title: RNA_monkey_PAC_rep2

city: Beijing

first: Wei

last: Xie

address: Zhongguancun north street

country: China

institute: Tsinghua University

data_processing:
Basecalls performed using CASAVA version 1.8
For Hi-C sapples: sisHi-C sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the mm9 reference genome in a two-step approach with bowtie2. Then the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb bin size was used and a 40Kb bin size was used for examination of local domain level contacts. The raw contact counts are normalized with iterative correction.
For methylation samples: STEM-seq reads were aligned to the rheMac2 genome using BSseeker2.0.8, and methylation value in bedGraph files were counted by the number of reads falling into 200bp bin in the genome.
For RNA-seq samples: SMART-seq2 reads were aligned to the rheMac2 or mm9 genome assembly using tophat2 version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2.
Genome_build: rheMac2, mm9
Supplementary_files_format_and_content: The bedgraph files contains the values  counted by the number of reads falling into 200bp bin in the genome. The gene fpkm txt file contains FPKM value for all samples. with number for each bin. While the validpair txt file indicates the paired interaction reads for each sample.

organism: Macaca mulatta

source_name: pachytene spermatocyte

extract_protocol:
The RNA extraction follows smart-seq2 protocol
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously with minor modification (Picelli et al., 2014). Cells were lysed in hypotonic lysis buffer (Amresco, M334), and the polyadenylated mRNAs were captured by the PolyT primers. After ~3–10 min lysis at 72 °C, the Smart-seq2 reverse transcription reactions were performed. After pre-amplification and AMPure XP beads purification, cDNAs were sheared by Covaris and were subject to Illumina TruSeq library preparation. All libraries were sequenced on Illumina HiSeq 2500 according to the manufacturer’s instruction.

value: pachytene spermatocyte


title: TR4PL21_19H

status: Public on Feb 11 2019

type: SRA

city: Oxford

first: Alba

last: Rodriguez-Meira

address: John Radcliffe Hospital/Headley Way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description: Rodriguez-Meira_et.al_3TARGET_counts.txt

library_source: transcriptomic

data_processing:
BCL files were demultiplexed into FASTQ files using bcl2fastq, using the first 8 bp obtained from R1, corresponding to a cell-specific barcode.
RNA-Seq:Short reads (63-bp) were trimmed for polyA tails and aligned to the human genome using STAR
RNA-Seq: primary alignments mapping to a set of RefSeq annotated transcripts were quantified using FeatureCounts
RNA-Seq: Expression values were quantified as counts and normalized per library size and a scale factor (mean library size:68,412)
Genome_build: GRCh37 assembly (hg19)
Supplementary_files_format_and_content: Normalized counts

molecule: polyA RNA

organism: Homo sapiens

source_name: TR4PL21_19H_Peripheral blood_WT

extract_protocol:
cDNA libraries were synthetized from single cells using 3'-TARGET-seq method
Illumina sequencing libraries were prepared using the Illumina Nextera XT DNA kit, using a custom P5 primer for PCR amplification. Samples were sequenced on Illumina NextSeq Instrument using a custom primer for Read1 (cell barcode)

treatment_protocol: HSPC (defined as Lineage-CD34+ cells) were isolated by Fluorescent Activated Cell Sorting from patients or normal donors

tag: subject id

tag: cell type

value: cd34+ HSPC

tag: tissue

value: Peripheral blood

tag: method

tag: disease timepoint

value: baseline

tag: diagnosis

value: healthy control

tag: donor type

value: normal

tag: primer mix

tag: batch

tag: plate

tag: mutation

value: WT

tag: multimap

value: realclone


title: Plasmodium falciparum clone 34F5; GB4 self-mating

type: genomic

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

country: USA

institute: NIH

hyb_protocol: Affymetrix GenomeWideSNP6_450 protocol.

scan_protocol: Affymetrix 3000 7G.

data_processing: Affymetrix power tools brlmm-p, specifically: apt-probeset-genotype --cdf-file Pf_SNP_2_geno_pm.cdf --analysis brlmm-p --write-models --read-genders gender.txt --chrX-snps x.chrx --out-dir

label: biotin-SAPE

molecule: genomic DNA

organism: Plasmodium falciparum

source_name: GB4 self-mating

label_protocol: Affymetrix GenomeWide 5.0/6.0 kit.

growth_protocol: Cultures presenting at least 0.5% stage-V gametocytes were used to membrane feed An. stephensi mosquitoes.

extract_protocol: Plasmodium falciparum genomic DNA was extracted with DNeasy Blood and Tissue Kit (Qiagen).

treatment_protocol: A total of 600 An. stephensi were fed with 400-600 μl of gametocyte cultures at 50% hematocrit, resulting in 369,540 sporozoites.

tag: clone


title: Plasmodium falciparum clone 85G7; 85G7


title: Plasmodium falciparum clone 43E5; 43E5


title: Plasmodium falciparum clone 39H5; 39H5


title: Plasmodium falciparum clone 37F12; GB4 self-mating


title: Plasmodium falciparum clone 38C7; 11C2 isogenic progeny

source_name: 11C2 isogenic progeny


title: Plasmodium falciparum clone 44F6; 44F6


title: Plasmodium falciparum clone 44D4; 44D4


title: Plasmodium falciparum clone 38E11; 38E11


title: RNAseq-Skin Fibroblast-treated with DMSO-1

city: Albany

first: Morgan

middle: A

last: Sammons

state: NY

address: 1400 Washington Ave, Life Sciences 2075

department: Biological Sciences

institute: University at Albany - SUNY

data_processing:
Raw fastq reads were processed for quality control using FastQC v0.11.5
Reads were aligned to the reference genome (hg19) using STAR v 2.5.3a. Genome indices for STAR were built using the parameters --runThreadN 12 --runMode genomeGenerate --sjdbOverhang 100
Indexes built in the aforementioned step were then used to align reads with STAR using the parameters --runThreadN 12 --genomeDir <genomeDir> --readFilesIn <Sample.fastq.gz> --readFilesCommand zcat --outSAMstrandField intronMotif --outFilterIntronMotifsRemoveNoncanonical --outSAMtype BAM SortedByCoordinate --outFileNamePrefix Sample. --limitBAMsortRAM 61675612266
Gene counts were calculated using HTSeq v 0.9.1 with -f bam -s no -I gene_id -m intersection-strict parameters
Genome_build: hg19
Supplementary_files_format_and_content: The count files are tab-delimited text files with first column as geneNames and second column as geneCounts

molecule: total RNA

source_name: Foreskin

growth_protocol: MCF10A epithelial cells were cultured in HuMEC Complete media (Gibco, #12752010) and skin fibroblast cells were cultured  in DMEM media (with 10% FBS and 1% Pen/Strep, Gibco)

extract_protocol:
For RNA-Seq: Total mRNA was extracted with E.Z.N.A. Total RNA kit (Omega; R6834-02) and Poly(A)+ RNA was isolated by double selection with poly-dT beads, using 2.5 mg total RNA, which is then followed by first- and second-strand synthesis
For RNA-Seq: Libraries were prepared using NEXTflex Rapid Illumina DNA-Seq Library Prep Kit (Bioo Scientific).
For ChIP-Seq: Cells were crosslinked at 80% confluency with 1% formaldehyde for 10 min at room temperature. Crosslinking was quenched with 125mM glycine and the resulting pellet was washed twice with cold PBS and lysed. Samples were subjected to sonication with Diagenode Bioruptor Plus for 40 cycles (30 sec on/off at high setting) for shearing chromatin to 150-500 bp average size. Immunoprecipitation reactions were performed with Diagenode IP-Star Compact Atuomated System with mentioned antibodies. Immunoprecipitated DNA was reverse-crosslinked at 65°C for 4 hours and then eluted from beads, purified using SPRI beads, and used to construct sequencing libraries.
For ChIP-Seq: Libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: To induce p53 activation, cells were treated with Nutlin-3A (5 mM final) or DMSO (vehicle control) for 6 hours.

tag: treatment

value: DMSO


title: Plasmodium falciparum clone 35C2; 35C2


title: Plasmodium falciparum clone 51G5; 36F11 isogenic progeny

source_name: 36F11 isogenic progeny


title: Plasmodium falciparum clone 11C2; 11C2 isogenic progeny


title: Plasmodium falciparum clone 39A4; 24G11 isogenic progeny

source_name: 24G11 isogenic progeny


title: Plasmodium falciparum clone 44A12; 24G11 isogenic progeny


title: Plasmodium falciparum clone 46E11; 46E11


title: Plasmodium falciparum clone 61D3; 61D3 isogenic progeny

source_name: 61D3 isogenic progeny


title: Plasmodium falciparum clone 40B12; 34B1 isogenic progeny

source_name: 34B1 isogenic progeny


title: Plasmodium falciparum clone 34D8; 36H9 isogenic progeny

source_name: 36H9 isogenic progeny


title: Plasmodium falciparum clone 76H10; 61D3 isogenic progeny


title: Plasmodium falciparum clone 44D7; 36F11 isogenic progeny


title: Plasmodium falciparum clone 43A6; 43A6 isogenic progeny

source_name: 43A6 isogenic progeny


title: Plasmodium falciparum clone 34B1; 34B1 isogenic progeny


title: Plasmodium falciparum clone 46G9; 46G9


title: Plasmodium falciparum clone 37D9; 37D9


title: Plasmodium falciparum clone 38A6; 36F11 isogenic progeny


title: Plasmodium falciparum clone 85D3; 61D3 isogenic progeny


title: Plasmodium falciparum clone 36H9; 36H9 isogenic progeny


title: Plasmodium falciparum clone 82D2; 87E7 isogenic progeny

source_name: 87E7 isogenic progeny


title: Plasmodium falciparum clone 39C5; 39C5


title: Plasmodium falciparum clone 87E7; 87E7 isogenic progeny


title: Plasmodium falciparum clone 39E8; GB4 self-mating


title: Plasmodium falciparum clone 71D6; 61D3 isogenic progeny


title: Plasmodium falciparum clone 39C3; 39C3


title: Plasmodium falciparum clone 43H3; 36F11 isogenic progeny


title: Plasmodium falciparum clone 36E5; 36E5


title: Plasmodium falciparum clone 50C5; 44E8 isogenic progeny

source_name: 44E8 isogenic progeny


title: Plasmodium falciparum clone 38B3; GB4 self-mating


title: Plasmodium falciparum clone 49G1; 43A6 isogenic progeny


title: Plasmodium falciparum clone 61A12; 61D3 isogenic progeny


title: Plasmodium falciparum clone 52B4; GB4 self-mating


title: Plasmodium falciparum clone 50G8; 36F11 isogenic progeny


title: Plasmodium falciparum clone 46A11; GB4 self-mating


title: Plasmodium falciparum clone 51D10; GB4 self-mating


title: Plasmodium falciparum clone 87A11; 61D3 isogenic progeny


title: Plasmodium falciparum clone 38G5; 38G5


title: Plasmodium falciparum clone 48C1; 48C1


title: Plasmodium falciparum clone GB4; GB4


title: Plasmodium falciparum clone 40E7; 40E7


title: Plasmodium falciparum clone 36D5; 36D5


title: Plasmodium falciparum clone 40G11; 43A6 isogenic progeny


title: Plasmodium falciparum clone 36F11; 36F11 isogenic progeny


title: Plasmodium falciparum clone 44E8; 44E8 isogenic progeny


title: Plasmodium falciparum clone 11H5; 36F11 isogenic progeny


title: Plasmodium falciparum clone 24G11; 24G11 isogenic progeny


title: GFP_pre, biological replicate2

type: RNA

city: Tampa

first: Daniel

last: Abate-Daga

state: Florida

address: 12902 Magnolia Dr.

department: Immunology

institute: H. Lee Moffitt Cancer Center and Research Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C to the Affymetrix U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: The data were analyzed with the Affymetrix Expression Console v 1.4 software using the MAS 5.0 algorithm with default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was set to 500. Using the Affymetrix Transcriptome Analysis Console v3.0, a one-way unpaired ANOVA analysis was performed and differentially expressed probe sets with fold changes > 2.0 and p-values < .05 were retained.

label: Biotin

source_name: ex vivo culture, at day of transfer

label_protocol: Biotinylated cRNA was prepared according to the Ambion Message Amp Premier protocol using 100 ng of total RNA (Ambion).

growth_protocol: Human peripheral blood mononuclear cells were stimulated with anti-CD3 antibody (OKT3) in presence of IL-2. Two days post-stimulation, they were transduced with retroviral vectors encoding either a second generation CAR (PSCA2), a third generation CAR (PSCA3), or GFP as a control. Cells were cultured for 2 weeks in presence of IL-2, until collection of samples (pre-infusion samples) or transfer into mice (Post-infusion samples).

extract_protocol: Isolation of total RNA was performed using the Qiagen RNeasy column (with QIAshredder) according to the manufacturer's instructions.

treatment_protocol: NSG mice bearing palpable subcutaneous tumors, derived from HPAC cells, were treated with human T cells. Treatment groups received CD8 T cells expressing either PSCA2 or PSCA3 CARs, plus untransduced CD4 cells for cytokine support. GFP-transduced CD8 T cells were used as a control, and 3 biological replicates were included per group. For the post-infusion samples, CD8+ T cells were isolated from the spleen (3 mice/group), using magnetic bead cell sorting.

tag: anti-psca car type

value: GFP

tag: infusion timepoint

value: pre-infusion

value: Cells expressing GFP


title: Plasmodium falciparum clone 40A5; 36F11 isogenic progeny


title: Plasmodium falciparum clone 803; 803


title: GFP_pre, biological replicate3


title: Plasmodium falciparum clone 39H4; 36F11 isogenic progeny


title: R42015-489pf_97-IR_L1

city: Bethesda

first: Matthew

middle: J

last: Brooks

state: MD

address: 6 Center Dr Bldg 6, Rm 303

department: NEI

data_processing:
Sequenced reads were trimmed for adaptors with Trimmomatic 0.36 and quality of raw FASTQs were checked with FastQC.
Reads were aligned to reference genome with STAR 2.5.2a.
Aligned reads were quantified as expacted counts at transcript level and collapsed to gene level using RSEM 1.2.31
Genome_build: GRCh38.p3/ENSEMBLv82
Supplementary_files_format_and_content: RSEM_gene_counts.tsv (tab delimited value file with raw gene counts)
Supplementary_files_format_and_content: Normalized_CPM.txt (tab delimited value file with normalized counts per million expression values)
Supplementary_files_format_and_content: DE_analysis.txt (space delimited value file with differential expression output)

source_name: Retina

extract_protocol:
Retina punches flash frozen in liquid nitrogren and stored in -80 C; retina homogenized and RNA isolated with TRIZol® protocol with additional washing steps
Randomized to batches and constructed with TruSeq® Stranded mRNA Library Preparation Kit

tag: age

tag: Sex

value: M

tag: rin

tag: pmi

value: retina punch


title: R42015-488pf_93-IR_L1

tag: tissue


title: R42016-133pf_95-IR_L5

value: F


title: R42016-131pf_92-IR_L4


title: R42016-134pf_96-IR_L5


title: R42016-136pf_99-IR_L5


title: R42016-132pf_94-IR_L4


title: R42016-135pf_98-IR_L5


title: R42015-487pf_91-IR_L1


title: GFP_post, biological replicate2

source_name: spleen of tumor-bearing mice, 30 days post transfer

value: post-infusion

tag: cell type


title: R42015-534pf_90-IR_L5


title: R42016-091pf_9-IR_L1


title: R42016-130pf_89-IR_L4


title: R42015-533pf_88-IR_L5


title: GFP_post, biological replicate3


title: R42015-532pf_87-IR_L5


title: PSCA2_pre, biological replicate1

value: Cells expressing a second generation CAR


title: PSCA3_pre, biological replicate2

value: Cells expressing a third generation CAR


title: PSCA3_pre, biological replicate1


title: PSCA3_pre, biological replicate3


title: PSCA2_post, biological replicate3


title: PSCA2_post, biological replicate2


title: PSCA2_pre, biological replicate3


title: PSCA3_post, biological replicate2


title: PSCA2_pre, biological replicate2


title: PSCA2_post, biological replicate1


title: R42015-530pf_85-IR_L5


title: R42015-529pf_84-IR_L5


title: R42015-527pf_82-IR_L5


title: R42015-526pf_80-IR_L5


title: R42015-531pf_86-IR_L5


title: R42015-480pf_8-IR_L1


title: R42015-524pf_75-IR_L4


title: PSCA3_post, biological replicate1


title: R42016-127pf_78-IR_L4


title: R42015-525pf_77-IR_L4


title: R42016-126pf_76-IR_L4


title: R42016-128pf_79-IR_L4


title: R42015-528pf_83-IR_L5


title: R42016-129pf_81-IR_L4


title: R42016-125pf_74-IR_L4


title: R42015-486pf_72-IR_L1


title: R42015-523pf_71-IR_L4


title: GFP_pre, biological replicate1


title: R42016-123pf_70-IR_L4


title: R42016-090pf_7-IR_L1


title: R42015-522pf_69-IR_L4


title: GFP_post, biological replicate1


title: R42016-122pf_67-IR_L4


title: R42015-519pf_62-IR_L4


title: R42015-521pf_68-IR_L4


title: R42016-121pf_66-IR_L4


title: R42016-118pf_60-IR_L3


title: R42015-520pf_63-IR_L4


title: R42016-089pf_6-IR_L1


title: R42016-119pf_61-IR_L3


title: R42016-124pf_73-IR_L4


title: R42016-116pf_57-IR_L3


title: R42015-518pf_58-IR_L4


title: R42015-517pf_54-IR_L4


title: R42016-114pf_55-IR_L3


title: R42016-402pf_526-IR_L7


title: R42016-115pf_56-IR_L3


title: R42016-117pf_59-IR_L3


title: R42015-516pf_53-IR_L4


title: R42016-424pf_524-IR_L5


title: R42016-427pf_529-IR_L5


title: R42016-425pf_525-IR_L5


title: R42016-396pf_527-IR_L8


title: R42016-423pf_522-IR_L5


title: R42016-394pf_521-IR_L8


title: R42016-395pf_523-IR_L8


title: R42016-120pf_65-IR_L3


title: R42016-426pf_528-IR_L5


title: R42015-515pf_52-IR_L4


title: R42016-393pf_520-IR_L8


title: R42016-392pf_519-IR_L8


title: R42016-401pf_518-IR_L7


title: R42016-400pf_517-IR_L7


title: R42016-429pf_513-IR_L5

value: no grade


title: R42016-389pf_514-IR_L8


title: R42016-390Cpf_515-IR_L8


title: R42016-391Cpf_516-IR_L8


title: R42016-388pf_511-IR_L8


title: R42015-485pf_51-IR_L1


title: R42016-387pf_509-IR_L8


title: R42016-399Cpf_506-IR_L7


title: R42016-419Cpf_507-IR_L8


title: R42016-418pf_505-IR_L8


title: R42016-421pf_510-IR_L8


title: R42016-417pf_504-IR_L8


title: R42016-398pf_503-IR_L8


title: R42016-385pf_500-IR_L7


title: R42016-420pf_508-IR_L8


title: R42016-113pf_50-IR_L3


title: R42016-384pf_499-IR_L7


title: R42016-416pf_502-IR_L8


title: R42016-088pf_5-IR_L1


title: R42016-386pf_501-IR_L7


title: R42016-428pf_498-IR_L5

value: 2 or 3


title: R42016-381pf_495-IR_L7


title: R42016-382Cpf_496-IR_L7


title: R42016-383pf_497-IR_L7


title: R42016-380pf_493-IR_L7


title: R42016-422pf_512-IR_L8


title: R42016-397pf_530-IR_L8


title: R42016-378pf_491-IR_L7


title: R42016-376pf_489-IR_L7


title: R42016-377pf_490-IR_L7


title: R42015-514pf_49-IR_L4


title: R42016-379pf_492-IR_L7


title: R42016-412pf_486-IR_L8


title: R42016-413pf_487-IR_L8


title: R42016-414pf_488-IR_L8


title: R42016-375pf_484-IR_L7


title: R42016-411pf_485-IR_L8


title: R42016-372Cpf_481-IR_L6


title: R42016-374pf_483-IR_L6


title: R42016-371pf_480-IR_L6


title: R42015-484pf_48-IR_L1


title: R42016-370pf_478-IR_L6


title: R42016-369pf_477-IR_L6


title: R42016-365pf_473-IR_L6


title: R42016-366pf_474-IR_L6


title: R42016-415pf_494-IR_L8


title: R42016-368pf_476-IR_L6


title: R42016-410Cpf_479-IR_L7


title: R42016-408pf_470-IR_L7


title: R42016-409pf_471-IR_L7


title: R42016-363pf_468-IR_L6


title: R42016-364Cpf_472-IR_L6


title: R42016-112pf_47-IR_L3


title: R42016-361Cpf_466-IR_L5


title: R42016-362pf_467-IR_L5


title: R42016-407pf_465-IR_L7


title: R42016-360Cpf_464-IR_L5


title: R42016-373pf_482-IR_L6


title: R42016-358pf_462-IR_L5


title: R42016-357pf_461-IR_L5


title: R42016-111pf_46-IR_L3


title: R42016-356pf_460-IR_L5


title: R42016-355pf_459-IR_L5


title: R42016-354pf_458-IR_L5


title: R42016-353pf_457-IR_L5


title: R42016-367pf_475-IR_L6


title: R42016-352pf_456-IR_L5


title: R42016-351pf_455-IR_L5


title: R42016-345Cpf_448-IR_L4


title: R42016-110pf_45-IR_L3


title: R42016-348Cpf_451-IR_L4


title: R42016-347Cpf_450-IR_L4


title: R42016-343Cpf_446-IR_L4


title: R42016-405pf_445-IR_L7


title: R42016-344Cpf_447-IR_L4


title: R42016-342Cpf_444-IR_L4


title: R42016-359Cpf_463-IR_L5


title: R42016-404pf_443-IR_L7


title: R42016-341Cpf_441-IR_L4


title: R42016-403pf_442-IR_L7


title: R42016-340Cpf_440-IR_L4


title: R42016-339Cpf_439-IR_L4


title: R42016-336pf_436-IR_L3


title: R42016-334Cpf_434-IR_L3


title: R42016-350Cpf_454-IR_L4


title: R42016-338pf_438-IR_L3


title: R42016-406pf_453-IR_L7


title: R42016-333pf_433-IR_L3


title: R42016-331pf_431-IR_L3


title: R42016-349Cpf_452-IR_L4


title: R42016-327pf_427-IR_L3


title: R42016-328pf_428-IR_L3


title: R42016-329Cpf_429-IR_L3


title: R42016-108pf_43-IR_L2


title: R42016-330pf_430-IR_L3


title: R42016-326pf_426-IR_L2


title: R42016-346Cpf_449-IR_L4


title: R42016-325pf_425-IR_L2


title: R42016-324pf_424-IR_L2


title: R42016-323pf_423-IR_L2


title: R42016-322Cpf_422-IR_L2


title: R42016-109pf_44-IR_L3


title: R42016-335pf_435-IR_L3


title: R42016-321Cpf_421-IR_L2


title: R42016-337pf_437-IR_L3


title: R42016-320pf_420-IR_L2


title: R42016-319pf_419-IR_L2


title: R42016-107pf_42-IR_L2


title: R42016-317pf_417-IR_L2


title: R42016-332pf_432-IR_L3


title: R42016-313pf_413-IR_L1


title: R42016-316pf_416-IR_L2


title: R42016-312pf_412-IR_L1


title: R42016-314pf_414-IR_L1


title: R42016-311pf_411-IR_L1


title: R42016-310pf_410-IR_L1


title: R42016-106pf_41-IR_L2


title: R42016-305pf_405-IR_L1


title: R42016-308pf_408-IR_L1


title: R42016-304pf_404-IR_L1


title: R42016-306pf_406-IR_L1


title: R42016-307pf_407-IR_L1


title: R42016-303pf_403-IR_L1


title: R42016-309pf_409-IR_L1


title: PSCA3_post, biological replicate3


title: R42015-551pf_400-IR_L1


title: R42015-418pf_402-IR_L7


title: R42015-417pf_401-IR_L7


title: R42015-431pf_40-IR_L8


title: R42016-087pf_4-IR_L1


title: R42016-318pf_418-IR_L2


title: R42015-416pf_399-IR_L7


title: R42016-315pf_415-IR_L2


title: R42015-415pf_398-IR_L7


title: R42015-414pf_397-IR_L7


title: R42015-410pf_393-IR_L7


title: R42015-413pf_396-IR_L7


title: R42015-411pf_394-IR_L7


title: R42015-407pf_390-IR_L6


title: R42016-105pf_39-IR_L2


title: R42015-406pf_389-IR_L6


title: R42015-404pf_387-IR_L6


title: R42015-403pf_386-IR_L6


title: R42015-401pf_384-IR_L6


title: R42015-400pf_383-IR_L6


title: R42015-550pf_381-IR_L1


title: R42015-398pf_379-IR_L6


title: R42015-430pf_38-IR_L8


title: R42015-397pf_378-IR_L6


title: R42015-402pf_385-IR_L6


title: R42015-412pf_395-IR_L7


title: R42015-549pf_380-IR_L6


title: R42015-408pf_391-IR_L7


title: R42015-548Cpf_374-IR_L6


title: R42015-409pf_392-IR_L7


title: R42015-390pf_370-IR_L5


title: R42015-392pf_372-IR_L5


title: R42015-395pf_376-IR_L5


title: R42015-405pf_388-IR_L6


title: R42015-388pf_368-IR_L5


title: R42015-389pf_369-IR_L5


title: R42015-386pf_366-IR_L5


title: R42015-483pf_37-IR_L1


title: R42015-385pf_365-IR_L5


title: R42015-384pf_364-IR_L5


title: R42015-391pf_371-IR_L5


title: R42015-383pf_363-IR_L4


title: R42015-399pf_382-IR_L6


title: R42015-382pf_362-IR_L4


title: R42015-380pf_360-IR_L4


title: R42015-396pf_377-IR_L6


title: R42015-381pf_361-IR_L4


title: R42015-429pf_36-IR_L8


title: R42015-379pf_359-IR_L4


title: R42015-378pf_358-IR_L4


title: R42015-394pf_375-IR_L5


title: R42015-393pf_373-IR_L5


title: R42015-375pf_355-IR_L4


title: R42015-376pf_356-IR_L4


title: R42015-374pf_354-IR_L4


title: R42015-370pf_350-IR_L3


title: R42015-373pf_353-IR_L4


title: R42016-104pf_35-IR_L2


title: R42015-368pf_348-IR_L3


title: R42015-366pf_346-IR_L3


title: R42015-372pf_352-IR_L4


title: R42015-371pf_351-IR_L3


title: R42015-365pf_345-IR_L3


title: R42015-369pf_349-IR_L3


title: R42015-362pf_342-IR_L3


title: R42015-363pf_343-IR_L3


title: R42015-361pf_341-IR_L3


title: R42015-367pf_347-IR_L3


title: R42015-360pf_340-IR_L3


title: R42015-428pf_34-IR_L8


title: R42015-364pf_344-IR_L3


title: R42015-359pf_339-IR_L2


title: R42015-356pf_336-IR_L2


title: R42015-357pf_337-IR_L2


title: R42015-377pf_357-IR_L4


title: R42015-355pf_335-IR_L2


title: R42015-353pf_333-IR_L2


title: R42015-387pf_367-IR_L5


title: R42015-350pf_330-IR_L2


title: R42015-351pf_331-IR_L2


title: R42015-354pf_334-IR_L2


title: R42015-349pf_329-IR_L2


title: R42015-346pf_326-IR_L1


title: R42015-352pf_332-IR_L2


title: R42015-347pf_327-IR_L1


title: R42015-345pf_325-IR_L1


title: R42015-348pf_328-IR_L2


title: R42015-343pf_323-IR_L1


title: R42015-342pf_322-IR_L1


title: R42015-340pf_320-IR_L1


title: R42016-102pf_32-IR_L2


title: R42015-339pf_319-IR_L1


title: R42015-341pf_321-IR_L1


title: R42015-338pf_318-IR_L1


title: R42015-344pf_324-IR_L1


title: R42015-358pf_338-IR_L2


title: R42015-276pf_314-IR_L8


title: R42015-337pf_317-IR_L1


title: R42015-277pf_315-IR_L8


title: R42015-336pf_316-IR_L1


title: R42015-275pf_313-IR_L8


title: R42015-273pf_311-IR_L8


title: R42015-274pf_312-IR_L8


title: R42015-272pf_310-IR_L8


title: R42015-547pf_309-IR_L6


title: R42016-103pf_33-IR_L2


title: R42015-270pf_307-IR_L8


title: R42015-268pf_305-IR_L8


title: R42015-269pf_306-IR_L8


title: R42015-267pf_303-IR_L8


title: R42015-512pf_300-IR_L3


title: R42016-086pf_3-IR_L1


title: R42015-513pf_301-IR_L3


title: R42015-266pf_302-IR_L8


title: R42015-510pf_298-IR_L3


title: R42015-511pf_299-IR_L3


title: R42015-504pf_292-IR_L3


title: R42015-508pf_296-IR_L3


title: R42015-505pf_293-IR_L3


title: R42015-264pf_288-IR_L7


title: R42015-427pf_31-IR_L8


title: R42015-507pf_295-IR_L3


title: R42015-263pf_287-IR_L7


title: R42015-506pf_294-IR_L3


title: R42015-503pf_291-IR_L3


title: R42015-509pf_297-IR_L3


title: R42015-502pf_290-IR_L3


title: R42015-261pf_285-IR_L7


title: R42015-262pf_286-IR_L7


title: R42015-260pf_284-IR_L7


title: R42015-259pf_283-IR_L7


title: R42015-265pf_289-IR_L7


title: R42015-257pf_281-IR_L7


title: R42015-271pf_308-IR_L8


title: R42015-258pf_282-IR_L7


title: R42015-255pf_279-IR_L7


title: R42015-425pf_28-IR_L8


title: R42015-254pf_278-IR_L7


title: R42016-101pf_29-IR_L2


title: R42015-256pf_280-IR_L7


title: R42015-249pf_273-IR_L6


title: R42015-253pf_276-IR_L6


title: R42015-250pf_274-IR_L6


title: R42015-251pf_275-IR_L6


title: R42015-252pf_277-IR_L6


title: R42015-426pf_30-IR_L8


title: R42015-248pf_272-IR_L6


title: R42015-247pf_271-IR_L6


title: R42015-246pf_270-IR_L6


title: R42015-245pf_269-IR_L6


title: R42015-243pf_267-IR_L6


title: R42015-244pf_268-IR_L6


title: R42015-240pf_264-IR_L5


title: R42015-241pf_265-IR_L5


title: R42015-237pf_261-IR_L5


title: R42015-239pf_263-IR_L5


title: R42015-424pf_27-IR_L8


title: R42016-100pf_26-IR_L2


title: R42015-235pf_258-IR_L5


title: R42015-238pf_262-IR_L5


title: R42015-234pf_257-IR_L5


title: R42015-546pf_255-IR_L6


title: R42015-233pf_256-IR_L5


title: R42015-232pf_254-IR_L5


title: R42015-231pf_253-IR_L5


title: R42015-230pf_252-IR_L5


title: R42015-229pf_251-IR_L4


title: R42015-227pf_249-IR_L4


title: R42015-228pf_250-IR_L4


title: R42015-225pf_247-IR_L4


title: R42015-224pf_246-IR_L4


title: R42015-242pf_266-IR_L6


title: R42016-099pf_25-IR_L2


title: R42015-226pf_248-IR_L4


title: R42015-223pf_245-IR_L4


title: R42015-221pf_243-IR_L4


title: R42015-219pf_241-IR_L4


title: R42015-222pf_244-IR_L4


title: R42015-236pf_259-IR_L5


title: R42015-218pf_240-IR_L4


title: R42015-216pf_237-IR_L3


title: R42015-423pf_24-IR_L8


title: R42015-220pf_242-IR_L4


title: R42015-214pf_235-IR_L3


title: R42015-217pf_239-IR_L3


title: R42015-212pf_233-IR_L3


title: R42015-213pf_234-IR_L3


title: R42015-211pf_232-IR_L3


title: R42015-210pf_231-IR_L3


title: R42015-209pf_230-IR_L3


title: R42015-215pf_236-IR_L3


title: R42015-422pf_23-IR_L8


title: R42015-207pf_228-IR_L3


title: R42015-208pf_229-IR_L3


title: R42015-206pf_227-IR_L3


title: R42015-205pf_226-IR_L2


title: R42015-203pf_224-IR_L2


title: R42015-204pf_225-IR_L2


title: R42015-201pf_222-IR_L2


title: R42015-202pf_223-IR_L2


title: R42015-200pf_221-IR_L2


title: R42015-199pf_220-IR_L2


title: R42015-197pf_218-IR_L2


title: R42015-196pf_217-IR_L2


title: R42015-198pf_219-IR_L2


title: R42016-098pf_22-IR_L2


title: R42015-195pf_216-IR_L2


title: R42015-190pf_211-IR_L1


title: R42016-097pf_21-IR_L2


title: R42015-192pf_213-IR_L1


title: R42015-185pf_206-IR_L1


title: R42015-191pf_212-IR_L1


title: R42015-193pf_214-IR_L1


title: R42015-186pf_207-IR_L1


title: R42015-182pf_203-IR_L1


title: R42015-189pf_210-IR_L1


title: R42015-187pf_208-IR_L1


title: R42015-194pf_215-IR_L2


title: R42015-183pf_204-IR_L1


title: R42015-180pf_202-IR_L3


title: R42015-421pf_20-IR_L8


title: R42015-178pf_200-IR_L3


title: R42015-179pf_201-IR_L3


title: R42016-085pf_2-IR_L1


title: R42015-176pf_198-IR_L3


title: R42015-175pf_197-IR_L3


title: R42015-168pf_190-IR_L2


title: R42015-169pf_191-IR_L3


title: R42015-174pf_196-IR_L3


title: R42015-171pf_193-IR_L3


title: R42015-170pf_192-IR_L3


title: R42015-172pf_194-IR_L3


title: R42015-162pf_184-IR_L2


title: R42015-164pf_186-IR_L2


title: R42015-184pf_205-IR_L1


title: R42015-173pf_195-IR_L3


title: R42015-188pf_209-IR_L1


title: R42015-167pf_189-IR_L2


title: R42015-420pf_19-IR_L8


title: R42015-158pf_180-IR_L2


title: R42015-155pf_177-IR_L1


title: R42015-160pf_182-IR_L2


title: R42015-165pf_187-IR_L2


title: R42015-157pf_179-IR_L2


title: R42015-156pf_178-IR_L1


title: R42015-154pf_176-IR_L1


title: R42015-153pf_175-IR_L1


title: R42015-166pf_188-IR_L2


title: R42015-159pf_181-IR_L2


title: R42015-151pf_173-IR_L1


title: R42015-152pf_174-IR_L1


title: R42015-150pf_172-IR_L1


title: R42015-149pf_171-IR_L1


title: R42015-501pf_167-IR_L2


title: R42015-163pf_185-IR_L2


title: R42015-147pf_169-IR_L1


title: R42016-096pf_18-IR_L1


title: R42015-161pf_183-IR_L2


title: R42015-145pf_164-IR_L1


title: R42016-180pf_162-IR_L8


title: R42015-499pf_165-IR_L2


title: R42015-500pf_166-IR_L2


title: R42016-177pf_158-IR_L8


title: R42016-094pf_16-IR_L1


title: R42016-178pf_159-IR_L8


title: R42016-179pf_160-IR_L8


title: R42016-172pf_150-IR_L8


title: R42016-175pf_155-IR_L8


title: R42016-173pf_151-IR_L8


title: R42015-544pf_156-IR_L6


title: R42015-542pf_152-IR_L6


title: R42015-543pf_154-IR_L6


title: R42015-482pf_15-IR_L1


title: R42015-146pf_168-IR_L1


title: R42015-541pf_147-IR_L6


title: R42016-168pf_145-IR_L7


title: R42015-498pf_163-IR_L2


title: R42015-540pf_143-IR_L6


title: R42016-095pf_17-IR_L1


title: R42016-169pf_146-IR_L8


title: R42015-545pf_161-IR_L6


title: R42016-166pf_142-IR_L7


title: R42016-164pf_140-IR_L7


title: R42016-165pf_141-IR_L7


title: R42016-174pf_153-IR_L8


title: R42016-176pf_157-IR_L8


title: R42016-167pf_144-IR_L7


title: R42015-539pf_138-IR_L6


title: R42016-162pf_137-IR_L7


title: R42016-163pf_139-IR_L7


title: BE21_17407_17406_CD49b_PNA_LUM

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description:
RNA-seq of luminal fraction of mammary gland of BN rats treated with E2.
mRNA

data_processing:
Quality check of the called bases of the reads were performed using the FastQC tool (Babraham Bioinformatics).
Datasets were aligned to the rat reference rn6 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b). Two-pass mapping was performed using the following modified parameters: --outSAMstrandField intronMotif, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.1, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outFilterType BySJout, --outFilterScoreMinOverLread 0.33, --outFilterMatchNminOverLread 0.33, --limitSjdbInsertNsj 1200000, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --twopassMode Basic.
The read counts for individual genes were generated using the htseq-count script of the HTSeq framework (version 0.6.1p1) using modified parameters (--stranded no) and the rn6 refGene annotation file available at the UCSC.
Genome_build: rn6
Supplementary_files_format_and_content: Tab-separated file of the raw read counts for each gene.

organism: Rattus norvegicus

source_name: mammary gland

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen). The total RNA was measured by Aligent 2100 Bioanalyzer.
RNA-seq libraries were prepared using Clontech Low Input mRNA Library (Clontech SMARTer) v4 kit from less than 10ng of purified total RNA according to the manufacturer’s protocol. The concentrations of finished dsDNA library were measured by Qubit Fluorometer, the size of library fragment was measured by Agilent TapeStation 2200, and RT-qPCR for adapted library molar concentration measurement according to manufacturer’s protocols. Uniquely indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq500 with Single-End 75bp (SE75) reads by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.

tag: strain

value: BN

tag: gender

value: Female

value: mammary gland

value: Luminal


title: BE21_17407_17406_BAS

description:
RNA-seq of basal fraction of mammary gland of BN rats treated with E2.
mRNA

value: Basal


title: R42016-171pf_149-IR_L8


title: R42015-497pf_136-IR_L2


title: BC21_9645_9646_CD49b_PNA_LUM

description:
RNA-seq of luminal fraction of mammary gland of BN rats.
mRNA

value: Control


title: R42015-538pf_135-IR_L6


title: BC21_9645_9646_BAS

description:
RNA-seq of basal fraction of mammary gland of BN rats.
mRNA


title: AE21_9382_CD49b_PNA_LUM

description:
RNA-seq of luminal fraction of mammary gland of ACI rats treated with E2.
mRNA

value: ACI


title: AE21_16757_CD49b_PNA_LUM


title: AE21_16757_BAS

description:
RNA-seq of basal fraction of mammary gland of ACI rats treated with E2.
mRNA


title: R42016-170pf_148-IR_L8


title: AC21_9641_CD49b_PNA_LUM

description:
RNA-seq of luminal fraction of mammary gland of ACI rats.
mRNA


title: R42015-537pf_134-IR_L5


title: AC21_9641_BAS

description:
RNA-seq of basal fraction of mammary gland of ACI rats.
mRNA


title: R42016-160pf_132-IR_L7


title: AC21_9639_CD49b_PNA_LUM


title: AC21_9639_BAS


title: KO_PR_ChIP

description: ChIP-seq for PR from mammary organoid cells from knockout ACI rat

library_source: genomic

data_processing:
ChIPseq aligner, bowtie
ChIPseq peak call, macs2 2.1.1.20160309
motif analysis with homer
CNV analysis using QDNAseq, true
genome_build: rn6
Supplementary_files_format_and_content: bed file (BED6+4) of factor peaks from MACS2 peakcaller.

extract_protocol:
Single cell suspensions were obtained from dissociated mammary organoids, 1 × 107 cells were fixed with fixing buffer (50 mM HEPES-NaOH (pH 7.5), 100 mM NaCl, 1mM EDTA) containing 1% paraformaldehyde (Electron Microscopy Sciences, 15714) and crosslinked for 10 min at 37 °C. Crosslinking was quenched by adding glycine to a final concentration of 0.125 M. The cells were washed with ice-cold PBS, harvested in PBS. The nuclear fraction was extracted by first resuspending the pellet in 1 ml of lysis buffer (50 mM HEPES-NaOH (pH 8.0), 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min at 4 °C. Cells were pelleted, and washed in 1 ml of wash buffer (10 mM Tris-HCL (pH 8.0), 200 mM NaCl, 1 mM EDTA) for 10 min at 4 °C. Cells were then pelleted and resuspended in 1 ml of shearing buffer (10 mM Tris-HCl (pH 8), 1 mM EDTA, 0.1% SDS) and sonicated in a Covaris sonicator. Lysate was centrifuged for 5 min at 14,000 rpm to purify the debris. Then 100 µl of 10% Triton X-100 and 30 µl of 5M NaCl were added. The sample was then incubated with 20 µl of Dynabeads Protein G (LifeTechnologies,10003D) for 1 h at 4 °C. Primary antibodies were added to each tube and immunoprecipitation (IP) was conducted overnight in the cold room. Cross-linked complexes were precipitated with Dynabeads Protein G for 2 hr at 4 °C. The beads were then washed in low salt wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C, high salt wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C and LiCl wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C. DNA was eluted in elution buffer (100 mM sodium bicarbonate and 1% SDS). Cross-links were reversed overnight at 65 °C. RNA and protein were digested with 0.2 mg ml−1 RNase A for 30 min at 37 °C followed by 0.2 mg ml−1 Proteinase K for 1 h at 55 °C. DNA was purified with phenol-chloroform extraction and isopropanol precipitation.
ChIP-seq libraries were prepared using the Rubicon ThruPLEX DNA-seq Kit from 1 ng of purified ChIP DNA or input DNA according to the manufacturer’s protocol.

tag: genotype

value: 9 weeks

value: mammary cells

tag: chip antibody

value: Anti-PR antibody (H-190, Santa Cruz, cat# sc-7208)


title: KO_PR_input

description: input for anti-PR from mammary organoid cells from knockout ACI rat

value: none (input)


title: R42016-159pf_131-IR_L7

value: F

value: retina punch


title: ACI_PR_input

description: input for anti-PR from mammary organoid cells from wild type ACI rat


title: R42016-161pf_133-IR_L7


title: ACI_PR_ChIP

description: ChIP-seq for PR from mammary organoid cells from wild type ACI rat


title: R42016-158pf_130-IR_L7


title: R42016-093pf_13-IR_L1


title: KOLM5.9_BAS

description: RNA-seq of basal/myoepithelial cells of prepubertal aminals (6 seeks old)

data_processing:
Quality check of the called bases of the reads were performed using the FastQC tool (Babraham Bioinformatics).
Datasets were aligned to the rat reference rn6 genome using the STAR RNA-Seq aligner (version STAR_2.5.1b). Two-pass mapping was performed using the following modified parameters: --outSAMstrandField intronMotif, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.1, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outFilterType BySJout, --outFilterScoreMinOverLread 0.33, --outFilterMatchNminOverLread 0.33, --limitSjdbInsertNsj 1200000, --chimSegmentMin 15, --chimJunctionOverhangMin 15, --twopassMode Basic.
he read counts for individual genes were generated using the htseq-count script of the HTSeq framework (version 0.6.1p1) using modified parameters (--stranded no) and the rn6 refGene annotation file available at the UCSC Genome Browser.
genome_build: rn6
Supplementary_files_format_and_content: Tab-separated file of the raw read counts for each gene.

value: 6 weeks

value: basal/myoepithelial (Cd24+ Cd29HIGH)


title: KOLM5.9_LUM

description: RNA-seq of luminal cells of prepubertal aminals (6 seeks old)

value: luminal (Cd24+ Cd29LOW)


title: KORU5.3_LUM


title: R42016-157pf_128-IR_L7

value: M


title: HiC_mouse_PAC_top6bl_KO_ZYGL

description: new_mouse_top6bl_KO_ZYGL_HiC_allValidPairs.gz

data_processing:
Basecalls performed using CASAVA version 1.8
For Hi-C sapples: sisHi-C sequencing reads were mapped, processed and iteratively corrected using HiC-Pro, a pipeline developed by Servant et al. Briefly, the read pairs were mapped to the mm9 reference genome in a two-step approach with bowtie2. Then the invalid read pairs including dangling end, self-circle ligation and duplicates were discarded. The genome was divided into bins of specific length to generate the contact maps. For global detection of contacts, a 100Kb bin size was used and a 40Kb bin size was used for examination of local domain level contacts. The raw contact counts are normalized with iterative correction.
For methylation samples: STEM-seq reads were aligned to the rheMac2 genome using BSseeker2.0.8, and methylation value in bedGraph files were counted by the number of reads falling into 200bp bin in the genome.
For RNA-seq samples: SMART-seq2 reads were aligned to the rheMac2 or mm9 genome assembly using tophat2 version 2.0.11, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.0.2.
Genome_build: rheMac2, mm9
Supplementary_files_format_and_content: The bedgraph files contains the values  counted by the number of reads falling into 200bp bin in the genome. The gene rpkm txt file contains FPKM value for all samples. with number for each bin. While the validpair txt file indicates the paired interaction reads for each sample.

organism: Mus musculus

source_name: pachytene spermatocyte

extract_protocol:
The DNA extraction follows Hi-C protocol
Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification

treatment_protocol: Testes in each adult animal were harvested via standard surgical procedure and immediately placed into DMEM medium. After removing laminae parietalis, the testicular tissues were placed in 10 ml dish with DMEM/F12 (Cat# 11330032, Life technology) and cut by surgical scissors into 1~2 mm3. Small pieces were washed twice in DMEM/F12 to remove blood cell contaimination and further minced through successive cutting. Frist digestion were incubated for 15 min with a DMEM solution (Cat# 11965-084, Life technology) containing 2mg/ml Collagenase IV (Cat# C5138, Sigma) and 2mg/ml DNaseⅠ(Cat# DN25, Sigma). After spinning down at 600g, the pellet was then incubated with second enzyme digestion containing 2mg/ml collagenase, 2mg/ml DNaseⅠ and 0.25% trypsin EDTA (Cat# 25200-114, Life technology) for approximately 15 min. Digestion were stopped by 10% Fetal Bovine Serum (Cat# 10099-141, Life technology) and the cell suspension were filtered through 100μm and 40μm Strainers (Cat# 352340, BD)

value: testes


title: R42015-496pf_129-IR_L2


title: WTRU5.9_BAS


title: HiC_mouse_PAC_top6bl_KO_LEPL

description: new_mouse_top6bl_KO_LEPL_HiC_allValidPairs.gz


title: AE21_9382_BAS

value: Female


title: WTLU5.9_LUM

value: mammary gland


title: Hi-C_mouse_PAC_rep4

extract_protocol:
Purified pachytene spermatocyte were isolated from 3-month-old C57BL/6J (B6) mice using STA-PUT velocity sedimentation cell separator. The DNA extraction follows Hi-C protocol
Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification


title: R42016-155pf_126-IR_L6


title: WTLU5.9_BAS


title: R42016-154pf_125-IR_L6


title: WTRM5.9_LUM


title: RNA_mouse_PAC_WT_RNA

value: pachytene spermatocyte

value: WT


title: Hi-C_mouse_PAC_amanitin_rep1

extract_protocol:
Purified pachytene spermatocyte were isolated using STA-PUT velocity sedimentation cell separator. The DNA extraction follows Hi-C protocol
Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification
TruSeq

treatment_protocol: Pachytene cells were cultured according to a previously published protocol in Mary Ann Handel’s lab (Salle et al., 2009). Briefly, cells were washed twice with enriched Krebs-Ringer bicarbonate medium and cultured with spermatocyte culture medium (Salle et al., 2009) containing 200µg/ml α-amanitin (Sigma Co, USA, Cat#A2263) at 32℃ incubator for overnight. Next day, cells were collected and purified through 25% Percoll gradients (Sigma Co, USA, Cat#P4937) to further get rid of the dead cells and debris. The majority of viable Pachytene cells were applied for Hi-C sequencing. The absence of transcription was verified by BrUTP fluorescent staining following the protocol of a commercial kit (Cell-Light™ EU Apollo®567 In Vitro Imaging Kit, RIBOBIO Co，China, Cat# C10316-1). Pictures were taken by confocal microscopy (LSM 700, Zeiss, Pleasanton, CA, USA).

tag: agent

value: amanitin


title: Hi-C_mouse_PAC_amanitin_rep2

treatment_protocol: Pachytene cells were cultured according to a previously published protocol in Mary Ann Handel’s lab (Salle et al., 2010). Briefly, cells were washed twice with enriched Krebs-Ringer bicarbonate medium and cultured with spermatocyte culture medium (Salle al., 2009) containing 200µg/ml α-amanitin (Sigma Co, USA, Cat#A2263) at 32℃ incubator for overnight. Next day, cells were collected and purified through 25% Percoll gradients (Sigma Co, USA, Cat#P4937) to further get rid of the dead cells and debris. The majority of viable Pachytene cells were applied for Hi-C sequencing. The absence of transcription was verified by BrUTP fluorescent staining following the protocol of a commercial kit (Cell-Light™ EU Apollo®567 In Vitro Imaging Kit, RIBOBIO Co，China, Cat# C10316-1). Pictures were taken by confocal microscopy (LSM 700, Zeiss, Pleasanton, CA, USA).


title: R42016-152pf_123-IR_L6


title: R42015-495pf_122-IR_L2


title: Hi-C_mouse_PAC_rep3

extract_protocol:
Purified pachytene spermatocyte were isolated from 3-month-old C57BL/6J (B6) mice using STA-PUT velocity sedimentation cell separator. The DNA extraction follows Hi-C protocol
Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification
TruSeq


title: WTRM5.9_BAS

value: ACI


title: Hi-C_mouse_PAC_rep2


title: KORM4_LUM

description: RNA-seq of luminal cells of prepubertal aminals (4 seeks old)

value: 4 weeks


title: R42015-177pf_199-IR_L3


title: KORM4_BAS

description: RNA-seq of basal/myoepithelial cells of prepubertal aminals (4 seeks old)


title: KORU5.3_BAS


title: HiC_mouse_PAC_SYCP2_KO

description: new_mouse_SYCP2_KO_PAC_HiC_allValidPairs.gz


title: R42016-156pf_127-IR_L6


title: Hi-C_mouse_PAC_rep1


title: KORD4_LUM


title: RNA_mouse_top6bl_KO_LEPL

source_name: spermatocyte


title: KORD4_BAS


title: R42015-481pf_12-IR_L1


title: KORUU4_LUM


title: RNA_mouse_top6bl_KO_ZYGL


title: R42016-149pf_119-IR_L6


title: arota_diabetic rats_rep3 [miRNA]

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

institute: Peking Union Medical College Hospital

description: miRNA expression data from diabetic rats

hyb_protocol: Labeled miRNA was hybridized to the array.

scan_protocol: After hybridization, the chips were scanned by using a Genechip Array Scanner 3000 (Affymetrix).

data_processing: The data were generated by Affymetrix Expression Console software v1.1.

label: biotin

source_name: diabetic rats, 17week

label_protocol: Affymetrix protocol

extract_protocol: Total RNA was extracted by mirVanaTM RNA Isolation Kit (ABI)

value: arota

value: 17 weeks


title: R42016-153pf_124-IR_L6


title: RNA_mouse_SYCP2_KO_spermatocyte


title: WTLUU4_LUM


title: R42016-148pf_118-IR_L6


title: R42016-151pf_121-IR_L6


title: WTLUU4_BAS


title: R42016-147pf_117-IR_L6


title: R42016-146pf_116-IR_L6


title: WTLUD4_LUM


title: WTLUD4_BAS


title: arota_diabetic rats_rep1 [miRNA]


title: R42016-150pf_120-IR_L6


title: WTRU3.4_LUM


title: Hi-C_monkey_SPA_rep3

source_name: spermatogonia

treatment_protocol: For the gonocyte or spermatogonia, we separated them from the testis tissue of half-year-old rhesus monkeys. Only spermatogonia could be observed in the seminiferous tubules of testis tissue at this age, through hematoxylin-eosin staining and stage-specific antibody staining (PGP9.5).   Testis cells were also collected through two step enzyme digestion. The first step used an enzyme solution in DMEM and the second step used an enzyme solution in 0.25% trypsin EDTA, both containing 1mg/ml  collagenase, 1mg/ml DNaseⅠand 2.5 mg/ml hyaluronidase (Cat# H3884, Sigma).


title: Hi-C_monkey_SPA_rep2


title: Hi-C_monkey_RS_rep2

source_name: round spermatid

extract_protocol:
STA-PUT velocity sedimentation cell separator (Chamber Cat#56700-012, ProScience INC, Canada) was applied to generate separation of suspensions of living spematogenic cells on the basis of differences in cell sedimentation rate through the gravity, followed the methods developed for mouse testis cells (Bryant et al., 2013) and the manual of STA-PUT (2010 edition, ProScience INC) . For adult monkeys（5Y）, 2-5×107cell/ml testis cell suspension in 1600ml was used with 3hr sedimentation. For neonate monkeys (0.5Y), 600 ml cell suspension was used with 1.5hr sedimentation. According to the visible sedimentation bands, cell suspension was gradually collected through an automatic collector (Cat#DBS-160F, Jinke, China) after velocity sedimentation. All steps for separation were performed at 4°C.And the DNA extraction follows Hi-C protocol.
Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification

treatment_protocol: Testes in each adult animal were harvested via standard surgical procedure and immediately placed into DMEM medium. After removing laminae parietalis, the testicular tissues were placed in 10 ml dish with DMEM/F12 (Cat# 11330033, Life technology) and cut surgical scissors into 1~2 mm3. Small pieces were washed twice in DMEM/F12 to remove blood cell contaimination and further minced through successive cutting. Frist digestion were incubated for 15 min with a DMEM solution (Cat# 11965-084, Life technology) containing 2mg/ml Collagenase IV (Cat# C5138, Sigma) and 2mg/ml DNaseⅠ(Cat# DN25, Sigma). After spinning down at 600g, the pellet was then incubated with second enzyme digestion containing 2mg/ml collagenase, 2mg/ml DNaseⅠ and 0.25% trypsin EDTA (Cat# 25200-114, Life technology) for approximately 15 min. Digestion were stopped by 10% Fetal Bovine Serum (Cat# 10099-141, Life technology) and the cell suspension were filtered through 100μm and 40μm Strainers (Cat# 352340, BD)


title: arota_liraglutide-treated_rep3 [miRNA]

description: miRNA expression data from liraglutide-treated rats

source_name: liraglutide-treated rats, 17week


title: R42015-494pf_114-IR_L2


title: WTRU3.4_BAS


title: R42016-145pf_115-IR_L6


title: RNA_monkey_RS_rep2

value: round spermatid


title: Single_cell_RNAseq

city: Farmington

first: Zhongyuan

last: Tian

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

description: single-cell RNA-seq

data_processing:
ChIA-Drop: FASTQ files were aligned to the Drosophila melanogaster reference genome (dm3) using the longranger wgs pipeline (v2.1.5)  with default parameters to generate BAM files and simultaneously identify GEMcodes. Only high quality reads (uniquely mapped reads with MAPQ ≥ 30 and read length ≥ 50 bp) were retained for downstream analyses. Reads with the same GEMcode and whose extended genomic coordinates overlapped were merged into a chromatin fragment. Based on the merged chromatin fragments and their GEMcodes, individual GEMs (chromatin interaction complexes) could then be categorized based on the number of fragments they contained.
ChIA-PET and in situ ChIA-PET: Pair-end read (PET) sequences were scanned for the bridge linker sequence and only PETs with the bridge linker were used for downstream processing.  After trimming the linkers, the sequences flanking the linker were mapped to the dm3 using bwa-mem and only uniquely aligned (MAPQ ≥ 30) PETs were retained.  PCR duplicates were removed using Picard.  Each PET was categorized as either a self-ligation PET (two ends of the same DNA fragment) or inter-ligation PET (two ends from two different DNA fragments in the same chromatin complex) by evaluating the genomic span between the two ends of a PET.
Single-cell RNA-Seq:  FASTQ files were aligned to the Drosophila melanogaster reference genome (dm3) using thecellranger count pipeline (v2.1.1)  with with a key parameter (recovered_cells = 6000). Any cells that expressed < 5 % of the total genes were excluded, and any genes that were expressed in < 5% of cells were excluded.
Genome_build: dm3
Supplementary_files_format_and_content: ChIA-Drop:  (a) GEMLINE, one row represents one GEM, and columns are "GEM_ID" ,"GEM_coordinate" ,"GEM_span" ,"Fragment_number" ,"List_of_fragment_coordinates". (b) BARCODE_READID, a list of readID and barcode. Read1 contents 16 bp barcode and 8 bp UMI from its left side, and read2 is biological read.
Supplementary_files_format_and_content: ChIA-PET and in situ ChIA-PET: (a) BEDPE files are the genomic coodinates with frequency of each interactive PET clusters; (b) BEDGRAPH files ares reads pileup files.
Supplementary_files_format_and_content: Single-cell RNA-Seq: (a) Genes.tsv, (b) Barcodes.tsv, and (c) Matrix.mtx.

organism: Drosophila melanogaster

extract_protocol:
The overall chromatin sample preparation for ChIA-Drop is very similar to Hi-C, except no proximity ligation in ChIA-Drop. And the overall chromatin sample preparation for RNAPII enriched ChIA-Drop is very similar to ChIA-PET, except no proximity ligation in ChIA-Drop.
Fragmented chromatin sample was mixed with BSA to prevent chromatin aggregation. About 0.5ng of chromatin DNA material was loaded to microfluidics device, Chromium Controller with reagents from Chromium Genome v2 Library Kit & Gel Bead Kit for partitioning of single chromatin complex into individual droplets with unique gel beads according to the manufacturer’s protocol with modification. The barcoded DNA amplicons of each chromatin complex were released from all droplets.The purified DNA fragments were subjected for end repair, A-tailing, adaptor ligation, Sample Index PCR and size selection.  The final ChIA-Drop library was sequenced (2× 150 bp) by MiSeq, NextSeq or Hiseq runs.
We applied microfluidics-based strategy for genome-wide analysis of multiplex chromatin interactions with single-molecule precision (ChIA-Drop). Here, individual chromatin complexes are isolated in droplets that contain a gel bead with unique DNA barcode, in which tethered chromatin DNA fragments are barcoded and amplified for sequencing and mapping to demarcate chromatin contacts.

tag: method

value: single-cell RNA-seq

tag: factor

value: Poly(A)+

tag: molecule subtype

value: nuclear chromatin


title: arota_diabetic rats_rep2 [miRNA]


title: R42016-144pf_113-IR_L5

value: F

value: retina punch


title: WT_PNA+_2

description: RNA-seq of luminal progenitor fraction of mammary gland of wild type ACI rats

value: 9 weeks

value: luminal progenitors (Cd24+ Cd29LOW PNA+)


title: arota_liraglutide-treated_rep1 [miRNA]


title: R42015-536pf_112-IR_L5

value: M


title: RNA_monkey_RS_rep1


title: ChIA-Drop-Rep2

description: ChIA-Drop

source_name: ChIA-Drop

value: ChIA-Drop

value: HindIII fragmented chromatin, including all chromatin associated proteins


title: ChIA-Drop-Rep1

description: ChIA-Drop


title: arota_liraglutide-treated_rep2 [miRNA]


title: WT_PNA+_1

value: mammary gland


title: RNA_monkey_PAC_rep1

value: pachytene spermatocyte


title: NOD_16w_C

city: San Francisco

first: Anil

last: Bhushan

state: CA

address: 513 Parnassus ave

department: Diabetes Center

institute: UCSF

data_processing:
Cell Ranger v2.0.0
Genome_build: mm10
Supplementary_files_format_and_content: filtered gene barcode matrices from cellranger output: genes.tsv, barcodes.tsv, matrix.mtx (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/2.0/output/overview)

source_name: Pancreatic islets

extract_protocol:
islets were extracted, single cell suspension was made and CD45 cells were depleted.
scRNA libraries were prepared for sequencing using standard 10X Genomics protocol

value: 16 weeks

value: NOD/ShiltJ

value: Pancreas


title: HiC_monkey_PAC_rep3

value: testes


title: RNA_monkey_fibroblast_rep2

source_name: fibroblast

value: fibroblast


title: R42015-493pf_111-IR_L2


title: WT_Luminal_2

description: RNA-seq of mature luminal fraction of mammary gland of wild type ACI rats

value: ACI

value: mature luminal (Cd24+ Cd29LOW Cd49b- PNA-)


title: R42016-143pf_110-IR_L5


title: RNA_monkey_fibroblast_rep1


title: R42016-092pf_11-IR_L1


title: WT_Luminal_1


title: NOD_16w_B


title: R42016-142pf_109-IR_L5


title: DNA methylation_monkey_Sperm

source_name: sperm

extract_protocol:
The DNA extraction follows Stem-seq protocol
The STEM-seq libraries were generated using the protocol as described previously(Zhang et al., 2018). Briefly, cells were lysed in lysis buffer (10mM Tris-Hcl PH 7.5, 10mM NaCl,0.5% NP-40, protease K (Roche)) for 3h at 55°C and heat-inactivated for 1h at 72°C. Then we added Lamda DNA as a control to calculate bisulfite conversion rate. The DNA mixture was digested by dsDNA fragmentase (NEB) and followed by bisulfite conversion using EpiTect Fast Bisulfite Conversion Kit (Qiagen). Finally, the purified single strand converted DNA is tailed by poly C, followed by extension with a biotinylated poly G containing primer. The extension product is ligated to an adaptor followed by PCR amplification for sequencing library preparation. All libraries were sequenced on Illumina HiSeq XTen according to the manufacturer’s instruction.
TELP

treatment_protocol: For mature sperms, we collected them through swimming from the epididymis of the five-year-old animals in a 38 °C water bath

value: sperm


title: WT_CD49b+_1

value: luminal progenitors (Cd24+ Cd29LOW Cd49b+)


title: NOD_16w_A


title: R42016-141pf_108-IR_L5

value: F

value: retina punch


title: NOD_14w_C

value: 14 weeks


title: WT_Basal_2

description: RNA-seq of basal/myoepithelial fraction of mammary gland of wild type ACI rats

value: 9 weeks

value: basal/myoepithelial (Cd24+ Cd29HIGH)


title: DNA methylation_monkey_RS

value: round spermatid


title: WT_CD49b+_2

value: mammary gland


title: NOD_14w_A


title: R42016-140pf_107-IR_L5


title: DNA methylation_monkey_PAC

value: pachytene spermatocyte


title: WT_Basal_1


title: NOD_08w_C

value: 8 weeks


title: R42016-139pf_106-IR_L5


title: DNA methylation_monkey_SPA

value: spermatogonia


title: p27KO_PNA+_2

description: RNA-seq of luminal progenitor fraction of mammary gland of knockout ACI rats

value: luminal progenitors (Cd24+ Cd29LOW PNA+)


title: Hi-C_monkey_Sperm_rep2

extract_protocol:
The DNA extraction follows Hi-C protocol
Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification
TruSeq


title: Hi-C_monkey_Sperm_rep1

treatment_protocol: For mature sperms, we collected them through swimming from the epididymis of the five-year-old animals in a 37 °C water bath


title: p27KO_PNA+_1


title: R42015-535pf_104-IR_L5


title: RNAPII-ChIA-Drop-Rep2

description: RNAPII-ChIA-Drop

source_name: RNAPII-ChIA-Drop

value: RNAPII-ChIA-Drop

value: RNAPII (Biolegend, catalog# 920102)

value: nuclear chromatin


title: R42015-492pf_105-IR_L2

value: M


title: NOD_08w_A

value: NOD/ShiltJ

value: Pancreas


title: R42015-148pf_170-IR_L1


title: p27KO_Basal_2

description: RNA-seq of basal/myoepithelial fraction of mammary gland of knockout ACI rats

value: ACI


title: p27KO_CD49b+_1

value: luminal progenitors (Cd24+ Cd29LOW Cd49b+)


title: p27KO_CD49b+_2


title: R42015-419pf_1-IR_L7

value: retina punch


title: RNAPII-ChIA-Drop-Rep1

description: RNAPII-ChIA-Drop


title: p27KO_Basal_1

value: 9 weeks


title: Hi-C_monkey_PAC_rep2

extract_protocol: TruSeq


title: Hi-C_monkey_PAC_rep1

extract_protocol:
STA-PUT velocity sedimentation cell separator (Chamber Cat#56700-012, ProScience INC, Canada) was applied to generate separation of suspensions of living spematogenic cells on the basis of differences in cell sedimentation rate through the gravity, followed the methods developed for mouse testis cells (Bryant et al., 2013) and the manual of STA-PUT (2010 edition, ProScience INC) . For adult monkeys（5Y）, 2-5×107cell/ml testis cell suspension in 1600ml was used with 3hr sedimentation. For neonate monkeys (0.5Y), 600 ml cell suspension was used with 1.5hr sedimentation. According to the visible sedimentation bands, cell suspension was gradually collected through an automatic collector (Cat#DBS-160F, Jinke, China) after velocity sedimentation. All steps for separation were performed at 4°C.And the DNA extraction follows Hi-C protocol.
Hi-C libraries were prepared using Hi-C protocal developed by Rao et al. with slightly modification
TruSeq


title: Hi-C_monkey_RS_rep1


title: R42015-491pf_102-IR_L2

value: F


title: R42016-138pf_103-IR_L5


title: R42015-490pf_100-IR_L2


title: p27KO_Luminal_1

description: RNA-seq of mature luminal fraction of mammary gland of knockout ACI rats

value: mature luminal (Cd24+ Cd29LOW Cd49b- PNA-)


title: Hi-C_monkey_fibroblast_rep1

description: monkey_fibroblast_rep12_allValidPairs.gz

value: fibroblast


title: In_situ_RNAPII-ChIA-PET


title: SAMPLE22: PE_noNP_rep4

city: Cardiff

first: Hannah

last: Scott

address: Hadyn Ellis Building, Maindy Road

department: UK Dementia Research Institute

institute: Cardiff University

description: ND_noNP_vs_PE_noNP.txt; PE_noNP_vs_PE_blankNP.txt; PE_noNP_vs_PE_MitoQNP.txt

hyb_protocol: Samples were hybridised using the NanoString nCounter Human v2 miRNA Expression Assay kit. See nCounter miRNA Expression Assay User Manual for protocol.

scan_protocol: Samples were analysed using the NanoString nCounter Analysis System (Gen2). See Gen2 Prep Station User Manual.

data_processing:
Raw output files were converted into lists of counts. To compare two groups, the respective raw counts were passed into RUVSeq for normalisation and removal of unwanted variation. Adjusted counts were then analysed for differential expression analysis using edgeR.
Normalised counts can be found in attached text files, as specified in the 'Description' column under the 'Samples' heading. Values are Reporter Probe signal intensities captured with the nCounter Analysis System and normalised using RUVSeq.

source_name: placenta conditioned medium, preeclampsia, MitoQ-NP administration

label_protocol: Samples were labelled using the NanoString nCounter human v2 miRNA Expression Assay kit. See nCounter miRNA Expression Assay User Manual for protocol.

growth_protocol: De-identified human tissue was obtained from Southmead Hospital (Bristol, UK) with patients’ written informed consent and ethical approval by the NHS Health Research Authority. Mild, moderate or severe preeclampsia was diagnosed based on NICE guidelines. Preeclamptic placentae were delivered by induction or caesarean section. Control samples were obtained from non-diseased women following elective term caesarean delivery. Within 30 min of delivery, explants of villous tissue (~0.5 cm3) were dissected from the placenta midway between chorionic and basal plates. Explants were allowed to settle for up to 24 h in Dubecco’s Modified Eagle’s Medium (DMEM) with F-12 (Sigma-Aldrich) containing 10% FBS (Thermo Fisher Scientific), 1.2 mM L-glutamine (Sigma-Aldrich), 100 μg/mL gentamicin and 40 U/mL penicillin-streptomycin (Thermo Fisher Scientific). Placental explants were then incubated for 24 h in Gibco Neurobasal media with 1x Gibco B-27 Supplement, 1x antibiotic-antimycotic (all Thermo Fisher Scientific) and 2 mM L-glutamine.

extract_protocol: Conditioned medium was centrifuged for 15 min at 3,800 x g to pellet debris. Total RNA was extracted from 200 μl conditioned medium using the Qiagen miRNeasy Mini Kit.

treatment_protocol: MitoQ-NPs were added at the start of the incubation period at a final dose of 0.5 μM MitoQ. Alternatively unloaded NPs (blank NPs) were used at equivalent volume.

value: female

tag: gestational age

value: Placenta

tag: maternal disease status

value: Preeclampsia + systemic lupus erythematosus nephritis, previous deep vein thrombosis/pulmonary embolus, baby has metabolic disorder

tag: drug administration

value: no NP

tag: disease severity

value: severe

tag: maternal age


title: NOD_14w_B

tag: age

value: 14 weeks


title: RNAPII-ChIA-PET

description: RNAPII-ChIA-PET

source_name: RNAPII-ChIA-PET

value: RNAPII-ChIA-PET

value: RNAPII (Biolegend, catalog# 920102)

value: nuclear chromatin


title: NOD_08w_B

value: 8 weeks

value: NOD/ShiltJ

value: Pancreas


title: R42016-137pf_101-IR_L5

tag: Sex

value: M

tag: rin

tag: pmi

value: retina punch


title: SAMPLE23: PE_blankNP_rep4

description: PE_blankNP_vs_PE_MitoQNP.txt; PE_noNP_vs_PE_blankNP.txt

tag: tissue

value: blank NP


title: T. congolense-Infected bovine serum 1 [2873TRYP]

city: Edinburgh

first: Liam

last: Morrison

state: Midlothian

address: Easter Bush

institute: The Roslin Institute, The University of Edinburgh

data_processing:
SmallRNA Illumina adapter trimming and read length filtering 20-39bp using Cutadapt v1.7.1
Novoalign v3.02.12 to align the trimmed reads to T.Congolense IL3000 genome
HTSeq to quantify alignment count based on TriTrypDB-v9.0 annotation
Reads normalised to RPM  (Reads per Million)  alignged reads
Genome_build: TriTrypDB-9.0_TcongolenseIL3000 http://tritrypdb.org
Supplementary_files_format_and_content: HTSeq raw count and aggregated normalised RPM value

organism:
Trypanosoma congolense
Bos taurus

source_name: bovine serum

growth_protocol: Infected cattle: cattle infected with T. congolense IL3000 and serum sampled at day 19 post-infection, at a parasitaemia of approximately 5 x 10^6 trypanosomes/m;. T. congolense sample was grown in in vitro culture (TcBSF3) and RNA extracted from ~4 x 10^7 cells.

extract_protocol:
Samples were extracted using Trizol LS.
TruSeq Small RNA library preparation kit (Illumina) with 10 µL total RNA as starting material (approximately 50 ng - 1.66 µg)
Samples were enriched using 15 cycles of PCR and library products of 145-160 bp were gel purified, quantified and pooled for sequencing.  The library pool was sequenced using a HiSeq 2500 with 50-base single end reads and V4 chemistry.

tag: infected with

value: T. congolense IL3000

tag: time point

value: day 19 post-infection

value: serum

value: small RNA


title: p27KO_Luminal_2

tag: strain

value: ACI

tag: genotype

value: 9 weeks

value: mammary gland

tag: cell type

value: mature luminal (Cd24+ Cd29LOW Cd49b- PNA-)


title: T. congolense-Infected bovine serum 2 [2874TRYP]


title: In vitro T. congolense cell pellet [TRYPA]

description: TRYPA

organism: Trypanosoma congolense

source_name: trypanosome in vitro culture


title: SAMPLE20: PE_blankNP_rep3

source_name: placenta conditioned medium, preeclampsia, blank-NP administration

tag: gender

value: female

value: Placenta

value: Preeclampsia + adult polycystic kidney disease

value: severe


title: SAMPLE21: PE_MitoQNP_rep3

description: PE_noNP_vs_PE_MitoQNP.txt; PE_blankNP_vs_PE_MitoQNP.txt

value: MitoQ-NP


title: Hi-C_monkey_SPA_rep1

value: spermatogonia


title: Hi-C_monkey_fibroblast_rep2

value: fibroblast


title: SAMPLE19: PE_noNP_rep3

value: no NP


title: SAMPLE17: PE_blankNP_rep2

value: Preeclampsia + type I diabetes

value: blank NP


title: SAMPLE16: PE_noNP_rep2

source_name: placenta conditioned medium, preeclampsia, no NP administration


title: SAMPLE18: PE_MitoQNP_rep2


title: SAMPLE15: PE_MitoQNP_rep1

value: Preeclampsia

value: mild


title: SAMPLE12: ND_MitoQNP_rep4

description: ND_noNP_vs_ND_MitoQNP.txt; ND_blankNP_vs_ND_MitoQNP.txt

source_name: placenta conditioned medium, non-diseased, MitoQ-NP administration

value: unknown

value: no disease


title: SAMPLE14: PE_blankNP_rep1


title: SAMPLE10: ND_noNP_rep4

description: ND_noNP_vs_PE_noNP.txt; ND_noNP_vs_ND_blankNP.txt; ND_noNP_vs_ND_MitoQNP.txt


title: SAMPLE11: ND_blankNP_rep4

description: ND_blankNP_vs_ND_MitoQNP.txt; ND_noNP_vs_ND_blankNP.txt


title: SAMPLE07: ND_noNP_rep3

source_name: placenta conditioned medium, non-diseased, blank-NP administration


title: SAMPLE13: PE_noNP_rep1


title: SAMPLE08: ND_blankNP_rep3


title: SAMPLE09: ND_MitoQNP_rep3


title: SAMPLE05: ND_blankNP_rep2


title: miRNA_DEX3

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: left ventricle

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray, Kamakura, Japan)

growth_protocol: Male Wistar rats weighing between 250 g and 350 g were used.

extract_protocol: RNA samples were extracted from cardiac tissue using RNeasy mini kit (Qiagen).

treatment_protocol: Rats were assigned to a control group in which saline was infused or a DEX group in which dexmedetomidine was administered for 30 min.

tag: treatment

value: administration of dexmedetomidine

value: Wistar

value: male

value: heart

tag: heart region

value: left ventricle


title: SAMPLE06: ND_MitoQNP_rep2

value: female

tag: gestational age

value: Placenta

tag: maternal disease status


title: miRNA_DEX4


title: SAMPLE04: ND_noNP_rep2

source_name: placenta conditioned medium, non-diseased, no NP administration

tag: drug administration

tag: disease severity


title: miRNA_DEX1


title: SAMPLE03: ND_MitoQNP_rep1

value: MitoQ-NP

tag: maternal age


title: miRNA_Control5

value: administration of saline

tag: Sex


title: SAMPLE02: ND_blankNP_rep1


title: miRNA_Control4


title: Control5

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc..

extract_protocol: RNA samples were extracted from cardiac tissue using RNesy mini kit (Qiagen).


title: miRNA_DEX5


title: miRNA_DEX2


title: miRNA_Control2


title: SAMPLE01: ND_noNP_rep1


title: Control1


title: DEX1


title: DEX5


title: DEX2


title: Control3


title: DEX3


title: Control2


title: DEX4


title: miRNA_Control1


title: miRNA_Control3


title: Gro-Seq minus TNFa

status: Public on Feb 10 2019

city: San Diego

first: Qi

last: Ma

address: 9500 Gilman Dr,

institute: UCSD

description: Gro-seq in MCF7 cells treated withEtOH(Control) + 2,5-Hexanediol

data_processing:
Library strategy: GRO-seq
Basecalls performed using CASAVA version 1.4, then all Raw fastq files are treated with prinseq-lite.pl to remove PCR amplification duplicates.
Then the remaining reads are trimmered 6 bp from the 5' end and keep 40bp for each reads for the mapping.
After that, all reads are mapped to the hg19 genome with bowtie ( -q --offrate 6 -m 1 --best --strata -t -v 3 --sam)
The common artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data. To determine transcription changes in gene body, the sequencing reads for RefSeq genes were counted over the first 13kb of the entire gene body, excluding the 500bp promoter-proximal region on the sense strand with respect to the gene orientation by using HOMER. EdgeR was used to compute the significance of the differential gene expression (FC ≥ 1.5, FDR ≤ 0.01). Additionally, a read density threshold (that is, normalized GRO-seq read counts per kb) was used to exclude lowly expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files are generated with HOMER using makeUCSCfile,

growth_protocol: MCF7, estrogen receptor alpha positive breast cancer cells were cultured in DMEM and 10%FBS under standard condition

extract_protocol:
MCF7 cells after treatment were incubated in swellinig ice-cold buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2) for 5min. Cells were lysed in lysis buffer (swelling buffer with 0.5% IGEPAL and 10% glycerol). The resultant nuclei were washed once again with 10 ml lysis buffer and then re-suspended in 100μl of freezing buffer (50mM Tris-Cl pH 8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA).
GRO-seq experiments were performed as previously reported (Li et al., 2013). Briefly, MCF7 cells were swollen in swelling buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2) for 5 min on ice and then lysed in lysis buffer (swelling buffer with 0.5% IGEPAL and 10% glycerol), before being re-suspended in 100µl of freezing buffer (50mM Tris-Cl pH8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA). For the run-on assay, re-suspended nuclei were mixed with an equal volume of reaction buffer (10mM Tris-Cl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of Superase.In, 1% sarkosyl, 500µM ATP, GTP, and Br-UTP, 2µM CTP) and incubated for 5 min at 300C. The nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol LS reagent (Invitogen) following manufacturer’s instructions. After base hydrolysis on ice for 40min and followed by treatment with DNase I and antarctic phosphatase, the Br-UTP labeled NRO-RNA was purified by an anti-BrdU argarose beads (Santa Cruz Biotech) in binding buffer (0.5XSSPE, 1mM EDTA, 0.05% tween) for 3hr at 4°C while rotating. Then T4 PNK (NEB) was used to repair the end of NRO-RNA. Subsequently, cDNA synthesis was performed as reported(9,33) with few modifications. The RNA fragments were subjected to poly-A tailing reaction by poly-A polymerase (NEB) for 30 min at 37°C. Reverse transcription was then performed using superscript III (Invitrogen) with oNTI223 primer. The cDNA products were separated on a 10% polyacrylamide TBE-urea gel with right product (~100-500bp) being excised and recovered by gel extraction. After that, the first-strand cDNA was circularized by CircLigase (Epicentre) and re-linearized by Ape1 (NEB). Re-linearized single strand cDNA were separated by TBE gel and the products of desired size was excised (~120-320bp) for gel extraction. Finally, cDNA template was amplified by PCR using the Phusion High-Fidelity enzyme (NEB) with primers oNTI200 and oNTI201 for deep sequencing.

treatment_protocol: MCF7 cells  grown in phenol red free DMEM and charcoal stripped FBS were treated with estrogen for 60 before collecting the samples for ChIP-Seq. Control samples were treated with ICI 182,780, and ER alpha antagonist

tag: cell line

value: Human breast cancer cells

value: WT


title: ChIP-Seq AP2g + E2 + 1,6-HD

data_processing:
Basecalls performed using CASAVA version 1.4, then all Raw fastq files are treated with prinseq-lite.pl to remove PCR amplification duplicates.
Then the remaining reads are trimmered 6 bp from the 5' end and keep 40bp for each reads for the mapping.
After that, all reads are mapped to the hg19 genome with bowtie ( -q --offrate 6 -m 1 --best --strata -t -v 3 --sam)
Peaks are determined using HOMER with the following parameters: -style factor -center -size 200 -minDist 500 -fdr 0.001 -fragLength 150.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files are generated with HOMER using makeUCSCfile,

source_name: AP2g ChIP-seq on MCF7 cell stimulated with Estrogen+ 1,6-Hexanediol

extract_protocol:
For ChIP-seq, samples were fixed for 8 minutes with 1% formaldehyde. Fixation was stopped by adding Glycine (0.125M). Chromatin DNA was sheared to 200–500 bp size by sonication. Soluble sheared chromatin was immunoprecipitated with specific antibodies overnight at 4°C. Next day, lysates were incubated in prewashed protein G dynabeads (Invitrogen). After washing and elution, the protein–DNA complex was decross-linked by heating at 65°C for 4 hours. Immunoprecipitated DNA was purified by using QIAquick PCR purificaion kit.
The libraries were constructed following Illumina’s Chip-Seq Sample prep kit.

treatment_protocol: MCF7 cells  grown in phenol red free DMEM and charcoal stripped FBS were treated with estrogen for 60 before collecting the samples for 4C. Control samples were treated with ICI 182,780, and ER alpha antagonist

tag: chip antibody

value: Santacruz biotechnology (H-77)


title: Gro-Seq minus TNFa + 1,6-Hexanediol

description: Gro-seq in MCF7 cells treated withEtOH(Control) + 1,6-Hexanediol


title: Gro-Seq minus E2

description:
Nascent RNA
Gro-seq in MCF7 cells treated with  ICI 182,780

data_processing:
Library strategy: GRO-seq
Basecalls performed using CASAVA version 1.4
Gro-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.0.1.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: ATCC

treatment_protocol: MCF7 cells  grown in phenol red free DMEM and charcoal stripped FBS were treated with estrogen for 60 before collecting the samples for GRO-seq. Control samples were treated with ICI 182,780, and ER alpha antagonist


title: Groseq-plus E2 + 2,5-HD

description: Gro-seq in MCF7 cells treated with E2 14hrs. + 2,5-Hexanediol


title: Groseq-plus E2 + 1,6-HD

description: Gro-seq in MCF7 cells treated with E2 14hrs. + 1,6-Hexanediol


title: Gro-Seq plus TNFa + 1,6-Hexanediol

description: Gro-seq in MCF7 cells treated with TNFa + 1,6-Hexanediol


title: Groseq-plus E2 (30min) + 2,5-HD

description:
Nascent RNA
Gro-seq in MCF7 cells treated with E2 30min + 2,5-Hexanediol


title: Gro-Seq plus TNFa

description: Gro-seq in MCF7 cells treated with TNFa + 2,5-Hexanediol


title: Groseq-plus E2 (14hrs) + E2 1hr + 2,5-HD

description:
Nascent RNA
Gro-seq in MCF7 cells treated withEtOH(Control) + 1,6-Hexanediol


title: T6 (PCV2-infected YL pig)

city: Tai'an

first: Gen

last: Liu

state: Shandong

address: Daizong Road No.61

department: College of Animal Science and Veterinary Medicine

institute: Shandong Agricultural University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Sscrofa10.2 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Cufflinks are used for assemble transcripts and remap and quanlity gene-expression level, which is estimate by FPKM value.
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample; FASTA file with transcriptome sequence of the new genes

organism: Sus scrofa

source_name: Spleen

extract_protocol:
RNA was extracted from spleen samples (stored at liquid nitrogen) according to the instruction manual of the TRIzol reagent. RNA sequencing libraries were generated using the NEB Next Ultra RNA Library Prep Kit for Illumina (Cat# E7420L).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: spleen

tag: age

value: 11 weeks

value: wild type


title: T4 (PCV2-infected YL pig)


title: T3 (mock-infected YL pig)


title: T1 (mock-infected YL pig)


title: T5 (PCV2-infected YL pig)


title: ChIP-Seq GATA3 + E2 + 1,6-HD

source_name: GATA3 ChIP-seq on MCF7 cell stimulated with Estrogen+ 1,6-Hexanediol

value: Santacruz biotechnology (HG3-31)


title: ChIP-Seq AP2g + E2

source_name: AP2g ChIP-seq on MCF7 cell stimulated with Estrogen


title: ChIP-Seq ER alpha + E2

source_name: ER alpha ChIP-seq on MCF7 cell stimulated with Estrogen

value: Santacruz biotechnology (HC-20)


title: ChIP-Seq GATA3 + E2

source_name: GATA3 ChIP-seq on MCF7 cell stimulated with Estrogen


title: ChIP-Seq ER alpha + E2 + 1,6-HD

source_name: ER alpha ChIP-seq on MCF7 cell stimulated with Estrogen + 1,6-Hexanediol


title: RNA-seq in GSK126-treated resistant clone 4 TOV21G cell line

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

data_processing:
RNA-Seq data analysis was done with bowtie2 and rsem (ver. 1.2.3) using hg19 genome with ensemble transcriptome information
DESeq2 was used for differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed files contain raw counts for each gene

source_name: resistant TOV21G cell line

growth_protocol: Ovarian clear cell carcinoma cell line TOV21G wes cultured in RPMI 1640 with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C supplied with 5% CO2

extract_protocol:
total RNA was isolated for RNA-Seq using Trizol reagent.
RNA-Seq library was prepared using the TruSeq Stranded Total RNA Library Preparation kit (Illumina).

treatment_protocol: The GSK126-resistant clones were generated from TOV21G cells by gradually increasing the  concentration of GSK126. Cells were treated started from 5 uM. The concentration was increased to 10 uM after the cells become stable. The concentration was then increased to 15 uM and 20 uM. After the cells become stable in 20 uM GSK126, clones were picked for further analysis.

value: resistant clone 4 TOV21G cell line (c4)

value: GSK


title: Groseq-minus E2 + 2,5-HD

description: Gro-seq in MCF7 cells treated with EtOH(Control) overnight + 2,5-Hexanediol


title: T2 (mock-infected YL pig)


title: RNA-seq in GSK126-treated resistant clone 3 TOV21G cell line

value: resistant clone 3 TOV21G cell line (c3)


title: AR2130 03: melanocyte precursor cells

city: kobe

first: Chieko

last: Hosaka

institute: kobe dermatology

hyb_protocol: Agilent standard protocol

scan_protocol: Agilent standard protocol

data_processing: The data were analyzed using the Gene Spring GX 13.1.1 software program (Agilent Technologies).The data processing was performed as follows; (i) Threshold raw signals were set to 1.0, (ii) Log base 2 transformation was performed, (iii) 75th percentile normalization was chosen as the normalized algorithm.

source_name: precursor cell

label_protocol: Agilent standard protocol

extract_protocol: Total RNA was isolated by Trizol reagent (Life Technologies) according to the manufacturer's instruction.

value: melanocyte precursor cells


title: AR2130 04: directly differentiated melanocytes

source_name: melanocyte

value: directly differentiated melanocytes


title: AR2130 05: indirectly differentiated melanocytes

value: indirectly differentiated melanocytes


title: AR2130 02: human epidermal melanocytes

value: human epidermal melanocytes


description:
BRG1 binding in resistant clone 3 of TOV21G cell line
CHIP.c3.BRG1

data_processing:
Chip-seq data was aligned using bowtie version 0.12.9 to human genome hg19
Peak calling in parental TOV21G and resistant cell lines was done with HOMER software using another sample as a control with -style histone -fdr 0.05 parameters.  TOVvsClone.BRG1_CHIPseq.txt = CHIP.TOV.BRG1 using CHIP.c3.BRG1 as a control.  ClonevsTOV.BRG1_CHIPseq.txt = CHIP.c3.BRG1 using CHIP.TOV.BRG1 as a control.  So each sample uses another one as a control.
Genome_build: hg19
Supplementary_files_format_and_content: Prosessed file contains HOMER peak calling output for TOV21G and resistant clone specific binding

extract_protocol:
Flag (Sigma, F1804) antibody was used on TOV21G and resistant endogenously Flag-tagged BRG1 cells. Chromatin were incubated overnight at 4°C and protein A+G Dynabeads were added to the reaction for another 1.5 hour. Magnetic beads were washed and chromatin was eluted and reversed. Chromatin was then treated with proteinase K and purified with Gel extraction kit (Qiagen, cat. no. 28706). ChIP DNA was used for ChIP-seq.
For CHIP-seq NEBNext Ultra DNA Library Prep Kit (NEB, E7645) was used to prepare sequencing library

value: anti-Flag (Sigma, catalog# F1804, lot# SLBT7654) antibody


title: AR2130 01: feeder-free iPSCs

source_name: FF-iPS

value: feeder-free iPSCs


title: RNA-seq in parental TOV21G cell line

description: RNA-seq in parental TOV21G cell line

source_name: TOV21G cell line

value: parental TOV21G cell line

value: ctr


title: RNA-seq in untreated resistant clone 3 TOV21G cell line


title: Gro-Seq plus KLA + 1,6-Hexanediol

description: Gro-seq in RAW cells treated with KLA + 1,6-Hexanediol

data_processing:
Library strategy: GRO-seq
Basecalls performed using CASAVA version 1.4, then all Raw fastq files are treated with prinseq-lite.pl to remove PCR amplification duplicates.
Then the remaining reads are trimmered 6 bp from the 5' end and keep 40bp for each reads for the mapping.
After that, all reads are mapped to the hg19 genome with bowtie ( -q --offrate 6 -m 1 --best --strata -t -v 3 --sam)
The common artifacts derived from clonal amplification were circumvented by considering maximal three tags from each unique genomic position as determined from the mapping data. To determine transcription changes in gene body, the sequencing reads for RefSeq genes were counted over the first 13kb of the entire gene body, excluding the 500bp promoter-proximal region on the sense strand with respect to the gene orientation by using HOMER. EdgeR was used to compute the significance of the differential gene expression (FC ≥ 1.5, FDR ≤ 0.01). Additionally, a read density threshold (that is, normalized GRO-seq read counts per kb) was used to exclude lowly expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files are generated with HOMER using makeUCSCfile.

growth_protocol: RAW264.7 cells are immortalized murine macrophase cell line. Cells were grown in DMEM media with 10% FBS

extract_protocol:
RAW264.7 cells after KLA treatment were incubated in swellinig ice-cold buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2) for 5min. Cells were lysed in lysis buffer (swelling buffer with 0.5% IGEPAL and 10% glycerol). The resultant nuclei were washed once again with 10 ml lysis buffer and then re-suspended in 100μl of freezing buffer (50mM Tris-Cl pH 8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA).
GRO-seq experiments were performed as previously reported (Li et al., 2013). Briefly, MCF7 cells were swollen in swelling buffer (10mM Tris-Cl pH7.5, 2mM MgCl2, 3mM CaCl2) for 5 min on ice and then lysed in lysis buffer (swelling buffer with 0.5% IGEPAL and 10% glycerol), before being re-suspended in 100µl of freezing buffer (50mM Tris-Cl pH8.3, 40% glycerol, 5mM MgCl2, 0.1mM EDTA). For the run-on assay, re-suspended nuclei were mixed with an equal volume of reaction buffer (10mM Tris-Cl pH 8.0, 5mM MgCl2, 1mM DTT, 300mM KCl, 20 units of Superase.In, 1% sarkosyl, 500µM ATP, GTP, and Br-UTP, 2µM CTP) and incubated for 5 min at 300C. The nuclear-run-on RNA (NRO-RNA) was then extracted with TRIzol LS reagent (Invitogen) following manufacturer’s instructions. After base hydrolysis on ice for 40min and followed by treatment with DNase I and antarctic phosphatase, the Br-UTP labeled NRO-RNA was purified by an anti-BrdU argarose beads (Santa Cruz Biotech) in binding buffer (0.5XSSPE, 1mM EDTA, 0.05% tween) for 3hr at 4°C while rotating. Then T4 PNK (NEB) was used to repair the end of NRO-RNA. Subsequently, cDNA synthesis was performed as reported(9,33) with few modifications. The RNA fragments were subjected to poly-A tailing reaction by poly-A polymerase (NEB) for 30 min at 37°C. Reverse transcription was then performed using superscript III (Invitrogen) with oNTI223 primer. The cDNA products were separated on a 10% polyacrylamide TBE-urea gel with right product (~100-500bp) being excised and recovered by gel extraction. After that, the first-strand cDNA was circularized by CircLigase (Epicentre) and re-linearized by Ape1 (NEB). Re-linearized single strand cDNA were separated by TBE gel and the products of desired size was excised (~120-320bp) for gel extraction. Finally, cDNA template was amplified by PCR using the Phusion High-Fidelity enzyme (NEB) with primers oNTI200 and oNTI201 for deep sequencing.

treatment_protocol: RAW264.7 cells  grown in  DMEM with 10% FBS were cultured in medium with 0.5% FBS overnight. Cells were treated with 8.5% 2,5 hexanediol or 1,6 hexanediol for 5 min before stimulation with 100nMKdo2-Lipid A (KLA) for 30min.

value: Mouse macrophage


title: Gro-Seq minus KLA

description: Gro-seq in untreated RAW cells + 2,5-Hexanediol


title: RNA-seq in untreated resistant clone 4 TOV21G cell line


title: Gro-Seq minus KLA + 1,6-Hexanediol

description: Gro-seq in untreated RAW cells  + 1,6-Hexanediol


title: pU6 MosIR transfected NIH3T3 cells, replicate 2

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

description: replicate 2

data_processing:
Raw .fastq files were trimmed in two rounds using bbduk 37.95. First, adapter was trimmed from 3’ end or reads:  bbduk.sh in=${FILE}.fastq.gz out=${FILE}.atrim.fastq.gz literal=TGGAATTCTCGGGTGCCAAGG ktrim=r k=19 rcomp=t mink=10 hdist=1 minoverlap=8   Next, 4 bases were trimmed from both 5’ and 3’ ends of adapter trimmed reads:  bbduk.sh in=${FILE}.atrim.fastq.gz out=${FILE}.trim.fastq.gz forcetrimright2=4 forcetrimleft=4 minlength=15
Trimmed reads were then mapped onto indexed genome using STAR 2.5.3a:   STAR --readFilesIn ${FILE}.trim.fastq.gz --genomeDir $ REF_GENOME_INDEX --runThreadN 10 --genomeLoad LoadAndRemove –limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix ${FILE}. --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMismatchNmax 2 --outFilterMismatchNoverLmax 1 --outFilterMismatchNoverReadLmax 1 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --outFilterMultimapNmax 99999 --outFilterMultimapScoreRange 0 --alignIntronMax 1 --alignSJDBoverhangMin 999999999999
Mapped .bam files were divided into reads aligning with 0, 1 or 2 allowed mismatches
Counts of mature miRNAs were computed in R over .gff3 annotation file downloaded from miRBase, v22, separately for reads with 0, 1 or 2 allowed mismatches:  GenomicAlignments::summarizeOverlaps(features = mirna_gr, reads = bamfiles, mode = "Union", singleEnd = TRUE, ignore.strand = FALSE)
Genome_build: mm10
Supplementary_files_format_and_content: mature_miRNA.NIH3T3_transfected.2018.counts.xlsx  - .xlsx table with counts of reads aligning to mature miRNAs annotated on mm10 genome from miRBase, v22  - counts are done separately for reads with 0, 1, or 2 mismatches allowed when aligning to the genome (separate sheets in .xlsx file)  - samples are in columns, rows represent annotated mature miRNA

growth_protocol: NIH3T3 cells were maintained in DMEM (Sigma) supplemented with 10 % fetal calf serum (Sigma), penicillin (100 U/mL, Invitrogen), and streptomycin (100 µg/mL, Invitrogen) at 37 °C and 5 % CO2 atmosphere

extract_protocol:
Cells were washed with PBS, and total RNA was isolated using RNAzol (MRC) according to the manufacturer’s protocol. RNA quality was verified by Agilent 2100 Bioanalyzer
Libraries were constructed from total RNA using NEXTflex Small RNA-Seq Kit v3 (Bio Scientific) according to manufacturer’s protocol and sequenced on the Illumina HiSeq2000 platform at the Genomics Core Facility at EMBL

treatment_protocol: Cells were plated on 6-well plates and grown to 50 % density. Cells grown in a 24-well plate were transfected with 250 ng/well of U6-MosIR, U6-Lin28aIR, CAG-EGFP-MosIR, or CAG-EGFP-Lin28IR plasmids and cultured for 48 hours.

value: pU6 MosIR


title: pU6 MosIR transfected NIH3T3 cells, replicate 1

description: replicate 1


title: Gro-Seq plus KLA

description: Gro-seq in RAW cells treated with KLA + 2,5-Hexanediol


title: s46m-N2

status: Public on Feb 09 2019

city: Wuhan

first: Ma

last: Siqi

address: No.1,Shizishan Street

institute: Huazhong Agricultural Uinveristy

data_processing:
For ChIP-seq, the reads were filtered by FASTP and mapped to the rice genome (MSU RGAP, release 7) using Bowtie 2 (version 2.3.4). And the peak calling was performed using MACS2 software (version 2.1.1) with the default parameters. Genes (including gene body and the 3-kb upstream and 3-kb downstream regions) overlapping with the peaks were considered to have the H2Bub1 occupancy. The differential modification of H2Bub1 was determined with a standard of Fold change ≥2 and P-value< 0.05. Gene Ontology (GO) analysis was performed on an online platform named BMKClould (http://www.biocloud.net), and the significance threshold was set at a P-value of 0.001.
Genome_build: RGAP 7.0
Supplementary_files_format_and_content: peak file; differential modification of H2Bub1

organism: Oryza sativa

source_name: osbzip46 mutant _normal condition_leaves_anti-H2Bub1

growth_protocol: Seedlings were grown in sand/paddy (1:3) soil under natural conditions (14 h sun light/ 10 h dark) at July in Wuhan area. Seedlings at the four-leaf stages were harvested and frozen in liquid nitrogen for RNA isolation.

extract_protocol: For The ChIP-Seq, 4 ng DNA were used to construct sequencing libraries following the protocol of TruSeq ChIP Library Preparation Kit (Illumina);

treatment_protocol: rice plants at 4-leaf stage growing in the paddy soil from natural rice field were subjected to progressively (slowly developed) drought stress with the soil water content monitored.

tag: germplasm background

tag: genotype/variation

value: osbzip46 mutant

tag: development stage

value: normal condition

value: leaves

value: anti-H2Bub1 (Millipore, 05-1312)


title: s46m-N2-in

source_name: osbzip46 mutant _normal condition_leaves_input

value: none (input)


title: s46m-N1-in


title: s46m-N1


title: pCag-EGFP MosIR transfected NIH3T3 cells, replicate 1

description: replicate 1

value: pCag-EGFP MosIR


title: pU6 Lin28IR transfected NIH3T3 cells, replicate 2

description: replicate 2

value: pU6 Lin28IR


title: pCag-EGFP MosIR transfected NIH3T3 cells, replicate 2

description: replicate 2


title: pCag-EGFP Lin28IR transfected NIH3T3 cells, replicate 2

description: replicate 2

value: pCag-EGFP Lin28IR


title: pU6 Lin28IR transfected NIH3T3 cells, replicate 1

description: replicate 1


description:
BRG1 binding in parental TOV21G cell line
CHIP.TOV.BRG1


title: s46m-D3-in

source_name: osbzip46 mutant _drought treatment_leaves_input

value: drought treatment


title: s46m-D3

source_name: osbzip46 mutant _drought treatment_leaves_anti-H2Bub1


title: s46m-D2


title: s46m-D1


title: s46m-D2-in


title: s46m-N3-in


title: s46m-D1-in


title: s46m-N3


title: s46CK-N2-in

source_name: wild type_normal condition_leaves_input

value: wild type


title: s46CK-N1-in 1


title: s46CK-N1


title: s46CK-N2


title: s46CK-D2


title: zh11_severe drought_2_RNA

description: zh11_severe drought_2_RNA.txt

data_processing:
For ChIP-seq, the reads were filtered by FASTP and mapped to the rice genome (MSU RGAP, release 7) using Bowtie 2 (version 2.3.4). And the peak calling was performed using MACS2 software (version 2.1.1) with the default parameters. Genes (including gene body and the 3-kb upstream and 3-kb downstream regions) overlapping with the peaks were considered to have the H2Bub1 occupancy. The differential modification of H2Bub1 was determined with a standard of Fold change ≥2 and P-value< 0.05. Gene Ontology (GO) analysis was performed on an online platform named BMKClould (http://www.biocloud.net), and the significance threshold was set at a P-value of 0.001.
For RNA-seq, sequence reads were filtered by FASTP and mapped to the rice genome (MSU RGAP, release 7) using HISAT2 (version 2.0.5) with default parameters. Differentially expressed genes, which were defined with an expression change fold ≥ 2 with P < 0.05, were analyzed using DESeq2 (version 1.20.0).
Genome_build: RGAP 7.0

source_name: zhonghua11（Oryza sativa）

extract_protocol: For The ChIP-Seq, 4 ng DNA were used to construct sequencing libraries following the protocol of TruSeq ChIP Library Preparation Kit (Illumina); For each sample, mRNA purified from 10 μg total RNA was used for constructing sequencing libraries with the TruSeq RNA Sample Preparation Kit (Illumina).

treatment_protocol: To define the moderate and severe drought stresses treatment, rice plants at 4-leaf stage growing in the paddy soil from natural rice field were subjected to progressively (slowly developed) drought stress with the soil water content monitored. It was regarded as moderate drought stress when the relative soil water content was about 20% and severe drought stress when the relative soil water content was about 10%. The relative soil water content was calculated as followings: 100% × (the weight of soil after stress – the weight of air-dried soil) / the weight of soil after stress.

value: severe drought treatment

tag: antibody


title: s46CK-D1


title: zh11_severe drought_3_RNA

description: zh11_severe drought_3_RNA.txt


title: s46CK-D2-in


title: zh11_moderate drought_3_RNA

description: zh11_moderate drought_3_RNA.txt

value: moderate drought treatment


title: zh11_normal_3_RNA

value: normal


title: zh11_moderate drought_2_RNA

description: zh11_moderate drought_2_RNA.txt


title: zh11_moderate drought_1_RNA

description: zh11_moderate drought_1_RNA.txt


title: zh11_normal_2_RNA


title: s46CK-D3


title: zh11_normal_1_RNA


title: zh11_severe drought_3_H2B

description: zh11_H2Bub1_severe_drought_peak_annoation.xls


title: zh11_severe drought_1_RNA

description: zh11_severe drought_1_RNA.txt


title: zh11_severe drought_1_H2B


title: zh11_moderate drought_3_H2B

description: zh11_H2Bub1_moderate_drought_peak_annoation.xls


title: zh11_moderate drought_2_H2B


title: zh11_normal_1_H2B


title: zh11_normal_3_H2B


title: s46CK-D3-in


title: zh11_moderate drought_1_H2B


title: pCag-EGFP Lin28IR transfected NIH3T3 cells, replicate 1

description: replicate 1


title: zh11_severe drought_3_input


title: zh11_severe drought_1_input


title: s46CK-N3


title: zh11_severe drought_2_input


title: s46CK-D1-in


title: zh11_moderate drought_3_input


title: zh11_normal_3_input


title: zh11_moderate drought_1_input


title: zh11_normal_1_input


title: Control4

source_name: left ventricle

value: administration of saline

tag: strain

value: Wistar

value: male

value: heart

value: left ventricle


title: zh11_severe drought_2_H2B

tag: treatment


title: zh11_normal_2_H2B


title: s46CK-N3-in

value: normal condition