title: Sample_N6D, hippocampal neuron

status: Public on Jan 07 2019

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

description:
processed data: combined_3utr_counts_per_gene.txt
processed data: individual_3utr_counts.txt

data_processing:
Reads were trimmed for adapter and poly-A sequence using in-house software and then mapped to the mouse genome (mm10) using STAR v2.4.0 (Dobin et al. 2013).
Uniquely mapped reads were used for gene quantification using VERSE v0.1.4 with parameters “-s 1 -z 3 --nonemptyModified” (Zhu et al. 2016, doi:https://doi.org/10.1101/053306)
The gene/UTR annotations were obtained from the following: Ensembl genes (downloaded from UCSC, Dec 2015); UCSC genes (downloaded from UCSC, Dec 2015); and ~2,000 new 3'UTRs determined by Miura et al. 2013 (Miura P, Shenker S, Andreu-Agullo C, Westholm JO, Lai EC. Widespread and extensive lengthening of 3' UTRs in the mammalian brain. Genome Res. 2013;23:812-25).
Genome_build: mm10
Supplementary_files_format_and_content: *.verse.exon.cnts.txt: tab delimited text files containing raw gene counts.
Supplementary_files_format_and_content: combined_3utr_counts_per_gene.txt: tab delimited text file. Summation of reads in all the 3'UTRs of each gene.
Supplementary_files_format_and_content: individual_3utr_counts.txt: tab delimited text file. Separate features for each alternative 3'UTR (but using only the last 500nt and merging some UTRs, as described in the paper).

source_name: hippocampal neuron

growth_protocol: Hippocampal neurons from embryonic day 18 (E18) mice (C57BL/6) were cultured as described in (Buchhalter and Dichter 1991) for 15 days.

extract_protocol:
A micropipette with a closed, tapered end was used to sever dendrites from the cell body. Another micropipette was used to aspirate the soma, which was deposited into a tube containing first strand synthesis buffer and RNase inhibitor and placed on ice. A separate micropipette was used to aspirate the dendrites, which were deposited into a separate tube as above. Samples were transferred to -80ºC within 30 minutes and stored there until first strand synthesis. Poly-adenylated RNA was amplified using two or three rounds of the aRNA in vitro transcription-based amplification method, as described in (Morris, Singh, and Eberwine 2011). The quality and quantity of the amplified RNA was verified using a Bioanalyzer RNA assay.
Strand-specific sequencing libraries were prepared using the Illumina TruSeq Stranded kit according to the manufacturer's instructions, except that the initial poly-A capture step was skipped because the aRNA amplification procedure already selects for poly-adenylated RNA. Samples were sequenced on a HiSeq (100bp paired-end) or NextSeq (75bp paired-end) to an average depth of 25 million reads.

tag: cell number

tag: cell compartment

value: Dendrite

tag: ercc spike-in dilution

tag: rounds of arna amplification


title: Sample_P1S, hippocampal neuron

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

tag: strain

value: Soma


title: Sample_P1D, hippocampal neuron


title: Sample_N6S, hippocampal neuron


title: Sample_M9S, hippocampal neuron


title: Sample_M6S, hippocampal neuron


title: Sample_N4D, hippocampal neuron


title: FOXP1 ChIPseq in human tonsilar Naïve IgD+ B cells

status: Public on Jan 16 2019

city: New York

first: Ashley

middle: Stephen

last: Doane

state: NY

address: 1300 York Ave

institute: Weill Cornell Medicine

library_source: genomic

data_processing:
Counts: Raw image data were converted into base calls via the Illumina pipeline CASAVA version 1.8 with default parameters. All 51-bp-long paired-end reads were mapped to the reference human genome sequence, hg38, using BWA aligner (Li H. and Durbin R. (2009) Bioinformatics, 25:1754-60) with the default parameters.
Peaks: Peak detection was performed with the ChIPseeqer program (Giannopoulou and Elemento, BMC Bioinformatics 2011, 12:277) and annotated to genes and/or promoters based on hg38 refseq genes downloaded from the UCSC Genome Browser
Genome_build: human hg38 build
Supplementary_files_format_and_content: bigwig, bigbed, narrowPeak, and bed formats

molecule: genomic DNA

organism: Homo sapiens

source_name: Naïve IgD+ B cells

growth_protocol: cultured cells, IMDM+10%FBS

extract_protocol:
Chromatin was sheared to 200-400bp, incubated with H3K27ac antibody (abcam 4729) overnight at 4C on a rocker, antibody chromatin complex was captured by ProteinA agarose beads, washed with low salt, high salt, LiCl, and TE buffer, eluted and then de-crosslinked at 65C with 0.3M NaCl final for at least 6 hr.  Final chormatin was purified using Qiagen PCR purification columns.
Libraries were prepared using the Illumina Truseq ChIPseq Library preparation Kit following the manufacture’s instructions (Illumina, CA).

tag: tissue

value: Primary tonsilar B cells

tag: chip antibody

value: FOXP1 (ab4729, Rabbit, 2 ug)


title: Sample_N5D, hippocampal neuron


title: Sample_M1D, hippocampal neuron


title: Sample_I6S, hippocampal neuron


title: Sample_I5S, hippocampal neuron


title: Sample_I5D, hippocampal neuron


title: Sample_I4S, hippocampal neuron


title: Sample_I4D, hippocampal neuron


title: Sample_P2D, hippocampal neuron


title: Sample_P2S, hippocampal neuron


title: Sample_I3S, hippocampal neuron


title: Sample_H5D, hippocampal neuron


title: Sample_N5S, hippocampal neuron


title: Sample_H3S, hippocampal neuron


title: Sample_I3D, hippocampal neuron


title: Sample_H5S, hippocampal neuron


title: Sample_H3D, hippocampal neuron


title: Sample_N4S, hippocampal neuron


title: Sample_M6D, hippocampal neuron


title: J1 (for Taf KOs) rep3

status: Public on Jan 01 2019

city: Melbourne

first: Partha

last: Das

state: Victoria

address: 211 Wellington Road

department: Anatomy & Developmental Biology

country: Australia

institute: Monash University

description:
processed data file:
Taf5l_Taf6l_Myc_KovsWT_RawCounts.tsv
Taf5l_Taf6l_Myc_KovsWT_NormalizedCounts.tsv
Taf5l_Taf6l_Myc_KovsWT_FPKM.tsv
Taf5l_Taf6l_Myc_KovsWT_TPM.tsv

data_processing:
Gene expression quantification, both raw counts and TPM (Transcripts Per Million) values, was done using Salmon (v0.8.2) with default parameters. The mm9-based GENCODE version M1 mouse transcriptome was used.
Normalized counts and FPKM (Fragments Per Kilobase per Million mapped reads) expression values were calculated using the DESeq2 R Bioconductor package (v1.14.1).
Genome_build: mm9
Supplementary_files_format_and_content: Comma-separated text files containing raw counts, normalized counts, FPKM expression values and TPM expression values.

molecule: total RNA

source_name: Embryonic Stem Cell

growth_protocol: Mouse ESCs (mESCs) were cultured in mouse ESC media that contains DMEM, supplemented with 15% fetal calf serum, 0.1mM b-mercaptoethanol, 2mM L-glutamine, 0.1mM NEAA, 1% of nucleoside mix , 1000 U/ml LIF/ESGRO, and 50U/ml Penicillin/Streptomycin. mESCs were cultured at 37ºC, 5% CO2.

extract_protocol:
Total RNA was isolated, and ribosomal RNAs were depleted using ribosomal RNA depletion kit (rRNA Depletion Kit, NEB).
Ribosomal depleted RNA was used to make the RNAseq libraries using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: mESCs were harvested, washed with 1X PBS- twice at 4C, followed by RNA isolation

tag: cell line

tag: genotype/variation

value: wildtype


title: Sample_B2S, hippocampal neuron


title: Sample_M1S, hippocampal neuron


title: Sample_B2D, hippocampal neuron


title: J1 (for Taf KOs) rep2


title: PRO-Cap of 96 h infected DMSO-treated HFF (Towne)

city: Iowa City

first: David

middle: H

last: Price

state: Iowa

address: 500 Newton Road

department: Biochemistry

institute: University of Iowa

data_processing:
Adapter trimming using trim_galore 0.4.4
Alignment of trimmed reads to hg38 using bowtie 1.2 (retain unmapped reads; Towne samples: --trim5 4 and --trim3 4)
Alignment of unmapped reads to Genbank FJ616285.1 using bowtie 1.2
Towne samples: filter duplicate mapped reads with dedup (https://github.com/P-TEFb/dedup)
Generate bedgraphs using bedtools genomecov 2.26
Convert bedgraphs to bigwigs using kentUtils
Upload hg38-mapped tracks to UCSC genome browser
Upload HCMV-mapped tracks to a custom track hub (https://github.com/P-TEFb/trackHub_HCMV)
Genome_build: hg38
Supplementary_files_format_and_content: bigwigs contain PRO-Seq pileups, PRO-Cap pileups, or PRO-Cap 5' read positions
Supplementary_files_format_and_content: bigbed files were generated from bed files using kentUtils bedToBigBed program

molecule: nuclear RNA

source_name: human foreskin fibroblast

growth_protocol: HFF were kept at 100% confluence at least one week before infection.

extract_protocol:
All PRO-Seq and PRO-Cap protocols are detailed in the manuscript. Nuclei were rapidly isolated as described in Nilson, et al. 2017 (10.1093/nar/gkx724).
Please consult the manuscript, Nilson, et al. 2017 (10.1093/nar/gkx724), and Mahat, et al. 2016 (10.1038/nprot.2016.086).

treatment_protocol: Infection details are in the manuscript. As indicated, 1 µM Flavopiridol or 0.1% DMSO were added to media 1 h before harvest.

tag: hcmv strain

value: Towne varS

tag: infection duration

tag: method

value: PRO-Cap


title: Sample_B1D, hippocampal neuron


title: Sample_B1S, hippocampal neuron


title: RRC1_rrn9

status: Public on Jan 03 2019

city: Bunkyo-ku

first: Tetsushi

last: Iida

state: Tokyo

address: 1-1-1 Yayoi

department: Research Center for Biological Visualization

country: Japan

institute: The Institute for Quantitative Biosciences (IQB), The University of Tokyo

description:
RRC_Mt002
Pooled linkage analysis. Mutant clones from ascospores of backcrossed yeast strains were cultured in YPD at 30 Celsius overnight. Prepared genomic DNA was sheared by Covaris S220 and purified. Sequencing libraries were prepared by KAPA kit and TruSeqHT-compatible adaptors.

data_processing:
Library strategy: Whole genome sequencing
ChIP-seq: The paired-end reads were merged to a set of single reads.
Low quality 15 bases were trimmed from the 3'-end of each read with Seqtk (https://github.com/lh3/seqtk).
Reads were mapped to the S. cerevisiae reference genome EF4.68 by means of bowtie-1.0.0 using the single-read mapping mode: “bowtie -S --best -k 1 -n 3 EF4.68.index Sample_trim.fastq > Sample_trim.sam”.
Mapped reads were counted by samtools-0.1.19.
The pileup data was generated by means of MACS2 (http://liulab.dfci.harvard.edu/MACS/).
ChIP-seq profile data were normalized by the number of mapped reads as fragment per million reads (fpm).
Whole genome sequencing: To identify causative rcc-mutations, FASTQ files were analyzed with the webtool Mudi (version2, http://naoii.nig.ac.jp/mudi_top.html).
Genome_build: Saccharomyces_cerevisiae.EF4.68
Supplementary_files_format_and_content: BedGraph files were generated by macs2 and normalized by mapped read number as fragment count per million (fpm).
Supplementary_files_format_and_content: *.tsv: Tab-delimited text files were generated by the webtool "mudi". Mutations called by the analysis were listed.

organism: Saccharomyces cerevisiae BY4741

source_name: Stationary phase yeast cells

growth_protocol: Yeast mutant clones were separately cultured in 1 ml of 1% Bacto Yeast Extract (BD), 2% Bacto Peptone and 2% Glucose (Wako) (YPD) at 30｡C with shaking in plate shaker.

extract_protocol:
Cells for each mutant group were harvested together by centrifugation at 3,000 g at room temperature, washed twice with water and suspended in 500 µl 0.2 M Tris-HCl pH8.0, 2.5% 2-ME. After 30 minutes incubation at 30°C, cells were resuspended in 500 µl 40 mM NaPhosphate pH6.8, 1 M sorbitol and 2% Zymolyase 100T (Nacali tesque, 07665-55) and incubated at 37°C for 1 hour. The resulting spheroplasts were harvested by centrifugation at 9,000 g at room temperature and resuspended in 500 µl of pre-warmed 50 mM Tris-HCl pH7.5, 0.2 M NaCl, 0.1 M EDTA and 5% SDS. After 30 minutes incubation at 65°C, the cell lysate was extracted twice with phenol/chloroform/isoamylalcohol (pH 8.0) and combined with1 ml of ethanol. The precipitated DNA was picked up, rinsed with 70% ethanol, dried and dissolved in 250 µl 10 mM Tris-HCl pH8.0, 1 mM EDTA and 0.4mg/ml RNase A (Nippon gene, 313-01461) and incubated at 37°C for 2 hours. The DNA was purified by phenol/chloroform/isoamylalcohol (pH 8.0) extraction and ethanol precipitated without salt and dissolved in 150 µl 10 mM Tris-HCl pH8.0, 1 mM EDTA.
For NGS sequencing, 2 µg DNA in 100 µl TE buffer was sheared at 4°C with a Covaris S220 ultrasonicator (Covaris) using a microtube AFA fiber (Covaris, 520045) with the following settings: peak power 140, duty factor 10, cycle/burst 200, duration 45 s. The resulting 400~500 bp DNA fragments were separated on an 1.5% agarose gel and purified with a NucleoSpin Gel and PCR Clean-up kit. Genomic DNA libraries for NGS sequencing were prepared with 100 ng gel-purified DNA and TruSeqHT (Illumina) compatible adaptors and amplified by 3 PCR cycles (98°C 15s, 50°C 30 s and 72°C 1 minute) using a KAPA library preparation kit (KAPA biosystems, KK8201). After purification of the PCR reactions with 1 volume AMpureXP beads (Beckman Coulter, A63881), equimolar mixtures of the libraries were sequenced on a MiSeq system (Illumina). Reactions for 200 bp, paired-end runs were prepared with the MiSeq Reagent Kit v3 (Illumina, MS-102-3003).

tag: strain name

tag: mating type

value: MATa and MAT alpha mixture

tag: growth phase

value: stationary


title: Sample_I6D, hippocampal neuron


title: J1 (for Taf KOs) rep1


title: Taf5l-KO rep1


title: Taf5l-KO rep2


title: Taf6l-KO rep1


title: Taf6l-KO rep2


title: GM12878 cell 2550

status: Public on Dec 20 2018

city: Stanford

first: Paul

last: Khavari

state: CA

address: 269 Campus Drive, CCSR 2150

institute: Stanford University

description:
277-59-Ad1-2-Ad2-11-AAGAGGCA-ATAGAGAG_S59
Peak_counts_GM12878_experiment2.txt.gz

data_processing:
For ATAC-seq data: adapter sequence trimming, mapping to Hg19 using Bowtie2, and PCR duplicate removal using Picard Tools was performed. ATAC-seq peaks were called with MACS2 and reads in each peak were counted for each sample.
Genome_build: hg19
Supplementary_files_format_and_content: ATAC-seq counts table file; adapter trimmed, reads aligned, pcr duplicates removed, and reads in ATAC-seq peaks counted

source_name: GM12878 cell line

growth_protocol: GM1878 cells were grown in RPMI 1640 with 10% FBS and 1% pen/strep. Human primary keratinocytes were cultured in 50/50 growth media and induced to differentiated for three or six days as previously described (Zarnegar et al., 2012)

extract_protocol: Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips and assayed using the single-cell ATAC-seq protocol. In a 96-well plate, 6-7 µL from a total of 15ul of harvested libraries were amplified in 50 µL PCR for an additional 14 cycles (1.25 µM custom Nextera dual-index PCR primers in 1x NEBnext High-Fidelity PCR Master Mix) using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. Pooled libraries were purified and quantified using qPCR prior to sequencing.

tag: cell type

value: GM12878 cell line


title: RRC5_uaf30

description:
RRC_Mt005
Pooled linkage analysis. Mutant clones from ascospores of backcrossed yeast strains were cultured in YPD at 30 Celsius overnight. Prepared genomic DNA was sheared by Covaris S220 and purified. Sequencing libraries were prepared by KAPA kit and TruSeqHT-compatible adaptors.


title: GFP plus sample from liver in SOX9-GFP mice at E18.5 labeled with Hy3, biological rep2

type: RNA

city: Brussels

first: Claude

last: Gérard

address: Avenue Hippocrate 75

department: de Duve Institute

country: Belgium

institute: Université catholique de Louvain

description: GFP plus_2

hyb_protocol: The samples were hybridized to the miRCURY LNA microRNA Array (7th Gen) by Exiqon S/A Profiling Services.

scan_protocol: The miRCURY LNA microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA).

data_processing: miRNAs with Benjamini-Hochberg adjusted p-values < 0.05 were selected.

source_name: Fraction SOX9-GFP plus from mice liver at E18.5

label_protocol: 200 ng of RNA were labeled using the miRCURY LNA microRNA Hi-Power Labeling Kit, Hy3/Hy5.

growth_protocol: For each biological replicate, a pool of 20 mouse embryonic livers at E18.5 were used.

extract_protocol: Total RNA was isolated from embryonic liver at E18.5 using Trizol (#1029602, Invitrogen, Life Technologies) according to the manufacturer's instructions.

treatment_protocol: For each biological replicate, 20 embryonic livers were pooled and cells were dissociated in a dispase/collagenase/DNase I solution. Cell suspensions were depleted in hematopoietic cells by using the Miltenyi Lineage Cell Depletion Kit (#130-110-470). Remaining cells were FACS-sorted based on their GFP expression.

tag: strain/background

tag: age

value: embryos at E18.5

value: liver

value: cholangiocytes


title: GFP neg sample from liver in SOX9-GFP mice at E18.5 labeled with Hy3, biological rep2

description: GFP neg_2

source_name: Fraction SOX9-GFP neg from mice liver at E18.5

value: hepatocytes


title: GFP neg sample from liver in SOX9-GFP mice at E18.5 labeled with Hy5, biological rep3

description: GFP neg_3


title: GFP plus sample from liver in SOX9-GFP mice at E18.5 labeled with Hy5, biological rep3

description: GFP plus_3


title: ProliHH in vivo Rep2

status: Public on Dec 19 2018

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

country: China

institute: CEMCS, CAS

data_processing:
Trimmed reads were aligned to the human genome (hg38, Genome Reference Consortium GRCh38) using Hisat2-2.0.0-beta
FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated by Cufflinks using default parameters for gene expression levels
The counts expression profiles were normalized  by Deseq2 using rlog function
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include log2 tranformed counts for each Sample

source_name: Fresh Human Hepatocytes isolated from ProliHH-repopulated Fah-/-Rag2-/-IL2rg-/- mouse liver

growth_protocol: Primary human hepatocytes or proliferating human hepatocytes were seeded at 2 x 104 cells/cm2 on 6-wells collagen-coated plates (Corning) in HM. The medium was changed every 3 days. At day 6 of the primary culture, cells cultured in the presence of HM were harvested via trypsinization

extract_protocol:
Proliferaitng human hepatocyte or mouse liver were removed, flash frozen on dry ice, total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Fresh Human Hepatocytes-repopulated Fah-/-Rag2-/-IL2rg-/- mouse liver

value: mouse liver

tag: passages

value: Fresh isolated human hepatocyte


title: ProliHH P4 Rep1

source_name: Proliferating Human Hepatocytes at P4 cultured for 24day in HM

value: Proliferating Human Hepatocytes at P4


title: PHH in vivo Rep2

source_name: Fresh Human Hepatocytes isolated from PHH-repopulated Fah-/-Rag2-/-IL2rg-/- mouse liver


title: PHH in vivo Rep1


title: ProliHH in vivo Rep1


title: Taf6l-KO rep3


title: GFP neg sample from liver in SOX9-GFP mice at E18.5 labeled with Hy3, biological rep3

description: GFP neg_3


title: GFP plus sample from liver in SOX9-GFP mice at E18.5 labeled with Hy3, biological rep1

description: GFP plus_1


title: GFP plus sample from liver in SOX9-GFP mice at E18.5 labeled with Hy3, biological rep3

description: GFP plus_3


title: Taf5l-KO rep3


title: ProliHH P4 Rep2


title: GFP plus sample from liver in SOX9-GFP mice at E18.5 labeled with Hy5, biological rep1

description: GFP plus_1


title: ProliHH P2 Rep2

source_name: Proliferating Human Hepatocytes at P2 cultured for 12day in HM

value: Proliferating Human Hepatocytes at P2


title: GFP neg sample from liver in SOX9-GFP mice at E18.5 labeled with Hy5, biological rep1

description: GFP neg_1


title: ProliHH P1 Rep2

source_name: Proliferating Human Hepatocytes at P1 cultured for 6day in HM

value: Proliferating Human Hepatocytes at P1


title: GFP plus sample from liver in SOX9-GFP mice at E18.5 labeled with Hy5, biological rep2

description: GFP plus_2


title: GFP neg sample from liver in SOX9-GFP mice at E18.5 labeled with Hy3, biological rep1

description: GFP neg_1


title: GFP neg sample from liver in SOX9-GFP mice at E18.5 labeled with Hy5, biological rep2

description: GFP neg_2


title: ProliHH P3 Rep2

source_name: Proliferating Human Hepatocytes at P3 cultured for 18day in HM

value: Proliferating Human Hepatocytes at P3


title: ProliHH P3 Rep1


title: ProliHH P1 Rep1


title: Fresh PHH Rep2

source_name: Fresh Primary Human Hepatocytes

value: Fresh Primary Human Hepatocytes


title: ProliHH P2 Rep1


title: Fresh PHH Rep1


title: GJ37

status: Public on Dec 05 2018

type: genomic

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

description: Genomic DNA extracted from blood was genotyped using HumanOmniExpress-24 v1.0 BeadChip (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48°C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol, dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Image data was analyzed using GenomeStudio v2.0.4 with GT module 2.0.4 (Illumina).

label: Cy3, Cy5

source_name: blood

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37°C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

value: blood

tag: northwest india population

value: Gujjar (GJ)


title: GJ33


title: GJ40


title: GJ32


title: GJ42


title: GJ43


title: GJ30


title: GJ36


title: GJ24


title: GJ17


title: KJ38

value: Kamboj (KJ)


title: GJ2


title: GJ20


title: GJ27


title: GJ21


title: KJ32


title: GJ16


title: KJ34


title: KJ31


title: KJ28


title: KJ29


title: KJ27


title: KJ06


title: KJ05


title: KJ12


title: KJ09


title: KJ26


title: KJ03


title: Ror_52

value: Ror


title: Ror_44


title: Ror_83


title: Ror_55


title: Ror_45


title: KJ02


title: Ror_56


title: Ror_49


title: BMDM ChIRP lincRNA-EPS input biological replicate 2

status: Public on Dec 04 2018

first: Howard

middle: Y

last: Chang

address: 269 Campus Drive

description:
Input DNA
BMDM_ChIRP_EPS_Input_Mean.bigwig
BMDM_ChIRP_EPS_Diff.bigwig

data_processing:
Library strategy: ChIRP-seq
Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Filtered reads were converted to a .hic file for visualization with Juicebox (PMID: 25497547)
Genome_build: mm10
Supplementary_files_format_and_content: validPairs output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.
Supplementary_files_format_and_content: HiC output from the Juicebox Tools pipeline. Matrix file to visualize long-range interactions with Juicebox.
Supplementary_files_format_and_content: Bam files were read into R through rsamtools and converted to a 250bp bin coverage object exported by rtracklayer.

source_name: Bone-marrow derived macrophages

growth_protocol: Grown in DMEM with 15% FBS and supplemented with L929

extract_protocol:
Input chromatin
Nextera

treatment_protocol: Crosslinked with 1% glutaraldehyde

value: Primary macrophage cells

tag: gender

value: male


title: Ror_12


title: Jatt_Jt2

description: Genomic DNA extracted from blood was genotyped using HumanOmniExpress-24 v1.1 BeadChip (Illumina).

value: Jatt


title: Ror_37


title: Ror_20


title: Ror_11


title: Ror_25


title: Ror_17


title: BMDM ChIRP lincRNA-EPS input biological replicate 1


title: Ror_10


title: BMDM ChIRP lincRNA-EPS odd

description:
RNA-enriched DNA
BMDM_ChIRP_EPS_Min_Even_Odd.bigwig
BMDM_ChIRP_EPS_Diff.bigwig

extract_protocol:
RNA enrichment of chromatin
Nextera


title: BMDM ChIRP lincRNA-EPS even


title: 233756

status: Public on Jan 18 2019

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

data_processing:
Data quality was assessed using FastQC v.0.11.2
Trimmed reads were screened for presence of rRNA and mtRNA sequences using FastQ-Screen v.0.3.7
RSeQC package v.2.6.1 was used to assess read distribution, positional read duplication and confirm strandedness of alignments
Raw trimmed reads were aligned to the reference genome hg19 using Tophat v.2.0.13
Tophat alignments were processed to extract raw read counts for genes using htseq-count v.0.5.4p2
Raw gene counts were loaded and sample-normalized using DESeq v.1.18.0
Differential analysis was performed also in edgeR v3.8.6
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq_count.txt
Supplementary_files_format_and_content: edgeR_merged_wRPKM_tn20150828_GLMM_20170614dm.txt: Differential expression results.

source_name: Peripheral blood

extract_protocol:
Total RNA was extracted using QIAGEN QIAsymphony DNA Midi kit.
RNA libraries were prepared using Illumina TruSeq RNA Sample prep kit V2

tag: task force

tag: harvesting time

value: VAL - ALL PHASES

tag: cohort

tag: post deployment time

tag: aggregatebatch

tag: phase

value: I

tag: ptsd diagnosis

tag: date processed

value: Male

tag: age group


title: Ror_29

tag: tissue


title: HT-144-ASO-SREBF1-S1-Rep-4

status: Public on Nov 20 2018

city: Charlestown

first: Su

last: Wu

state: MA

address: Building 149 7-330, 13th Street

department: Cancer Center

institute: Mass General Hospital

description: polyadenylated mRNA

data_processing:
For RNA-Seq, Illumina sequencing reads (FASTQ files) were checked with FASTQC for quality control and then aligned to the human genome (GRCh38.94).
Genome index generation and sequence alignment were performed using STAR software (2.6.1a).
Sequence alignment were performed using STAR software (2.6.1a) with arguments including “--quantMode TranscriptomeSAM GeneCounts --twopassMode Basic”.
Genome_build: GRCh38.94
Supplementary_files_format_and_content: Tab-delimited files (*ReadsPerGene.out.tab) include gene counts generated by STAR from individual samples.

source_name: melanoma cell line HT-144

growth_protocol: Transfected HT-144 cells were cultured in 1% ITS medium. That is composed of RPMI-1640 medium with 1 x Insulin-Transferrin-Selenium (ITS-G, Thermo Fisher Scientific), 2 mM L-glutamine (Gibco) and 50 U/ml penicillin-streptomycin (Gibco).

extract_protocol:
RNA samples were harvested and treated with RNase-free DNase (Qiagen). RNA quality was verified with the RNA ScreenTape (Agilent) on Agilent 2200 TapeStation (Agilent). mRNAs were isolated from total RNA for RNA library preparation using NEBNext® Poly(A) mRNA magnetic isolation module (NEB).
100 ng of purified mRNA was used for RNA-Seq library synthesis with NEBNext® Ultra™ directional RNA library prep kit for Illumina® (NEB). The final RNA-Seq libraries were quantified with KAPA Library Quantification Kit (KAPABiosystem). Adaptor indexed strand-specific RNA-Seq libraries were pooled and sequenced using the pair-end 75-bp per read setting for NextSeq® 500 High Output v2 Kit (150 cycles) on the NextSeq® 500 sequencer (Illumina).

treatment_protocol: HT-144 cells were transfected with ASOs (5 nM) or pooled siRNAs (50 nM) in 1% ITS medium for three days using Lipofectamine RNAiMAX transfection reagent (Thermo Fisher Scientific) and the reverse transfection protocol suggested by the manufacture.

tag: cell line

value: Malignant Melanoma; Derived From Metastatic Site

tag: treatment

value: ASO-1 for SREBF1


title: Sample4_LSK2_3w

status: Public on Nov 04 2018

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

institute: Australian Institute for Bioengineering and Nanotechnology

description:
gene_count_frags.txt
gene_count_frags_TMM_RPKM_log2.txt

data_processing:
Individual fastq files were aligned to the reference genome (GRCm38 assembly and ENSEMBL version 86) with Rsubread 1.20.6 with default settings in R version 3.2.2.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text files include raw counts or TMM scaled, median centered RPKM Log2 values.

source_name: lin-sca1+cKit+ cells from 3 week old mice

growth_protocol: Cells were originated from WT mice

extract_protocol:
RNA was isolated using either the RNeasy Mini kit (Qiagen) or Arcturus PicoPure kit (Fisher Scientific) and total RNA converted to cDNA using the High Capacity cDNA Reverse Transcription Kit (Invitrogen) as per manufacturers’ instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For isolation of LSK cells (transplanted in control mice and for RNA-seq analysis), BM cells were stained with lineage cocktail with the following biotinylated antibodies: CD3, CD4, CD8a, B220, CD11-b, Gr-1 and Ter119. Followed anti-biotin MicroBeads staining for lineage cells depletion in LS Columns (Miltenyi Biotec) in the magnetic field of a MACS Separator (Miltenyi Biotec). The lineage-negative population were staining with Sca1 PE-Cy7, cKit ACP-Cy7 and Streptavidin V450.

tag: cell type

value: murine lin-sca1+cKit+

tag: mice age

value: 3 weeks

value: Bone marrow


title: Sample4_LSK52w

source_name: lin-sca1+cKit+ cells from 52 week old mice

value: > 52 weeks


title: Sample2_LSK2_3w


title: Sample3_LSK2_3w


title: Sample3_LSK52w


title: Sample2_LSK52w


title: Sample1_LSK52w


title: MF.B220n6Cn64pTim4p.PC.6

status: Public on Nov 03 2018

city: Boston

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: Macrophage

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.5.4a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM16)
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts

source_name: Peritoneal Cavity

growth_protocol: 6 week old C57BL/6J mice from the Jackson Laboratory (Bar Harbor, ME) housed in facility at least one week before harvesting cells

extract_protocol:
Extractions follow ImmGen standard operating protocol (available on https://www.immgen.org/). Briefly, organs are harvested at 9am on day of sort, perterbed as little as possible during preparation, and 1000 cells are double sorted into TCL buffer (Qiagen, Hilden, Germany) containing 1% BME.
Libraries are constructed according to the standard protocol for Smart-seq2 (Picelli et al, 2013) at the Broad Techology Labs in Cambridge, MA

tag: strain

tag: age

value: 6 weeks old

tag: sorting markers

value: live  single  B220-  Ly6C-  F480+  CD11b+  CD64+  Tim4+

value: Macrophage


title: Sample_M9D, hippocampal neuron

source_name: hippocampal neuron

tag: cell number

tag: cell compartment

value: Dendrite

tag: ercc spike-in dilution

tag: rounds of arna amplification


title: Sample1_LSK2_3w


title: MF.B220n6Cn64pTim4p.PC.5

description: Macrophage


title: MF.B220n6Cn64pTim4p.PC.3

description: Macrophage


title: MF.B220n6Cn64pTim4p.PC.1

description: Macrophage


title: MF.B220n6Cn64pTim4p.PC.2

description: Macrophage


title: MF.B220n6Cn64pTim4p.PC.4

description: Macrophage


title: MF.B220n6Cn64pTim4n.PC.3

description: Macrophage

value: live  single  B220-  Ly6C-  F480+  CD11b+  CD64+  Tim4-


title: MF.B220n6Cn64pTim4n.PC.2

description: Macrophage


title: MF.B220n6Cn64pTim4n.PC.1

description: Macrophage


title: RJ356_RST9_aCGH

status: Public on Nov 28 2018

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

institute: University of Guelph

hyb_protocol: 2ug of sample and reference DNA were hybridised to Agilent 244K whole mouse genome CGH arrays (Agilent, G4415A). Samples were prepared using the direct method with hybridizization and microarray washing carried out according to the manufacturer’s protocol.

scan_protocol: Scanned on an Agilent G2505C scanner

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: mammary tumor  (IGF-IR independent)

label_protocol: DNA was prepared for array hybridisation using the Agilent Genomic DNA Enzymatic Labeling kit and labelled with Cy-5. Cy3-labelled genomic DNA extracted from mouse spleen was used as a common reference.

extract_protocol: Genomic DNA was isolated from snap frozen tissue pieces using the Qiagen DNAeasy kit

value: recurrent mammary tumor

value: FVB (MTB-IGFIR transgenic mouse)

source_name: Normal splenic DNA (reference)

value: spleen


title: RJ286_PMT6_aCGH

source_name: mammary tumor  (IGF-IR induced)

value: primary mammary tumor


title: RJ348_RST8_aCGH


title: Mo.64p6ChiGFPp.inj.d4.Ht.3

description: Heart Monocyte from injured mice day 4

source_name: Heart

value: Tnnt2-DTR  CCR2GFP  Flt3-Cre  Rosa26-tdTomato

value: 17 weeks old


title: Mo.64p6ChiGFPp.inj.d4.Ht.4

description: Heart Monocyte from injured mice day 4


title: Mo.64p6ChiGFPp.inj.d4.Ht.1

description: Heart Monocyte from injured mice day 4

value: Monocyte


title: Mo.64p6ChiGFPp.inj.d2.Ht.4

description: Heart Monocyte from injured mice day 2


title: PMT11_aCGH


title: Mo.64p6ChiGFPp.inj.d2.Ht.3

description: Heart Monocyte from injured mice day 2


title: Mo.64p6ChiGFPp.inj.d2.Ht.2

description: Heart Monocyte from injured mice day 2


title: Mo.64p6ChiGFPp.inj.d2.Ht.1

description: Heart Monocyte from injured mice day 2


title: RJ281_PMT9_aCGH


title: MF.CCR2nFlt3n64p6CloGFPntdTomaton.inj.d2.Ht.4

description: Heart Macrophage from injured Flt3-Cre mice day 2


title: MF.CCR2nFlt3n64p6CloGFPntdTomatop.Ht.1

description: Macrophage


title: MF.CCR2nFlt3n64p6CloGFPntdTomaton.Ht.4

description: Heart Macrophage from Flt3-Cre mice


title: RJ301_PMT8_aCGH


title: MF.CCR2nFlt3n64p6CloGFPntdTomaton.inj.d2.Ht.1


title: RJ236_PMT7_aCGH


title: RJ309_PMT5_aCGH


title: MF.CCR2nFlt3n64p6CloGFPntdTomatop.Ht.2

description: Macrophage


title: PMT4_aCGH


title: MF.CCR2nFlt3n64p6CloGFPntdTomaton.Ht.3

description: Heart Macrophage from Flt3-Cre mice


title: PMT10_aCGH


title: MF.CCR2nFlt3n64p6CloGFPntdTomaton.Ht.1

description: Heart Macrophage from Flt3-Cre mice


title: MF.CCR2p64p6CnGFPp.inj.d4.Ht.1

description: Heart Macrophage from injured mice day 4


title: MF.CCR2p64p6CnGFPp.inj.d4.Ht.2

description: Heart Macrophage from injured mice day 5


title: Mo.64p6ChiGFPp.inj.d4.Ht.2

description: Heart Monocyte from injured mice day 4


title: MF.CCR2p64p6CnGFPp.inj.d2.Ht.3


title: RJ279_PMT2_aCGH


title: PMT1_aCGH


title: MF.CCR2p64p6CnGFPp.inj.d2.Ht.1

description: Heart Macrophage from injured mice day 2


title: RJ307_RST4_aCGH


title: RJ407_RST1_aCGH


title: DC.preDC.SigHn6Cp.Sp.3

description: preDC from Spleen

source_name: Spleen

value: Dendritic Cell


title: RJ323_RST5_aCGH


title: DC.preDC.SigHn6Cp.Sp.2

description: preDC from Spleen


title: RJ422_RST6_aCGH


title: DC.preDC.SigHn6Cp.BM.3

description: preDC from Bone Marrow

source_name: Bone Marrow


title: DC.preDC.SigHn6Cp.BM.2

description: preDC from Bone Marrow


title: MF.CCR2nFlt3n64p6CloGFPntdTomaton.Ht.2

description: Heart Macrophage from Flt3-Cre mice


title: MF.CCR2p64p6CnGFPp.inj.d4.Ht.3

description: Heart Macrophage from injured mice day 6


title: DC.preDC.SigHn6Cp.BM.1

description: preDC from Bone Marrow


title: DC.preDC.DP.BM.2

description: Double Positive preDC from Bone Marrow


title: DC.preDC.SigHp6Cn.BM.2

description: preDC from Bone Marrow


title: DC.preDC.DN.Sp.3

description: Splenic Double Negative preDC


title: RJ324_PMT3_aCGH


title: RJ323_RST3_aCGH


title: DC.preDC.DN.Sp.2

description: Splenic Double Negative preDC


title: DC.preDC.DP.BM.3

description: Double Positive preDC from Bone Marrow


title: RJ433_RST2_aCGH


title: DC.preDC.DN.Sp.1

description: Splenic Double Negative preDC

value: 8 weeks old


title: MF.CCR2p64p6CnGFPp.inj.d2.Ht.4


title: DC.preDC.DN.BM.2

description: Double Negative preDC from Bone Marrow


title: MF.CCR2p64p6CloGFPp.Ht.2

description: Macrophage


title: DC.preDC.SigHn6Cp.Sp.1

description: preDC from Spleen


title: DC.preDC.DN.BM.1

description: Double Negative preDC from Bone Marrow


title: MF.CCR2p64p6CloGFPp.Ht.3

description: Macrophage


title: MF.E10.5.YS.2

description: Yolk Sac Macrophage

source_name: yolk sac

value: E10.5 weeks old


title: MCF-7 FAT1 CR rep2

status: Public on Nov 02 2018

city: NEW YORK

first: Sarat

last: CHANDARLAPATY

address: 417 E 68th Street

department: HOPP

institute: Memorial Sloan-Kettering Cancer Center

data_processing:
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
The STAR aligner is uses a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Using DESeq2, a comparison of gene expression between the groups of samples was performed.
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files

source_name: Human breast cancer cell line

growth_protocol: MCF-7 parental cells and FAT1 crispr cells were grown in DMEM/F-12 medium supplied with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
RNA was extracted from MCF7 cells or FAT1-CR-1 cells using the RNeasy Mini kit (Qiagen). RNA samples were quantified using Qubit 2.0 Fluorometer and RNA integrity was checked with 4200 TapeStation .
RNA sequencing library preparation used the NEBNext Ultra RNA Library Prep Kit for Illumina

value: FAT1 CR

tag: passages


title: DC.preDC.SigHp6Cn.BM.3

description: preDC from Bone Marrow


title: MCF-7 parental rep2

value: parental


title: MF.CCR2p64p6CnGFPp.inj.d2.Ht.2

description: Heart Macrophage from injured mice day 3


title: MF.E10.5.YS.1

description: Yolk Sac Macrophage


title: des20

status: Public on Oct 31 2018

city: Msida

first: Brendon

last: Scicluna

address: Msida campus

country: Malta

institute: University of Malta

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

label: biotin

source_name: lung

label_protocol: standard Affymetrix protocol

extract_protocol: RNA was isolated from lung homogenate using the Nucleospin RNA isolation kit (Macherey-Nagel, Düren, Germany) as described by the manufacturer.

value: 8-10 weeks

tag: gender

value: female

tag: experimental group


title: des29

value: cryo


title: des12

value: cult


title: des11


title: des46


title: des35

value: n


title: des10


title: des33


title: des28


title: des45


title: des27


title: des36


title: des25


title: des42


title: des39


title: des24


title: des31


title: des32


title: des14


title: des40


title: des2


title: des22


title: des38


title: des3


title: des26


title: des30


title: des8


title: des17


title: 101-C

status: Public on Oct 30 2018

city: Seattle

first: Timothy

middle: M

last: Rose

state: WA

address: 1900 Ninth Ave., 8th floor

institute: Seattle Children’s Research Institute

data_processing:
Image analysis and base calling was performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4 (http://support.illumina.com/downloads /bcl2fastq_conversion_software_184.html).
Reads of low quality were filtered out prior to alignment to the KSHV (HHV-8) reference genome using TopHat v2.0.14.  Counts were generated from TopHat alignments for each viral gene using the Python package HTSeq v0.6.1 ( http://www-huber.embl.de/users/anders/ HTSeq/doc/overview.html) using the KSHV NC_009333 UCDS ver 121715.gff, available on the series record.
Genome_build: NC_009333.1
Supplementary_files_format_and_content: tab-delimited text files include raw read count for feature in each sample; GFF file defines those features relative to NC_009333.1 genome
Supplementary_files_format_and_content: KSHV_reads_normalization_and_primary_transcript_calculations.xls: matrix table for all samples including raw read counts and counts normalized by the length of each feature in kilobases  (RPK units) and additionally by sequencing depth (TPM units)

organism: Human gammaherpesvirus 8

source_name: KS skin tumor

extract_protocol:
Total RNA was isolated using the RNeasy mini kit with DNAse treatment step following manufacturer instructions. Total RNA from the 6 tumor samples analyzed by stranded sequencing were extracted using the NucleoSpin RNA kit (Machery-Nagle, Bethlehem, PA, USA). RNA was further concentrated and purified using the RNA Clean and Concentrator kit (Zymo Research, Irvine, CA, USA).
Unstranded RNA-seq libraries were prepared from 300 ng of total RNA using the TruSeq RNA Sample Prep Kit v2. In addition four KS tumor libraries were prepared using the TruSeq Stranded mRNA Library Kit (Illumina) from 100 ng of total RNA.  Library size distributions were validated using an Agilent 2200 TapeStation (Agilent Technologies, Santa Clara, CA, USA).  Additional library QC, pooling of indexed libraries, and cluster optimization was performed using Life Technologies’ Invitrogen Qubit® 2.0 Fluorometer (Life Technologies-Invitrogen, Carlsbad, CA, USA).  The unstranded RNA-seq libraries were pooled (5-plex) and the stranded libraries were pooled (4-plex) and each pool was clustered onto a flow cell lane.  Sequencing was performed using an Illumina HiSeq 2500 in “High Output” mode with a paired-end, 50 base reads (PE50) sequencing strategy for the unstranded libraries and non-paired end for the stranded libraries.  Image analysis and base calling was performed using Illumina's Real Time Analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.2.

value: KSHV (HHV-8)

tag: patient diagnosis

value: Kaposi's sarcoma

value: skin biopsy

tag: genotype

value: wild type (Uganda-101)

tag: host gender

value: M

tag: morphotype

value: Fungating

tag: hiv viral loads (log)

tag: cd4 blood counts


title: 088-C

tag: tissue

value: wild type (Uganda-X)

value: Macular


title: 092-C

tag: strain

value: wild type (Uganda-?)


title: 037-B

value: wild type (Uganda-C)


title: des1

tag: age


title: des13


title: des41


title: des4


title: des15


title: des5


title: des21


title: 034-B

value: F


title: des47


title: 032-B

value: wild type (Uganda-A)


title: des6

value: 8-10 weeks


title: des19

value: female


title: 030-C

value: wild type (Uganda-E)

value: Nodular


title: des23


title: des9

value: cult


title: des7


title: des37

value: n


title: 030-B

value: KSHV (HHV-8)

value: Kaposi's sarcoma


title: des43


title: des34


title: 099-C

value: skin biopsy


title: des44


title: MF.CCR2nFlt3n64p6CloGFPntdTomaton.inj.d2.Ht.2

value: Tnnt2-DTR  CCR2GFP  Flt3-Cre  Rosa26-tdTomato

value: 17 weeks old

tag: sorting markers

tag: cell type

value: Macrophage


title: des16


title: des18


title: MF.CCR2nFlt3n64p6CloGFPntdTomaton.inj.d2.Ht.3


title: 028-B

value: M

value: Macular


title: 029-B


title: 022-B

value: wild type (Uganda-D)


title: 015-B

value: wild type (Uganda-B)


title: 026-B

value: wild type (Uganda-A)

value: F


title: 020-B


title: 011-D

value: wild type (Uganda-C)


title: 014-B


title: 010-C

value: Fungating


title: 023-B


title: 011-C

value: Nodular


title: 024-B


title: 005-C

value: wild type (Uganda-?)


title: 010-B


title: 012-C

value: wild type (Uganda-F)


title: 018-B

value: KSHV (HHV-8)


title: 026-C

value: Kaposi's sarcoma


title: 013-B

value: skin biopsy


title: 006-C


title: 009-B


title: 007-B


title: 013-C


title: 004-D


title: 012-D


title: 006-B


title: 029-C


title: 028-D


title: 001-C


title: 003-C


title: 008-B

value: wild type (Uganda-C:translocation)


title: 008-C


title: Grey IL22 TGFlo

status: Public on Oct 26 2018

city: Montreal

first: Naglaa

last: Shoukry

state: QC

address: Tour Viger, Local 09.414, 900 rue St-Denis

institute: CRCHUM

description:
mRNA
processed data file: raw_data_GEO-20180814.csv
processed data file: norm_data_GEO-20180814.csv

data_processing:
Raw Count Matrix was obtained from the standard workflow used at The McGill University and Génome Québec Innovation Centre.
Features with at least one count per million (CPM) were kept prior to transformation.
Raw Counts were transformed into log2-CPM values using the voom method from the limma Bioconductor R package.
Genome_build: GRCh37
Supplementary_files_format_and_content: raw_data_GEO-20180814.csv: Comma-separated text file includes raw counts. Matrix table with features as rows. First column is the feature ID and each subsequent column represent one sample.
Supplementary_files_format_and_content: norm_data_GEO-20180814.csv: Comma-separated text file includes normalized counts, filtered. Matrix table with features as rows. First column is the feature ID and each subsequent column represent one sample.

source_name: Primary Hepatic Stellate Cells

extract_protocol:
RNA extracted with RNeasy Mini kit plus (QIAGEN).
cDNA libraries and RNA-seq were performed by The McGill University and Génome Québec Innovation Centre, Montreal, QC. 100 bp paired-end sequencing was performed on an Illumina-Hiseq (depth was above 150 million reads).

treatment_protocol: Each lot was stimulated for 48h with either PBS, TGFlo (0.1ng/mL), TGFhi (2,5ng/mL), IL-17A (40ng/mL), IL-17A + TGFlo, IL-22 (40ng/mL) or IL-22 + TGFlo.

value: Primary hepatic stellate cells

tag: stimulation

value: IL22 TGFlo

tag: lot

value: Grey

tag: barcode


title: Grey IL17A TGFlo

value: IL17A TGFlo


title: Grey IL22


title: Yellow IL17A

value: Yellow


title: Yellow TGFhi

value: TGFhi


title: Yellow IL22


title: Blue PBS

value: PBS

value: Blue


title: Blue IL22 TGFlo


title: Grey TGFlo

value: TGFlo


title: Grey TGFhi


title: Grey PBS


title: Yellow IL17A TGFlo


title: Blue IL17A TGFlo


title: Grey IL17A


title: Yellow IL22 TGFlo


title: Blue TGFlo


title: Yellow PBS


title: Blue IL22


title: Blue TGFhi


title: Blue IL17A


title: Yellow TGFlo


title: 001-B

value: wild type (Uganda-A)

value: M

value: Macular


title: AI.Treated.180B

status: Public on Oct 22 2018

city: London

first: Alice

last: Gao

state: London

address: 237 Fulham Road

department: Breast Cancer Now

country: United Kingdom

institute: The Institute of Cancer Research

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol of iScan

data_processing: The data was filtered to remove any non-expressed probes using the detection p-value from Illumina. Across all samples probes for which the intensity values were not significantly different (p>0.01) from the negative controls were removed from the analysis. Following filtering the data was transformed and normalized using variance-stabilizing transformation and robust spline normalization (RSN) method in the lumi package in R. The RSN combines the features of quantile and loess normalization

source_name: breast tumour

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: mRNA from baseline (B) and surgery (S) tumour biopsies were extracted with RNeasy Mini Kit (Qiagen), as per the manufacturer's instructions, and quantification performed using the Agilent 2100 Bioanalyzer (Santa Clara, CA, USA).

tag: group

value: treated

tag: Sex

value: female

tag: timepoint

value: baseline (B)

value: Negative


title: AI.Treated.181B


title: AI.Treated.178B


title: AI.Treated.183B


title: AI.Treated.176B


title: AI.Treated.179B


title: AI.Treated.174B


title: AI.Treated.177B


title: AI.Treated.169B


title: AI.Treated.168B


title: AI.Treated.165B


title: AI.Treated.151B


title: AI.Treated.170B


title: AI.Treated.167B


title: AI.Treated.172B


title: AI.Treated.175B


title: AI.Treated.159B


title: AI.Treated.149B


title: AI.Treated.142B


title: AI.Treated.154B


title: AI.Treated.153B


title: AI.Treated.146B


title: AI.Treated.161B


title: AI.Treated.173B


title: AI.Treated.155B


title: AI.Treated.140B


title: AI.Treated.143B


title: AI.Treated.166B


title: AI.Treated.147B


title: AI.Treated.144B


title: AI.Treated.139B


title: AI.Treated.137B


title: AI.Treated.138B


title: AI.Treated.133B


title: AI.Treated.136B


title: AI.Treated.135B


title: AI.Treated.134B


title: AI.Treated.132B


title: AI.Treated.125B


title: AI.Treated.128B


title: AI.Treated.123B


title: AI.Treated.124B


title: AI.Treated.122B


title: AI.Treated.130B


title: AI.Treated.127B


title: AI.Treated.116B


title: AI.Treated.120B


title: AI.Treated.118B


title: AI.Treated.119B


title: AI.Treated.112B


title: AI.Treated.115B


title: AI.Treated.111B


title: AI.Treated.121B


title: AI.Treated.104B


title: AI.Treated.95B


title: AI.Treated.108B


title: AI.Treated.96B


title: AI.Treated.109B


title: AI.Treated.107B


title: AI.Treated.105B


title: AI.Treated.92B


title: AI.Treated.93B


title: AI.Treated.88B


title: AI.Treated.87B


title: AI.Treated.85B


title: AI.Treated.90B


title: AI.Treated.81B


title: AI.Treated.94B


title: AI.Treated.78B


title: AI.Treated.91B


title: AI.Treated.97B


title: AI.Treated.84B


title: AI.Treated.79B


title: AI.Treated.75B


title: AI.Treated.82B


title: AI.Treated.80B


title: AI.Treated.77B


title: AI.Treated.70B


title: AI.Treated.73B


title: AI.Treated.68B


title: AI.Treated.67B


title: AI.Treated.76B


title: AI.Treated.74B


title: AI.Treated.55B


title: AI.Treated.53B


title: AI.Treated.64B


title: AI.Treated.52B


title: AI.Treated.71B


title: AI.Treated.69B


title: AI.Treated.63B


title: AI.Treated.160B


title: AI.Treated.66B


title: AI.Treated.58B


title: AI.Treated.62B


title: AI.Treated.54B


title: AI.Treated.44B


title: AI.Treated.48B


title: AI.Treated.50B


title: AI.Treated.43B


title: AI.Treated.45B


title: AI.Treated.59B


title: AI.Treated.40B


title: AI.Treated.56B


title: AI.Treated.47B


title: AI.Treated.49B


title: AI.Treated.39B


title: AI.Treated.36B


title: AI.Treated.38B


title: AI.Treated.34B


title: AI.Treated.24B

value: Positive


title: AI.Treated.19B


title: AI.Treated.31B


title: AI.Treated.23B


title: AI.Treated.35B


title: AI.Treated.30B


title: AI.Treated.126B


title: AI.Treated.37B


title: AI.Treated.32B


title: AI.Treated.28B


title: AI.Treated.33B


title: AI.Treated.27B


title: AI.Treated.20B


title: AI.Treated.22B


title: AI.Treated.18B


title: AI.Treated.12B


title: AI.Treated.10B


title: AI.Treated.17B


title: AI.Treated.16B


title: AI.Treated.7B


title: AI.Treated.9B


title: AI.Treated.8B


title: AI.Treated.15B


title: AI.Treated.5B


title: 16-071I2_LUNG

status: Public on Oct 19 2018

first: Ilsa

last: Coleman

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

description: 15-090H1 CRPC lung metastasis

data_processing:
Image analysis and base calling were performed using Illumina's Real Time Analysis v1.18.X software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files, using Illumina's bcl2fastq Conversion Software v1.8.4
Reads were mapped to the hg19 human genome build using TopHat v2.X and bowtie2 v2.2.X.
Mean and standard deviation of fragment size were calculated with picard-tools v2.18.1
Transcript abundance was determined from the TopHat alignments in R using the Genomic Alignments Bioconductor package v1.12.2 using the summarizeOverlaps function with mode=IntersectionStrict, counting reads mapping to the exonic regions of genes.

source_name: CRPC lung metastasis

extract_protocol:
Total RNA was isolated from sections of frozen tissue using RNA STAT-60 (Tel-Test) while incorporating Phase Lock Gel Heavy tubes (5 Prime) into the protocol to better facilitate phase separation.   RNA yield and purity was obtained on a NanoDrop 2000 (Thermo Fisher Scientific).  RNA Integrity was evaluated on a 2100 Bioanalyzer (Agilent Technologies).
RNA-seq libraries were constructed from 1 ug total RNA using the Illumina TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol.
Barcoded libraries were pooled and sequenced six per lane on the Illumina HiSeq 2500 generating 50 bp paired end reads.

tag: gender

value: male

value: Castration Resistant Prostate Cancer (CRPC)

tag: tumor type

value: CRPC metastasis

tag: tumor site

value: lung

tag: patient


title: 16-052K1_LN

description: 15-023AA1 CRPC lymph node (LN) metastasis

source_name: CRPC lymph node (LN) metastasis

value: lymph node


title: 16-052H1_LIVER

description: 13-122H1 CRPC liver metastasis

source_name: CRPC liver metastasis

value: liver


title: 16-071H10_LIVER

description: 14-077N15 CRPC liver metastasis


title: 15-096FF1_BONE

description: 14-043H6 CRPC bone metastasis

source_name: CRPC bone metastasis

value: bone


title: AI.Treated.13B


title: 15-069K1_LIVER

description: 14-091E1 CRPC liver metastasis


title: 15-023K2_SPLEEN

description: 03-192C3 CRPC spleen metastasis

source_name: CRPC spleen metastasis

value: spleen


title: 15-090KK1_BONE

description: 13-012M3 CRPC bone metastasis


title: 15-090H1_LIVER

description: 13-101K3 CRPC liver metastasis


title: 15-010K4_LN

description: 15-090KK1 CRPC lymph node (LN) metastasis


title: 15-023L2_LN

description: 15-010K4 CRPC lymph node (LN) metastasis


title: 15-069P5_LN

description: 15-096FF1 CRPC lymph node (LN) metastasis


title: 15-003H1_LIVER

description: 14-053H3 CRPC liver metastasis


title: AI.Treated.14B


title: 15-010H1_LIVER

description: 14-053O7 CRPC liver metastasis


title: 14-053AA3_BONE

description: 12-005H6 CRPC bone metastasis


title: 14-039K4_LIVER

description: 14-039E3 CRPC liver metastasis


title: AI.Treated.3B


title: 15-023AA1_BONE

description: 12-011J3 CRPC bone metastasis


title: 14-043H6_LIVER

description: 12-021H6 CRPC liver metastasis


title: 13-122H1_PELVIC_MASS

description: 16-052K1 CRPC pelvic mass metastasis

source_name: CRPC pelvic mass metastasis

value: pelvic mass


title: 13-101H1_LN

description: 15-069P5 CRPC lymph node (LN) metastasis


title: 13-104AA2_BONE

description: 12-005K3 CRPC bone metastasis


title: 13-104K7_LN

description: 13-099J2 CRPC lymph node (LN) metastasis


title: 14-039E3_LUNG

description: 15-010H1 CRPC lung metastasis


title: AI.Treated.1B


title: 14-077N15_LIVER

description: 14-053AA3 CRPC liver metastasis


title: 14-053H3_LIVER

description: 14-039K4 CRPC liver metastasis


title: 13-099J2_LUNG

description: 16-052H1 CRPC lung metastasis


title: 12-021H6_LIVER

description: 12-021J3 CRPC liver metastasis


title: 12-011J3_BLADDER

description: 12-011I8 CRPC bladder metastasis

source_name: CRPC bladder metastasis

value: bladder


title: 12-011I8_LN

description: 11-028L3 CRPC lymph node (LN) metastasis


title: 12-005K3_RENAL

description: 16-071I2 CRPC renal metastasis

source_name: CRPC renal metastasis

value: renal


title: 11-028L3_LUNG

description: 15-023K2 CRPC lung metastasis


title: 13-099H7_LIVER

description: 13-099H7 CRPC liver metastasis


title: 12-005H6_LIVER

description: 12-021FF6 CRPC liver metastasis


title: WT255_small RNA

status: Public on Oct 11 2018

description: small RNA

data_processing:
RNA-Seq reads were algined to GRCm38 using STAR (v2.4.0.1). Raw counts were generated using FeatureCounts (v1.50).
small-RNA-Seq reads were aligned to GRCm38 using Bowtie (v1.0) and quantified using miRDeep2 (v2.0.0.7).
Genome_build: GRCm38
Supplementary_files_format_and_content: text file with read counts

source_name: normal lung

growth_protocol: SPC-rtTA mice were bred with tetO-IGF1R mice to generate SPC-IGF1R mice.

extract_protocol:
Lung tumor nodules or normal lung tissue was dissected and flash frozen. Total RNA was isolated using the miRVana miRNA isolation kit with Phenol (ThermoFisher).
mRNASeq (stranded) using firststrand TrueSeq RNA protocol.
miRNA (size select) with Illumina TruSeq smRNA adaptors

treatment_protocol: Tumors were induced by feeding SPC-IGF1R mice with rodent chow supplemented with 2g/kg of doxycycline

value: FVB

tag: genotype

value: wildtype


title: WT217_small RNA

description: small RNA


title: IGFIR538_small RNA

description: small RNA

source_name: lung tumor

value: lung tumor

value: SPC-IGF1R transgenic


title: 03-192C3_LN

description: 15-069K1 CRPC lymph node (LN) metastasis


title: WT214_small RNA

description: small RNA


title: WT239_small RNA

description: small RNA


title: IGFIR464_small RNA

description: small RNA


title: IGFIR534_Total RNA


title: IGFIR464_Total RNA


title: WT214_Total RNA


title: WT239_Total RNA


title: IGFIR538_Total RNA


title: 13-084H5_LIVER

description: 13-084H5 CRPC liver metastasis


title: 15_3

status: Public on Oct 04 2018

city: Moscow

first: Maria

middle: Vladimirovna

last: Suntsova

address: Miklukho-Maklaya, 16/10

department: Department of Genetics and Postgenomic Technologies

country: Russia

institute: M.M. Shemyakin and Yu.A. Ovchinnikov  Institute of  bioorganic chemistry of the Russian Academy of Sciences

data_processing:
Runing STAR aligner in "Gene_counts" mode
Merging STAR output ("ReadPerGene.out" files) with R into a single table
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw gene counts for each sample

source_name: Stomach

extract_protocol:
For solid tissue biosamples, RNA extraction was performed immediately before preparation of sequencing libraries using QIAGEN RNeasy Kit (Qiagen) for tissues in RNAlater and using the RecoverAll™ Total Nucleic Acid Isolation Kit for FFPE (Invitrogen) following the manufacturer ’s protocol. Then RNA Integrity Number (RIN) was measured using Agilent 2100 bio-Analyzer. Agilent RNA 6000 Nano or Qubit RNA Assay Kits were used to measure RNA concentration. The Kit for further depletion of ribosomal RNA was selected based on total amount of RNA in every sample: (i) when total amounts of RNA were less than 25 ng, Clontech Smarter stranded total RNA kit-pico (Mammalian only) was used; (ii) when total amount of RNA exceeded 25ng, KAPA RNA Hyper with RiboErase (KAPA Biosystem) kits were used.
For library preparations, we used Ovation® Universal RNA-Seq System 1-96 and KAPA HyperPrep Kit according to the manufacturer’s recommendations. Different adaptors were used for multiplexing samples in one sequencing run. Library concentrations and quality were measured using Qubit ds DNA HS Assay kit (Life Technologies) and Agilent Tapestation (Agilent). RNA sequencing was performed using Illumina HiSeq 3000 equipment for single-end sequencing, 50 bp read length, for approx. 30 million raw reads per each sample. Data quality check was done on Illumina SAV. De-multiplexing was performed with Illumina Bcl2fastq2 v 2.17 program.

value: Stomach

tag: disease

value: healthy


title: 13-012M3_LUNG

description: 15-003H1 CRPC lung metastasis

value: male

tag: tissue


title: WT255_Total RNA

tag: strain


title: 15_4

source_name: Prostate

value: Prostate


title: 12-021FF6_BONE

description: 13-104K7 CRPC bone metastasis

value: Castration Resistant Prostate Cancer (CRPC)

value: CRPC metastasis


title: Rgt1_10aaD_genomic_B3

status: Public on Oct 03 2018

first: Seungsoo

last: Kim

address: 265 Campus Dr

department: Chemical and Systems Biology

description:
fixed-locus_ko_barcodes.fa
Rgt1_10aaD_associations.txt

data_processing:
Library strategy: Rgt1 deletion trans MAP-C
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were trimmed to a fixed length of 25 bp and mapped to the set of possible barcodes using Bowtie2. Barcodes were associated with Rgt1 mutants based on programmed barcode associations.
Genome_build: Barcode file fixed-locus_ko_barcodes.fa
Supplementary_files_format_and_content: tab-delimited text files ending in "counts.txt" include the last amino acid position before the 10 amino acid Rgt1 deletion and the number of reads containing each barcode. FASTA files ending in ".fa" contain the possible barcodes used for mapping. tab-delimited text files ending in "associations.txt" include the Rgt1 deletion associated with each barcode.

organism: Saccharomyces cerevisiae

source_name: Cells

growth_protocol: Cells were grown overnight, shaking at 30C in YPD media (1% yeast extract, 2% peptone, 2% dextrose).

extract_protocol:
Cells were lysed using glass beads and chromatin was extracted, digested using restriction enzyme, and ligated. Crosslinks were reversed and DNA was purified by phenol/chloroform extraction.
DNA was amplified with primers containing sequencing and flowcell adapter sequences.

treatment_protocol: Cells were crosslinked by addition of 37% formaldehyde to a 1% final concentration, for 20 minutes at room temperature, and then quenched by addition of 2.5M glycine, incubation for 5 minutes, and a TBS (Tris-buffered saline) wash.

tag: growth conditions

value: saturated in YPD

tag: restriction enzyme

value: EcoRI-HF


title: Rgt1_10aaD_genomic_A3


title: Rgt1_10aaD_genomic_A1


title: Rgt1_10aaD_3C_B2


title: Rgt1_10aaD_genomic_B1


title: Rgt1_10aaD_genomic_B2


title: Rgt1_10aaD_3C_B3


title: Rgt1_10aaD_3C_B1


title: Rgt1_10aaD_genomic_A2


title: Rgt1_10aaD_3C_A3


title: Rgt1_10aaD_3C_A2


title: IGFIR534_small RNA

description: small RNA


title: IGFIR466_small RNA

description: small RNA


title: Rgt1_10aaD_3C_A1


title: IGFIR466_Total RNA


title: WT217_Total RNA

value: lung


title: SER8

status: Public on Aug 24 2018

city: Ann Arbor

first: Qianyi

last: Ma

state: MI

address: 1141 E Catherine St

department: Human Genetics

institute: University of Michigan

description:
mixed-species samples
72297_1_CGCAAGCCGA_S1

data_processing:
Two paired-end fastq files were converted to one query-sorted bam file using Picard tools v2.6.0 and samtools v1.2.
Sequence reads were tagged with cell and molecular barcodes, filtered for low base quality in cell or molecular barcodes, trimmed for starting sequence and polyA tail using Drop-seq tools v1.12.
The barcode-tagged, filtered and trimmed bam file is converted back to fastq file using Picard tools v2.6.0.
Alignment was performed using Star v2.5.2b.
Aligned reads were tagged with gene exons and cleaned for bead synthesis errors using Drop-seq tools v1.12.
Gene expressoin matrix was generated using Drop-seq tools v1.12.
For mixed-species samples, mouse cells were separated from other species based on UMI data and extracted from the unaligned fastq file.
For unaligned fastq file for mouse cells, repeat the above steps from alignment to gene expression matrix generation.
Genome_build: GRCm38, Mmul_1
Supplementary_files_format_and_content: tab-delimited text files include raw UMI counts for each cell (column) and each gene (row)

source_name: Adult testis

extract_protocol:
Sertoli cells were enriched by selection of Sox9 positive cells. For Sox9+ cell selection, Sox9-eGFP (MGI ID: 3844824) mice were used to collect GFP+ cells by flow cytometry.
Briefly, cells, barcoded microparticle beads and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, and cDNA synthesis occurred on the bead. Excess oligos were removed by exonuclease I digestion. cDNA amplification was done from a pool of 2,000 bead. Individual PCRs were purified and pooled for library generation. A total of 600 pg of amplified cDNA was used for a Nextera XT library preparation (Illumina).

value: Testis

tag: cell type enrichment

value: sertoli

tag: age

value: 8 wk

tag: non-mouse cell line

tag: spike-in species

value: Macaca mulatta


title: SER5

description:
mixed-species samples
63757_6_S9
72297_3_GAGTTACGCT_S3

extract_protocol:
Sertoli cells were enriched by selection of Amh positive cells. For Amh+ cell selection, 129S.FVB-Tg(Amh-cre)8815Reb/J (JAX®mice, stock no. 007915) mice were crossed with RosamT/mG. Amh-cre; RosamT/mG were used to collect all live Amh positive (GFP expressing) and tdTomato negative cells by flow cytometry.
Briefly, cells, barcoded microparticle beads and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, and cDNA synthesis occurred on the bead. Excess oligos were removed by exonuclease I digestion. cDNA amplification was done from a pool of 2,000 bead. Individual PCRs were purified and pooled for library generation. A total of 600 pg of amplified cDNA was used for a Nextera XT library preparation (Illumina).

value: 7 wk


title: SER7

description:
mixed-species samples
63757_5_S8

data_processing:
Two paired-end fastq files were converted to one query-sorted bam file using Picard tools v2.6.0 and samtools v1.2.
Sequence reads were tagged with cell and molecular barcodes, filtered for low base quality in cell or molecular barcodes, trimmed for starting sequence and polyA tail using Drop-seq tools v1.12.
The barcode-tagged, filtered and trimmed bam file is converted back to fastq file using Picard tools v2.6.0.
Alignment was performed using Star v2.5.2b.
Aligned reads were tagged with gene exons and cleaned for bead synthesis errors using Drop-seq tools v1.12.
Gene expressoin matrix was generated using Drop-seq tools v1.12.
For mixed-species samples, mouse cells were separated from other species based on UMI data and extracted from the unaligned fastq file.
For unaligned fastq file for mouse cells, repeat the above steps from alignment to gene expression matrix generation.
Genome_build: GRCm38, GRCh37
Supplementary_files_format_and_content: tab-delimited text files include raw UMI counts for each cell (column) and each gene (row)

value: Homo sapiens


title: SER4

description:
mixed-species samples
63757_3_S6


title: Cdiphtheriae1737deltadtxR_10iron_rep3

status: Public on Sep 07 2018

city: Silver Spring

first: Michael

last: Schmitt

state: MD

address: 10903 New Hampshire Ave

institute: US Food and Drug Administration

description:
deltaDtxR10iron(3)
Gene expression following growth in high iron conditions.

hyb_protocol: 0.6 µg of Cy3-labelled cRNA (specific activity > 30 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 m in a reaction volume of 25 µl. An equal volume (25 µl) of 2x Hi-RPM Hybridization Buffer was added to stop the fragmentation reaction. 40 µl of each sample was hybridized to Agilent Custom Microarrays designed using the Corynebacterium diphtheriae strain NCTC 13129 for 17 h at 65°C in a rotating hybridization oven. After hybridization, microarrays were washed 1 m at room temperature with Gene Expression Wash Buffer 1 and 1 m at 37°C using Gene Expression Wash Buffer 2. Slides were scanned immediately.

scan_protocol: Slides were scanned on the Agilent G2505C Microarray Scanner using settings recommended by the manufacturer (Dye channel: G (green), Scan region: Scan Area 61 x 21.6 mm, Scan Resolution: 3 µm, and 100% Green PMT gain).

data_processing:
The scanned images were analyzed with Feature Extraction Software version 12.0.3.1 (Agilent) using default parameters to obtain gProcessedSignal values. Median gProcessedSignal values were divided by the entire sample set mean and log2 transformed.
J5_analysis.txt: Data presented in this file were subjected to the J5 test described in Jordan et al. "Efficiency Analysis of Competing Tests for Finding Differentially Expressed Genes in Lung Adenocarcinoma" (PMID 19259419). This analysis was used for the identification of significantly differentially regulated genes presented in the associated manuscript.

organism: Corynebacterium diphtheriae

source_name: Cdiphtheriae 1737 deltadtxR, 10uM iron

label_protocol: Cyanine-3 labeled cRNA was prepared from 0.1 µg RNA using the Low Input Quick Amp WT Labeling Kit (Agilent) following the manufacturer’s instructions. cRNA was purified using the RNeasy kit (QIAGEN). Dye incorporation and cRNA yield were assessed with the GE NanoVue Plus.

growth_protocol: Wild-type C. diphtheriae or the dtxR mutant were grown overnight in the semi-defined medium mPGT supplemented with 1 µM FeCl3. Overnight cultures were diluted 1:1 with fresh media and allowed to grow for 2-3 h. The optical density of cultures was measured (A600) and the cells diluted to an optical density of 0.1 into mPGT supplemented with either 0.5 or 10 µM FeCl3. For the dtxR mutant, cultures were only diluted into 10 µM FeCl3. Cells were harvested by centrifugation at mid-logarithmic growth.

extract_protocol: Cells were lysed in phosphate buffered saline supplemented with 10% ethanol, 0.2% phenol, and 14.3 mM beta-mercaptoethanol in Lysing Matrix B (MP Biomedicals). Appropriate volumes of TriZOL LS reagent (Thermo Fisher Scientific) were added to lysates and samples were briefly vortexed. RNA was purified following the Zymo Direct-zol RNA MiniPrep Plus protocol (Zymo Research Corporation). RNA was treated with Ambion Turbo DNase I (Invitrogen). The RNA concentration and integrity were assessed by the Agilent Bioanalyzer 2100 following the RNA 6000 Nano protocol.

tag: strain/background

tag: genotype/variation

value: delta dtxR

tag: treatment

value: 10uM iron


title: SER6

description:
mixed-species samples
72297_2_TTTATCGTTC_S2

value: 9 wk


title: Cdiphtheriae1737deltadtxR_10iron_rep1

description:
deltaDtxR10iron(1)
Gene expression following growth in high iron conditions.


title: Cdiphtheriae1737_0.5iron_rep3

description:
wildtype0.5iron(3)
Gene expression following growth in low iron conditions.

source_name: Cdiphtheriae 1737, 0.5uM iron

value: wild type

value: 0.5uM iron


title: Cdiphtheriae1737_0.5iron_rep2

description:
wildtype0.5iron(2)
Gene expression following growth in low iron conditions.


title: Cdiphtheriae1737deltadtxR_10iron_rep2

description:
deltaDtxR10iron(2)
Gene expression following growth in high iron conditions.


title: Cdiphtheriae1737_0.5iron_rep1

description:
wildtype0.5iron(1)
Gene expression following growth in low iron conditions.


title: Cdiphtheriae1737_10iron_rep1

description:
wildtype10iron(1)
Gene expression following growth in high iron conditions.

source_name: Cdiphtheriae 1737, 10uM iron


title: SER3

extract_protocol:
Sertoli cells were enriched by selection of Amh positive cells. For Amh+ cell selection, 129S.FVB-Tg(Amh-cre)8815Reb/J (JAX®mice, stock no. 007915) mice were crossed with RosamT/mG. Amh-cre; RosamT/mG were used to collect all live Amh positive (GFP expressing) and tdTomato negative cells by flow cytometry. Human HEK293T cells were added at 20% of the total sample.
Briefly, cells, barcoded microparticle beads and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, and cDNA synthesis occurred on the bead. Excess oligos were removed by exonuclease I digestion. cDNA amplification was done from a pool of 2,000 bead. Individual PCRs were purified and pooled for library generation. A total of 600 pg of amplified cDNA was used for a Nextera XT library preparation (Illumina).

value: 11 wk

value: HEK 293T cell line


title: SER1


title: SER2

value: 7 and 11 wk


title: INT6

extract_protocol:
Interstitial cells were enriched by selection of Sca1 positive cells. For Sca1 (Ly6a)+ cell selection, combined cell suspensions were stained with biotinylated anti-Ly6a (1:200) for 20 min followed by streptavidin conjugated Alexa Fluor 488 (1:1000; Life Technologies Cat# S11223; RRID: AB_2336881) for 20 min prior to flow cytometry.
Briefly, cells, barcoded microparticle beads and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, and cDNA synthesis occurred on the bead. Excess oligos were removed by exonuclease I digestion. cDNA amplification was done from a pool of 2,000 bead. Individual PCRs were purified and pooled for library generation. A total of 600 pg of amplified cDNA was used for a Nextera XT library preparation (Illumina).

value: interstitial


title: INT4

extract_protocol:
Interstitial cells were enriched by selection of Sca1 positive cells. For Sca1 (Ly6a)+ cell selection, combined cell suspensions were stained with biotinylated anti-Ly6a (1:200) for 20 min followed by streptavidin conjugated Alexa Fluor 488 (1:1000; Life Technologies Cat# S11223; RRID: AB_2336881) for 20 min prior to flow cytometry. Human A549 cells were added at 25% of the total sample.
Briefly, cells, barcoded microparticle beads and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, and cDNA synthesis occurred on the bead. Excess oligos were removed by exonuclease I digestion. cDNA amplification was done from a pool of 2,000 bead. Individual PCRs were purified and pooled for library generation. A total of 600 pg of amplified cDNA was used for a Nextera XT library preparation (Illumina).

value: 18 wk

value: A549 cell line


title: INT2

description:
mixed-species samples
79087_ATTGCTTCCA_S4

extract_protocol:
Interstitial cells were enriched by selection of Thy1 positive cells. For Thy1+ selection, collagenase and whole tubule cell suspensions were stained with anti-CD90-PerCP cyanine5.5 (1:200; Life Technologies, Cat# 45090082; RRID: AB_2573662) for 20 min prior to flow cytometry.
Briefly, cells, barcoded microparticle beads and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, and cDNA synthesis occurred on the bead. Excess oligos were removed by exonuclease I digestion. cDNA amplification was done from a pool of 2,000 bead. Individual PCRs were purified and pooled for library generation. A total of 600 pg of amplified cDNA was used for a Nextera XT library preparation (Illumina).

value: Testis

value: 10 wk


title: INT3

extract_protocol:
Interstitial cells were enriched by gental digestion with collagenase (shake first by hand to get tubules into strands, then rocked 37C/215rpm/~1min and shaken by hand again). Tubules were settled and the suspension was kept, washed with PBS, and used for FACS to collect live interstitial cells. Human HEK293T cells were added at 10% of the total sample.
Briefly, cells, barcoded microparticle beads and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, and cDNA synthesis occurred on the bead. Excess oligos were removed by exonuclease I digestion. cDNA amplification was done from a pool of 2,000 bead. Individual PCRs were purified and pooled for library generation. A total of 600 pg of amplified cDNA was used for a Nextera XT library preparation (Illumina).

value: 15 wk


title: Cdiphtheriae1737_10iron_rep2

description:
wildtype10iron(2)
Gene expression following growth in high iron conditions.


title: SPG2

description:
mouse-only sample
78014_TTTATCGTTC_S2

extract_protocol:
Spermatogonia were enriched by selection of Gfra1+ cells. For Gfra1+ selection, tamoxifen inducible Gfrα1CreERT2 mice on a C57BL/6 background (kindly provided by Dr. Shosei Yoshida, National Institute for Basic Biology, Okazaki, Japan) were crossed with B6.Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo (RosamT/mG; JAX®mice, stock no. 007676). Labeling of Gfra1+ spermatogonia was conducted by injecting a Gfrα1CreERT2; RosamT/mG mouse with 2mg of 4OH-tamoxifen (dissolved in ethanol and then in corn oil, Sigma) per day for 3.5 weeks prior to euthanasia at 8 weeks of age. All live Gfra1 positive (GFP expressing) and tdTomato negative cells were collected by flow cytometry.
Briefly, cells, barcoded microparticle beads and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, and cDNA synthesis occurred on the bead. Excess oligos were removed by exonuclease I digestion. cDNA amplification was done from a pool of 2,000 bead. Individual PCRs were purified and pooled for library generation. A total of 600 pg of amplified cDNA was used for a Nextera XT library preparation (Illumina).

value: spermatogonia

value: 8 wk


title: SPG3

extract_protocol:
Spermatogonia were enriched by selection of C-kit+ cells. C-kit+ (CD117) cells were isolated from whole tubule cell suspensions on a magnetic cell-sorting separator (Miltenyi Biotec) using an anti-CD117 (Miltenyl Biotec) antibody. Cells were additionally stained with a biotinylated anti-CD117 antibody (1:200) for 20 min followed by streptavidin conjugated Alexa Fluor 488 (1:1000, Life Technologies) for 20 min prior to flow cytometry. All live 488 positive cells were collected by flow cytometry. Human A549 cells were added at 25% of the total sample.
Briefly, cells, barcoded microparticle beads and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, and cDNA synthesis occurred on the bead. Excess oligos were removed by exonuclease I digestion. cDNA amplification was done from a pool of 2,000 bead. Individual PCRs were purified and pooled for library generation. A total of 600 pg of amplified cDNA was used for a Nextera XT library preparation (Illumina).

value: 20 wk

value: Homo sapiens


title: INT1

description:
mouse-only sample
63757_1_S4

extract_protocol:
Interstitial cells were enriched by selection of Thy1 and Sca1 positive cells. For Thy1+ selection, collagenase and whole tubule cell suspensions were combined and isolation was performed on a magnetic cell-sorting separator (Miltenyi Biotec) using anti-CD90.2 (Miltenyi Biotec) antibody. Cells were additionally stained anti-CD90-PerCP cyanine5.5 (1:200; Life Technologies, Cat# 45090082; RRID: AB_2573662) for 20 min prior to flow cytometry. For Sca1 (Ly6a)+ cell selection, combined cell suspensions were stained with anti-Ly6a-PerCP cyanine5.5 (1:200; Life Technologies, Cat# 45-5981-82; RRID: AB_914372) for 20 min. Cells were sorted by flow cytometry and combined prior to Drop-seq.
Briefly, cells, barcoded microparticle beads and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, and cDNA synthesis occurred on the bead. Excess oligos were removed by exonuclease I digestion. cDNA amplification was done from a pool of 2,000 bead. Individual PCRs were purified and pooled for library generation. A total of 600 pg of amplified cDNA was used for a Nextera XT library preparation (Illumina).

value: 16 wk


title: 1nDepleted1

description:
mixed-species samples
63757_2_S5

extract_protocol:
Haploid cells were depleted by performing two sequential incubations of whole seminiferous tubule cell suspensions in MACS buffer containing Hoechst 33342 (Life Technologies) at 0.6μg per million cells for 20 min at 35ºC / 150 rpm as described previously. Immediately before flow cytometry, propidium iodide was added at 2μg/ml. All live cells were collected, excluding those recognized as haploid with low Hoechst 33342 fluorescence.
Briefly, cells, barcoded microparticle beads and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, and cDNA synthesis occurred on the bead. Excess oligos were removed by exonuclease I digestion. cDNA amplification was done from a pool of 2,000 bead. Individual PCRs were purified and pooled for library generation. A total of 600 pg of amplified cDNA was used for a Nextera XT library preparation (Illumina).

value: diploid (due to depletion of haploid cells)


title: SPG1

description:
mouse-only sample
78013_CGCAAGCCGA_S1


title: 1nDepleted2

description:
mixed-species samples
63757_4_S7

value: 7 wk


title: INT5

extract_protocol:
Interstitial cells were enriched by selection of Thy1 positive cells. For Thy1+ selection, collagenase and whole tubule cell suspensions were combined and isolation was performed on a magnetic cell-sorting separator (Miltenyi Biotec) using anti-CD90.2 (Miltenyi Biotec) antibody. Cells were additionally stained with anti-CD90-FITC conjugated (1:200; Abcam, Cat# ab62009; RRID: AB_940927) for 20 min prior to flow cytometry. Human A549 cells were added at 10% of the total sample.
Briefly, cells, barcoded microparticle beads and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, and cDNA synthesis occurred on the bead. Excess oligos were removed by exonuclease I digestion. cDNA amplification was done from a pool of 2,000 bead. Individual PCRs were purified and pooled for library generation. A total of 600 pg of amplified cDNA was used for a Nextera XT library preparation (Illumina).

value: 14 wk


title: ST6

description:
mouse-only sample
73590_ATTGCTTCCA_S4

extract_protocol:
Testes from adult C57BL/6 (JAX®mice, stock no. 000664) and transgenic mice were excised and the tunica albuginea was removed with fine tweezers. Seminiferous tubules were transferred to collagenase IA digest buffer (200 μg/ml (Sigma) dissolved in Advanced DMEM:F12 media(Life Technologies) plus 400 units/ml DNaseI (Worthington Biochemical Corp.)) and dispersed by gently shaking by hand, and allowed to settle for 1 min at room temperature. Tubules were then digested twice in trypsin (200 μg/ml dissolved in Advanced DMEM:F12 media plus 400 units/ml DNaseI) at 35ºC / 215 rpm for 5 min each and quenched with the addition of fetal bovine serum (FBS). Cells were filtered through a 100 μm strainer, rinsed in PBS, and re-suspended in MACS rinsing solution containing 0.5% BSA (MACS buffer; Miltenyi Biotec). For interstitial cell enrichment, supernatants from collagenase IA digests were collected after incubating at 35ºC / 150rpm for 5 min, gently shaken by hand, quenched with FBS, and used independently or combined with trypsin digests. For all preparations, live single-cell suspensions were collected by flow cytometry by exclusion of DAPI or propidium iodide without or with fluorescent markers (see below) using FACSARIA II/III (BD Biosciences) and Synergy SY3200 (Sony) cell sorters.
Briefly, cells, barcoded microparticle beads and lysis buffer were co-flown into a microfluidic device and captured in nanoliter sized droplets. After droplet collection and breakage, the beads were washed, and cDNA synthesis occurred on the bead. Excess oligos were removed by exonuclease I digestion. cDNA amplification was done from a pool of 2,000 bead. Individual PCRs were purified and pooled for library generation. A total of 600 pg of amplified cDNA was used for a Nextera XT library preparation (Illumina).

value: 9 wk


title: ST5

description:
mouse-only sample
73589_GAGTTACGCT_S3


title: Cdiphtheriae1737_10iron_rep3

description:
wildtype10iron(3)
Gene expression following growth in high iron conditions.

value: wild type

value: 10uM iron


title: ST4


title: ST3


title: ST1

description:
mixed-species samples
73587_CGCAAGCCGA_S1


title: ST2

description:
mixed-species samples
73588_TTTATCGTTC_S2


title: M95_w_3

status: Public on Aug 20 2018

city: bronx

first: Nicholas

last: Baker

address: 1300 Morris Park Avenue

department: genetics

institute: albert einstein college of medicine

data_processing:
The library is sequenced using Illumina HiSeqTM 2000
Then raw reads is subjected to quality control (QC)
After QC, raw reads are filtered into clean reads for alignment to the reference sequences.
Genome_build: dm6
Supplementary_files_format_and_content: Excel files include FPKM values for each Sample; Excel files for different expression between wildtype (frt82_w) and two types of Rp+/- (M67_w and M95_w), as well as RpS3+/- Xrp1+/- (M2-73_M95)

organism: Drosophila melanogaster

source_name: 3rd instar wing disc

growth_protocol: eggs laid in 4h cohorts were raised at 25°C on yeast-glucose medium supplemented with 20μg/ml tetracycline to minimize potential differences in microbiome between genotypes.

extract_protocol:
from each genotype, ~50 wing discs were dissected into Trizol reagent (25 discs into 250μL) and frozen at -80°C. Following thawing and centrifugation (12000g 15 min 4°C), the aqueous phase was precipitated with an equal volume of isopropanol (10 min room temperature). The pellet was recovered by centrifugation (12000g 15 min 4°C), washed with RNAse-free 75% ethanol twice, and air dried (5-10 min room temperature) after removing the remaining ethanol with a filtered RNAse-free pipette tip. Samples were resuspended in RNAse-free water, analyzed by nanodrop spectroscopy and Bioanalyzer and satisfactory samples stored at -80°C
library was constructed by Beijing Genomics Institute. After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes) or by removing rRNAs from the total RNA (for prokaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library.

treatment_protocol: third-instar larvae were harvested 24±2h before puparium formation

tag: strain/genotype

value: w11-18(y w p{ ry+ hsF}); p{ ry+ hs-neor FRT}82D M(3R)RpS3plac92 p{ w+ arm-LacZ}/+

tag: developmental stage

value: 3rd instar

value: wing disc


title: m2-73_M95_1

value: w11-18(y w p{ ry+ hsF}); p{ ry+ hs-neor FRT}82D M(3R)RpS3plac92 p{ w+ arm-LacZ}/ p{ ry+ hs-neor FRT}82D Xrp1m2-73


title: M95_w_2


title: M67_w_2

value: w11-18(y w p{ ry+ hsF}); M(3L)67C p{ w+ ubi-GFP} p{ ry+ hs-neor FRT}80B/+


title: M67_w_3


title: frt82_w_3


title: m2-73_M95_2


title: M95_w_1


title: m2-73_M95_3


title: CT RS

status: Public on Aug 08 2018

city: Berkeley

first: Marina

last: Volegova

address: 748 Stanley Hall, MS 3220

department: Molecular and Cell Biology

institute: University of California - Berkeley

description:
This GEO Sample represents 3 biological replicates.
Total mRNA
processed data file: RS.genes.fpkm_tracking (q1)
processed data file: RS.gene_exp.diff (sample_1)

data_processing:
Illumina CASAVA_v1.8.0 software used for basecalling.
Adapters removed using fastx_clipper -a <adapter seq> -l 25 -c -n -v -Q 33 -i <file>.fastq -o <file_trim>.fastq, and rRNA reads removed using bowtie2 -L 23 --un /<file_norRNA>.fastq -x /<Human_rRNA> -q /<file_trim>.fastq > /<file_rRNA>.map
Reads were mapped to genome using tophat --no-novel-juncs -o <output-directory-name> -G ~/<path-to-gtf-file>/<filename>.gtf --transcriptome-index=~/<path-to-gtf-file> ~/<path-to-file>/<genome-and-indexed-genome-file-name-without-extension> <input-file>.fastq
Raw read counts and FPKM were obtained using Cufflinks (cufflinks -o <output directory name> --compatible-hitsnorm -u -b <path to genome.fa> -G <path to .gtf file> <aligned_reads.bam>) and Cuffdiff (cuffdiff -o <outpit directory> -p <thread #> --compatible-hits-norm <path to .gtf file> <sample 1_accepted hits_rep1.bam, __rep2.bam, __rep3.bam> <sample 2_accepted hits_rep1.bam, __rep2.bam, __rep3.bam>)
Genome_build: GRCh38
Supplementary_files_format_and_content: *.gene_exp.diff: Cufflinks/Cuffdiff output; raw read count measurements.
Supplementary_files_format_and_content: *.genes.fpkm_tracking: Cufflinks/Cuffdiff output; FPKM measurements.

source_name: HEK293T cells

growth_protocol: Lentiviral engineered HEK293T cells were grown in DMEM media with 10% FBS. Each biological replicate was thawed separately into a 10cm plate and passaged twice before collection.

extract_protocol:
Extract was prepared according to protocol published in (Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M., and Weissman, J. S. 2013. Genome-wide annotation and quantitation of translation by ribosome proﬁling. Curr. Protoc. Mol. Biol.103:4.18.1-4.18.18.doi: 10.1002/0471142727.mb0418s103).
Ribosome profiling libraries were prepared according to protocol published in (Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M., and Weissman, J. S. 2013. Genome-wide annotation and quantitation of translation by ribosome proﬁling. Curr. Protoc. Mol. Biol.103:4.18.1-4.18.18.doi: 10.1002/0471142727.mb0418s103). RNA-seq libraries were prepared according to Illumina TruSeq RNA Library Prep kit manufacturer's instructions.

tag: cell line

tag: passages

tag: lentivirus 1

value: anti-EIF3A shRNA

tag: lentivirus 2

value: Control (CT) EIF3A


title: HLH RS

description:
This GEO Sample represents 3 biological replicates.
Total mRNA
processed data file: RS.genes.fpkm_tracking (q2)
processed data file: RS.gene_exp.diff (sample_2)

value: HLH mutant EIF3A


title: HLH RP

description:
This GEO Sample represents 3 biological replicates.
Ribosome-protected mRNA
Ribosome profiling
processed data file: RP.genes.fpkm_tracking (q2)
processed data file: RP.gene_exp.diff (sample_2)

data_processing:
Library strategy: Ribo-seq
Illumina CASAVA_v1.8.0 software used for basecalling.
Adapters removed using fastx_clipper -a <adapter seq> -l 25 -c -n -v -Q 33 -i <file>.fastq -o <file_trim>.fastq, and rRNA reads removed using bowtie2 -L 23 --un /<file_norRNA>.fastq -x /<Human_rRNA> -q /<file_trim>.fastq > /<file_rRNA>.map
Reads were mapped to genome using tophat --no-novel-juncs -o <output-directory-name> -G ~/<path-to-gtf-file>/<filename>.gtf --transcriptome-index=~/<path-to-gtf-file> ~/<path-to-file>/<genome-and-indexed-genome-file-name-without-extension> <input-file>.fastq
Raw read counts and FPKM were obtained using Cufflinks (cufflinks -o <output directory name> --compatible-hitsnorm -u -b <path to genome.fa> -G <path to .gtf file> <aligned_reads.bam>) and Cuffdiff (cuffdiff -o <outpit directory> -p <thread #> --compatible-hits-norm <path to .gtf file> <sample 1_accepted hits_rep1.bam, __rep2.bam, __rep3.bam> <sample 2_accepted hits_rep1.bam, __rep2.bam, __rep3.bam>)
Genome_build: GRCh38
Supplementary_files_format_and_content: *.gene_exp.diff: Cufflinks/Cuffdiff output; raw read count measurements.
Supplementary_files_format_and_content: *.genes.fpkm_tracking: Cufflinks/Cuffdiff output; FPKM measurements.


title: CT RP

description:
This GEO Sample represents 3 biological replicates.
Ribosome-protected mRNA
Ribosome profiling
processed data file: RP.genes.fpkm_tracking (q1)
processed data file: RP.gene_exp.diff (sample_1)


title: frt82_w_2

tag: tissue


title: M67_w_1


title: frt82_w_1


title: interactor_ko_genomic_3

status: Public on Aug 05 2018

city: Stanford

institute: Stanford University

description:
fixed-locus_ko_barcodes.fa
interactor_ko_associations.txt

data_processing:
Library strategy: fixed-locus trans MAP-C
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were trimmed to a fixed length of 25 bp and mapped to the set of possible barcodes using Bowtie2. Barcodes were associated with gene knockouts based on programmed barcode associations.
Genome_build: Barcode file fixed-locus_ko_barcodes.fa
Supplementary_files_format_and_content: tab-delimited text files ending in "counts.txt" include an identifier for each barcoded construct, the systematic name of the gene knockout, and the number of reads containing each barcode. FASTA files ending in ".fa" contain the possible barcodes used for mapping. tab-delimited text files ending in "associations.txt" include the gene knockout (including "r" for replicates) and the systematic gene name.

extract_protocol:
Cells were lysed using glass beads and chromatin was extracted, digested using restriction enzyme, and ligated. Crosslinks were reversed and DNA was purified by phenol/chloroform extraction.
DNA was amplified with primers containing sequencing and flowcell adapter sequences.

value: saturated in YPD

value: EcoRI-HF


title: interactor_ko_3C_3


title: interactor_ko_genomic_1


title: interactor_ko_3C_2


title: error-prone_WT

description:
plasmid DNA
error-prone.fa

data_processing:
Library strategy: error-prone PCR cis MAP-C
Basecalls were converted to FASTQ using bcl2fastq 2.17
Sequencing reads were trimmed of adapter sequences and merged using PEAR
Reads were mapped were trimmed of the first 4 bp (corresponding to a randomized region for Illumina clustering purposes) to the mutagenized subset of the S. cerevisiae HAS1pr-TDA1pr region using Bowtie2. The read alignments were scored for the number of substitutions, insertions, and deletions, and the frequency of each substitution and the total number of reads were calculated.
Genome_build: Saccharomyces cerevisiae R64.2.1 from SGD
Supplementary_files_format_and_content: tab-delimited text files ending in "mutcounts.txt" include the 1) set of mutations, 2) the total number of mutations, 3) the number of substitutions, 4) the number of deletions, 5) the number of insertions, 6) the number of reads with this set of mutations. tab-delimited text files ending in "subcounts.txt" include the number of reads with each substitution and the total number of reads. FASTA files ending in ".fa" include the names and sequences of the regions used as references for alignment.

organism: synthetic construct

extract_protocol:
E. coli plasmid DNA was prepared using Qiagen miniprep kit.
DNA was amplified with primers containing sequencing and flowcell adapter sequences.


title: P187_09_Cln3_dex7-8_1068_light_Mino

status: Public on Aug 17 2018

city: Cologne

first: Thomas

last: Langmann

address: Kerpener Strasse 62

department: Department of Ophthalmology

country: Germany

institute: University of Cologne

description: total retina transcripts from Cln3_dex7-8 light plus minocycline

hyb_protocol: 15 µg of fragmented cRNA was hybridized to Affymetrix mouse Clariom S arrays

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 Blank7G (Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression Console and Genomatix Software using Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

source_name: Retina from Cln3_dex7-8 light plus Minocycline

label_protocol: Biotinylated cRNA was prepared from 150 ng total RNA according to the standard Affymetrix protocol

growth_protocol: All experimental procedures were in compliance with the German law on animal protection and the ARVO Statement for the Use of Animals in Ophthalmic and Vision Research.

extract_protocol: Retinas were removed and RNA was harvested using Qiagen RNeasy Kit.

treatment_protocol: Wild type littermates and Cln3Δex7/8 mice were dark-adapted for 16 h before light exposure. To test low light and high light conditions, pupils were dilated with 2.5 % Phenylephrin and 1 % Tropicamid under dim red light and the mice were placed into aluminum foil-coated cages. A light intensity of 10,000 lux for 30 min for low light conditions and a light intensity of 15,000 lux for 60 min were used for high light conditions, respectively. Mice of both genotypes without light exposure served as controls. Then mice were then kept in dark-reared conditions over night. For the therapy study with minocycline only Cln3Δex7/8 mice and low light conditions were used. Minocycline (45 mg/kg dissolved in 0.9 % NaCl solution, Sigma) was injected intraperitoneally starting one day before light exposure and then daily until one day before the final experiment. Cln3Δex7/8 mice were injected with the same volume and frequency of 0.9 % NaCl solution as a solvent control

value: retina

value: light plus Minocycline

tag: strain

value: Cln3 delta ex7/8


title: P187_06_Cln3_dex7-8_1077_nolight_2

description: total retina transcripts from Cln3_dex7-8 no light

source_name: Retina from Cln3_dex7-8 no light

value: no light


title: P187_01_Cln3_WT_1127_nolight

description: total retina transcripts fromCln3 WT no light

source_name: Retina from Cln3 WT no light

value: Balb/c


title: P187_07_Cln3_dex7-8_1067_light_NaCl

description: total retina transcripts from Cln3_dex7-8 light plus Nacl

source_name: Retina from Cln3_dex7-8 light plus Nacl

value: light plus Nacl


title: P187_02_Cln3_WT_1133_nolight


title: P187_03_Cln3_WT_1082_highlight

description: total retina transcripts fromCln3 WT high light

source_name: Retina from Cln3 WT high light

value: high light


title: validation_ko_genomic_3

description:
fixed-locus_ko_barcodes.fa
validation_ko_associations.txt

tag: growth conditions


title: fixed-locus_ko_offtarget_3

description:
fixed-locus_ko_barcodes.fa
fixed-locus_ko_associations.txt

tag: restriction enzyme


title: interactor_ko_3C_1


title: P187_10_Cln3_dex7-8_1074_light_Mino


title: P187_05_Cln3_dex7-8_1076_nolight