title: 20160118_C30_170330_6


title: F5.1001200134

status: Public on Dec 31 2018

type: SRA

city: Stanford

first: Qingyun

last: Li

state: CA

address: 299 Campus Drive

department: Neurobiology

country: USA

institute: Stanford University

description: Single_myeloid_1922_cells_processed_data.csv

library_source: transcriptomic

data_processing:
Prinseq (version 0.20.4) was first used to filter sequencing reads shorter than 30 bp (-min_len 30), trim the first 10 bp at the 5’-end (-trim_left 10) of the reads, trim reads with low quality from the 3’-end (-trim_qual_right 25) and remove low complexity reads (-lc_method entropy, -lc_threshold 65).
Trim Galore (version 0.4.3) was applied to trimmed the Nextera adapters (--stringency 1).
The remaining reads were aligned to the mm10 genome by calling STAR (version 2.5.3a) with the following options: --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMstrandField intronMotif.
Picard was then used to remove the duplicate reads (VALIDATION_STRINGENCY=LENIENT, REMOVE_DUPLICATES=true).
The aligned reads were converted to counts for each gene by using HTSeq (-m intersection-nonempty, -s no)
To filter out cells with low sequencing quality, three criteria, namely the number of total reads, the number of total detected genes and correlation coefficient between ERCC spike-ins input and corresponding read counts, were each evaluated based on the distributions of the data. The distribution of the total reads (in logarithmic scale) was fitted by a truncated Cauchy distribution, and data points in two tails of the estimated distribution were considered as outliers and eliminated. Fitting and elimination were then applied to the remaining data. This process was run iteratively until the estimated distribution became stable. The threshold was set to the value where the cumulative distribution function of the estimated distribution reaches 0.05. Similarly, cells with small numbers of detected genes, and poor correlation coefficients for ERCC (low sequencing accuracy) were dropped. After filtering, 1816 cells, out of 1922, were retained.
Genome_build: mm10
Supplementary_files_format_and_content: Common delimited file (csv) containing all 1922 cells and mapped gene counts (including counts for ERCC spike-ins)

molecule: total RNA

organism: Mus musculus

source_name: Brain myeloid cell

extract_protocol:
For the E14.5 stage, whole brains were dissected out from timed embryos, and collected into 1ml PBS with 1% fetal bovine serum (added 10ul Ambion DNase I, 2ul RNase inhibitor) on ice. The sample was passed through a 26G needle 5-10 times to create single cell suspension. Cells were spun down (500g) at 4˚C for 5min, and suspended in 1ml PBS for FACS staining. Single live cells in the cKit-CD45+ gate were sorted into 96-well plates for library preparation.  For P7 and P60 stages, cortex (CTX), cerebellum (CB), hippocampus (HIP), striatum (STR), olfactory bulb (OB) and choroid plexus (CP) were dissected out. Tissues from the same region were pooled from multiple mice (3-8 depending on the ages and regions) into a 6cm petri dish with 200ul cold medium A on ice (15mM HEPES, 0.5% glucose in 1 X Hanks' Balanced Salt Solution (HBSS without phenol red)). Microglia (myeloid cells) extraction was carried out on ice following a published protocol (Bennett et al. PNAS. 2016) through douncing, MACS myelin removal and FACS staining. Single live cells in the CD45lowCD11b+ (microglia) or CD45hiCD11b+ (myeloid cells) gate were sorted into 96-well plates for library preparation.
Sequencing libraries were prepared following the published Smart-seq2 protocol with the aid of liquid handling robotics (Picelli et al. Nature Protocols. 2014). Briefly, plates with sorted cells were thawed on ice and incubated at 72˚C for 3 min in order to anneal RNAs to the Oligo-dT30VN primer. After that, 6ul reverse transcription mixture (95U SMARTScribe™ Reverse Transcriptase (100U/ul, Clontech 639538), 10U RNase inhibitor (40U/ul), 1XFirst-Strand buffer, 5mM DTT, 1M Betaine, 6mM MgCl2, 1uM TSO (Exiqon, Rnase free HPLC purified)) was added into each well, and RT was performed at 42˚C for 90 min, followed by 70˚C, 5 min. To amplify cDNA, 15ul PCR amplification mix (1X KAPA HIFI Hotstart Master Mix (Kapa Biosciences KK2602), 0.1uM ISPCR Oligo (AAGCAGTGGTATCAACGCAGAGT), 0.56U Lambda Exonuclease (5U/ul, New England BioLabs M0262S)) was added, and the following PCR program was used: (1) 37˚C 30 min; (2)95˚C 3 min; (3) 21 cycles of 98˚C 20 sec, 67˚C 15 sec, 72˚C 4 min; (4) 72˚C 5 min. Amplified cDNA samples were then purified with PCRClean DX beads (0.7:1 ratio, Aline C-1003-50), and resuspended in 20ul EB buffer. cDNA quality was examined with a Fragment Analyzer (AATI, High Sensitivity NGS Fragment Analysis Kit:1 bp - 6000 bp) following the manufacture’s instruction. Samples with sufficient amount of cDNA content (>0.05ng/ul) and normal peaks on the quantification graphs were retained for library preparation. To make libraries, all samples were first diluted down to 0.15ng/ul (only if higher than 0.15ng/ul) in 384-well plates using Mantis Liquid Handler (Formulatrix) and Mosquito X1 (TTP Labtech) with customized scripts. Nextera XT DNA Sample Prep Kit (Illumina FC-131-1096) was used at 1/10 of recommendation volume, with the help of a Mosquito HTS robot for liquid transfer. Specifically, tagmentation was done in 1.6ul (1.2ul Tagment enzyme mix, 0.4ul diluted cDNA) at 55˚C, 10 min. Neutralization buffer was added 0.4ul per well and incubated at room temperature for 5 min to stop the reaction. Then 0.8ul Illumina Nextera XT 384 Indexes (0.4ul each, 5uM from 4 sets of 96 indexes) and 1.2ul PCR master mix were added to amplify whole transcriptomes using the following program: (1) 72˚C 3 min; (2) 95˚C 30 sec; (3) 10 cycles of 95˚C 10 sec, 55˚C 30 sec, 72˚C 1 min; (4) 72˚C 5 min. Libraries from a single 384 plate were pooled together in an Eppendorf tube and purified twice with PCRClean DX beads. The quality and concentrations of the final mixed libraries were measured with Bioanalyzer and Qubit, respectively, before Illumina Nextseq sequencing.

tag: strain

tag: genotype

value: wild type

tag: tissue

value: HIP

tag: age

tag: gate

value: Y


title: 20160118_C29_170330_6

city: Ramat Gan

first: Isabelle

last: Stévant

address: Institute of Nanotechnology and Advanced Materials, Building 206

country: Israel

institute: University of Bar Ilan

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Some libraries were sequenced twice because of a technical issue and the Fastq files of the two runs were merged and are annotated as « merged » in the sample and fastq file name.
FastQ files were mapped with GemTools (version 1.7.1) to the mouse reference genome (GRCm38.p3) and the genome annotation (version M4) downloaded from GENCODE, with an extra fake “Z” chromosome  with the GFP sequence.
RPKM (Reads Per Kilobase of exon per Million reads mapped) were computed with an in house pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include RPKM values for each sample

molecule: polyA RNA

source_name: XX gonad

extract_protocol:
XX gonads were collected in PBS at room temperature. PBS was removed and tissues were digested 10 minutes at 37°C with trypsin/EDTA 0.05% and filtered through a 40µm cell strainer to obtain single cell suspension. Nr5a1-eGFP+ cells were then sorted by fluorescent-active cell sorting (BD FACSARIA II) with Draq7TM dye to exclude dead cells and collected in PBS for the single-cell capture. Cells were centrifuged at low speed to be concentrated at an average of 400 million cells per mL prior cell capture. Single cells were capture on small size IFC microfluidic chips using the C1 Single-Cell Auto Prep System (Fluidigm) following the manufacturer recommended protocol. Reverse-transcription and pre-amplification of the single-cell cDNAs were achieved within the IFC chip using the SMARTer Ultra Low RNA kit for Illumina (Clontech) according to the C1 protocol.
RNA-sequencing libraries of the single-cell cDNA were prepared using the Illumina Nextera XT DNA Sample Preparation kit using the modified protocol described in the C1 documentation.

value: Mixed background

value: NR5A1-eGFP positive cells

tag: c1 ifc size

value: small

tag: sequencing depth

value: 10M reads 100bp p-e


title: 20160118_C28_170330_5


title: 20160118_C27_170330_5


title: E4.1001200134


title: 20160118_C25_170330_5


title: C10.1001200130


title: 20160118_C23_170330_4


title: D5.1001200133

value: STR


title: D8.1001200132

value: CTX


title: F9.1001200133


title: 20160118_C22_170330_5


title: D5.1001200125

value: CB


title: E10.1001200129


title: A8.1001200134


title: B7.1001200133


title: 20160118_C21_170330_4


title: 20160118_C40_170330_7


title: 20160118_C20_170330_4


title: 20160118_C18_170330_3


title: 20160118_C17_170330_3


title: 20160118_C19_170330_4


title: D4.1001200130


title: G4.1001200132


title: D4.1001200132


title: 20160118_C16_170330_3


title: 20160118_C26_170330_5


title: F11.1001200129


title: 20160118_C15_170330_3


title: D3.1001200125


title: F4.1001200131

value: OB


title: 20160118_C14_170330_3


title: 20160118_C12_170330_2


title: E3.1001200125


title: 20160118_C11_170330_2


title: G11.1001200125


title: 20160118_C13_170330_3


title: B1.1001200125


title: F3.1001200125


title: E5.1001200130


title: A4.1001200131


title: 20160118_C07_170330_2


title: 20160118_C10_170330_2


title: H10.1001200125


title: 20160118_C06_170330_1


title: 20160118_C09_170330_1


title: F4.1001200125


title: 20160118_C04_170330_1


title: A3.1001200125


title: 20160118_C01_170330_1


title: 20151201_C96_170330_8


title: 20151201_C94_170330_8


title: A12.1001200131


title: G12.1001200125


title: A7.1001200129


title: H5.1001200132


title: 20151201_C93_170330_8


title: D4.1001200131


title: 20151201_C89_170330_8


title: B9.1001200134


title: F6.1001200131


title: 20151201_C87_170330_7


title: B4.1001200130


title: 20151201_C85_170330_7


title: H6.1001200131


title: 20151201_C84_170330_6


title: 20151201_C86_170330_7


title: F9.1001200131


title: G1.1001200129


title: 20151201_C82_170330_7


title: 20151201_C77_170330_6


title: 20151201_C81_170330_6


title: G10.1001200132


title: E9.1001200125


title: G5.1001200132


title: 20151201_C73_170330_5


title: 20151201_C83_170330_7


title: 20151201_C71_170330_5


title: 20151201_C70_170330_5


title: C12.1001200130


title: 20151201_C68_170330_4


title: 20151201_C66_170330_4


title: C7.1001200133


title: B2.1001200129


title: E1.1001200125


title: E6.1001200132


title: 20151201_C92_170330_8


title: H9.1001200133


title: 20151201_C64_170330_4


title: 20151201_C63_170330_3


title: G7.1001200125


title: 20151201_C58_170330_2


title: C9.1001200132


title: 20151201_C57_170330_2


title: E8.1001200130


title: 20151201_C56_170330_2


title: C6.1001200132

value: N


title: 20151201_C55_170330_2


title: 20151201_C54_170330_1


title: F12.1001200129


title: 20151201_C53_170330_1


title: B4.1001200134


title: A1.1001200131


title: 20151201_C52_170330_1


title: A10.1001200129


title: E5.1001200134


title: 20151201_C48_170330_8


title: H10.1001200134


title: H5.1001200125


title: 20151201_C49_170330_1


title: B10.1001200130


title: 20151201_C46_170330_8


title: 20151201_C44_170330_8


title: H4.1001200133


title: 20151201_C43_170330_8


title: G5.1001200133


title: 20151201_C39_170330_7


title: D11.1001200125


title: 20151201_C35_170330_6


title: E12.1001200125


title: 20151201_C34_170330_6


title: D9.1001200134


title: 20151201_C33_170330_6


title: B4.1001200131


title: 20151201_C32_170330_6


title: D5.1001200132


title: 20151201_C51_170330_1


title: 20151201_C31_170330_6


title: 20151201_C28_170330_5


title: 20151201_C29_170330_5


title: E3.1001200131


title: B12.1001200129


title: H2.1001200125


title: 20151201_C23_170330_4


title: 20151201_C24_170330_4


title: H10.1001200129


title: D6.1001200131


title: 20151201_C20_170330_4


title: B5.1001200134


title: G5.1001200129


title: G10.1001200130


title: 20151201_C21_170330_4


title: 20151201_C18_170330_3


title: D10.1001200133


title: A12.1001200132


title: 20151201_C16_170330_3


title: 20151201_C17_170330_3


title: 20151201_C13_170330_3


title: B3.1001200129


title: H8.1001200132


title: 20151201_C10_170330_2


title: C6.1001200130


title: B11.1001200132


title: F10.1001200133


title: 20151201_C09_170330_1


title: 20151201_C07_170330_2


title: G1.1001200131


title: 20151201_C04_170330_1


title: 20151201_C01_170330_1


title: E7.1001200125


title: D7.1001200133


title: 20151126_C94_170330_8


title: H2.1001200132


title: A3.1001200134


title: 20151126_C92_170330_8


title: 20151126_C87_170330_7


title: 20151126_C86_170330_7


title: H2.1001200134


title: C11.1001200131


title: 20151201_C12_170330_2


title: 20151126_C83_170330_7


title: A11.1001200130


title: 20151126_C81_170330_6


title: 20151126_C79_170330_6


title: D2.1001200132


title: B9.1001200130


title: D11.1001200132


title: 20151126_C77_170330_6


title: 20151126_C74_170330_5


title: D8.1001200133


title: D7.1001200129


title: F3.1001200132


title: A2.1001200129


title: C11.1001200132


title: 20151126_C85_170330_7


title: 20151126_C72_170330_5


title: 20151126_C95_170330_8


title: E7.1001200133


title: B5.1001200132


title: A1.1001200132


title: 20151126_C59_170330_3


title: 20151126_C51_170330_1


title: 20151126_C55_170330_2


title: F6.1001200133


title: B2.1001200134


title: 20151126_C50_170330_1


title: 20151126_C49_170330_1


title: D5.1001200134


title: G3.1001200134


title: 20151126_C73_170330_5


title: 20151126_C43_170330_8


title: D9.1001200125


title: 20151126_C71_170330_5


title: 20151126_C68_170330_4


title: B3.1001200133


title: C8.1001200134


title: 20151126_C42_170330_7


title: 20151126_C37_170330_7


title: 20151126_C41_170330_7


title: G6.1001200133


title: 20151126_C62_170330_3


title: 20151126_C35_170330_6


title: D10.1001200131


title: 20151126_C30_170330_6


title: 20151126_C26_170330_5


title: 20151126_C25_170330_5


title: 20151126_C23_170330_4


title: E12.1001200134


title: 20151126_C44_170330_8


title: 20151126_C19_170330_4


title: 20151126_C22_170330_5


title: 20151126_C21_170330_4


title: 20151126_C18_170330_3


title: 20151126_C17_170330_3


title: F6.1001200134


title: 20151126_C16_170330_3


title: C8.1001200125


title: G11.1001200132


title: 20151126_C07_170330_1


title: 20151126_C04_170330_1


title: 20151126_C02_170330_1


title: G7.1001200134


title: 20151119_C94_170330_8


title: 20151119_C93_170330_8


title: 20151119_C90_170330_7


title: 20151119_C92_170330_8


title: F11.1001200132


title: F5.1001200132


title: 20151119_C89_170330_8


title: E10.1001200131


title: 20151119_C80_170330_6


title: E12.1001200129


title: 20151119_C78_170330_6


title: 20151119_C74_170330_5


title: 20151119_C76_170330_6


title: G6.1001200134


title: D12.1001200125


title: 20151119_C68_170330_4


title: 20151119_C70_170330_5


title: 20151119_C66_170330_4


title: D2.1001200134


title: 20151119_C65_170330_4


title: H1.1001200131


title: F1.1001200132


title: 20151119_C62_170330_3


title: 20151119_C61_170330_3


title: 20151119_C60_170330_3


title: F8.1001200133


title: 20151119_C85_170330_7


title: 20151119_C59_170330_2


title: 20151119_C58_170330_2


title: C2.1001200125


title: 20151119_C57_170330_2


title: NEBNext12: ApcMin adenomas rep 3

city: Cambridge

first: Laurens

middle: Moore

last: van Tienen

state: Cambridgeshire

address: Francis Crick Avenue

department: PNAC

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

description: replicate 3

data_processing:
Reads for each sample were demultiplexed according to the barcodes at the CRUK Genomics Core, Cambridge, and transcript-level abundances were quantified by quasi-mapping the reads against an index build from the GRCm38 transcriptome using Salmon.
These quantifications were subsequently imported into the R environment using the tximport package, and differentially expressed genes were identified using the DESeq2 package.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Salmon gene-level estimated counts

source_name: inestinal adenomas

extract_protocol: Tissue was flash-frozen in liquid nitrogen and stored at -80 °C for <24 months. Frozen samples were thawed on ice in RLT buffer containing 1% β-mercaptoethanol, and homogenized with a Qiagen TissueRuptor followed by QIAshredder columns according to the manufacturer’s instructions. RNA was extracted from tissue lysates with the RNeasy Kit, and libraries were constructed using the NEBNext Ultra II Directional RNA Library Prep Kit with 1µg total RNA input.

value: ApcMin/+

value: inestinal adenomas

tag: tissue extraction method

value: excision


title: H9.1001200125


title: 20151119_C55_170330_2


title: 20151119_C69_170330_4


title: 20151119_C49_170330_1


title: H1.1001200132


title: NEBNext10: ApcMin adenomas rep 1

description: replicate 1


title: F5.1001200130


title: 20151119_C44_170330_8


title: 20151119_C45_170330_8


title: 20151119_C54_170330_1


title: NEBNext09: Apc1322T adenomas rep 3

description: replicate 3


title: NEBNext08: Apc1322T adenomas rep 2

description: replicate 2


title: 20151119_C42_170330_7


title: 20151119_C46_170330_8


title: 20151119_C47_170330_8


title: C7.1001200131


title: 20151119_C41_170330_7


title: B12.1001200134


title: 20151119_C40_170330_7


title: 20151119_C56_170330_2


title: NEBNext07: Apc1322T adenomas rep 1

description: replicate 1


title: 20151119_C39_170330_7


title: 20151119_C34_170330_6


title: A4.1001200134


title: 20151119_C31_170330_6


title: 20151119_C28_170330_5


title: NEBNext11: ApcMin adenomas rep 2

description: replicate 2


title: 20151119_C26_170330_5


title: G10.1001200134


title: 20151119_C25_170330_5


title: 20151119_C30_170330_6


title: 20151119_C24_170330_4


title: G8.1001200131


title: F7.1001200133


title: 20151119_C23_170330_4


title: 20151119_C22_170330_5


title: 20151119_C20_170330_4


title: G4.1001200134


title: 20151119_C17_170330_3


title: 20151119_C19_170330_4


title: 20151119_C14_170330_3


title: B10.1001200132


title: H11.1001200125


title: 20151119_C12_170330_2


title: 20151119_C11_170330_2


title: D8.1001200134


title: F1.1001200125


title: 20151119_C10_170330_2


title: 20151119_C07_170330_1


title: 20151119_C06_170330_1


title: A6.1001200125


title: 20151119_C02_170330_1


title: duodenum_Glu_negative_4665

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

data_processing:
data was demultiplexed using the Casava pipeline
data was mapped to the mouse genome GRCm38 using Tophat v2.1.0 and raw fragment counts generated with Cufflinks v2.2.1
Genome_build: GRCm38
Supplementary_files_format_and_content: mouse_duo_Neurod1_GluVenus_raw_count.txt is a tab delimited file of number of counts for ensembl gene ids of each biological sample

source_name: duodenum

growth_protocol: mice were grown on a 12h dark/light cycle with ad libitum access to water and standard chow

extract_protocol:
duodenum epithelium was single-cell digestedand FACS sorted for positive cells and similar number of negative cells. RNA was extracted using microplus RNeasy kit (Qiagen) and quality checked on a picochip bioanalyzer (RIN >7)
Library was constructed with 2ng of total RNA using the Ovation RNAseq system v2 kit and the Ovation Rapid DR multiplex 1-96 kit (Nugen)

value: duodenum

value: GluVenus

tag: cell population

value: negative


title: H8.1001200125

value: wild type


title: F3.1001200129

value: Y


title: duodenum_Glu_positive_4665

value: positive


title: 20140709_C82_150331_7

value: Mixed background

value: NR5A1-eGFP positive cells


title: 20151119_C01_170330_1

value: small

value: 10M reads 100bp p-e


title: G5.1001200125


title: 20140709_C83_150331_6


title: 20140709_C81_150331_5


title: C5.1001200132

value: CTX


title: A5.1001200130

value: HIP


title: duodenum_Glu_negative_5254


title: 20151119_C18_170330_3


title: 20140709_C80_150331_6


title: 20140709_C77_150331_7


title: B11.1001200129

value: STR


title: 20151119_C13_170330_3


title: duodenum_Glu_positive_5254


title: duodenum_NeuroD1_negative_6362


title: 20140709_C76_150331_5


title: 20140709_C68_150331_3


title: 20140709_C70_150331_3


title: 20140709_C72_150331_4


title: 20140709_C71_150331_4


title: duodenum_NeuroD1_negative_6361


title: E4.1001200133


title: F12.1001200134


title: duodenum_NeuroD1_negative_6360


title: 20140709_C67_150331_3


title: 20140709_C66_150331_2


title: duodenum_Glu_positive_5160


title: 20140709_C65_150331_2


title: B6.1001200131

value: OB


title: duodenum_NeuroD1_positive_6362


title: duodenum_NeuroD1_positive_6361


title: 20140709_C62_150331_1


title: 20140709_C64_150331_1


title: 20140709_C61_150331_8


title: 20140709_C60_150331_7


title: 20140709_C59_150331_7


title: B3.1001200125

value: CB


title: duodenum_NeuroD1_positive_6360


title: 20140709_C57_150331_5


title: B8.1001200134


title: F10.1001200132


title: 20140709_C50_150331_3


title: mouse28_pancreas_mRNAseq

city: Boston

first: Maxim

last: Gerashchenko

state: Massachusetts

address: 77 Louis Pasteur Ave, NRB 435

department: Medicine

institute: Brigham and Women's Hospital

description:
processed data file:
organs_mRNAseq_count.txt

data_processing:
To remove illumina adapter from Ribo-seq libraries run "cutadapt -u 1 -m 23 -a AGATCGGAAGAGCACACGTCT --discard-untrimmed -o output.fastq input.fastq"
mRNA-seq sequences were aligned with TopHat 2.1.0 using following settings: tophat --transcriptome-index --no-discordant --no-mixed --no-novel-juncs
The NCBI mouse genome build GRCm38.p3 and the Mus musculus Annotation Release 105 were used as a reference. When aligning mRNA-seq and ribosome profiling reads for expression and translation efficiency estimation we used the following strategy. Only full chromosomes were left and all non-chromosomal and mitochondrial records removed. Furthermore, only RefSeq and BestRefSeq records were left in the transcriptome annotation, while Gnomon predictions were discarded along with pseudogenes. Read count per gene was accessed by HTseq-count software
To plot time-dependent ribosome occupancy, we employed a different strategy. First, using a gene bank (gbk) file, which comes in a package with the genome assembly and annotation, we extracted RefSeq and BestRefSeq records for every gene including CDS, 5’-UTR and 3’-UTR lengths and sequences. Among them, we identified the longest isoform for every gene, prioritized as CDS > 5’UTR > 3’UTR. 5’-UTRs were trimmed by 100 nucleotides. If either or UTRs were shorter than 100 nucleotides, we filled it with up to 100 based on genomic coordinates. The full list of sequences is collected in the mRNA_100.fna file. To prepare a list of non-redundant genes, we run blast of all vs. all (blastall -p blastn -m 8 -b 500 -v 500 -e 0.001). Gene pairs that are too similar at the level of nucleotide sequence were excluded. In addition to the e-score, we enforced a requirement of the high-homology stretch being at least 50 nt long, and if it was longer, the similarity had to be at least 90% to treat these genes as homologous and redundant. A total of 13,685 genes passed every threshold. This reference set ensured unambiguous alignment of ribosome footprints. Resulting sequences are collected in the mRNA_100unique.fna file.
Custom Perl and R scripts were used to calculate the footprint coverage profiles of individual genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: read counts contain raw read count of individual genes; footprint coverage contains gene coverage profiles

extract_protocol: Total RNA was extracted with Trizol (Invitrogen), according to the manual. After phase separation, upper aqueous phase was collected and mixed with 1.5 volumes of isopropanol. This mixture was applied to the column from the RNAqueous kit and proceeded as described in the manual. After elution 1 ul of Superase-In was added before storing at -80.

tag: internal animal id

value: 13 weeks old mouse

tag: inhibitors

tag: injection route

value: pancreas


title: H3.1001200134


title: D9.1001200130


title: mouse27_pancreas_mRNAseq


title: 20140709_C56_150331_5


title: mouse26_pancreas_mRNAseq


title: 20140709_C36_150331_6


title: 20140709_C37_150331_7


title: 20140709_C34_150331_6


title: mouse28_lung_mRNAseq

value: lung


title: C10.1001200134


title: 20140709_C54_150331_4


title: 20140709_C33_150331_5


title: 20140709_C32_150331_5


title: 20140709_C35_150331_6


title: F11.1001200125


title: mouse27_lung_mRNAseq


title: 20140709_C29_150331_4


title: mouse26_lung_mRNAseq


title: 20140709_C30_150331_7


title: 20140709_C31_150331_5


title: D8.1001200130


title: H4.1001200125


title: 20140709_C25_150331_4


title: 20140709_C28_150331_4


title: mouse28_testis_mRNAseq

value: testis


title: B10.1001200131


title: mouse27_tastis_mRNAseq


title: 20140709_C23_150331_3


title: mouse26_testis_mRNAseq


title: 20140709_C20_150331_2


title: mouse28_brain_mRNAseq

value: brain


title: F8.1001200132

value: wild type


title: C11.1001200133

value: Y


title: B4.1001200133


title: 20140709_C16_150331_1


title: 20140709_C17_150331_1


title: 20140709_C19_150331_2


title: 20140709_C18_150331_1


title: mouse27_brain_mRNAseq


title: 20140709_C14_150331_7


title: A8.1001200132


title: mouse26_brain_mRNAseq


title: 20140709_C15_150331_7


title: 20140709_C12_150331_6


title: 20140709_C24_150331_3


title: mouse29_heart_mRNAseq

value: heart


title: A11.1001200131


title: 20140709_C10_150331_7

value: Mixed background


title: 20140709_C11_150331_6

value: NR5A1-eGFP positive cells


title: 20140709_C09_150331_4

value: small


title: 20140709_C21_150331_2

value: 10M reads 100bp p-e


title: E2.1001200132

value: CTX


title: B6.1001200132


title: mouse28_heart_mRNAseq


title: 20140709_C08_150331_5


title: 20140709_C05_150331_3


title: mouse26_heart_mRNAseq


title: 20140709_C04_150331_4


title: mouse28_skeletal_mRNAseq

value: skeletal muscle


title: F6.1001200130

value: HIP


title: E7.1001200134


title: 20140709_C02_150331_2


title: 20140414_C93_150331_6


title: mouse27_skeletal_mRNAseq


title: mouse26_skeletal_mRNAseq


title: F9.1001200125


title: 20140414_C92_150331_6


title: mouse28_kidney_mRNAseq

extract_protocol: Total RNA was extracted with a column based RNAqueous mini kit (Ambion). After elution 1 ul of Superase-In was added before storing at -80.

value: kidney


title: 20140414_C91_150331_6


title: E12.1001200131

value: OB


title: 20140414_C90_150331_5


title: F10.1001200131


title: mouse27_kidney_mRNAseq

value: 13 weeks old mouse


title: 20140414_C88_150331_5


title: mouse26_kidney_mRNAseq


title: 20140709_C07_150331_5


title: F9.1001200132


title: 20140414_C87_150331_4


title: 20140414_C85_150331_5


title: 20140414_C83_150331_4


title: mouse28_liver_mRNAseq

value: liver


title: 20140414_C84_150331_4


title: B6.1001200125

value: CB


title: 20140414_C81_150331_3


title: F4.1001200129

value: STR


title: 20140709_C03_150331_2


title: 20140414_C78_150331_8


title: mouse27_liver_mRNAseq


title: 20140414_C73_150331_2


title: D7.1001200131


title: mouse26_liver_mRNAseq


title: 20140414_C64_150331_7


title: 20140414_C55_150331_5


title: 20140414_C46_150331_6


title: H3.1001200132


title: Treg_MT HiChIP H3K27ac biological replicate 2

city: San Francisco

first: Simone

last: Giacometti

address: 513 Parnassus Avenue

institute: UCSF

library_source: genomic

data_processing:
Library strategy: HiChIP-Seq
For CHIP-Seq: Reads were mapped to the mouse mm10 genome sequence (GRCm38) with BWA (version 0.7.16a-r1181), and BAM files were generated with SAMtools (version 1.5), using the following commands: bwa aln -o 1 -l 32 -t 4 -k 2 -m 80000000 [reference] [fastq] > [aln] ; bwa samse -n 10 [reference] [aln] [fastq] | samtools view -Sbh - > [bamfile]
Duplicates removal was performed using PICARD MarkDuplicates tool (version 2.17.10)
Bigwig files were generated from BAM files using deepTools bamCoverage (version 3.0.1) with parameters --binSize 10 --normalizeUsing RPGC --ignoreForNormalization chrX ---extendReads [insert size]
ChIP-seq peaks were called using MACS2 callpeak (version 2.1.1.20160309) with parameters --bdg -q 0.01 --keep-dup all
Differential peaks between the WT and MT samples were calculated using bdgdiff module in MACS2
Bigwig files and aligned peaks were visualised using the Interactive Genome Browser (IGV)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files containing the number of reads per 10 bp bins normalized to 1x sequencing depth (Reads Per Genomic Content)
Supplementary_files_format_and_content: text files containing ChIP-Seq peak genomic coordinates, length, summit, pileup, pvalue, fold enrichment, qvalue and name over input as determined by MACS2
For RNA-Seq: Quality of raw FASTQ sequences was assessed using FASTQC (v0.11.5).
Raw reads were adaptor-trimmed and quality-filtered using Cutadapt version 1.14 (-q 20,20)
Reads were aligned to the GRCm38/mm10 mouse genome reference with the STAR Aligner (version 020201)
Gene expression quantification was done with STAR (using the --quantMode GeneCounts option) to generate uniquely mapped read counts at the gene level
Differential expression analysis was performed with DESeq2 (v.1.16.0) using the count matrix as input
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing the raw reads count matrix
For HiChIP: Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Genome_build: mm9
Supplementary_files_format_and_content: Output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.

molecule: genomic DNA

source_name: Treg transgene

growth_protocol: Treg cells sorted from lymph nodes and spleens

extract_protocol:
Cells were harvested from mice that were approximately 3-4 weeks old. Lymph nodes and spleen cells were sorted based on CD4, CD25,GITR and Fr4 or CD4, CD25, Foxp3-GFP. Cells were fixed with formaldehyde, nuclei were extracted and sonicated. For RNA-seq total RNA was extracted using Quiagen's RNeasy Kit and TRIzol reagent
ChIP DNA was prepared for high throughput sequencing library using Accel-NGS 2S Plus DNA library kit
ChIP-seq and HiChIP with Illumina Hiseq4000, Illumina HiSeq 2500 single-end 50bp sequencing platform for RNA-seq

treatment_protocol: Crosslinked with 1% formaldehyde. IP with Foxp3 antibody; custom polyclonal antibody that has been affinity purified, IP with H3K27ac antibody for HiChIP (Abcam ab4729)

tag: cell type

value: Treg cells

tag: genotype/variation

value: mutant M370I

tag: antibody


title: 20140414_C44_150331_6


title: F3.1001200130

value: wild type

value: Y


title: 20140414_C38_150331_4

value: Mixed background


title: Treg_MT HiChIP H3K27ac biological replicate 1


title: 20140414_C37_150331_4

value: NR5A1-eGFP positive cells


title: D7.1001200125


title: 20140414_C35_150331_3

value: small


title: E2.1001200133


title: 20140414_C33_150331_8

value: 10M reads 100bp p-e


title: 20140414_C32_150331_8


title: 20140414_C36_150331_3


title: C9.1001200133


title: Treg_WT HiChIP H3K27ac biological replicate 2

source_name: Treg wild-type

value: Wild-type


title: 20140414_C30_150331_2


title: 20140414_C27_150331_1


title: Treg_WT Foxp3 Input

data_processing:
For CHIP-Seq: Reads were mapped to the mouse mm10 genome sequence (GRCm38) with BWA (version 0.7.16a-r1181), and BAM files were generated with SAMtools (version 1.5), using the following commands: bwa aln -o 1 -l 32 -t 4 -k 2 -m 80000000 [reference] [fastq] > [aln] ; bwa samse -n 10 [reference] [aln] [fastq] | samtools view -Sbh - > [bamfile]
Duplicates removal was performed using PICARD MarkDuplicates tool (version 2.17.10)
Bigwig files were generated from BAM files using deepTools bamCoverage (version 3.0.1) with parameters --binSize 10 --normalizeUsing RPGC --ignoreForNormalization chrX ---extendReads [insert size]
ChIP-seq peaks were called using MACS2 callpeak (version 2.1.1.20160309) with parameters --bdg -q 0.01 --keep-dup all
Differential peaks between the WT and MT samples were calculated using bdgdiff module in MACS2
Bigwig files and aligned peaks were visualised using the Interactive Genome Browser (IGV)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files containing the number of reads per 10 bp bins normalized to 1x sequencing depth (Reads Per Genomic Content)
Supplementary_files_format_and_content: text files containing ChIP-Seq peak genomic coordinates, length, summit, pileup, pvalue, fold enrichment, qvalue and name over input as determined by MACS2
For RNA-Seq: Quality of raw FASTQ sequences was assessed using FASTQC (v0.11.5).
Raw reads were adaptor-trimmed and quality-filtered using Cutadapt version 1.14 (-q 20,20)
Reads were aligned to the GRCm38/mm10 mouse genome reference with the STAR Aligner (version 020201)
Gene expression quantification was done with STAR (using the --quantMode GeneCounts option) to generate uniquely mapped read counts at the gene level
Differential expression analysis was performed with DESeq2 (v.1.16.0) using the count matrix as input
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file containing the raw reads count matrix
For HiChIP: Sequencing reads were aligned and paired, filtered for long-range contacts, and removed of duplicates using the HiC-Pro pipeline (PMID: 26619908)
Genome_build: mm9
Supplementary_files_format_and_content: Output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.

source_name: WT Treg cells


title: Treg_MT Foxp3 Input

source_name: M370I Treg cells


title: 20140414_C34_150331_3


title: 20140414_C31_150331_8


title: Treg_WT HiChIP H3K27ac biological replicate 1


title: 20140414_C26_150331_1


title: B10.1001200125


title: 20140414_C24_150331_5


title: 20140414_C29_150331_2


title: 20140414_C25_150331_6


title: Treg_MT Foxp3 ChIP


title: Treg_WT Foxp3 ChIP


title: 20140414_C23_150331_6


title: G8.1001200125


title: 20140414_C21_150331_7


title: H2.1001200131


title: 20140414_C20_150331_7


title: E12.1001200132

value: CTX


title: 20140414_C19_150331_8


title: A12.1001200129


title: sth1 recovery, 1h [RNA-Seq]

city: Jerusalem

first: Avital

last: Klein Brill

address: Edmond J. Safra Campus

institute: The hebrew university

data_processing:
mapped to the yeast (sacCer3) genomes using bowtie2 default parameters. We used UMI to filter duplicate reads.
For the analysis of the spike-in data, we used bowtie2 to align the sequenced library twice: to S. cerevisiae (sacCer3 R64) and to K. lactis (ASM251v1). We discarded reads that mapped to both strains.
For 5' data, G tracks were trimmed from read start before alignment
Genome_build: sacCer3
Supplementary_files_format_and_content: The wig file were generaged using bedtools genomeCoverageBed, full coverage for 3' data and with -5 option for 5' data.

organism: Saccharomyces cerevisiae

source_name: sth1 recovery, 1h

growth_protocol: yeast cells were grown in YPD at 24ºC with constant shaking to OD 0.3-0.6

extract_protocol:
Yeast cells were either fixed in formaldehyde or (for the stress experiment) cell pellet was flash frozen in liquid nitrogen and kept in -80C. For the spike-in experiments both fixed Sth1-degron and Kluyveromyces lactis cells were resuspended in water and cell concentration was determined under the microscope using a hemocytometer.  5% lactis were added to each sample.
For the spike-in experiments both fixed Sth1-degron and Kluyveromyces lactis cells were resuspended in water and cell concentration was determined under the microscope using a hemocytometer.  5% lactis were added to each sample.
for 3' libraries: RNA purification was performed as previously described (Dye, Hao, and Ahlquist 2005). Total RNA was incubated with oligo-dT RT primers with 7bp barcode and 8bp UMI  and transferred  to ice. RT reaction was performed with SmartScribe enzyme  followed by incubation at 70oC. Barcoded samples were then pooled and purified using SPRI beads X1.2. DNA-RNA hybrids were tagmented using Tn5 transposase  and 0.2% SDS was added to strip off the Tn5 from the DNA , followed by a SPRI X2 cleanup.
for 5' libraries: Cell pellet was resuspended in proteinase K solution in the presence of oligo(dt)25 beads that were pre-washed with Proteinase K buffer. RNA was released from the cells, followed by  mRNA hybridization to polyT beads. Beads-mRNA complexes were washed according to the manufacturer protocol except that buffer B was prepared without EDTA. Reverse transcription was performed on the beads with SmartScribe enzyme in the presence of Template Switching Oligo. cDNA was washed on beads and second strand synthesis was performed using barcoded oligo. Pooled samples were then tagmented as above. Supernatant was transferred to a new tube followed by a SPRI X2 clean up. NGS sequences were added to the tagmented DNA by PCR and the DNA was purified using 0.8x SPRI beads.

treatment_protocol: Auxin (3-indolo acetic acid, Sigma) was added at final concentration of 0.5mM

tag: experiment type

value: recovery

tag: treatment protocol

value: mid-log cells were incubated with auxin for 2 hours. Auxin was washed. Cells were sampled after 1h.


title: sth1 recovery, 3h [RNA-Seq]

source_name: sth1 recovery, 3h

tag: strain

value: mid-log cells were incubated with auxin for 2 hours. Auxin was washed. Cells were sampled after 3h.


title: C4.1001200131

tag: genotype

value: OB

value: N


title: 20140414_C16_150331_7

tag: tissue


title: sth1 recovery, 0h [RNA-Seq]

source_name: sth1 recovery, 0h

value: mid-log cells were incubated with auxin for 2 hours. Auxin was washed. Cells were sampled after 0h.


title: 20140414_C15_150331_3

tag: age


title: 20140414_C14_150331_3


title: 20140414_C17_150331_4


title: 20140414_C13_150331_3


title: sth1 depletion, 5h [RNA-Seq]

source_name: sth1 depletion, 5h

value: depletion

value: Auxin was added to mid-log culture. Cells were sampled after 5h.


title: sth1 depletion, 0.5h [RNA-Seq]

source_name: sth1 depletion, 0.5h

value: Auxin was added to mid-log culture. Cells were sampled after 30m.


title: 20140414_C12_150331_5


title: sth1 depletion, 2h [RNA-Seq]

source_name: sth1 depletion, 2h

value: Auxin was added to mid-log culture. Cells were sampled after 120m.


title: sth1 recovery, 5h [RNA-Seq]

source_name: sth1 recovery, 5h

value: mid-log cells were incubated with auxin for 2 hours. Auxin was washed. Cells were sampled after 5h.


title: 20140414_C09_150331_2

value: Mixed background


title: sth1 depletion, 0h [RNA-Seq]

source_name: sth1 depletion, 0h

value: Auxin was added to mid-log culture. Cells were sampled after 0m.


title: 20140414_C08_150331_2

value: NR5A1-eGFP positive cells

value: small


title: 20140414_C18_150331_4

value: 10M reads 100bp p-e


title: C2.1001200134

value: wild type

value: HIP

tag: gate

value: Y


title: 20140414_C07_150331_2

tag: c1 ifc size


title: E3.1001200134


title: B4.1001200132

value: CTX


title: A6.1001200134


title: 20140414_C06_150331_1

tag: sequencing depth


title: F5.1001200125

value: CB


title: 20140414_C03_150331_3


title: 20140414_C05_150331_1


title: 20140414_C11_150331_5


title: sth1 stress auxin KCl-45m [RNA-Seq]

source_name: sth1 stress auxin KCl-45m

value: stress

value: auxin was added to mid-log culture for 20m. KCl was added. Cells were sampled after 45m.


title: D4.1001200133

source_name: Brain myeloid cell

value: STR


title: B6.1001200133


title: 20160111_C93_170330_8

source_name: XX gonad


title: 20140414_C10_150331_5


title: 20140414_C04_150331_1


title: G10.1001200131

value: OB


title: G4.1001200129


title: sth1 stress auxin KCl-20m [RNA-Seq]

source_name: sth1 stress auxin KCl-20m

value: auxin was added to mid-log culture for 20m. KCl was added. Cells were sampled after 20m.


title: 20140414_C01_150331_1


title: sth1 stress auxin KCl-30m [RNA-Seq]

source_name: sth1 stress auxin KCl-30m

value: auxin was added to mid-log culture for 20m. KCl was added. Cells were sampled after 30m.


title: H11.1001200132


title: sth1 stress auxin KCl-10m [RNA-Seq]

source_name: sth1 stress auxin KCl-10m

value: auxin was added to mid-log culture for 20m. KCl was added. Cells were sampled after 10m.


title: 20160111_C91_170330_8

value: Mixed background


title: sth1 stress auxin KCl-60m [RNA-Seq]

source_name: sth1 stress auxin KCl-60m

value: auxin was added to mid-log culture for 20m. KCl was added. Cells were sampled after 60m.


title: 20160111_C90_170330_7

value: NR5A1-eGFP positive cells


title: D2.1001200131


title: 20160111_C88_170330_8

value: small


title: sth1 stress auxin KCl-0m [RNA-Seq]

source_name: sth1 stress auxin KCl-0m

value: auxin was added to mid-log culture for 20m. KCl was added. Cells were sampled after 0m.


title: 20160111_C86_170330_7

value: 10M reads 100bp p-e


title: 20140414_C02_150331_1


title: sth1 stress KCl only-60m [RNA-Seq]

source_name: sth1 stress KCl only-60m

value: EtOH was added to mid-log culture for 20m. KCl was added. Cells were sampled after 60m.


title: H7.1001200131

value: wild type

value: Y


title: 20160111_C85_170330_7


title: 20160111_C83_170330_7


title: 20160111_C81_170330_6


title: sth1 stress KCl only-45m [RNA-Seq]

source_name: sth1 stress KCl only-45m

value: EtOH was added to mid-log culture for 20m. KCl was added. Cells were sampled after 45m.


title: C12.1001200133


title: B7.1001200125

value: CB


title: 20160111_C92_170330_8


title: 20160111_C78_170330_6


title: 20160111_C79_170330_6


title: 20160111_C77_170330_6


title: sth1 stress KCl only-20m [RNA-Seq]

source_name: sth1 stress KCl only-20m

value: stress

value: EtOH was added to mid-log culture for 20m. KCl was added. Cells were sampled after 20m.


title: sth1 stress KCl only-30m [RNA-Seq]

source_name: sth1 stress KCl only-30m

value: EtOH was added to mid-log culture for 20m. KCl was added. Cells were sampled after 30m.


title: 20160111_C74_170330_5


title: 20160111_C76_170330_6


title: G5.1001200131

value: OB


title: sth1 stress KCl only-10m [RNA-Seq]

source_name: sth1 stress KCl only-10m

value: EtOH was added to mid-log culture for 20m. KCl was added. Cells were sampled after 10m.


title: 20160111_C73_170330_5


title: H8.1001200129

value: STR


title: 20160111_C71_rep_170330_5

value: Mixed background


title: 20160111_C71_170330_5


title: sth1 stress KCl only-0m [RNA-Seq]

source_name: sth1 stress KCl only-0m

value: EtOH was added to mid-log culture for 20m. KCl was added. Cells were sampled after 0m.


title: 20160111_C69_170330_4

value: NR5A1-eGFP positive cells


title: F7.1001200131


title: sth1 stress auxin only-60m [RNA-Seq]

source_name: sth1 stress auxin only-60m

value: Auxin was added to mid-log culture for 20m. Cells were sampled after 60m.


title: 20160111_C67_170330_4

value: small


title: sth1 stress auxin only-45m [RNA-Seq]

source_name: sth1 stress auxin only-45m

value: Auxin was added to mid-log culture for 20m. Cells were sampled after 45m.


title: 20160111_C66_170330_4

value: 10M reads 100bp p-e


title: B3.1001200134

value: wild type

value: HIP


title: 20160111_C64_170330_4


title: 20160111_C65_170330_4


title: 20160111_C63_170330_3


title: 20160111_C61_170330_3


title: 20160111_C58_170330_2


title: G5.1001200130

value: Y


title: 20160111_C60_170330_3


title: 20160111_C57_170330_2


title: G12.1001200133


title: sth1 stress auxin only-20m [RNA-Seq]

source_name: sth1 stress auxin only-20m

value: Auxin was added to mid-log culture for 20m. Cells were sampled after 20m.


title: 20160111_C56_170330_2


title: 20160111_C52_170330_1


title: sth1 stress auxin only-10m [RNA-Seq]

source_name: sth1 stress auxin only-10m

value: stress

value: Auxin was added to mid-log culture for 20m. Cells were sampled after 10m.


title: 20160111_C55_170330_2


title: sth1 stress auxin only-0m [RNA-Seq]

source_name: sth1 stress auxin only-0m

value: Auxin was added to mid-log culture for 20m. Cells were sampled after 0m.


title: F4.1001200130

source_name: Brain myeloid cell


title: 20160111_C51_170330_1

source_name: XX gonad


title: E11.1001200134


title: A5.1001200134


title: 20160111_C50_170330_1


title: 5p, sth1 depletion, 0.5h [RNA-Seq]

source_name: 5p, sth1 depletion, 0.5h

value: Auxin was added to mid-log culture. Cells were sampled after 30m.


title: D9.1001200129


title: 20160111_C49_170330_1


title: 20160111_C45_170330_8


title: sth1 stress auxin only-30m [RNA-Seq]

source_name: sth1 stress auxin only-30m

value: Auxin was added to mid-log culture for 20m. Cells were sampled after 30m.


title: 5p, sth1 depletion, 0h [RNA-Seq]

source_name: 5p, sth1 depletion, 0h

value: Auxin was added to mid-log culture. Cells were sampled after 0m.


title: C5.1001200125

value: CB


title: 20160111_C44_170330_8

value: Mixed background


title: A9.1001200129

value: STR


title: F12.1001200131

value: OB


title: 20160111_C38_170330_7

value: NR5A1-eGFP positive cells

value: small


title: 5p, sth1 depletion, 1h [RNA-Seq]

source_name: 5p, sth1 depletion, 1h

value: Auxin was added to mid-log culture. Cells were sampled after 60m.


title: B1.1001200133

value: wild type


title: G7.1001200133


title: 20160111_C40_170330_7

value: 10M reads 100bp p-e


title: 20160111_C42_170330_7


title: sth1 replication recovery, no alpha, wash-3h

description: replication recovery sample 14

data_processing:
mapped to the yeast (sacCer3) genomes using bowtie2 default parameters. Reads longer than 200 bp were filtered out.
For paired end data, we used read centers position. For single end data, we estimated read center as 75 bp downstream/upstream to the read position.
Mnase coverage was calculated using matlab “ksdensity” function with read centers count as weights and 30bp width.
Genome_build: sacCer3
Supplementary_files_format_and_content: Mnase coverage over the genome
count of read centers (measured / estimated) over the genome

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. The reaction was stopped by adding glycine to a final concentration of 125 mM, and cells were harvested by centrifugation and washed. Pellet were kept in -80oC. Yeast cells were resuspended in Zymolyase buffer and treated with zymolyase (6U/od) and incubated for 25 min at 30 °C to generate spheroplasts. cells were centrifuged, washed and resuspended NP buffer. Lysed Spheroplasts were treated with MNAse (Micrococcal nuclease, worthington). MNAse concentration was calibrated to generate 80% mono nucleosomes (1 unit for 2.5od, 37C, 20m). The reactions were stopped by adding 100 μl of 5% SDS and 50 mM EDTA.
MNase digested chromatin was reverse cross linked, and MNase sequencing libraries were prepared (Blecher-Gonen et al. 2013).

treatment_protocol: mid-log cells were not incubated with alpha factor and auxin for 2 hours. Auxin and alpha factor was washed. Cells were sampled after 3h.

value: replication recovery


title: sth1 replication recovery, no alpha, wash-30m

description: replication recovery sample 13

treatment_protocol: mid-log cells were not incubated with alpha factor and auxin for 2 hours. Auxin and alpha factor was washed. Cells were sampled after 30m.


title: 20160111_C30_170330_6


title: 20160111_C28_170330_5


title: 20160111_C34_170330_6


title: G1.1001200130

value: HIP

value: Y


title: 20160111_C26_170330_5


title: A7.1001200131


title: 20160111_C20_170330_4


title: A9.1001200130


title: 20160111_C19_170330_4


title: sth1 replication recovery, no alpha, wash-2h30m

description: replication recovery sample 11

treatment_protocol: mid-log cells were not incubated with alpha factor and auxin for 2 hours. Auxin and alpha factor was washed. Cells were sampled after 2h30m.


title: 20160111_C18_170330_3


title: C4.1001200125


title: sth1 replication recovery, no alpha, wash-4h

description: replication recovery sample 15

treatment_protocol: mid-log cells were not incubated with alpha factor and auxin for 2 hours. Auxin and alpha factor was washed. Cells were sampled after 4h.


title: 20160111_C39_170330_7


title: sth1 replication recovery, no alpha, wash-1h

description: replication recovery sample 10

treatment_protocol: mid-log cells were not incubated with alpha factor and auxin for 2 hours. Auxin and alpha factor was washed. Cells were sampled after 1h.


title: 20160111_C17_170330_3


title: 20160111_C16_170330_3


title: sth1 replication recovery, no alpha, wash-1h30m

description: replication recovery sample 9

treatment_protocol: mid-log cells were not incubated with alpha factor and auxin for 2 hours. Auxin and alpha factor was washed. Cells were sampled after 1h30m.


title: 20160111_C32_170330_6


title: C10.1001200131


title: 20160111_C15_170330_3


title: sth1 replication recovery, no alpha, wash-0m

description: replication recovery sample 8

treatment_protocol: mid-log cells were not incubated with alpha factor and auxin for 2 hours. Auxin and alpha factor was washed. Cells were sampled after 0h.


title: 20160111_C11_170330_2


title: 20160111_C12_170330_2


title: sth1 replication recovery, no alpha, wash-2h

description: replication recovery sample 12

treatment_protocol: mid-log cells were not incubated with alpha factor and auxin for 2 hours. Auxin and alpha factor was washed. Cells were sampled after 2h.


title: 20160111_C10_170330_2


title: sth1 replication recovery, alpha, wash-4h

description: replication recovery sample 7

treatment_protocol: mid-log cells were not incubated with alpha factor and auxin for 2 hours. Auxin was washed. Cells were sampled after 4h.


title: G3.1001200132

value: CTX


title: sth1 replication recovery, alpha, wash-3h

description: replication recovery sample 6

treatment_protocol: mid-log cells were not incubated with alpha factor and auxin for 2 hours. Auxin was washed. Cells were sampled after 3h.


title: 20160111_C08_170330_1


title: F1.1001200131


title: 20160111_C07_170330_2


title: 20160111_C02_170330_1


title: 20160111_C01_170330_1


title: A3.1001200132


title: 20160111_C03_170330_1


title: 20141022_C89_150331_8


title: sth1 replication recovery, alpha, wash-2h

description: replication recovery sample 4


title: G3.1001200129


title: 20141022_C87_150331_5


title: sth1 replication recovery, alpha, wash-30m

description: replication recovery sample 5

treatment_protocol: mid-log cells were not incubated with alpha factor and auxin for 2 hours. Auxin was washed. Cells were sampled after 30m.


title: 20141022_C85_150331_5


title: D12.1001200131


title: sth1 replication recovery, alpha, wash-2h30m

description: replication recovery sample 3

treatment_protocol: mid-log cells were not incubated with alpha factor and auxin for 2 hours. Auxin was washed. Cells were sampled after 2h30m.


title: 20141022_C81_150331_4


title: sth1 replication recovery, alpha, wash-1h

description: replication recovery sample 2

treatment_protocol: mid-log cells were not incubated with alpha factor and auxin for 2 hours. Auxin was washed. Cells were sampled after 1h.


title: G9.1001200125


title: sth1 replication recovery, alpha, wash-1h30m

description: replication recovery sample 1

treatment_protocol: mid-log cells were not incubated with alpha factor and auxin for 2 hours. Auxin was washed. Cells were sampled after 1h30m.


title: C1.1001200134


title: 20141022_C80_150331_2


title: F3.1001200131


title: 20141022_C79_150331_2


title: sth1 replication no alpha, IAA-60m

description: replication sample 6

source_name: sth1 replication no alpha, IAA-60m

treatment_protocol: mid-log cells were not incubated with alpha factor for 3 hours. Auxin was added. Cells were sampled after 60m.

value: replication


title: 20141022_C78_150331_4


title: 20141022_C75_150331_8


title: 20141022_C74_150331_1


title: C7.1001200134


title: sth1 replication no alpha, IAA-30m

description: replication sample 5

source_name: sth1 replication no alpha, IAA-30m

treatment_protocol: mid-log cells were not  incubated with alpha factor for 3 hours. Auxin was added. Cells were sampled after 30m.


title: 20141022_C83_150331_6


title: 20141022_C70_150331_7


title: 20141022_C71_150331_2


title: C10.1001200125


title: 20141022_C72_150331_8


title: sth1 replication no alpha, IAA-0m

description: replication sample 4

source_name: sth1 replication no alpha, IAA-0m

treatment_protocol: mid-log cells were not incubated with alpha factor for 3 hours. Auxin was added. Cells were sampled after 0m.


title: sth1 replication 3h alpha, IAA-60m

description: replication sample 3

source_name: sth1 replication 3h alpha, IAA-60m

treatment_protocol: mid-log cells were incubated with alpha factor for 3 hours. Auxin was added. Cells were sampled after 60m.


title: E1.1001200134


title: 20141022_C62_150331_4


title: sth1 replication 3h alpha, IAA-30m

description: replication sample 2

source_name: sth1 replication 3h alpha, IAA-30m

treatment_protocol: mid-log cells were incubated with alpha factor for 3 hours. Auxin was added. Cells were sampled after 30m.


title: 20141022_C68_150331_6


title: 20141022_C69_150331_6


title: 20141022_C65_150331_6


title: A12.1001200125


title: 20141022_C61_150331_4


title: sth1 replication 3h alpha, IAA-0m

description: replication sample 1

source_name: sth1 replication 3h alpha, IAA-0m

treatment_protocol: mid-log cells were incubated with alpha factor for 3 hours. Auxin was added. Cells were sampled after 0m.


title: E10.1001200130


title: sth1 stress auxin KCl-60m

description: stress sample 18

source_name: sth1 stress auxin KCl-60m

treatment_protocol: auxin was added to mid-log culture for 20m. KCl was added. Cells were sampled after 60m.

value: stress


title: 20141022_C58_150331_4


title: 20141022_C59_150331_4


title: 20141022_C56_150331_3


title: G1.1001200125


title: A10.1001200131


title: sth1 stress auxin KCl-45m

description: stress sample 17

source_name: sth1 stress auxin KCl-45m

treatment_protocol: auxin was added to mid-log culture for 20m. KCl was added. Cells were sampled after 45m.


title: 20141022_C50_150331_2


title: 20141022_C54_150331_2


title: 20141022_C55_150331_2


title: sth1 stress auxin KCl-30m

description: stress sample 16

source_name: sth1 stress auxin KCl-30m

treatment_protocol: auxin was added to mid-log culture for 20m. KCl was added. Cells were sampled after 30m.


title: C5.1001200134


title: 20141022_C49_150331_1


title: 20141022_C44_150331_8


title: 20141022_C43_150331_8


title: F2.1001200125


title: 20141022_C42_150331_8


title: sth1 stress auxin KCl-10m

description: stress sample 14

source_name: sth1 stress auxin KCl-10m

treatment_protocol: auxin was added to mid-log culture for 20m. KCl was added. Cells were sampled after 10m.


title: 20141022_C38_150331_7


title: F5.1001200131


title: D1.1001200125


title: 20141022_C36_150331_6


title: 20141022_C37_150331_7


title: C1.1001200133


title: 20141022_C35_150331_6


title: sth1 stress KCl only-60m

description: stress sample 12

source_name: sth1 stress KCl only-60m

treatment_protocol: EtOH was added to mid-log culture for 20m. KCl was added. Cells were sampled after 60m.


title: 20141022_C34_150331_3


title: 20141022_C33_150331_4


title: B1.1001200134

source_name: Brain myeloid cell

value: N


title: 20141022_C32_150331_4

source_name: XX gonad


title: sth1 stress KCl only-45m

description: stress sample 11

source_name: sth1 stress KCl only-45m

treatment_protocol: EtOH was added to mid-log culture for 20m. KCl was added. Cells were sampled after 45m.


title: sth1 stress KCl only-30m

description: stress sample 10

source_name: sth1 stress KCl only-30m

treatment_protocol: EtOH was added to mid-log culture for 20m. KCl was added. Cells were sampled after 30m.


title: 20141022_C29_150331_1


title: 20141022_C31_150331_4


title: G11.1001200134


title: C12.1001200131


title: sth1 stress auxin KCl-20m

description: stress sample 15

source_name: sth1 stress auxin KCl-20m

treatment_protocol: auxin was added to mid-log culture for 20m. KCl was added. Cells were sampled after 20m.


title: 20141022_C28_150331_1


title: 20141022_C26_150331_8


title: sth1 stress KCl only-10m

description: stress sample 8

source_name: sth1 stress KCl only-10m

treatment_protocol: EtOH was added to mid-log culture for 20m. KCl was added. Cells were sampled after 10m.


title: sth1 stress KCl only-20m

description: stress sample 9

source_name: sth1 stress KCl only-20m

treatment_protocol: EtOH was added to mid-log culture for 20m. KCl was added. Cells were sampled after 20m.


title: 20141022_C25_150331_8


title: sth1 stress auxin KCl-0m

description: stress sample 13

source_name: sth1 stress auxin KCl-0m

treatment_protocol: auxin was added to mid-log culture for 20m. KCl was added. Cells were sampled after 0m.


title: 20141022_C19_150331_6


title: D3.1001200130


title: sth1 stress KCl only-0m

description: stress sample 7

source_name: sth1 stress KCl only-0m

treatment_protocol: EtOH was added to mid-log culture for 20m. KCl was added. Cells were sampled after 0m.


title: 20141022_C24_150331_6


title: F2.1001200134


title: sth1 stress auxin only-60m

description: stress sample 6

source_name: sth1 stress auxin only-60m

treatment_protocol: Auxin was added to mid-log culture for 20m. Cells were sampled after 60m.


title: 20141022_C13_150331_4


title: 20141022_C17_150331_5


title: F10.1001200125


title: sth1 stress auxin only-45m

description: stress sample 5

source_name: sth1 stress auxin only-45m

treatment_protocol: Auxin was added to mid-log culture for 20m. Cells were sampled after 45m.


title: 20141022_C18_150331_8


title: 20141022_C12_150331_3


title: D10.1001200130


title: 20141022_C11_150331_3


title: 20141022_C10_150331_3


title: sth1 stress auxin only-30m

description: stress sample 4

source_name: sth1 stress auxin only-30m

treatment_protocol: Auxin was added to mid-log culture for 20m. Cells were sampled after 30m.


title: D8.1001200125


title: sth1 stress auxin only-20m

description: stress sample 3

source_name: sth1 stress auxin only-20m

treatment_protocol: Auxin was added to mid-log culture for 20m. Cells were sampled after 20m.


title: 20141022_C03_150331_1


title: H7.1001200125


title: 20141022_C08_150331_2


title: F3.1001200134


title: 20141022_C02_150331_1


title: C3.1001200125


title: sth1 stress auxin only-0m

description: stress sample 1

source_name: sth1 stress auxin only-0m

treatment_protocol: Auxin was added to mid-log culture for 20m. Cells were sampled after 0m.


title: 20140317_C93_150331_7


title: 20140317_C92_150331_8


title: 20141022_C01_150331_1


title: sth1 stress auxin only-10m

description: stress sample 2

source_name: sth1 stress auxin only-10m

treatment_protocol: Auxin was added to mid-log culture for 20m. Cells were sampled after 10m.


title: 20140317_C90_150331_7


title: H10.1001200131


title: sth1 recovery repeat-1h

description: recovery sample 10

source_name: sth1 recovery repeat-1h

treatment_protocol: mid-log cells were incubated with auxin for 2 hours. Auxin was washed. Cells were sampled after 1h.

value: recovery


title: E11.1001200130


title: 20140317_C84_150331_5


title: 20140317_C87_150331_6


title: sth1 recovery repeat-0h

description: recovery sample 9

source_name: sth1 recovery repeat-0h

treatment_protocol: mid-log cells were incubated with auxin for 2 hours. Auxin was washed. Cells were sampled after 0h.


title: 20140317_C81_150331_5


title: B8.1001200125

source_name: Brain myeloid cell

value: CB


title: 20141022_C07_150331_2

source_name: XX gonad

value: Mixed background


title: 20140317_C74_150331_2


title: sth1 recovery control-5h

description: recovery sample 8

source_name: sth1 recovery control-5h

treatment_protocol: mid-log cells were incubated with EtOH for 2 hours. EtOH was washed. Cells were sampled after 5h.


title: 20140317_C77_150331_3


title: 20140317_C69_150331_1


title: A10.1001200132


title: 20140317_C71_150331_1


title: D10.1001200125


title: 20140317_C70_150331_1


title: sth1 recovery control-0h

description: recovery sample 7

source_name: sth1 recovery control-0h

treatment_protocol: mid-log cells were incubated with EtOH for 2 hours. EtOH was washed. Cells were sampled after 0h.


title: sth1 recovery-5h

description: recovery sample 6

source_name: sth1 recovery-5h

treatment_protocol: mid-log cells were incubated with auxin for 2 hours. Auxin was washed. Cells were sampled after 5h.


title: 20140317_C68_150331_8


title: 20140317_C67_150331_7


title: sth1 recovery-3h

description: recovery sample 5

source_name: sth1 recovery-3h

treatment_protocol: mid-log cells were incubated with auxin for 2 hours. Auxin was washed. Cells were sampled after 3h.


title: 20140317_C65_150331_7


title: D11.1001200131


title: sth1 recovery-2h

description: recovery sample 4

source_name: sth1 recovery-2h

treatment_protocol: mid-log cells were incubated with auxin for 2 hours. Auxin was washed. Cells were sampled after 2h.


title: 20140317_C64_150331_7


title: 20140317_C61_150331_5


title: B12.1001200130


title: F12.1001200132


title: 20140317_C59_150331_5


title: 20140317_C60_150331_5


title: sth1 recovery-1h

description: recovery sample 3

source_name: sth1 recovery-1h


title: 20140317_C58_150331_5


title: sth1 recovery-0h

description: recovery sample 2

source_name: sth1 recovery-0h


title: 20140317_C55_150331_4


title: sth1 recovery-0.5h

description: recovery sample 1

source_name: sth1 recovery-0.5h

treatment_protocol: mid-log cells were incubated with auxin for 2 hours. Auxin was washed. Cells were sampled after 0.5h.


title: 20140317_C54_150331_3


title: 20140317_C51_150331_2


title: B4.1001200129

value: STR


title: G12.1001200129


title: A4.1001200125


title: 20140317_C53_150331_3


title: A2.1001200125


title: 20140317_C49_150331_2


title: 20140317_C45_150331_7


title: wt depletion-3h

description: depletion sample 18

source_name: wt depletion-3h

treatment_protocol: Auxin was added to mid-log culture. Cells were sampled after 3h.

value: depletion

value: wt


title: A5.1001200125


title: 20140317_C42_150331_8

value: NR5A1-eGFP positive cells

value: small


title: wt depletion-0m

description: depletion sample 17

source_name: wt depletion-0m

treatment_protocol: Auxin was added to mid-log culture. Cells were sampled after 0m.


title: 20140317_C41_150331_8


title: H6.1001200125

value: wild type


title: F8.1001200130


title: 20140317_C39_150331_6

value: 10M reads 100bp p-e


title: 20140317_C36_150331_5


title: sth1 depletion repeat-4.5h

description:
depletion sample 15
repeat of dep_4.5h

source_name: sth1 depletion repeat-4.5h

treatment_protocol: Auxin was added to mid-log culture. Cells were sampled after 4.5h.


title: 20140317_C50_150331_2


title: wt depletion-60m

description: depletion sample 19

source_name: wt depletion-60m

treatment_protocol: Auxin was added to mid-log culture. Cells were sampled after 60m.


title: sth1 depletion repeat-30m

description:
depletion sample 14
repeat of dep_30m

source_name: sth1 depletion repeat-30m

treatment_protocol: Auxin was added to mid-log culture. Cells were sampled after 30m.


title: 20140317_C32_150331_3


title: sth1 depletion repeat-0m

description:
depletion sample 13
repeat of dep_0m

source_name: sth1 depletion repeat-0m


title: 20140317_C31_150331_3


title: D5.1001200130


title: 20140317_C30_150331_3


title: 20140317_C28_150331_3


title: sth1 depletion control-6h

description: depletion sample 12

source_name: sth1 depletion control-6h

treatment_protocol: EtOH was added to mid-log culture. Cells were sampled after 6h.


title: C5.1001200131

source_name: Brain myeloid cell

value: OB


title: 20140317_C26_150331_2

source_name: XX gonad


title: 20140317_C40_150331_8


title: 20140317_C25_150331_2


title: H7.1001200134

value: HIP


title: 20140317_C24_150331_1


title: sth1 depletion repeat-60m

description:
depletion sample 16
repeat of dep_60m

source_name: sth1 depletion repeat-60m


title: sth1 depletion control-60m

description: depletion sample 11

source_name: sth1 depletion control-60m

treatment_protocol: EtOH was added to mid-log culture. Cells were sampled after 60m.


title: 20140317_C38_150331_5


title: 20140317_C23_150331_1


title: B12.1001200132

value: Y


title: 20140317_C21_150331_7


title: C4.1001200132

value: CTX


title: sth1 depletion-60m

description: depletion sample 9

source_name: sth1 depletion-60m


title: 20140317_C34_150331_5


title: 20140317_C20_150331_7


title: A4.1001200130


title: sth1 depletion-4.5h

description: depletion sample 8

source_name: sth1 depletion-4.5h


title: 20140317_C27_150331_2


title: 20140317_C17_150331_6


title: G9.1001200129


title: B9.1001200125


title: sth1 depletion-45m

description: depletion sample 7

source_name: sth1 depletion-45m

treatment_protocol: Auxin was added to mid-log culture. Cells were sampled after 45m


title: 20140317_C12_150331_4


title: C6.1001200133


title: 20140317_C10_150331_4


title: 20140317_C18_150331_6


title: sth1 depletion-3h

description: depletion sample 6

source_name: sth1 depletion-3h


title: 20140317_C08_150331_1


title: sth1 depletion-6h

description: depletion sample 10

source_name: sth1 depletion-6h

treatment_protocol: Auxin was added to mid-log culture. Cells were sampled after 6h.


title: G6.1001200131


title: 20140317_C07_150331_4


title: 20140317_C02_150331_2


title: sth1 depletion-30m

description: depletion sample 5

source_name: sth1 depletion-30m


title: 20140317_C06_150331_2


title: sth1 depletion-2h

description: depletion sample 4

source_name: sth1 depletion-2h

treatment_protocol: Auxin was added to mid-log culture. Cells were sampled after 2h.


title: H4.1001200131


title: 20140901_C83_150331_8


title: 20140901_C82_150331_8


title: sth1 depletion-20m

description: depletion sample 3

source_name: sth1 depletion-20m

treatment_protocol: Auxin was added to mid-log culture. Cells were sampled after 20m.


title: 20140901_C81_150331_7


title: D10.1001200132


title: 20140317_C16_150331_6


title: 20140901_C79_150331_7


title: 20140901_C77_150331_6


title: sth1 depletion-10m

description: depletion sample 2

source_name: sth1 depletion-10m

treatment_protocol: Auxin was added to mid-log culture. Cells were sampled after 10m.


title: C3.1001200134


title: 20140901_C76_150331_7


title: sth1 depletion-0m

description: depletion sample 1

source_name: sth1 depletion-0m


title: 20140901_C75_150331_4


title: A3.1001200133


title: 20140901_C74_150331_4


title: 20140901_C73_150331_6


title: G12.1001200130


title: MG-63_RNA_1

city: New York

first: John

middle: A

last: Morris

state: New York

address: 101 Avenue of the Americas, 4th Floor

institute: New York Genome Center

data_processing:
RNA-Seq: Raw reads were trimmed for quality (phred33 ≥ 30) and length (n ≥ 32), and Illumina adapters were clipped off using Trimmomatic v. 0.3564.
RNA-Seq: Filtered reads were aligned to the GRCh37 human reference using STAR v. 2.5.1b65.
RNA-Seq: Raw read counts of genes were obtained using HTseq-count v.0.6.166.
ATAC-Seq; DNAse-Seq: Illumina adapters were trimmed using Trimmomatic v. 0.3664.
ATAC-Seq; DNAse-Seq: Reads were aligned to the hg38 human reference using BWA v.0.7.15 65.
ATAC-Seq; DNAse-Seq: Peak calling was performed using hotspot2 with a cutoff of 1% FDR and converted to hg19 reference coordinates using UCSC liftOver.
Genome_build: hg19 (RNA-Seq); hg38 (ATAC-Seq; DNase-Seq)
Supplementary_files_format_and_content: bedGraph; Tab delimited peak files in starch format

organism: Homo sapiens

source_name: Human osteosarcoma

extract_protocol: RNA library preparations were carried out on 500 ng of RNA from SaOS-2, U2OS, MG63 and HOS cells with RNA integrity number (RIN) > 7 using the Illumina TruSeq Stranded Total RNA Sample preparation kit, according to manufacturer's protocol.

value: osteoblast cell line

tag: cell line


title: HOS_RNA_1

value: HOS


title: 20140901_C71_150331_4


title: G3.1001200125

value: N


title: 20140901_C69_150331_8


title: 20140901_C68_150331_8


title: B3.1001200131


title: 20140901_C67_150331_2


title: SaOS-2_RNA_1


title: 20140901_C66_150331_1


title: 20140901_C65_150331_6


title: 20140901_C64_150331_6


title: H11.1001200130


title: SaOS-2_ATACseq_1

extract_protocol:
Standard protocol was followed with the following modifications: Reduced the transposase reaction volume from 50 µl to 25 µl, increased the transposase concentration from 1x to 40x, and used 12 cycles of PCR to enrich each library.
Libraries were quantified by Q-PCR, Picogreen and LabChip, then were sequenced on the Illumina HiSeq 2500 to 125 bp in pair-ended mode, using the Nextera sequencing primers.


title: D1.1001200132


title: 20140901_C58_150331_7


title: 20140901_C61_150331_7


title: 20140901_C57_150331_3


title: E9.1001200132


title: H1.1001200125


title: 20140901_C55_150331_5


title: 20140901_C70_150331_3


title: CWP_sequence

city: Nantong

first: hao

last: wu

state: Jiangsu

address: XiSi Road,No.20

country: China

institute: Affiated hospital of nantong unversity

data_processing:
Basecalls performed using CASAVA version 1.8
circRNA-seq reads were mapped to human genome by BWA-MEM software by default parameters except -T = 19
circRNAs were detected and annotated with CIRI software
Genome_build: hg19
Supplementary_files_format_and_content: Number of raw junction read

source_name: Adjacent tissue specimens

extract_protocol:
Fresh TSSC tissue specimens (n=3) and adjacent tissue specimens (n=3) were homogenized. Total RNA was extracted from the frozen TSCC tissues and adjacent tissues with using TRIzol reagent (Life Technologies, Carlsbad, CA, USA). The RNA concentration of each sample was measured by NanoDrop ND-1000 analysis (Agilent Inc. USA). The OD260/OD280 ratio was used as the RNA purity index. The RNA purity is qualified if the OD260/OD280 ratio ranges from 1.8 to 2.1, then QC Results are marked as "Pass".
Total RNA from each sample was used to prepare the circRNA sequencing library, which included the following steps:1) 5 μg total RNA were pretreated to enrich circRNA using CircRNA Enrichment Kit (Cloud-seq Inc, USA). 2) RNA libraries were constructed by using pretreated RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.3) Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.Paired-end reads were harvested from Illumina HiSeq Sequencer after quality filtering. The reads were aligned to the reference genome/transcriptome with BWA-MEM software and circRNAs were detected and annotated with CIRI software. circBase database and circ2Trait disease database were used to annotated the identified circRNAs. Raw junction reads for all samples were normalized by total reads number and log2 transformed. Differentially expressed circRNAs were identified by t-test between two groups. Fold change >2.0 and P-value ≤0.05 were used as cutoffs for differential circRNAs. R package was used to perform cluster analysis for the normalized junction reads that were differentially expressed.

value: tongue

tag: tissue type

value: Adjacent tissue specimens

tag: molecule subtype

value: circular RNA


title: NCML_sequence


title: N_sequence


title: 20140901_C52_150331_1

value: Mixed background


title: U-2_OS_RNA_1


title: 20140901_C51_150331_1


title: CCML_sequence

source_name: TSCC tissue specimens

value: Tongue squamous cell carcinoma (TSCC) tissue specimens


title: A11.1001200125

source_name: Brain myeloid cell

value: CB


title: 20140901_C50_150331_1

source_name: XX gonad

value: NR5A1-eGFP positive cells


title: B7.1001200131


title: A2.1001200130


title: 20140901_C49_150331_3

value: small


title: H11.1001200134

value: wild type


title: 20140901_C33_150331_8

value: 10M reads 100bp p-e


title: 20140901_C32_150331_8


title: F6.1001200125


title: 20140901_C56_150331_5


title: 20140901_C31_150331_7


title: 20140901_C30_150331_6


title: C_sequence


title: A10.1001200134


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TCCTGAGC-TCTTACGC

city: Atlanta

first: Steven

last: Sloan

state: GA

address: 615 Michael Street, Whitehead Building Room 375

department: Human Genetics

institute: Emory University

description: Single cell

data_processing:
Read alignment: reads were aligned to the hg38 genome with STAR using the following options (-outFilterType BySJout \--outFilterMultimapNmax 20 \--alignSJoverhangMin 8 \--alignSJDBoverhangMin 1 \--outFilterMismatchNmax 999 \--outFilterMismatchNoverLmax 0.04 \--alignIntronMin 20 \--alignIntronMax 1000000 \--alignMatesGapMax 1000000 \--outSAMstrandField intronMotif ).
Per-gene read assignement: aligned reads were converted to counts for every gene using FeatureCounts (-p -t exon -g gene_id -a ).
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files with raw read values for each sample

source_name: human oligodendrocyte spheroids

growth_protocol: Human induced pluripotent stem cells (hiPSCs) grown in feeder free conditions were enzymatically dissociated and plated in microwells to form spheroids. The following day the spheroids were flushed from the microwellsand transferred into ultra-low attachment plastic dishes (Thermo Fisher Scientific) in EssentialTM 6 medium (Thermo Fisher Scientific) supplemented with two SMAD pathway inhibitors– dorsomorphin (DM, 2.5 μM, Sigma-Aldrich, P5499-CONF) and SB-431542 (10 μM, R&D systems, 1614) for five days. On day 6 in suspension the spheroids were transferred to differentiation and maintenance medium (DMM) containing DMEM/F12 (Thermo Fisher Scientific), B-27 Supplement without vitamin A (Thermo Fisher Scientific), N-2 Supplement (Thermo Fisher Scientific), MEM Non-Essential Amino Acids (1:100, Thermo Fisher Scientific), GlutaMax (1:100, Thermo Fisher Scientific), human insulin (25 μg/mL, Sigma-Aldrich), and penicillin-streptomycin (1:100, Thermo Fisher Scientific). The DMM medium was supplemented with 20 ng/ml EGF (R&D Systems) and 20 ng/ml bFGF (Peprotech) for 19 days. IWP-2 (5 μM, Selleckchem) was added from day 4 until day 24, and SAG (1 μM, Millipore Sigma) was added from day 12 to day 24. From day 25 to day 36, hOLS were cultured in DMM supplemented with T3 (60 ng/mL, Sigma Aldrich), biotin (100 ng/mL, Sigma Aldrich), NT-3 (20 ng/mL, Peprotech), BDNF (20 ng/mL, Peprotech), cAMP (1 μM, Sigma Aldrich), HGF (5 ng/mL, Peprotech), IGF-1 (10 ng/mL, VWR), and PDGFaa (10 ng/mL, R&D Systems). From day 37 onwards, hOLs were cultured in complete DMM (DMM supplemented with T3, biotin, cAMP, and ascorbic acid (AA, 20 μg/mL, Wako Pure Chemical).

extract_protocol:
Single cells were sorted into lysis buffer according to a published Smartseq2  protocol (Picelli, S. et al. 2014). ERCC RNA Spike-In Mix was added at 1: 2.4X10^7  dilution in the buffer.
Sorted cells in 96-well plates were used for library preparation following the  Smartseq2 protocol (Picelli, S. et al. 2014) with modifications. Briefly, plates were  incubated at 72˚C, 3 min for annealing with Oligo-dT 30 VN. Reverse transcription  mixture was added 6ul per well, and RT was performed at 42˚C for 90 min, followed  by 70˚C, 5 min. To amplify the whole transcriptome, 15ul of DNA amplification  mixture was added and cDNA was amplified for 21 cycles. Amplified cDNA was then  purified using PCRClean DX beads. cDNA quality and quantity were assessed using a  Fragment Analyzer (AATI, High Sensitivity NGS Fragment Analysis Kit:1 bp - 6000  bp), and samples with concentrations below 0.08ng/ul or abnormal peak patterns  were filtered out. A total of 295 cDNA samples (retaining 88.9% of initially sorted)  were diluted down to 0.15ng/ul (only if above it) and consolidated into a 384-well  plate using a Mosquito X1 (TTP Labtech). Library preparation was performed using  Nextera XT DNA Sample Prep Kit (Illumina, Cat: FC-131-1096) and Nextera XT 384  dual index primers, with the help of a Mosquito HTS machine for liquid transfer.  Tagmentation was performed in 1.2ul at 55˚C for 10 min and amplification was  performed in 4ul system, 10 cycles. In the end, all samples were pooled (0.5ul each)  together into a 1.5ml Eppendorf tube, and the mixed libraries were purified twice  with PCRClean DX beads. The final sample was reconstituted in 50ul EB buffer, and  the concentration and peaks were measured by Qubit and Bioanalyzer before  Illumina sequencing (Hiseq).
Single cell RNA-seq

tag: plate id

value: plate 1

value: Day 421

tag: line


title: 20140901_C29_150331_6


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TCCTGAGC-TCGCATAA

description: Single cell

value: Day 420


title: C12.1001200125

value: Y


title: 20140901_C27_150331_4


title: E6.1001200131

value: OB


title: 20140901_C26_150331_4


title: 20140901_C24_150331_8


title: F9.1001200129

value: STR


title: 20140901_C22_150331_3


title: 20140901_C20_150331_2


title: 20140901_C21_150331_1


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TCCTGAGC-TACTCCTT

description: Single cell

value: Day 418


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TCCTGAGC-TAAGGCTC

description: Single cell

value: Day 417


title: Ca_sequence

value: tongue


title: 20140901_C19_150331_2


title: A7.1001200132

value: CTX


title: 20140901_C17_150331_8

value: Mixed background


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TCCTGAGC-CTTAATAG

description: Single cell

value: Day 416


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TCCTGAGC-CTCCTTAC

description: Single cell

value: Day 415


title: 20140901_C18_150331_7

value: NR5A1-eGFP positive cells


title: C5.1001200133


title: 20140901_C28_150331_6

value: small


title: 20140901_C16_150331_5


title: 20140901_C34_150331_7


title: 20140901_C13_150331_7


title: 20140901_C12_150331_3


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TCCTGAGC-CTAGTCGA

description: Single cell

value: Day 414


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TCCTGAGC-TATGCAGT

description: Single cell

value: Day 419


title: E6.1001200125

value: wild type

value: CB


title: G12.1001200132


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TCCTGAGC-CGGAGAGA

description: Single cell

value: plate 1

value: Day 413


title: 20140901_C11_150331_3

value: 10M reads 100bp p-e


title: 20140901_C09_150331_1


title: E1.1001200132

value: Y


title: 20140901_C08_150331_5


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TCCTGAGC-ATTAGACG

description: Single cell

value: Day 412


title: H7.1001200129

value: STR


title: 20140901_C07_150331_5


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TCCTGAGC-ATAGCCTT

description: Single cell

value: Day 411


title: 20140901_C06_150331_1


title: E4.1001200125


title: 20140901_C03_150331_2


title: 20140901_C02_150331_3


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TCCTGAGC-ATAGAGAG

description: Single cell

value: Day 410


title: H3.1001200133


title: 20140708_C82_150331_8

value: Mixed background


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TCCTGAGC-AGGCTTAG

description: Single cell

value: Day 409


title: H5.1001200130

value: HIP


title: 20140708_C79_150331_5

value: NR5A1-eGFP positive cells


title: 20140708_C83_150331_7

value: small


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TCCTGAGC-AGCTAGAA

description: Single cell

value: Day 408


title: 20140708_C80_150331_5


title: F7.1001200130


title: 20140708_C78_150331_3


title: 20140708_C77_150331_7


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TCCTGAGC-AGAGGATA

description: Single cell

value: Day 407


title: 20140901_C10_150331_4


title: 20140708_C74_150331_2


title: 20140708_C73_150331_2


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TCCTGAGC-ACTCTAGG

description: Single cell

value: Day 406


title: G2.1001200133

value: wild type


title: 20140708_C71_150331_1


title: 20140708_C76_150331_7


title: D9.1001200133


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGGCATG-TCTTACGC

description: Single cell

value: plate 1

value: Day 405


title: C2.1001200129


title: E2.1001200131

value: OB


title: 20140708_C70_150331_1

value: 10M reads 100bp p-e


title: 20140708_C69_150331_8


title: 20140708_C68_150331_2


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGGCATG-TCGCATAA

description: Single cell

value: Day 404


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGGCATG-TATGCAGT

description: Single cell

value: plate 2

value: Day 403


title: H8.1001200131

value: Y


title: 20140708_C67_150331_7

value: Mixed background


title: 20140708_C60_150331_4


title: 20140708_C64_150331_6


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGGCATG-TACTCCTT

description: Single cell

value: Day 402


title: 20140708_C59_150331_4


title: 20140708_C58_150331_4


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGGCATG-TAAGGCTC

description: Single cell

value: Day 401


title: C8.1001200132

value: CTX


title: 20140708_C56_150331_3

value: NR5A1-eGFP positive cells

value: small


title: 20140708_C55_150331_3


title: C6.1001200129

value: STR


title: 20140708_C52_150331_2


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGGCATG-CTCCTTAC

description: Single cell

value: Day 399


title: E10.1001200132

value: wild type


title: 20140708_C35_150331_7


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGGCATG-CTAGTCGA

description: Single cell

value: plate 1

value: Day 398


title: 20140708_C39_150331_8


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGGCATG-CGGAGAGA

description: Single cell

value: Day 397


title: 20140708_C36_150331_7

value: 10M reads 100bp p-e


title: A1.1001200129


title: 20140708_C34_150331_8


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGGCATG-CTTAATAG

description: Single cell

value: Day 400


title: B2.1001200132


title: 20140708_C38_150331_8


title: G10.1001200125

value: CB


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGGCATG-ATTAGACG

description: Single cell

value: plate 2

value: Day 396


title: 20140708_C53_150331_2

value: Mixed background


title: 20140708_C33_150331_5


title: D4.1001200125

value: Y


title: 20140708_C32_150331_5


title: 20140708_C31_150331_5


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGGCATG-ATAGCCTT

description: Single cell

value: Day 395


title: F7.1001200125


title: 20140708_C30_150331_3


title: 20140708_C28_150331_3


title: H3.1001200125


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGGCATG-ATAGAGAG

description: Single cell

value: Day 394


title: 20140708_C27_150331_4

value: NR5A1-eGFP positive cells


title: 20140708_C26_150331_4

value: small


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGGCATG-AGGCTTAG

description: Single cell

value: Day 393


title: 20140708_C25_150331_1


title: F4.1001200134

value: HIP


title: 20140708_C23_150331_8


title: B1.1001200131

value: wild type

value: OB


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGGCATG-AGAGGATA

description: Single cell

value: plate 1

value: Day 391


title: B11.1001200130


title: 20140708_C22_150331_8

value: 10M reads 100bp p-e


title: 20140708_C20_150331_6


title: 20140708_C19_150331_6


title: 20140708_C21_150331_6


title: 20140708_C18_150331_8


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGGCATG-ACTCTAGG

description: Single cell

value: Day 390


title: H10.1001200132

value: CTX


title: 20140708_C17_150331_5


title: 20140708_C16_150331_6


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGCGCTC-CTCCTTAC

description: Single cell

value: plate 5

value: Day 388


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGGCATG-AGCTAGAA

description: Single cell

value: Day 392


title: 20140414_C22_150331_6

value: Mixed background


title: 20140708_C11_150331_4


title: D2.1001200125

value: CB

value: Y


title: E11.1001200131


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGCGCTC-TATGCAGT

description: Single cell

value: Day 389


title: 20140708_C10_150331_4

value: NR5A1-eGFP positive cells

value: small


title: D7.1001200130

value: HIP


title: 20140708_C09_150331_2


title: 20140708_C24_150331_8


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGCGCTC-ATAGAGAG

description: Single cell

value: Day 386


title: 20140708_C08_150331_2


title: E1.1001200133

value: wild type

value: STR


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGCGCTC-AGCTAGAA

description: Single cell

value: Day 385


title: 20140708_C07_150331_3

value: 10M reads 100bp p-e


title: 20140708_C05_150331_1


title: 20140708_C02_150331_1


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGCGCTC-AGAGGATA

description: Single cell

value: Day 384


title: E4.1001200131

value: OB


title: D11.1001200134


title: 20140505_C96_150331_8


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGCGCTC-ACTCTAGG

description: Single cell

value: plate 5

value: Day 383


title: 20140708_C01_150331_1


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TACGCTGC-TCTTACGC

description: Single cell

value: Day 382


title: 20140708_C06_150331_1

value: Mixed background


title: 20140505_C94_150331_8


title: A9.1001200134


title: 20140505_C92_150331_7


title: A7.1001200134


title: 20140505_C91_150331_7


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TACGCTGC-TCGCATAA

description: Single cell

value: plate 4

value: Day 381


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAGCGCTC-CTAGTCGA

description: Single cell

value: Day 387


title: 20140505_C90_150331_8

value: NR5A1-eGFP positive cells


title: F2.1001200131

value: Y


title: A3.1001200129


title: 20140505_C89_150331_8

value: small


title: 20140505_C88_150331_7


title: F12.1001200125

value: CB


title: 20140505_C87_150331_6


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TACGCTGC-TACTCCTT

description: Single cell

value: Day 379


title: 20140505_C86_150331_6


title: H9.1001200130

value: wild type

value: HIP


title: 20140505_C85_150331_6

value: 10M reads 100bp p-e


title: A10.1001200125


title: B6.1001200134


title: E6.1001200130


title: 20140505_C84_150331_4


title: 20140505_C74_150331_1


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TACGCTGC-CTCCTTAC

description: Single cell

value: Day 376


title: F12.1001200130


title: 20140505_C80_150331_3


title: 20140505_C77_150331_2


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TACGCTGC-CGGAGAGA

description: Single cell

value: Day 374


title: 20140505_C69_150331_7


title: 20140505_C83_150331_5


title: 20140505_C70_150331_1


title: 20140505_C82_150331_5


title: 20140505_C68_150331_7


title: F8.1001200134


title: B1.1001200132

value: CTX


title: 20140505_C79_150331_3


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TACGCTGC-TAAGGCTC

description: Single cell

value: Day 378


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TACGCTGC-ATTAGACG

description: Single cell

value: Day 373


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TACGCTGC-CTTAATAG

description: Single cell

value: Day 377


title: 20140505_C72_150331_1

value: Mixed background


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TACGCTGC-TATGCAGT

description: Single cell

value: plate 4

value: Day 380


title: 20140505_C67_150331_7

value: NR5A1-eGFP positive cells


title: B4.1001200125

value: Y


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TACGCTGC-ATAGCCTT

description: Single cell

value: Day 372


title: 20140505_C78_150331_2

value: small


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TACGCTGC-CTAGTCGA

description: Single cell

value: Day 375


title: 20140505_C66_150331_6


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TACGCTGC-AGGCTTAG

description: Single cell

value: Day 370


title: 20140505_C65_150331_6


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TACGCTGC-AGCTAGAA

description: Single cell

value: Day 369


title: 20140505_C63_150331_5

value: 10M reads 100bp p-e


title: F9.1001200134

value: wild type

value: HIP


title: 20140505_C62_150331_5


title: F7.1001200132

value: CTX


title: 20140505_C59_150331_4


title: 20140505_C61_150331_5


title: 20140505_C54_150331_2


title: F1.1001200133

value: STR


title: 20140505_C57_150331_3


title: 20140505_C56_150331_1


title: 20140505_C51_150331_2


title: H4.1001200134


title: 20140505_C48_150331_8


title: 20140505_C58_150331_4


title: 20140505_C60_150331_4


title: G10.1001200129


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TACGCTGC-ACTCTAGG

description: Single cell

value: Day 367


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAAGGCGA-TCGCATAA

description: Single cell

value: plate 1

value: Day 365


title: 20140505_C46_150331_8

value: Mixed background


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TACGCTGC-ATAGAGAG

description: Single cell

value: plate 4

value: Day 371


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAAGGCGA-TATGCAGT

description: Single cell

value: Day 364


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TACGCTGC-AGAGGATA

description: Single cell

value: Day 368


title: F8.1001200125

value: CB

value: Y


title: B7.1001200129


title: F8.1001200131

value: OB

value: N


title: 20140505_C52_150331_2

value: NR5A1-eGFP positive cells

value: small

value: 10M reads 100bp p-e


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAAGGCGA-TCTTACGC

description: Single cell

value: Day 366


title: 20140505_C40_150331_6


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAAGGCGA-TAAGGCTC

description: Single cell

value: Day 362


title: 20140505_C41_150331_6


title: 20140505_C39_150331_5


title: E11.1001200133

value: wild type

value: STR


title: 20140505_C34_150331_4


title: G12.1001200134

value: HIP


title: 20140505_C33_150331_3

value: Mixed background


title: 20140505_C38_150331_5


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAAGGCGA-CTTAATAG

description: Single cell

value: plate 1

value: Day 361


title: 20140505_C36_150331_4


title: C1.1001200129


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAAGGCGA-CTCCTTAC

description: Single cell

value: Day 360


title: 20140505_C32_150331_3


title: 20140505_C37_150331_5


title: 20140505_C31_150331_3


title: 20140505_C42_150331_8


title: C11.1001200134


title: 20140505_C30_150331_2


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAAGGCGA-CTAGTCGA

description: Single cell

value: Day 359


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAAGGCGA-CGGAGAGA

description: Single cell

value: Day 358


title: 20140505_C29_150331_2


title: 20140505_C25_150331_1


title: B9.1001200132

value: CTX

value: Y


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAAGGCGA-TACTCCTT

description: Single cell

value: Day 363


title: 20140505_C27_150331_1

value: NR5A1-eGFP positive cells


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAAGGCGA-ATTAGACG

description: Single cell

value: Day 357


title: G11.1001200133


title: B7.1001200134


title: 20140505_C24_150331_8

value: small

value: 10M reads 100bp p-e


title: 20140505_C23_150331_8


title: G6.1001200125

value: CB


title: 20140505_C21_150331_6


title: 20140505_C22_150331_8


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAAGGCGA-AGGCTTAG

description: Single cell

value: Day 354


title: B7.1001200132

value: wild type


title: 20140505_C17_150331_6


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAAGGCGA-ATAGCCTT

description: Single cell

value: Day 356


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAAGGCGA-ATAGAGAG

description: Single cell

value: Day 355


title: 20140505_C16_150331_6

value: Mixed background


title: 20140505_C18_150331_5


title: B2.1001200133

value: STR


title: 20140505_C15_150331_4


title: 20140505_C19_150331_7


title: B8.1001200133


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAAGGCGA-AGCTAGAA

description: Single cell

value: plate 1

value: Day 353


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAAGGCGA-AGAGGATA

description: Single cell

value: Day 352


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_TAAGGCGA-ACTCTAGG

description: Single cell

value: Day 351


title: 20140505_C08_150331_3


title: B8.1001200130

value: HIP

value: Y


title: 20140505_C07_150331_3

value: NR5A1-eGFP positive cells


title: C7.1001200125


title: H5.1001200131

value: OB


title: C9.1001200125


title: 20140505_C04_150331_2

value: small


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GTAGAGGA-TCTTACGC

description: Single cell

value: Day 350


title: 20140505_C03_150331_1

value: 10M reads 100bp p-e


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GTAGAGGA-TCGCATAA

description: Single cell

value: plate 2

value: Day 349


title: 20140505_C20_150331_7


title: 20140505_C02_150331_1


title: 20140505_C01_150331_1


title: A12.1001200134

value: wild type


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GTAGAGGA-TATGCAGT

description: Single cell

value: Day 348


title: A10.1001200130


title: 20140505_C11_150331_4

value: Mixed background


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GTAGAGGA-TAAGGCTC

description: Single cell

value: Day 346


title: G7.1001200132

value: CTX


title: RNA-Seq CTL2

city: Bukgu

first: Jihwan

last: Park

state: Gwangju

address: 123 Cheomdangwagi-ro

country: South Korea

institute: GWANGJU INSTITUTE OF SCIENCE /TECHNOLOGY

description: control

data_processing:
For mRNA-Seq data, adaptor and lower-quality bases were trimmed with Trim-galore.
Reads were aligned to the Gencode mouse genome (GRCm38) using STAR-2.4.1d.
Read counts for each sample was obtained using HTSeq-0.6.1 (htseq-count).
Genome_build: mm10
Supplementary_files_format_and_content: mRNA-Seq: HTSeq count file

source_name: Tubule epithelial cells from kidney

growth_protocol: Cell suspensions were cultured in RPMI 1640 (Corning#10-040-CM) supplement with 10% fetal bovine serum (Atlanta Biologicals#S11950), 20 ng/ml EGF (Peprotech#AF-100-15), 1× ITS (Gibco#51500-056), and 1% penicillin-streptomycin (Corning#30-002-CI) at 5% CO2, at 37°C

extract_protocol:
RNA was isolated from harvested cells using Trizol (Invitrogen)
RNA (100 ng) was used to isolate poly(A)-purified mRNA using the Illumina TruSeq RNA Preparation Kit.

treatment_protocol: When cell confluence reached 70%, the media were changed with serum-free RPMI for 24h. After that, cells were treated with 50 ng/ml TGF-β1 (Peprotech#100-21) for 24 h

value: FvB

value: kidney

value: 4 to 6 weeks


title: RNA-Seq CTL1

description: control


title: RNA-Seq TGFB1-1

description: TGF-b1 treated


title: RNA-Seq TGFB1-3

description: TGF-b1 treated


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GTAGAGGA-CTCCTTAC

description: Single cell

value: Day 344


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GTAGAGGA-TACTCCTT

description: Single cell

value: Day 347


title: G8.1001200129

value: STR

value: Y


title: 20140505_C06_150331_2

value: NR5A1-eGFP positive cells

value: small


title: E2.1001200125

value: CB


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GTAGAGGA-CTTAATAG

description: Single cell

value: plate 2

value: Day 345


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GTAGAGGA-CTAGTCGA

description: Single cell

value: Day 343


title: D6.1001200128

value: wild type

value: N


title: TG IN treated 2

city: Cincinnati

first: Mei-Ling

last: Bermudez

state: Ohio

address: 160 Panzeca Way

department: Environmental Health

institute: University of Cincinnati

data_processing:
none provided by the submitter
Supplementary_files_format_and_content: entrez gene ID and counts

source_name: Midbrain

extract_protocol:
RNA was extracted using the mirVana miRNA Isolation Kit  following the manufacturer’s protocol for total RNA extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Two months old WT and TG mice were treated for 2-months

tag: treatment

value: carnosine


title: TG DW treated 3

value: drinking water


title: TG DW treated 1


title: TG IN treated 3


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GTAGAGGA-CGGAGAGA

description: Single cell

value: Day 342


title: TG DW treated 2


title: RNA-Seq TGFB1-2

description: TGF-b1 treated

value: FvB

value: kidney


title: C3.1001200128


title: TG IN treated 1


title: TG Control 2

value: control


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GTAGAGGA-ATTAGACG

description: Single cell

value: Day 341


title: TG Control 3


title: G8.1001200123

value: OB


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GTAGAGGA-ATAGCCTT

description: Single cell

value: Day 340


title: RNA-Seq CTL3

description: control

value: 4 to 6 weeks


title: F9.1001200128

value: STR

value: Y


title: H3.1001200124

value: CB


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GTAGAGGA-ATAGAGAG

description: Single cell

value: plate 2

value: Day 339


title: WT IN Treated 1


title: WT IN Treated 2


title: WT Control 3


title: A9.1001200128

value: wild type


title: WT Control 1


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GTAGAGGA-AGCTAGAA

description: Single cell

value: Day 337


title: B11.1001200128


title: TG Control 1


title: SCGPM_Rebecca-Oligo_HMMKJ_L7_GTAGAGGA-ACTCTAGG

description: Single cell

value: Day 335