title: RRMM1_C91


title: RRMM2_C08

status: Public on Nov 17 2018

type: SRA

city: Rochester

first: Jie

last: Sun

state: MN

address: 200 First Street SW

country: USA

institute: Mayo Clinic

library_source: transcriptomic

data_processing:
Basecalls performed using Illumina bcl2fastq2 versions bcl2fastq-1.8.4 (before therapy) and 2.17.1.14 after therapy)
Sequence reads were aligned to the hg19 genome assembly using TopHat2
Raw and normalized gene counts (RPKM) are generated by Featuregenecounts
Raw gene counts are converted to TPM
Genome_build: hg19
Supplementary_files_format_and_content: raw counts

molecule: polyA RNA

organism: Homo sapiens

source_name: plasma cells from perpheral blood

extract_protocol: Bone marrow aspirates were collected from 15 patients after informed consent and subjected to ACK lysis and mononuclear cell isolation. Plasma cells were separated by positive selection using CD138 coated magnetic beads (MACS; Miltenyi Biotec, CA) in a RoboSep system (STEMCELL Technology, Canada). CD138 positive cells were examined using Vi-CELL XR (Beckman Coulter, CA) to determine cell number, viability and average size. A microfluidic mRNA-Seq chip (Fluidigm, CA) was used for capturing cells from each sample at a concentration of 500 cells/μl and run in the Fluidigm C1 system to  generate double stranded cDNA using SMARTer Ultra Low RNA kit for Illumina (Takara, CA).  All samples were assessed for cell capture in a C1 chip by direct observation under a microscope and for cDNA quality using Fragment Analyzer (HS Large Fragment kit, Advanced Analytical Technologies, IA).

tag: tumor stage

value: RRMM

tag: patient


title: RRMM1_C79


title: RRMM2_C02


title: RRMM1_C57


title: RRMM2_C01


title: RRMM1_C63


title: RRMM1_C69


title: RRMM2_C51


title: RRMM1_C56


title: RRMM2_C53


title: RRMM1_C52


title: RRMM1_C50


title: RRMM1_C46


title: RRMM1_C48


title: RRMM1_C41


title: RRMM1_C42


title: RRMM1_C37


title: RRMM1_C40


title: RRMM1_C33


title: RRMM1_C34


title: RRMM1_C39


title: RRMM1_C32


title: RRMM1_C73


title: RRMM1_C28


title: RRMM1_C27


title: RRMM1_C29


title: RRMM1_C25


title: RRMM1_C22


title: RRMM1_C21


title: RRMM1_C49


title: RRMM1_C16


title: RRMM1_C31


title: RRMM1_C19


title: RRMM1_C13


title: RRMM1_C17


title: RRMM1_C44


title: RRMM1_C11


title: RRMM1_C09


title: RRMM1_C12


title: RRMM1_C05


title: RRMM1_C08


title: RRMM1_C06


title: RRMM1_C35


title: RRMM1_C02


title: RRMM1_C01


title: NDMM8_C96

value: NDMM


title: RRMM1_C03


title: NDMM8_C91


title: RRMM1_C24


title: NDMM8_C95


title: RRMM1_C20


title: NDMM8_C85


title: RRMM1_C04


title: RRMM1_C18


title: NDMM8_C83


title: NDMM8_C78


title: NDMM8_C93


title: NDMM8_C82


title: NDMM8_C80


title: NDMM8_C72


title: NDMM8_C69


title: NDMM8_C74


title: NDMM8_C68


title: NDMM8_C90


title: NDMM8_C67


title: NDMM8_C63


title: NDMM8_C66


title: NDMM8_C58


title: NDMM8_C65


title: NDMM8_C60


title: NDMM8_C61


title: NDMM8_C57


title: NDMM8_C56


title: NDMM8_C55


title: NDMM8_C92


title: NDMM8_C54


title: NDMM8_C76


title: NDMM8_C53


title: NDMM8_C46


title: NDMM8_C44


title: NDMM8_C41


title: NDMM8_C39


title: NDMM8_C40


title: NDMM8_C86


title: NDMM8_C62


title: NDMM8_C37


title: NDMM8_C33


title: NDMM8_C35


title: NDMM8_C59


title: NDMM8_C30


title: NDMM8_C24


title: NDMM8_C28


title: NDMM8_C50


title: NDMM8_C27


title: NDMM8_C29


title: NDMM8_C10


title: NDMM8_C15


title: NDMM8_C09


title: NDMM8_C13


title: NDMM8_C06


title: NDMM8_C14


title: NDMM8_C12


title: NDMM8_C45


title: NDMM8_C05


title: NDMM8_C23


title: NDMM8_C04


title: NDMM8_C51


title: NDMM7_C95


title: NDMM8_C07


title: NDMM7_C92


title: NDMM7_C88


title: NDMM7_C91


title: NDMM7_C90


title: NDMM7_C87


title: NDMM7_C94


title: NDMM7_C86


title: NDMM7_C85


title: NDMM7_C82


title: NDMM7_C67


title: NDMM7_C83


title: NDMM8_C16


title: NDMM7_C84


title: NDMM7_C80


title: NDMM7_C70


title: NDMM7_C65


title: NDMM7_C50


title: NDMM7_C51


title: NDMM7_C54


title: NDMM7_C47


title: NDMM7_C55


title: NDMM7_C49


title: NDMM7_C63


title: NDMM7_C62


title: NDMM8_C02


title: NDMM7_C58


title: NDMM7_C35


title: NDMM7_C56


title: NDMM7_C30


title: NDMM7_C66


title: NDMM7_C59


title: NDMM7_C61


title: NDMM7_C53


title: NDMM7_C42


title: NDMM7_C24


title: NDMM7_C41


title: NDMM7_C36


title: NDMM7_C74


title: NDMM7_C28


title: NDMM7_C25


title: NDMM7_C43


title: NDMM7_C17


title: NDMM7_C23


title: NDMM7_C21


title: NDMM7_C22


title: NDMM7_C40


title: NDMM7_C15


title: NDMM7_C05


title: NDMM7_C10


title: NDMM7_C09


title: NDMM7_C11


title: NDMM7_C04


title: NDMM6_C79


title: NDMM7_C03


title: NDMM6_C78


title: NDMM6_C93


title: NDMM6_C75


title: NDMM6_C74


title: NDMM6_C69


title: NDMM7_C12


title: NDMM6_C91


title: NDMM6_C63


title: NDMM6_C58


title: NDMM6_C61


title: NDMM6_C62


title: NDMM6_C57


title: NDMM6_C56


title: NDMM6_C52


title: NDMM7_C16


title: NDMM6_C51


title: NDMM6_C48


title: NDMM6_C50


title: NDMM6_C44


title: NDMM6_C41


title: NDMM6_C43


title: NDMM6_C40


title: NDMM6_C36


title: NDMM6_C37


title: NDMM6_C34


title: NDMM6_C31


title: NDMM6_C33


title: NDMM6_C38


title: NDMM6_C25


title: NDMM6_C28


title: NDMM6_C32


title: NDMM6_C39


title: NDMM6_C29


title: NDMM6_C19


title: NDMM6_C21


title: NDMM6_C30


title: NDMM6_C18


title: NDMM6_C24


title: NDMM6_C22


title: NDMM6_C16


title: NDMM6_C11


title: NDMM6_C14


title: NDMM6_C10


title: NDMM6_C07


title: NDMM6_C03


title: NDMM5_C89


title: NDMM5_C96


title: NDMM6_C12


title: NDMM5_C95


title: NDMM6_C17


title: NDMM6_C05


title: NDMM5_C82


title: NDMM5_C79


title: NDMM5_C73


title: NDMM5_C72


title: NDMM5_C66


title: NDMM5_C71


title: NDMM5_C68


title: NDMM5_C70


title: NDMM5_C55


title: NDMM5_C51


title: NDMM5_C50


title: NDMM5_C54


title: NDMM5_C48


title: NDMM5_C22


title: NDMM5_C26


title: NDMM5_C24


title: NDMM5_C19


title: NDMM5_C34


title: NDMM5_C16


title: NDMM5_C37


title: NDMM5_C13


title: NDMM5_C17


title: NDMM5_C12


title: NDMM5_C78


title: NDMM3_C96


title: NDMM5_C01


title: NDMM5_C10


title: NDMM5_C04


title: NDMM5_C05


title: NDMM3_C87


title: NDMM3_C91


title: NDMM3_C84


title: NDMM3_C86


title: NDMM3_C77


title: NDMM3_C71


title: NDMM3_C70


title: NDMM5_C43


title: NDMM3_C82


title: NDMM3_C69


title: NDMM3_C83


title: NDMM3_C68


title: NDMM3_C66


title: NDMM3_C64


title: NDMM3_C63


title: NDMM3_C61


title: NDMM3_C62


title: NDMM3_C60


title: NDMM3_C56


title: NDMM3_C55


title: NDMM3_C53


title: NDMM3_C54


title: NDMM3_C52


title: NDMM3_C50


title: NDMM3_C47


title: NDMM3_C45


title: NDMM3_C41


title: NDMM3_C43


title: NDMM3_C79


title: NDMM3_C40


title: NDMM3_C39


title: NDMM3_C37


title: NDMM3_C34


title: NDMM3_C36


title: NDMM3_C35


title: NDMM3_C33


title: NDMM3_C24


title: NDMM3_C31


title: NDMM3_C32


title: NDMM3_C30


title: NDMM3_C26


title: NDMM3_C58


title: NDMM3_C19


title: NDMM3_C29


title: NDMM3_C17


title: NDMM3_C49


title: NDMM3_C15


title: NDMM3_C12


title: NDMM3_C09


title: NDMM3_C51


title: NDMM3_C13


title: NDMM3_C11


title: NDMM3_C06


title: NDMM3_C05


title: NDMM3_C38


title: NDMM3_C07


title: NDMM3_C02


title: NDMM3_C04


title: MGUS5_C35

value: MGUS


title: MGUS5_C63


title: MGUS5_C29


title: MGUS5_C24


title: MGUS5_C82


title: IgM-MGUS3_C74

value: IgM-MGUS


title: IgM-MGUS3_C83


title: IgM-MGUS3_C89


title: IgM-MGUS3_C65


title: NDMM3_C03


title: IgM-MGUS3_C49


title: IgM-MGUS3_C64


title: IgM-MGUS3_C90


title: IgM-MGUS3_C30


title: IgM-MGUS3_C36


title: MGUS5_C23


title: IgM-MGUS3_C32


title: IgM-MGUS3_C31


title: IgM-MGUS3_C17


title: IgM-MGUS3_C21


title: IgM-MGUS1_C93


title: IgM-MGUS1_C84


title: MGUS5_C78


title: IgM-MGUS1_C91


title: IgM-MGUS1_C65


title: IgM-MGUS1_C72


title: IgM-MGUS1_C60


title: IgM-MGUS3_C61


title: IgM-MGUS3_C37


title: IgM-MGUS1_C53


title: IgM-MGUS3_C09


title: IgM-MGUS1_C62


title: IgM-MGUS1_C50


title: IgM-MGUS1_C42


title: IgM-MGUS1_C37


title: IgM-MGUS1_C40


title: IgM-MGUS3_C33


title: IgM-MGUS1_C21


title: IgM-MGUS1_C30


title: IgM-MGUS1_C19


title: IgM-MGUS1_C11


title: IgM-MGUS1_C25


title: IgM-MGUS1_C04


title: IgM-MGUS1_C39


title: IgM-MGUS1_C31


title: IgM-MGUS1_C26


title: u130

city: Beijing

first: Bingjie

last: Dong

address: No.5, Yiheyuan Street, Haidian District

country: China

institute: Peking University

description: polyA RNA

data_processing:
Basecalls performed using Illumina CASAVA version 1.8
Barcode information in read2 of paired-end data were used to de-multiplex raw reads
Unique molecular identifier (UMI) information from read2 were added into the corresponding read 1
Reads were then trimed for polyA tail sequence and template switch oligo (TSO) sequence.
Reads with adaptor contaminates and low-quality bases (N>10%) were removed
Clean reads were aligned to the NCBIM37 genome by Tophat version 2.0.12 (Trapnell et al., 2009) with default parameters
Mapped reads were counted by Htseq version 0.6.0 with parameters -s no and -a 10
Based on the UMI information, duplicated transcripts with the same UMI barcode of each gene were removed.
TPM (transcript-per-million) was calculated by the number of UMIs of each gene divided by all the number of UMIs of a given cell, then multiplying by 1,000,000.
Genome_build: NCBIM37
Supplementary_files_format_and_content: tab-delimited text files include UMI and TPM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Mouse thymus T-ALL cells

extract_protocol:
A modified Smart-seq2 protocol was applied for single-cell RNA-seq. Briefly, a single cell was sorted into the lysis buffer by mouth pippete. The reverse transcription reaction was performed with 24 oligo (dT) primer anchored with the 8 bp cell specific barcode, and also with 8 bp unique molecular identifiers (UMIs).
After the first-strand reaction, the cDNA was amplified by 17 cycles. Then the amplified cDNA of the cells of the same fetal sample were pooled together to proceed the following steps. Biotinylated pre-indexed primer was used to amplify the PCR product by additional 4 cycles to introduce biotin tags to the 3’ end of the amplified cDNA. About 300 ng DNA was sheared to around 300 bp by Covaris S2 and the 3’ ternimal of the DNA was captured by Dynabeads® MyOne™ Streptavidin C1 beads (Thermo Fisher). RNA seq library was constructed using Kapa Hyper Prep Kit (Kapabiosystems) and subjected to 150 bp paired-end sequencing on illumina HiSeq 4000 platform.

tag: subpopulation

value: Blast

tag: turmor stage

value: blast crisis

tag: gender

value: Female


title: u146

description: polyA RNA


title: u143

description: polyA RNA


title: u128

description: polyA RNA


title: u152

description: polyA RNA


title: u153

description: polyA RNA


title: u134

description: polyA RNA


title: u154

description: polyA RNA


title: u145

description: polyA RNA


title: Pachynema replicate 2

city: La Jolla

first: Kevin

last: Corbett

state: CA

address: 9500 Gilman Drive

department: Department of Cellular and Molecular Medicine

institute: University of California, San Diego

description:
pachynema_overall.hic
pachynema_interhomolog.hic

library_source: genomic

data_processing:
base-calling used bcl2fastq version 2.17
alignment used bwa-mem
haplotype assignment used WASP
Hi-C contact maps construction used Juicer
Genome_build: mm10
Supplementary_files_format_and_content: zygonema_overall.hic is a Juicer-formatted Hi-C matrix file containing all read pairs from samples Zygo_rep1 and Zygo_rep2
Supplementary_files_format_and_content: zygonema_interhomolog.hic is a Juicer-formatted Hi-C matrix file containing only those read pairs from samples Zygo_rep1 and Zygo_rep2 where one read originated from C57BL6/J and the other read originated from CAST/EiJ
Supplementary_files_format_and_content: pachynema_overall.hic is a Juicer-formatted Hi-C matrix file containing all read pairs from samples Pachy_rep1, Pachy_rep2, and Pachy_rep3
Supplementary_files_format_and_content: pachynema_interhomolog.hic is a Juicer-formatted Hi-C matrix file containing only those read pairs from samples Pachy_rep1, Pachy_rep2, and Pachy_rep3 where one read originated from C57BL6/J and the other read originated from CAST/EiJ

molecule: genomic DNA

source_name: testes

extract_protocol: 600,000-800,000 cells were cross-linked with 2% formaldehyde for 10 min at room temperature, then the reaction was quenched using 200 mM glycine for 5 min at room temperature, then 15 minutes on ice, then samples were frozen in liquid nitrogen. Nuclei were isolated and directly applied for digestion using the 4-base cutter restriction enzyme MboI (NEB) at 37°C overnight. The single strand overhang was filled with biotin-14-dATP (Life Technologies) using Klenow DNA polymerase (New England Biolabs). In contrast to traditional Hi-C,  the ligation was performed when the nuclear membrane was still intact (in situ protocol). DNA was ligated for 4 hours at 16°C using T4 ligase (New England Biolabs). Protein was degraded by proteinase K (New England Biolabs) treatment at 55°C for 30 min. The crosslinking was reversed with addition of 500 mM NaCl and incubation at 65°C overnight. DNA was purified by ethanol precipitation, sonicated to 300-700 bp fragments, and size-selected using SPRI magnetic beads as described 33. Biotinylated DNA was selected with Dynabeads MyOne T1 Streptavidin beads (Life Technologies). Sequencing libraries were prepared on beads, checked using an Agilent Bioanalyzer 2100 and quantified using a Qubit (Life Technologies).

treatment_protocol: Male C57BL/6J x CAST/EiJ F1 hybrid neonates were treated with the retinoic acid inhibitor WIN 18,446 at two days post-partum to block spermatogonial differentiation, then injected retinoic acid at 9 days post-partum. Treated animals were allowed to recover for 25-47 days to enable isolation of synchronized cell populations in zygonema and pachynema of the third through fifth waves, with harvesting times calculated as previously described. Spermatocytes from synchronized testes were isolated and stained with Hoechst 33342 to allow isolation of cells with 4C DNA content (prophase I) by flow cytometry. Zygonema replicate #1 was isolated at 25 days post-injection (dpi; third wave of synchronous meiosis), Zygonema replicate #2 at 33 dpi (fourth wave), Pachynema replicate #1 at 30 dpi (third wave), Pachynema replicate #2 at 47 dpi (fifth wave), and Pachynema replicate #3 at 21 dpi (second wave).

tag: cell type

value: Pachynema-stage spermatocytes

tag: strain

value: C57BL6/J x CAST/EiJ hybrid

tag: tissue

value: spermatocytes

tag: developmental stage

value: pachynema


title: Zygonema replicate 1

description:
zygonema_overall.hic
zygonema_interhomolog.hic

value: Zygonema-stage spermatocytes

value: zygonema


title: Zygonema replicate 2


title: Pachynema replicate 1


title: IgM-MGUS1_C35


title: u122

description: polyA RNA


title: IgM-MGUS1_C58


title: Pachynema replicate 3


title: u144

description: polyA RNA


title: u126

description: polyA RNA


title: u118

description: polyA RNA


title: u111

description: polyA RNA


title: u112

description: polyA RNA


title: u121

description: polyA RNA


title: u114

description: polyA RNA


title: u151

description: polyA RNA


title: u110

description: polyA RNA


title: u127

description: polyA RNA


title: u105

description: polyA RNA


title: u106

description: polyA RNA


title: r776

description: polyA RNA


title: u103

description: polyA RNA


title: u113

description: polyA RNA


title: r778

description: polyA RNA


title: r775

description: polyA RNA


title: u104

description: polyA RNA


title: r768

description: polyA RNA


title: r761

description: polyA RNA


title: r729

description: polyA RNA


title: r727

description: polyA RNA


title: r728

description: polyA RNA


title: r754

description: polyA RNA


title: r737

description: polyA RNA


title: r719

description: polyA RNA


title: r722

description: polyA RNA


title: r704

description: polyA RNA


title: r712

description: polyA RNA


title: r736

description: polyA RNA


title: r714

description: polyA RNA


title: r762

description: polyA RNA


title: r713

description: polyA RNA


title: r760

description: polyA RNA


title: r695

description: polyA RNA


title: r691

description: polyA RNA


title: r683

description: polyA RNA


title: r770

description: polyA RNA


title: r670

description: polyA RNA


title: r675

description: polyA RNA


title: r767

description: polyA RNA


title: r777

description: polyA RNA


title: r668

description: polyA RNA


title: r653

description: polyA RNA


title: r637

description: polyA RNA


title: r636

description: polyA RNA


title: r628

description: polyA RNA


title: r603

description: polyA RNA


title: r619

description: polyA RNA


title: r604

description: polyA RNA


title: r592

description: polyA RNA


title: r590

description: polyA RNA


title: r591

description: polyA RNA


title: r644

description: polyA RNA


title: r584

description: polyA RNA


title: r581

description: polyA RNA


title: r576

description: polyA RNA


title: r582

description: polyA RNA


title: r575

description: polyA RNA


title: r583

description: polyA RNA


title: r568

description: polyA RNA


title: r573

description: polyA RNA


title: r574

description: polyA RNA


title: r567

description: polyA RNA


title: r661

description: polyA RNA


title: r652

description: polyA RNA


title: r559

description: polyA RNA


title: r566

description: polyA RNA


title: r565

description: polyA RNA


title: r560

description: polyA RNA


title: r557

description: polyA RNA


title: r558

description: polyA RNA


title: r550

description: polyA RNA


title: r549

description: polyA RNA


title: r535

description: polyA RNA


title: r543

description: polyA RNA


title: r589

description: polyA RNA


title: r527

description: polyA RNA


title: r534

description: polyA RNA


title: r526

description: polyA RNA


title: r519

description: polyA RNA


title: r511

description: polyA RNA


title: r517

description: polyA RNA


title: r518

description: polyA RNA


title: r502

description: polyA RNA


title: r602

description: polyA RNA


title: r487

description: polyA RNA


title: r486

description: polyA RNA


title: r509

description: polyA RNA


title: r485

description: polyA RNA


title: r484

description: polyA RNA


title: r482

description: polyA RNA


title: r483

description: polyA RNA


title: r479

description: polyA RNA


title: r478

description: polyA RNA


title: r475

description: polyA RNA


title: r470

description: polyA RNA


title: r551

description: polyA RNA


title: r468

description: polyA RNA


title: r542

description: polyA RNA


title: r466

description: polyA RNA


title: r533

description: polyA RNA


title: r463

description: polyA RNA


title: r462

description: polyA RNA


title: r461

description: polyA RNA


title: r460

description: polyA RNA


title: r458

description: polyA RNA


title: r510

description: polyA RNA


title: r459

description: polyA RNA


title: r451

description: polyA RNA


title: r447

description: polyA RNA


title: r450

description: polyA RNA


title: r443

description: polyA RNA


title: r439

description: polyA RNA


title: r436

description: polyA RNA


title: r437

description: polyA RNA


title: r429

description: polyA RNA


title: r428

description: polyA RNA


title: r430

description: polyA RNA


title: r438

description: polyA RNA


title: r423

description: polyA RNA


title: r422

description: polyA RNA


title: r421

description: polyA RNA


title: r426

description: polyA RNA


title: r419

description: polyA RNA


title: r427

description: polyA RNA


title: r418

description: polyA RNA


title: r414

description: polyA RNA


title: r415

description: polyA RNA


title: r445

description: polyA RNA


title: r431

description: polyA RNA


title: r455

description: polyA RNA


title: r446

description: polyA RNA


title: r406

description: polyA RNA


title: r402

description: polyA RNA


title: r403

description: polyA RNA


title: r412

description: polyA RNA


title: r394

description: polyA RNA


title: r395

description: polyA RNA


title: r405

description: polyA RNA


title: r390

description: polyA RNA


title: r404

description: polyA RNA


title: r386

description: polyA RNA


title: r385

description: polyA RNA


title: r387

description: polyA RNA


title: r384

description: polyA RNA


title: r383

description: polyA RNA


title: r377

description: polyA RNA


title: r382

description: polyA RNA


title: r378

description: polyA RNA


title: r371

description: polyA RNA


title: r379

description: polyA RNA


title: r375

description: polyA RNA


title: r376

description: polyA RNA


title: r368

description: polyA RNA


title: r369

description: polyA RNA


title: r363

description: polyA RNA


title: r410

description: polyA RNA


title: r370

description: polyA RNA


title: r362

description: polyA RNA


title: r366

description: polyA RNA


title: r359

description: polyA RNA


title: r358

description: polyA RNA


title: r361

description: polyA RNA


title: r391

description: polyA RNA


title: r360

description: polyA RNA


title: r355

description: polyA RNA


title: r352

description: polyA RNA


title: r351

description: polyA RNA


title: r347

description: polyA RNA


title: r345

description: polyA RNA


title: r344

description: polyA RNA


title: r343

description: polyA RNA


title: r338

description: polyA RNA


title: r331

description: polyA RNA


title: r337

description: polyA RNA


title: r335

description: polyA RNA


title: r329

description: polyA RNA


title: r328

description: polyA RNA


title: r327

description: polyA RNA


title: r322

description: polyA RNA


title: r320

description: polyA RNA


title: r315

description: polyA RNA


title: r318

description: polyA RNA


title: r354

description: polyA RNA


title: r312

description: polyA RNA


title: r342

description: polyA RNA


title: r313

description: polyA RNA


title: r319

description: polyA RNA


title: r310

description: polyA RNA


title: r330

description: polyA RNA


title: r271

description: polyA RNA


title: r334

description: polyA RNA


title: r268

description: polyA RNA


title: r258

description: polyA RNA


title: r270

description: polyA RNA


title: r259

description: polyA RNA


title: r247

description: polyA RNA


title: r275

description: polyA RNA


title: r236

description: polyA RNA


title: r231

description: polyA RNA


title: r227

description: polyA RNA


title: r211

description: polyA RNA


title: r207

description: polyA RNA


title: r213

description: polyA RNA


title: r202

description: polyA RNA


title: r186

description: polyA RNA


title: r203

description: polyA RNA


title: r276

description: polyA RNA


title: r185

description: polyA RNA


title: r183

description: polyA RNA


title: r176

description: polyA RNA


title: r174

description: polyA RNA


title: r175

description: polyA RNA


title: r169

description: polyA RNA


title: r170

description: polyA RNA


title: r167

description: polyA RNA


title: Thymus_LSC_4

data_processing:
Pair-end reads were aligned to the mouse reference genome (Version mm9 from UCSC) using Tophat (v2.0.13)
The expression value was generated as the number of fragments per kilobase of transcript per million mapped reads (FPKM) using Cufflinks (v2.2.1)
Genome_build: mm9
Supplementary_files_format_and_content: A tab-delimited text file include FPKM values for each Sample

source_name: mouse Thymus LSC cells

extract_protocol:
Total RNA from FACS sorted cells was extracted using the RNeasy Micro Kit (QIAGEN, 74004)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Blast crisis

tag: age

value: 60 day after born


title: r230

description: polyA RNA


title: Thymus_LSC_3


title: r321

description: polyA RNA


title: r162

description: polyA RNA


title: Thymus_LSC_2

value: Male


title: r160

description: polyA RNA


title: r163

description: polyA RNA


title: Thymus_LSC_1


title: r158

description: polyA RNA


title: Thymus_BLAST_3

source_name: mouse Thymus blast cells


title: r155

description: polyA RNA


title: Thymus_BLAST_4


title: Thymus_BLAST_2


title: r184

description: polyA RNA


title: r153

description: polyA RNA


title: r182

description: polyA RNA


title: Thymus_BLAST_1


title: r152

description: polyA RNA


title: r151

description: polyA RNA


title: Spleen_LSC_3

source_name: mouse spleen LSC cells


title: r150

description: polyA RNA


title: r147

description: polyA RNA


title: r161

description: polyA RNA


title: Spleen_BLAST_4

source_name: mouse spleen blast cells


title: Spleen_LSC_1


title: r146

description: polyA RNA


title: Spleen_BLAST_3


title: Spleen_LSC_2


title: r145

description: polyA RNA


title: Spleen_BLAST_2


title: r143

description: polyA RNA


title: Spleen_BLAST_1


title: r142

description: polyA RNA


title: r139

description: polyA RNA


title: BM_LSC_4

source_name: mouse BM LSC cells


title: r144

description: polyA RNA


title: BM_LSC_2


title: r137

description: polyA RNA


title: r138

description: polyA RNA


title: BM_LSC_1


title: Spleen_LSC_4


title: r136

description: polyA RNA


title: BM_BLAST_4


title: r131

description: polyA RNA


title: BM_BLAST_3

source_name: mouse BM blast cells


title: r135

description: polyA RNA


title: BM_BLAST_2


title: r130

description: polyA RNA


title: Thymus_LIC

description: RRBS

data_processing:
BS-seq reads were aligned to reference genome (mm9) by BS-Seeker2.
The lollipop plot and region-specific distribution profiles are generated by CGmapTools.
Genome_build: mm9
Supplementary_files_format_and_content: CGmap

extract_protocol:
Blast- and LSC-enriched subpopulations were collected by FACS sorting and genomic DNA were extracted using DNA micro kit or DNA mini kit (Qiagen)
Genomic DNA was digested with MspI (Fermentas), followed by end repair, adapter ligation and bisulfite modification (QIAGEN, #59104). The converted DNA library was sequenced on HiSeq 4000 (illumina) after two–round PCR amplification and size-selection

value: LSC

tag: turmor cell or normal cells

value: tumor


title: Spleen_LIC

description: RRBS

source_name: Mouse spleen T-ALL cells


title: r154

description: polyA RNA


title: WT

description: RRBS

source_name: Mouse thymus  cells

value: DP t cell

value: WT

value: normal


title: BM_LSC_3


title: BM_LIC

description: RRBS

source_name: Mouse BM T-ALL cells


title: r122

description: polyA RNA


title: r126

description: polyA RNA


title: r115

description: polyA RNA


title: r119

description: polyA RNA


title: BM_BLAST

description: RRBS

value: Blast


title: r114

description: polyA RNA

value: blast crisis


title: Thymus_BLAST

description: RRBS


title: Spleen_BLAST

description: RRBS


title: r112

description: polyA RNA

value: Female


title: r113

description: polyA RNA


title: r127

description: polyA RNA


title: r111

description: polyA RNA


title: BM_BLAST_1


title: r129

description: polyA RNA


title: r326

description: polyA RNA


title: r110

description: polyA RNA


title: r107

description: polyA RNA


title: r128

description: polyA RNA


title: r105

description: polyA RNA


title: r106

description: polyA RNA


title: r104

description: polyA RNA


title: pcDNA2_S2_R1_001

city: New York

first: Shahar

last: Barbash

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description: Cells transfected with empty vector.

data_processing:
Quality control was verified with qualilmap
Adaptor cutting.
Read alignment with STAR.
Cufflink was used to produce FPKM
Genome_build: GRCh38
Supplementary_files_format_and_content: Files include FPKM values and the format is FPKM-tracking-file.

growth_protocol: HEK293T cells were cultured in cell medium and 300,000 cells were seeded onto poly-D-lysine mol wt 70,000-150,000 (Sigma-Aldrich) coated cover glasses (18-mm, thickness No. 1.5H, Marienfeld Superior) placed in 60-mm tissue culture dishes.

extract_protocol:
After 24 h incubation at 37°C, RNA was extracted using the miRneasy kit (QIAGEN) for RNA sequencing.
Extracted RNA samples were examined with Bioanalyzer for RNA integrity and concentration before sequencing. RNA integrity number was 9.62 with 0.98 standard deviation. 100 ng of total RNA was used to generate RNA-Seq libraries using Illumina TruSeq stranded mRNA LT kit (Cat# RS-122-2101).   Libraries prepared with unique barcodes were pooled at equal molar ratios. The pool was denatured and sequenced on Illumina NextSeq 500 sequencer using high output V2 reagents and NextSeq Control Software v1.4 to generate 75 bp single reads, following manufactures protocol (Cat# 15048776 Rev.E).

treatment_protocol: The next day, cells were transfected with 2 µg plasmid DNA for RNA sequencing, using Lipofectamine 2000 (Thermo Fisher Scientific) according to manufacturer’s protocol. Plasmid DNA included RAMP2 with a FLAG-tag epitope sequence following the signal peptide, OLLAS-epitope, tag on the C-terminus in pcDNA3.1, codon optimized for expression in human cell lines.

tag: cell line

tag: transfection

value: empty vector


title: UnTfx3_S9_R1_001

description: Non-transfected cells.


title: pcDNA3_S3_R1_001

description: Cells transfected with empty vector.


title: RAMP2-2_S5_R1_001

description: HEK293T cells were transfected with pcDNA3.1 vector containing codon optimized sequence for (Receptor Activity Modifying Protein 2) RAMP2


title: RAMP2-3_S6_R1_001


title: r103

description: polyA RNA


title: CRCLM_23T

type: genomic

city: Taipei

first: yi-chiung

last: hsu

address: 128 Academia Road, Section 2

country: Taiwan

institute: academia sinica

hyb_protocol: in situ oligonucleotide

scan_protocol: The array scanning and image generation were performed by the GenePixTM Reader (Personal 4000B, Axon Instruments, Molecular Devices, Sunnyvale, CA) and GenePix® Pro 6.0 software.

data_processing:
Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.
Generation of log intensity ratio data with normalization was performed by NimbleScanTM version 2.4, SignalMapTM version 1.9 software
normalized log2 ratio (Cy5/Cy3)

source_name: Colon

label_protocol: Labeling, hybridization and washing were processed according to the manufacturer's protocol.

extract_protocol: DNA from frozen cancer tissue of each sample, with quality checked by agarose electrophoresis, against the normal DNA extracted from the PBMC of one male and one female in a community cohort.

value: Tumor

tag: Stage

value: III

value: female

tag: synchronous metastasis

value: Synchronous meta:no

tag: distant metastasis

value: yes

tag: vital status

tag: survival month

tag: recur status

tag: recurrence month

source_name: PBMC

value: Normal


title: r102

description: polyA RNA

tag: subpopulation

tag: turmor stage


title: CRCLM_22T

tag: gender

value: male


title: CRCLM_23N


title: D10-PATS13-Tconv

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description: Tconv cells isolated from RA patients

data_processing:
FastQC v0.11.4 is used to check the quality of the samples
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic v0.35 with parameters ILLUMINACLIP:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:35
Sequenced reads were then mapped to mm10 transcriptome using Tophat2 v2.1.0 with parameters --library-type fr-unstranded --min-intron-length 50 --no-coverage-search
The mapping files were then filtered using samtools v0.1.18 (samtools view with parameters -bq 20) and sorted using samtools sort
Reads were counted using HTSeqCount v0.6.1p1 with parameters -f bam -m intersection-strict -s no -a 10 -t exon -i gene_id
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files including raw counts (output HTSeqCount) for each sample

source_name: RA disease, Tconv cells

extract_protocol: All methods listed in Venken et al, (REF NCOMMS-17-18476)

value: Peripheral blood

tag: disease state

value: Rheumatoid arthritis

tag: cell

value: Conventional T cell


title: CRCLM_22N

tag: tissue


title: D11-PAT148-Tconv

description: Tconv cells isolated from RA patients


title: D12-PATS14-Tconv

description: Tconv cells isolated from RA patients


title: D9-PAT146-Tconv

description: Tconv cells isolated from RA patients


title: pcDNA1_S1_R1_001

description: Cells transfected with empty vector.


title: D8-PATS11-Tconv

description: Tconv cells isolated from RA patients


title: CRCLM_20N

tag: age

value: II

value: no


title: UnTfx2_S8_R1_001

description: Non-transfected cells.


title: CRCLM_19T

value: IV

value: Synchronous meta:yes


title: CRCLM_20T


title: UnTfx1_S7_R1_001

description: Non-transfected cells.


title: D6-PATB1-Tconv

description: Tconv cells isolated from SpA patients

source_name: SpA disease, Tconv cells

value: Spondyloarthritis


title: D5-PATG5-Tconv

description: Tconv cells isolated from SpA patients


title: D7-PATG6-Tconv

description: Tconv cells isolated from SpA patients


title: CRCLM_19N


title: CRCLM_18T


title: D3-PATG3-Tconv

description: Tconv cells isolated from SpA patients


title: RAMP2-1_S4_R1_001


title: CRCLM_18N


title: CRCLM_17T


title: CRCLM_15T


title: C12-PATS14-TCRgd

description: TCRgd cells isolated from RA patients

source_name: RA disease, TCRgd cells

value: Gamma delta T cell


title: CRCLM_15N


title: C11-PAT148-TCRgd

description: TCRgd cells isolated from RA patients


title: CRCLM_14T


title: CRCLM_14N


title: C10-PATS13-TCRgd

description: TCRgd cells isolated from RA patients


title: C9-PAT146-TCRgd

description: TCRgd cells isolated from RA patients


title: C7-PATG6-TCRgd

description: TCRgd cells isolated from SpA patients

source_name: SpA disease, TCRgd cells


title: CRCLM_13T


title: CRCLM_13N


title: C5-PATG5-TCRgd

description: TCRgd cells isolated from SpA patients


title: CRCLM_12T


title: C6-PATB1-TCRgd

description: TCRgd cells isolated from SpA patients


title: CRCLM_12N


title: C4-PATG4-TCRgd

description: TCRgd cells isolated from SpA patients


title: CRCLM_11T


title: C3-PATG3-TCRgd

description: TCRgd cells isolated from SpA patients


title: D1-PATG1-Tconv

description: Tconv cells isolated from SpA patients


title: CRCLM_11N


title: CRCLM_17N


title: C2-PATG2-TCRgd

description: TCRgd cells isolated from SpA patients


title: CRCLM_10T


title: CRCLM_10N


title: CRCLM_9T


title: C8-PATS11-TCRgd

description: TCRgd cells isolated from RA patients


title: A11-PAT148-NKT

description: iNKT cells isolated from RA patients

source_name: RA disease, iNKT cells

value: Invariant natural killer cell


title: C1-PATG1-TCRgd

description: TCRgd cells isolated from SpA patients


title: D4-PATG4-Tconv

description: Tconv cells isolated from SpA patients


title: A9-PAT146-NKT

description: iNKT cells isolated from RA patients


title: CRCLM_9N


title: CRCLM_8T

value: Tumor


title: beclo treated_non amputated_rep3

city: Leiden

first: Yufei

last: Xie

address: Einsteinweg 55

country: Netherlands

institute: Leiden University

data_processing:
Image analysis and base calling were done by the Illumina HCS version 2.2.68, and RTA version 1.18.66.
cDNA sequencing data were analyzed by mapping the reads to the Danio rerio GRCz10 reference genome with annotation version 80 using Tophat (v2.1.0).
The DESeq (v1.26.0) R package was used to test for differential expression. Before each analysis, the genes with low reads were removed (i.e. those genes for which the sum of reads from three replicates of the analyzed two groups was lower than 30). The output data were used for transcriptome analysis.
Genome_build: RNAseq reads from individual samples were mapped against D. rerio GRCz10.80
Supplementary_files_format_and_content: tab-separated values files include id and reads for each gene

organism: Danio rerio

source_name: 3dpf zebrafish embryo treated with beclomethasone, not amputated

growth_protocol: Zebrafish were maintained and handled according to the guidelines from the Zebrafish Model Organism Database (http://zfin.org) and in compliance with the directives of the local animal welfare committee of Leiden University. They were exposed to a 14 hours light and 10 hours dark cycle to maintain circadian rhythmicity. Fertilization was performed by natural spawning at the beginning of the light period. Eggs were collected and raised at 28°C in egg water (60 µg/ml Instant Ocean sea salts and 0.0025% methylene blue).

extract_protocol:
Macrophages were sorted from Tg(mpeg1.4:mCherry-F) embryos as previously described (Rougeot et al., 2014; Zakrzewska et al., 2010). Dissociation was performed with 100-150 embryos for each sample at 4 hours post amputation (hpa) using Liberase TL (Roche) and stopped by adding Fetal Calf Serum (FCS) to a final concentration of 10%. Isolated cells were resuspended in Dulbecco’s PBS (DPBS), and filtered through a 40 μm cell strainer. Actinomycin D (Sigma Aldrich) was added  (final concentration of 1 µg/ml) to each step to inhibit transcription. Macrophages were sorted based on their red fluorescent signal using a FACSAria III cell sorter (BD Biosciences). The sorted cells were collected in QIAzol lysis reagent (Qiagen) for RNA isolation. Extracted total RNA was amplified using the SMART-seq V4 kit (Clontech) for sequencing.
The RNA seq libraries generated with the SMART-seq V4 kit were sequenced using an Illumina HiSeq 2500 instrument according to the manufacturer’s instructions with a read length of 50 nucleotides

treatment_protocol: After anesthesia with 0.02% aminobenzoic acid ethyl ester (tricaine, Sigma Aldrich), the tails of 3 days post fertilization (dpf) embryos were partially amputated (Figure 1A) with a 1mm sapphire blade (World Precision Instruments) on 2% agarose-coated Petri dishes under a Leica M165C stereomicroscope (Chatzopoulou et al., 2016). Amputated and non-amputated (control) embryos were pretreated for 2 hours with 25 μM beclomethasone (Sigma Aldrich) or vehicle (0.05% dimethyl sulfoxide (DMSO)) in egg water prior to amputation and received the same treatment after the amputation.

tag: drug treatment

value: 25uM beclomethasone in egg water

tag: tail amputation

value: without tail amputation

tag: developmental stage


title: control_non amputated_rep3

source_name: 3dpf zebrafish embryo treated with vehicle, not amputated

value: 0.05% DMSO in egg water


title: beclo treated_amputated_rep3

source_name: 3dpf zebrafish embryo treated with beclomethasone, tail amputated

value: tail amputated


title: control_amputated_rep3

source_name: 3dpf zebrafish embryo treated with vehicle, tail amputated


title: A7-PATG6-NKT

description: iNKT cells isolated from SpA patients

source_name: SpA disease, iNKT cells


title: CRCLM_8N

value: Normal

tag: Stage


title: beclo treated_amputated_rep2


title: control_amputated_rep2


title: control_non amputated_rep2


title: A6-PATB1-NKT

description: iNKT cells isolated from SpA patients


title: CRCLM_7T

value: female

tag: synchronous metastasis

value: yes


title: control_amputated_rep1


title: A5-PATG5-NKT

description: iNKT cells isolated from SpA patients

value: Peripheral blood


title: beclo treated_amputated_rep1


title: CRCLM_7N

tag: distant metastasis


title: beclo treated_non amputated_rep2


title: A4-PATG4-NKT

description: iNKT cells isolated from SpA patients


title: beclo treated_non amputated_rep1


title: control_non amputated_rep1


title: A12-PATS14-NKT

description: iNKT cells isolated from RA patients

value: Rheumatoid arthritis


title: CRCLM_6T

value: II

value: male

value: Synchronous meta:no

tag: vital status


title: CRCLM_6N

tag: survival month


title: A2-PATG2-NKT

description: iNKT cells isolated from SpA patients


title: A1-PATG1-NKT

description: iNKT cells isolated from SpA patients


title: B4: 35S::KNAT1_PAC_GA_rep2

city: Valencia

first: David

last: Alabadi

state: Valencia

address: Av de los Naranjos s/n, Campus UPV, Edificio 8E

department: Biologia del Desarrollo

country: Spain

institute: Instituto de Biologia Molecular y Celular de Plantas (CSIC-UPV)

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw data preprocessing (clipping adapters, and filter sequences <20 nt, 3’ end quality-trimmed threshold Q28) :cutadapt v1.8.3. FASTQC (v0.11.5) was used to assess data quality
All sequenced libraries were mapped to the Arabidopsis thaliana genome (Arabidopsis_thaliana.TAIR10.22) with GTF information (Arabidopsis_thaliana.TAIR10.22.gtf) using TopHat(v.2.1). Seqmonk v.1.35 was used to generate per gene raw count matrix from unique mapped reads with the same GTF file used for the alignment step (opposing strand specific, merge transcript isoforms).
Differential expression analysis performed with DESeq2 v.1.16.1 and edgeR v.3.0.2 (P-adj.value cutoff 0.05)
Genome_build: Arabidopsis_thaliana.TAIR10.22
Supplementary_files_format_and_content: tab-delimited text files include raw counts values for each sample.

organism: Arabidopsis thaliana

source_name: Seven-day-old seedlings

extract_protocol:
Total RNAwas extracted with RNeasy Plant Mini Kit (Qiagen) according to manufacturer’s instructions, treated with the DNase Kit (Ambion), and then frozen at −80°C until analyzed.RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using Truseq Stranded mRNA  Illumina protocols

tag: accession

value: Nossen

value: whole seedlings

tag: genotype/variation

tag: treatment

value: 10 μM PAC+100 μM GA3


title: B3: 35S::KNAT1_PAC_rep2

value: 10 μM PAC


title: CRCLM_4T

value: Tumor

value: IV

value: Synchronous meta:yes

value: no

tag: recur status

tag: recurrence month


title: C4: 35S::KNAT1_PAC_GA_rep3


title: A4: 35S::KNAT1_PAC_GA_rep1


title: CRCLM_5N

value: III

tag: gender


title: CRCLM_4N

value: Normal


title: A3: 35S::KNAT1_PAC_rep1


title: CRCLM_3T


title: CRCLM_3N


title: KO_Input

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Raw reads were filtered by BGI to remove low quality reads, N reads, and adaptor sequences to obtain clean data.    Raw reads were removed if: 1) The ratio of N in whole read was over 10%; 2) unknown bases are more than 10%; or  3) The ratio of base whose quality was less than 20 was over 10%.
The resulting clean data was algined to the mm10 reference genome using SOAPaligner/SOAP2 (Version: 2.21t) allowing no more than 2 mismatches.
Peak calling was performed using using MACS (Model-based Analysis for  ChIP -Seq, version: MACS-1.4.2) with a p-value cutoff of 0.05.  The parameters used were: macs2 -g hs -s 50 -p 1e-5 -m 10 30 --broad -B --trackline
Genome_build: mm10
Supplementary_files_format_and_content: wig files were generated using the bam2wig program from samtools and represent the mapped read locations

growth_protocol: C57BL/6 T and/or B cell STAT3 conditional knockout (cKO) mice (STAT3fl/flCD2Cre/+ and STAT3fl/flCD19Cre/+) were generated by interbreeding STAT3fl/flCD2+/+CD19+/+ mice 15 (control) with STAT3+/+CD2Cre/Cre or STAT3+/+CD19Cre/Cre mice (The Jackson Laboratory), respectively. Mice at 6–8 weeks of age with both sexes were used for experiments. All mice were housed and bred in a conventional facility at the University of Louisville. Animal care and experiments were conducted in accordance with the National Institutes of Health guidelines and were approved by the Institutional Animal Care and Use Committee at the University of Louisville

extract_protocol:
In vitro cultured GC B cells from STAT3 control and cKO mice were used for ChIP studies as described previously (Tripathi et al. 2017. Cell Reports). In brief, cells were subjected to sonication using a sonicator (AFA Focused ultrasonicator S220) to obtain chromatin fragements of 100-500 bp. Fragemented chromatin was incubated with STAT3 Ab (124H6, Cell Signaling Technology) or isotype control Ab and incubated for crosslinking with the beads (Dynabeads Protein G, Invitrogen). After crosslinking, crosslinks were reversed (65C for 12-16 h), and precipitated DNA was treated with Proteinase K and then purified (QIAquick PCR purification kit, Qiagen).
DNA was DNA-end repaired, with a 3'-dA overhang and ligation of methylated sequencing adaptor.  Sequences were PCR amplified and size selected in the range of 100-500bp (including adapter sequence).  Selected sequences were then prepared using the BGISEQ-500 ChIP-Seq sample preparation workflow.

tag: strain

tag: genotype

value: STAT3 knockout

tag: cell type

value: in vitro cultured GC B cells

tag: chip antibody


title: CRCLM_2T

tag: age

tag: tissue


title: C2: WT_PAC_GA_rep3

value: wild-type (No-0)


title: A3-PATG3-NKT

description: iNKT cells isolated from SpA patients

value: Peripheral blood

tag: disease state

value: Spondyloarthritis

tag: cell

value: Invariant natural killer cell


title: B2: WT_PAC_GA_rep2


title: Planktonic with no biofilm 3

type: RNA

city: Madrid

first: Patricia

last: Romero Lastra

address: Plaza de Ramon y Cajal s/n

institute: Universidad Complutense de Madrid

description:
Gene expression after 96h Planktonic 3 sample 3 of 3
PgP3

hyb_protocol: Preparation of probes and hybridization was performed as described (One-Color Microarray Based Gene Expression Analysis Manual Ver. 6.5, Agilent Technologies). For each hybridization, 600 ng of Cy3 probes were mixed and added to 5 µL of 10x Blocking Agent and Nuclease free water in a 25 µL reaction. Then, 25 µL from 2x GExHybridization buffer was added and mixed carefully. The samples were placed on ice and quickly loaded onto arrays, hybridized at 65ºC for 17 h in a rotating Agilent hybridization oven. After hybridization, microarrays were washed once in GE wash buffer 1 at room temperature (1 min) and once in GE Wash Buffer 2 at 37ºC (1 min).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x15K array slides

data_processing: Images from Cy3 channel were equilibrated and captured with a high-resolution scanner (Agilent) and spots quantified using Feature Extraction software (Agilent). Background correction and normalization of data expression were performed using LIMMA.

organism: Porphyromonas gingivalis ATCC 33277

source_name: Porphyromonas gingivalis culture 96h_no biofilm

label_protocol: Fluorescently labeled cDNA for microarray hybridizations was obtained by using the SuperScript Indirect cDNA Labeling System (Invitrogen)

growth_protocol: Planktonic cultures of P. gingivalis were grown anaerobically at 37ºC for 24 h in a protein-rich medium containing brain-heart infusion (BHI). A volume of 1.5 mL of P. gingivalis inoculums (concentration 10^8 CFU/mL) was placed in pre-sterilized polystyrene 24-well tissue culture plates (Greiner Bio-one) with or without the presence of sterile ceramic calcium hydroxyapatite discs (HA discs)

extract_protocol: After 96h of incubation, free-floating P. gingivalis cells from both planktonic conditions were harvested and total RNA was extracted and purified. Total RNA was extracted from the harvested samples listed above, using the TRIzol® Max Bacterial RNA Isolation Kit (Ambion, Life Technologies, Carlsbad, CA, USA). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Plates were incubated in anaerobic conditions at 37°C for 96 h


title: KO_3

value: STAT3 Ab (124H6, Cell Signaling Technology)


title: Planktonic in the presence of HA disc 2

description:
Gene expression after 96h Planktonic in the presence of HA disc sample 2 of 3
PgPD2

source_name: Porphyromonas gingivalis culture 96h_with biofilm


title: Planktonic in the presence of HA disc 3

description:
Gene expression after 96h Planktonic in the presence of HA disc sample 3 of 3
PgPD3


title: A2: WT_PAC_GA_rep1

value: Nossen


title: Planktonic with no biofilm 2

description:
Gene expression after 96h Planktonic 2 sample 2 of 3
PgP2


title: CRCLM_5T

tag: Stage

value: male

tag: synchronous metastasis

value: Synchronous meta:no

tag: distant metastasis


title: Planktonic with no biofilm 1

description:
Gene expression after 96h Planktonic 1 sample 1 of 3
PgP1


title: C3: 35S::KNAT1_PAC_rep3

tag: accession

value: whole seedlings

value: 10 μM PAC


title: Planktonic in the presence of HA disc 1

description:
Gene expression after 96h Planktonic in the presence of HA disc sample 1 of 3
PgPD1


title: KO_2


title: CRCLM_2N

tag: vital status

tag: survival month


title: C1: WT_PAC_rep3

tag: genotype/variation

tag: treatment


title: Control_Input

value: control


title: B1: WT_PAC_rep2


title: CRCLM_1T

value: Tumor

value: IV

tag: gender

value: female

value: Synchronous meta:yes

value: yes

tag: recur status

tag: recurrence month


title: DHA Treatment (biological rep2)

city: Cape Town

first: Luiz

middle: F

last: Zerbini

address: Wernher and Beit Building (South), Anzio Road

country: South Africa

institute: ICGEB

description: Gene expression data from DU145cells treated with DHA

hyb_protocol: The hybridization and subsequent washing and staining were performed on the Affymetrix GeneChip® Array Station (GCAS) automation platform.

scan_protocol: The arrays were scanned on the GeneChip® HT Array Plate Scanner (Affymetrix 00-0332)

data_processing: affymetrix-algorithm-name = ExpressionStat  affymetrix-algorithm-version = 5.0  affymetrix-progid = GeneChip.CallGEBaseCall.1  program-name = Expression Console

label: biotin

source_name: DU145 treated with DHA

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.1 µg of total RNA was used to prepare complementary RNA (cRNA) target with the Genechip® HT One-Cycle cDNA synthesis Kit (Affymetrix 900687) and the GeneChip® HT IVT Labeling Kit (Affymetrix 900688)

growth_protocol: DU145 cells were grown in DMEM medium (BioWhitaker, Walkersville, MD, USA).The medium was supplemented with 10% fetal bovine serum (FBS), 50 units/ml penicillin, and 50 µg/ml streptomycin (all from Life Technologies, Inc.). Cells were maintained in a 5% CO2-humidified incubator at 37°C

extract_protocol: Total RNA was obtained using QIAshredder (Qiagen) and RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions

treatment_protocol: DHA was dissolved in dimethyl sulfoxide (DMSO) and cells were treated in DMEM medium for 6h . The final concentration of DHA was 5 μM. For the control, cells were treated with 0.1% DMSO. Biological duplicates were used for this analysis

tag: cell type

value: Prostate Cancer cell line

tag: cell line


title: CRCLM_1N

tag: age

value: Normal


title: A1: WT_PAC_rep1

tag: tissue

value: wild-type (No-0)


title: E40_3

status: Public on Nov 16 2018

first: Yang

last: Li

address: No.10, west end of right 'an gate, fengtai district, Beijing

institute: Capital Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Tophat mapping to reference genome
Genome_build: Sscrofa10.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: The Extracellular Matrix of Developing Deciduous Teeth in Miniature Pigs

growth_protocol: We chose E40, E50 and E60 stage corresponding to the cap stage

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: pregnant miniature pigs at embryonic days 40, 50 and 60 (E40, E50 and E60) were anesthetized with a combination of 6 mg/kg ketamine chloride and 0.6 mg/kg xylazine. The timed gestation of the pregnant miniature pigs was determined starting the day following insemination and verified by B-type ultrasonic inspection. After removing the fetuses by cesarean section, the pregnant sows were sacrificed by over-anesthetization.

value: tooth germ

tag: developmental stage

value: E40 stage


title: E50_2

value: E50 stage


title: E40_2


title: E50_1


title: E60_1

value: E60 stage


title: E60_3


title: E60_2


title: E50_3


title: E40_1


title: Control        (biological rep2)

description: Gene expression data from DU145cells treated with DMSO

source_name: DU145 treated with DMSO


title: Yo2

city: Changchun

first: Bo

last: Gu

state: China

address: Jilin Agricultural University

institute: Jilin Agricultural University

data_processing:
illumina Casava 1.8 software used for basecalling.
The library preparations were sequenced on an Illumina Hiseq 2500 platform and 50bp single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie  without mismatch to analyze their expression and distribution on the reference.  Known miRNA alignment   Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures. Custom scripts were used to obtain the miRNA counts as well as base bias on the first position of identified miRNA with certain length and on each position of all identified miRNA respectively.  Novel miRNA prediction   The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA. The available software miREvond mirdeep2 were integrated to predict novel miRNA through exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the small RNA tags unannotated in the former steps. At the same time, custom scripts were used to obtain the identified miRNA counts as well as base bias on the first position with certain length and on each position of all identified miRNA respectively.  Differential expression analysis of two conditions/groups was performed using the DESeq R package (1.8.3). The P-values was adjusted using the Benjamini& Hochberg method. Corrected P-value of 0.05 was set as the threshold for significantly differential expression by default. Predicting the target gene of miRNA was performed by miRanda.

organism: Ovis aries

source_name: ovary

growth_protocol: All sheep were raised under the same environment with natural light and free intake of food and water.

extract_protocol:
RNA was harvested using Trizol reagent. A total amount of 3 μg total RNA per sample was used as input material for the small RNA library.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The tissue samples were immediately snap-frozen in liquid nitrogen for total RNA extraction.

value: ovary

tag: breed

value: Small Tail Han Sheep


title: Jo3


title: Yo1


title: Yo3


title: Jo1


title: Jo2


title: Fo3


title: Control       (biological rep1)


title: DHA Treatment (biological rep1)


title: Fo1


title: Fo2


title: Control_2

tag: strain

tag: genotype

value: in vitro cultured GC B cells

tag: chip antibody

value: STAT3 Ab (124H6, Cell Signaling Technology)


title: r282

description: polyA RNA

source_name: Mouse thymus T-ALL cells

tag: subpopulation

tag: turmor stage

value: blast crisis

value: Female


title: r278

description: polyA RNA


title: T47D Pol II T60 gv_072_01_01_chipseq

city: Barcelona

first: François

last: Le Dily

address: Dr Aiguader, 88

institute: CRG

data_processing:
All steps inidicated in https://github.com/4DGenome/pipelines/tree/master/hic-16.05
Genome_build: hg38
Supplementary_files_format_and_content: TSV file containing the number of contacts observed between each pair of 100-Kb bins in the genome

growth_protocol: T47D, MCF-7, BT474, MCF10A, SKBR3 were routinely grown in their optimal medium according the ATCC recommendations. Stable T47D clones expressing shRNA empty or shRNA against PR are described elsewhere (Verde et al., 2017*).  For RNA interference experiments, T47D cells were transiently transfected as previously described (Nacht et al. 2016) with scramble siRNA (siRNA-Control) or siRNA directed against ERα (siRNA-ER; sc-29305, Santa-Cruz Biotechnology).

extract_protocol:
In Situ Hi-C was performed according previously described protocol (Rao et al., 2014) with some modifications (Le Dily et al., 2017).
Paired-end libraries were generated with Truseq adaptors (Illumina) according previously published Hi-C protocols (Rao et al., 2014).

treatment_protocol: For the experiments cells were grown 48 hours in medium without phenol red complemented with 10% charchoal-dextran treated Fetal Bovine Serum (which corresponds to steroid depleted condition). After further synchronization in G0/G1 by overnight culture in medium without phenol red in absence of FBS, cells were harvested (steroid depleted (-H) condition). In the case of hormonal treatments, cells were further treated for the times indicated with 10-8 M Estradiol (E2) or with 10-8 M of the progestin analogue R5020 (Pg).

value: ER+/PR+

tag: target protein

tag: pre treatment

value: Untreated

tag: pre treatment time

value: Progesterone

tag: treatment time

tag: sequencing core

value: CRG

tag: send for sequencing on

tag: illumina machine

value: Illumina HiSeq 2000

tag: application

value: ChIP-seq

tag: read length

tag: sequencing type

value: SE

tag: library type

value: Unknown


title: T47D BRD4 T30 gv_105_01_01_chipseq

tag: cell type

tag: treatment

tag: sequencing index

value: GTGAAA


title: T47D H3K27ac T30 gv_115_01_01_chipseq

value: GTCCGC

value: Unstranded


title: T47D BRD4 T0 gv_104_01_01_chipseq

value: ACAGTG


title: T47D Pol II T0 gv_071_01_01_chipseq


title: MCF7 ER T30 E2 gv_005_01_01_chipseq

value: ChIP-ER

value: Estrogen

value: CTTGTA


title: WT rep3

city: Yangzhou

first: Zhen

address: Wenhui

institute: Yangzhou University

data_processing:
Bcl2fastq (v2.17.1.14) used for basecalling.
3’ adaptor-trimming and low quality reads removing by Cutadapt（version 1.9.1）
The high quality trimmed reads (clean reads) were aligned to the human reference genome (UCSC HG19) using Hisat2(v2.0.1).
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Htseq (V0.6.1).
Differential expression analysis used the DESeq2 (V1.6.3).
Genome_build: HG19
Supplementary_files_format_and_content: Excel files include RPKM values for each Sample

source_name: kidney

growth_protocol: Cells were grown in Eagle’s Minimum Essential Medium (MEM) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin solution. The cells were maintained at 37% in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA of cells was extracted using TRIzol according to the manufacturer’s instructions. The poly(A) mRNA isolation was performed using Ribo-Zero™ rRNA removal Kit
Next generation sequencing libraries were constructed according to the manufacturer’s protocol (NEBNext® Ultra™ RNA Library Prep Kit for Illumina®).

treatment_protocol: The NSUN2-deficient HEK293 cell line was generated using a CRISPR-Cas9-mediated method

tag: strain

tag: passages


title: WT rep1


title: NSUN2-KO rep1


title: NSUN2-KO rep2


title: WT rep2


title: T47D H3K27ac T0 gv_114_01_01_chipseq


title: MCF7 ER T0 gv_001_02_01_chipseq

value: GCCAAT


title: MCF7 PR T30 R5020 gv_004_01_01_chipseq

value: ChIP-PR


title: T47D R6 fd_005_01_01_rnaseq

value: ER+/PR+

value: ATCACG

value: RNA-seq

value: PE

value: Reverse-stranded


title: T47D R180 e4aa8d54f_0e24fcc35

value: Untreated

value: Progesterone

value: CNAG

value: AGTCAA

value: Illumina HiSeq 2000

value: INHIC

tag: restriction enzyme

value: DpnII

value: hic


title: T47D R180 e4aa8d54f_51720e9cf

value: CRG


title: T47D T0 dc3a1e069_db4f304ee

value: ACAGTG


title: MCF7 PR T0 gv_003_01_01_chipseq

tag: target protein

value: ChIP-seq

value: SE

value: Unknown


title: T47D T0 fd_004_01_01_rnaseq

value: ER+/PR+

tag: pre treatment

value: GTGAAA


title: NSUN2-KO rep3


title: T47D R30 9a7c4a68d_db4f304ee

tag: pre treatment time

value: CAGATC

value: PE


title: T47D E6 fd_006_01_01_rnaseq

value: Untreated

value: Estrogen

tag: treatment time

value: ACTTGA

value: RNA-seq

value: Reverse-stranded


title: M4724: E18.5 ureters, Tbx2/Tbx3cDKO vs control, rep1

city: Hannover

first: Andreas

last: Kispert

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

country: Germany

institute: Medizinische Hochschule Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the 'Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7' (Agilent Technologies), except that 2500ng of each labeled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing:
Data extraction, processing and intra-array normalization of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE2_107_Sep09.xml’.
Measurements of on-chip replicates were averaged using the geometric mean of ProcessedSignal (PS) values (for each channel independently) to retrieve one resulting value per probe, sample, and channel. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per feature that exceeded 0.5.
For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500) by the 75th Percentile of the microarray dataset to be normalized. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:
normalized PSArray i = PSArray i  x (1500 / 75th Percentile gPSArray i)
Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 15 normalized PS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 15.

source_name: control

label_protocol: Synthesis of AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA was performed with the 'Amino Allyl MessageAmp™ II aRNA Amplification Kit' (#AM1753, Life Technologies) according to the manufacturer's recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1) and that reaction volumes were halved.

extract_protocol: Total RNA was extracted using peqGOLD RNAPure™ (VWR) according to the manufacturer's recommendations

value: NMRI

tag: genotype

tag: gender

value: male

tag: developmental stage

tag: tissue

value: Ureter


title: T47D T0 dc3a1e069_51720e9cf

tag: sequencing core

value: CRG

tag: send for sequencing on

tag: illumina machine

value: Illumina HiSeq 2000

tag: application

value: INHIC

tag: read length

value: DpnII

value: hic


title: M5339: E13.5 ureters, Tbx2-GOF vs control, rep1


title: M5340: E13.5 ureters, Tbx2-GOF vs control, rep2


title: M4725: E18.5 ureters, Tbx2/Tbx3cDKO vs control, rep2

value: female


title: T47D R30 9a7c4a68d_51720e9cf

tag: cell type

value: ER+/PR+

tag: treatment

value: Progesterone

tag: sequencing index

tag: sequencing type

tag: library type


title: T47D E30 7824bad60_51720e9cf

tag: pre treatment

value: CCGTCC

tag: restriction enzyme

value: PE


title: T47D E30 7824bad60_0e24fcc35

value: Untreated

tag: pre treatment time

value: Estrogen

tag: treatment time

value: CNAG


title: T47D E180 1618f57a8_0e24fcc35

value: GTGAAA


title: T47D E180 1618f57a8_51720e9cf


title: MCF7 T0 cont for ICI 66950b082_f708c2c20

value: CTTGTA

value: MboI


title: t47D siER

data_processing:
library strategy: In Situ Hi-C
All steps inidicated in https://github.com/4DGenome/pipelines/tree/master/hic-16.05
Genome_build: hg38
Supplementary_files_format_and_content: raw matrices TSV file containing the number of contacts observed between each pair of 100-Kb bins in the genome

tag: cell line

tag: pre-treatment

value: si ER

tag: pre-treatment time

value: ACAGTG


title: BT474 T0

tag: sequencing core

value: CRG


title: Capture-C R60 split 2

tag: send for sequencing on

value: TGACCA


title: Capture-C R60 split 1


title: Capture-C T0 split 2

value: CGATGT


title: SKBR3 T0

value: ER-/PR-

value: CAGATC

value: INHIC


title: T47D shempty

value: ER+/PR+

value: sh empty

value: ATGTCA


title: T47D siCont

value: si control

value: Untreated


title: Capture-C T0 split 1


title: ChIC T47D E60

value: Estrogen

value: GTCCGC

value: CHIC


title: T47D E180

value: MboI


title: Capture-C E60

value: GCCAAT


title: ChiC T47D T0

value: ACAGTG


title: ChIC T47D E180

value: CRG

value: GTGAAA


title: MCF10 T0

value: AGTCAA


title: MCF-7 T0

value: CNAG

value: CGATGT


title: T47D E30

value: AGTTCC

value: INHIC


title: T47D R180

value: ER+/PR+

value: Progesterone


title: ChIC T47D R180


title: ChiC T47D R60

value: CTTGTA


title: T47D R30

value: Untreated

value: CAGATC


title: T47D T0


title: ChIP-Seq POL2 T660 R5020 rf_087_01_01_chipseq

tag: target protein

value: GCACTA

tag: illumina machine

value: Illumina NextSeq 500

value: ChIP-seq

value: SE

value: Unknown


title: T47D ChIP-H3K27ac R30 fd_034_01_01_chipseq

value: CAGGCG

tag: application

tag: read length


title: ChIP-Seq POL2 T0 rf_086_01_01_chipseq

tag: cell type

tag: treatment

value: AGTGAG


title: T47D ChIP-BRD4 R30 fd_028_01_01_chipseq

tag: sequencing index

value: CACGAT

tag: sequencing type


title: T47D ChIP-H3K27ac T0 fd_033_01_01_chipseq

tag: pre treatment

value: untreated

value: CACTCA

tag: library type


title: T47D ChIP-BRD4 T0 fd_027_01_01_chipseq

tag: pre treatment time

value: CAACTA


title: T47D shPR

value: sh PR

tag: treatment time

value: CRG

value: CCGTCC

value: INHIC

tag: restriction enzyme

value: MboI


title: Hi-C SKBR3 ee060a665_48f314007

value: ER-/PR-

value: Untreated

value: PE

value: hic


title: Hi-C BT474 7dc7dba2e_8feda926a

value: ER+/PR+

value: CATGGC

value: Illumina NextSeq 502


title: T47D ChIP-ER Red medium fd_023_01_01_chipseq

value: ChIP-ER

value: Red medium

value: Illumina NextSeq 500

value: ChIP-seq

value: SE

value: Unknown


title: T47D ChIP-ER Day 2 fd_024_01_01_chipseq

value: FBSdes

value: CATTTT


title: GM ChIP CTCF yc_001_01_01_chipseq

source_name: GM

value: ChIP-CTCF

value: AACCAG


title: Normal-B272c

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

data_processing:
STAR for alignment to hg19
featureCount for RPKM counting
voom-limma for differential gene expression
Genome_build: hg19
Supplementary_files_format_and_content: An Excel file including RPKM of each gene for all 24 samples

source_name: interneurons

growth_protocol: interneurons were generated from iPSCs according to previously published protocols (Kim, T.G., et al. Efficient specification of interneurons from human pluripotent stem cells by dorsoventral and rostrocaudal modulation. Stem cells 32, 1789-1804, 2014), and were harvested for RNA preparation after 8 weeks of differentiation.

extract_protocol:
Samples were harvested using Trizol reagent (Invitrogen).
TruSeq Stranded HT mRNA kit

tag: tissue

value: iPSC-derived interneurons

tag: disease

value: healthy control


title: Hi-C MCF10A 36c337b3a_8454e00e3

value: Untreated

tag: sequencing core

value: CAGGCG

value: Illumina NextSeq 501

value: INHIC

value: MboI

value: PE


title: Normal-B190c


title: Normal-B367b


title: Normal-B226a


title: Normal-B190b


title: Normal-B367a


title: Normal-B367c


title: Normal-B226c


title: Normal-B226b


title: Schizophrenia-A212b

value: schizophrenia


title: Normal-B272a


title: Schizophrenia-A162b


title: Schizophrenia-A162c


title: Schizophrenia-A162a


title: Schizophrenia-A128c


title: T47D ChIP-ER Day 12 fd_025_01_01_chipseq

value: ER+/PR+

value: ChIP-ER

tag: send for sequencing on

value: CCAACA

value: Illumina NextSeq 500


title: Schizophrenia-A128a


title: Schizophrenia-A67c


title: Schizophrenia-A67b


title: Schizophrenia-A128b


title: Normal-B272b


title: Normal-B190a


title: Schizophrenia-A212c


title: Schizophrenia-A212a


title: Schizophrenia-A67a


title: 87_spln_Id3pos_eTR [lib16893]

city: Seattle

first: Daniel

middle: J

last: Campbell

state: Washington

address: 1201 Ninth Avenue

institute: Benaroya Research Institute

data_processing:
Base-calling was performed automatically by Illumina real time analysis software and demultiplexing was performed on Illumina BaseSpace.
Hard trimming was performed in Galaxy; 1 3'-end base was removed from all reads using the FASTQ Trimmer tool (v1.0.0)
Quality-based trimming was performed in Galaxy; reads were trimmed from both ends using the FASTQ Quality Trimmer tool (v1.0.0) until minimum base quality for each read was >= 30.
Reads were aligned in Galaxy using bowtie and TopHat (Tophat for Illumina tool, v.1.4.0)
Read counts per Ensembl gene ID were computed in Galaxy using htseq-count (htseq-count tool, v.0.4.1).
Sequencing, alignment, and quantitation metrics were obtained for FASTQ, BAM/SAM, and count files in Galaxy using FastQC, Picard, TopHat, Samtools, and htseq-count.
Genome_build: mouse NCBI genome build 37
Supplementary_files_format_and_content: raw _counts.txt: Read counts as quantified by htseq-count.
Supplementary_files_format_and_content: norm_counts.txt: Lowly expressed genes and non-protein coding genes were filtered out and the ensembl gene IDs mapped to MGI gene symbols. Count data was normalized using TMM (Robinson & Oshlack, 2010)

extract_protocol:
CD4+ T cells were isolated using CD4 microbreads (Miltenyi) from either peripheral LNs or spleens of 3 littermate Id3-GFP x Foxp3-mRFP mice. Cells were sorted based on viability, CD4, CD44, CD62L, Id3-GFP and Foxp3-mRFP expression on a FACs Aria II (BD Biosciences). 500 cells were sorted directly into SMART-Seq v4 Ultra Low Input RNA Kit (Takara) lysis buffer and protocol followed to produce cDNA.
Library construction was performed using a modified protocol of the NexteraXT DNA sample preparation kit (Illumina).

tag: strain background

tag: genotype/variation

value: Id3-GFP x Foxp3-mRFP

value: Spleen

value: CD4+ T cells

tag: cell population

value: Id3+CD62LloCD44hi effector TR (Id3pos_eTR)


title: 87_spln_Id3pos_cTR [lib16894]

value: Id3+CD62LhiCD44lo central TR (Id3pos_cTR)


title: 86_spln_Id3pos_cTR [lib16891]


title: 84_LN_Id3pos_eTR [lib16896]

value: Lymph node


title: 87_LN_Id3neg_eTR [lib16901]

value: Id3- effector TR (Id3neg_eTR)


title: 86_LN_Id3neg_eTR [lib16898]


title: 86_spln_Id3neg_eTR [lib16889]


title: 84_spln_Id3neg_eTR [lib16886]


title: 87_LN_Id3pos_eTR [lib16902]


title: 84_spln_Id3pos_eTR [lib16887]


title: 86_LN_Id3pos_eTR [lib16899]


title: 84_LN_Id3pos_cTR [lib16897]


title: 87_spln_Id3neg_eTR [lib16892]


title: 84_spln_Id3pos_cTR [lib16888]


title: 86_spln_Id3pos_eTR [lib16890]


title: 87_LN_Id3pos_cTR [lib16903]


title: F123_WGBS_Rep2

first: Guoqiang

state: Beijing

address: No.5 Yiheyuan Rd

institute: Biomedical Pioneering Innovation Center,Peking University

data_processing:
Analysis of methylation data: Raw reads were first trimmed as paired-end reads using Trimmomatic with default parameters to remove the adapters and low quality reads. Trimmed reads were aligned to mm9 using Bismark (v12.5). PCR duplications were removed with Picard (http://broadinstitute.github.io/picard/). Cpg methylation level were calculated by Bis-SNP in bissnp_easy_usage.pl with default parameters.
Analysis of Hi-C data: All sequence data were produced using Illumina paired-end sequencing. Each end of the raw reads was mapped separately to the mm9 reference genome using BWA-mem.  Filtered reads were then paired and de-duplicated (Picard). Reads that map to the same fragment were further removed. Contact matrices were generated at different resolution using Juicer pipeline with KR normalization and visualized using Juicebox. Loops were then called by HICCUPS.
Methyl-HiC reads mapping by Bhmem: Raw reads were first trimmed as paired-end reads using Trimmomatic with default parameters to remove the adapters and low-quality reads. All C in reference genome is converted to T to make C_to_T reference genome, and all G is converted to A to make G_to_A reference genome in mm9. On paired end reads, C is converted to T in end 1 and G is converted to A in end 2. The converted end 1 and end 2 are joined as single paired fragment when both of them were mapped to C_to_T reference genome or G_to_A reference genome by BWA-MEM. Only unique mapped and passed VendorQualityFilter reads on both ends were joined.
The best paired reads were selected based on the following priorities: (1) mapping quality on both ends are bigger than 0. (2) the sum of mapping quality score is larger. (3) both ends of reads are mapped into the same chromosome. (4) the sum of alignment score is larger. (5) the sum of mismatches is smaller. (6).the sum of matched cigar string length is larger. Only best paired reads were output for the following analysis. Low quality reads (not unique mapped on both ends, PCR duplicate and mapping quality score < 30) were removed for the following downstream analysis. Only bases with quality score more than 5 were included in the downstream methylation analysis. Details were implemented in Bhmem.java
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Bed files contain DNA methylation called from MethylHiC and WGBS data.
Supplementary_files_format_and_content: Bedpe files contain HICCUPS loops and Methylation Concordance called from MethylHiC data.
Supplementary_files_format_and_content: Hic file contains binary contact matrix for in situ HiC data.

source_name: F123 embryonic stem cells

growth_protocol: The F1 Mus musculus castaneus × S129/SvJae mouse ESC line (F123) was cultured in KSR medium as described previously. Cells were collected and plated on 0.2% gelatin-coated feeder-free plates for 30mins before harvesting to remove feeder cell contamination.

extract_protocol:
Cell pellets were washed with cold PBS and lysed with lysis buffer to get nuclei pellets. Nucleus were permeabilized with 0.5% SDS. DNA was in situ digested with 100 units of DpnII (NEB) overnight. The ends of restriction fragments were filled with biotinylated nucleotides and in situ ligated. After reversal of crosslinks, ligated DNA was ethanol precipitate and sheared to a length of ∼400 bp by sonication (Covaris). Sonicated products were pulled down with streptavidin beads. Library construction was then performed on beads. After adapter ligation, beads were suspended in 20ul TE buffer and subjected to bisulfite conversion with EZ DNA Methylation-Gold™ Kit (Zymo). Unmethylated lambda DNA was sonicated and ligated with the same adapter for Methyl-HiC sample and then was spiked in at 0.5% before bisulfite conversion. After conversion, streptavidin beads were removed with magnet and the supernatant were purified. Purified bisulfite converted DNA was amplified with Hifi Hotstart Uracil+Ready Mix (KAPA).
Libraries were prepared according to Illumina's standard DNA library protocol, in which genomic DNA was fragmented by sonication (Covaris), end-repaired, dA-tailed and ligated to cytosine methylated Illumina TruSeq adapter.

treatment_protocol: About two million cells were cross-linked with 1% formaldehyde for 10 min at room temperature. Reaction was then quenched with 0.2M Glycine.

tag: cell line

tag: strain

value: F1 Mus musculus castaneus x S129/SvJae

value: mouse ESC line

tag: culture condition

value: serum+LIF


title: F123_in_situ_HiC_Rep2

description:
Data from 4 replicates were merged to calculate processed files.
processed data file: JL.merged.sorted.nodup.long.juice.q30.hic

tag: cell type


title: F123_WGBS_Rep1


title: F123_Methyl-HiC_Rep3

description:
Data from 4 replicates were merged to calculate processed files.
processed data file: F123.mESC.MethylHic.mapQ30.25k_res.enhancedHicMatrix.txt.gz
processed data file: F123.MethylHic.mm9.calmd.cpg.filtered.sort.CG.strand.6plus2.bed
processed data file: F123.MethylHic.mm9.calmd.long.hic.mapQ30.5k_res.all_chr.hiccups.txt
processed data file: F123.MethylHic.mm9.calmd.long.hic.mapQ30.5k_res.methy_corr.minMapQ30.methyCor.txt.gz
processed data file: F123.MethylHic.mm9.calmd.long.hic.mapQ30.10k_res.all_chr.hiccups.txt
processed data file: F123.MethylHic.mm9.calmd.long.hic.mapQ30.10k_res.methy_corr.minMapQ30.methyCor.txt.gz
processed data file: F123.MethylHic.mm9.calmd.long.hic.mapQ30.25k_res.all_chr.hiccups.txt
processed data file: F123.MethylHic.mm9.calmd.long.hic.mapQ30.25k_res.methy_corr.minMapQ30.methyCor.txt.gz

data_processing:
Library strategy: Methyl-HiC
Analysis of methylation data: Raw reads were first trimmed as paired-end reads using Trimmomatic with default parameters to remove the adapters and low quality reads. Trimmed reads were aligned to mm9 using Bismark (v12.5). PCR duplications were removed with Picard (http://broadinstitute.github.io/picard/). Cpg methylation level were calculated by Bis-SNP in bissnp_easy_usage.pl with default parameters.
Analysis of Hi-C data: All sequence data were produced using Illumina paired-end sequencing. Each end of the raw reads was mapped separately to the mm9 reference genome using BWA-mem.  Filtered reads were then paired and de-duplicated (Picard). Reads that map to the same fragment were further removed. Contact matrices were generated at different resolution using Juicer pipeline with KR normalization and visualized using Juicebox. Loops were then called by HICCUPS.
Methyl-HiC reads mapping by Bhmem: Raw reads were first trimmed as paired-end reads using Trimmomatic with default parameters to remove the adapters and low-quality reads. All C in reference genome is converted to T to make C_to_T reference genome, and all G is converted to A to make G_to_A reference genome in mm9. On paired end reads, C is converted to T in end 1 and G is converted to A in end 2. The converted end 1 and end 2 are joined as single paired fragment when both of them were mapped to C_to_T reference genome or G_to_A reference genome by BWA-MEM. Only unique mapped and passed VendorQualityFilter reads on both ends were joined.
The best paired reads were selected based on the following priorities: (1) mapping quality on both ends are bigger than 0. (2) the sum of mapping quality score is larger. (3) both ends of reads are mapped into the same chromosome. (4) the sum of alignment score is larger. (5) the sum of mismatches is smaller. (6).the sum of matched cigar string length is larger. Only best paired reads were output for the following analysis. Low quality reads (not unique mapped on both ends, PCR duplicate and mapping quality score < 30) were removed for the following downstream analysis. Only bases with quality score more than 5 were included in the downstream methylation analysis. Details were implemented in Bhmem.java
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: Bed files contain DNA methylation called from MethylHiC and WGBS data.
Supplementary_files_format_and_content: Bedpe files contain HICCUPS loops and Methylation Concordance called from MethylHiC data.
Supplementary_files_format_and_content: Hic file contains binary contact matrix for in situ HiC data.


title: F123_in_situ_HiC_Rep1


title: F123_Methyl-HiC_Rep2


title: F123_in_situ_HiC_Rep4


title: 86_LN_Id3pos_cTR [lib16900]


title: F123_Methyl-HiC_Rep1


title: 84_LN_Id3neg_eTR [lib16895]


title: siA_2745L-170901Bur_D17-7550_NA_sequence

city: Cambridge

first: Peter

last: Sudmant

state: MA

address: 77 Massachusetts Ave

institute: MIT

description: genome build: mm10

library_source: other

data_processing:
Library strategy:  ribo-Seq
Reads were aligned to the mouse genome using STAR version 2.5.1b. ENSEMBL version 75 gene annotations were used.

source_name: NIH-3T3 cell line

extract_protocol:
ribosome footprinting
SMARTer smRNA Kit - Takara

tag: treatment

value: ABCE1 siRNA


title: PQ_2745L-170901Bur_D17-7551_NA_sequence

description: genome build: mm10

value: 100uM paraquat


title: siC_2745L-170901Bur_D17-7549_NA_sequence

description: genome build: mm10

value: control siRNA


title: Tgd.Sp#1.8

city: Boston

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

description:
Gamma Delta T Cell
Gene_count_table.csv

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

source_name: Spleen

growth_protocol: 5 week old C57BL/6J mice from the Jackson Laboratory (Bar Harbor, ME) housed in facility at least one week before harvesting cells

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

tag: age

value: 6 weeks old

tag: sorting markers

value: T Cell


title: Tgd.Sp#1.7

description:
Gamma Delta T Cell
Gene_count_table.csv


title: T.4.Nve.Sp#1.7

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: Tgd.Sp#1.1

description:
Gamma Delta T Cell
Gene_count_table.csv


title: Tgd.Sp#1.3

description:
Gamma Delta T Cell
Gene_count_table.csv


title: T.4.Nve.Sp#1.14

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: T.4.Nve.Sp#1.2

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: T.4.Nve.Sp#1.15

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: T.4.Nve.Sp#1.6

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: Tgd.Sp#1.6

description:
Gamma Delta T Cell
Gene_count_table.csv


title: Tgd.Sp#1.4

description:
Gamma Delta T Cell
Gene_count_table.csv


title: F123_singlecellMethyl-HiC_naive_Cell_41-44

city: Beijing


title: T.4.Nve.Sp#1.16

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: Tgd.Sp#1.2

description:
Gamma Delta T Cell
Gene_count_table.csv


title: T.4.Nve.Sp#1.3

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: T.4.Nve.Sp#1.13

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: T.4.Nve.Sp#1.4

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: T.4.Nve.Sp#1.8

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: F123_singlecellMethyl-HiC_naive_Cell_25-28


title: T.4.Nve.Sp#1.5

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: T.4.Nve.Sp#1.9

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: Tgd.Sp#1.5

description:
Gamma Delta T Cell
Gene_count_table.csv


title: F123_singlecellMethyl-HiC_naive_Cell_37-40


title: T.4.Nve.Sp#1.11

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: F123_singlecellMethyl-HiC_naive_Cell_45-47


title: T.4.Nve.Sp#1.12

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: F123_singlecellMethyl-HiC_naive_Cell_17-20


title: F123_singlecellMethyl-HiC_naive_Cell_33-36


title: F123_singlecellMethyl-HiC_naive_Cell_29-32


title: F123_singlecellMethyl-HiC_naive_Cell_21-24


title: T.4.Nve.Sp#1.10

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: F123_singlecellMethyl-HiC_naive_Cell_5-8


title: T.4.Nve.#2.1

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: T.4.Nve.#2.2

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: NK.Sp#1.8

description:
Spleenic NK Cell
Gene_count_table.csv

value: 7 weeks old

value: NK Cell


title: F123_singlecellMethyl-HiC_primed_Cell_96-99


title: NK.Sp#1.6

description:
Spleenic NK Cell
Gene_count_table.csv


title: F123_singlecellMethyl-HiC_naive_Cell_9-12


title: F123_singlecellMethyl-HiC_primed_Cell_88-91


title: NK.Sp#1.3

description:
Spleenic NK Cell
Gene_count_table.csv


title: F123_singlecellMethyl-HiC_primed_Cell_92-95


title: NK.Sp#1.2

description:
Spleenic NK Cell
Gene_count_table.csv


title: F123_singlecellMethyl-HiC_primed_Cell_72-75


title: F123_singlecellMethyl-HiC_primed_Cell_76-79


title: F123_singlecellMethyl-HiC_naive_Cell_1-4


title: NK.Sp#1.18

description:
Spleenic NK Cell
Gene_count_table.csv


title: F123_singlecellMethyl-HiC_primed_Cell_100-103


title: F123_singlecellMethyl-HiC_naive_Cell_13-16


title: NK.Sp#1.4

description:
Spleenic NK Cell
Gene_count_table.csv


title: F123_singlecellMethyl-HiC_primed_Cell_80-83


title: F123_singlecellMethyl-HiC_primed_Cell_60-63


title: NK.Sp#1.5

description:
Spleenic NK Cell
Gene_count_table.csv


title: NK.Sp#1.16

description:
Spleenic NK Cell
Gene_count_table.csv


title: NK.Sp#1.17

description:
Spleenic NK Cell
Gene_count_table.csv


title: F123_singlecellMethyl-HiC_primed_Cell_64-67


title: F123_singlecellMethyl-HiC_primed_Cell_68-71


title: T.4.Nve.Sp#1.1

description:
Naïve CD4 T Cell
Gene_count_table.csv


title: F123_singlecellMethyl-HiC_primed_Cell_56-59


title: NK.Sp#1.9

description:
Spleenic NK Cell
Gene_count_table.csv


title: NK.Sp#1.7

description:
Spleenic NK Cell
Gene_count_table.csv


title: F123_singlecellMethyl-HiC_primed_Cell_84-87


title: F123_singlecellMethyl-HiC_primed_Cell_44-47


title: F123_singlecellMethyl-HiC_primed_Cell_52-55


title: NK.Sp#1.10

description:
Spleenic NK Cell
Gene_count_table.csv


title: F123_singlecellMethyl-HiC_primed_Cell_40-43


title: NK.Sp#1.1

description:
Spleenic NK Cell
Gene_count_table.csv


title: NK.Sp#1.12

description:
Spleenic NK Cell
Gene_count_table.csv


title: F123_singlecellMethyl-HiC_primed_Cell_48-51


title: F123_singlecellMethyl-HiC_primed_Cell_20-23


title: F123_singlecellMethyl-HiC_primed_Cell_24-27


title: MF.PC#2.6

description:
Peritoneal Macrophage
Gene_count_table.csv

source_name: Peritoneal Cavity

value: Peritoneal Cavity

value: Macrophage


title: F123_singlecellMethyl-HiC_primed_Cell_16-19


title: MF.PC#2.5


title: MF.PC#2.7


title: F123_singlecellMethyl-HiC_primed_Cell_12-15


title: MF.PC#2.4


title: MF.PC#2.3


title: F123_singlecellMethyl-HiC_primed_Cell_32-35


title: MF.PC#2.8


title: F123_singlecellMethyl-HiC_primed_Cell_9-11


title: F123_singlecellMethyl-HiC_primed_Cell_5-8


title: MF.PC#2.1

value: Spleen


title: NK.Sp#1.13

description:
Spleenic NK Cell
Gene_count_table.csv


title: NK.Sp#1.15

description:
Spleenic NK Cell
Gene_count_table.csv


title: NK.Sp#1.14

description:
Spleenic NK Cell
Gene_count_table.csv


title: NK.Sp#1.11

description:
Spleenic NK Cell
Gene_count_table.csv


title: F123_singlecellMethyl-HiC_primed_Cell_1-4


title: F123_singlecellMethyl-HiC_primed_Cell_36-39


title: F123_singlecellMethyl-HiC_primed_Cell_28-31


title: MF.PC#1.9


title: F123_in_situ_HiC_Rep3


title: MF.PC#1.7


title: NSUN2-KO HEK293 RNA-Bisulfite-Seq

last: Sun

data_processing:
Library strategy: RNA-Bisulfite-Seq
Illumina HiSeq 4000 sequencer used for basecalling.
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
The high quality trimmed reads (clean reads) were aligned to the human reference genome (UCSC HG19) using meRanGh (one component of meRanTK) software with default parameters.
The methylation status of each C within the genome was extracted by meRanCall (one component of meRankTK) software.
meRanCompare (one component of meRanTK) software was used to identify differentially methylated sites (DMSs). The methylated sites and DMSs were annotated using Ensembl genome features.
Genome_build: HG19
Supplementary_files_format_and_content: bed file include 5-methylcytosine sites for each Sample

extract_protocol:
Total RNA of cells was extracted using TRIzol according to the manufacturer’s instructions. Total RNA for each sample was rRNA depleted using NEBNext® rRNA Depletion Kit.
rRNA-depleted RNA was bisulfite-converted and purified using the EZ RNA methylation Kit (Zymo Research). RNA libraries were later constructed with TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

tag: passages

value: NSUN2 KO


title: MF.PC#1.8


title: MF.PC#1.5


title: WT HEK293 RNA-Bisulfite-Seq

value: Wildtype


title: F123_Methyl-HiC_Rep4


title: MF.PC#1.4


title: MF.PC#1.3


title: MF.PC#1.2


title: MF.PC#1.16


title: MF.PC#1.15


title: MF.PC#2.2


title: MF.PC#1.14


title: MF.PC#1.13


title: M4 (ATR6): Renal Biopsy Mixed ATN+AIN

city: Indianapolis

first: Michael

middle: Thomas

last: Eadon

state: IN

address: 950 W. Walnut St R2 202

department: Medicine

institute: Indiana University

data_processing:
For the RNA-seq data, sequence reads were aligned to the human reference genome hg38 with STAR-2.5.2b.
featureCounts (subread-1.5.0) was used to quantify gene expression (parameters applied: "“-s 2 –p –Q 10")
Genome_build: hg38
Supplementary_files_format_and_content: csv file of read counts fro all samples

source_name: Kidney

extract_protocol:
Kidney tissue was obtained from a clinical biopsy, placed in Michels solution and frozen on OCT within 24 h. 20 um of cross-sectional biopsy tissue was cut on a cryotome and placed in Arcturus Picopure extraction buffer. RNA was extracted according to protocol.
SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input
RNA seq, 10 millions input reads per sample

value: Kidney

value: Mixed ATN and AIN

tag: sepsis

value: N

tag: storage

value: OCT at -80C

tag: gender

value: Female


title: M7 (ATR29): Renal Biopsy Mixed ATN+AIN

tag: tissue

tag: disease

value: not included in comparison

value: male


title: M2 (AIR3): Renal Biopsy Mixed ATN+AIN


title: I8 (ATR24): Renal Biopsy AIN

value: AIN


title: M3 (ATR4): Renal Biopsy Mixed ATN+AIN


title: M8 (ATR33): Renal Biopsy Mixed ATN+AIN

value: Y


title: M5 (ATR7): Renal Biopsy Mixed ATN+AIN


title: MF.PC#1.12

value: 6 weeks old


title: M6 (ATR28): Renal Biopsy Mixed ATN+AIN


title: I7 (AIR13): Renal Biopsy AIN


title: M1 (AIR2): Renal Biopsy Mixed ATN+AIN


title: MF.PC#1.11


title: MF.PC#1.6


title: MF.PC#1.10


title: I5 (AIR8): Renal Biopsy AIN


title: I4 (AIR7): Renal Biopsy AIN


title: B.fo.Sp#1.9

description:
Follicular B Cell
Gene_count_table.csv

value: B Cell


title: I3 (AIR6): Renal Biopsy AIN


title: I6 (AIR10): Renal Biopsy AIN


title: I1 (AIR1): Renal Biopsy AIN


title: B.fo.Sp#1.8

description:
Follicular B Cell
Gene_count_table.csv


title: I2 (ATR2): Renal Biopsy AIN


title: B.fo.Sp#1.5

description:
Follicular B Cell
Gene_count_table.csv


title: T11 (ATR27): Renal Biopsy ATN

value: ATN


title: B.fo.Sp#1.4

description:
Follicular B Cell
Gene_count_table.csv


title: T10 (ATR26): Renal Biopsy ATN


title: B.fo.Sp#1.3

description:
Follicular B Cell
Gene_count_table.csv


title: B.fo.Sp#1.16

description:
Follicular B Cell
Gene_count_table.csv


title: T7 (ATR22): Renal Biopsy ATN


title: T8 (ATR23): Renal Biopsy ATN


title: T9 (ATR25): Renal Biopsy ATN


title: B.fo.Sp#1.15

description:
Follicular B Cell
Gene_count_table.csv


title: B.fo.Sp#1.2

description:
Follicular B Cell
Gene_count_table.csv


title: B.fo.Sp#1.6

description:
Follicular B Cell
Gene_count_table.csv


title: day2-B-cell-RNA.rep3

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

data_processing:
Basecalls performed by Annoroad Co. Ltd. (naïve B and Day2 B) / BerryGenomics Co. Ltd. (Day3 B and day3 PCs)
RNA-Seq data were mapped by STAR aligner v2.5.2b and quantitified by Cufflinks and Cuffdiff.
Genome_build: GENCODE M12 (mm10)
Supplementary_files_format_and_content: The transcription levels (RPKM) were quantified with Cufflinks (v2.0.2) software.

source_name: antigen stimulated day2 B

extract_protocol:
Total RNA from at least 50,000 isolated mouse B cells was extracted by Trizol (Life Technology) and precipitated by RNase-free glycogen(Life technology). Immediately, we isolated mRNA from total RNA with NEBNext® Poly(A) mRNA Magnetic isolation Module(E7490S).
high throughput sequencing library was constructed with NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®(E7770S).

value: primary lymphocytes

tag: stimulation

value: antigen stimulated day2 B cells

value: wild type

value: spleen

tag: developmental stage

value: 8 weeks


title: T5 (ATR15): Renal Biopsy ATN

value: Kidney


title: MF.PC#1.1

value: Peritoneal Cavity

value: Macrophage


title: T6 (ATR18): Renal Biopsy ATN

value: OCT at -80C


title: day2-B-cell-RNA.rep2

tag: strain background

tag: genotype/variation


title: day2-B-cell-RNA.rep1


title: naive-B-cell-RNA.rep3

source_name: naive B cells

value: naive B cells


title: B.fo.Sp#1.13

description:
Follicular B Cell
Gene_count_table.csv

value: Spleen


title: T4 (ATR14): Renal Biopsy ATN

value: N

value: male


title: naive-B-cell-RNA.rep2


title: naive-B-cell-RNA.rep1


title: T3 (ATR10): Renal Biopsy ATN

value: not included in comparison

value: Female


title: P10 Pkd1V/V cystic kidney-4

city: Baltimore

first: Feng

last: Qian

address: 655 W. Baltimore Street

department: School of medicine, Department of medicine

institute: University of Maryland

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label_protocol: standard

extract_protocol: Total RNAs were extracted from the kidneys using the RNeasy mini kit (Qiagen) and the quality of total RNA samples were verified by a 260/280 ratio in NanoDrop and agarose gel electrophoresis.

tag: genotype

value: Pkd1V/V cystic


title: P10 Pkd1V/V cystic kidney-1


title: klp10a-KD rep3_mRNAseq

first: Charlotte

middle: Park

last: Choi

state: MD

address: 3400 North Charles Street

department: Department of Biology

institute: Johns Hopkins University

description:
MRNA_KLP10_03
mRNA_normalized_counts.txt.gz

data_processing:
Basecalling was performed using Illumina's default Real Time Analysis (RTA) basecalling and quality scoring software application.
Conversion from qseq files to fastq files and demultiplexing was performed using custom Awk and Python scripts.
Reads were adapter-trimmed and quality filtered (Q30) using  Trimmomatic 0.27  (Bolger et al., 2014).
Reads were aligned to the D. melanogaster genome (Dm3) by STAR-2.6.0a while allowing for up to 100 multi-alignments per read (Dobin et al., 2013).
Feature and abundance estimation were determined using TEtranscripts 2.0.3 (Jin et al., 2015).
Genome_build: dm3
Supplementary_files_format_and_content: Processed data files contains a matrix of genes (rows) and counts in each library (columns).

organism: Drosophila melanogaster

source_name: Testis

extract_protocol: 300 pairs of testes were removed and Total RNAs were extracted by the Trizol method. For mRNA sequencing, 2.5 µg of total RNAs were treated with DNase I (Amplification Grade, ThermoFisher) and recovered by RNA Clean & Concentrator-25 columns (Zymo). DNase I treated RNAs were then treated with Ribo-Zero Gold rRNA Removal Kit (Illumina). Libraries were generated from rRNA depleted RNAs using TruSeq Stranded Total RNA Sample Prep Kit (Illumina).

value: testis

value: 0-2 days


title: P10 wild-type kidney-1

value: Wild type


title: P10 Pkd1V/V cystic kidney-2


title: P10 wild-type kidney-3


title: P10 wild-type kidney-4


title: P10 wild-type kidney-2


title: T2 (ATR9): Renal Biopsy ATN

value: ATN


title: klp10a-KD rep2_mRNAseq

description:
MRNA_KLP10_02
mRNA_normalized_counts.txt.gz


title: klp10a-KD rep1_mRNAseq

description:
MRNA_KLP10_01
mRNA_normalized_counts.txt.gz


title: B.fo.Sp#1.14

description:
Follicular B Cell
Gene_count_table.csv

tag: strain

value: 6 weeks old

value: B Cell


title: B.fo.Sp#1.10

description:
Follicular B Cell
Gene_count_table.csv


title: T1 (ATR5): Renal Biopsy ATN

value: Kidney

value: Y


title: WT rep3_mRNAseq

description:
MRNA_CONT_03
mRNA_normalized_counts.txt.gz

value: wild type


title: WT rep2_mRNAseq

description:
MRNA_CONT_02
mRNA_normalized_counts.txt.gz


title: kidney sample 20

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

institute: University of Washington

data_processing:
Illumina's CASAVA 1.8.2 was used for basecalling.
After first assessing sequence quality using FastQC and then trimming the adaptor and lower-quality bases using Trim-galore, RNA-seq reads were aligned to the human genome (hg19/GRCh37) using STAR (v2.4.1d) based on GENCODE v19 annotations.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tab-delimited text files include log2 (RPKM) for each Sample

extract_protocol:
Collected tissue was immersed in RNAlater solution at 4°C for several hours prior to being stored at -80°C in RNAlater. Tissue was thawed on ice, placed in RNAlater, and manually microdissected for glomerulus and tubule compartments.
RNA quality was assessed with the Agilent Bioanalyzer 2100. Only samples with RIN scores above 7 and a minimum total RNA of 100 ng were used for cDNA production. Non-strand specific, polyA+ selected RNA-seq libraries were generated using the Illumina TruSeq protocol. Libraries were sequenced to a median depth of 35 million 100-bp single end reads.

value: Kidney (glomerular and tubular portions)

tag: disease state

value: Healthy