title: complex nitrogen

city: Wuxi

first: xiaopeng

last: Xu

address: Jiangnan University, Wuxi 214122, Jiangsu, China

department: school of biotechnology

institute: Jiangnan University

data_processing:
The reads from the three samples were pooled, then were respectively applied for de novo genome assembly using the scaffolding contig algorithm of CLC Genomics Workbench (ver. 6.0.4) using word size = 45 and minimum contig length ≥ 200. The derived splicing sequences were designated as primary reads.
The primary UniGene was further assembled using the CAP3 EST assembly program to obtain a final UniGene sequence assembly. First, the primary UniGene was assembled using loose parameters to produce the first contig. Then, the second contig was generated using strict parameters.
According to the polycistronic characteristic of prokaryotic mRNA, Unigenes with lengths of ≥ 500 were predicted using the Glimmer software as gene-encoding segments. Each unigene may contain more than one gene, and finally, the predicted gene sequences, unigenes without predicted gene sections, and unigene lengths of < 500 were merged to generate the total gene sequence file, which contained a total of 3,899 gene sequences.
Gene annotation was first conducted based on ab initio prediction of protein-coding sequences. The assembled gene sequences were blasted against trEMBL + SWISS-PROT UniProt (Date: March 2014) database (blastx with the nucleic acid sequences translated into protein). The UniProt database is the most detailed and accurate protein database of protein structure and function, which presumably includes a total of 54,789,971 entries. The filter criteria included an E-value of < 1e-−5.
Genome_build: polycistronic characteristic of prokaryotic mRNA
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for three samples

organism: Sphingomonas sp. ATCC 31555

source_name: bacteria

growth_protocol: The mRNAs of Sphingomonas sp. ATCC 31555 cultured in IN, ON, and CN media for 12 h at 37°C.

extract_protocol:
Total RNAs were extracted from seed coats using TRIzol reagent (Life Technologies, USA) and purified using Qiagen RNeasy Micro kit and RNase-Free DNase set (Germany). Poly(A) mRNAs were isolated using Oligotex mRNA mini kit (Qiagen, Germany). RNA concentration was measured in a UV spectrophotometer (Shanghai Mapada Instrument Corp., Shanghai, China) to ensure that the samples had optimal OD260/OD280 ratios between 1.8–2.0. RNA quality and integrity of the 23S and 16S rRNAs and its corresponding ratio (~2:1) were checked in agarose gels.
cDNA library construction and sequencing by illumina genome analyzer

treatment_protocol: After culturing in fermentation media for 3 days, Sphingomonas were harvested by centrifugation, washed with distilled water, and dried at 80°C for 24 h to a constant weight. Dry cell weight (DCW) was determined from at least three 10-mL cell suspensions, The concentration of gum was measured following a previously reported method.

tag: cultured

value: :NaNO3 (1.5 g/L) + beef extract (2.5 g/L) as complex nitrogen (CN)


title: DPY27 RNAi L1 rep3

status: Public on Mar 25 2016

type: SRA

city: Ann Arbor

first: Gyorgyi

last: Csankovszki

state: MI

address: 830 N. University Ave.

department: MCDB

country: USA

institute: University of Michigan

library_source: transcriptomic

data_processing:
Reads were trimmed for quality using the TrimGalore program from Babraham Bioinformatics and aligned to the C. elegans genome version WS235 with Tophat v 2.0.13. Default parameters allow up to 20 hits for each read. Gene expression was quantified using Cufflinks v2.2.1 with use of “rescue method” for multi-reads and supplying gene annotation for WS235. Gene count estimation was performed using HTSeq-count tool v0.6.0 in the default “union” mode.  Differential expression analysis was performed using DESeq2 v1.6.3 in R version 3.2.3. All analyses were performed which genes that had average expression level above 1 RPKM (reads per kilobase per million, as calculated by Cufflinks).
Genome_build: C. elegans genome version WS235
Supplementary_files_format_and_content: tab-delimited text files include RPKM values, and values from DESeq2 (log2 fold change of (mutant/control) and p-values after adjustment for multiple test correction)

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: L1 worms_DPY27 RNAi L1

growth_protocol: Worms were synchronized by bleaching gravid adults to isolate embryos and allowing worms to hatch overnight. Newly hatched L1 larval worms were plated and grown for 3 hours on NGM plates with OP50.

extract_protocol:
RNA was extracted and precipitated using the manufacturer's instructions. Total RNA was cleaned using the Qiagen RNeasy kit.
Non-stranded mRNA-seq libraries were prepared using TruSeq RNA Library Preperation Kit.

treatment_protocol: Packed larvae were resuspended in 10V of Trizol and frozen at -80C.

tag: strain/genotype

value: N2, DPY-27 RNAi

tag: developmental stage

tag: tissue

value: worms; packed larvae


title: mRNA_Zli_E10.5

city: Old Westbury

first: Ying-Tao

last: Zhao

state: NY

address: Riland building, Room 024 Northern Boulevard, P.O. Box 8000

department: Biomedical Sciences

institute: New York Institute of Technology

data_processing:
Illumina Casava software used for basecalling.
Paired-end sequencing (100 bp) was performed on an Illumina HiSeq2000 platform at the Next Generation Sequencing Core (Perelman School of Medicine, University of Pennsylvania) to a depth of 62 million reads.
Raw sequences were filtered to retain only high quality reads. Sequences were processed with RNA-Seq Unified Mapper (RUM)49 that aligns reads to the set of known transcripts in RefSeq, UCSC, ENSEMBL, and the mouse genome (mm9), and outputs feature-level quantitation (transcript, exon, and intron).
To analyze global gene expression profiles, the number of uniquely aligning read counts to mRNA transcripts were extracted from the RUM output and processed using a custom script49. Transcripts with a fragment per kilobase of exon per million fragments mapped (FPKM) value >2 were considered as expressed.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph file was generated using RUM; tab-delimited text file includes read count values

molecule: total RNA

organism: Mus musculus

extract_protocol:
RNA-seq. The 429M20eGFP BAC reporter line48 was used to guide the dissection of Shh expressing cells from the ventral midbrain, ventroposterior diencephalon and zli of E10.5 embryos under a fluorescent stereomicroscope. Total RNA was extracted from GFP+ brain tissue isolated from approximately 30 embryos using the miRNeasy Micro Kit (Qiagen, Valencia, CA).
The RNA-seq library was prepared from 1µg of total RNA according to the manufacturer's protocol for TruSeq RNA Sample Prep Kits (Illumina).

tag: strain

tag: developemental stage

value: zona limitans intrathalamica (ZLI)


title: M2_KO1

city: Cambridge

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

institute: MIT

description: Liver tissue

data_processing:
Illumina pipeline version 1.8 used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes estimated read counts (from rsem) per gene for each sample

source_name: PKM2 KO Liver

growth_protocol: RNA was isolated from flash frozen ground whole liver tissue.

extract_protocol:
RNA was isolated from flash frozen ground whole tissue following manufacturer’s instructions for Trizol (Invitrogen).
RNA libraries were prepared for sequencing with the Illumina TruSeq kit according to the manufacturer's instructions.

treatment_protocol: No treatment

tag: cell-type

value: Liver tissue

tag: genotype

value: C57BL/6J x 129SvJ


title: E7.0 single cell region P (93_L1_I055)

status: Public on Mar 24 2016

city: Guangzhou

first: Guangdun

last: Peng

address: 190 Kaiyuan Road

department: Guangzhou Institutes of Biomedicine and Health

country: China

institute: Chinese Academy of Sciences

description:
Sample name: 93_L1_I055.P
processed data file: E7.0.single.cell.gene.expression.txt

data_processing:
The reads for all samples are mapped to the mm10 using Tophat v2.0.8b with parameter: -p 20 -g 1 -N 4 --read-edit-dist 4 --microexon-search
The mapped reads were used to estimate transcriptomic alignment rates, and were also used as input in Cufflinks v2.1.1 (Trapnell et al., 2013) to quantify gene expression levels (fragment per kilobase per million, FPKM) with the default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for all single cells

source_name: Mouse embryonic cells

growth_protocol: E7.0 C57BL/6E embryos were harvested and incubated in 0.5% Trypsin at 4°C.

extract_protocol:
Single cell RNA-seq was performed according to Smart2-seq (Picelli et al., 2013) protocol.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit

treatment_protocol: The epiblast with the extraembryonic and mesoderm/endoderm parts removed were bisected into the anterior (A) and posterior (P) parts. These fragments were further dissociated into single cells. Individual cells were picked up by mouth pipette and marked (A or P).

value: Late mid-streak embryo (E7.0)

tag: region

value: P


title: inorganic nitrogen

value: :NaNO3 (4.0 g/L) as inorganic nitrogen (IN)


title: E7.0 single cell region P (94_L1_I034)

description:
Sample name: 94_L1_I034.P
processed data file: E7.0.single.cell.gene.expression.txt


title: organic nitrogen

value: :Beef extract (4.0 g/L) as organic nitrogen (ON)


title: PacBio_Spombe

city: Berlin

first: Lydia

last: Herzel

address: Takustr. 6

department: Biology, Chemistry and Pharmacy

country: Germany

institute: Freie Universität

description: Nascent RNA

data_processing:
PacBio SMRT Analysis v2.3.0 software was used to obtain CCS reads (reads of inserts protocol).
Fastq files were filtered and trimmed for the 3’ end DNA adaptor and downstream Clontech adaptor sequences with cutadapt 1.8 (-a CTGTAGGCACCATCAAT -n 1 -O 17 -e 0.1 –match-read-wildcards –discard-untrimmed -m 15).
Also the reverse-complement adaptor was trimmed (-g ATTGATGGTGCCTACAG) and the read was reverse-complemented.
Demultiplexing (MS2_reads_of_insert.fastq) was also done similarly using the sample identifier and its reverse-complement identifier.
Trimmed fastq-files were catenated and the remaining 5 nt random 3’ barcode was removed using the FASTX toolkit (fastx_trimmer -Q 33 -t 5, version 0.0.13).
Reads with 5’ and 3’ end adaptors were trimmed and retained for mapping (cutadapt -g AAGCAGTGGTATCAACGCAGAGTACATGGG -n 3 -O 30 -e 0.1 –match-read-wildcards –discard-untrimmed -m 10).
Processed fastq-data were mapped to the genome version  S. cerevisiae sacCer3 or S. pombe EF2 using gmap 2013-05-09 (-d <genome_index> –min-intronlength=30 –intronlength=1010 (850 S. pombe) –localsplicedist=1010 (850 S. pombe) –totallength=1010 ( 850 S. pombe) –trimendexons=0 –microexon-spliceprob=0.5 –direction=auto –find-shifted-canonical –allow-close-indels=2 –npaths=1 –nofails –fails-as-input –mapboth -A –format=samse).
genome build: sacCer3 and S. pombe EF2
processed data files format and content: mapped data in sam- or bed-format

organism: Schizosaccharomyces pombe

source_name: cells in exponential growth (Glucose)

growth_protocol: Cell cultures were grown in complete media (YPD or YES, respectively) at 30°C and 250 rpm. For cell growth with Galactose as carbon source, cells were grown in YP containing 1% Raffinose and 2% D-Galactose. Cells were harvested in exponential growth at an OD (595nm) of 0.5-1.

extract_protocol:
Nascent RNA was prepared using a nascent RNA isolation protocol for yeast (Carrillo Oesterreich et al. 2010) and Phenol:Chloroform:IAA, 25:24:1, pH 6.6 extraction.
Nascent RNA was 3’ end ligated to the DNA adaptor (/5rApp/NNNNNCTGTAGGCACCATCAAT/3ddC/) and reverse transcribed into cDNA with a slight modification of the SMARTer PCR cDNA Synthesis Kit (Clontech).
A custom primer reverse-complement to the 3’ end adaptor was used (AAGCAGTGGTATCAACGCAGAGTACATTGATGGTGCCTACAG). Maximal 1 µg of RNA was used per reaction.
The subsequent low cycle PCR was carried out with the Advantage 2 PCR Kit according to the instructions provided by the kit.
Double-stranded cDNA was further used for Pacific Biosciences library preparation and sequencing with standard protocols and kit from Pacific Biosciences (SMRTbell™ Template Prep Kit 1.0).
SMRT DNA sequencing (Pacific Biosciences)

treatment_protocol: For nascent RNA extraction, 1l of cells was pelleted, washed with ice-cold PBS, quick-frozen in liquid nitrogen in 6 aliquots and kept at -80°C.

value: Wild-type h-


title: E7.0 single cell region P (83_L1_I047)

description:
Sample name: 83_L1_I047.P
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region P (90_L1_I054)

description:
Sample name: 90_L1_I054.P
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region P (88_L1_I052)

description:
Sample name: 88_L1_I052.P
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region P (85_L1_I050)

description:
Sample name: 85_L1_I050.P
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region P (80_L1_I032)

description:
Sample name: 80_L1_I032.P
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region P (86_L1_I051)

description:
Sample name: 86_L1_I051.P
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region P (78_L1_I046)

description:
Sample name: 78_L1_I046.P
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region P (76_L1_I030)

description:
Sample name: 76_L1_I030.P
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region P (76_L1_I045)

description:
Sample name: 76_L1_I045.P
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region P (74_L1_I043)

description:
Sample name: 74_L1_I043.P
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region P (75_L1_I044)

description:
Sample name: 75_L1_I044.P
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region P (72_L1_I029)

description:
Sample name: 72_L1_I029.P
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTSWRzJzOBz171

city: Los Angeles

first: Yehudit

last: Hasin-Brumshtein

state: CA

address: 695 Charles E. Young Drive South

department: David Geffen School of Medicine, Cardiology

institute: UCLA

data_processing:
FastQC read quality assessment
Alignment to mm10 wirh GENCODE_M2 annotation, using STAR 2.3.1 with --outFilterMismatchNmax 3, --outFilterIntronMotifs RemoveNoncanonicalUnannotated and --outFilterMultimapNmax 10
Transcript assembly with Cufflinks 2.2.0, using -g, -b and -u options
Merging of assemblies with GENECODE_M2, using Cuffmerge
Quantification of transcripts with Cuffquant and Cuffnorm v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Expression profile (FPKM), merged assembly (GTF)

source_name: hypothalamus

extract_protocol:
Qiagen miRNAeasy kit
Truseq v3

treatment_protocol: high fat diet described in Parks BW, 2013 PMID: 23312289

value: SWR/J

tag: Sex

value: male

tag: diet

value: high fat


title: E7.0 single cell region P (69_L1_I028)

description:
Sample name: 69_L1_I028.P
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTSMzJzOBz1467

value: SM/J


title: E7.0 single cell region P (84_L1_I048)

description:
Sample name: 84_L1_I048.P
processed data file: E7.0.single.cell.gene.expression.txt


title: met-2 set-25, Vector RNAi L1 rep1

source_name: L1 worms_met-2 set-25, Vector RNAi L1

value: EKM99, Vector


title: E7.0 single cell region P (68_L1_I046)

description:
Sample name: 68_L1_I046.P
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTSMzJzOBz1354


title: HypoTSJLzJzOBz1391

value: SJL/J


title: HypoTSMzJzOBz1353


title: HypoTRIIISzJzOBz617

value: RIIIS/J


title: HypoTSEAzGnJzOBz529

value: SEA/GnJ


title: HypoTSEAzGnJzOBz528


title: E7.0 single cell region P (66_L1_I026)

description:
Sample name: 66_L1_I026.P
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTRIIISzJzOBz618


title: HypoTSWRzJzOBz172


title: E7.0 single cell region P (64_L1_I024)

description:
Sample name: 64_L1_I024.P
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTRIIISzJzOBz616


title: HypoTNZWzLacJzOBz1371

value: NZW/LacJ


title: E7.0 single cell region P (61_L8_I023)

description:
Sample name: 61_L8_I023.P
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTPLzJzOBz585

value: PL/J


title: HypoTNZWzLacJzOBz1269


title: E7.0 single cell region P (68_L1_I027)

description:
Sample name: 68_L1_I027.P
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTSEAzGnJzOBz530


title: E7.0 single cell region P (5_L4_I002)

description:
Sample name: 5_L4_I002.A
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region P (57_L1_I021)

description:
Sample name: 57_L1_I021.P
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTNZBzBlNJzOBz1474

value: NZB/BlNJ


title: HypoTNZBzBlNJzOBz1473


title: HypoTNONzSHiLtJzOBz72

value: NON/LtJ


title: HypoTNONzSHiLtJzOBz71


title: E7.0 single cell region P (59_L1_I022)

description:
Sample name: 59_L1_I022.P
processed data file: E7.0.single.cell.gene.expression.txt

value: Late mid-streak embryo (E7.0)


title: HypoTNONzSHiLtJzOBz656


title: E7.0 single cell region P (56_L5_I012)

description:
Sample name: 56_L5_I012.P
processed data file: E7.0.single.cell.gene.expression.txt

value: P


title: HypoTNZBzBlNJzOBz1475


title: E7.0 single cell region P (54_L1_I011)

description:
Sample name: 54_L1_I011.P
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTPLzJzOBz586


title: HypoTMAzMyJzOBz637

value: MA/MyJ


title: HypoTMAzMyJzOBz635


title: HypoTMAzMyJzOBz636


title: E7.0 single cell region P (50_L2_I032)

description:
Sample name: 50_L2_I032.P
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region P (51_L5_I010)

description:
Sample name: 51_L5_I010.P
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTKKzHlJzOBz1308

value: KK/HlJ


title: HypoTLGzJzOBz319

value: LG/J


title: E7.0 single cell region P (50_L1_I009)

description:
Sample name: 50_L1_I009.P
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTKKzHlJzOBz109


title: HypoTLGzJzOBz318


title: WT1

description: Liver tissue

source_name: WT Liver

value: Liver tissue

value: C57BL/6J x 129SvJ


title: HypoTDBAz2JzOBz600

value: male

value: high fat


title: HypoTLGzJzOBz317


title: E7.0 single cell region P (51_L2_I033)

description:
Sample name: 51_L2_I033.P
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region A (47_L1_I008)

description:
Sample name: 47_L1_I008.A
processed data file: E7.0.single.cell.gene.expression.txt

value: A


title: HypoTCXB6zByJzOBz274


title: HypoTCXB6zByJzOBz273


title: HypoTIzLnJzOBz1452

value: I/LnJ


title: HypoTKKzHlJzOBz110


title: E7.0 single cell region A (46_L1_I030)

description:
Sample name: 46_L1_I030.A
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region P (79_L1_I031)

description:
Sample name: 79_L1_I031.P
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region A (4_L1_I002)

description:
Sample name: 4_L1_I002.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTDBAz2JzOBz601


title: HypoTSJLzJzOBz1390

value: SJL/J


title: HypoTCXB4zByJzOBz654

value: CXBH


title: HypoTCXB3zByJzOBz422


title: HypoTDBAz2JzOBz599


title: HypoTCXB7zByJzOBz678


title: E7.0 single cell region A (43_L2_I028)

description:
Sample name: 43_L2_I028.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTCXB7zByJzOBz677


title: HypoTCXB3zByJzOBz420


title: HypoTCXB13zHiAJzOBz225


title: HypoTCXB12zHiAJzOBz681


title: HypoTCXB6zByJzOBz272


title: E7.0 single cell region A (47_L1_I042)

description:
Sample name: 47_L1_I042.A
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region P (82_L1_I033)

description:
Sample name: 82_L1_I033.P
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region A (40_L1_I006)

description:
Sample name: 40_L1_I006.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTCXB12zHiAJzOBz452


title: HypoTCXB4zByJzOBz653


title: E7.0 single cell region A (45_L8_I007)

description:
Sample name: 45_L8_I007.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTCXB13zHiAJzOBz812


title: E7.0 single cell region A (45_L2_I029)

description:
Sample name: 45_L2_I029.A
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region A (49_L1_I031)

description:
Sample name: 49_L1_I031.P
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region P (65_L1_I025)

description:
Sample name: 65_L1_I025.P
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTCXB4zByJzOBz287


title: HypoTCXB7zByJzOBz676


title: E7.0 single cell region A (39_L1_I025)

description:
Sample name: 39_L1_I025.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTCXB3zByJzOBz421


title: E7.0 single cell region P (94_L1_I056)

description:
Sample name: 94_L1_I056.P
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTCXB12zHiAJzOBz680


title: HypoTCEzJzOBz1343

value: CE/J


title: E7.0 single cell region A (42_L2_I027)

description:
Sample name: 42_L2_I027.A
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region A (41_L2_I026)

description:
Sample name: 41_L2_I026.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTCXB11zHiAJzOBz268


title: E7.0 single cell region A (37_L1_I041)

description:
Sample name: 37_L1_I041.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTCXB11zHiAJzOBz187


title: HypoTCXB13zHiAJzOBz224


title: HypoTCXB11zHiAJzOBz267


title: HypoTCBAzJzOBz260

value: CBA/J


title: HypoTCBAzJzOBz691


title: HypoTSWRzJzOBz170

value: SWR/J


title: HypoTC57LzJzOBz493


title: E7.0 single cell region A (33_L5_I004)

description:
Sample name: 33_L5_I004.A
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region A (34_L1_I022)

description:
Sample name: 34_L1_I022.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTC57BLKSzJzOBz85


title: HypoTC57BLKSzJzOBz84


title: E7.0 single cell region A (37_L1_I024)

description:
Sample name: 37_L1_I024.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTCEzJzOBz1341


title: HypoTCBAzJzOBz261


title: HypoTCEzJzOBz1342


title: HypoTC57BLKSzJzOBz83


title: E7.0 single cell region A (35_L1_I023)

description:
Sample name: 35_L1_I023.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTC57LzJzOBz492


title: E7.0 single cell region A (36_L1_I005)

description:
Sample name: 36_L1_I005.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTC57BLz6JzOBz607


title: E7.0 single cell region A (32_L1_I038)

description:
Sample name: 32_L1_I038.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTNZWzLacJzOBz1370

value: NZW/LacJ


title: HypoTC57BLz6JzOBz606


title: HypoTC57BLz6JzOBz605


title: HypoTC57LzJzOBz491


title: E7.0 single cell region A (31_L1_I003)

description:
Sample name: 31_L1_I003.A
processed data file: E7.0.single.cell.gene.expression.txt

value: Late mid-streak embryo (E7.0)


title: E7.0 single cell region A (33_L2_I021)

description:
Sample name: 33_L2_I021.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTBXH6zTyJzOBz321


title: E7.0 single cell region A (33_L1_I039)

description:
Sample name: 33_L1_I039.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTC3HzHeJzOBz65


title: HypoTC3HzHeJzOBz64


title: HypoTC3HzHeJzOBz66


title: E7.0 single cell region A (31_L2_I012)

description:
Sample name: 31_L2_I012.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTBXH9zTyJzOBz753


title: HypoTBXH4zTyJzOBz365


title: HypoTBXH22zKccJzOBz483


title: HypoTBXH9zTyJzOBz752


title: HypoTBXH9zTyJzOBz751


title: E7.0 single cell region A (31_L1_I037)

description:
Sample name: 31_L1_I037.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTBXH22zKccJzOBz458


title: HypoTBXH6zTyJzOBz323


title: HypoTBXH6zTyJzOBz322


title: E7.0 single cell region A (30_L1_I036)

description:
Sample name: 30_L1_I036.A
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region A (27_L1_I009)

description:
Sample name: 27_L1_I009.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTBXH19zTyJzOBz532


title: HypoTBXH4zTyJzOBz367


title: E7.0 single cell region A (30_L1_I011)

description:
Sample name: 30_L1_I011.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTBXD9zTyJzOBz298


title: E7.0 single cell region A (25_L1_I008)

description:
Sample name: 25_L1_I008.A
processed data file: E7.0.single.cell.gene.expression.txt


title: E7.0 single cell region A (29_L2_I010)

description:
Sample name: 29_L2_I010.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTBXH22zKccJzOBz457


title: E7.0 single cell region A (29_L1_I035)

description:
Sample name: 29_L1_I035.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTBXH20zKccJzOBz535


title: HypoTBXD87zRwwJzOBz996


title: E7.0 single cell region A (20_L1_I007)

description:
Sample name: 20_L1_I007.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTBXD87zRwwJzOBz995


title: E7.0 single cell region A (1_L1_I001)

description:
Sample name: 1_L1_I001.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTBXH4zTyJzOBz366


title: E7.0 single cell region A (19_L1_I006)

description:
Sample name: 19_L1_I006.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTBXD86zRwwJzOBz1319


title: HypoTBXD85zRwwJzOBz1198


title: HypoTBXD86zRwwJzOBz1320


title: HypoTBXH20zKccJzOBz534


title: HypoTBXD86zRwwJzOBz1321


title: E7.0 single cell region A (17_L1_I004)

description:
Sample name: 17_L1_I004.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTBXH19zTyJzOBz533


title: HypoTBXD85zRwwJzOBz1196


title: E7.0 single cell region A (16_L1_I003)

description:
Sample name: 16_L1_I003.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTBXD84zRwwJzOBz1169


title: HypoTBXD84zRwwJzOBz1155


title: HypoTBXD84zRwwJzOBz1168


title: HypoTBXD9zTyJzOBz299


title: HypoTBXD79zRwwJzOBz928


title: HypoTBXD79zRwwJzOBz1041


title: HypoTBXD79zRwwJzOBz929


title: HypoTBXD87zRwwJzOBz997


title: HypoTBXD75zRwwJzOBz1080


title: RNA_WT_rep2

city: Urbana

first: Hans

middle: Tomas

last: Rube

state: Illinois

address: 1110 West Green Street

department: Physics

institute: University of Illinois at Urbana Champaign

data_processing:
ChIP-Seq: The MeCP2 ChIP-seq and Input reads were aligned to the mm9 reference genome using Bowtie 2 using the options --sensitive --score-min L,-1.5,-0.3. Reads mapping to multiple sites in the genome were discarded. PCR-duplicates were removed by keeping at most one mapped read at each position in the genome. The fragment coverages of the ChIP and Input sets were calculated after extending the map coordinate by 200 bp  (the experimentally determined fragment length).
MNase-Seq:The MNase-seq reads were aligned to the mm9 reference genome using Bowtie 2 using the options --sensitive --score-min L,-1.5,-0.3. Reads mapping to multiple sites in the genome were discarded. The nucleosome occupancy was calculated by extending the map coordinates 146 bp and tabulating the coverage.
RNA-Seq: The RNA-seq reads were aligned to the mm9 refGene using TopHat 2. Only reads mapping uniquely, in proper pairs, and to the same chromosome were retained, leaving 65M, 55M and 56M reads in the WT replicates and 58M, 51M and 51M reads in the KO replicates. Differential gene expression and statistical significance were calculated for the refGene transcripts using cufflinks and cuffdiff with default parameters but keeping only uniquely mapped and proper read pairs.
Bisulfite-Seq: Deduplication of the raw sequencing reads resulted in 161M and 152M reads constituting combined 21x genomic coverage. We aligned the deduplicated reads to the mm9 reference assembly using Bismark (Krueger et al. 2011) package with Bowtie2 aligner, using default Bowtie2 alignment scoring. Methylation calls were performed by Bismark package.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files were generated using bedTools genomeCoverageBed and UCSC bedGraphToBigWig. The genes.fpkm_tracking were generated using cufflinks. The Bisulfite-Seq tables were generated usin Bismark.

growth_protocol: Animal care and experimental procedures were conducted in accordance with institution guidelines and complied with the National Institute of Health (NIH) policy. To ensure minimum and equal olfactory stimulation, experimental animals are individually housed in circulating clean air cages for minimum of 24 hours before use. Male Mecp2-/y (KO) and Mecp2+/y (WT) littermates were obtained by crossing heterozygous Mecp2-/+ female (Jackson Laboratory strain: B6.129P2(C)-Mecp2tm1.1Bird/J, stock number 003890) (Guy et al. 2001) with inbred C57BL/6J male.

extract_protocol:
Olfactory neuroepithelia were collected from three different WT and KO mice respectively. Total RNA was extracted with TRIzol Reagent (Life Technologies, Grand Island, NY). The quality of the RNA was determined with an Agilent 2100 BioAnalyzer. Equal amounts of total RNA (13 µg) were used for subsequent isolation of mRNA using Dynabeads mRNA purification kit (Invitrogen). Construction of RNA-seq libraries was done using NEXTflex Directional RNA-Seq kit (Bioo Scientific). cDNA library sequencing was performed with Illumina Hi-Seq 2500 at QB3 Vincent J. Coates Genomics Sequencing Laboratory in the UC Berkeley.
library construction protocol

tag: strain background

value: B6.129P2(C)-Mecp2tm1.1Bird/J X C57BL/6J

tag: genotype/variation

value: wild-type, MeCP2(+/y)

tag: age

value: 8 weeks

value: Olfactory epithelium


title: RNA_MeCP2_KO_rep2

value: knockout, MeCP2(-/y)


title: RNA_MeCP2_KO_rep3


title: RNA_MeCP2_KO_rep1


title: HypoTBXD75zRwwJzOBz1014


title: RNA_WT_rep3


title: HypoTBXD73zRwwJzOBz1264


title: HypoTBXD73zRwwJzOBz1263


title: RNA_WT_rep1


title: HypoTBXD71zRwwJzOBz922


title: HypoTBXD74zRwwJzOBz1121


title: HypoTBXD74zRwwJzOBz1120


title: E7.0 single cell region A (18_L1_I005)

description:
Sample name: 18_L1_I005.A
processed data file: E7.0.single.cell.gene.expression.txt


title: HypoTBXD70zRwwJzOBz1245


title: HypoTBXD71zRwwJzOBz921


title: HypoTBXD74zRwwJzOBz1071


title: HypoTBXD85zRwwJzOBz1197


title: HypoTBXD6zTyJzOBz292


title: HypoTBXD70zRwwJzOBz1246


title: HypoTBXD9zTyJzOBz297


title: HypoTBXD71zRwwJzOBz891


title: Embryo 3 section 11 position L

description:
Sample name: E3.11L
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx

data_processing:
The reads for all samples are mapped to the mm10 using Tophat v2.0.8b with parameter: -p 20 -g 1 -N 4 --read-edit-dist 4 --microexon-search
The mapped reads were used to estimate transcriptomic alignment rates, and were also used as input in Cufflinks v2.1.1 (Trapnell et al., 2013) to quantify gene expression levels (fragment per kilobase per million, FPKM) with the default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each embryo

growth_protocol: Embryos from late mid-streak mouse were embedded with OCT and subjected to cryosection.

extract_protocol:
RNA from LCM samples were extracted by 5M GuSCN (Invitrogen, # 20012-043), then RNA was precipitated by ethanol with the help of RNA carrier.
Libraries were constructed using illumina Nextera XT DNA sample preparation kit

treatment_protocol: Sample from sections were laser-microdissected and collected for single-cell based RNA sequencing.

tag: embryo

tag: section

tag: position

value: L


title: Embryo 3 section 11 position A

description:
Sample name: E3.11A
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD6zTyJzOBz291

value: male


title: Embryo 3 section 10 position R

description:
Sample name: E3.10R
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx

value: R


title: HypoTBXD68zRwwJzOBz979

value: high fat


title: Embryo 3 section 11 position R

description:
Sample name: E3.11R
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: Embryo 3 section 10 position L

description:
Sample name: E3.10L
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD68zRwwJzOBz978


title: HypoTBXD66zRwwJzOBz941


title: HypoTBXD68zRwwJzOBz977


title: Embryo 3 section 10 position P

description:
Sample name: E3.10P
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx

value: P


title: Embryo 3 section 10 position A

description:
Sample name: E3.10A
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx

value: A


title: HypoTBXD64zRwwJzOBz1114


title: HypoTBXD64zRwwJzOBz1187


title: HypoTBXD64zRwwJzOBz1113


title: Embryo 3 section 11 position P

description:
Sample name: E3.11P
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: Embryo 3 section 9 position L

description:
Sample name: E3.9L
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: Embryo 3 section 9 position R

description:
Sample name: E3.9R
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD70zRwwJzOBz1244


title: HypoTBXD62zRwwJzOBz1049


title: HypoTBXD62zRwwJzOBz1051


title: HypoTBXD61zRwwJzOBz1146


title: Embryo 3 section 9 position P

description:
Sample name: E3.9P
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD62zRwwJzOBz1050


title: Embryo 3 section 9 position A

description:
Sample name: E3.9A
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD61zRwwJzOBz1144


title: HypoTBXD73zRwwJzOBz1262


title: HypoTBXD5zTyJzOBz504


title: HypoTBXD66zRwwJzOBz896


title: Embryo 3 section 8 position R

description:
Sample name: E3.8R
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD61zRwwJzOBz1145


title: Embryo 3 section 8 position A

description:
Sample name: E3.8A
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD60zRwwJzOBz873


title: HypoTBXD56zRwwJzOBz832


title: HypoTBXD60zRwwJzOBz1107


title: HypoTBXD56zRwwJzOBz830


title: Embryo 3 section 8 position L

description:
Sample name: E3.8L
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD55zRwwJzOBz972


title: HypoTBXD66zRwwJzOBz897


title: HypoTBXD56zRwwJzOBz831


title: HypoTBXD60zRwwJzOBz1106


title: HypoTBXD5zTyJzOBz494


title: Embryo 3 section 7 position R

description:
Sample name: E3.7R
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD5zTyJzOBz505


title: Embryo 3 section 7 position P

description:
Sample name: E3.7P
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD50zRwwJzOBz1162


title: HypoTBXD55zRwwJzOBz971


title: HypoTBXD55zRwwJzOBz970


title: Embryo 3 section 7 position A

description:
Sample name: E3.7A
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD75zRwwJzOBz1013


title: HypoTBXD51zRwwJzOBz879


title: Embryo 3 section 7 position L

description:
Sample name: E3.7L
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: Embryo 3 section 6 position L

description:
Sample name: E3.6L
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: Embryo 3 section 6 position R

description:
Sample name: E3.6R
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: Embryo 3 section 6 position A

description:
Sample name: E3.6A
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD51zRwwJzOBz877


title: HypoTBXD50zRwwJzOBz1161


title: HypoTBXD51zRwwJzOBz878


title: HypoTBXD50zRwwJzOBz1160


title: Embryo 3 section 5 position R

description:
Sample name: E3.5R
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD49zRwwJzOBz958


title: Embryo 3 section 5 position L

description:
Sample name: E3.5L
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD49zRwwJzOBz959


title: Embryo 3 section 6 position P

description:
Sample name: E3.6P
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD45zRwwJzOBz1117


title: HypoTBXD48zRwwJzOBz1128


title: HypoTBXD48zRwwJzOBz1127


title: HypoTBXD49zRwwJzOBz883


title: HypoTBXD44zRwwJzOBz1024


title: HypoTBXD48zRwwJzOBz965


title: HypoTBXD45zRwwJzOBz1148


title: Embryo 3 section 5 position P

description:
Sample name: E3.5P
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: Embryo 3 section 5 position A

description:
Sample name: E3.5A
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD45zRwwJzOBz1147


title: HypoTBXD44zRwwJzOBz918


title: HypoTBXD39zTyJzOBz251


title: HypoTBXD44zRwwJzOBz917


title: Embryo 3 section 4 position R

description:
Sample name: E3.4R
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: Embryo 3 section 3 position L

description:
Sample name: E3.3L
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: Embryo 3 section 4 position L

description:
Sample name: E3.4L
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD40zTyJzOBz668


title: HypoTBXD43zRwwJzOBz1138


title: HypoTBXD36zTyJzOBz176


title: Embryo 3 section 4 position P

description:
Sample name: E3.4P
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD36zTyJzOBz175


title: HypoTBXD40zTyJzOBz667


title: HypoTBXD39zTyJzOBz252


title: Embryo 3 section 4 position A

description:
Sample name: E3.4A
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD38zTyJzOBz708


title: HypoTBXD36zTyJzOBz174


title: HypoTBXD43zRwwJzOBz1137


title: Embryo 3 section 2 position R

description:
Sample name: E3.2R
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD34zTyJzOBz472


title: HypoTBXD38zTyJzOBz709


title: HypoTBXD43zRwwJzOBz1136


title: HypoTBXD34zTyJzOBz473


title: HypoTBXD32zTyJzOBz558


title: Embryo 3 section 3 position A

description:
Sample name: E3.3A
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD39zTyJzOBz250


title: HypoTBXD40zTyJzOBz666


title: Embryo 3 section 2 position L

description:
Sample name: E3.2L
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: Embryo 3 section 3 position R

description:
Sample name: E3.3R
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD32zTyJzOBz556


title: HypoTBXD24zTyJzOBz379


title: HypoTBXD38zTyJzOBz800


title: HypoTBXD32zTyJzOBz557


title: Embryo 3 section 2 position P

description:
Sample name: E3.2P
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: Embryo 3 section 3 position P

description:
Sample name: E3.3P
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD24zTyJzOBz378


title: HypoTBXD21zTyJzOBz296


title: HypoTBXD24zTyJzOBz377


title: Embryo 3 section 1 position P

description:
Sample name: E3.1P
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD20zTyJzOBz191


title: HypoTBXD20zTyJzOBz192


title: HypoTBXD20zTyJzOBz559


title: Embryo 2 section 11 position R

description:
Sample name: E2.11R
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTBXD21zTyJzOBz293


title: HypoTBXD16zTyJzOBz221


title: Embryo 3 section 1 position A

description:
Sample name: E3.1A
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: Embryo 2 section 11 position P

description:
Sample name: E2.11P
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: Embryo 2 section 11 position L

description:
Sample name: E2.11L
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: Embryo 2 section 11 position A

description:
Sample name: E2.11A
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTBXD19zTyJzOBz369


title: HypoTBXD19zTyJzOBz371


title: HypoTBXD16zTyJzOBz220


title: HypoTBXD15zTyJzOBz278


title: HypoTBXD16zTyJzOBz222


title: HypoTBXD19zTyJzOBz370


title: HypoTBXD15zTyJzOBz1415


title: Embryo 3 section 2 position A

description:
Sample name: E3.2A
processed data files: E3.gene.expression.txt, E3_mapping.ratio.xlsx


title: HypoTBXD14zTyJzOBz746


title: HypoTBXD15zTyJzOBz1414


title: HypoTBXD21zTyJzOBz294


title: HypoTBXD14zTyJzOBz745


title: HypoTBXD14zTyJzOBz698


title: HypoTBXD12zTyJzOBz838


title: HypoTBXD12zTyJzOBz547


title: HypoTBXD12zTyJzOBz546


title: HypoTBXD11zTyJzOBz795


title: HypoTBXD11zTyJzOBz847


title: ES si- (1)

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

description: ES cells transfected with scrambled siRNA ( replicate 1)

data_processing:
RNA-seq reads were aligned to the mm9 genome assembly using tophat  (Galaxy Tool Version 1.1.2)
Cuffdiff (Galaxy Tool Version 2.2.1.2) was used to find genes differentially expressed between the two conditions
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff output files corresponding to gene and transcript differential expression

source_name: 46C ES cells

growth_protocol: ES cells expressing a TAP-tagged Atad2 were cultured according to a standard in DMEM medium containing LIF (ESG1107, Millipore), non essential aminoacids, antibiotics (Penicillin and streptomycin), beta-mercaptoethanol and supplemented with 15% fetal bovine serum (Invitrogen), on 0.1% gelatin-coated tissue culture dishes at 37°C in CO2 incubator.

extract_protocol:
Total RNA was isolated using RNAeasy kit from Quiagen following the manufacturer´s instruction.
Approximately 500ng of total RNA were used for sequencing library preparation with the TruSeq RNA protocol from Illumina.
Four libraries were multiplexed in a single lane (10pm) and subsequently sequenced on a HiSeq1000 (Illumina) with the paired end protocol and 50 cycle each.

treatment_protocol: 46C ES tag cells were treated with an active anti-Atad2 siRNA (si Atad2) and an inactive siRNA (si ctrl)

tag: cell type

value: 46C ES cells

tag: knock in

value: Atad2 TAP-tag

tag: si rna

value: si control


title: ES wild type_antiHA_antiFlag

library_source: genomic

data_processing:
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie for illumina  (Galaxy Tool Version 1.1.2)
peaks were called using Sicer (Galaxy Tool Version 0.0.1)
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using Sicer (Galaxy Tool Version 0.0.1)

molecule: genomic DNA

growth_protocol: ES cells expressing a TAP-tagged Atad2 or not (wild type 46C ES cells) were cultured according to a standard in DMEM medium containing LIF (ESG1107, Millipore), non essential aminoacids, antibiotics (Penicillin and streptomycin), beta-mercaptoethanol and supplemented with 15% fetal bovine serum (Invitrogen), on 0.1% gelatin-coated tissue culture dishes at 37°C in CO2 incubator.

extract_protocol:
The DNA was precipitated with ethanol in the presence of glycogen, and solubilized in water. The purified DNA was size-selected at 150 base pairs and processed for sequencing onto an Illumina analyzer
Approximately 10ng of IP DNA from each samples were used for library preparation using the TruSeq ChIP Sample Prep protocol (Illumina) as described in the TruSeq ChIP Sample Preparation Data Sheet (Illumina).

treatment_protocol: ChIP-seq was perfomed after formaldehyde crosslinking and a tandem purification of Atad2-associated regions by anti-Ha followed by anti-Flag immunoprecipitation.

value: Atad2 wild-type

tag: chip antibody

value: Anti-HA and anti-Flag


title: Embryo 2 section 10 position R

description:
Sample name: E2.10R
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx

tag: strain

tag: developmental stage

value: Late mid-streak embryo (E7.0)


title: ES Atad2tag_antiHA_antiFlag


title: HypoTBXA8zPgnJzOBz1423


title: Embryo 2 section 9 position R

description:
Sample name: E2.9R
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: Embryo 2 section 10 position P

description:
Sample name: E2.10P
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: Embryo 2 section 9 position L

description:
Sample name: E2.9L
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: ES siATAD2 (2)

description: ES cells transfected with siATAD2 ( replicate 2)

value: si Atad2


title: HypoTBXA8zPgnJzOBz1359


title: ES siATAD2 (1)

description: ES cells transfected with siATAD2 ( replicate 1)


title: Embryo 2 section 9 position P

description:
Sample name: E2.9P
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: Embryo 2 section 10 position L

description:
Sample name: E2.10L
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTBXA7zPgnJzOBz313


title: ES wild type_antiHA

treatment_protocol: Native ChIP protocol with a single anti-Ha immunoprecipitation

tag: chip antibodies

value: Anti-HA


title: ES_Atad2tag_AntiHA


title: HypoTBXA7zPgnJzOBz312


title: HypoTBXA7zPgnJzOBz311


title: Embryo 2 section 9 position A

description:
Sample name: E2.9A
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: ES si- (2)

description: ES cells transfected with scrambled siRNA ( replicate 2)


title: HypoTBXA4zPgnJzOBz308


title: HypoTBXA4zPgnJzOBz309


title: Embryo 2 section 10 position A

description:
Sample name: E2.10A
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: Embryo 2 section 8 position L

description:
Sample name: E2.8L
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: Embryo 2 section 8 position R

description:
Sample name: E2.8R
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTBXA8zPgnJzOBz1424


title: HypoTBXA2zPgnJzOBz816


title: HypoTBXA2zPgnJzOBz108


title: HypoTBXA24zPgnJzOBz209


title: HypoTBXA2zPgnJzOBz107


title: Embryo 2 section 8 position A

description:
Sample name: E2.8A
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: Embryo 2 section 7 position R

description:
Sample name: E2.7R
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTBXA14zPgnJzOBz200


title: HypoTBXA24zPgnJzOBz208


title: Embryo 2 section 8 position P

description:
Sample name: E2.8P
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: Embryo 2 section 7 position L

description:
Sample name: E2.7L
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTBXA12zPgnJzOBz672


title: HypoTBXA12zPgnJzOBz670


title: HypoTBXA11zPgnJzOBz580


title: HypoTBXA14zPgnJzOBz199


title: HypoTBXA14zPgnJzOBz201


title: HypoTBXA11zPgnJzOBz579


title: Embryo 2 section 6 position R

description:
Sample name: E2.6R
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTBUBzBnJzOBz506

value: BUB/BnJ


title: HypoTBUBzBnJzOBz507


title: HypoTBUBzBnJzOBz399


title: HypoTBXA11zPgnJzOBz1362


title: HypoTBALBzcJzOBz807

value: BALB/cJ


title: Embryo 2 section 6 position L

description:
Sample name: E2.6L
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTBXA4zPgnJzOBz307


title: Embryo 2 section 6 position P

description:
Sample name: E2.6P
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: Embryo 2 section 6 position A

description:
Sample name: E2.6A
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTBALBzcJzOBz806


title: Embryo 2 section 7 position P

description:
Sample name: E2.7P
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: Embryo 2 section 5 position R

description:
Sample name: E2.5R
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTAzJzOBz1430

value: A/J


title: Embryo 2 section 5 position L

description:
Sample name: E2.5L
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx

value: L


title: HypoTBALBzcJzOBz589

value: male


title: HypoTAXB8zPgnJzOBz628


title: HypoTAXB6zPgnJzOBz540


title: HypoTAXB5zPgnJzOBz1422


title: HypoTAXB5zPgnJzOBz1421


title: HypoTAzJzOBz1432


title: HypoTAzJzOBz1431


title: Embryo 2 section 4 position L

description:
Sample name: E2.4L
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: Embryo 2 section 7 position A

description:
Sample name: E2.7A
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTAXB5zPgnJzOBz1420


title: HypoTAXB19zPgnJzOBz755


title: HypoTAXB8zPgnJzOBz629


title: HypoTAXB8zPgnJzOBz627


title: HypoTAXB19zPgnJzOBz286


title: Embryo 2 section 5 position A

description:
Sample name: E2.5A
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTAXB2zPgnJzOBz265


title: Embryo 2 section 4 position P

description:
Sample name: E2.4P
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTAXB2zPgnJzOBz264


title: Embryo 2 section 4 position A

description:
Sample name: E2.4A
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTAXB19bzPgnJzOBz276


title: HypoTAXB19zPgnJzOBz285


title: HypoTAXB19bzPgnJzOBz1205


title: Embryo 2 section 3 position P

description:
Sample name: E2.3P
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: Embryo 2 section 3 position R

description:
Sample name: E2.3R
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx

value: R


title: HypoTAXB19bzPgnJzOBz277

value: high fat


title: HypoTAXB19azPgnJzOBz788


title: Embryo 2 section 3 position A

description:
Sample name: E2.3A
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTAXB19azPgnJzOBz789


title: Embryo 2 section 2 position L

description:
Sample name: E2.2L
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTAXB15zPgnJzOBz573


title: HypoTAXB15zPgnJzOBz572


title: HypoTAXB15zPgnJzOBz571


title: HypoTAXB19azPgnJzOBz787


title: HypoTAXB6zPgnJzOBz541


title: Embryo 2 section 4 position R

description:
Sample name: E2.4R
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTAXB13zPgnJzOBz1387


title: HypoTAXB13zPgnJzOBz1388


title: Embryo 2 section 2 position P

description:
Sample name: E2.2P
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx

value: P


title: F3 2nd trigger rep 3

city: Tel-Aviv

first: Leah

last: Houri-Ze'evi

address: Haim Levanon

department: Neurobiology

country: Israel

institute: Tel-Aviv University

description: Sample 24

data_processing:
Adapter trimming - cutadapt
Quality examination - fastQC
Alignment - butter
Counting - htseq count
Comparisons - DESeq2
Genome_build: ce10
Supplementary_files_format_and_content: sum of counts

source_name: F3 2nd trigger_Whole animal

extract_protocol:
TRIZOL
NEBNext® Multiplex Small RNA Library Prep Set for Illumina®

treatment_protocol: RNAi by feeding/regular growth on emtpy vector bacteria

value: WT

value: Day 1 adult

tag: sample group

value: F3 - repetitive RNAi exposure in P0&F1

tag: tissue

value: Whole animal


title: Embryo 2 section 2 position A

description:
Sample name: E2.2A
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx

value: A


title: F3 2nd trigger rep 2

description: Sample 23


title: HypoTAKRzJzOBz1400

value: AKR/J

tag: Sex


title: Embryo 2 section 3 position L

description:
Sample name: E2.3L
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx

value: Late mid-streak embryo (E7.0)


title: F3 2nd trigger rep 1

description: Sample 22


title: HypoTAKRzJzOBz1399

tag: diet


title: HypoTAXB12zPgnJzOBz1346


title: HypoTAKRzJzOBz1398


title: Embryo 2 section 1 position P

description:
Sample name: E2.1P
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: F3 control RNAi rep 3

description: Sample 21

source_name: F3 control RNAi_Whole animal

value: F3 - RNAi exposure in the P0 generation


title: F3 control RNAi rep 2

description: Sample 20


title: HypoT129X1zSvJzOBz1302


title: HypoT129X1zSvJzOBz1303


title: HypoT129X1zSvJzOBz1301


title: F3 control RNAi rep 1

description: Sample 19


title: Embryo 2 section 1 position A

description:
Sample name: E2.1A
processed data files: E2.gene.expression.txt, E2_mapping.ratio.xlsx


title: HypoTAXB13zPgnJzOBz1462


title: F2 2nd trigger rep 3

description: Sample 18

source_name: F2 2nd trigger_Whole animal

value: F2 - repetitive RNAi exposure in P0&F1


title: Embryo 1 section 11 position R

description:
Sample name: E1.11R
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Embryo 1 section 11 position P

description:
Sample name: E1.11P
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Embryo 1 section 11 position L

description:
Sample name: E1.11L
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: HOMO2

first: Jacqueline

middle: Gire

last: O'Rourke

address: 8700 Beverly Blvd

institute: Cedars Sinai Medical Center

description: 3 mo RNA Seq C9null

data_processing:
fastq reads were alignd to the mouse genome (mm9) with tophat v2.0.8b with parameters -G --no-novel-juncs
bam files were annotated in using Partek software to generate RPKM numbers for each Refseq annotated gene
Genome_build: mm9 (3 month) and mm10 (17 month)

source_name: spinal cord (3 months)

growth_protocol: Mouse  spinal cords (lumbar region) were collected at 3 month and 17 months

extract_protocol:
Lumbar spinal cords were flash frozen on dry ice, and RNA was harvested using Trizol. Total RNA isolated using the PureLink™ RNA Mini Kit (Catalog # 12183018A) and 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard  Illumina (3 month) or Iontorrent (17 month) protocols.  RNA sequencing libraries were constructed with the TruSeq RNA Sample Prep Kits v2 from Illumina. 9 RNA samples were indexed with different adapters and pooled for sequencing.

value: lumbar spinal cord

tag: genotype


title: F2 2nd trigger rep 2

description: Sample 17


title: HOMO1

description: 3 mo RNA Seq C9null


title: Evx1as ChIRP D4

city: Rochester

first: jinlong

last: lu

address: 213 Hutchinson Hall

institute: University of Rochester

description:
none
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, ChIRP retrived RNA was fragmentated by NEBNext Magnesium RNA Fragmentation Module at 94 ℃ for 210 seconds. The fragementated RNA was reverse transcribed by SuperScript III First-Strand Synthesis System for RT-PCR kit (Life Technology), 2'nd strand was then synthesized by NEBNext mRNA Second Strand Synthesis Module , the end repair, dA-tailing and adaptor ligation were also following the instruments by respect module. the adaptor for the libary was sythersized from IDT with the first 7nt is "TCACGTT" as a barcode. After liagation, the DNA was amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Genome Analyzer following the manufacturer's protocols.

data_processing:
Basecalls performed using CASAVA version
Sequenced reads were trimmed for barcode sequence
ChIRP retrived DNA-Seq reads were aligned to the mm9 genome assembly using Bowtie version 1.0.0 with the default parameters
Peaks of each sample were called using MACS v. 1.4.2
Genome_build: mm9

source_name: 46C mES cells

growth_protocol: Wild-type ESCs were maintained in standard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). Differentiated ESCs were cultured in standard ES medium without LIF.

extract_protocol:
Wild-type  ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
ChIRP retrieved DNA-seq were prepared by library preparation modules (New England Biolabs)

value: embryonic stem cells

tag: treatment

value: LIF withdrawal, day4

tag: chirp probes

value: ChIRP probes targeting Evx1as  mRNA


title: HEMI3

description: 3 mo RNA Seq C9null


title: HEMI2

description: 3 mo RNA Seq C9null


title: CTR3

description: 3 mo RNA Seq C9null


title: F2 control RNAi rep 3

description: Sample 15

source_name: F2 control RNAi_Whole animal

value: F2 - RNAi exposure in the P0 generation


title: F2 2nd trigger rep 1

description: Sample 16


title: Embryo 1 section 10 position L

description:
Sample name: E1.10L
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx

tag: embryo

value: L


title: F2 control RNAi rep 2

description: Sample 14


title: CTR1

description: 3 mo RNA Seq C9null


title: Embryo 1 section 10 position P

description:
Sample name: E1.10P
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx

tag: section


title: CTR2

description: 3 mo RNA Seq C9null


title: F2 control RNAi rep 1

description: Sample 13


title: Bisulfite_WT_rep1

extract_protocol:
500 nanograms (ngs) of DNA was isolated from two wild-type olfactory epithelia (OE) and bisulfite converted using the EZ DNA methylation-Lightning kit (Zymo Research, Irvine, CA). 100 ngs of bisulfite converted DNA from each OE was then used to make indexed, Illumina sequencing compatible libraries using the Epignome Methyl-Seq Kit (Epicentre, Madison WI) and Epignome Index PCR Primers (Epicentre). Each bisulfite converted OE sample had a separate sequencing index allowing for paired end sequencing of both samples in one lane. Whole genome bisulfite-treated DNA libraries were sequenced with 100 pb paired end reads by Beijing Research Institute (BGI), Sacramento, CA. We performed sequencing in two biological replicates obtaining 173M and 161M pair-end reads, respectively.
library construction protocol

tag: strain background

value: B6.129P2(C)-Mecp2tm1.1Bird/J X C57BL/6J

tag: genotype/variation

value: wild-type, MeCP2(+/y)

tag: age

value: 8 weeks

value: Olfactory epithelium


title: HOMO3

description: 3 mo RNA Seq C9null


title: F1 2nd trigger rep 3

description: Sample 12

source_name: F1 2nd trigger_Whole animal

value: WT

value: Day 1 adult

value: F1 - repetitive RNAi exposure


title: MNase_WT

extract_protocol:
For MNase digestion, olfactory neuroepithelia were harvested from Mecp2 KO and WT littermate adult mice and resuspended in PIPES buffer (5mM PIPES, 85mM KCl, 0.5% NP-40, pH 8.0) at 4 °C. After disruption with a dounce homogenizer, nuclei were collected by centrifugation. Collected nuclei were washed once, resuspended in the MNase buffer and digested with 0.5 units of MNase (New England Biolabs, Ipswich, MA) per microliter volume for 15 min at 37 °C. MNase digestion was stopped by putting the samples on ice and adding EDTA to a concentration of 10 mM. After digestion with 0.1 µg/µl RNase A (Fermentas, Pittsburgh, PA), DNAs were purified with DNA Purification Magnetic Beads (Life Technologies, Grand Island, NY), and pellets were dissolved in H2O. DNA fragments corresponding to mononucleosomes (about 150 bp) were confirmed by using 2100 Bioanalyzer (Agilent Technologies Santa Clara, CA). MNase-seq libraries were prepared as described (Bioo Scientific, Austin, TX) using 5140-01 NEXTflex DNA Sequencing kit and 514101 NEXTflex DNA Barcodes-6. High throughput sequencing was done with Illumina Hi-Seq 2000.
library construction protocol


title: Input_WT_rep2

extract_protocol:
ChIP-seq was done based on methods established previously (Li, Y et al. 2014). Two independent chromatin immunoprecipitation assays were performed using MAGnify chromatin immunoprecipitation kit (Life Technologies, Grand Island, NY). Specifically, main olfactory neuroepithelia (MOE) were dissected from the nasal cavity and dissociated mechanically via trituration in phosphate buffer saline (PBS). Equal number of cells was used for subsequent steps. Protein-DNA complexes were cross linked by incubating dissociated MOE cells with 1% formaldehyde for 5 minutes on a rocker at room temperature. The cross-linking was quenched by adding Glycine. After washing off the media, MOE cells were lysed briefly in SDS containing buffer followed by sonication for 15 minutes with 30 second intervals to shear genomic DNA using a BioruptorTM 300 (Diagenode, Denville, NJ). Sheared DNA was evaluated by 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and selected for sizes ranging between 200 bp and 300 bp. Each sheared genomic DNA preparation was split into two equal portions and incubated with MeCP2 antibody (Diagenode, pAb-052-050) or Rabbit IgG (Millipore, Cat# 12-370) for the negative control. MeCP2-genomic DNA complexes were pulled down and reverse cross-linked by DNase-free Proteinase K and subsequently purified. MeCP2 ChIP-seq and input DNA library were prepared according to manufacturer’s instruction (Bioo Scientific, Austin, TX) using 5143-01 NEXTflex ChIP-Seq kit and 514120 NEXTflex ChIP-Seq Barcodes-6. ChIP and Input DNAs were PCR amplified, cleaned up and sequenced on Illumina Hi-Seq 2000 at QB3 Vincent J. Coates Genomics Sequencing Laboratory in the UC Berkeley.
library construction protocol


title: Embryo 1 section 9 position R

description:
Sample name: E1.9R
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx

tag: position

value: R


title: F1 2nd trigger rep 2

description: Sample 11

value: Whole animal


title: Input_WT_rep1


title: MeCP2_ChIP_WT_rep1

tag: chip antibody

value: MeCP2 antibody

tag: chip antibody vendor

value: Diagenode

tag: chip antibody cat. #


title: Embryo 1 section 10 position R

description:
Sample name: E1.10R
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx

tag: strain

tag: developmental stage

value: Late mid-streak embryo (E7.0)


title: HEMI1

description: 3 mo RNA Seq C9null

tag: tissue

value: lumbar spinal cord


title: F1 2nd trigger rep 1

description: Sample 10

tag: sample group


title: MeCP2_ChIP_WT_rep2


title: Embryo 1 section 9 position L

description:
Sample name: E1.9L
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Embryo 1 section 9 position P

description:
Sample name: E1.9P
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx

value: P


title: Evx1as ChIRP D0

description:
none
The library was constructed by library preparation modules (New England Biolabs) according to manufacturer's instructions. Briefly, ChIRP retrived RNA was fragmentated by NEBNext Magnesium RNA Fragmentation Module at 94 ℃ for 210 seconds. The fragementated RNA was reverse transcribed by SuperScript III First-Strand Synthesis System for RT-PCR kit (Life Technology), 2'nd strand was then synthesized by NEBNext mRNA Second Strand Synthesis Module , the end repair, dA-tailing and adaptor ligation were also following the instruments by respect module. the adaptor for the libary was sythersized from IDT with the first 7nt is "AGCTCAT" as a barcode. After liagation, the DNA was amplified by primer 1.0 (AATGATACGGCGACCACCGAGATCTACAC, synthersized from IDT) and 2.0 (CAAGCAGAAGACGGCATACGAGAT, synthersized from IDT) for 15 cycles. After this, the product was further purified and size selected by Ampure XP beads (Beckman Coulter). The library was sequenced on the Genome Analyzer following the manufacturer's protocols.

extract_protocol:
Wild-type ESCs were maintained in strandard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore).
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
ChIRP retrieved DNA-seq were prepared by library preparation modules (New England Biolabs)

tag: cell type

value: embryonic stem cells

value: ChIRP probes targeting Evx1as mRNA


title: Embryo 1 section 11 position A

description:
Sample name: E1.11A
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx

value: A


title: F1 control RNAi rep 3

description: Sample 9

source_name: F1 control RNAi_Whole animal

value: F1 - RNAi exposure in the P0 generation


title: Single HSC H9_old

city: Oxford

first: Claus

last: Nerlov

address: John Radcliffe Hospital, University of Oxford

department: MRC Molecular Haematology Unit

country: United Kingdom

institute: Weatheral Institute of Molecular Medicine

description: Vwf-eGFP reporter mouse

data_processing:
RNA-Seq: Alignment by Tophat (version 2.0.10) to mm10 reference genome.
RNA-Seq: Non-uniquely mapped reads were discarded.
RNA-Seq: Expression values were quantified based on RefSeq using rpkmforgenes (Ramskold et al., 2009).
Genome_build: mm10
Supplementary_files_format_and_content: Read counts and RPKM values from RNA sequencing

source_name: Old Vwf-eGFP mouse

extract_protocol:
From single FACS sorted cells, cDNA was generated according to C1™ Single-Cell Auto Prep IFC for mRNA Sequencing (Fluidigm) using the Fluidigm C1 system and following manufacturer protocol.
Illumina sequenecing libraries were constructed in 96-well plates using the Illumina Nextera XT DNA Sample Preparation kit according to a protocol supplied by Fluidigm.
RNA-Seq samples were sequenced on Illumina HiSeq 2000

treatment_protocol: Cell populations isolated by FACS sorting from mouse Bone marrow

value: old (20-25 months)

value: Bone marrow

value: hsc

tag: phenotype


title: Bisulfite_WT_rep2

value: B6.129P2(C)-Mecp2tm1.1Bird/J X C57BL/6J

value: wild-type, MeCP2(+/y)

value: 8 weeks

value: Olfactory epithelium


title: F1 control RNAi rep 2

description: Sample 8

value: WT

value: Day 1 adult

value: Whole animal


title: Single HSC H7_old

description: Vwf-eGFP reporter mouse


title: Single HSC H6_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 9 position A

description:
Sample name: E1.9A
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx

value: Late mid-streak embryo (E7.0)


title: Single HSC H8_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 10 position A

description:
Sample name: E1.10A
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Single HSC H5_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 8 position R

description:
Sample name: E1.8R
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx

value: R


title: Single HSC H2_old

description: Vwf-eGFP reporter mouse


title: F1 control RNAi rep 1

description: Sample 7


title: Embryo 1 section 8 position L

description:
Sample name: E1.8L
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx

value: L


title: Single HSC H1_old

description: Vwf-eGFP reporter mouse


title: P0 RNAi rep 3

description: Sample 6

source_name: P0 RNAi_Whole animal

value: P0 RNAi exposure


title: Single HSC H12_old

description: Vwf-eGFP reporter mouse


title: Single HSC H11_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 8 position P

description:
Sample name: E1.8P
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx

value: P


title: Single HSC G9_old

description: Vwf-eGFP reporter mouse


title: Single HSC G6_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 8 position A

description:
Sample name: E1.8A
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx

value: A


title: Embryo 1 section 7 position R

description:
Sample name: E1.7R
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Control rep 3

description: Sample 3

source_name: Control_Whole animal

value: Control - no dsRNA exposure


title: Single HSC G3_old

description: Vwf-eGFP reporter mouse

value: old (20-25 months)


title: P0 RNAi rep 1

description: Sample 4


title: Single HSC G5_old

description: Vwf-eGFP reporter mouse

value: Bone marrow


title: Single HSC G2_old

description: Vwf-eGFP reporter mouse

value: hsc


title: Embryo 1 section 7 position L

description:
Sample name: E1.7L
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx

source_name: Mouse embryonic cells


title: Control rep 2

description: Sample 2


title: Single HSC H4_old

description: Vwf-eGFP reporter mouse


title: Single HSC G12_old

description: Vwf-eGFP reporter mouse


title: Single HSC G10_old

description: Vwf-eGFP reporter mouse


title: Single HSC F9_old

description: Vwf-eGFP reporter mouse


title: Single HSC F8_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 7 position P

description:
Sample name: E1.7P
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Single HSC F7_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 6 position R

description:
Sample name: E1.6R
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Single HSC F5_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 7 position A

description:
Sample name: E1.7A
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Embryo 1 section 6 position L

description:
Sample name: E1.6L
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: SIN rep1

city: Bethesda

first: Shaohe

last: Wang

state: Maryland

address: 9000 Rockville Pike, Bldg 30, Rm 403

department: DIR

institute: NIDCR, NIH

data_processing:
A genome index was first generated using the Ensembl  C. elegans genome WBcel235 and the Ensembl gene annotation file (version WBcel235.82)  by the command: “STAR --runThreadN 8 --runMode genomeGenerate --genomeDir <output  folder> --genomeFastaFiles <path to genome fasta> --sjdbGTFfile <path to .gtf gene  annotation file> --sjdbOverhang 49 --genomeSAindexNbases 12”.
Reads from all six samples were then mapped onto the genome using: “STAR --runThreadN 8 --genomeDir  <path to genome index> --readFilesIn <list of sequence files> --outFileNamePrefix <Prefix  for output files> --outFilterMismatchNmax 3 --outFilterMultimapNmax 10”.
Reads that uniquely mapped to annotated genes were counted by htseq-count using the command: “htseq-count --stranded=no <.sam file> <.gtf gene annotation file> > <output file name>”.
DESeq2 (Love et al., 2014) was used to perform differential analysis of gene  expression between different groups. First, a DESeq2 data set was created by: “(dds <-  DESeqDataSetFromMatrix(countData = countdata, colData = coldata, design = ~  genotype))”. Second, the size factors (normalization for sequence depth) for each group  were estimated by: “dds <- estimateSizeFactors(dds)”.
Differential analysis was performed by calling “dds <- DESeq(dds)” and pairwise  comparison was performed at a false discovery rate of 0.05 by: “res_group1_group2_alpha.05 <- results(dds, contrast=c("genotype", "group1", "group2"), alpha = .05)”.
Genome_build: WBcel235
Supplementary_files_format_and_content: csv file that contains counts, normalized expression (rpkm), log2FoldChange(SIN/WT), adjusted p-values as well as useful published information for each gene annotation and each of the six samples

source_name: adult worms

growth_protocol: Worms of the three genotypes were grown at 20°C on NGM plates seeded with OP50 E. coli as food

extract_protocol:
100 gravid adults were picked and washed in M9 for each sample. For OD1463 (WT) and OD1175 (SIN), worms homozygous for both transgenes and csr-1(tm892) were isolated from balanced heterozygous csr-1(tm892) mothers based on their differential motility. Total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA, 15596-026) and was assessed for quality using an Agilent Tapestation; the RNA Integrity Number (RIN) for samples ranged from 7.9 to 8.9.
RNA libraries were generated using Illumina’s TruSeq Stranded mRNA Sample Prep Kit using 500 ng of total RNA following manufacturer instructions. RNA libraries were multiplexed and sequenced with 50 basepair (bp) single end reads (SR50) to a depth of approximately 40 million reads per sample on an Illumina HiSeq2500 using V4 chemistry. All samples were run on the same lane.

value: whole worm

value: adult


title: WT rep2


title: WT rep1


title: Single HSC F1_old

description: Vwf-eGFP reporter mouse


title: Single HSC F10_old

description: Vwf-eGFP reporter mouse


title: Single HSC F12_old

description: Vwf-eGFP reporter mouse


title: Single HSC F3_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 6 position A

description:
Sample name: E1.6A
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: N2 rep2


title: Embryo 1 section 6 position P

description:
Sample name: E1.6P
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Control rep 1

description: Sample 1


title: Single HSC E7_old

description: Vwf-eGFP reporter mouse


title: N2 rep1


title: Embryo 1 section 5 position L

description:
Sample name: E1.5L
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: SIN rep2


title: Single HSC E3_old

description: Vwf-eGFP reporter mouse


title: Single HSC E8_old

description: Vwf-eGFP reporter mouse


title: Single HSC E5_old

description: Vwf-eGFP reporter mouse


title: Single HSC E12_old

description: Vwf-eGFP reporter mouse


title: Single HSC E11_old

description: Vwf-eGFP reporter mouse


title: Single HSC E1_old

description: Vwf-eGFP reporter mouse


title: Single HSC F4_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 5 position P

description:
Sample name: E1.5P
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Single HSC D9_old

description: Vwf-eGFP reporter mouse


title: Single HSC E10_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 5 position A

description:
Sample name: E1.5A
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Embryo 1 section 4 position R

description:
Sample name: E1.4R
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Single HSC E9_old

description: Vwf-eGFP reporter mouse


title: Single HSC D8_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 5 position R

description:
Sample name: E1.5R
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Embryo 1 section 4 position L

description:
Sample name: E1.4L
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Single HSC D12_old

description: Vwf-eGFP reporter mouse


title: Single HSC D4_old

description: Vwf-eGFP reporter mouse


title: Single HSC D6_old

description: Vwf-eGFP reporter mouse


title: Single HSC D7_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 4 position A

description:
Sample name: E1.4A
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Single HSC D1_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 4 position P

description:
Sample name: E1.4P
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Single HSC C9_old

description: Vwf-eGFP reporter mouse


title: Single HSC D11_old

description: Vwf-eGFP reporter mouse


title: Single HSC C8_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 3 position R

description:
Sample name: E1.3R
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Single HSC C5_old

description: Vwf-eGFP reporter mouse


title: Single HSC C7_old

description: Vwf-eGFP reporter mouse


title: Single HSC C6_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 3 position P

description:
Sample name: E1.3P
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Single HSC C1_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 3 position L

description:
Sample name: E1.3L
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Single HSC C4_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 2 position R

description:
Sample name: E1.2R
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Single HSC G1_old

description: Vwf-eGFP reporter mouse


title: Single HSC C3_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 2 position L

description:
Sample name: E1.2L
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Single HSC C12_old

description: Vwf-eGFP reporter mouse


title: Single HSC C11_old

description: Vwf-eGFP reporter mouse


title: Single HSC B9_old

description: Vwf-eGFP reporter mouse


title: Single HSC C10_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 2 position P

description:
Sample name: E1.2P
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Embryo 1 section 1 position P

description:
Sample name: E1.1P
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Single HSC B5_old

description: Vwf-eGFP reporter mouse


title: Single HSC B7_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 2 position A

description:
Sample name: E1.2A
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Single HSC B4_old

description: Vwf-eGFP reporter mouse


title: Single HSC B3_old

description: Vwf-eGFP reporter mouse


title: Single HSC B6_old

description: Vwf-eGFP reporter mouse


title: Embryo 1 section 1 position A

description:
Sample name: E1.1A
processed data files: E1.gene.expression.txt, E1_mapping.ratio.xlsx


title: Single HSC B11_old

description: Vwf-eGFP reporter mouse


title: SON-N ChIP-seq

city: BALTIMORE

first: Linda

last: Resar

address: 720 Rutland Avenue

department: Department of Medicine / Division of Hematology

institute: Johns Hopkins University

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie version 0.12.9 with the following standard parameters.
peaks were called using MACS version 1.4.2 using default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated using BEDtools.

organism: Homo sapiens

source_name: K562 cells

growth_protocol: RPMI 1640 medium with 10% fetal bovine serum

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Gnomegen Library Preparation Kits (Gnomegen) and ChIP-seq libraries were cluster-amplified and sequenced with the Illumina HiSeq2000 sequencer (50-nucleotide pair-ended read) following the manufacturer's protocols.

tag: cell line

value: Chronic myelogenous leukemia

value: SON antibody recognizing the N-terminus of SON (amino acids 74-88 of human SON)


title: Single HSC A7_old

description: Vwf-eGFP reporter mouse


title: Single HSC A6_old

description: Vwf-eGFP reporter mouse


title: Single HSC A8_old

description: Vwf-eGFP reporter mouse


title: SON-C ChIP-seq

value: SON antibody (Abcam, ab121759)


title: Single HSC A1_old

description: Vwf-eGFP reporter mouse


title: Single HSC A2_old

description: Vwf-eGFP reporter mouse


title: Single HSC A12_old

description: Vwf-eGFP reporter mouse


title: Single HSC A5_old

description: Vwf-eGFP reporter mouse


title: Single HSC A11_old

description: Vwf-eGFP reporter mouse


title: Wild Type_7

city: Baltimore

first: S. Amer

last: Riazuddin

address: 600 N. Wolfe St

institute: Johns Hopkins University School of Medicine

description: mRNA Library

data_processing:
The RNA sequencing (FASTQ) reads were subjected to two independent software protocols for analysis, namely TopHat2/DESeq and DNASTAR. In the first protocol, the sequencing reads were evaluated for their quality by FastQC followed by removal of adapter sequences. The processed sequencing reads were aligned to the human reference genome (hg19) with TopHat2 (version 2.0.3.1) using the default settings whereas duplicate reads from PCR amplification were removed by the rmdup option of samtools. Differential gene expression analysis was performed by the DESeq R/Bioconductor package with raw read count as input data. Raw read counts were calculated using the RPKM_count.py tool in the RSeQC software. In parallel, sequencing reads were processed and analyzed using Lasergene Genomics Suite (DNASTAR). The paired-end reads were assembled with SeqMan NGen version 11, using default parameters while ArrayStar Version 11 was used for a) normalization, b) differential gene expression, and c) statistical analysis of uniquely mapped paired-end reads with default parameters. The quantification and normalization were performed using RPKM value for each transcript.
Genome_build: hg19
Supplementary_files_format_and_content: xls files include RPKM values for each Sample

source_name: Wild Type, HEK293FT

growth_protocol: HEK293FT cells were grown in Dulbecco's Modified Eagle's Medium (DMEM) with 10% fetal bovine serum (FBS) at 37°C (5% CO2).

extract_protocol:
The cells were dissolved in the Trizol reagent (Invitrogen; Carlsbad, CA) 24-hours post-transfection to extract total RNA.
Total RNA was used for the preparation of next-generation messenger RNA (mRNA) sequencing libraries with the TruSeq RNA Sample Preparation v2 kit (Illumina) according to manufacturer's instructions. Briefly, four µg of total RNA was used for polyA mRNA selection using streptavidin-coated magnetic beads followed by thermal fragmentation of selected mRNA. The fragmented mRNA was used as a template for cDNA synthesis by reverse transcriptase with random primers. The cDNA was further converted into double stranded DNA and end-repaired to incorporate specific index adapters for multiplexing. The quality of RNA-Seq libraries was examined by qPCR and the DNA high sensitivity chip on Agilent 2100 Bioanalyzer (Agilent; Palo Alto, CA) according to manufacturer’s instructions. The libraries having unique index sequences were pooled in equimolar ratio for a final size selection (400-500bp) on a Caliper Lab XT DNA 750 chip (Caliper life Sciences, Hopkinton, MA).

treatment_protocol: HEK293FT cells were transfected with the expression vector (pT-RexTM-DEST30) harboring either the wild type or the mutant (C240*) FOXE3 ORF.

value: Transfected with wild type FOXE3 expression vector


title: Wild Type_8

description: mRNA Library


title: Single HSC A10_old

description: Vwf-eGFP reporter mouse


title: Wild Type_5

description: mRNA Library


title: Wild Type_6

description: mRNA Library


title: Single HSC H8_young

description: Vwf-eGFP reporter mouse

source_name: Young Vwf-eGFP mouse

value: young (2-3 months)


title: Wild Type_4

description: mRNA Library


title: Single HSC H5_young

description: Vwf-eGFP reporter mouse


title: Single HSC H6_young

description: Vwf-eGFP reporter mouse


title: Single HSC H4_young

description: Vwf-eGFP reporter mouse


title: Wild Type_3

description: mRNA Library


title: Single HSC B10_old

description: Vwf-eGFP reporter mouse


title: Single HSC H11_young

description: Vwf-eGFP reporter mouse


title: Wild Type_2

description: mRNA Library


title: Single HSC H3_young

description: Vwf-eGFP reporter mouse


title: Single HSC G8_young

description: Vwf-eGFP reporter mouse


title: Wild Type_1

description: mRNA Library


title: Single HSC G7_young

description: Vwf-eGFP reporter mouse


title: Single HSC G6_young

description: Vwf-eGFP reporter mouse


title: Single HSC G5_young

description: Vwf-eGFP reporter mouse


title: Single HSC G4_young

description: Vwf-eGFP reporter mouse


title: Mutant_7

description: mRNA Library

source_name: Mutant, HEK293FT

value: Transfected with mutant FOXE3 (p.C240*) expression vector


title: Single HSC G3_young

description: Vwf-eGFP reporter mouse


title: Single HSC A4_old

description: Vwf-eGFP reporter mouse


title: Mutant_6

description: mRNA Library


title: Mutant_5

description: mRNA Library


title: Single HSC G1_young

description: Vwf-eGFP reporter mouse


title: Single HSC G11_young

description: Vwf-eGFP reporter mouse


title: Single HSC F8_young

description: Vwf-eGFP reporter mouse


title: Single HSC H12_young

description: Vwf-eGFP reporter mouse


title: Single HSC F6_young

description: Vwf-eGFP reporter mouse


title: Single HSC F5_young

description: Vwf-eGFP reporter mouse


title: Single HSC F2_young

description: Vwf-eGFP reporter mouse


title: Single HSC F3_young

description: Vwf-eGFP reporter mouse


title: Mutant_2

description: mRNA Library


title: Mutant_1

description: mRNA Library


title: Mutant_3

description: mRNA Library


title: Single HSC E7_young

description: Vwf-eGFP reporter mouse


title: Control_8

description: mRNA Library

source_name: Control, HEK293FT

value: No FOXE3 Expression


title: Single HSC F1_young

description: Vwf-eGFP reporter mouse


title: Mutant_8

description: mRNA Library


title: Single HSC E6_young

description: Vwf-eGFP reporter mouse


title: Control_7

description: mRNA Library


title: Single HSC G2_young

description: Vwf-eGFP reporter mouse


title: Single HSC B2_old

description: Vwf-eGFP reporter mouse


title: Single HSC E2_young

description: Vwf-eGFP reporter mouse


title: Single HSC E3_young

description: Vwf-eGFP reporter mouse


title: Single HSC F9_young

description: Vwf-eGFP reporter mouse


title: Single HSC G12_young

description: Vwf-eGFP reporter mouse


title: Single HSC E11_young

description: Vwf-eGFP reporter mouse


title: Mutant_4

description: mRNA Library


title: Single HSC E1_young

description: Vwf-eGFP reporter mouse


title: Single HSC D9_young

description: Vwf-eGFP reporter mouse


title: Control_6

description: mRNA Library


title: Single HSC D8_young

description: Vwf-eGFP reporter mouse


title: Control_5

description: mRNA Library


title: Control_4

description: mRNA Library


title: Single HSC D7_young

description: Vwf-eGFP reporter mouse


title: Single HSC D3_young

description: Vwf-eGFP reporter mouse


title: Single HSC D6_young

description: Vwf-eGFP reporter mouse


title: Control_3

description: mRNA Library


title: Single HSC D1_young

description: Vwf-eGFP reporter mouse


title: Control_2

description: mRNA Library


title: Single HSC C5_young

description: Vwf-eGFP reporter mouse


title: Single HSC C7_young

description: Vwf-eGFP reporter mouse


title: Single HSC C8_young

description: Vwf-eGFP reporter mouse


title: Single HSC C6_young

description: Vwf-eGFP reporter mouse


title: Single HSC C4_young

description: Vwf-eGFP reporter mouse


title: Control_1

description: mRNA Library


title: Single HSC C1_young

description: Vwf-eGFP reporter mouse


title: Single HSC C11_young

description: Vwf-eGFP reporter mouse


title: Single HSC C3_young

description: Vwf-eGFP reporter mouse


title: Single HSC B7_young

description: Vwf-eGFP reporter mouse


title: Single HSC C12_young

description: Vwf-eGFP reporter mouse


title: Single HSC B2_young

description: Vwf-eGFP reporter mouse


title: Single HSC B12_young

description: Vwf-eGFP reporter mouse


title: Single HSC B5_young

description: Vwf-eGFP reporter mouse


title: Single HSC A9_young

description: Vwf-eGFP reporter mouse


title: Single HSC F10_young

description: Vwf-eGFP reporter mouse


title: Single HSC B1_young

description: Vwf-eGFP reporter mouse


title: Single HSC A7_young

description: Vwf-eGFP reporter mouse


title: Single HSC B3_young

description: Vwf-eGFP reporter mouse


title: Single HSC A5_young

description: Vwf-eGFP reporter mouse


title: PbfRNAi;o2 rep1

city: Piscataway

first: Joachim

last: Messing

state: NJ

address: 190 Frelinghuysen Rd

institute: Waksman Institute of Microbiology, Rutgers University

data_processing:
FastQC is used for quality control checks on raw sequence data combining with NGS QC TOOLKIT v2.3.3
Clean reads are aligned to the B73 reference genome (download in ftp://ftp.ensemblgenomes.org/pub/plants/release-26/fasta/zea_mays/dna/Zea_mays.AGPv3.26.dna.genome.fa) and the B73 reference gene model (download in ftp://ftp.ensemblgenomes.org/pub/plants/release-26/fasta/zea_mays/cdna/Zea_mays.AGPv3.26.cdna.all.fa) using tophat/bowtie2
The gene expression value is normalized as fragments per kilobase of transcript per million mapped reads (FPKM) from "Trapnell C, et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc 7(3):562-578."

organism: Zea mays

source_name: endosperm 16 day after pollination (DAP)

growth_protocol: The four maize genetic materials are cultivated in the field of the Institute of Plant Physiology & Ecology in Shanghai, China.

extract_protocol:
Total RNA are extracted from 16-DAP endosperm using TRIzol reagent (Invitrogen) and purified with the RNeasy Mini Kit (Qiagen). The mRNA are captured by Epicenter Ribo-Zero™ Magnetic Kit (No. MRZPL116-6).
The libraries are prepared according Illumina Standard library preparation kit (Illumina USA) and sequenced to generate 125nt paired-end reads on Illumina HiSeqTM2500

treatment_protocol: Fresh materials

value: endosperm


title: Single HSC A3_young

description: Vwf-eGFP reporter mouse


title: PbfRNAi;o2 rep2


title: o2 rep3


title: Single HSC A11_young

description: Vwf-eGFP reporter mouse


title: o2 rep2


title: Single HSC A10_young

description: Vwf-eGFP reporter mouse


title: PbfRNAi rep3

value: PbfRNAi


title: o2 rep1


title: Single HSC B8_young

description: Vwf-eGFP reporter mouse


title: P0 RNAi rep 2

description: Sample 5

value: WT

value: Day 1 adult

value: P0 RNAi exposure

value: Whole animal


title: PbfRNAi rep2


title: PbfRNAi rep1


title: Single HSC B11_young

description: Vwf-eGFP reporter mouse

value: Bone marrow


title: KO_EVX1_D4_3

description:
NO_8
E1-3

data_processing:
Basecalls performed using CASAVA version
Sequenced reads were trimmed for barcode sequence
RNA-seq reads were aligned to the mm10 genome assembly using Tophat v2.0.11,allowing for uniquely mapped reads and mapping both spliced and unspliced reads.
FPKM was calculated by Cufflink 2.1.1
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all the samples

source_name: CJ9 mES cells (-LIF, day4)

growth_protocol:
ESCs  were cultured in ESC differentiation medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and without recombinant leukemia inhibitory factor (LIF, millipore) for six days.
Wild-type ESCs or XH lncRNA-knockdown ESCs were maintained in standard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). Differentiated ESCs were cultured in standard ES medium without LIF or N2B27 standard medium with RA.

extract_protocol:
Differentiated ES cells were harvested at day 6. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
Library was prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

value: embryonic stem cells

value: EVX1 KO

tag: treatment

value: LIF withdrawal

tag: time


title: KO_EVX1_D4_2

description:
NO_7
E1-2


title: KO_Evx1as_D4_3

description:
NO_5
AS-3

growth_protocol:
ESCs  were cultured in ESC differentiation medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and without recombinant leukemia inhibitory factor (LIF, millipore) for four days.
Wild-type ESCs or XH lncRNA-knockdown ESCs were maintained in standard ES medium supplemented with 15% heat-inactivated FCS, 1% of nucleoside mix (100 × stock, Millipore), Penicillin-Streptomycin Solution (100 × stock, Life Technologies), 2 mM Glutamax (100 × Life Technology), 0.1 mM non-essential amino acid, 0.1 mM 2-mercaptoethanol and supplied with 1000 U/ml recombinant leukemia inhibitory factor (LIF, millipore). Differentiated ESCs were cultured in standard ES medium without LIF or N2B27 standard medium with RA.

extract_protocol:
Differentiated ES cells were harvested at day 4. TRIzol reagent was added directly into the plate after cold 1 × PBS wash once. The total RNA was extracted according to manufacturer's instructions. mRNA was further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instructions.
Library was prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.
Total RNA of RNA-Seq were extracted by TRIzol reagent according to manufacturer's instruction. mRNA were further isolated by Dynabeads mRNA purification kit (Life Technologies) according to manufacturer's instruction.
Libraries were prepared by illumina TruSeq Stranded mRNA LT Sample Prep Kit (RS-122-2101) according to the standard protocols of the manufacturer.

value: Evx1as KO


title: PbfRNAi;o2 rep3


title: WT rep3

value: Wild type


title: KO_Evx1as_D4_2

description:
NO_4
AS-2


title: KO_WT_D4_2

description:
NO_2
WT-2


title: KO_Evx1as_D4_1

description:
NO_3
AS-1


title: WT rep1


title: WT rep2


title: Single HSC A4_young

description: Vwf-eGFP reporter mouse

value: hsc


title: KO_WT_D4_1

description:
NO_1
WT-1