title: Kcng4_2la_A5

description: single end RNA-seq data


title: Kcng4_2Ra_H9

status: Public on Aug 25 2016

type: SRA

city: Cambridge

first: Karthik

last: Shekhar

state: MA

address: 415 Main St.

country: USA

institute: Broad Institute

description: single end RNA-seq data

library_source: transcriptomic

data_processing:
Reads were aligned to a reference genome (mm10 Ensembl) using Tophat v2.0.10
Expression levels were quantified using RSEM v1.2.28 (inferred counts and tpm values)
Genome_build: mm10
Supplementary_files_format_and_content: text file with tab delimiters

molecule: total RNA

organism: Mus musculus

source_name: Mus musculus retina, P17

extract_protocol:
Dissociated retina were FACS sorted into 96-well plates (single cells) containing lysis buffer
Smart-seq2 (Picelli et al., Nature Methods, 2014)

tag: tissue

value: retina

tag: developmental stage

tag: retina id


title: Kcng4_2Ra_H8

description: single end RNA-seq data


title: Kcng4_2Ra_H7

description: single end RNA-seq data


title: Kcng4_2Ra_H6

description: single end RNA-seq data


title: Kcng4_2Ra_H5

description: single end RNA-seq data


title: Kcng4_2Ra_H4

description: single end RNA-seq data


title: Kcng4_2la_A10

description: single end RNA-seq data


title: Kcng4_2la_A1

description: single end RNA-seq data


title: Kcng4_2Ra_H3

description: single end RNA-seq data


title: Kcng4_2Ra_H12

description: single end RNA-seq data


title: Kcng4_2Ra_H2

description: single end RNA-seq data


title: Kcng4_2la_A11

description: single end RNA-seq data


title: Kcng4_2Ra_H11

description: single end RNA-seq data


title: Kcng4_2Ra_H10

description: single end RNA-seq data


title: Kcng4_2Ra_G9

description: single end RNA-seq data


title: Kcng4_2Ra_H1

description: single end RNA-seq data


title: Kcng4_2la_A8

description: single end RNA-seq data


title: Kcng4_2Ra_G8

description: single end RNA-seq data


title: Kcng4_2Ra_G7

description: single end RNA-seq data


title: Kcng4_2Ra_G6

description: single end RNA-seq data


title: Kcng4_2Ra_G5

description: single end RNA-seq data


title: Kcng4_2Ra_G2

description: single end RNA-seq data


title: Kcng4_2Ra_G11

description: single end RNA-seq data


title: Kcng4_2Ra_G3

description: single end RNA-seq data


title: Kcng4_2Ra_G12

description: single end RNA-seq data


title: Kcng4_2Ra_G1

description: single end RNA-seq data


title: Kcng4_2Ra_G10

description: single end RNA-seq data


title: Kcng4_2Ra_F9

description: single end RNA-seq data


title: Kcng4_2la_B12

description: single end RNA-seq data


title: Kcng4_2Ra_F4

description: single end RNA-seq data


title: Kcng4_2Ra_F6

description: single end RNA-seq data


title: Kcng4_2Ra_F7

description: single end RNA-seq data


title: Kcng4_2Ra_F3

description: single end RNA-seq data


title: Kcng4_2Ra_F8

description: single end RNA-seq data


title: Kcng4_2Ra_F10

description: single end RNA-seq data


title: Kcng4_2Ra_F1

description: single end RNA-seq data


title: Kcng4_2Ra_F12

description: single end RNA-seq data


title: Kcng4_2Ra_E8

description: single end RNA-seq data


title: Kcng4_2Ra_F2

description: single end RNA-seq data


title: Kcng4_2Ra_E6

description: single end RNA-seq data


title: Kcng4_2Ra_E7

description: single end RNA-seq data


title: Kcng4_2Ra_E5

description: single end RNA-seq data


title: Kcng4_2Ra_E4

description: single end RNA-seq data


title: Kcng4_2Ra_G4

description: single end RNA-seq data


title: Kcng4_2Ra_E1

description: single end RNA-seq data


title: Kcng4_2Ra_E3

description: single end RNA-seq data


title: Kcng4_2Ra_E11

description: single end RNA-seq data


title: Kcng4_2Ra_D9

description: single end RNA-seq data


title: Kcng4_2Ra_D8

description: single end RNA-seq data


title: Kcng4_2Ra_F5

description: single end RNA-seq data


title: Kcng4_2Ra_E10

description: single end RNA-seq data


title: Kcng4_2Ra_E9

description: single end RNA-seq data


title: Kcng4_2Ra_D4

description: single end RNA-seq data


title: Kcng4_2Ra_D7

description: single end RNA-seq data


title: Kcng4_2Ra_F11

description: single end RNA-seq data


title: Kcng4_2Ra_D6

description: single end RNA-seq data


title: Kcng4_2Ra_D5

description: single end RNA-seq data


title: Kcng4_2Ra_D3

description: single end RNA-seq data


title: Kcng4_2Ra_D1

description: single end RNA-seq data


title: Kcng4_2Ra_D12

description: single end RNA-seq data


title: Kcng4_2Ra_D10

description: single end RNA-seq data


title: Kcng4_2Ra_D2

description: single end RNA-seq data


title: Kcng4_2Ra_C7

description: single end RNA-seq data


title: Kcng4_2Ra_D11

description: single end RNA-seq data


title: Kcng4_2Ra_C5

description: single end RNA-seq data


title: Kcng4_2Ra_C9

description: single end RNA-seq data


title: Kcng4_2Ra_C4

description: single end RNA-seq data


title: Kcng4_2Ra_C6

description: single end RNA-seq data


title: Kcng4_2Ra_C2

description: single end RNA-seq data


title: Kcng4_2Ra_E2

description: single end RNA-seq data


title: Kcng4_2Ra_E12

description: single end RNA-seq data


title: Kcng4_2Ra_C1

description: single end RNA-seq data


title: Kcng4_2Ra_C3

description: single end RNA-seq data


title: Kcng4_2Ra_C12

description: single end RNA-seq data


title: Kcng4_2Ra_C11

description: single end RNA-seq data


title: Kcng4_2Ra_B9

description: single end RNA-seq data


title: Kcng4_2Ra_B6

description: single end RNA-seq data


title: Kcng4_2Ra_B7

description: single end RNA-seq data


title: Kcng4_2Ra_B5

description: single end RNA-seq data


title: Kcng4_2Ra_B2

description: single end RNA-seq data


title: Kcng4_2Ra_B12

description: single end RNA-seq data


title: Kcng4_2Ra_C8

description: single end RNA-seq data


title: Kcng4_2Ra_B11

description: single end RNA-seq data


title: Kcng4_2Ra_B4

description: single end RNA-seq data


title: Kcng4_2Ra_A9

description: single end RNA-seq data


title: Kcng4_2Ra_B1

description: single end RNA-seq data


title: Kcng4_2Ra_A7

description: single end RNA-seq data


title: Kcng4_2Ra_B10

description: single end RNA-seq data


title: Kcng4_2Ra_A5

description: single end RNA-seq data


title: Kcng4_2Ra_A4

description: single end RNA-seq data


title: Kcng4_2Ra_A6

description: single end RNA-seq data


title: Kcng4_2Ra_A2

description: single end RNA-seq data


title: Kcng4_2Ra_B3

description: single end RNA-seq data


title: Kcng4_2Ra_A12

description: single end RNA-seq data


title: Kcng4_2Ra_A11

description: single end RNA-seq data


title: Kcng4_1la_H9

description: single end RNA-seq data


title: Kcng4_2Ra_A8

description: single end RNA-seq data


title: Kcng4_2Ra_A3

description: single end RNA-seq data


title: Kcng4_1la_H8

description: single end RNA-seq data


title: Kcng4_2Ra_A10

description: single end RNA-seq data


title: Kcng4_2Ra_C10

description: single end RNA-seq data


title: Kcng4_1la_H6

description: single end RNA-seq data


title: Kcng4_1la_H7

description: single end RNA-seq data


title: Kcng4_2Ra_B8

description: single end RNA-seq data


title: Kcng4_2Ra_A1

description: single end RNA-seq data


title: Kcng4_1la_H4

description: single end RNA-seq data


title: Kcng4_1la_H3

description: single end RNA-seq data


title: Kcng4_1la_H1

description: single end RNA-seq data


title: Kcng4_1la_H11

description: single end RNA-seq data


title: Kcng4_1la_H2

description: single end RNA-seq data


title: Kcng4_1la_G7

description: single end RNA-seq data


title: Kcng4_1la_G8

description: single end RNA-seq data


title: Kcng4_1la_G9

description: single end RNA-seq data


title: Kcng4_1la_G4

description: single end RNA-seq data


title: Kcng4_1la_G5

description: single end RNA-seq data


title: Kcng4_1la_G12

description: single end RNA-seq data


title: Kcng4_1la_F8

description: single end RNA-seq data


title: Kcng4_1la_F6

description: single end RNA-seq data


title: Kcng4_1la_F7

description: single end RNA-seq data


title: Kcng4_1la_F9

description: single end RNA-seq data


title: Kcng4_1la_G3

description: single end RNA-seq data


title: Kcng4_1la_G1

description: single end RNA-seq data


title: Kcng4_1la_G10

description: single end RNA-seq data


title: Kcng4_1la_F5

description: single end RNA-seq data


title: Kcng4_1la_F4

description: single end RNA-seq data


title: Kcng4_1la_H5

description: single end RNA-seq data


title: Kcng4_1la_F2

description: single end RNA-seq data


title: Kcng4_1la_F1

description: single end RNA-seq data


title: Kcng4_1la_F3

description: single end RNA-seq data


title: Kcng4_1la_F12

description: single end RNA-seq data


title: Kcng4_1la_F10

description: single end RNA-seq data


title: Kcng4_1la_H12

description: single end RNA-seq data


title: Kcng4_1la_H10

description: single end RNA-seq data


title: Kcng4_1la_E9

description: single end RNA-seq data


title: Kcng4_1la_F11

description: single end RNA-seq data


title: Kcng4_1la_G6

description: single end RNA-seq data


title: Kcng4_1la_E8

description: single end RNA-seq data


title: Kcng4_1la_E5

description: single end RNA-seq data


title: Kcng4_1la_G2

description: single end RNA-seq data


title: Kcng4_1la_E4

description: single end RNA-seq data


title: Kcng4_1la_E7

description: single end RNA-seq data


title: Kcng4_1la_G11

description: single end RNA-seq data


title: Kcng4_1la_E3

description: single end RNA-seq data


title: Kcng4_1la_E2

description: single end RNA-seq data


title: Kcng4_1la_E1

description: single end RNA-seq data


title: Kcng4_1la_D9

description: single end RNA-seq data


title: Kcng4_1la_D8

description: single end RNA-seq data


title: Kcng4_1la_E11

description: single end RNA-seq data


title: Kcng4_1la_D6

description: single end RNA-seq data


title: Kcng4_1la_E12

description: single end RNA-seq data


title: Kcng4_1la_D5

description: single end RNA-seq data


title: Kcng4_1la_E10

description: single end RNA-seq data


title: Kcng4_1la_D7

description: single end RNA-seq data


title: Kcng4_1la_D2

description: single end RNA-seq data


title: Kcng4_1la_D3

description: single end RNA-seq data


title: Kcng4_1la_D11

description: single end RNA-seq data


title: Kcng4_1la_D1

description: single end RNA-seq data


title: Kcng4_1la_D12

description: single end RNA-seq data


title: Kcng4_1la_D10

description: single end RNA-seq data


title: Kcng4_1la_D4

description: single end RNA-seq data


title: Kcng4_1la_C6

description: single end RNA-seq data


title: Kcng4_1la_C7

description: single end RNA-seq data


title: Kcng4_1la_C5

description: single end RNA-seq data


title: Kcng4_1la_E6

description: single end RNA-seq data


title: Kcng4_1la_C8

description: single end RNA-seq data


title: Kcng4_1la_C9

description: single end RNA-seq data


title: Kcng4_1la_C4

description: single end RNA-seq data


title: Kcng4_1la_C12

description: single end RNA-seq data


title: Kcng4_1la_C3

description: single end RNA-seq data


title: Kcng4_1la_C11

description: single end RNA-seq data


title: Kcng4_1la_C10

description: single end RNA-seq data


title: Kcng4_1la_B9

description: single end RNA-seq data


title: Kcng4_1la_B7

description: single end RNA-seq data


title: Kcng4_1la_B2

description: single end RNA-seq data


title: Kcng4_1la_B3

description: single end RNA-seq data


title: Kcng4_1la_B4

description: single end RNA-seq data


title: Kcng4_1la_B1

description: single end RNA-seq data


title: Kcng4_1la_B6

description: single end RNA-seq data


title: Kcng4_1la_B5

description: single end RNA-seq data


title: Kcng4_1la_B11

description: single end RNA-seq data


title: Kcng4_1la_B12

description: single end RNA-seq data


title: Kcng4_1la_A7

description: single end RNA-seq data


title: Kcng4_1la_A6

description: single end RNA-seq data


title: Kcng4_1la_A4

description: single end RNA-seq data


title: Kcng4_1la_A3

description: single end RNA-seq data


title: Kcng4_1la_A8

description: single end RNA-seq data


title: Kcng4_1la_A12

description: single end RNA-seq data


title: Kcng4_1la_C1

description: single end RNA-seq data


title: Kcng4_1la_A9

description: single end RNA-seq data


title: Kcng4_1la_A5

description: single end RNA-seq data


title: Kcng4_1la_A11

description: single end RNA-seq data


title: Kcng4_1la_B8

description: single end RNA-seq data


title: Kcng4_1Ra_H9

description: single end RNA-seq data


title: Kcng4_1la_A10

description: single end RNA-seq data


title: Kcng4_1Ra_H7

description: single end RNA-seq data


title: Kcng4_1la_B10

description: single end RNA-seq data


title: Kcng4_1Ra_H3

description: single end RNA-seq data


title: Kcng4_1la_C2

description: single end RNA-seq data


title: Kcng4_1Ra_H10

description: single end RNA-seq data


title: Kcng4_1Ra_H5

description: single end RNA-seq data


title: Kcng4_1Ra_H4

description: single end RNA-seq data


title: Kcng4_1Ra_G7

description: single end RNA-seq data


title: Kcng4_1Ra_G4

description: single end RNA-seq data


title: Kcng4_1Ra_H1

description: single end RNA-seq data


title: Kcng4_1Ra_G3

description: single end RNA-seq data


title: Kcng4_1Ra_H12

description: single end RNA-seq data


title: Kcng4_1Ra_G8

description: single end RNA-seq data


title: Kcng4_1Ra_G1

description: single end RNA-seq data


title: Kcng4_1Ra_G11

description: single end RNA-seq data


title: Kcng4_1la_A2

description: single end RNA-seq data


title: Kcng4_1Ra_F8

description: single end RNA-seq data


title: Kcng4_1Ra_H2

description: single end RNA-seq data


title: Kcng4_1Ra_G6

description: single end RNA-seq data


title: Kcng4_1Ra_F6

description: single end RNA-seq data


title: Kcng4_1Ra_G5

description: single end RNA-seq data


title: Kcng4_1Ra_G2

description: single end RNA-seq data


title: Kcng4_1Ra_H11

description: single end RNA-seq data


title: Kcng4_1Ra_F5

description: single end RNA-seq data


title: Kcng4_1Ra_H8

description: single end RNA-seq data


title: Kcng4_1Ra_G12

description: single end RNA-seq data


title: Kcng4_1Ra_G10

description: single end RNA-seq data


title: Kcng4_1la_A1

description: single end RNA-seq data


title: Kcng4_1Ra_F9

description: single end RNA-seq data


title: Kcng4_1Ra_F7

description: single end RNA-seq data


title: Kcng4_1Ra_H6

description: single end RNA-seq data


title: Kcng4_1Ra_F4

description: single end RNA-seq data


title: Kcng4_1Ra_F3

description: single end RNA-seq data


title: Kcng4_1Ra_F12

description: single end RNA-seq data


title: Kcng4_1Ra_E9

description: single end RNA-seq data


title: Kcng4_1Ra_E8

description: single end RNA-seq data


title: Kcng4_1Ra_F2

description: single end RNA-seq data


title: Kcng4_1Ra_G9

description: single end RNA-seq data


title: Kcng4_1Ra_F10

description: single end RNA-seq data


title: Kcng4_1Ra_E7

description: single end RNA-seq data


title: Kcng4_1Ra_E6

description: single end RNA-seq data


title: Kcng4_1Ra_E4

description: single end RNA-seq data


title: Kcng4_1Ra_E2

description: single end RNA-seq data


title: Kcng4_1Ra_F1

description: single end RNA-seq data


title: Kcng4_1Ra_E5

description: single end RNA-seq data


title: Kcng4_1Ra_E11

description: single end RNA-seq data


title: Kcng4_1Ra_D9

description: single end RNA-seq data


title: Kcng4_1Ra_D8

description: single end RNA-seq data


title: Kcng4_1Ra_D7

description: single end RNA-seq data


title: Kcng4_1Ra_E12

description: single end RNA-seq data


title: Kcng4_1Ra_E1

description: single end RNA-seq data


title: Kcng4_1Ra_E3

description: single end RNA-seq data


title: Kcng4_1Ra_D5

description: single end RNA-seq data


title: acLDL+C1q rep3

city: Long Beach

first: Deborah

middle: A.

last: Fraser

state: California

address: 1250 Bellflower Blvd

department: Biological Sciences

institute: California State University, Long Beach

description: barcode: CGCTCATT-GTACTGAC

data_processing:
Base-calling was performed with Illumina HiSeq 2500
Libraries were demultiplexed depending on barcode
Alignment was performed using CASAVA version 1.8.2
Reads Per Kilobase per Million of mapped reads (RPKM) and raw counts were generated using CASAVA version 1.8.2
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited files contain RPKM values and raw counts for all samples in a matrix table.

organism: Homo sapiens

source_name: HMDM treated with 10 µg/ml acetylated LDL+ 75 µg/ml C1q

growth_protocol: Human monocytes obtained from healthy human blood samples were isolated by counter current flow elutriation. Isolated monocytes were cultured in 100mm petri dishes for 8 days in RMPI1640, 10% FCS, 2mM L-Glutamine and 1% penicillin/streptomycin containing 25ng/ml rhM-CSF to stimulate differentiation into human monocyte-derived macrophages. Cells were harvested with Cellstripper and added to 24-well tissue culture treated plates at a concentration of 5x10⁵ cells per well.

extract_protocol:
Total RNA from samples was isolated using the Qiagen RNeasy Mini kit
RNA libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Preparation Kit

treatment_protocol: Cells were cultured for 3 hours at 37°C in 5% CO2 with 10 µg protein /ml oxLDL or 10 µg protein /ml acLDL in the absence or presence of 75 µg/ml C1q.

value: blood

tag: cell type

value: Human monocyte-derived macrophages


title: Kcng4_1Ra_D3

description: single end RNA-seq data


title: acLDL+C1q rep2

description: barcode: TCCGGAGA-GTACTGAC


title: Kcng4_1Ra_D6

description: single end RNA-seq data


title: Kcng4_1Ra_D2

description: single end RNA-seq data


title: acLDL+C1q rep1

description: barcode: ATTACTCG-GTACTGAC


title: Kcng4_1Ra_D1

description: single end RNA-seq data


title: Kcng4_1Ra_F11

description: single end RNA-seq data


title: Kcng4_1Ra_E10

description: single end RNA-seq data


title: Kcng4_1Ra_D4

description: single end RNA-seq data


title: acLDL rep2

description: barcode: CGCTCATT-CAGGACGT

source_name: HMDM treated with 10 µg/ml acetylated LDL


title: acLDL rep3

description: barcode: GAGATTCC-CAGGACGT


title: Input DNA S-phase time course 3

city: Montpellier

first: Marta

last: Radman-Livaja

address: 1919 route de Mende

department: IGMM

country: France

institute: CNRS

description:
MNase digest time course from synchronized cells in S-phase.
Strand-specific MNase-seq.
Processed data file: Sync_EdU_input_tss_aligned.txt

library_source: genomic

data_processing:
Illumina OLB-1.8.0/CASAVA_v1.7.0 were used for base calling.
Time points were separated by barcode and the 5bp barcode was removed from the read sequence.
Reads were mapped to the yeast S288C genome using BLAT.
Paired end read count distribution in 1bp windows was determined separately for Watson (marked as F in the processed data files) and Crick (marked as R in the processed data files) strands.
The average read count value was calculated and the data were normalized to one.
Genome_build: S288C (S. cerevisiae)
Supplementary_files_format_and_content: Tab-delimited text files of nucleosome occupancy for every gene at indicated time points (lines), showing every 20th bp from -500bp to the end of the gene coding sequence surrounding the transcription start site (marked as tss). Occupancy data start after the GWEIGHT header.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Input DNA S-phase time course

growth_protocol:
For the synchronization experiment cells were grown over night at 30°C in Synthetic Complete- URA + Dextrose media to OD 0.3. After 3.75hrs of incubation at 30°C with alpha factor (0.25μg/ml), cells were pelleted and transferred into preheated and premixed SCD-URA+ 10μM EdU(Carbosynth), with freshly added 20μg/ml pronase (Sigma). 200ml aliquots were taken at 25, 32, 40, 47 and 55 min after release. Time points were fixed with 1% formaldehyde.
In the EdU-Thymidine pulse chase experiments, cells were grown in SCD-URA over night at 30°C to an OD of 1.0. The next day the culture was diluted to OD=0.25 and cells were allowed to double once. Cell pellets were then transferred to preheated and premixed SCD-URA+ 10μM EdU media. Thymidine (to a final concentration of 5mM) was added after 5,10 or 20min incubation with EdU at 30°C and incubated for another 5 or 10 min. Cells were then pelleted and transferred into fresh media with 5mM Thymidine (and 15μg/ml nocodazole 5(Sigma) or 3μg/ml thiolutin (Abcam) when indicated) and 200ml aliquots were taken at indicated time points (after the Thymidine incubation) and fixed as above.

extract_protocol:
Cells were washed in water, cell walls were broken with bead beating and spheroplasts were treated with micrococcal nuclease. EdU from isolated nascent DNA fragments was biotinylated using Click chemistry and nascent DNA was purified with streptavidin coated beads. An input DNA aliquot was set aside prior to biotinylation.
Nascent and input DNA samples, were treated with calf intestinal phosphatase (NEB), blunt-ended, A-tailed, and ligated (Epicentre) to Illumina genomic PE adaptors with custom 5bp inline barcodes (first 5bp in raw data read), and PCR amplified and size selected by gel purification. For nascent libraries, the nascent strand was separated from its complement with primer extension in the presence of dUTP and the dUTP strand was then digested with the USER enzyme cocktail prior to PCR amplification. All the steps for nascent libraries were done on streptavidin coated magnetic beads.

treatment_protocol: Cells were fixed in 1% formaldehyde.

tag: strain

value: wt yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase

tag: cell cycle

value: S-phase

tag: edu incubation

value: from beginning of release from G1 arrest

tag: thymidine incubation (min)

tag: time point

value: 55min after release, total S-phase chromatin


title: Input DNA S-phase time course 2

value: 40min after release, total S-phase chromatin


title: Input DNA S-phase time course 1

value: 32min after release, total S-phase chromatin


title: Nascent DNA S-phase time course 4

description:
MNase digest time course followed by nascent DNA purification by EdU-biotin pulldown from synchronized cells in S-phase.
Strand-specific MNase-seq.
Processed data file: Sync_EdU_input_tss_aligned.txt

source_name: Nascent DNA S-phase time course

value: 47min after release, nascent S-phase chromatin


title: Kcng4_1Ra_D10

description: single end RNA-seq data


title: Nascent DNA S-phase time course 1

value: 25min after release, nascent S-phase chromatin.


title: oxLDL+C1q rep3

description: barcode: ATTACTCG-CAGGACGT

source_name: HMDM treated with 10 µg/ml oxidized LDL+ 75 µg/ml C1q


title: oxLDL rep2

description: barcode: ATTACTCG-TAATCTTA

source_name: HMDM treated with 10 µg/ml oxidized LDL


title: Nascent DNA S-phase time course 5

value: 55min after release, nascent S-phase chromatin


title: Kcng4_1Ra_D12

description: single end RNA-seq data


title: Kcng4_1Ra_C4

description: single end RNA-seq data


title: Kcng4_1Ra_C5

description: single end RNA-seq data


title: HMDM rep3

description: barcode: CGCTCATT-AGGCGAAG

source_name: Untreated HMDM


title: Kcng4_1Ra_D11

description: single end RNA-seq data


title: p110g-/- CD11b+Gr1-4

city: La Jolla

first: Judith

last: Varner

state: CA

address: 3855 Health Sciences Drive #0819

institute: Univeristy of California San Diego

description:
p110gko_CD11b_plus_Gr1_minus_4
Processed data file: tumor_macro_wt_ko.txt

data_processing:
Sequence files from Illumina HiSeq 2000 were aligned to the mouse transcriptome (mm9 genome build) using the Bowtie2 aligner.
Gene-level count summaries were analyzed for statistically significant changes using DESeq.
Individual p-values were adjusted for multiple testing by calculating Storey's q-values using fdrtools.
For each gene, the q-value is the smallest false discovery rate at which the gene is found significant.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *wt_ko.txt: Text files contain raw counts of sequencing reads.

source_name: CD11b+Gr1- TAMs, p110g-/- mice

growth_protocol: Lewis lung carcinoma cells were inoculated into the flanks of WT and p110g-/- mice and allowed to grow for 14 days.

extract_protocol:
RNA was extracted from 30 mg of whole tumor or 1 x 10^6 sorted cells using the Qiagen RNeasy kit according to manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For CD11b+Gr1- cells, single cell suspensions were produced from whole tumor, and CD11b+Gr1- cells were isolated by flow cytometry.

tag: strain/background

tag: genotype/variation

value: PI3Kinase-gamma-null (p110g-/-)

value: CD11b+Gr1- cells isolated from tumor

tag: timepoint

value: day 14 post tumor implantation


title: acLDL rep1

description: barcode: TCCGGAGA-CAGGACGT


title: p110g-/- CD11b+Gr1-1

description:
p110gko_CD11b_plus_Gr1_minus_1
Processed data file: tumor_macro_wt_ko.txt


title: Kcng4_1Ra_C2

description: single end RNA-seq data


title: Nascent DNA S-phase time course 3

value: 40min after release, nascent S-phase chromatin


title: Kcng4_1Ra_C7

description: single end RNA-seq data


title: Nascent DNA S-phase time course 2

value: 32min after release, nascent S-phase chromatin


title: HMDM rep1

description: barcode: ATTACTCG-AGGCGAAG


title: WT CD11b+Gr1-3

description:
WT_CD11b_plus_Gr1_minus_3
Processed data file: tumor_macro_wt_ko.txt

source_name: CD11b+Gr1- TAMs, WT mice

value: wild type


title: p110g-/- CD11b+Gr1-3

description:
p110gko_CD11b_plus_Gr1_minus_3
Processed data file: tumor_macro_wt_ko.txt


title: WT CD11b+Gr1-2

description:
WT_CD11b_plus_Gr1_minus_2
Processed data file: tumor_macro_wt_ko.txt


title: Kcng4_1Ra_C9

description: single end RNA-seq data

value: retina


title: Kcng4_1Ra_C8

description: single end RNA-seq data


title: oxLDL+C1q rep2

description: barcode: GAGATTCC-TAATCTTA

value: blood

value: Human monocyte-derived macrophages


title: oxLDL+C1q rep1

description: barcode: CGCTCATT-TAATCTTA


title: oxLDL rep3

description: barcode: TCCGGAGA-TAATCTTA


title: Kcng4_1Ra_C6

description: single end RNA-seq data


title: N2_mock(RNAi)_L1toL4_20°C_rep2

city: Basel

first: Sarah

last: Carl

address: Maulbeerstrasse 66

department: Epigenetics

country: Switzerland

institute: Friedrich Miescher Institute

data_processing:
Basecalling was performed using RTA v. 1.13.48.
Reads were aligned to the ce10 (WS220) genome assembly using the qAlign function from the QuasR R package (v. 3.2) with the parameter "splicedAlignment = TRUE", which calls the SpliceMap aligner with default parameters.
Gene expression was quantified using WS220 annotations downloaded from WormBase. The qCount function in the QuasR package was used to count reads overlapping all annotated exons for each gene.
Genome_build: ce10 (WS220)
Supplementary_files_format_and_content: Tab-delimited file. First column contains gene names (WormBase identifiers), following columns contain raw counts of reads overlapping each gene for each sample.

organism: Caenorhabditis elegans

source_name: whole body

extract_protocol:
Worms were harvested, washed three times with M9 medium, resuspended in 1 ml of TRI Reagent (Molecular Research Center, Cincinnati, OH, USA) and frozen in liquid nitrogen. Worms were broken open by five repeats of freeze and thaw, and RNA was extracted and purified according to the supplier’s protocol with the modification that RNA was incubated with 50% 2-propanol at −80°C overnight for efficient precipitation. The purified RNA was treated with DNA-free Kit (Thermo Fischer Scientific, Waltham, MA, USA) to remove DNA.
Libraries were prepared using the TruSeq Standard mRNA Library Prep Kit (Illumina, San Diego, CA, USA).

treatment_protocol: RNAi by feeding

tag: replicate


title: N2_xrn-2(RNAi)_L1toL4_20°C_rep1


title: WT whole tumor3

description:
WT_whole_tumor3
Processed data file: whole_tumor_wt_ko.txt

source_name: LLC tumor, WT mice

value: whole tumor


title: oxLDL rep1

description: barcode: GAGATTCC-AGGCGAAG


title: WT whole tumor2

description:
WT_whole_tumor2
Processed data file: whole_tumor_wt_ko.txt


title: Kcng4_1Ra_C10

description: single end RNA-seq data


title: Kcng4_1Ra_C3

description: single end RNA-seq data


title: p110g-/- CD11b+Gr1-2

description:
p110gko_CD11b_plus_Gr1_minus_2
Processed data file: tumor_macro_wt_ko.txt


title: N2_mock(RNAi)_L1toL4_20°C_rep1


title: Kcng4_1Ra_B9

description: single end RNA-seq data


title: HMDM rep2

description: barcode: TCCGGAGA-AGGCGAAG


title: WT CD11b+Gr1-4

description:
WT_CD11b_plus_Gr1_minus_4
Processed data file: tumor_macro_wt_ko.txt


title: IN-WT

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

state: Missouri

address: Washington University School of Medicine

description: CLIP-seq with wild-type IN

data_processing:
CLIP-seq reads were trimmed off of the adapters and collapsed using FASTX-toolkit
Resulting reads were mapped to the viral and human genomes using bowtie
Samtools mpileup and custom scripts were used to generate read density (i.e. number of reads that map to each nucleotide of the viral genome) graphs on viral RNAs.
Genome_build: HIV-1 NL4-3 strain, hg19
Supplementary_files_format_and_content: tab-delimited files showing read density on each nucleotide of the viral genome as well as nucleotide substitutions.

organism: Human immunodeficiency virus 1

source_name: HIV-1 NL4-3 virions

growth_protocol: Cells transfected with HIV-1 NL4-3-based proviral plasmids were utilized for harvesting virus particles.

extract_protocol:
Virions collected from cells were pelleted on sucrose cushions, lysed in detergent containing buffers and IN-RNA complexes were immunoprecipitated from these lysates.
Libraries were constructed based on previously published methodologies as explained before (Kutluay et al,m 2014, Cell). The 3' adapter is common to all samples and has the sequence: TCG TAT GCC GTC TTC TGC TTG. The 5' adapters are:Sample 1 (rGUU CAG AGU UCU ACA GUC CGA CGA UC AGU NNN UC); Sample 2 ( rGUU CAG AGU UCU ACA GUC CGA CGA UC GAU NNN UC); Sample 3 ( rGUU CAG AGU UCU ACA GUC CGA CGA UC GUG NNN UC); Sample 4 (rGUU CAG AGU UCU ACA GUC CGA CGA UC ACG NNN UC); Sample 5 (rGUU CAG AGU UCU ACA GUC CGA CGA UC  AUC NNN UC).

treatment_protocol: Prior to isolation of HIV-1 particles, cells were treated with 4-thiouridine to enhance UV crosslinking. Some samples were treated with allosteric integrase inhibitor BI-B2.

tag: antibody

value: monoclonal anti-integrase

value: wild-type IN


title: deltaIN

institute: Washington University School of Medicine

description: CLIP-seq with integrase deletion

value: integrase deletion


title: Kcng4_1Ra_B7

description: single end RNA-seq data


title: Kcng4_1Ra_B8

description: single end RNA-seq data


title: EdU pulse (20min) Thymidine chase (10min) input DNA time course 8

description:
Mnase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 20min EdU pulse and a 10min Thymidine chase.
Strand-specific MNase-seq.
processed data file: PC_20_10_EdU_tss_aligned.txt

value: wt yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase

value: asynchronous

value: 22 min after Thymidine chase, nascent chromatin


title: WT CD11b+Gr1-1

description:
WT_CD11b_plus_Gr1_minus_1
Processed data file: tumor_macro_wt_ko.txt


title: N2_xrn-2(RNAi)_L1toL4_20°C_rep2


title: Kcng4_1Ra_C12

description: single end RNA-seq data


title: p110g-/- whole tumor3

description:
p110gko_whole_tumor3
Processed data file: whole_tumor_wt_ko.txt

source_name: LLC tumor, p110g-/- mice


title: Kcng4_1Ra_C1

description: single end RNA-seq data


title: Kcng4_1Ra_C11

description: single end RNA-seq data


title: Cauda 2

city: Newcastle

first: Brett

last: Nixon

state: NSW

address: University Drive, Callaghan

country: Australia

institute: University of Newcastle

data_processing:
Basecalls were dones using CASAVA pipeline version 1.8.2.
Reads were screened and trimmed based on matches to Illumina smallRNA adaptors, PhiX, ChrM and rRNAs using flicker script with Illumina smallRNA kit with default settings
Cleaned reads were aligned using the bowtie ver 1.1.1 against human genome and miRNA database version 21
miRNA gene counts were summarised with custom shell scripts
Differential expression analysis was performed using the R-bioconductor libraies: limma and voom
Genome_build: miRNA database version 21

source_name: Epididymosomes

extract_protocol:
Total RNA was extracted from purified epididymal epididymosomes (caput, corpus and cauda) using a Direct-zol™ RNA MiniPrep Kit (Zymo Research Corporation, Irvine, CA, USA) according to manufacturer’s instructions before being incubated with 1% DNase (Promega) to eliminate genomic DNA contamination.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: epididymosomes type

value: cauda

value: Swiss

tag: age

value: 8 Weeks

tag: Sex

value: Male


title: p110g-/- whole tumor2

description:
p110gko_whole_tumor2
Processed data file: whole_tumor_wt_ko.txt

value: PI3Kinase-gamma-null (p110g-/-)

tag: tissue

value: day 14 post tumor implantation


title: Cauda 1


title: Kcng4_1Ra_B6

description: single end RNA-seq data

tag: developmental stage


title: p110g-/- whole tumor1

description:
p110gko_whole_tumor1
Processed data file: whole_tumor_wt_ko.txt


title: Corpus 3

value: corpus


title: Cauda 3


title: Kcng4_1Ra_B3

description: single end RNA-seq data

value: retina

tag: retina id


title: EdU pulse (20min) Thymidine chase (10min) input DNA time course 3

value: 3 min after Thymidine chase, nascent chromatin


title: EdU pulse (20min) Thymidine chase (10min) input DNA time course 4

value: 4 min after Thymidine chase, nascent chromatin


title: WT whole tumor1

description:
WT_whole_tumor1
Processed data file: whole_tumor_wt_ko.txt

value: wild type

value: whole tumor


title: Caput 3

value: caput


title: Kcng4_1Ra_B12

description: single end RNA-seq data


title: Kcng4_1Ra_B11

description: single end RNA-seq data


title: Kcng4_1Ra_B1

description: single end RNA-seq data


title: Caput 1


title: EdU pulse (20min) Thymidine chase (10min) input DNA time course 7

value: 16 min after Thymidine chase, nascent chromatin


title: EdU pulse (20min) Thymidine chase (10min) input DNA time course 5

value: wt yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase

value: 8 min after Thymidine chase, nascent chromatin


title: E14.5mouseCerebralCortexTbr2EGFP+_1

city: Chicago

first: Xiaochang

last: Zhang

state: IL

address: 920 E 58th St, CLSC 507A

department: Human Genetics

institute: The University of Chicago

description: FACS sorted

data_processing:
Tophat 2.0.7
Genome_build: mm9
Supplementary_files_format_and_content: Cuffdiff output, genes fpkm tracking ("vz" (ventricular zone) = NPCs and "oz" = Neurons)

molecule: polyA RNA

source_name: E14.5 mouse dorsal cortical neurons

growth_protocol: FVB mice were maintained in a 12 hour light/dark cycle, with food and water ad-libitum, in the animal facility at Boston Children's Hospital. All animal experimental protocols were performed with Institutional Animal Care and Use Committee approval

extract_protocol:
Total RNA from sorted cells were extracted using RNeazy Mini Kit (Qiagen) and treated with Turbo DNase (Ambion). The integrity of DNase-treated total RNA was measured by RNA Nano chips on Bioanalyzer (Agilent), and the RIN for all samples were above 9.0. 500-2000ng total RNA was treated with Ribo-Zero Gold (Epicentre) to remove ribosomal RNAs, and mRNA was further enriched using Oligo(dT)25 Dynabeads (Life Tech).
RNA-Seq libraries were prepared and barcoded using ligation-based directional RNA-Seq kit (Bioo Scientific), and sequenced on Illumina HiSeq2000 using single end 50 bp reactions.

tag: stain

value: FVB

value: dorsal cerebral cortex Neurons

value: Embryonic day 14.5


title: Kcng4_1Ra_B4

description: single end RNA-seq data


title: EdU pulse (20min) Thymidine chase (10min) input DNA time course 6

tag: strain

value: asynchronous

value: 12 min after Thymidine chase, nascent chromatin


title: Corpus 2

value: Swiss

value: 8 Weeks

value: Male


title: Corpus 1

value: corpus


title: E14.5mouseCerebralCortexTbr2EGFP+_2

description: FACS sorted


title: HSPC_shSCR_p300_ChIPSeq_2

city: New York

first: Beatriz

last: Aranda-Orgilles

address: 522 First Avenue

institute: NYU School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 0.12.7
Processed reads were slopped by 250bp
Duplicates were removed with Picard tools and bedgraphs were normalized to reads per million.
MACS version 1.4.2 was used for ChIP-sequencing peak discovery.
Bedtools,  GenomicTools version 2.7.2, Seqminer and deepTools weee used for performing genomic interval mathematical operations, genomic interval annotation, ChIP-seq heatmap generation and ChIP-seq profile construction.
Genome_build: mm9
Supplementary_files_format_and_content: BigWigs of data normalized to reads per million

growth_protocol: HPC7 were grown in IMDM supplemented with 5%FBS, MTG, pen/Strep and 100ng/ml SCF

extract_protocol:
Cells were harvested, washed with PBS and crosslinked with 1% Formaldehyde for 30 min at 37C.
Libraries were constructed with  KAPA Hyper Prep Kit  and Multiplexed with NextFlex Barcodes from Biooscientific

tag: cell line

value: hematopoietic cell line HPC7

tag: protocol

value: shSCR

tag: chip antibody

value: p300 (santa cruz sc-585 X, lot j2214)


title: Kcng4_1Ra_B2

description: single end RNA-seq data

value: retina


title: Kcng4_1Ra_A5

description: single end RNA-seq data


title: HSPC_p300_ChIPSeq_2


title: HSPC_Med12_ChIPSeq_2

value: Med12 (bethyl-A300-774A, lot 1)


title: Kcng4_1Ra_B10

description: single end RNA-seq data


title: Kcng4_1Ra_A9

description: single end RNA-seq data


title: E14.5mouseCerebralCortexTbr2EGFP-_2

description: FACS sorted

source_name: E14.5 mouse dorsal cortical neural progenitors

value: dorsal cerebral cortex NPCs


title: Kcng4_1Ra_A8

description: single end RNA-seq data

source_name: Mus musculus retina, P17


title: Caput 2

value: caput


title: Kcng4_1Ra_A1

description: single end RNA-seq data


title: HSPC_Med12_ChIPSeq_1


title: Kcng4_1Ra_A2

description: single end RNA-seq data


title: E14.5mouseCerebralCortexTbr2EGFP-_1

description: FACS sorted


title: Kcng4_1Ra_A7

description: single end RNA-seq data


title: Kcng4_1Ra_B5

description: single end RNA-seq data


title: Kcng4_1Ra_A10

description: single end RNA-seq data


title: Kcng4_1Ra_A6

description: single end RNA-seq data


title: 4C-seq-kit enhancer2

description: 4C analysis from enhancer view point

data_processing:
library strategy: 4C-Seq
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.0.17
Counts and wig files were normalized with DeSeq
Genome_build: mm9
Supplementary_files_format_and_content: Normalized wigs
Supplementary_files_format_and_content: csv files reporting normalized counts

source_name: enriched c-kit cells from mice

extract_protocol:
Cells were washed with PBS and crosslinked with 2% of formaledehyde for 10 minutes
Library was prepared according to previously published protocols (Rocha PP, Micsinai M, Kim JR, Hewitt SL, Souza PP, Trimarchi T, Strino F, Parisi F, Kluger Y, Skok JA. 2012. Close proximity to Igh is a contributing factor to AID-mediated translocations. Mol Cell 47: 873-885.)

tag: cell type

value: hematopoietic stem and progenitor cells

value: enriched c-kit cells

tag: primer set


title: 4C-seq-kit enhancer1

description: 4C analysis from enhancer view point


title: HSPC_shMed12_p300_ChIPSeq2


title: EdU pulse (20min) Thymidine chase (10min) input DNA time course 1

description:
MNase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 20min EdU pulse and a 10min Thymidine chase.
Strand-specific MNase-seq.
Processed data file: PC_20_10_EdU_tss_aligned.txt

value: wt yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase

tag: cell cycle

tag: edu incubation

tag: thymidine incubation (min)

tag: time point

value: 0 min after Thymidine chase, nascent chromatin


title: 4C-seq-kit Promoter3

description: 4C analysis from promoter view point

source_name: expanded HSPCs sorted from mice

value: expanded HSPCs, sorted

tag: culture

value: 5 days in culture


title: Kcng4_1Ra_A3

description: single end RNA-seq data


title: 4C-seq-kit Promoter2

description: 4C analysis from promoter view point


title: Kcng4_1Ra_A12

description: single end RNA-seq data


title: HSPC_p300_ChIPSeq_1


title: Input-KO

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie version 2.017
Processed reads were slopped by 250bp
Duplicates were removed with Picard tools and bedgraphs were normalized to reads per million.
MACS version 1.4.2 was used for ChIP-sequencing peak discovery.
Bedtools,  GenomicTools version 2.7.2, Seqminer and deepTools weee used for performing genomic interval mathematical operations, genomic interval annotation, ChIP-seq heatmap generation and ChIP-seq profile construction.
Genome_build: mm9
Supplementary_files_format_and_content: BigWigs of data normalized to reads per million

source_name: HSPCs

growth_protocol: HSPCs (Lineage-, c-kit+, Sca1+) were sorted using Fluorescence Activated Cell Sorting  4 days after injection with pI:pC

extract_protocol:
Cells from bone marrow were isolated from mice and eriched for c-Kit+ cells,crosslinked for 10 minutes with 1% formaldehyde and stained with Lineage antibodies (CD11b, Gr1, Ter119, B220, CD4, CD8), Sca1 and c-Kit and then sorted and snap frozen
Libraries were generated as previously published (Lara Astiaso et al, 2014) Briefly, sonicated chromatin was immunoprecipitated with H3 and libraries were generated on chromatin bound to beads. Libaries with multiplexed with NextFlex Barcoded primers from Bioo Scientific. ChIp with specific histone modifications were performed with barcoded chromatin and released DNA was amplified with ilumina standard primers

treatment_protocol: Mice were injected every other day with pI:pC (10mg/Kg)

tag: genotype/variation

value: KO

tag: chip antibody 1

value: none (input)

tag: chip antibody 2


title: Kcng4_1Ra_A11

description: single end RNA-seq data

tag: tissue

tag: developmental stage


title: H3K4me1_ChIPSeq_Med12KO3

description: bowtie.K4me1KO.LSK.total.dd.sort.slop.bw


title: 5htr3a_rep1

data_processing:
Reads were aligned to a reference genome (mm10 Ensembl) using Tophat v2.0.10
Expression levels were quantified using RSEM v1.2.28 (inferred counts and tpm values)
Genome_build: mm10
Supplementary_files_format_and_content: text file with tab delimiters (1 column per sample) containing tpm values for both samples.

source_name: Mus musculus retina

extract_protocol:
Dissociated retina were FACS sorted into RNAlater
Ovationa RNA-seq system V2 (Nugen, 7102-32)

value: Type 5 retinal bipolar cells


title: H3K4me1_ChIPSeq_Med12KO1


title: 4C-seq-kit enhancer3

description: 4C analysis from enhancer view point


title: 5htr3a_rep2


title: H3K4me1_ChIPSeq_Med12WT4

description: bowtie.K4me1WT.LSK.total.dd.sort.slop.bw

value: WT


title: Kcng4_1Ra_A4

description: single end RNA-seq data

tag: retina id


title: Input

value: hematopoietic cell line HPC7


title: H3K4me1_ChIPSeq_Med12KO4

tag: strain


title: H3K4me1_ChIPSeq_Med12KO2


title: cv16 rep3

city: Durham

first: Christopher

last: Vockley

state: NC

address: 101 science drive rm 2193

institute: Duke University

description:
[7] contains the reporter assay specific RNA-seq from plasmids described in [1].
Plasmid DNA-seq

data_processing:
Base-calling was performed on instrument using CASAVA software
Reads were aligned to the hg19 version of the human genome using bowtie2-align version 2.1.0, and the  -p 32 --end-to-end --very-sensitive t" alignment options
Reads were converted from .sam to .bam files using samtools view version 0.1.19-44428cd with the  "-bS" option
Bam files were sorted using Samtools sort version 0.1.19-44428cd with the options "32 -m 2G"
Bam files were indexed using Samtools Index version 0.1.19-44428cd
Fragments were counted using in-house software
Genome_build: hg19
Supplementary_files_format_and_content: *.fragments files contain counts of each fragment tested.  *.fragments files include the following columns:   Chromosome, Start, Stop, counts per fragment.  In the context of [4] and [7] this is the location and abundance of a test element in the plasmid DNA that was transfected into cells.

molecule: other

source_name: tagmented human BACs clones into Starr-seq vector

growth_protocol: 6 human BACs (CTD_2340K24, RP11_139K17, RP11_435L21, RP11_769H22, RP11_788A16, RP11_806F7) were tagmented and cloned into the STARR-seq backbone (the reporter assay plasmids) as described in methods

extract_protocol:
Promega plasmid DNA maxiprep
PCR to amplify library and add indexed adapters

treatment_protocol: Grown 12H and harvested

tag: cell line

tag: transfection

value: transfected with STARR-seq library


title: H3K4me3_ChIPSeq_Med12KO1

description: bowtie.K4me3KO.LSK.total.dd.sort.slop.bw


title: cv16 rep4


title: cv16 rep2


title: H3K4me3_ChIPSeq_Med12WT2

description: bowtie.K4me3WT.LSK.total.dd.sort.slop.bw


title: H3K4me1_ChIPSeq_Med12WT3


title: H3K4me1_ChIPSeq_Med12WT2


title: ETOH2_GR chip seq library_STARRseq

description: STARR-seq- Reporter-RNA-seq

data_processing:
Base-calling was performed on instrument using CASAVA software
Reads were aligned to the hg19 version of the human genome using bowtie2-align version 2.1.0, and the  -p 32 --end-to-end --very-sensitive t" alignment options
Reads were converted from .sam to .bam files using samtools view version 0.1.19-44428cd with the  "-bS" option
Bam files were sorted using Samtools sort version 0.1.19-44428cd with the options "32 -m 2G"
Bam files were indexed using Samtools Index version 0.1.19-44428cd
Bam files were converted to Bed files for down stream analysis using BamtoBed function of the bedTools suite.
Genome_build: hg19
Supplementary_files_format_and_content: .bed (columns: Chromosome, Start, Stop, Bed Name (RNAME field in the BAM alignment)/ mate (1 or 2), Counts, Strand). bed files report the abundance of fragments generated in a reporter plasmid-specific RNA-seq experiment performed after transfecting the reporter plasmids contained in [4] into A549 cells and treating the cells with either 100 nM dexamethasone or ethanol.  In the context of [1] and [5], the files contain the abundance of RNA transcribed from the reporter vectors (from the plasmid pools described in [4] and [7]). [1] and [5] contain the location and abundance of the RNA species transcribed from the transfected reporter plasmids after treatment with either 100 nM dexamethasone or with ethanol as a control.

source_name: human GR chip seq library cloned into STARR-seq plasmid

growth_protocol: A549 cells grown in F12K medium with 10%FCS

extract_protocol:
Qiagen total RNAmidi-prep, two rounds of oligodT dynabead (invitrogen) to harvest mRNA
gene specific RT primer used to reverse transcribe only the mRNA encoded by the plasmid pool, then nested PCR to amplify spliced reporter transcripts and index for sequencing

treatment_protocol: transfected with STARR-seq library at 50% confluence, after 48H treated with 100 nM DEX or etoh control for 3 h, then harvested

tag: agent

value: etoh


title: H3K4me1_ChIPSeq_Med12WT1

tag: cell type


title: H3K4me3_ChIPSeq_Med12KO3


title: cv16 rep7


title: cv16 rep5


title: H3K4me3_ChIPSeq_Med12KO2


title: cv16 rep6


title: DEX1_GR chip seq library_STARRseq

description: STARR-seq- Reporter-RNA-seq

value: dex


title: H3K4me3_ChIPSeq_Med12WT4


title: 4C-seq-kit Promoter1

description: 4C analysis from promoter view point

tag: protocol

tag: primer set


title: H3K27Ac_ChIPSeq_Med12WT4

description: bowtie.all.final.WT.H3K27Ac.LSK.dd.sort.slop.bw


title: cv16 rep1


title: Input-WT


title: ChIP-reporter_input_pool4

description: DNA sequencing

data_processing:
Base-calling was performed on instrument using CASAVA software
Reads were aligned to the hg19 version of the human genome using bowtie2-align version 2.1.0, and the  -p 32 --end-to-end --very-sensitive t" alignment options
Reads were converted from .sam to .bam files using samtools view version 0.1.19-44428cd with the  "-bS" option
Bam files were sorted using Samtools sort version 0.1.19-44428cd with the options "32 -m 2G"
Bam files were indexed using Samtools Index version 0.1.19-44428cd
Counted fragments using in-house software
Genome_build: hg19
Supplementary_files_format_and_content: *.fragments files contain counts of each fragment tested.  *.fragments files include the following columns:   Chromosome, Start, Stop, counts per fragment.  *.fragments files contain the abundance of each reporter plasmid produced by cloning the GR ChIP-seq library into the reporter vector. In the context of [4] and [7] this is the location and abundance of a test element in the plasmid DNA that was transfected into cells.

growth_protocol: Plasmids containing human GR ChIP libraries were grown for 12H in LB +ampicillin

extract_protocol:
Promega plasmid DNA maxiprep
PCR of library from STARR_seq vector


title: H3K4me3_ChIPSeq_Med12WT3


title: H3K4me3_ChIPSeq_Med12KO4


title: ETOH3_GR chip seq library_STARRseq

description: STARR-seq- Reporter-RNA-seq


title: H3K4me3_ChIPSeq_Med12WT1


title: ETOH1_GR chip seq library_STARRseq

description: STARR-seq- Reporter-RNA-seq


title: H3K27Ac_ChIPSeq_Med12KO4

description: bowtie.all.final.KO.H3K27Ac.LSK.dd.sort.slop.bw


title: H3K27Ac_ChIPSeq_Med12KO3


title: H3K27Ac_ChIPSeq_Med12WT2


title: DEX3_GR chip seq library_STARRseq

description: STARR-seq- Reporter-RNA-seq


title: H3K27Ac_ChIPSeq_Med12KO2


title: DEX2_GR chip seq library_STARRseq

description: STARR-seq- Reporter-RNA-seq


title: H3K27Ac_ChIPSeq_Med12KO1


title: Plasmid_translocation_DEX_rep2

description: Plasmid DNA from isolated nuclei

data_processing:
Base-calling was performed on instrument using CASAVA software
Reads were aligned to the hg19 version of the human genome using bowtie2-align version 2.1.0, and the  -p 32 --end-to-end --very-sensitive t" alignment options
Reads were converted from .sam to .bam files using samtools view version 0.1.19-44428cd with the  "-bS" option
Bam files were sorted using Samtools sort version 0.1.19-44428cd with the options "32 -m 2G"
Bam files were indexed using Samtools Index version 0.1.19-44428cd
Read depth per library was calculated using  Samtools flagstat version  version 0.1.19-44428cd
Genome coverage was normalized for read depth using genomeCoverageBed with the options "-bg" -"1/reads per library"
Genome_build: hg19
Supplementary_files_format_and_content: *.bedgraph data files (columns: chr, start,stop, abundance) contain the read-depth normalized counts of fragments that were contained in the plasmids that were recovered from the transfected nuclei after treatment with either dexamethasone or with ethanol control.

source_name: A549 cells transfected with STARR-seq plasmid pool

growth_protocol: A549 cells were grown to 90% confluence according to standard protocols in F12K medium

extract_protocol:
After 3 hours of treatment, nuclei were isolated using the Sigma EZ prep nuclar isolation protocol. Plasmid DNA was harvested from nuclei using the Qiagen plasmid miniprep kit.
Libraries were constructed from transfected plasmids via PCR amplification.
Plasmids containing Illumina adapters were transfected into cells, then isolated. PCR was performed to amplify the DNA fragments contained on the plasmids and to index the libraries for sequencing.

treatment_protocol: Cells were transfected with BAC-starr-seq libraries (containing DNA fragments from the following BACs: CTD_2340K24, RP11_139K17, RP11_435L21, RP11_769H22, RP11_788A16, RP11_806F7, pBACe3.6, pBeloBAC11) using Fugene HD. Cells were treated with 100 nM Dexamethasone or .02% EtOH as vehicle control.

value: transfected with STARR-seq plasmid pool


title: Plasmid_translocation_DEX_rep1

description: Plasmid DNA from isolated nuclei


title: etoh3_BAC_STARRseq_exp

description: library strategy: STARR-seq- Reporter-RNA-seq

data_processing:
Base-calling was performed on instrument using CASAVA software
Reads were aligned to the custom reference as described in experimental methods using bowtie2-align version 2.1.0, and the  -p 32 --end-to-end --very-sensitive t" alignment options
Reads were converted from .sam to .bam files using samtools view version 0.1.19-44428cd with the  "-bS" option
Bam files were sorted using Samtools sort version 0.1.19-44428cd with the options "32 -m 2G"
Bam files were indexed using Samtools Index version 0.1.19-44428cd
fragments were counted using in -house software
Genome_build: custom genome (using human BAC clones: CTD_2340K24, RP11_139K17, RP11_435L21, RP11_769H22, RP11_788A16, RP11_806F7, pBACe3.6, and pBeloBAC11,  as described in methods)
Supplementary_files_format_and_content: *.fragments files include the following columns:   Chromosome, Start, Stop, counts per fragment.   *.fragments files contain counts of each fragment tested.  *.fragments files contain the location and abundance of the RNA species transcribed from the transfected reporter plasmids after treatment with either 100 nM dexamethasone or with ethanol as a control.  In the context of [1] and [5], the files contain the abundance of RNA transcribed from the reporter vectors (from the plasmid pools described in [4] and [7]). [1] and [5] contain the location and abundance of the RNA species transcribed from the transfected reporter plasmids after treatment with either 100 nM dexamethasone or with ethanol as a control.

source_name: human BACs, tagmented and cloned into starr-seq


title: EdU pulse (5min) Thymidine chase (5min) nascent DNA time course during Thiolutin treatment 4

description:
MNase digest time course during Thiolutin treatment followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after an 5min EdU pulse and a 5min Thymidine chase.
Strand-specific MNase-seq.
Processed data file: PC_5_5_EdU_+-Thiolutin_tss_aligned.txt

tag: cell cycle

value: asynchronous

tag: edu incubation

value: 25 min after Thymidine chase, nascent chromatin, with thiolutin


title: Growth competition glucose

city: Rehovot

first: Leeat

last: Keren

state: Israel

address: Herzl 706

department: Mathematics and Computer Science

country: Israel

institute: Weizmann Institute of Science

description:
The strains used in this study were constructed by us. They are derivatives of strain Y8205 (Tong A. and Boone C., 2005).
Barcoded cells, differing in expression of one of 81 target genes, were grown in glucose. After 13, 23 and 35 hours, samples were taken and genomic DNA was extracted. The barcode region was amplified by PCR and sequenced.
The study was initially designed on 96 genes. Of these, 85 were mapped with decent quality. Further post-processing eliminated 4 more genes, which did not give smooth fitness-to-expression curves. The final results presented in the manuscript are for 81 genes.

data_processing:
The reads for the different timepoints are combined in the fastq files. There is a barcode at the beginning of each read indicating the timepoint to which it belongs.
NGS reads were mapped to a reference sequence set that contained all barcode combinations of promoter, target gene and experimental timepoint. Example of a read: TGGGG*TCCGA*TACGTGAACCATCACCCTAATCAA*GGGAGAT*GTTTTTTGGGGACCAGGTGCCGTAAG*CTACACATGT*. Read structure: Random nucleotides (5bp) - experimental timepoint (5bp) - constant region (24bp) - target gene barcode (7bp)- constant region (26bp) - synthetic promoter barcode (10bp). Barcodes are listed in Tables S3-5 of the associated publication.
Mapping barcodes from reads to designed barcodes by custom software.
Calculating fitness advantage by custom software.
Genome_build: Not applicable.
Supplementary_files_format_and_content: The processed data files are tab-delimited text files that contain the number of reads mapped to each combination of synthetic promoter (row) and target gene (column) for the three timepoints assayed in the experiment, with either glucose or galactose medium. The first column contains a unique identifier for the synthetic promoter, defined by Sharon et al., 2012. The second column contains the log2 expression of the synthetic promoter as measured by fluorescent reporters. Columns 3-87 are the sequencing-derived data for the first experimental time. They indicate the number of reads mapped for each combination of synthetic promoter upstream of a specific target gene. Columns 88-172 are for the second timepoint and columns 173-257 are for the third timepoint.

source_name: Synthetic construct, glucose

growth_protocol: Cells were grown for 20 generations in 50ml glucose or galactose media.

extract_protocol:
Genomic DNA was extracted using YeaStar Genomic DNA Kit (Zymo Catalog # D2002).
A fragment of 300bp, containing the strain and promoter barcodes, was amplified from the gDNA by PCR. In order to maintain the complexity of the library amplified from gDNA, PCR reactions were carried out on a total of 1200ng of gDNA, an amount calculated to contain >10^7 yeast genomes. To minimize erroneous representation of the strains in the final product due to PCR bias, 12 separate reactions of PCR were performed for each sample (each with 100ng gDNA) and reactions were limited to 24 cycles. PCR was performed with 3 alternatively barcoded 5' primers, used to barcode the different experimental timepoints. Primers also included 5 random nucleotides at their 5' to increase sequence complexity and facilitate cluster calling during sequencing. 51'- NNNNNCTACTTACGTGAACCATCACCCTAATCAA 52'- NNNNNCTACTTACGTGAACCATCACCCTAATCAA 53'- NNNNNTCCGATACGTGAACCATCACCCTAATCAA 3'- NNNNNCTTTGCCTTCGTTTATCTTGCC. Italic nucleotides denote the timepoint barcodes. Following PCR, products were united and separated from unspecific fragments by electrophoresis on a 2% agarose gel stained by EtBr, cut from the gel, and cleaned in 2 steps: QIAquick Gel Extraction Kit (Qiagen Catalog # 28704) and SPRI beads (Agencourt AMPure XP Catalog A63881). Concentration was measured using a monochromator (Tecan i-control). The samples were assessed for size and purity at the Tapestation, using high-sensitivity D1K screenTape (Agilent Technologies, Catalog # 5067-5582). 50 ng DNA were used for library preparation for next-generation sequencing; specific Illumina adaptors were added, and DNA was amplified using 8 amplification cycles (protocol adopted from Blecher-Gonen et al.). Samples were run on the NextSeq (Illumina) with 75bp single-end kits (Catalog # FC-404-1001).
Illumina adaptors ligation.

treatment_protocol: At defined timepoints, genomic DNA was extracted and subjected to PCR amplification of the barcode region.

tag: strain/background

value: derivative of strain Y8205

tag: growth media

value: glucose

tag: timepoint

value: 13, 23 and 35 hours


title: EdU pulse (5min) Thymidine chase (5min) nascent DNA time course during Thiolutin treatment 3

value: wt yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase

tag: thymidine incubation (min)

tag: time point

value: 16 min after Thymidine chase, nascent chromatin, with thiolutin


title: H3K27Ac_ChIPSeq_Med12WT3

value: hematopoietic stem and progenitor cells

tag: genotype/variation

tag: chip antibody 1

tag: chip antibody 2


title: ChIP-reporter_input_pool3

description: DNA sequencing


title: ChIP-reporter_input_pool2

description: DNA sequencing


title: H3K27Ac_ChIPSeq_Med12WT1

tag: strain


title: EdU pulse (5min) Thymidine chase (5min) nascent DNA time course 4

description:
MNase digest time course followed by nascent DNA purification by EdU-biotin pulldown from asynchronous cells after a 5min EdU pulse and a 5min Thymidine chase.
Strand-specific MNase-seq.
Processed data file: PC_5_5_EdU_+-Thiolutin_tss_aligned.txt

value: 16 min after Thymidine chase, nascent chromatin, without thiolutin


title: EdU pulse (5min) Thymidine chase (5min) nascent DNA time course 2

value: 8 min after Thymidine chase, nascent chromatin, without thiolutin


title: Plasmid_translocation_EtOH_Rep3

description: Plasmid DNA from isolated nuclei

tag: cell line


title: IN-WT-(+)BIB2

description: CLIP-seq with BI-B2-treated wild-type IN

tag: antibody

value: monoclonal anti-integrase

value: BI-B2-treated wild-type IN


title: ChIP-reporter_input_pool1

description: DNA sequencing


title: Plasmid_translocation_EtOH_Rep2

description: Plasmid DNA from isolated nuclei

tag: transfection

tag: agent


title: A128T-IN-WT-(+)BIB2

description: CLIP-seq with BI-B2-treated A128T mutant IN

value: BI-B2-treated A128T mutant IN


title: IN-WT (mock)

description: CLIP-seq with mock-treated wild-type IN

value: mock-treated wild-type IN


title: Plasmid_translocation_EtOH_Rep1

description: Plasmid DNA from isolated nuclei

value: etoh


title: dex2_BAC_STARRseq_exp

value: transfected with STARR-seq library

value: dex


title: Plasmid_translocation_DEX_rep3

description: Plasmid DNA from isolated nuclei

value: transfected with STARR-seq plasmid pool


title: Growth competition galactose

description:
The strains used in this study were constructed by us. They are derivatives of strain Y8205 (Tong A. and Boone C., 2005).
Barcoded cells, differing in expression of one of 81 target genes, were grown in galactose. After 22, 35 and 49 hours, samples were taken and genomic DNA was extracted. The barcode region was amplified by PCR and sequenced.
The study was initially designed on 96 genes. Of these, 85 were mapped with decent quality. Further post-processing eliminated 4 more genes, which did not give smooth fitness-to-expression curves. The final results presented in the manuscript are for 81 genes.

source_name: Synthetic construct, galactose

value: galactose

value: 22, 35 and 49 hours


title: etoh2_BAC_STARRseq_exp


title: E06_MS03T27

status: Public on Aug 24 2016

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description:
SC3-seq protocol
Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E06
processed data file: SC3seq_Cy_ProcessedData.txt

data_processing:
All the reads were surveyed and the adaptor or the poly-A sequences were trimmed by cutadapt-1.3 with options "-c -m 30 -a CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -g CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -a AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA". The trimmed reads with less than 30 bp were discarded.
Untrimmed and trimmed reads of 30 bp or longer were mapped onto the mouse genome mm10 or Macsca fascicularis genome Macaca_fascicularis_5.0 and the ERCC spike-in RNA sequences with tophat-1.4.1/bowtie1.0.1 with the “—no-coverage-search” option.
Mapped reads on the genome and the ERCC were separated, and the reads on the genome were converted into the expression levels by cufflinks-2.2.0 using the “—compatible-hits-norm”, “—no-length-correction” and “—library-type fr-secondstrand” options and mm10 reference gene annotations with extended TTSs. We also set the cufflinks option “—max-mle-iterations” to 50,000, because default iterations (5,000) resulted in “FAILED” when estimating the expression levels of some genes. For the reference gene annotations used in cufflinks, we extended the TTSs of the reference genes up to 10 kb downstream to correctly estimate the expression levels of genes whose transcripts are longer than the reference toward the 3 prime.
Genome_build: mm10, Macaca_fascicularis_5.0
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each Sample ...

organism: Macaca fascicularis

source_name: Cynomolgus monkey embryo E06

growth_protocol:
For cultivation on feeders, cyESCs were cultured with conventional hESC medium [DMEM/F12 supplemented with 20% (vol/vol) of KSR, 1 mM of sodium pyruvate, 2 mM of GlutaMax, 0.1 mM of non-essential amino acids, 0.1 mM of 2-mercaptoethanol, 1000 U/ml of ESGRO mouse LIF, and 4 ng/ml of recombinant human bFGF] on mouse embryonic feeders (MEFs).
For cultivation in feeder free condition, CMK6 was cultured using the same condition applied for human ESC/iPSC as reported previously [Nakagawa, M., et al. (2014). Scientific Reports, 4, 3594.]
The mouse ESC line BVSC R8 was cultured in a 2i+LIF, feeder-free culture condition as reported previously [Hayash, K., et al. (2011). Cell, 146, 519].
The mouse EpiLC was induced from 2i+LIF ESCs for two days in N2B27 medium containing activin A (20 ng/ml), bFGF (12 ng/ml), and KSR (1%) as reported previously [Hayash, K., et al. (2011). Cell, 146, 519].

extract_protocol:
For single cell isolation from cy pre-implantation embryos, a whole embryo was incubated with 0.25% trypsin/PBS  for around 10 min at 37℃, then dissociated into single cells by repeated pipetting, and dispersed in 0.1 mg/ml of PVA/PBS  for preparation of single-cell cDNAs.
For single cell isolation from cy post-implantation embryos, the implantation site was dissected out from the uterus and the embryonic fragment containing the epiblast (EPI), amnion, hypoblast, and yolk sac endoderm was isolated manually. The fragment was incubated with 0.25% trypsin/PBS for around 10 min at 37℃, then dissociated into single cells by repeated pipetting, and dispersed in 0.1 mg/ml of PVA/PBS.
For single cell isolation from mouse E5.5 and E6.5 embryos, the embryos were dissected out from decidua and the extra-embryonic ectoderm was removed manually. The EPI/visceral endoderm (VE) were incubated in 0.25% Pancreatin/0.5 % Trypsin/Polyvinylpyrrolidone, and EPI and VE were separated by mild pipetting. For E5.5 embryos, EPI and VE were incubated with 0.25% trypsin/PBS separately for around 10 min at 37℃. For E6.5 EPI, their proximal parts were dissected out manually, and the proximal EPI and whole VE were incubated with 0.25% trypsin/PBS separately for around 10 min at 37℃. The proximal EPI and VE were dissociated into single cells by repeated pipetting, and dispersed in 0.1 mg/ml of PVA/PBS.
For single cell isolation from cyESCs, cells were first detached as clumps with CTK solution, incubated in 0.25% trypsin/PBS (Sigma-Aldrich) for around 10 min at 37℃, and dispersed into single cells in 1% (vol/vol) KSR/PBS containing 10 M of the ROCK inhibitor Y-27632. Cells under feeder-free condition were directly incubated in TrypLE Select for around 5 min at 37℃, and dispersed into single cells in 1% (vol/vol) KSR/PBS containing 10 M of the ROCK inhibitor Y-27632.
For single cell isolation from mESCs and EpiLCs, cells were incubated in TrypLE Select for around 5 min at 37℃, and dispersed into single cells in 1% (vol/vol) KSR/PBS.
For SC3-seq analysis, cDNA synthesis / amplification from single cells and library construction from the cDNAs were performed as described previously [Nakamura et al. 2015, NAR, 43, e60].

tag: tissue

value: embryo

tag: developmental stage


title: E06_MS03T25


title: E06_MS03T21


title: E06_MS68T13


title: E06_MS03T24


title: E06_MS68T15


title: E06_MS03T19


title: EdU pulse (5min) Thymidine chase (5min) nascent DNA time course during Thiolutin treatment 2

data_processing:
Illumina OLB-1.8.0/CASAVA_v1.7.0 were used for base calling.
Time points were separated by barcode and the 5bp barcode was removed from the read sequence.
Reads were mapped to the yeast S288C genome using BLAT.
Paired end read count distribution in 1bp windows was determined separately for Watson (marked as F in the processed data files) and Crick (marked as R in the processed data files) strands.
The average read count value was calculated and the data were normalized to one.
Genome_build: S288C (S. cerevisiae)
Supplementary_files_format_and_content: Tab-delimited text files of nucleosome occupancy for every gene at indicated time points (lines), showing every 20th bp from -500bp to the end of the gene coding sequence surrounding the transcription start site (marked as tss). Occupancy data start after the GWEIGHT header.

tag: cell cycle

value: asynchronous

value: 8 min after Thymidine chase, nascent chromatin, with thiolutin


title: EdU pulse (5min) Thymidine chase (5min) nascent DNA time course during Thiolutin treatment 1

value: wt yeast derived from W303 with the h-ENT1 nucleotide transporter and HPV-Thymidine kinase

tag: edu incubation

value: 6 min after Thymidine chase, nascent chromatin, with thiolutin


title: dex1_BAC_STARRseq_exp


title: dex3_BAC_STARRseq_exp


title: E06_MS03T17


title: etoh1_BAC_STARRseq_exp


title: E09_MS03T91

description:
SC3-seq protocol
Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E09
processed data file: SC3seq_Cy_ProcessedData.txt

source_name: Cynomolgus monkey embryo E09


title: E06_MS03T30


title: EdU pulse (5min) Thymidine chase (5min) nascent DNA time course 1

value: 4 min after Thymidine chase, nascent chromatin, without thiolutin


title: EdU pulse (5min) Thymidine chase (5min) nascent DNA time course 3

value: 12 min after Thymidine chase, nascent chromatin, without thiolutin


title: E09_MS03T82


title: E08_MS03T01

description:
SC3-seq protocol
Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E08
processed data file: SC3seq_Cy_ProcessedData.txt

source_name: Cynomolgus monkey embryo E08


title: E09_MS03T79


title: E06_MS03T29


title: E08_MS02T93


title: E06_MS03T22


title: E06_MS03T16


title: E09_MS03T83


title: E09_MS03T85


title: E08_MS02T92


title: E08_MS02T85


title: E08_MS02T89


title: E08_MS02T59


title: E08_MS02T57


title: E08_MS02T55


title: E08_MS02T44


title: E08_MS02T48


title: E08_MS02T38


title: E08_MS02T45


title: E08_MS02T43


title: E08_MS02T52


title: E08_MS02T30


title: E08_MS02T17


title: E08_MS02T31


title: E08_MS02T16


title: E08_MS02T06


title: E08_MS02T05


title: E08_MS02T01


title: E08_MS02T02


title: E07_MS03T70

description:
SC3-seq protocol
Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E07
processed data file: SC3seq_Cy_ProcessedData.txt

source_name: Cynomolgus monkey embryo E07


title: E07_MS08T41


title: E07_MS03T52


title: E07_MS03T65


title: E17_MS61T42

description:
SC3-seq protocol
Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E17
processed data file: SC3seq_Cy_ProcessedData.txt

source_name: Cynomolgus monkey embryo E17


title: E17_MS61T41


title: E17_MS61T62


title: E08_MS02T47


title: E17_MS61T40


title: E17_MS61T39


title: E08_MS02T36


title: E17_MS61T38


title: E17_MS11T80


title: E17_MS11T78


title: E17_MS61T37


title: E17_MS11T79


title: E07_MS08T42


title: E17_MS13T95


title: E17_MS10T94


title: E17_MS11T81


title: E17_MS11T46


title: E17_MS11T84


title: E17_MS11T49


title: E17_MS10T93


title: E17_MS10T91


title: E17_MS10T92


title: E17_MS10T86


title: E17_MS10T85


title: E17_MS10T88


title: E17_MS61T43


title: E17_MS10T87


title: E17_MS10T84


title: E17_MS10T82


title: E17_MS10T81


title: E17_MS10T77


title: E17_MS10T72


title: E17_MS10T73


title: E17_MS10T68


title: E17_MS10T71


title: E17_MS10T66


title: E16_MS09T41

description:
SC3-seq protocol
Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E16
processed data file: SC3seq_Cy_ProcessedData.txt

source_name: Cynomolgus monkey embryo E16


title: E16_MS09T21


title: E16_MS08T75


title: E16_MS09T28


title: E16_MS09T36


title: E16_MS08T69


title: E16_MS08T74


title: E16_MS08T68


title: E16_MS08T66


title: E16_MS08T65


title: E16_MS08T63


title: E16_MS08T61


title: E14_MS61T73

description:
SC3-seq protocol
Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E14
processed data file: SC3seq_Cy_ProcessedData.txt

source_name: Cynomolgus monkey embryo E14


title: E14_MS61T71


title: E14_MS61T72


title: E14_MS61T70


title: E14_MS61T68


title: E14_MS61T67


title: E14_MS61T64


title: E16_MS08T71


title: E14_MS61T61


title: E16_MS08T77


title: E14_MS61T63


title: E14_MS13T78


title: E14_MS10T63


title: E14_MS10T62


title: E16_MS08T60


title: E14_MS10T60


title: E14_MS13T76


title: E16_MS08T62


title: E14_MS08T56


title: E14_MS61T60


title: E14_MS13T74


title: E14_MS08T55


title: E16_MS08T64


title: E14_MS10T61


title: E14_MS08T48


title: E14_MS61T69


title: E14_MS08T53


title: E13_MS61T59

description:
SC3-seq protocol
Single cell transcriptome of amplified cDNA from cynomolgus monkey embryo at E13
processed data file: SC3seq_Cy_ProcessedData.txt

source_name: Cynomolgus monkey embryo E13


title: E14_MS08T49


title: E13_MS61T57


title: E14_MS61T66


title: E13_MS61T56


title: E13_MS61T53


title: E13_MS61T48


title: E14_MS08T54


title: E13_MS10T59


title: E13_MS13T92


title: E13_MS10T57


title: E13_MS10T56


title: E13_MS10T55


title: E14_MS08T52


title: E13_MS10T58


title: E14_MS08T50


title: E13_MS10T43


title: E13_MS10T50


title: E13_MS10T54


title: E13_MS10T52


title: E13_MS10T39


title: E13_MS10T37


title: E13_MS61T58


title: E13_MS10T35


title: E13_MS10T51


title: E13_MS61T55


title: E13_MS10T40


title: E13_MS10T34


title: E13_MS61T52


title: E16_MS09T43


title: E13_MS61T47


title: E13_MS61T46


title: E16_MS09T42


title: E14_MS13T86


title: E14_MS13T81


title: E14_MS09T11


title: E14_MS09T10


title: E14_MS09T07


title: E14_MS09T04


title: E14_MS09T06


title: E06_MS68T08


title: E06_MS68T12


title: E06_MS68T09


title: E06_MS68T11


title: E13_MS10T36


title: E14_MS09T02


title: E06_MS68T10


title: E14_MS09T01


title: E06_MS68T07


title: E06_MS68T04


title: E06_MS68T06


title: E06_MS68T02


title: E06_MS68T03


title: E06_MS68T01


title: E06_MS68T05


title: E06_MS03T38


title: E06_MS03T34


title: E06_MS03T28


title: E06_MS03T26


title: E06_MS03T23


title: E06_MS03T13


title: E06_MS03T14


title: E06_MS03T20


title: E06_MS03T12


title: E06_MS03T15


title: E06_MS03T10


title: E06_MS03T07


title: E06_MS03T11


title: E06_MS03T05


title: E06_MS03T04


title: E06_MS03T03


title: E09_MS03T81


title: E09_MS03T80


title: E09_MS03T93


title: E06_MS03T06


title: E06_MS03T08


title: E09_MS03T89


title: E08_MS03T02


title: E09_MS03T78


title: E09_MS03T95


title: E08_MS02T77


title: E08_MS02T80


title: E08_MS02T67


title: E09_MS03T88


title: E08_MS02T68


title: E08_MS02T81


title: E08_MS02T66


title: E08_MS02T63


title: E08_MS02T54


title: E08_MS02T56


title: E08_MS02T49


title: E08_MS02T53


title: E08_MS02T71


title: E08_MS02T50


title: E08_MS02T46


title: E08_MS02T42


title: E08_MS02T40


title: E08_MS02T41


title: E08_MS02T28


title: E08_MS02T26


title: E08_MS02T22


title: E08_MS02T35


title: E08_MS02T37


title: E08_MS02T32


title: E08_MS02T18


title: E08_MS02T20


title: E08_MS02T21


title: E08_MS02T39


title: E08_MS02T15


title: E08_MS02T13


title: E08_MS02T14


title: E08_MS02T12


title: E08_MS02T09


title: E08_MS02T08


title: E08_MS02T03


title: E07_MS03T72


title: E07_MS08T43


title: E07_MS03T64


title: E08_MS02T23


title: E07_MS03T62


title: E07_MS03T61


title: E07_MS03T56


title: E07_MS03T53


title: E17_MS13T94


title: E17_MS13T96


title: E17_MS10T96


title: E17_MS10T83


title: E16_MS08T76


title: E16_MS09T24


title: E17_MS10T95


title: E16_MS09T22


title: E16_MS09T33


title: E17_MS11T47


title: E16_MS08T67


title: E14_MS08T51


title: E16_MS09T25


title: E17_MS10T89


title: E07_MS03T71


title: E08_MS02T29


title: E07_MS03T57


title: E17_MS10T75


title: E17_MS10T67


title: E17_MS10T76


title: E17_MS10T69


title: E07_MS03T54


title: E16_MS08T72


title: E17_MS10T65


title: E16_MS08T59


title: E14_MS13T90


title: E14_MS13T87


title: E17_MS10T70


title: E17_MS11T83


title: E14_MS13T82


title: E17_MS11T82


title: E17_MS10T78


title: E17_MS10T64


title: E17_MS11T48


title: E14_MS13T80


title: E16_MS08T58


title: E16_MS09T30


title: E16_MS08T57


title: E14_MS13T85


title: E14_MS61T65


title: E16_MS09T35


title: E17_MS11T77


title: E16_MS09T40


title: E14_MS13T79


title: E14_MS13T89


title: E16_MS08T73


title: E14_MS09T19


title: E14_MS13T83


title: E14_MS13T77


title: E13_MS61T45


title: E14_MS13T88


title: E14_MS09T15


title: E14_MS09T05


title: E14_MS13T75


title: E14_MS09T17


title: E16_MS09T27


title: E14_MS09T20


title: E13_MS61T54


title: E14_MS09T03


title: E14_MS09T16


title: E13_MS61T49


title: E14_MS09T13


title: E14_MS09T14


title: E14_MS09T09


title: E13_MS13T72


title: E14_MS09T08


title: E14_MS09T12


title: E13_MS13T68


title: E13_MS13T66


title: E13_MS61T50


title: E13_MS13T67


title: E13_MS10T48


title: E13_MS61T51


title: E13_MS13T73


title: E13_MS10T49


title: E13_MS61T44


title: E13_MS10T46


title: E13_MS10T45


title: E13_MS13T69


title: C9oF_MS05T70

description:
SC3-seq protocol
Single cell transcriptome of amplified cDNA from cyESC, CMK9 cultivated on feeder
processed data file: SC3seq_Cy_ProcessedData.txt

source_name: cyESC, on feeder


title: C9oF_MS05T74


title: C9oF_MS05T72


title: C9oF_MS05T73


title: C9oF_MS05T75


title: E13_MS13T71


title: C9oF_MS05T71


title: C6oF_MS05T65

description:
SC3-seq protocol
Single cell transcriptome of amplified cDNA from cyESC, CMK6 cultivated on feeder
processed data file: SC3seq_Cy_ProcessedData.txt


title: C6oF_MS05T67


title: C9oF_MS05T69


title: E13_MS13T70


title: C6oF_MS05T66


title: C6oF_MS05T63


title: C6oF_MS05T64


title: C6oF_MS05T61


title: C6oF_MS05T60


title: C6oF_MS05T59


title: C6oF_MS05T58


title: C6oF_MS05T57


title: C6oF_MS05T56


title: C6oF_MS05T53


title: C6oF_MS05T54


title: C6FF_MS11T94

description:
SC3-seq protocol
Single cell transcriptome of amplified cDNA from cyESC, CMK6 cultivated in feeder free condition
processed data file: SC3seq_Cy_ProcessedData.txt

source_name: cyESC, feeder free


title: C6FF_MS11T95


title: C9oF_MS05T68


title: C6FF_MS11T92


title: C6FF_MS11T91


title: C6FF_MS11T86


title: C6FF_MS11T87


title: C6FF_MS11T89


title: C6oF_MS05T55


title: C6FF_MS11T85


title: E16_MS09T31


title: E17_MS13T91


title: E13_MS13T65


title: E16_MS09T29


title: C6FF_MS11T88


title: E09_MS03T87


title: E14_MS09T18


title: E09_MS03T90


title: E09_MS03T86


title: E09_MS03T75


title: E09_MS03T76


title: E09_MS03T77


title: E09_MS03T84


title: E08_MS02T95


title: E08_MS02T94


title: E08_MS02T90


title: E08_MS02T86


title: E08_MS02T87


title: E08_MS02T79


title: E08_MS02T83


title: E09_MS03T94


title: E08_MS02T75


title: E08_MS02T74


title: E08_MS02T88


title: E08_MS02T96


title: E08_MS02T78


title: E08_MS02T70


title: E08_MS02T65


title: E08_MS02T69


title: E08_MS02T61


title: E08_MS02T64


title: E08_MS02T72


title: E08_MS02T73


title: E08_MS02T34


title: E08_MS02T62


title: E08_MS02T58


title: E08_MS02T27


title: E08_MS02T33


title: E08_MS02T60


title: E08_MS02T19


title: E08_MS02T82


title: E08_MS02T10


title: E08_MS02T25


title: E08_MS02T91


title: E08_MS02T11


title: E08_MS02T07


title: E08_MS02T24


title: E08_MS02T04


title: E07_MS08T46


title: E07_MS08T45


title: E07_MS03T58


title: E07_MS03T60


title: E07_MS08T44


title: E07_MS03T59


title: E07_MS03T48


title: E07_MS03T46


title: E07_MS03T45


title: E07_MS03T44


title: E07_MS03T68


title: E07_MS03T49


title: E07_MS03T47


title: E07_MS03T42


title: E07_MS03T40


title: E07_MS03T41


title: E07_MS03T43


title: E06_MS68T16


title: E07_MS03T67


title: MN_Spombe_TetO_3h_Rep1

city: Madrid

first: Enrique

last: Vazquez de Luis

state: Madrid

address: Melchor Fernandez Almagro, 3

country: Spain

institute: CNIC

description: Mononucleosomal DNA

data_processing:
Alignment: bowtie 0.12.7
The smoothed profiles were generated by using a modified version of NUCwave (Quintales et al. 2015) to normalize signal against repeated sequences.
Genome_build: S. pombe 2007 (ASM294v2)

organism: Schizosaccharomyces pombe

source_name: Mononucleosomal DNA

growth_protocol: Yeast cultures were grown in YES medium

extract_protocol:
200 ml cultures at 0.4x10⁷ cells/ml were supplemented with EtOH or TetO and incubated 3 h. Then were collected  for preparation of mononucleosomal DNA. Cells were treated with 8 mg of Zymolyase  20T during 30 minutes at 30 ºC to induce spheroplasts formation. Mononucleosomal fragments were generated by digesting DNA with 200 units/ml of micrococcal nuclease (MNase) at 37 ºC during 45 minutes. The amount of MNase was optimized experimentally to generate a 80:20 ratio of mononucleosomes to dinucleosomes, as described (Lantermann et al. 2010). Mononucleosomal DNA was recovered from 1.5% agarose gels and sequenced in an Illumina NextSeq 500 using the 2x41 pair-end sequencing protocol.
Mononucleosomal DNA libraries were prepared for sequencing using standard Illumina protocols

tag: time

value: 3h with 5ug/ml of Anhydrotetracycline (AnTet)


title: E07_MS03T63


title: MN_Spombe_TetO_3h_Rep2

description: Mononucleosomal DNA


title: MN_Spombe_EtOH_3h_Rep1

description: Mononucleosomal DNA

value: 3h with EtOH


title: E07_MS03T55


title: Day16-3_GES13_05288_ACTTGA

city: Bar Harbor

first: Gregory

last: Carter

state: Maine

address: 600 Main Street

institute: The Jackson Laboratory

description:
Germ cells from mouse 3 at age 16 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt

data_processing:
Sequenced reads were filtered to keep reads for which 70% of the base pair quality score was > 20, and the 3’ end was trimmed if the base pair quality score was < 20
Two technical replicates for each paired-end were run in different lanes and then merged.
All RNA-seq samples were aligned with Bowtie 1.0.0 and expression levels were estimated by RSEM 1.2.8
A Bowtie index was prepared for alignment to a combined (mm10) transcriptome of Ensembl Genome Reference Consortium, build 38, release 75, NONCODE v4 lncRNA, and piRNA precursor transcripts. The 214 piRNA precursors were obtained from Dr. Christian Roy. Both the NONCODE lncRNA and piRNA precursors were converted to mm10 coordinates using liftOver.
We used log2(TPM+1) as the expression level, where TPM is transcripts per million, defined by RSEM
Only transcripts having TPM >= 3 for at least one of the 28 samples was used in this study.
Genome_build: (mm10) Ensembl Genome Reference Consortium, build 38, release 75
Supplementary_files_format_and_content: GeneLists.xlsx: Lists of substage-concordant, substage-negatively concordant, and X-linked genes. Genes are ranked by how closely the expression pattern follows the substage pattern (rank=1 is best). Gene ids and Gene names for piRNA precursors and NONCODE lncRNAs have prefix "pi-" and "NON", respectively. Expression is given in log2(TPM+1).
Supplementary_files_format_and_content: GeneExpressionTPM.txt : Gene expression in Transcripts per Million (TPM) by RSEM of genes with at least one sample having TPM >=3. Tab delimited text file. Substage associations given. Gene ids for piRNA precursors and NONCODE lncRNAs have prefix "pi-" and "NON", respectively.
Supplementary_files_format_and_content: TranscriptExpressionTPM.txt : Transcript (isoform) expression in Transcripts per Million (TPM) by RSEM of genes with at least one sample having TPM >=3. Tab delimited text file. Substage associations given. Gene ids for piRNA precursors and NONCODE lncRNAs have prefix "pi-" and "NON", respectively.

source_name: Germ cells

extract_protocol:
The procedure was as previously described with some modifications (Cobb 1997, La Salle 2009). Briefly, seminiferous tubules were transferred into 20 ml DMEM (Gibco, Life Technologies, Carlsbad, CA, USA) containing 0.5 mg of Liberase TL Research Grade (05401020001, Roche, Basel, Switzerland) and incubated for 20 min at 32 °C. To remove interstitial cells, tubules were washed three times with the same media.
Isolated germ cell samples were resuspended in QIAzol Lysis Reagent according to the manufacturer's instructions, and total RNAs were purified from homogenized cells using Qiagen RNeasy Mini Kit (74104).

tag: age

value: 16 dpp

tag: Sex

value: male


title: Day16-5_GES13_05290_TAGCTT

description:
Germ cells from mouse 5 at age 16 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day18-2_GES13_05292_CTTGTA

description:
Germ cells from mouse 2 at age 18 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt

value: 18 dpp


title: Day16-1_GES13_05286_GCCAAT

description:
Germ cells from mouse 1 at age 16 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day18-1_GES13_05291_GGCTAC

description:
Germ cells from mouse 1 at age 18 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day12-5_GES13_05280_ATGTCA

description:
Germ cells from mouse 5 at age 12 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt

value: 12 dpp


title: Day12-3_GES13_05278_AGTCAA

description:
Germ cells from mouse 3 at age 12 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day14-7_GES13_05285_ACAGTG

description:
Germ cells from mouse 5 at age 14 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt

value: 14 dpp


title: Day14-3_GES13_05283_TTAGGC

description:
Germ cells from mouse 3 at age 14 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day18-5_GES13_05295_ATGTCA

description:
Germ cells from mouse 5 at age 18 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day14-2_GES13_05282_CGATGT

description:
Germ cells from mouse 2 at age 14 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day14-6_GES13_05284_TGACCA

description:
Germ cells from mouse 4 at age 14 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day16-2_GES13_05287_CAGATC

description:
Germ cells from mouse 2 at age 16 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day12-4_GES13_05279_AGTTCC

description:
Germ cells from mouse 4 at age 12 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day18-4_GES13_05294_AGTTCC

description:
Germ cells from mouse 4 at age 18 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: MN_Spombe_EtOH_3h_Rep2

description: Mononucleosomal DNA


title: Day18-3_GES13_05293_AGTCAA

description:
Germ cells from mouse 3 at age 18 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day12-2_GES13_05277_CTTGTA

description:
Germ cells from mouse 2 at age 12 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day10-4_GES13_05274_GATCAG

description:
Germ cells from mouse 4 at age 10 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt

value: 10 dpp


title: Day8-2_GES13_05267_CGATGT

description:
Germ cells from mouse 2 at age 8 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt

value: 8 dpp


title: Day8-1_GES13_05266_ATCACG

description:
Germ cells from mouse 1 at age 8 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day8-3_GES13_05268_TTAGGC

description:
Germ cells from mouse 3 at age 8 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day10-2_GES13_05272_CAGATC

description:
Germ cells from mouse 2 at age 10 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day16-4_GES13_05289_GATCAG

description:
Germ cells from mouse 4 at age 16 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day10-3_GES13_05273_ACTTGA

description:
Germ cells from mouse 3 at age 10 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day14-1_GES13_05281_ATCACG

description:
Germ cells from mouse 1 at age 14 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: ExomeSeq_M2

city: Stanford

first: Joseph

last: Wu

state: Carlifornia

address: Stanford University School of Medicine

institute: Stanford University School of Medicine

data_processing:
Library strategy: Exome-seq
Exome sequences processing Torrent Suite 5.0.4
Depth of reads= 30 million/sample
genome build: hg19
processed data files format and content: text file with identified SNVs.

extract_protocol:
QIAGEN DNeasy Blood and Tissue Kit
Exome-Seq libraries prepared from 100ng gDNA, using the Ion AmpliSeq Exome RDY Library Preparation kit

treatment_protocol: Daily for 7 days

tag: treatment

value: Untreated

tag: reagent/antibody (company

value: cat #):Not applicable

value: Skin fibroblasts


title: ExomeSeq_M1


title: ExomeSeq_F5


title: ExomeSeq_F2


title: ExomeSeq_F4


title: ExomeSeq_F1


title: ExomeSeq_F3


title: AmpliSeq_F2_Untreated

data_processing:
Library strategy: Ampli-seq
Ampliseq processing: Torrent Suite 5.0.4
Depth of reads= 5 million/sample
genome build: hg19
processed data files format and content: text file with FPKM values

growth_protocol:
RPMI-B27
Cardiac differentiation of iPSCs grown in E8 media, using RPMI-B27 medium with 6uM CHIR induction for 2 days (d0-d2) and 2.5uM C59 treatment for two days (d3-d5)

extract_protocol:
QIAGEN RNeasy Mini Kit
Ampli-Seq libraries prepared from 10ng RNA, using the Ion AmpliSeq Transcriptome Human Gene Expression Kit

value: hiPSC-derived cardiomyocytes


title: AmpliSeq_F2_Tacrolimus

value: Tacrolimus

value: cat #):Tocris Bioscience:#3631


title: Day12-1_GES13_05276_GGCTAC

description:
Germ cells from mouse 1 at age 12 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: AmpliSeq_F5 + PPP3CC_Tacrolimus

source_name: AmpliSeq_F5 + PPP3CC_Tacrolimus


title: AmpliSeq_F5_Tacrolimus


title: AmpliSeq_M2


title: AmpliSeq_F5_Rosiglitazone

value: Rosiglitazone

value: cat #):Tocris Bioscience:#5325


title: AmpliSeq_F5 + PPP3CC_Rosiglitazone

source_name: AmpliSeq_F5 + PPP3CC_Rosiglitazone


title: AmpliSeq_P3_hiPSC_CM


title: AmpliSeq_F2_Rosiglitazone


title: AmpliSeq_M1


title: Day10-5_GES13_05275_TAGCTT

description:
Germ cells from mouse 5 at age 10 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: Day10-1_GES13_05271_GCCAAT

description:
Germ cells from mouse 1 at age 10 dpp
GeneLists.xlsx
GeneExpressionTPM.txt
TranscriptExpressionTPM.txt


title: AmpliSeq_P2_hiPSC_CM


title: AmpliSeq_P1_hiPSC_CM


title: AmpliSeq_P1_LV

value: Human left ventricular tissue


title: AmpliSeq_P3_LV


title: 2iLESC_MS61T83

description:
SC3-seq protocol
Single cell transcriptome of amplified cDNA from ESC cultivated under 2i/LIF condition
processed data file: SC3seq_Ms_ProcessedData.txt

source_name: 2i/LIF ESC

value: BVSC R8

tag: cell type

value: ESC


title: AmpliSeq_P2_LV


title: AmpliSeq_F5 + PPP3CC_Untreated

source_name: AmpliSeq_F5 + PPP3CC_Untreated


title: rep4_GES14_04765_TGACCA

description:
pachytene and diplotene spermatocytes
processed data: STA-PUT_TPM.txt

data_processing:
Two technical replicates for each paired-end were run in different lanes and then merged.
All RNA-seq samples were aligned with Bowtie 1.0.0 and expression levels were estimated by RSEM 1.2.8
A Bowtie index was prepared for alignment to a combined (mm10) transcriptome of Ensembl Genome Reference Consortium, build 38, release 75, NONCODE v4 lncRNA, and piRNA precursor transcripts. The 214 piRNA precursors were obtained from Dr. Christian Roy. Both the NONCODE lncRNA and piRNA precursors were converted to mm10 coordinates using liftOver.
We used log2(TPM+1) as the expression level, where TPM is transcripts per million, defined by RSEM
Genome_build: (mm10) Ensembl Genome Reference Consortium, build 38, release 75
Supplementary_files_format_and_content: STA-PUT_TPM.txt: Gene expression in Transcripts per Million (TPM) by RSEM of genes for each replicate. Tab delimited file.  Gene ids for piRNA precursors and NONCODE lncRNAs have prefix "pi-" and "NON", respectively.

source_name: Pachytene and diplotene spermatocytes

extract_protocol:
Each enriched population (4 biological replicates) of pachytene/diplotene spermatocytes was obtained from the testes of 6 9-week old mice by sedimentation at unit gravity [3] (Bellvé, 1993). Mixed germ-cell suspensions were prepared as described above, and after the three 0.5% BSA/KRB washes, cells were allowed to separate by cellular sedimentation at unit gravity in a 2–4% BSA gradient generated over 2.5 h in a STA-PUT apparatus (ProScience Inc., GlassShop, Toronto, ON, Canada).  Following the sedimentation process, 10 ml fractions were collected and examined using light microscopy and differential interference contrast Nomarski optics. Cells were identified based on morphological criteria and size [3] (Bellvé 1993). Populations of pachytene/diplotene spermatocytes of average purity= ~90% were collected. For every cell separation, and for each population of cells collected, an aliquot of cells was snap-frozen for subsequent RNA extraction.
Isolated germ cell samples were resuspended in QIAzol Lysis Reagent according to the manufacturer's instructions, and total RNAs were purified from homogenized cells using Qiagen RNeasy Mini Kit (74104).

value: 9 weeks

value: male


title: 2iLESC_MS61T81


title: AmpliSeq_F5_Untreated


title: rep2_GES14_04763_CGATGT


title: rep3_GES14_04764_TTAGGC


title: rep1_GES14_04762_ATCACG


title: 2iLESC_MS61T79


title: 2iLESC_MS61T78


title: 2iLESC_MS61T80


title: 2iLESC_MS61T76


title: 2iLESC_MS61T77


title: 2iLESC_MS61T74


title: scramble_RNASeq, 3

city: Salt Lake City

first: Bethany

last: Buck-Koehntop

state: Utah

department: Chemistry

institute: University of Utah

data_processing:
Basecalls were performed using CASAVA version 1.8.2
Illumina fastq files were aligned to the hg19 genome with all known and theoretical splice junctions using Novocraft’s novoalign aligner with the following parameters: -r All 50 -t 40 -o SAM 90 –k. The USeq NovoalignParser application was then used to parse the alignment files into binary point data by setting the posterior probability to 0 and alignment score threshold to 60.
The MultipleReplicaDefinedRegionScanseqs USeq application, which utilizes the DESeq R package22, identified statistically significant differentially expressed genes between cells treated with the scrambled siRNA and CTCF depleted cells.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

growth_protocol: Cell were cultured in Dulbecco's Modified Eagle medium supplemented with 4.5 g/L glucose, 10% FBS and 2 nM glutamine in humidified incubator at 37 deg. C with 5% CO2.

extract_protocol:
Transfected cells were washed with PBS and resuspended in TRIzol prior to RNA extraction with the Direct-zol RNA Kit (Zymo Research). RNA quality was measured on a Bioanalyzer RNA 6000 Nano Chip. Total RNA was further purified with the RiboMinus Eukaryote Kit for RNA-Seq (Thermo Fisher Scientific – Life Technologies).
RNA libraries were prepared for sequencing by Illumina TruSeq Stranded mRNA Sample Prep with poly(A) selection

treatment_protocol: HeLa cells were transfected with either a scrambled siRNA or one of two CTCF siRNAs (Thermo Fisher Scientific – Life technologies) using Lipofectamine RNAiMAX (Thermo Fisher Scientific – Life technologies) and incubated for 24 hr.

value: HeLa S3

tag: passage

value: 5 to 8

tag: sirna

value: scrambled siRNA


title: siRNA2_CTCF_RNASeq, 3


title: 2iLESC_MS61T75

tag: strain


title: siRNA1_CTCF_RNASeq, 2

tag: cell line


title: EpiLC_MS61T94

description:
SC3-seq protocol
Single cell transcriptome of amplified cDNA from day2 EpiLC
processed data file: SC3seq_Ms_ProcessedData.txt

source_name: EpiLC

value: EpiLC


title: siRNA2_CTCF_RNASeq, 2


title: siRNA1_CTCF_RNASeq, 3


title: siRNA1_CTCF_RNASeq, 1


title: EpiLC_MS61T96


title: EpiLC_MS61T91


title: 2iLESC_MS61T82


title: EpiLC_MS61T92


title: scramble_RNASeq, 1


title: EpiLC_MS61T90


title: scramble_RNASeq, 2


title: siRNA2_CTCF_RNASeq, 1


title: EpiLC_MS61T93