title: 128-cell, polysome-unbound

description: rRNA-depleted RNA


title: Rao-2017-CHIP030-NIPBL-treated

status: Public on Oct 13 2017

type: SRA

city: Houston

first: Suhas

last: Rao

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

library_source: genomic

data_processing:
The paired end reads were aligned separately using BWA against the b37 human build
PCR duplicates, low mapping quality and unligated reads were removed using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Contact matrices were constructed at various resolutions and normalized using Juicer (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
loops were annotated using HiCCUPS (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016), domains were annotated using Arrowhead (see Rao, Huntley, et al Cell 2014; Durand, Shamim, et al Cell Systems 2016)
Genome_build: b37 (human)
Supplementary_files_format_and_content: .hic file (contains contact matrices at various resolutions in an easy to visualize and access format) (see Durand, Robinson, et al Cell Systems 2016)

molecule: genomic DNA

organism: Homo sapiens

source_name: Colorectal carcinoma

growth_protocol: Cell lines were cultured according to manufacturer's instructions

extract_protocol:
Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeqX Ten, NextSeq 500, or HiSeq 2500 following the manufacturer's protocols
Hi-C; Specific library strategies are indicated as additional columns in the SAMPLES section

treatment_protocol: Cells were treated with 500uM auxin as described in the characteristics above

tag: cell line

tag: protocol

value: ChIP-Seq

tag: treatment

value: 500uM auxin (360 min)


title: 5.3 hpf, polysome-bound

status: Public on Oct 14 2017

city: Warsaw

first: Cecilia

middle: Lanny

last: Winata

state: Mazovia

address: 4 Ks. Trojdena

country: Poland

institute: International Institute of Molecular and Cell Biology in Warsaw

description: rRNA-depleted RNA

library_source: transcriptomic

data_processing:
Basecalling was performed by Illumina RTA 1.18.61. Files were translated into demultiplexed FASTQ files by Illumina bcl2fastq2 2.16.10.
For the RNA-Seq data analysis sequencing reads were aligned to the GRCz10 zebrafish genome using STAR v2.4.2a (Dobin et al. 2012).
For the novel transcript discovery sequencing reads were trimmed using cutadapt 1.9.1 (-e 0.1; -q 20; -O 3; -m 20; -a  AGATCGGAAGAGC). Subsequently the reads were aligned to the GRCz10 zebrafish genome using GSNAP version 2015-12-31 (--filter-chastity=both; --max-mismatches=5; --novelsplicing=1). Transcriptome was assembled using cufflinks 2.2.1 (--multi-read-correct; --library-type fr-secondstrand) with Ensembl release 83 genome annotation. Cuffcompare was run to compare and annotate the newly assembled transcripts.
Transcript level abundances were generated using Salmon 0.6.0 algorithm (Patro et al., 2015). The abundances were summarized to gene level and imported to DESeq2 using tximport 1.0.2. Subsequently data was normalized to library size using DESeq2 „median ratio method” (Anders and Huber 2010).
Genome_build: GRCz10
Supplementary_files_format_and_content: Salmon's quantification files, tab-delimited text files, contain abundance measurements for each sample. normalizedCounts.txt tab-delimited text file contains counts for all the samples, normalized using DESeq2.

molecule: total RNA

organism: Danio rerio

source_name: whole zebrafish embryo

growth_protocol: Zebrafish embryos were maintained according to standard protocol (Westerfield et al., 2000) and staged according to standard morphological criteria (Kimmel et al., 1995).

extract_protocol:
rRNA-depletion was performed using RiboZero Magnetic Gold Kit (Epicentre), unfractionated, polysome-associated and non associated RNA were subsequently isolated using Qiagen RNAeasy kit (Qiagen, USA).
Sequencing library was constructed using Stranded RNA-seq libraries were generated using ScriptSeq v2 RNA Library Preparation Kit (Illumina, USA).

tag: strain

value: wild-type (AB)

tag: developmental stage

value: 5.3 hpf

tag: tissue

value: whole embryo


title: Rao-2017-CHIP029-NIPBL-untreated


title: CN_pc5_+_HJag

city: Stockholm

first: Urban

last: Lendahl

address: Von Eulers vag 3

country: Sweden

institute: Karolinska Insttitutet

description: RPKM CN_pc5_+_HJag

data_processing:
Reads were aligned using STAR to genomes mm9 and hg19
Reads were separated for different species using S^3 (https://github.com/danielramskold/S3_species-specific_sequencing) with settings -Ms 3 -Mu 3 -D 2
Reads that mapped uniquely in the target species' genome were selected
Gene expression values were calculated using rpkmforgenes.py (see link above) with options -rmnameoverlap -bothendsceil -u and using RefSeq annotation from 7 April 2013 and unique alignment positions from http://sandberg.cmb.ki.se/multo/
Genome_build: mm9 and hg19
Supplementary_files_format_and_content: Tab-delimited text of normalised expression values and read counts

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus

source_name: Cell lines

growth_protocol: Mouse C2C12 control and C2C12-FLNotch1 (latter with 1ug/mL puromycin selection; Puromycin dihydrochloride from Streptomyces alboniger, Sigma-Aldrich®, cat. no. P7255), and human HEK-293-Flp-In cells (Hansson et al., 2010): HEK293-Flp control (Flp Ctrl), HEK293-Flp-Jag1WT (Flp Jag1+), HEK293-Flp-Jag1Ndr (Flp Jag1Ndr) (latter two with 300 ug/mL hygromycin selection; Hygromycin B, Gibco®, cat. no. 10687-010) were cultured in complete medium, composed of DMEM, high glucose, pyruvate (Gibco®, cat. no. 41966-029) supplemented with 10% fetal bovine serum (Gibco®, cat. no. 10270-106) and 1% penicillin-streptomycin (10,000 U/mL, Gibco®, cat. no. 15140-122), at 37°C in a humidified 5% CO2 atmosphere.

extract_protocol:
RNA extraction for all cell lysates from the two-species co-culture and immobilized ligand assay was performed using the RNeasy Mini Kit (cat. no. 74104, QIAGEN), including on-column DNase I digestion (cat. no. 79254, QIAGEN).
cDNA libraries for all samples were created using the TruSeq® RNA Sample Prep Kit v2–48, Set A (cat. no. RS-122-2001, Illumina®,) as per the TruSeq® RNA Sample Preparation v2 Guide, Low-Throughput Protocol.

treatment_protocol: In one 12-well plate, we seeded 3 wells of mouse C2C12 control cells and 3 wells of C2C12-FLN1 cells, with 3.6x105 cells in 1 mL antibiotic-free medium per well. Cells were allowed to settle for 8 hours. C2C12 control and C2C12-FLN1 cells were transfected with pcDNA5 (1.6 ug/well). All transfections were done using Lipofectamine® 2000 (InvitrogenTM, cat. no. 11668-019) with Opti-MEM® I Reduced Serum Medium (Gibco®, cat. no. 31985-062), according to manufacturer’s instructions. The following day (18 hours post transfection), 3.6x105 cells in 0.5 mL antibiotic-free medium of Flp Ctrl, Flp Jag1+, or Flp Jag1Ndr cells were added. Cells were co-cultured for 6 hours, then lysed in 350 L per well Buffer RLT (QIAGEN, cat. no. 79216) with 1% 2-Mercaptoethanol (Sigma-Aldrich®, cat. no. M3148) and stored at -80°C until RNA extraction.

tag: cell line (receptor side)

value: C2C12 cells

tag: mouse cell genotype/variation

value: Notch1 expression

tag: cocultured with

value: human HEK-293-Flp-In cells

tag: ligand side

value: Jag1 WT (Flp Jag1+)

tag: human cell genotype/variation

value: Jag1 expression


title: CN_pc5_+_Hwt

description: RPKM CN_pc5_+_Hwt

value: control (Flp Ctrl)

value: wild type


title: 3.5 hpf, polysome-bound

description: rRNA-depleted RNA

value: 3.5 hpf


title: Rao-2017-CHIP025-H4K20me3-untreated


title: Cwt_pc5_+_HJag

description: RPKM Cwt_pc5_+_HJag


title: Rao-2017-CHIP028-H2AZ-treated


title: Cwt_pc5_+_HNdr

description: RPKM Cwt_pc5_+_HNdr

value: Jag1 Ndr (Flp Jag1Ndr)

value: Jag1Ndr expression


title: CN_pc5_+_HNdr

description: RPKM CN_pc5_+_HNdr


title: Rao-2017-CHIP024-H3K79me2-treated


title: Rao-2017-CHIP027-H2AZ-untreated


title: RNA Bind-N-Seq: Bead control for YTH purification; sample 1

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description:
processed data file:
GEO_bind_n_seq.txt.gz

data_processing:
Library strategy: RNA Bind-N-Seq
For RNA Bind-n-Seq experiment the reads were sorted into individual libraries based on the barcodes and the 3′ adapter sequences were removed using cutadapt . Only reads of final length of 21 nucleotides with A at 10th position were kept for further analysis using R (R Core Team, 2017) and Bioconductor (Huber et al., 2015). Frequencies of individual nucleotides were calculated for each position as well as enrichment vs. the bead control. MEME - Motif discovery tool (Bailey and Elkan, 1994)  was used to search for a motif in a collection of 9-mers (read positions 6-14) centred around the  m6A at position 10.
genome build: N/A
processed data files format and content: The files for RNA Bind-n-Seq experiment contains the comparison of frequencies of 9mers centered on m6A.

organism: synthetic construct

source_name: random 21 nt ssRNAs with a central m6A moiety (N10-m6A-N10)

growth_protocol: To get the Ythdc2 knock-out mice, endogenous Ythdc2 locus of the C57BL/6J mouse embryos was targeted with two guide RNAs (gRNAs) that direct the DNA endonuclease Cas9 to create a 152 bp deletion that removes all of the exon 7 (Line #2). Additionally, a 181 nt single-stranded DNA (ssDNA) repair template (IDT) that carries a triple-stop codon (and 80 nt homology arms on each side of triple-stop codon) was co-injected into single-cell mouse embryos. This resulted in a knock-in line that has the triple-stop codon cassette introduced into the exon 7, truncating the coding sequence within the RNA helicase domain (Line #1).

extract_protocol:
For RNA Bind-n-Seq experiment  randomized 21 nt single-stranded RNAs carrying a central m6A moiety were mixed with Ni-NTA agarose beads alone or bound to 6xHis-SUMO-YTH domain (of hYTHDC2). RNA bound to the beads was phenol chloroform extracted.
For m6a IP experiment testicular RNA was isolated using the Trizol reagent and polyA+ transcripts were purified, fragmented and the fragments were immunopurified using anti-m6A antibody. Total testicular and ovarian RNAs were isolated using the Trizol reagent.
Sequencing libraries  of RNA Bind-n-Seq and m6a IP experiments were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Cat No:E7300) according to manufacturer instructions and sequenced on Illumina 2000 HiSeq platform (EMBL Heidelberg Gene core facility). Sequencing libraries of total testicular and ovarian RNAs were prepared by TruSeq Stranded Total RNA kit with Ribo-Zero Gold and sequenced on the Illumina HiSeq 4000 sequencer (iGE3 Genomics Platform, University of Geneva)

tag: purification

value: Ni-NTA beads

tag: background strain

tag: age


title: Cwt_pc5_+_Hwt

description: RPKM Cwt_pc5_+_Hwt


title: Rao-2017-CHIP023-H3K79me2-untreated


title: Rao-2017-CHIP016-H3K36me3-treated


title: Rao-2017-CHIP014-H3K4me1-treated


title: Rao-2017-CHIP022-H4K16Ac-treated


title: Rao-2017-CHIP015-H3K36me3-untreated


title: Rao-2017-CHIP021-H4K16Ac-untreated


title: Rao-2017-CHIP013-H3K4me1-untreated


title: Rao-2017-CHIP018-H3K27me3-treated


title: Rao-2017-CHIP017-H3K27me3-untreated


title: Rao-2017-CHIP026-H4K20me3-treated


title: Rao-2017-CHIP011-H3K4me3-untreated


title: Rao-2017-CHIP010-H3K27Ac-treated


title: Rao-2017-CHIP008-CTCF-treated


title: Rao-2017-CHIP009-H3K27Ac-untreated


title: Rao-2017-CHIP002-RAD21-treated


title: Rao-2017-CHIP001-RAD21-untreated


title: H2_cell_9

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: National Institutes of Health

data_processing:
Paired-end reads were mapped to the hg19 genome with RSubread, featureCounts function within the Rsubread package was applied to summarize data to integer-based, gene-level read counts with annotation of ENSEMBL.
log(TPM+1) was calculated and used to represent gene expression, then expression of each gene was normlazation cross cells.
Genome_build: hg19
Supplementary_files_format_and_content: comma separated file containing normalized, centered transcripts per million (log(tpm+1)) values for filtered cells from healthy donors and patients.

source_name: Bone Marrow

extract_protocol: The C1 Single-cell Auto Prep System (Fluidigm) was employed to perform SMARTer (Clontech) WTA on up to 96 individual cells, according to the manufacturer’s protocols (full details available at www.fluidigm.com). WTA products were converted to Illumina sequencing libraries using Nextera XT (Illumina). Samples with single cell and bulk controls were sequenced on an Illumina HiSeq 2500 or 3000 Systems using a 75-bp paired-end sequencing strategy

tag: markers

tag: Sex

value: Male

tag: subject

tag: disease

value: bone marrow cells from healthy donors


title: H2_cell_95


title: Rao-2017-CHIP019-H3K9me3-untreated

tag: cell line

tag: protocol

value: ChIP-Seq


title: H2_cell_94


title: H2_cell_96


title: H2_cell_93


title: H2_cell_92


title: Rao-2017-CHIP020-H3K9me3-treated

tag: treatment

value: 500uM auxin (360 min)


title: H2_cell_91


title: H2_cell_90


title: Rao-2017-CHIP012-H3K4me3-treated


title: H2_cell_8


title: H2_cell_89


title: H2_cell_88


title: H2_cell_84


title: H2_cell_81


title: H2_cell_82


title: H2_cell_80


title: H2_cell_83


title: Rao-2017-CHIP007-CTCF-untreated


title: H2_cell_87


title: H2_cell_85


title: H2_cell_86


title: H2_cell_79


title: H2_cell_78


title: H2_cell_76


title: H2_cell_77


title: H2_cell_7


title: H2_cell_75


title: H2_cell_74


title: H2_cell_6


title: H2_cell_67


title: H2_cell_68


title: H2_cell_72


title: H2_cell_71


title: H2_cell_66


title: H2_cell_73


title: H2_cell_64


title: H2_cell_65


title: H2_cell_63


title: H2_cell_62


title: H2_cell_60


title: H2_cell_58


title: H2_cell_5


title: H2_cell_59


title: H2_cell_57


title: H2_cell_54


title: H2_cell_53


title: H2_cell_55


title: H2_cell_52


title: H2_cell_50


title: H2_cell_51


title: H2_cell_4


title: H2_cell_47


title: H2_cell_49


title: H2_cell_48


title: H2_cell_69


title: H2_cell_70


title: H2_cell_46


title: H2_cell_41


title: H2_cell_43


title: H2_cell_42


title: H2_cell_45


title: H2_cell_44


title: H2_cell_61


title: H2_cell_56


title: H2_cell_40


title: H2_cell_3


title: H2_cell_38


title: H2_cell_32


title: H2_cell_39


title: H2_cell_36


title: H2_cell_37


title: H2_cell_35


title: H2_cell_33


title: H2_cell_31


title: H2_cell_2


title: H2_cell_29


title: H2_cell_26


title: H2_cell_27


title: H2_cell_30


title: H2_cell_28


title: H2_cell_24


title: H2_cell_22


title: H2_cell_1


title: H2_cell_21


title: H2_cell_15


title: H2_cell_19


title: H2_cell_23


title: H2_cell_25


title: H2_cell_18


title: H2_cell_17


title: H2_cell_34


title: H2_cell_16


title: H2_cell_14


title: H2_cell_12


title: H2_cell_13


title: H2_cell_10


title: H2_cell_11


title: H1_cell_98


title: H1_cell_99


title: H1_cell_92


title: H1_cell_94


title: H1_cell_91


title: H1_cell_89


title: H1_cell_93


title: H2_cell_20


title: H1_cell_97


title: H1_cell_85


title: H1_cell_88


title: H1_cell_8


title: H1_cell_81


title: H1_cell_9


title: H1_cell_82


title: H1_cell_7


title: H1_cell_96


title: H1_cell_95


title: H1_cell_80


title: H1_cell_86


title: H1_cell_79


title: H1_cell_84


title: H1_cell_90


title: H1_cell_76


title: H1_cell_77


title: H1_cell_78


title: H1_cell_74


title: H1_cell_73


title: H1_cell_87


title: H1_cell_75


title: H1_cell_83


title: H1_cell_72


title: H1_cell_70


title: H1_cell_71


title: H1_cell_65


title: H1_cell_6


title: H1_cell_63


title: H1_cell_62


title: H1_cell_64


title: H1_cell_68


title: H1_cell_67


title: H1_cell_69


title: H1_cell_57


title: H1_cell_58


title: H1_cell_66


title: H1_cell_61


title: H1_cell_52


title: H1_cell_60


title: H1_cell_53


title: H1_cell_59


title: H1_cell_50


title: H1_cell_4


title: H1_cell_5


title: H1_cell_56


title: H1_cell_54


title: H1_cell_55


title: H1_cell_49


title: H1_cell_46


title: H1_cell_45


title: H1_cell_48


title: H1_cell_51


title: H1_cell_43


title: H1_cell_42


title: H1_cell_41


title: H1_cell_3


title: H1_cell_40


title: H1_cell_38


title: H1_cell_44


title: H1_cell_39


title: H1_cell_47


title: H1_cell_31


title: H1_cell_37


title: H1_cell_36


title: H1_cell_35


title: H1_cell_33


title: H1_cell_29


title: H1_cell_32


title: H1_cell_19


title: H1_cell_21


title: H1_cell_1


title: H1_cell_30


title: H1_cell_20


title: H1_cell_18


title: H1_cell_2


title: H1_cell_34


title: H1_cell_17


title: H1_cell_28


title: H1_cell_27


title: H1_cell_26


title: H1_cell_24


title: H1_cell_25


title: H1_cell_23


title: H1_cell_22


title: H1_cell_15


title: Rao-2017-HIC047

extract_protocol:
Cells were crosslinked and then lysed with nuclei permeabilized but still intact. DNA was then restricted and the overhangs filled in incorporating a biotinylated base. Free ends were then ligated together in situ. Crosslinks were reversed, the DNA was sheared to 300-500bp and then biotinylated ligation junctions were recovered with streptavidin beads.
standard Illumina library construction protocol, Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 8-12 cycles and library fragments of 400-600 bp (insert plus adaptor and PCR primer sequences) were purified using SPRI beads. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq X Ten, Illumina NextSeq 500, or HiSeq 2500 following the manufacturer's protocols
Hi-C; Specific library strategies are indicated as additional columns in the SAMPLES section

value: in situ Hi-C

value: 500uM auxin (360 min), 180 min withdrawal


title: Rao-2017-HIC046


title: H1_cell_13


title: H1_cell_14


title: H1_cell_11


title: Rao-2017-HIC040

value: 500uM auxin (360 min), 60 min withdrawal


title: Rao-2017-HIC043


title: Rao-2017-HIC042


title: H1_cell_12


title: H1_cell_116


title: H1_cell_117


title: Rao-2017-HIC045


title: Rao-2017-HIC038

value: 500uM auxin (360 min), 40 min withdrawal


title: H1_cell_118


title: H1_cell_16


title: H1_cell_113


title: Rao-2017-HIC039


title: H1_cell_115


title: Rao-2017-HIC044


title: Rao-2017-HIC037


title: Rao-2017-HIC035

value: 500uM auxin (360 min), 20 min withdrawal


title: H1_Bulk


title: Rao-2017-HIC036


title: Rao-2017-HIC034


title: Rao-2017-HIC033


title: Rao-2017-HIC041


title: H1_cell_112


title: Rao-2017-HIC031


title: Rao-2017-HIC032


title: H1_cell_10


title: H1_cell_110


title: H1_cell_109


title: Rao-2017-HIC030


title: H1_cell_107


title: H1_cell_108


title: Rao-2017-HIC027


title: H1_cell_106


title: Rao-2017-HIC026


title: Rao-2017-HIC028


title: Rao-2017-HIC025


title: Rao-2017-HIC029


title: Rao-2017-HIC023


title: H1_cell_102


title: Rao-2017-HIC022

value: G1/S arrest, 500uM auxin (360min)


title: H1_cell_101


title: H1_cell_111


title: H1_cell_104


title: H1_cell_105


title: Rao-2017-HIC021


title: Rao-2017-HIC024


title: H4_cell_9


title: H1_cell_103


title: Rao-2017-HIC019


title: H1_cell_100


title: H4_cell_99


title: Rao-2017-HIC020


title: H4_cell_98


title: Rao-2017-HIC017

value: G1/S arrest


title: Rao-2017-HIC016


title: Rao-2017-HIC015


title: H4_cell_96


title: H4_cell_97


title: H4_cell_95


title: Rao-2017-HIC014


title: H4_cell_94


title: Rao-2017-HIC013


title: Rao-2017-HIC012


title: Rao-2017-HIC011


title: H4_cell_8


title: H4_cell_91


title: H4_cell_90


title: H4_cell_89


title: Rao-2017-HIC007


title: Rao-2017-HIC008


title: H4_cell_88


title: H4_cell_87


title: Rao-2017-HIC018


title: H4_cell_86


title: H4_cell_82


title: H4_cell_83


title: H4_cell_85


title: H4_cell_84


title: H4_cell_81


title: H4_cell_80


title: H4_cell_77


title: H4_cell_78


title: H4_cell_79


title: H4_cell_93


title: H4_cell_76


title: H4_cell_92


title: Rao-2017-HIC010


title: H4_cell_74


title: H4_cell_75


title: H4_cell_71


title: H4_cell_70


title: H4_cell_73


title: H4_cell_67


title: H4_cell_66


title: H4_cell_69


title: Rao-2017-HIC009


title: H4_cell_6


title: H4_cell_68


title: LT-3

city: Nanjing

first: Mantang

last: Qiu

state: Jiangsu

address: 42 Baiziting

department: Thoracic Surgery

country: China

institute: Cancer Institute of Jiangsu Province

description:
ribosome RNA depleted total RNA
this smaple was prepared with lung adenocarcinoma tisses of patient 7, 8, 9

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.1.8 mapping to reference genome
count counting
Genome_build: hg19_GRCh37
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Lung: adenocarcinoma tissues

growth_protocol: Normal posterior longitudinal ligament were dissected during the surgery, all tissues were obtained with written informed consent signed by the donors voluntarily for research. Ligaments were further cut into pieces and cultured in DMEM supplemented with 20% fetal bovine serum, and cells of passage 3 were used for the experiments.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
The complementary DNA (cDNA) libraries for single-end sequencing were prepared using Ion Total RNA-Seq Kit v2.0 (Life Technologies) according to the manufacturer’s instructions. The cDNA libraries were then processed for the Proton Sequencing process according to the commercially available protocols. Samples were diluted and mixed, the mixture was processed on a OneTouch 2 instrument (Life Technologies) and enriched on a OneTouch 2 ES station (Life Technologies) for preparing the template-positive Ion PI™ Ion Sphere™ Particles (Life Technologies) according to Ion PI™ Template OT2 200 Kit v2.0 (Life Technologies). After enrichment, the mixed template-positive Ion PI™ Ion Sphere™ Particles of samples was loaded on to 1 P1v2 Proton Chip (Life Technologies) and sequenced on Proton Sequencers according to Ion PI Sequencing 200 Kit v2.0 (Life Technologies) by NovelBio Corp. Laboratory, Shanghai.

treatment_protocol: Primary lung adenocarcinoma tissues and paired nontumor tissues were snap frozen with liquid nitrogen immediately after resection and stored in liquid nitrogen till RNA extraction.

value: Lung

tag: histology

value: lung adenocarcinoma

tag: lymph node metastasis

value: Negative


title: H4_cell_7


title: H4_cell_64


title: LT-2

description:
ribosome RNA depleted total RNA
this smaple was prepared with lung adenocarcinoma tisses of patient 4, 5, 6

tag: tissue


title: P7_cell_274

value: Female

value: patients with bone marrow failure and cytogenetic abnormalities


title: LN-3

description:
ribosome RNA depleted total RNA
this smaple was prepared with nontumor tisses of patient 7, 8, 9

source_name: Lung: nontumor tissues

value: normal lung tissues


title: P7_cell_275


title: P7_cell_272


title: P7_cell_276


title: P7_cell_268


title: P7_cell_270


title: H4_cell_72

value: Male


title: H4_cell_62

value: bone marrow cells from healthy donors


title: P7_cell_267


title: H4_cell_63


title: P7_cell_266


title: P7_cell_273


title: H4_cell_65


title: P7_cell_264


title: LN-1

description:
ribosome RNA depleted total RNA
this smaple was prepared with nontumor tisses of patient 1, 2, 3


title: P7_cell_265


title: H4_cell_60


title: P7_cell_262


title: H4_cell_5


title: LT-1

description:
ribosome RNA depleted total RNA
this smaple was prepared with lung adenocarcinoma tisses of patient 1, 2, 3


title: P7_cell_263


title: Rao-2017-CHIP005-CTCF-untreated

value: ChIP-Seq


title: H4_cell_61


title: P7_cell_271


title: H4_cell_59


title: P7_cell_269


title: LN-2

description:
ribosome RNA depleted total RNA
this smaple was prepared with nontumor tisses of patient 4, 5, 6


title: P7_cell_260


title: P7_cell_259


title: H4_cell_58


title: Rao-2017-CHIP003-SMC1-untreated


title: Rao-2017-CHIP004-SMC1-treated

value: 500uM auxin (360 min)


title: H4_cell_57


title: P7_cell_258


title: P7_cell_256


title: P7_cell_257


title: P7_cell_255


title: Rao-2017-HIC045S

value: in situ Hi-C


title: P7_cell_254


title: H4_cell_56


title: P7_cell_261


title: P7_cell_252


title: H4_cell_55


title: P7_cell_253


title: Rao-2017-HIC044S

value: 500uM auxin (360 min), 180 min withdrawal


title: H4_cell_54


title: P7_cell_251


title: Rao-2017-HIC041S

value: 500uM auxin (360 min), 60 min withdrawal


title: H4_cell_53


title: P7_cell_249


title: P7_cell_250


title: Rao-2017-HIC040S


title: P7_cell_248


title: Rao-2017-HIC037S

value: 500uM auxin (360 min), 40 min withdrawal


title: P7_cell_247


title: H4_cell_52


title: P7_cell_246


title: Rao-2017-HIC036S


title: H4_cell_51


title: H4_cell_50


title: P7_cell_244


title: P7_cell_243


title: Rao-2017-HIC033S

value: 500uM auxin (360 min), 20 min withdrawal


title: P7_cell_242


title: Rao-2017-HIC032S


title: P7_cell_240


title: P7_cell_241


title: Rao-2017-HIC068

value: 500uM auxin (360 min), 1440 min withdrawal


title: Rao-2017-HIC069


title: H4_cell_48


title: H4_cell_49


title: P7_cell_237


title: H4_cell_4


title: Rao-2017-HIC067

value: 500uM auxin (360 min), 1080 min withdrawal


title: H4_cell_47


title: Rao-2017-HIC066


title: P7_cell_233


title: P7_cell_234


title: P7_cell_236


title: P7_cell_235


title: P7_cell_232


title: H4_cell_46


title: P7_cell_245


title: Rao-2017-HIC065

value: 500uM auxin (360 min), 360 min withdrawal


title: P7_cell_231


title: P7_cell_229


title: H4_cell_45


title: P7_cell_230


title: H4_cell_44


title: P7_cell_239


title: Rao-2017-HIC064


title: P7_cell_228


title: P7_cell_238


title: H4_cell_43


title: P7_cell_227


title: Rao-2017-HIC063


title: P7_cell_226


title: Rao-2017-HIC062


title: H4_cell_42


title: H4_cell_41


title: P7_cell_224


title: P7_cell_223


title: P7_cell_222


title: P7_cell_219


title: Rao-2017-HIC059


title: P7_cell_221


title: H4_cell_3


title: Rao-2017-HIC060


title: P7_cell_220


title: H4_cell_40


title: P7_cell_218


title: P7_cell_216


title: Rao-2017-HIC057

value: 500uM auxin (240 min)


title: P7_cell_215


title: Rao-2017-HIC058


title: H4_cell_39


title: H4_cell_38


title: H4_cell_37


title: P7_cell_217


title: Rao-2017-HIC061


title: Rao-2017-HIC056


title: P7_cell_225


title: Rao-2017-HIC055

value: 500uM auxin (60 min)


title: P7_cell_212

value: Female


title: P7_cell_211

value: patients with bone marrow failure and cytogenetic abnormalities


title: P7_cell_210


title: Rao-2017-HIC054


title: H4_cell_35


title: P7_cell_208


title: P7_cell_206


title: Rao-2017-HIC053

value: 500uM auxin (40 min)


title: Rao-2017-HIC052


title: H4_cell_34

value: Male


title: H4_cell_33

value: bone marrow cells from healthy donors


title: P7_cell_214


title: P7_cell_204


title: P7_cell_213


title: P7_cell_203


title: H4_cell_32


title: P7_cell_202


title: Rao-2017-HIC051

value: 500uM auxin (20 min)


title: Rao-2017-HIC050


title: P7_cell_201


title: H4_cell_31


title: P7_cell_209


title: H4_cell_30


title: Rao-2017-HIC049


title: P7_cell_150


title: P7_cell_149


title: Rao-2017-HIC048


title: H4_cell_36


title: P7_cell_151


title: H4_cell_2


title: P7_cell_147


title: P7_cell_148


title: P7_cell_207


title: P7_cell_205


title: H4_cell_29


title: 80996

city: Boston

first: Kevin

middle: Meyer

last: Elias

state: MA

address: 75 Francis Street

department: OB/GYN

institute: Brigham and Women's Hospital

description: Processed file Cohort 2

data_processing:
After sequencing adapters were trimmed off as part of the base calling, trimming of adapters from the dataset revealed distinct peaks representing microRNA (~18-22nt). Novel microRNAs not in standard miRBase or Rfam classification were identified based on the prediction algorithm miRPara
Expression levels were quantified in tags per million (TPM).
Genome_build: Sequence tags were mapped to miRbase 20 (http://www.mirbase.org/).
Supplementary_files_format_and_content: .xls include total reads, raw counts, and TPM for each sample

source_name: serum

extract_protocol:
500 ul of human serum were submitted for each sample. SMall RNA from each serum sample was isolated using the miRCURYTM RNA isolation kit (Exiqon, Vedbæk, Denmark) according to the manufacturer’s protocol optimized for serum. The quality of the isolated RNA was checked using qPCR.
Total RNA was converted into microRNA NGS libraries using the NEBNEXT library generation kit (New England Biolabs Inc., Ipswich, MA) according to the manufacturer’s instructions. Each individual RNA sample had adaptors ligated to its 3’ and 5’ ends and converted into cDNA. Then the cDNA was pre-amplified with specific primers containing sample specific indices. After 18 cycles of pre-PCR the libraries were purified on QiaQuick columns and the insert efficiency evaluated by a Bioanalyzer 2100 instrument on a high sensitivity DNA chip (Agilent Inc., Lexington, MA). The microRNA cDNA libraries were size fractionated on a LabChip XT (PerkinElmer Waltham, MA) and a band representing adaptors and 15-40 bp insert excised using the manufacturer’s instructions. Samples were then quantified using qPCR and concentration standards. Based on the quality of the inserts and the concentration measurements, the libraries were pooled in equimolar concentrations (all concentrations of libraries to be pooled were of the same concentration). The library pools were finally quantified again with qPCR and the optimal concentration of the library pool used to generate the clusters on the surface of a flowcell before sequencing using v3 sequencing methodology according to the manufacturer instructions (Illumina Inc., Dedham, MA). Samples were sequenced on the Illumina NextSeq 500 system (Illumina Inc., Dedham, MA) using a single-end read length of 50 nucleotides at an average of 10 million reads per sample.

tag: Stage

value: Stage I/II

value: Endo/Clear Cell

tag: diagnosis

value: Cancer


title: P7_cell_146


title: 80846

description: Processed file Cohort 2

value: Endometrioma

value: Benign


title: P7_cell_144


title: P7_cell_145


title: H4_cell_28


title: P7_cell_143


title: 81176

description: Processed file Cohort 2

value: Serous

value: Borderline


title: 81027

description: Processed file Cohort 2


title: H4_cell_27


title: P7_cell_141


title: P7_cell_142


title: P7_cell_140


title: H4_cell_26


title: H4_cell_25


title: P7_cell_138


title: P7_cell_137


title: 80676

description: Processed file Cohort 2


title: P7_cell_139


title: P7_cell_135


title: P7_cell_136


title: H4_cell_24


title: P7_cell_134


title: H4_cell_23


title: P7_cell_133


title: P7_cell_132


title: H4_cell_22


title: P7_cell_131


title: H4_cell_21


title: P7_cell_129


title: 81204

description: Processed file Cohort 2


title: 81004

description: Processed file Cohort 2


title: 1487

description: Processed file Cohort 2

value: Stage III/IV


title: 80148

description: Processed file Cohort 2


title: P7_cell_128


title: H4_cell_20


title: 2390

description: Processed file Cohort 2


title: 80476

description: Processed file Cohort 2


title: P7_cell_127


title: P7_cell_126


title: P7_cell_125


title: P7_cell_123


title: 80938

description: Processed file Cohort 2


title: H4_cell_19


title: P7_cell_121


title: 2324

description: Processed file Cohort 2


title: P7_cell_124


title: 2131

description: Processed file Cohort 2


title: H4_cell_17


title: Rao-2017-CHIP006-CTCF-treated

value: ChIP-Seq

value: 500uM auxin (360 min)


title: H4_cell_1


title: P7_cell_120


title: P7_cell_122


title: P7_cell_130


title: H4_cell_18


title: P7_cell_119


title: 1229

description: Processed file Cohort 2


title: H4_cell_16


title: 80624

description: Processed file Cohort 2


title: P7_cell_117


title: H4_cell_15


title: 2026

description: Processed file Cohort 2


title: P7_cell_115


title: P7_cell_114


title: P7_cell_113


title: P7_cell_112


title: 50509

description: Processed file Cohort 2

value: Control


title: H4_cell_151


title: P7_cell_110

value: Female


title: 80198

description: Processed file Cohort 2


title: H4_cell_14


title: P7_cell_111

value: patients with bone marrow failure and cytogenetic abnormalities


title: P7_cell_108


title: 80296

description: Processed file Cohort 2


title: H4_cell_149


title: P7_cell_107


title: H4_cell_148


title: P7_cell_106


title: P7_cell_105


title: P7_cell_118


title: 80832

description: Processed file Cohort 2


title: P7_cell_104


title: 80261

description: Processed file Cohort 2


title: P7_cell_116


title: P7_cell_102


title: H4_cell_146


title: P7_cell_103


title: H4_cell_147


title: 50655

description: Processed file Cohort 2


title: P7_cell_101


title: 1608

description: Processed file Cohort 2


title: H4_cell_150


title: H4_cell_145


title: P6_cell_361


title: 81062

description: Processed file Cohort 2


title: P7_cell_109


title: P6_cell_360


title: P6_cell_359


title: H4_cell_144


title: 1666

description: Processed file Cohort 2


title: P6_cell_358


title: P6_cell_357


title: P6_cell_356


title: H4_cell_143


title: 80751

description: Processed file Cohort 2


title: P6_cell_355


title: H4_cell_142


title: P6_cell_354


title: P6_cell_353


title: 80971

description: Processed file Cohort 2


title: 81206

description: Processed file Cohort 2


title: P6_cell_352


title: H4_cell_141


title: P6_cell_351


title: P6_cell_349


title: P6_cell_350


title: H4_cell_13


title: H4_cell_140


title: P6_cell_348


title: 70159

description: Processed file Cohort 2


title: P6_cell_347


title: P6_cell_346


title: P6_cell_345


title: H4_cell_139


title: H4_cell_138


title: 80593

description: Processed file Cohort 2


title: H4_cell_137


title: P6_cell_343


title: P6_cell_342


title: 2085

description: Processed file Cohort 2


title: P6_cell_341


title: 2525

description: Processed file Cohort 2


title: P6_cell_340


title: H4_cell_135


title: H4_cell_136


title: P6_cell_339


title: H4_cell_134


title: P6_cell_336


title: P6_cell_338


title: 80879

description: Processed file Cohort 2


title: P6_cell_337


title: 50809

description: Processed file Cohort 2


title: P6_cell_335


title: H4_cell_133


title: 80103

description: Processed file Cohort 2


title: P6_cell_334


title: H4_cell_132


title: P6_cell_331


title: 50363

description: Processed file Cohort 2


title: 1286

description: Processed file Cohort 2


title: H4_cell_131


title: P6_cell_344


title: 2113

description: Processed file Cohort 2


title: P6_cell_330


title: P6_cell_329


title: H4_cell_130


title: 80999

description: Processed file Cohort 2


title: P6_cell_327


title: H4_cell_12


title: P6_cell_325


title: 81196

description: Processed file Cohort 2


title: H4_cell_129


title: 50057

description: Processed file Cohort 2


title: P6_cell_322


title: P6_cell_323


title: P6_cell_332


title: P6_cell_321


title: P6_cell_333


title: H4_cell_127


title: 70088

description: Processed file Cohort 2


title: P6_cell_319


title: P6_cell_320


title: P6_cell_318


title: 80638

description: Processed file Cohort 2


title: H4_cell_126


title: P6_cell_317


title: P6_cell_328


title: P6_cell_316


title: 1282

description: Processed file Cohort 2


title: H4_cell_125


title: P6_cell_315


title: P6_cell_314


title: 81010

description: Processed file Cohort 2


title: 1108

description: Processed file Cohort 2


title: P6_cell_312


title: P6_cell_324


title: H4_cell_124


title: P6_cell_313


title: 80655

description: Processed file Cohort 2


title: H4_cell_128


title: H4_cell_123


title: P6_cell_310


title: 81070

description: Processed file Cohort 2


title: 2115

description: Processed file Cohort 2


title: P6_cell_309


title: H4_cell_122


title: H4_cell_121


title: P6_cell_308


title: P6_cell_306


title: P6_cell_307


title: 1859

description: Processed file Cohort 2


title: P6_cell_304


title: 80876

description: Processed file Cohort 2


title: P6_cell_305


title: P6_cell_302


title: H4_cell_120


title: 1024

description: Processed file Cohort 2


title: P6_cell_301


title: H4_cell_119


title: 80301

description: Processed file Cohort 2


title: H4_cell_11


title: P6_cell_303


title: P6_cell_258


title: H4_cell_118


title: P6_cell_311


title: P6_cell_259


title: 1331

description: Processed file Cohort 2


title: H4_cell_116


title: H4_cell_117


title: P6_cell_253


title: 80250

description: Processed file Cohort 2


title: P6_cell_252


title: P6_cell_256


title: 80542

description: Processed file Cohort 2


title: P6_cell_257


title: 1789

description: Processed file Cohort 2


title: P6_cell_251


title: 80285

description: Processed file Cohort 2


title: P6_cell_255


title: H4_cell_114


title: P6_cell_250


title: P6_cell_247


title: P6_cell_248


title: P6_cell_246


title: H4_cell_110


title: H4_cell_111


title: H4_cell_112


title: P6_cell_245


title: P6_cell_241


title: 80703

description: Processed file Cohort 2


title: P6_cell_254


title: 81131

description: Processed file Cohort 2


title: P6_cell_243


title: H4_cell_10


title: P6_cell_240


title: 81106

description: Processed file Cohort 2


title: P6_cell_244


title: 2320

description: Processed file Cohort 2


title: P6_cell_242


title: P6_cell_238


title: 80263

description: Processed file Cohort 2


title: P6_cell_239


title: H4_cell_109


title: 81195

description: Processed file Cohort 2


title: H4_cell_108


title: P6_cell_237


title: P6_cell_236


title: 80453

description: Processed file Cohort 2


title: H4_cell_113


title: P6_cell_249


title: H4_cell_115


title: P6_cell_235


title: H4_cell_107


title: P6_cell_234


title: P6_cell_233


title: 50782

description: Processed file Cohort 2


title: 80953

description: Processed file Cohort 2


title: P6_cell_231


title: H4_cell_104


title: P6_cell_230


title: 80280

description: Processed file Cohort 2


title: P6_cell_225


title: P6_cell_226


title: P6_cell_229


title: P6_cell_232


title: 80504

description: Processed file Cohort 2


title: P6_cell_227


title: H4_cell_105


title: H4_cell_103


title: 80840

description: Processed file Cohort 2


title: 80872

description: Processed file Cohort 2


title: P6_cell_228


title: P6_cell_224


title: P6_cell_222


title: 81118

description: Processed file Cohort 2


title: P6_cell_221


title: H4_cell_106


title: H4_cell_100


title: H4_cell_102


title: H3_cell_9


title: P6_cell_223


title: 50078

description: Processed file Cohort 2


title: P6_cell_217


title: H4_cell_101


title: P6_cell_216


title: P6_cell_218


title: H3_cell_96


title: P6_cell_213


title: P6_cell_212


title: P6_cell_211


title: H3_cell_95


title: 81034

description: Processed file Cohort 2


title: 80556

description: Processed file Cohort 2


title: H3_cell_98


title: P6_cell_214


title: 80398

description: Processed file Cohort 2


title: 80704

description: Processed file Cohort 2


title: 50067

description: Processed file Cohort 2


title: P6_cell_209


title: H3_cell_94


title: P6_cell_208


title: P6_cell_210


title: P6_cell_219


title: P6_cell_207


title: P6_cell_206


title: P6_cell_215


title: H3_cell_92


title: H3_cell_97


title: P6_cell_220


title: H3_cell_91


title: P6_cell_205


title: H3_cell_90


title: P6_cell_201


title: 50145

description: Processed file Cohort 2


title: P6_cell_204


title: H3_cell_8


title: 80014

description: Processed file Cohort 2


title: P6_cell_202


title: P6_cell_164


title: 1863

description: Processed file Cohort 2


title: P6_cell_165


title: 2187

description: Processed file Cohort 2


title: P6_cell_162


title: P6_cell_163


title: 80254

description: Processed file Cohort 2


title: 81203

description: Processed file Cohort 2


title: P6_cell_161


title: 2579

description: Processed file Cohort 2


title: P6_cell_160


title: H3_cell_88


title: P6_cell_159


title: H3_cell_87


title: P6_cell_158


title: H3_cell_86


title: 50247

description: Processed file Cohort 2


title: P6_cell_203


title: 2224

description: Processed file Cohort 2


title: P6_cell_157


title: P6_cell_156


title: P6_cell_155


title: 80633

description: Processed file Cohort 2


title: P6_cell_153


title: P6_cell_154


title: H3_cell_85


title: P6_cell_152


title: H3_cell_84


title: H3_cell_82


title: P6_cell_151


title: P6_cell_150


title: P6_cell_149


title: H3_cell_83


title: P6_cell_148


title: 1478

description: Processed file Cohort 2


title: H3_cell_81


title: P6_cell_147


title: P6_cell_146


title: 50096

description: Processed file Cohort 2


title: H3_cell_80


title: 80292

description: Processed file Cohort 2


title: H3_cell_7


title: P6_cell_145


title: P6_cell_144


title: P6_cell_142


title: P6_cell_143


title: 81102

description: Processed file Cohort 2


title: H3_cell_79


title: H3_cell_89


title: P6_cell_141


title: 81120

description: Processed file Cohort 2


title: P6_cell_140


title: P6_cell_138


title: H3_cell_78


title: 50831

description: Processed file Cohort 2


title: 80358

description: Processed file Cohort 2


title: H3_cell_76


title: 80357

description: Processed file Cohort 2


title: P6_cell_137


title: P6_cell_134


title: P6_cell_136


title: P6_cell_135


title: H3_cell_75


title: 1247

description: Processed file Cohort 2


title: P6_cell_132


title: H3_cell_74


title: 527

description: Processed file Cohort 2


title: H3_cell_73


title: P6_cell_130


title: 2572

description: Processed file Cohort 2


title: P6_cell_131


title: P6_cell_129


title: P6_cell_128


title: 1446

description: Processed file Cohort 2


title: P6_cell_127


title: H3_cell_77


title: H3_cell_72


title: 81123

description: Processed file Cohort 2


title: P6_cell_126


title: 2622

description: Processed file Cohort 2


title: P6_cell_124


title: H3_cell_70


title: P6_cell_123


title: H3_cell_71


title: 2082

description: Processed file Cohort 2


title: P6_cell_125


title: 80098

description: Processed file Cohort 2


title: P6_cell_133


title: P6_cell_122


title: 80858

description: Processed file Cohort 2


title: P6_cell_121


title: P6_cell_120


title: H3_cell_6


title: P6_cell_119


title: H3_cell_69


title: P6_cell_139


title: 81065

description: Processed file Cohort 2


title: H3_cell_68


title: P6_cell_118


title: P6_cell_115


title: P6_cell_116


title: P6_cell_117


title: H3_cell_67


title: 80091

description: Processed file Cohort 2


title: H3_cell_66


title: P6_cell_114


title: 81043

description: Processed file Cohort 2


title: P6_cell_111


title: P6_cell_110


title: P6_cell_113


title: H3_cell_65


title: P6_cell_112


title: P6_cell_109


title: H3_cell_64


title: P6_cell_107


title: 2392

description: Processed file Cohort 2


title: 2555

description: Processed file Cohort 2


title: 2110

description: Processed file Cohort 2


title: H3_cell_62


title: P6_cell_106


title: H3_cell_63


title: 81099

description: Processed file Cohort 2


title: P6_cell_105


title: H3_cell_61


title: P6_cell_104


title: P6_cell_108


title: P6_cell_103


title: H3_cell_60


title: P6_cell_101


title: P6_cell_102


title: 80627

description: Processed file Cohort 2


title: P4_cell_252


title: H3_cell_5


title: P4_cell_251


title: 1809

description: Processed file Cohort 2


title: 2601

description: Processed file Cohort 2


title: P4_cell_249


title: H3_cell_59


title: 2317

description: Processed file Cohort 2


title: H3_cell_58


title: 81063

description: Processed file Cohort 2


title: P4_cell_246


title: P4_cell_247


title: P4_cell_248


title: P4_cell_245


title: H3_cell_57


title: 80675

description: Processed file Cohort 2


title: H3_cell_55


title: H3_cell_56


title: P4_cell_242


title: P4_cell_244


title: E-1021

description: Processed file Cohort 1


title: P4_cell_241


title: E-1022

description: Processed file Cohort 1


title: P4_cell_240


title: P4_cell_250


title: H3_cell_54


title: P4_cell_239


title: H3_cell_53


title: E-1035

description: Processed file Cohort 1


title: P4_cell_237


title: E-1031

description: Processed file Cohort 1


title: H3_cell_52


title: P4_cell_234


title: P4_cell_235


title: E-1056

description: Processed file Cohort 1

value: Mucinous


title: P4_cell_232

value: Male


title: 50217

description: Processed file Cohort 2


title: P4_cell_243


title: H3_cell_50

value: bone marrow cells from healthy donors


title: P4_cell_231


title: H3_cell_4


title: P4_cell_228


title: P4_cell_229


title: H3_cell_49


title: E-1058

description: Processed file Cohort 1

value: Brenner tumor


title: P4_cell_227


title: P4_cell_238


title: P4_cell_225


title: E-1032

description: Processed file Cohort 1


title: H3_cell_48


title: P4_cell_226


title: P4_cell_236


title: E-1057

description: Processed file Cohort 1

value: Endometrial Adenocarcinoma


title: P4_cell_224


title: P4_cell_223


title: H3_cell_51


title: H3_cell_47


title: P4_cell_233


title: P4_cell_222


title: E-1002

description: Processed file Cohort 1


title: P4_cell_221


title: E-1040

description: Processed file Cohort 1

value: Brenner tumor with mucinous cystadenofibroma


title: H3_cell_45


title: P4_cell_219


title: E-1012

description: Processed file Cohort 1


title: P4_cell_220


title: H3_cell_46


title: P4_cell_230


title: E-1009

description: Processed file Cohort 1

value: Cancer


title: P4_cell_218


title: P4_cell_217


title: H3_cell_44


title: H3_cell_43


title: P4_cell_215


title: E-1053

description: Processed file Cohort 1

value: Atypical leiomyoma


title: E-1016

description: Processed file Cohort 1

value: Stage I/II

value: Clear cell


title: P4_cell_213


title: E-1030

description: Processed file Cohort 1

value: Serous


title: P4_cell_212


title: H3_cell_41


title: E-1013

description: Processed file Cohort 1

value: Borderline


title: P4_cell_214


title: P4_cell_211


title: H3_cell_40


title: E-1011

description: Processed file Cohort 1

value: Stage III/IV


title: P4_cell_208


title: P4_cell_207


title: E-1006

description: Processed file Cohort 1

value: Fibrothecoma

value: Benign


title: H3_cell_3

value: Female


title: H3_cell_42


title: P4_cell_210

value: patients with bone marrow failure and cytogenetic abnormalities


title: E-1027

description: Processed file Cohort 1


title: H3_cell_39


title: P4_cell_206


title: P4_cell_216


title: E-1050

description: Processed file Cohort 1


title: P4_cell_204


title: P4_cell_205


title: P4_cell_203


title: P4_cell_202


title: E-1055

description: Processed file Cohort 1


title: H3_cell_37


title: P4_cell_201


title: E-1010

description: Processed file Cohort 1

value: Simple cyst


title: P4_cell_126

value: Male


title: H3_cell_36

value: bone marrow cells from healthy donors


title: P4_cell_209


title: P4_cell_125


title: H3_cell_35


title: E-1005

description: Processed file Cohort 1


title: P4_cell_124


title: P4_cell_123


title: E-1062

description: Processed file Cohort 1


title: H3_cell_33


title: P4_cell_121


title: H3_cell_34


title: E-1063

description: Processed file Cohort 1

value: Leiomyoma


title: P4_cell_120


title: P4_cell_122


title: P4_cell_119


title: E-1023

description: Processed file Cohort 1

value: Endometrioid


title: E-1054

description: Processed file Cohort 1

value: Mucinous


title: P4_cell_118


title: H3_cell_31


title: P4_cell_116


title: P4_cell_115


title: H3_cell_32


title: H3_cell_38


title: H3_cell_30


title: P4_cell_113


title: P4_cell_114


title: H3_cell_2


title: P4_cell_111


title: P4_cell_110


title: P4_cell_112


title: H3_cell_29


title: E-1020

description: Processed file Cohort 1

value: Cancer


title: P4_cell_109


title: P4_cell_117


title: P4_cell_108


title: P4_cell_107


title: E-1052

description: Processed file Cohort 1


title: H3_cell_28


title: H3_cell_27


title: E-1001

description: Processed file Cohort 1


title: E-1060

description: Processed file Cohort 1

value: Fibroma


title: P4_cell_106


title: P4_cell_103


title: P4_cell_105


title: H3_cell_26


title: P4_cell_102


title: P2_Bulk_3


title: E-1014

description: Processed file Cohort 1

value: Stage I/II


title: H3_cell_22


title: E-1042

description: Processed file Cohort 1


title: P2_cell_383


title: E-1039

description: Processed file Cohort 1


title: H3_cell_24


title: P2_cell_386


title: P2_cell_385


title: P4_cell_104


title: H3_cell_23


title: P2_cell_380


title: E-1024

description: Processed file Cohort 1


title: E-1003

description: Processed file Cohort 1


title: P2_cell_384


title: H3_cell_20


title: P4_cell_101


title: E-1004

description: Processed file Cohort 1


title: P2_cell_382


title: P2_cell_377


title: P2_cell_376


title: P2_cell_387


title: H3_cell_21


title: P2_cell_378


title: P2_cell_379


title: E-1061

description: Processed file Cohort 1


title: E-1034

description: Processed file Cohort 1

value: Endometrial Adenocarcinoma


title: H3_cell_1


title: H3_cell_25


title: P2_cell_375


title: P2_cell_374


title: H3_cell_19


title: H3_cell_18


title: P2_cell_373


title: E-1015

description: Processed file Cohort 1

value: Serous


title: P2_cell_372


title: E-1049

description: Processed file Cohort 1


title: E-1017

description: Processed file Cohort 1


title: E-1038

description: Processed file Cohort 1


title: E-1033

description: Processed file Cohort 1

value: Epithelioid Leiomyosarcoma


title: P2_cell_371


title: H3_cell_16


title: P2_cell_370


title: P2_cell_369


title: P2_cell_366


title: P2_cell_368


title: E-1019

description: Processed file Cohort 1

value: Stage III/IV


title: P2_cell_364


title: P2_cell_367


title: H3_cell_15


title: P2_cell_363


title: H3_cell_14


title: P2_cell_365


title: E-1008

description: Processed file Cohort 1


title: E-1046

description: Processed file Cohort 1

value: Borderline


title: H3_cell_13


title: E-1029

description: Processed file Cohort 1

value: Mixed Mullerian adenofibroma

value: Benign


title: H3_cell_12

value: Female


title: P2_cell_362

value: patients with bone marrow failure and cytogenetic abnormalities


title: P2_cell_361

value: Male


title: P2_cell_360


title: E-1047

description: Processed file Cohort 1


title: H3_cell_17

value: bone marrow cells from healthy donors


title: P2_cell_358


title: H3_cell_11


title: E-1043

description: Processed file Cohort 1


title: P2_cell_357


title: P2_cell_356


title: P2_cell_355


title: P2_cell_353


title: E-1045

description: Processed file Cohort 1


title: P2_cell_354


title: H3_cell_10


title: P2_cell_352


title: E-1037

description: Processed file Cohort 1


title: P2_cell_351


title: E-1007

description: Processed file Cohort 1


title: H3_cell_109


title: H3_cell_108


title: E-1041

description: Processed file Cohort 1


title: P2_cell_349


title: P2_cell_359


title: P2_cell_348


title: H3_cell_107


title: P2_cell_347


title: P2_cell_346


title: H3_cell_106


title: E-1026

description: Processed file Cohort 1

value: Myxoid Leiomyosarcoma


title: E-1044

description: Processed file Cohort 1


title: H3_cell_110


title: P2_cell_344


title: P2_cell_343


title: E-1051

description: Processed file Cohort 1


title: P2_cell_345


title: H3_cell_104


title: H3_cell_105


title: P2_cell_342


title: P2_cell_350


title: P2_cell_340


title: H3_cell_103


title: H3_cell_102


title: P2_cell_341


title: E-1059

description: Processed file Cohort 1

value: Granulosa Cell


title: E-1036

description: Processed file Cohort 1


title: P2_cell_338


title: P2_cell_336


title: P2_cell_337


title: H3_cell_101


title: P2_cell_335


title: H3_cell_100


title: P2_cell_333


title: P2_cell_331


title: P1_cell_99


title: P2_cell_330


title: P1_cell_9


title: P2_cell_332


title: SKOM day5_Vc+_Tet1CD+shDnmt1_RNA

city: Guangzhou

first: Hui

last: Zheng

state: Guangdong

address: 190 Kaiyuan Avenue

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

description:
processed data file: Vc+.tsv
grown in media with Vitamin C (Vc)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie
Transcripts Per Million were  calculated using a protocol from RSEM
Genome_build: mm10
Supplementary_files_format_and_content: TPM

organism: Mus musculus

source_name: mouse embryonic fibroblasts

growth_protocol: MEFs were derived from 13.5-day mouse embryos and maintained in Dulbecco’s modified Eagle medium (DMEM, Gibco) supplemented with 10% FBS (Gibco), non-essential amino acids (NEAA, Gibco), penicillin/streptomycin and L-glutamine. In the reprogramming group, MEFs was infected with retrovirus containing Oct4, Klf4, c-Myc and Sox2 (OKMS), and maintained in mESC or mESC-Vc medium containing high-glucose DMEM (Hyclone), NEAA, penicillin/streptomycin, lglutamine, leukaemia inhibitory factor (LIF), β-mercaptoethanol, pyruvate and 15% FBS without or with Vc (Vitamin C). Cells were harvested on day 5 after retrovirus infection.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were infected by retrovirus carried the indicated genes for 48 hours.

tag: cell type

value: mouse embryonic fibroblasts_reprogrammed by SKOM-induction

tag: passages

tag: strain

value: ICR


title: P2_cell_329


title: P2_cell_328


title: SKOM day5_Vc+_shp53+shDnmt1_RNA


title: P2_cell_339


title: E-1048

description: Processed file Cohort 1


title: SKOM day5_Vc+_Flag+shLuc_RNA


title: SKOM day5_Vc+_shDnmt1_RNA


title: P1_cell_97


title: P2_cell_326


title: P2_cell_327


title: P1_cell_98


title: P1_cell_96


title: P2_cell_325


title: P2_cell_324


title: SKOM day5_Vc+_Tet1CD+Dmnt1_RNA


title: SKOM day5_Vc+_Tet1CD_RNA


title: SKOM day5_Vc+_Dnmt1_RNA


title: P1_cell_95


title: P2_cell_323


title: P2_cell_334


title: P2_cell_322


title: P1_cell_94


title: SKOM day5_Vc-_Tet1CD_RNA

description:
processed data file: Vc-.tsv
grown in media without Vitamin C (Vc)


title: P2_cell_321


title: P2_cell_320


title: SKOM day5_Vc-_shp53+shDnmt1_RNA


title: P2_cell_319


title: P1_cell_93


title: P2_cell_318


title: P1_cell_92


title: P2_cell_317


title: SKOM day5_Vc-_Tet1CD+shDnmt1_RNA


title: P2_cell_315


title: P2_cell_316


title: SKOM day5_Vc-_shDnmt1_RNA


title: P1_cell_90


title: P2_cell_314


title: P1_cell_8


title: SKOM day5_Vc-_Tet1CD+Dmnt1_RNA


title: SKOM day5_Vc-_Flag+shLuc_RNA


title: P2_cell_313


title: P2_cell_311


title: P2_cell_310


title: P2_cell_312


title: P2_cell_309


title: P1_cell_89


title: P2_cell_308


title: P2_cell_307


title: MEF_shp53_RNA

description: processed data file: MEF.tsv

value: mouse embryonic fibroblasts


title: SKOM day5_Vc-_Dnmt1_RNA


title: MEF_Tet1-CD_RNA

description: processed data file: MEF.tsv


title: P1_cell_88


title: P2_cell_306


title: P2_cell_305


title: P1_cell_87


title: MEF_Flag+shLuc_RNA

description: processed data file: MEF.tsv


title: P2_cell_304


title: P1_cell_91


title: P2_cell_303


title: P2_cell_302


title: P1_cell_86


title: MEF_shp53+shDnmt1_RNA

description: processed data file: MEF.tsv


title: P2_cell_301


title: P2_Bulk_2


title: P1_cell_85


title: P2_cell_280


title: P2_cell_279


title: P2_cell_278


title: P1_cell_84


title: P1_cell_83


title: MEF_Dnmt1_RNA

description: processed data file: MEF.tsv


title: P2_cell_275


title: MEF_shDnmt1_RNA

description: processed data file: MEF.tsv


title: P2_cell_277


title: P2_cell_273


title: P1_cell_81


title: P2_cell_272


title: P1_cell_82


title: P1_cell_80


title: Liver_Ctrl3

description: RPKM L10_NonAlagillePatient2

data_processing:
Reads were aligned using STAR to genomes mm10 and hg19
Reads were separated for different species using S^3 (https://github.com/danielramskold/S3_species-specific_sequencing) with default settings (-Ms 1 -Mu 1 -D 2)
Unique reads were selected using mapping quality threshold 255
Gene expression values were calculated using rpkmforgenes.py (see link above) with options -rmnameoverlap -bothendsceil and using RefSeq annotation from 1 July 2014
MicroRNAs and snoRNAs were removed
RPKM values were TMM normalized
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text of normalised expression values and read counts

source_name: control_liver needle biopsy

extract_protocol:
RNA extraction of homogenized human liver biopsies was performed using Direct-zol™ RNA MiniPrep (cat. no. R2050, Zymo Research), including on-column DNase I digestion (cat. no. E1009, Zymo Research).
cDNA libraries for all samples were created using the TruSeq® RNA Sample Prep Kit v2–48, Set A (cat. no. RS-122-2001, Illumina®,) as per the TruSeq® RNA Sample Preparation v2 Guide, Low-Throughput Protocol.

tag: subject status

value: Progressive familial intrahepatic cholestasis type 2, PFIC2

value: Liver


title: P1_cell_7

tag: age


title: P2_cell_270

tag: markers


title: P2_cell_271

tag: Sex


title: P2_cell_268

tag: subject


title: P1_cell_79

tag: disease


title: Liver_Ctrl2

description: RPKM L8_NonAlagillePatient1

value: Autoimmune hepatitis


title: Liver_Ctrl_adult

description: RPKM T5_NonAlagillePatientAdult

value: patient with gallbladder cancer


title: P2_cell_267


title: P2_cell_266


title: Liver_Ctrl1

description: RPKM L11_NonAlagillePatient3


title: Liver_ALGS4

description: RPKM L6_AlagillePatient5

source_name: Alagille syndrome_liver needle biopsy

value: Alagille syndrome


title: P1_cell_78


title: 5C_Flag+shLuc_RNA

description: processed data file: MEF.tsv


title: P1_cell_77


title: P2_cell_263


title: P2_cell_274


title: Liver_ALGS2

description: RPKM L5_AlagillePatient4


title: Liver_Ctrl4

description: RPKM L12_NonAlagillePatient4

value: Autoimmune hepatitis with sclerosing cholangitis


title: P2_cell_262


title: P2_cell_261


title: Liver_ALGS1

description: RPKM L4_AlagillePatient3


title: P2_cell_260


title: P2_cell_259


title: P1_cell_75


title: P2_cell_269


title: P2_cell_258


title: P1_cell_74


title: P2_cell_257


title: P2_cell_256


title: Liver_ALGS3

description: RPKM HF207_AlagillePatient1


title: P2_cell_255


title: P2_cell_265


title: P2_cell_264


title: P2_cell_254


title: P1_cell_72


title: P2_cell_251


title: P2_cell_250


title: P2_cell_249


title: P2_cell_252


title: P1_cell_76


title: P2_cell_253


title: P2_cell_248


title: P2_cell_247


title: P2_cell_246


title: Liver_ALGS5

description: RPKM L2_AlagillePatient2


title: P2_cell_245


title: P1_cell_6


title: P1_cell_70


title: P1_cell_71


title: P1_cell_69


title: P2_cell_244


title: P2_cell_243


title: P1_cell_68


title: P1_cell_73


title: P2_cell_242


title: P2_cell_240


title: P1_cell_66


title: P2_cell_276


title: P2_cell_238


title: P2_cell_237


title: P1_cell_65


title: P2_cell_239


title: P2_cell_236


title: P1_cell_63


title: P2_cell_233


title: P2_cell_232


title: P2_cell_235


title: P1_cell_62


title: P2_cell_234


title: P2_cell_231


title: P1_cell_64


title: P2_cell_230


title: P1_cell_61


title: P2_cell_229


title: P2_cell_227


title: P2_cell_226


title: P2_cell_225


title: P2_cell_228


title: P1_cell_67


title: P1_cell_5


title: P1_cell_60


title: P2_cell_224


title: P2_cell_223


title: P1_cell_59


title: P2_cell_241


title: P2_cell_222


title: P2_cell_221


title: P1_cell_57


title: P2_cell_220


title: P2_cell_218


title: P1_cell_58


title: P1_cell_56


title: P2_cell_219


title: P2_cell_217


title: P2_cell_216


title: P1_cell_54


title: P2_cell_213


title: P2_cell_214


title: P2_cell_212


title: P1_cell_53


title: P2_cell_211


title: P2_cell_209


title: P2_cell_210


title: P1_cell_51


title: P2_cell_208


title: P2_cell_207


title: P2_cell_206


title: P2_cell_204


title: P1_cell_50


title: P1_cell_52


title: P2_cell_203


title: P2_cell_202


title: P1_cell_4


title: P2_cell_205


title: P1_cell_49


title: P2_Bulk_1


title: P2_cell_215


title: P1_cell_47


title: P2_cell_201


title: P2_cell_168


title: P1_cell_55


title: P2_cell_171


title: P1_cell_48


title: P2_cell_167


title: P1_cell_46


title: P1_cell_45


title: P2_cell_165


title: P2_cell_163


title: P2_cell_164


title: P1_cell_44


title: P2_cell_162


title: P2_cell_161


title: P1_cell_43


title: P2_cell_160


title: P1_cell_42


title: P1_cell_41


title: P2_cell_158


title: P2_cell_170


title: P2_cell_155


title: P2_cell_154


title: P2_cell_169


title: P2_cell_156


title: P2_cell_153


title: P1_cell_3


title: P2_cell_166


title: P2_cell_152


title: P2_cell_151


title: P1_cell_38


title: P1_cell_37


title: P1_cell_39


title: P2_cell_150


title: P2_cell_149


title: P1_cell_36


title: P2_cell_148


title: P2_cell_147


title: P1_cell_34


title: P1_cell_35


title: P2_cell_159


title: P2_cell_146


title: P1_cell_33


title: Peritoneal tissue-resident macrophage 2

city: Frederick

first: Luke

middle: Cynlais

last: Davies

state: MARYLAND

address: 1050 Boyles Street

department: Cancer and Inflammation Program

institute: National Cancer Institute

description:
RES_2.star.count.txt
Peritoneal tissue-resident macrophage 2

data_processing:
Alignment to mm10 genome with STAR
Trimmed mean of end values after filtering out genes with 5 counts of less
Limma-Voom paired test
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited *Fold.txt  file is limma voom paired test comparison of peritoneal macrophages vs BMDM (higher fold indicates this is higher in peritoneal resident cells); *CPM.txt containing CPM values

source_name: Peritoneal cavity

growth_protocol: M-CSF for bone-marrow derived macrophages

extract_protocol:
RNA-extraction (column)
Illumina TruSeq - HiSeq 2500, two lanes of paired-end 125bp reads

treatment_protocol: No additional treatement

tag: strain background

value: C57BL/6 J

tag: tissue/cell type

value: Peritoneal tissue-resident macrophage


title: P2_cell_145


title: P1_cell_40

value: Female


title: P1_cell_32

value: patients with bone marrow failure and cytogenetic abnormalities


title: P2_cell_144

value: Male


title: P2_cell_157


title: P1_cell_31


title: P2_cell_142


title: Bone marrow derived macrophage 2

description:
BM2.star.count.txt
Bone marrow derived macrophage 2

source_name: Bone marrow derived macrophage 2

value: Bone marrow derived macrophage


title: P2_cell_143


title: P1_cell_30


title: Bone marrow derived macrophage 1

description:
BM1.star.count.txt
Bone marrow derived macrophage 1

source_name: Bone marrow derived macrophage 1


title: P2_cell_141


title: P1_cell_2


title: MEF_shp53+Dnmt1

data_processing:
Base calls performed using CASAVA version 1.4
Reads were filtered by using perl trim_galore v 0.3.7 with the following parameters: -q 20 –paired -a AGATCGGAAGAGC –a2 GATCGGAAGAGC --phred33 --gzip --rrbs --keep --fastqc --fastqc_args --threads 2 FastqFile -o OutFile.
BS-seq reads were aligned to the mm10 genome assembly using bismark version 0.9.0 with the following configurations: -pe -N 1 --bowtie2 --path_to_bowtie Bowtie2Path --bam --samtools_path SamtoolsPath –o OutFile <genome_folder> -1 fastq1 -2 fastq2.
Methylation calls were obtained using bismark version 0.9.0.
Genome_build: mm10
Supplementary_files_format_and_content: See README.txt

growth_protocol: MEFs were derived from 13.5-day mouse embryos and maintained in Dulbecco’s modified Eagle medium (DMEM, Gibco) supplemented with 10% FBS (Gibco), non-essential amino acids (NEAA, Gibco), penicillin/streptomycin and L-glutamine. In the reprogramming group, MEFs was infected with retrovirus containing Oct4, Klf4, c-Myc and Sox2 (OKMS), and maintained in mESC or mESC-Vc medium containing high-glucose DMEM (Hyclone), NEAA, penicillin/streptomycin, lglutamine, leukaemia inhibitory factor (LIF), β-mercaptoethanol, pyruvate and 15% FBS without or with Vc. Cells were harvested on day 5 after retrovirus infection.

extract_protocol:
Around 3×106 cells were harvested by 0.25 % trypsin digestion. DNA was extracted according to the instructions of Wizard® Genomic DNA Purification Kit (Promega A1125). Purity of DNA was determined by K5500 spectrophotometer, DNA quantification was performed using Qubit® 3.0 Fluorometer.
DNA was digested by MspI followed by end-repairing. The 3’end of the end-repaired, phosphorylated fragments were tailed with dA, and the single A overhangs were ligated by the methylated adaptors. Library fragments of 40~220 bp were band isolated from 2% agarose gel, converted by bisulfite treatment, and amplified by PCR. The RRBS library was sequenced on an Illumina HiSeq2500 sequencers as paired-end 50 bp reads.


title: MEF_shp53+shDnmt1


title: P1_cell_28


title: P1_cell_29


title: P2_cell_139


title: MEF_Tet1-CD


title: P1_cell_27


title: P2_cell_138


title: P1_cell_26


title: MEF_shp53


title: Peritoneal tissue-resident macrophage 1

description:
RES_1.star.count.txt
Peritoneal tissue-resident macrophage 1


title: P1_cell_25


title: MEF_shDnmt1


title: P2_cell_136


title: P2_cell_135


title: MEF_Flag+shLuc


title: P1_cell_23


title: P1_cell_24


title: P2_cell_134


title: P1_cell_22


title: P2_cell_140


title: SKOM day5_Vc+_Tet1CD+shDnmt1


title: P2_cell_133


title: 5C_Flag+shLuc


title: P1_cell_21


title: SKOM day5_Vc+_Tet1CD+Dmnt1


title: P1_cell_20


title: P2_cell_132


title: SKOM day5_Vc+_shp53+shDnmt1


title: P1_cell_1


title: P2_cell_130


title: SKOM day5_Vc+_shp53+Dnmt1


title: SKOM day5_Vc+_Tet1CD


title: P1_cell_19


title: P2_cell_137


title: P2_cell_129


title: MEF_Dnmt1


title: P1_cell_18


title: P2_cell_128


title: SKOM day5_Vc+_shDnmt1


title: SKOM day5_Vc+_Dnmt1


title: P2_cell_127


title: P2_cell_126


title: P1_cell_16


title: P1_cell_17


title: P2_cell_125


title: P1_cell_15


title: SKOM day5_Vc+_Flag+shLuc


title: SKOM day5_Vc-_Tet1CD+shDnmt1


title: P1_cell_14


title: P2_cell_124


title: P2_cell_131


title: P2_cell_123


title: SKOM day5_Vc-_Tet1CD+Dmnt1


title: SKOM day5_Vc-_shp53+shDnmt1


title: P2_cell_122


title: P1_cell_13


title: P1_cell_11


title: P1_cell_12


title: P2_cell_121


title: SKOM day5_Vc-_shDnmt1


title: P2_cell_120


title: P2_cell_118


title: SKOM day5_Vc-_Flag+shLuc


title: P1_bulk


title: P2_cell_119


title: P2_cell_116


title: MEF_G1

description:
Processed data file: WGBS_chr1_processed.txt
Processed data file: WGBS_chr2_processed.txt
Processed data file: WGBS_chr3_processed.txt
Processed data file: WGBS_chr4_processed.txt
Processed data file: WGBS_chr5_processed.txt
Processed data file: WGBS_chr6_processed.txt
Processed data file: WGBS_chr7_processed.txt
Processed data file: WGBS_chr8_processed.txt
Processed data file: WGBS_chr9_processed.txt
Processed data file: WGBS_chr10_processed.txt
Processed data file: WGBS_chr11_processed.txt
Processed data file: WGBS_chr12_processed.txt
Processed data file: WGBS_chr13_processed.txt
Processed data file: WGBS_chr14_processed.txt
Processed data file: WGBS_chr15_processed.txt
Processed data file: WGBS_chr16_processed.txt
Processed data file: WGBS_chr17_processed.txt
Processed data file: WGBS_chr18_processed.txt
Processed data file: WGBS_chr19_processed.txt

data_processing:
Basecalls performed using CASAVA version 1.4.
BS-seq reads were aligned to the mm10 genome assembly using bismark version 0.9.0 with the following configurations: -p -n -1 -2 -un --bowtie2 -path_to_bowtie –bam -samtool s_path -o
Methylation calls were obtained using bismark version 0.9.0.
Methylation level was calculated as: the number of reads in support of 5mC/total reads at this site*100%. All CpG sites with depth over 4X were analyzed in the processed data.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: WGBS_chr*_processed.txt: Tab-delimited text files include methylation levels. See the README.txt file for additional details.

source_name: mouse embryonic fibroblasts, G1 phase

growth_protocol: MEFs were derived from 13.5-day mouse embryos and maintained in Dulbecco's modified Eagle medium (DMEM, Gibco) supplemented with 10% FBS (Gibco), non-essential amino acids (NEAA, Gibco), penicillin/streptomycin and L-glutamine.

extract_protocol:
Around 3x10^6 cells were sorted by FACS. DNA was extracted according to the instructions of Wizard® Genomic DNA Purification Kit (Promega A1125). Purity of DNA was determined by K5500 spectrophotometer. DNA quantification was performed using Qubit® 3.0 Fluorometer.
Bisulfite-Seq DNA libraries were prepared for sequencing using standard Illumina protocols. Briefly, DNA was fragmented to ~300bp by sonication and followed by end-repair. The blunt, phosphorylated ends were tailed by dA of the 3' end, and the single A overhangs were ligated by the methylated adaptors. Library fragments of ~350 bp were band isolated from 2% agarose gel, converted by bisulfite treatment, and amplified by PCR. The WGBS library was sequenced on an Illumina HiSeq2500 sequencers as paired-end 125-bp reads.

treatment_protocol: MEFs were digested by 0.25% trypsin, followed by fixation with 70% ethanol for overnight. Fixed cells were treated with 0.25mg/mL RNase A at 37℃ for 30 minutes to remove RNA, and stained with 50μg/L PI for 30 minutes. The resulted cell suspension was used for fluorescence-activated cell sorting (FACS) with BD FACSAria II flow cytometer.

tag: strain/background

value: mouse embryonic fibroblasts (MEFs)

tag: cell cycle phase

value: G1 phase


title: P2_cell_115


title: P2_cell_117


title: MEF_G2

source_name: mouse embryonic fibroblasts, G2 phase

value: G2 phase


title: P2_cell_114


title: P2_cell_113


title: chicken_claw_2_sample_C126C

city: Heidelberg

first: Jacob

last: Musser

address: Meyerhofstrasse 1

country: Germany

institute: European Molecular Biology Laboratory

data_processing:
Basecalls performed using CASAVA
reads mapped to chicken or emu genome using Tophat2 version 2.0.6. using default parameters and setting the -GTF option
read counts generated using HTSEQ version 0.5.3p9 implemented in python version 2.7.2. We set the option requiring reads to map to the correct strand, and resolved issues with multiple mappings using the option "intersection-nonempty".
TPM (transcript per million) relative expression values were calculated for all genes using the following method: Wagner GP, Kin K, Lynch VJ. 2012. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theor Biosci. 131:281-285.
We applied a scaling factor to all emu TPM values (.55x) to account for differences in the number of annotated genes. This value was calculated using the method outlined here: Musser, J. M. & Wagner, G. P. Character trees from transcriptome data: Origin and individuation of morphological characters and the so-called ‘species signal’. J Exp Zool (Mol Dev Evol) 324, 588–604 (2015).
Genome_build: Chicken reads were mapped to ensembl WASHUC2 release version 68. Emu reads were mapped to a preliminary version of the Emu genome generated by the Alan Baker Lab at the University of Toronto.
Supplementary_files_format_and_content: concerted_evolution_scaled_tpms.txt is a tabular format text file that contains the final scaled TPM values for all chicken and emu one-to-one orthologs that were used for analyses.

organism: Gallus gallus

source_name: chicken_claw placode tract epidermis

growth_protocol: Bird eggs were incubated with rotation in a G.Q.F 1502 Sportsmen Incubator at 37.8 degrees celsius (chicken) or 35.5 degrees celsius (emu)

extract_protocol:
Total RNA was extracted using a Qiagen Rneasy kit.
polyA enriched strand-specific library was constructed using a proprietary method developed by the Yale Center for Genome Analysis

treatment_protocol: Skin samples were dissected and placed in a minimal amount of 10 mg/mL dispase and incubated at 4 degrees celsius for 13 hours to permit clean separation of epidermis.

tag: developmental stage

value: Hamburger and Hamilton Stage 36

value: claw placode tract epidermis


title: chicken_reticulate_scale_2_sample_C113R

source_name: chicken_reticulate scale placode tract epidermis

value: Hamburger and Hamilton Stage 39

tag: tissue


title: emu_claw_1_sample_E23C

organism: Dromaius novaehollandiae

source_name: emu_claw placode tract epidermis


title: chicken_claw_1_sample_C99C


title: SKOM day5_Vc-_Tet1CD

value: ICR

value: mouse embryonic fibroblasts


title: P2_cell_112


title: chicken_reticulate_scale_1_sample_C91R

value: reticulate scale placode tract epidermis


title: SKOM day5_Vc-_shp53+Dnmt1


title: chicken_scutate_scale_2_sample_C116S

source_name: chicken_scutate scale placode tract epidermis

value: Hamburger and Hamilton Stage 37

value: scutate scale placode tract epidermis


title: P1_cell_10


title: emu_reticulate_scale_1_sample_E21R

source_name: emu_reticulate scale placode tract epidermis


title: P2_cell_111

source_name: Bone Marrow


title: SKOM day5_Vc-_Dnmt1


title: P2_cell_110


title: emu_scutate_scale_2_sample_E11S

source_name: emu_scutate scale placode tract epidermis


title: chicken_scutate_scale_1_sample_C103S


title: emu_scutate_scale_1_sample_E10S


title: Hcc1954

first: John

middle: M

last: Coffin

address: 136 Harrison Ave.

department: Molecular Biology & Microbiology

institute: Tufts University

data_processing:
Basecalling was accomplished using Illumina's CASAVA-1.8.2.
Reads were trimmed to clip off Illumina adapters and filter out low-quality reads. Any overlapping paired-end reads were merged.
Both stranded and unstranded alignments were performed using TopHat v2.0.10 and Bowtie v2.1.0.
All aligned reads were filtered for uniquely mapping reads only.
Transcript abundance levels were generated using Cuffdiff and values are provided as FPKM.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Cuffdiff_Results.xls: Excel spreadsheet includes the normalized FPKM values of each HERV-K (HML-2) provirus in the four cell lines sequenced. There are two sheets included in the file: one that contains the results of the unstranded alignments and one that contains the results from the stranded alignments.
Supplementary_files_format_and_content: *FPKM.txt: Results by individual cell line are provided as separate tab-delimited text files.

source_name: human mammary epithelial cells, tumorigenic

growth_protocol: The Hcc1954 cell line was cultured in RPMI 1640 Media, supplemented with 10% FBS and 1% Pen-Strep, and were incubated at 37ºC with 5% CO2.

extract_protocol:
Total RNA was extracted using the TRIzol-PureLink RNA Mini Kit system and all traces of DNA were removed by DNase treatment.
Libraries were constructed using Illumina’s TruSeq Stranded Total RNA Kit with Ribo-Zero Gold and sequencing was done on the MiSeq benchtop sequencer using Illumina's MiSeq Reagent Kit v3.

tag: cell line

value: HCC1954; Cell type:Human mammary epithelial cell line; Transformation stage:Tumorigenic


title: HMLE-Ras

growth_protocol: The HMLE-Ras cell line was cultured using the MEGM BulletKit, according to the manufacturer’s protocol (Lonza, Walkersville, MD, USA) and incubated at 37ºC with 5% CO2.

value: HMLE-Ras; Cell type:Human mammary epithelial cell line; Transformation stage:Tumorigenic


title: HME

source_name: human mammary epithelial cells, immortalized, non-transformed

growth_protocol: The HME cell line was cultured using the MEGM BulletKit, according to the manufacturer’s protocol (Lonza, Walkersville, MD, USA) and incubated at 37ºC with 5% CO2.

value: HME; Cell type:Human mammary epithelial cell line; Transformation stage:Immortalized, non-transformed


title: HMLE-Her2

growth_protocol: The HMLE-Her2 cell line was cultured using the MEGM BulletKit, according to the manufacturer’s protocol (Lonza, Walkersville, MD, USA) and incubated at 37ºC with 5% CO2.

value: HMLE-Her2; Cell type:Human mammary epithelial cell line; Transformation stage:Tumorigenic


title: chicken_feather_2_sample_C14F

source_name: chicken_feather placode tract epidermis

value: Hamburger and Hamilton Stage 33/34

value: feather placode tract epidermis


title: P2_cell_109

value: Male

value: patients with bone marrow failure and cytogenetic abnormalities


title: P2_cell_108


title: chicken_feather_1_sample_C17F


title: emu_feather_1_sample_E6FL

source_name: emu_feather placode tract epidermis


title: emu_feather_2_sample_E9FL


title: P2_cell_107


title: Jag1Ndr/Ndr rep 3

description:
1337_2_Jag1ndr
RPKM Jag1ndr_rep3

data_processing:
Reads were aligned using STAR to genome mm10
Reads with multiple alignments were removed
Gene expression values were calculated using rpkmforgenes.py (https://github.com/danielramskold/Allelic_patterns_in_clonal_somatic_cells) with options -rmnameoverlap -bothendsceil and using RefSeq annotation from February 2015
RPKM values were TMM normalized
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text of normalised expression values and read counts

growth_protocol: Livers collected at postnatal day 10.

extract_protocol:
Mouse livers were collected fresh and stored in RNAlater® (cat. no. AM7020, Ambion) at -80 °C. RNA was extracted from one lobe using the RNeasy Mini Kit (cat. no. 74104, QIAGEN), including on-column DNase I digestion (cat. no. 79254, QIAGEN).
cDNA libraries for all samples were created using the TruSeq® RNA Sample Prep Kit v2–48, Set A (cat. no. RS-122-2001, Illumina®,) as per the TruSeq® RNA Sample Preparation v2 Guide, Low-Throughput Protocol.

treatment_protocol: No treatment.

tag: genotype/variation

value: postnatal day 10

value: liver


title: P2_cell_105


title: Jag1Ndr/Ndr rep 2

description:
1329_3_Jag1ndr
RPKM Jag1ndr_rep2


title: P2_cell_106


title: IBDV infection

city: Beijing

first: Shijun J.

state: beijing

address: 2 Yuan-Ming-Yuan West Road

department: College of Veterinary Medicine

institute: China Agricultural University

data_processing:
the raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and then the dataset was further processed with a program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 21.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment.
Genome_build: from miRBase21.0 version
Supplementary_files_format_and_content: differences in miRNA expression between IBDV-infected and Mock-infected DF-1 cells, xlsx

source_name: DF-1 cells

growth_protocol: DF-1 cells (immortal chicken embryo fibroblast) were cultured in 100mm cell culture dish in Dulbecco modified Eagle medium (DMEM) (Invitrogen, USA) supplemented with 10% fetal bovine serum (FBS) in a 5% CO2 incubator.

extract_protocol:
total RNA was extracted using the TRIzol reagent (LC Science, China) following the manufacturer’s protocol.
RNA libraries were prepared for sequencing using TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA)

tag: cell type

value: immortal chicken embryo fibroblast

value: no more than 10

tag: virus strain

value: Lx


title: s213F2

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

data_processing:
Illumina Casava 1.8 software used for basecalling.
Removal of adapter sequences for each sample was manually confirmed from FastQC output. Sequenced reads were mapped to hg19 whole genome using bowtie2 v2.2.5 with the default parameters, and Tophat2 2.1.0 to detect splicing junctions.
Raw read counts were extracted using a bioconductor package Rsubread with the default parameters. Raw read counts were then normalized by a bioconductor package applys an edgeR or DESeq2 normalization method.
Genome_build: hg19
Supplementary_files_format_and_content: [rcsym.txt] Raw read counts
Supplementary_files_format_and_content: [rcmat.txt] a single tab-delimited text file includes normalized counts for all samples

source_name: Humanized mouse

extract_protocol:
RNA was extracted from splenic human mononuclear cells using QIAamp RNA Blood Mini kit (Qiagen)
RNA libraries were prepared for sequencing in Medical & Biological Laboratories, co (Nagoya, Japan).

treatment_protocol: HIV-1 was intraperitoneally inoculated into the 2 humanized mice. PegIFN was subcutaneously treated into the 2 humanized mice.

tag: treatment of humanized mice

value: PegIFN treated

tag: time

value: 1 week post-treatment

value: Splenic human CD4-positive T cells


title: s235M3

tag: infection of humanized mice

value: HIV-1 infected

value: 6 weeks post-infection


title: Jag1Ndr/Ndr rep 1

description:
1022_3_Jag1ndr
RPKM Jag1ndr_rep1


title: s214F2


title: P2_cell_104

tag: markers

tag: age


title: P2_cell_103

tag: Sex

tag: subject


title: s244M2_3


title: Jag1+/+ rep 2

description:
1329_1_Jag1wt
RPKM Jag1wt_rep2

tag: strain background


title: s214F1M3

value: Mock infected


title: P2_cell_102

tag: disease


title: Jag1+/+ rep 3

description:
1337_1_Jag1wt
RPKM Jag1wt_rep3


title: Jag1+/+ rep 1

description:
1022_1_Jag1wt
RPKM Jag1wt_rep1


title: P2_cell_101


title: Mock infection

tag: passages

value: Mock


title: Myod1_control rep1

status: Public on Oct 12 2017

first: Xueying

last: Mai

address: 7 Science Park Road ZGC Life Science Park

institute: National Institute of Biological Sciences, Beijing

data_processing:
Use cutadapt v1.11 to remove the low quality bases and trimmed the sequence in 50nt length.
Use TopHat v2.1.1 to aligned the reads with default parameter.
Use Cufflinks 2.2.1 to calculate the gene expression level.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM for each sample in text.

source_name: mouse liver

extract_protocol:
RNA was extracted using the Direct-zol™ RNA MiniPrep Kit (Zymo Research).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype

value: Myod1 Control


title: SunTag rep2

tag: tissue

value: SunTag


title: s213F1


title: WT rep2

value: Wild Type


title: Myod1_control rep2


title: Myod1_active rep1

value: Myod1 active


title: Day_20_5hmC

city: Stanford

first: Nidhi

last: Bhutani

state: California

address: 300 Pasteur Drive, R164 Edwards Bldg

department: Orthopaedic Surgery

institute: Stanford University

data_processing:
QC and filtering: An iterative quality check (FastQC http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and filtering procedure (Cutadapt http://code.google.com/p/cutadapt/) was performed to obtain good quality reads after trimming of the initial 7 bases.
Alignment: The Burrows-Wheeler Aligner, version 0.7.5a-r405 (http://bio-bwa.sourceforge.net/) (Li and Durbin 2009), was used with default parameters to align the filtered and trimmed reads to the mouse reference genome (GRCm38/mm10 http://genome.UCSC.edu) and alignments with a MAPQ score of greater than 5 were used for downstream analyses.
QC: MEDIPS (Lienhard et al. 2014) was used to assess the sequencing depth and coverage across the genome.
Peak calling: MACS version 1.4.2 (http://liulab.dfci.harvard.edu/MACS/) (Zhang et al. 2008), was used to call peaks using default settings. The MACS peaks annotated with Cisgenome version 2.0 (http://www.biostat.jhsph.edu/~hji/cisgenome/) (Ji et al. 2008), are based on the GRCm38/mm10 (http://genome.UCSC.edu) annotation file.
Data visualizaiton: To identify the distribution of 5mC/5hmC throughout the gene body and around the TSS, ngs.plot (Shen et al. 2014) was used with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: All processed data files contain peak calls generated using MACS and are in .txt files.

source_name: ATDC5 chondrogenic cell line D20 (replicate) enriched for hydroxymethylated DNA

growth_protocol: ATDC5 chondroprogenitor cells were maintained in DMEM/F12, 5% fetal bovine serum, 2mM L-Glutamine, 1x Antibiotic-Antimycotic (all Fisher Scientific) and 12.5μg/mL ascorbic acid (Eastman). To differentiate the cells into chondrocytes, 1x Insulin-Transferrin-Selenite (Invitrogen) was added to the basal media for 20 days.

extract_protocol:
Total DNA was extracted at appropriate timepoint. Extracted DNA was enriched for either 5mC (MIRA-base enrichment -  MethylCollector Ultra, Active Motif) or 5hmC (Hydroxymethyl Collector, Active Motif).
Libraries were prepared using enrichmed DNA and the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB) as per manufacturers guidelines.  200-500ng of enriched DNA was used for each library.

tag: developmental stage

value: Chondrocyte

tag: enrichment type

tag: method for enrichment

value: Hydroxymethyl Collector (Active Motif) as per manufacturer's guidelines.


title: Day_0_5hmC

source_name: ATDC5 chondrogenic cell line D0 enriched for hydroxymethylated DNA

value: Chondroprogenitor


title: Day_0B_5hmC

source_name: ATDC5 chondrogenic cell line D0 (replicate) enriched for hydroxymethylated DNA


title: WT mESC

city: Chicago

first: Ian

last: Roundtree

state: IL

address: 929 E 57th Street E307

department: Department of Chemistry

institute: University of Chicago

description: WT mESC

data_processing:
After adaptor trimming with Cutadapt (v1.4.1) and quality control, 50 bp sequence reads were mapped to the human genome (hg19) using TopHat (v.2.0.11) and Bowtie (v1.0.1). 150 bp reads from paired-end sequencing were mapped directly to the mouse genome (mm9) using TopHat.
PAR-CLIP peaks were called using PARalyzer (v.1.5) with default parameters.
RIP-seq and RNA-seq differential expression was quantified between replicate experiments using Cufflinks (v.2.2.1)
Differential splicing was analyzed using MATS (v3.0.8) (rMATS) below a FDR of 0.05.
Genome_build: hg19 (human), mm9 (mouse)

source_name: WT mECS

growth_protocol: HeLa cells (ATCC CCL-2) were cultured in DMEM supplemented with 10% FBS and 1% Pen/Strep. mESCs (CGR8) were cultured in GMEM supplemented with 10% FBS, Non-Essential Amino Acids, 1 mM sodium pyruvate, 1 mM 2-mercaptoethanol and 1,000 U/mL LIF. All cells were cultured at 37 degrees C in 5% CO2 incubators.

extract_protocol:
PAR-CLIP was performed as previously described (Xu et al., 2014). Breifly, Flag-tagged YTHDC1 was immunoprecipitated from transfected HeLa cells and treated with Rnase. Bound RNA fragments were isolated with TriZol following Proteinase K digestion and subject to ibrary construction.
RIP was performed according to literature procedure (Peritz et al., 2006) using polyA selected RNA and ribosomal RNA depleted RNA as biological replicates.
HeLa cells were fractionated using NE-PER Nuclear and Cytoplasmic Extraction Reagents (Thermo Scientific) according to manufacturer protocol with the following modifications: following cytoplasmic isolation, nuclei were washed extensively (4 x 200 μL) with PBS. RNA from each portion was collected using Directzol RNA miniprep (Zymo Research) and treated with DNaseI. Samples were depleted of ribosomal RNA prior to sequencing.
mESC mRNA was isolated using TriZol reagent and purified using poly-T oligo magnetic beads.
PAR-CLIP libraries were constructed using Illumina TruSeq Small RNA (Rep 1) or NEBNext Small RNA (Rep 2) library construction kits. RIP-seq and subcellular RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA kit. mESC mRNA libraries were constructed using the NEBNext Ultra Directional RNA library construction kit.

treatment_protocol: Transfections were carried out using Lipofectamine 2000, Lipofectamine LTX (multiple plasmids) or Lipofectamine RNAiMAX according to manufacturers protocol in the absence of antibiotics.

tag: cell line

value: HeLa

tag: culture media

value: GMEM


title: Ythdc1 KO mESC re

description: Ythdc1 KO mESC re

source_name: Ythdc1 KO mESC


title: Ythdc1 KO mESC

description: Ythdc1 KO mESC


title: WT mESC re

description: WT mESC re


title: CD11b_inflamed_2

city: Cologne

first: Sebastian

last: Brähler

address: Joseph-Stelzmann-Str. 26

department: Nephrology

institute: University Hospital of Cologne

data_processing:
RNA-Seq reads were aligned to the Ensembl release 76 assembly with STAR version 2.0.4b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
All gene-level and counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Genes or transcripts not expressed in any sample were excluded from further analysis.
Genome_build: Mus musculus Ensembl release 76 assembly
Supplementary_files_format_and_content: File is an excel sheet with 3 columns with gene identifiers (including the official gene symbols in column 1), followed by columns for the 12 replicates, the values are normalized abundance measurements obtained with EdgeR.

source_name: kidney

growth_protocol: does not apply

extract_protocol:
For RNA sequencing kidney single cells suspensions were prepared. In brief, Kidneys were cut into small pieces and then stirred for 30 min at 37 °C in 5 ml of complete RPMI (Thermo Fisher Scientific) with 30 U/ml DNase I and 250 μg/ml collagenase B (Sigma-Aldrich). For removal of debris, cells were passed through a 100 μm strainer before red blood cells were lysed with ammonium chloride–potassium bicarbonate lysis buffer (150 mM NH4Cl, 10 mM KHCO3, 0.1 mM EDTA) for 3 min at room temperature and then passed through a 70 μm cell strainer. Immune cells were enriched with anti-mouse CD45-beads and LS columns (Miltenyi Biotec, San Diego, CA) according to the manufacturer’s instructions, before proceeding to surface. Cell sorting was performed on a FACS Aria II flow cytometer (BD) and sorted directly into the lysis buffer of the RNAqueous micro isolation kit (ThermoFisher). Lysates were immediately frozen on dry ice and stored at -80°C until RNA preparation and DNase treatment according to the manufacturer’s standard protocol. RNA integrity was determined using an Agilent bioanalyzer.
Library preparation was performed with total RNA after integrity was determined using an Agilent bioanalyzer.  Double stranded cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara Bio USA, Mountain View, CA) per the manufacturer’s protocol. cDNA was fragmented using a Covaris E210 sonicator using duty cycle 10, intensity 5, cycles/burst 200, time 180 seconds. cDNA was blunt ended, had an adenine added to the 3’ ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-2500 (Illumina, San Diego, CA) using single reads extending 50 bases.

treatment_protocol: 3 mice were sacrificed in the healthy situation, 3 mice were sacrificed 7 days after injection of the nephrotoxic nephritis antiserum (NTN).

value: male

value: 8-12 weeks

tag: cell type

value: CD11b+ kidney denritic cell

tag: treatment

value: 7 days of nephrotoxic nephritis (experimental glomerulonephritis)


title: CD11b_inflamed_3


title: CD11b_inflamed_1


title: CD103_inflamed_2

value: CD103+ kidney dendritic cell


title: Day_19_5hmC

source_name: ATDC5 chondrogenic cell line D19 enriched for hydroxymethylated DNA


title: CD11b_healthy_2

value: healthy


title: CD103_inflamed_1


title: CD11b_healthy_3


title: CD103_inflamed_3


title: CD103_healthy_2


title: CD103_healthy_3


title: CD11b_healthy_1


title: CD103_healthy_1


title: IR_PB1

city: Hangzhou

first: Haiyan

last: Lin

state: Zhejiang

address: No 28, Rice Road, Fuyang Dist

institute: China National Rice Research Insititution

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: OS-Nipponbare-IRGSP-1.0
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Oryza sativa

growth_protocol: Rice submergence-intolerant variety IR64 plants were grown in plastic pots (25 cm in length, 18cm in width, and 8 cm in height) filled with 2.0 kg mixture of dry paddy soil and special seedling substrate (NPK content ≥ 5%, organic material ≥ 15%) in a 4:1 ratio, a 24-15-15 (N-P2O5-K2O) fertilizer was applied at 0.8 g per pot rate once before seeding. Thirty IR64 pre-germination seeds were sown in each pot. Irrigation was applied as needed to prevent any visible drought stress during seedling growth. Plants were thinned to twenty seedlings per pot 10 days after sowing.

extract_protocol:
Total RNA was extracted from leaves of seedlings using the Trizol (Invitrogen, Carlsbad, U.S.A.) according to the manufacturer’s protocols. The total RNA quantity and purifity were analysis of Bioanalyzer 2100 and RNA 6000 Nano Labchip Kit (Agilent, CA, USA) with RIN number>7. 0.5 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligo attached magnetic beads (Invitrogen, Carlsbad, U.S.A.). The mRNA is fragmented into small pieces using divalent-cation under elevated temperature after purification, then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, U.S.A.), the average insert size for the paired-end libraries was 300 bp (±50 bp).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PB and GA stock solutions were made by pre-dissolving 300 mg and 150 mg powders in 2 mL 95% ethanol and then diluted to 200 mg.L-1 and 100 mg.L-1 by water, respectively. Twenty DAG seedlings were sprayed with 25ml of 200 mg.L-1 PB, 100 mg.L-1 GA, or ethanol solvent (0.1% final concentration) as control at two days prior to the submergence. Plants were completely submerged and water depth was maintained at 100 cm for 0, 4, 8, 12, and 16 days in concrete tanks (180 cm in length, 120 cm in width and 100 cm in height), respectively.

tag: variety

tag: genotype/phenotype

value: submergence-intolerant variety

tag: treated with

value: Paclobutrazol (PB)

tag: condition

value: four days in submergence

value: leaves


title: IR_PB3


title: IR_GA1

value: gibberellic acid (GA)


title: IR_GA2


title: IR_GA3


title: IR_CK3

value: ethanol solvent (untreated control)


title: IR_CK1


title: siYT521_PE150

description: siYT521 PE_150

data_processing:
After adaptor trimming with Cutadapt (v1.4.1) and quality control, 150 bp sequence reads were mapped to the human genome (hg19) using TopHat (v.2.0.11) and Bowtie (v1.0.1) in paired-end mode.
RIP-seq and RNA-seq differential expression was quantified between replicate experiments using Cufflinks (v.2.2.1)
Genome_build: hg19 (human)
Supplementary_files_format_and_content: Differential splicing was analyzed using MISO v.0.5.3.

source_name: HeLa transfected with YT521 siRNA

growth_protocol: HeLa cells (ATCC CCL-2) were cultured in DMEM supplemented with 10% FBS and 1% Pen/Strep.

extract_protocol:
RNA from each portion was collected using Directzol RNA miniprep (Zymo Research) and treated with DNaseI. RNA was purufied by Ribo(-) and used to construct sequencing libraries.
Libraries were constructed using the Illumina TruSeq Stranded mRNA kit.

treatment_protocol: Transfections were carried out using Lipofectamine RNAiMAX according to manufacturers protocol in the absence of antibiotics.

value: DMEM

value: ATCC CCL-2


title: siControl_2_PE150

description: siControl PE_150

source_name: HeLa transfected with control siRNA


title: siYTHDC1_PE150

description: siYTHDC1 PE_150

source_name: HeLa transfected with YTHDC1 siRNA


title: siControl_1_PE150

description: siControl PE_150