title: BXD79 Chow Diet_scWAT

description: Gene expression data


title: BXD80 Chow Diet_scWAT

status: Public on Mar 08 2019

type: RNA

city: Lausanne

first: Johan

last: Auwerx

address: Station 15

department: SV IBI NCEM

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

description: Gene expression data

hyb_protocol: Labeled cDNA was hybridized according to Affymetrix protocols. Approximately 16hr incubation and then washed and stained according to Affymetrix protocols on Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned on Affymetrix GSC3000 7G Scanner

data_processing: Samples were analyzed using Affymetrix Expression Console using RMA-sketch

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Mouse subcutaneous white adipose tissue

label_protocol: 100ng of total RNA was amplified using Ambion® WT Expression Kit from life technologies (Part Number 4411974) according to manufactures protocols, then 5500ng cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit (part number 900671) according to manufactures protocols.

growth_protocol: Mice are housed 5 per cage in IVC GM500 cages (Tecniplast, 500 cm2) according to the Swiss cantonal rules.

extract_protocol: Trizol extraction of total RNA was performed on all individuals -- approximately 5 per cohort, for roughly 400 animals in all. Sample concentrations were then measured by Nanodrop, and then all individuals from a cohort were evenly pooled together. These cohort pools were then cleaned up with a Qiagen RNEasy kit prior to preparation for microarray.

treatment_protocol: Male mice in chow diet cohorts were Harlan 2018 throughout their lifetime until sacrifice at 29 weeks. Male mice in the high fat diet cohorts were fed Harlan 06414 from week 8 until sacrifice at 29 weeks of age. Food was ad libitum except prior to sacrifice, when all animals were fasted overnight (6pm to 9am).

tag: tissue

value: subcutaneous white adipose tissue

tag: diet

value: Chow

tag: strain

tag: Sex

value: male

tag: age

value: 29 weeks


title: EXP1_COL06_ROW11

type: SRA

city: New York

first: Kemal

middle: Marc

last: Akat

state: NY

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

description:
exp1_counts.txt
exp1_spike_counts.txt

library_source: transcriptomic

data_processing:
Files were demultiplexed using Perl script mRNASeqHT_demultiplex.pl provided by Fluidigm
Demultiplexed FASTQ files were polyA trimmed using cutadapt (v 1.11)
polyA trimmed reads were aligned to the mouse genome using the STAR aligner (2.4.2a) allowing 2 mismatches and otherwise default parameters; if applicable, reads unmapped to the mouse genome were mapped to an ERCC spike-in reference using the BWA aligner (0.7.17-r1188) allowing 2 mismatches.
gene counting with featureCounts (1.5.1) counting multimappers fractionally
Genome_build: mm10

source_name: single-cell suspension from whole glomerulus, kidney

extract_protocol:
Glomerular cells were isolated by perfusing mice with PBS, followed by Dynabead solution and then 2 ml bead solution with enzymatic digestion buffer containing collagenase type II 300U/ml, Pronase E (1mg/ml) and DNase I (50μg/ml). Kidneys were then removed, decapsulated, minced into 1 mm3 pieces, and digested in 3 ml digestion buffer at 37°C for 15 minutes on a rotator (100 rpm). Digested tissue was then passed through a 100 μm cell strainer and collected by centrifugation. The pellet was resuspended in 2 ml of Hank's buffered salt solution and glomeruli were washed three times and collected using a magnet. Separated glomeruli were resuspended in 2 ml digestion buffer and incubated at 37°C for an additional 40 minutes rotating on a thermomixer. During the digestion period, the solution was vortexed every 10 minutes and sheared with a 27G needle every 15 minutes. The solution was then put on magnetic particle concentrator, and supernatants were pooled. The suspension was sieved through a 40 μm cell strainer and centrifuged at 1,500rpm for 5 minutes at 4°C.
RNA libraries were prepared for sequencing using version 2 of the Fluidigm C1 800-cell IFC protocol

tag: treatment

value: Control

tag: cell count

tag: genotype

value: Postnatal week 10


title: pEX0383_ME_8mer_10794

type: protein

city: Toronto

first: Samuel

last: Lambert

state: ON

address: 160 College St.

department: Donnelly Centre for Cellular and Biomolecular Research

country: Canada

institute: University of Toronto

hyb_protocol: After a 2-h incubation at 37oC, 12.5 ml of the mix was added to 137.5 ml of protein-binding solution for a final mix of PBS/2% skim milk/0.2 mg per ml BSA/50 μM zinc acetate/0.1% Tween-20. This mixture was added to an array previously blocked with PBS/2% skim milk and washed once with PBS/0.1% Tween-20 and once with PBS/0.01% Triton-X 100. After a 1-h incubation at room temperature, the array was washed once with PBS/0.5% Tween-20/50 mM zinc acetate and once with PBS/0.01% Triton-X 100/50 mM zinc acetate. Cy5-labeled anti-GST antibody was added, diluted in PBS/2% skim milk/50 mM zinc acetate. After a 1-h incubation at room temperature, the array was washed three times with PBS/0.05% Tween-20/50 mM zinc acetate and once with PBS/50 mMzinc acetate.

scan_protocol: The array was imaged using an Agilent microarray scanner at 2 mM resolution. Images were scanned at two power settings: 100% photomultiplier tube (PMT) voltage (high), and 10% PMT (low). The two resulting grid images were then manually examined, and the scan with the fewest number of saturated spots was used. Image spot intensities were quantified using ImaGene software (BioDiscovery).

data_processing: We provide several scores for each 8-mer in each experiment. The VALUE column contains the median intensity for the 8mer sequence. Z-Score – transformed kmer median intensity; E-score – Enrichment Score. E-scores are a modified version of AUC, and describe how well each kmer ranks the intensities of the spots. Please see the supplementary files on the platform record (GPL11260) to match the raw data files with the array probes.

molecule: protein

organism: synthetic construct

source_name: ANIA_09395, ME design

label_protocol: We used 150 ng of plasmid DNA in a 15 μl in vitro transcription/ translation reaction using a PURExpress In Vitro Protein Synthesis Kit (New England BioLabs) supplemented with RNase inhibitor and 50 μM zinc acetate.

extract_protocol: DBD sequences along with 50 amino acid residues on either side of the DBD in the native protein were cloned as AscI–SbfI fragments into pTH6838, a modified T7-driven GST expression vector.

value: ME


title: pEX0385_HK_8mer_10812

source_name: ANIA_01298, HK design

value: HLH

value: HK


title: pEX0384_HK_8mer_10988

source_name: ANIA_09516, HK design


title: pEX0381_ME_8mer_10792

source_name: ANIA_11818, ME design


title: EXP1_COL06_ROW07

description:
exp1_counts.txt
exp1_spike_counts.txt


title: BXD79 High Fat Diet_scWAT

description: Gene expression data

value: High fat


title: BXD75 Chow Diet_scWAT

description: Gene expression data


title: BXD75 High Fat Diet_scWAT

description: Gene expression data


title: BXD73 Chow Diet_scWAT

description: Gene expression data


title: BXD73 High Fat Diet_scWAT

description: Gene expression data


title: pEX0383_HK_8mer_10810

source_name: ANIA_09395, HK design


title: BXD71 High Fat Diet_scWAT

description: Gene expression data


title: pEX0379_ME_8mer_10790

source_name: ANIA_07661, ME design


title: pEX0380_HK_8mer_10807

source_name: ANIA_07788, HK design


title: EXP1_COL06_ROW05

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0378_ME_8mer_10789

source_name: ANIA_10976, ME design


title: EXP1_COL06_ROW06

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0378_HK_8mer_10805

source_name: ANIA_10976, HK design


title: EXP1_COL06_ROW04

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0377_ME_8mer_10788

source_name: ANIA_07553, ME design


title: pEX0384_ME_8mer_10795

source_name: ANIA_09516, ME design


title: pEX0381_HK_8mer_10808

source_name: ANIA_11818, HK design


title: pEX0376_HK_8mer_10803

source_name: ANIA_07508, HK design


title: pEX0377_HK_8mer_10804

source_name: ANIA_07553, HK design


title: EXP1_COL06_ROW02

description:
exp1_counts.txt
exp1_spike_counts.txt


title: BXD71 Chow Diet_scWAT

description: Gene expression data


title: BXD70 High Fat Diet_scWAT

description: Gene expression data


title: BXD69 High Fat Diet_scWAT

description: Gene expression data


title: BXD69 Chow Diet_scWAT

description: Gene expression data


title: pEX0376_ME_8mer_10787

source_name: ANIA_07508, ME design


title: BXD70 Chow Diet_scWAT

description: Gene expression data

source_name: Mouse subcutaneous white adipose tissue


title: pEX0374_ME_8mer_10785

source_name: ANIA_06998, ME design


title: pEX0373_ME_8mer_10784

source_name: ANIA_10912, ME design


title: pEX0373_HK_8mer_10800

source_name: ANIA_10912, HK design


title: EXP1_COL05_ROW36

description:
exp1_counts.txt
exp1_spike_counts.txt

source_name: single-cell suspension from whole glomerulus, kidney


title: EXP1_COL05_ROW35

description:
exp1_counts.txt
exp1_spike_counts.txt


title: BXD68 Chow Diet_scWAT

description: Gene expression data


title: EXP1_COL06_ROW03

description:
exp1_counts.txt
exp1_spike_counts.txt


title: BXD66 High Fat Diet_scWAT

description: Gene expression data


title: BXD68 High Fat Diet_scWAT

description: Gene expression data


title: pEX0374_HK_8mer_10801

source_name: ANIA_06998, HK design


title: pEX0300_HK_8mer_10562

source_name: ANIA_02672, HK design


title: EXP1_COL05_ROW22

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0304_ME_8mer_10015

source_name: ANIA_07592, ME design


title: EXP1_COL05_ROW39

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0379_HK_8mer_10806

source_name: ANIA_07661, HK design


title: pEX0299_HK_8mer_9827

source_name: ANIA_02725, HK design


title: pEX0299_ME_8mer_9855

source_name: ANIA_02725, ME design


title: BXD66 Chow Diet_scWAT

description: Gene expression data


title: BXD65 Chow Diet_scWAT

description: Gene expression data


title: pEX0298_HK_8mer_9864

source_name: ANIA_02785, HK design


title: pEX0305_ME_8mer_9817

source_name: ANIA_02122, ME design


title: pEX0296_ME_8mer_9998

source_name: ANIA_02839, ME design


title: pEX0306_HK_8mer_9866

source_name: ANIA_00937, HK design


title: pEX0306_ME_8mer_9850

source_name: ANIA_00937, ME design


title: pEX0298_ME_8mer_9848

source_name: ANIA_02785, ME design


title: pEX0295_ME_8mer_9997

source_name: ANIA_03050, ME design


title: EXP1_COL05_ROW15

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0305_HK_8mer_9833

source_name: ANIA_02122, HK design


title: EXP1_COL05_ROW23

description:
exp1_counts.txt
exp1_spike_counts.txt


title: BXD62 High Fat Diet_scWAT

description: Gene expression data

source_name: Mouse subcutaneous white adipose tissue


title: EXP1_COL05_ROW18

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW13

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0295_HK_8mer_10560

source_name: ANIA_03050, HK design


title: EXP1_COL05_ROW20

description:
exp1_counts.txt
exp1_spike_counts.txt

source_name: single-cell suspension from whole glomerulus, kidney


title: EXP1_COL05_ROW17

description:
exp1_counts.txt
exp1_spike_counts.txt


title: BXD63 Chow Diet_scWAT

description: Gene expression data


title: BXD64 High Fat Diet_scWAT

description: Gene expression data


title: pEX0300_ME_8mer_9999

source_name: ANIA_02672, ME design


title: BXD65 High Fat Diet_scWAT

description: Gene expression data


title: pEX0296_HK_8mer_10561

source_name: ANIA_02839, HK design


title: pEX0287_ME_8mer_9788

source_name: ANIA_02553, ME design


title: pEX0292_ME_8mer_9809

source_name: ANIA_03217, ME design


title: BXD62 Chow Diet_scWAT

description: Gene expression data


title: BXD64 Chow Diet_scWAT

description: Gene expression data


title: BXD63 High Fat Diet_scWAT

description: Gene expression data


title: pEX0286_ME_8mer_9787

source_name: ANIA_02422, ME design


title: pEX0289_ME_8mer_9790

source_name: ANIA_11169, ME design


title: EXP1_COL05_ROW12

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0283_ME_8mer_9785

source_name: ANIA_10295, ME design


title: pEX0292_HK_8mer_9825

source_name: ANIA_03217, HK design


title: pEX0289_HK_8mer_9806

source_name: ANIA_11169, HK design


title: EXP1_COL05_ROW10

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0287_HK_8mer_9804

source_name: ANIA_02553, HK design


title: pEX0380_ME_8mer_10791

source_name: ANIA_07788, ME design


title: pEX0279_ME_8mer_9782

source_name: ANIA_01848, ME design


title: EXP1_COL05_ROW03

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0283_HK_8mer_9801

source_name: ANIA_10295, HK design


title: EXP1_COL05_ROW04

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0286_HK_8mer_9803

source_name: ANIA_02422, HK design


title: EXP1_COL05_ROW07

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0279_HK_8mer_9798

source_name: ANIA_01848, HK design


title: pEX0277_ME_8mer_9780

source_name: ANIA_01812, ME design


title: pEX0278_HK_8mer_9797

source_name: ANIA_01824, HK design


title: pEX0278_ME_8mer_9781

source_name: ANIA_01824, ME design


title: pEX0277_HK_8mer_9796

source_name: ANIA_01812, HK design


title: pEX0275_ME_8mer_9778

source_name: ANIA_01729, ME design


title: EXP1_COL04_ROW33

description:
exp1_counts.txt
exp1_spike_counts.txt

source_name: single-cell suspension from whole glomerulus, kidney


title: pEX0274_HK_8mer_9793

source_name: ANIA_01705, HK design


title: BXD55 Chow Diet_scWAT

description: Gene expression data

source_name: Mouse subcutaneous white adipose tissue


title: EXP1_COL04_ROW35

description:
exp1_counts.txt
exp1_spike_counts.txt


title: BXD61 High Fat Diet_scWAT

description: Gene expression data


title: EXP1_COL05_ROW01

description:
exp1_counts.txt
exp1_spike_counts.txt


title: BXD55 High Fat Diet_scWAT

description: Gene expression data


title: BXD60 Chow Diet_scWAT

description: Gene expression data


title: BXD51 High Fat Diet_scWAT

description: Gene expression data


title: BXD51 Chow Diet_scWAT

description: Gene expression data


title: BXD61 Chow Diet_scWAT

description: Gene expression data


title: pEX0275_HK_8mer_9794

source_name: ANIA_01729, HK design


title: pEX0274_ME_8mer_9777

source_name: ANIA_01705, ME design


title: BXD56 Chow Diet_scWAT

description: Gene expression data


title: pEX0269_HK_8mer_9772

source_name: ANIA_01518, HK design


title: EXP1_COL04_ROW22

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0273_ME_8mer_9776

source_name: ANIA_01678, ME design


title: pEX0268_ME_8mer_9755

source_name: ANIA_10192, ME design


title: pEX0273_HK_8mer_9792

source_name: ANIA_01678, HK design


title: EXP1_COL04_ROW29

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW27

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0269_ME_8mer_9756

source_name: ANIA_01518, ME design


title: EXP1_COL04_ROW21

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW20

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0267_ME_8mer_9754

source_name: ANIA_08902, ME design


title: pEX0268_HK_8mer_9771

source_name: ANIA_10192, HK design


title: pEX0263_ME_8mer_9750

source_name: ANIA_08978, ME design


title: pEX0267_HK_8mer_9770

source_name: ANIA_08902, HK design


title: pEX0261_HK_8mer_9764

source_name: ANIA_09047, HK design


title: pEX0263_HK_8mer_9766

source_name: ANIA_08978, HK design


title: pEX0261_ME_8mer_9748

source_name: ANIA_09047, ME design


title: BXD50 High Fat Diet_scWAT

description: Gene expression data


title: EXP1_COL04_ROW17

description:
exp1_counts.txt
exp1_spike_counts.txt

source_name: single-cell suspension from whole glomerulus, kidney


title: BXD49 Chow Diet_scWAT

description: Gene expression data


title: pEX0258_ME_8mer_9693

source_name: ANIA_06846, ME design


title: pEX0258_HK_8mer_9709

source_name: ANIA_06846, HK design


title: EXP1_COL04_ROW18

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0259_HK_8mer_9710

source_name: ANIA_06849, HK design


title: EXP1_COL04_ROW15

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW14

description:
exp1_counts.txt
exp1_spike_counts.txt


title: BXD50 Chow Diet_scWAT

description: Gene expression data

source_name: Mouse subcutaneous white adipose tissue


title: BXD45 High Fat Diet_scWAT

description: Gene expression data


title: EXP1_COL04_ROW13

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0256_HK_8mer_9644

source_name: ANIA_06790, HK design


title: EXP1_COL04_ROW12

description:
exp1_counts.txt
exp1_spike_counts.txt


title: BXD48 Chow Diet_scWAT

description: Gene expression data


title: BXD48 High Fat Diet_scWAT

description: Gene expression data


title: circ-sh2

city: Nanjing

first: shouyu

last: wang

address: 22 Hankou Road

country: China

institute: Nanjing university medical school

data_processing:
Solexa pipeline version 1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to HG19 whole genome using Hisat 2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Ballgown software. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: HG19
tab-delimited text files include RPKM values for each Sample (FPKM >= 0.5).
Supplementary_files_format_and_content: FPKM

organism: Homo sapiens

source_name: breast cancer cells

growth_protocol: The cells cultured in DMEM medium. The media were supplemented with 10% fetal bovine serum (FBS). Cultures were incubated at 37°C in a humidified chamber with 5% CO2.

extract_protocol:
Total RNA extracted using RNeasy Plus Mini Kit with QIAshredder columns (Qiagen) following manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: MDA-MB-231 lung metastatic cells LM2


title: pEX0256_ME_8mer_9628

source_name: ANIA_06790, ME design


title: BXD49 High Fat Diet_scWAT

description: Gene expression data


title: circ-sh1


title: pEX0255_HK_8mer_9643

source_name: ANIA_06788, HK design


title: EXP1_COL04_ROW11

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW10

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0253_ME_8mer_9625

source_name: ANIA_06747, ME design


title: pEX0252_HK_8mer_10987

source_name: ANIA_06062, HK design


title: EXP1_COL04_ROW09

description:
exp1_counts.txt
exp1_spike_counts.txt


title: BXD44 Chow Diet_scWAT

description: Gene expression data


title: BXD44 High Fat Diet_scWAT

description: Gene expression data


title: BXD43 High Fat Diet_scWAT

description: Gene expression data


title: BXD43 Chow Diet_scWAT

description: Gene expression data


title: pEX0252_ME_8mer_9624

source_name: ANIA_06062, ME design


title: pEX0251_ME_8mer_9623

source_name: ANIA_06173, ME design


title: WtSau_2

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence.
Trimmed reads were aligned to reference genome using Tophat.
Read count estimates per gene were obtained using HTSeq.
Genome_build: WBcel235 (Ensembl release 67)
Supplementary_files_format_and_content: *.count: Tab-delimited text files include count values for each sample.

organism: Caenorhabditis elegans

source_name: WT

growth_protocol: Animals were synchronized using hypochlorite solution and eggs were plated on NGM plates seeded with OP50 until they reached L4/young adult stage (approximately 48 hours).

extract_protocol:
RNA was extracted using Trizol and purified using Qiagen RNeasy columns. RNA samples were processed for RNA-seq analysis at Novogene Inc.
RNA-seq libraries were generated via polyA+ selection of mRNA from total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina).

treatment_protocol: Synchronized L4/young adult animals were harvested with M9 buffer and plated on either OP50 plates or infection plates seeded with S. aureus for 4 hours. Animals were then harvested again, washed twice with M9 buffer, and pellets were flash frozen in liquid nitrogen.

tag: genotype/variation

value: WT

tag: developmental stage

value: L4-young adult

value: whole body

value: Staphylococcus aureus (MW2)


title: WtSau_3


title: pEX0250_ME_8mer_9622

source_name: ANIA_10789, ME design


title: pEX0251_HK_8mer_9639

source_name: ANIA_06173, HK design


title: pEX0254_ME_8mer_9626

source_name: ANIA_06762, ME design


title: BXD45 Chow Diet_scWAT

description: Gene expression data


title: pEX0259_ME_8mer_9694

source_name: ANIA_06849, ME design


title: WtSau_1


title: pEX0250_HK_8mer_9638

source_name: ANIA_10789, HK design


title: pEX0253_HK_8mer_9641

source_name: ANIA_06747, HK design


title: EXP1_COL04_ROW04

description:
exp1_counts.txt
exp1_spike_counts.txt

source_name: single-cell suspension from whole glomerulus, kidney


title: pEX0254_HK_8mer_9642

source_name: ANIA_06762, HK design


title: pEX0246_ME_8mer_9596

source_name: ANIA_06430, ME design


title: WtOP50_3

value: Escherichia coli OP50


title: con-sh

source_name: breast cancer cells


title: EXP1_COL04_ROW02

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL03_ROW40

description:
exp1_counts.txt
exp1_spike_counts.txt


title: AAKSau_3

value: aak-1; aak-2


title: WtOP50_2


title: pEX0245_ME_8mer_9595

source_name: ANIA_11099, ME design


title: pEX0244_ME_8mer_9594

source_name: ANIA_11093, ME design


title: EXP1_COL03_ROW38

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0242_ME_8mer_9592

source_name: ANIA_08655, ME design


title: pEX0242_HK_8mer_9608

source_name: ANIA_08655, HK design


title: pEX0244_HK_8mer_9610

source_name: ANIA_11093, HK design


title: pEX0245_HK_8mer_9611

source_name: ANIA_11099, HK design


title: pEX0241_ME_8mer_9591

source_name: ANIA_10541, ME design


title: EXP1_COL03_ROW36

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL03_ROW37

description:
exp1_counts.txt
exp1_spike_counts.txt


title: AAKSau_1


title: pEX0241_HK_8mer_9607

source_name: ANIA_10541, HK design


title: pEX0246_HK_8mer_9612

source_name: ANIA_06430, HK design


title: AAKSau_2


title: pEX0239_HK_8mer_9605

source_name: ANIA_10550, HK design


title: pEX0239_ME_8mer_9589

source_name: ANIA_10550, ME design


title: WtOP50_1

source_name: WT


title: EXP1_COL03_ROW35

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL05_ROW09

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0237_ME_8mer_9567

source_name: ANIA_04524, ME design


title: pEX0237_HK_8mer_9583

source_name: ANIA_04524, HK design


title: EXP1_COL03_ROW34

description:
exp1_counts.txt
exp1_spike_counts.txt

source_name: single-cell suspension from whole glomerulus, kidney


title: AAKOP_2


title: pEX0236_ME_8mer_9566

source_name: ANIA_04562, ME design


title: EXP1_COL03_ROW33

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0231_HK_8mer_9580

source_name: ANIA_03835, HK design


title: pEX0236_HK_8mer_9582

source_name: ANIA_04562, HK design


title: AAKOP_3


title: pEX0235_ME_8mer_9587

source_name: ANIA_04606, ME design


title: AAKOP_1


title: pEX0235_HK_8mer_9603

source_name: ANIA_04606, HK design


title: pEX0228_ME_8mer_9562

source_name: ANIA_03911, ME design


title: pEX0234_HK_8mer_9581

source_name: ANIA_04933, HK design


title: pEX0228_HK_8mer_9578

source_name: ANIA_03911, HK design


title: pEX0227_ME_8mer_9561

source_name: amdR, ME design


title: pEX0227_HK_8mer_9577

source_name: amdR, HK design


title: pEX0231_ME_8mer_9564

source_name: ANIA_03835, ME design


title: EXP1_COL03_ROW27

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL04_ROW05

description:
exp1_counts.txt
exp1_spike_counts.txt


title: cNSC-WT_Cntrl_Rep3

city: San Francisco

first: Tomasz

last: Nowakowski

state: Ca

institute: UCSF

description: Pnky(+/+) Cntrl Rep3

data_processing:
For NSC culture RNA-seq, reads were psuedoaligned to Genocde GRCm38.p5 mouse transriptome with kallisto v0.43.0 using 100 bootstrap replications. DESeq2 was used to perform differential expression analysis.
Genome_build: mouse mm10, Gencode GRCm38.p5 mouse transriptome

molecule: polyA RNA

source_name: cultured cortical NSCs

growth_protocol: Acutely dissected cortical NSCs cultured with media containing EGF/FGF.

extract_protocol:
Total RNA was isolated by Trizol (Life Technologies), purified using Direct-zol (Zymo) kit with on-column DNAse treatment.
Strand-specific, poly(A) selected cDNA libraries were generated using TruSeq Stranded mRNA kit (Illumina, #20020594).

value: cultured cortical neural stem cells (NSCs)

value: Derived from embryonic day 12.5

value: Pnky(+/+) Cntrl


title: cNSC-FF_Cre_Rep3

description: Pnky(fl/fl) +Ad:Cre Rep3

value: Pnky(fl/fl) +Ad:Cre


title: pEX0234_ME_8mer_9565

source_name: ANIA_04933, ME design


title: EXP1_COL03_ROW31

description:
exp1_counts.txt
exp1_spike_counts.txt

value: Control


title: cNSC-WT_Cre_Rep3

description: Pnky(+/+) +Ad:Cre Rep3

value: Pnky(+/+) +Ad:Cre


title: cNSC-FF_Cntrl_Rep3

description: Pnky(fl/fl) Cntrl Rep3

value: Pnky(fl/fl) Cntrl


title: EXP1_COL03_ROW32

description:
exp1_counts.txt
exp1_spike_counts.txt

value: Postnatal week 10


title: cNSC-BAC_Cre_Rep3

description: Pnky(fl/fl);BAC-Pnky +Ad:Cre Rep3

value: Pnky(fl/fl);BAC-Pnky +Ad:Cre


title: pEX0225_HK_8mer_9575

source_name: ANIA_04175, HK design

value: HK


title: EXP1_COL03_ROW25

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0223_HK_8mer_9573

source_name: ANIA_07923, HK design


title: pEX0223_ME_8mer_9557

source_name: ANIA_07923, ME design

value: ME


title: cNSC-BAC_Cntrl_Rep3

description: Pnky(fl/fl);BAC-Pnky Cntrl Rep3

value: Pnky(fl/fl);BAC-Pnky Cntrl


title: pEX0222_ME_8mer_9556

source_name: ANIA_07921, ME design


title: EXP1_COL03_ROW29

description:
exp1_counts.txt
exp1_spike_counts.txt

source_name: single-cell suspension from whole glomerulus, kidney


title: EXP1_COL03_ROW22

description:
exp1_counts.txt
exp1_spike_counts.txt


title: cNSC-WT_Cre_Rep2

description: Pnky(+/+) +Ad:Cre Rep2


title: EXP1_COL03_ROW20

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0218_ME_8mer_9552

source_name: ANIA_10670, ME design


title: pEX0225_ME_8mer_9559

source_name: ANIA_04175, ME design


title: pEX0215_ME_8mer_9533

source_name: ANIA_05609, ME design


title: EXP1_COL03_ROW15

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL03_ROW14

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL03_ROW23

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL03_ROW13

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0218_HK_8mer_9568

source_name: ANIA_10670, HK design


title: pEX0213_ME_8mer_9531

source_name: ANIA_05220, ME design


title: GFP_1371

city: Morgantown

first: Roberta

last: Leonardi

state: WV

address: 1 Medical Center Drive

institute: West Virginia University

data_processing:
Read quality was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc) and deemed to require no trimming
The reads were quantified using Salmon (Patro, R., Duggal, G., Love, M. I., Irizarry, R. A., and Kingsford, C., 2017, Nature methods 14, 417-419) with transcripts obtained from ensemble, version GRCm38.84
Using tximport (Soneson, C., Love, M. I., and Robinson, M. D., 2015, F1000Res 4, 1521) the data was imported into R and differential expression was computing using DESeq2 (Love, M. I., Huber, W., and Anders, S., 2014, Genome Biol 15, 550)
Genome_build: Ensembl, version GRCm38.84
Supplementary_files_format_and_content: sf.txt files produced by salmon give a list of Ensembl transcript IDs with TPM and estimated number of counts.

extract_protocol:
Livers were removed, flash frozen in liquid nitrogen and stored at -80 C until processed. RNA was extracted using Trizol reagent.
Libraries were built using 500 ng of RNA as input material for the stranded mRNA library preparation kit from KAPA Biosystems following the manufacturer’s recommended protocol with 9 cycles of PCR

treatment_protocol: 8-week-old C57BL/6J mice were injected with 2.5*10^11 particles of adeno-associated virus carrying mouse Nudt7 or GFP in 150 µl of sterile phosphate buffered saline via tail vein. Liver samples were collected 3-4 weeks after the injection from mice that were fasted for 24 h

value: 11-12 weeks

tag: transgene expressed

value: GFP

tag: nutritional status

value: 24h fasted

value: Liver


title: GFP_1369


title: pEX0215_HK_8mer_9549

source_name: ANIA_05609, HK design


title: GFP_1343


title: pEX0213_HK_8mer_9547

source_name: ANIA_05220, HK design


title: GFP_1347


title: pEX0222_HK_8mer_9572

source_name: ANIA_07921, HK design


title: pEX0212_ME_8mer_9530

source_name: ANIA_08535, ME design


title: Nudt7_2305

value: mouse Nudt7


title: EXP1_COL03_ROW09

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL03_ROW08

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0212_HK_8mer_9546

source_name: ANIA_08535, HK design


title: cNSC-WT_Cntrl_Rep2

description: Pnky(+/+) Cntrl Rep2

source_name: cultured cortical NSCs

value: cultured cortical neural stem cells (NSCs)


title: cNSC-FF_Cre_Rep2

description: Pnky(fl/fl) +Ad:Cre Rep2

value: Derived from embryonic day 12.5


title: Nudt7_1357


title: pEX0210_ME_8mer_9528

source_name: ANIA_08506, ME design


title: EXP1_COL03_ROW11

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL03_ROW06

description:
exp1_counts.txt
exp1_spike_counts.txt


title: cNSC-FF_Cre_Rep1

description: Pnky(fl/fl) +Ad:Cre Rep1


title: EXP1_COL03_ROW05

description:
exp1_counts.txt
exp1_spike_counts.txt


title: cNSC-WT_Cntrl_Rep1

description: Pnky(+/+) Cntrl Rep1

value: Pnky(+/+) Cntrl


title: Nudt7_1359


title: cNSC-FF_Cntrl_Rep2

description: Pnky(fl/fl) Cntrl Rep2


title: Nudt7_1365


title: EXP1_COL03_ROW04

description:
exp1_counts.txt
exp1_spike_counts.txt


title: cNSC-BAC_Cre_Rep1

description: Pnky(fl/fl);BAC-Pnky +Ad:Cre Rep1


title: pEX0210_HK_8mer_9544

source_name: ANIA_08506, HK design


title: pEX0208_ME_8mer_9526

source_name: ANIA_08391, ME design


title: cNSC-BAC_Cntrl_Rep2

description: Pnky(fl/fl);BAC-Pnky Cntrl Rep2


title: cNSC-BAC_Cre_Rep2

description: Pnky(fl/fl);BAC-Pnky +Ad:Cre Rep2


title: pEX0208_HK_8mer_9542

source_name: ANIA_08391, HK design


title: EXP1_COL03_ROW03

description:
exp1_counts.txt
exp1_spike_counts.txt


title: cNSC-BAC_Cntrl_Rep1

description: Pnky(fl/fl);BAC-Pnky Cntrl Rep1


title: pEX0255_ME_8mer_9627

source_name: ANIA_06788, ME design


title: Emx1-Cre-Pnky-cKO-Rep3

description: Pnky(fl/fl);Emx1-Cre Rep3 (litter 5)

data_processing:
For Emx1-Cre RNA-seq, reads were aligned to mm10 by Hisat2 and FeatureCounts was used to summarize gene abundance. DESeq2 was used to perform differential expression analysis.
Genome_build: mouse mm10, Gencode GRCm38.p5 mouse transriptome

source_name: acutely dissected cortex

value: acutely dissected cortex


title: EXP1_COL02_ROW39

description:
exp1_counts.txt
exp1_spike_counts.txt

source_name: single-cell suspension from whole glomerulus, kidney

value: Control


title: cNSC-FF_Cntrl_Rep1

description: Pnky(fl/fl) Cntrl Rep1


title: pEX0204_HK_8mer_9538

source_name: ANIA_00568, HK design


title: pEX0203_HK_8mer_9537

source_name: ANIA_10105, HK design


title: EXP1_COL02_ROW38

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL02_ROW36

description:
exp1_counts.txt
exp1_spike_counts.txt


title: Emx1-Cre-Pnky-cKO-Rep2

description: Pnky(fl/fl);Emx1-Cre Rep2 (litter 2)


title: pEX0202_ME_8mer_9520

source_name: ANIA_01368, ME design


title: flcn1

description: Biological replicate 1 of 4. Flcn-mutant.

hyb_protocol: The labeled cRNA was normalized at 1.65 µg, fragmented and hybridized to C. Elegans 4x44k oligonucleotide microarrays as per manufacturer's instructions.

scan_protocol: We used an Agilent Microarray Scanner System, an Agilent Scanner C type.

data_processing: Flexarray Software was used for background subtraction and normalization using the vsn algorithm.

source_name: flcn-1 L4-young adult animals

label_protocol: Cyanine 3-labeled CTP cRNA was produced from total RNA using the Low Input Quick Amp Labeling Kit, according to manufacturer’s instructions (Agilent Technologies, Inc).

growth_protocol: Synchronized Wt and flcn-1 animals were plated on OP50 plates and grown for 48 hours.

extract_protocol: RNA was extracted using Trizol and purified using Qiagen columns.

treatment_protocol: Synchronized animals grown on NGM OP50 plates were harvested at the L4 - young adult stage.

value: flcn

value: L4-young adult

value: whole body


title: flcn2

description: Biological replicate 2 of 4. Flcn-mutant.


title: Emx1-Cre-Control-Rep3

description: Cntrl Rep3 (litter 5)

value: Cntrl


title: EXP1_COL02_ROW34

description:
exp1_counts.txt
exp1_spike_counts.txt

value: Postnatal week 10


title: Emx1-Cre-Control-Rep2

description: Cntrl Rep2 (litter 2)


title: EXP1_COL02_ROW33

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL02_ROW40

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0204_ME_8mer_9522

source_name: ANIA_00568, ME design

value: ME


title: pEX0304_HK_8mer_10563

source_name: ANIA_07592, HK design

value: HK


title: pEX0202_HK_8mer_9536

source_name: ANIA_01368, HK design


title: Emx1-Cre-Control-Rep1

description: Cntrl Rep1 (litter 1)


title: pEX0201_ME_8mer_10544

source_name: ANIA_11222, ME design


title: EXP1_COL02_ROW32

description:
exp1_counts.txt
exp1_spike_counts.txt


title: wt2

description: Biological replicate 2 of 4. Wild-type.

source_name: Wild-type L4-young adult animals

value: WT


title: pEX0203_ME_8mer_9521

source_name: ANIA_10105, ME design


title: Emx1-Cre-Pnky-cKO-Rep1

description: Pnky(fl/fl);Emx1-Cre Rep1 (litter 1)


title: flcn4

description: Biological replicate 4 of 4. Flcn-mutant.


title: SAM24348567: Vemu Regressed

city: South San Francisco

first: Dorothee

last: Nickles

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Illumina v1.8 software used for basecalling
The number of reads for all ~700k possible cell barcodes were tallied and data demultiplexed for cell barcodes represented by at least 10k reads. Transcript reads were aligned to the reference genome GRCm38 using GSNAP version ‘2013-10-10’ (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1); only uniquely mapping reads were considered. The number of transcripts per gene was inferred based on the number of unique molecular identifiers (UMIs) per gene (for reads overlapping exons in sense orientation) allowing for one mismatch between UMI sequences to account for errors in sequencing or PCR amplification. After excluding cells with <300 UMIs and removing non-expressed features, data were further processed using the Seurat R package version 2.2.0. Subsequent to normalization using the “LogNormalize” setting, data were scaled based on the total number of UMIs per cell. Then a principle component (PC) analysis was run on the most variably expressed genes and the first 30 PCs were used to perform t-distributed statistical neighbor embedding (tSNE) analysis and density clustering.
For each sample the R1 file provides the barcode representing the cell and the R2 file provides the insert sequence
Genome_build: mm10

source_name: melanoma tumor

extract_protocol:
Samples were processed for single cell RNA sequencing (scRNAseq) using the Chromium Single Cell 3’ Library and Gel bead kit v2, following the manufacturer’s manual (10x Genomics, San Francisco, CA). Cell density and viability of the single-cell suspensions were determined by Vi-CELL XR cell counter (Beckman Coulter). All of the processed samples had very high percentage of viable cells. Cell density was used to impute the volume of single cell suspension needed in the reverse transcription (RT) master mix, aiming to achieve ~6,000 cells per sample. cDNAs and libraries were prepared following the manufacturer’s manual (10x Genomics, San Francisco, CA). Libraries were profiled by Bioanalyzer High Sensitivity DNA kit (Agilent Technologies, Santa Clara, CA) and quantified using Kapa Library Quantification Kit (Kapa Biosystems, Wilmington, MA). Each library was sequenced in one lane of HiSeq4000 (Illumina, San Diego, CA) following the manufacturer’s sequencing specification (10x Genomics, San Francisco, CA).
cDNAs and libraries were prepared according to manufacturer instructions (10× Genomics)

tag: background

value: Genetically engineered mouse model (GEMM) tumor


title: wt1

description: Biological replicate 1 of 4. Wild-type.


title: pEX0200_ME_8mer_9502

source_name: ANIA_07820, ME design


title: SAM24348329: Vemu Progressed


title: flcn3

description: Biological replicate 3 of 4. Flcn-mutant.


title: wt4

description: Biological replicate 4 of 4. Wild-type.


title: wt3

description: Biological replicate 3 of 4. Wild-type.


title: AS1842856  (Donor 11)

city: Paris

first: Marianne

last: Mangeney

address: rue Méchain

country: France

institute: CNRS/Inserm/Université Paris Descartes

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® ClariomS Human (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. Brain array CDF file V22 was used for annotation.

source_name: primary T lymphocytes treated with AS1842856 (Donor 11)

label_protocol: 250 ng of total RNA is reverse transcribed  following the Genechip Whole transcript (WTplus) Sense Target labelling assay kit (Affymetrix). Briefly, the resulting double strand cDNA is used for in vitro transcription with T7 RNA pol. This cRNA is reverse transcribed in single stranded sens DNA which is fragmented and biotin labelled

extract_protocol: Total RNA is purified from 10^7 cells with the RNeasy Mini Kit (Qiagen, #74104)

treatment_protocol: AS1842856 is a pharmacological FOXO1 inhibitor. To investigate the modification of gene expression patterns after FOXO1 inhibition in primary T lymphocytes, we treated 7 days peripheral blood T cells from 3 heathly donnors (8,10,11) with 500 nM AS1842856. cells were harvested and RNA was extracted and hybridized on Affymetrix microarrays.

tag: cell type

value: primary T lymphocytes

tag: donor id


title: EXP1_COL02_ROW26

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL02_ROW25

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0199_ME_8mer_9501

source_name: ANIA_11003, ME design


title: SAM24348328: Untreated


title: pEX0200_HK_8mer_9518

source_name: ANIA_07820, HK design


title: ChIP-H2AZ-rep2

city: ILLKIRCH-GRAFFENSTADEN

first: Christophe

last: Papin

address: 1 rue Laurent Fries

institute: IGBMC - CNRS UMR 7104 - Inserm U 964

library_source: genomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Adapter dimer reads were removed using DimerRemover v0.9.2.
Reads were mapped to the mouse genome (mm9) using Bowtie v1.0.0 with the following arguments: -m 1 --strata --best -y -S –l 40 -p 2.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b). Scores represent tag numbers per total uniquely mapped reads.

molecule: genomic DNA

source_name: skeletal muscle cells

extract_protocol:
Hind limbs muscles were collected and placed in tube with 4 ml of cold buffer A (300 mM sucrose, 10 mM NaCl, 1.5 mM MgCl2, 15 mM Tris HCl pH 8.0 and protease inhibitor cocktail (Sigma)). The tissue was first mince with scissor and then transfer in a dounce homogenizer where 50 strokes of the loose pestle was slowly applied.The extract was then passed through a 100 µm cell strainer to remove myofibrils debris and placed back into a clean cold dounce homogenizer. To release nuclei, NP-40 was added to a final concentration of 0.5% and incubated for 15 min at 4°C. An additional 50 strokes with the tight pestle is then applied. Lastly extract was further clarified by passing through a 40 µm cell strainer, centrifuged at 2000 g for 10 min at 4°C and was washed in cold buffer A. Nuclei were resuspended in a small volume of buffer A before ChIP or immunoblot analysis.
Libraries were prepared using the Diagenode MicroPlex Library Preparation kit v2.

value: skeletal muscle cells

tag: antibody

value: H2A-Z.1flox/flox :H2A-Z.2 flox/flox

value: 7 weeks-old


title: ChIP-H2AZ-rep1

tag: tissue


title: EXP1_COL02_ROW24

description:
exp1_counts.txt
exp1_spike_counts.txt

source_name: single-cell suspension from whole glomerulus, kidney


title: untreated  (Donor 11)

source_name: untreated primary T lymphocytes (Donor 11)


title: EXP1_COL02_ROW23

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL02_ROW30

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0197_ME_8mer_9499

source_name: ANIA_07516, ME design


title: pEX0199_HK_8mer_9517

source_name: ANIA_11003, HK design


title: untreated  (Donor 10)

source_name: untreated primary T lymphocytes (Donor 10)


title: EXP1_COL02_ROW19

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0197_HK_8mer_9515

source_name: ANIA_07516, HK design


title: EXP1_COL02_ROW21

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL02_ROW16

description:
exp1_counts.txt
exp1_spike_counts.txt


title: Control plasma exosomal miRNA [Z3]

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

institute: Renji Hospital

description:
small RNA
Z3

data_processing:
We use AASRA  to map clean reads to reference genome and other sRNA database, except Rfam which was performanced by using cmsearch
Genome_build: miRBase v20
Supplementary_files_format_and_content: RPKM-NB-exomalmiRNA.xls file includes RPKM values

source_name: Normal control

extract_protocol:
Total RNA of plasma exosomes was using Qiazol and RNeasy Minelute spin column following the manufacturer’s user guide.RNA concentration was determined using Nanodrop. The content and quality of exosomal RNAs were determined using the 2100 Bioanalyzer instrument.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: patient diagnosis

value: Normal control

value: plasma

tag: tissue compartment

value: exosome


title: Control plasma exosomal miRNA [Z1]

description:
small RNA
Z1


title: ChIP-Input-rep2

value: input

tag: strain


title: Control plasma exosomal miRNA [Z2]

description:
small RNA
Z2


title: ChIP-Input-rep1

tag: age


title: AS1842856  (Donor 10)

source_name: primary T lymphocytes treated with AS1842856 (Donor 10)


title: pEX0195_ME_8mer_9497

source_name: ANIA_07163, ME design


title: pEX0201_HK_8mer_10986

source_name: ANIA_11222, HK design


title: EXP1_COL02_ROW10

description:
exp1_counts.txt
exp1_spike_counts.txt

tag: treatment

value: Control


title: pEX0195_HK_8mer_9513

source_name: ANIA_07163, HK design


title: RNA-Muscle-Innerv-dKO-rep3

data_processing:
The libraries were sequenced on Illumina Hiseq 4000 sequencer as single-end 50 bp reads following Illumina's instructions.
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Adapter dimer reads were removed using DimerRemover v0.9.2.
Reads were mapped to the mouse genome (mm9) using Tophat v2.0.14 and Bowtie v2-2.1.0.
Quantification of gene expression was performed using HTSeq v0.6.1 and gene annotations from Ensembl release 67.
Genome_build: mm9
Supplementary_files_format_and_content: Processed expression data were summarized in one single Excel file containing the following informations for each sample: gene name/ensemble_gene_id/raw read count/normalized read count, and for each pairwise comparison: log2 fold change/p-value/p-value adjusted for multi-testing.

source_name: Mouse skeletal muscle cells

extract_protocol:
To extract total RNA, 500 µl of TRI Reagent (Sigma) was added to frozen tibialis anterior and homogenized with PreCellys (Bertin Technologies) (6500 RPM, 3 × 10 s) in tube containing ceramics beads (Lysing Matrix D – MP biomedicals). After centrifugation, TRI Reagent was removed and beads were washed one time with 500 µl of TRI reagent. Total RNA was then extracted following provider’s instruction.
Libraries of template molecules suitable for strand-specific high-throughput DNA sequencing were created using a TruSeq Stranded Total RNA with Ribo-Zero Gold Prep Kit (RS-122-2301; Illumina)

treatment_protocol: Section of the left sciatic nerve was used to induce denervation. Briefly, after the mice were anesthetized with an intraperitoneal injection of ketamine (100 mg.kg−1) and xylazine (10 mg.kg−1), the sciatic nerve was exposed in the thigh and doubly cut (5 mm apart) just distal to the sciatic notch. Contralateral muscles that were not operated on were used as controls. 48 hours post-denervation control and denervated tibialis anterior was collected and snap frozen in liquid nitrogen.

value: Control tibialis anterior


title: RNA-Muscle-Denerv-dKO-rep2

value: Denervated tibialis anterior


title: RNA-Muscle-Denerv-dKO-rep3


title: untreated  (Donor 8)

source_name: untreated primary T lymphocytes (Donor 8)


title: Patients plasma exosomal miRNA [N13]

description:
small RNA
N13

source_name: Patients

value: NB


title: RNA-Muscle-Denerv-dKO-rep1


title: EXP1_COL02_ROW14

description:
exp1_counts.txt
exp1_spike_counts.txt

tag: cell count

value: Postnatal week 10


title: AS1842856  (Donor 8)

source_name: primary T lymphocytes treated with AS1842856 (Donor 8)


title: pEX0194_ME_8mer_9496

source_name: ANIA_07170, ME design

value: HLH

value: ME


title: pEX0194_HK_8mer_9512

source_name: ANIA_07170, HK design

value: HK


title: Patients plasma exosomal miRNA [N14]

description:
small RNA
N14


title: RNA-Muscle-Innerv-dKO-rep2


title: EXP1_COL02_ROW09

description:
exp1_counts.txt
exp1_spike_counts.txt

source_name: single-cell suspension from whole glomerulus, kidney

tag: genotype


title: Patients plasma exosomal miRNA [N12]

description:
small RNA
N12

value: GNBi


title: RNA-Muscle-Denerv-WT-rep3

value: H2A-Z.1flox/flox :H2A-Z.2 flox/flox HSA Cre WT


title: RNA-Muscle-Innerv-dKO-rep1


title: EXP1_COL02_ROW20

description:
exp1_counts.txt
exp1_spike_counts.txt


title: Patients plasma exosomal miRNA [N15]

description:
small RNA
N15


title: EXP1_COL02_ROW07

description:
exp1_counts.txt
exp1_spike_counts.txt


title: Patients plasma exosomal miRNA [N10]

description:
small RNA
N10


title: pEX0189_ME_8mer_9491

source_name: ANIA_07223, ME design


title: pEX0189_HK_8mer_9507

source_name: ANIA_07223, HK design


title: pEX0193_HK_8mer_9511

source_name: ANIA_07189, HK design


title: RNA-Muscle-Denerv-WT-rep1


title: RNA-Muscle-Denerv-WT-rep2


title: EXP1_COL02_ROW06

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL02_ROW05

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0188_HK_8mer_9506

source_name: ANIA_07332, HK design


title: EXP1_COL02_ROW04

description:
exp1_counts.txt
exp1_spike_counts.txt


title: RNA-Muscle-Innerv-WT-rep2


title: Patients plasma exosomal miRNA [N9]

description:
small RNA
N9


title: EXP1_COL02_ROW03

description:
exp1_counts.txt
exp1_spike_counts.txt


title: Patients plasma exosomal miRNA [N8]

description:
small RNA
N8


title: RNA-Muscle-Innerv-WT-rep3


title: pEX0188_ME_8mer_9490

source_name: ANIA_07332, ME design


title: pEX0193_ME_8mer_9495

source_name: ANIA_07189, ME design


title: Patients plasma exosomal miRNA [N7]

description:
small RNA
N7


title: Patients plasma exosomal miRNA [N11]

description:
small RNA
N11


title: Patients plasma exosomal miRNA [N6]

description:
small RNA
N6


title: EXP1_COL02_ROW08

description:
exp1_counts.txt
exp1_spike_counts.txt


title: pEX0187_ME_8mer_9489

source_name: ANIA_07343, ME design


title: pEX0187_HK_8mer_9505

source_name: ANIA_07343, HK design


title: EXP1_COL02_ROW02

description:
exp1_counts.txt
exp1_spike_counts.txt


title: RNA-Muscle-Innerv-WT-rep1


title: Patients plasma exosomal miRNA [N5]

description:
small RNA
N5


title: EXP1_COL01_ROW39

description:
exp1_counts.txt
exp1_spike_counts.txt


title: Patients plasma exosomal miRNA [N3]

description:
small RNA
N3


title: Patients plasma exosomal miRNA [N4]

description:
small RNA
N4


title: EXP1_COL01_ROW36

description:
exp1_counts.txt
exp1_spike_counts.txt


title: EXP1_COL01_ROW24

description:
exp1_counts.txt
exp1_spike_counts.txt


title: yjw1864-tripleKO_starved_plusChx_mrna

first: Daniel

middle: A

last: Santos

address: 1700 4th Street

department: Cellular and Molecular Pharmacology

description: rRNA-depleted total RNA

data_processing:
Base calls were called with Illumina CASAVA software.
For RNA-seq libraries, reads were reverse-complemented and 3' adapter sequences (if present) were removed using FASTX-clipper.
For ribosome profiling libraries, 3' linker sequences were removed from reads and samples were de-multiplexed using FASTX-clipper and -barcode splitter, respectively.
Unique molecular identifiers (UMIs) and sample barcodes were removed from ribosome profiling reads using a custom Python script. UMIs were appended to the FASTQ header of each read immediately following the cluster y-coordinate (e.g. if UMI=AGTAG, header will resemble @K00153:418:HKMLHBBXX:1:1101:3437:1191_AGTAG ...).
Bowtie v1.1.2 was used to filter out reads aligning to S. cerevisiae rRNAs and tRNAs, and all surviving reads were aligned to the sacCer3 genome using tophat v2.1.1.
Counts per gene and normalized counts per gene (in reads per kilobase per million mapped reads, or RPKM) were calculated using the plastid cs program, with counts assigned to ribosomal P-sites determined by plastid’s psite program (for ribosome profiling) or assigned to the 5'-most aligned base (for RNA-seq). Regions of the genome that could not be uniquely mapped from a 26-base read with 2 mismatches were identified using plastid’s crossmap program, and these regions, along with the first 30 and last 5 codons of each coding sequence, were masked from RPKM calculations.
Genome_build: sacCer3
Supplementary_files_format_and_content: Tab delimited file containing count and RPKM data

organism: Saccharomyces cerevisiae

source_name: yeast cell lysate

extract_protocol:
Cells were cryogenically pulverized and lysates were clarified by centrifugation. A portion of the lysate was treated with RNase I and then subjected to ultracentrifugation for ribosome profiling. RNA was purified from monosome pellets (ribosome profiling) or clarified lysate (RNA-seq) using TRIzol reagent
Ribosome profiling libraries were generated essentially as described in MGlincy, N.J. and Ingolia, N.T., 2017, Methods, 126:112–129 . RNA-seq libraries were generated from rRNA-depleted total RNA using an Illumina TruSeq stranded total RNA kit.

value: MATa dot6::LEU2 tod6::URA3 stb3::kanMX6 his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0

tag: condition

value: 20 min amino acid starvation

tag: cells pretreated with cycloheximide

value: TRUE


title: EXP1_COL01_ROW28

description:
exp1_counts.txt
exp1_spike_counts.txt


title: Patients plasma exosomal miRNA [N1]

description:
small RNA
N1


title: Patients plasma exosomal miRNA [N2]

description:
small RNA
N2


title: EXP1_COL01_ROW26

description:
exp1_counts.txt
exp1_spike_counts.txt


title: yjw1861-Pccw12-nop2_starved_plusChx_mrna

description: rRNA-depleted total RNA

value: MATa nop2::klNOP2 yhrcdelta14::PCCW12-NOP2::kanMX6 his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0


title: multiple myeloma cell line MM.1S_OTX015_0nM_72hr

city: Suzhou

first: Wenzhuo

last: Zhuang

state: Jiangsu

address: Ren Ai Road 199

department: Department of Cell Biology, School of Biology & Basic Medical Sciences

institute: Soochow University

description: Gene expression after 72hr in 0nM OTX015-exposured in MM.1S

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: multiple myeloma cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted by TRIZOL (Invitrogen, USA) according to the manufacturer’s instructions.

treatment_protocol: multiple myeloma cell lines were incubated for 72 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell line

value: MMIS

tag: gender

value: female


title: multiple myeloma cell line u266_OTX015_1.5uM_72hr

description: Gene expression after 72hr in 40nM OTX015-exposured in U266


title: yjw1861-Pccw12-nop2_replete_plusChx_mrna

description: rRNA-depleted total RNA

value: replete


title: multiple myeloma cell line MM.1S_OTX015_40nM_72hr

description: Gene expression after 72hr in 40nM OTX015-exposured in MM.1S


title: meso_obese_rep3

city: RTP

first: Benjamin

last: Buehrer

state: NC

address: 3200 East Hwy 54, Suite 100

institute: ZenBio, Inc.

description:
replicate 3
SAMPLE 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using Expression Analysis' proprietary Quantile Scrunch method

source_name: omental mesothelium

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

growth_protocol: Human adult mesothelial cells were seeded at subconfluence and allowed to grow to confluence using Mesothelial Growth Medium (ZenBio, Inc.) prior to harvesting for total RNA extraction.

extract_protocol: RNA was extracted with RLT buffer, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: No treatments

value: omental mesothelium

tag: bmi

tag: age avg

tag: donors


title: EXP1_COL01_ROW22

description:
exp1_counts.txt
exp1_spike_counts.txt

value: Control


title: EXP1_COL01_ROW20

description:
exp1_counts.txt
exp1_spike_counts.txt


title: meso_obese_rep2

description:
replicate 2
SAMPLE 5


title: yjw1864-tripleKO_replete_plusChx_mrna

description: rRNA-depleted total RNA


title: meso_lean_rep2

description:
replicate 2
SAMPLE 2


title: meso_obese_rep1

description:
replicate 1
SAMPLE 4


title: EXP1_COL01_ROW23

description:
exp1_counts.txt
exp1_spike_counts.txt


title: multiple myeloma cell line u266_OTX015_0nM_72hr

description: Gene expression after 72hr in 0nM OTX015-exposured in U266


title: meso_lean_rep3

description:
replicate 3
SAMPLE 3


title: EXP1_COL01_ROW18

description:
exp1_counts.txt
exp1_spike_counts.txt


title: multiple myeloma cell line 8226_OTX015_1600nM_72hr

description: Gene expression after 72hr in 1600nM OTX015-exposured in 8226

value: male


title: cNSC-WT_Cre_Rep1

description: Pnky(+/+) +Ad:Cre Rep1

source_name: cultured cortical NSCs

value: cultured cortical neural stem cells (NSCs)

tag: developmental stage

value: Derived from embryonic day 12.5

tag: genotype/variation

value: Pnky(+/+) +Ad:Cre


title: multiple myeloma cell line 8226_OTX015_0nM_72hr

description: Gene expression after 72hr in 0nM OTX015-exposured in 8226


title: yjw1863-Pnop2-gfp_replete_plusChx_mrna

description: rRNA-depleted total RNA

value: MATa yhrcdelta14::PNOP2-5'UTRADH1-EGFP-3'UTRADH1::kanMX6 his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0


title: yjw1863-Pnop2-gfp_starved_plusChx_mrna

description: rRNA-depleted total RNA


title: meso_lean_rep1

description:
replicate 1
SAMPLE 1

tag: tissue


title: yjw1862-Pnop2-nop2_starved_plusChx_mrna

description: rRNA-depleted total RNA

value: MATa nop2::klNOP2 yhrcdelta14::PNOP2-NOP2::kanMX6 his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0


title: ID 89, visit 4

city: OSLO

first: Mari

last: Myhrstad

address: Postboks 4, St. Olavs plass

department: Department of health

country: Norway

institute: Oslo and Akershus University College

description: wk 7

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

label_protocol: Labelled extracts were prepared using Illumina TotalPrep RNA Amplification Kit (Illumina Inc, CA 92122, USA).

extract_protocol: Total RNA was isolated from all PBMC samples using RNeasy mini kit (Qiagen) with lysis buffer added -mercaptoethanol according to the manufacturer’s instructions,  and stored at -80C. Quality control was performed with Agilent Bioanalyser.

value: F

value: Peripheral blood mononuclear cells

tag: n6 level tertiles (1=low, 2=middle, 3=high)

tag: n3 level tertiles (1=low, 2=middle, 3=high)

tag: sfa/pufa ratio tertiles (1=low, 2=middle, 3=high)


title: EXP1_COL01_ROW11

description:
exp1_counts.txt
exp1_spike_counts.txt

data_processing:
Files were demultiplexed using Perl script mRNASeqHT_demultiplex.pl provided by Fluidigm
Demultiplexed FASTQ files were polyA trimmed using cutadapt (v 1.11)
polyA trimmed reads were aligned to the mouse genome using the STAR aligner (2.4.2a) allowing 2 mismatches and otherwise default parameters; if applicable, reads unmapped to the mouse genome were mapped to an ERCC spike-in reference using the BWA aligner (0.7.17-r1188) allowing 2 mismatches.
gene counting with featureCounts (1.5.1) counting multimappers fractionally
Genome_build: mm10

tag: strain

tag: age

value: Postnatal week 10


title: ITGA6  positive keratinocytesfrom K14ΔNLef1 epidermis, biological rep3

city: London

first: Giacomo

last: Donati

address: Guy's Hospital, Great Maze Pond

country: United Kingdom

institute: King's College London

description: sorted bulge

hyb_protocol: Samples were hybridised to GeneChip Mouse Exon 1.0ST Arrays (Affymetrix) according to the FL-Ovationô cDNA Biotin Module V2 protocol (NuGEN Technologies). Arrays were washed and stained in the Affymetrix GeneChip Fluidics Station 450 using protocol FS450_0001.

scan_protocol: Affymetrix GeneChip Scanner 3000 with AGCC software

data_processing:
RMA normalistion via Affymetrix Power Tools (apt-1.12.0)
MoEx-1_0-st-v1.r2.pgf
MoEx-1_0-st-v1.r2.dt1.mm9.core.ps

source_name: ITGA6+ keratinocytes, K14ΔNLef1 epidermis, back skin

label_protocol: cDNA synthesis and amplification was performed using the WT-Ovationô Pico RNA Amplification System (NuGEN Technologies). PolyA controls (Affymetrix, part no. 900433) were included at the same concentration as the sample. Sense transcript cDNA was then obtained using the WT-Ovationô Exon Module (NuGEN Technologies). Sense transcript cDNA was fragmented and labelled using the FL-Ovationô cDNA Biotin Module V2 (NuGEN Technologies).

growth_protocol: unfractionated and sorted epidermal cells  (back skin) from wild type mice and K14ΔNLef1

extract_protocol: After FACS sorting, RNA was extracted according to Rnaeasy micro kit (qiagen)

treatment_protocol: not applicable

tag: cell type

value: ITGA6+ keratinocytes

value: epidermis, back skin


title: ID 9, visit 4

description: wk 7


title: EXP1_COL01_ROW17

description:
exp1_counts.txt
exp1_spike_counts.txt

extract_protocol:
Glomerular cells were isolated by perfusing mice with PBS, followed by Dynabead solution and then 2 ml bead solution with enzymatic digestion buffer containing collagenase type II 300U/ml, Pronase E (1mg/ml) and DNase I (50μg/ml). Kidneys were then removed, decapsulated, minced into 1 mm3 pieces, and digested in 3 ml digestion buffer at 37°C for 15 minutes on a rotator (100 rpm). Digested tissue was then passed through a 100 μm cell strainer and collected by centrifugation. The pellet was resuspended in 2 ml of Hank's buffered salt solution and glomeruli were washed three times and collected using a magnet. Separated glomeruli were resuspended in 2 ml digestion buffer and incubated at 37°C for an additional 40 minutes rotating on a thermomixer. During the digestion period, the solution was vortexed every 10 minutes and sheared with a 27G needle every 15 minutes. The solution was then put on magnetic particle concentrator, and supernatants were pooled. The suspension was sieved through a 40 μm cell strainer and centrifuged at 1,500rpm for 5 minutes at 4°C.
RNA libraries were prepared for sequencing using version 2 of the Fluidigm C1 800-cell IFC protocol

tag: treatment

tag: cell count

tag: genotype


title: EXP1_COL01_ROW38

description:
exp1_counts.txt
exp1_spike_counts.txt


title: ITGA6  positive keratinocytesfrom K14ΔNLef1 epidermis, biological rep2

description: sorted bulge


title: ITGA6  positive keratinocytesfrom K14ΔNLef1 epidermis, biological rep1

description: sorted bulge


title: ID 88, visit 4

description: wk 7

value: M


title: yjw1862-Pnop2-nop2_replete_plusChx_mrna

description: rRNA-depleted total RNA

tag: condition

tag: cells pretreated with cycloheximide

value: TRUE


title: ITGA6  positive keratinocytes from wild type epidermis, biological rep3

description: sorted bulge

source_name: ITGA6+ keratinocytes, wild type epidermis, back skin

tag: gender

value: female

value: wild type


title: ITGA6  positive keratinocytes from wild type epidermis, biological rep2

description: sorted bulge


title: EXP1_COL01_ROW09

description:
exp1_counts.txt
exp1_spike_counts.txt


title: by4741_starved_minusChx_mrna

description: rRNA-depleted total RNA

value: MATa his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0

value: 20 min amino acid starvation

value: FALSE


title: EXP1_COL01_ROW08

description:
exp1_counts.txt
exp1_spike_counts.txt

value: Control


title: by4741_starved_plusChx_mrna

description: rRNA-depleted total RNA


title: EXP1_COL01_ROW06

description:
exp1_counts.txt
exp1_spike_counts.txt


title: ITGA6  positive keratinocytes from wild type epidermis, biological rep1

description: sorted bulge


title: EXP1_COL01_ROW02

description:
exp1_counts.txt
exp1_spike_counts.txt


title: by4741_replete_minusChx_mrna

description: rRNA-depleted total RNA

value: replete


title: by4741_replete_plusChx_mrna

description: rRNA-depleted total RNA


title: ID 81, visit 4

description: wk 7


title: Br7_7

city: Zurich

first: Francesc

last: Castro-Giner

address: Otto-Stern-Weg 7

institute: ETH Zurich

data_processing:
Basecalls performed using CASAVA version 1.4
Trim Galore (v0.4.2; parameters : --phred33 --length 36 --clip_R1 9).
Mapping using STAR (v 2.5.2a; parameters: --runMode alignReads --genomeLoad LoadAndExit) to a combined human (GRCh38) and mouse (GRCm38) genome reference
The gene-level expression counts computed with featureCounts (v1.5.1) using the gene annotations obtained from RefSeq (release 70).
To normalize gene counts for cell-specific biases, we used size factors computed utilizing the deconvolution strategy developed by Lun et al. (2016) implemented in the scran (v1.6.5) package available on R/Bioconductor
Genome_build: GRCh38 and GRCm38
Supplementary_files_format_and_content: raw_counts.txt.gz are tab-delimited files containing the gene counts as obtained from featureCounts; processed_normalized_matrix_hs.txt.gz and processed_normalized_matrix_mm.txt.gz contain normalized counts for human and mouse, respectively, using the method implemented in scran R/bioconductor package; sce_hs.rds.gz and sce_mm.rds.gz are R Data Format files containing a SingleCellExperiment class object for human and mouse, respectively.

extract_protocol:
Individual cells from CTC-WBC-clusters were mechanically separated with gentle micromanipulation (CellCelector, ALS). AF488/FITC-positive (or GFP-positive) and BV605-negative CTCs or AF488/FITC-negative and BV605-positive WBCs were immediately transferred into individual tubes (#321-032-501, Axygen) containing 2.5 μl RLT Plus lysis buffer (#1053393, Qiagen) and 1U/μl SUPERase In RNase Inhibitor (#AM2694, Invitrogen). Samples were immediately frozen on dry ice and kept at -80°C until further processing
Libraries were prepared with Smart -Seq2 protocol

tag: origin

value: patient

tag: number of cells

tag: number of ctc

tag: number of wbc attached

tag: sample type

value: CTC-cluster

value: CTC

tag: ctc-cluster size

tag: ctc-cluster id

tag: sample cell type

tag: sample cell type cat

tag: mouse type

tag: donor


title: CD34 ITGA6 double positive keratinocytesfrom K14ΔNLef1 epidermis, biological rep3

description: sorted basal

source_name: CD34+ ITGA6+ keratinocytes, K14ΔNLef1 epidermis, back skin

tag: cell type

value: CD34+ ITGA6+ keratinocytes

tag: tissue


title: Br7_4

value: CTC-single


title: Br61_CTC___46


title: cenpk_ymc_16_plusChx_mrna

description: rRNA-depleted total RNA

tag: strain

tag: genotype

value: MATa

value: YMC  time point 16


title: hmcn_2

city: Cambridge

first: Peter

middle: W

last: Reddien

state: MA

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

data_processing:
Basecalling was performed by Illumina CASAVA 1.9
Sequenced were quality trimmed using cutadapt v1.8 with parameteres -m 20 -q 30,30 and mapped to the ddv4 transcriptome using Bowtie v1.2.2 with parameter --best.
Raw read counts were generated with Samtools v1.9 idxstats and transcripts from different isoforms were summed (sum of counts for dd_v6_Smed_XXX_Y_Z for all Z)
Differential expression was determined with DESeq2 v1.2.2 using R 3.4.4
Genome_build: Dresden S. mediterranea Transcriptome Assembly (ddv6, http://planmine.mpi-cbg.de/ ) (Brandl et al, Nucleic Acids Res 2016)
Supplementary_files_format_and_content: Tab-separated text files

organism: Schmidtea mediterranea

source_name: tail fragment

growth_protocol: Standard planarian culture conditions

extract_protocol:
Total RNA extracted from tail fragments with TriZOL reagent with 5 tails per replicate. Tissue was homogenized with TissueLyser II at 30.0 Hz for 30 sec and an extra 1:1 chloroform extractation was performed to removed excess phenol. RNA was quantified by Qubit and Agilent Bioanalyser.
Kapa Stranded mRNA-Seq Kit Illumina Platform (Kapa Biosystems)

treatment_protocol: Animals fed in-vitro transcribed dsRNA mixed with liver 4 times over 13 days.

value: tail fragment

tag: RNAi

tag: RNAi feedings


title: hmcn_3


title: cenpk_ymc_15_plusChx_mrna

description: rRNA-depleted total RNA

tag: condition

value: YMC  time point 15

tag: cells pretreated with cycloheximide


title: Br7_3

tag: origin

tag: number of cells

tag: number of ctc


title: ID 78, visit 4

description: wk 7

tag: gender

value: M

value: Peripheral blood mononuclear cells

tag: n6 level tertiles (1=low, 2=middle, 3=high)

tag: n3 level tertiles (1=low, 2=middle, 3=high)

tag: sfa/pufa ratio tertiles (1=low, 2=middle, 3=high)


title: ID 8, visit 4

description: wk 7


title: ID 77, visit 4

description: wk 7


title: ID 70, visit 4

description: wk 7

value: F


title: ID 7, visit 4

description: wk 7


title: ID 72, visit 4

description: wk 7


title: CD34 ITGA6 double positive keratinocytesfrom K14ΔNLef1 epidermis, biological rep2

description: sorted basal

value: female

value: epidermis, back skin


title: CD34 ITGA6 double positive keratinocytes from wild type epidermis, biological rep3

description: sorted basal

source_name: CD34+ ITGA6+ keratinocytes, wild type epidermis,

value: wild type


title: CD34 ITGA6 double positive keratinocytes from wild type epidermis, biological rep2

description: sorted basal


title: CD34 ITGA6 double positive keratinocytesfrom K14ΔNLef1 epidermis, biological rep1

description: sorted basal


title: cenpk_ymc_14_plusChx_mrna

description: rRNA-depleted total RNA

value: YMC  time point 14

value: TRUE


title: cenpk_ymc_11_plusChx_mrna

description: rRNA-depleted total RNA

value: YMC  time point 11


title: hmcn_1


title: cenpk_ymc_13_plusChx_mrna

description: rRNA-depleted total RNA

value: YMC  time point 13


title: CD34 ITGA6 double positive keratinocytes from wild type epidermis, biological rep1

description: sorted basal


title: Br61_CTC___19

value: patient

tag: number of wbc attached

tag: sample type

value: CTC-cluster

value: CTC

tag: ctc-cluster size

tag: ctc-cluster id

tag: sample cell type

tag: sample cell type cat

tag: mouse type


title: ID 69, visit 4

description: wk 7

tag: tissue


title: ctrl_3

tag: strain

tag: RNAi

tag: RNAi feedings


title: cenpk_ymc_12_plusChx_mrna

description: rRNA-depleted total RNA

tag: genotype

value: MATa

tag: condition

value: YMC  time point 12

tag: cells pretreated with cycloheximide


title: ID 67, visit 4

description: wk 7

tag: gender

tag: n6 level tertiles (1=low, 2=middle, 3=high)


title: ID 68, visit 4

description: wk 7

tag: n3 level tertiles (1=low, 2=middle, 3=high)

tag: sfa/pufa ratio tertiles (1=low, 2=middle, 3=high)


title: Br61_CTC___1

tag: origin

tag: number of cells

tag: number of ctc

tag: number of wbc attached

tag: sample type

value: CTC-single

tag: cell type

tag: donor


title: cenpk_ymc_08_plusChx_mrna

description: rRNA-depleted total RNA

tag: strain

value: YMC  time point 8


title: ctrl_2

tag: tissue

value: tail fragment

tag: RNAi


title: Br39_6

tag: ctc-cluster size

tag: ctc-cluster id

tag: sample cell type

tag: sample cell type cat

tag: mouse type


title: ctrl_1

tag: RNAi feedings


title: cenpk_ymc_07_plusChx_mrna

description: rRNA-depleted total RNA

tag: genotype

tag: condition

value: YMC  time point 7

tag: cells pretreated with cycloheximide


title: cenpk_ymc_10_plusChx_mrna

description: rRNA-depleted total RNA

value: YMC  time point 10


title: input DNA

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using the BWA alignment program
Peak calling was performed with Homer (Heinz et al., 2010)
Genome_build: mm9

source_name: primary keratinocytes

growth_protocol: Primary mouse keratinocytes were isolated from dorsal skin and cultured on confluent irradiated 3T3-J2 fibroblast feeders in FAD medium (DMEM: Ham’s F12, 3:1, 1.8 × 10−4  M adenine) supplemented with 10% FCS, hydrocortisone (0.5 μg/ml), insulin (5 μg/ml), cholera toxin (8.4 ng/ml) and epidermal growth factor (10 ng/ml).

extract_protocol:
Lysates were clarified from sonicated nuclei and ∆NLef1-DNA complexes were isolated with antibody.
Immunoprecipitated DNA was prepared for sequencing as previously described (Schmidt et al., 2009). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~200/300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: keratinocytes


title: Br39_33

tag: origin

tag: number of cells

tag: number of ctc


title: Br39_5

tag: number of wbc attached

tag: sample type

tag: cell type


title: hWM2_12w

city: Amsterdam

first: Vincent

middle: M.

last: Christoffels

state: N/A (NA)

address: Meibergdreef 15  K2-159

department: Medical Biology

country: Netherlands

institute: Amsterdam UMC

description: processed data file: SAN_vs_RA_counts_hg19.xlsx

data_processing:
Reads were mapped to mm10 or hg19 build of the mouse and human transcriptome, respectively, using STAR (Dobin et al. 2013).
Reads generated with SOLID sequencing were converted to fastqsanger with FASTQ Groomer and and aligned with TopHat using default settings
Differential expression analysis was performed using the DESeq2 package based on a model using the negative binomial distribution (Love, Huber, and Anders 2014).
Genome_build: mm10 and hg19
Supplementary_files_format_and_content: Excel files with normalized (DESeq2) count data per gene & differential expression analysis: VENUS_vs_KATUSHKA_E17.5_sorted_counts_mm10.xlsx; VENUS_vs_KATUSHKA_adult_RNA-seq_mm10.xlsx; SAN_vs_RA_counts_hg19.xlsx

source_name: Human RA tissue

growth_protocol: Human + adult and fetal mouse E17.5 SAN and working myocardium tissue was obtained in strict accordance with the Academic Medical Center Amsterdam and the Aix Marseille University

extract_protocol:
RNA from isolated SANs and chamber myocardial cells was obtained using the Nucleospin RNA XS isolation kit (Bioke, MN 740902.50), according to manufacturer’s protocol. The quality of total RNA was assessed by micro-electrophoresis on acrylamide gel (Agilent 2100 Bioanalyser, Agilen).
RNA template was processed with the Ovation V2 RNA-seq system (Nugen, 7102-32), according to manufacturer’s protocol. Libraries were generated using the Ovation Ultra-low system V2 1-96 (Nugen, 0344NB-A01). Amplified cDNA was bead-purified (AmpureXP, Beckman-Coulter).

tag: tissue

value: Right atrial tissue

tag: developmental tissue

value: 12 weeks fetal

tag: cell population


title: Negative_control(Flag Antibody)_ChIPSeq

tag: strain

tag: chip antibody

value: Flag (Sigma)


title: Br39_2

tag: ctc-cluster size

tag: ctc-cluster id

tag: sample cell type

tag: sample cell type cat

tag: donor


title: cenpk_ymc_05_plusChx_mrna

description: rRNA-depleted total RNA

tag: genotype

tag: condition

value: YMC  time point 5

tag: cells pretreated with cycloheximide

value: TRUE


title: ∆NLef1_ChIPSeq

value: Lef1 (Cell Signaling)


title: cenpk_ymc_06_plusChx_mrna

description: rRNA-depleted total RNA

value: YMC  time point 6


title: cenpk_ymc_09_plusChx_mrna

description: rRNA-depleted total RNA

value: YMC  time point 9


title: Br39_3

tag: origin

value: patient

tag: number of cells

tag: number of ctc

value: CTC

tag: mouse type


title: hSAN3_9w

source_name: Human SAN tissue

tag: tissue

value: sinoatrial node

value: 9 weeks fetal


title: R11-6h-D3

city: Stockholm

first: Sunjay

middle: Jude

last: Fernandes

address: Karolinska University Sjukhuset, CMM L8:05, Solna

department: Department of Medicine, Solna

country: Sweden

institute: Karolinska Institutet

description: Illumina Stranded mRNA libraries

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads per gene were counted using HT-Seq with the parameters -m union -s reverse. Genes with greater than 1 cpm in all samples were retained.
Conditional quantile normalization was used to correct for GC content, gene length and library size. Output was log2 count of gene expression.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2 count values for each Sample

source_name: CD4+ T cells

growth_protocol: Human peripheral blood leucocytes were purified from fresh buffy coats by gradient centrifugation using Ficoll-Paque Plus (GE Healthcare). Monocyte depletion was then performed by plastic adherence in RPMI 1640 medium containing 10% FCS (Invitrogen). “Untouched” CD4+CD25− Tcons were isolated using the CD4+ T cell Isolation Kit II, human (Miltenyi Biotec) and were additionally depleted from CD25+ cells with CD25 specific MACS beads (6 µl per 107 cells).

extract_protocol:
AllPrep DNA/RNA/Protein Mini Kit
Illumina Stranded mRNA Protocol

treatment_protocol: CD4+ T cells from 3 donors were treated with either control or PPP1R11 siRNA for 4.5 days and either stimulated with cross linked CD3/CD28 for 6h or left unstimulated for RNAseq analysis

value: Blood

tag: cell type

value: CD4+ T cells

tag: knockdown

tag: stimulation

value: 6h CD3/CD28


title: Br39_32

tag: number of wbc attached

tag: sample type

value: CTC-cluster


title: Br39_31

tag: ctc-cluster size

tag: ctc-cluster id


title: hSAN2_12w

tag: developmental tissue

tag: cell population


title: cenpk_ymc_04_plusChx_mrna

description: rRNA-depleted total RNA

tag: strain

tag: genotype

value: MATa

value: YMC  time point 4


title: Br39_29

value: CTC-cluster-WBC

tag: sample cell type

tag: sample cell type cat

tag: donor


title: hWM3_9w

value: Right atrial tissue


title: cenpk_ymc_01_plusChx_mrna

description: rRNA-depleted total RNA

tag: condition

value: YMC  time point 1

tag: cells pretreated with cycloheximide


title: Br39_30

tag: origin

tag: number of cells

tag: number of ctc

value: CTC-WBC

tag: mouse type


title: ID 90, visit 4

description: wk 7

tag: gender

value: F

tag: tissue

value: Peripheral blood mononuclear cells

tag: n6 level tertiles (1=low, 2=middle, 3=high)

tag: n3 level tertiles (1=low, 2=middle, 3=high)

tag: sfa/pufa ratio tertiles (1=low, 2=middle, 3=high)


title: yjw1864-tripleKO_starved_plusChx_footprints

description: Ribosome protected mRNA fragment

data_processing:
Library strategy: Ribo-seq
Base calls were called with Illumina CASAVA software.
For RNA-seq libraries, reads were reverse-complemented and 3' adapter sequences (if present) were removed using FASTX-clipper.
For ribosome profiling libraries, 3' linker sequences were removed from reads and samples were de-multiplexed using FASTX-clipper and -barcode splitter, respectively.
Unique molecular identifiers (UMIs) and sample barcodes were removed from ribosome profiling reads using a custom Python script. UMIs were appended to the FASTQ header of each read immediately following the cluster y-coordinate (e.g. if UMI=AGTAG, header will resemble @K00153:418:HKMLHBBXX:1:1101:3437:1191_AGTAG ...).
Bowtie v1.1.2 was used to filter out reads aligning to S. cerevisiae rRNAs and tRNAs, and all surviving reads were aligned to the sacCer3 genome using tophat v2.1.1.
Counts per gene and normalized counts per gene (in reads per kilobase per million mapped reads, or RPKM) were calculated using the plastid cs program, with counts assigned to ribosomal P-sites determined by plastid’s psite program (for ribosome profiling) or assigned to the 5'-most aligned base (for RNA-seq). Regions of the genome that could not be uniquely mapped from a 26-base read with 2 mismatches were identified using plastid’s crossmap program, and these regions, along with the first 30 and last 5 codons of each coding sequence, were masked from RPKM calculations.
Genome_build: sacCer3
Supplementary_files_format_and_content: Tab delimited file containing count and RPKM data

value: MATa dot6::LEU2 tod6::URA3 stb3::kanMX6 his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0

value: 20 min amino acid starvation

value: TRUE


title: ID 62, visit 4

description: wk 7


title: cenpk_ymc_03_plusChx_mrna

description: rRNA-depleted total RNA

value: YMC  time point 3


title: Br39_26

value: patient

tag: number of wbc attached

tag: sample type

tag: cell type

value: CTC

tag: ctc-cluster size

tag: ctc-cluster id


title: ID 64, visit 4

description: wk 7


title: ID 6, visit 4

description: wk 7


title: ID 63, visit 4

description: wk 7


title: ID 58, visit 4

description: wk 7


title: ID 59, visit 4

description: wk 7

value: M


title: ID 56, visit 4

description: wk 7


title: Br39_25

value: CTC-single

tag: sample cell type

tag: sample cell type cat

tag: donor


title: cenpk_ymc_02_plusChx_mrna

description: rRNA-depleted total RNA

tag: strain

tag: genotype

tag: condition

value: YMC  time point 2

tag: cells pretreated with cycloheximide


title: Br39_27

tag: origin

tag: number of cells

tag: number of ctc

value: CTC-cluster

tag: mouse type


title: R11-6h-D2

description: Illumina Stranded mRNA libraries

tag: tissue

value: Blood

value: CD4+ T cells

tag: knockdown

tag: stimulation

value: 6h CD3/CD28


title: R11-6h-D1

description: Illumina Stranded mRNA libraries

tag: cell type


title: ID 57, visit 4

description: wk 7

tag: gender

tag: n6 level tertiles (1=low, 2=middle, 3=high)

tag: n3 level tertiles (1=low, 2=middle, 3=high)

tag: sfa/pufa ratio tertiles (1=low, 2=middle, 3=high)


title: ID 53, visit 4

description: wk 7


title: R11-0h-D3

description: Illumina Stranded mRNA libraries

value: 0h CD3/CD28

tag: donor


title: ID 52, visit 4

description: wk 7


title: Br39_24

tag: number of wbc attached

tag: sample type

tag: ctc-cluster size

tag: ctc-cluster id

tag: sample cell type

tag: sample cell type cat


title: ID 49, visit 4

description: wk 7


title: yjw1861-Pccw12-nop2_replete_plusChx_footprints

description: Ribosome protected mRNA fragment

tag: strain

tag: genotype

value: MATa nop2::klNOP2 yhrcdelta14::PCCW12-NOP2::kanMX6 his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0

tag: condition

value: replete

tag: cells pretreated with cycloheximide


title: R11-0h-D2

description: Illumina Stranded mRNA libraries

tag: tissue

tag: knockdown

tag: stimulation


title: R11-0h-D1

description: Illumina Stranded mRNA libraries

tag: cell type


title: yjw1864-tripleKO_replete_plusChx_footprints

description: Ribosome protected mRNA fragment


title: Br39_19

tag: origin

tag: number of cells

tag: number of ctc

tag: mouse type


title: ID 50, visit 4

description: wk 7

tag: gender

value: F

value: Peripheral blood mononuclear cells

tag: n6 level tertiles (1=low, 2=middle, 3=high)

tag: n3 level tertiles (1=low, 2=middle, 3=high)

tag: sfa/pufa ratio tertiles (1=low, 2=middle, 3=high)


title: Br39_22

tag: number of wbc attached

tag: sample type

tag: ctc-cluster size

tag: ctc-cluster id

tag: sample cell type

tag: sample cell type cat

tag: donor


title: ID 51, visit 4

description: wk 7

tag: tissue


title: yjw1861-Pccw12-nop2_starved_plusChx_footprints

description: Ribosome protected mRNA fragment

tag: strain

tag: genotype

tag: condition

value: 20 min amino acid starvation

tag: cells pretreated with cycloheximide


title: Br39_21

tag: origin

tag: number of cells

tag: number of ctc

tag: cell type

tag: mouse type


title: Br39_18

tag: number of wbc attached


title: yjw1863-Pnop2-gfp_starved_plusChx_footprints

description: Ribosome protected mRNA fragment

value: MATa yhrcdelta14::PNOP2-5'UTRADH1-EGFP-3'UTRADH1::kanMX6 his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0

value: TRUE


title: CONTROL-6h-D3

description: Illumina Stranded mRNA libraries

tag: knockdown

value: siControl

tag: stimulation


title: CONTROL-6h-D2

description: Illumina Stranded mRNA libraries


title: yjw1863-Pnop2-gfp_replete_plusChx_footprints

description: Ribosome protected mRNA fragment


title: CONTROL-0h-D2

description: Illumina Stranded mRNA libraries


title: CONTROL-6h-D1

description: Illumina Stranded mRNA libraries


title: yjw1862-Pnop2-nop2_starved_plusChx_footprints

description: Ribosome protected mRNA fragment

value: MATa nop2::klNOP2 yhrcdelta14::PNOP2-NOP2::kanMX6 his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0


title: ID 46, visit 4

description: wk 7

tag: gender

tag: n6 level tertiles (1=low, 2=middle, 3=high)

tag: n3 level tertiles (1=low, 2=middle, 3=high)

tag: sfa/pufa ratio tertiles (1=low, 2=middle, 3=high)


title: Br30_8

value: patient

tag: sample type

value: CTC-single-WBC

value: CTC-WBC

tag: ctc-cluster size

tag: ctc-cluster id

tag: sample cell type

tag: sample cell type cat

tag: donor


title: by4741_starved_plusChx_footprints

description: Ribosome protected mRNA fragment

tag: strain

tag: genotype

value: MATa his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0

tag: condition

tag: cells pretreated with cycloheximide


title: ID 4, visit 4

description: wk 7

value: M

tag: tissue


title: ID 43, visit 4

description: wk 7


title: yjw1862-Pnop2-nop2_replete_plusChx_footprints

description: Ribosome protected mRNA fragment


title: CONTROL-0h-D3

description: Illumina Stranded mRNA libraries

value: Blood

tag: cell type

value: CD4+ T cells

tag: knockdown


title: CONTROL-0h-D1

description: Illumina Stranded mRNA libraries

tag: stimulation

value: 0h CD3/CD28


title: ID 45, visit 4

description: wk 7

tag: gender

tag: n6 level tertiles (1=low, 2=middle, 3=high)


title: Br39_17

tag: origin

tag: number of cells

tag: number of ctc

tag: number of wbc attached

value: CTC-single

value: CTC

tag: mouse type


title: Br37_4

tag: sample type

tag: ctc-cluster size

tag: ctc-cluster id

tag: sample cell type

tag: sample cell type cat


title: by4741_replete_minusChx_footprints

description: Ribosome protected mRNA fragment

tag: strain

tag: genotype

tag: condition

value: replete

tag: cells pretreated with cycloheximide

value: FALSE


title: Br30_6

tag: cell type

tag: donor


title: by4741_starved_minusChx_footprints

description: Ribosome protected mRNA fragment

value: 20 min amino acid starvation


title: by4741_replete_plusChx_footprints

description: Ribosome protected mRNA fragment


title: Br30_7


title: ID 44, visit 4

description: wk 7

tag: gender

tag: tissue

value: Peripheral blood mononuclear cells

tag: n6 level tertiles (1=low, 2=middle, 3=high)

tag: n3 level tertiles (1=low, 2=middle, 3=high)

tag: sfa/pufa ratio tertiles (1=low, 2=middle, 3=high)


title: synchronized control 10 hours post release

city: Norwich

first: Conrad

last: Nieduszynski

address: Norwich Research Park

institute: Earlham Institute

description:
BrdU genomic DNA
Control_10h

data_processing:
Library strategy: RepliSeq
Alignment to hg38 using STAR version 2.5.3a.
Data were filtered for uniquely mapping, non duplicated reads, and binned into 1kb windows. Bins with signal spikes (z score > 2.5) were removed.
1kb windows were binned into 50kb windows. Quantile normalization was applied across the sample set.
Replication timing was calculated as log2(reads in early sample /reads in late sample), where 'early' corresponds to S phase bin 1 or 4h for the asynchronous and synchronized experiment, respectively. 'Late' corresponds to S phase bin 3 or 10h for the asynchronous and synchronized experiments, respectively.
Loess smooting was applied to the final replication timing values.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated from the smoothed replication timing score (log2(S phase bin 1/S phase bin 3) for asynchronous cells. log2(4h/10h) for synchronized cells)

source_name: HCT116 Scc1-mAID-mClover

growth_protocol: Grown in MyCoy's 5A media with 10% FBS, 100U/mL penicillin, 100µg/mL streptomycinat 37degreesC with 5% CO2.

extract_protocol:
Phenol chloroform extraction followed with isopropa nol precipitation. BrdU-containing DNA was isolated using BD347580 antibody and the protocol outlined in : Peace et al, 2016 (doi:10.1101/gr.196857.115)
Libraries were prepared according to Illumina's instructions.

treatment_protocol: "Treated" samples were subjected to 500µM indole-3-acetic acid (IAA, auxin) for at least 2 hours.

tag: time

value: 10 hours post release

tag: cell line

value: HCT116 Scc1-mAID-mClover

tag: treatment

value: control

tag: growth

value: thymidine-nocodazole-mitotic shakeoff


title: Br39_20

tag: origin

value: patient

tag: number of cells

tag: number of ctc

tag: number of wbc attached

tag: sample type

tag: ctc-cluster size

tag: ctc-cluster id

tag: sample cell type

tag: mouse type


title: synchronized control 7 hours post release

description:
BrdU genomic DNA
Control_7h

value: 7 hours post release


title: ID 87, visit 4

description: wk 7

tag: gender

tag: tissue


title: cenpk_ymc_15_plusChx_footprints

description: Ribosome protected mRNA fragment

tag: strain

tag: genotype

value: MATa

tag: condition

value: YMC  time point 15

tag: cells pretreated with cycloheximide

value: TRUE


title: cenpk_ymc_13_plusChx_footprints

description: Ribosome protected mRNA fragment

value: YMC  time point 13


title: synchronized control 4 hours post release

description:
BrdU genomic DNA
Control_4h

tag: time

value: 4 hours post release

tag: cell line

tag: treatment


title: Br30_1

tag: origin

tag: number of cells

value: CTC-single

tag: cell type

tag: sample cell type cat

tag: donor


title: cenpk_ymc_16_plusChx_footprints

description: Ribosome protected mRNA fragment

value: YMC  time point 16


title: cenpk_ymc_12_plusChx_footprints

description: Ribosome protected mRNA fragment

value: YMC  time point 12


title: cenpk_ymc_14_plusChx_footprints

description: Ribosome protected mRNA fragment

value: YMC  time point 14


title: ID 36, visit 4

description: wk 7

value: F

tag: n6 level tertiles (1=low, 2=middle, 3=high)

tag: n3 level tertiles (1=low, 2=middle, 3=high)

tag: sfa/pufa ratio tertiles (1=low, 2=middle, 3=high)


title: synchronized auxin treated 10 hours post release

description:
BrdU genomic DNA
IAA_10h

value: auxin treated

tag: growth


title: ID 41, visit 4

description: wk 7

tag: gender

tag: tissue

value: Peripheral blood mononuclear cells


title: ID 32, visit 4

description: wk 7


title: ID 30, visit 4

description: wk 7


title: ID 3, visit 4

description: wk 7


title: ID 27, visit 4

description: wk 7


title: synchronized auxin treated 4 hours post release

description:
BrdU genomic DNA
IAA_4h

value: HCT116 Scc1-mAID-mClover


title: synchronized auxin treated 7 hours post release

description:
BrdU genomic DNA
IAA_7h


title: cenpk_ymc_11_plusChx_footprints

description: Ribosome protected mRNA fragment

tag: strain

tag: genotype

value: YMC  time point 11


title: ID 31, visit 4

description: wk 7


title: ID 33, visit 4

description: wk 7


title: cenpk_ymc_10_plusChx_footprints

description: Ribosome protected mRNA fragment

tag: condition

value: YMC  time point 10

tag: cells pretreated with cycloheximide


title: ID 22, visit 4

description: wk 7


title: ID 25, visit 4

description: wk 7


title: cenpk_ymc_09_plusChx_footprints

description: Ribosome protected mRNA fragment

value: YMC  time point 9


title: asynchronous control S phase bin 4

description:
BrdU genomic DNA
Control_S4

tag: cell line

value: control

value: asynchronous


title: asynchronous control S phase bin 3

description:
BrdU genomic DNA
Control_S3

tag: treatment


title: asynchronous control S phase bin 2

description:
BrdU genomic DNA
Control_S2


title: cenpk_ymc_06_plusChx_footprints

description: Ribosome protected mRNA fragment

value: MATa

value: YMC  time point 6


title: cenpk_ymc_08_plusChx_footprints

description: Ribosome protected mRNA fragment

value: YMC  time point 8

value: TRUE


title: ID 24, visit 4

description: wk 7


title: cenpk_ymc_07_plusChx_footprints

description: Ribosome protected mRNA fragment

value: YMC  time point 7


title: asynchronous control S phase bin 1

description:
BrdU genomic DNA
Control_S1


title: cenpk_ymc_05_plusChx_footprints

description: Ribosome protected mRNA fragment

value: YMC  time point 5


title: cenpk_ymc_04_plusChx_footprints

description: Ribosome protected mRNA fragment

value: YMC  time point 4


title: ID 21, visit 4

description: wk 7


title: asynchronous auxin treated S phase bin 3

description:
BrdU genomic DNA
IAA2h_S3


title: cenpk_ymc_03_plusChx_footprints

description: Ribosome protected mRNA fragment

value: YMC  time point 3


title: asynchronous auxin treated S phase bin 1

description:
BrdU genomic DNA
IAA2h_S1


title: asynchronous auxin treated S phase bin 2

description:
BrdU genomic DNA
IAA2h_S2


title: cenpk_ymc_02_plusChx_footprints

description: Ribosome protected mRNA fragment

value: YMC  time point 2


title: WT_bioifilm_S1

first: Vanessa

last: Dumeaux

state: Ontario

address: Elgin Dr

department: Anatomy and Cell Biology

institute: Western University

data_processing:
RNA sequencing reads were pre-processed with the sequence-grooming tool cutadapt version 0.4.1(MARTIN 2011) with the following quality trimming and filtering parameters (`--phred33 --length 36 -q 5 --stringency 1 -e 0.1`). Each set of paired-end reads was mapped against the C. albicans SC5314 haplotype A, version A22 downloaded from the Candida Genome Database (CGD) (www.candidagenome.org) using HISAT2 version 2.0.4. SAMtools was then used to sort and convert SAM files. The read alignments and C. albicans SC5314 genome annotation were provided as input into StringTie v1.3.3 (PERTEA et al. 2015) which returned gene abundances for each sample. We imported gene abundances into R and conducted differential analysis of gene count data using the DESeq2 R package (Love et al. 2014).
Genome_build: C. albicans SC5314 haplotype A, version A22
Supplementary_files_format_and_content: Tab-delimited gene abundances files

organism: Candida albicans

source_name: yeast cells

extract_protocol:
Total RNA isolation was performed as previously described (Tebbji et al, PloSGenetics 2014)
Libraries were prepared according to Illumina's mRNASeq stranded library preparation kit

treatment_protocol: RPMI-MOPS medium at 37oC

tag: genotype/variation

value: wild type yeast cells


title: ILS1_Biofilm_L1

value: ILS1 mutated yeast cells


title: ID 13, visit 4

description: wk 7

value: F

value: Peripheral blood mononuclear cells


title: WT_bioifilm_S2


title: ILS1_Biofilm_L2


title: cenpk_ymc_01_plusChx_footprints

description: Ribosome protected mRNA fragment

value: YMC  time point 1


title: WT_planktonic_S1

treatment_protocol: YPD medium at 30°C


title: HCT116-3ex-nc-2

status: Public on Mar 07 2019

city: beijing

first: wanru

last: ma

address: 52 Fucheng Road,Haidian District,Beijing

institute: beijing cancer hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The remaining reads were filtered against the rRNA database to remove possible ribosomal RNA contamination,  and then mapped to the hg19 whole genome using Hisat2 v2.1.0 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and counts for each Sample

source_name: colon cell line

extract_protocol:
RNA was extract though Magzol Reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: colon cancer cell line


title: asynchronous auxin treated S phase bin 4

description:
BrdU genomic DNA
IAA2h_S4

value: HCT116 Scc1-mAID-mClover

value: auxin treated


title: HCT116-3ex-siauf1-2


title: HCT116-ctrl-siauf1-2


title: HCT116-3ex-siauf1-1


title: HCT116-3ex-nc-1


title: ID 18, visit 4

description: wk 7


title: HCT116-ctrl-nc-2


title: WT_planktonic_S2


title: ID 16, visit 4

description: wk 7


title: HCCy19

city: chongqing

first: lei

last: bo

address: gaotan yan

institute: Army Medical University

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HiSat2 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: PBMCs

growth_protocol: The study included 7 samples, of which 4 were HCC samples and 3 were normal controls.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 10 ml of peripheral blood was centrifuged in700x g at room temperature. Removing the plasma, then dilute it by volume with precooled PBS 1 to 1, then add it slowly to the lymphocyte isolate at room temperature, and centrifuge it in 700x g. Carefully absorb the middle layer of white membrane with straw and wash it 2 times with pre cooled PBS at room temperature.The ratio of serum and DMSO to volume ratio was 9 to 1, and suspended cells were frozen with liquid nitrogen.

value: Peripheral blood

tag: disease

value: hepatocellular carcinoma


title: ID 20, visit 4

description: wk 7

value: M


title: HCCy18


title: HCCy14


title: HCCy15


title: ID 12, visit 4

description: wk 7


title: ID 11, visit 4

description: wk 7