate-3-male

source_name: male_splenic B cell_mock

value: mock


title: mock-sample-replicate-3-female

source_name: female_splenic B cell_mock


title: mock-sample-replicate-2-male


title: FVB/N_WT_24w_#1


title: FVB/N_WT_20w_#3


title: mock-sample-replicate-2-female


title: sMOsrsf5a_rep2

first: Marine

last: Joris

address: Chemin de la vallée 4 Quartier de la vallée 1

department: Life Sciences

data_processing:
Reads quality was assessed using fastXtool Kit
Reads were mapped using TopHat .2.0.9 (-r 200, -p1, -m2, --solexa1.3-quals)
Gene expression was measured from the mapped reads by using HT-seq-count (intersection-strict mode)
Differentially expressed genes were determined using the R package DESeq2
MATS version 3.0.9 was used to detect differential alternative splicing events(-t paired -len 101 -a 8 -r1 178,176 –r2 183,195 -sd1 60,60 –sd2 61,67 –analysis P, a gtf file coming from the Zv9 version of the genome was also given to MATS). Insert sizes were calculated using Picard Tools.
Genome_build: Zv9
Supplementary_files_format_and_content: txt file containing read counts for all genes in all samples, csv file containing deseq2 output, directories containing all MATS results in txt files

organism: Danio rerio

source_name: whole zebrafish embryos

growth_protocol: Embryos were raised and staged according to standard protocol. Embryos were kept in E3 medium at 28°C until harvested.

extract_protocol:
For each conditions, 80 (previously dechorionated) embryos were euthanized at 48hpf with tricaine (at the recommended dose). Embryos were lysed and homogenized in TRIzol Reagent (Sigma Aldrich) using a G22 and G26 needle. RNA were extracted using chloroform and precipitated with isopropanol. Another purification stage was performed using the Rneasy mini kit (Qiagen).
True Seq Kit (Illumina). 1 µg of RNA was used for library construction.

treatment_protocol: The night prior to injection fish were set up in breeding tanks. The following morning the male and female were allowed to mate and eggs were collected in petri dishes in E3 medium. Eggs were injected at one cell stage with 3ng of control or sMOsrsf5a morpholino and replaced in petri dishes in E3 at 28°C. At the end of the day, dead embryos were removed and sorted using rhodamine Dextran.

value: AB

value: whole embryos

tag: morpholino target


title: mock-sample-replicate-1-male


title: mock-sample-replicate-1-female


title: sMOsrsf5a_rep1


title: CtrlMO_rep2

value: control


title: AU565_MBD2-2

city: Lyon

first: Robert

last: Dante

address: 28, rue Laennec

department: Department of Tumoral Escape

country: France

institute: Cancer Research Center – Lyon

description:
processed data file:
AU565_NT_vs_AU565_MBD2_Cuffdiff.txt

data_processing:
Reads were aligned on the UCSC Homo sapiens hg19 genome using TopHat2.
Differential expression analysis was performed using Cuffdiff from Galaxy web site
Genome_build: hg19
Supplementary_files_format_and_content: Cuffdiff  txt files contain, FPKM,  log2 of the fold change, and Pvalue, and qvalue for each studied of conditions.

molecule: polyA RNA

growth_protocol: SKBR3 and AU565 cell lines were cultivated as the manufacturer’s instructions (ATCC).

extract_protocol:
Total RNA was extracted with the NucleoSpin RNA kit (Macherey-Nagel, Hoerdt, France) following the manufacturer's instructions. RNA purity and integrity were examined on agarose gel, and quantified with a NanoDrop 1000 (Thermo Scientific, Wilmington, DE).
Illumina TruSeq RNA sample preparation Kit.

treatment_protocol: SKBR3 and AU565 were treated by CAF-CMs or DAC or sictrl and siMBD2 as specified in the methods section

tag: cell line

tag: treatment


title: AU565_MBD2-1


title: AU565_ctrl-2

description:
processed data file:
AU565_NT_vs_AU565_ctrl_Cuffdiff.txt

value: siCtrl


title: AU565_ctrl-1


title: AU565_DAC-2

description:
processed data file:
AU565_NT_vs_AU565_DAC_Cuffdiff.txt

value: DAC


title: Z8-1

city: Berkeley

first: Abraham

last: Morales-Cruz

state: California

address: 1 Cyclotron Road

institute: Joint Genome Institute

data_processing:
Quality trimming of raw reads was done with Sickle v.1.210 with a threshold of 20 (Q>20).
Quality filtering was done with Scythe v.0.991 with a prior of 0.4
Bowtie2 v.2.1.0  was used to map the processed reads to the reference with the following options: -q --end-to-end --sensitive --no-unal -p20.
Read counts were extracted from the bowtie2 alignments using the script sam2counts.py v.0.91
Genome_build: Vitis vinifera cv. PN40024 (http://www.genoscope.cns.fr/externe/Download/Projets/Projet_ML/data/12X/annotation/)
Supplementary_files_format_and_content: xf_raw_counts-early.txt and : tab delimited text file, raw read counts determined by mapping the sequencing reads
Supplementary_files_format_and_content: xf_raw_counts-late.txt: tab delimited text file, raw read counts determined by mapping the sequencing reads

organism: Vitis vinifera

source_name: petiole

growth_protocol: We used wild type X. fastidiosa strain Temecula1 and a wzy mutant strain. X. fastidiosa wild type and wzy mutant strains were grown for 7 days at 28°C on solid PD3 medium without or with kanamycin at 5μg/mL, respectively.

extract_protocol:
Total RNA was extracted from 0.1 g of ground tissue per sample. The frozen tissue was homogenized by inversion in 500 µl of extraction buffer (PureLink Plant RNA Reagent, Ambion cat# 12322-012) for 5 min at room temperature. After homogenization, 100µl of Plant RNA isolation Aid (Ambion cat# AM9690) was added to the suspension and mixed by inversion for 5 min at room temperature. Samples were centrifuged at top speed for 5 min at room temperature to pellet insoluble debris and other contaminants. The supernatant was transferred to a new tube and then 100µl of 5M NaCl and 300µl chloroform were added and mixed for 5 min by inversion. Samples were centrifuged at 12,000 xg for 10 min at 4oC to separate the phases, and the upper aqueous phase was transferred to a new tube. Samples were treated with DNase RNase-free (5 U) and incubated for 20 min at 37oC. After DNase treatment, 500µl of chloroform was added and mixed for 5 min as described above. To separate the phases, the samples were centrifuged again at 12,000 xg for 10 min at 4oC, and the upper aqueous phase was transferred to a new tube. An equal volume of isopropyl alcohol was added, after the samples were mixed by inversion and incubated at room temperature for 10 min. Precipitated RNA was centrifuged at 12,000 xg for 10 min at 4oC, and the supernatant was discarded. The RNA pellets were washed with 1mL of 80 % ethanol and centrifuged at 12,000 xg for 2 min at room temperature. Then the pellets were air-dried at room temperature and re-suspended in 30µl RNase-free water.
Illumina TruSeq RNA Sample Prep Kit v2 protocol

treatment_protocol: Vitis vinifera ‘Cabernet Sauvignon’ vines were needle-inoculated with either X. fastidiosa wild type, wzy mutant, or 1X PBS buffer control. Cells of X. fastidiosa strains were harvested from plates of PD3 media in 1X PBS buffer, and suspensions were adjusted to OD600 0.25. Each vine was inoculated twice (with a 20μL drop) on the main stem. Petioles were harvested at each time point and then immediately placed into liquid nitrogen.

tag: inoculation

value: X. fastidiosa wzy

tag: time point

value: 8 hours

tag: tissue position

value: local

tag: biorep


title: Z24-3

value: 24 hours


title: Z8-3


title: Z8-2


title: Z24-1


title: AU565_DAC-1


title: AU565_CAF15-1

description:
processed data file:
AU565_NT_vs_AU565_CAF15_Cuffdiff.txt

value: CAF-CM


title: Z0-3

value: 0 hours


title: Z0-2


title: AU565_CAF11-2

description:
processed data file:
AU565_NT_vs_AU565_CAF11_Cuffdiff.txt


title: naive-sample-replicate-1-female

value: C57BL/6 yy1 f/f

value: female

tag: cell type


title: AU565_CAF15-2


title: Z24-2


title: AU565_CAF12-2

description:
processed data file:
AU565_NT_vs_AU565_CA12_Cuffdiff.txt


title: Z0-1


title: AU565_CAF11-1


title: W8-3

value: X. fastidiosa wild type


title: W8-2


title: AU565_CAF8-2

description:
processed data file:
AU565_NT_vs_AU565_CAF8_Cuffdiff.txt


title: CtrlMO_rep1

tag: developmental stage


title: AU565_CAF8-1


title: AU565_NT-2


title: W24-3


title: AU565_NT-1


title: W0-3


title: W24-1


title: AU565_CAF12-1


title: SKBR3_MBD2-2

description:
processed data file:
SKBR3_NTpool_vs_SKBR3_MBD2_Cuffdiff.txt


title: W0-2


title: SKBR3_MBD2-1


title: SKBR3_ctrl-2

description:
processed data file:
SKBR3_NTpool_vs_SKBR3_ctrl_Cuffdiff.txt


title: W0-1


title: SKBR3_ctrl-1


title: C8-2

value: Control


title: C8-3


title: SKBR3_DAC-2

description:
processed data file:
SKBR3_NTpool_vs_SKBR3_DAC_Cuffdiff.txt


title: SKBR3_CAF15-1

description:
processed data file:
SKBR3_NTpool_vs_SKBR3_CAF15_Cuffdiff.txt


title: SKBR3_DAC-1


title: SKBR3_CAF12-2

description:
processed data file:
SKBR3_NTpool_vs_SKBR3_CAF12_Cuffdiff.txt


title: SKBR3_CAF15-2


title: C24-1


title: C24-3


title: SKBR3_CAF12-1


title: C0-3


title: W8-1


title: SKBR3_CAF11-2

description:
processed data file:
SKBR3_NTpool_vs_SKBR3_CAF11_Cuffdiff.txt


title: W24-2


title: C0-2


title: C0-1


title: SKBR3_CAF8-2

description:
processed data file:
SKBR3_NTpool_vs_SKBR3_CAF8_Cuffdiff.txt


title: SKBR3_CAF11-1


title: SKBR3_NT-4


title: SKBR3_CAF8-1


title: SKBR3_NT-2


title: SKBR3_NT-1


title: SKBR3_NT-3


title: WZY4WKS2

value: 4 weeks

value: systemic


title: WZY4WKS3


title: C8-1


title: WZY4WKS1


title: Visible (GS8) 8-3*,visible

city: LA

first: Sungyong

last: You

address: Beverly Blvd 8400

department: Surgery

institute: Cedars-Sinai Medical Center

description: MRI Visible (GS8)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the GRCh37/hg19 build of the Homo sapiens genome using the Subread aligner, implemented in the R subread software package.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include tag count values for every sample.

source_name: Prostate cancer tissue, FFPE

extract_protocol:
RNA was extracted from nine 10-μm sections. Tumor sections were placed in 2.0-ml RNase-free Eppendorf tubes. Sections were treated twice with 1.9 ml xylene for 5 min (min) at 55 °C while rocking. The sections were washed twice with 100% ethanol. RNA was extracted from the paraffin samples using the MasterPure™ RNA Purification Kit (Epicenter Biotechnologies, Madison, WI, USA). In an attempt to further increase RNA yield, FFPE samples were treated with 200 μg Proteinase K for 3 h at 55 °C. RNA was then treated with 20 units DNase I (Ambion, Austin, TX, USA) for 30 min and checked for residual genomic DNA by TaqMan RT-PCR targeting ACTB. If there was measurable DNA after 34 PCR cycles using 50 ng input RNA, the samples were treated with 20 units DNase I for an additional 15 min, and the assay for residual DNA was repeated. The final RNA concentration (A260:0.025) and purity (A260:A280 ratio) was measured using a NanoDrop ND-2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA).
300 ng total RNA were sent to Beijing Genomics Institute- Hong Kong. Sample quality was tested by Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, USA; supplemental Figure 2). For library preparation, total RNA was hybridized with the Probe, RNase H treated and rRNA-depleted. Then RNA was subjected to fragmentation, cDNA synthesis, adaptor ligation and PCR.
Amplified PCR product was sequenced on Illumina HiSeqTM 4000 (Illumina Inc, San Diego, CA, USA). The average depth of sequencing for each library was 26 million reads.

value: prostate

tag: tumor size


title: C24-2


title: Visible (GS8) 8-1*,visible

description: MRI Visible (GS8)


title: Visible (GS7) 7-7*,visible

description: MRI Visible (GS7)


title: Visible (GS8) 8-2*,visible

description: MRI Visible (GS8)


title: WZY4WKL3


title: WZY4WKL2


title: Visible (GS7) 7-4*,visible

description: MRI Visible (GS7)


title: Invisible (GS7) 7-1,invisible

description: MRI Invisible (GS7)


title: WZY48HS3

value: 48 hours


title: Visible (GS7) 7-5*,visible

description: MRI Visible (GS7)


title: Invisible (GS7) 7-3,invisible

description: MRI Invisible (GS7)


title: WZY48HS2


title: WZY4WKL1


title: WZY48HS1


title: Visible (GS7) 7-6*,visible

description: MRI Visible (GS7)


title: Invisible (GS6) 6-7,invisible

description: MRI Invisible (GS6)


title: WZY48HL2


title: Invisible (GS6) 6-6,invisible

description: MRI Invisible (GS6)


title: WZY48HL3


title: Visible (GS6) 6-5*,visible

description: MRI Visible (GS6)


title: WZY1WKS3

value: 1 week


title: Invisible (GS6) 6-4,invisible

description: MRI Invisible (GS6)


title: WZY48HL1


title: Invisible (GS6) 6-3,invisible

description: MRI Invisible (GS6)


title: Invisible (GS6) 6-2,invisible

description: MRI Invisible (GS6)


title: WZY1WKS2


title: WZY1WKS1


title: WZY1WKL3


title: WZY1WKL2


title: Invisible (GS6) 6-1,invisible

description: MRI Invisible (GS6)


title: WZY0HS3


title: WZY0HS2


title: WZY1WKL1


title: WZY0HL2


title: WZY0HL3


title: WZY0HL1


title: WT4WKS3


title: WT4WKL3


title: WT4WKL2


title: WT4WKS2


title: WT4WKS1


title: WT48HS3


title: WT48HS2


title: WT4WKL1


title: WT48HS1


title: WT48HL3


title: WT1WKS3


title: WT1WKS2


title: WT48HL1


title: WT1WKL3


title: WZY0HS1


title: WT1WKL1


title: WT0HS1


title: WT0HS3


title: WT0HL3


title: PNW20_C13R

city: Amherst

first: Alexander

last: Suvorov

address: 149A Goessman, 686 N.Pleasant Str

department: Environmental Health Sciences

institute: University of Massachusetts

data_processing:
Reads were mapped to the reference mouse genome (MM10) using TopHat 2 aligner.
Aligned reads were used for assembly of novel transcriptsand differential expression of novel and reference transcripts with Cuffdiff 2.1.1.
Genome_build: MM10
Supplementary_files_format_and_content: XLSX files showing Log2(FPKM) for control and exposed condition and Log2 of their FPKM ratio for each tanscript, as well as transcript coordinates and gene names.

source_name: liver

growth_protocol: Eight-week old male (30–35 g) and female (27–30 g) CD-1 mice were obtained from Charles River Laboratories (Kingston, NY, USA) and housed in a temperature (23±2◦C)- and humidity (40±10%)-controlled environment, with a 12-h light/dark cycle, and food and water available ad libitum. After 3 days of acclimation, the animals were bred and the day of vaginal plug detection was considered pregnancy day 1.

extract_protocol:
Total RNA was isolated from liver tissue using TRIzol reagent (Invitrogen).
The NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, New England BioLabs Inc., Ipswich, MA) was then used to isolate intact poly(A)+ RNA from 3 µg of total RNA. Libraries were constructed using NEBNext mRNA Library Prep Reagent Set for Illumina with multiplexing indexes from NEBNext Multiplex Oligos for Illumina (E6100 and E7335 respectively, New England BioLabs Inc., Ipswich, MA).

treatment_protocol: The dams were assigned to one of two treatment groups (n=5 per group) based on weight match, and were exposed to tocopherol-stripped corn oil (MP Biomedicals, Solon, OH) or 0.2 mg/ml solution of BDE-47 (AccuStandard, Inc., New Haven, CT; 100% purity) in tocopherol-stripped corn oil daily from pregnancy day 8 through postpartum day 21; the females were fed 1 µl/gram BW from the tip of a pipette, resulting in exposure of 0.2 mg/kg BW/day. One male pup per litter were euthanized on PND21 and 1 male pup per litter was euthanized on PNW20.

value: liver

tag: Sex

value: male

tag: exposure

value: 0.2 mg/kg BDE-47

value: postnatal week 20

tag: strain


title: PNW20_C8L

tag: tissue


title: PNW20_C19N


title: WT0HL2

value: local


title: WT0HL1


title: PNW20_X90

value: Vehicle


title: PBS4WKS3


title: PBS4WKS2


title: PNW20_X31R


title: PBS4WKS1


title: WT1WKS1


title: PNW20_X10N


title: PNW20_X31N


title: BhRE100%RWC-2

city: Beijing

first: Lihong

last: Xiao

address: No.105 North Road of West 3rd-ring Road.Haidian District

institute: Capital Normal University

data_processing:
Basecalls performed using the Illumina GA Pipeline.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity (unknown bases are less than 10%) or low-quality sequence (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read), then mapped to Bhy_V1.0 (unpublished) whole genome using SOAPaligner/soap2.
The transcript abundance of each gene were normalized by RPKM.
Genome_build: Bhy_V1.0
Supplementary_files_format_and_content: tab-delimited text files include read number for each Sample.

organism: Dorcoceras hygrometricum

source_name: Gametophores

extract_protocol:
Total RNA extracted from  desiccated (10% RWC), rehydrated to 50% RWC  (RE50% RWC) and rehydrated to 100% RWC (RE100% RWC) leaf tissues of B. hygrometrica.
Illumina standard protocol for HiSeq 2000 platform

treatment_protocol: Plants growing in MS mediums were subjected to desiccated (10% RWC), rehydrated to 50% RWC (RE50% RWC) and rehydrated to 100% RWC (RE100% RWC) treatments.

value: rehydrated to 100% RWC


title: BhRE100%RWC-1


title: BhRE50%RWC-3

value: rehydrated to 50% RWC


title: BhRE100%RWC-3


title: WT1WKL2


title: WT0HS2

value: 0 hours


title: BhRE50%RWC-2


title: PNW20_X1N


title: PNW20_C30N


title: PBS4WKL2


title: BhRE50%RWC-1


title: Bh10%RWC-3

value: dehydrated to 10% RWC


title: PND21_C8

value: postnatal day 21


title: PBS48HS2

value: Control


title: PND21_X1


title: Bh10%RWC-1


title: PBS48HS3


title: Bh10%RWC-2


title: PND21_C13


title: PND21_C22


title: PBS48HS1


title: PND21_X31


title: PBS4WKL3

value: 4 weeks


title: PBS48HL3


title: AD012_elt2Delt7D_sorted_4

city: Fort Collins

first: Erin

last: Osborne Nishimura

state: CO

address: 1870 Campus Delivery, 200 W. Lake St.

department: Biochemistry and Molecular Biology

institute: Colorado State University

description:
elt2Delt7D_sorted_4
elt-7elt-2_avg.bw

data_processing:
Raw sequence reads were mapped as single-end reads by Dr. Paul Gordon, (Genomics and Bioinformatics, University of Calgary) to the WS220 ce10 version of the C. elegans genome using Lifescope ver. 2.5. Quality control of sequence reads was assessed using FastQC version 0.52.
RNA-seq alignment files in .bam format were tabulated for read counts associated with each gene model using HTseq 0.6.1 (Anders et al., 2015), Samtools 1.3.1 (Li et al., 2011 ), and the WS235 genome feature file (WS235, Ensemble 78). The genome feature file was filtered for protein coding sequences and lifted over to the ce10 genome and renamed C_elegans_WS235_liftover_ce10.gtf. HTseq’s HTseq.scripts.count function was performed with the following options: --mode=union --stranded=no --minaqual=20. Raw counts generated by this analysis are tabulated in the document 2017-07-12_raw_counts.xlsx. Note that samples that elt-2(-) samples that did not show sufficient elt-2 gene expression reduction were filtered from analysis. This removed the sample elt2Delt7D_sorted_4.
RNA-seq count data was analyzed using DESeq2 (Love et al., 2014). An initial distance matrix analysis illustrated that the sample 'AD012_elt2Delt7D_sorted_4' did not have sufficient suppression of elt-2 expression. For this reason, this sample was filtered out of downstream analysis. DESeq2 differential gene epxression was performed by initially filtering for detected genes (> 10 counts across all samples) then analyzing using DESeq2 with Cook’s cutoff filtering set to FALSE. Count data was normalized, variance-stabilized, and log transformed using the rlog utility.
RNA-seq alignment files in .bam format were normalized for read depth, averaged, and converted into BigWig format using automated scripts that employed bedtools (bamtobed, sort, and genomecov) v2.26.0 (Quinlan et al., 2010 ), java-genomics-toolkit wigmath.Average, and the UCSC Kent utility wigToBigWig v4.
Genome_build: ce10
Supplementary_files_format_and_content: .bw files for individual samples; avg.bw files that merge like-conditions;

organism: Caenorhabditis elegans

source_name: L1 staged worms

growth_protocol: Worms were grown on NGM plates seeded with E. coli OP50 and allowed to develop at 20ºC until gravid. Embryos were collected by centrifugation (~200g, 5 min, room temperature), washed once with 50 ml of M9 buffer, bleached (5ml 6% hypochlorite with 12.5 ml 1M NaOH) until ~50% of the gravid adults had burst (4 - 6 min), then mixed with an equal volume of alkaline bleach stop solution (0.95 M Tris-HCl with 0.05 M Tris Base), vortexed briefly and centrifuged as above. Collected embryos were suspended in M9 buffer, re-centrifuged, re-suspended in 50 ml of filtered  M9 buffer, transferred to a 75 cm2 tissue culture flask and allowed to hatch overnight on a shaker at room temperature.

extract_protocol:
Starved L1 larvae were passed twice through a 27 μm nylon mesh and placed on a shaker in 50 ml tubes. Filtered worms were then passed as continual batches through a Union Biometrica Complex Object Parametric Analyzer and Sorter (COPAS) platform with Biosort Device (488 nm excitation) capable of sorting green larvae from non-green. For each sort of strains JM147 and JM199, a total of 50,000 GFP positive and 50,000 GFP negative worms were isolated and two consecutive sorts  of each type were usually pooled into one sample.  Pooled larvae were pelleted and preserved in 1 ml of TRizol and 10 μl of β-mercaptoethanol, flash frozen, and stored at -80ºC.
Total RNA extractions were performed using the Ambion PureLink RNA Mini Kit. Poly-A+ mRNA was isolated using the Life Technologies Dynabeads mRNA Direct Kit (part #61021; standard method).
Whole transcriptome libraries were prepared with the Life Technologies Solid Total RNA-Seq kit (part #4445374; standard method) using chemical fragmentation and Array Script reverse transcriptase.

tag: replicate


title: PBS48HL1


title: AD011_elt2Delt7D_sorted_3

description:
elt2Delt7D_sorted_3
elt-7elt-2_avg.bw


title: PBS48HL2


title: PND21_C19


title: PBS1WKS3

value: systemic


title: AD010_elt2Delt7D_sorted_2

description:
elt2Delt7D_sorted_2
elt-7elt-2_avg.bw


title: PND21_X10


title: PND21_C30


title: PND21_X90


title: PBS4WKL1


title: AD004_elt2D_sorted_4

description:
elt2D_sorted_4
elt-2_avg.bw


title: AD009_elt2Delt7D_sorted_1

description:
elt2Delt7D_sorted_1
elt-7elt-2_avg.bw


title: PBS1WKS2


title: PBS1WKS1


title: AD003_elt2D_sorted_3

description:
elt2D_sorted_3
elt-2_avg.bw


title: WT48HL2

value: X. fastidiosa wild type


title: AD002_elt2D_sorted_2

description:
elt2D_sorted_2
elt-2_avg.bw


title: PBS1WKL1


title: PBS1WKL2


title: AD032_elt7D_sorted_3

description:
elt7D_sorted_3
elt-7_avg.bw


title: MM_c rep3

first: Runmao

last: Lin

address: No. 12 Zhongguancun South Street, Haidian District

institute: The Institute of Vegetables and Flowers, CAAS

data_processing:
Low quality based were splited and reads length of at least 80 bp were used for analysis.
We calculated FPKM values following protocol provided by study by Trapnell et al., Nat Protoc, 2012.
Genome_build: Pochonia chlamydosporia 170 (Accession: LSBJ00000000)
Supplementary_files_format_and_content: One text file included FPKM values for genes.

organism: Pochonia chlamydosporia

source_name: mycelium

growth_protocol: The fungal strains were grown on potato dextrose agar.

extract_protocol:
RNA isolation was carried out using the RNeasy Plant Mini Kit (Qiagen) and performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Treatments were: (1) CD (nutrient rich medium) that was predicted to repress parasitism; (2) MM (nutrient-poor liquid minimal medium) that was predicted to de-repress genes associated with parasitism; and (3) MM-eggs (minimal medium with root-knot nematode eggs) that was prepared to induce parasitism.

tag: subculture

value: nutrient-poor liquid minimal medium


title: egg_b rep2

value: minimal medium with root-knot nematode eggs


title: AD001_elt2D_sorted_1

description:
elt2D_sorted_1
elt-2_avg.bw


title: egg_c rep3


title: egg_a rep1


title: MM_b rep2


title: PBS0HS3


title: PBS0HS2


title: PBS0HS1


title: AD030_elt7D_sorted_1

description:
elt7D_sorted_1
elt-7_avg.bw


title: AD031_elt7D_sorted_2

description:
elt7D_sorted_2
elt-7_avg.bw


title: AD025_wt_sorted_3

description:
wt_sorted_3
wt_avg.bw


title: CD_b rep2

value: nutrient rich medium


title: CD_c rep3


title: AD026_wt_sorted_4

description:
wt_sorted_4
wt_avg.bw


title: PBS0HL2


title: PBS0HL3


title: AD024_wt_sorted_2

description:
wt_sorted_2
wt_avg.bw


title: CD_a rep1


title: AD023_wt_sorted_1

description:
wt_sorted_1
wt_avg.bw


title: PBS1WKL3

value: 1 week


title: PBS0HL1


title: E14_GSK3βKO+βLGc1 5uM 3MB_2

status: Public on Feb 21 2018

city: Los Angeles

first: Liang

last: Hu

address: 1425 San Pablo Street

department: Department of Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

description:
processed data files:
Partek_GSK3_Mar2017_gene_counts.txt
GSK3β targets.xls

data_processing:
Partek Flow software used for Pre-alignment QA/QC
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using TopHat2
Quantification to the transcriptome was performed by Partek expectation maximization (EM)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include expression values for each sample and Excel table with total reads, p-value and  fold change for each groups

source_name: embryonic stem cells

extract_protocol:
Two cell lines,  E14 Gsk3α-/-+Gsk3α-L195G and Gsk3β-/-+ Gsk3β-L132G ES cells were treated with or without 3MB-PP1 for 2 hrs respectively after serum starvation using N2B27 medium for 6 hrs. Total RNA was extracted from the above cells with the Qiagen RNeasy kit.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 0.5 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: GSK3Beta knock-out with transgenic mutant GSK3Beta-L132G

value: 5µM 3MB-PP1


title: E14_GSK3βKO+βLGc1 5uM 3MB_1


title: E14_GSK3βKO+βLGc1 NT_2


title: E14_GSK3αKO+αLGc2 5uM 3MB_2

description:
processed data files:
Partek_GSK3_Mar2017_gene_counts.txt
GSK3α targets.xls

value: GSK3alpha knock-out with transgenic mutant GSK3alpha-L195G


title: E14_GSK3αKO+αLGc2 5uM 3MB_1


title: E14_GSK3αKO+αLGc2 NT_2


title: E14_GSK3αKO+αLGc2 NT_1


title: MM_a rep1


title: Fetal liver

city: Worcester

first: Merav

last: Socolovsky

address: 364 Plantation St

department: Molecular, Cell and Cancer Biology

institute: University of Massachusetts Medical School

description:
FL
The barcode reads are: SRR5010991 SRR5010993 SRR5010995 SRR5010997
The cDNA reads are: SRR5010992 SRR5010994 SRR5010996 SRR5010998

data_processing:
The barcode read was first filtered based on presence of two sample barcode components separated by the W1 adaptor sequence (GAGTGATTGCTTGTGACGCCTT), as previously described (Klein et al., Cell 2015).
The cDNA read was then trimmed using Trimomatic (5) (version 0.32; parameters: LEADING:28 SLIDINGWINDOW:4:20  MINLEN:30).
Barcodes for each read were matched against a list of the pre-determined barcodes, and errors of up to two nucleotides mismatch were corrected. Reads with a barcode separated by more than two nucleotides from the reference list were discarded. The reads were then split into barcode-specific files for mapping and UMI filtering.  All files were submitted to SRA.
The trimmed reads were aligned using Bowtie (version 1.1.1, parameters: -n 1 -l 15 -e 100 -m 200 -best -strata -a) to the mouse transcriptome. The reference transcriptome was built using annotations from ENSEMBL (GRCm38.81) including all annotations with ""Transcript Support Levels"" of 1, 2, or NA (only accepted for protein coding genes).
A custom Python and PySAM script to process mapped reads into counts of UMI-filtered transcripts per gene, as previously described (Zilionis et al., Nature Protocols in press)
Genome_build: GRCm38
Supplementary_files_format_and_content: The raw_umifm_counts files include raw unique molecular identifier (UMI)-filtered counts for all transcriptomes (prior to filtering). The filtered_normalized_counts files have normalized counts for transcriptomes passing all filtering steps. In both cases, columns = genes (with exception of first 5 columns), rows = cells. Column 1 contains cell identifier. Column 2 contains matching cell barcode. Column 3 contains library ID. Column 4 contains sequencing run ID (cells with same run ID were run on same flow cell). Column 5 contains flag for cell pass filtering (0=fail, 1=pass). Columns 6+ contain counts for each gene.

source_name: Fetal liver Kit+ cells

extract_protocol:
Cells were encapsulated using the inDrops platform, into droplets on ice and lysed in the 4nL microfluidic droplets using a final concentration of 0.4% NP-40. Single cell lysates were subject to reverse transcription at 50°C without purification of RNA (as previously described in Klein et al., Cell 2015).
Libraries were prepared as in Zilionis et al., Nature Protocols (in press), with the exception of the first round of libraries, for which the final PCR step was carried out as in Klein et al., Cell 2015.

treatment_protocol: For bone-marrow preparation, femurs and tibiae were harvested immediately following euthanasia and placed in cold (4°C) ‘staining buffer’ (phosphate- buffered saline (PBS) containing 0.2% Bovine Serum Albumin (BSA) and 0.08% Glucose). Bones were flushed using a 2 mL syringe with a 26-gauge needle and then crushed with a pestle and mortar to obtain all cells. Harvested bone marrow cells were filtered through a 40 μm strainer and washed in cold ‘Easy Sep’ buffer (PBS; 2% fetal bovine serum (FBS); 1mM EDTA). Fetal livers were prepared by mechanical dissociation in staining buffer and a wash in ‘Easy-Sep’ buffer. Bone marrow and fetal liver cell samples were each enriched for Kit expressing cells using magnetic beads, with the Mouse Biotin Selection Kit (STEMCELL technologies [Cat # 18556]) and Biotin Rat Anti-Mouse CD117 antibody (clone 2B8 , BD Bioscience), following the manufacturer’s protocol. Dead cells and debris were removed from the bone marrow and fetal liver samples using density centrifugation in OptiPrep (Sigma, Cat # D1556). Briefly, cells were re-suspended in 0.5ml staining buffer, mixed with 1mL of 40% of Optiprep in PBS, and placed in a 5 mL tube. The cell suspension was carefully over-layered with 2 mL of 20% OptiPrep solution, and 1mL of 5% OptiPrep solution, and centrifuged at 800g for 15 min (Centrifuge break OFF). The top visible cell band that formed during centrifugation contained the live, Kit+ single cells, confirmed by flow cytometric analysis. This layer was carefully aspirated and used directly in the inDrops platform.

value: BALB/cJ

tag: age

value: embryonic day 13.5

value: fetal liver

value: Kit+ hematopoietic progenitors


title: Gen


title: fresh_H3__IM834-703-511_S77

city: Stanford

first: Wanxin

last: Wang

address: James H Clark Center, 318 Campus Drive, room E300

institute: Stanford Univeristy

data_processing:
STAR for alignment
Piccard for marking duplicates
HTSeq for quantification
Genome_build: GRCm38
Supplementary_files_format_and_content: comma separated file including HTSeq count for each cell

source_name: primary resident immune cells in mouse kidney

extract_protocol:
Single cells were lysed following the Smartseq2 protocol
RNA libraries were prepared for sequencing using standard Illumina Nextera-XT protocols

tag: time

value: fresh


title: fresh_H5__IM834-705-511_S79


title: fresh_H1__IM834-701-511_S75


title: fresh_H4__IM834-704-511_S78


title: fresh_G7__IM834-707-510_S69


title: fresh_H2__IM834-702-511_S76


title: fresh_H11__IM834-714-511_S85


title: fresh_H6__IM834-706-511_S80


title: fresh_G9__IM834-711-510_S71


title: fresh_G4__IM834-704-510_S66


title: fresh_G6__IM834-706-510_S68


title: fresh_G3__IM793-703-510_S75


title: fresh_G2__IM834-702-510_S64


title: fresh_G5__IM834-705-510_S67


title: fresh_H7__IM834-707-511_S81


title: fresh_H10__IM834-712-511_S84


title: fresh_G2__IM793-702-510_S74


title: E14_GSK3βKO+βLGc1 NT_1

tag: cell line

tag: treatment


title: fresh_G3__IM834-703-510_S65


title: fresh_H9__IM834-711-511_S83


title: fresh_G10__IM834-712-510_S72


title: fresh_H8__IM834-710-511_S82


title: fresh_G1__IM793-701-510_S73


title: fresh_F9__IM834-711-508_S59


title: fresh_G12__IM834-715-510_S74


title: fresh_F9__IM793-711-508_S69


title: fresh_F8__IM834-710-508_S58


title: fresh_F8__IM793-710-508_S68


title: fresh_F7__IM793-707-508_S67


title: fresh_F6__IM834-706-508_S56


title: fresh_F6__IM793-706-508_S66


title: fresh_F4__IM793-704-508_S64


title: fresh_G1__IM834-701-510_S63


title: fresh_F2__IM793-702-508_S62


title: fresh_G11__IM834-714-510_S73


title: fresh_F5__IM793-705-508_S65


title: fresh_F10__IM834-712-508_S60


title: fresh_F11__IM834-714-508_S61


title: fresh_E9__IM793-711-507_S57


title: fresh_F3__IM793-703-508_S63


title: fresh_E8__IM793-710-507_S56


title: fresh_F2__IM834-702-508_S52


title: fresh_E9__IM834-711-507_S48


title: fresh_F1__IM834-701-508_S51


title: fresh_F1__IM793-701-508_S61


title: fresh_E6__IM793-706-507_S54


title: fresh_E6__IM834-706-507_S47


title: fresh_E3__IM834-703-507_S46


title: fresh_F12__IM834-715-508_S62


title: fresh_F12__IM793-715-508_S72


title: fresh_F10__IM793-712-508_S70


title: fresh_F7__IM834-707-508_S57


title: fresh_E3__IM793-703-507_S51


title: fresh_E5__IM793-705-507_S53


title: fresh_E7__IM793-707-507_S55


title: fresh_E2__IM834-702-507_S45


title: fresh_F11__IM793-714-508_S71


title: fresh_E2__IM793-702-507_S50


title: fresh_E1__IM834-701-507_S44


title: fresh_D9__IM834-711-506_S40


title: fresh_E12__IM793-715-507_S60


title: fresh_E12__IM834-715-507_S50


title: fresh_E11__IM793-714-507_S59


title: fresh_E10__IM793-712-507_S58


title: fresh_D9__IM793-711-506_S45


title: fresh_D6__IM834-706-506_S37


title: fresh_D8__IM834-710-506_S39


title: fresh_D8__IM793-710-506_S44


title: fresh_D4__IM793-704-506_S40


title: fresh_D6__IM793-706-506_S42


title: fresh_D7__IM793-707-506_S43


title: fresh_D7__IM834-707-506_S38


title: fresh_D3__IM834-703-506_S35


title: fresh_D5__IM834-705-506_S36


title: fresh_D5__IM793-705-506_S41


title: fresh_D2__IM793-702-506_S38


title: fresh_D3__IM793-703-506_S39


title: fresh_E4__IM793-704-507_S52


title: fresh_D12__IM834-715-506_S43


title: fresh_D2__IM834-702-506_S34


title: fresh_D1__IM834-701-506_S33


title: fresh_D11__IM834-714-506_S42


title: fresh_E1__IM793-701-507_S49


title: fresh_D10__IM793-712-506_S46


title: fresh_D11__IM793-714-506_S47


title: fresh_C9__IM834-711-505_S29


title: fresh_D10__IM834-712-506_S41


title: fresh_C9__IM793-711-505_S33


title: fresh_E11__IM834-714-507_S49


title: fresh_C8__IM834-710-505_S28


title: fresh_C7__IM834-707-505_S27


title: fresh_C7__IM793-707-505_S31


title: fresh_C6__IM793-706-505_S30


title: fresh_C8__IM793-710-505_S32


title: fresh_C6__IM834-706-505_S26


title: fresh_C2__IM834-702-505_S24


title: fresh_C1__IM834-701-505_S23


title: fresh_D12__IM793-715-506_S48


title: fresh_C1__IM793-701-505_S25


title: fresh_C2__IM793-702-505_S26


title: fresh_C4__IM834-704-505_S25


title: fresh_C12__IM793-715-505_S36


title: fresh_C10__IM834-712-505_S30


title: fresh_C4__IM793-704-505_S28


title: fresh_C11__IM793-714-505_S35


title: fresh_C3__IM793-703-505_S27


title: fresh_C10__IM793-712-505_S34


title: fresh_B9__IM834-711-503_S19


title: fresh_C12__IM834-715-505_S32


title: fresh_B8__IM834-710-503_S18


title: fresh_C11__IM834-714-505_S31


title: fresh_B9__IM793-711-503_S21


title: fresh_B7__IM834-707-503_S17


title: fresh_B6__IM834-706-503_S16


title: fresh_B4__IM834-704-503_S14


title: fresh_D1__IM793-701-506_S37


title: fresh_B3__IM834-703-503_S13


title: fresh_B6__IM793-706-503_S18


title: fresh_B8__IM793-710-503_S20


title: fresh_C5__IM793-705-505_S29


title: fresh_B5__IM834-705-503_S15


title: fresh_B2__IM834-702-503_S12


title: fresh_B12__IM834-715-503_S22


title: fresh_B1__IM793-701-503_S13


title: fresh_B2__IM793-702-503_S14


title: fresh_B3__IM793-703-503_S15


title: fresh_B1__IM834-701-503_S11


title: fresh_B12__IM793-715-503_S24


title: fresh_B11__IM793-714-503_S23


title: fresh_B11__IM834-714-503_S21


title: fresh_A9__IM834-711-502_S7


title: fresh_B10__IM834-712-503_S20


title: fresh_B10__IM793-712-503_S22


title: fresh_B7__IM793-707-503_S19


title: fresh_B5__IM793-705-503_S17


title: fresh_A9__IM793-711-502_S9


title: fresh_A7__IM793-707-502_S7


title: fresh_A6__IM834-706-502_S5


title: fresh_A6__IM793-706-502_S6


title: fresh_A7__IM834-707-502_S6


title: fresh_A8__IM793-710-502_S8


title: fresh_A5__IM793-705-502_S5


title: fresh_A5__IM834-705-502_S4


title: fresh_A4__IM793-704-502_S4


title: fresh_A4__IM834-704-502_S3


title: fresh_A2__IM793-702-502_S2


title: fresh_B4__IM793-704-503_S16


title: fresh_A3__IM793-703-502_S3


title: fresh_A2__IM834-702-502_S1


title: fresh_A12__IM834-715-502_S10


title: fresh_A12__IM793-715-502_S12


title: fresh_A1__IM793-701-502_S1


title: fresh_A10__IM793-712-502_S10


title: day4_H1__IM790-710-511_S92

value: day 4


title: day4_H4__IM834-721-521_S256


title: day4_H11__IM793-714-522_S287


title: day4_H12__IM793-715-522_S288


title: day4_G6__IM834-720-521_S255


title: day4_G2__IM834-720-520_S249


title: day4_G2__IM790-704-510_S76


title: day4_E9__IM834-720-515_S225


title: day4_F11__IM790-702-510_S74


title: day4_G10__IM790-704-511_S88


title: day4_E6__IM834-719-518_S242


title: day4_E7__IM834-719-520_S248


title: day4_E3__IM834-719-513_S218


title: day4_E6__IM790-705-508_S65


title: day4_F7__IM790-715-508_S72


title: day4_E11__IM790-714-508_S71


title: day4_E2__IM790-705-507_S53


title: day4_C6__IM834-722-511_S133


title: fresh_A11__IM793-714-502_S11


title: day4_E11__IM834-720-518_S243


title: fresh_A10__IM834-712-502_S8


title: day4_D8__IM790-714-505_S35


title: day4_C3__IM790-714-503_S23


title: day4_E2__IM834-718-522_S258


title: day4_C10__IM790-712-505_S34


title: fresh_A11__IM834-714-502_S9


title: day4_C10__IM834-718-518_S241


title: day4_G6__IM790-702-511_S86


title: day4_B6__IM834-720-503_S95


title: day4_B9__IM790-705-502_S5


title: day4_B8__IM834-720-506_S107


title: day4_B1__IM834-720-502_S89


title: day4_B11__IM790-710-503_S20


title: fresh_A3__IM834-703-502_S2


title: day4_B12__IM834-721-506_S108


title: day4_A3__IM834-716-503_S92


title: day3_H9__IM834-711-522_S213

value: day 3


title: day3_H5__IM834-705-522_S211


title: day4_A7__IM834-716-510_S122


title: day3_H4__IM834-704-522_S210


title: day3_G9__IM834-711-521_S205


title: day3_G7__IM834-707-521_S204


title: day3_H10__IM834-712-522_S214


title: day3_G6__IM834-706-521_S203


title: day3_H7__IM834-707-522_S212


title: day4_A8__IM834-718-507_S111


title: day3_H2__IM834-702-522_S208


title: day3_G3__IM834-703-521_S200


title: day3_G4__IM834-704-521_S201


title: day3_H11__IM834-714-522_S215


title: day4_B10__IM834-720-507_S113


title: day3_G10__IM834-712-521_S206


title: day3_G11__IM834-714-521_S207


title: day3_F9__IM834-711-520_S195


title: day3_F6__IM834-706-520_S192


title: day3_G1__IM834-701-521_S198


title: day3_F7__IM834-707-520_S193


title: day3_H3__IM834-703-522_S209


title: day3_F5__IM834-705-520_S191


title: day3_G2__IM834-702-521_S199


title: day3_F8__IM834-710-520_S194


title: day3_F2__IM834-702-520_S188


title: day3_F4__IM834-704-520_S190


title: day3_F3__IM834-703-520_S189


title: day3_F10__IM834-712-520_S196


title: day3_E8__IM834-710-518_S183


title: day3_E10__IM834-712-518_S185


title: day3_E11__IM834-714-518_S186


title: day3_E6__IM834-706-518_S181


title: day3_E3__IM834-703-518_S178


title: day3_E2__IM834-702-518_S177


title: day3_E12__IM834-715-518_S187


title: day3_D5__IM834-705-517_S170


title: day3_D8__IM834-710-517_S172


title: day3_E5__IM834-705-518_S180


title: day3_D2__IM834-702-517_S168