title: Evx1as+/- M7_2

source_name: laser capture microdissected Evx1as+/- E7.0 mesoderm layer 7

value: Evx1as+/- mesoderm layer


title: Evx1as+/- M9

status: Public on Feb 15 2018

type: SRA

city: Rochester

first: jinlong

last: lu

state: NY

address: 213 Hutchinson Hall

country: USA

institute: University of Rochester

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version
RNA-seq reads were aligned to the mm10 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
FPKM was calculated by Cufflink 2.1.1
Genome_build: mm10
Supplementary_files_format_and_content: bigwig; reads signal

molecule: total RNA

organism: Mus musculus

source_name: laser capture microdissected Evx1as+/- E7.0 mesoderm layer 9

growth_protocol: Wild-type ESCs or 4x polyA KI ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).

extract_protocol:
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction. For embryo sections, embryo was freshly embedded in OCT and subjected to cryosection and followed by Geo-seq for spatial transcritpome analysis.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

tag: development stage

value: Embryonic day 7 embryo

tag: strain

tag: cell type


title: MCF7_Y537S_H3K27Ac_Rep1

city: Boston

first: Rinath

last: Jeselsohn

state: MD

address: 450 Brookline Ave, D728

department: Medical Oncology

institute: DFCI

library_source: genomic

data_processing:
ChIP-seq reads were aligned using bowtie
Peaks were called using MACS2 with default parameters, including a q value < 0.001
bedgraph to wig file conversion was done using the UCSC tool bedGraphToBigWig
A binding intensity matrix was generated using bamliquidator
Differential Binding analysis was peformed using custom R code, and further analysis was done using DeepTools v2.2.3
Genome_build: hg19
Supplementary_files_format_and_content: bigwig  files for ER ChIP
RNA-seq reads were aligned to hg19 genome using STAR v2.5.1, and a raw count file was generated using STAR output
Transcipt Assembly and FPKM values were determined using cufflinks v2.2.1 and a normzlized RPKM matrix was generated using the cufflinks output
Quality Control steps tp ensure read quality were performed using rRNA STAR v2.5.1 and RseQC v2.6.2
Further differential expressions analysis was done using DEseq2 v1.1, gage v2.21, clusterprofiler 2.4.3, gostats v2.36; heatmaps were generated using complexheatmap v1.6
All analysis was performed by inputting fastq files into VIPER: https://bitbucket.org/cfce/viper/overview
Association of ChIP-seq data with RNAseq data was done using BETA v1.0.7
Genome_build: hg19
Supplementary_files_format_and_content: Count Matrix Files

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: MCF7 cells were grown in DMEM supplemented with Penstrep and L-glutamine and 10% FBS.

extract_protocol: Cell lines before ChIP were grown in   White Medium DMEM with CDT. Cells expressing the Y537S mutation were grown in Doxycyclin.The cells with WT-ER were stimulated with E2 x45 minutes prior to cross linking for the ChIP experiment. Cells were sonicated, then cell lysate was incubated with antibody to extract protein-DNA complex of interest, Library Preparation is performed using the Rubicon 48S kit

tag: cell line

tag: genotype/variation

tag: condition

value: White Medium+Doxycycline

tag: antibody


title: MCF7_Y537S_H3K27Ac_Rep3


title: Evx1as+/- S7

source_name: laser capture microdissected Evx1as+/- E7.0 Primtive streak layer 7

value: Evx1as+/- Primtive streak layer


title: Reninoma from Rotterdam (RotB1)

city: Montreal

first: Timothy

middle: L

last: Reudelhuber

state: Quebec

address: 110 Avenue des Pins Ouest

country: Canada

institute: IRCM

data_processing:
Base calls were made using the Illumina CASAVA 1.8 pipeline.
Low-quality bases (any leading or trailing base with a quality below 3, and any window of 4 bases with an average quality below 15) were removed with Trimmomatic (v0.22).
The sequences were aligned to the human reference genome hg19 using Tophat (v2.0.6).
Assembly and abundance were determined using Cufflinks (v2.0.2).
The gene expression levels are represented as Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text file with FPKM values of protein-coding genes for each sample. Outputted by Cuffdiff.

source_name: Reninoma tumor

extract_protocol:
Biopsies of reninomas were obtained at surgery from 4 anonymous patients (Paris1, Paris2, Montreal, Rotterdam) and snap frozen in liquid nitrogen. Total RNA was isolated using Trizol (Invitrogen) from 10 mg pieces of each tumor or biopsy and was further purified using RNeasy MinElute Cleanup spin (#74204, QIAGEN) according to manufacturer's instructions and eluted in a final volume of 10 μL.
RNA libraries were prepared for sequencing using standard Illumina protocols. Eight microliters of RNA was used as input and library preparation was conducted according to manufacturer's instructions ("Low-Throughput (LT) Protocol" TruSeq RNA Sample Preparation Guide, Illumina). Resulting library preps were assessed for quality and concentration using the Agilent 2100 Bioanalyzer (Agilent Technologies).

tag: tissue

value: reninoma tumor

tag: patient

value: Rotterdam


title: subject7_after_low_carbohydrate_diet

city: Solna

first: Adil

last: Mardinoglu

address: Tomtebodavägen 23B

department: Systems biology

country: Sweden

institute: SciLifeLab, KTH

data_processing:
standard Illumina RNA-Seq protocol was used for processing.
Kallisto(version 0.43.0) used to generate Transcripts Per Million (TPM) values
Genome_build: GRch38
Supplementary_files_format_and_content: tab-delimited text files include Transcripts Per Million (TPM) values for each sample

extract_protocol:
Liver biopsies were collected in tubes with RNAlater (Qiagen, Hilden, Germany) and stored at -80°C. Total RNA was extracted from the tissue samples using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: obese with  non-alcoholic fatty liver disease (NAFLD)

tag: subject id

tag: time point

value: liver


title: Reninoma from Montreal (Mon)

value: Montreal


title: Evx1as+/- M7


title: subject7_before_low_carbohydrate_diet


title: Evx1as+/- S5

source_name: laser capture microdissected Evx1as+/- E7.0 Primtive streak layer 5


title: Evx1as+/- M3


title: Reninoma from Paris (Par1B1)


title: subject6_after_low_carbohydrate_diet


title: Homogenate_mRNA_rep2

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

data_processing:
Sequencing reads were trimmed by trim galore 0.3.7 with --RRBS option for RRBS and default option for RNA-seq.
RRBS reads were aligned using bismark v0.14.0 and bowtie 1.1.1. RNA-seq reads were aligned by TopHat v2.1.1.
Genome_build: hg19 or mm9
Supplementary_files_format_and_content: bedgraph files of CpG methylation were generated using bismark_methylation_extractor. fpkm_tracking files were generated by Cufflinks.

source_name: Cerebellum

growth_protocol: GM12878 cells were cultured in RPMI 1640 medium (11875-093, Gibco) plus 15% fetal bovine serum (26140-079, Gibco) and 100 U/ml penicillin-streptomycin (15140-122, Gibco) at 37 ℃ in a humidified incubator with 5% CO2. Cells were sub-cultured every 2-3 days to maintain them in exponential growth phase.

extract_protocol:
The mouse line C57Bl/6 was bred and maintained in groups of 3-4 per cage with food ad libitum. 8-10 week old mice were anesthetized with isoflurane and decapitated. The cerebellum was rapidly dissected and frozen on dry ice and stored at -80 ℃ until used for nuclei isolation.  Cerebellum was placed in 5 ml ice-cold nuclei extraction buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ac)2, 0.1 mM EDTA, 10 mM Tris-HCl and 0.1% Triton X-100) with freshly added 50 μl protease inhibitor cocktail (P8340, Sigma-Aldrich), 5 μl 100 mM PMSF and 5 μl 1 M DTT. In addition, 7.5 μl 40 U/μl RNase inhibitor (N2611, Promega) was also added when RNA-seq was conducted. Once thawed, the tissue was homogenized by slowly doucing for 15 times with a loose pestle (D9063, Sigma-Aldrich) and 25 times with a tight pestle (D9063, Sigma-Aldrich). The homogenate was transferred into an ultracentrifugation tube (355631, Beckman Coulter) and underlayered with 9.5 ml sucrose cushion (1.8 M sucrose, 3 mM Mg(Ac)2 and 10 mM Tris-HCl). The homogenate was centrifuged at 32,300 rpm (107,164g) for 2.5 h at 4 ℃ with 70 Ti rotor (Optima L-90K Ultracentrifuge, Beckman Counter). The spinning was slowly braked to avoid disturbing the nuclei pellet. All the supernatant was removed and the nuclei was gently resuspended in 0.4 ml 10% normal goat serum (50062Z, Life Technologies) and 1.6 ml Dulbecco's phosphate-buffered saline (14190144, Life Technologies). For RNA-seq, 3 μl 40 U/μl RNase inhibitor was added into nuclei suspension. The integrity and the number of nuclei were checked under the microscope. 32 μl 2 ng/μl anti-NeuN antibody conjugated with Alexa 488 (MAB377X, EMD Millipore) was incubated with the nuclei suspension (2 ml) for 1 h at 4 ℃ on an end-to-end rotator. The stained samples were sorted using a FACS (BD FACSAria, BD Biosciences) with 50,000 to 100,000 unlabeled nuclei used as non-staining control. Human genomic DNA was purified from GM 12878 cells using QIAamp DNA Blood Mini Kit (Qiagen) following the manufacturer’s protocol and suspended in 50 µl EB buffer. Mouse genomic DNA was purified using QIAamp DNA Blood Midi Kit (Qiagen) from nuclei and suspended in 200 µl AE buffer (10 mM Tris-Cl, 0.5 mM EDTA, pH 9.0). The eluate was reloaded on the column membrane and spun to maximize DNA yield. Mouse DNA was concentrated by ethanol precipitation to 20 µl EB buffer. RNA was extracted from ~10,000 nuclei using RNeasy Mini Kit (Qiagen). DNase treatment step was included following kit instructions to remove gDNA contamination.
RRBS library construction. 5 µl genomic DNA (0.2-6 ng/µl) was digested by adding 1 µl of 20 U/µl MspI enzyme (R0106S, NEB), 2 µl NEB buffer2 and 12 µl H2O at 37 ℃ for 1 h and inactivated at 80 ℃ for 20 min. The fragment size was examined using 2.5% agarose gel (16550100, Thermo Fisher) in 0.5× TBE buffer (15581044, Thermo Fisher). The 3’ terminal of digested DNA was end-repaired and an extra A which was required by adapter ligation was added on both strands in a single reaction. 1 µl of 5 U/µl Klenow exo- enzyme (M0212M, NEB) and 1.1 µl dNTP mixture (10 mM dATP, 1 mM dGTP and 1 mM dCTP, N0446S, NEB) were added into 20 µl digested sample. Ten-fold excess of dATP was added to increase A-tailing efficiency. The sample was incubated at 30 ℃ for 20 min (end-repair), 37 ℃ for 20 min (A-tailing) and 75 ℃ for 20 min (enzyme inactivation). The DNA (22.1 µl) was then purified by phenol–chloroform extraction and ethanol precipitation. DNA pellet was then resuspended in 17 μl EB buffer. 16.4 µl sample was transferred to a new 200 µl PCR tube. 1 µl of 2000 U/µl T4 ligase (M0202T, NEB), 2 µl of supplied 10× T4 ligase buffer, 0.6 µl NEXTflex bisulfite-seq barcode (1.6-6 µM) were mixed with the sample for ligation. The ligation reaction was carried out at 16 ℃ for 16 h and followed by 65 ℃ for 10 min for heat inactivation. The heating of the thermal cycler lid was turned off to protect the T4 ligase. Gel-free procedure 17, 28 instead of gel cutting was used for RRBS library construction. Ligated DNA (20 µl) was purified using AMPure XP beads with bead suspension to sample volumetric ratio of 1.5: 1. The DNA was eluted from Ampure beads by 20 µl EB buffer. The elute was concentrated by ethanol precipitation and then suspended in 0.7 µl to facilitate loading into the microfluidic device. The converted DNA was amplifed by PCR (13 cycles for 10 ng, and 16-18 cycles for 1-0.3 ng). After PCR amplification, a double size selection using AMPure XP beads was performed. Large DNA fragments were removed by adding 30 μl AMPure bead suspension and incubating for 5 min. The beads that had large DNA bound were discarded and the supernatant was preserved. 30 μl AMPure bead suspension were then added into the supernatant and incubated for 5 min. The supernatant was discarded and DNA bound to beads was eluted into 7 μl EB buffer.mRNA-seq library construction. RNA was extracted from ~100,000 nuclei using RNeasy Mini Kit (Qiagen). DNase treatment was included following manufacturer instructions to remove gDNA contamination. The RNA quality was detected by High Sensitivity RNA ScreenTape System (Agilent) to yield RNA integrity number (RIN) > 6. mRNA-seq libraries were prepared using SMART-seq v4 Ultra Low Input RNA kit (Clontech) and Nextera XT DNA library prep kit (Illumina) following instructions.

tag: age

value: 8-10 weeks


title: subject6_before_low_carbohydrate_diet


title: subject5_before_low_carbohydrate_diet


title: subject4_after_low_carbohydrate_diet


title: subject5_after_low_carbohydrate_diet


title: Evx1as-/- M11

source_name: laser capture microdissected Evx1as-/- E7.0 mesoderm layer 11

value: Evx1as-/- mesoderm layer


title: Evx1as-/- S11

source_name: laser capture microdissected Evx1as-/- E7.0 Primtive streak layer 11

value: Evx1as-/- Primtive streak layer


title: Evx1as-/- S9

source_name: laser capture microdissected Evx1as-/- E7.0 Primtive streak layer 9


title: subject4_before_low_carbohydrate_diet


title: Evx1as+/- S3

source_name: laser capture microdissected Evx1as+/- E7.0 Primtive streak layer 3


title: Evx1as-/- 4-6A control

source_name: laser capture microdissected Evx1as-/- E7.0 anterior epiblast cells, layer 4-6

value: Evx1as-/- anterior epiblast cells


title: subject2_after_low_carbohydrate_diet


title: Evx1as-/- M7

source_name: laser capture microdissected Evx1as-/- E7.0 mesoderm layer 7


title: subject3_after_low_carbohydrate_diet


title: Evx1as-/- S7

source_name: laser capture microdissected Evx1as-/- E7.0 Primtive streak layer 7


title: subject2_before_low_carbohydrate_diet


title: subject1_after_low_carbohydrate_diet


title: Evx1as-/- S5

source_name: laser capture microdissected Evx1as-/- E7.0 Primtive streak layer5


title: subject1_before_low_carbohydrate_diet


title: Evx1as-/- S3

source_name: laser capture microdissected Evx1as-/- E7.0 mesoderm layer layer 3


title: Evx1as-/- M3


title: KDM4ARNAi_INPUT4_filtered.fastq.gz

city: berkeley

first: serafin

last: colmenares

address: 1 cyclotron road MS977R180A

institute: lawrence berkeley national lab

data_processing:
Read filtering by FastX
Bowtie alignment to Release 5.22 Drosophila genome assembly
broadPeak calling by Macs2
Bowtie alignment to repetitive DNA library
Genome_build: Release 5.22 Drosophila genome assembly
Supplementary_files_format_and_content: Mean enrichment of H3K9me3 or H3K36me3 at various repetitive regions

organism: Drosophila melanogaster

source_name: Drosophila S2 cells

growth_protocol: 25ºC in Schneider medium + 10% FBS

extract_protocol:
chromatin crosslinking with 1% paraformaldehyde for 10 minutes, shearing with Bioruptor sonicator (30 cycles), immunoprecipitation with anti-H3K9me3 or anti-H3K36me3 antibodies with Protein-A Dynabeads
standard Illumina TruSeq protocol

treatment_protocol: 5-day dsRNA treatment with DOTAP transfection reagent

value: embryonic

tag: treatment


title: KDM4ARNAi_INPUT3_filtered.fastq.gz


title: Evx1as-/- S1

source_name: laser capture microdissected Evx1as-/- E7.0 Primtive streak layer 1


title: KDM4ARNAi_H3K9Me3ChIP4_filtered.fastq.gz


title: Evx1as-/- M9

source_name: laser capture microdissected Evx1as-/- E7.0 mesoderm layer 9


title: Evx1as+/- 4-6A control

source_name: laser capture microdissected Evx1as+/- E7.0 anterior epiblast cells, layer 4-6

value: Evx1as+/- anterior epiblast cells


title: Evx1as+/- M11

source_name: laser capture microdissected Evx1as+/- E7.0 mesoderm layer 11


title: subject3_before_low_carbohydrate_diet


title: KDM4ARNAi_H3K36Me3ChIP3_filtered.fastq.gz


title: KDM4ARNAi_H3K36Me3ChIP4_filtered.fastq.gz


title: Evx1as+/- S1

source_name: laser capture microdissected Evx1as+/- E7.0 Primtive streak layer 1


title: KDM4ARNAi_H3K9Me3ChIP3_filtered.fastq.gz


title: GFPRNAi_INPUT3_filtered.fastq.gz

value: GFPRNAi


title: GFPRNAi_H3K9Me3ChIP4_filtered.fastq.gz


title: GFPRNAi_INPUT4_filtered.fastq.gz


title: PD Homozygote

source_name: Evx1as-/- E7.0 proximal posterier

value: Evx1as-/- proximal posterier


title: 4x polyA KI-3 (D4)

source_name: 4x polyA KI mES cells (-LIF, day4)

value: 4x polyA KI in embryonic stem cells

value: LIF withdrawal, day4


title: PD Heterozygote

source_name: Evx1as+/- E7.0 proximal posterier

value: Embryonic day 7 embryo

value: Evx1as+/- proximal posterier


title: GFPRNAi_H3K36Me3ChIP4_filtered.fastq.gz


title: PP Heterozygote

source_name: Evx1as+/- E7.0 distal posterier

value: Evx1as+/- distal posterier


title: PP Homozygote

source_name: Evx1as-/- E7.0 distal posterier

value: Evx1as-/- distal posterier


title: GFPRNAi_H3K9Me3ChIP3_filtered.fastq.gz


title: GFPRNAi_H3K36Me3ChIP3.filtered.fastq.gz


title: 4x polyA KI-2 (D4)


title: NeuN-_mRNA_rep1

source_name: Glial cell from cerebellum


title: HP1aRNAi_RNASeq2

data_processing:
Read filtering by FastX
TopHat alignment of genes to Release 5.25 Drosophila genome assembly
Bowtie alignment to repetitive DNA library
DESeq2 read count analysis
Genome_build: Release 5.25 Drosophila genome assembly
Supplementary_files_format_and_content: described in subheadings

extract_protocol:
Trizol extraction, oligo-dT purification
standard Illumina TruSeq protocol

value: HP1a RNAi

tag: cells


title: KDM4ARNAi_RNASeq2


title: Evx1as+/- S11

source_name: laser capture microdissected Evx1as+/- E7.0 Primtive streak layer 11

value: Evx1as+/- Primtive streak layer


title: GFPRNAi_RNASeq2

value: GFP


title: WT-3 (D4)

source_name: CJ9 mES cells (-LIF, day4)

value: embryonic stem cells


title: WT-1 (D4)


title: HP1aRNAi_RNASeq1


title: Control AT2 cells rep3

city: Cincinnati

first: John

middle: M.

last: Snowball

state: OH

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

description:
524_ATII_Control
mRNA
Processed data file: Counts_AT2_All.xlsx
Processed data file: RPKMs_AT2_All.xlsx

data_processing:
Paired reads were aligned against mm10 using bowtie2-2.1.0 and tophat-2.0.8.
Reads Per Kilobase of transcript Per Million mapped reads (RPKM) values were computed using cufflinks-2.0.2.
Bioconductor package GenomicAlignments was used to calculate Raw counts.
DESeq was used to normalize raw counts and calculate differential expression.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Counts_AT2_All.xlsx: Excel file includes Raw Counts.
Supplementary_files_format_and_content: RPKMs_AT2_All.xlsx: Excel file includes FPKM values.

source_name: Adult AT2 purified, control

growth_protocol: Mice were housed in filtered cages and all experiments were performed in accordance with approved IACUC protocols.

extract_protocol:
AT2 cells were purified by cell depletion as described by Corti et al. "Isolation and primary culture of murine alveolar type II cells."
Total RNA was isolated from adult AT2 cells with the RNeasy Plus Mini Kit (Qiagen, Valencia, CA). RNA amplification was performed utilizing the Ovation RNA-Seq System v2 (NuGEN).
RNA libraries were prepared using Nextera XT DNA Sample Preparation kits (Illumina Technologies).

treatment_protocol: Adult mice were given Tamoxifen for 6 days prior to harvest.

tag: strain/background

value: mixed

value: control

value: adult

value: alveolar type 2 cells


title: Evx1as-/- M5

source_name: laser capture microdissected Evx1as-/- E7.0 mesoderm layer layer 5

value: Evx1as-/- mesoderm layer


title: Control AT2 cells rep2

description:
529_ATII_Control
mRNA
Processed data file: Counts_AT2_All.xlsx
Processed data file: RPKMs_AT2_All.xlsx


title: GFPRNAi_RNASeq1

value: embryonic


title: Control AT2 cells rep1

description:
526_ATII_Control
mRNA
Processed data file: Counts_AT2_All.xlsx
Processed data file: RPKMs_AT2_All.xlsx


title: E. coli hhahha2

city: Barcelona

first: Mario

last: Huttener Queiroz

address: Av. Diagonal 643

country: Spain

institute: Universitat de Barcelona

description: Strain-expression.xlsx

data_processing:
We used an Illumina NextSeq 500 system and a MID 150 Kit with 1x75 bp read length. Base-calling was perform online during the sequencing procedure with the Real-Time Analysis (RTA) software version 2.4.11 and System Suite Version 2.1.2.1.
Illumina sequencing instruments generate per-cycle BCL base call files as primary sequencing output in bcl2 format. Conversion of the bcl2 file to gzipped fastq files was performed using the bcl2fastq script v. 2.18.0.12 provided by Illumina.
Quality and adapter trimming was performed with the CLC Genomics Workbench 9.0 software package using the 'Trim Sequences' tool with standard parameters.
Mapping of the trimmed reads to the reference sequences was also performed with the CLC Genomics Workbench 9.0 using the 'Map Reads to Reference' tool with standard parameters.
For quantification of gene expression (read counting), the alignments generated with the Genomics Workbench were exported in BAM format. Read counting was then performed with the FeatureCounts v. 1.5.0-p1 program using the following parameters; Level : meta-feature leve. Paired-end : no. Strand specific : yes. Multimapping reads : counted (as fractions). Multi-overlapping reads : not counted. Overlapping bases : 30. Read orientations : fr
Genome_build: NCBI reference sequence (NC_017626.1)
Supplementary_files_format_and_content: Strain-expression.xlsx archive contains expression values in RPKM (Reads Per Kb exon (contig) per Million mapped  reads ( see Mortazavi et al. 2008, Nat Methods. 5(7):621-8 ) and can be directly compared to each other)  tab-delimited text files include RPKM values for each Sample.

organism: Escherichia coli 042

source_name: cell pellets

growth_protocol: LB medium at 37ºC with 200rpm agitation.

extract_protocol:
Total RNA was isolated from the cell pellets using a bead mill and the mirVana RNA isolation kit (Ambion) including DNase treatment. From the total RNA samples, ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina).
From the rRNA depleted RNA samples, first-strand cDNA was synthesized using a N6 randomized primer. After fragmentation, the Illumina TruSeq sequencing adapters were ligated in a strand specific manner to the 5' and 3' ends of the cDNA fragments. The cDNA was finally amplified with PCR (15 PCR cycles) using a proof reading enzyme. For Illumina sequencing, cDNA libraries were pooled in a 25:1 ratio. The library pool was fractionated in the size range of 250-500 bp using a differential clean- up with the Agencourt AMPure kit. The cDNA pool was sequenced on an Illumina NextSeq 500 system using 75 bp read length.

tag: genotype

value: mutant hhahha2


title: E. coli 042 WT

description: Strain-expression.xlsx

value: wild type


title: E. coli hnshns2

description: Strain-expression.xlsx

value: mutant hnshns2


title: E. coli hns

description: Strain-expression.xlsx

value: mutant hhs


title: E. coli hns2

description: Strain-expression.xlsx

value: mutant hns2


title: Abca3 cko AT2 cells rep1

description:
525_ATII_Knockout
mRNA
Processed data file: Counts_AT2_All.xlsx
Processed data file: RPKMs_AT2_All.xlsx

source_name: Adult AT2 purified, Abca3 cKO

value: Abca3 cKO


title: Abca3 cko AT2 cells rep2

description:
527_ATII_Knockout
mRNA
Processed data file: Counts_AT2_All.xlsx
Processed data file: RPKMs_AT2_All.xlsx


title: Abca3 cko AT2 cells rep3

description:
528_ATII_Knockout
mRNA
Processed data file: Counts_AT2_All.xlsx
Processed data file: RPKMs_AT2_All.xlsx


title: GnRH

city: New York

first: Frederique

last: Ruf-Zamojski

address: 1468 Madison Avenue

department: Neurology

institute: Mount Sinai Medical Center

data_processing:
Single-cell RNA-seq data were processed using the Cell Ranger pipeline v1.3, which provides a data matrix of expression for all genes and all cells.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited file for the UMIs of all genes and all single cells

molecule: polyA RNA

source_name: pituitary gonadotrope-derived cells

growth_protocol: LβT2 cells were cultured at 37°C in DMEM (Mediatech, Herndon, VA) supplemented with 10% fetal bovine serum (FBS; Gemini, Calabasas, CA) in a humidified air atmosphere of 5% CO2.

extract_protocol:
Cells were then trypsinized and resuspended in medium before being washed and resuspended in 1x PBS/0.04% BSA. Following filtration of the cell suspension, cells were counted on a Countess instrument, and viability was assessed to be above 90% using Trypan Blue. Final concentration was set at 1,000 cells/μl in 1x PBS/0.04% BSA. As a starting point, ~8,000 cells from each sample were loaded into the fluidics chip.
Reverse-transcription was performed in the emulsion and cDNA was amplified for 12 cycles before library construction (see Zheng et al., 2017 PMID: 28091601). Quality control and quantification of the amplified cDNA were assessed using the High-Sensitivity DNA Bioanalyzer kit. Library quality control and quantification were evaluated.
GEM Drop-Seq, Chromium™ Single Cell 3’ Library & Gel Bead Kit v2

treatment_protocol: LβT2 cells were seeded at 350,000 cells per well in 12-well plates for 48 h, and treated on day 3 with either 2 nM GnRH or vehicle for 40 min.

value: immortalized gonadotrope cells

value: 2 nM GnRH for 40 min

tag: passages

value: anterior pituitary


title: Vehicle

value: Vehicle


title: Rep1 + GnRH

data_processing:
Primary data analysis involved read mapping via bowtie2 to GRCm38 (mm10).
Duplicate read removal and peak calling were done via MACS2 with parameters “-g dm –nomodel –shiftsize 100 extsize 200”.
Genome_build: mm10
Supplementary_files_format_and_content: narrowPeak

extract_protocol:
Briefly, cells were then trypsinized and resuspended in medium; 4,500 cells were washed with cold PBS at 4ºC and lysed for 10 min at 4ºC. Cell pellets were resuspended in the transposase reaction mix (5 μl 2x TD buffer, 0.5 μl transposase (Illumina) and 4.5 μl nuclease free water) and incubated at 37ºC for 30 min. DNA from the transposase reaction was purified with a DNA Clean & Concentrator-5 Kit (Zymo Research).
PCR amplification was performed using Nextera PCR primers. The optimal number of cycles was determined via quantitative real-time PCR (qPCR) to stop the amplification before saturation. Libraries were purified with AMPure beads, then quantified using a  KAPA Library Quantification Kit (Kapa Biosystems) and High-Sensitivity DNA Bionalyzer kit (Agilent).

treatment_protocol: LβT2 cells were treated with 2 nM GnRH pulses every 2 h for a duration of 6 h and 45 min (4 pulses in total; cells harvested 45 min after last pulse).


title: Rep2 + GnRH

value: 2 nM GnRH pulses every 2 h for a duration of 6 h and 45 min


title: 4x polyA KI-1 (D4)

value: 4x polyA KI in embryonic stem cells

value: LIF withdrawal, day4

tag: strain


title: Junb KO, Th17 cell, replicate 1

city: Fukuoka

first: Hiromitsu

last: Araki

address: 744 Motooka Nishi-Ku

country: Japan

institute: Kyushu University

data_processing:
Reads were trimmed for adapter sequences and low-quality reads using Trimmomatic version 0.32 (Bolger et al., 2014) and were then aligned to the mouse reference genome mm9 using TopHat version 2.0.13 (Kim et al. 2013).  For each gene, reads were counted using featureCounts (Liao et al., 2014). Finally, edgeR was used to normalize read count by the TMM procedure and perform differential expression analyses (Robinson et al., 2010).
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: Junb KO mouse, Th17 cell

growth_protocol: Junbf/f mice were generated according to the standard technique (Gomi et al., 1995; Endo et al., 1995), and crossed with Meox2Cre/+ mice (Tallquist et al., 2000) (Jackson laboratory) for generation of Junb-deficient (Junbf/f;Meox2Cre/+) mice.

extract_protocol:
Total RNA was extacted using TRIsure (BIOLINE, London, UK) and treated with Rnase-free DNase (Promega, Madison).
Two and a half micrograms of total RNA was subjected to ribosomal RNA depletion using Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat) (Epicentre) followed by RNA-seq library preparation using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions.  Each library was quantified using Kapa Library Quantitation Kit (Kappa) and sequenced on Illumina HiSeq2500 to generate 101-bp paired-end reads.

treatment_protocol: Naive CD4+ T cells were prepared from the spleen and lymph nodes of 6–9 week old mice by magnetic sorting using DynabeadsⓇ Mouse CD4 (L3T4, Invitrogen) and DETACHaBEADⓇ Mouse CD4 (Invitrogen), as described previously (Tanaka et al., 2007).  The CD4+ T cells were activated for 3 days via TCR with plate-bound 5 ug/ml of an anti-CD3 antibody (145-2C11, BioLegend) and soluble 2.5 ug/ml of an anti-CD28 antibody (35.71, BioLegend) under the following differentiation conditions: 10 ug/ml of an anti-IFN- antibody (XMG 1.2, BioLegend) and 10 ug/ml of an anti-IL-4 antibody (11B11, BioLegend) for Th0; 10 ug/ml of the anti-IFN- antibody, 10 ug/ml of the anti-IL-4 antibody, 40 ng/ml of mouse IL-6 (Peprotech), and 4 ng/ml of human TGF-1 (R&D) for Th17; 10 ug/ml of the anti-IL-4 antibody and 40 ng/ml of mouse IL-12 p70 (BioLegend) for Th1; 10 ug/ml of the anti-IFN- antibody and 40 ng/ml of mouse IL-4 (Peprotech) for Th2; 10 ug/ml of the anti-IFN- antibody, 10 ug/ml of the anti-IL-4 antibody, 4 ng/ml of human TGF-1 for Treg.

tag: cell type

value: Th17 cell

value: Junb-/-


title: Junb KO, Th17 cell, replicate 2


title: Junb KO, Th0 cell

source_name: Junb KO mouse, Th0 cell


title: Junb KO, naïve T cell

source_name: Junb KO mouse, naïve T cell

value: naive T cell


title: WT-2 (D4)

value: embryonic stem cells


title: KDM4ARNAi_RNASeq1

source_name: Drosophila S2 cells

value: embryonic


title: WT, Th17 cell, replicate 2

source_name: WT mouse, Th17 cell

value: wild type


title: WT, Th17 cell, replicate 1


title: WT, Th0 cell

source_name: WT mouse, Th0 cell

value: Th0 cell


title: WT, naïve T cell

source_name: WT mouse, naïve T cell


title: E12.5 Pitx1 KO Rep2

status: Public on Feb 14 2018

city: Dallas

first: Jialiang

last: Wang

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Sequenced libraries were evaluated and trimmed with FastQC.
Sequenced reads were aligned to mm9 using Tophat2 on the Galaxy platform
Cuffdiff was used to generate qualified RPKM and to identify differentially expressed genes and transcripts
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and log2(fold_change)

source_name: Hindlimb

extract_protocol:
Hindlimbs were collected and total RNA was isolated using the mirVana RNA Isolation Kit (ThermoFisher Scientific).
Libraries were constructed with TruSeq Stranded mRNA Sample Prep Kit for Illumina and sequenced on the Illumina NextSeq platform.

value: Hindlimb

tag: developmental stage

value: Pitx1 KO


title: E12.5 WT Rep3


title: E12.5 Pitx1 KO Rep1


title: m6A-irCLIP rep1

city: Stanford

first: Howard

last: Chang

state: CA

address: 269 Campus Drive

department: Dermatology

institute: Stanford University School of Medicine

data_processing:
Library strategy: CLIP-seq
FASTQ files first demultiplexed by sample, PCR duplicates removed, and all adaptor sequences trimmed as previously described (PMID: 25411354)
Processed sequencing reads were mapped to mouse genome indices, RT stop positions extracted, and replciate experiments intersected to obtain highly reproducible binding sites for further analysis as per FAST-iCLIP (PMID: 25411354)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files containing RT stops of m6A-irCLIP datasets mapped to mm10 build of mouse genome.

source_name: WT CD4+ T cells

extract_protocol:
Cells were lysed and total RNA collected, RNA was polyA selected, and fragmented to ~30-60 nts, m6A residues were isolated by crosslinking anti-m6A antibody to fragmented RNA
RNA ligation for library construction was perfromed on affinity beads and RNA was subsequenctly transformed into dsRNA libraries using RT, cDNA circularization, and PCR amplification

value: CD4+ T cells

value: m6A, Synaptic Systems, 202 003


title: m6A-irCLIP rep2


title: E12.5 Pitx1 KO Rep3


title: E12.5 WT Rep2


title: E12.5 WT Rep1


title: E11.5 Pitx1 KO Rep1


title: E11.5 WT Rep2


title: E11.5 WT Rep1


title: E11.5 Pitx1 KO Rep3


title: E11.5 WT Rep3


title: E9.5 WT Rep1

source_name: Hindlimb field and associated trunk

value: Hindlimb field and associated trunk


title: E9.5 WT Rep2


title: E9.5 WT Rep3


title: E9.5 Pitx1 KO Rep2


title: Foxd1Tdt+_2

city: Los Angeles

first: Andrew

middle: P

last: McMahon

state: California

address: 1425 San Pablo St, BCC 312

department: Stem Cell Biol & Regen Med

institute: University of Southern California

description:
processed data file:
TPM.ms_Foxd1+_Foxd1-.txt

data_processing:
Fastq files were aligned using TopHat2
Gene-level quantification was presented as TPM and calculated by Partek Genomic Suite
Genome_build: mm10
Supplementary_files_format_and_content: text file with TPM

source_name: Foxd1+ cells in developing kidneys

extract_protocol:
Ambion Recoverall Total Nucleic Acid Isolation Kit and QIAGEN Rneasy Micro Kit; Qiagen Rneasy micro kit
Kapa stranded mRNA-Seq library (#KK8420)

value: kidney

value: CFW

tag: allele


title: E9.5 Pitx1 KO Rep1


title: Foxd1Tdt-_2

source_name: Foxd1- cells in developing kidneys


title: Foxd1Tdt-_1


title: Foxd1Tdt+_1


title: Six2GFP+_3

description:
processed data file:
TPM.ms_Six2+_Six2-_GFP+_GFP-_NZC.txt

source_name: Six2GFP+ cells indeveloping kidneys


title: Six2GFP+_2

source_name: Six2GFP+ cells in developing kidneys


title: Six2GFP+_1


title: Six2GFP-_3

source_name: Six2GFP- cells in developing kidneys


title: Six2GFP-_2

source_name: Six2GFP- cells indeveloping kidneys


title: mMARIS_SIX2+_3

source_name: Six2+ cells in NZC


title: mMARIS_SIX2+_2


title: mMARIS_SIX2-_2

source_name: Six2- cells in NZC


title: E11.5 Pitx1 KO Rep2


title: mMARIS_SIX2+_1


title: mMARIS_SIX2-_1


title: mMARIS_NZC_3

source_name: nephrogenic zone cells (NZC) in developing kidneys


title: E9.5 Pitx1 KO Rep3


title: mMARIS_SIX2-_3


title: mMARIS_NZC_2


title: mMARIS_NZC_1


title: M203_ATII_N_HOILKO_4

city: Chicago

first: Jacob

middle: Iasha

last: Sznajder

state: IL

address: 240 East Huron

department: Medicine

institute: Northwestern University

data_processing:
Illumina bcl2fastq2 v2.17 was used for demultiplexing and conversion to FASTQ files.
Normalized counts were estimated using edgeR v3.14.0(Version 0.11.5).
Genome_build: mm10
Supplementary_files_format_and_content: normalized mRNA molecule count values for each sample

extract_protocol:
ATII sorted cells were immediately lysed with RLT plus buffer a RNA isolations were performed using Qiagen RNeasy Plus Mini kit (Qiagen).
5 ug of total RNA was used for full-length cDNA synthesis and library preparation with NEBNext Ultra™ RNA (New England Biolabs, Inc).
sequencing was performed on the Illumina NextSeq 500 instrument using the V1 chemistry high-output 150 cycles sequencing kit (Illumina).

treatment_protocol: Mice were provided with food and water ad libitum, maintained on a 14:10-hour light-dark cycle, and handled according to National Institutes of Health guidelines and the Northwestern University Institutional Animal Care and Use Committee–approved experimental protocol.

value: Lung

value: ATII cells

value: 8-10 weeks

value: HOIL-1L -/-


title: M204_ATII_N_HOILKO_5


title: M200_ATII_N_WT_5


title: M201_ATII_N_WT_6


title: M199_ATII_N_WT_4


title: M189_ATII_N_HOILKO_3


title: M188_ATII_N_HOILKO_2


title: M187_ATII_N_HOILKO_1


title: M184_ATII_N_WT_3


title: mES_H1-TKO_repl_I

city: Madrid

first: Maria

last: Gomez

address: Nicolas Cabrera, 1

institute: CBMSO(CSIC/UAM)

description: molecule: short DNA replication intermediates

data_processing:
Library strategy: SNS-Seq
Sequenced reads were aligned to mm10 genome using bwa-mem standard parameters.
Low quality reads and multihits were removed with samtools view -q 1
bedGraph files were generated with bedtools genomeCoverage, and artifacts detected by visual inspection were removed. bigWig files were obtained with the bedGraphToBigWig tool.
Peak-calling was performed with scanquantile program (Picard et al., 2014), parameters p-value 1E-16 and windowsize=500bp. Peaks separated by less than 200bp and peaks with a p-value higher than a threshold were removed with custom perl scripts.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files with density of each sample; bigBed files with SNS called peaks.

source_name: Embryonic stem cells

growth_protocol: mES cells were grown at 37ºC and 5% CO2 in DMEM supplemented with 10% fetal calf serum, 1x non-essential  aminoacids, 2 mM L-glutamine, 50 mM b-mercaptoethanol, 1 mM sodium piruvate, 100 U/ml penicillin,  100 μg/ml streptomycin  and 10E3 U/ml LIF.

extract_protocol:
Cells were lysed and DNA was purified by phenol/cloroform extraction. DNA was denaturated (boiling) and size fractionated through a sucrose gradient centrifugation. Fractions containing the sizes of interest (F4 and F5) were digested three times with lambda-exonucleasa. Finally, ssDNA was converted into dsDNA prior library preparation.
DNA libraries were prepared for sequencing using Illumina standard protocols

value: Embryonic stem cells

tag: genotype/variation

value: triple-KO for three somatic histone H1 genes


title: MEFs_HMGB1-KO_repl_II

source_name: Embryonic fibroblasts

growth_protocol: MEFS were derived from 14.5 dpc (Balb/C) embryos and grown in DMEM high glucose medium supplemented with 10% FBS, 100 U/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine, 1x non-essential aminoacids and 50 mM b-mercaptoethanol.

value: Embryonic fibroblasts


title: mES_WT_repl_II

value: WT


title: Six2GFP-_1


title: M183_ATII_N_WT_2

value: wild type


title: mES_H1-TKO_repl_II


title: mES_WT_repl_I


title: MEFs_WT_repl_II


title: Control_Jejunum_Tissue D3

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description: Barcode: GTTACC

data_processing:
Raw data were quality trimmed to minimum Q20 and minimum length 20bp with Trimmomatic v. 0.32 using "LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:20" settings.
Trimmed reads were mapped to reference genome mm10 using BWA MEM.
Gene expression was quantified against UCSC gene annotations for mm10 using HTSeq.
Normalizing according to protocol within the Limma method ( , first TMM normalization using Edge (Storey JD, Leek JT and Bass AJ (2015). edge: Extraction of Differential Gene Expression. R package version 2.8.0) then  correction using precision weights using Voom ( Law, CW, Chen, Y, Shi, W, and Smyth, GK (2014). Voom: precision weights unlock  linear model analysis tools for RNA-seq read counts. Genome Biology 15, R29 ) from the Limma package (Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W and Smyth GK (2015). “limma powers differential expression analyses for RNA-sequencing and microarray studies.” Nucleic Acids Research, 43(7), pp. e47).
Genome_build: mm10
Supplementary_files_format_and_content: exprs.raw.csv:  raw counts generated from the individual fastq.gz files.  exprs.norm.csv: comman separated file containing the adjusted counts after TMM normalization (EdgeR, Bioconductor 3.4) adjustment with Voom (Limma, Bioconductor 3.4) and  logCPM transformation.

growth_protocol: Organoids are grown according Sato  and Clevers et al 2009

extract_protocol:
RNA for organoids was extracted by Qiagen mini kit
Lexogen QuantSeq 3' mRNA-Seq Library Prep

treatment_protocol: Mice were treated with chronic 15% EtOH or water for 8 weeks

tag: donorid

value: Control

tag: organtype

value: Jejunum

tag: organoidtissue

value: Tissue

tag: txtissue

tag: txtissueorganoid


title: MEFs_WT_repl_I


title: EtOH_Jejunum_Tissue D4

description: Barcode: GGAGGT

value: EtOH


title: EtOH_Jejunum_Tissue D2

description: Barcode: CGATCT


title: EtOH_Colon_Tissue D4

description: Barcode: CAATGC

value: Colon


title: Control_Jejunum_Tissue D1

description: Barcode: AAGACA


title: EtOH_Colon_Tissue D3

description: Barcode: TGGCGA


title: EtOH_Colon_Tissue D2

description: Barcode: GCGAAT


title: Control_Colon_Tissue D1

description: Barcode: CGAAGG


title: EtOH_Jejunum_Tissue D1

description: Barcode: GCAGCC


title: EtOH_Jejunum_Organoid D4

description: Barcode: CAACAG

value: Organoid


title: Control_Colon_Tissue D2

description: Barcode: AACGCC


title: Control_Colon_Tissue D4

description: Barcode: CACACT


title: Control_Jejunum_Organoid D4

description: Barcode: GACGAT


title: EtOH_Jejunum_Organoid D3

description: Barcode: AACCGA


title: EtOH_Colon_Organoid D2

description: Barcode: GAAGTG


title: MEFs_HMGB1-KO_repl_I


title: Control_Jejunum_Organoid D2

description: Barcode: CGGTTA


title: Control_Colon_Organoid D2

description: Barcode: GAACCT


title: Control_Jejunum_Organoid D1

description: Barcode: GGTGAG


title: EtOH_Colon_Organoid D1

description: Barcode: AGGCAT


title: EtOH_Jejunum_Organoid D1

description: Barcode: ACCTAC


title: EtOH_Jejunum_Tissue D3

description: Barcode: CACTAA


title: Control_Jejunum_Tissue D2

description: Barcode: CAGATG


title: Tg

city: Beijing

first: Zinan

last: Li

address: #5 Dong Dan San Tiao

department: Immunology

country: China

institute: Institute of Basic Medical Sciences of the Chinese Academy of Medical Sciences

description: thymus from one male and one femal were mixed to form a pool

data_processing:
Raw reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence to get clean reads using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
Clean reads were mapped against Mus musculus genome using HotHap software
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nat Methods, 2008.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

source_name: Thymus

extract_protocol:
Thymuses were removed and washed twice in precooled PBS, then frozen in liquid nitrogen and grined into powders. Total RNA was harvested using Trizol reagent and then purified using Dynabeads Oligo (dt) 25 kit. NEB Next Ultra RNA Library Prep Kit for Illumina was used with 100 ng purified total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing according to introduction of NEB Next Ultra RNA Library Prep Kit for Illumina

value: Balb/c

value: miR-146a transgenic

value: 5 to 6 weeks


title: EtOH_Colon_Tissue D1

description: Barcode: TGGATT


title: Control_Colon_Tissue D3

description: Barcode: CAAGCA


title: WT

value: wild-type


title: 3037 dKO

city: San Francisco

first: Biao

address: 555 Mission Bay Blvd South

department: CVRI

institute: University of California, San Francisco

description:
Barcode ID: L2V18DR-BC15
Barcode Sequence: CACAGT

data_processing:
Known adapters and low-quality regions of reads were trimmed using Fastq-mcf. Sequence quality control was assessed using the program FastQC and RSeQC.
Reads were aligned to mouse mm9 genome. Reads were assigned to genes using "featureCounts", part of the Subread suite (http://subread.sourceforge.net/)
We first filter out any genes where there were not at least two samples with a CPM (counts per million) between 0.5 and 5000.  Then remaining ones were re-normalize  using "calcNormFactors" in edgeR. The sum of CPM in each sample is always exactly 1,000,000. Genes that would have had too-high or too-low CPM are reported as "NA".
Genome_build: mm9
Supplementary_files_format_and_content: [.xlsx] CPM, FPKM, Raw counts

source_name: dKO

extract_protocol:
RNA was prepared using RNeasy Mini kit (Qiagen)
cDNA libraries were prepared using Ovation RNA-seq Systems V2 and Ovation Ultralow Library Systems V2 (Nugen) according to manufacturers instructions.

value: AdipoqCre LKB1 F/F; HDAC4 F/F

tag: tissue

value: inguinal white adipose tissue


title: 971 KO

description:
Barcode ID: L2V18DR-BC4
Barcode Sequence: GCACTA

source_name: KO

tag: age

value: AdipoqCre LKB1 F/F


title: 966 KO

description:
Barcode ID: L2V18DR-BC9
Barcode Sequence: AAGAGG


title: 2837 dKO

description:
Barcode ID: L2V18DR-BC16
Barcode Sequence: TTGGCA


title: 1753-2 dKO

description:
Barcode ID: L2V18DR-BC13
Barcode Sequence: CGTAGA


title: 660 KO

description:
Barcode ID: L2V18DR-BC10
Barcode Sequence: GGAGAA


title: 1753 dKO

description:
Barcode ID: L2V18DR-BC12
Barcode Sequence: GAGTCA


title: 662 KO

description:
Barcode ID: L2V18DR-BC11
Barcode Sequence: AGCATG


title: 3035 dKO

description:
Barcode ID: L2V18DR-BC14
Barcode Sequence: TCAGAG


title: 963 KO

description:
Barcode ID: L2V18DR-BC3
Barcode Sequence: AGTGAG


title: EtOH_Jejunum_Organoid D2

description: Barcode: AGAATC

tag: treatment


title: Control_Jejunum_Organoid D3

description: Barcode: GCGCTG


title: 970 WT

description:
Barcode ID: L2V18DR-BC7
Barcode Sequence: AAGCCT

source_name: WT

value: LKB1 F/F


title: 1047 WT

description:
Barcode ID: L2V18DR-BC5
Barcode Sequence: ACCTCA


title: Female GLI1-3xFLAG Day 0 ChIP rep2

city: Boston

first: Brian

middle: C

last: Del Rosario

state: MA

address: 185 Cambridge St, CPZN-7250

department: Molecular Biology

institute: Massachusetts General Hospital

description:
BDa0-FG1-Day0-chip.allchr.s20_1e-4.allchr.bed
BDa0-FG1-Day0-chip.enrichment.wig

data_processing:
Basecalls performed using CASAVA version 1.7
Subsequent to demultiplexing and adapter trimming, fastqs were mapped to mouse genome build mm9 with the aligner BWA.
Genome_build: mm9
Supplementary_files_format_and_content: Input-normalized coverages (.wig), ChIPseq peak calls (.bed)

source_name: Female GLI1-3xFLAG Day 0 ChIP rep2

growth_protocol: Female (F1-2.1) mouse Tet-on (rtTA) ES cells bearing stable transgenes for GLI1-3xFLAG or GLI2-3xFLAG regulated by tetracycline response elements were generated.  These were maintained on gamma-irradiated feeder MEFs in DMEM GlutaMAX 4.5g/L D-glucose, 110mg/L sodium pyruvate, 15% FBS, 25mM HEPES pH 7.5, 0.1mM MEM non-essential amino acids, 0.1mM 2-mercaptoethanol, 100U/mL penicillin, 100ug/mL streptomycin, 100ug/mL hygromycin, and 500U/mL LIF.

extract_protocol:
Frozen cell pellets were resuspended in Lysis buffer 1 (50mM Tris-HCl pH 8.0, 10mM EDTA, 0.5% SDS). Chromatin was sheared in a Qsonica Q800R for 2 minutes at 40% power 30sec on 30sec off at 4C to ~500bp. 4 volumes of Lysis buffer 2 (50mM Tris-HCl pH 7.5, 187.5mM NaCl, 0.625% Triton X-100, 0.625% sodium deoxycholate, EDTA-free cOmplete Protease Inhibitor (Roche)) were added with 0.5mg RNaseA. Chromatin samples were incubated at 37C for 30minutes. Sepharose 4B (Sigma-Aldrich) was washed with ChIP Buffer (50mM Tris-HCl pH 7.6, 150mM NaCl, 0.5% Triton X-100, 0.5% sodium deoxycholate, 0.1% SDS, 2mM EDTA) with protease inhibitors and used to preclear RNase A treated chromatin samples. 20uL/IP anti-FLAG M2 agarose (Sigma-Aldrich) was blocked in ChIP buffer, 100ug/mL Acyclovir, 100ug/mL Zalcitabine, 5% Gly-Gly (Sigma-Aldrich), and protease inhibitors. Precleared chromatin and blocked anti-FLAG agarose were incubated together overnight at 4C with rotation. 10% of the precleared chromatin input was saved.  IP samples were washed with ChIP Wash Buffer (50mM Tris-HCl pH 7.5, 250mM LiCl, 10mM EDTA, 1% Triton X-100, 0.5% sodium deoxycholate, protease inhibitors) and with TEN (50mM Tris-HCl pH 8.0, 1mM EDTA, 50mM NaCl). Elution buffer (50mM Tris-HCl pH7.5, 10mM EDTA, 1% SDS) was added and the samples were heated to 65C.  Eluates and inputs were digested with 40ug Proteinase K.  Both IP and input cross-links were reversed and then samples were phenol:chloroform extracted.   DNA was alcohol precipitated and resuspended in TE.
ChIP-seq libraries were generated from both IP and Input DNA samples using the NEBNext ChIP-seq Library Prep Master Mix for Illumina with NEBNext Muliplex Oligos for Illumina (NEB).  DNA was quantified with both a Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher) and a KAPA Library Quantification Kit (KAPA Biosystems).  Libraries were size selected using Agencourt AMPure XP resin (Beckman Coulter) and sizes confirmed on a 2100 Bioanalyzer (Agilent).

treatment_protocol: Cells were cultured for 72hrs in media supplemented with 1ug/mL doxycycline and 100nM SAG prior to harvesting for Day 0 (D0) samples.  Irradiated MEFs were settled away from ES cells upon harvesting.  Two biological replicates for D0 Female GLI1-3xFLAG and GLI2-3xFLAG samples were generated.  For Day 3 (D3) samples, ES colonies were first detached from irradiated MEFs and then differentiated in suspension in media containing 1ug/mL doxycycline and 100nM SAG without LIF for 72 hours. Cells were trypsinized and 10^7 cells were fixed with 1% formaldehyde for 10 minutes at room temperature and quenched in 125mM glycine followed by PBS washes.  Cells were then frozen at -80C prior to chromatin extraction.

tag: antibody

value: Anti-FLAG

tag: cell line

tag: Sex

value: Female

tag: transgene


title: Female GLI2-3xFLAG Day 0 Input rep1

description:
D0_GLI2.allchr_s50_1e-5.bed
D0_GLI2.density.bw

source_name: Female GLI2-3xFLAG Day 0 Input rep1


title: Female GLI1-3xFLAG Day 0 Input rep2

source_name: Female GLI1-3xFLAG Day 0 Input rep2

value: none, input


title: Female GLI2-3xFLAG Day 0 Input rep2

description:
BDa0-FG2-Day0-chip.allchr.s20_1e-5.allchr.bed
BDa0-FG2-Day0-chip.enrichment.wig

source_name: Female GLI2-3xFLAG Day 0 Input rep2


title: Female GLI1-3xFLAG Day 0 Input rep1

description:
D0_GLI1.allchr_s50_1e-4.bed
D0_GLI1.density.bw

source_name: Female GLI1-3xFLAG Day 0 Input rep1


title: w96h3 (miRNA)

first: zhongyi

last: wang

address: No.27, Taiping road, Haidian district, Beijing

institute: Academy of Military Medical Sciences

description: miRNA.All.Counts.txt

data_processing:
[mRNA&ncRNA] Reads filtering under criteria removing reads with 20% of the base quality lower than 13
[mRNA&ncRNA] HISAT2 mapping to reference genome
[mRNA&ncRNA] count counting
[miRNA] Reads filtering under criteria removing reads with 20% of the base quality lower than 13
[miRNA] Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Homo sapiens miRNA database and Homo sapiens genome.
[miRNA] count counting
Genome_build: GRCh38, miRBase 21.0
Supplementary_files_format_and_content: TXT files contain counts for each sample

source_name: w96h3, 293T cells

growth_protocol: 293T cells grow in DMEM medium with 5% fetal bovine serum

extract_protocol:
Total RNA was extracted from cells using TRIzol reagent (Invitrogen)
cDNA Library Construction:  The cDNA libraries were constructed for each pooled RNA sample using the VAHTSTM Total RNA-seq (H/M/R) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: depletion of rRNA and fragmented into 150-200 bp using divalent cations at 94 ℃ for 8 min. The cleaved RNA fragments were reverse-transcribed into first-strand cDNA, second-strand cDNA synthesis, fragments were end repaired, A-tailed and ligated with indexed adapters. Target bands were harvested through VAHTSTM DNA Clean Beads .The products were purified and enriched by PCR to create the final cDNA libraries and quantified by Agilent2200. The tagged cDNA libraries were pooled in equal ratio and used for 150 bp paired-end sequencing in a single lane of the Illumina Xten with 51 plus 7 cycles by NovelBio Corp. Laboratory, Shanghai.   miRNA Library Construction and RNA Sequencing:  The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA library had been size selected by PAGE Gel electrophoresis for miRNA sequencing. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies) by NovelBio Corp. Laboratory, Shanghai.

treatment_protocol: P1 trVLPs were used to infect 293T cells, which were pre-transfected with pCAGGS-L, pCAGGS-NP, pCAGGS-VP30, pCAGGS-VP35 and pCAGGS-Tim1 (24 hours before infection). The TCID50 of P1 trVLPs was 10-6.5/ml. Approximately 4×10^5 cells were present in each well of a 6-well plate, and P1 trVLPs used for infection in this experiment were applied in a volume of 2 ml per well.

tag: infection

value: trVLP

tag: time

value: 96 hours post virus infection


title: Female GLI2-3xFLAG Day 0 ChIP rep1

source_name: Female GLI2-3xFLAG Day 0 ChIP rep1


title: w96h2 (miRNA)

description: miRNA.All.Counts.txt

source_name: w96h2, 293T cells


title: w96h1 (miRNA)

description: miRNA.All.Counts.txt

source_name: w96h1, 293T cells


title: w72h3 (miRNA)

description: miRNA.All.Counts.txt

source_name: w72h3, 293T cells

value: 72 hours post virus infection


title: 979 WT

description:
Barcode ID: L2V18DR-BC8
Barcode Sequence: GTCGTA

tag: strain


title: w48h3 (miRNA)

description: miRNA.All.Counts.txt

source_name: w48h3, 293T cells

value: 48 hours post virus infection


title: 957 WT

description:
Barcode ID: L2V18DR-BC2
Barcode Sequence: TGGTGA


title: w72h2 (miRNA)

description: miRNA.All.Counts.txt

source_name: w72h2, 293T cells


title: Control_Colon_Organoid D1

description: Barcode: ACATTA

value: Control

value: Colon


title: w72h1 (miRNA)

description: miRNA.All.Counts.txt

source_name: w72h1, 293T cells


title: 2961 WT

description:
Barcode ID: L2V18DR-BC6
Barcode Sequence: GTGCTT


title: w24h2 (miRNA)

description: miRNA.All.Counts.txt

source_name: w24h2, 293T cells

value: 24 hours post virus infection


title: w48h1 (miRNA)

description: miRNA.All.Counts.txt

source_name: w48h1, 293T cells


title: human week 16 kidney cortex single cell RNA-Seq

data_processing:
Base call by bcl2fastq v. 2.17; adaptor and index sequences were trimmed
Reads were mapped using STAR 2.5.1b and the NCBI GTF annotation accession NCBI:GCA_000001405.14
Count tables were generated from the FASTQ files using the Cell Ranger software version 1.3.1 with default parameters.
Read 1 is the Cell Barcode + UMI and read 2 is the actual RNA sequence
bam file contains cell barcode for each read at CB:Z tag
Genome_build: GRCh37.p13
Supplementary_files_format_and_content: text file with count table of read counts for each cell barcode.

source_name: human kidney cortex

extract_protocol: 10X Genomics: Chromium Single Cell 3’ v2 for single cell RNA-Seq of poly A selected mRNA

tag: developmental stage

value: week 16

value: kidney cortex


title: w24h3 (miRNA)

description: miRNA.All.Counts.txt

source_name: w24h3, 293T cells


title: Female GLI1-3xFLAG Day 0 ChIP rep1

source_name: Female GLI1-3xFLAG Day 0 ChIP rep1


title: w0h3 (miRNA)

description: miRNA.All.Counts.txt

source_name: w0h3, 293T cells

value: control

value: 0 hours post virus infection


title: Female GLI2-3xFLAG Day 0 ChIP rep2

source_name: Female GLI2-3xFLAG Day 0 ChIP rep2


title: w24h1 (miRNA)

description: miRNA.All.Counts.txt

source_name: w24h1, 293T cells


title: w0h1 (miRNA)

description: miRNA.All.Counts.txt

source_name: w0h1, 293T cells


title: w0h2 (miRNA)

description: miRNA.All.Counts.txt

source_name: w0h2, 293T cells


title: hMARIS_SIX2-_polyA#2

data_processing:
Fastq files were aligned using TopHat2
Gene-level quantification was presented as TPM and calculated by Partek Genomic Suite
hg38
Genome_build: txt files containing TPM values by gene

source_name: developing kidneys

extract_protocol:
Ambion Recoverall Total Nucleic Acid Isolation Kit and QIAGEN Rneasy Micro Kit
Kapa stranded mRNA-Seq library (numberKK8420)
polyA selected RNA-Seq

tag: developing stage

value: 17 wk


title: hMARIS_SIX2-_polyA#3

value: 15 wk


title: hMARIS_SIX2-_MEIS1-_polyA#2


title: hMARIS_SIX2-_polyA#1

value: 16 wk


title: hMARIS_SIX2-_MEIS1-_polyA#1


title: hMARIS_SIX2-_MEIS1+_polyA#1


title: hMARIS_SIX2+_polyA#5


title: w48h2 (miRNA)

description: miRNA.All.Counts.txt

source_name: w48h2, 293T cells


title: hMARIS_SIX2+_polyA#2


title: hMARIS_SIX2+_polyA#3


title: hMARIS_SIX2+_polyA#4


title: hMARIS_SIX2+_polyA#1


title: hMARIS_SIX2+_MEIS1+_polyA#1


title: hMARIS_SIX2-_polyA#4


title: hMARIS_NZC_polyA#3

description: TPM.huNZC.txt


title: hMARIS_NZC_polyA#4

description: TPM.huNZC.txt


title: hMARIS_NZC_polyA#2

description: TPM.huNZC.txt


title: huKidney_17wk_RNASeq_2

data_processing:
Base call by bcl2fastq v. 2.17; adaptor and index sequences were trimmed
Fastq files were aligned using TopHat2
Gene-level quantification was presented as TPM and calculated by Partek Genomic Suite
Genome_build: hg38
Supplementary_files_format_and_content: txt files containing TPM values by gene

extract_protocol:
phenol chloroform and isopropenol precipitation
Kapa stranded mRNA-Seq library (#KK8420)
polyA selected RNA-Seq


title: hMARIS_NZC_polyA#1

description: TPM.huNZC.txt


title: huKidney_9.5wk_RNASeq_2


title: huKidney_9.5wk_RNASeq_3


title: huKidney_11.3wk_RNASeq_1


title: huKidney_13wk_RNASeq_2


title: huKidney_17wk_RNASeq_1


title: hMARIS_NZC_polyA#5

description: TPM.huNZC.txt


title: huKidney_13wk_RNASeq_1


title: hMARIS_SIX2-_MEIS1+_polyA#2


title: Untreated replicate 3

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

description:
Sample name: YM-NT-3_S4_0
Processed data file: Cuffnorm_CountMatrix.txt

data_processing:
Illumina BaseSpace FastQ v1.0.0 used for basecalling.
Raw sequences were checked for quality values using fastQC v0.10.1. Quality trimming was not deemed necessary.
Raw sequences were mapped to the hg38 genome assembly using tophat2 v2.0.13 generating alignments in bam format, using an Ensembl gene and transcript gtf as a guide.
Mapped reads were assembled according to the Ensembl hg38.gtf file using cufflinks v2.2.1.
Differentially expressed genes were identified for the treated vs. untreated conditions using cuffdiff v2.2.1.
The resulting mapped files from cufflinks were normalized and concatenated into a single tab-delimited gene matrix file using cuffnorm.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Cuffnorm_CountMatrix.txt: Tab-delimited text file includes cuffnorm results.

source_name: HeLa cells, untreated

growth_protocol: HeLa cells were grown in Dulbecco's modified Eagle's medium (Sigma) containing 1 mM sodium pyruvate, 0.1 mM nonessential amino acids and supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin at 37 °C in a humidified environment containing 5% CO2 and 95% air.

extract_protocol:
Total RNA was extracted using Quick-RNA MiniPrep (Plus) from Zymo Research.
Using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA).

treatment_protocol: The ON-TARGETplus Human PARP1 siRNAs (purchased from Dharmacon) and DharmaFECT 1 transfection reagent were used to deliver siRNAs into HeLa cells according to manufacturer's protocol. In brief, 2x10^5 cells/well were starved by incubating the cells in 2 ml of antibiotic-free complete medium with 10% serum for 2 hours. 50 nM of the ON-TARGETplus Human PARP1 siRNAs were added to serum-free DMEM (180 μl) in one tube, and DharmaFECT 1 (2.4 μl) was added to 197.6 μl of serum-free medium in another tube. The contents of each tube were individually gently mixed and after 5 min incubation at room temperature, were mixed together. This mixture was then incubated at room temperature for an additional 20 min. (For control samples, 2.4 μl of DharmaFECT 1 was added to 400 μl serum-free medium). Subsequently, an additional serum-free medium (1600 μl) was added to each mixture of 400 μl for a final volume of 2000 μl transfection medium and a final siRNA concentration of 50 nM. The starvation media from the cells was then removed and replaced with the 2000 ul transfection mixture. Cells were further incubated for 1 hour at 37°C, before 10% serum was added. Cells were then allowed to grow for 24 - 48 hours. This procedure was repeated three times, every 24-48 hours. After that, the cells were collected and analyzed for mRNA or PARP1-protein to check the target gene knockdown efficiency. 3 independent experiments were performed.

value: HeLa

value: untreated


title: Treated replicate 3

description:
Sample name: YM-T-3_S1_0
Processed data file: Cuffnorm_CountMatrix.txt

source_name: HeLa cells, PARP knockdown

value: PARP knockdown


title: hMARIS_SIX2+_MEIS1+_polyA#2


title: Treated replicate 1

description:
Sample name: YM-T-1_S3_0
Processed data file: Cuffnorm_CountMatrix.txt


title: Untreated replicate 1

description:
Sample name: YM-NT-1_S6_0
Processed data file: Cuffnorm_CountMatrix.txt


title: Untreated replicate 2

description:
Sample name: YM-NT-2_S5_0
Processed data file: Cuffnorm_CountMatrix.txt


title: Root untreated 48 hrs repeat 2

city: Milwaukee

first: Dazhong

last: Zhao

state: WI

address: 3209 N. Maryland Ave

department: Biological Sciences Department

institute: University of Wisconsin-Milwaukee

data_processing:
Evaluate read quality (FASTQC 0.11.5)
Remove adapter sequence (scythe-0.99)
Filter reads by quality (sickle-quality-based-trimming_version_1.0)
Align RNA-Seq reads to reference genome (Tophat2-SE)
Assemble transcripts (Cufflinks2)
Merge transcripts (Cuffmerge2)
Compare gene expression (Cuffdiff2)
Supplementary_files_format_and_content: text file with FPKM values for each Sample and file with statistical analysis from Cuffdiff2.

organism: Arabidopsis thaliana

source_name: Roots

growth_protocol: Seedlings were grown on the Murashige and Skooge (MS) medium in square Petri dishes under a 16-hour light/8-hour dark photoperiod regime at 22°C and 50% humidity.

extract_protocol:
Roots from hundred seedlings were collected and thern were used for RNA extraction by RNeasy Plant Mini Kit (Qiagen).
RNA-seq libraries were constructed using the Illumina's TruSeq Stranded Total RNA with Ribo-Zero Plant kit.

treatment_protocol: Roots of 4-day old seedlings were inoculated with the LB grown Rhizobium sp. IRBG74 strain and the plain LB (control). Roots were collected at 24 and 48 hours after inoculation.

value: Roots

tag: rhizobium strain used for treatment

value: Rhizobium sp. IRBG74

value: untreated 48 hrs


title: Root untreated 48 hrs repeat 1


title: Root treated 48 hrs repeat 3

value: treated 48 hrs


title: Root untreated 48 hrs repeat 3


title: Root treated 48 hrs repeat 1


title: Root treated 24 hrs repeat 2

value: treated 24 hrs


title: Root treated 48 hrs repeat 2


title: huKidney_9.5wk_RNASeq_1


title: Root treated 24 hrs repeat 3


title: Root untreated 24 hrs repeat 3

value: untreated 24 hrs


title: Treated replicate 2

description:
Sample name: YM-T-2_S2_0
Processed data file: Cuffnorm_CountMatrix.txt


title: Root untreated 24 hrs repeat 2


title: Root untreated 24 hrs repeat 1


title: Uninduced

city: London

first: Andrea

last: Streit

address: Centre for Craniofacial & Regenerative Biology, King's College London

country: United Kingdom

institute: Kings College London

description: Data from Claudio Stern's laboratory

data_processing:
Illumina Casava1.7 software used for basecalling.
Alignment was performed with Tophat2 with following parameters: -N 4 --read-edit-dist 6 -m 1 --max-insertion-length 5 --max-deletion-length 5 --no-discordant --no-mixed --microexon-search --library-type fr-unstranded
Normalized FPKM for each gene was generated with cuffdiff2 with following parameters: -u -N --library-type fr-unstranded --library-norm-method geometric --dispersion-method blind
easyRNAseq(R package) was used to get the raw count.
Genome_build: Gallus_gallus-4.0 (galGal4.71)

organism: Gallus gallus

source_name: Area opaca control epiblast

growth_protocol: Chicken embryos were grown to stage EGKXII/XIII, HH4-/4, or HH6/7

extract_protocol:
Total RNA were extracted by using the RNAqueous-Micro Kit (Ambion AM1931)
RNASeq library was prepared using the TrueSeq RNA sample preparation V2 kit (Illumina).

treatment_protocol: Tissue: Neural plate, anterior and posterior pre-placodal region, non-neural/ non-placodal head ectoderm were dissected from HH6/7 embryos. Anterior prestreak and central epiblast from  pre-streak  EGKXII/XIII embryos. Hensen's node was grafted into the area opaca of HH4 chick embryos and the epiblast in contact with the node was collected after 5 hours (5hrs induced); the contralateral area opaca from the same embryos was collected a the same time (uninduced area opaca).

tag: tissue type

value: Area of opaca epiblast from the contralateral side of embryos which had received a graft of Hensen's node for 5 hours


title: NNE_RNASeq

department: Centre for Craniofacial & Regenerative Biology

description: Data from Andrea streit's laboratory

source_name: Non-placoda, non-neural ectoderm

value: Embryonic Ectoderm - anterior head ectoderm


title: aPPR_RNASeq

description: Data from Andrea streit's laboratory

source_name: Anterior preplacodal region

value: Embryonic Ectoderm - preplacodal region


title: cPS_RNASeq

description: Data from Claudio Stern's laboratory

source_name: Central pre-streak epiblast

value: Central pre-streak epiblast

value: Pre-streak EGKXII/XIII


title: pPPR_RNASeq

description: Data from Andrea streit's laboratory

source_name: Posterior preplacodal region

value: Embryonic Ectoderm - pre-placodal region


title: NP_RNASeq

description: Data from Claudio Stern's laboratory

source_name: Neural plate epiblast

value: Embryonic ectoderm - Neural plate


title: control eutopic endometrium miRNA, patient 25

first: Luyang

address: 28 Fuxing Road, HaiDian District

department: Department of Gynecology and Obstetrics

institute: People’s Liberation Army (PLA) Medical School, Chinese PLA General Hospital

data_processing:
Data Filtering:Remove low-quality reads (reads of which more than 15% bases are with Phred Quality Score<19);Remove reads without 3’ adaptor; Remove reads without insert sequence, that is 3’ adaptor is directly ligated to 5’adaptor;Remove ploy(A)/poly(T)-contained reads;Remove reads with unfit length.
Alignment:To ensure accuracy of subsequent analysis, we filtered reads according to their length (for animals 17-35nt), then we aligned filtered reads against reference genome using Bowtie(version 1.1.2), then get the reads location in the genome.
Analysis of known miRNA:Either according to the genome annotation information in miRBase database (Release 21), or align miRNA sequence in miRBase againse reference genome to obtain genome location of all known mature miRNA and its precursors. To compare reads location with miRNA location in the genome to identify known miRNA. This step uses the miRDeep2_V2.After that,we got reads count of known miRNA.
Genome_build: Homo_sapiens.GRCh38.83

source_name: eutopic endometrium

extract_protocol:
Total RNA was extracted using a single-step acid guanidinium thiocyanate-phenol-chloroform method. The quality and purity of RNA were examined by a Nanodrop 8000 spectrophotometer (Thermo Scientific, Waltham, MA, USA). RNA integrity was analyzed using the RNA 6000 Nano Kit and Small RNA Kit with the and a Bioanalyzer 2100 (Agilent, Santa Clara, CA). The samples with the absorbance wavelength ratio (A260/A280) ≥1.9 and a the RNA integrity number ≥ 8 were included. For small RNA sequencing, 3 μg of total RNA was used for library preparation. For mRNA sequencing, 3 μg of RNA per sample was prepared for library preparation.
The purified libraries were sequenced on an Illumina HiSeq 2000 platform in Annoroad Genome (Beijing, China).

tag: disease state

value: control

tag: patient

tag: rafs stage

value: IV


title: Induced-5h

description: Data from Claudio Stern's laboratory

source_name: Area opaca epiblast

value: Area opaca epiblast exposed to Hensen's node for 5 hours


title: aPS_RNASeq

description: Data from Claudio Stern's laboratory

source_name: Anterior pre-streak epiblast

value: Anterior pre-streak epiblast


title: control eutopic endometrium miRNA, patient 18

value: III


title: control eutopic endometrium miRNA, patient 21


title: control eutopic endometrium miRNA, patient 6


title: control eutopic endometrium miRNA, patient 7


title: huKidney_21wk_RNASeq_1


title: ectopic endometrium miRNA, patient 21

source_name: ectopic endometrium

value: case


title: ectopic endometrium miRNA, patient 18


title: ectopic endometrium miRNA, patient 5


title: ectopic endometrium miRNA, patient 6


title: ectopic endometrium miRNA, patient 25


title: control eutopic endometrium miRNA, patient 1


title: SMC-IL rep3

city: Madison

first: Lianwang

last: Guo

address: 1111 Highland Avenue

department: Surgery

institute: University of Wisconsin at Madison

data_processing:
Illumina CASAVA pipeline (released version 1.8, Illumina) was used to obtain de-multiplexed sequencing reads (fastq files) passed the default purify filter.
quality filtering used FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit) to keep only reads that have at least 80% of bases with a quality score of 20 or more (conducted by fastq_quality_filter function) and reads left with N10 bases after being trimmed with reads with a quality score of b20 (conducted by fastq_quality_trimmer function)
Tthe short read sequences of each sample were aligned onto the human genome  human genome version 19 (HG19) to generate transcripts by TopHat2 program23 withusing human genome annotation data of HG19.
Cuffdiff program in the Cufflinks2.0 package was then applied to calculate differential gene expression using the accepted alignments of samples and controls in SMC and EC with  TNFα and IL-1β treatments, respectively from the TopHat2 output and HG19 gene annotations as input data.
gene_exp files including gene expression results from the CuffDiff were normalized using a Perl script to integrate with gene names and to calculate fold changes (FC).
Genome_build: HG19

source_name: SMC-IL

growth_protocol: Human aortic SMCs and ECs were purchased from Lonza, and cultured at 37 °C with 5% CO2 in their respective optimal media (SmGM-2 with 5% FBS and EGM-2 with 2% FBS, Lonza).

extract_protocol:
total RNAs were isolated from SMCs or ECs using TRIzol reagents (Invitrogen) followed by removal of ribosomal RNA using the RiboMinus Kit (Invitrogen). Confirming high quality of purified mRNAs, the A260/A280 ratio was determined to be > 1.9 by NanoDrop (Thermo Scientific), and the RNA integrity number was measured to be > 7 using the BioAnalyzer RNA 6000 Pico Kit (Agilent).
The cDNA libraries were prepared using Ovation RNA-seq System v2 (NuGEN), and unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The size distribution and concentration of the final product were assessed using the BioAnalyzer High Sensitivity DNA Kit (Agilent) and the Kapa Library Quantification Kit (Kapa Biosystems).
The libraries were pooled and diluted to 2 nM in EB buffer (Qiagen). Before loading to an Illumina HiSeq 2000 sequencing analyzer (with TruSeq SR v3 flow cells), the libraries were denatured and diluted to 10 pM in pre-chilled hybridization buffer. After 75 cycles using a single-read recipe (TruSeq SBS Kit v3, Illumina), de-multiplexed sequencing reads (fastq files) that passed the default purify filter were obtained using the Illumina CASAVA pipeline (version 1.8).

treatment_protocol: For cytokine stimulation, cells at ~70% confluency were starved overnight in basal medium containing 0.5% fetal bovine serum (FBS) and then treated for 4h with recombinant TNF-α or IL-1β (R&D Systems, MN) at a final concentration of 20 ng/mL. The same experiments without adding TNFα or IL-1β were conducted as solvent control. Three replicate experiments were conducted for each cytokine treatment or control condition.

tag: cell

value: Smooth muscle cells (SMCs)


title: SMC-IL rep 2


title: SMC-TNF rep3

source_name: SMC-TNF


title: ectopic endometrium miRNA, patient 1


title: SMC-TNF rep2


title: ectopic endometrium miRNA, patient 7


title: SMC-TNF rep1


title: control eutopic endometrium miRNA, patient 11


title: SMC-CTR rep2

source_name: SMC-CTR


title: SMC-IL rep1


title: EC-IL rep2

source_name: EC-IL

value: Endothelial cells (ECs)


title: EC-IL rep3


title: SMC-CTR rep1


title: control eutopic endometrium miRNA, patient 5


title: EC-IL rep 1


title: EC-TNF rep 3

source_name: EC-TNF


title: EC-TNF rep2


title: EC-TNF rep1


title: EC-CTR rep3

source_name: EC-CTR


title: EC-CTR rep2


title: EC-CTR rep1


title: SMC-CTR rep3


title: C_6

city: Durham

first: Yarui

last: Diao

state: NC

address: 307 Research Drive, Box3709

institute: Duke University

data_processing:
TopHat v1.3.3 was used for aligning to the hg19 genome, assembling transcripts, and estimating abundance as FPKM values.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx file contains FPKM values for each sample.

source_name: human bone osteosarcoma epithelial cells

growth_protocol: Human U2OS cell line was purchased from ATCC and cultured following the manufacturer's protocol.

extract_protocol:
RNeasy Mini Kit (QIAGEN) was used to extract cytoplasmic RNA from transfected cells following the manufacturer's protocols.
cDNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with control siRNA or Pan3 isoform-specific siRNAs using RNAiMAX (Invitrogen) according to the manufacturer’s protocol.

value: Control knockdown

tag: time (hours)


title: S_2

tag: treatment

value: Short isoform knockdown


title: L_1

value: Long isoform knockdown


title: LS_2

value: Both knockdown


title: LS_1


title: LS_0-5


title: S_0


title: S_1


title: L_0


title: LS_4


title: S_0-5


title: L_2


title: L_0-5


title: LS_6


title: S_4


title: C_4


title: C_0-5


title: C_0


title: L_4


title: S_6


title: w96h2 (total RNA)

description: All.Counts.txt

source_name: w96h2, 293T cells

value: trVLP

value: 96 hours post virus infection


title: w96h3 (total RNA)

description: All.Counts.txt

source_name: w96h3, 293T cells


title: w96h1 (total RNA)

description: All.Counts.txt

source_name: w96h1, 293T cells


title: LS_0


title: L_6


title: C_2


title: w72h3 (total RNA)

description: All.Counts.txt

source_name: w72h3, 293T cells

value: 72 hours post virus infection


title: C_1


title: w72h2 (total RNA)

description: All.Counts.txt

source_name: w72h2, 293T cells


title: w48h1 (total RNA)

description: All.Counts.txt

source_name: w48h1, 293T cells

value: 48 hours post virus infection


title: w48h2 (total RNA)

description: All.Counts.txt

source_name: w48h2, 293T cells


title: w24h3 (total RNA)

description: All.Counts.txt

source_name: w24h3, 293T cells

value: 24 hours post virus infection


title: w72h1 (total RNA)

description: All.Counts.txt

source_name: w72h1, 293T cells


title: w48h3 (total RNA)

description: All.Counts.txt

source_name: w48h3, 293T cells


title: w0h2 (total RNA)

description: All.Counts.txt

source_name: w0h2, 293T cells

value: control

value: 0 hours post virus infection


title: w0h1 (total RNA)

description: All.Counts.txt

source_name: w0h1, 293T cells


title: w24h2 (total RNA)

description: All.Counts.txt

source_name: w24h2, 293T cells


title: w24h1 (total RNA)

description: All.Counts.txt

source_name: w24h1, 293T cells


title: w0h3 (total RNA)

description: All.Counts.txt

source_name: w0h3, 293T cells


title: mutants_replicate2

city: Bad Nauheim

first: Jason

last: Lai

state: Hessen

address: Ludwigstrasse 43

department: Developmental Genetics

country: Germany

institute: Max Planck Institute For Heart and Lung Research

data_processing:
Reads trimming: Trimmomatic v0.33 (LEADING:3 TRAILING:3 SLIDINGWINDOW:5:20 CROP:500 MINLEN:15)
Alignment: STAR 2.4.0a (--outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMatchNmin 30 --outFilterMultimapNmax 999 --alignEndsProtrude 10 ConcordantPair
normalization and statistics: Cufflinks suite v2.2.1 (standard parameters)
Genome_build: Zv10
Supplementary_files_format_and_content: fpkm_tracking

organism: Danio rerio

source_name: tails

extract_protocol:
RNA extraction was performed with Qiagen miRNeasy kit
Library was prepared with Truseq Stranded mRNA library preparation kit

tag: tissue

value: posterior body up to S-III

tag: genotype/variation

value: yap1/wwtr1 double homozygous mutants


title: Control 24hpf sea urchin embryos replicate 1 run 1

city: Barcelona

first: Demian

last: Burguera

address: Diagonal 643

department: Genetics, Faculty of Biology

institute: University of Barcelona

description:
Embr_24h_Esrp_Cont_e
cRPKM_Spu_ESRP_KD.tab

data_processing:
Full genomic sequences for the analyzed species were downloaded from the UCSC Genome Browser database. Full transcriptomic sequences were downloaded from Ensembl for zebrafish and from Echinobase from sea urchin. For each gene, the canonical transcript was selected for gene expression analysis based on ORF lenght.
For each species, we assembled all canonical transcript (as defined above) sequences. In order to calculate the effective number of unique mappable positions in each transcript (i.e. the effective length) we performed the following steps. For each read length k, we extracted the L-k+1 (L being the transcript length) k-mer sequences from each canonical transcript and then aligned the full set of k-mers against the respective genome using Bowtie, allowing for a maximum of two mismatches. k-mers with no or one unique genomic alignment were then likewise aligned back to the canonical transcriptome. For each transcript, the number of such k-mers having a unique transcriptomic alignment was determined. This corresponds to the transcript’s effective number of unique mappable positions for k-mer mRNA-Seq reads. For each sample, the corresponding mRNA-Seq data were aligned against the respective genome using Bowtie, allowing for a maximum of two mismatches. Reads with one unique genomic alignment were then aligned against the canonical transcriptome and, for each transcript, the number of reads with one unique transcriptomic alignment were counted. Gene expression levels were determined as reads per thousand mappable positions of target transcript sequence per million of reads, where the reads uniquely align to the analyzed transcriptome. This procedure for estimating gene expression levels is a corrected version of the widely used RPKM (reads per kilobase of target transcript sequence per million of total reads) metric, and is referred to as “cRPKM” [Labbe RM et al. Stem Cells (2012)].
Genome_build: zebrafish: danRer10. sea urchin: Spur_v3.1
Supplementary_files_format_and_content: Tab-delimited text files include cRPKM values (as defined above) for each gene's canonical transcript in each condition

organism: Strongylocentrotus purpuratus

source_name: Purple sea urchin embryos 24hpf

extract_protocol:
mRNA was purified using QIAGEN RNA purification kit for zebrafish and AMBION kit for sea urchin
RNA libraries were prepared for sequencing using standard Illumina Truseq kit protocols

value: Wild type


title: siblings_replicate1

value: siblings


title: Control 24hpf sea urchin embryos replicate 2 run 1

description:
Embr_24h_Esrp_Cont_f
cRPKM_Spu_ESRP_KD.tab


title: Esrp SplMO knockdown 24hpf sea urchin embryos replicate 2 run 1

description:
Embr_24h_Esrp_KD_f
cRPKM_Spu_ESRP_KD.tab

value: Esrp KD


title: siblings_replicate2


title: mutants_replicate1


title: Esrp SplMO knockdown 24hpf sea urchin embryos replicate 1 run 1

description:
Embr_24h_Esrp_KD_e
cRPKM_Spu_ESRP_KD.tab


title: 40

city: wuhan

first: juan

last: ling

address: lion street 1

institute: Huazhong Agricultural University

description:
Four weeks old mutant plants and the experimental design used to impose treatment conditions on independent plants: methoxyfenozide (Inducer) and distilled water (Control). After leaves from each treatment were gathered and RNA isolated
4h_gene_exp.diff

data_processing:
short-read alignment and mapping of reads were carried on Arabidopsis genome annotation (TAIR 10) with the software TopHat v2.0.11 using the default parameters
Cufflinks v2.2.1 programme was used to estimate transcript abundance and differential gene expression.
Reads mapping to annotated transcripts were summed for each gene model and normalized by FPKM
Genome_build: TAIR10.gtf
Supplementary_files_format_and_content: tab-delimited text files include different expression genes for treatment and no-treatment

source_name: Arabidopsis thaliana

extract_protocol:
The TRIzol Reagent Kit (Ambion™) was used following manufacturer’s instructions to extract total RNA from leaf
12 samples were used to construct cDNA library with Illumina® TruSeq™ RNA Sample Preparation Kit following the manufacturer’s instructions.

value: leaf

tag: age

value: 4 weeks

tag: ecotype

value: Columbia

tag: protocol

value: Stable multi copy insertion line, after 4h non-induced


title: 31

value: Stable multi copy insertion line, after 4h induced


title: 38


title: 39


title: 34


title: 32


title: 17

description:
Four weeks old mutant plants and the experimental design used to impose treatment conditions on independent plants: methoxyfenozide (Inducer) and distilled water (Control). After leaves from each treatment were gathered and RNA isolated
2h_gene_exp.diff

value: Stable multi copy insertion line, after 2h non-induced


title: 19


title: 18


title: 13

value: Stable multi copy insertion line, after 2h induced


title: 12


title: PITX1_ChIPseq_Rep2

city: Dallas

first: Jialiang

last: Wang

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

data_processing:
Sequencing read quality was evaluated using FastQC (version 0.5.1)
ChIP-seq reads were aligned to the Anolis carolinensis genome (anoCar2) using bowtie (version 0.12.8)
Peaks were identified using MACS2 with default parameters except for the effective genome size set for lizard (anoCar2)
Genome_build: anoCar2
Supplementary_files_format_and_content: Bigwig files were converted from bedGraph files generated by MACS2

organism: Anolis carolinensis

source_name: embryonic hindlimb tissue

growth_protocol: Hindlimbs were collected from stage 6-7 Anolis carolinensis embryos.

extract_protocol:
Lysates were clarified from sonicated hindlimb tissues and PITX1-DNA complexes were isolated with antibody.
Libraries were prepared according to instructions accompanying the NEBNext Ultra DNA Library Prep Kit (NEB #E6240S/L). Libraries were sequenced on the HiSeq platform.

value: stage 6-7

tag: antibody

value: Pitx1(Santa Cruz, sc-18922X, Lot G0105)

value: hindlimb


title: PITX1_ChIPseq_Rep1


title: WT.H1N1.D2B

city: New York

first: Christian

last: Forst

address: One Gustave L. Levy Place

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The sequencing reads were aligned to the human hg19 genome using star aligner (version 2.5.0b).
featureCounts was used to quantify gene expression at the gene and exon levels based on Ensembl gene model GRCh37.70. Genes with at least 1 count per million (CPM) reads in at least 1 sample were considered expressed, otherwise absent and hence discarded.
The gene level read counts data was normalized using edgeR, multi-dimensional scaling and cluster analysis were performed to check for potential sample outliers.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited tex file using log2-tranformed CPM values for each sample

source_name: A549 cells

growth_protocol: A549-wt and A549-DOCK5-ko cells were seeded into T-75 tissue culture flasks to approximately 80% confluency (~ 2.5 x 10^6 cells/flask) at the time of infection.

extract_protocol:
Total RNA was extracted from each sample using Qiagen RNeasy Mini Kit, with genomic DNA removed by on-column DNase digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A549-WT and A549-DOCK5-c28 cells were each infected at MOI of  0.5 TCID50/cell of the PR8 (H1N1) virus, the A/New York/238/2015 (H3N2) virus, or Mock infected. The infected cells were incubated at 37C incubator with 5% CO2 for 1 or 2 days.

tag: genotype

value: wild type

tag: dpi


title: 11


title: WT.H1N1.D1C


title: WT.H1N1.D2A


title: WT.H1N1.D2C


title: Input_DNA

tag: developmental stage


title: WT.H1N1.D1B


title: WT.Mock.D1C

value: Mock


title: DOCK5.H1N1.D2B

value: DOCK5 -/-


title: WT.Mock.D1A


title: WT.H1N1.D1A


title: WT.H3N2.D2A


title: WT.H3N2.D2B


title: DOCK5.H1N1.D2A


title: DOCK5.H1N1.D1C


title: WT.H3N2.D1B


title: WT.Mock.D1B


title: WT.H3N2.D2C


title: DOCK5.H1N1.D1B


title: DOCK5.Mock.D1B


title: DOCK5.Mock.D1C


title: DOCK5.Mock.D1A


title: DOCK5.H3N2.D2B


title: DOCK5.H3N2.D2A


title: DOCK5.H3N2.D2C


title: DOCK5.H3N2.D1B


title: DOCK5.H3N2.D1A


title: F2-7 PDX-P5

city: Aurora

last: Kabos

state: CO

address: 12801 E. 17th Avenue

department: Division of Medical Oncology

institute: University of Colorado School of Medicine

data_processing:
After demultiplexing, the resulting reads were trimmed with cutadapt to remove 3' adaptor sequences and low quality 3' bases (Q<10)
The trimmed reads were then aligned to both the human (hg19/GRCh37) and mouse (mm10) genomes using Tophat2
Reads were then assigned to either the human or mouse genome using disambiguate and ambiguous reads were discarded.
Unambiguous reads were assigned to features using Rsubread and normalized read counts were produced using the rlog function in DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file containing normalized (log2) counts for each sample

source_name: breast cancer brain metastasis

growth_protocol: PDXs grown in the mammary fat pad of NSG mice

extract_protocol:
RNA was isolated from tumor samples using trizol followed by RNA cleanup using RNEeasy MinElute Cleanup kit (Qiagen), and RNA concentration was measured in a Nanodrop 2000 (Thermo Scientific)
The Genomics and Microarray core facility at the University of Colorado AMC performed RNA quality control using an Agilent 2100 Bioanalyzer, and prepared RNA-seq libraries using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit.

tag: cell type

value: patient-derived xenograft

tag: labelling

value: Not Labelled

tag: er-status

value: Negative


title: DOCK5.H1N1.D2C


title: WT.H3N2.D1A


title: CSF-1 PDX-P3


title: DOCK5.H3N2.D1C


title: DOCK5.H1N1.D1A


title: F2-7 Cells

value: Cell Line


title: Root treated 24 hrs repeat 1

source_name: Roots

value: Roots

tag: rhizobium strain used for treatment

value: Rhizobium sp. IRBG74

value: treated 24 hrs


title: E22-1 PDX-P0-i1

value: Labelled


title: H12

city: West Lafayette

first: Nadia

middle: Marie

last: Atallah

state: IN

address: 201 S. University St

department: Center for Cancer Research

institute: Purdue University

data_processing:
Illumina Casava1.7 software used for basecalling.
Read quality was observed using FastQC v. 0.11.2
quality trimming was performed using FastX-Toolkit version 0.0.14 with a trimscore of 30 and a trim length of 50
Topha2t version 2.1.0 was used to align trimmed reads to the human genome with default parameters other than that 1 mismatch was allowed
The htseq-count script was used in HTSeq v 0.6.1 to count the number of reads mapping to each gene.  HTSeq used Biopython v.2.7.3.
BPSC in R, version 0.99.1 was used to determine normalize genes based on library size and to identify differentially expressed genes. A Benjamini-Hochmerg FDR of 0.05 was used as the cutoff.
IPA version
Genome_build: ENSEMBL version GrCh38.p7
Supplementary_files_format_and_content: counts generated from HTSeq are provided, along with 5 rows at the end of the matrix which include information about where reads aligned in the genome, how many alignments there were for each, etc.

source_name: low passage patient-derived PDAC cells

growth_protocol: All cells were maintained at 37 degrees Celsius in 5% Carbon dioxide and grown in DMEM.

extract_protocol:
The C1 fluidigm instrument was used to capture single cells, extract RNA, reverse transcribe cDNA using the SMARTer system.
The Nextera kit was used to prepare the library.

treatment_protocol: To transfect cells 1x10^5 cells were plated per well of a 6-well plate and allowed to attach overnight.  The next dat Lipofectamine RNAiMax reagent was used to transfect according to the manufacturer's protocol.

tag: transfection

value: scrambled siRNA


title: SQCC

city: Wuhan

first: Mingxiong

address: Luojia Hill

institute: Wuhan University

data_processing:
To get clean reads, the adaptor sequences, contaminated reads, low quality reads, less than 17nt reads and poly-A/T/C/G/N repeat sequences were removed.
Next, the clean reads (17-45nt) were mapped to the human genome database using Burrows-Wheeler Aligner (BWA) software. Uniquely aligned reads were categorized and annotated to known non-coding small RNA transcripts using Rfam version 11.0 for YRNA, rRNA, snRNA, snoRNA, and tRNA. miRBase version 21 was used for miRNA, and piRNABank was used for piRNA.
Next, the quantity of small RNA in each sample was obtained and normalized as RPM (number of mapped reads per million clean reads). The clean reads of miRNA, containing the entire reference sequence from the miRBase database and a length difference within 4nt, were confirmed, as well as miRNA generated from the same end of the same precursor and a length discrepancy below 3nt. Considering sequencing error, reads with less than ten copies were removed.
Significant differences in miRNA expression were determined using R package edgeR, with thresholds of a P-value <0.05 and a |log2 (Fold Change)| ≥ 1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including raw counts and normalized values of miRNAs for each sample

source_name: plasma exosomes

extract_protocol:
Blood was collected from non-small cell lung cancer patients or healthy controls, and dispensed into an EDTA anticoagulation tube. Plasma was separated by centrifugation at 5 000 rpm for 5 minutes at 4℃. The clear supernatant was transferred to a labeled tube, and stored at -80℃. Exosomes from plasma were isolated using Ribo Exosome Isolation Reagent (for serum or plasma) (Ribobio) according to the manufacturer’s protocol. Then the total RNA in plasma exosomes was extracted and small RNA fractions were separated by electrophoresis.
The small RNA fractions (<60nt) from plasma exosomes were ligated to 5’-adapters and 3’-adapters, and then reverse-transcribed and PCR amplified, with indexes included in the PCR reaction. PCR products were run on a 6% polyacrylamide gel and size-selected to include RNAs with an insert size < 51 nt. The DNA-containing index was eluted from the gel, precipitated, and dissolved in nuclease-free water. Small RNA inserts were sequenced using a HiSeq 2500 high-throughput sequencing system (Illumina).

value: plasma exosomes

tag: disease

value: lung squamous cell carcinoma


title: E22-1 PDX-P0

first: Peter


title: 6TGscreen_library1

city: Madrid

first: Oscar

last: Fernandez-Capetillo

address: MFA 3

department: Genomic Instability Group

institute: CNIO

description: HAP1, haploid for all chromosomes, derives from near-haploid KBM7 parent line which was in turn obtained from a chronic myeloid leukemia patient in blast crisis phase (Carette et al. Nature 477:340-343, 2011).

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina Real Time Analysis software. Conversion of Illumina BCL files to bam format was performed with the Illumina2bam tool (Wellcome Trust Sanger Institute - NPG). Bam files containing unaligned reads were prepared by sorting (samtools sort -n) and subsequent conversion to fastq format (bamToFastq from bedtools.)
For the evaluation of gene expression fastq files were aligned to the transcriptome with Tophat-2.0.10 on bowtie2. No --fusion-search nor PB sequences were used here. For visualization of alignments in the UCSC genome browser bigwig files were obtained after successive format conversions. bamToBed and genomeCoverageBed, both from bedtools, respectively converted accepted_hits.bam from Tophat into bed and then bed to bedGraph. Track definition line was manually removed from bedGraph which was finally converted to bigWig with bedGraphToBigWig from UCSC.
For the mapping of PiggyBac (PB) insertions a custom Bowtie index was prepared to attach selected PB (Cadiñanos and Bradley, Nucl Acids Res 35:e87, 2007) fragments to the human genome assembly. Specifically, up to 1,300 bases from the start of the 5'-PB terminal repeat to the start of Puro, plus 150 bases from the 3'-PB terminal repeat's 3'end were added as fasta segments to the multifasta UCSC hg19 file and indexed with bowtie-build. The length of PB sequence used from the 5' terminal repeat side could have been shorter, including just terminal repeat boundaries and location of the official SA plus some added length, according to library fragment size, to allow the read mapping. Some cryptic SA site suggested however an extended version would do no harm. Each pair of sample-specific fastq files was aligned to this bowtie index with TopHat-2.0.10 with the --fusion-search option turned on. Other options were --bowtie1, --no-coverage-search, -r 30, --mate-std-dev 80, --max-intron-length 10000, --fusion-min-dist 200000000, --fusion-anchor-length 13, --fusion-ignore-chromosomes chrM.
In order to extract the PB insertions Tophat accepted_hits.bam file outputs were converted to sam format with samtools view. Lines containing "XF:Z:" or "XP:Z:" as markers for fusion alignments were extracted from accepted_hits.sam.txt files with egrep (egrep '^@|(5TR\+150|SA\+150|3TR-150)\>' accepted_hits.sam.txt | egrep '^@|\<XF:Z:|\<XP:Z:' > PBfrags.sam.txt). Read names from these simplified sam files were used on the initial fastq files to extract corresponding read1 and read2 sequences (egrep with the -A 1 option), which were transferred to MS-Excel for examination as explained in the manuscript of reference.
Genome_build: Human GRCh37/hg19 assembly, extended as described with PiggyBac (Cadiñanos and Bradley, Nucl Acids Res (2007) 35:e87) fragments for the mapping of PB insertions.
Supplementary_files_format_and_content: Samples analyzed for gene expression are represented with bigWig files, compatible with the UCSC genome browser. Samples analyzed for PB insertions are represented by sam files containing only lines with tags "XF:Z" or "XP:Z", extracted as described.

source_name: chronic myeloid leukemia

growth_protocol: HAP1 cells  were maintained in IMDM (Invitrogen) supplemented with 15% FBS and 1% penicillin-streptomycin

extract_protocol:
RNA from HAP1 cells was isolated using Absolutely RNA Miniprep Kit (Agilent). RNA Integrity Numbers were in the range 9.1-10 when assayed on an Agilent 2100 Bioanalyzer.
PolyA+ fraction was purified from 1 µg of total RNA and randomly fragmented, converted to double stranded cDNA and processed through subsequent end-repair, dA-tailing, and ligation to adapters as in Illumina's "TruSeq Stranded mRNA Sample Preparation Part # 15031047 Rev. D". Adapter-ligated library was completed by PCR with Illumina PE primers (8 cycles). The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation and sequenced on an Illumina HiSeq2500 instrument.

treatment_protocol: For 6TG, 6 million cells of the two independent piggyBac-mutagenized libraries were plated at low density. A concentration of 20 μM 6-TG was used during the complete incubation period (15 days). In the case of ATRi, 6 million cells were exposed for 9 days to 0.3 μM of ATRi (Toledo et al., 2011).

tag: cell line

value: chronic myeloid leukemia

tag: ploidy

value: near haploid


title: 6TGscreen_library2


title: 6TGscreen-clone


title: CTRL

value: healthy


title: H9


title: H10


title: Mix_of_clones


title: library unselected


title: H11


title: H6

value: APE1 siRNA


title: H8


title: H5


title: H2


title: H7


title: H1


title: ADC

value: lung adenocarcinoma


title: H4


title: G12


title: G11


title: G9


title: ATRi_screen


title: G8


title: G10


title: G7


title: G6


title: F12


title: G4


title: F10


title: F11


title: F8


title: G1


title: G3


title: F6


title: F7


title: F5


title: F9


title: F2


title: F1


title: E10


title: E9


title: ectopic endometrium miRNA, patient 11

city: Beijing

source_name: ectopic endometrium

tag: disease state

value: case

tag: patient

tag: rafs stage

value: III


title: E11


title: F4


title: E7


title: E5


title: G5


title: G2


title: E8


title: F3


title: E4


title: E3


title: D9


title: D12


title: D10


title: D7


title: D8


title: D11


title: D5


title: D4


title: H3


title: D3


title: D1


title: D2


title: C9


title: C8


title: C6


title: C7


title: E12


title: C11


title: C4


title: E1


title: E2


title: C5


title: C3


title: C2


title: D6


title: C1


title: B10


title: B9


title: B8


title: C12


title: B11


title: B5


title: C10


title: A11


title: A10


title: A8


title: A9


title: B1


title: A2


title: A1


title: A5


title: A3


title: A4


title: B12


title: B7


title: B6