title: Kit+_SingleCells_SSCs_48


title: Kit+_SingleCells_SSCs_52

status: Public on Oct 05 2017

type: SRA

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

country: USA

institute: University of Utah School of Medicine

library_source: transcriptomic

data_processing:
Raw RNA sequencing reads (fastq files) were aligned to a custom genome index using Novoalign (v2.8, Novocraft) using the following parameters: -o SAM –r ALL 50. Index was generated using MakeTranscriptome application (USeq package v8.8.8), accounting for splicing junctions.  The raw splice juction alignments were converted to genomic cooradinates using SamTranscriptomeParser (USeq package v8.8.8).
Raw reads were counted across all individual exons and subsequently merged by corresponsing ensembl gene annotation using DefinedRegionDifferentialSeq application (USeq package v8.8.8) with default options. FPKMs were then counted based on reads mapped to genes.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

molecule: polyA RNA

organism: Homo sapiens

source_name: human SSCs

extract_protocol:
Isolated SSEA4+ or Kit+ germline stem cells were diluted into 15,000-20,000 cells/ml and loaded into 5-10 μm integrated fluidic circuits (IFCs) using Fluidigm C1 instrument. Single cells captured in IFCs were scored under microscope. Only cells with normal morphology were scored high for sequencing. Single cells in IFCs were lysed and total RNA was harvested for polyadenylation selection, reverse transcription and PCR amplification.
Library constructions were performed according to Fluidigm Library preparation with Nextera XT protocol and sequenced on a 50-cycle single end run on an Illumina HiSeq 2500 instrument.

tag: cell type

value: Spermatogonial Stem Cells

tag: marker

value: KIT+

tag: tissue

value: Testis


title: Kit+_SingleCells_SSCs_49


title: Kit+_SingleCells_SSCs_47


title: Kit+_SingleCells_SSCs_69


title: Kit+_SingleCells_SSCs_51


title: Kit+_SingleCells_SSCs_46


title: Kit+_SingleCells_SSCs_50


title: Kit+_SingleCells_SSCs_63


title: Kit+_SingleCells_SSCs_45


title: Kit+_SingleCells_SSCs_44


title: Kit+_SingleCells_SSCs_42


title: Kit+_SingleCells_SSCs_43


title: Kit+_SingleCells_SSCs_37


title: Kit+_SingleCells_SSCs_39


title: Kit+_SingleCells_SSCs_34


title: Kit+_SingleCells_SSCs_32


title: Kit+_SingleCells_SSCs_31


title: Kit+_SingleCells_SSCs_41


title: Kit+_SingleCells_SSCs_35


title: Kit+_SingleCells_SSCs_38


title: Kit+_SingleCells_SSCs_40


title: Kit+_SingleCells_SSCs_36


title: Kit+_SingleCells_SSCs_27


title: Kit+_SingleCells_SSCs_29


title: Kit+_SingleCells_SSCs_28


title: Kit+_SingleCells_SSCs_33


title: Kit+_SingleCells_SSCs_26


title: Kit+_SingleCells_SSCs_22


title: Kit+_SingleCells_SSCs_23


title: Kit+_SingleCells_SSCs_21


title: Kit+_SingleCells_SSCs_17


title: Kit+_SingleCells_SSCs_25


title: Kit+_SingleCells_SSCs_18


title: Kit+_SingleCells_SSCs_24


title: Kit+_SingleCells_SSCs_20


title: Kit+_SingleCells_SSCs_16


title: Kit+_SingleCells_SSCs_19


title: Kit+_SingleCells_SSCs_15


title: Kit+_SingleCells_SSCs_14


title: Kit+_SingleCells_SSCs_13


title: Kit+_SingleCells_SSCs_30


title: Kit+_SingleCells_SSCs_11


title: Kit+_SingleCells_SSCs_9


title: Kit+_SingleCells_SSCs_6


title: Kit+_SingleCells_SSCs_8


title: Kit+_SingleCells_SSCs_10


title: Kit+_SingleCells_SSCs_7


title: Rao-2017-HIC006

city: Houston

first: Suhas

last: Rao

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

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

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 following the manufacturer's protocols

tag: cell line

tag: protocol

value: in situ Hi-C

value: Colorectal carcinoma


title: Rao-2017-HIC003


title: Rao-2017-HIC005


title: Kit+_SingleCells_SSCs_5


title: Rao-2017-HIC004


title: Rao-2017-HIC002


title: Kit+_SingleCells_SSCs_4


title: Rao-2017-HIC001


title: Kit+_SingleCells_SSCs_1


title: Kit+_SingleCells_SSCs_2


title: SSEA4+_SingleCells_SSCs_101


title: SSEA4+_SingleCells_SSCs_98


title: SSEA4+_SingleCells_SSCs_100


title: SSEA4+_SingleCells_SSCs_99


title: SSEA4+_SingleCells_SSCs_97


title: SSEA4+_SingleCells_SSCs_94


title: SSEA4+_SingleCells_SSCs_95


title: SSEA4+_SingleCells_SSCs_96


title: SSEA4+_SingleCells_SSCs_91


title: SSEA4+_SingleCells_SSCs_93


title: Kit+_SingleCells_SSCs_12


title: SSEA4+_SingleCells_SSCs_89


title: SSEA4+_SingleCells_SSCs_88


title: SSEA4+_SingleCells_SSCs_90


title: SSEA4+_SingleCells_SSCs_92


title: SSEA4+_SingleCells_SSCs_85


title: SSEA4+_SingleCells_SSCs_87


title: SSEA4+_SingleCells_SSCs_86


title: SSEA4+_SingleCells_SSCs_84


title: SSEA4+_SingleCells_SSCs_81


title: SSEA4+_SingleCells_SSCs_80


title: Kit+_SingleCells_SSCs_3


title: SSEA4+_SingleCells_SSCs_79


title: SSEA4+_SingleCells_SSCs_77


title: SSEA4+_SingleCells_SSCs_83


title: SSEA4+_SingleCells_SSCs_82


title: SSEA4+_SingleCells_SSCs_78


title: SSEA4+_SingleCells_SSCs_76


title: SSEA4+_SingleCells_SSCs_73


title: SSEA4+_SingleCells_SSCs_74


title: SSEA4+_SingleCells_SSCs_66


title: SSEA4+_SingleCells_SSCs_67


title: SSEA4+_SingleCells_SSCs_72


title: SSEA4+_SingleCells_SSCs_75


title: RNA-HCC95-WT-B

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

institute: University of Utah

data_processing:
STAR alignment
RSEM quantification
edgeR normalization
Limma analysis
Genome_build: hg19
Supplementary_files_format_and_content: txt file; RSEM output

molecule: total RNA

source_name: Cancer cell line

extract_protocol:
RNA was extracted using Qiagen RNeasy kit (74104) and mRNA was subsequently isolated using NEB poly(A) module (E7490)
Following NEB RNA-seq library preparation kit (E7420S)

tag: tumor type

value: Lung squamous cell carcinoma

tag: treatment

value: HCC95 overexpressing KLF5 WT


title: SSEA4+_SingleCells_SSCs_71


title: SSEA4+_SingleCells_SSCs_70


title: SSEA4+_SingleCells_SSCs_65


title: SSEA4+_SingleCells_SSCs_64


title: RNA-HCC95-Empty-B

value: HCC95 overexpressing an empty vector


title: SSEA4+_SingleCells_SSCs_63


title: RNA-HCC95-Empty-A


title: RNA-HCC95-E419Q-A

value: HCC95 overexpressing KLF5 E419Q


title: SSEA4+_SingleCells_SSCs_61


title: SSEA4+_SingleCells_SSCs_62


title: SSEA4+_SingleCells_SSCs_59


title: V5-HCC95-Empty

data_processing:
BWA alignment
MACS2 Peak-calling
Genome_build: hg19
Supplementary_files_format_and_content: BigWig; ChIP-seq signal

extract_protocol:
Chromatin-IP
Following NEB ChIP-seq library preparation kit (E6200S)

tag: antibody

value: V5, Thermo Scientific, R960-25

value: Over-expressing Empty vector


title: V5-HCC95-E419Q-A

value: Over-expressing KLF5 E419Q


title: V5-HCC95-WT-A

value: Over-expressing KLF5 WT


title: SSEA4+_SingleCells_SSCs_60


title: V5-HCC95-WT-B


title: V5-HCC95-E419Q-B

value: Over-expressing KLF5 D418N


title: SSEA4+_SingleCells_SSCs_69


title: SSEA4+_SingleCells_SSCs_58


title: H3K27ac-HCC95-WT-B

value: H3K27ac, Abcam, ab4729


title: H3K27ac-HCC95-WT-A


title: SSEA4+_SingleCells_SSCs_68


title: H3K27ac-HCC95-E419Q-B


title: H3K27ac-BICR31-siNC-A

value: Head and neck squamous cell carcinoma

value: siNC


title: RNA-HCC95-WT-A


title: H3K27ac-BICR31-siNC-B


title: SSEA4+_SingleCells_SSCs_56

value: Spermatogonial Stem Cells


title: H3K27ac-BICR31-siNC-C


title: H3K27ac-HCC95-E419Q-A


title: H3K27ac-BICR31-siKLF5-C


title: RNA-HCC95-E419Q-B


title: SSEA4+_SingleCells_SSCs_55


title: H3K27ac-BICR31-siKLF5-A


title: SSEA4+_SingleCells_SSCs_54


title: H3K27ac-BICR31-siKLF5-B


title: SSEA4+_SingleCells_SSCs_57


title: H3K27ac-BICR31-sg-e134-Rep2

value: Head and neck squamous cell carcinomas

tag: chip antibody


title: SSEA4+_SingleCells_SSCs_53

value: Testis


title: H3K27ac-BICR31-sg-e134-Rep1


title: H3K27ac-BICR31-sgControl-2


title: SSEA4+_SingleCells_SSCs_52


title: SSEA4+_SingleCells_SSCs_51


title: H3K27ac-BICR31-sgControl-1


title: SSEA4+_SingleCells_SSCs_49


title: SSEA4+_SingleCells_SSCs_50


title: V5KLF5-HEK293-E419Q-A


title: V5KLF5-HEK293-WT-A


title: V5KLF5-HEK293-WT-B


title: V5KLF5-HEK293-D418N-B


title: V5KLF5-HEK293-D418N-A


title: SSEA4+_SingleCells_SSCs_48


title: SSEA4+_SingleCells_SSCs_47


title: SSEA4+_SingleCells_SSCs_46


title: SSEA4+_SingleCells_SSCs_45


title: BICR31-siNC-B

data_processing:
STAR alignment
RSEM normalization
quartile normalization
Genome_build: hg19
Supplementary_files_format_and_content: txt file; RSEM output (read counts) processed by quartile normalization

value: siNC (siRNA negative control)


title: BICR31-siKLF5-B

value: siKLF5 (siRNA silencing KLF5)


title: BICR31-siNC-C


title: V5KLF5-HEK293-E419Q-B


title: BICR31-siKLF5-C


title: p300-BICR31


title: BICR31-siKLF5-A


title: H3K27ac-YD8


title: V5-HEK293-Empty

value: Over-expressing an empty vector


title: BICR31-siNC-A


title: SSEA4+_SingleCells_SSCs_44


title: KLF5-BICR31

value: KLF5, Abcam, ab137676


title: V5KLF5-HEK293-E419K-A

value: Over-expressing KLF5 E419K


title: H3K27ac-TT

value: Esophageal carcinomas

value: TT


title: SSEA4+_SingleCells_SSCs_43


title: H3K27ac-TE6


title: V5KLF5-HEK293-E419K-B

value: V5, Thermo Scientific, R960-25


title: H3K27ac-TE10


title: SSEA4+_SingleCells_SSCs_41


title: SSEA4+_SingleCells_SSCs_40


title: H3K27ac-GSU

value: Stomach adenocarcinomas

value: GSU


title: H3K27ac-HSC4


title: H3K27ac-KATOIII

value: KATOIII


title: H3K27ac-Detroit562

value: H3K27ac, Abcam, ab4729


title: H3K27ac-CAL33


title: SSEA4+_SingleCells_SSCs_39


title: H3K27ac-BICR31


title: SSEA4+_SingleCells_SSCs_42


title: SSEA4+_SingleCells_SSCs_38


title: SSEA4+_SingleCells_SSCs_37


title: Input control for WT_thymus1

city: Stockholm

first: Nik

middle: V

last: Kuznetsov

address: Nobels vag 16

country: Sweden

institute: Karolinska Institute

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph files contain processed NGS data for WASp ChIP genomic DNA

organism: Mus musculus

source_name: Input control for WT thymus sample 1

extract_protocol:
Lysates were clarified from sonicated nuclei and WASp-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions.

value: thymocytes

tag: source

value: thymus

tag: strain

value: no antibody added


title: SSEA4+_SingleCells_SSCs_33

value: Spermatogonial Stem Cells


title: H3K27ac-AGS

value: AGS


title: WT_thymus1_ChIPSeq

description: ChIP Sample 2

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm9
Supplementary_files_format_and_content: wig files contain processed NGS data for WASp ChIP genomic DNA

source_name: WT thymus sample 1

value: WASp F-8 (Santa Cruz)


title: SSEA4+_SingleCells_SSCs_35

value: Testis


title: H3K27ac-BHY

value: Head and neck squamous cell carcinomas

value: BHY


title: Input control for WT_spleen_CD4+Tcells

source_name: Input control for WT spleen CD4+ Tcells sample

value: spleen CD4+ T cells

value: spleen


title: WT_spleen_CD4+Tcells_ChIPSeq

description: ChIP Sample 4

source_name: WT spleen CD4+ T cells sample


title: SSEA4+_SingleCells_SSCs_36


title: H3K27ac-BICR16


title: Naa10-KO biological replicate #2

city: Taipei

first: Li-Jung

last: Juan

address: 128 Academia Road, Section 2, Nankang

department: Genomic Research Center

country: Taiwan

institute: Academia Sinica

description: RNA enriched by poly-dT oligo

data_processing:
RNAseq reads trimmed for adaptor sequence and masked for low-complexity or low-quality sequence were aligned to mm9 reference using TopHap
The aligend reads were annotated and called for Reads Per Kilobase of exon per Megabase  (RPKM) for gene expression using Cufflinks
RNAseq reads were mapped to B6 and JF1 genomes for allele specific expression by Allele-specific Alignment Pipeline (ASAP) developed by Felix Krueger (Bioinformatics Department, Babraham Institute) (Strogantsev et al., 2015).
Only reads specific to either genome were retained as maternal B6 or paternal JF1 reads.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample, bedgraph files for allele specific reads were generated using genomeCoverageBed of bedtools with option -d and -split

source_name: mouse embryonic stem cell

growth_protocol: The C57BL/6-JF1 F1-ESCs were generated in our lab by crossing Naa10-/X C57BL/6 female with WT JF1 male mice according to a previous report (Bryja et al., 2006) with the following modifications. Naa10-KO and littermate WT ES cells were cultured in N2B27 supplemented with Mek inhibitor PD325901 (1 mM, Stemgen), Gsk3 inhibitor Chir99021 (3 mM, Stemgen), and LIF (1x103 units/ml, ESGRO, Millipore) in the presence of irradiated MEF feeder

extract_protocol:
Total RNAs purified from mouse embryonic stem cells using RNeasy® Plus Mini Kit (Qiagen) were treated with DNase I to remove residual genomic DNA.
RNA enriched by oligo-dT magnetic beads, and sonicated (Bioruptor®, Diagenode) into roughly 200 bp fragments. cDNAs were synthesized with random hexamer-primers, purified by silicon-coated magnetic beads, blunted in the ends, added with a single adenine at 3'-end, ligated with sequencing adaptors and PCR-amplified. The quality and quantity of the resulting library were determined by Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System, respectively. The library products were sequenced by Illumina HiSeqTM 2000.

tag: genetic background

value: C57BL6/JF1 F1

tag: origin

value: Inner cell mass of blastocyst

tag: passages

value: 5 passages with MEF feader plus 5 passages without MEF feeder


title: Naa10-KO biological replicate #1

description: RNA enriched by poly-dT oligo


title: WT_thymus2_ChIPSeq

description: ChIP Sample 12

source_name: WT thymus sample 2


title: WT_thymus_WASpI296T_ChIPSeq

description: ChIP Sample 13

source_name: WASp  thymus I296T sample


title: WT biological replicate #1

description: RNA enriched by poly-dT oligo


title: WT biological replicate #2

description: RNA enriched by poly-dT oligo


title: SSEA4+_SingleCells_SSCs_31


title: SSEA4+_SingleCells_SSCs_28


title: SSEA4+_SingleCells_SSCs_29


title: Ab-free_negative_control

description: ChIP Sample 5

source_name: Ab-free WT spleen negative control


title: H3K27ac-BICR6


title: SSEA4+_SingleCells_SSCs_32


title: SSEA4+_SingleCells_SSCs_25


title: SSEA4+_SingleCells_SSCs_34


title: SSEA4+_SingleCells_SSCs_24


title: SSEA4+_SingleCells_SSCs_23


title: SSEA4+_SingleCells_SSCs_22


title: SSEA4+_SingleCells_SSCs_21


title: SSEA4+_SingleCells_SSCs_20


title: SSEA4+_SingleCells_SSCs_17


title: SSEA4+_SingleCells_SSCs_16


title: SSEA4+_SingleCells_SSCs_19


title: SSEA4+_SingleCells_SSCs_18


title: SSEA4+_SingleCells_SSCs_30


title: SSEA4+_SingleCells_SSCs_15


title: SSEA4+_SingleCells_SSCs_13


title: AGO2-CLIP-seq low RNase I let-7a

city: Seoul

first: Young-Soo

last: Kwon

address: Nungdongro 209, Gwangjingu

department: Department of Bioscience and Biotechnology

country: South Korea

institute: Sejong University

description:
CLIP-enriched RNA
Processed data file: AGO2_CLIP_H1_let-7_coverage_neg.bedgraph.gz
Processed data file: AGO2_CLIP_H1_let-7_coverage_pos.bedgraph.gz

data_processing:
Reads were demultiplexed by using codes in the id of each reads by using the ShortRead package in BioConductor. Identical sequences were collapsed using the occurrenceFilter function in the ShortRead package.
3' adapter sequences were trimmed using the trimLRPatterns function in the ShortRead package. The 3' adapter sequences trimmed were sequences containing CCTGTGGTCGTAGCATCAGCTA.
The trimmed sequences were collapsed and converted to reverse complementary sequences.
CLIP-seq reads were sequentially mapped to rRNA, snRNA, snoRNA, tRNA and microRNA precursors sequences using Bowtie versions 1.12.7 with the following configurations -q –m 50 -n 2 -l 44 -5 1 -3 5 -a --best --strata -p 7 --sam for noncoding RNAs. The remaining reads were aligned with the hg19 human genome with the configuration -q –m 1 -n 0 -l 44 -5 1 -3 5 -a --best --strata -p 7 --sam unique genomic sequences to generate bedGraph files.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: bedGraph. Scores stand for CLIP-seq read coverage.

source_name: H1 human embryonic stem cells (knock-in cells containing a Flag tag at the N-terminus of AGO2) with let-7a mimic transfected

growth_protocol: Generation of the H1 human embryonic stem cell (hESC) line that expresses flag-tagged AGO2 from its native genomic locus was described previously. The modified hESCs were dissociated using TrypLE, harvested and resuspended in 30% Matrigel diluted with DMEM/F12. Approximately 2 million cells were subcutaneously injected into SCID mice. After 6 weeks, teratomas were harvested, minced and incubated in DMEM complemented with 10% FBS, 1X MEM non-essential amino acids solution, 1X Glutamax, 1X penicillin-streptomycin solution and 55 μM 2-mercaptoethanol. The outgrowing cells were passaged using Trypsin-EDTA. Teratoma-derived fibroblasts (TDFs) at passage 10-15 were used for all experiments. hESCs were maintained on a mitotically inactivated mouse feeder (MEF) layer in DMEM/F12 supplemented with 20% KSR, 1X MEM non-essential amino acids solution, 1X Glutamax, 55 μM 2-mercaptoethanol and 4ng/ml bFGF. Before analyses, hESCs were cultured for at least two passages without the feeder layer on Matrigel-coated plates in MEF-conditioned media supplemented with 50 ng/ml bFGF. For CLIP analysis of let-7a-transfected hESCs, the cells were trypsinized, transfected with 50 nM of each miR-302a/b/c hairpin inhibitor using Lipofectamine 2000, and plated on Matrigel-coated plates. After 24 hrs, the transfected cells were transfected again with 50 nM of let-7a mimic and incubated for another 24 hrs before UV-crosslinking.

extract_protocol:
Two million cells were resuspended in 250 μl lysis buffer (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 1 mM MgCl2, 0.1 mM CaCl2, 1% NP-40, 0.5% sodium deoxycholate, 0.1% SDS) containing EDTA-free protease inhibitor cocktail (Roche) and RNase inhibitor (Ambion) and briefly sonicated by using the Bioruptor.
The lysates were treated with 5 μl of Turbo DNase (Ambion) and 10 μl of 10 U/μl or 1 U/μl RNase I (Ambion) at 37°C for 3 min. Cellular debris was removed by centrifugation at 13,000 rpm for 15 min. Protein-RNA complexes were immunopurified with an anti-Flag or anti-DGCR8 antibody (Bethyl laboratories) bound to Protein A/G Dynabeads. Beads were washed twice with high-salt wash buffer (50 mM Tris-HCl pH 7.4, 1 M NaCl, 1 mM EDTA, 1% NP-40, 0.5% sodium deoxycholate, and 0.1% SDS) followed by two washes with PNK buffer (20 mM Tris-HCl pH 7.4, 10 mM MgCl2, and 0.2% Tween-20). For dephosphorylation of 3’ ends, 1U of FastAP alkaline phosphatase (Fermentas) was added to the beads and incubated at 37°C for 20 min. After washing the beads twice with PNK buffer, protein-bound RNAs were ligated to a pre-adenylylated 3’ adaptor overnight at 16°C. Beads were washed twice with PNK buffer again and labeled with [γ- 32P] ATP for visualization. The labeled RNAs were separated by 4-12% NuPAGE Bis-Tris gel (Invitrogen), transferred to a nitrocellulose membrane, and excised from the membrane. The protein was degraded by proteinase K treatment, and RNA was recovered by phenol/chloroform/isoamyl alcohol extraction and ethanol precipitation. Protein-associated RNAs purified by IP or CLIP were ligated to a pre-adenylylated 3’ adaptor that contains a 2-nt adapter code for de-multiplexing and a 3-nt random sequence to minimize the loss of information after collapsing identical sequences. The RNA-adapter hybrids were converted into cDNAs with RT primer and SuperScript III reverse transcriptase (Invitrogen). The cDNAs were size-fractionated by electrophoresis on a 12% denaturing polyacrylamide gel and circularized by single-stranded DNA ligase (Epicentre). Circularized cDNAs were amplified with PCR primers, in which one of them contained a 6-nt primer code for de-multiplexing. PCR products were purified by agarose gel elution and subjected to next-generation sequencing.

treatment_protocol: For CLIP experiments, TDF and H1 cells were irradiated with 300 mJ/cm2 of UVC light (254 nm) by using the CL-1000 ultraviolet crosslinker (UVP).

value: embryonic stem cells

tag: genotype/variation

tag: rnase i

value: low

tag: transfection

value: let-7a mimic

tag: ip antibody

value: M1 anti-Flag (Waco)


title: SSEA4+_SingleCells_SSCs_12

tag: cell type

tag: marker


title: SSEA4+_SingleCells_SSCs_27

tag: tissue


title: SSEA4+_SingleCells_SSCs_26


title: AGO2-CLIP-seq low RNase I scRNA

description:
CLIP-enriched RNA
Processed data file: AGO2_CLIP_H1_control_coverage_neg.bedgraph.gz
Processed data file: AGO2_CLIP_H1_control_coverage_pos.bedgraph.gz

source_name: H1 human embryonic stem cells (knock-in cells containing a Flag tag at the N-terminus of AGO2) with scrambled small RNA

tag: cell line

value: scrambled small RNA


title: IgG-CLIP-seq low RNase I scRNA

description:
CLIP-enriched RNA
Processed data file: IgG_CLIP_H1_control_coverage_neg.bedgraph.gz
Processed data file: IgG_CLIP_H1_control_coverage_pos.bedgraph.gz

value: knock-in cells containing a Flag tag at the N-terminus of AGO2

value: rabbit IgG (Bethyl laboratories)


title: AGO2-CLIP-seq replicate 2 low RNase I

description:
CLIP-enriched RNA
Processed data file: AGO2_CLIP_TDF_coverage_neg.bedgraph.gz
Processed data file: AGO2_CLIP_TDF_coverage_pos.bedgraph.gz

source_name: teratoma-derived fibroblasts (knock-in cells containing a Flag tag at the N-terminus of AGO2)

value: teratoma-derived fibroblasts


title: SSEA4+_SingleCells_SSCs_11

value: Spermatogonial Stem Cells


title: SSEA4+_SingleCells_SSCs_14

value: Testis


title: IgG-CLIP-seq low RNase I

description:
CLIP-enriched RNA
Processed data file: IgG_CLIP_TDF_coverage_neg.bedgraph.gz
Processed data file: IgG_CLIP_TDF_coverage_pos.bedgraph.gz


title: AGO2-CLIP-seq replicate 2 high RNase I

value: high


title: AGO2-CLIP-seq replicate 1 low RNase I


title: AGO2-CLIP-seq replicate 1 high RNase I


title: Ad-KLF4 2

city: La Jolla

first: John

last: Shyy

state: California

address: 9500 Gilman Dr., BRF2 Rm 1217 Bay LL

department: Medicine

institute: University of California, San Diego

data_processing:
Base calling and quality scoring were performed by an updated implementation of Real-Time Analysis (RTA), termed RTA v2, on the NextSeq 500 system. bcl2fastq Conversion Software v1.8.4 was used to demultiplex data and convert BCL files to FASTQ file formats.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the hg19 whole genome using tophat v2.0.14 with parameters -p -G -o
Reads per kilobase of exon per megabase of library size (RPKM) were calculated using cufflinks v2.2.1, which assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: HUVEC

growth_protocol: Human umbelical vein endothelial cells (HUVECs) between 6-8 passages were grown to confluence in M199 media supplemented with 15% fetal bovine serum, 5 ng/mL b-endothelial cell growth factor, 4 U/mL haparin, and 100 U/mL penicillin-streptomycin.

extract_protocol:
Total RNA was exracted and purified using the mirVana mRNA isolation kit (Thermo Fisher Scientific) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HUVECs were grown to 70% confluency and infected with adenovirus containing KLF4 (Ad-KLF4) or empty vector control (Ad-null) for 48 hr.

value: Umbilical vein endothelial cells

tag: passage


title: SSEA4+_SingleCells_SSCs_10


title: SSEA4+_SingleCells_SSCs_9


title: Ad-Null 2


title: SSEA4+_SingleCells_SSCs_8


title: Ad-KLF4 1


title: IgG-CLIP-seq low RNase I let-7a

description:
CLIP-enriched RNA
Processed data file: IgG_CLIP_H1_let-7_coverage_neg.bedgraph.gz
Processed data file: IgG_CLIP_H1_let-7_coverage_pos.bedgraph.gz


title: SSEA4+_SingleCells_SSCs_7


title: SSEA4+_SingleCells_SSCs_6


title: SSEA4+_SingleCells_SSCs_5


title: SSEA4+_SingleCells_SSCs_4


title: SSEA4+_SingleCells_SSCs_2


title: Wild-type (m5C) IP2

city: Singapore

first: Hao

last: Yu

address: Science Drive 4

country: Singapore

institute: National University of Singapore

data_processing:
Sequence data were analyzed according to the procedure previously described (Dominissini et al., 2013), BWA was run to align the input and IP-sequenced samples to the Columbia reference genome and annotation file (TAIR10). Non-unique reads with MAPQ less 13 were discarded from downstream analysis. The peak-caller MACS was used for peak detection; the ‘effective genome size’ parameter was adjusted to the calculated transcriptome size (65084215).Peaks were considered if their P value < 0.00001 and fold change >2.
Genome_build: TAIR10
Supplementary_files_format_and_content: Wig files were generated using the MACS2. Scores represent pileup normalized to 1M reads.

organism: Arabidopsis thaliana

source_name: Whole plant

growth_protocol: Arabidopsis thaliana plants were grown on MS plates in growth chambers under long day conditions (16 hr light/8 hr dark) at 23°C ± 2°C.

extract_protocol:
Plant samples were aliquot and total RNA was extracted using the RNeasy Plus Mini kit (QIAGEN) according to the manufacturer’s instructions and pooled together. RNA samples were fragmented into ~100-nucleotide-long fragments by RNA fragmentation buffer (100 mM Tris-HCl, pH 7.0, 100 mM ZnCl2). Fragmented RNA was incubated for 2 h at 4 °C with anti-m5C monoclonal antibody (Diagenode) in IP buffer (150 mM NaCl, 0.1% Igepal CA-630, 10 mM Tris-HCl, pH 7.4) supplemented with RNasin® Plus RNase inhibitor (Promega). The mixture was then immunoprecipitated by incubation with Protein A/G Plus-Agarose (Santa Cruz) that was pre-bound with bovine serum albumin (BSA) at 4 °C for an additional 2 h. After extensive washing, bound RNA was eluted from the beads with 6.7 mM 5-methylcytosine  (Sigma-Aldrich) in IP buffer, and precipitated by ethanol.
NEBNext® UltraTM Directional RNA Library Prep Kit for illumina® (NEB) was used to construct the library from immunoprecipitated RNA and input RNA. Sequencing was done on Illumina Hiseq 2500 platform.

tag: ecotype

tag: age

value: Nine-day-old


title: Wild-type (m5C) Input2

tag: antibody


title: Naa10p-ChIPseq_KO-mES

description: male hybrid-ES was generated by crossing Naa10-heterozygous female with JF male

data_processing:
All sequencing reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence.
All sequencing reads were mapped to NCBI build 37 (mm9) of the mouse genome using the Bowtie with default configurations and suppressing all alignments for reads that align to more than 1 locations on the reference (-m 1).
Mapped reads were subjected to the MACS program and bound regions (peaks) were determined using sequencing reads from Naa10-KO ESC as negative controls. The statistical cutoff used for peak calling was p<10-5 and >5-fold enrichment over the Naa10-KO control.
Allele-specific analysis of ChIPseq data was performed with Allele-specific Alignment Pipeline (ASAP) developed by Felix Krueger (Bioinformatics Department, Babraham Institute). The reads were mapped to B6 and JF1 genomes and only reads specific to either genome were retained as maternal B6 or paternal JF1 reads.
Genome_build: NCBI build 37 (mm9)
Supplementary_files_format_and_content: Bigwig files were generated using Bedtools followed by converting bedgraph to bigwig

growth_protocol: The C57BL6/JF1 F1 mES cells were generated in our lab by crossing Naa10-/X C57BL/6 female with WT JF1 male mice according to a previous report (Bryja et al., 2006) with the following modifications. Naa10-KO and littermate WT male ES cells were cultured in N2B27 supplemented with Mek inhibitor PD325901 (1 mM, Stemgen), Gsk3 inhibitor Chir99021 (3 mM, Stemgen), and LIF (1x10^3 units/ml, ESGRO, Millipore) in the presence of irradiated MEF feeder.

extract_protocol:
The mES cells were fixed with 1% formaldehyde for 10 min, followed by 0.125 M glycine quenching for 5 min. Cells were lysed in 1% SDS, 10 mM EDTA and 50 mM Tris-HCl (pH 8.0) and the DNA was fragmented by sonication to approximately 150-300 bp (Bioruptor, Diagenode). Immunoprecipitation was performed with 10 μg of rabbit polyclonal Naa10p for overnight at 4 °C. Antibody-bound samples were isolated by protein G agarose beads (Active Motif), washed, eluted and reverse cross-linked. ChIPed DNA was extracted by phenol/chloroform, ethanol precipitated and quantified by Qubit assay (Invitrogen).
The Naa10p Ab (generated by our lab) for ChIP is a rabbit polyclonal Ab antigen affinity-purified from serum of rabbits immunized with E. coli-purified mouse Naa10p (235 aa) by GenScript Inc., USA.
The ChIPed DNA library for NextSeq 500 sequencing was constructed using the NEBNext DNA library Prep Master Mix Set for Illumina (New England Bio Labs) according to the manufacturer's instruction. Briefly, the ChIPed DNA was blunt ended and a dA tail was added. The DNA with dA overhangs was ligated with multiplex oligos for illumina with individual index sequences (New England Bio Labs). Adaptor-ligated DNA was amplified by PCR for 12 cycles, followed by size selection using magnetic beads (KAPA Pure Beads, KAPA Biosystem). The purified DNA was quantified by Qubit assay (Invitrogen) and qualified by Agilent Bioanalyzer.

treatment_protocol: The mES cells were cultured without feeders for 5 passages for depleting feeder cells

tag: genotype

value: Blastocyst-derived embryonic stem cell

tag: chip antibody

value: rabbit polyclonal Naa10p (made in-house)


title: Ch25h-KO1

data_processing:
Base calling and quality scoring were performed by an updated implementation of Real-Time Analysis (RTA), termed RTA v2, on the NextSeq 500 system. bcl2fastq Conversion Software v1.8.4 was used to demultiplex data and convert BCL files to FASTQ file formats.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the mm9 whole genome using tophat v2.0.14 with parameters -p -G -o
Reads per kilobase of exon per megabase of library size (RPKM) were calculated using cufflinks v2.2.1, which assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Peritoneal macrophages

extract_protocol:
Mice were injected with 3% thioglycolate three days prior to sacrifice. PMs were isolated from the mouse peritoneal cavity with PBS. Cells were cultured in DMEM containing 10% fetal bovine serum and 1% penicillin-streptomycin. Total RNA was exracted and purified using the mirVana mRNA isolation kit (Thermo Fisher Scientific) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: 6 week old

value: Peritoneal macrophages


title: Wild-type (m5C) IP1


title: SSEA4+_SingleCells_SSCs_3

source_name: human SSCs


title: Wild-type (m5C) Input1


title: SSEA4+_SingleCells_SSCs_1


title: Ch25h-KO2


title: Wild-type 2

data_processing:
Clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data, then the clean reads were aligned to the Arabidopsis reference TAIR10 using TopHat v2.0.12. The mapped reads were assembled by Cufflinks v2.1.1. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. Cuffdiff was used to calculate FPKMs of each gene.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

extract_protocol:
9-day-old Arabidopsis wild-type and trm4b-4 seedlings were harvested for total RNA extraction. The amount and quality of RNA were tested by Qubit RNA Assay Kit (Life Technologies), gel electrophoresis and Agilent Bioanalyzer 2100 system. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB) was used to construct the libraries according to the manufacturer’s instructions, and sequencing was performed on Illumina Hiseq 4000 platform.

value: Nine-day old

value: wild type


title: Ch25h-WT1


title: Naa10p-ChIPseq_WT-mES

value: C57BL6/JF1 F1


title: Ch25h-WT2


title: H3K36me2-ChIP-in-siMrg15

status: Public on Oct 04 2017

city: Beijing

first: Zhuqiang

address: 15 Datun Road, Chaoyang District.

country: China

institute: Institute of Biophysics, CAS

data_processing:
Basecalls performed by BGI, Shenzhen
ChIP-seq reads were aligned to the dm3 genome assembly using bowtie v1.1.0 with only unique mapped reads were kept
Data were filtered using samtools rmdup to remove potential PCR duplicates
peaks were called using MACS2 (v2.1.1.20160309)
RNA-Seq data were mapped by TopHat and quantitified by Crosslinks.
Genome_build: dm3
Supplementary_files_format_and_content: bigwig files were generated using IGV tools with fragment extension 250 bp

organism: Drosophila melanogaster

source_name: siMrg15 treated S2 cells

extract_protocol:
Cells for ChIP assays were crosslinked in 1% formaldehyde for 8-10 min at room temperature. The reaction was terminated by adding 2 M glycine to a final concentration of 125 mM. After being washed with PBS, the cells were resuspended in lysis buffer 1 (50 mM HEPES, pH 7.9, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% IGEPAL CA-630 and 0.25% Triton X-100) and incubated for 10 min on ice. After centrifugation, the cells were resuspended in lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA) and incubated for 10 min at room temperature. The chromatin fraction was resuspended in lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate and 0.5% sodium N-lauroyl sarcosine) and sonicated into 200-400 base-pair (bp) fragments (Bioruptor, Diagenode). Chromatin fragments were immunoprecipitated overnight with antibodies against Ash1 and Mrg15. The protein-antibody complexes were incubated with pre-washed Dynabeads Protein A or G (Life Technologies) for 1 hr. The beads were sequentially washed with the following buffers: once with FA-lysis buffer (150 mM NaCl, 1% Triton X-100, 50 mM HEPES, pH 7.9, 2 mM EDTA and 0.5% sodium deoxycholate), twice with FA high salt buffer (500 mM NaCl, 1% Triton X-100, 50 mM HEPES, pH 7.9, 2 mM EDTA and 0.5% sodium deoxycholate), once with LiCl buffer (250 mM LiCl, 0.5% IGEPAL CA-630, 0.5% sodium deoxycholate, 1 mM EDTA and 10 mM Tris-HCl, pH 8.0) and twice with TE buffer (10 mM Tris-HCl, pH 8.0 and 1 mM EDTA). Protein complexes were eluted by incubation with 250 μl of freshly prepared elution buffer (1% SDS and 100 mM sodium bicarbonate) for 15 min at room temperature. The elution step was repeated once, and the eluted fractions were combined.  After crosslinking reversal and RNase A and proteinase K treatment, DNA was extracted with phenol-chloroform and precipitated with ethanol.  For mRNA deep sequencing analysis, total RNA was isolated by TRIzol Reagent (Life Technologies), and mRNA with a poly (A) tail was purified and subjected to sequencing library construction.
The ChIP-seq libraries were constructed using NEBNext DNA Sample Prep Master Mix (NEB).DNA libraries were subjected to size-selection using AMPure XP beads (Beckman Coulter) and PCR amplification (18-20 cycles for ChIP-seq DNA libraries).

value: Schneider 2 cell-line

value: somatic cell

value: late embryos (20h-24h AEL)

tag: chip antibody info.

value: ab9049, Abcam


title: H3K36me2-ChIP-in-siAsh1

source_name: siAsh1 treated S2 cells


title: H3K27me3-ChIP-in-siMrg15

value: ab6002, Abcam


title: ZIP10 positive cells isolated from hair follicles of mice

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

institute: POSTECH

data_processing:
Illumina CASAVA1.8.2 software used for basecalling.
We first removed the adapter sequences (TrueSeq universal and index adapters), and then trimmed the ends of the adapter-free reads for which PHRED scores were lower than 20 using Cutadapt software
Remaining reads were then aligned to the mouse reference genome (UCSC mm9) using the TopHat aligner. After aligning, we quantified the gene expression using Cufflinks (RPKM).
Genome_build: UCSC mm9
Supplementary_files_format_and_content: tab-delimited text file including normalized read counts for each sample

extract_protocol:
Ventral skins excised from 7-day-old C57BL/6 mice were minced with a scalpel and incubated overnight with Dispase II (2.4 U/ml, Roche), Collagenase (50 U/ml, Worthington Biochemical Corporation, Lakewood, NJ), and 10% FBS in DMEM (Invitrogen) at 4 ºC. Next, the tissues were pipetted vigorously to dissociate the cells, which were filtered through a 40-μm cell strainer (Greiner Bio-One) and incubated with anti-ZIP10 polyclonal antibody or normal rabbit IgG for 30 min on ice, and then with Alexa Fluor 488-conjugated anti-rabbit IgG for 15 min on ice. The cells were also stained with 7-AAD (BD), and ZIP10+ and ZIP10− cells were sorted with a FACSAria II (BD).
The RNA-sequencing library was constructed from total RNA (10 ng) using a NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Inc., Ipswich, MA). The prepared libraries were sequenced using an Illumina HiSeq 1500 in 50-base single-end mode.

value: Ventral skins

value: ZIP10 positive cells


title: H3K36me2-ChIP-in-S2

source_name: WT S2 cells

value: WT


title: H3K27me3-ChIP-in-siAsh1


title: H3K27me3-ChIP-in-S2


title: ZIP10 negative cells isolated from hair follicles of mice

value: ZIP10 negative cells


title: input-of-siMrg15


title: input DNA

city: Freising

first: Franziska

last: Greulich

address: Gregor-Mendel-Str. 2

department: Metabolic Programming

country: Germany

institute: TU München

data_processing:
Reads were aligned to the mouse mm9 reference genome using BWA-MEM version 0.7.13 with default parameter settings.
PCR duplicates were removed using Picard Tools version 1.119.
Peaks  were  called  using  MACS2 version  2.1.0 with a FDR threshold of 0.01.
Genome_build: mm9
Supplementary_files_format_and_content: The .bed files containing the peak positions were generated with MACS2 version 2.1.0.

source_name: neuronal stem cells

growth_protocol: Embryonic NSCs   from  E12.5  embryos  were  cultured  under  proliferation  conditions  in  Neurobasal-A   medium supplemented with GlutaMAX (1%), glutamine (0.5%), Penicillin/Streptomycin   (1%), rhFGF-2 (20 ng/ml), B-27 minus Vitamin A (2%) (all from Invitrogen) and rhEGF   (20 ng/ml, Sigma-Aldrich).

extract_protocol:
Embryonic  NSCs  (approx.  10  x  10^6 cells)  were  fixed  with  1.5  mM  ethylene  glycol bis[succinimidyl  succinate]  in  DMSO  for  20  min  at  RT, followed  by  adding formaldehyde  to  a  final  concentration  of  1%,  incubated  for  10  min  at  RT  and  finally quenched by 0.2 M glycine. Cells were then lysed and sonicated with a microtip for 10 seconds  followed  by  a  1  min  break  for  10  cycles.  After  adding  1%  Triton-X  to  the sonicated lysates, ChIP was performed overnight at 4°C with Dynabeads M-280 Sheep anti-Rabbit IgG (Thermo Fisher, 11203D) linked to rabbit anti-E2A (1.5 µg, sc-349X, Santa Cruz Biotechnology). 10% of sonicated suspension was kept as input control. After washing and  elution  of  chromatin-antibody  complexes  from  the  beads  at  65°C  overnight, crosslinking  was  reversed  by  proteinase  K  and  RNase  digestion.  Genomic  DNA  and DNA  from  the  sonicated  input  were  purified  using  a  PCR  Purification  Kit  (Qiagen).
Library preperation was performed from 2 ng of ChIP DNA using the Kapa Hyper Prep Kit with PCR library amplification (#KK8504, KapaBiosystems) according to the manufactur's protocol. Shortly, ChIP DNA was end-repaired and A-tailed before adapter ligation. After adapter ligation, the ChIP DNA was purified with Agencourt AMPure XP beads (#A63880, Beckman Coulter) and size-selected for 360-600 bp using the Pippin Prep System from Saga Science. The size-selected library is amplified by PCR using the Kapa Hyper Prep Kit (#KK8504,KapaBiosystems) and purified terminally with Agencourt AMPure XP beads (#A63880, Beckman Coulter).

value: wildtype

value: E12.5 embryo

tag: fixation


title: Ad-Null 1

value: Umbilical vein endothelial cells


title: trm4b-4 2

tag: genotype/variation


title: E2A_wt_rep1_ChIP-Seq

value: E2A (sc-349X, Santa Cruz Biotechnology)


title: input-of-ChIP-in-WT-S2

data_processing:
Basecalls performed by BGI, Shenzhen
ChIP-seq reads were aligned to the dm3 genome assembly using bowtie v1.1.0 with only unique mapped reads were kept
Data were filtered using samtools rmdup to remove potential PCR duplicates
peaks were called using MACS2 (v2.1.1.20160309)
RNA-Seq data were mapped by TopHat and quantitified by Crosslinks.
Genome_build: dm3
Supplementary_files_format_and_content: wig files were generated using IGV tools with fragment extension 250 bp


title: IgG-ctrl-ChIP-in-WT-S2

value: Normal Rabbit IgG #2729 from CST Ltd.


title: Mrg15-ChIP-in-WT-S2-rep1

value: polyclonal antibody against fly Mrg15 from rabbit


title: Mrg15-ChIP-in-siAsh1-S2


title: Mrg15-ChIP-in-siMrg15-S2


title: Ash1-ChIP-in-WT-S2-rep2

value: polyclonal antibody against fly Ash1 from rabbit


title: Ash1-ChIP-in-WT-S2-rep1


title: HuD-immunized 2

city: Rotterdam

first: Martijn

middle: Maurice

last: vanDuijn

state: ZH

address: Wytemaweg 80

department: Neurology

country: Netherlands

institute: ERASMUS MEDICAL CENTER

data_processing:
Combining (overlapping) paired end reads with PEAR 0.9.8
Processing of UMI tags and error correction with MIGEC-1.2.1b
Alignment and characterization of immunoglobulin reads by IMGT-HighV-QUEST (http://www.imgt.org/HighV-QUEST/)
Genome_build: NA
Supplementary_files_format_and_content: tab-delimited text files containing IMGT-VQUEST output

organism: Rattus norvegicus

source_name: HuD-immunized rat

extract_protocol:
Trizol lysis of whole spleen cell suspension, RNA fraction
c-DNA synthesis with gene-specific primer against the immunoglobulin heavy chain constant domain adjacent to the variable region, and including an UMI tag. c-DNA was futher amplified by a multiplex PCR method with primers complementary to the 5'UTR of the immunoglobulins. The 6-base random UMI tag is located ajacent to the (T7) reverse priming site (CTCCCTATAGTGAGTCGTATTA) that was also introduced during cDNA synthesis

treatment_protocol: Immunized once with Freunds complete adjuvans, and three boosts in incomplete adjuvans. 5 animals immunized with recombinant human HuD, 5 animals immunized with a keyhole limpet hemocyanone carrier that was modified with dinitrophenol residues.

value: Wistar

value: Splenocyte

tag: immunogen

value: HuD


title: HuD-immunized 5


title: HuD-immunized 3


title: HuD-immunized 1


title: DNP-immunized 5

source_name: DNP-immunized rat

value: DNP


title: DNP-immunized 4


title: DNP-immunized 3


title: DNP-immunized 2


title: input-of-siAsh1

value: Schneider 2 cell-line

value: somatic cell

value: late embryos (20h-24h AEL)


title: 4Ne_clone_336

city: Boulder

first: Amber

middle: Lynne

last: Scott

state: CO

address: 3415 Colorado Ave

department: Department of Molecular, Cellular, and Developmental Biology

institute: University of Colorado

description:
4Ne Clone 336
mRNA-seq, single-end

data_processing:
Trimmed Reads with trimmomatic v0.32 ILLUMINACLIP:TruSeq2-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Mapped Reads to custom genome with rRNA genes only with Bowtie2 v2.0.2 - bowtie2 -q --phred33 --sensitive-local -p32 -x --un -U -S
Mapped the non-ribosomal reads to S288c genome (SGDv3) with Bowtie2 v2.0.2 bowtie2 -q --phred33 --sensitive-local -p64 -x -U -S
Counted reads using htseq counts htseq_0.5.4p5- htseq-count -f bam -s yes -m intersection-strict -t gene -i ID
Differential expression DESeq_1.10.1 method=c("blind")
Genome_build: R63.1.1, 2010-01-05 (SGD)
Supplementary_files_format_and_content: htseq counts files, DESeq output files.

organism: Saccharomyces cerevisiae

source_name: evolved tetraploid

growth_protocol: Yeast were grown to saturation overnight at 30C in SC+2% raffinose media. The cells were cut back to 0.2 ODU in 5mL cultures in the morning and grown to log phase (0.6-0.8 ODU) at 30C in SC+2%Raffinose Media. Cells were pelleted, washed, snap-frozen, and stored at -80C.

extract_protocol:
Hot-Acid Phenol RNA isolation - Frozen cell pellets were r/s in TES and Phenol:Chloroform:Isoamyla alcohol (25:24:1) pH 4. RNA was extracted at 65C for 1hr.
Poly(A) tailed RNA was isolated from total RNA with the Oligotex mRNA mini kit and RNA Strand specific RNA libraries were prepared using the Illumina RNA ligation library protocol.

tag: strain/background

tag: ploidy

tag: generation

tag: media

value: SC+2% Raffinose


title: 4Ne_clone_337

description:
4Ne Clone 337
mRNA-seq, single-end


title: 4Ne_clone_335

description:
4Ne Clone 335
mRNA-seq, single-end


title: 4Ne_clone_334

description:
4Ne Clone 334
mRNA-seq, single-end


title: 2Ne_clone_233

description:
2Ne Clone 233
mRNA-seq, single-end

source_name: evolved diploid


title: 2Ne_clone_232

description:
2Ne Clone 232
mRNA-seq, single-end


title: Ash1-ChIP-in-siMrg15-S2

tag: cell type

tag: tissue


title: ID_274

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

data_processing:
For data analysis, FASTQ files were generated using CASAVA v1.8.1.
FastQC software (Version 0.9.6) was used to evaluate the quality of the files.
The trimming of adapter sequences from the reads was performed using fastq-mcf utility
RSEM was used to map single-end reads to reference transcriptome hg38 (Ensembl) and to provide read counts and normalized expression values for each case analyzed.
Genome_build: hg38 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text file includes read counts values for each sample

source_name: FFPE breast tumor

extract_protocol:
Hematoxylin and eosin-stained slides were evaluated by a pathologist to estimate the percentage of tumor present in the paraffin block selected. For cases with more than 60% of tumor content, five 10µm sections were used for RNA extraction. For cases with less than 60% of tumor content, areas that contained tumor were marked to obtain 5 tumor cores using a 1-mm punch needle. RNA extraction was done using the RecoverAll™ Total Nucleic Acid Isolation Kit (Life Technologies®) following the manufacturer’s recommendations.
Library preparation was performed  from 1µg of total RNA using the TruSeq® Stranded RNA Sample Preparation kit (Illumina Inc., San Diego, CA). Briefly, isolated RNA was depleted of ribosomal RNA using the rRNA Removal Mix provided by the kit. Random hexamers were used for cDNA synthesis. Subsequently, cDNA was subjected to end repair, adapter ligation and size selection using AMPure XP beads (Beckman Coulter Inc., Brea, CA). Fragmentation step was omitted due to the sample quality, as recommended by the protocol. Libraries were quantified by Qubit dsDNA HS Assay Kit (Life Technologies, Carlsbad, CA) and the validation of the library size was performed in an Agilent Bioanalyzer using a DNA 1000 kit (© Agilent Technologies) to verify the presence of a 260 base pair fragment

value: breast tumor

tag: intrinsic subtype

value: Luminal A


title: HuD-immunized 4


title: Mrg15-ChIP-in-WT-S2-rep2

tag: cell line

value: WT


title: Ash1-ChIP-in-siAsh1-S2


title: ID_266


title: Wild-type 1

tag: ecotype

tag: age

value: Nine-day old

value: wild type


title: trm4b-4 1


title: 1Ne_clone_131

description:
1Ne Clone 131
mRNA-seq, single-end

source_name: evolved haploid


title: ID_265


title: 1Ne_clone_132

description:
1Ne Clone 132
mRNA-seq, single-end


title: Z_Stim

city: Milwaukee

first: Sridhar

state: WI

address: 8727 Watertown Plank Road

department: Blood Research Institute

institute: BloodCenter of Wisconsin

data_processing:
The raw fastq files were aligned to mouse MM9 genome build using STAR version 2
Differentail expression analysis was done using DESEQ
The whole workflow for RNA seq data was performed in Basepairtech.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include abundance measurements, foldchange and Pvalues values for each gene

source_name: Spleen

growth_protocol: Naïve CD8 T cells were isolated from the spleens of WT and DGKzeta deficinet mice and stimulated for 24hrs.

extract_protocol:
RNA was extracted using Trizol and following the manufacturer's protocol
Library construction was performed using the NEBNext Ultra RNA Library Prep Kit for Illumina (E7530)

treatment_protocol: Naïve CD8+ T cells isolated following the Stem Cell kit protocol  (#19858) were stimulated with plate bound anti-CD3 and anti-CD28 for 24hrs at 37°C.

value: CD8+ T cells

tag: genotype

value: DGK{zeta}-/-

value: 6 weeks


title: 2N_ancestor_6006

description:
Diploid Ancestral Strain
mRNA-seq, single-end

source_name: diploid ancestor


title: ID_249


title: WT_Stim

value: 7 weeks


title: DNP-immunized 1

value: Wistar


title: ID_234

value: Luminal B


title: ID_229


title: Nsa2_deproteinized_1M7_2

city: Edinburgh

first: Sander

last: Granneman

address: Mayfield Road, Kings Buildings, Waddington building, room 3.06

department: Centre for Synthetic and Systems Biology

country: United Kingdom

institute: University of Edinburgh

description:
purified 27SB deproteinized pre-ribosomal RNP treated with 1M7
High-throughput RNA structure probing library

data_processing:
Library strategy: CRAC
Base-calling by Illumina
Raw data processing was carried out using tools described in the pyCRAC software package (Webb et al Genome Biology 2014; https://bitbucket.org/sgrann/pycrac)
The pyBarcodeFilter tool was used to split reads based on barcoded indexes.  Random nucleotide information from the in-read adapter is included in the headers of the forward reads. See characters after the two hashes (##).
PyFastqDuplicateRemover was used to remove potential PCR duplicates using random nucleotide information in the 5? adapter sequence
pyPileup and pyGTF2sgr.py were used to generate count data for the genes of interest. Raw 1M7 reactivities were calculated according to Tang et al Bioinformatics 2015
Genome_build: Reads were mapped to the Saccharomyces cerevisiae 35S gene (RDN37-1) using Novoalign version 2.07
Burlacu et al Table S2 contains all the calculated 1M7 reactivity for each RNA as well as the categorisations of the nucleotides. To calculate 1M7 reactivities we pooled the sequencing data of the biological replicates.

growth_protocol: S.cerevisiae strains were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) or YPG/R (YP with 2% Galactose and 2% Raffinose) at 30ºC.

extract_protocol:
Immunoprecipitations with HTP-and TAP-tagged proteins were performed with TNM150 buffer (50 mM Tris-HCl pH 7.8, 1.5 mM MgCl2, 150 mM NaCl, 0.1% NP-40 and 5 mM b-mercaptoethanol), essentially as previously described (Granneman et al., 2009). RNA was extracted using a GTC phenol solution (4 M guanidine thiocyanate, 0.05 M Tris at pH 8.0, 0.01 M EDTA, 2% sarcosyl, 1% β-mercaptoethanol, 50% [v/v] phenol) as previously described (Sambrook, 1989).
cDNA libraries were generated from purified ribosomal RNA using an RT oligonucteotide containing random hexamers (SuperScript III, Invitrogen). 5' adapters were ligated on (CircLigase II, EpiCentre) and 3' adaptors generated during PCR amplification.

value: BY4741 with nsa2-TAP::K.I.HIS3

tag: rna type

value: pre-ribosomal RNA


title: Nsa2_deproteinized_1M7_1

source_name: purified 27SB deproteinized pre-ribosomal RNP treated with 1M7

tag: strain


title: Nsa2_DMSO_deproteinized_1

description:
purified 27SB deproteinized pre-ribosomal RNP treated with DMSO
High-throughput RNA structure probing library


title: Nsa2_DMSO_deproteinized_2

source_name: purified 27SB deproteinized pre-ribosomal RNP treated with DMSO


title: ID_226


title: Rrp5_DMSO_deproteinized_2

description:
purified 27SA2 deproteinized pre-ribosomal RNP treated with DMSO
High-throughput RNA structure probing library

value: BY4741 with rrp5-TAP::K.I.HIS3


title: ID_215


title: Rrp5_deproteinized_1M7_1

description:
purified 27SA2 deproteinized pre-ribosomal RNP treated with 1M7
High-throughput RNA structure probing library


title: ID_224


title: ID_208


title: Rrp5_DMSO_deproteinized_1

source_name: purified 27SA2 deproteinized pre-ribosomal RNP treated with DMSO


title: ID_201


title: ID_190


title: Nsa2_1M7_in_vitro_2

description:
purified 27SB pre-ribosomal RNP treated with 1M7
High-throughput RNA structure probing library


title: Nsa2_DMSO_in_vitro_1

description:
purified 27SB pre-ribosomal RNP treated with DMSO
High-throughput RNA structure probing library


title: Nsa2_DMSO_in_vitro_2

source_name: purified 27SB pre-ribosomal RNP treated with DMSO


title: Rrp5_1M7_in_vitro_3

description:
purified 27SA2 pre-ribosomal RNP treated with 1M7
High-throughput RNA structure probing library


title: ID_230


title: Nsa2_1M7_in_vitro_1

source_name: purified 27SB pre-ribosomal RNP treated with 1M7


title: ID_165


title: ID_172


title: ID_174


title: Rrp5_1M7_in_vitro_2

source_name: purified 27SA2 pre-ribosomal RNP treated with 1M7


title: ID_160


title: Rrp5_DMSO_in_vitro_3

description:
purified 27SA2 pre-ribosomal RNP treated with DMSO
High-throughput RNA structure probing library


title: Rrp5_1M7_in_vitro_1


title: ID_158


title: Rrp5_DMSO_in_vitro_2

source_name: purified 27SA2 pre-ribosomal RNP treated with DMSO


title: ID_152


title: ID_151


title: Rrp5_deproteinized_1M7_2

source_name: purified 27SA2 deproteinized pre-ribosomal RNP treated with 1M7


title: Rrp5_DMSO_in_vitro_1


title: Mrd1_1M7_in_vitro_2

description:
purified 35S pre-ribosomal RNP treated with 1M7
High-throughput RNA structure probing library

value: BY4741 with mrd1-deltaRDB5-TAP::K.I.TRP1, pGAL-HA-MRD1::URA3


title: ID_149


title: Mrd1_DMSO_in_vitro_2

description:
purified 35S pre-ribosomal RNP treated with DMSO
High-throughput RNA structure probing library


title: ID_148


title: ID_145


title: ID_188


title: ID_187


title: ID_144


title: Mrd1_DMSO_in_vitro_1

source_name: purified 35S pre-ribosomal RNP treated with DMSO


title: ID_134


title: ID_133


title: ID_128


title: ID_81


title: ID_98


title: ID_114


title: ID_130


title: ID_76


title: ID_75


title: ID_29


title: ID_52


title: ID_47


title: ID_37


title: ID_101


title: ID_127


title: ID_36


title: ESC2

city: Guangzhou

first: Lihui

last: Lin

state: Guangdong

address: No.190, Kaiyuan Street

department: Stem cell

institute: Guangzhou Institutes Of Biomedicine and Health Chinese Academy Of Science

description: OG2 transgenetic mouse embryonic stem cells(OG2ES)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
The number of raw reads mapped to genes was calculated by RSEM (rsem-1.2.4), the reference genome using mm10, then put all the samples results together and normalized by EDAseq (1.99.1),  genes expression fold change were calculated using normalized raw reads.
Genome_build: mm10
Supplementary_files_format_and_content: Each files contain Rsem output, including raw reads, TPM and RPKM, raw_counts contain all samples reads counts mapped to genes and tpm file contains all samples normalized tpm value.

source_name: mouse embryonic stem cells(mESCs)

extract_protocol:
Total RNA was extracted by Trizol-based protocol.
The libraries were prepared according to Illumina TruSeq® RNA sample preparation Kit.

tag: passage

value: Oct4-GFP transgenic allele carrying mice (CBA/CaJ X C57BL/6J) to 129Sv/Jae female mice


title: pHeps_2

description: pHeps isolated from mouse adult liver

source_name: mouse adult liver

value: pHeps isolated from mouse adult liver

value: Oct4-GFP transgenic allele carrying mice (CBA/CaJ X C57BL/6J)


title: R7.1

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description:
s_140401_R01
Arabidopsis thaliana unifected roots 14dpi
processed data file:
20140401_tableCount.txt

data_processing:
Lifescope v2.5 smallRNA pipeline. Mapping with mapreads, default parameters.
Bam files were then merged per samples with keeping read group per lane.
Bam files were then processed with a java home made class, based on picard java classes to perform identification and produce raw data count for Arabidopsis thaliana smallRNAs including mirbase release 20 miRNAs and tRNAs from UCSC web server (UCSC tables).
Genome_build: TAIR10.21 + minc v3
Supplementary_files_format_and_content: SmallRNAs count based on arab.thal. mirbase v20 and tRNA from UCSC table browser

source_name: Arabidopsis thaliana uninfected roots 7dpi

growth_protocol: Seeds of A. thaliana (ecotype Wassilewskija) were surface-sterilised and sown on Murashige & Skoog (Duchefa) medium agar plates (0.5 x MS, 1% sucrose, 0.8% agar, pH 6.4). Plates were kept at 4°C for two days, and then transferred to a growth chamber (20°C with 8 h light and 16 h darkness). M. incognita strain “Morelos” was multiplied on tomato plants in a growth chamber (25°C, 16 h light and 8 h darkness).

extract_protocol:
Total RNA, including small RNAs (less than 200 nt long), was isolated from galls or uninfected roots at 7 and 14 dpi. Approximately 150 galls or internode fragments from uninfected roots were independently ground into powder in liquid nitrogen, with a mortar. Total RNA was extracted from these samples with the miRNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions, with three additional washes in RPE buffer. The quality and integrity of the RNA were assessed with a Bioanalyzer (Agilent)
2 µg of total RNA were ligated, reverse transcribed and amplified (11 cycles) with the reagents from the NEBNext Small RNA Library Prep Set for SOLiD. Amplified libraries were size-selected from 115 nt to 130 nt with the LabChip XT DNA 300 Assay Kit (Caliper Lifesciences). Libraries were subjected to 4 additional PCR rounds with the primers from the 5500 W Conversion Primers Kit (Life Technologies) and converted with the enzyme kit from the 5500 W Conversion Primers Kit (Life Technologies). Libraries were then quantified with the Bioanalyzer High Sensitivity DNA Kit (Agilent).

treatment_protocol: For in vitro nematode infection, J2 larvae were surface-sterilised with HgCl2 (0.01%) and streptomycin (0.7%) as described elsewhere (Caillaud & Favery, 2016). We inoculated 25-day-old seedlings grown in vitro individually with 200 sterilised J2s each, resuspended in Phytagel. Seven and 14 days post inoculation (dpi), galls were hand dissected from the infected roots. We also dissected internodes from uninfected roots (without apical and lateral root meristems) at the same time point than gall samples for use as a negative control. Samples were immediately frozen in liquid nitrogen and stored at -80°C. Three independent biological replicates were established for each set of conditions.

value: roots

tag: strain/ecotype

value: Wassilewskija

tag: days post-infection

tag: concentration sample (ng/nl)

tag: rin number


title: R7.2

description:
s_140401_RH
Arabidopsis thaliana unifected roots 14dpi
processed data file:
20140401_tableCount.txt


title: R7.3

description:
s_140401_R03
Arabidopsis thaliana unifected roots 14dpi
processed data file:
20140401_tableCount.txt


title: Mrd1_1M7_in_vitro_1

source_name: purified 35S pre-ribosomal RNP treated with 1M7


title: pHeps_1

description: pHeps isolated from mouse adult liver


title: R14.1

description:
s_140729_R02
Arabidopsis thaliana unifected roots 7dpi
processed data file:
20140729_tableCount.txt

source_name: Arabidopsis thaliana uninfected roots 14dpi


title: R14.2

description:
s_140729_R03
Arabidopsis thaliana unifected roots 7dpi
processed data file:
20140729_tableCount.txt


title: R14.3

description:
s_140729_R04
Arabidopsis thaliana unifected roots 7dpi
processed data file:
20140729_tableCount.txt


title: MEF_ciHeps_3

description: ciHeps from MEFs derived ciEPCs

source_name: mouse embryonic fibroblasts (MEFs)

value: ciHeps from MEFs derived ciEPCs

value: passage 3-10 (ciEPCs)


title: MEF_ciHeps_2

description: ciHeps from MEFs derived ciEPCs


title: MNF_ciHeps_2

description: ciHeps from MNFs derived ciEPCs

source_name: mouse neonatal fibroblasts

value: ciHeps from MNFs derived ciEPCs


title: ESC1

value: OG2 transgenetic mouse embryonic stem cells(OG2ES)


title: MEF_ciHeps_1

description: ciHeps from MEFs derived ciEPCs


title: MNF_ciHeps_1

description: ciHeps from MNFs derived ciEPCs


title: ESC_EPC1

description: EPCs derived from mESCs

value: EPCs derived from mESCs

value: passage10-15 (mESCs)


title: MNF_ciEPC1

description: ciEPCs derived from MNFs

value: ciEPCs derived from MNFs


title: MNF_ciEPC2

description: ciEPCs derived from MNFs


title: ciEPC2_P22

description: ciEPCs derived from MEFs

value: ciEPCs derived from MEFs


title: ciEPC1_P22

description: ciEPCs derived from MEFs


title: ciEPC2_P5

description: ciEPCs derived from MEFs


title: ciEPC2_P1

description: ciEPCs derived from MEFs


title: ciEPC1_P6

description: ciEPCs derived from MEFs


title: ciEPC1_P2

description: ciEPCs derived from MEFs


title: ciEPC1_P10

description: ciEPCs derived from MEFs


title: ciEPC1_P4

description: ciEPCs derived from MEFs


title: MNF2

description: mouse neonatal dermal fibroblast

value: mouse neonatal dermal fibroblast


title: MNF1

description: mouse neonatal dermal fibroblast


title: MEF3

description: E13.5 mouse embryo derived  fibroblast

value: E13.5 mouse embryo derived  fibroblast


title: MEF2

description: E13.5 mouse embryo derived  fibroblast


title: MEF1

description: E13.5 mouse embryo derived  fibroblast


title: RNAseq-of-siMrg15-S2

source_name: siMrg15 treated S2 cells

value: Schneider 2 cell-line

value: somatic cell

tag: genotype/variation

value: late embryos (20h-24h AEL)


title: trap_sham_mut3

last: Leach

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Reads were mapped to the mouse genome (mm10)
read counts quantified using STAR (version 2.5)
Differentially expressed genes were detected by using R package DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: read count matrix

source_name: heart

growth_protocol: Adult mice 8-10 weeks old under went surgically induced myocardial infarction (MI).

extract_protocol:
Total whole heart RNA, or cardiomyocyte specific TRAP RNA
Ion Total RNA-Seq kit v2 for whole transcriptome libraries

treatment_protocol: Mice underwent Sham or LAD ligation 6 weeks prior to RNA collection.

tag: rna isolation

value: translating ribosomal affinity purified (TRAP)

tag: surgery

value: Sham

value: Adult 8-10 weeks

value: Salv cKO


title: A5_5d

city: Shanghai

first: Zhihua

last: Shao

address: No.1239, Siping Road

institute: Tongji University

data_processing:
Bowtie2 v2.2.5 was used for building the genome index, and clean data was mapped to the reference genome using TopHat v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0. Fragment per kilobases per million mapped reads were calculated by Cufflinks(v2.2.1).
Genome_build: hg 19
Supplementary_files_format_and_content: tab-delimited text file includes count values for each sample.

source_name: primary ahRPE

growth_protocol: Cells were routinely passaged with 0.05% Trypsin-EDTA and cultivated in DMEM/F12 with 10% FBS at a density of 2.5-5x104 cells/cm2 in a 10cm culture dish. All cells were maintained and cultured in a humidified incubator, keeping at 37°C in 5% CO2. The media was half changed every 2 days.

extract_protocol:
Total RNA was extracted using TRIzol® Regeant (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols. Libraries were sequenced on the Illumina HiSeq2000 and single-end reads of 50bp were obtained.

tag: cell type

value: retina pigment epithelium

tag: passages

tag: Stage

value: 5 days


title: A5_4d

value: 4 days


title: RNAseq-of-siAsh1-S2

source_name: siAsh1 treated S2 cells

tag: cell line

tag: tissue


title: RNAseq-of-WT-S2

source_name: WT S2 cells

value: WT


title: A6_5d

source_name: ARPE-19 cell line


title: A5_3d

value: 3 days


title: trap_sham_mut2

city: Houston

tag: age


title: ciEPC2_P10

description: ciEPCs derived from MEFs

value: Oct4-GFP transgenic allele carrying mice (CBA/CaJ X C57BL/6J) to 129Sv/Jae female mice


title: ESC_EPC2

description: EPCs derived from mESCs

value: EPCs derived from mESCs

value: passage10-15 (mESCs)


title: A5_2d

value: 2 days


title: trap_sham_mut1

tag: genotype


title: ciEPC1_P3

description: ciEPCs derived from MEFs

value: ciEPCs derived from MEFs


title: trap_sham_ctrl3

value: control


title: H358-sh3+D5 rep 3

first: Bin

last: Xiang

address: Building 3, 4218 Jinke Road, Pudong

institute: novartis institutes for biomedical research

data_processing:
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using STAR v2.5.3 with parameters --bamRemoveDuplicatesType UniqueIdentical --outSAMmultNmax 1;
Raw reads and Reads Per Kilobase per Megabase of library size (RPKM) were calculated using HOMER (PMID: 20513432).
Differential gene expression was analyzed using R package DESeq2 using the raw reads.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw reads and RPKM values for each Sample.

source_name: lung/bronchiole; derived from metastatic site: alveolus

growth_protocol: H358 cells were cultured in RMPI 1640 medium (GIBCO) supplemented with 10% fetal bovine serum (FBS, GIBCO) and 100 U/mL penicillin-streptomycin (GIBCO) at 37°C with 5% CO2.

extract_protocol:
RNA isolation is performed using Trizol and RNeasy MinElute Cleanup Kit from cells. Following extraction, evaluate the quantity on Nanodrop and the integrity of total RNA using RNA 6000 Nano Kit on Aligent 2100 Bioanalyzer.
RNA library is constructed using TruSeq RNA Sample Preparation Kit. The first step in the workflow involves purifying the poly-A containing mRNA molecules using oligo-dT attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Second strand cDNA synthesis follows, using DNA PolymeraseI and RNase H. The cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.
The clusters of the cDNA library are generated on HiSeq X HD PE flow cell. Then the clusters are sequenced on HiSeq X system.

treatment_protocol: Doxycycline was added to induce the shRNA knockdown of FXR1 expression

value: H358 cell line

value: FXR1 KD

tag: time point


title: A4_5d

source_name: fhRPE-13A cell line


title: trap_sham_ctrl2

value: translating ribosomal affinity purified (TRAP)


title: H358-sh3+D5 rep 2


title: H358-sh3+D5 rep 1


title: trap_MI_mut3

value: myocardial infarction


title: H358-sh3-D5 rep 3


title: A4_2d


title: A4_4d


title: trap_MI_mut2

value: Adult 8-10 weeks


title: trap_MI_mut1

value: Salv cKO


title: H358-sh3-D5 rep 2


title: H358-sh3-D5 rep 1


title: H358-sh3+D3 rep 3


title: trap_MI_ctrl3


title: A3_4d

value: retina pigment epithelium


title: A3_5d

value: 5 days


title: A3_3d


title: trap_MI_ctrl1


title: H358-sh3+D3 rep 2


title: A2_5d


title: trap_MI_ctrl2


title: H358-sh3+D3 rep 1


title: A2_4d

value: 4 days


title: H358-sh3-D3 rep 3


title: total_MI_mut2

value: total whole-heart RNA


title: H358-sh3-D3 rep 2

value: 3 days


title: A2_3d


title: A4_3d


title: total_MI_mut1


title: trap_sham_ctrl1

value: Sham


title: H358-sh3-D3 rep 1


title: total_MI_ctrl2


title: total_MI_ctrl3


title: A2_2d


title: H358-ctrl+D3 rep 3

value: ctrl


title: H358-ctrl+D3 rep 2


title: A1_4d

source_name: fhRPE-13B cell line


title: A1_5d


title: A3_2d


title: sfl2 CO2-2

first: guanghua

last: huang

address: NO.1 West Beichen Road, Chaoyang District

institute: Institute of Microbiology

data_processing:
Illumina OLB_1.9.4 were used for basecalling
Filter dirty raw reads by removing reads with adaptors and low quality, the obtained clean reads were mapped to reference sequences using SOAPaligner/soap2 according to Li et al., Bioinformatics, 2009. Mismatches no more than 2 bases were allowed in the alignment.
Relative gene expression levels were calculated using the FPKM (Fragments Per kb per Million reads) method; FPKM=106C/(NL/103), where “C” is the number of fragments that uniquely aligned to gene A, “N” represents the total number of fragments that uniquely aligned to all genes, and “L” is the number of bases of gene A.
Genome_build: Candida albicans SC5314 genome (ASM18296v1)
Supplementary_files_format_and_content: Excel file containing FPKM  and count values for all samples

organism: Candida albicans

source_name: candida albicans

growth_protocol: Cells of the WT and sfl2/sfl2 mutant were first grown at 25°C in liquid Lee’s glucose medium for 24 h, then spread onto YPD medium plates and incubated at 37°C in air or in 5% CO2 for 22 h.

extract_protocol:
Cells were lysed by Mini-beadbeater and total RNA was harvested using GeneJET RNA Purification Kit (Thermo Scientific #K0731, #K0732)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth condition


title: total_MI_mut3


title: A1_3d


title: total_MI_ctrl1


title: H358-ctrl-D3 rep 3


title: H358-ctrl+D3 rep 1


title: H358-ctrl-D3 rep 2


title: sfl2 CO2-1


title: sfl2 air-1

value: air


title: A1_2d

value: 2 days


title: H358-ctrl-D3 rep 1


title: sfl2 air-2


title: WT CO2-2

value: wild type


title: WT CO2-1


title: WT air-1


title: NSCs_E47wt_RNA-Seq_rep3

description:
E47wt_rep3
RNA-Seq on wildtype neuronal stem cells (E47-/- litter mates) at E14.5, replicate 3
processed data file: NSCs_E47KOvsWt_DESeq.txt

data_processing:
The reads were mapped to the mouse genome mm9 (Ensembl build 37.67) and reads per gene counted using STAR version 2.5 with the following settings: --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 -- alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 100000 --quantMode GeneCounts.
Counts were filtered for their expression strength by selecting only genes with counts above 50 as expressed in embryonic NSCs. Gene count normalization and differential expression analysis was performed with DESeq2.
For gene annotation Ensembl Transcript Ids were mapped to mgi_symbol using the Bioconductor package biomaRt version 2.32.1 and information from Ensembl (build 37.67).
Genome_build: mm9
Supplementary_files_format_and_content: _DESeq.txt files contain the unfiltered results from the DESeq2 analysis for differential expression on either E12+/+ versus E12-/- (NSCs_E12KOvsWt_DESeq.txt) or E47+/+ versus E47-/- (NSCs_E47KOvsWt_DESeq.txt) neuronal stem cells.
Supplementary_files_format_and_content: _countsPerGene.tab.txt files contain the raw count data per gene as a result of mapping the reads to mm9 genome with STAR version 2.5.

growth_protocol: Embryonic NSCs   from  E14.5  embryos  were  cultured  under  proliferation  conditions  in  Neurobasal-A   medium supplemented with GlutaMAX (1%), glutamine (0.5%), Penicillin/Streptomycin   (1%), rhFGF-2 (20 ng/ml), B-27 minus Vitamin A (2%) (all from Invitrogen) and rhEGF   (20 ng/ml, Sigma-Aldrich).

extract_protocol:
RNA was extracted using the Quiagen Rneasy Mini Kit according to manufacture's manual.
The quality of the RNA was verified by Agilent 2100 Bioanalyzer with RNA 6000Nano Reagents (Agilent Technologies). Library preparation and rRNA depletion was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina) according to manufacture's manual. 500 ng RNA were used as input for each sample.
stranded mRNA-Seq

tag: strain background

value: E14.5 embryo

value: neuronal stem cells


title: NSCs_E47wt_RNA-Seq_rep2

description:
E47wt_rep2
RNA-Seq on wildtype neuronal stem cells (E47-/- litter mates) at E14.5, replicate 2
processed data file: NSCs_E47KOvsWt_DESeq.txt


title: NSCs_E47KO_RNA-Seq_rep1

description:
E47KO_rep1
RNA-Seq on E47-/- neuronal stem cells at E14.5, replicate 1
processed data file: NSCs_E47KOvsWt_DESeq.txt


title: NSCs_E47KO_RNA-Seq_rep3

description:
E47KO_rep3
RNA-Seq on E47-/- neuronal stem cells at E14.5, replicate 3
processed data file: NSCs_E47KOvsWt_DESeq.txt


title: NSCs_E47KO_RNA-Seq_rep2

description:
E47KO_rep2
RNA-Seq on E47-/- neuronal stem cells at E14.5, replicate 2
processed data file: NSCs_E47KOvsWt_DESeq.txt


title: Wild Type strain overexpressing dam, replicate 2

city: Montpellier

first: Anne

last: Lanois

address: 75 rue du Truel CC54

institute: INRA

description:
Dam_B
P. luminescens TT01
Processed data file: raw_reads_count.txt
Processed data file: normalized_reads_count_TT01(pBBR1MCS-5)_versus_TT01(pBB-Dam).txt

data_processing:
Image analyses and basecalling were performed using the Illumina HiSeq Control Software and Real-Time Analysis component.
Demultiplexing was performed using Illumina's conversion software (bcl2fastq 2.17).
The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer). Potential contaminants were investigated with the FastQ Screen software from the Babraham Institute.
In a first step, the RNA-Seq data quality was assessed by including option like reads trimming or merging/split paired-end reads.
In a second step, reads were mapped onto the Photorhabdus luminescens TT01 genome sequence using the SSAHA2 package (Ning et al., 2001) that combines the SSAHA searching algorithm (sequence information is encoded in a perfect hash function) aiming at identifying regions of high similarity, and the cross-match sequence alignment program (Ewing et al., 1998), which aligns these regions using a banded Smith-Waterman-Gotoh algorithm. An alignment score equal to at least half of the read is required for a hit to be retained.
To lower false positives discovery rate, the SAMtools (v.0.1.8) were then used to extract reliable alignments from SAM formatted files.
The number of reads matching each genomic object harbored by the reference genome was subsequently computed with the Bioconductor-GenomicFeatures package.
The Bioconductor-DESeq package with default parameters was used to analyze raw counts data and test for differential expression between conditions.
Genome_build: Photorhabdus luminescens TT01 (NC_005126.1)
Supplementary_files_format_and_content: raw_reads_count.txt: Tab-delimited text file includes raw number of reads mapped to individual genes of the Photorhabdus luminescens TT01 genome, for all samples.
Supplementary_files_format_and_content: normalized_reads_counts_TT01(pBBR1MCS-5)_versus_TT01(pBB-Dam).txt: Tab-delimited text file includes normalized reads count compute by DESeq package for the diferential expression between the two conditions : TT01 (pBBR1MCS-5) versus TT01 (pBB-Dam).

organism: Photorhabdus laumondii subsp. laumondii TTO1

source_name: TT01 (pBB-Dam)

growth_protocol: Logarithmic culture phase in LB broth supplemented with gentamycine at 28°C.

extract_protocol:
RNeasy miniprep QIAGEN kit.
Ribo-Zero rRNA Removal Kit Bacteria (Illumina, San Diego, CA) was used to remove ribosomal RNA from 4 µg of total RNA. For each sample, 100 ng of rRNA-depleted RNA was used to construct sequencing libraries using Illumina’s TruSeq Stranded mRNA Sample Prep Kit (Low throughput). The mRNA was chemically fragmented. The first cDNA strand was generated by reverse transcription with random hexamer primers, SuperScript IV Reverse Transcriptase (Life Technologies), Actinomycine D. The second strand cDNA was synthesized by replacing dTTP with dUTP. A single ‘‘A’’ nucleotide was added to the 3' end and ligation was carried out with Illumina’s indexed adapters. After 15 cycles of PCR, libraries were validated on a Fragment Analyzer (AATI, Ankeny, IA) and quantified with a KAPA qPCR kit.
On a sequencing lane of a flowcell V4, nine libraries were pooled in equal proportions, denatured with NaOH and diluted to 8 pM before clustering. Clustering and 50nt single read sequencing were performed according to the manufacturer’s instructions.
Cluster formation, primer hybridisation and single end-read 50 cycles sequencing were performed on cBot and HiSeq2500 (Illumina, San Diego, CA) respectively.

treatment_protocol: RNAprotect Bacteria reagent 5 min.

tag: overexpression

value: Dam


title: Wild Type strain overexpressing dam, replicate 1

description:
Dam_A
P. luminescens TT01
Processed data file: raw_reads_count.txt
Processed data file: normalized_reads_count_TT01(pBBR1MCS-5)_versus_TT01(pBB-Dam).txt


title: Wild Type strain overexpressing dam, replicate 3

description:
Dam_C
P. luminescens TT01
Processed data file: raw_reads_count.txt
Processed data file: normalized_reads_count_TT01(pBBR1MCS-5)_versus_TT01(pBB-Dam).txt


title: NSCs_E12KO_RNA-Seq_rep1

description:
E12KO_rep1
RNA-Seq on E12-/- neuronal stem cells at E14.5, replicate 1
processed data file: NSCs_E12KOvsWt_DESeq.txt


title: Wild Type strain harbouring empty plasmid, replicate 3

description:
pBB_C
P. luminescens TT01
Processed data file: raw_reads_count.txt
Processed data file: normalized_reads_count_TT01(pBBR1MCS-5)_versus_TT01(pBB-Dam).txt

source_name: TT01 (pBBR1MCS-5)

value: control


title: Wild Type strain harbouring empty plasmid, replicate 2

description:
pBB_B-2
P. luminescens TT01
Processed data file: raw_reads_count.txt
Processed data file: normalized_reads_count_TT01(pBBR1MCS-5)_versus_TT01(pBB-Dam).txt


title: NSCs_E12wt_RNA-Seq_rep3

description:
E12wt_rep3
RNA-Seq on wildtype neuronal stem cells  (E12-/- litter mates) at E14.5, replicate 3
processed data file: NSCs_E12KOvsWt_DESeq.txt


title: NSCs_E12wt_RNA-Seq_rep2

description:
E12wt_rep2
RNA-Seq on wildtype neuronal stem cells  (E12-/- litter mates) at E14.5, replicate 2
processed data file: NSCs_E12KOvsWt_DESeq.txt


title: NSCs_E12KO_RNA-Seq_rep2

description:
E12KO_rep2
RNA-Seq on E12-/- neuronal stem cells at E14.5, replicate 2
processed data file: NSCs_E12KOvsWt_DESeq.txt


title: WT air-2


title: G7.3

description:
s_140401_G1
Galls from Meloidogyne incognita infecting Arabidopsis thaliana 14dpi
processed data file:
20140401_tableCount.txt

organism:
Arabidopsis thaliana
Meloidogyne incognita

source_name: Galls from Meloidogyne incognita infecting Arabidopsis thaliana 7dpi

tag: pathogen

value: Meloidogyne incognita

value: root gall

tag: strain/ecotype

value: Morelos

tag: days post-infection


title: E2A_E47KO_ChIP-Seq

description: E2A ChIP-Seq in E47-/- NSCs

data_processing:
Reads were aligned to the mouse mm9 reference genome using BWA-MEM version 0.7.13 with default parameter settings.
PCR duplicates were removed using Picard Tools version 1.119.
Peaks  were  called  using  MACS2 version  2.1.0 with a FDR threshold of 0.1.
Genome_build: mm9
Supplementary_files_format_and_content: The .bed files containing the peak positions were generated with MACS2 version 2.1.0.

source_name: neuronal stem cells

tag: strain

value: E47 KO

value: E12.5 embryo

tag: fixation

tag: antibody

value: E2A (sc-349X, Santa Cruz Biotechnology)


title: E2A_E12KO_ChIP-Seq

description: E2A ChIP-Seq in E12-/- NSCs

value: E12 KO


title: Nematode J2.2

description:
s_140401_NC
Nematode J2
processed data file:
20140401_tableCount.txt

organism: Meloidogyne incognita

source_name: Nematode J2

value: whole body

tag: developmental stage

tag: concentration sample (ng/nl)

tag: rin number


title: E2A_wt_rep2_ChIP-Seq

description: E2A ChIP-Seq in wildtype NSCs

value: wildtype


title: G7.2

description:
s_140401_G2
Galls from Meloidogyne incognita infecting Arabidopsis thaliana 14dpi
processed data file:
20140401_tableCount.txt


title: NSCs_E12KO_RNA-Seq_rep3

description:
E12KO_rep3
RNA-Seq on E12-/- neuronal stem cells at E14.5, replicate 3
processed data file: NSCs_E12KOvsWt_DESeq.txt

tag: genotype/variation

tag: cell type


title: Nematode J2.1

description:
s_140401_NJ2
Nematode J2
processed data file:
20140401_tableCount.txt

tag: tissue


title: E2A_wt_rep3_ChIP-Seq

description: E2A ChIP-Seq in wildtype NSCs

tag: genotype

tag: age


title: Wild Type strain harbouring empty plasmid, replicate 1

description:
pBB_A
P. luminescens TT01
Processed data file: raw_reads_count.txt
Processed data file: normalized_reads_count_TT01(pBBR1MCS-5)_versus_TT01(pBB-Dam).txt


title: NSCs_E47wt_RNA-Seq_rep1

description:
E47wt_rep1
RNA-Seq on wildtype neuronal stem cells (E47-/- litter mates) at E14.5, replicate 1
processed data file: NSCs_E47KOvsWt_DESeq.txt


title: G7.1

description:
s_140401_G3
Galls from Meloidogyne incognita infecting Arabidopsis thaliana 14dpi
processed data file:
20140401_tableCount.txt


title: G14.3

description:
s_140729_G06
Galls from Meloidogyne incognita infecting Arabidopsis thaliana 7dpi
processed data file:
20140729_tableCount.txt

source_name: Galls from Meloidogyne incognita infecting Arabidopsis thaliana 14dpi

value: Wassilewskija


title: G14.1

description:
s_140729_G01
Galls from Meloidogyne incognita infecting Arabidopsis thaliana 7dpi
processed data file:
20140729_tableCount.txt


title: 120716_Bcd_Chip_Post

city: Berkeley

first: Mustafa

last: Mir

state: CA

address: 1951 Oxford St., Room 485, Li Ka Shing Center

institute: University of California, Berkeley

description: ChIP'd DNA

data_processing:
The sequencing reads were aligned to a combined D. pseudoobscura (Flybase Release 1.0) and D. melanogaster genome (Flybase Release 5) using Bowtie with options set as -3 70 -n 2 -m 1.
The aligned reads were converted to wig files using custom scripts available upon request
Wig files were normalized to 10 million mapped reads
Genome_build: The sequencing reads were aligned to a combined D. pseudoobscura (Flybase Release 1.0) and D. melanogaster genome (Flybase Release 5).
Supplementary_files_format_and_content: Normalized Wig files contain a wig score associated with each position that is normalized to 10 million reads that mapped to either genome.

organism:
Drosophila melanogaster
Drosophila pseudoobscura

source_name: Stage 3-5 embryos

growth_protocol: OregonR Drosophila melanogaster embryos were collected for 90 minutes and aged for 2 hours to enrich for embryos at developmental stage 5.

extract_protocol:
Embryo halves were then homogenized in homogenization buffer containing 15mM NaCl, 15mM TrisHCl pH 7.5, 60mM KCl, 1mM EDTA, and 0.1% Triton-X100, with 1mM DTT, 0.1 mM PMSF, and protease inhibit cocktail (Roche) added before use. After homogenization, 0.5% NP40 was added, and following a 5 minute incubation, samples were spun down at a low speed. Nuclei in the pellet were then washed once with the homogenization buffer containing 0.2M NaCl. The low speed centrifugation was repeated, and the recovered nuclei pellet was then re-suspended in nuclear lysis buffer (10 mM TrisCl, pH 7.9, 100 mM NaCl, 1 mM EDTA, 0.5 % Sarkosyl) +1%SDS, +1.5% sarkosyl. The chromatin was recovered by spinning the sample at full speed in a micro-centrifuge at 4oC for 1 hour and was re-suspended in a small volume of nuclear lysis buffer. Chromatin was sheared to an average size of 300bp using a Covaris sonicator (peak power= 140, duty factor = 10, cycle burst = 200, time = 3 minutes). Chromatin immunoprecipitation was performed using 72ng of chromatin and 1.5ug of an anti-Bicoid polyclonal antibody described previously (Li et al., 2008). The Bicoid antibody was coupled to Dynabead M-280 sheep anti-rabbit magnetic beads and the immunoprecipitation was conducted with the standard protocol from the manufacturer.
DNA libraries for the chromatin immunoprecitation samples were prepared using the Rubicon genomics thru-plex DNA-seq kit using 16 PCR cycles for posterior and whole samples and 22 cycles for anterior, middle, and input samples.

treatment_protocol: Embryos were fixed with formaldehyde as previously described (Li et al., 2008) and sorted by morphology for those at early stage 5. The posterior thirds of embryos were sliced off by hand with a scalpel. A pool of the embryo segments from approximately 300 embryos was combined with 20 µg of whole Drosophila pseudoobscura embryos at stage 5 (to serve as carrier).

tag: d. melanogaster fly line

value: Oregon R

tag: chip antibody

value: House-made Bicoid antibody (Paris et al 2013)


title: 120716_Bcd_Chip_Input_Whole

description: Input DNA - sonicated chromatin


title: ΔcnaBΔcchA-salt

city: Huzhou

first: Sha

last: Wang

address: No.759 Er Huan East Rd

institute: Huzhou University

data_processing:
Raw reads were cleaned, including removal of reads with adapters. Furthermore, reads with “N” (representative of an ambiguous base) and reads that contained more than 20% bases with Q < 20 were discarded. Clean reads were then mapped to the A. nidulans genome using TopHat version v2.0.12. Default parameter settings were used for TopHat alignment except “mismatch” was set to 2.
Gene expression analysis was performed via RNA-seq by expectation-maximization (RSEM). Briefly, the transcript abundance for a given gene was quantified by calculating the frequency of RNA-seq reads aligned to it, and this was expressed as an RPKM value.
Genome_build: Aspergillus nidulans FGSC A4 (assembly ASM14920v1)
Supplementary_files_format_and_content: tab-delimited text files include Read count for each Sample …

organism: Aspergillus nidulans

source_name: conidia

growth_protocol: MMPDRUU minimal medium with 2% glucose, nitrate salts, trace elements, 0.5 mg/l pyridoxine, 2.5 mg/l riboflavin, 5 mM uridine, and 10 mM uracil, pH 6.5

extract_protocol:
For RNA isolation, a total of 1×108 conidia from the relevant strains were incubated in 100 ml MMPDRUU at 37°C with shaking at 220 rpm for 18 h. Then, cultures underwent an additional incubation supplemented with or without NaCl (800 mM ﬁnal concentration) at 37°C for 30 min. The samples were harvested by filtration and ground to a fine powder in liquid nitrogen. Total RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT, ΔcnaB, and ΔcnaBΔcchA strains cultured on MMPDRUU, and the same strains cultured on MMPDRUU plus 800 mM NaCl

value: pyrG89 delta_cnaB::pyrG; nkuA::argB2;deltacchA::pyrG; veA1

tag: treatment

value: treatment with NaCl


title: G14.2

description:
s_140729_G03
Galls from Meloidogyne incognita infecting Arabidopsis thaliana 7dpi
processed data file:
20140729_tableCount.txt

tag: pathogen


title: ΔcnaB-salt

value: pyrG89 delta_cnaB::pyrG; riboB2; pyroA4nkuA::argB2; veA1


title: in vitro rep2

city: Yangling

first: bo

last: wang

state: Shaanxi

address: No. 3 Taicheng Road

institute: Northwest A&F University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to CPC 18961 whole genome using TopHat v. 2.0.9 with parameters --bowtie1 -p 8 -g 1
A gene expression profile was created using Cufflinks v. 2.2.1.
FPKM of transcripts with a significant P-value (< 0.05) and a greater than twofold change (log2) in transcript level were considered to be differently expressed. All P-values were corrected for false discoveries resulting from multiple hypothesis testing using the Benjamini-Hochberg procedure.
Genome_build: CPC 18961, reference genome deposited at DDBJ/EMBL/GenBank under the accession MTSC00000000 (version MTSC01000000)
Supplementary_files_format_and_content: [gene_exp-proc.diff.txt] Gene expression profile was created using Cufflinks v. 2.2.1
Supplementary_files_format_and_content: [Genes-exp-annot.txt] Expression profile with annotations
Supplementary_files_format_and_content: [genes.count-proc_tracking.txt] Counts of reads per each gene

organism: Ramichloridium luteum

source_name: liquid Czapek-Dox medium

extract_protocol:
Total RNA was extracted according to the instruction manual of the Trizol Reagent (Life technologies, California, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: 7 days

value: mycelium


title: in vitro rep3


title: NSCs_E12wt_RNA-Seq_rep1

description:
E12wt_rep1
RNA-Seq on wildtype neuronal stem cells (E12-/- litter mates) at E14.5, replicate 1
processed data file: NSCs_E12KOvsWt_DESeq.txt

tag: strain background

value: E14.5 embryo

value: neuronal stem cells


title: in vitro rep1


title: Nematode J2.3

description:
s_140401_NJ
Nematode J2
processed data file:
20140401_tableCount.txt

tag: strain/ecotype

value: Morelos


title: WT-salt

tag: strain

value: pyrG89; riboB2; pyroA4 nkuA::argB2; veA1


title: ΔcnaB-control

value: treatment without NaCl


title: in planta rep2

source_name: apple surface

value: 3 months


title: ΔcnaBΔcchA-control


title: in planta rep1


title: WT-control


title: in planta rep3


title: MALAT1 5590_CMC+

status: Public on Oct 03 2017

first: Chengqi

last: Yi

address: 5 Yiheyuan Road, Haidian District

institute: Peking University

data_processing:
Sequenced reads were trimmed for low-quality reads, adaptor sequences, and paired reads without any adaptor sequence(as our insert is only 65-85 bp).
Duplicative reads were removed according to their unique molecular identifier (6 random bases adjacent to each side of insert added during adaptor ligation: 5'-CGCGNNNNNNACT-3').
The remaining reads were mapped with Bowtie2 to the human mRNA or lncRNA reference (downloaded from NCBI).
Misincorporation information were analyzed based on translated Pileup files.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include numbers of miscorporation events of different types at each site on the reference

source_name: HEK293T cells

growth_protocol: HEK293T cells were maintained in DMEM medium supplemented with 10% FBS and 1% penicillin/streptomycin and grown at 37 ℃ with 5% CO2.

extract_protocol:
Total RNA was extracted, fragmented and then CMC-reacted or mock-treated, followed by developed reverse transcription using our method. The RT-PCR products of specific qPCR amplicons were subjected to high-throughput sequencing.
Libraries were prepared using NEBNext® Ultra II DNA Library Prep Kit. Briefly, DNA was end-repaired by an enzyme mix to yield a protruding 3'- 'A' base for ligation with our in-house synthesized adaptors which have a single 'T' base overhang at the 3’ end. After adaptor ligation, DNA was PCR amplified with Illumina primers for 15 cycles, followed by size-selection and purification using AMPure XP beads (New England Biolabs). Libraries were sequenced on Illumina HiSeq X Ten with double end reads (150 bp).

value: wild type


title: EEF1A1 519_CMC-


title: MALAT1 5590_CMC-


title: Gst_0_No_KDE_rep4

first: Heather

middle: Marie

last: Jensen

address: 1 Cyclotron Road, Mailstop 978-4110K

institute: Lawrence Berkeley National Laboratory

description: Biorep analysis

data_processing:
Library strategy: BAR-Seq
log2 fitness values for bar-coded strains processed using the published FEBA analysis method with "Time0_control" as Time0; Wetmore et. al (2015) mBio;open access code available at https://bitbucket.org/berkeleylab/feba
Supplementary_files_format_and_content: Excel file includes log2 fitness (bar code abundance) values for each bar-coded gene disruption.  Time0_control is the sample used as the initial abundance of each barcode (i.e.,  would have a 0 value in all fields).

organism: Escherichia coli BW25113

source_name: E. coli BW25113 transposon library (TnLib)

growth_protocol: Grown and induced in 0.42mL EZ rich + 1% glucose + kanamycin + chloramphenicol in 48 well plates at 30degC for 6 hours

extract_protocol:
Sorted cells were pelleted, and genomic DNA was purified using the Qiagen DNeasy Blood and Tissue Kit.
Barcodes were amplified as described in Wetmore (2015). In brief, barcodes were amplified using Q5 DNA polymerase with a common primer and indexed primer. Amplicons were checked with gel electrophoresis and purified using the Zymo Clean and Concentrator kit. Finally, concentrations were measured with Qubit HS assay, and samples were multiplexed.

treatment_protocol: Cells were sorted by FACS according to GFP signal intensity.

tag: tnlib

value: TnLib/gstA-GFP

tag: iptg (mm)

tag: sorting gate

value: No GFP


title: TnLib_0_No_KDE_rep6

description: Biorep analysis

value: TnLib


title: Lep_0_No_KDE_rep3

description: Biorep analysis

value: TnLib/lepI-GFP


title: Lep_diversity

description: Library diversity confirmation

value: Not sorted


title: Cyo_0_No_KDE_rep3

description: Biorep analysis

value: TnLib/cyoB-GFP


title: Mdl_100_Low_rep2

description: Bar codes in sorted sample

value: TnLib/mdlB-GFP

value: Low GFP


title: Cyo_0_No_KDE_rep2

description: Biorep analysis


title: Yid_0_No_KDE_rep4

description: Biorep analysis

value: TnLib/yidC-GFP


title: TnLib_diversity

description: Library diversity confirmation


title: Mdl_diversity

description: Library diversity confirmation


title: Yid_diversity

description: Library diversity confirmation


title: Yid_0_No_KDE_rep3

description: Biorep analysis


title: Time0_control

description: Time0 control


title: Cyd_diversity

description: Library diversity confirmation

value: TnLib/cydB-GFP


title: Gst_diversity

description: Library diversity confirmation


title: Mdl_100_High_rep1

description: Bar codes in sorted sample

value: High GFP


title: Mdl_0_No_KDE_rep3

description: Biorep analysis


title: Cyo_diversity

description: Library diversity confirmation


title: Gst_0_No_KDE_rep3

description: Biorep analysis


title: Cyd_0_No_KDE_rep4

description: Biorep analysis


title: TnLib_0_No_KDE_rep5

description: Biorep analysis


title: 18S rRNA 1045+1056_CMC-


title: Mdl_0_No_KDE_rep4

description: Biorep analysis


title: EEF1A1 519_CMC+


title: Lep_0_No_KDE_rep4

description: Biorep analysis


title: Cyd_0_No_KDE_rep3

description: Biorep analysis


title: TnLib_0_No_KDE_rep4

description: Biorep analysis


title: 18S rRNA 1045+1056_CMC+


title: TnLib_0_No_KDE_rep3

description: Biorep analysis


title: Yid_0_No_KDE_rep2

description: Biorep analysis