title: p53 null rep2

city: Stanford

first: Stephano

last: Spano Mello

address: 269 Campus Drive

institute: Stanford University

data_processing:
Basecalls performed using CASAVA 1.8
STAR aligner was used for alignment to mouse genome version mm10
DESeq2 was used for statistical analysis and to generate a variance stabilized table of counts used for subsequent analysis
Genome_build: mm10
Supplementary_files_format_and_content: normalized abundance measurements

source_name: p53 null_PanIN cells

extract_protocol:
Pancreas was resected, dissociated and labeled. Living CD133+ ductal epithelial cells that make up the PanINs were sorted and RNA was harvested using PicoPure RNA Isolation Kit. Illumina TruSeq Stranded RNA LT Kit (Cat#15032612) was used and 1 µg of total RNA was entered for the construction of sequencing libraries. To achieve a minimum of 1 µg of total RNA for each library, RNA samples from 2 mice of the same genotype were combined
The libraries were prepared using the manufacturer's standard protocol

tag: genotype/variation

value: pancreas

value: pancreatic intraepithelial neoplasia (PanIN) cells


title: MEF cells treated with Nudt21 siRNA and induced to express OKSM for 3 days _D3_replicate 2  [PAS-seq]

status: Public on Oct 26 2017

type: SRA

city: Irvine

first: Elmira

last: Forouzmand

state: CA

address: B228 Medical Science I

department: Department of Microbiology and Molecular Genetics

country: USA

institute: University of California Irvine

library_source: transcriptomic

data_processing:
Reads with a string of As (at least 15) were trimmed and kept. These reads were mapped to mouse genome (mm9), using TopHat v2.1.0 with the setting -g 1.
Alignmnet with the possibility of internal priming were removed if a read had 6 or more consecutive As or more than 7 As in the 10 nucleotide downstream of polyA site.
Bigwig files were generated from the remaing reads, using deepTools 2.4
From the remaing reads those with their 3' end in the interval of -40nt to +40nt of potential polyA sites were used to generate the count table.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include read counts for polyA sites for each Sample

molecule: total RNA

organism: Mus musculus

source_name: MEF

growth_protocol: MEFs were derived from mice carrying an inducible, polycistronic OKSM cassette in the 3’ UTR of Col1a1, the M2-rtTA transactivator at the Rosa26 locus, and an EGFP reporter construct under control of Pou5f1 regulatory elements. MEFs cells were grown in MEF growth media (500 ml DMEM (Life Technologies) 10% fetal bovine serum (Hyclone), 1X non-essential amino acids (Life Technologies), 1X Glutamax (Life Technologies), 55 μM beta-mercaptoethanol (Sigma)) and cultured at 37°C at 4% oxygen.

extract_protocol:
RNA isolation was performed using the miRNeasy mini kit (Qiagen). RNA was eluted from the columns using RNase-free water and quantified using a Nanodrop ND-1000.
Total RNA was extracted with Trizol as per manual (Life technologies), 10 μg total RNA was fragmented with fragmentation reagent (Ambion) at 70 oC for 10 minutes followed by precipitation with ethanol. After centrifugation, RNA was dissolved and Reverse transcription was performed with PASSEQ7-2 RT oligo : [phos]NNNNAGATCGGAAGAGCGTCGTGTTCGGATCCATTAGGATCCGAGACGTGTGCTCTTCCGATCTTTTTTTTTTTTTTTTTTTT[V-Q] and Superscript III. cDNA was recovered by ethanol precipitation and centrifugation. 120-200 nucleotides of cDNA was gel-purified and eluted from 8% Urea-PAGE. Recovered cDNA was circularized with CircligaseTM II (Epicentre) at 60 oC overnight. Buffer E (Promega) was added in cDNA and heated at 95 oC for 2 minutes, and then cool to 37 oC slowly. Circularized cDNA was linearized by adding BamH I (Promega). cDNA was centrifugated after ethanol precipitation. PCR was carried out with primers PE1.0 and PE2.0 contaning index. Around 200 bp of PCR products was gel-purified and submitted for sequencing (single read 100 nucleotides).

treatment_protocol: To induce expression of the pluripotency factors, reprogrammable MEFs were seeded at a density of 15,000 cells per well of a 12 well plate coated with 0.2% gelatin (Sigma). Induction media contained ES culture media (500 ml KO-DMEM (Life Technologies) 15% fetal bovine serum (Hyclone), 1X non-essential amino acids (Life Technologies), 1X Glutamax (Life Technologies), 1000 U/ml leukemia inhibitory factor, 55 μM beta-mercaptoethanol (Sigma)) supplemented with 50 μg/ml ascorbic acid (Sigma) and 2 μg/ml doxycycline hyclate (Sigma). Unless otherwise indicated, reprogrammable MEFs were induced for 10 days, followed by 4 days of doxycycline withdrawal to ensure transgene independence.

tag: treatment


title: p53 null rep1

tag: strain background

value: B6/129 hybrid

tag: tissue

tag: cell type


title: siCtrl day3_1

city: Houston

first: Bruno

last: Di Stefano

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: siCTRL transfected MEF induced with OSKM for 3 days replicate 1

library_source: genomic

data_processing:
ATAC-seq reads were aligned to the mm10 genome assembly using BWA-MEM with default parameter
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files were generated using deeptools

molecule: genomic DNA

growth_protocol: Mouse embryonic fibroblasts (MEFs) were derived from E13.5 embryos. The head, limbs, spinal cord, gonads, and internal organs were removed and the remaining tissue was minced in 200 μl of Trypsin-EDTA. Following a 5 minutes incubation at 37°C, the Trypsin-EDTA was quenched in 10 ml of MEF growth media (500 ml DMEM,  10% fetal bovine serum, 1X non-essential amino acids, 1X Glutamax, 55 μM beta-mercaptoethanol) and cultured at 37°C at 4% oxygen. iPSCs were cultured on mitomycin C treated MEF feeder cells in KO-DMEM (Invitrogen) supplemented withL-glutamine, penicillin/streptomycin, nonessential amino acids, β-mercaptoethanol, 1,000 U/ml LIF (ESC medium) and 15% fetal bovine serum (FBS, Invitrogen).reprogrammable MEFs were seeded at a density of 15,000 cells per well of a 12 well plate coated with 0.2% gelatin (Sigma). For cell reprogramming experiments, OSKM inducible MEF were cul;tured in induction media contained ES culture media (500 ml KO-DMEM (Life Technologies) 15% fetal bovine serum (Hyclone), 1X non-essential amino acids (Life Technologies), 1X Glutamax (Life Technologies), 1000 U/ml leukemia inhibitory factor, 55 μM beta-mercaptoethanol (Sigma)) supplemented with 50 μg/ml ascorbic acid (Sigma) and 2 μg/ml doxycycline hyclate (Sigma).

extract_protocol:
60.000 cells were washed once with 100µl PBS and resuspended in 50µl lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.2% IGEPAL CA-630)
The suspension of nuclei was then centrifuged for 10min at 500g at 4°C, followed by the addition of 50µl transposition reaction mix (25µl TD buffer, 2.5µl Tn5 Transposase and 22.5µl Nuclease Free H2O) and incubation at 37°C for 30min. DNA was isolated using MinElute Kit (Qiagen). Libraries were amplified by PCR (13 cycles). After the PCR reaction, the library was selected for fragments between 100 and 1000bp with AmpureXP beads (Beckman Coulter). Libraries were purified with Qiaquick PCR (Qiagen) and integrity checked on a Bioanalyzer before sequencing.

treatment_protocol: Cells were trypsinized

tag: developmental stage

value: E13.5 embryo

value: Mouse Embryonic fibroblasts (MEFs)

tag: transfected with

value: siCtrl

tag: induced with

value: OSKM for 3 days

tag: time points

value: day 3


title: p53 wt rep1

source_name: p53 wt_PanIN cells

value: wild-type; KrasG12D;Pdx1-Cre;p53+/+


title: p53 wt rep2


title: Untransfected MEF cells induced to express OKSM for 6 days _replicate 1  [PAS-seq]

value: induced to express OKSM for 6 days


title: SAM24295060 mRPTEC 24hrs TWEAK NIK SMI1

city: South San Francisco

first: Mark

last: McCreary

state: California

address: 1 DNA Way, MS 93

department: Bioinformatics

institute: Genentech

description: SAM24295060 mRPTEC 24hrs TWEAK NIK SMI1

data_processing:
Processing and analysis of the RNA sequencing data were performed using the R programming language (http://www.rproject.org) along with packages from the Bioconductor project (http://bioconductor.org).
Raw RNA sequencing reads were processed using the HTSeqGenie Bioconductor package. Reads were aligned to the reference mouse genome sequence (National Center for Biotechnology Information build 37) using the Genomic ShortRead Nucleotide Alignment Program algorithm (Thomas D Wu, 2010).
Uniquely aligned read pairs that fell within exons were counted to estimate individual gene expression levels. For inclusion, genes were required to have >10 reads in 14 samples.
To calculate differential expression, we used the DESeq2 Bioconductor package (M. I. Love, 2014) that fits a negative binomial generalized linear model to determine the log-fold change and P value for differences between groups. The default library size estimation method was used to account for differences in sequencing depth. Data were analyzed using Expression Plot (B. A. Friedman, 2011) and plotted using Prism software. STATS, unpaired t-test with Welch’s correction. * p<0.05, ** p<0.005, *** p<0.0001.
Genome_build: GRCm37
Supplementary_files_format_and_content: Processed data files were created for each sample using the Bioconductor package, HTSeqGenie. The tab-delimited text files contain 4 columns: entrez gene IDs, gene exonic counts, gene length, and RPKM values

source_name: Kidney

growth_protocol: Mouse (C57BL/6) renal tubulointerstitial epithelial cells (ScienCell) were cultured in EpiCM-a medium with supplements as per vendor’s protocol.

extract_protocol:
RNA was prepared using RNEasy micro (Qiagen)
Total RNA (RNA integrity number >5; 250 ng) was put into the Illumina TruSeq RNA Sample Preparation Kit v2 protocol and run in conjunction with Biomek liquid handling platforms (Beckman Coulter Life Sciences, Brea, CA). RNA libraries were evaluated using the Agilent 2200 TapeStation HighSensitivity D1K Tape and quantitative polymerase chain reaction (qPCR) with the KAPA Library Quantification Kit for Illumina sequencing. Then 2 nM of library (12 samples per lane) was loaded for cluster generation and sequenced on the Illumina HiSeq 2000 Sequencing System at 250 base pairs read length plus index read. Reads that passed quality filters were deter- mined, and fastq files were generated by Illumina CASAVA v1.8

treatment_protocol: 5x10^6 cells were stimulated with recombinant mouse TWEAK (100 ng/mL, R&D Systems) for 6 and 24 hours in the presence or absence of NIK SMI1 (~IC90 = 3 µM) or vehicle (DMSO) with 3 replicates per treatment.

tag: inventory sample name

value: mRPTEC

tag: primary tissue

value: Kidney

tag: agent

value: TWEAK NIK SMI1

tag: tweak

value: Yes

tag: time point

tag: strain


title: SAM24295058 mRPTEC 24hrs TWEAK

description: SAM24295058 mRPTEC 24hrs TWEAK

value: TWEAK


title: SAM24295057 mRPTEC 24hrs TWEAK

description: SAM24295057 mRPTEC 24hrs TWEAK


title: SAM24295055 mRPTEC 24hr

description: SAM24295055 mRPTEC 24hr

value: Vehicle

value: No


title: SAM24295056 mRPTEC 24hrs TWEAK

description: SAM24295056 mRPTEC 24hrs TWEAK


title: SAM24295054 mRPTEC 24hr

description: SAM24295054 mRPTEC 24hr


title: SAM24295053 mRPTEC 24hr

description: SAM24295053 mRPTEC 24hr


title: SAM24295052 mRPTEC 6hrs TWEAK NIK SMI1

description: SAM24295052 mRPTEC 6hrs TWEAK NIK SMI1


title: SAM24295047 mRPTEC 6hrs TWEAK

description: SAM24295047 mRPTEC 6hrs TWEAK


title: SAM24295049 mRPTEC 6hrs TWEAK

description: SAM24295049 mRPTEC 6hrs TWEAK


title: SAM24295050 mRPTEC 6hrs TWEAK NIK SMI1

description: SAM24295050 mRPTEC 6hrs TWEAK NIK SMI1


title: SAM24295051 mRPTEC 6hrs TWEAK NIK SMI1

description: SAM24295051 mRPTEC 6hrs TWEAK NIK SMI1


title: SAM24295046 mRPTEC 6hrs

description: SAM24295046 mRPTEC 6hrs


title: SAM24295044 mRPTEC 6hrs

description: SAM24295044 mRPTEC 6hrs


title: SAM24295045 mRPTEC 6hrs

description: SAM24295045 mRPTEC 6hrs


title: MEF cells treated with luciferase siRNA and induced to express OKSM for 3 days _D3_replicate 1  [PAS-seq]


title: SAM24295059 mRPTEC 24hrs TWEAK NIK SMI1

description: SAM24295059 mRPTEC 24hrs TWEAK NIK SMI1


title: SAM24295061 mRPTEC 24hrs TWEAK NIK SMI1

description: SAM24295061 mRPTEC 24hrs TWEAK NIK SMI1


title: Mat-B_3

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

data_processing:
Quality checked using fastqc
Reads were aligned using HiSat
Reads counted using iGenomes annotation using Rsubread
Counts normalised and differentials found using DESeq
Genome_build: mm10
Supplementary_files_format_and_content: Two columns per file, the first giving gene name, and the second giving DESeq normlised expression levels.

source_name: Bone marrow B-cell progenitors

extract_protocol:
Total RNA was isolated from using RNAeasy MicroKit (Qiagen)
Libraries were made using Nugen Ovation RNA-Seq System kits and Nugen Ovation Ultralow System V2 kits.

treatment_protocol: B-cell populations were isolated from single cell suspension of BM cells by FACS

tag: age

value: 8 weeks

tag: genotype

value: hCD25-lambda5, Rag1-GFP


title: Imm-B_2


title: Mat-B_1


title: Mat-B_2


title: Imm-B


title: pre-B3_2


title: Mat-B

value: 9 weeks


title: Imm-B_1


title: pre-B3_1


title: pre-B2_2


title: pre-B2_1


title: pre-B1_3


title: pre-B1_1


title: SAM24295048 mRPTEC 6hrs TWEAK

description: SAM24295048 mRPTEC 6hrs TWEAK


title: pre-B2


title: pro-B2_2

value: CD19+Igk-Igl-IgM-IgD-RaghiLambda5hi big


title: pre-B1_2


title: pre-B1


title: pro-B2_1


title: undifferentiated hESC Ctrl_P24

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

country: Germany

institute: Ludwig-Maximilians University Munich

data_processing:
Raw fastq data was demultiplexed according to the i7 Index using deML (Renaud et al., 2015)
Paired fastq-files were processed to count tables using the zUMIs pipeline (Parekh et al., 2017)
Reads were mapped with STAR (Dobin et al., 2015) to the human genome (hg38) and gene expression quantified with ENSEMBL gene models (GRCh38.84)
Genome_build: hg38
Supplementary_files_format_and_content: gene- and cell-wise UMI count table

organism: Homo sapiens

source_name: human embryonic stem cell line H9

growth_protocol: H9 cell line was grown on Geltrex-coated plates in mTESR1 medium

extract_protocol:
Single-cells were FACS-sorted directly into 384-well plates containing 5µl lysis buffer (1/500 dilution of Phusion HF buffer)
Libraries were constructed using the SCRB-seq protocol (Soumillon et al., 2014) as previously described (Ziegenhain et al., 2017)

treatment_protocol: For trophoblast differentiation, cells were seeded at 100% confluency on Matrigel-coated plates containing KSR-based differentiation medium and 50 ng/ml BMP4. During the time course, medium was changed every 24 hours.

tag: cell line


title: pro-B1


title: pro-B2


title: pro-B1_1


title: pro-B1_2


title: undifferentiated hESC Ctrl_P23


title: undifferentiated hESC Ctrl_P21


title: undifferentiated hESC Ctrl_P22


title: undifferentiated hESC Ctrl_P20


title: undifferentiated hESC Ctrl_P18


title: undifferentiated hESC Ctrl_P17


title: pre-B3


title: undifferentiated hESC Ctrl_P19


title: undifferentiated hESC Ctrl_P14


title: undifferentiated hESC Ctrl_P13


title: undifferentiated hESC Ctrl_P11


title: undifferentiated hESC Ctrl_P12


title: undifferentiated hESC Ctrl_P16


title: undifferentiated hESC Ctrl_P10


title: undifferentiated hESC Ctrl_P15


title: undifferentiated hESC Ctrl_P8


title: undifferentiated hESC Ctrl_P7


title: undifferentiated hESC Ctrl_P6


title: undifferentiated hESC Ctrl_P1


title: undifferentiated hESC Ctrl_P5


title: undifferentiated hESC Ctrl_P2


title: undifferentiated hESC Ctrl_O24


title: undifferentiated hESC Ctrl_P4


title: undifferentiated hESC Ctrl_P9


title: undifferentiated hESC Ctrl_P3


title: undifferentiated hESC Ctrl_O21


title: undifferentiated hESC Ctrl_O22


title: undifferentiated hESC Ctrl_O20


title: undifferentiated hESC Ctrl_O19


title: undifferentiated hESC Ctrl_O16


title: undifferentiated hESC Ctrl_O17


title: undifferentiated hESC Ctrl_O14


title: undifferentiated hESC Ctrl_O15


title: undifferentiated hESC Ctrl_O10


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title: undifferentiated hESC Ctrl_O13


title: undifferentiated hESC Ctrl_O7


title: undifferentiated hESC Ctrl_O12


title: undifferentiated hESC Ctrl_O8


title: undifferentiated hESC Ctrl_O5


title: undifferentiated hESC Ctrl_O4


title: undifferentiated hESC Ctrl_O9


title: undifferentiated hESC Ctrl_O2


title: undifferentiated hESC Ctrl_N23


title: undifferentiated hESC Ctrl_N22


title: undifferentiated hESC Ctrl_N19


title: undifferentiated hESC Ctrl_O1


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title: undifferentiated hESC Ctrl_O18


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title: undifferentiated hESC Ctrl_N13


title: undifferentiated hESC Ctrl_O6


title: undifferentiated hESC Ctrl_N10


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title: undifferentiated hESC Ctrl_M24


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title: undifferentiated hESC Ctrl_F5


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title: undifferentiated hESC Ctrl_F14


title: undifferentiated hESC Ctrl_F4


title: undifferentiated hESC Ctrl_E20


title: undifferentiated hESC Ctrl_E24


title: undifferentiated hESC Ctrl_E18


title: undifferentiated hESC Ctrl_E22


title: undifferentiated hESC Ctrl_E19


title: undifferentiated hESC Ctrl_E21


title: undifferentiated hESC Ctrl_E17


title: undifferentiated hESC Ctrl_F9


title: undifferentiated hESC Ctrl_F12


title: undifferentiated hESC Ctrl_E16


title: undifferentiated hESC Ctrl_E14


title: undifferentiated hESC Ctrl_E23


title: undifferentiated hESC Ctrl_E13


title: undifferentiated hESC Ctrl_E9


title: undifferentiated hESC Ctrl_E12


title: undifferentiated hESC Ctrl_E2


title: undifferentiated hESC Ctrl_E10


title: undifferentiated hESC Ctrl_E11


title: undifferentiated hESC Ctrl_E8


title: undifferentiated hESC Ctrl_E4


title: undifferentiated hESC Ctrl_E6


title: undifferentiated hESC Ctrl_E7


title: undifferentiated hESC Ctrl_E5


title: undifferentiated hESC Ctrl_D24


title: undifferentiated hESC Ctrl_D22


title: undifferentiated hESC Ctrl_D23


title: Mouse wild type erythroid cells CTCF ChIP biological replicate 3

city: Oxford

first: Jelena

middle: M

last: Telenius

address: MRC Weatherall Institute of Molecular Medicine University of Oxford John Radcliffe Hospital Headington

department: Weatherall Institute of Molecular Medicine (WIMM)

country: United Kingdom

institute: Oxford University

data_processing:
All analysis was done using NGseqBasic pipeline, using default parameters ( http://userweb.molbiol.ox.ac.uk/public/telenius/NGseqBasicManual/external/ )
Including the following steps:
Mapping : bowtie -m 2 --maxIns 350
For un-mapping reads : trim_galore -- length 10, flash -m 9 -x 0.125
Combining trimmed+flashed and originally mapped reads, mapping again with bowtie -m 2 --maxIns 350
Removing read pairs overlapping Blacklisted regions
Removing duplicates : samtools rmdup
Reconstructing sequenced fragments from R1+R2 read pairs ( bedtools bedpe | cut -f 1,2,6) - for visualisation
Pileup of fragments (bedtools genomecov -counts)
Generating bigwig tracks (ucsctools bedGraphToBigWig)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig of Reconstructed sequenced fragments

source_name: Ter119+ Erythroid cells

growth_protocol: C57BL/6 mice were treated with phenylhydrazine (three doses of 40 mg/g body weight given 12 hours apart; mice were sacrificed after five days)

extract_protocol:
A single cell suspension was made by gently dissociating the spleen of a phenyhydrazine treated mouse and passing it through a 70um filter. Ter119 selection was performed by staining the cells with phycoerythrin conjugated anti-ter119 antibodies (BD biosciences). The cells were subsequently washed and then incubated with MACS anti-phycoerythrin beads. Cells were then separated using an auto-MACS (Miltenyi Biotec).
NEBnext ultra library prep kit

treatment_protocol: Ter119+ cells were isolated from mouse spleens

value: Phenylhydrazine treated spleen

tag: antibody

value: anti-CTCF, Millipore 07-729


title: undifferentiated hESC Ctrl_E1


title: undifferentiated hESC Ctrl_D21


title: undifferentiated hESC Ctrl_D17


title: undifferentiated hESC Ctrl_D18


title: undifferentiated hESC Ctrl_D20


title: undifferentiated hESC Ctrl_D19


title: undifferentiated hESC Ctrl_D16


title: undifferentiated hESC Ctrl_E15


title: undifferentiated hESC Ctrl_D14


title: undifferentiated hESC Ctrl_D15


title: undifferentiated hESC Ctrl_D11


title: undifferentiated hESC Ctrl_D12


title: undifferentiated hESC Ctrl_E3


title: undifferentiated hESC Ctrl_D13


title: undifferentiated hESC Ctrl_D10


title: undifferentiated hESC Ctrl_D4


title: Warm_TRPM2-KD_case

city: Beijing

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description:
1000ng
Warm-TRPM2-sh1_case_RPKM

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. (Reads containing more than 5 adapter-polluted bases were regarded as adaptor-polluted reads and would be filtered out; 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: neural stem cells from brain

extract_protocol:
The in utero electroporation was employed to introduce the TRPM2 knockdown or control plasmids into the E13 embryonic cortex. and then the GFP+ neural progenitor cell isolated from E15 mice by using FACS. RNA utilized for global transcriptome analysis were extracted from these GFP+ neural stem cells
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: stain

value: ICR

tag: development stage

tag: genotype/variation


title: undifferentiated hESC Ctrl_D1


title: undifferentiated hESC Ctrl_C24


title: undifferentiated hESC Ctrl_D7


title: undifferentiated hESC Ctrl_D3


title: undifferentiated hESC Ctrl_D5


title: undifferentiated hESC Ctrl_D6


title: undifferentiated hESC Ctrl_C22


title: undifferentiated hESC Ctrl_D2


title: Warm_Control_ctrl

description:
1000ng
Warm-Control_ctrl_RPKM

value: Ctrl


title: undifferentiated hESC Ctrl_C20


title: undifferentiated hESC Ctrl_C23


title: undifferentiated hESC Ctrl_D9


title: undifferentiated hESC Ctrl_C21


title: undifferentiated hESC Ctrl_C18


title: undifferentiated hESC Ctrl_C17


title: undifferentiated hESC Ctrl_C19


title: undifferentiated hESC Ctrl_C16


title: AntNPC_PE_LHX5null_3

city: Koeln

first: Milos

last: Nikolic

state: Nordrhein-Westfalen

address: Robert Koch Str. 21

institute: Center for Molecular Medicine Cologne

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and read statistics were obtained with SAMtools
Reads were mapped to the mouse reference assembly, version GRCm38, using TopHat2
Read count means, fold-change (FC) and p-values were calculated with DEseq2
gene expression for the individual samples was calculated with Cufflinks as FPKMs.
Genome_build: mm10
Supplementary_files_format_and_content: Txt file containing Read count means, fold-change (FC) and p-values  calculated with DEseq2 and FPKMs calculated with Cufflinks for each ENSEMBL mouse gene.

molecule: polyA RNA

source_name: AntNPC (anterior neural progenitors derived from mESC)

growth_protocol: WT (E14) mESC and mESC lines with the PE Lhx5(-109) deletion were cultured on gelatin-coated plates using Knock-out DMEM (KO-DMEM, Life Technologies) supplemented with 15% FBS (Life Technologies) and LIF. These mESC lines were differentiated into AntNPC according to a previously described protocol (Gouti et al., 2014), with slight modifications. Briefly, mESC were plated at a density of 10000 cells/cm2 on gelatin-coated plates and grown for three days in N2B27 medium supplemented with 10 ng/ml bFgf (Life Technologies) and without serum or LIF (Advanced Dulbecco’s Modified Eagle Medium F12 (Life Technologies) and Neurobasal medium (Life Technologies) (1:1), supplemented with 1x N2 (Life Technologies), 1x B27 (Life Technologies), 2 mM L-glutamine (Life Technologies), 40 mg/ml BSA (Life Technologies), 0.1 mM 2-mercaptoethanol (Life Technologies)). Subsequently, cells were grown for another two days in N2B27 medium without bFgf (D3–D5).  Moreover, to improve the homogeneity of the differentiation, from D2-D5 the N2B27 medium was also supplemented with 5μM Xav939 (Sigma), a potent WNT inhibitor (Matsuda and Kondoh, 2014).

extract_protocol:
Total RNA was isolated using Tripure reagent according to the manufacturer’s instructions (Roche). Libraries were prepared with the RNA sample preparation kit (TruSeq v2; Ilumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: To generate the PE Lhx5(-109) deletion in mESC, pairs of gRNAs were selected flanking the PE according to the instructions of the genome engineering toolbox (http://www.genome-engineering.org/crispr/). For each selected sgRNA, two oligonucleotides were synthesized, annealed and phosphorylated. The CRISPR-Cas9 expression vector (pX330-U6-Chimeric_BB-CBh-hSpCas9 (42230, Addgene) or pX330-hCas9-long-chimeric-grna-g2p (provided by Leo Kurian's laboratory)) was digested with BbsI (R0539L, NEB) and gel or column purified. Pairs of annealed oligos and the digested vector were ligated overnight at 16°C using T4 ligase (NEB). Following transformation, the gRNA-Cas9 expression vectors were purified and sequenced to confirm that the gRNAs were correctly cloned.   E14 mESC were transfected with a pair of gRNAs-Cas9 expressing vectors specific forthe PE Lhx5(-109) using X-tremeGENE HP DNA transfection reagent (Roche). After 16 hours, puromycin selection was performed for 48 hours. Subsequently, surviving cells were isolated in 96-well plates by serial dilution and, following expansion, clones with the desired deletions were identified by PCR . 20-40 mESC clones were screened for each PE candidate. Finally, the intended PE deletions were confirmed by Sanger sequencing in all the clonal mESC lines selected for downstream characterization.

tag: cell type

tag: treatment

value: mESC differentiation into AntNPC


title: AntNPC_PE_LHX5null_1

value: AntNPC (anterior neural progenitors derived from mESC)


title: AntNPC_PE_LHX5null_4


title: AntNPC_PE_LHX5null_2


title: undifferentiated hESC Ctrl_C15


title: undifferentiated hESC Ctrl_D8


title: AntNPC_WT_4

value: WT


title: AntNPC_WT_3


title: undifferentiated hESC Ctrl_C14


title: Mouse wild type erythroid cells: sonication INPUT, sequenced with the Rad21 ChIP, as its input sample

tag: tissue


title: undifferentiated hESC Ctrl_C13


title: AntNPC_WT_1


title: undifferentiated hESC Ctrl_C10


title: undifferentiated hESC Ctrl_C12


title: AntNPC_WT_2


title: undifferentiated hESC Ctrl_C11


title: NAP1l3_3

city: Stockholm

first: David

last: Brodin

address: Hälsovägen 7-9

department: Department of Biosciences and Nutrition

institute: Karolinska Institute

data_processing:
Illumina bcl2fastq2 Conversion Software v2.19.0 software was used for basecalling and demultiplexing
Sequenced reads were mapped to Ensembl Homo_sapiens.GRCh38.dna.primary_assembly using STAR v2.5.2b
Mapped reads were summarized to gene counts using featureCounts v1.5.1 software with Ensembl Homo_sapiens.GRCh38.90 gene reference
Counts were normalized using DESeq2 v1.14.1
Genome_build: hg38/GRCh38
Supplementary_files_format_and_content: matrix of normalized counts

source_name: NAP1l3, umbilical cord blood cells

growth_protocol: Umbilical cord blood cells were propagated for 72h post transduction before harvesting of total RNA in SFEMII media supplemented with hIL-3, hIL6, TPO, FLT3l, SCF.

extract_protocol:
RNA extraction was done by using Qiagen micro RNAeasy extraction kit.
TotalScriptTM RNA-seq kit (Epicentre, Madison, WI) was used to prepare strand specific RNA libraries according to the manufacturer’s instructions.

treatment_protocol: UCBs transduced with lentiviral shRNA virus agaist Nap1l3 and SC control and cells were harvested 72h after transduction

value: UCBs

tag: hematopoietic lineage markers

tag: cell selection

value: FACS sorted cells

tag: vector type

value: shRNA targeting NAP1L3

value: NAP1L3 Knockdown


title: undifferentiated hESC Ctrl_C6


title: undifferentiated hESC Ctrl_B16


title: undifferentiated hESC Ctrl_B22


title: undifferentiated hESC Ctrl_C7


title: undifferentiated hESC Ctrl_B20


title: undifferentiated hESC Ctrl_C1


title: NAP1l3_2


title: undifferentiated hESC Ctrl_B24


title: undifferentiated hESC Ctrl_B17


title: undifferentiated hESC Ctrl_C8


title: undifferentiated hESC Ctrl_B18


title: undifferentiated hESC Ctrl_B19


title: undifferentiated hESC Ctrl_C4


title: undifferentiated hESC Ctrl_B23


title: undifferentiated hESC Ctrl_C2


title: undifferentiated hESC Ctrl_C9


title: undifferentiated hESC Ctrl_C3


title: undifferentiated hESC Ctrl_C5


title: NAP1l3_1


title: undifferentiated hESC Ctrl_B15


title: undifferentiated hESC Ctrl_B14


title: undifferentiated hESC Ctrl_B21


title: undifferentiated hESC Ctrl_B11


title: undifferentiated hESC Ctrl_B12


title: EXO.3

city: Tokyo

first: Rulan

last: Bai

address: 1-1-1 Yayoi, Bunkyouku

country: Japan

institute: The University of Tokyo

data_processing:
The Illumina Hiseq generates raw images utilizing HCS (HiSeq Control Software v2.2) for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq (v1.8.4). Adapters are not trimmed away from the reads.
Trimmed sequences were analyzed on the basis of the TopHat/Cufflinks pipeline based on the porcine genome and reference annotations obtained from Ensembl genome browser (https://www.ensembl.org).
Differential and significant gene expression analysis was performed with the use of gene-level FPKM (fragments per kilo- base of gene locus summarized mRNA per million reads) expression levels. Genes were selected with the criteria of an absolute expression level >1 FPKM in normal medium or exosome-treated samples.
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for all samples

organism: Sus scrofa

source_name: seminal fluid exosome treatment group

growth_protocol: Porcine uteri were obtained from  healthy animals in a local slaughterhouse within 1 h after death. The organs were washed immediately with PBS, and cut into pieces (approximate length 1 cm, width 1cm and height 0.3 cm), then put into 50 ml tube with 0.76% EDTA・4Na (pH=7.4) solution and incubated at 37ºC for 75 min. Transferred the suspension into a new 15 ml tube, and centrifuged at 200 x g for 8 min. Re-suspend the pellet with Hanks’ balanced salt solution (HBSS) supplemented with 100 IU/ml penicillin and 100 g/ml streptomycin, 0.1% collagenase I , 0.01% DNase I (Type IV) , and incubated at 37ºC for 45 min. Epithelial cells were collected after washed 3 times by centrifugation (5 min at 200 x g) with Dulbecco’s modified Eagle’s medium, then cultured on collagen type IA-coated six-well plates in DMEM/F12 (1:1) medium supplemented with 10% FBS, 2 mM glutamine, antibiotic/antimycotic solution, and maintained at 37°C in air with 5% CO2.

extract_protocol:
Rneasy Mini Kit extraction of total RNA according to the manufactuture's instractions
TruSeq Stranded mRNA Sample Preparation Guide, Part # 15031047 Rev. E

treatment_protocol: Exosomes were isolated from 1 ml of sperm-rich fraction of porcine seminal fluid (SF) (n = 3) by adding 200 μl exosome precipitation solution (Exo-Quick-TC, System Biosciences, Mountain View, CA). The SFs with Exo-Quick-TC were incubated overnight at 4°C and then centrifuged at 1,500 x g for 30 min at 4°C to pellet exosomes. Exosomes were suspended and their protein concentration adjusted in PBS (1 μg/μl), treated endometrial epithelial cells with 10  μg per well (6-well dish) for 48h at 37°C in air with 5% CO2.

value: uterus

value: endometrial epithelial cells

tag: passage

tag: culture type

value: primary culture


title: undifferentiated hESC Ctrl_B13


title: SC_1

source_name: SC, umbilical cord blood cells

value: Negative control vector

value: control


title: undifferentiated hESC Ctrl_B7


title: undifferentiated hESC Ctrl_B8


title: CTRL.2

source_name: control group


title: undifferentiated hESC Ctrl_A22


title: undifferentiated hESC Ctrl_B3


title: undifferentiated hESC Ctrl_B4


title: SC_2


title: CTRL.1


title: EXO.2


title: undifferentiated hESC Ctrl_B9


title: undifferentiated hESC Ctrl_A23


title: undifferentiated hESC Ctrl_B2


title: EXO.1


title: SC_3


title: CTRL.3


title: undifferentiated hESC Ctrl_B1


title: undifferentiated hESC Ctrl_B6


title: undifferentiated hESC Ctrl_B5


title: undifferentiated hESC Ctrl_A17


title: undifferentiated hESC Ctrl_A16


title: undifferentiated hESC Ctrl_A18


title: undifferentiated hESC Ctrl_A20


title: undifferentiated hESC Ctrl_A19


title: undifferentiated hESC Ctrl_A24


title: undifferentiated hESC Ctrl_A12


title: undifferentiated hESC Ctrl_A15


title: undifferentiated hESC Ctrl_B10


title: undifferentiated hESC Ctrl_A21


title: undifferentiated hESC Ctrl_A10


title: undifferentiated hESC Ctrl_A8


title: undifferentiated hESC Ctrl_A11


title: undifferentiated hESC Ctrl_A5


title: undifferentiated hESC Ctrl_A7


title: undifferentiated hESC Ctrl_A9


title: APA-positive trophoblast progenitors Apa_P24


title: undifferentiated hESC Ctrl_A4


title: undifferentiated hESC Ctrl_A6


title: undifferentiated hESC Ctrl_A2


title: undifferentiated hESC Ctrl_A3


title: APA-positive trophoblast progenitors Apa_P20


title: APA-positive trophoblast progenitors Apa_P16


title: APA-positive trophoblast progenitors Apa_P22


title: APA-positive trophoblast progenitors Apa_P13


title: APA-positive trophoblast progenitors Apa_P23


title: undifferentiated hESC Ctrl_A1


title: APA-positive trophoblast progenitors Apa_P18


title: APA-positive trophoblast progenitors Apa_P17


title: undifferentiated hESC Ctrl_A13


title: APA-positive trophoblast progenitors Apa_P12


title: APA-positive trophoblast progenitors Apa_P19


title: undifferentiated hESC Ctrl_A14


title: APA-positive trophoblast progenitors Apa_P21


title: APA-positive trophoblast progenitors Apa_P15


title: APA-positive trophoblast progenitors Apa_P14


title: APA-positive trophoblast progenitors Apa_P9


title: APA-positive trophoblast progenitors Apa_P10


title: APA-positive trophoblast progenitors Apa_P8


title: APA-positive trophoblast progenitors Apa_P11


title: APA-positive trophoblast progenitors Apa_P7


title: APA-positive trophoblast progenitors Apa_P6


title: APA-positive trophoblast progenitors Apa_P5


title: APA-positive trophoblast progenitors Apa_P3


title: APA-positive trophoblast progenitors Apa_P2


title: APA-positive trophoblast progenitors Apa_P1


title: APA-positive trophoblast progenitors Apa_O24


title: APA-positive trophoblast progenitors Apa_P4


title: APA-positive trophoblast progenitors Apa_O22


title: APA-positive trophoblast progenitors Apa_O23


title: APA-positive trophoblast progenitors Apa_O16


title: APA-positive trophoblast progenitors Apa_O17


title: APA-positive trophoblast progenitors Apa_O14


title: APA-positive trophoblast progenitors Apa_O12


title: APA-positive trophoblast progenitors Apa_O20


title: APA-positive trophoblast progenitors Apa_O9


title: APA-positive trophoblast progenitors Apa_O18


title: APA-positive trophoblast progenitors Apa_O19


title: APA-positive trophoblast progenitors Apa_O21


title: APA-positive trophoblast progenitors Apa_O15


title: APA-positive trophoblast progenitors Apa_O13


title: APA-positive trophoblast progenitors Apa_O7


title: APA-positive trophoblast progenitors Apa_O8


title: APA-positive trophoblast progenitors Apa_O6


title: APA-positive trophoblast progenitors Apa_O5


title: APA-positive trophoblast progenitors Apa_O4


title: APA-positive trophoblast progenitors Apa_O3


title: APA-positive trophoblast progenitors Apa_O11


title: APA-positive trophoblast progenitors Apa_O2


title: APA-positive trophoblast progenitors Apa_N24


title: APA-positive trophoblast progenitors Apa_N21


title: APA-positive trophoblast progenitors Apa_O10


title: APA-positive trophoblast progenitors Apa_O1


title: APA-positive trophoblast progenitors Apa_N20


title: APA-positive trophoblast progenitors Apa_N18


title: APA-positive trophoblast progenitors Apa_N19


title: APA-positive trophoblast progenitors Apa_N17


title: APA-positive trophoblast progenitors Apa_N14


title: APA-positive trophoblast progenitors Apa_N16


title: APA-positive trophoblast progenitors Apa_N13


title: APA-positive trophoblast progenitors Apa_N11


title: APA-positive trophoblast progenitors Apa_N10


title: APA-positive trophoblast progenitors Apa_N23


title: APA-positive trophoblast progenitors Apa_N22


title: APA-positive trophoblast progenitors Apa_N8


title: APA-positive trophoblast progenitors Apa_N5


title: APA-positive trophoblast progenitors Apa_N9


title: APA-positive trophoblast progenitors Apa_N4


title: APA-positive trophoblast progenitors Apa_N3


title: APA-positive trophoblast progenitors Apa_N12


title: APA-positive trophoblast progenitors Apa_N2


title: APA-positive trophoblast progenitors Apa_N15


title: APA-positive trophoblast progenitors Apa_M24


title: APA-positive trophoblast progenitors Apa_N1


title: APA-positive trophoblast progenitors Apa_M23


title: APA-positive trophoblast progenitors Apa_M21


title: APA-positive trophoblast progenitors Apa_M19


title: APA-positive trophoblast progenitors Apa_M17


title: APA-positive trophoblast progenitors Apa_M16


title: APA-positive trophoblast progenitors Apa_M18


title: APA-positive trophoblast progenitors Apa_M15


title: APA-positive trophoblast progenitors Apa_N7


title: APA-positive trophoblast progenitors Apa_M14


title: APA-positive trophoblast progenitors Apa_N6


title: APA-positive trophoblast progenitors Apa_M11


title: APA-positive trophoblast progenitors Apa_M5


title: APA-positive trophoblast progenitors Apa_M7


title: APA-positive trophoblast progenitors Apa_M2


title: APA-positive trophoblast progenitors Apa_M10


title: APA-positive trophoblast progenitors Apa_L22


title: APA-positive trophoblast progenitors Apa_M22


title: APA-positive trophoblast progenitors Apa_L24


title: APA-positive trophoblast progenitors Apa_M9


title: APA-positive trophoblast progenitors Apa_L23


title: APA-positive trophoblast progenitors Apa_M4


title: APA-positive trophoblast progenitors Apa_M8


title: APA-positive trophoblast progenitors Apa_M3


title: APA-positive trophoblast progenitors Apa_M1


title: APA-positive trophoblast progenitors Apa_L20


title: APA-positive trophoblast progenitors Apa_L19


title: APA-positive trophoblast progenitors Apa_M20


title: APA-positive trophoblast progenitors Apa_L18


title: APA-positive trophoblast progenitors Apa_L17


title: APA-positive trophoblast progenitors Apa_L14


title: APA-positive trophoblast progenitors Apa_M13


title: APA-positive trophoblast progenitors Apa_M12


title: APA-positive trophoblast progenitors Apa_L15


title: APA-positive trophoblast progenitors Apa_L13


title: APA-positive trophoblast progenitors Apa_M6


title: APA-positive trophoblast progenitors Apa_L12


title: APA-positive trophoblast progenitors Apa_L21


title: APA-positive trophoblast progenitors Apa_L10


title: APA-positive trophoblast progenitors Apa_L9


title: APA-positive trophoblast progenitors Apa_L8


title: APA-positive trophoblast progenitors Apa_L7


title: APA-positive trophoblast progenitors Apa_L2


title: APA-positive trophoblast progenitors Apa_L4


title: APA-positive trophoblast progenitors Apa_K22


title: APA-positive trophoblast progenitors Apa_K21


title: APA-positive trophoblast progenitors Apa_L3


title: APA-positive trophoblast progenitors Apa_K23


title: APA-positive trophoblast progenitors Apa_L6


title: APA-positive trophoblast progenitors Apa_K24


title: APA-positive trophoblast progenitors Apa_L16


title: APA-positive trophoblast progenitors Apa_K18


title: APA-positive trophoblast progenitors Apa_K19


title: APA-positive trophoblast progenitors Apa_K17


title: APA-positive trophoblast progenitors Apa_L11


title: APA-positive trophoblast progenitors Apa_K15


title: APA-positive trophoblast progenitors Apa_K14


title: APA-positive trophoblast progenitors Apa_K13


title: APA-positive trophoblast progenitors Apa_K12


title: APA-positive trophoblast progenitors Apa_K10


title: APA-positive trophoblast progenitors Apa_K9


title: APA-positive trophoblast progenitors Apa_K8


title: APA-positive trophoblast progenitors Apa_K7


title: APA-positive trophoblast progenitors Apa_L1


title: APA-positive trophoblast progenitors Apa_L5


title: APA-positive trophoblast progenitors Apa_K6


title: APA-positive trophoblast progenitors Apa_K20


title: APA-positive trophoblast progenitors Apa_K3


title: APA-positive trophoblast progenitors Apa_K4


title: APA-positive trophoblast progenitors Apa_K2


title: APA-positive trophoblast progenitors Apa_K1


title: APA-positive trophoblast progenitors Apa_J24


title: APA-positive trophoblast progenitors Apa_J21


title: APA-positive trophoblast progenitors Apa_J22


title: APA-positive trophoblast progenitors Apa_K16


title: APA-positive trophoblast progenitors Apa_K5


title: APA-positive trophoblast progenitors Apa_J19


title: APA-positive trophoblast progenitors Apa_J20


title: APA-positive trophoblast progenitors Apa_J18


title: APA-positive trophoblast progenitors Apa_J23


title: APA-positive trophoblast progenitors Apa_J17


title: APA-positive trophoblast progenitors Apa_J16


title: APA-positive trophoblast progenitors Apa_J15


title: APA-positive trophoblast progenitors Apa_J13


title: APA-positive trophoblast progenitors Apa_J14


title: APA-positive trophoblast progenitors Apa_J12


title: APA-positive trophoblast progenitors Apa_K11


title: APA-positive trophoblast progenitors Apa_J10


title: APA-positive trophoblast progenitors Apa_J8


title: APA-positive trophoblast progenitors Apa_J11


title: APA-positive trophoblast progenitors Apa_J7


title: APA-positive trophoblast progenitors Apa_J4


title: APA-positive trophoblast progenitors Apa_J3


title: APA-positive trophoblast progenitors Apa_J2


title: APA-positive trophoblast progenitors Apa_I22


title: APA-positive trophoblast progenitors Apa_I23


title: APA-positive trophoblast progenitors Apa_I21


title: APA-positive trophoblast progenitors Apa_I16


title: APA-positive trophoblast progenitors Apa_I18


title: APA-positive trophoblast progenitors Apa_I19


title: APA-positive trophoblast progenitors Apa_I20


title: APA-positive trophoblast progenitors Apa_I11


title: APA-positive trophoblast progenitors Apa_I12


title: APA-positive trophoblast progenitors Apa_I13


title: APA-positive trophoblast progenitors Apa_I9


title: APA-positive trophoblast progenitors Apa_I8


title: APA-positive trophoblast progenitors Apa_I14


title: APA-positive trophoblast progenitors Apa_I6


title: APA-positive trophoblast progenitors Apa_I7


title: APA-positive trophoblast progenitors Apa_I5


title: APA-positive trophoblast progenitors Apa_I10


title: APA-positive trophoblast progenitors Apa_I4


title: APA-positive trophoblast progenitors Apa_I3


title: APA-positive trophoblast progenitors Apa_I2


title: APA-positive trophoblast progenitors Apa_I24


title: APA-positive trophoblast progenitors Apa_J9


title: APA-positive trophoblast progenitors Apa_J1


title: APA-positive trophoblast progenitors Apa_I17


title: APA-positive trophoblast progenitors Apa_J5


title: APA-positive trophoblast progenitors Apa_H23


title: APA-positive trophoblast progenitors Apa_H24


title: APA-positive trophoblast progenitors Apa_J6


title: APA-positive trophoblast progenitors Apa_I15


title: APA-positive trophoblast progenitors Apa_H18


title: APA-positive trophoblast progenitors Apa_H21


title: APA-positive trophoblast progenitors Apa_H20


title: APA-positive trophoblast progenitors Apa_H17


title: APA-positive trophoblast progenitors Apa_H16


title: APA-positive trophoblast progenitors Apa_H15


title: APA-positive trophoblast progenitors Apa_H13


title: APA-positive trophoblast progenitors Apa_H14


title: APA-positive trophoblast progenitors Apa_I1


title: APA-positive trophoblast progenitors Apa_H9


title: APA-positive trophoblast progenitors Apa_H10


title: APA-positive trophoblast progenitors Apa_H11


title: APA-positive trophoblast progenitors Apa_H6


title: APA-positive trophoblast progenitors Apa_H7


title: APA-positive trophoblast progenitors Apa_H5


title: APA-positive trophoblast progenitors Apa_H8


title: APA-positive trophoblast progenitors Apa_H4


title: APA-positive trophoblast progenitors Apa_H3


title: APA-positive trophoblast progenitors Apa_H2


title: APA-positive trophoblast progenitors Apa_G24


title: APA-positive trophoblast progenitors Apa_H1


title: APA-positive trophoblast progenitors Apa_H22


title: APA-positive trophoblast progenitors Apa_H19


title: APA-positive trophoblast progenitors Apa_G20


title: APA-positive trophoblast progenitors Apa_G23


title: APA-positive trophoblast progenitors Apa_G22


title: APA-positive trophoblast progenitors Apa_G17


title: APA-positive trophoblast progenitors Apa_G21


title: APA-positive trophoblast progenitors Apa_G19


title: APA-positive trophoblast progenitors Apa_G15


title: APA-positive trophoblast progenitors Apa_G14


title: APA-positive trophoblast progenitors Apa_G18


title: APA-positive trophoblast progenitors Apa_G16


title: APA-positive trophoblast progenitors Apa_G13


title: APA-positive trophoblast progenitors Apa_H12


title: APA-positive trophoblast progenitors Apa_G12


title: APA-positive trophoblast progenitors Apa_G11


title: APA-positive trophoblast progenitors Apa_G10


title: APA-positive trophoblast progenitors Apa_G9


title: APA-positive trophoblast progenitors Apa_G6


title: APA-positive trophoblast progenitors Apa_G2


title: APA-positive trophoblast progenitors Apa_G5


title: APA-positive trophoblast progenitors Apa_G3


title: APA-positive trophoblast progenitors Apa_G8


title: APA-positive trophoblast progenitors Apa_G7


title: APA-positive trophoblast progenitors Apa_G4


title: APA-positive trophoblast progenitors Apa_G1


title: APA-positive trophoblast progenitors Apa_F23


title: APA-positive trophoblast progenitors Apa_F22


title: APA-positive trophoblast progenitors Apa_F19


title: APA-positive trophoblast progenitors Apa_F21


title: APA-positive trophoblast progenitors Apa_F24


title: APA-positive trophoblast progenitors Apa_F17


title: APA-positive trophoblast progenitors Apa_F15


title: APA-positive trophoblast progenitors Apa_F18


title: APA-positive trophoblast progenitors Apa_F13


title: APA-positive trophoblast progenitors Apa_F20


title: APA-positive trophoblast progenitors Apa_F11


title: APA-positive trophoblast progenitors Apa_F16


title: APA-positive trophoblast progenitors Apa_F10


title: APA-positive trophoblast progenitors Apa_F12


title: APA-positive trophoblast progenitors Apa_F14


title: APA-positive trophoblast progenitors Apa_F7


title: APA-positive trophoblast progenitors Apa_F9


title: APA-positive trophoblast progenitors Apa_F3


title: APA-positive trophoblast progenitors Apa_F6


title: APA-positive trophoblast progenitors Apa_F4


title: APA-positive trophoblast progenitors Apa_F2


title: APA-positive trophoblast progenitors Apa_E23


title: APA-positive trophoblast progenitors Apa_E24


title: APA-positive trophoblast progenitors Apa_E20


title: APA-positive trophoblast progenitors Apa_E21


title: APA-positive trophoblast progenitors Apa_E22


title: APA-positive trophoblast progenitors Apa_E19


title: APA-positive trophoblast progenitors Apa_F1


title: APA-positive trophoblast progenitors Apa_E17


title: APA-positive trophoblast progenitors Apa_E16


title: APA-positive trophoblast progenitors Apa_E14


title: APA-positive trophoblast progenitors Apa_F8


title: APA-positive trophoblast progenitors Apa_E18


title: APA-positive trophoblast progenitors Apa_E15


title: APA-positive trophoblast progenitors Apa_E13


title: APA-positive trophoblast progenitors Apa_E12


title: APA-positive trophoblast progenitors Apa_E11


title: APA-positive trophoblast progenitors Apa_E10


title: APA-positive trophoblast progenitors Apa_F5


title: APA-positive trophoblast progenitors Apa_E8


title: APA-positive trophoblast progenitors Apa_E4


title: APA-positive trophoblast progenitors Apa_D22


title: APA-positive trophoblast progenitors Apa_E3


title: APA-positive trophoblast progenitors Apa_E7


title: APA-positive trophoblast progenitors Apa_D19


title: APA-positive trophoblast progenitors Apa_E1


title: APA-positive trophoblast progenitors Apa_D20


title: APA-positive trophoblast progenitors Apa_E5


title: APA-positive trophoblast progenitors Apa_D18


title: APA-positive trophoblast progenitors Apa_E6


title: APA-positive trophoblast progenitors Apa_E9


title: APA-positive trophoblast progenitors Apa_D21


title: APA-positive trophoblast progenitors Apa_E2


title: RPMI-8226 500nM CB-5083

city: Burlingame

first: Daniel

last: Anderson

address: 866 Malcolm Rd #100

institute: Cleave Biosciences

data_processing:
The pipeline mRNAv8-RSEM (EA-Quintiles) was used to analyze RNA-seq data.
Reads were aligned to External RNA Controls Consortium (ERCC) sequences. A subset of the reads (~1 million reads) were aligned to spiked-in control sequences (PhiX and other Illumina controls used during library preparation), residual sequences (globin and ribosomal RNA), and poly-A/T sequences that persisted after clipping.  The reads were also aligned to a sampling of intergenic regions to assess DNA contamination level and set the RPK (reads per thousand bases) threshold to call a transcript as present.
RSEM v1.2.0  was used to quantify normalized gene counts using parameters optimized for Illumina 50x50 paired-end sequencing
The UCSC knownGene transcriptome was used
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized RSEM gene counts, gene name, gene function and chromosone location

growth_protocol: Cells were grown according to ATCC protocols

extract_protocol:
RNA was isolated with the PureLink® RNA Mini Kit (Ambion™)
RNA samples were converted into cDNA libraries using the Illumina TruSeq Stranded mRNA sample preparation kit

treatment_protocol: Cells were treated with compound in 0.25% DMSO for 8 hr

value: multiple myeloma cell line

tag: treated with


title: RPMI-8226 100nM CB-5083


title: APA-positive trophoblast progenitors Apa_D15


title: APA-positive trophoblast progenitors Apa_D17


title: APA-positive trophoblast progenitors Apa_D14


title: RPMI-8226 10nM Bortezomib

value: Bortezomib


title: APA-positive trophoblast progenitors Apa_D16


title: RPMI-8226 DMSO

value: DMSO


title: APA-positive trophoblast progenitors Apa_D13


title: APA-positive trophoblast progenitors Apa_D12


title: MM.1S 500nM CB-5083


title: APA-positive trophoblast progenitors Apa_D24


title: APA-positive trophoblast progenitors Apa_D23


title: APA-positive trophoblast progenitors Apa_D11


title: MM.1S 100nM CB-5083


title: APA-positive trophoblast progenitors Apa_D9


title: APA-positive trophoblast progenitors Apa_D10


title: APA-positive trophoblast progenitors Apa_D8


title: AMO-1 10nM Bortezomib


title: AMO-1 500nM CB-5083


title: MM.1S DMSO


title: APA-positive trophoblast progenitors Apa_D5


title: MM.1S 10nM Bortezomib


title: APA-positive trophoblast progenitors Apa_D3


title: APA-positive trophoblast progenitors Apa_D7


title: AMO-1 100nM CB-5083


title: APA-positive trophoblast progenitors Apa_D2


title: APA-positive trophoblast progenitors Apa_D6


title: APA-positive trophoblast progenitors Apa_C23


title: AMO-1 DMSO


title: APA-positive trophoblast progenitors Apa_C24


title: APA-positive trophoblast progenitors Apa_C22


title: APA-positive trophoblast progenitors Apa_C21


title: APA-positive trophoblast progenitors Apa_C19


title: APA-positive trophoblast progenitors Apa_C20


title: APA-positive trophoblast progenitors Apa_C17


title: APA-positive trophoblast progenitors Apa_C18


title: APA-positive trophoblast progenitors Apa_C16


title: Shep2_shControl_rep2

city: Amsterdam

first: Wouter

last: Moolenaar

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

data_processing:
Sequencing reads were mapped against the human genome build 38 using tophat 2.0.12 with parameters --bowtie1 --prefilter-multihits --no-coverage-search --transcriptome-index --library-type firststrand
Readcounts were calculated using a custom script that uses the same strategy as HTSeq-count with union mode
Genes that have zero expression across all samples are removed from the dataset.
Genome_build: hg38
Supplementary_files_format_and_content: The file readcounts.txt contains the absolute gene expressions values for each of the samples.

source_name: neuroblastoma cells

growth_protocol: 2-3 x 106  cells were seeded in 10-cm dishes and grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) at 37°C under 5% CO2 for 2 days.

extract_protocol:
Cells were cooled on ice and  RNA was harvested using 2 ml of Trizol reagent.
RNA libraries were prepared for sequencing using standard Kapa protocols

tag: shRNA

value: shControl


title: Shep2_shGDE2(#4)_rep2


title: Shep2_shGDE2(#4)_rep1


title: Shep2_shControl_rep1


title: APA-positive trophoblast progenitors Apa_D4


title: APA-positive trophoblast progenitors Apa_C13


title: APA-positive trophoblast progenitors Apa_C15


title: APA-positive trophoblast progenitors Apa_D1


title: APA-positive trophoblast progenitors Apa_C12


title: APA-positive trophoblast progenitors Apa_C11


title: APA-positive trophoblast progenitors Apa_C14


title: APA-positive trophoblast progenitors Apa_C9


title: APA-positive trophoblast progenitors Apa_C5


title: APA-positive trophoblast progenitors Apa_C6


title: APA-positive trophoblast progenitors Apa_C10


title: APA-positive trophoblast progenitors Apa_C8


title: APA-positive trophoblast progenitors Apa_C7


title: APA-positive trophoblast progenitors Apa_C4


title: APA-positive trophoblast progenitors Apa_C3


title: APA-positive trophoblast progenitors Apa_B23


title: APA-positive trophoblast progenitors Apa_C2


title: APA-positive trophoblast progenitors Apa_C1


title: APA-positive trophoblast progenitors Apa_B22


title: APA-positive trophoblast progenitors Apa_B20


title: APA-positive trophoblast progenitors Apa_B19


title: APA-positive trophoblast progenitors Apa_B18


title: APA-positive trophoblast progenitors Apa_B21


title: APA-positive trophoblast progenitors Apa_B17


title: APA-positive trophoblast progenitors Apa_B16


title: APA-positive trophoblast progenitors Apa_B15


title: APA-positive trophoblast progenitors Apa_B13


title: APA-positive trophoblast progenitors Apa_B12


title: APA-positive trophoblast progenitors Apa_B14


title: APA-positive trophoblast progenitors Apa_B11


title: APA-positive trophoblast progenitors Apa_B9


title: APA-positive trophoblast progenitors Apa_B7


title: APA-positive trophoblast progenitors Apa_B10


title: APA-positive trophoblast progenitors Apa_B8


title: APA-positive trophoblast progenitors Apa_B6


title: APA-positive trophoblast progenitors Apa_B24


title: APA-positive trophoblast progenitors Apa_B3


title: APA-positive trophoblast progenitors Apa_B2


title: APA-positive trophoblast progenitors Apa_B1


title: APA-positive trophoblast progenitors Apa_B4


title: APA-positive trophoblast progenitors Apa_B5


title: APA-positive trophoblast progenitors Apa_A23


title: APA-positive trophoblast progenitors Apa_A21


title: APA-positive trophoblast progenitors Apa_A19


title: APA-positive trophoblast progenitors Apa_A22


title: APA-positive trophoblast progenitors Apa_A24


title: APA-positive trophoblast progenitors Apa_A20


title: APA-positive trophoblast progenitors Apa_A17


title: APA-positive trophoblast progenitors Apa_A18


title: APA-positive trophoblast progenitors Apa_A15


title: APA-positive trophoblast progenitors Apa_A14


title: APA-positive trophoblast progenitors Apa_A16


title: APA-positive trophoblast progenitors Apa_A13


title: APA-positive trophoblast progenitors Apa_A12


title: APA-positive trophoblast progenitors Apa_A11


title: APA-positive trophoblast progenitors Apa_A7


title: APA-positive trophoblast progenitors Apa_A8


title: APA-positive trophoblast progenitors Apa_A6


title: APA-positive trophoblast progenitors Apa_A2


title: APA-positive trophoblast progenitors Apa_A1


title: pos_rep3

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

description: genotype: ΔgsrN vanA::pMT552-gsrN(37)PP7hp

data_processing:
FastQ files were inputed into Rockhopper v1.0 (Tjaden et al., 2015)
FastQ files were also processed with EDGE-pro/Deseq pipeline (Magoc et al., 2013, Anders and Huber, 2010). Custom genome files were created to handle the mapping of each of the GsrN-PP7hp constructs
Genome_build: custom CP001340 files (G12, G17)
Supplementary_files_format_and_content: tab delimited files from EDGE-pro and Rockhopper

organism: Caulobacter vibrioides

source_name: Bacterial Cells

growth_protocol: Cultures harboring GsrN-PP7hp constructs were grown in 50mL flasks in M2X media until an OD660 ~0.85-0.9 were reached

extract_protocol:
Amylose elutions were treated with Acid-Phenol, cleaned with Chloroform and preciptated with Ethanol. RNA was then immobilized on an RNeasy Mini Kit column (Qiagen 74106) and treated with TURBO™ Dnase (ThermoFisher AM2238)
Ribosomal RNA was reduced using 4 ug of total RNA according to Gram negative Ribo-Zero rRNA Removal Kit (Illumina, CA). 100 ng of rRNA reduced RNA was processed  to strand specific RNA-Seq library construction, following Ovation Complete Prokaryotic RNA-Seq DR Multiplex System (Nugen, CA)

treatment_protocol: Cells were pelleted, lysed, and loaded onto a amylose column with immobilized MBP-PP7cp-HIS protein

tag: strain

value: deltagsrN vanA::pMT552-gsrN(37)PP7hp


title: APA-positive trophoblast progenitors Apa_A3


title: mock_rep2

description: genotype: ΔgsrN vanA::pMT552-PgsrN-gsrN(1-5)-PP7hp-gsrN(56-112)

tag: genotype


title: gsrN-OE_rep5

data_processing:
FastQ files were mapped and quantified using the CLC Bioinformatic Workbench program from Qiagen.
Genome_build: ncbi CP001340.1
Supplementary_files_format_and_content: tab-delimited text files exported from CLC Bioinformatic Workbench program from Qiagen
Supplementary_files_format_and_content: Name  "Chromosome"    "Region"        "Expression value"      "TPM"   "RPKM"  "Gene length"   "Unique gene reads"     "Total gene reads"

growth_protocol: strains were grown in M2X defined medium, cells were passaged over two days and harvested when their OD 660 reached ~0.85-0.9

extract_protocol:
Cultures were pelled and RNA was harvested using Trizol reagent. RNA was then immobilized on an RNeasy Mini Kit column (Qiagen 74106) and treated with TURBO™ Dnase (ThermoFisher AM2238)
Ribosomal RNA was reduced using 4 ug of total RNA according to Gram negative Ribo-Zero rRNA Removal Kit (Illumina, CA). 100 ng of rRNA reduced RNA was processed  to strand specific RNA-Seq library construction, following Ovation Complete Prokaryotic RNA-Seq DR Multiplex System (Nugen, CA)


title: gsrN-OE_rep4


title: pos_rep1


title: gsrN-OE_rep3


title: gsrN-OE_rep2


title: APA-positive trophoblast progenitors Apa_A4

tag: cell line


title: mock_rep1


title: gsrN-KO_rep5

description: ΔgsrN, CCNA_R0081

value: deltagsrN, CCNA_R0081


title: gsrN-KO_rep4

description: ΔgsrN, CCNA_R0081


title: APA-positive trophoblast progenitors Apa_A10


title: 49_3; Native CRP, basal cAMP levels

city: Albany

first: Kathleen

last: McDonough

state: NY

address: 120 New Scotland Ave

institute: Wadsworth Center, NYSDOH

description:
49_3_632J2AAXX_ChIP_405_BCG
processed data file:
CRP Binding Sites_GEO Sub.txt

data_processing:
Sequencing was performed on the Illumina platform, using a GAIIx (Boston University, sequencing core).
Coverage along the genome was calculated using Bowtie2 and SamTools.
Enriched regions were called using log-normal distributions.
The criteria for a region to be considered ‘enriched’ were a minimum region length of 150 nt and at least 60 nt shift between its forward and reverse peaks.
Region coverage was normalized using mean coverage of an experiment, correcting for the number of reads amongst experiments
Genome_build: M. bovis BCG Pasteur
Supplementary_files_format_and_content: Analyzed data is provided as text files. Sample Name; BCG_start and BCG_Stop are the co-ordinates of the binding site mapped to the M. bovis BCG Pasteur genome; enrichment of a particular region is indicated by the peak height; Site type indicates whether the binding site maps to region between genes (intergenic) or within open reading framr of annotated genes (genic)

organism: Mycobacterium tuberculosis variant bovis BCG str. Pasteur 1173P2

source_name: Broth culture of M. bovis BCG WT, Ambient (21% O2, 0% CO2) shaking, 10 days, washed and resuspended in fresh media for 24 h

growth_protocol: Liquid cultures of all strains used- M. bovis BCG WT, M. bovis BCG (p0805:Rv1264cat), M. bovis BCG (pMBC357) were started from frozen seed stocks and grown shaking for 7 days in mycomedium, with gentle rocking in 225-cm2 tissue culture flasks at a shallow depth of 2 mm. Bacterial cultures were either grown in ambient air conditions (21% O2) or in CO2 supplemented low oxygen conditions (1.3% O2, 5% CO2) in a controlled atmospher incubator.

extract_protocol:
A total of 50 ml culture volume of mid-log phase bacterial culture was cross-linked with 1% formaldehyde, for 30 min at room temperature, on a slow rocking platform. Cross-linking was quenched by addition of 250mM glycine and incubation for 15 min at room temperature with slow rocking. The cells were harvested, washed with cold PBS and resuspended in 0.5-0.6 ml of Buffer I (20 mM HEPES pH 7.9, 50 mM KCl, 0.5 M DTT, 10% glycerol) with protease inhibitor cocktail (Sigma). Bacterial cells were lysed and DNA sheared by sonication for 25 min (Covaris). The salt concentration of the cleared cell lysate was adjusted to a final concentration of 10 mM Tris-HCl pH 8.0, 150 mM NaCl, 0.1% NP-40 (IPP150 buffer). Immunoprecipitation was carried out by incubation of lysate with 10ul of Cmr antiserum, on nutator at 4°C. A total of 50ul of Protein A agarose beads were rinsed with IPP150 buffer, and added to the lysate-antiserum mixture. Protein A agarose-lysate-antiserum mixture was incubated at 4°C for 30 min and room temperature for 1.5 h. The beads were washed at least five times with IPP150 buffer followed by two washes with TE buffer (10mMTris HCl pH 8.0, 1mM EDTA).DNA from agarose beads was eluted by incubation with 150ul elution buffer (50 mMTris HCl pH 8.0, 10mM EDTA, 1% SDS) at 65°C for 15 min. A second elution was carried out by incubation of pellet with 100ul of TE buffer+ 1% SDS at 65°C for 5 min. Both elutions were pooled and de-crosslinked by incubating with 1 mg/ml Proteinase K at 37°C for 2 h and 65°C overnight. DNA was purified using PCR purification kit (QIAGEN).
Standard manufacturer (Illumina) recommended protocol was used for library construction

treatment_protocol: All bacterial cultures were grown under the mentioned O2 and CO2 conditions for 7 days (mid-log phase of growth). For exogenous cAMP treatment, 10mM dibutyryl-cAMP was added to the bacterial cutlure on day 3 and returned to the controlled atmospheric incubator. dbcAMP is a cell permeable compound, which gets cleaved upon internalization by bacteria to produce cAMP. For endogenous cAMP supplementation, M. bovis BCG (p0805:Rv1264cat) strain was used. In this strain, constitutive expression of the catalytic domain of Rv1264 adenylyl cyclase, driven by the Rv0805 promoter, increases the cAMP level within the bacterial cytoplasm.

tag: chip antibody

value: Anti-CRP antiserum

tag: transcription factor expression level

value: Native CRP

tag: camp treatment/level

value: Basal


title: 54_1; Native CRP, basal cAMP

description:
54_1_64Y9CAAXX_030612_ChIP_446_BCG
processed data file:
CRP Binding Sites_GEO Sub.txt

source_name: Broth culture of M. bovis BCG_hypoxia supplemented with CO2 (1.3% O2, 5% CO2) shaking, 7 days,


title: APA-positive trophoblast progenitors Apa_A9


title: gsrN-KO_rep3

description: ΔgsrN, CCNA_R0081


title: 49_4; Native CRP, basal cAMP levels, starvation

description:
49_4_632J2AAXX_ChIP_406_BCG
processed data file:
CRP Binding Sites_GEO Sub.txt

source_name: Broth culture of M. bovis BCG WT, Ambient (21% O2, 0% CO2) shaking, 10 days, washed and resuspended in PBS for 24 h


title: 34_1; Native CRP, endogenous cAMP supplementation

description:
34_1_70AYPAAXX_041511_ChIP_308_BCG
processed data file:
CRP Binding Sites_GEO Sub.txt

source_name: Broth culture of M. bovis BCG (p0805:Rv1264cat)/ hypoxia supplemented with CO2 (1.3% O2, 5% CO2) shaking, 7 days,

value: Endogenous cAMP supplementation


title: APA-positive trophoblast progenitors Apa_A5


title: gsrN-KO_rep1

description: ΔgsrN, CCNA_R0081


title: 33_2; Native CRP, basal cAMP

description:
33_2_630C4AAXX_040111_ChIP_307_BCG
processed data file:
CRP Binding Sites_GEO Sub.txt


title: WT_rep4

value: wild-type


title: 33_1; Native CRP, exogenous cAMP supplementation

description:
33_1_630C4AAXX_040111_ChIP_306_BCG
processed data file:
CRP Binding Sites_GEO Sub.txt

source_name: Broth culture of M. bovis BCG_hypoxia supplemented with CO2 (1.3% O2, 5% CO2) shaking, 7 days,10mM final dibutyrl cAMP added on day 3

value: Exogenous cAMP supplementation


title: WT_rep3


title: 33_3; Cmr overexpression, exogenous cAMP supplementation

description:
33_3_630C4AAXX_040111_ChIP_309_BCG
processed data file:
Cmr Binding sites_GEO Sub.txt

source_name: Broth culture of M. bovis BCG (pMBC357)/ hypoxia supplemented with CO2 (1.3% O2, 5% CO2) shaking, 7 days; 10mM final dibutyrl cAMP added on day 3

value: Anti-Cmr antiserum

value: Cmr overexpression


title: pos_rep2


title: WT_rep2


title: gsrN-OE_rep1


title: 54_2; Native CRP, endogenous cAMP supplementation

description:
54_2_64Y9CAAXX_030612_ChIP_447_BCG
processed data file:
CRP Binding Sites_GEO Sub.txt


title: 33_4; Cmr overexpression, basal cAMP levels

description:
33_4_630C4AAXX_040111_ChIP_310_BCG
processed data file:
Cmr Binding sites_GEO Sub.txt

source_name: Broth culture of M. bovis BCG (pMBC357)/ hypoxia supplemented with CO2 (1.3% O2, 5% CO2) shaking, 7 days,


title: WT_rep1


title: 54_3; Native Cmr, basal cAMP levels

description:
54_3_64Y9CAAXX_030612_ChIP_448_BCG
processed data file:
Cmr Binding sites_GEO Sub.txt

source_name: Broth culture of M. bovis BCG WT, Ambient (21% O2, 0% CO2) shaking, 7 days

value: Native Cmr


title: gsrN-KO_rep2

description: ΔgsrN, CCNA_R0081


title: Cells at aw 0.11

city: St. Cloud

first: Ryan

middle: Cristiano

last: Fink

state: MN

address: 720 4th Ave S

department: Biology

institute: St. Cloud State University

description: cells equilibrated to aw 0.11

data_processing:
Base call files for each cycle of sequencing were generated by Real-Time Analysis software (Illumina Inc., San Diego, CA). Primary analysis and de-multiplexing were performed using CASAVA software v1.8.2 (Illumina Inc., San Diego, CA).
The reads ends were trimmed using the Auto trim option available in the DNASTAR software package. The ends were trimmed to best match the alignment to the template. SeqMan Ngen marked the portion of the read that aligns well to the template and set the trimming to skip any of the poorly aligned portions of the read.
RPKM (reads assigned per kilobase of target per million mapped reads) normalization was applied. Briefly, the signal values for each experiment were divided by the totaltarget sequence divided by one thousands; and the resulting number divided by the total number of reads divided by the total number of mapped reads divided by one million.
Genome_build: Salmonella enterica serovar Typhimurium strain LT2

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. ATCC 14028

source_name: Biological replicate 1, 2, and 3

growth_protocol: Working cultures of Salmonella Typhimurium ATCC14028 were freshly inoculated in TSB and grown for 3 h at 37°C shaking at 250 rpm. The cultures were collected through centrifugation (10 min at 5,000×g) and washed twice with distilled sterile water (DSW) to eliminate nutrient residues. Approximately 10^9 CFU were spotted on 0.2 µm polycarbonate filters (Merck Millipore Ltd., Billerica, MA).

extract_protocol:
The total RNA was extracted from Salmonella cells using the RNAprotect Bacteria Reagent and RNeasy Mini Kit (Qiagen, Hilden, Germany). The experiments were repeated three times in different days. Each time, three technical replicates were performed. The total RNA was extracted individually for each replicate and then the RNA was pooled together from all the replicates for the same conditions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were allowed to air-dry for 24 h at room temperature. Filters were placed in desiccators containing water or a saturated solution of lithium chloride 99% (Acros Organics, Thermo Fisher Scientific, Waltham, MA) to allow equilibration to aw 1.0 and 0.11 respectively. Filters were kept in the desiccators for 4 days at 25°C.

tag: serovar

value: Typhimurium


title: Cells at aw 1.0

description: cells equilibrated to aw 1.0


title: C3684: XX d43 DSD gonad

status: Public on Oct 25 2017

city: Ithaca

first: Jennifer

middle: K

last: Grenier

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.5 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
tophat v2.0.13 was used to map reads to the Dog CanFam3 reference genome, guided by the CanFam3 annotated transcriptome (Ensembl).
Novel transcripts were analyzed with cufflinks v2.2.1 (cufflinks, cuffmerge) guided by the CanFam3 annotated transcriptome (Ensembl). File: GuidedDiscovery_genes.gtf.gz
Transcripts were quantified with cuffquant v2.2.1 (-max-bundle-frags 5000000 to handle intervals with high read counts). Analyses included annotated genes only (CanFam3 gtf file with Amh added; --no-novel-juncs) and 'discovery' guided by annotated genes (cuffmerge output: GuidedDiscovery_genes.gtf.gz).
FPKM values were generated with cufflinks v2.2.1: cuffnorm was used for analysis of all samples in parallel for both annotated genes only (+Amh) and for the set of novel genes in GuidedDiscovery_genes.gtf.gz (guided by CanFam3 annotated genes); cuffdiff was used to call differentially expressed annotated genes for age-matched XX cohorts at d37 and d43.
Genome_build: CanFam3 (Ensembl)
Supplementary_files_format_and_content: Tab delimited text files generated with Cufflinks including FPKM values for all samples (Annotated_genes_FPKM.txt, GuidedDiscovery_genes_FPKM.txt) and differential gene expression analysis, including q-values reflecting multiple hypothesis testing correction, for age-matched XX cohorts at d37 and d43 (XX_d37_gene_exp.diff, XX_d43_gene_exp.diff).

organism: Canis lupus familiaris

source_name: embryonic gonad

extract_protocol:
Total RNA was isolated with the RNeasy Plus Mini Kit (Qiagen)
Standard polyA+ RNAseq libraries were prepared with the TruSeq RNA Library Prep Kit v2 (Illumina) by the Cornell Biotechnology Resource Center Genomics Facility

treatment_protocol: gonadal tissue was dissected from embryos and then flash frozen and stored in liquid nitrogen

value: embryonic gonad

tag: developmental age

tag: sex chromosomes

value: XX

tag: pedigree

value: DSD


title: A1107: XX d44 age matched control gonad

tag: tissue

value: Control


title: C3659: XX d44 DSD gonad


title: A1104: XX d44 age matched control gonad


title: A1109: XY d44 age matched control gonad

value: XY


title: C3518: XY d42 DSD littermate gonad


title: C3517: XX d42 DSD gonad


title: A1106: XY d44 age matched control gonad


title: C3688: XX d43 DSD gonad


title: C3696: XX d41 DSD gonad


title: C3694: XX d41 DSD gonad


title: A1095: XY d39 age matched control gonad


title: C3522: XY d42 DSD littermate gonad


title: A1089: XX d39 age matched control gonad


title: A1086: XX d39 age matched control gonad


title: A1091: XY d39 age matched control gonad


title: C3516: XY d37 DSD littermate gonad


title: A1110: XX d44 age matched control gonad


title: C3512: XX d37 DSD gonad


title: C3515: XX d37 DSD gonad


title: A1096: XY d37 age matched control gonad


title: A1100: XY d37 age matched control gonad


title: A1108: XY d44 age matched control gonad


title: A1101: XX d37 age matched control gonad


title: A1098: XX d37 age matched control gonad


title: C3691: XY d41 DSD littermate gonad


title: A1097: XX d37 age matched control gonad


title: Jeko NR4A1 sgRNA#2

city: Madison

first: Lixin

last: Rui

state: WI

address: 1111 Highland ave, Room 4053

institute: Wisconsin Ins for Medical Res

data_processing:
RNAseq reads were filtered for average QC score>30. Reads were mapped to hg19 genome.
RNAseq fpkm were generated by tophat and cufflink by following Trapnell et al.(2012).
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq (txt file: gene fpkm)

source_name: mantle cell lymphoma cell line

growth_protocol: Mantle cells were grown in RPMI1640 media plus 20%FBS,1%  penicillin, 1% streptomycin.

extract_protocol:
RNA was extracted by Rneasy plus mini kit (Qiagen) following the manufacturer’s instructions.
cDNA library was construbuted by using Illumina Truseq RNA Library Prep Kit (RS-122-2002)

treatment_protocol: sgRNA was induced by Doxycycline for 48H

tag: treatment

value: Jeko cell line transduced with NR4A1 sgRNA#2, and induced with Doxycyclin for 48H


title: ARD_EZH2i_R_Rep2

city: Pamplona

first: Teresa

last: Ezponda

state: Navarra

address: Pio XII 55

department: Hematology/Oncology

country: Spain

institute: Center for Applied Medical Research

description:
A GSK343 resistant cell line was generated by growing ARD cells in the presence of increasing concentrations of the drug. Resistant cells were maintained in the presence of 4 uM of GSK343 for at least 3 weeks before RNA extraction.
ARD-ARP-FPKMs.csv

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw files were QC_processed to remove any reads which failed Illumina's purity filer, and were then trimmed using the Sickle tool
Reads were alinged using STAR (v 2.3.0e_r291)
Read counts per gene were calculated using HTSeq (v0.6.0).
The R (v3.1.1) Bioconductor package, edgeR (v3.8.5) was used to identify statistically significant differentially expressed genes
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited files containing FPKMs for all genes.

source_name: ARD

extract_protocol:
Cell pellets were frozen at -80 C and total RNA was extracted using the Rneasy mini kit (Qiagen), including the on column Dnase step. Libraries were prepared using the TruSeq RNA sample kit (Illumina) and multiplexed samples were sequenced on a Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: multiple myeloma

tag: utx status

tag: culture condition

value: Advanced RPMI + 4% Fetal Bovine Serum + glutamax + 4 μM GSK343


title: Jeko control

value: Jeko cell line transduced with the CRISPR/cas9 empty vector as a control, and induced with Doxycyclin for 48H


title: Rec-1 NR4A1 sgRNA#1

value: Rec-1 cell line transduced  with NR4A1 sgRNA#1, and induced with Doxycyclin for 48H


title: ARD_EZH2i_R_7d_release_Rep2

description:
ARD cells resistant to GSK343 were maintained in the absence of the drug for 7 days
ARD-ARP-FPKMs.csv

value: Advanced RPMI + 4% Fetal Bovine Serum + glutamax


title: Rec-1 NR4A1 sgRNA#2

value: Rec-1 cell line transduced with NR4A1 sgRNA#2, and induced with Doxycyclin for 48H


title: ARD_EZH2i_R_Rep1


title: A1094: XY d39 age matched control gonad


title: Rec-1 control

value: Rec-1 cell line transduced  with the CRISPR/cas9 empty vector as a control, and induced with Doxycyclin for 48H


title: ARP-1_GSK669_Rep2

description:
ARP-1 cells were grown in the presence of the EZH2 inhibitor GSK343 (4 uM) or a control compound (GSK669) for 7 days
ARD-ARP-FPKMs.csv

value: wild-type

value: Advanced RPMI + 4% Fetal Bovine Serum + glutamax + 4 μM GSK669


title: ARP-1_GSK669_Rep1


title: ARP-1_GSK343_Rep2


title: A1088: XX d39 age matched control gonad


title: A1099: XY d37 age matched control gonad


title: ARP-1_GSK343_Rep1


title: ARD_GSK669_Rep1

description:
ARD cells were grown in the presence of the EZH2 inhibitor GSK343 (4 uM) or a control compound (GSK669) for 7 days
ARD-ARP-FPKMs.csv


title: ARD_EZH2i_R_7d_release_Rep1


title: ARD_GSK343_Rep2


title: ARD_GSK669_Rep2


title: ARD_GSK343_Rep1


title: ARD_pUTX_6d_Rep2

description:
ARD cells were transduced with a plasmid to express UTX in a doxycyline inducible manner. Cells were grown in the absence (pUTX) or presence (pUTXDox) of doxycycline for 6 days.
ARP-UTX-Dox-FPKMs.csv


title: ARD_pUTXDox_6d_Rep2

value: Add-back in null cells

value: Advanced RPMI + 4% Fetal Bovine Serum + glutamax + 25 ng/mL doxycycline


title: ARD_pUTXDox_6d_Rep1


title: ARD_pUTX_6d_Rep1


title: ARP-1_Rep2

description:
ARP-1 cells were grown in regular culture conditions as indicated in column G
ARP-UTX-Dox-FPKMs.csv


title: ARD_pUTXDox_3d_Rep1

description:
ARD cells were transduced with a plasmid to express UTX in a doxycyline inducible manner. Cells were grown in the absence (pUTX) or presence (pUTXDox) of doxycycline for 3 days.
ARP-UTX-Dox-FPKMs.csv


title: ARD_pUTX_3d_Rep2


title: ARD_pUTXDox_3d_Rep2


title: Jeko NR4A1 sgRNA#1

value: Jeko cell line transduced with NR4A1 sgRNA#1, and induced with Doxycyclin for 48H


title: ARP-1_Rep1


title: dCLIP Parental Control

city: Boston

first: Michael

last: Rosenberg

state: MA - Massachusetts

address: 185 Cambridge street

department: Molecular Biology

institute: Massachusetts General Hospital, Harvard Medical School

description:
RNA extracted from membrane
dCLIP-seq Library.
dCLIP-seq

data_processing:
Base-calling was performed with Illumina real time analysis (RTA) basecaller v1.17.21.3
Adaptor sequences were trimmed from libraries with either Trim Galore! v0.3.3 (for CLIP-seq and RNA-seq; stringency 15 and allowed error rate 0.2) or Cutadapt v1.0 (for ChIP-seq; allowed error rate 0.2). PCR duplicates were removed by custom programs prior to alignment. Reads were aligned to the reference hg19 genome. RNA was aligned with Tophat (v2.0.8 or greater), while DNA was aligned using Novoalign (3.00.03). Post-processing of mm9 alignments was performed with custom C and Perl programs and bash shell scripts, SAMtools v0.1.18, and BEDtools v2.17.0. These included accounting, alignment file-type conversion, extracting and sorting uniquely/paired-end reads (SAMtools), and obtaining wig coverage files (DNA: BEDtools genomecov; RNA: SAMtools depth).
For dCLIP, Fragment per million (fpm) wig files were then created by scaling uniquely aligned wig files to total number of fragments per million in each library (determined by SAMtools flagstat combining reads “with itself and mate mapped” and “singletons”).
dCLIP-seq enriched tag density wig files were viewed in UCSC genome browser (7) or Integrated Genome Browser (IGB) (8). Then consecutive wig entries of equal coverage were merged forming bed files that were used for peak calling. The peak caller software PeakRanger (v.16)  was used. The software requires an even distribution of watson/crick entries, thus, prior to peak calling, strand specific bed file entries were randomized per each strand. PeakRanger was called with arguments ranger –p 0.01 –-format bed –gene_annot_file (hg19), –d experiment and –c mock-transfected control, to identify narrow peaks with p-value 0.01 or less. Peaks were called once over parental control (3.1 and 4.1) and once over GFP control (3.2 and 4.2).
Genome_build: hg19

source_name: HEK293 cells

growth_protocol: HEK293 cells were routinely maintained in DME + 10% FBS.

extract_protocol:
UV-cross-linked cells, expressing BirA biotinylase and Biotin-tagged hCBX7 or mock vector, were isolated and lysed. Lysates were DNase-treated and RNAse-treated. Cleared lysates were incubated 2hrs with Streptavidin beads. After stringent washing and 2nd DNase treatment, CLIP-tags on beads were radiolabelled with [γ-32P]ATP, run on Bis-Tris SDS-PAGE in MOPS buffer, and transferred to nitrocellulose membrane. Membrane fragments containing CLIP signal and corresponding positions on control lanes were excised, and RNA was eluted by proteinase K, followed by Trizol extraction and ethanol precipitation.
Multiplex Compatible NEBNext Small RNA Library Prep Set for Illumina (NEB). Illumina barcode #2, CGATGT. Paired-end 50bp reads
none provided by the submitter

treatment_protocol: UV cross-linking

tag: cells

value: Human Embryonic Kidney cells with stable expression of BirA biotinylase, clone 1C

tag: Sex

value: Female


title: dCLIP GFP Control

extract_protocol:
UV-cross-linked cells, expressing BirA biotinylase and Biotin-tagged Cbx7 or mock vector, were isolated and lysed. Lysates were DNase-treated and RNAse-treated. Cleared lysates were incubated 2hrs with Streptavidin beads. After stringent washing and 2nd DNase treatment, CLIP-tags on beads were radiolabelled with [γ-32P]ATP, run on Bis-Tris SDS-PAGE in MOPS buffer, and transferred to nitrocellulose membrane. Membrane fragments containing CLIP signal and corresponding positions on control lanes were excised, and RNA was eluted by proteinase K, followed by Trizol extraction and ethanol precipitation.
Multiplex Compatible NEBNext Small RNA Library Prep Set for Illumina (NEB).  Illumina barcode #4, TGACCA. Paired-end 50bp reads
none provided by the submitter

value: Human Embryonic Kidney cells with stable expression of BirA biotinylase and Avi-GFP control, clone 3C


title: Non-targeting control 3

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

description: NTC.txt

data_processing:
Base calls using CASAVA
Spliced reads were aligned to the genome using tophat 2.0.9 (calling bowtie 2.1.0)
cufflinks 2.1.0 was used to quantify expression based on the reference transcriptome
cuffdiff 2.1.1  was used to normalize counts and obtain abundance estimates for each sample and differential expression calls beween the PUMKD and NTC conditions
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Text files contain FPKM estimates for each gene from the genes.fpkm_tracking cuffdiff output file; results are pooled across replicates for each condition

growth_protocol: HEK293 cells were cultured at 37°C under 5% CO2 in DMEM with glucose and 1 x Penicillin/Streptomycin/Glutamine and 10% FBS (Gibco)

extract_protocol:
RNA was isolated using the Maxwell simplyRNA cells kit (Promega) and a MaxWell16 instrument, and subsequently poly-A purified
Prepared using a TruSeq RNA kit following the manufacturer's instructions

treatment_protocol: PUMs were knocked down in HEK293 cells using On-target Plus Smartpool siRNAs for PUM1 (L-014179-00), PUM2 (L-014031-02), or non-targeting control siRNAs (GE Dharmacon). HEK293 cells (2 x 10^5 cells per well) were plated into a 12-well culture plate. Three replicates were performed for each condition. After 24 hours, 500 μL culture medium was removed and cells were transfected with 100 fmoles of siRNAs using Dharmafect-I (Dharmacon). After 4-8 hours of siRNA treatment, 500 μL culture medium was refreshed. After 24 hours, 500 μL culture medium was removed and cells were transfected again with 100 fmoles of siRNAs using Dharmafect-I. After 4-8 hours of siRNA treatment, 650 μL culture medium was refreshed. Cells were harvested 48 hours after last transfection for RNA purification and RNA Seq experiments

value: immortalized human cell line HEK293

tag: shRNA

value: Non-target control


title: PUM knockdown 1

description: PUMKD.txt


title: Non-targeting control 2

description: NTC.txt


title: PUM knockdown 2

description: PUMKD.txt


title: d3MGT-shPtbp1-2

city: WAUWATOSA

first: ZIQING

last: LIU

address: 8701 W Watertown Plank Rd, BSB 5320

institute: Medical College of Wisconsin

data_processing:
QC: Qualities of de-barcoded raw sequence reads were checked by fastqc.
Mapping: Mapping to the merged genome of mm10 was performed with Tophat2 (2.1.0) using default settings.
Counting: Gene expression was counted with Htseq-count (0.6.1p1) using the union mode and counts per million were calculated for each gene.
Genome_build: mm10
Supplementary_files_format_and_content: csv file containing CPM for each gene in each sample.

source_name: d3CF transduced with MGT and shPtbp2

growth_protocol: P1.5 neonatal hearts were isolated from CD1 mice and cardiac fibroblasts were isolated with the enzyme digestion method followed by MACS purification of Thy1+ cells. P1.5 cardiomyocytes were isolated using the neonatal cardiomyocytes isolation system (Worthington Biochemical Corporation). For reprogramming, CF cells were seeded onto 0.1% gelatin-coated plates at 2 x 104/cm2 in fibroblast media (IMDM + 20% FBS). After overnight culturing, media was replaced before retroviral transduction to remove unattached cells.

extract_protocol:
After three days, cells were collected and lysed in TRIzol.
Illumina libraries were prepared for sequencing using the TruSeq Stranded mRNA Library Prep Kit (Illumina)

treatment_protocol: Retroviruses encoding MGT were packaged by transfecting platE cells (Cell Biolabs) with lipofectamine 2000 (Life Technology) and lentiviruses encoding non-targeting shRNA control (shRNA) or shPtbp1 were packaged by transfecting 293T cells. Viruses collected from one 10 cm2 dish were resuspended in 100 µl iCM media. For RNA-seq of Ptbp1-silencing experiments, 2.5 x 105 CF were seeded into one well in a 6-well plate. On the following day, 50 µl of pMXs-puro/ pMXs-puro-MGT or 50 µl each of pMXs-puro-MGT and shNT/ shPtbp1-271 were added to the cells.

tag: strain

tag: age

tag: transduction

value: MGT and shPtbp1


title: Lib1_Rods_Rep3

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description:
RNA Barcodes in Rods
processed data file: Lib1Results.tab

data_processing:
Library strategy: Parallel Reporter Assay
A custom pipeline was created to assign barcodes to each tested sequences. Then sequence activity was calculated as the ratio of barcode abundance in the RNA sample compare to its abundance in the AAV pool.
Barcode sequences were extracted from 50bp reads by taking only reads starting with the expected backbone sequence: “TCCTGCTGGAGTTCGTGACCTGCATGCGCCGAA”. From these reads the sequence at position 34-48 was extracted. The frequency of each barcode sequence was calculated to get counts for each sample. Counts of barcodes were normalized to library size. Enrichment of barcodes in the RNA sample was calculated over their representation in the AAV input. Barcodes not sufficiently covered in the AAV sequencing were discarded (depending on sequencing depth 2-16 reads). The median activity of all barcodes per CRE was calculated. Only CREs that were covered in at least 2 out of 3 biological replicates with at least three barcodes were used for downstream analysis.
processed data: Tab delimited, summary table of the expression values for each tested seqeunce in the tested cell types
Genome_build: mm9

source_name: Rods

extract_protocol:
RNA was isolated from sorted cells using Qiagen RNeasy® Mini Kit with on-column DNase digestion followed by reverse transcription using Takara PrimeScript RT Reagent Kit (#RR047A).
barcodes were amplified with KAPA HIFI Hotstart using Primer #1 and indexing primers (Primers #3-11)

value: Rods

tag: mouse strain

value: b2-Cre x B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J # 007913


title: Lib1_wholeRetina_Rep2

source_name: whole Retina

value: whole Retina


title: Lib1_wholeRetina_Rep3


title: Lib1_wholeRetina_Rep1


title: Lib1_Rods_Rep2