title: Sample_6_MG4

city: Atlanta

first: Rajneesh

last: Jha

state: Georgia

address: 2015 Uppergate Dr

department: Pediatric Cardiology

institute: Emory University School of Medicine

data_processing:
Illumina Casava1.8.2 software was used for basecalling and demultiplexing.
Reads were mapped to hg19 genome assembly with the STAR (v2.4.0g1) aligner.
Per sample read counts were calculated with htseq-count, mode: union, feature type: exon, id attribute: gene_id, and all other defaults.
Normalized read count abundance was estimated and differential expression was calculated with DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file containing raw or normalized read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: Microgravity_Replicate 3

extract_protocol:
IMR90 iPSCs were induced for cardiac differentiation using a growth factor-guided protocol.  Cardiac spheres were generated from cells at differentiation day 4 and subjected to simulated microgravity or standard gravity.   RNA samples from cells at differentiation day 8 were prepared using Bio-Rad RNA extraction kit and 1 µg of total RNA/sample was used for the construction of sequencing libraries using Illumina TruSeq RNA Sample Prep Kit.
Libraries were generated using the Illumina standard TruSeq Low-Throughput protocol.  Libraries were validated by microelectrophoresis, quantified, pooled and clustered on Illumina TruSeq v3 flowcell.  Clustered flowcell was sequenced on an Illumina HiSeq 1000 in 101-base single-read reactions.

value: IMR90 iPSC derived cardiac progenitor cells

tag: developmental stage

value: Day 8 differentiated cells

tag: condition

value: Microgravity


title: Sample_5_MG3

status: Public on Aug 08 2016

type: SRA

country: USA

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

source_name: Microgravity_Replicate 2

tag: cell type


title: Sample_4_MG2

source_name: Microgravity_Replicate 1


title: Sample_1_SG2

source_name: Standard gravity_Replicate 1

value: Standard gravity


title: Sample_2_SG3

source_name: Standard gravity_Replicate 2


title: GA1838-mouse-9732-Input

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

description:
input
GA1842_mouse_9732_H4K16ac_noDup-W200-G400-islands-summary-FDR0.001.txt.gz

library_source: genomic

data_processing:
Basecalls performed using GAPipeline 1.3.2
Sequence reads were obtained and mapped to the mouse (mm8) genomes with bowtie (0.12.7). Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained.
ChIP-Seq read enriched regions were called by using SICER v 1.03 (window size = 200, gap size = 400, FDR = 0.001) (PMID: PMC2732366)
Genome_build: mm8
Supplementary_files_format_and_content: The seven-column files are outputs from SICER. From left to right the columns are for:
chrom, start, end, ChIP_island_read_count, CONTROL_island_read_count, p_value, fold_change, FDR_threshold

molecule: genomic DNA

organism: Mus musculus

source_name: liver

growth_protocol: Mice are maintained at a 12-h light environment. At the experiments time, mice were sacrificedbetween 9AM to 11AM by Avertin injection. Blood were drained. Fresh liver samples were snap frozen with liquid nitrogen.

extract_protocol:
The fresh liver samples were snap frozen with liquid nitrogen, then powdered by Bessman Tissue Pulverizer. Chromatins were extracted from the hepatic powder based on previous publication (Cell. 2007 May 18;129(4):823-37.)
Library constructions for ChIP-Seq follow the protocol as described previously in (Cell. 2007 May 18;129(4):823-37. PMID: 17512414).

tag: strain

value: mix genetic background of 129/FVB/Black Swiss

tag: genotype/variation

value: SIRT1 KO

tag: age

value: 3 months

tag: antibody (vendor, batch/lot#, catalog#) or reference


title: GA1839-mouse-9905-Input

description:
input
GA1843_mouse_9905_H4K16ac_noDup-W200-G400-islands-summary-FDR0.001.txt.gz

value: wild type


title: GA1842-mouse-9732-H4K16ac

description:
Chromatin IP against H4K16ac
GA1842_mouse_9732_H4K16ac_noDup-W200-G400-islands-summary-FDR0.001.txt.gz

value: anti-H4K16ac, Santa Cruz, sc-8662-R


title: bra mac e10.5_2

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

description: mouse Macs from brain at day E10.5

data_processing:
After de-multiplexing and adapter removal, we aligned reads using Bowtie v 1.1.1 (parameters: -q -p 6 -a -m 100 --minins 0 --maxins 5000 --fr --sam --chunkmbs 200) to the Ensembl cDNA reference. We used BitSeq (v 1.12.0) to quantify transcript levels.
Raw read counts were loaded into R and all transcripts that were detected with at least 50 reads in at least four samples (n = 37,521), were processed with DESeq2's variance stabilizing transformation to output normalized read counts, which we subsequently further adjusted by accounting for batch effect with ComBat.
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated text file

source_name: brain Mac, E10.5

extract_protocol:
SMART-Seq2
SMART-Seq2

value: Mac

tag: tissue

value: brain

tag: tissue group

value: Head / brain

tag: time


title: bra mac e18.5_2

description: mouse Macs from brain at day E18.5

source_name: brain Mac, E18.5


title: 0-1_h_smg_Chx_RPF_43

city: Cambridge

first: Stephen

last: Eichhorn

state: MA

address: 9 Cambridge Center

department: Biology

institute: Whitehead Institute for Biomedical Research

data_processing:
Library strategy: Ribosome Footprint Profiling
RPF and RNA-seq reads were mapped to ORFs of representative transcript models as described, which excluded the first 50 nt of each ORF to eliminate signal from ribosomes that initiated after adding cycloheximide (Subtelny et al., 2014).  PAL-seq tags were mapped to 3' UTRs of representative transcript models, and PAL-seq fluorescence intensities were converted to tail lengths as described (Subtelny et al., 2014).
Genome_build: dm6
Supplementary_files_format_and_content: Processed data files contain RNA and RPF abundance measurements, poly(A)-tail length measurements, and information about whether a given gene passed certain expression cutoffs.

molecule: total RNA

organism: Drosophila melanogaster

source_name: embryos

growth_protocol: All flies were kept at 18, 22 or 25 °C according to standard procedure.  Oregon R flies were used as a wild-type control.  The null png1058 allele was previously described (Shamanski and Orr-Weaver, 1991; Fenger et al., 2000).  The wispy hemizygote mutants were derived from a cross between wisp41/FM6 (Cui et al., 2008); kindly provided by Mariana Wolfner, Cornell) and Df(1)RA47/FM7c flies (BL961, obtained from the Bloomington Drosophila Stock Center).  Smaug hemizygote mutants resulted from a cross between smg1/TM3, Sb[1] (BL5930, obtained from the Bloomington Drosophila Stock Center) and Df(3L)Scf-R6, Diap1[1] st[1] cu[1] sr[1] e[s] ca[1]/TM3, Sb[1] flies (BL4500, obtained from the Bloomington Drosophila Stock Center).  Unfertilized eggs were collected from crosses to twineHB5 mutant males, which fail to make sperm (Courtot et al., 1992).

extract_protocol:
Samples were transferred to RPF lysis buffer (10 mM Tris-HCl, pH 7.4, 5 mM MgCl2, 100 mM KCl, 2 mM DTT, 100 µg ml–1 cycloheximide, 1% Triton X-100, 500 U ml–1 RNasin Plus, and protease inhibitor (1x complete, EDTA-free, Roche)), centrifuged at 10000 rpm for 5 min, with obtained supernatants flash frozen in liquid nitrogen to be stored at –80 °C. Thawed lysates were then used for ribosome footprint profiling, or total RNA was extracted with TRIreagent and used for RNA-seq and PAL-seq. Samples Stage_14_wt_No_chx_RNA_1, Stage_14_wt_No_chx_RPF_7, Stage_14_wt_No_chx_PAL_46, Activated_egg_wt_No_chx_RNA_2, Activated_egg_wt_No_chx_RPF_8, and Activated_egg_wt_No_chx_PAL_47 were prepared using lysates made with RPF lysis buffer that did not contain cycloheximidie.
Samples were split and prepared for ribosome-footprint profiling and RNA-seq as described (Kronja et al., 2014b), as well as for PAL-seq as described (Subtelny et al., 2014).  Detailed protocols are available at http://bartellab.wi.mit.edu/protocols.html. For each stage, RNA, RPF, and tail length measurements were from the same sample.

treatment_protocol: Egg chambers were hand-dissected in Grace’s Unsupplemented Insect Media (Gibco) from three-day old flies that had been fattened for two days with wet yeast at 22 °C.  Approximately 300 egg chambers were collected per oogenesis stage.  Stages 11 to 14 were distinguished using morphological criteria. Embryos were collected at 25 °C by discarding two initial one-hour collections to avoid collecting embryos held within females for prolonged time.  Only the subsequent 0–1 h collection was then processed for sequencing analysis.  The same embryo collection strategy was applied wisp mutants.  For these samples, collection was extended to 0–2 h as one hour was too short to gather a sufficient number of laid eggs for sequencing.  Although wispy mutant eggs do not undergo the oocyte-to-embryo transition, eggs are laid that can be collected for mRNA analysis.  To obtain OrR 2–3 h, 3–4 h and 5–6 h embryo samples, 0–1 h embryos (collected after two previous one-hour collections were discarded) were incubated in a “humid chamber” at 25 °C for additional 2, 3 or 5 h, respectively.

value: OregonR

value: 0-1 h embryo

value: embryos

tag: genotype

value: smg


title: Stage_11_wt_Chx_RPF_36

source_name: oocytes

value: Stage 11 oocyte

value: oocytes

value: wt


title: Stage_13_wisp_Chx_RNA_41

data_processing:
RPF and RNA-seq reads were mapped to ORFs of representative transcript models as described, which excluded the first 50 nt of each ORF to eliminate signal from ribosomes that initiated after adding cycloheximide (Subtelny et al., 2014).  PAL-seq tags were mapped to 3' UTRs of representative transcript models, and PAL-seq fluorescence intensities were converted to tail lengths as described (Subtelny et al., 2014).
Genome_build: dm6
Supplementary_files_format_and_content: Processed data files contain RNA and RPF abundance measurements, poly(A)-tail length measurements, and information about whether a given gene passed certain expression cutoffs.

value: Stage 13 oocyte

value: wisp


title: 0-1_h_smg_Chx_RNA_40


title: 5-6_h_wt_Chx_RPF_25_33

value: 5-6 h embryo


title: 5-6_h_wt_Chx_RNA_21_29


title: 3-4_h_wt_Chx_RNA_20_28

value: 3-4 h embryo


title: 0-2_h_wisp_Chx_RNA_38

value: 0-2 h embryo


title: Stage_14_png_Chx_PAL_59

data_processing:
Library strategy: PAL-Seq
RPF and RNA-seq reads were mapped to ORFs of representative transcript models as described, which excluded the first 50 nt of each ORF to eliminate signal from ribosomes that initiated after adding cycloheximide (Subtelny et al., 2014).  PAL-seq tags were mapped to 3' UTRs of representative transcript models, and PAL-seq fluorescence intensities were converted to tail lengths as described (Subtelny et al., 2014).
Genome_build: dm6
Supplementary_files_format_and_content: Processed data files contain RNA and RPF abundance measurements, poly(A)-tail length measurements, and information about whether a given gene passed certain expression cutoffs.

value: Stage 14 oocyte

value: png


title: Stage_13_wisp_Chx_RPF_44


title: 3-4_h_wt_Chx_RPF_24_32


title: 0-2_h_wisp_Chx_RPF_39


title: Stage_11_wt_Chx_RNA_34


title: 0-1_h_smg_Chx_PAL_58


title: 2-3_h_wt_Chx_RNA_19_27

value: 2-3 h embryo


title: GA1843-mouse-9905-H4K16ac

description:
Chromatin IP against H4K16ac
GA1843_mouse_9905_H4K16ac_noDup-W200-G400-islands-summary-FDR0.001.txt.gz

value: mix genetic background of 129/FVB/Black Swiss

value: wild type

value: 3 months

value: anti-H4K16ac, Santa Cruz, sc-8662-R


title: Sample_3_SG4

source_name: Standard gravity_Replicate 3

value: IMR90 iPSC derived cardiac progenitor cells

value: Day 8 differentiated cells

value: Standard gravity


title: Stage_11_wt_Chx_PAL_55

value: OregonR

value: Stage 11 oocyte

value: oocytes


title: 2-3_h_wt_Chx_RPF_23_31

value: embryos

value: wt


title: Stage_14_png_Chx_RPF_18


title: Stage_13_wisp_Chx_PAL_56

value: Stage 13 oocyte

value: wisp


title: 3-4_h_wt_Chx_PAL_53

value: 3-4 h embryo


title: 0-1_h_wt_Chx_RPF_22_30

value: 0-1 h embryo


title: ME35_20150325_IDXX15

city: Boston

first: Kevin

middle: Meyer

last: Elias

address: 75 Francis Street

department: OB/GYN

institute: Brigham and Women's Hospital

data_processing:
Sequencing was performed on a HiSeq 2000 platform
Reads were aligned to the hg19 genome assembly using STAR
Genome_build: hg19
Supplementary_files_format_and_content: Excel files contain transcript ID, closest gene, average log fold change among knockdown experiments versus controls, p-value, and q-value
Supplementary_files_format_and_content: List of transcript ID, closest known gene or non-coding RNA, and log fold change of all siRNAs compared to controls with raw p-values and adjusted p-values

source_name: cell line

growth_protocol: Cancer cell lines were cultured in DMEM:F12 media (Mediatech, Inc, Manassas, VA) supplemented with 10% fetal bovine serum (Atlanta Biologicals, Norcross, GA) and 1% penicillin/streptomycin (Gibco, Life Technologies, Grand Island, NY).  FT33, FT194, and FT246 cells were derived from human fallopian tube secretory cells as previously described and were cultured in DMEM:F12 supplemented with 2% UltraserTM G (Pall Corporation, Port Washington, NY) and 1% penicillin/streptomycin.

extract_protocol:
For extraction, cells were lysed using RLT buffer then the lysate was homogenized using Qiashredder spin columns (Qiagen, Hilden, Germany).  RNA was isolated using RNeasy mini columns (Qiagen, Hilden, Germany) and quantitated using a Nanodrop (Thermo Fisher, Wilmington, DE), followed by Turbo DNAse treatment (Thermo Fisher, Wilmington, DE) at 37°C for 30 minutes and re-quantification.
After repairing the RNA ends, sequencing adaptors (Illumina, San Diego, CA) were ligated to the purified RNA, and the RNA was amplified for sequencing.

treatment_protocol: Reverse transfection with RNAiMAX Lipofectamine (Life Technologies, Grand Island, NY) using three different pre-designed siRNA oligonulceotides (catalogue numbers s15403, s15404, and s15405, abbreviated 403, 404, and 405, respectively, Ambion, Life Technologies, Grand Island, NY), a pool of all three siRNA oligonucleotides targeting PAX8, a control siRNA oligonucleotide targeting no known mammalian genes, or a no siRNA control was performed for each cell line. Samples were plated in duplicated 6 well plates, with one plate assigned for RNA-seq and the other for Western blot confirmation.  All cells were incubated for 72 hours before cells were harvested for protein or RNA.

tag: cell line

value: OVSAHO

tag: cell line type

value: High grade serous ovarian carcinoma

tag: sirna

value: PAX8 siRNA pool

tag: sirna source

value: Catalogue s15403, s15404, s15405, Ambion


title: 2-3_h_wt_Chx_PAL_52

value: 2-3 h embryo


title: Stage_12_wt_Chx_RPF_16

value: Stage 12 oocyte


title: 0-2_h_wisp_Chx_PAL_57

value: 0-2 h embryo


title: 5-6_h_wt_Chx_PAL_54

value: 5-6 h embryo


title: ME34_20150325_IDX5

value: PAX8 siRNA 405

value: Catalogue s15405, Ambion


title: Stage_13_wt_Chx_PAL_50

value: OregonR

value: oocytes


title: 0-1_h_wt_Chx_PAL_51

value: embryos

value: wt


title: Activated_egg_png_Chx_PAL_48

source_name: activated eggs

value: Activated egg

value: activated eggs

value: png


title: Activated_egg_wt_No_chx_PAL_47

description: Sample was prepared without any cycloheximide present in any solutions


title: Stage_13_wt_Chx_RPF_17

value: Stage 13 oocyte


title: 0-1_h_wt_Chx_RNA_26

value: 0-1 h embryo


title: ME33_20150325_IDX4

value: OVSAHO

value: High grade serous ovarian carcinoma

value: PAX8 siRNA 404

value: Catalogue s15404, Ambion


title: Stage_12_wt_Chx_PAL_49

value: Stage 12 oocyte


title: Stage_14_wt_No_chx_PAL_46

value: Stage 14 oocyte


title: ME31_20150325_IDX3

value: non-targeting siRNA control


title: ME30_20150325_IDX2

value: non-transfection control


title: Activated_egg_png_Chx_RPF_12

description: previously submitted as: GSM1276400

value: OregonR


title: ME29_20150325_IDX1

value: Immortalized fallopian tube secretory cell

value: PAX8 siRNA pool

value: Catalogue s15403, s15404, s15405, Ambion


title: Activated_egg_wt_No_chx_RPF_8

description:
Sample was prepared without any cycloheximide present in any solutions
previously submitted as: GSM1276396

value: Activated egg

value: wt


title: ME28_20150325_IDX27

value: PAX8 siRNA 405

value: Catalogue s15405, Ambion


title: ME27_20150325_IDX25

value: PAX8 siRNA 403

value: Catalogue s15403, Ambion


title: Activated_egg_png_Chx_RNA_6

description: previously submitted as: GSM1276394

value: activated eggs

value: png


title: Activated_egg_wt_No_chx_RNA_2

description:
Sample was prepared without any cycloheximide present in any solutions
previously submitted as: GSM1276390


title: Stage_14_wt_No_chx_RNA_1

description:
Sample was prepared without any cycloheximide present in any solutions
previously submitted as: GSM1276389

value: oocytes


title: ME23_20150407_IDX21


title: ME24_20150325_IDX22


title: ME25_20150325_IDX23


title: ME26_20150325_IDX14


title: Stage_13_wt_Chx_RNA_14

value: Stage 13 oocyte


title: Stage_14_png_Chx_RNA_15

value: Stage 14 oocyte


title: ME20_20150325_IDX18

value: non-targeting siRNA control


title: ME21_20150325_IDX19


title: ME22_20150407_IDX20

value: PAX8 siRNA 404

value: Catalogue s15404, Ambion


title: ME17_20150325_IDX15

value: High grade serous ovarian carcinoma


title: ME18_20150325_IDX13

value: PAX8 siRNA pool


title: ME16_20150325_IDX14


title: ME15_20150325_IDX13


title: ME14_20150325_IDX12


title: ME12_20150325_IDX10

value: Immortalized fallopian tube secretory cell

value: Catalogue s15403, s15404, s15405, Ambion


title: Stage_12_wt_Chx_RNA_13

value: OregonR

value: Stage 12 oocyte

value: wt


title: ME8_20150325_IDX7


title: ME13_20150325_IDX11

value: non-transfection control


title: ME5_20150325_IDX4

value: Kurmomachi

value: PAX8 siRNA 405

value: Catalogue s15405, Ambion


title: ME11_20150325_IDX9


title: ME6_20150325_IDX5


title: ME10_20150325_IDX12


title: Stage_14_wt_No_chx_RPF_7

description:
Sample was prepared without any cycloheximide present in any solutions
previously submitted as: GSM1276395

value: oocytes


title: ME2_20150407_IDX11


title: ME3_20150325_IDX2

value: PAX8 siRNA 403

value: Catalogue s15403, Ambion


title: ME4_20150325_IDX3


title: ME9_20150325_IDX8


title: ME1_20150325_IDX1


title: ME7_20150325_IDX6


title: JHOS4_chip

data_processing:
Sequencing was performed on a HiSeq 2000 platform
ChIP-seq reads were aligned to the hg19 genome assembly using : bwa (alignment via Burrows-Wheeler transformation) version 0.7.4-r385.
Data were filtered using Max 2 mismatches to ref genome during alignment
Peaks were called using macs2 version 2.1.0 with a q-value cutoff of 1e-5.
Motif enrichment analysis was done using the HOMER package (http://homer.salk.edu//homer/ngs/peaks.html)
Genome_build: hg19
Supplementary_files_format_and_content: Text files contains information on each experiment, chromosomal location of each peak, fold enrichement over input, p-value, and q-value

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with PAX8 antibody (Novus, Product #NBP1-32440, Littleton, CO).
After repairing the DNA ends, sequencing adaptors (Illumina, San Diego, CA) were ligated to the purified chromatin, and the DNA was amplified for sequencing

tag: antibody


title: OVSAHO_chip

source_name: OVSAHO

value: OVSAHO


title: KURAMOCHI_chip

source_name: KURAMOCHI

value: KURAMOCHI

value: PAX8 antibody (Novus, Product #NBP1-32440, Littleton, CO)


title: JHOS4_input

value: High grade serous ovarian carcinoma


title: ME19_20150325_IDX16


title: FT194_chip


title: KURAMOCHI_input


title: FT33_input


title: FT246_input


title: OVSAHO_input


title: FT194_input


title: FT246_chip


title: VSD-05 VSD

city: Berlin

first: Silke

last: Sperling

state: Berlin

address: Lindenberger Weg 80

department: Cardiovascular Genetics

country: Germany

institute: Experimental and Clinical Research Center (ECRC), Charité / MDC for Molecular Medicine

description: VSD

data_processing:
base calling using Illumina Casava pipeline 1.8.0
read mapping using Bowtie v0.12.7 (zero mismatches in the first 28 nucleotides; only unique paired reads were retained and both fragments must be located within 400 bp of each other on the reference genome)
calculating methylation score for each CpG site using BALM v1.0.1 (enrichment level of 0.99)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab separated text file with the chromosome number, coordinate and CpG methylation score (between 0 and 1)

source_name: right atrium

extract_protocol:
Genomic DNA from cardiac samples was extracted using Phenol:Chloroform:Isoamyl Alcohol (25:24:1) and treated with RNase A (Invitrogen) according to manufacturer’s instructions. DNA fragmentation was performed on a Covaris S3 to obtain fragments with an average length of 200 bp. The fragment distribution was examined on a high sensitivity DNA chip. Methylated DNA was captured using the MethylCap kit (Diagenode AF-100-0048, Belgium). The concentrations of the fragmented and captured DNA were determined on a Fluostar Optima plate reader (BMG Labtech, Offenburg, Germany) with the Quant-iTTN Picogreen dsDNA assay kit (Invitrogen P7589, Merelbeke, Belgium).
Library preparation and amplification were performed according to the ‘multiplexed paired-end ChIP protocol’ (with modifications) including the indexes from the ‘Multiplexing Sample Preparation Oligo Kit’ (Illumina, San Diego, California, USA). The libraries were 2 x 51 bp paired-end sequenced on an Illumina HiSeq 2000 platform. Base calling was performed with the Illumina Casava pipeline version 1.8.0. Initial sequencing quality assessment was based on data passing the Illumina Chastity filter.

value: heart

tag: disease state

value: ventricular septal defect


title: VSD-04 VSD

description: VSD


title: VSD-07 VSD

description: VSD


title: VSD-06 VSD

description: VSD


title: VSD-02 VSD

description: VSD


title: TOF-12 TOF

description: TOF

source_name: right ventricle

value: Tetralogy of Fallot


title: VSD-08 VSD

description: VSD


title: VSD-01 VSD

description: VSD


title: TOF-09 TOF

description: TOF


title: TOF-18 TOF

description: TOF


title: TOF-06 TOF

description: TOF


title: TOF-08 TOF

description: TOF


title: 363

city: Shanghai

first: Zilong

last: Qiu

address: No.320, Rd. Yueyang

country: China

institute: Chinese Academic of Science

data_processing:
Filtering Adaptor and low-quality reads
Mapping with BWA according to mmu9 genome and mouse miRNA database to detect the miRNA
miRNA Counting according to Bam file of the mapping result of the BWA
Genome_build: mm9
Supplementary_files_format_and_content: counts of miRNA

source_name: mouse hippocampups

extract_protocol:
Using Qiagen miRNA Kit to extract and purify the miRNA from RNA
Using Illumina Protocol

tag: genetic background

value: hippocampus

value: post natal day 30


title: Neu_076 Control Neurons Immortalized

city: Memphis

first: Quynh

last: Tran

state: TN

address: 262 Danny Thomas Place, C4029, Mail Stop 250

department: Pathology

institute: St. Jude Children's Research Hospital

data_processing:
These samples were run on Ion Torrent PGM.
These were aligned to the human genome (Enembl GRCh38.77) using TopHat version 2.0.10, Bowtie 2 version 2.1.0 and Samtools version 0.1.18
Reads were mapped to known genes using HTseq.  Gene expression was analyzed using DESeq2 version 1.2.10
Genome_build: GRCh38.77
Supplementary_files_format_and_content: RPKM

source_name: Human Dental Pulp Stem Cells

extract_protocol:
Control teeth were obtained through the Department of Pediatric Dentistry at the University of Tennessee Health Science Center (UTHSC). The UTHSC Institutional Review Board (IRB) approved this study and informed consent was obtained in accordance with IRB policy. Immediately following extraction, the teeth were placed in transportation media (DMEM/F12 with HEPES and 100 U/ml penicillin, 100μg/ml streptomycin). DPSC were isolated and culture as previously described in (Kiraly et al (2009) Neurochemistry International 55: 323-332) with slight modifications. Briefly, the pulp was minced and digested in a solution of 3 mg/ml Collagenase type I and 4 mg/ml Dispase II for 1 h at 37°C. Cells were seeded in poly-D-Lysine 12-well dishes and maintained under standard conditions (37°C, 5% CO2) in DMEM/F12 1:1, 10% fetal bovine serum (FBS), 10% newborn calf serum (NCS) and 100 U/ml penicillin, 100μg/ml streptomycin. Sub-confluent cultures were passaged regularly with 0.1μM HyQTase (HyClone).
Total RNA was extracted from ~3 week cultured Neurons and DPSCs using the miRNeasy Mini kit from Qiagen.
Total RNA was checked for quantity and quality on an Agilent Bioanalyzer 6000 pico chip and determined to have an RNA Integrity Number (RIN) of >8.0. NuGen amplified material was sheared on a Covaris S2 with a duty cycle of 10%, intensity of 5, 100 cycles/burst, and 6 X 60 sec cycles (total processing time 6 min).  500ng of this sheared dscDNA then used to prepare libraries for sequencing using the Ion plus Core Library Module for AB Library Builder System. Libraries were used from this point without amplification. Before sequencing, small aliquots of this material pooled and sequenced on an Ion Torrent PGM 314 chip. Barcode quantification data from the PGM were used to balance the barcodes for final pooling before sequencing. Following this final pooling the library pools were sized to a target size of 260bp on a Pippin Prep instrument. The sized libraries were examined on an Agilent High Sensitivity DNA chip, quantified using real-time PCR, and used to prepare spheres using a One-Touch 2 device. These spheres were then sequenced on an Ion Torrent Proton sequencer with a P1 chip.

treatment_protocol: 20,000 cells/cm2 were seeded in poly-D-lysine coated 12 well plates in DMEM/F12 (1:1), 2.5% FCS, 100 U/ml penicillin and 100 μg streptomycin, and culture for 24 hours. Epigenetic reprogramming was performed by exposing the DPSCs to 10 μM 5-azacytidine in DMEM/F12 containing 2.5% FCS and 10 ng/ml bFGF for 48 hours. Neural differentiation was induced by exposing the cells to 250μM IBMX, 50μM forskolin, 200 nM TPA, 1mM dbcAMP, 10ng/ml bFGF, 10 ng/ml NGF, 30 ng/ml NT-3, and 1% insulin-transferrin-sodium selenite premix (ITS) in DMEM/F12 for 3 days. At the end of the neural induction treatment, the cells were washed with 1X PBS. Neuronal maturation was performed by maintaining the cells in Neurobasal A media supplemented with 1mM dbcAMP, 1% N2, 1% B27, and 30 ng/ml NT-3 and 1X Glutamax for 3 days.

value: Neurons

value: Neurotypical Control

tag: immortalized

value: Yes


title: NH-12 normal heart

description: normal heart

value: normal


title: NH-11 normal heart

description: normal heart


title: NH-10 normal heart

description: normal heart


title: TP_037 Control DPSC Immortalized

tag: cell type

value: DPSC


title: 359

value: wild type male mouse


title: FT33_chip

value: Immortalized fallopian tube secretory cell


title: VSD-03 VSD

description: VSD


title: TP_076 Control DPSC Immortalized


title: TOF-02 TOF

description: TOF


title: NH-04 normal heart

description: normal heart


title: TOF-04 TOF

description: TOF


title: Neu_076 Control Neurons

value: No


title: TOF-01 TOF

description: TOF


title: TP_076 Control DPSC


title: AA respiratory tree

city: Yantai

first: Ye

last: Zhao

state: Shandong Province

address: Qingquan Road No.30

institute: Yantai University

description: mRNA

data_processing:
The original image data was transferred into sequence data by base calling (using CASAVA version 1.5+) (defined as "raw reads") and saved as fastq files that include the detailed reads sequences and the reads quality information.
To obtain clean reads, it is necessary to remove the dirty raw reads prior to data analysis. This process encompasses the following procedures: (1) remove reads with adaptors; (2) remove reads in which unknown bases are greater than 10%; (3) remove low-quality reads (the percentage of the low-quality bases of quality value ≤ 5 is more than 50% in a read).
A comparison of "clean reads" by SOAPaligner/soap2 (parameters:-m 0 -x 1000 -s 28 -l 32 -v 2 -r 2) was carried out using the reference databases from large-scale transcriptome profiling.
Genome_build: PMID 22428017
Supplementary_files_format_and_content: Tab-delimited text files include RPKMs. Details are in the supplementary readme.txt file that is linked to the Series record.

organism: Apostichopus japonicus

source_name: Apostihopus japonicus respiratory tree, AA

extract_protocol:
Total RNA from NA, DA and AA respiratory trees was extracted and DNase-treated using RNeasy Mini Kit and RNase-Free DNase Set (Qiagen, Germany), following the manufacturer's instructions.
The quality and concentration of RNA were measured by NanoDrop 1000 (Thermo) after which the mRNA in total RNA was enriched by using the oligo(dT) magnetic beads. After the addition of fragmentation buffer, the mRNA was interrupted and formed short fragments (~200 bp). The first strand cDNA was then synthesized by the random hexamer-primer, using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double strand cDNA was purified using the QiaQuick PCR extraction kit, and washed with EB buffer so as to facilitate end repair and the addition of a single nucleotide A (adenine). Finally, sequencing adaptors were ligated to the fragments. The required fragments were purified by means of agarose gel electrophoresis and enriched by PCR amplification.

value: respiratory tree

tag: Stage

value: arousal from aestivation


title: Neu_037 Control Neurons Immortalized


title: NA respiratory tree

description: mRNA

source_name: Apostihopus japonicus respiratory tree, NA

value: non-aestivation


title: NH-09 normal heart

description: normal heart


title: Neu_037 Control Neurons


title: Neu_023 Control Neurons Immortalized


title: TP_037 Control DPSC


title: TP_023 Control DPSC Immortalized


title: NH-06 normal heart

description: normal heart


title: DA respiratory tree

description: mRNA

source_name: Apostihopus japonicus respiratory tree, DA

value: deep aestivation


title: Chimp PR01209 Neurons 8week

status: Public on Aug 07 2016

city: La Jolla

first: Inigo

last: Narvaiza

state: CA

address: 10010 N Torrey Pines Rd

department: Laboratory of Genetics

institute: Salk Institute

description:
PolyA+ RNA (strand specific)
Processed data file: TPM_NPC_Neuron_hg19.txt

data_processing:
Reads from all libraries were mapped to both the human (hg19, GRCh37) and chimpanzee (panTro4, CGSC 2.1.3) genomes using STAR (v2.2.0c). Due to the lack of annotation in the chimpanzee genome, human gene models (RefSeq) were used to quantify gene expression. To avoid bias introduced by genome insertions and deletions, only reads mapping to both the human and chimpanzee genomes uniquely were used from each sample when comparing gene expression values (~4% of reads mapped to only one genome per sample). To calculate gene expression, read counts in the exons of RefSeq transcripts were calculated using HOMER.
Gene expression was calculated in TPM with Kallisto (version 0.42.1) against a custom catalog of human transcripts, including all human RefSeq transcripts with the three BOLA2 isoforms. RefSeq isoforms nearly identical to the canonical BOLA2 isoform (NM_001039182 and NM_001031827) were not included in the catalog of transcripts.
Since the RNA-seq datasets are a mix of PE100 and SE100 reads, we quantified gene expression by using only the first read of PE100 sequencing.
Genome_build: hg19 (GRCh37)
Genome_build: panTro4 (Pan_troglodytes-2.1.4)
Supplementary_files_format_and_content: TPM_NPC_Neuron_hg19.txt: Tab-delimited text file with TPM values from all experiments, RefSeq based with custom bola2 transcripts, and gene annotation information for RefSeq genes BOLA2 characterized isoforms (hg19 assembly).

organism: Pan troglodytes

source_name: neurons (8 week) derived from PR01209 iPSC line

growth_protocol: Human iPSC lines (WT-33 and ADRC-40) and chimpanzee iPSC lines (PR00818 and PR01209) have been previously described (Marchetto et al. Nature 2013, GEO GSE47626). To obtain NPCs from human and chimpanzee iPSCs, embryoid bodies (EBs) were formed by mechanical dissociation of iPSC clusters and plated into low-adherence dishes in DMEM/F12 plus N2 and B27 (Invitrogen) medium in the presence of Noggin (R&D) for forebrain induction for approximately 7 days. Then, floating EBs were plated onto poly-ornithine/laminin (Sigma)-coated dishes in DMEM/F12 plus N2 and B27 (Invitrogen) with addition of Noggin. Rosettes were visible to collect after 7 days. Rosettes were then dissociated with accutase (Chemicon) and plated again onto coated dishes in DMEM/F12 plus N2 and B27 and 10ng/ml of FGF2 (R&D). Homogeneous populations of NPCs were achieved after 1-2 passages with accutase in the same conditions. To obtain mature neurons, NPCs were cultured with DMEM/F12 plus N2 and B27 with addition of 1ug/ml of Laminin, BDNF (20 ng/ml), GDNF (20 ng/ml) and cyclic AMP (500 ug/ml) for 8 weeks.

extract_protocol:
Total cellular RNA was extracted from ~1-5x10^6 cells using the RNeasy Protect Mini kit or RNeasy Plus kit (Qiagen, Valencia, CA), according to the manufacturer's instructions.
For RNA library generation from human and chimpanzee NPCs and eight-week-old neurons, polyA+ RNA was fragmented and prepared into sequencing libraries using the Illumina TruSeq RNA sample preparation kit. NPC-derived sequencing libraries were analyzed on an Illumina HiSeq 2000 sequencer at the UCSD Biomedical Genomics Laboratory (BIOGEM). cDNA libraries were prepared from two human and two chimpanzee NPC lines (two clones each) derived from human WT-33 and ADRC-40 iPSC lines and chimpanzee PR00818 and PR01209 iPSC lines, respectively. Libraries were sequenced using single-end 100 bp reads at a depth of 15-30 million reads per library. Sequencing libraries derived from eight-week-old neurons were analyzed on an Illumina HiSeq 2500 sequencer at the Salk Next Generation Sequencing Core. cDNA libraries were prepared from two human (WT-33 and ADRC-40) and two chimpanzee (PR00818 and PR01209) neurons, one clone each. Libraries were sequenced using paired-end 100 bp reads at a depth of 15-30 million reads per library.

value: neurons

value: 8 weeks

tag: origin

value: PR01209 induced pluripotent stem cell (iPSC) line


title: TP_023 Control DPSC


title: NH-02 normal heart

description: normal heart

value: heart


title: WT15 +CMC

first: Thomas

middle: M

last: Carlile

state: Massachusetts

address: 77 Massachusetts Ave

institute: MIT

description: RNA was fragmented, treated with CMC as indicated, and captured by 3' adaptor ligation. RT was perfromed with AMV-RT, and truncated cDNA fragments were size selected on a gel, circularized, PCR amplified, and sequenced.

data_processing:
Reads were trimmed of adapter sequence
Reads were mapped to the longest spliced coding transcripts from the indicated transcriptomes using bowtie1
Mapped reads were processed using custom bash and python scripts
Mapped reads were processed using custom bash and python scripts
Genome_build: mm10 (5/13/2015)
Supplementary_files_format_and_content: Tab delimited text file of Pseudo-seq peak values for sites of pseudouridylation in the mouse rRNA.

extract_protocol:
Total spleens of C57BL/6J mice were harvested, and total RNA was isolated using the RNeasy Mini Kit following manufacturer’s protocol (Qiagen)
Pseduo-seq libraries were prepared as described (Carlile et al. Nature 2014) Briefly, total RNA was fragmented, and was subsequently derivatized with CMC followed by reversal of CMC adducts. Fragments were size selected, followed by 3′ adapter ligation, and reverse transcription. Truncated RT fragents were size selected, circularized, and PCR amplified. PCR products were gel purified, and sequenced on an Illumina HiSeq 2000.
OTHER: Pseudo-seq

tag: strain

value: spleen

tag: rna

value: Total RNA

tag: cmc use


title: WT7 +CMC

tag: tissue


title: WT8 +CMC


title: HET11 -CMC


title: WT8 -CMC


title: HET10 +CMC


title: WT9 -CMC


title: HET12 -CMC


title: Chimp PR01209 NPC B

description:
PolyA+ RNA-Seq (not strand-specific)
Processed data file: TPM_NPC_Neuron_hg19.txt

source_name: NPCs derived from PR01209 iPSC line

value: neural progenitor cells (NPCs)


title: HET10 -CMC


title: Neu_023 Control Neurons

value: Neurons

value: Neurotypical Control


title: Human WT-33 NPC A

source_name: NPCs derived from WT-33 iPSC line

value: WT-33 induced pluripotent stem cell (iPSC) line


title: WT15 -CMC


title: HET11 +CMC


title: Human ADRC-40 NPC B

source_name: NPCs derived from ADRC-40 iPSC line

value: ADRC-40 induced pluripotent stem cell (iPSC) line


title: Human WT-33 NPC B


title: WT7 -CMC


title: WT9 +CMC


title: Sample SC EMP preMac Mac e10.25

description: Single-cells mouse EMPs preMac Macs from whole embryo at day E10.25

data_processing:
After de-multiplexing, Cell barcode and RMT were extracted from Read 2 and stored in Read 1. Reads with a Phred<27 for any RMT base were removed from further analysis. Next, we removed contamination, by alignment against the e.coli genome and de-multiplexed the unmapped reads by pool barcode and cell barcode. Reads were aligned using Bowtie v 1.1.1 (parameters:“-m 1 -t --best --chunkmbs 64 –strata) to the Ensembl mouse mm10 + ERCC pseudo genome assembly. We used HTSeq-count (v 0.6.0) to quantify gene count levels based on the ensembl exon-model for mm10. Following UMI sequencing errors were filtered nad a gene expression matrix was generated.
Raw molecule counts were loaded into R and all cells with a mito-to-endogenous gene molecule count of 0.15, with less than 320 unique molecule counts or 150 unique genes were removed from further analysis. In addition we filtered for mitichondrial, ribosomal and predicted genes.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text file

source_name: whole_embryo EMPs_preMac_Mac, E10.25

extract_protocol:
MARS-seq
MARS-seq

value: EMPs preMac Mac

value: whole embryo

tag: tissue group

tag: time


title: Human ADRC-40 NPC A


title: Chimp PR01209 NPC A


title: exo4.2

status: Public on Aug 06 2016

city: New York

first: Eleni

last: Mimitou

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

data_processing:
Mapping of the reads onto the S288c reference genome (SacCer2) was performed using the SHRiMP mapper50 (gmapper-ls) with arguments: -E -U -n 1 -Q --sam-unaligned --strata -o 10001 -N 20 Before mapping, adaptor sequences were removed using fastx_clipper (http://hannonlab.cshl.edu/fastx_toolkit/) and a custom script. Code used for read processing and mapping is available online at https://github.com/soccin/S1Seq. After mapping, the reads were separated into unique and multiple-mapping sets, but only uniquely mapping reads were analyzed in this study. Analyses were performed using the R package (RStudio version 0.99.879, R version 3.1.2).
Maps were curated by masking (set to NA) 500 bp at the ends of each chromosome, because telomeres represent naturally occurring resected DNA ends and therefore give a high frequency of reads.
We masked regions that gave a high frequency of meiotic DSB-independent reads, defined as positions with more than 10 reads in the high-depth biological replicates and/or more than 5 reads in the lower depth biological replicates from the 0-h maps from wild type, spo11-Y135F, dmc1 null, and exo1-D173A plus the 4-h map from spo11-Y135F. A table of mask coordinates is provided at https://github.com/soccin/S1Seq.
Reads mapping to mitochondrial DNA or the 2 μ plasmid were excluded.
Each map was normalized to reads per million remaining mapped reads (provided here as processed data files) and biological replicates were averaged.
Genome_build: Reads were mapped to the SGD assembly released in June 2008, called "SacCer2" by UCSC.
Supplementary_files_format_and_content: txt files include RPM (reads per million mapped) for each genotype and biological replicate over the experimental meiotic time points examined. Column names: letter "w" or "c" denotes watson (top) or crick (bottom) strand respectively, followed by a number indicating meiotic  time point.

organism: Saccharomyces cerevisiae

source_name: meiotic culture

growth_protocol: Cells were grown in YPA (1% yeast extract, 2% Bacto Peptone, 1% potassium acetate) for 14 hr at 30°C, harvested, resuspended to OD600=6.0 in 2% potassium acetate and sporulated at 30°C.

extract_protocol: Ten plugs of each sample to be analyzed were equilibrated in 500 μl 1× S1 buffer (50 mM sodium acetate pH 4.5, 0.28 M NaCl, 4.5 mM ZnSO4) per plug in 2 ml conical tubes for 30 min and this was repeated three times. Fresh 1× S1 buffer (500 ul) containing 9 U of S1 nuclease (Promega) was added to each tube and the plugs were incubated on ice for 15 min to allow the enzyme diffuse into the plugs, followed by 20 min incubation at 37°C. S1 nuclease was inactivated by addition of EDTA pH 8.0 to a final concentration 10 mM and incubation on ice for 15 min. Plugs were rinsed with 1× TE and further equilibrated in 500 μl T4 polymerase buffer (1× T4 DNA ligase buffer (NEB), 1× BSA, 100 μM dNTPs), four times for 30 min each. Fresh T4 polymerase buffer (500 μl) containing 30 U of T4 DNA polymerase (NEB) was added to each tube and the plugs were incubated on ice for 15 min, followed by 30 min incubation at 12°C. T4 polymerase was inactivated by addition of EDTA pH 8.0 to a final concentration of 10 mM and incubation on ice for 15 min. At this point all buffer was aspirated,the plugs were rinsed with 1× TE and incubated at 75°C for 20 min to fully inactivate T4 polymerase. Plugs were allowed to gradually cool and solidify, before equilibrating in 250 μl 1× T4 ligase buffer (NEB), four times for 15 min each. After the last equilibration step, 200 μl of the buffer were removed leaving each plug immersed in 50 μl 1× T4 DNA ligase buffer, to which 1 μl of 50 μM adaptor and 1 μl of 2000 U/μl T4 DNA ligase were added. Ligation took place at 4°C for ≥18 h. The adaptor was prepared the day of the experiment by mixing oligos P5-top (5BiosG/ACACTCTTTCCCTACACGACGCTCTTCCGATCT, biotin attached to the 5′- end of the oligo) and P5-bottom (5Phos/AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT/3InvdT, 5′- end phosphorylated with inverted dT incorporated at the 3′-end to block ligation) at equimolar concentration, boiling for 5 min and cooling down at room temperature for at least 1 h.  To retrieve the DNA from the agarose plugs, the Epicentre GELase Enzyme Digestion protocol was used, followed by phenol extraction and ethanol precipitation. During this process plugs of DNA from a single culture and time point were pooled. The purified DNA was then subjected to size selection by electrophoresis through a 1% LMP 1× TAE agarose gel at 80 V/cm for 2 h to separate the high-molecular-weight genomic DNA from the excess unligated adaptor. The genomic DNA was excised and extracted from the gel using the Epicentre GELase enzyme protocol, phenol extraction and ethanol precipitation; then the DNA was dissolved in 100 μl 1× TE. To ensure complete removal of unligated adaptor, each sample was further purified by passing three times through Chroma Spin-1000 (Clontech) columns. The eluates were then subjected to shearing according to the Covaris instrument protocol to DNA fragment sizes ranging between 200-500 bp.  Following shearing, fragments containing the biotinylated adaptor were enriched by affinity purification with streptavidin. For each sample, 50 μl of streptavidin M-280 beads (Roche) were used, prewashed twice with 1× TE and twice with 1× B&W (binding and washing buffer, 10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2 M NaCl), according to the manufacturer’s instructions. Binding was carried out at 20°C for 30 min, followed by two washes with 500 μl 1x B&W buffer and two washes with 500 μl 10 mM Tris-HCl pH 7.5. The remaining steps were performed with the DNA fragments still bound to the streptavidin beads. Because sheared ends are not always readily ligatable, an end-repair step was included according to Epicentre’s End-it DNA Repair kit protocol. The beads for each sample were incubated in 100 μl of reaction mix according to manufacturer’s instructions and incubated at 20°C for 45 min. Following washes with 500 μl 1× B&W buffer (twice) and 500 μl 10 mM Tris-HCl pH 7.5 (twice), the beads were incubated in 100 μl of 1× T4 DNA ligase buffer containing 400 U T4 ligase and 1 μM P7 adaptor. The adaptor was prepared by annealing oligos P7 top (5Phos/GATCGGAAGAGCACACGTCTGAACTCCAGTCAC/3InvdT) and P7 bottom (GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC) at equimolar concentration, boiling for 5 min and allowing to cool down at room temperature for at least one hour. Ligation of the P7 adaptor was allowed at 20°C for 4 h and was followed by washes with 500 μl 1× TE and 500 μl 10 mM Tris-HCl pH 7.5 (three times each). Beads of each sample were resuspended in 20 μl 10 mM Tris-HCl pH 7.5.  Each sample of beads was split into two PCR reactions in a total of 50 μl containing 10 μl of the resuspended beads, 1× Phusion HF buffer, 0.2 mM dNTP, 1 U Phusion HF polymerase (Thermo Scientific), 0.4 μM P5 universal primer (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC T) and 0.4 μM P7 indexed primer (CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTG, shown here with Illumina TruSeq index 1 underlined). PCR was initiated by a denaturation step at 98°C for 30 sec, followed by 16 cycles of amplification (98°C for 10 sec, 65°C for 20 sec, and 72°C for 20 sec). PCR products were pooled, and the DNA was precipitated by adding ammonium acetate to 2.5 M and 2.5 volumes of ice-cold 100% ethanol. Following an overnight incubation at -20°C, the samples were spun at 16000 g for 30 min, washed with ice-cold 70% ethanol, air-dried and dissolved in 20 μl 10 mM Tris, pH 7.5. PCRs from each sample were pooled and separated on a 5% non-denaturing polyacrylamide gel in 1× TBE. The gel piece between 200–600 bp was excised, crushed, and eluted in 300 μl 10 mM Tris pH 8.0 at 37°C overnight. The elution mixture was spun through a SPIN-X column, and DNA was precipitated with ammonium acetate and ethanol as above. The DNA pellet was dissolved in 20 μl 10 mM Tris pH 7.5 and sequenced on the Illumina HiSeq platform (50 bp single-end) in the Integrated Genomics Operation at Memorial Sloan Kettering Cancer Center.

tag: genotype

tag: meiotic time-point

value: 4 h


title: exo2.2

value: 2 h


title: Chimp PR00818 Neurons 8week

source_name: neurons (8 week) derived from PR00818 iPSC line

tag: age

value: PR00818 induced pluripotent stem cell (iPSC) line


title: Human ADRC-40 Neurons 8week

source_name: neurons (8 week) derived from ADRC-40 iPSC line


title: Chimp PR00818 NPC A

source_name: NPCs derived from PR00818 iPSC line


title: HU-2

city: North Chicago

first: Weihang

last: Chai

state: Illinois

address: 3333 N Green Bay Rd, IRP 257

department: Center for Genetic Diseases

institute: Rosalind Franklin University of Medicine and Sciences, Chicago Medical School

description: Myc-tagged hSTN1 is stably expressed in HeLa by retroviral transduction.

data_processing:
Reads quality from each sample was assessed with FASTQC and adapters were removed with Cutadapt
Processed reads were aligned to hg19 using Bowtie 2 (no gaps, alignment of individual read pairs allowed).
Peaks were called with MACS 1.4.2 (band width = 300, model fold = 10,30, p-value = 1e-3 or 1e-5, shiftsize = 160 and 158)
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph files generated using MACS 1.4.2, bedgraph values indicate number of tags mapped to a given genomic position

source_name: HeLa

growth_protocol: Cells were grown in DMEM supplemented with 10% calf serum in 5% CO2, synchronized to G1/S boundary with double-thymidine block. After cells were released into S phase for 3 hours, 2 mM hydroxyurea was added into media for 3 hours. Cells were then crosslinked with formaldehyde.

extract_protocol:
Lysates were clarified from sonicated whole cells and hSTN1-DNA complexes were isolated with antibody.
Libraries were prepared by Otogenetics Corporation (Atlanta, US) according to Illumina's instructions. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: Hydroxyurea was added to media for 3 hours.

tag: chip antibody

value: Myc


title: exo4.1


title: HET12 +CMC


title: PANC 354

city: Bronx

first: Yiting

last: Yu

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

data_processing:
We used the BWA aligner (version 0.6.1) with default parameters to align the sequencing reads for each sample to the NCBI reference human genome sequence (Build 37/hg19). Peak calling for each sample was performed using MACS (version 1.4.2) (Zhang et al., 2008) with default parameters. GEO accession number is pending.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include hydroxymethylation peaks for each Sample

source_name: xenograft PANC 354

growth_protocol: Cells were maintained in Dulbecco’s Modified Eagle’s Medium (Invitrogen #11965) supplemented with 10% FBS, 1% Pen-Strep, and 5μg/mL Plasmocin (Invivogen). Pa02C was cultured in RPMI1640 medium (Invitrogen #11875) supplemented with 20% FBS, 1% Pen-Strep, and 5μg/mL Plasmocin (Invivogen).

extract_protocol: Genomic DNA from cell lines were isolated by Puregene Core Kit A (Qiagen)

tag: tissue origin

value: Primary pancreatic tumor


title: exo0.2

value: 0 h


title: HU-1


title: Pa39X

source_name: xenograft Pa39X


title: Chimp PR00818 NPC B


title: Human WT-33 Neurons 8week

source_name: neurons (8 week) derived from WT-33 iPSC line

value: neurons

value: 8 weeks


title: PANC219

source_name: xenograft PANC219


title: PANC215

source_name: xenograft PANC215


title: input


title: spo0.2


title: spo4.1


title: PANC198

source_name: xenograft PANC198


title: Pa38X

source_name: xenograft Pa38X


title: dmc8.1

value: dmc1 null

value: 8 h


title: Pa37X

source_name: xenograft Pa37X


title: Pa43X

source_name: xenograft Pa43X


title: Pa136X

source_name: xenograft Pa136X


title: Pa10X

source_name: xenograft Pa10X


title: spo0.1


title: spo4.2


title: dmc6.1

value: 6 h


title: Pa135X

source_name: xenograft Pa135X


title: dmc6.2

source_name: meiotic culture


title: Pa09C

source_name: cell line Pa09C

tag: cell line


title: dmc4.2


title: dmc4.1


title: exo0.1


title: MIAPACA2

source_name: cell line MIAPACA2


title: dmc0.2


title: PANC1

source_name: cell line PANC1


title: M5G_treat

first: Michael

last: Laub

address: 31 Ames St

description: Cultures were grown to mid-exponential phase at 30 degrees C in rich medium (PYE).

data_processing:
Reads were mapped to the Caulobacter crescentus NA1000 reference genome using BWA (Li and Durbin, 2010 (PMID: 20080505)).
860,000 uniquely mapping reads were analyzed for each sample.
Read extension and pileup was performed using MACS software analysis package (Zhang et al., 2008, PMID:18798982).
Data were analyzed using custom Python scripts and peaks were called by comparing local maxima in the treat sample to the control sample with a p-value < 10^-5
Genome_build: NC_011916.1
Supplementary_files_format_and_content: The processed wig files contain the output of MACS software analysis, with 10 bp genomic bins containing the number of reads.

organism: Caulobacter vibrioides NA1000

source_name: mixed population of Caulobacter crescentus

extract_protocol:
Cross-linked DNA was extracted as in Fioravanti et al., 2013 (PMID: 23737758) with modifications: mid-exponential phase cultures were cross-linked in 10 mM sodium phosphate (pH 7.6) and 1% formaldehyde at room temperature for 10 minutes. Reactions were quenched with 0.1 M glycine at room temperature for 5 minutes, and on ice for 15 minutes. Cells were washed 3X in phosphate buffered saline (PBS) and lysed with Ready-Lyse lysozyme solution (Epicentre, Madison, WI) according to manufacturer instructions. Lysates were diluted 1:1 in ChIP buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl (pH 8.1), 167 mM NaCl) plus Roche Protease Inhibitor Tablets (Roche) and incubated at 37 °C for 10 minutes. Lysates were sonicated (Branson Sonicator) on ice for 6 bursts of 10 seconds each at 15% amplitude, and then cleared by centrifugation at 14,000 rpm for 5 minutes at 4 °C. Cleared supernatants were normalized by protein content in 1 mL of ChIP buffer + 0.01% SDS, and pre-cleared with 50 μL of Protein-A DynaBeads (Invitrogen) (pre-blocked with 100 μg Ultra Pure BSA in ChIP buffer + 0.01% SDS) by 1 hour rotation at 4 °C.  10% of each supernatant was removed and used as total chromatin input sample. The remaining supernatant was incubated with a 1:1000 dilution of anti-M2 antibody overnight at 4 °C. Each sample was then incubated with 50 μL of pre-blocked Protein-A DynaBeads for 6 hours at 4 °C with rotation. DynaBeads were washed consecutively at 4 °C for 15 minutes with 1 mL of the following buffers: low salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 150 mM NaCl), high salt wash buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl (pH 8.1), 500 mM NaCl), LiCl wash buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl (pH 8.1)), and twice with TE buffer (10 mM Tris-HCl (pH 8.1), 1 mM EDTA). Complexes were eluted twice by incubation with 250 μL freshly prepared elution buffer (1% SDS, 0.1 M NaHCO3) at 30 °C for 15 minutes.  Cross-links were reversed by addition of 300 mM NaCl and 2 μL of 0.5 mg/mL RNase A and overnight incubation at 65 °C. Samples were treated with 5 μL of Proteinase K (20 mg/mL, NEB) in 40 mM EDTA and 40 mM Tris-HCl (pH 6.8) for 2 hours at 45 °C. DNA was extracted using a PCR purification kit (Qiagen) and resuspended in 80 μL of water.  Libraries were prepared using the SPRI-works system and sequenced on an Illumina MiSeq (MIT BioMicroCenter).
Libraries were prepared using the SPRI-works system

treatment_protocol: Mid-exponential phase cultures were cross-linked in 10mM sodium phosphate and 1% formaldehyde.

tag: phob genotype

tag: psts genotype

value: pstS (wt)

tag: antibody

value: anti-FLAG M2 (Sigma-Aldrich,F1804)


title: pstS_PYE_control

growth_protocol: Cultures were grown to mid-exponential phase at 30 degrees C in rich medium (PYE).

value: phoB (wt)

value: pstS::Tn5 (kanamycin-marked Tn5 disruption pstS allele)


title: dmc8.2


title: Pa04C

description: JD

source_name: cell line Pa04C


title: M5G_control


title: dmc0.1


title: wt6.2

value: wild type


title: pstS_PYE_treat


title: PYE_treat


title: wt6.1


title: BXPC3

source_name: cell line BXPC3


title: Pa21C

source_name: cell line Pa21C


title: wt4.1


title: PYE_control


title: Pa07C

source_name: cell line Pa07C


title: ino4.1

value: ino4 null


title: ino4.2

value: 4 h


title: wt2.2

value: 2 h


title: bas4.2

value: bas1 null


title: wt4.2


title: Pa16C

source_name: cell line Pa16C


title: wt2.1


title: Pa02C

source_name: cell line Pa02C


title: wt0.2


title: Pa08C

source_name: cell line Pa08C


title: bas4.1


title: Pa03C

source_name: cell line Pa03C


title: tel4.1

value: tel1 null


title: wt0.1


title: tel2.2


title: HPDE

description: HPDE

source_name: cell line HPDE

value: Normal pancreatic duct

value: HPDE


title: sgs4.2


title: sgs4.1


title: tel2.1


title: O5

city: Hefei

first: Yulong

last: Wang

address: 130 West Changjiang Road

institute: Anhui Agricultural University

description:
mycelial mat reached 4 cm
T. versicolor was obtained from CICC 14001 (China Center of Industrial Culture Collection)

data_processing:
Reads were mapped to the T. versicolor genome from (EBI, http://www.ebi.ac.uk/ena/data/view/PRJNA56097)
Differential gene expression levelss were calculated with using the program Cufflinks software (v.2.0.1)
DAnnotations of differentially expressed genes (DEGs) including Pfam, were annotated using including Pfam database were obtained from the reference annotation of available T. versicolor genome database at the NCBI website.
For each differentially expressed peach gene, up-to-datelatest Gene Ontology (GO) annotations were obtained using Blast2GOv.2.3.5 with the default parameters., Theand “GO slim” option was employedset to reduce the number of functional classes.
GO slim annotations results were then used as queries against the AgBase database to perform their classify genesication according into to the three main classes categories (molecular function, biological process and cellular component), and to be further assigned to secondary categories
Genome_build: GCA_000271585.1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Trametes versicolor

source_name: T.versicolor grown on the a glucose carbon medium of glucose for 9 days

growth_protocol: on PDA and 25ºC

extract_protocol:
Total RNA was isolated separately from T. versicolor with RNA extraction Kit
RNA samples were first treated with RNAse-free DNAse I to remove contaminatinged DNA. Then, the mRNA wais enriched by using the oligo(dT) magnetic beads. After mixed with theadding fragmentation buffer, the mRNA was fragmented into short fragments (about 200 bp). NextThen, the first strand of cDNA was synthesized by using random hexamer-primers. Buffer, dNTPs, RNase H, and DNA polymerase I were added to synthesize the second cDNA strand. The double- stranded cDNA was then purified usingwith magnetic beads. End reparation and 3’-end single nucleotide A (adenine) addition was then performed. Finally, sequencing adaptors were ligated to the fragments. The fragments were enriched by PCR amplification. During the QC step, an Agilent 2100 Bioanaylzer (Agilent Technologies, Germany) and ABI StepOnePlus Real-Time PCR System (Applied Biosystems, USA) were used to perform qualitfy-control steps  and to quantify the sample library. The library products wasere then ready for sequencing using anvia Illumina HiSeqTM 2000 (GATC Biotech, Germany), or another sequencer when if necessary

tag: protocol

value: Mycelium


title: M4

source_name: T.versicolor grown on PDA medium for 9 days

value: PDA medium for 9 days


title: exo2.1


title: tel4.2


title: HPNE

description: HPNE

source_name: cell line HPNE

value: HPNE


title: Derivative_3-3-seedling

status: Public on Aug 05 2016

city: Wuhan

first: Handong

last: Su

state: Hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

description: processed data file: seedling.gene_exp.diff

data_processing:
Basecalls performed using Illumina CASAVA.
ChIP-seq reads were mapped to maize B73 genome with BWA version 0.6.1 with the following configurations.
Only uniquely mapping reads were chosen for further analysis, and only a random one was picked for duplicates (reads mapped to the same location).
RPM values were calculated with 10 kb windows along the genome to make it comparable between different samples.
Genome_build: Maize B73 RefGen_v3
Supplementary_files_format_and_content: *exp.diff containing FPKM and log2 foldchange values between samples; txt files with methylation-level data

organism: Zea mays

source_name: maize

growth_protocol: Suitable materials were planted in the greenhouse or in the field for RNA-seq and ChIP-seq experiments.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and was subjected to the Illumina RNA-seq protocol, followed by sequencing using the HiSeq2000 platform. Seedling and young leaf tissues harvested from plant materials with and without Derivative 3-3 were used for RNA-seq analysis. Extracted nuclei were digested with micrococcal nuclease (Sigma-Al drich) for ChIP experiments using the maize CENH3 antibody.The ChIP-enriched DNA of Derivative 3-3 was treated with sodium bisulfite and then performed Illumina sequence. The maize CENH3 is a rabbit polyclonal antiserum and was raised against the peptides: C-RPGTVALREIRKYQKS; STSATPERAAGTGGR-C. Keyhole limpet hemocyanin (KLH)-conjugated peptide was used to immunize rabbits.
RNA libraries were prepared according to standared Illumina's instructions. ChIP libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).180-400 bp fragments (contained the joint) were selected by gel extraction.

tag: genotype/variation

value: seedling


title: Derivative_3-3-bisulfite-CENH3

data_processing:
library strategy: ChIP-bisulfite-seq
Basecalls performed using Illumina CASAVA.
ChIP-seq reads were mapped to maize B73 genome with BWA version 0.6.1 with the following configurations.
Only uniquely mapping reads were chosen for further analysis, and only a random one was picked for duplicates (reads mapped to the same location).
RPM values were calculated with 10 kb windows along the genome to make it comparable between different samples.
Genome_build: Maize B73 RefGen_v3
Supplementary_files_format_and_content: *exp.diff containing FPKM and log2 foldchange values between samples; txt files with methylation-level data

value: young leaves


title: Gem5nm87_GCTACGC-GCGTAAG_L001_RNA-seq

city: Ann Arbor

first: Joshua

middle: D.

last: Welch

state: MI

address: 100 Washtenaw Ave.

institute: The University of Michigan

description: RNA

data_processing:
Read alignment using MapSplice 2
Gene expression quantification using RSEM
Genome_build: hg19
Supplementary_files_format_and_content: Gene expression quantification (FPKMs)

source_name: CFPAC-1_Gemcitabine (5nM)_Microraft

extract_protocol:
ClonTech SMARTer kit
Nextera XT

tag: treated with

value: Gemcitabine (5nM)

tag: isolation

value: Microraft

tag: num. cells

value: Unknown

tag: proliferative?

value: No


title: Control_seedling

value: control

tag: tissue


title: Y6

source_name: T.versicolor grown on poplar medium for 9 days

value: poplar medium for 9 days


title: Gem5nmH20_AAGAGGC-TATCCTC_L001_RNA-seq

description: RNA


title: Gem5nm88_CGAGGCT-CTCTCTA_L001_RNA-seq

description: RNA


title: Derivative_3-3-leaf

description: processed data file: leaf.gene_exp.diff


title: Gem5nm85_CTCTCTA-AAGGAGT_L001_RNA-seq

description: RNA


title: Gem5nm84_TAGGCAT-ACTGCAT_L001_RNA-seq

description: RNA


title: Gem5nm81_AGGCAGA-TATCCTC_L001_RNA-seq

description: RNA


title: Gem5nm76_GTAGAGG-CTAAGCC_L001_RNA-seq

description: RNA

value: Yes


title: Gem5nm86_CAGAGAG-CTAAGCC_L001_RNA-seq

description: RNA


title: Gem5nm73_GCTACGC-GTAAGGA_L001_RNA-seq

description: RNA


title: Gem5nm78_CGTACTA-CTCTCTA_L001_RNA-seq

description: RNA


title: Gem5nm72_CAGAGAG-AGAGTAG_L001_RNA-seq

description: RNA


title: Gem5nm77_TAAGGCG-GCGTAAG_L001_RNA-seq

description: RNA


title: Gem5nm74_CGAGGCT-ACTGCAT_L001_RNA-seq

description: RNA


title: Gem5nm75_AAGAGGC-AAGGAGT_L001_RNA-seq

description: RNA


title: Gem2nM68_CGAGGCT-CTCTCTA_L001_RNA-seq

description: RNA

source_name: CFPAC-1_Gemcitabine (2nM)_Microraft

value: Gemcitabine (2nM)


title: Gem2nMH20_AAGAGGC-TATCCTC_L001_RNA-seq

description: RNA


title: Gem2nM65_CTCTCTA-AAGGAGT_L001_RNA-seq

description: RNA


title: Gem2nM67_GCTACGC-GCGTAAG_L001_RNA-seq

description: RNA


title: Control_leaf

description: processed data file: leaf.gene_exp.diff


title: Gem2nM66_CAGAGAG-CTAAGCC_L001_RNA-seq

description: RNA


title: Gem2nM64_TAGGCAT-ACTGCAT_L001_RNA-seq

description: RNA


title: Gem5nm71_CTCTCTA-TATCCTC_L001_RNA-seq

description: RNA


title: Gem2nM63_GGACTCC-GTAAGGA_L001_RNA-seq

description: RNA


title: Gem2nM58_CGTACTA-CTCTCTA_L001_RNA-seq

description: RNA


title: Gem5nm83_GGACTCC-GTAAGGA_L001_RNA-seq

description: RNA


title: Gem2nM56_GTAGAGG-CTAAGCC_L001_RNA-seq

description: RNA


title: Gem2nM62_TCCTGAG-AGAGTAG_L001_RNA-seq

description: RNA


title: Gem2nM57_TAAGGCG-GCGTAAG_L001_RNA-seq

description: RNA


title: Gem2nM53_GCTACGC-GTAAGGA_L001_RNA-seq

description: RNA


title: Gem2nM61_AGGCAGA-TATCCTC_L001_RNA-seq

description: RNA


title: Gem5nm82_TCCTGAG-AGAGTAG_L001_RNA-seq

description: RNA


title: Gem2nM55_AAGAGGC-AAGGAGT_L001_RNA-seq

description: RNA


title: Gem2nM52_CAGAGAG-AGAGTAG_L001_RNA-seq

description: RNA


title: PlaceboH20_GGACTCC-GCGTAAG_L001_RNA-seq

description: RNA

value: Saline


title: Placebo47_AGGCAGA-AAGGAGT_L001_RNA-seq

description: RNA


title: Placebo46_CGTACTA-ACTGCAT_L001_RNA-seq

description: RNA


title: Placebo45_TAAGGCG-GTAAGGA_L001_RNA-seq

description: RNA


title: Placebo48_TCCTGAG-CTAAGCC_L001_RNA-seq

description: RNA


title: Gem2nM51_CTCTCTA-TATCCTC_L001_RNA-seq

description: RNA


title: Placebo38_CAGAGAG-CTAAGCC_L001_RNA-seq

description: RNA


title: Placebo43_AAGAGGC-TATCCTC_L001_RNA-seq

description: RNA


title: Placebo41_GCTACGC-GCGTAAG_L001_RNA-seq

description: RNA


title: Placebo42_CGAGGCT-CTCTCTA_L001_RNA-seq

description: RNA


title: Placebo44_GTAGAGG-AGAGTAG_L001_RNA-seq

description: RNA


title: Placebo36_TAGGCAT-ACTGCAT_L001_RNA-seq

description: RNA


title: Placebo37_CTCTCTA-AAGGAGT_L001_RNA-seq

description: RNA


title: Placebo35_GGACTCC-GTAAGGA_L001_RNA-seq

description: RNA


title: Gem2nM54_CGAGGCT-ACTGCAT_L001_RNA-seq

description: RNA


title: Placebo34_TCCTGAG-AGAGTAG_L001_RNA-seq

description: RNA


title: Placebo32_CGTACTA-CTCTCTA_L001_RNA-seq

description: RNA


title: NotreatH20_GGACTCC-GCGTAAG_L001_RNA-seq

description: RNA


title: Placebo33_AGGCAGA-TATCCTC_L001_RNA-seq

description: RNA


title: Notreat22_CGAGGCT-CTCTCTA_L001_RNA-seq

description: RNA


title: Notreat16_TAGGCAT-ACTGCAT_L001_RNA-seq

description: RNA


title: Notreat17_CTCTCTA-AAGGAGT_L001_RNA-seq

description: RNA


title: Notreat27_AGGCAGA-AAGGAGT_L001_RNA-seq

description: RNA


title: Notreat14_TCCTGAG-AGAGTAG_L001_RNA-seq

description: RNA


title: Notreat25_TAAGGCG-GTAAGGA_L001_RNA-seq

description: RNA


title: Notreat28_TCCTGAG-CTAAGCC_L001_RNA-seq

description: RNA


title: Notreat26_CGTACTA-ACTGCAT_L001_RNA-seq

description: RNA


title: Notreat13_AGGCAGA-TATCCTC_L001_RNA-seq

description: RNA


title: Notreat21_GCTACGC-GCGTAAG_L001_RNA-seq

description: RNA


title: Notreat24_GTAGAGG-AGAGTAG_L001_RNA-seq

description: RNA


title: Notreat11_TAAGGCG-GCGTAAG_L001_RNA-seq

description: RNA


title: C1SCN5_AAGAGGC-TATCCTC_L001_RNA-seq

description: RNA

source_name: CFPAC-1_None_Fluidigm C1

value: Fluidigm C1


title: Notreat12_CGTACTA-CTCTCTA_L001_RNA-seq

description: RNA


title: C1SCN71_AGGCAGA-AAGGAGT_L001_RNA-seq

description: RNA


title: C1MCN61_GCTACGC-TAGATCG_L001_RNA-seq

description: RNA


title: Notreat15_GGACTCC-GTAAGGA_L001_RNA-seq

description: RNA


title: Notreat18_CAGAGAG-CTAAGCC_L001_RNA-seq

description: RNA


title: C1SCN25_TAAGGCG-GTAAGGA_L001_RNA-seq

description: RNA


title: C1SCN17_GTAGAGG-AGAGTAG_L001_RNA-seq

description: RNA


title: C1MCN89_CGAGGCT-CTCTCTA_L001_RNA-seq

description: RNA


title: C1MCN33_CTCTCTA-AAGGAGT_L001_RNA-seq

description: RNA


title: Placebo31_TAAGGCG-GCGTAAG_L001_RNA-seq

description: RNA


title: C1MCN19_TAGGCAT-ACTGCAT_L001_RNA-seq

description: RNA


title: C1EN96_GGACTCC-GTAAGGA_L001_RNA-seq

description: RNA


title: Notreat23_AAGAGGC-TATCCTC_L001_RNA-seq

description: RNA


title: C1EN91_TCCTGAG-AGAGTAG_L001_RNA-seq

description: RNA


title: C1MCN43_CAGAGAG-CTAAGCC_L001_RNA-seq

description: RNA


title: TwoCells7_TCCTGAG-AGAGTAG_L001_RNA-seq

description: RNA


title: C1EN81_AGGCAGA-TATCCTC_L001_RNA-seq

description: RNA


title: TwoCells8_GGACTCC-AGAGTAG_L001_RNA-seq

description: RNA


title: TwoCells4_CGTACTA-AGAGTAG_L001_RNA-seq

description: RNA


title: OneCell8_GGACTCC-CTCTCTA_L001_RNA-seq

description: RNA


title: C1EN61_CGTACTA-CTCTCTA_L001_RNA-seq

description: RNA


title: TwoCells6_AGGCAGA-AGAGTAG_L001_RNA-seq

description: RNA


title: C1SCN49_CGTACTA-ACTGCAT_L001_RNA-seq

description: RNA


title: Rnd2Water_TCCTGAG-TATCCTC_L001_RNA-seq

description: RNA


title: TwoCells3_TAAGGCG-AGAGTAG_L001_RNA-seq

description: RNA


title: OneCell6_TCCTGAG-CTCTCTA_L001_RNA-seq

description: RNA


title: OneCell2_TAAGGCG-CTCTCTA_L001_RNA-seq

description: RNA


title: OneCell3_CGTACTA-CTCTCTA_L001_RNA-seq

description: RNA


title: mCh2Rnd2_CGTACTA-TATCCTC_L001_RNA-seq

description: RNA

value: Bulk


title: mCh1Rnd1_TAAGGCG-TATCCTC_L001_RNA-seq

description: RNA


title: OneCell5_AGGCAGA-CTCTCTA_L001_RNA-seq

description: RNA


title: Empty8_GGACTCC-GCGTAAG_L001_RNA-seq

description: RNA


title: Water-1_CGTACTA-TATCCTC_L001_RNA-seq

description: RNA


title: RAFTST16_CGTACTA-AAGGAGT_L001_RNA-seq

description: RNA


title: RAFTST9_AGGCAGA-GTAAGGA_L001_RNA-seq

description: RNA


title: C1EN31_TAAGGCG-TAGATCG_L001_RNA-seq

description: RNA


title: Water-2_GGACTCC-AAGGAGT_L001_RNA-seq

description: RNA


title: RAFTST15_TAAGGCG-AAGGAGT_L001_RNA-seq

description: RNA


title: Empty2_TAAGGCG-GCGTAAG_L001_RNA-seq

description: RNA


title: RAFTST11_TCCTGAG-GTAAGGA_L001_RNA-seq

description: RNA


title: RAFTST13_GGACTCC-GTAAGGA_L001_RNA-seq

description: RNA


title: RAFTSO9_AGGCAGA-TATCCTC_L001_RNA-seq

description: RNA


title: RAFTSE9_TAAGGCG-GCGTAAG_L001_RNA-seq

description: RNA


title: RAFTSE13_GGACTCC-GCGTAAG_L001_RNA-seq

description: RNA


title: RAFTSE12_TCCTGAG-GCGTAAG_L001_RNA-seq

description: RNA


title: RAFTSE11_AGGCAGA-GCGTAAG_L001_RNA-seq

description: RNA


title: RAFTSO15_CGTACTA-GTAAGGA_L001_RNA-seq

description: RNA


title: mch2-1_TAAGGCG-TATCCTC_L001_RNA-seq

description: RNA


title: Kasumi-3_input

city: Madison

first: Kyle

last: Hewitt

state: Wisconsin

address: 1111 Highland Ave.

institute: University of Wisconsin

description:
Input DNA in a human AML cell line
untreated cells

data_processing:
Sequence reads were aligned to the genome using the Eland alignment program.
Data was scored using Sole-Search based on sequence reads (length ~30 bps) that align uniquely to human genome (build hg19 ). From the mapped tags, a signal map of ChIP DNA fragments (average fragment length ~ 200 bp) was constructed where the signal height is the number of overlapping fragments at each nucleotide position in the genome.
Peaks were called using Sole-search (false-discovery rate, 0.0001; α value 0.001) with sequenced Kasumi-3 input DNA as background.
Genome_build: hg19
Supplementary_files_format_and_content: sgr files were generated using Sole-search

source_name: Kasumi-3 cells

growth_protocol: Kasumi-3 cells were maintained in RPMI 1640 medium (Invitrogen/Thermo Fisher Scientific, Waltham, MA, USA) containing 1% penicillin-streptomycin and 20% fetal bovine serum (FBS).

extract_protocol:
ChIP-Seq was performed by Peggy J. Farnham at University of Southern California. Immunoprecipitated DNA was processed into Illumina libraries using standard procedures, and libraries were sequenced on Illumina GenomeAnalyzer Iix.
Immunoprecipitated DNA was processed into Illumina libraries using standard procedures.

treatment_protocol: Samples containing 3 x 10^6 cells were crosslinked with 1% formaldehyde for 10 min.  Crosslinking reaction was extinguished by adding glycine to 125 mM. Lysates were immunoprecipitated with rabbit polyclonal anti-GATA-2 antibody.


title: Empty7_TCCTGAG-GCGTAAG_L001_RNA-seq

description: RNA


title: Kasumi-3_GATA2_N2

description:
GATA-2 ChIP-seq in a human AML cell line
untreated cells


title: RAFTSE10_CGTACTA-GCGTAAG_L001_RNA-seq

description: RNA


title: Empty6_AGGCAGA-GCGTAAG_L001_RNA-seq

description: RNA


title: P1

city: Skudai

first: Chun Shiong

last: Chong

state: Johor

address: Building T02, Faculty of Biosciences and Medical Engineering Universiti Teknologi Malaysia

department: Department of Biotechnology and Medical Engineering

country: Malaysia

institute: Universiti Teknologi Malaysia

data_processing:
The raw data obtained from RNA-seq was further base-calling, aligned filtered by ChunLab, Inc. Seoul National University, Bldg 105-1, Suite #307, 1 Gwanak-ro, Gwanak-gu,  eoul, Korea 151-742
The relative transcript abundance was computed by counting the trimmed mean of M values (TMM) (Robinson et al., 2010)
Genome_build: C289
Supplementary_files_format_and_content: The total read count for each samples was generate using CLRNA-seq software in xlsx.file

organism: Anoxybacillus ayderensis

source_name: Hot spring

growth_protocol: Anoxybacillus sp. SK 3-4 was streaked on the Thermus Medium (TM) agar plate aseptically. The plate was sealed and incubated at 55°C overnight (generally 18 hours). The bacteria inoculum was prepared by inoculated the Anoxybacillus sp. SK 3-4 from the plate into conical flask containing 25 mL of TM broth and then incubated at 55°C and 200 rpm for 18 hours.

extract_protocol:
The RNA was extracted using RNeasy Protect Bacteria Mini Kit (Qiagen) according to the instructions detailed by the manufacturer.
The cDNA was synthesized from total RNA using ScriptSeq™ Complete Kit (Bacteria).

treatment_protocol: The inoculum was transferred into two sterile conical flasks containing medium with 0 mg L-1 and 600 mg L-1 aluminum, respectively. Then, the flasks were incubated at 55°C and 200 rpm for 3 hours.

tag: strain

tag: treatment

value: 0 MG l-1 aluminum


first: Dario

last: Beraldi

address: Robinson Way

country: United Kingdom

institute: Cambridge Research Institute

description:
rhh175_ChIPwthacat_704_502_entst_26082015
processed data file: rhh175_ChIPwthacat_704_502_entst_26082015_peaks.narrowPeak.gz

data_processing:
Library strategy: BG4-ChIP
bcl files were converted to fastq using bcl2fastq v2.15.0.4 with default options.
See https://github.com/sblab-bioinformatics/dna-secondary-struct-chrom-lands/blob/master/Methods.md
Genome_build: hg19
Supplementary_files_format_and_content: For narrowPeak format see MACS2 documentation at https://github.com/taoliu/MACS/.   The text format files are differential binding and differential expression tables with columns:   logFC: the log-abundance ratio, i.e.  fold change, for each tag in the two groups being compared,   logCPM: the log-average concentration/abundance for each tag in the two groups being compared,  PValue exact p-value for differential expression using the NB model,  FDR the p-value adjusted for multiple testing

source_name: cell line

extract_protocol:
See methods section in the associated manuscript
See methods section in the associated manuscript

value: HACAT

value: Control


title: rhh174_ChIP9_701_503_entst_26082015

description:
rhh_ChIP_entst_26082015
processed data file: rhh_ChIP_entst_26082015_peaks.narrowPeak.gz

value: Entinostat


title: V2

value: 600 mg L-1 aluminum


title: P3


title: RAFTSO13_GGACTCC-TATCCTC_L001_RNA-seq

description: RNA


description:
rhh178_inputwthacat_703_517_entst_26082015
BG-input


title: RAFTSO14_TAAGGCG-GTAAGGA_L001_RNA-seq

description: RNA


title: RAFTSO12_TCCTGAG-TATCCTC_L001_RNA-seq

description: RNA


title: P2


title: rhh172_ChIP4_704_504_entst_17082015

description:
rhh_ChIP_entst_17082015
processed data file: rhh_ChIP_entst_17082015_peaks.narrowPeak.gz


title: rhh173_ChIP8_706_502_entst_26082015


title: rhh171_ChIP3_703_503_entst_17082015


title: rhh169_ChIP1_702_502_entst_17082015


title: rhh153_25cyc_BG4_Rep2_702_502_12082015

description:
rhh_25cyc_BG4_12082015
processed data file: rhh_25cyc_BG4_12082015_peaks.narrowPeak.gz


title: MCH2-2_AGGCAGA-AAGGAGT_L001_RNA-seq

description: RNA


title: rhh177_Input_705_517_entst_26082015

description:
rhh177_Input_705_517_entst_26082015
BG-input


title: rhh151_25cyc_BG4_Rep1_701_517_12082015


title: Kasumi-3_GATA2_N1


title: rhh150_untreatedRep2P70327052014

description:
rhh149-150_untreat_27052014_atact_hacat
processed data file: rhh149-150_untreat_27052014_atact_hacat_peaks.narrowPeak.gz

data_processing:
Library strategy: ATAC-Seq
bcl files were converted to fastq using bcl2fastq v2.15.0.4 with default options.
See https://github.com/sblab-bioinformatics/dna-secondary-struct-chrom-lands/blob/master/Methods.md
Genome_build: hg19
Supplementary_files_format_and_content: For narrowPeak format see MACS2 documentation at https://github.com/taoliu/MACS/.   The text format files are differential binding and differential expression tables with columns:   logFC: the log-abundance ratio, i.e.  fold change, for each tag in the two groups being compared,   logCPM: the log-average concentration/abundance for each tag in the two groups being compared,  PValue exact p-value for differential expression using the NB model,  FDR the p-value adjusted for multiple testing


title: V5


title: rhh148_untreated_rep1_14102014

description:
rhh147-148_untreat_14102014_atac_hacat
processed data file: rhh147-148_untreat_14102014_atac_hacat_peaks.narrowPeak.gz


title: Empty4_CGTACTA-GCGTAAG_L001_RNA-seq

description: RNA


title: V3


title: rhh147_unteated_rep2_14102014


title: rhh146_K4_N711_N501

description:
rhh145-146_K3_K4_atac_hacat
processed data file: rhh145-146_K3_K4_atac_hacat_peaks.narrowPeak.gz


title: rhh155_25cyc_input_703_503_12082015

description:
rhh155_25cyc_input_703_503_12082015
BG-input


title: rhh145_K3_N710_N501


title: rhh114_HEKnp_ATAC_702_502_24022015

description:
rhh_HEKnp_ATAC_24022015
processed data file: rhh_HEKnp_ATAC_24022015_peaks.narrowPeak.gz

value: NHEK


title: rhh077_Input2_N702_N502_HEKnp_FAIRE_BG4DIPseq_09112014

description:
rhh_hek_09112014_FAIRE
processed data file: rhh_hek_09112014_FAIRE.narrowPeak.gz

data_processing:
bcl files were converted to fastq using bcl2fastq v2.15.0.4 with default options.
See https://github.com/sblab-bioinformatics/dna-secondary-struct-chrom-lands/blob/master/Methods.md
Genome_build: hg19
Supplementary_files_format_and_content: For narrowPeak format see MACS2 documentation at https://github.com/taoliu/MACS/.   The text format files are differential binding and differential expression tables with columns:   logFC: the log-abundance ratio, i.e.  fold change, for each tag in the two groups being compared,   logCPM: the log-average concentration/abundance for each tag in the two groups being compared,  PValue exact p-value for differential expression using the NB model,  FDR the p-value adjusted for multiple testing


title: rhh116_HEKnp_ATAC_701_517_27032015

description:
rhh_HEKnp_ATAC_27032015
processed data file: rhh_HEKnp_ATAC_27032015_peaks.narrowPeak.gz


title: rhh056_FAIRE_Input2_N703_N501_05082014

description:
rhh_hacat_05082014_FAIRE
processed data file: rhh_hacat_05082014_FAIRE.narrowPeak.gz


title: rhh170_ChIP10_702_504_entst_26082015


title: rhh113_HEKnp_ATAC_701_517_24022015


title: rhh0188_705_517_ATAC_entinostat_bio2_2_23102015

description:
rhh_ATAC_entinostat_bio2_23102015
processed data file: rhh_ATAC_entinostat_bio2_23102015_peaks.narrowPeak.gz


title: rhh0184_703_503_ATAC_entinostat_bio1_3_23102015

description:
rhh_ATAC_entinostat_bio1_23102015
processed data file: rhh_ATAC_entinostat_bio1_23102015_peaks.narrowPeak.gz


title: rhh118_HEKnp_ATAC_704_504_27032015


title: rhh074_Input1_N701_N501_HEKnp_FAIRE_BG4DIPseq_09112014


title: rhh063_HEKnp_FAIREinp_N701_N502_18092014

description:
rhh_hek_18092014_FAIRE
processed data file: rhh_hek_18092014_FAIRE.narrowPeak.gz


title: rhh0181_706_502_ATAC_entinostat_bio2_3_23102015


title: rhh050_FAIRE_Input_P705_14062014

description:
rhh_hacat_14062014_FAIRE
processed data file: rhh_hacat_14062014_FAIRE.narrowPeak.gz


title: rhh0179_701_517_ATAC_entinostat_bio1_1_23102015


title: rhh051_FAIRE_Input_P706_14062014


title: rhh0180_704_504_ATAC_entinostat_bio2_1_23102015


title: rhh149_untreatedRep1P70127052014


title: rhh117_HEKnp_ATAC_702_502_27032015


title: merged_14_and_15072015_input_heknplonza

description:
merged_14_and_15072015_input_heknplonza
BG-input


title: HaCaT_3


title: HaCaT_4


title: HaCaT_1


title: HEKnp_Lonza_1472015_BG4

description:
HEKnp_Lonza_1472015_BG4
processed data file: HEKnp_Lonza_1472015_BG4.1e4_peaks.narrowPeak.gz


title: HaCaT_2


title: rhh115_HEKnp_ATAC_703_503_24022015


title: HEKnp_Lonza_1572015_BG4

description:
HEKnp_Lonza_1572015_BG4
processed data file: HEKnp_Lonza_1572015_BG4.1e4_peaks.narrowPeak.gz


title: rhh0183_702_502_ATAC_entinostat_bio1_2_23102015


title: Entinostat_3


title: Entinostat_4


title: Entinostat_2


title: HEK_Gibco_1


title: Entinostat_1


title: L/L, cre rep2

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

data_processing:
Basecalling performed with MSR: Generate FASTQ v1.0.0
Sequenced reads were aligned to the mouse genome (GRCm38) with HISAT 0.1.6 (--fr --rna-strandness RF). Reads that aligned to the mitochondria were extracted and subsequently realigned with identical parameters, but spliced alignment disabled, to reflect the un-spliced nature of the mitochondrial transcriptome and prevent the introduction of spurious splice junctions.
Gene-specific counts were summarized with featureCounts 1.3.5-p4 (-p -s 2 -Q 10) using the Ensembl 75 gene annotation for nuclear-encoded genes, and a modified annotation for mitochondrial genes. The modified annotation was based on the Ensembl 75 MT annotation, but contains merged mt-Atp8/mt-Atp6 and mt-Nd4l/mt- Nd4 annotations to reflect their bicistronic nature and accurately determine read counts.
Initially, mt-tRNAs and genes with a zero count in any sample were filtered from the count table, followed by loess and upper quartile normalization for GC-content and sequencing depth, performed with EDASeq 2.3.2.
Differential expression analysis was performed in R 3.2.0 with edgeR 3.11.2 using a GLM with tagwise dispersion estimates and the offsets generated by EDASeq.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files containing raw counts, normalized counts and differential expression results

source_name: L/L cre, heart mitochondria

growth_protocol: To generate conditional Polrmt knockout mice, exon 3 was loxP-flanked (Taconic Artemis GmbH, Cologne, Germany) and excised by breeding to mice expressing cre from the muscle creatinine kinase promoter.

extract_protocol:
RNA was isolated from crude heart mitochondria using the miRNeasy mini kit (QIAGEN) and the concentration, purity, and integrity was confirmed using a BioAnalyser.
RNA sequencing libraries were constructed using the Illumina TruSeq Sample Prep Kit. Paired end deep sequencing of the mitochondrial RNAs was performed on an Illumina MiSeq according to the manufacturer’s instructions.

value: heart

tag: genotype

value: Polrmt -/-

value: 3-4 weeks

tag: molecule subtype

value: mitochondrial RNA


title: L/L, cre rep1

tag: age


title: L/L, rep3

source_name: L/L, heart mitochondria

value: Polrmt +/+


title: L/L, rep1


title: L/L, rep2


title: SW780 foxp3 delta 3_3

first: Kelvin

last: Zhang

address: 35 CambridgePark Drive, Suite 500

institute: Codiak Biosciences

data_processing:
We first filtered out reads with low quality and reads containing sequencing adapters and then mapped raw reads (single-end, 50bp in length) to the Homo sapiens reference genome (UCSC hg19) with the gapped aligner Tophat allowing up to two mismatches.
We supplied the UCSC hg19 gene model to Tophat as the reference genome annotation. Only reads uniquely aligned were collected.
Transcript expression levels were quantified using RPKM units (Reads Per Kilobase of exon per Million reads mapped) using customized scripts written in Perl.
Genome_build: hg19
Supplementary_files_format_and_content: a txt file contains RPKMs of all samples

growth_protocol: cells overexpressing foxp3 (delta3 and full length) were maintained in G418 for selection

extract_protocol:
RNA was isolated with Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: bladder cancer cells

tag: overexpression

value: foxp3 delta3


title: SW780 parental_3


title: HEK_Gibco_4

tag: cell line


title: SW780 foxp3 delta 3_1


title: SW780 parental_2


title: SW780 foxp3 full length_1

value: full length foxp 3


title: L/L, cre rep3


title: SW780 foxp3 full length_2


title: SW780 parental_1


title: Stress Male 3

status: Public on Aug 04 2016

first: Immanuel

last: Purushothaman

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description:
Sample name: sm3
Processed data file: counts.txt
Processed data file: Stress_vs_Control_lists_all.xls

data_processing:
Bowtie2: 2.1.0, defaults
TopHat2: 2.0.9, --no-novel-juncs --b2-very-sensitive
HTSeq: 0.6.0, -s no
Genome_build: NCBIM37 (NCBI Build 37, MGSCv37, UCSC mm9)
Supplementary_files_format_and_content: counts.txt: Raw count matrix
Supplementary_files_format_and_content: Excel files: Differential list. "logFC" refers to log2(Fold change) and "AveExpr" refers to average expression across all samples.

source_name: Brain tissue, WT, male, stress

extract_protocol:
NAc samples were collected and processed as described previously (Golden et al., 2013). Bilateral 14-gauge NAc dorsal striatum punches were collected on ice after rapid decapitation and then immediately placed on dry ice and stored at -80°C until use. RNA was isolated using homogenization in Trizol (Invitrogen) followed by chloroform layer separation. The clear RNA layer was then processed (RNeasy MicroKit, QIAGEN) and analyzed with NanoDrop (Thermo Scientific). A total of 500 ng of RNA was then reverse transcribed to cDNA (qScript Kit, VWR).
Library construction was performed following a previously published protocol (Feng et al., 2014). Bilateral 14 gauge NAc dorsal striatum punches were collected on ice and stored as described above. RNA was purified with RNeasy Micro columns, and Bioanalyzer confirmed that the RNA integrity numbers were >8.0. Total RNA (4 μg) was used for mRNA library construction following instructions of Illumina mRNA sample prep kit (catalog #RS-100-0801). Libraries were created from pooled mRNA samples (n = 4 mice/library and run in independent biological replicates of 3 libraries per sex/stress).

tag: strain/background

value: WT

tag: virus

tag: Sex

value: Male

value: Nucleus accumbens

value: Stress


title: Stress Male 2

description:
Sample name: sm2
Processed data file: counts.txt
Processed data file: Stress_vs_Control_lists_all.xls

tag: genotype/variation


title: Stress Male 1

description:
Sample name: sm1
Processed data file: counts.txt
Processed data file: Stress_vs_Control_lists_all.xls


title: Stress Female 2

description:
Sample name: sf2
Processed data file: counts.txt
Processed data file: Stress_vs_Control_lists_all.xls

source_name: Brain tissue, WT, female, stress

value: Female


title: Stress Female 3

description:
Sample name: sf3
Processed data file: counts.txt
Processed data file: Stress_vs_Control_lists_all.xls


title: Stress Female 1

description:
Sample name: sf1
Processed data file: counts.txt
Processed data file: Stress_vs_Control_lists_all.xls


title: Control Male 3

description:
Sample name: cm3
Processed data file: counts.txt
Processed data file: Stress_vs_Control_lists_all.xls

source_name: Brain tissue, WT, male, control

value: Control


title: HEK_Gibco_2


title: Control Male 1

description:
Sample name: cm1
Processed data file: counts.txt
Processed data file: Stress_vs_Control_lists_all.xls


title: Control Female 3

description:
Sample name: cf3
Processed data file: counts.txt
Processed data file: Stress_vs_Control_lists_all.xls

source_name: Brain tissue, WT, female, control


title: SW780 foxp3 full length_3


title: Control Female 1

description:
Sample name: cf1
Processed data file: counts.txt
Processed data file: Stress_vs_Control_lists_all.xls


title: GFP Male 2

description:
Sample name: GFP_m2
Processed data file: counts.txt
Processed data file: GFP_CRE_comparisons.xls

source_name: Brain tissue, Dnmt3a2lox/2lox, GFP, male, stress

value: AAV-GFP


title: SW780 foxp3 delta 3_2


title: rhh055_FAIRE_Input1_N701_N501_05082014

description:
rhh_hacat_05082014_FAIRE
processed data file: rhh_hacat_05082014_FAIRE.narrowPeak.gz

value: HACAT


title: Control Female 2

description:
Sample name: cf2
Processed data file: counts.txt
Processed data file: Stress_vs_Control_lists_all.xls


title: HEK_Gibco_3

value: NHEK


title: GFP Female 3

description:
Sample name: GFP_f3
Processed data file: counts.txt
Processed data file: GFP_CRE_comparisons.xls

source_name: Brain tissue, Dnmt3a2lox/2lox, GFP, female, stress


title: CRE Male 2

description:
Sample name: CRE_m2
Processed data file: counts.txt
Processed data file: GFP_CRE_comparisons.xls

source_name: Brain tissue, Dnmt3a2lox/2lox, CRE, male, stress

value: AAV-CRE


title: Control Male 2

description:
Sample name: cm2
Processed data file: counts.txt
Processed data file: Stress_vs_Control_lists_all.xls


title: CRE Female 1

description:
Sample name: CRE_f1
Processed data file: counts.txt
Processed data file: GFP_CRE_comparisons.xls

source_name: Brain tissue, Dnmt3a2lox/2lox, CRE, female, stress


title: CRE Female 3

description:
Sample name: CRE_f3
Processed data file: counts.txt
Processed data file: GFP_CRE_comparisons.xls


title: GFP Female 2

description:
Sample name: GFP_f2
Processed data file: counts.txt
Processed data file: GFP_CRE_comparisons.xls


title: CRE Male 3

description:
Sample name: CRE_m3
Processed data file: counts.txt
Processed data file: GFP_CRE_comparisons.xls


title: CRE Male 1

description:
Sample name: CRE_m1
Processed data file: counts.txt
Processed data file: GFP_CRE_comparisons.xls


title: KO-65

data_processing:
Basecalling was performed by HiSeq Control Software
Quality and adapter trimming was performed with Flexbar v2.5
To analyse the nuclear transcriptome:
Reads were aligned to the mouse genome using HiSat v.0.1.6-beta.
Guided transcriptome assembly (GRCm38.81) was done using StringTie v.1.1.0.
Cufflinks v.2.2.1 was then used for analysis of differential expression. Briefly, cuffmerge was used to merge all assemblies with the reference assembly as template, and cuffquant followed by cuffdiff (--dispersion-method per-condition) for quantification and differential analysis.
genome build: GRCm38
Tab-delimited txt containing FPKM values for each sample calculated by CuffDiff
To analyse the mitochondrial trancriptome:
Sequenced reads were initially aligned to the mouse genome with HISAT2 v2.0.1-beta (--very-sensitive --fr --rna-strandness RF --phred33 --no-mixed --no-discordant). The read IDs of all mitochondrial primary alignments were extracted with SAMtools v1.3, and used to filter the original alignments into nuclear and mitochondrial alignment files with Picard v1.23. The mitochondrial alignments were converted back to their original read sequence in fastq format with Picard, and realigned to the mitochondrial genome as before with the additional parameter --no-spliced-alignment.
Primary mitochondrial alignments were extracted and separated according to their template strand-of-origin with SAMtools and converted to template strand-specific fragment BED files with BEDtools and awk.
Per-base depth of strand-specific fragment BED files were generated with BEDtools normalized by the total number of properly mapped pairs per million across the whole genome (nuclear and mitochondrial) and converted to bedGraph format.
genome build: mm10
Strand-specific fragment coverage for each sample in bedGraph format, in reads per million (RPM)

growth_protocol: Mice were housed in standard cages (45 cm × 29 cm × 12 cm) under a 12-h light/dark schedule (lights on 7 am to 7 pm) in controlled environmental conditions of 22 ± 2 °C and 50 + 10% relative humidity and fed a normal chow diet (Rat & Mouse Chow, Specialty Foods, Glen Forrest, Western Australia) and water were provided ad libitum.

extract_protocol:
RNA was isolated from total hearts or heart mitochondria using the miRNeasy Mini kit (Qiagen) incorporating an on-column RNase-free DNase digestion to remove all DNA.
Total RNA libraries were prepared according to the Illumina TruSeq protocol, using random hexamer primers for cDNA generation and the Ribo-Zero rRNA removal kit for cytoplasmic RNA deptetion. Mitochondrial RNA was prepared according to the PARE protocol as described by German et al. (Nature Protocols, Vol.4 No.3, 2009).

value: Heart

value: 11 weeks

value: Mrpp3^loxP/loxP, +/Ckmm

tag: molecule

value: total cellular RNA from heart


title: WT-523


title: GFP Female 1

description:
Sample name: GFP_f1
Processed data file: counts.txt
Processed data file: GFP_CRE_comparisons.xls


title: WT-522


title: Naïve_CD4_rep3 (Sample 85)

first: Hyein

middle: Sophia

last: Cho

address: 430 E 67th St

department: Developmental Biology

institute: Memorial Sloan Kettering Cancer Center

description: LCMV-specific GP66-tetramer+ memory CD4 T cells were isolated 60 days p.i and transferred to congenically marked recipients. Recipients were infected with LCMV and 60 days later primary and secondary memory T cells were isolated. Naïve CD4 T cells from recipient mice were used as controls

data_processing:
Sequences mapped using STAR 2.5.0
Expression level was quantified with refGene annotation
DESeq2 analysis was run with q-value cutoff of 0.05
Genome_build: mm9
Supplementary_files_format_and_content: [htseq.txt and bam-genes.txt] DESeq2-normalized read counts for RNA-Seq samples
Supplementary_files_format_and_content: [countsatatacseqpeaks.txt] peaks for ATAC-Seq and ChIP-Seq samples

extract_protocol: Sorted cells were lysed with TRIzol and stored at -80 degree. RNA was extracted according to the manufacturer’s manual (Life Technologies). cDNA libraries were generated using SMARTer amplification (Clontech) and individually indexed. Libraries were sequenced on HiSeq 2000 platform (Illumina).

value: Spleen

value: naive CD4 T cells

tag: activating stimulus

value: Uninfected control

tag: days post-stimulus


title: Wild type Stomach [ChIP-seq]

first: Abby

last: Sarkar

address: 185 Cambridge Street

department: Cancer Center

institute: Harvard University

data_processing:
Sequencing reads were mapped to the mouse genome (mm9 build) using the aligner Bowtie2.
Sox2 peak calling was performed with MACS (Zhang, et a. 2008) for both the WT and KO samples.
Supplementary_files_format_and_content: MACS peak bed files

source_name: Stomach

extract_protocol:
Gastric glands were isolated from mouse antrum as described (Barker et al., 2010) and cross-linked with 1% formaldehyde for 10 min at room temperature. Chromatin fractions were sheared by sonication. ChIP-enriched and input DNA were purified and genomic libraries were prepared as described (Sulahian et al., 2014), using four micrograms of goat anti-SOX2 (AF2018, R&D).
Genomic libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Both Sox2 KO mice (Rosa26CreER; Sox2 fl/fl) and Sox2 WT mice (Rosa26WT; Sox2fl/fl) were treated with Tamoxifen at 8 weeks of age. Stomaches from these mice were isolated 2 weeks later.

tag: strain background

value: C57BL/6 x 129 mixed

value: wild type

value: 8 weeks

value: Stomach

tag: chip antibody

value: goat anti-SOX2 (AF2018, R&D).


title: Naïve_CD4_rep1 (Sample 83)

tag: tissue

tag: strain


title: Naïve_CD4_rep2 (Sample 84)


title: Sox2 KO Stomach  [ChIP-seq]

value: RosaCreER;; Sox2fl/fl


title: Wild type Stomach [input]


title: GFP Male 1

description:
Sample name: GFP_m1
Processed data file: counts.txt
Processed data file: GFP_CRE_comparisons.xls

value: AAV-GFP

value: Male

value: Nucleus accumbens

tag: treatment

value: Stress


title: GP66+_secondary_memory_rep3 (Sample 82)

value: GP66 tetramer+ secondary memory CD4 T cells

value: LCMV-infection

value: 60 days


title: GFP Male 3

description:
Sample name: GFP_m3
Processed data file: counts.txt
Processed data file: GFP_CRE_comparisons.xls


title: WT-521

value: Heart

value: 11 weeks

tag: genotype

value: total cellular RNA from heart


title: GP66+_primary_memory_rep2 (Sample 78)

value: Spleen

value: GP66 tetramer+ primary memory CD4 T cells


title: GP66+_secondary_memory_rep2 (Sample 81)


title: GP66+_secondary_memory_rep1 (Sample 80)


title: Foxp3_GFPKO_post_Tfx_rep1 (Sample 75)

description: GFP+ CD45.1+ CD4 T cells were isolated from animals hemizigous for the Foxp3GFPKO allele. and transferred into Foxp3-GFP-DTR mice. Recipients underwent suboptimal Treg depletion prior to transfer to increase recovery of donor cells. GFP+CD45.1+ cells were isolated 1 month post-transfer for RNA-seq

value: Spleen and peripheral lymph nodes

value: Inflammation-experienced cells expressing a Foxp3 reporter-null allele

tag: source

value: Foxp3-GFPKO CD45.1

value: Genetic Treg cell deficiency


title: Foxp3_GFPKO_post_Tfx_rep2 (Sample 76)

tag: cell type


title: GP66+_primary_memory_rep1 (Sample 77)


title: GP66+_primary_memory_rep3 (Sample 79)


title: CRE Female 2

description:
Sample name: CRE_f2
Processed data file: counts.txt
Processed data file: GFP_CRE_comparisons.xls

value: AAV-CRE

value: Female


title: Foxp3_GFPKO_rep2 (Sample 73)

description: GFP+ CD45.1+ CD4 T cells were isolated from animals hemizigous for the Foxp3GFPKO allele

value: Activated cells expressing a Foxp3 reporter-null allele


title: KO-66

tag: age

value: Mrpp3^loxP/loxP, +/Ckmm


title: aTr_post_Tfx_rep2 (Sample 70)

description: Activated Treg cells were isolated from Foxp3-GFP-DTR CD45.1 mice on day 11 post DT treatment and transferred into Foxp3GFP-DTR recipients 2 days after suboptimal Treg cell depletion. GFP+CD45.1+ cells were isolated one month post-transfer for RNA-seq

value: Inflammation-experienced Treg cells

value: Foxp3-GFP-DTR CD45.1

value: Transient Treg cell depletion

value: 11 days


title: Foxp3_GFPKO_rep3 (Sample 74)


title: aTr_post_Tfx_rep3 (Sample 71)


title: Foxp3_GFPKO_rep1 (Sample 72)


title: aTr_post_Tfx_rep1 (Sample 69)


title: KO-89

value: Heart


title: aTr_rep3 (Sample 68)

description: Treg cells were isolated from diphtheria toxin treated animals based on GFP expression

source_name: aTr

value: Activated Treg cells


title: rTr_rep2 (Sample 65)

description: Treg cells were isolated from untreated animals based on GFP expression

source_name: rTr

value: Resting Treg cells


title: aTr_rep1 (Sample 66)


title: aTr_rep2 (Sample 67)