title: Rec1 DMSO rep1 BNDME1


title: Rec1 DMSO rep1 BNDME2

status: Public on Jun 03 2018

type: SRA

city: Ann Arbor

first: Russell

middle: James Hubbard

last: Ryan

state: MI

address: 4306 Rogel Cancer Center, 1500 E Medical Center Dr.

department: Pathology

country: USA

institute: University of Michigan Medical School

library_source: genomic

data_processing:
Library strategy: 4C-Seq
There is no single accepted processed  format for 4C-Seq, so we are providing the raw sequencing data only.
Genome_build: hg19

molecule: genomic DNA

organism: Homo sapiens

source_name: Rec-1 cell line

extract_protocol:
Cells were crosslinked with 2% formaldehyde in PBS at room temperature for 10 minutes, followed by glycine quenching, washing in PBS, isolation of nuclei by hypotonic buffer lysis, and resuspension in primary restriction enzyme buffer. Primary digestion was accomplished by sequential addition of SDS, Triton-X100, and primary restriction enzyme while mixing at 37°C, followed by heat inactivation at 65°C. Ligation was performed after sample dilution in T4 ligase buffer by addition of T4 ligase at 16°C. Ligated DNA was isolated by proteinase K and RNAase A digestion, phenol-chloroform extraction, and ethanol precipitation. DNA was then digested with secondary restriction enzyme, heat inactivated, ligated with T4 ligase, and isolated by ethanol precipitation and QIAquick PCR purification columns.
To generate each 4C-Seq library, a total of 3.2 micrograms of 4C DNA was amplified across 16 separate 50-microliter PCR reactions containing Q5 high-fidelity polymerase mix (NEB) and oligonucleotides pairs consisting of universal illumina adaptor sequences, sample-specific barcodes, and viewpoint-specific primer sequences. Equal portions of each reaction were pooled and the PCR-amplified library was purified with 0.8 volumes of Ampure XP per volume of PCR product.

tag: cell line

tag: cell type

value: Mantle cell lymphoma cell line

tag: drug treatment

value: DMSO:Grown for 72 h in media containing vehicle (DMSO) only

tag: data type

tag: 4c-seq primary enzyme

value: NlaIII

tag: 4c-seq secondary enzyme

value: DpnII

tag: 4c-seq viewpoint primer 1 (reading)

value: GAAGTAATAATGCCTGCATG

tag: 4c-seq viewpoint primer 2 (non-reading)

value: TATGTAAGGAACCACACAGAGA


title: Rec1 GSI rep2 BNDME1

value: GSI:Grown for 72 h in media containing Compound E (1μM)

value: AAAGAATGAGTGTGGCCATG

value: AGTTCAGGTATGCAAAGTGG


title: Rec1 DMSO rep1 MYCP

value: AGCTGCTGGGAGGAGACATG

value: CCACGTCCTAACACCTCTAG


title: PDX98848_8_RNA-Seq_dbz

library_source: transcriptomic

data_processing:
Reads were aligned to the hg19 genome assembly and iGenomes UCSC annotation using TopHat2.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq was used to quantify reads mapping to the iGenomes UCSC genes hg19 transcript annotation, with read-through genes removed to prevent exon exclusion.

molecule: polyA RNA

source_name: MCL PDX 98848

growth_protocol: Xenografts were established in NOD-SCID-gamma (NSG) mice via tail vein injection of 1.5 million cells from the mantle cell lymphoma PDX model DFBL-98848.

extract_protocol:
Mouse spleens were dissociated on ice, red blood cells were lysed, and human cells were isolated by EasySep Mouse/Human Chimera Isolation Kit (STEMCELL Technologies) per the manufacturer?s protocol and flash-frozen in liquid nitrogen. RNA was extracted from pellets via Qiagen Qiashredder and RNAeasy columns.
Strand-specific RNA-Seq libraries were generated as follows: Oligo dT beads were used to isolate the poly-adenylated fraction of total RNA, followed by zinc-mediated fragmentation and DNAase treatment. A 3' single-stranded RNA adaptor was ligated to RNA fragments, and an adaptor-seated primer used for first-strand cDNA synthesis. RNA was then hydrolyzed, and a 3' DNA adaptor was ligated to ssDNA fragments, which were then PCR enriched with barcoded, adaptor-seated illumina PCR primers. Final libraries were isolated by SPRI purification (forward SPRI x2), and paired-end sequenced on illumina NextSeq (38 bp x2).

treatment_protocol: Upon appearance of MCL cells in the peripheral blood at d32, mice were treated with IP injection of DBZ (10?Mol/kg) in 0.5% CMC + 1% Tween 80 or vehicle alone every other day for 5 d.

tag: tissue

value: Mouse spleen

tag: tissue/cell type

value: Mantle cell lymphoma xenograft

value: DBZ


title: PDX98848_9_RNA-Seq_dbz


title: PDX98848_5_RNA-Seq_veh

value: Vehicle


title: PDX98848_6_RNA-Seq_dbz


title: Gorilla_GON_VPFC

status: Public on Jun 04 2018

city: Okazaki

first: Yasuhiro

last: Go

address: 38 Nishigonaka Myodaiji

department: Department of Brain Sciences, Center for Novel Science Initiatives

country: Japan

institute: National Institutes of Natural Sciences

data_processing:
Raw reads of four species were aligned to the reference genomes (human, hg19; chimpanzee, panTro4; gorilla, gorGor3; gibbon, nomLeu1) by “STAR” (parameters: outFilterMultimapNmax = 1, outFilterMatchNminOverLread = 0.95, outFilterMismatchNoverLmax = 0.05, outFilterIntronMotifs = RemoveNoncanonical).
PCR duplicates removal was then conducted using SAMtools and only uniquely mapped reads were considered as validity to avoid the estimation ambiguity.
We obtained chimpanzee, gorilla and gibbon orthologs of human genes (GENCODE v19) by reciprocal liftOver requiring the same exon orders and no less than 50% exons preserved.
Based on the annotations, numbers of reads were counted per gene per sample using htseq-count within HTSeq. Only genes with counts greater than 0 in all four species in at least one brain region were used in the following analysis
We took advantage of the median ratio method implemented in DESeq2 to normalize the gene abundance data for further comparisons across species and brain regions.
Genome_build: human, hg19; chimpanzee, panTro4; gorilla, gorGor3; gibbon, nomLeu1
Supplementary_files_format_and_content: tab-delimited text files include raw count, normalized count, and RPKM for each sample

organism: Gorilla gorilla

source_name: ventrolateral prefrontal cortex

extract_protocol:
Brain dissection was performed from either fresh specimens or frozen tissue slabs by the same person to ensure sampling consistency between specimens. About 100 mg of dissected tissues were used and total RNA were extracted using RNeasy Plus Universal Kit (Qiagen). Quality and quantity measurements of extracted RNA were performed using NanoDrop (Thermo Fisher Scientific) and Qubit Fluorometer (Thermo Fisher Scientific), respectively, and the RNA Integrity Number (RIN) were determined using Bioanalyzer RNA 6000 Nano Kit (Agilent).
Sequencing libraries were prepared using the NEBNext mRNA Library Prep Kit for non-directional libraries and the NEBNext Ultra Directional RNA Library Prep Kit for directional libraries (New England BioLabs) according to the manufacturer’s instructions.

tag: individual id

value: GON

tag: age (year)

tag: Sex

value: male

tag: rin

tag: processing date


title: PDX98848_4_RNA-Seq_veh


title: PDX98848_3_RNA-Seq_veh


title: dper_Jul_1_ATAC

city: Vienna

first: Jelle

last: Jacobs

address: Campus-Vienna-Biocenter 1

department: VBC

country: Austria

institute: Institute of molecular Pathology

data_processing:
Cleaning (fastq-mcf)
Mapping to their respective genomes using bowtie2
peaks were called for each sample using macs2 callpeak with parameter -g dm --nomodel
Genome_build: dana-all-chromosome-r1.3; dere-all-chromosome-r1.3; dmel-all-chromosome-r6.02; dmoj-all-chromosome-r1.3; dper-all-chromosome-r1.3; dpse-all-chromosome-r3.1; dsec-all-chromosome-r1.3; dsim-all-chromosome-r1.4; dvir-all-chromosome-r1.2; dwil-all-chromosome-r1.3; dyak-all-chromosome-r1.3
Supplementary_files_format_and_content: BigWigs for all ATAC-samples

organism: Drosophila persimilis

source_name: D. Persimilis_eye-antennal discs

growth_protocol: Normal flyfood, 25 degrees

extract_protocol:
Eye-antennal imaginal Disc were dissected from 3rd instar wandering larvae. The discs were immediately lysed and ATAC-seq was performed
Tn5 and nextera library prep

tag: genotype/species

value: Drosophila Persimilis

tag: age

value: 3rd instar-wandering

tag: treatment

value: Hand Dissections

value: eye-antennal discs


title: Rec1 DMSO rep2 MYCP

tag: cell line

tag: cell type

value: Mantle cell lymphoma cell line

value: DMSO:Grown for 72 h in media containing vehicle (DMSO) only

value: NlaIII

value: DpnII


title: PDX98848_1_RNA-Seq_veh

tag: drug treatment


title: Rec1 DMSO rep2 BNDME1

tag: data type

tag: 4c-seq primary enzyme

value: AAAGAATGAGTGTGGCCATG

value: AGTTCAGGTATGCAAAGTGG


title: SP49_gsi-wo_RNA-Seq_r3

description: Poly-A RNA

data_processing:
RNA-Seq: Reads were aligned to the hg19 genome assembly and iGenomes UCSC annotation using TopHat-1.4.1.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: RNA-Seq: Gene-level read count matrices were generated with HTSeq, using the iGenomes UCSC genes hg19 transcript annotation, with read-through genes removed to prevent exon exclusion.

molecule: total RNA

source_name: SP-49 cell line

growth_protocol: Cell lines were grown in RPMI medium 1640 (Invitrogen) supplemented with 10% fetal calf serum, penicillin/streptomycin, nonessential amino acids, 1mM sodium pyruvate and 5μM 2-mercaptoethanol.

extract_protocol:
RNA-Seq: Cells were pelleted and flash-frozen in liquid nitrogen. RNA was extracted from pellets via Qiagen QIAshredder and RNeasy columns.
RNA-Seq: Strand-specific RNA-Seq libraries were generated as follows: Oligo dT beads were used to isolate the poly-adenylated fraction of total RNA, followed by zinc-mediated fragmentation and DNase treatment. A 3' single-stranded RNA adaptor was ligated to RNA fragments, and an adaptor-seated primer used for first-strand cDNA synthesis. RNA was then hydrolyzed, and a 3' DNA adaptor was ligated to ssDNA fragments, which were then PCR enriched with barcoded, adaptor-seated Illumina PCR primers. Final libraries were isolated by SPRI purification (forward SPRI x2), and paired-end sequenced on Illumina NextSeq (38 bp x2).

treatment_protocol: GSI-washout: Treated with Compound E (1μM) for 72 h, washed 1x in media containing vehicle (DMSO) only, and then cultured for 4 h in media containing vehicle (DMSO) only.

value: GSI-washout


title: SP49_gsi-wo_RNA-Seq_r2

description: Poly-A RNA


title: SP49_gsi-wo_RNA-Seq_r1

description: Poly-A RNA


title: PDX98848_7_RNA-Seq_dbz

value: Mouse spleen


title: SP49_gsi-gsi_RNA-Seq_r3

description: Poly-A RNA

treatment_protocol: GSI-mock-washout: Treated with Compound E (1μM) for 72 h, washed 1x in media containing 1μM Compound E, and then cultured for 4 h in media containing 1μM Compound E.

value: GSI-mock-washout


title: SP49_gsi-gsi_RNA-Seq_r2

description: Poly-A RNA


title: SP49_dmso_RNA-Seq_r3

description: Poly-A RNA

treatment_protocol: DMSO: Grown for 76 h in media containing vehicle (DMSO) only.

value: DMSO


title: SP49_dmso_RNA-Seq_r2

description: Poly-A RNA


title: SP49_gsi-gsi_RNA-Seq_r1

description: Poly-A RNA


title: Mino_DLL1-IgG-gsi-wo_RNA-Seq_r3

description: Poly-A RNA

source_name: Mino cell line

treatment_protocol:
GSI-washout: Treated with Compound E (1μM) for 48 h, washed 1x in media containing vehicle (DMSO) only, and then cultured for 4 h in media containing vehicle (DMSO) only.
Plated on immobilized Notch ligand (DLL1-IgG).

value: Mino

tag: other treatment

value: Notch ligand (DLL1-IgG)


title: Mino_DLL1-IgG-gsi-wo_RNA-Seq_r1

description: Poly-A RNA


title: Mino_DLL1-IgG-gsi-gsi_RNA-Seq_r3

description: Poly-A RNA

treatment_protocol:
GSI-mock-washout: Treated with Compound E (1μM) for 48 h, washed 1x in media containing 1μM Compound E, and then cultured for 4 h in media containing 1μM Compound E.
Plated on immobilized Notch ligand (DLL1-IgG).


title: Mino_DLL1-IgG-gsi-gsi_RNA-Seq_r1

description: Poly-A RNA


title: Mino_DLL1-IgG-DMSO_RNA-Seq_r3

description: Poly-A RNA

treatment_protocol:
DMSO: Grown for 52 h in media containing vehicle (DMSO) only.
Plated on immobilized Notch ligand (DLL1-IgG).


title: Mino_DLL1-IgG-gsi-gsi_RNA-Seq_r2

description: Poly-A RNA


title: Mino_DLL1-IgG-gsi-wo_RNA-Seq_r2

description: Poly-A RNA


title: Mino_DLL1-IgG-DMSO_RNA-Seq_r2

description: Poly-A RNA


title: SP49_dmso_RNA-Seq_r1

description: Poly-A RNA


title: Mino_DLL1-IgG-DMSO_RNA-Seq_r1

description: Poly-A RNA


title: Mino_ctrl-IgG-DMSO_RNA-Seq_r3

description: Poly-A RNA

treatment_protocol:
DMSO: Grown for 52 h in media containing vehicle (DMSO) only.
Plated on immobilized control ligand (IgG).

value: Control ligand (IgG)


title: Mec-1_wce

data_processing:
ChIP-Seq: Reads were aligned to the hg19 genome assembly using bwa-aln and bwa-sampe (bwa version 0.7.12).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-Seq: Data were filtered to remove PCR duplicates and reads mapping to >2 genomic sites. Then .tdf display files were generated with igvtools count.

source_name: Mec-1 cell line

extract_protocol:
ChIP-Seq: Cells were crosslinked by addition of 1% formaldehyde to media at 37 C for 10 minutes, followed by glycine quenching and 2x washing in PBS. Nuclei were isolated by hypotonic buffer lysis, and chromatin was fragmented with a Branson sonifier in a 1% SDS-containing lysis buffer. Samples were diluted 1:10 and chromatin complexes containing the target of interest were isolated by immunoprecipitation, followed by reverse crosslinking and DNA purification by SPRI. For input samples, 1:10 diluted sonicated chromatin (whole cell extract; wce) was added directly to the reverse crosslinking step without immunoprecipitation.
ChIP-Seq: Purified ChIP or input DNA was end-repaired and A-tailed. Illumina barcoded adaptors were ligated and PCR amplified. Final library was isolated by double SPRI purification (sequential reverse and forward SPRI) and paired-end sequenced (38 bp x 2) on Illumina NextSeq.

value: Chronic lymphocytic leukemia cell line

tag: chip antibody

value: input


title: Mino_ctrl-IgG-DMSO_RNA-Seq_r2

description: Poly-A RNA


title: Mino_ctrl-IgG-DMSO_RNA-Seq_r1

description: Poly-A RNA


title: PDX98848_2_RNA-Seq_veh

tag: tissue

value: Mantle cell lymphoma xenograft

value: Vehicle


title: Mec-1_H3K27ac

value: H3K27ac (Active Motif, catalog #39133)


title: Z138_wce

source_name: Z138 cell line

value: Mantle cell lymphoma cell line


title: SP-49_gsi-wo_H3K27ac-r3


title: SP-49_gsi-wo_H3K27ac-r2


title: Z138_H3K27ac


title: SP-49_RBPJ

value: RBPJ (Cell Signaling, catalog #5313)


title: SP-49_gsi-wo_H3K27ac-r1


title: SP-49_gsi-gsi_H3K27ac-r2


title: SP-49_MAML1

value: MAML1 (Cell Signaling, catalog #12166)


title: SP-49_wce


title: SP-49_dmso_H3K27ac-r3


title: SP-49_gsi-gsi_H3K27ac-r3


title: Rec-1_RBPJ_gsi-wo-r1


title: Rec-1_RBPJ_gsi-gsi-r2


title: Rec-1_NICD1_gsi-gsi-r2

value: NICD1 (Cell Signaling, catalog #4147)


title: SP-49_dmso_H3K27ac-r2


title: Rec-1_NICD1_gsi-gsi-r1


title: SP-49_dmso_H3K27ac-r1


title: Rec-1_RBPJ_gsi-wo-r2


title: Rec-1_NICD1_gsi-wo-r2


title: Mino_DLL1-IgG-DMSO_NICD1


title: Mino_DLL1-IgG-gsi-wo_H3K27ac_r2


title: Mino_DLL1-IgG-gsi-gsi_H3K27ac_r2


title: Rec-1_H3K27ac_gsi-wo-r2


title: Mino_DLL1-IgG-DMSO_RBPJ


title: Rec-1_H3K27ac_gsi-gsi-r2


title: Rec-1_MAML1


title: Rec-1_RBPJ


title: Rec-1_H3K27ac_gsi-gsi-r1


title: Mino_DLL1-IgG-DMSO_H3K27ac_r2


title: Mino_DLL1-IgG-gsi-wo_H3K27ac_r1


title: Maver-1_H3K27ac

source_name: MAVER-1 cell line


title: Sample_E3_CaMac9

city: Clayton

first: Traude

last: Beilharz

state: VIC

address: Wellington Rd

department: Biomedicine Discovery Institute

country: Australia

institute: Monash University

description: Illumina index 9

data_processing:
In order to assign reads to C. albicans or M. musculus: Reads are first stripped of poly(A) sequence and adaptors using Tail Tools (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools). Reads are then aligned to both genomes using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Finally Xenomapper (https://github.com/genomematt/xenomapper) is used to assign reads to one or other genome based on the alignment score.
Reads assigned to each genome are then processed separately using the Tail Tools pipeline (https://github.com/Victorian-Bioinformatics-Consortium/tail-tools):  Reads are aligned using bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml). Multi-mapping reads are assigned to one location at random.  Alignments are extended where the stripped poly(A) sequence matches As present in the genome. A poly(A) tail is called present if there are at least four untemplated As remaining in the stripped sequence.  Reads aligning to genes are counted. As 3'UTR annotations are not always accurate, reads up to 400 bases down-strand of a gene, but not extending into another gene on the same strand, are counted towards that gene. Total reads per gene, reads with a poly(A) tail per gene, and average poly(A) tail length are tabulated.
Genome_build: C. albicans SC5314 assembly 21, and M. musculus from release 82 of Ensembl
Supplementary_files_format_and_content: Data is provided both for C. alibicans in the calbicans_... files, and for M. musculus in the mouse_... files.  Names in calbicans_... files are identifiers from C. albicans assembly 21. Names in mouse_... files are Ensembl gene ids.    ..._count.csv files give read counts for each gene in each sample. ..._tail.csv files give average poly(A) tail length for each gene in each sample. ..._tail_count.csv give the number of reads having a poly(A) tail. (The average poly(A) tail length is a less accurate estimate of tail length where there are fewer reads with a poly(A) tail.)

organism: Candida albicans

source_name: Candida/macrophages

growth_protocol: For dual RNA-seq experiment, BMDMs were infected with the C. albicans clinical isolate SC5314 at the multiplicity of infection of 3 Candida cells to 1 macrophage, and samples taken over a time course. Candida only and macrophage only samples were also grown in parallel, as controls.

extract_protocol:
Candida infected macrophage cultures were harvested by adding Trizol reagent to lyse macrophages. Two independent experiments were performed. These Trizol samples were centrifuged to divide the Candida fraction as pellet, and macrophages as supernatant. To obtain a sufficient yield of both Candida and macrophage RNA, total RNA isolation of the macrophage fraction was performed by the Trizol method, and Candida RNA was extracted by the hot phenol method. After preparation of total RNA, Candida and macrophage samples were pooled. The quality of total RNA was checked with the Bioanalyzer. One microgram of total RNA was used for library preparation by the PAT-seq method (Harrison et al., 2015).
Library construction was by the PAT-seq approach (Harrison et al 2015)
Cluster Generation: 9pM of libraries per lane using Illumina c-bot. Illumina protocol 15006165 Rev J, July 2012
Sequencing chemistry: 1 x 150bp sequencing using Illumina protocol 15035788 Rev A, Oct 2012

tag: strain backround

value: Wild type Candida/Mouse bone marrow derived macrophage


title: Sample_E3_CaMac6

description: Illumina index 6


title: JVM2_H3K27ac

source_name: JVM2 cell line


title: Mino_DLL1-IgG-DMSO_H3K27ac_r1


title: Rec-1_RBPJ_gsi-gsi-r1


title: Mino_ctrl-IgG-DMSO_H3K27ac_r2


title: CLL-B08_RNA-Seq-Notch1Mut-ICN1high

data_processing:
Reads were aligned to the hg19 genome assembly and iGenomes UCSC annotation using STAR.
Genome_build: hg19
Supplementary_files_format_and_content: HTSeq was used to quantify reads mapping to the iGenomes UCSC genes hg19 transcript annotation, with read-through genes removed to prevent exon exclusion.

source_name: Chronic lymphocytic leukemia B08

extract_protocol:
Frozen sections of lymph nodes containing >90% CLL cells were processed with Trizol per manufacturer's instructions to isolate RNA.
100ng of total RNA was used as input for library construction with the Next Ultra RNA Library Prep Kit for Illumina (New England BioLabs).

value: Lymph node

tag: tissue/cell type

value: Chronic lymphocytic leukemia biopsy

tag: notch1 mutation/expression

value: NOTCH1-PESTmut, ICN1-positive


title: Rec-1_H3K27ac_gsi-wo-r1

value: GSI-washout


title: Maver-1_wce


title: Mino_ctrl-IgG-DMSO_H3K27ac_r1

value: Mino

value: DMSO


title: Mino_DLL1-IgG-gsi-gsi_H3K27ac_r1

value: GSI-mock-washout

value: Notch ligand (DLL1-IgG)


title: Sample_E3_Ca6

description: Illumina index 4

source_name: Candida

value: wild type Candida


title: Sample_E1_CaMac9

description: Illumina index 12


title: Sample_E3_Ca1

description: Illumina index 1


title: JVM2_wce

value: input


title: CLL-B07_RNA-Seq-Notch1Mut-ICN1high

source_name: Chronic lymphocytic leukemia B07


title: Sample_E3_Mac6

description: Illumina index 5

organism: Mus musculus

source_name: macrophages

value: Mouse bone marrow derived macrophages


title: Sample_E1_CaMac1

description: Illumina index 18


title: HBL2_H3K27ac

source_name: HBL2 cell line

value: H3K27ac (Active Motif, catalog #39133)


title: HBL2_wce

value: Mantle cell lymphoma cell line


title: Sample_E1_Ca9

description: Illumina index 10


title: Sample_E3_CaMac1

description: Illumina index 3


title: Sample_E3_Ca9

description: Illumina index 7


title: Rec-1_NICD1_gsi-wo-r1


title: Sample_E1_Mac6

description: Illumina index 23


title: CLL-B01_RNA-Seq-Notch1WT-ICN1low

source_name: Chronic lymphocytic leukemia B01

value: NOTCH1-WT, ICN1-negative


title: SP-49_gsi-gsi_H3K27ac-r1


title: Sample_E1_Mac1

description: Illumina index 17


title: Sample_E1_Ca1

description: Illumina index 15


title: CLL-B05_RNA-Seq-Notch1Mut-ICN1high

source_name: Chronic lymphocytic leukemia B05


title: Sample_E3_Mac9

description: Illumina index 8


title: CLL-B06_RNA-Seq-Notch1Mut-ICN1high

source_name: Chronic lymphocytic leukemia B06


title: CLL-B04_RNA-Seq-Notch1WT-ICN1low

source_name: Chronic lymphocytic leukemia B04


title: CLL-B02_RNA-Seq-Notch1WT-ICN1low

source_name: Chronic lymphocytic leukemia B02


title: Sample_E1_Ca6

description: Illumina index 21


title: Sample_E3_Mac1

description: Illumina index 2


title: pH 6.3_36h

status: Public on Jun 02 2018

city: Philadelphia

first: Chi

middle: Van

last: Dang

state: PA

address: 3601 Spruce St

institute: Wistar Institute

description: RNA from U2OS cells in media of pH 6.3 for 36 hours

data_processing:
aligned to reference genome (h38) using Spliced Transcripts Alignment to a Reference (STAR) aligner (https://github.com/alexdobin/STAR)  using GENCODE v22 annotation as the guiding transcriptome.
aligned RNA-Seq reads (BAM files) were processed through Cufflinks (http://cole-trapnell-lab.github.io/cufflinks/) to assemble and quantify transcripts using GENCODE v22 as the reference transcriptome annotation
Fragments per kilobase per million mapped reads (FPKM) calculation was used to normalize read count by dividing it by the gene length and total number of reads mapped to genes
Filtered to protein coding genes (using GENCODE v22 annotation)
Processed data file (matrix) available here includes all protein coding genes. Data was further filtered to only those protein coding genes with mean FPKM over all 26 timepoints (pH 7.4 and pH 6.3 combined) greater than 2 for analyses presented in associated publication.
Genome_build: hg38
Supplementary_files_format_and_content: txt file; FPKM (fragments per killobase per million)

source_name: U2OS cells

growth_protocol: Human U2OS osteosarcoma cells expressing a circadian clock reporter (Arntl::dLUC) were maintained in standard DMEM (4 mM L-glutamine, 25 mM glucose) supplemented with 10% FBS and 1x penicillin/streptomycin in standard 5% CO2 37°C humidified tissue culture incubators.

extract_protocol:
TRIzol extraction (Invitrogen) according to the manufacturer's instructions. Media was aspirated from cells growing in 35 mm dishes. 1 mL of TRIzol Reagent was added to plates. A cell scraper was then used to collect cells and lysate which was frozen at -80 until RNA isolation following the manufacturer’s instructions with substitution of 1-Bromo-3-chloropropane for chloroform. RNA integrity was verified by bioanalyzer (Agilent Technologies) (RNA integrity number (RIN) 8.7-10.0, median = 9.7).
Illumina TruSeq Stranded mRNA Library Preparation kit

treatment_protocol: Total RNA was collected every 4 hours from U2OS cells treated with media of pH 7.4 or pH 6.3. In detail, each arm (pH 7.4 and pH 6.3) of this 52-hour timecourse with 4-hour intervals of RNA harvest was collected as a pair of staggered 24- and 28-hour parallel timecourses. Three days prior to the timecourse start, 375,000 U2OS Arntl::dLUC cells were seeded in 35 mm dishes and allowed to grow in normal DMEM in 5% CO2. Twenty-four hours later, another set of plates was seeded in identical fashion. Twenty-four hours later, cells of the first set were then synchronized and half were treated with media of pH 7.4 and half with media of pH 6.3.  Twenty-four hours later, the second set of plates was synchronized and treated with media of pH 7.4 and 6.3 in identical fashion. Harvest of RNA began four hours later with the 4-hour and 28-hour samples of each arm being collected together, followed four hours later by the 8-hour and 32-hour samples and so forth. Medias of pH 7.4 and 6.3 were DMEM medias with 5% FBS and 0.25x penicillin/streptomycin buffered with 25 mM PIPES and 25 mM HEPES (in place of the bicarbonate/5% CO2 buffering system) and adjusted to the indicated pH. Media additionally contained 0.1 uM dexamethasone to synchronize cells in circadian time at timecourse initiation. After application of pH 7.4 or 6.3 media, plates were sealed with vacuum grease to prevent desiccation and moved to atmospheric CO2 incubators.

tag: media ph

tag: time point

value: 36 hours

value: osteosarcoma

value: U-2 OS


title: pH 6.3_28h

description: RNA from U2OS cells in media of pH 6.3 for 28 hours

value: 28 hours


title: pH 6.3_4h

description: RNA from U2OS cells in media of pH 6.3 for 4 hours

value: 4 hours


title: pH 6.3_48h

description: RNA from U2OS cells in media of pH 6.3 for 48 hours

value: 48 hours


title: pH 6.3_44h

description: RNA from U2OS cells in media of pH 6.3 for 44 hours

value: 44 hours


title: pH 6.3_24h

description: RNA from U2OS cells in media of pH 6.3 for 24 hours

value: 24 hours


title: CLL-B03_RNA-Seq-Notch1WT-ICN1low

source_name: Chronic lymphocytic leukemia B03

value: Lymph node

value: Chronic lymphocytic leukemia biopsy


title: Sample_E1_CaMac6

description: Illumina index 24

value: Wild type Candida/Mouse bone marrow derived macrophage


title: pH 7.4_48h

description: RNA from U2OS cells in media of pH 7.4 for 48 hours


title: pH 6.3_20h

description: RNA from U2OS cells in media of pH 6.3 for 20 hours

value: 20 hours


title: pH 6.3_32h

description: RNA from U2OS cells in media of pH 6.3 for 32 hours

value: 32 hours


title: pH 6.3_16h

description: RNA from U2OS cells in media of pH 6.3 for 16 hours

value: 16 hours


title: Sample_E1_Mac9

description: Illumina index 11

value: Mouse bone marrow derived macrophages


title: pH 7.4_28h

description: RNA from U2OS cells in media of pH 7.4 for 28 hours


title: pH 7.4_4h

description: RNA from U2OS cells in media of pH 7.4 for 4 hours


title: pH 7.4_44h

description: RNA from U2OS cells in media of pH 7.4 for 44 hours


title: pH 6.3_52h

description: RNA from U2OS cells in media of pH 6.3 for 52 hours

value: 52 hours


title: pH 7.4_40h

description: RNA from U2OS cells in media of pH 7.4 for 40 hours

value: 40 hours


title: pH 7.4_32h

description: RNA from U2OS cells in media of pH 7.4 for 32 hours


title: RNAseq_PRMT5KD_2

city: New York

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

data_processing:
RNA-seq: Reads were mapped to mm9 build of the mouse genome from University of California Santa Cruz (UCSC) genome database using TopHat version 2.0.12 with the aligner Bowtie [41] with their default parameters and by supplying the gene model annotations from Ensemble (version NCBIM37.65).
RNA-seq: Differential expression analysis was performed by Cuffdiff 2.2.1 with threshold of FDR less than 0.05 and fold change more than 1.5.
ChIPseq: The ChIP-seq data was first checked for quality using the various metrics generated by FastQC (v0.11.2).
ChIPseq: Raw sequencing reads were then aligned to the mouse mm10 genome using default settings of Bowtie (v2.2.0).
ChIPseq: Peak-calling was performed using MACS (v2.1.1) with default settings.
Genome_build: mm9 and mm10
Supplementary_files_format_and_content: A single text file with tabulated RPKM values for all RNAseq samples and genes
Supplementary_files_format_and_content: One bigWig file per ChIPseq sample

source_name: primary OPCs

growth_protocol: OPCs were cultured in plates coated with Poly-D-lysine and proliferation medium supplemented with bFGF and PDGFA.

extract_protocol:
mRNAs were extracted with Tryzol and the RNeasy kit from Qiagen; chromatin from the cells were extracted and digested with Mnase for the ChIP experiments.
Library construction for the RNA-seq was performed with the TruSeq Total RNA Stranded kit from Illumina; library construction for the ChIP-seq was performed with a constomized protocol at the laboratory of Emily Bernstein.

treatment_protocol: OPCs were infected by lenti-EGFP-CRISPR (control) and lenti-PRMT5-CRISPR (PRMT5-KD) respectively, and harvested after 6 days of infection

value: oligodendrocyte progenitor cells

tag: derived from

value: P6 C57Black /6J mice

tag: genotype/variation

value: without PRMT5 expression


title: RNAseq_Control_2

value: control


title: pH 7.4_20h

description: RNA from U2OS cells in media of pH 7.4 for 20 hours

value: osteosarcoma

value: U-2 OS


title: pH 7.4_16h

description: RNA from U2OS cells in media of pH 7.4 for 16 hours


title: pH 7.4_12h

description: RNA from U2OS cells in media of pH 7.4 for 12 hours

value: 12 hours


title: Gfi1KD Young - moue 83395

status: Public on Jun 01 2018

city: Montreal

first: Möröy

last: Tarik

state: Quebec

address: 110 Pine avenue West

country: Canada

institute: Insititut de Recherches Cliniques

data_processing:
RNA-Seq reads were aligned to mm10 using Tophat v2.0.10
Reads were processed with Samtools.
For differential expression, countfiles were generated by mapping reads to Ensembl genes using HTSeq. Further analysis was carried out using the DESeq R package
Genome_build: mm10
Supplementary_files_format_and_content: txt files are tab-delimited text files containing counts on GRCm38 v77 Ensembl genes

source_name: total bone marrow

extract_protocol:
RNA was extracted using a MagMax-96 Total RNA Isolation kit (Ambion) and quality-checked with a RNA 6000 Pico kit (Agilent).
RNA-Seq, libraries were prepared from RNA extracts using the TruSeq Stranded mRNA kit from Illumina according to the manufacturer’s instructions and sequenced using using the TruSeq PE Clusterkit v3-cBot-HS.

tag: strain

tag: age (days)

tag: leukemia status

value: no AML


title: pH 7.4_36h

description: RNA from U2OS cells in media of pH 7.4 for 36 hours

value: 36 hours

tag: cell type

tag: cell line


title: Gfi1KO Old - mouse 81346


title: pH 7.4_52h

description: RNA from U2OS cells in media of pH 7.4 for 52 hours


title: pH 6.3_12h

description: RNA from U2OS cells in media of pH 6.3 for 12 hours


title: RNAseq_PRMT5KD_3


title: pH 7.4_24h

description: RNA from U2OS cells in media of pH 7.4 for 24 hours

value: 24 hours


title: pH 6.3_8h

description: RNA from U2OS cells in media of pH 6.3 for 8 hours

value: 8 hours


title: RNAseq_PRMT5KD_0


title: RNAseq_PRMT5KD_1


title: RNAseq_Control_0


title: bulked_168h_rep2

city: Geneva

first: Leonardo

last: Beccari

address: 30 Quai Ernest Ansermet

department: Genetics and Evolution

country: Switzerland

institute: University of Geneva

description: pool of 5 orgaoids collected at 168h after aggregation

data_processing:
Illumina Casava1.8.2 software used for basecalling.Replicate data set was concatenated together.
Demultiplexed RNA-seq reads were mapped onto the public available GRCm38 (mm10). using TopHat release 2.0.9 (Kim et al., 2013). TopHat output files were processed with SAMTools (Li et al., 2009) and BedTools (Quinlan, 2014) to extract the unique read coverage along the genome. For visualisation and comparison across samples, the read coverage was divided by the number of millions of mapped reads in each sample.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of the RNAseq read coverage, divided by the number of millions of mapped reads in each sample.

source_name: gastruloids

growth_protocol: mESCs were cultured on gelatinised tissue-culture flasks in a humidified incubator (5% CO2, 37°C). mESCs were cultured in GMEM supplemented with 10% foetal bovine serum (FBS), non-essential amino acids (NEAA), sodium pyruvate, GlutaMax, beta-mercaptoethanol and LIF (ESL).

extract_protocol:
Gastruloids were collected at different time points after aggregation, pooled in 15ml Falcon tubes and pelleted by centrifuging at 1000 rpm for 5min. After washing with cold PBS gastruloids were re-suspended in 100ml of RNA (Thermo fisher) and stored at -80°C until RNA extraction. The number of gastruloids collected for each replicate varied depending on their size: 295 at 24h AA; 105 at 48h AA; 37 at 72h AA; 14 for 96h AA and 5 for 120, 144 and 168h AA.  The RNA was extracted using the RNAeasy mini kit (Qiagen) following the manufacturer’s instructions. Contaminant DNA was eliminated using the on-column DNAase digestion and RNA was eluted in RNAase free water. RNA was quantified with the Qubit HS RNA quantification kit (Thermo fisher) and the integrity assessed with bioanalyser.
RNA-seq libraries were prepared from 100ng of pure total RNA using the TruSeq Stranded mRNA protocol from Illumina with polyA selection

treatment_protocol: mESCs were harvested from tissue-culture flasks, centrifuged and washed twice with warm PBS (containing Ca2+ and Mg2+). After the final wash, cells were re-suspended in a volume (~3-4ml) of fresh, warm N2B27 (NDiff) and the cell concentration determined. The number of cells required to form gastruloids with a diameter at 48h of ~150µm (~300 cells) was determined and seeded in each well of a round-bottomed, low-adherence 96-well plate as 40µl droplets of N2B27. A 24h pulse of 150µl 3µM Chi was added at 48h after aggregation (AA). Medium (150µl) was replaced with the same volume of fresh N2B27 daily.

tag: age

value: Whole gastruloid

tag: genotype


title: bulked_96h_rep2

description: pool of 14 orgaoids collected at 96h after aggregation


title: bulked_72h_rep2

description: pool of 37 orgaoids collected at 72h after aggregation


title: pH 6.3_40h

description: RNA from U2OS cells in media of pH 6.3 for 40 hours


title: Gfi1KD Sick - mouse 66513

value: AML


title: bulked_48h_rep2

description: pool of 105 orgaoids collected at 48h after aggregation


title: Gfi1KO Young - mouse 83095


title: Gfi1KO Old - mouse 79445


title: Gfi1KD Young - mouse 83425


title: pH 7.4_8h

description: RNA from U2OS cells in media of pH 7.4 for 8 hours


title: bulked_144h_rep2

description: pool of 5 orgaoids collected at 144h after aggregation


title: bulked_144h_rep1


title: Gfi1KO Young - mouse 83200


title: bulked_24h_rep1

description: pool of 295 orgaoids collected at 24h after aggregation


title: bulked_72h_rep1


title: bulked_120h_rep2

description: pool of 5 orgaoids collected at 120h after aggregation


title: RNAseq_Control_1


title: bulked_168h_rep1


title: bulked_24h_rep2


title: bulked_96h_rep1


title: bulked_120h_rep1


title: RNAseq_Control_3


title: bulked_48h_rep1


title: A_SMAD4_WT_3

city: Nashville

first: Jing

last: Zhu

state: TN

institute: Vanderbilt University

description:
SMAD4_WT
Colon epithelium from Smad4ΔLrig1 and from Smad4+ control mice was isolated. Total RNA was isolated from these tissues using RNeasy kit (Qiagen).
DEG_P3027_S15_20_May10_2017.txt

data_processing:
Casava and bcl2fastq v2.16 were used for demultiplexing data from HiSeq2500 and HiSeq3000, seperately.
We mapped the reads to the mouse genome mm10 using TopHat-2.1.0 (Kim et al. 2013). Then, following the method of Anders (Anders et al. 2013), we counted the number of reads that fall into annotated genes by samtools-1.3.1 (Li et al. 2009) and HTSeq-0.5.4p5 (Anders et al. 2014).
Finally, we performed count-based differential expression analysis using edgeR_3.4.2 (McCarthy et al. 2012) which implements general differential analyses based on the negative binomial model.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized count values and differential expression analysis results for each Sample

source_name: Colon

extract_protocol:
Total RNA was isolated using RNeasy kit (Qiagen). Processing of RNA using a TruSeq Stranded mRNA sample prep kit was conducted according to the manufacturer’s instructions (Illumina, San Diego, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colon epithelia


title: A_SMAD4_KO_3

description:
SMAD4_KO
Colon epithelium from Smad4ΔLrig1 and from Smad4+ control mice was isolated. Total RNA was isolated from these tissues using RNeasy kit (Qiagen).
DEG_P3027_S15_20_May10_2017.txt


title: SJMMNORM014682_G1

city: Memphis

first: David

last: Finkelstein

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

data_processing:
Basecalling was performed using Illumina Casava 1.7
FASTQ sequences adapter trimmed (curtadapt) and mapped to the mouse mm9 genome by a pipeline that serially  employs STAR and BWA
Mapped reads were counted with HTSEQ
Genome_build: mm9
Supplementary_files_format_and_content: count files are txt format files that contain raw read counts that map  to  transcripts for each defined gene.

source_name: ceca 21 days following TM infection

growth_protocol: not applicable

extract_protocol:
Total RNA was isolated using QIAzol and the RNeasy Mini Kit (Qiagen) from enriched cecal epithelial cells of uninfected Villin-Cre+::Riox2(flox/flox) and Villin-Cre+::Riox2(+/+) littermates; and from ceca of Riox2(-/-) and Riox2(+/+) littermates 21 days following TM infection.
Libraries were prepared from ~500 ng total RNA with the TruSeq RNA Library Preparation Kit v2 according to manufacturer’s instructions (Illumina, San Diego CA)

treatment_protocol: 21 day infection with parasitic gastrointestinal nematodes

tag: infection

value: 21 day long  GI infection by TM

value: ceca


title: SJMMNORM014677_G1


title: A_SMAD4_WT_2


title: Mutant_L1_H3K27ac_ChIPseq

city: Haining

first: Chaochen

last: Wang

address: 718 East Haizhou Rd

department: ZJU-UoE Institute

country: China

institute: Zhejiang University

data_processing:
Basecalls performed using the CASAVA software
ChIP-seq reads were aligned to the mm10 genome assembly using the Bowtie2 program (Langmead et al., Nature method, 2012)
The HOMER ((http://homer.salk.edu/homer/) software was used to convert alignment map files into bedGraph files with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: BedGraph files can be used to check ChIP-seq peaks through the UCSC genome browser.

source_name: L1 mammary gland

growth_protocol: Mutant mice were generated by CRIPSR/Cas9 genome editing. All animals were handled and housed in accordance with the guidelines of the NIH and experiments were approved by the ACUC of NIDDK.

extract_protocol:
Frozen-stored mammary tissues were broken into powder with mortar and pestle. Nuclei were extracted in Farnham lysis buffer (5mM PIPES pH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitors). Antibodies against H3K27ac (Abcam, Ab4729), H3K4me3 (Millipore, 17-614), PolII (Abcam, ab5408) were used for ChIP.
Libraries were prepared for sequencing using standard Illumina protocols.

value: Mammary gland

tag: time

value: Lactation day 1

value: MutA

tag: chip antibody

value: H3K27ac (Abcam, Ab4729)


title: A_SMAD4_WT_1

tag: tissue


title: ui_LPS

city: La Tronche

first: Alexandre

last: Bougdour

state: Isère

address: Domaine de la Merci, Campus santé

department: Prevention and Therapy of Chronic diseases

country: France

institute: Centre de Recherche Inserm U1209 / CNRS UMR5309 / UGA

data_processing:
The RNA-Seq reads (FASTQ) were processed and analyzed using the Lasergene Genomics Suite version 14 (DNASTAR, Madison, WI, USA) using default parameters.
The paired-end reads were uploaded onto the SeqMan NGen (version 14, DNASTAR. Madison, WI, USA) platform for reference-based assembly using either the Mus musculus genome package (GRCm38.p3) or the Toxoplasma Type II ME49 strain (ToxoDB-24, ME49 genome) as reference template.
The ArrayStar module (version 14, DNASTAR. Madison, WI, USA) was used for normalization, differential gene expression and statistical analysis of uniquely mapped paired-end reads using the default parameters.
The expression data quantification and normalization were calculated using the RPKM (Reads Per Kilobase of transcript per Million mapped reads) normalization method.
Genome_build: Mus musculus genome package (GRCm38.p3)
Genome_build: Toxoplasma Type II ME49 strain (ToxoDB-24, ME49 genome)
Supplementary_files_format_and_content: xlsx format. The matrix table includes RPKM values and log2 transformed values for each Sample for both BMDM and T. gondii transcripts.

source_name: BMDMs

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) supplemented with 10% heat-inactivated FBS (Invitrogen), 20% conditioned medium from macrophage-colony stimulating factor-secreting L929 fibroblasts (Aziz et al., 2009), 50 μM 2-mercaptoethanol, 1X non-essential amino acids (Thermo Fisher Scientific), 10 mM Hepes buffer, pH 7.2, 2 mM L-glutamine, and 50 μg/ml penicillin and streptomycin (Thermo Fisher Scientific). Cells were incubated at 37°C in 5% CO2.

extract_protocol:
Total RNAs were extracted and purified using TRIzol (Invitrogen, Carlsbad, CA, USA) and RNeasy Plus Mini Kit (Qiagen). RNA quantity and quality were measured by NanoDrop 2000 (Thermo Scientific). RNA integrity was assessed by standard non-denaturing 1.2% TBE agarose gel electrophoresis. The ribosomal large subunits from Toxoplasma and the host cells was used to verify that the ratio between Toxoplasma RNA versus host RNA was equivalent between the different biological samples, thus indicating that the samples had equivalent infection rates.
RNA libraries were prepared for sequencing using standard Illumina protocols (Illumina TruSEQ RNA library prep).

treatment_protocol: 18 hours after infection, cells were subjected or not to LPS stimulation for 4 hours before being harvested for RNA extraction.

tag: mice strain

value: BALB/c

tag: parasite strain

value: Macrophages

tag: treatment

value: LPS

tag: parasite genotype


title: ui


title: SJMMNORM013210_G1-NJ3755

source_name: enriched cecal epithelial cells

value: uninfected

value: cecal epithelial cells


title: A_SMAD4_KO_1


title: Clone6_R2

city: Baltimore

first: Jie

state: Maryland

address: 400 N Broadway

institute: Johns Hopkins University

data_processing:
After removing adaptors using Trimmomatic, 101-base paired-end reads were mapped to the hg19 genome assembly using STAR
We then calculated the counts of reads for each gene through HTSeq
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text files include the counts of genes for each Sample following columns: Ensembl ID, Symbol of gene, Count of genes

source_name: Mutated SVG

growth_protocol: The human astroglial cell line SVG-10B1 was originally established by Dr. Major and obtained via a material transfer agreement

extract_protocol: Samples were subjected to Illumina HiSeq next generation sequencing following the standard amplification and library construction protocol provided by the Johns Hopkins Deep Sequencing and Microarray Core Facility

treatment_protocol: SVG cells were cultured in Dulbecco’s Minimum Essential Media (DMEM, Thermo Fisher Scientific, Grand Island, NY) supplemented with 10%  fetal calf serum (FCS, Gemini Bio-products, West Sacramento, CA). Cells were incubated in a humidified incubator containing 5% CO2/95% air at 37°C, and passaged every 2-4 days

tag: cell line background

value: human astroglial cell line

value: IDH1 R132H/WT

tag: clone

value: clone 6

tag: replicate


title: Clone6_R1

tag: genotype/variation


title: Microspace fiber rep3

city: Lincoln

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence then mapped to rice genome using bowtie bowtie -v 0 -S -a --best --strata
Reads counts for each gene with  htseq-count
Genome_build: Human genome GRC37/Hg19
Supplementary_files_format_and_content: Tab-delimited plain text files: the first column is gene IDs and the second column is reads counts

source_name: Embryonic Stem Cell

growth_protocol: H9s were cultued in 2D, static 3D and dynamic 3D suspension and in the microspace cell culture system in Essential 8 medium for 3 days. mRNAs were sequenced.

extract_protocol:
Cells were harvested on day 3 and total RNA was isolated with RNAeasy isolation kit (Qiagen) according to manufacturer’s instructions. On-column DNAse treatment was performed to remove genomic DNA contamination (Qiagen).
Libraries were prepared using TruSeq RNA v2 library preparation reagents. 12 samples were sequenced per lane.

treatment_protocol: no treatment

value: Embryonic Stem Cell

tag: strain


title: Microspace fiber rep2

tag: cell type


title: Mutant_L1_H3K4me3_ChIPseq

value: H3K4me3 (Millipore, 17-614)


title: SJMMNORM014679_G1


title: SJMMNORM014680_G1


title: SJMMNORM013212_G1-NJ3705


title: SJMMNORM014678_G1


title: Dynamic 3D rep3


title: Gfi1KD Sick - mouse 63542

tag: age (days)

tag: leukemia status

value: AML


title: Dynamic 3D rep1


title: SJMMNORM014676_G1

tag: genotype

value: 21 day long  GI infection by TM


title: SJMMNORM013211_G1-NJ3759

tag: infection


title: Static 3D rep3


title: Static 3D rep1


title: A_SMAD4_KO_2

value: Colon epithelia


title: Clone2_R1

value: clone 2


title: SVG_R2

source_name: Wild-type astroglial cell line SVG

value: wild-type

value: clone 1


title: 2D rep3


title: SVG_R1


title: 2D rep2


title: 2D rep1


title: Microspace fiber rep1


title: Dynamic 3D rep2


title: Static 3D rep2


title: UM-UC3_sh#1

city: Guang zhou

first: Changhao

last: Chen

state: Guangdong

address: yanjiang road

department: Department of Urology

institute: Sun Yat-Sen Memorial Hospital

description:
UM-UC-3 cells were infected by lentivirus using sh1 to obtain stable expression cell  lines.
processed_data.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome（version:hg38）using Hisat2（version:2.0.4）.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Anders S, et al., Bioinformatics 2015, 31(2):166-169 and Robinson MD, et al. Genome Biol 2010, 11(3):R25. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: bladder cancer cell UM-UC-3

growth_protocol: The human bladder cancer cell lines UM-UC-3 and 5637 from American Type Culture Collection. UM-UC-3 cells were cultured in Dulbecco's modified eagle's medium and 5637 cells were cultured in RPMI 1640. All media contained fetal bovine serum, 100 U/ml penicillin, and 100 μg/ml streptomycin. All Cells were cultured in an incubator with 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.
The library was prepared with TruSeq Stranded mRNA LT Sample Prep Kit (Cat. No.15032612,Illumina) according to manufacturer’s instructions.

treatment_protocol: After 72 hr transfection, the viral supernatants of 293T cells were collected. Lentiviral particles were concentrated using a LentiX™ Concentrator overnight at 4°C. UM-UC-3 and 5637 cells (5×105 cells per well) were seeded in six-well culture plates and infected with lentivirus and polybrene for 24 hr. Cells were infected by lentivirus with the presence of polybrene and selected by puromycin for 2 weeks to obtain stable expression cell lines.

tag: cell line

value: LNMAT1 was depleted with shRNA#1


title: SJMMNORM013209_G1-NJ3725


title: 5 days WNT5A 1

city: Houston

first: Malgorzata

last: Borowiak

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description:
mRNA
Processed data file: GEO WNT5A FC_bio repeats.xls
Processed data file: GEO FPKM Wnt5a 5d.xlsx

data_processing:
For 'GEO_WNT5A_FC_bio_repeats.xls':
NextSeq Control Software v2.0 used for base calling.
Quality control and trimming were performed using FastQC.
The resulting reads were mapped to the reference genome (UCSC hg19) using STAR (Dobin et al., 2013) with NCBI RefSeq genes as the reference.
In order to reduce possible PCR biases, we removed the read duplicates using Picard tools (http://broadinstitute.github.io/picard/).
HTseq (http://www-huber.embl.de/users/anders/HTSeq) was used to determine the number of reads falling in the known genes.
EdgeR (Robinson et al., 2010) and DESeq2 (Love et al., 2014) were used to analyze the gene-based read counts to detect differentially expressed genes between the groups of interest.
The false discovery rate (FDR) of the differentially expressed genes was estimated using Benjamini and Hochberg method. FDR < 0.1 was considered statistically significant.
For 'GEO_WNT5A_FC_tech_repeats.xlsx':
NextSeq Control Software v2.0 used for base calling.
Two replicates were concatenated and analysed as single samples.
Quality control and trimming were performed using FastQC.
Remaining reads were uniquely mapped to the reference genome (assembly GRCh38) utilizing STAR.
Number of raw reads and TPM (Transcript per Million) values were used for differential expression analysed with EBSeq package.
Fragment per kilobase million of library size (FPKM) were calculated using Cufflinks Assembly & DE v1.1.0.
Enrichment of Gene Ontology terms and metabolic pathways were analysed using ConsensusPathDB.
Genome_build: GEO_WNT5A_FC_bio_repeats.xls: GRCh37 (UCSC hg19); GEO_WNT5A_FC_tech_repeats.xlsx: GRCh38
Supplementary_files_format_and_content: GEO_WNT5A_FC_bio_repeats.xls file includes FC from EdgeR and DESeq analysis and false discovery rate (FDR).
Supplementary_files_format_and_content: GEO_WNT5A_FC_tech_repeats.xlsx file includes PPEE (posterior probability), PostFC (posterior fold change FC) and RealFC (real fold change) values for WNt5A treatment sample/UT sample from EBSeq analysis.
Supplementary_files_format_and_content: GEO_FPKM_Wnt5a_5d.xlsx file includes FPKM values for the samples treated for 5 days.

source_name: hESC-derived EPs, WNT5A for 5 days

growth_protocol: hESC-derived endocrine progenitors (EPs).

extract_protocol:
Phenol-chloroform with TRIzol.
TruSeq Stranded mRNA kit.

treatment_protocol: Untreated control samples (maintained in B27) and samples treated with WNT5A for 12h or 5 days.

value: WNT5A for 5 days

tag: developmental stage

value: pancreatic beta cell


title: 12hr Untreated 1

description:
mRNA
Processed data file: GEO WNT5A FC_bio repeats.xls

source_name: hESC-derived EPs, untreated for 12 hr

value: hESC-derived endocrine progenitors (EPs)

value: untreated for 12 hr

value: endocrine progenitor (EP)


title: 12hr Untreated 2

description:
mRNA
Processed data file: GEO WNT5A FC_tech repeats.xlsx
Processed data file: GEO WNT5A FC_bio repeats.xls


title: 5 days WNT5A 2

description:
mRNA
Processed data file: GEO WNT5A FC_tech repeats.xlsx
Processed data file: GEO WNT5A FC_bio repeats.xls
Processed data file: GEO FPKM Wnt5a 5d.xlsx


title: 5 days Untreated 1

source_name: hESC-derived EPs, untreated for 5 days

value: untreated for 5 days


title: UM-UC3_NC

description:
UM-UC-3 cells were infected by lentivirus using NC to obtain stable expression cell  lines.
processed_data.txt

value: Negative control


title: 5637_sh#1

description:
5637 cells were infected by lentivirus using sh1 to obtain stable expression cell  lines.
processed_data.txt

source_name: bladder cancer cell 5637


title: SJMMNORM014681_G1

tag: tissue

value: ceca


title: UM-UC3_sh#2

description:
UM-UC-3 cells were infected by lentivirus using sh2 to obtain stable expression cell  lines.
processed_data.txt

value: LNMAT1 was depleted with shRNA#2


title: 5637_sh#2

description:
5637 cells were infected by lentivirus using sh2 to obtain stable expression cell  lines.
processed_data.txt


title: 12hr WNT5A 1

source_name: hESC-derived EPs, WNT5A for 12 hr

value: WNT5A for 12 hr


title: 5 days Untreated 2


title: Mutant_L1_PolII_ChIPseq

value: Mammary gland

tag: time

value: Lactation day 1

value: MutA

tag: chip antibody

value: PolII (Abcam, ab5408)


title: BCa4

city: Guangzhou

address: Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, 107 Yan-Jiang Xi Road, Guangzhou, 510120, China

institute: Sun yat-sen university

description: Total RNA was extracted using Trizol reagent and was further purified using Qiagen RNeasy Mini Kit. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and was quantitated spectrophotometrically.

data_processing:
HCS1.5.15.1,RTA1.13.48 and OLB 1.9.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome（version:hg19）using TopHat（TopHat v2.0.10）.
cufflinks v2.2.1 was used to assembles transcripts, estimates their abundances, and tests for differential expression
Assess the protein-coding potential of novel transcripts by CPC(v0.9-r2)
iSeeRNA was used to perform identification of long intergenic non-coding RNA transcripts
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

source_name: bladder cancer tissue

growth_protocol: The formalin-fixed, paraffin-embedded bladder cancer specimens were collected from patients who underwent surgery at Sun Yat-sen Memorial Hospital of Sun Yat-sen University. All samples were immediately snap-frozen in liquid nitrogen and stored at −80 ˚C until required. All samples were pathologically confirmed by two pathologists with hematoxylin-eosin (H&E) staining. Ethical consent was approved by Committees for Ethical Review of Research involving Human Subjects of Sun Yat-sen University. The written informed consent was obtained from all patients before sample collection.

extract_protocol:
Total RNA was extracted from tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. After DNase I treatment, Ribo-Zero Magnetic Kit is used to remove rRNA before constructing the RNA-seq libraries.By using the fragmentation buffer, the mRNAs and non-coding RNAs are fragmented into short fragments(about 200~500nt), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates, and dTTP is substituted by dUTP during the synthesis of the second strand. 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, then the second strand is degraded using UNG(Uracil-N-Glycosylase) finally. 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.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: bladder cancer tissue

tag: gender

value: Male

tag: age


title: 5637_NC

description:
5637 cells were infected by lentivirus using NC to obtain stable expression cell  lines.
processed_data.txt

tag: treatment


title: BCa2

treatment_protocol: All samples were pathologically confirmed by two pathologists with hematoxylin-eosin (H&E) staining. Ethical consent was approved by Committees for Ethical Review of Research involving Human Subjects of Sun Yat-sen University.


title: 12hr WNT5A 2


title: BCa5


title: NAT4

source_name: normal adjacent tissue

value: normal adjacent tissue


title: BCa3


title: LN(+)_5

source_name: lymph node-positive bladder cancer tissue


title: LN(-)_4

source_name: lymph node-negative bladder cancer tissues


title: LN(+)_4

value: lymph node-positive bladder cancer tissue


title: LN(-)_3

value: lymph node-negative bladder cancer tissues


title: NAT5


title: LN(-)_2


title: LN(+)_3


title: LN(+)_2


title: NAT2


title: NAT1


title: LN(-)_1


title: DK-S46

city: Durham

first: Liuyang

state: NC

address: 0049 CARL Building

institute: Duke University

description: Infected by Salmonella Typhimurium

data_processing:
RNA-seq data were processed using the TrimGalore toolkit (Krueger, 2017), which employs Cutadapt (Martin, 2011) to trim low quality bases and Illumina sequencing adapters from the 3’ end of the reads. Only reads that were 20nt or longer were kept for further analysis. Reads were mapped to the GrCh37v75 version of the human genome and transcriptome (Kersey et al., 2012) using the STAR RNA-seq alignment tool (Dobin et al., 2013).
Reads were kept for subsequent analysis if they mapped to a single genomic location. Gene counts were compiled using the HTSeq tool (Anders et al., 2015). Only genes that had at least 10 reads in any given library were used in subsequent analysis.
Normalization and differential expression was carried out using the DESeq2 (Love et al., 2014)
Genome_build: GRCH37v75
Supplementary_files_format_and_content: tab-delimited text files include read counts for each Sample

source_name: Lymphoblastoid Cell lines

extract_protocol:
RNA was harvested 24 hours post infection with RNAprotect and RNeasy Plus kit (Qiagen)
Library preparation was performed using Illumina TruSeq Stranded RNA-Seq kit by the Duke University Sequencing and Genomic Technologies Core Facility.

treatment_protocol: LCLs GM19154 and GM19203 were plated at 2 million cells per well of a 24-well plate and infected with wild-type or ΔsarA S. Typhimurium at MOI50. After 1 hour, gentamicin (50ug/mL) was added to kill extracellular bacteria.

value: GM19203 B cell line

value: Salmonella Typhimurium


title: NAT3


title: DK-S48

description: Infected by ΔsarA Salmonella Typhimurium

value: ΔsarA Salmonella Typhimurium


title: DK-S28

value: GM19154 B cell line


title: BCa1


title: LN(-)_5


title: DK-S30

description: Infected by Salmonella Typhimurium


title: DK-S44


title: LN(+)_1


title: DK-S32


title: DK-S14

description: Infected by Salmonella Typhimurium


title: Lck-I rep2

city: Providence

first: Nikos

last: Tapinos

state: RHODE ISLAND

address: 593 Eddy street

department: Neurosurgery

institute: Brown University

data_processing:
Illumina BCL2fastq v.1.8.4 was used for basecalling and masking of adapter sequences
Sequence reads were mapped to the hg19 build of the human genome using gsnap with default parameters, looking for know and novel splice sites with the options -N 1 -s Has_37_67_splicesites
Read with a mapping quality of 20 or greater were summarized at the gene level, by counting all reads mapping to any region of any isoform of a gene, using in-house scripts and information from the refGene.txt file of Refseq (http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz)
The number of reads mapped to a gene was standardized to Read per Million (RPM), and genes expressing less than 5 RPM in at least two samples were discarded, leaving 12152 genes for analysis
Gene expression analysis was done in R, with the limma package and using the Benjamini-Hochberg method to control the False Discovery Rate
Genome_build: hg19
Supplementary_files_format_and_content: Tab-separated text files with RPM values for the 12152 genes use for gene expression analysis

source_name: Lck-I treated_Glioblastoma

extract_protocol:
Human glioblastomas were microdissected from the brains of Nu/L mice, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human glioma stem cells were orthotopically transplanted in the brain of NU/J mice under stereotactic guidance. Following the cell transplantation, 2 mice were treated with intraventricular delivery of Lck-I for 4 weeks through an ALZET pump, while 3 mice received the diluent (Controls).

tag: host mouse strain

value: NU/J mice

tag: tranplanted with

value: human glioma stem cells

value: brain

tag: treated with

value: Lck-I


title: DK-S16


title: DK-S42

description: Infected by Salmonella Typhimurium


title: Control rep3

value: Control (Kolliphor ELP + PBS)


title: DK-S12


title: DK-S10

description: Infected by Salmonella Typhimurium


title: msh1 memory 33

city: State College

first: Sally

middle: A

last: Mackenzie

address: 362 North Frear

department: Biology

institute: Penn State University

data_processing:
Illumina for basecalling
Alignments were performed using RUM 2.0.4 (default parameters) (Grant et al., 2011) keeping only uniquely mapped reads
The read count data were generated from the SAM files by using QoRTs software package (Hartley and Mullikin, 2015) --stranded --singleEnded --minMAPQ 25 --dropChrom Pt,Mt
DESeq2 (Love, M.I., Huber, W., Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 Genome Biology 15(12):550 2014) was used for gene count normalization and to identify differentially expressed genes (FDR < 0.05, |log2FC| > 0.5. GTF file TAIR10.31
Genome_build: TAIR 10
Supplementary_files_format_and_content: Text file with GENEID and COUNTS to be used with DESeq2

organism: Arabidopsis thaliana

growth_protocol: clean seeds were sown on peat mix in square pots, with stratification at 4 °C for 2 days before moving to growth chamber (22 °C, 120-150 μmol/(m^2*s) light)

extract_protocol:
total RNA from each sample was extracted by NucleoSpin RNA Plant kit (Macherey-Nagel, Germany) following manufacturer’s protocol, including genomic DNA removal.
RNA libraries were constructed as described in the TruSeq RNA Sample Preparation v2 Guide.
These libraries were sequenced with the 150-bp reads option, in Hi-Seq 4000 analyzer (Illumina, USA) at BGI-Tech (Shenzhen, China).

treatment_protocol: three individual plants of wild type Arabidopsis thaliana ecotype Col-0 and three isogenic msh1 memory line plants were used. Whole plants at early bolting were flash frozen in liquid nitrogen.  Tissues were ground by motor and pestle in liquid nitrogen

tag: genotype/variation

value: msh1 memory


title: Control rep2


title: Control rep1


title: DK-S26

description: Infected by Salmonella Typhimurium


title: msh1 memory 32


title: wildtype 24

value: wild type


title: msh1 memory 31


title: wildtype 23


title: msh1 memory [33]

data_processing:
The sequences were trimmed using trim_galore 0.4.1 with options --paired --trim1 --gzip --phred33 --fastqc and cutadapt 1.9.1  with cutoff 20
The sequences were aligned using Bismark 0.15.0 with options --bam --multicore 8 --bowtie2 -p 16 -phred33-quals
tab-delimited file generated with bismark2bedGraph with options -CX --ample_memory
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-delimited file, 1-based genomic with chr, start, strand, number of cytosines (methylated bases)   #' and number of thymines (unmethylated bases),context, trinucletide context fields

source_name: msh1 memory

extract_protocol:
genomic DNA extraction using DNeasy Plant kit (Qiagen, Germany). Genomic DNA from three individual plants for both WT and msh1 memory line were used for subsequent Bisulfite methylome sequencing experiment.
Genomic DNA Sonicated to 100-300 bp fragments and purified with MiniElute PCR Purification Kit (Qiagen, Germany), incubated at 20 ℃ after add End Repair Mix. Then purified and added a single ‘A’ nucleotide to the 3’ ends of the blunt fragments, purified again and add Methylated Adapter to the 5’ and 3’ ends of each fragment. Then fragments with 300bp-400bp size-range were purified with QIAquick Gel Extraction kit (Qiagen, Germany) and subjected to bisulfite treatment by using Methylation-Gold kit (ZYMO). Followed with PCR and gel purification (350bp-400bp range fragments were selected). Qualified libraries sequenced pair end on the HiSeq X-ten system.

treatment_protocol: three individual plants of wild type Arabidopsis thaliana ecotype Col-0 and three isogenic msh1 memory line plants were used. Whole plants at early bolting were flash frozen in liquid nitrogen.  Tissues were ground by motor and pestle in liquid nitrogen

tag: ecotype

value: msh1 memory


title: msh1 memory [32]


title: indivi_120h_rep10

description: RNAseq on whole gastruloid collected 120h AA

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Demultiplexed RNA-seq reads were mapped onto the public available GRCm38 (mm10). using TopHat release 2.0.9 (Kim et al., 2013). TopHat output files were processed with SAMTools (Li et al., 2009) and BedTools (Quinlan, 2014) to extract the unique read coverage along the genome. For visualisation and comparison across samples, the read coverage was divided by the number of millions of mapped reads in each sample.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph of the RNAseq read coverage, divided by the number of millions of mapped reads in each sample.

source_name: single gastruloid

extract_protocol:
For RNAseq of individual gastruloids, 10 from each stage (24h, 72h and 120h AA) were individually collected and transferred to 1.5ml Eppendorf tube. After centrifugation, gastruloids were washed once with cold PBS, re-suspended in lysis buffer, and RNA extracted immediately using the RNAeasy micro kit (Qiagen) with on column DNAase digestion. RNA was quantified with the Qubit HS RNA quantification kit (Thermo fisher) and the integrity assessed with bioanalyser.
For each of the replicates of the 24h AA gastruloids, a total of 0.65ng RNA were used for the library preparation while 8ng total RNA from 72h and 120h AA were used for the RNA sequencing. Libraries were prepared using the SMART-seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech) and the Nextera XT library preparation kit (Illumina) following the manufacturer’s instructions.

tag: strain

value: Whole gastruloid


title: indivi_120h_rep9


title: indivi_120h_rep5


title: indivi_120h_rep7


title: indivi_120h_rep6


title: indivi_120h_rep1


title: wildtype 22


title: indivi_120h_rep4


title: indivi_120h_rep8


title: wildtype [22]

source_name: wildtype

value: wildtype


title: indivi_120h_rep2


title: wildtype [24]


title: msh1 memory [31]


title: wildtype [23]


title: indivi_24h_rep10

description: RNAseq on whole gastruloid collected 24h AA


title: indivi_24h_rep8


title: indivi_24h_rep7


title: indivi_24h_rep9


title: indivi_24h_rep4


title: indivi_24h_rep3


title: indivi_120h_rep3


title: indivi_24h_rep2


title: indivi_24h_rep1


title: 25_rep1

city: Davis

first: Susan

middle: E.

last: Lott

state: CA

address: 2320 Storer Hall

department: Evolution and Ecoloty

institute: University of California, Davis

data_processing:
adapters were removed from reads using Cutadapt 1.7.1
reads were (pseudo)aligned and transcript abundances quantified using Kallisto 0.43.1
Genome_build: Ensembl assembly BDGP6

organism: Drosophila melanogaster

source_name: 25% food, replicate 1

growth_protocol: 50 eggs placed in food of differing percentages, which hatched, fed as larvae on different food treatments, and became adults. Adults were placed into egg collection bottles (10 female, 10 male), and stage 2 embryos (Bownes' stages) were collected for RNA extractions.

extract_protocol:
TRIzol reagent extraction of total RNA from single embryos.
Standard Illumina mRNA-Seq library prep protocols, using KAPA mRNA stranded reagents

treatment_protocol: Parents of harvested eggs were raised during their larval stages on food of different percentages. Food was either provided at full strength (100%, or diluted to 25% or 5% of normal concentration with agar and water.

value: single stage 2 embryo

value: larval

tag: maternal food


title: 25_rep3

source_name: 25% food, replicate 3


title: 100_rep3

source_name: 100% food, replicate 3


title: 5_rep1

source_name: 5% food, replicate 1


title: 100_rep2

source_name: 100% food, replicate 2


title: 25_rep2

source_name: 25% food, replicate 2


title: 5_rep2

source_name: 5% food, replicate 2


title: smallRNA-Seq_MCF-7/S0.5

city: Aarhus

first: Jian

last: Li

address: The Bartholin Building

department: Institute of Biomedicine

country: Denmark

institute: Aarhus University

description:
estrogen-dependent and tamoxifen sensitive
Small RNA
LB-new8
processed data file: LCCs_TAMRs_miRNA_processed_data.txt

data_processing:
Base calling software: Illumina Casava1.7
Sequenced reads were trimmed for adaptor sequence, then the miRNA sequences were subject to alignment to known human mature miRNA sequence from miRBase using miRNAkey software.
Estimation of the expression levels of the identified miRNAs was performed by calculating the value of RPKM (Reads Per Kilobase of exon per Million fragments mapped) using miRNAkey software.
Genome_build: hg19, miRBase release 20
Supplementary_files_format_and_content: Tab-delimited text files include the significantly differented expression miRNAs and the correpsonding RPKM values between the tamoxifen-resistant cell lines and their parental cell line in the LCC cell line model or the TAMR cell line model.

source_name: Breast cancer cell line derived from MCF-7

growth_protocol: The TAMR cell lines were maintained in DME/F12 (1:1) medium supplemented with 1% FCS and 1 μM tamoxifen. The LCC cell lines were cultured in DMEM/F12 without phenol red, supplemented with 5% DCC and 1% penicillin/streptomycin. The cells were maintained at 37°C in a humidified atmosphere of 95% ambient air and 5% CO2.

extract_protocol:
Total RNA was extracted from the cell lines with TRI Reagent (Sigma) according to the manufacturer’s protocol. The extracted total RNA was verified by agarose gel electrophoresis, and the concentration was estimated by NanoDrop (Thermo Scientific). Furthermore, BioAnalyzer 2100 RNA Chip (Agilent) were used to ensure the quality, quantity and integrity for the messenger RNA (mRNA). Subsequently, the total RNA was subject to digestion of DNase I (New England BioLabs), and then purified by ethanol precipitation for subsequent analyses.
RNA libraries were prepared for sequencing using standard Small RNA Illumina protocol

treatment_protocol: For the TAMR cell line model, the MCF-7 cells were gradually adapted to grow in low serum concentration (initially 0.5% fetal calf serum (FCS) and 1% FCS  after phenol-red was omitted from the culture medium) and the tamoxifen-sensitive sub-line MCF-7/S0.5 was used to establish tamoxifen-resistant (TAMR) cell lines by extended treatment with 1 µM tamoxifen. The 4 TAMR cell lines:  MCF-7/TAMR-1 (TAMR-1), MCF-7/TAMR-4 (TAMR-4), MCF-7/TAMR-7 (TAMR-7) and MCF-7/TAMR-8 (TAMR-8) were derived from distinct colonies that emerged in cultures of MCF-7/S0.5 cells treated with 1 µM tamoxifen. For the LCC cell line model, LCC0 is derived from MCF-7 presenting estrogen-dependent and tamoxifen-responsive phenotype. LCC1 was established from the estrogen-dependent parent cell line MCF-7 through prolonged withdrawal from potent estrogenic stimuli both in vivo and in vitro. The above in vivo selected cell line was further passaged in ovary-comprised nude mice and re-established in vitro to generate a new cell line, MCF-7/LCC1, which is estrogen-independent, but tamoxifen-responsive as its parent cell line. Furthermore, a new cell hormone-independent, tamoxifen-resistant subline, LCC2 was developed through growth of LCC1 in incrementally increased dosages of tamoxifen in vitro. And a new cell hormone-independent, cross-resistance to tamoxifen and fluvestrant subline, LCC9 was developed through growth of LCC1 in incrementally increased dosage of fluvestrant.

value: Breast cancer


title: smallRNA-Seq_LCC2

description:
derived from LCC1 with increased small-dosage tamoxifen treatment, estrogen-independent, and tamoxifen-resistant
Small RNA
LB-new2
processed data file: LCCs_TAMRs_miRNA_processed_data.txt


title: smallRNA-Seq_LCC9

description:
derived from LCC1 with increased small-dosage fluvestrant treatment, estrogen-independent, and cross-resistance to fluvestrant and tamoxifen
Small RNA
LB-new1
processed data file: LCCs_TAMRs_miRNA_processed_data.txt


title: smallRNA-Seq_TAMR1

description:
tamoxifen-resistant
Small RNA
LB-new9
processed data file: LCCs_TAMRs_miRNA_processed_data.txt


title: smallRNA-Seq_LCC1

description:
estrogen-independent and tamoxifen sensitive
Small RNA
LB-new3
processed data file: LCCs_TAMRs_miRNA_processed_data.txt


title: smallRNA-Seq_TAMR8

description:
tamoxifen-resistant
Small RNA
LB-new12
processed data file: LCCs_TAMRs_miRNA_processed_data.txt


title: smallRNA-Seq_TAMR7

description:
tamoxifen-resistant
Small RNA
LB-new11
processed data file: LCCs_TAMRs_miRNA_processed_data.txt


title: smallRNA-Seq_LCC0

description:
estrogen-dependent and tamoxifen sensitive
Small RNA
LB-new4
processed data file: LCCs_TAMRs_miRNA_processed_data.txt


title: 100_rep1

source_name: 100% food, replicate 1


title: indivi_24h_rep5

tag: genotype


title: smallRNA-Seq_TAMR4

description:
tamoxifen-resistant
Small RNA
LB-new10
processed data file: LCCs_TAMRs_miRNA_processed_data.txt


title: indivi_24h_rep6


title: WT_5

city: Nanjing

first: You-Qiang

last: Su

state: Jiangsu

address: 140 Hanzhong Road

department: State Key Laboratory of Reproductive Medicine

institute: Nanjing Medical University

data_processing:
All RNA-seq reads passed filter were trimmed to remove low-quality bases and adaptor sequences. Reads then were aligned to the mm10 reference genome using tophat2 (v2.0.13)
Reads aligned to genes are counted by cufflinks (v2.2.1). The FPKMs are normalized usingcuffnorm. Differentially expressed genes are calculated using cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: ovary

extract_protocol:
Total RNA was extracted with RNeasy Mini Kit (Qiagen, Germantown, MD, USA) according to manufacturer's instructions, and 500 ng was then taken out from each of them and subjected to mRNA isolation using NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB, Ipswich, MA, USA).
The mRNA library was constructed using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, Ipswich, MA) according to the instruction manual, which includes sequential RNA fragmentation, reverse transcription using random primers, second strand cDNA synthesis, end repair, dA-tailing, adapter ligation, U excision, and PCR enrichment.

treatment_protocol: Mice used for the experiment were initially primed with PMSG at the dose of 5 IU/mouse. Forty-six  hours later, they were euthanized, and their ovariaies were collected and lysed in 350ul RLT buffer for RNA extraction.

value: 6 months

value: Wild type

value: ovary


title: 50_120L_20W_C3

city: Blacksburg

first: Chang

last: Lu

state: VA

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

department: Chemical Engineering

institute: Virginia Tech

description: LIFE-ChIP-seq data. Name format: Cell Number_Loading Volume_Washing Time_Chamber Number_Device Number(If applicable)

data_processing:
Raw reads were trimmed with TrimGalore 0.4.1
Trimmed reads were aligned using bowtie 1.1.2
Reads were extended to 250bp
Sample was normalized and input subtracted
Sample was converted to BigWig format
Genome_build: hg19
Supplementary_files_format_and_content: Normalized ChIP-seq signal in BigWig format

source_name: GM12878 cell line

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

extract_protocol:
Sample containing 10^6 cells was used as the starting material and centrifuged at 1,600 g for 5 min and washed twice with 1 ml cold PBS. Cells were crosslinked by adding 1 ml freshly made 1% formaldehyde and incubating at room temperature for 5 min on a shaker. Crosslinking was promptly terminated by adding 50 µl of 2.5 M glycine and shaking for 5 min. The pellet was resuspended in 130 μl Covaris buffer (10 mM Tris-HCl, pH 8.1, 1 mM EDTA, 0.1% SDS and 1× protease inhibitor cocktail) and sonicated using the following conditions. Using Covaris M 220 (Covaris), the sample was sheared at 4 oC with 75 W peak incident power, 5% duty factor, and 200 cycles per burst for 12 min. The sheared sample was centrifuged in a 4 oC centrifuge at 14,000g for 10 min, and the supernatant was transferred to a new tube. Sheared chromatin was diluted with IP buffer (20 mM Tris-HCl, pH 8.0, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% (w/v) sodium deoxycholate, 0.1% SDS, 1% (v/v) Triton X-100, with 1% freshly added PMSF and PIC) and aliquoted into 25 μl samples containing 250, 500, 1500, and 5,000 cell samples and stored at -80 oC.
Library preparation was performed using the Swift Bio S2 library preparation kit (Swift Biosciences) using 40 μl of purified DNA. 2.5 μl of the low EDTA TE buffer in the 50 μl amplification cycle reaction mix was replaced with 2.5 μl of 20x EvaGreen, and amplification was terminated after samples saw an >3000 RFU increase (BioRad CFX Connect). Amplified DNA was then eluted into 7 μl low EDTA TE buffer where 2 μl could be used for qPCR analysis for preliminary quality control analysis, Kappa DNA quantification, and Tapestation fragment size analysis and the other 5 μl for library pooling. Libraries were pooled at 10 nM for sequencing by Illumina HiSeq 4000 with single-end 50 nt read. LIFE-ChIP-seq (Low-Input Fluidized-bed Enabled Chromatin Immunoprecipitation combined with sequencing), procedures are detailed in our paper

tag: antibody

value: Anti-trimethyl-Histone H3 (Lys4), Millipore 07-473

tag: cell number


title: 50_120L_20W_C1

tag: cell line


title: 100_120L_20W_C4_Device6


title: 50_120L_20W_C4


title: WT_7

tag: tissue


title: 5_rep3

source_name: 5% food, replicate 3

tag: developmental stage


title: WT_6


title: input


title: WT_2


title: WT_4


title: WT_3


title: 100_120L_20W_C1_Device6


title: 100_120L_20W_C2_Device6


title: 100_120L_20W_C3_Device6


title: 50_120L_20W_C2


title: 100_120L_20W_C3_Device5


title: WT_1


title: 100_120L_20W_C4_Device5


title: 100_120L_20W_C2_Device5


title: 100_120L_20W_C1_Device5


title: 300_30L_10W_C3


title: CKO_5

value: Gdf9-Cre mediated Mtor Oocyte-Conditional Knockout (CKO)


title: CKO_2


title: CKO_4


title: 300_30L_10W_C4


title: CKO_3


title: 300_30L_10W_C2


title: CKO_1


title: 300_120L_20W_C2_Device4


title: 300_120L_20W_C3_Device4


title: 300_120L_20W_C4_Device4


title: 300_120L_20W_C1_Device4


title: 300_120L_20W_C3_Device3


title: 300_120L_20W_C2_Device3


title: 300_30L_10W_C1


title: 300_120L_20W_C4_Device3


title: 300_120L_20W_C1_Device3


title: 1K_120L_30W_C4


title: 1K_120L_30W_C3


title: 1K_120L_30W_C2


title: 1K_120L_20W_C4_Device2


title: 1K_120L_20W_C3_Device2


title: 1K_120L_20W_C1_Device2


title: 1K_120L_20W_C2_Device1


title: 1K_120L_20W_C2_Device2


title: 1K_120L_20W_C1_Device1


title: 1K_30L_20W_C1


title: 1K_120L_10W_C3


title: 1K_30L_20W_C3


title: 1K_120L_20W_C4_Device1


title: 1K_120L_20W_C3_Device1


title: 1K_30L_20W_C4


title: 1K_120L_10W_C4


title: 1K_120L_10W_C2


title: 1K_120L_10W_C1


title: 1K_120L_0W_C1


title: 1K_30L_20W_C2


title: 1K_120L_0W_C4


title: rnh1∆rnh201∆_RNAseq_rep2

first: Frederic

last: Chedin

address: 1 Shields Avenue

department: MCB

institute: UC Davis

description:
total RNA
RNA-seq
1x50 bp Hiseq 2500

data_processing:
DRIPc-seq and RNA-seq: All fastq files were trimmed with fastq-mcf before mapping.
DRIPc-seq: Trimmed fastq reads were mapped to hg19 using Bowtie2.1.0. DRIPc-seq peak calling was performed using HMM as described in methods.
RNA-seq: Trimmed fastq reads were mapped to S.pombe genome version ASM294v2 using TopHat 2.0.5. Normalized count table and log2 fold change were generated using DESeq2
Genome_build: ASM294v2
Supplementary_files_format_and_content: tsv: DESeq2 table count and log2Fold change. bigWig: binary of wiggle file

organism: Schizosaccharomyces pombe

source_name: Schizosaccaromyces pombe

growth_protocol: For RNA-seq analysis, cells were grown in PMG medium and shifted at 34°C for 3 hours before being collected. For DRIPc-seq, cells were grown at 30°C, in PMG or in YES as indicated

extract_protocol:
Total RNA was extracted from Schizosaccaromyces pombe cells using hot phenol.
NEXTflex™ Rapid Directional mRNA-Seq Kit
For RNA-seq, total RNA were extracted with hot phenol according to the classic procedure. For DRIPc-seq, genomic DNA was extracted after spheroplasting S.pombe cells.
RNA-seq: according ot the manufacturer's instructions. DRIPc-seq: according to the manusfacturer's instructions omitting the step of poly-A enrichment and the step of RNA fragmentation.

treatment_protocol: DRIPc-seq samples were either treated with RNase A alone, RNase A + RNase H or RNase A + RNase III as indicated.

tag: mutation

value: rnh1delta rnh201delta


title: pRnhA_RNAseq_rep2

description:
total RNA
RNA-seq
1x50 bp Hiseq 2500

value: E.coli rnhA o/e


title: 1K_120L_0W_C3


title: 1K_120L_0W_C2


title: pRnhA_RNAseq_rep3

description:
total RNA
RNA-seq
1x50 bp Hiseq 2500


title: pRnhA_RNAseq_rep1

description:
total RNA
RNA-seq
1x50 bp Hiseq 2500


title: 1K_120L_30W_C1


title: WT_RNAseq_rep3

description:
total RNA
RNA-seq
1x50 bp Hiseq 2500


title: rnh1∆rnh201∆_RNAseq_rep1

description:
total RNA
RNA-seq
1x50 bp Hiseq 2500


title: WT_RNAseq_rep1

description:
total RNA
RNA-seq
1x50 bp Hiseq 2500


title: WT_RNAseq_rep2

description:
total RNA
RNA-seq
1x50 bp Hiseq 2500


title: WT_smallRNAseq_rep3

description:
small RNA
RNA-seq (size fractionation)
1x50 bp Hiseq 2500

extract_protocol:
Small RNA was extracted from Schizosaccaromyces pombe cells.
NEXTflex™ Rapid Directional mRNA-Seq Kit
For RNA-seq, total RNA were extracted with hot phenol according to the classic procedure. For DRIPc-seq, genomic DNA was extracted after spheroplasting S.pombe cells.
RNA-seq: according ot the manufacturer's instructions. DRIPc-seq: according to the manusfacturer's instructions omitting the step of poly-A enrichment and the step of RNA fragmentation.

value: WT


title: WT_smallRNAseq_rep2


title: WT_smallRNAseq_rep1


title: TBP_Rap1_Sth1aa_V

city: Geneva

first: Slawomir

last: Kubik

address: quai Ernest-Ansermet 30

department: Molecular Biology Department

institute: University of Geneva

data_processing:
Raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
Data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For nucleosome occupancy tracks, each paired-end read was trimmed by 15 bp at each end to improve separation of nucleosome peaks.
For ChEC-seq experiments, the mapped reads were extended by 1 bp only to indicate cut sites.
For ChIP-seq, the reads were shifted by 150 bp and extended by 50 bp.
Genome_build: sacCer3 (R64)
Supplementary_files_format_and_content: bigWig files were obtained using HTSStation (http://htsstation.epfl.ch).

organism: Saccharomyces cerevisiae

source_name: whole organism

growth_protocol: Cells were grown at 30 degrees in YPD to mid-log phase before treatment.

extract_protocol:
TBP-myc and Rpb1 ChIP-seq was performed as described previously (Ribaud et al., 2012) (PMID: 21952045).
TruSeq ChIP library preparation kit (Illumina).

treatment_protocol: No rapamycin.

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 STH1-FRB-KanMX RAP1-FRB-RAP1-LEU2 SPT15-13xmyc-KanMX

tag: chip antibody

value: anti-Myc (homemade)


title: TBP_Reb1_Sth1aa_R

treatment_protocol: 60 minutes rapamycin.

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 STH1-FRB-KanMX REB1-FRB-HIS3MX SPT15-13xmyc-KanMX


title: TBP_Abf1_Sth1aa_V

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 STH1-FRB-KanMX ABF1-FRB-KanMX SPT15-13xmyc-KanMX


title: TBP_Rap1aa_R

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 RAP1-FRB-RAP1-LEU2 SPT15-13xmyc-KanMX


title: Rpb3_Sth1aa_R

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 STH1-FRB-KanMX SPT15-13xmyc-KanMX

value: Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) (Abcam ab5131)


title: TBP_Abf1_Sth1aa_R


title: Lck-I rep1

source_name: Lck-I treated_Glioblastoma

value: NU/J mice

value: human glioma stem cells

value: brain

value: Lck-I


title: TBP_Reb1_Sth1aa_V


title: Rpb3_Sth1aa_V


title: TBP_Rap1_Sth1aa_R


title: TBP_Reb1aa_V

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 REB1-FRB-HIS3MX SPT15-13xmyc-KanMX


title: TBP_Abf1aa_V

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 ABF1-FRB-KanMX SPT15-13xmyc-KanMX


title: TBP_Rap1aa_V


title: TBP_Reb1aa_R


title: TBP_Sth1aa_R


title: freeMNase_2m30s

data_processing:
Library strategy: ChEC-seq
Raw reads were aligned to the sacCer3 genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
Data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For nucleosome occupancy tracks, each paired-end read was trimmed by 15 bp at each end to improve separation of nucleosome peaks.
For ChEC-seq experiments, the mapped reads were extended by 1 bp only to indicate cut sites.
For ChIP-seq, the reads were shifted by 150 bp and extended by 50 bp.
Genome_build: sacCer3 (R64)
Supplementary_files_format_and_content: bigWig files were obtained using HTSStation (http://htsstation.epfl.ch).

growth_protocol: Cells were grown at 30 degrees in YPD to OD600=0.7.

extract_protocol:
DNA was prepared as described in Zentner et al., 2015 (PMID: 26490019).
Libraries were prepared as described in Zentner et al., 2015 (PMID: 26490019).

treatment_protocol: 2.5 minutes of 5 mM calcium.

value: W303 PReb1-3xFLAG-MNase-HphMX


title: Rsc8-MNase_30s

treatment_protocol: 30 seconds of 5 mM calcium.

value: W303 RSC8-3xFLAG-MNase-HphMX


title: Rsc8-Mnase_10s

treatment_protocol: 10 second of 5 mM calcium.


title: TBP_Sth1aa_V


title: TBPaa_R_highMNase

extract_protocol:
Chromatin for MNase digestion was prepared essentially as described in Kubik et al., 2015 (GSE73337) (PMID: 26545077).
Libraries were prepared essentially as described in Henikoff et al., 2011 (GSE30551) (PMID: 22025700).

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 SPT15-FRB-KanMX


title: freeMNase_20m

treatment_protocol: 20 minutes of 5 mM calcium.


title: TBPaa_V_highMNase


title: TBPaa_R_lowMNase


title: Rap1_Sth1aa_R_highMNase

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 STH1-FRB-KanMX RAP1-FRB-RAP1-LEU2


title: TBPaa_V_lowMNase


title: Rap1_Sth1aa_V_lowMNase


title: Reb1_Sth1aa_R_highMNase

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 STH1-FRB-KanMX REB1-FRB-HIS3MX


title: Abf1_Sth1aa_R_highMNase

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 STH1-FRB-KanMX ABF1-FRB-KanMX


title: PRIM3

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

data_processing:
Reads from RNAsequencing were aligned to the mouse reference genome GRCm38 using STAR. Number of reads aligned to genes were counted using FeatureCounts and count-per-million (CPM) values were calculated using edgeR.
Genome_build: mm10

source_name: skin

extract_protocol:
Skin samples were finely minced using scissors and digested for 45 min at 37 °C in RPMI medium containing DNase I, Collagenase I, Liberase and Dispace. For adult skin, epidermis was removed prior to cutting in an additional Dispase digestion step.
Full length cDNA were generated from 10 ng of total RNA using the SMART-Seq v4 Ultra Low Input RNA kit for Sequencing (Clontech, Part number 634890) according to manufacturer’s instructions with 10 cycles of PCR for cDNA amplification by Seq-Amp polymerase (Clontech). Six hundreds ng of pre-amplified cDNA were then used as input for Tn5 transposon tagmentation by the Nextera XT kit (Illumina, Part number FC-131-1096) followed by 12 cycles of library amplification. Following purification using Agencourt AMPure XP beads (Beckman Coulter, Part number A63882), the size and concentration of library DNA were assessed on an Agilent 2100 Bioanalyzer.

treatment_protocol: Cdh5CreERT2 mice pulsed with 4OHT at E7.5 and analyzed either at E16.5 or in the adult

tag: sort strategy

tag: age


title: DEF2

value: adult


title: Abf1_Sth1aa_V_highMNase


title: Reb1_Sth1aa_V_highMNase


title: Reb1_Sth1aa_V_lowMNase


title: DEF1


title: TBP_Abf1aa_R

value: anti-Myc (homemade)


title: Reb1_Sth1aa_R_lowMNase


title: PRIM2


title: Sth1aa_V_highMNase

value: W303 tor1-1 fpr1::NAT RPL13A-2XFKB12::TRP1 STH1-FRB-KanMX


title: Sth1aa_R_highMNase


title: Abf1_Sth1aa_V_lowMNase


title: Sth1aa_R_lowMNase


title: Sth1aa_V_lowMNase


title: OnM2_m_rep1

city: Rockville

first: Shunyuan

last: Xiao

state: MD

address: 9600 Gudelsky Drive

department: Institute of Bioscience and Biotechnology Research

institute: University of Maryland

description:
Oidium neolycopersici UMSG2
OnM2_cuffdiff.result.txt

data_processing:
We performed pair-end 100 bp sequencing on the HiSeq1500 Sequencing System. Sequenced reads were quality trimmed using Trimmomatic and adapters were removed with Cutadapt. Then, we used TopHat2 (v2.0.10) with parameters  "-g 1". The bam files from TopHat2, mapped reads at the gene-level were processed with cufflinks to get the expression value.
Genome_build: Gene structural prediction was performed using MAKER2 (Holt and Yandell 2011)
Supplementary_files_format_and_content: Tab limited text files that are generated from Cufflinks by using TopHat2 mapped reads. Each file contains fpkm value at gene level.
Supplementary_files_format_and_content: Tab limited text files that are generated from Cuffdiff by using TopHat2 mapped reads. Each file contains fpkm value at gene level.
Supplementary_files_format_and_content: The gff files contain the annotation for OnM2, GcM3 and GcC1

organism: Erysiphe neolycopersici

source_name: Mycelia

growth_protocol: All powdery mildew fungi were respectively maintained on sow thistle (for GcM1), tomato (for OnM2), or tobacco (for GcM3) plants in separate plant growth chambers (8 h light at ~125 µmol.m-2.S-1, 16 h dark) at The University of Maryland, Shady grove campus.

extract_protocol:
The samplels are collected at 6 days post inoculation. The infected leaves were used for mycelium collection by gently brushing the mycelia off from leaves using TRIzol reagent. Then the haustorium-containing leaves with surface mycelia and spores removed at 6 dpi were further washed with ddH2O, frozen in liquid N2 and stored at -80°C for extraction of total plant and fungal RNA. Total RNA extraction and purification from mycelia or haustorium-containing host cells was conducted using TRIzol reagent (Cat. No. 15596026, Thermo Fisher Scientific) after grinding harvested mycelia or plant tissue with a pestle.
The cDNA libraries were prepared using Illumina TruSeq™ RNA Sample Preparation Kit v2 and transcriptome sequencing was performed on Illumina Hiseq 1500 at the UM-IBBR Sequencing Core at the University of Maryland.

value: Mycelia

tag: time point

value: 6 dpi

tag: biotype


title: OnM2_h_rep2

source_name: Haustoria

value: Haustoria


title: Rap1_Sth1aa_V_highMNase


title: OnM2_h_rep3


title: Abf1_Sth1aa_R_lowMNase


title: OnM2_h_rep1


title: NO shh 11

city: Milwaukee

first: Ross

middle: F

last: Collery

state: Wisconsin

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

description: no shh vs shh expression.xlsx

data_processing:
Primary sequencing data produced by Illumina HiSeqTM 2000 generates raw reads.
Raw reads are subjected to quality control (QC) to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which are aligned to the reference sequences.
"Dirty" raw reads are reads which contain the sequence of adaptor, high content of unknown bases and low quality reads, and are removed before analysis.
Bowtie2  was used to map clean reads to reference gene, and HISAT used to reference genome.
The Fragments Per Kilobase of transcript per Million mapped reads (FPKM)  method is used to calculated expression level.
Genome_build: GRCz10 (GCA_000002035.3)
Supplementary_files_format_and_content: Excel files containing FKPM values for expression levels.

organism: Danio rerio

source_name: whole larval eyes

growth_protocol: Zebrafish (Danio rerio) were maintained at 28.5C on an  Aquatic Habitats recirculating filtered water system in reverse-osmosis purified water supplemented  with Instant Ocean salts (60 mg/l) on a 14 h light: 10 h  dark lighting cycle and fed a standard diet

extract_protocol:
Eyes were dissected were removed, stored overnight at 4C in RNAlater, and RNA was harvested using Trizol reagent.
RNA quality was determined using an Agilent BioAnalyzer. RNA libraries were prepared for sequencing using the low-input Illumina protocol.

value: wild-type

value: 5 days post-fertilization


title: shh 13

description: no shh vs shh expression.xlsx

value: Transgenic (hsp70l:shha-eGFP)


title: NO shh 13

description: no shh vs shh expression.xlsx


title: NO shh 12

description: no shh vs shh expression.xlsx


title: Atg3bp1_hrcC_3

city: Thuwal

first: Naganand

last: Rayapuram

address: KAUST

country: Saudi Arabia

institute: KAUST

data_processing:
Sequenced reads were checked for quality.
Low quality reads were trimed using trimmomatic.
Trimmed reads were mapped to TAIR10 genome using TOPHAT.
FPKM was calculated using cufflinks.
Differential analysis was performed using cuffdiff.
Genome_build: TAIR10
Supplementary_files_format_and_content: txt, FPKM values

source_name: 14 day old seedlings

growth_protocol: Plants were grown on sterile one-half-strength Murashige and Skoog (MS) medium with a 16-8h photoperiod for 14 days at 21° C.

extract_protocol:
Total RNA was extracted using NucleoSpin® Plant RNA kit and First-strand complementary DNA was synthesized from 1 μg of total RNA using reverse transcriptase, SuperScript® III First-Strand Synthesis SuperMix kit (Invitrogen).
Libraries were prepared using Illumina TruSeq stranded mRNA kits

treatment_protocol: Plants were treated with Pst DC3000 hrcC- for 24 hours

tag: cell type

value: Whole seedlings

tag: treatment

value: PstDC3000 hrcC-

value: Atg3bp1 mutant


title: shh 12

description: no shh vs shh expression.xlsx


title: Rap1_Sth1aa_R_lowMNase

tag: genotype/variation


title: PRIM1


title: DEF3


title: Atg3bp1_hrcC_2

tag: ecotype


title: Atg3bp1_hrcC_1


title: NO bmp4 12

description: no bmp vs bmp expression.xlsx


title: NO bmp4 13

description: no bmp vs bmp expression.xlsx


title: colo_hrcC_2

value: wild type


title: col0_hrcC_1


title: lrp2 1 mpf sclera 12

description: ZDR(wt) vs lrp2 expression.xlsx

source_name: choroid/sclera

value: 1 month post-fertilization


title: Atg3bp1_mock_2

value: Mock


title: lrp2 1 mpf sclera 13

description: ZDR(wt) vs lrp2 expression.xlsx


title: Atg3bp1_mock_1


title: bmp4 12

description: no bmp vs bmp expression.xlsx

value: Transgenic (hsp70l:eGFP-bmp4)


title: NO bmp4 11

description: no bmp vs bmp expression.xlsx


title: bmp4 11

description: no bmp vs bmp expression.xlsx


title: bmp4 13

description: no bmp vs bmp expression.xlsx


title: lrp2 1 mpf retina 13

description: ZDR(wt) vs lrp2 expression.xlsx

source_name: retina


title: lrp2 1 mpf retina 12

description: ZDR(wt) vs lrp2 expression.xlsx


title: Atg3bp1_mock_3


title: col0_mock_3


title: col0_mock_2


title: lrp2 1 mpf retina 11

description: ZDR(wt) vs lrp2 expression.xlsx


title: lrp2 1 mpf RPE 21

description: ZDR(wt) vs lrp2 expression.xlsx

source_name: retinal pigment epithelium


title: lrp2 1 mpf RPE 12

description: ZDR(wt) vs lrp2 expression.xlsx


title: lrp2 1 mpf eyes 3

description: ZDR(wt) vs lrp2 expression.xlsx

source_name: whole eyes


title: TH104_input_control

city: Oslo

first: Siv

last: Gilfillan

address: Gaustadaleen 21

department: Norwegian Center for Molecular Medicine

country: Norway

institute: University of Oslo

data_processing:
Reads were mapped to the human reference genome using bowtie version 1.1.2
Filtering of alignment files to identify uniquely mapping, non-duplicate reads, was performed using samtools version 1.3.1
Peak calling was performed by HOMER 4.7.2
Genome_build: hg19
Supplementary_files_format_and_content: peak files from HOMER

source_name: Cultured HCT8 INPUT control

extract_protocol:
ThruPLEX, Rubicon Genomics
Twenty five microliters of immunoprecipitated, FAIRE or input DNA was used for library preparation. For CHIP samples Illumina (San Diego, CA) TruSeq™ DNA Sample Preparation reagents were used, with ligation of 1/10th the manufacturers recommended adapter amounts and agarose gel selection of DNA fragments in the 200-500 bp size range. For FAIRE samplesThruPLEX DNA-Seq reagents was used (Rubicon Genomics, Ann Arbor, MI, USA), following manufacturer’s instructions”.


title: TH103_HCT8_MC1061_E.coli

source_name: Cultured HCT8 5h with vesicles from MC1061_E.coli


title: lrp2 1 mpf eyes 2

description: ZDR(wt) vs lrp2 expression.xlsx


title: TH99_input control

extract_protocol:
Illumina TruSeq™ DNA Sample Preparation
Twenty five microliters of immunoprecipitated, FAIRE or input DNA was used for library preparation. For CHIP samples Illumina (San Diego, CA) TruSeq™ DNA Sample Preparation reagents were used, with ligation of 1/10th the manufacturers recommended adapter amounts and agarose gel selection of DNA fragments in the 200-500 bp size range. For FAIRE samplesThruPLEX DNA-Seq reagents was used (Rubicon Genomics, Ann Arbor, MI, USA), following manufacturer’s instructions”.


title: TH101_control_HCT8 cells non treated

source_name: Cultured HCT8 control