title: FLC-375mimic3

city: Ithaca

first: Praveen

last: Sethupathy

address: T7 006 Vet Research Tower

institute: Cornell University

data_processing:
Sequencing quality was assess using fastqc/0.11.3
Reads were aligned using STAR/2.4.2 to the  hg38 reference genome.
Alignments were quantified using Salmon/0.8.2.
Gene level counts were read into R/3.1.1 using tximport. DESeq2/1.12.4 was used to normalize counts and conduct differential gene expression analysis. A table of normalized counts for each gene and sample is included as processed data.
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited text files include normalized (using DESeq2) count values for each sample

source_name: Fibrolamellar carcinoma cell line

extract_protocol:
48 hours post-transfection, total RNA was isolated using the Norgen Total RNA Purification kit.
Libraries were prepared using the NEBNext Ultra II Directional RNAseq kit per manufacturer's instructions by the RNA sequencing core of the Cornell Veterinary College. Paired end sequencing was performed on an Illumina NextSeq 500.

treatment_protocol: FLC cells were transfected with 50 nM miR-375 mimic or scramble control using Lipofectamine 3000.

value: miR-375 mimic

tag: cell type

value: Fibrolamellar carcinoma cell line


title: ID 17, visit 4

status: Public on Mar 08 2019

type: RNA

city: OSLO

first: Mari

last: Myhrstad

address: Postboks 4, St. Olavs plass

department: Department of health

country: Norway

institute: Oslo and Akershus University College

description: wk 7

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: Labelled extracts were prepared using Illumina TotalPrep RNA Amplification Kit (Illumina Inc, CA 92122, USA).

extract_protocol: Total RNA was isolated from all PBMC samples using RNeasy mini kit (Qiagen) with lysis buffer added -mercaptoethanol according to the manufacturer’s instructions,  and stored at -80C. Quality control was performed with Agilent Bioanalyser.

tag: gender

value: F

tag: tissue

value: Peripheral blood mononuclear cells

tag: n6 level tertiles (1=low, 2=middle, 3=high)

tag: n3 level tertiles (1=low, 2=middle, 3=high)

tag: sfa/pufa ratio tertiles (1=low, 2=middle, 3=high)


title: ID 2, visit 4

description: wk 7


title: ID 1, visit 4

description: wk 7

value: M


title: FLC-375mimic1

status: Public on Mar 07 2019

type: SRA

state: NY

country: USA

library_source: transcriptomic

molecule: polyA RNA

tag: treatment


title: HCT116-ctrl-siauf1-1

city: beijing

first: wanru

last: ma

address: 52 Fucheng Road,Haidian District,Beijing

country: China

institute: beijing cancer hospital

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. The remaining reads were filtered against the rRNA database to remove possible ribosomal RNA contamination,  and then mapped to the hg19 whole genome using Hisat2 v2.1.0 with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and counts for each Sample

source_name: colon cell line

extract_protocol:
RNA was extract though Magzol Reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: colon cancer cell line


title: FLC-Neg3

value: scramble mimic


title: FLC-Neg2


title: FLC-Neg1


title: HCT116-ctrl-nc-1


title: ATc-treated (Test) Vs ATc-untreated cells (Control) - Biological replicate 2

city: Faridabad

first: Nisheeth

last: Agarwal

state: Haryana

address: 3rd Milestone, Faridabad-Gurugram Expressway

department: Infection and Immunity

country: India

institute: Translational Health Science and Technology Institute

hyb_protocol: Labeled cDNAs and hybridization buffer (10X SSC, 50% Formamide and 0.2% SDS containing 10µg Salmon sperm DNA and 8µg yeast tRNA) were added, and samples were applied to microarrays enclosed in hybridization chambers. After hybridization, slides were washed sequentially with buffers containing decreasing concentrations of SSC and SDS.

scan_protocol: Scanned on a GenePix 4000A microarray scanner (Axon Instruments). Images were quantified using GenePix Pro 7.2.22 software (Axon Instruments).

data_processing: Normalized, background subtracted data obtained from processed Red signal and processed Green signal.

label: Alexa Fluor 647

organism: Mycobacterium tuberculosis

source_name: ATc-untreated cells

label_protocol: 4 µg of total RNA were primed with 0.5 µg of random hexamer primer at 70°C for 10 min, then reversed transcribed at 46°C for 3 h in the presence of Alexa Fluor 647- or 555-aha-dCTP by using SuperScript Direct cDNA labeling system (Invitrogen) according to manufacturer's instructions.

extract_protocol: Total RNA extracted using RNA iso plus (Takara) following manufacturer's instructions.

treatment_protocol: Cells grown in 7H9-OADS medium for 4 days at 37°C.

tag: strain/background

value: H37Ra, transformed with ptetInt-dcas9 and pGrna-gyrB

value: ATc-untreated

label: Alexa Fluor 555

source_name: ATc-treated cells

treatment_protocol: Cells grown in 7H9-OADS medium containing 20ng/ml ATc for 4 days at 37°C.

value: ATc-treated


title: ATc-treated (Test) Vs ATc-untreated cells (Control) - Biological replicate 1


title: FLC-375mimic2


title: A2_W4_1_N17

city: Stanford

first: Michelle

middle: Berkeley

last: Chen

address: 318 Campus Drive

institute: Stanford

description:
Young2pos_N17
Sample barcode: N479Barcode_721.521
mRNA

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: rawdata_natmed.csv: Comma-separated text file includes raw count table (genes X cells).

organism: Mus musculus

source_name: Young

growth_protocol: Mice 3 (young) and 19 (Old) months.

extract_protocol:
Hippocampi (pooled n=4 per sample) were dissected using Miltenyi neural dissociation kit. Brain endothelial cells were isolated via FACS.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: primary murine brain endothelial cell

value: Male

tag: age

value: Young (3 months)


title: H1_W4_1_A23

description:
Young2neg_A23
Sample barcode: N479Barcode_728.502
mRNA


title: C10_W4_1_N19

description:
Young2neg_N19
Sample barcode: N479Barcode_723.521
mRNA


title: E5_W4_1_A21

description:
Young2pos_A21
Sample barcode: N479Barcode_726.502
mRNA


title: D1_W4_1_A20

description:
Young2neg_A20
Sample barcode: N479Barcode_724.502
mRNA


title: C2_W4_1_F19

description:
Young2pos_F19
Sample barcode: N479Barcode_723.516
mRNA


title: A6_W1_1_F1

description:
Old2pos_F1
Sample barcode: N479Barcode_701.516
mRNA

source_name: Aged

value: Old (19 months)


title: D8_W1_1_K3

description:
Old2pos_K3
Sample barcode: N479Barcode_703.508
mRNA


title: H9_W1_1_O5

description:
Old2pos_O5
Sample barcode: N479Barcode_705.511
mRNA


title: F4_W1_1_C4

description:
Old2neg_C4
Sample barcode: N479Barcode_704.503
mRNA


title: B8_W4_1_P18

description:
Young2pos_P18
Sample barcode: N479Barcode_722.522
mRNA


title: F3_W4_1_K21

description:
Young2neg_K21
Sample barcode: N479Barcode_726.508
mRNA


title: C11_W1_1_B3

description:
Old2neg_B3
Sample barcode: N479Barcode_703.513
mRNA


title: E8_W4_1_D21

description:
Young2neg_D21
Sample barcode: N479Barcode_726.515
mRNA


title: G3_W1_1_N4

description:
Old2pos_N4
Sample barcode: N479Barcode_704.521
mRNA


title: F10_W1_1_I4

description:
Old2pos_I4
Sample barcode: N479Barcode_704.507
mRNA


title: BEAS-2B cells treated with 60 nm of silica nanoparticles, biological rep2

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: BEAS-2B cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: BEAS-2B cells were seeded in petri dishes at density of 1×105 cells/mL and allowed to attach for 24 h, then treated with silica nanoparticles suspended in DMEM culture medium or DMEM culture mediun only for another 24 h.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Suspension of silica nanoparticles was dispersed by sonicator, and diluted to 25 μg/ml, then add to BEAS-2B cells immediately.Cells maintained in DMEM culture medium without silica nanoparticles were used as control group.

value: bronchial epithelial cells


title: B1_W4_1_I18

description:
Young2neg_I18
Sample barcode: N479Barcode_722.507
mRNA


title: BEAS-2B cells as control (dataset II), biological rep1

description: cells as normal control


title: BEAS-2B cells treated with 40 nm of silica nanoparticles, biological rep3


title: BEAS-2B cells treated with 200 nm of silica nanoparticles, biological rep2


title: BEAS-2B cells treated with 40 nm of silica nanoparticles, biological rep1


title: D1_W1_1_D3

description:
Old2neg_D3
Sample barcode: N479Barcode_703.515
mRNA


title: BEAS-2B cells treated with 200 nm of silica nanoparticles, biological rep1


title: G2_W1_1_M4

description:
Old2pos_M4
Sample barcode: N479Barcode_704.510
mRNA


title: A7_W1_1_G1

description:
Old2neg_G1
Sample barcode: N479Barcode_701.506
mRNA


title: BEAS-2B cells treated with 200 nm of silica nanoparticles, biological rep3


title: F2_W4_1_J21

description:
Young2neg_J21
Sample barcode: N479Barcode_726.518
mRNA


title: BEAS-2B cells as control (dataset II), biological rep2

description: cells as normal control


title: H4_W4_1_D23

description:
Young2neg_D23
Sample barcode: N479Barcode_728.515
mRNA


title: BEAS-2B cells treated with 40 nm of silica nanoparticles, biological rep2


title: BEAS-2B cells as control (dataset II), biological rep3

description: cells as normal control


title: C9_W4_1_M19

description:
Young2neg_M19
Sample barcode: N479Barcode_723.510
mRNA


title: BEAS-2B cells treated with 60 nm of silica nanoparticles, biological rep1


title: D3_W1_1_F3

description:
Old2neg_F3
Sample barcode: N479Barcode_703.516
mRNA


title: G9_W1_1_D5

description:
Old2neg_D5
Sample barcode: N479Barcode_705.515
mRNA


title: A8_W1_1_H1

description:
Old2neg_H1
Sample barcode: N479Barcode_701.517
mRNA


title: G2_W4_1_F22

description:
Young2pos_F22
Sample barcode: N479Barcode_727.516
mRNA


title: F6_W4_1_N21

description:
Young2neg_N21
Sample barcode: N479Barcode_726.521
mRNA


title: H9_W4_1_I23

description:
Young2pos_I23
Sample barcode: N479Barcode_728.507
mRNA


title: H10_W4_1_J23

description:
Young2pos_J23
Sample barcode: N479Barcode_728.518
mRNA


title: B2_W4_1_J18

description:
Young2neg_J18
Sample barcode: N479Barcode_722.518
mRNA


title: H8_W1_1_N5

description:
Old2pos_N5
Sample barcode: N479Barcode_705.521
mRNA


title: E7_W4_1_C21

description:
Young2neg_C21
Sample barcode: N479Barcode_726.503
mRNA


title: A4_W1_1_D1

description:
Old2pos_D1
Sample barcode: N479Barcode_701.515
mRNA


title: G12_W4_1_P22

description:
Young2neg_P22
Sample barcode: N479Barcode_727.522
mRNA


title: G12_W1_1_F5

description:
Old2neg_F5
Sample barcode: N479Barcode_705.516
mRNA


title: C8_W4_1_L19

description:
Young2neg_L19
Sample barcode: N479Barcode_723.520
mRNA


title: D12_W4_1_L20

description:
Young2pos_L20
Sample barcode: N479Barcode_724.520
mRNA


title: E3_W4_1_O20

description:
Young2pos_O20
Sample barcode: N479Barcode_724.511
mRNA


title: C11_W4_1_O19

description:
Young2neg_O19
Sample barcode: N479Barcode_723.511
mRNA


title: D9_W1_1_L3

description:
Old2pos_L3
Sample barcode: N479Barcode_703.520
mRNA


title: A10_W1_1_J1

description:
Old2neg_J1
Sample barcode: N479Barcode_701.518
mRNA


title: H11_W4_1_K23

description:
Young2pos_K23
Sample barcode: N479Barcode_728.508
mRNA


title: G4_W4_1_H22

description:
Young2pos_H22
Sample barcode: N479Barcode_727.517
mRNA


title: B7_W4_1_O18

description:
Young2pos_O18
Sample barcode: N479Barcode_722.511
mRNA


title: C1_W1_1_H2

description:
Old2pos_H2
Sample barcode: N479Barcode_702.517
mRNA


title: G6_W4_1_J22

description:
Young2pos_J22
Sample barcode: N479Barcode_727.518
mRNA


title: D10_W4_1_J20

description:
Young2pos_J20
Sample barcode: N479Barcode_724.518
mRNA


title: C6_W4_1_J19

description:
Young2pos_J19
Sample barcode: N479Barcode_723.518
mRNA


title: D7_W1_1_J3

description:
Old2pos_J3
Sample barcode: N479Barcode_703.518
mRNA


title: D11_W1_1_N3

description:
Old2pos_N3
Sample barcode: N479Barcode_703.521
mRNA


title: B1_W1_1_M1

description:
Old2neg_M1
Sample barcode: N479Barcode_701.510
mRNA


title: H10_W1_1_P5

description:
Old2pos_P5
Sample barcode: N479Barcode_705.522
mRNA


title: F12_W4_1_D22

description:
Young2pos_D22
Sample barcode: N479Barcode_727.515
mRNA


title: H3_W1_1_I5

description:
Old2neg_I5
Sample barcode: N479Barcode_705.507
mRNA


title: F9_W4_1_A22

description:
Young2pos_A22
Sample barcode: N479Barcode_727.502
mRNA


title: F8_W1_1_G4

description:
Old2pos_G4
Sample barcode: N479Barcode_704.506
mRNA


title: B6_W1_1_B2

description:
Old2neg_B2
Sample barcode: N479Barcode_702.513
mRNA


title: A11_W4_1_G18

description:
Young2neg_G18
Sample barcode: N479Barcode_722.506
mRNA


title: F5_W4_1_M21

description:
Young2neg_M21
Sample barcode: N479Barcode_726.510
mRNA


title: A9_W1_1_I1

description:
Old2neg_I1
Sample barcode: N479Barcode_701.507
mRNA


title: C5_W4_1_I19

description:
Young2pos_I19
Sample barcode: N479Barcode_723.507
mRNA


title: C3_W4_1_G19

description:
Young2pos_G19
Sample barcode: N479Barcode_723.506
mRNA


title: G8_W4_1_L22

description:
Young2neg_L22
Sample barcode: N479Barcode_727.520
mRNA


title: H7_W4_1_G23

description:
Young2pos_G23
Sample barcode: N479Barcode_728.506
mRNA


title: F1_W4_1_I21

description:
Young2neg_I21
Sample barcode: N479Barcode_726.507
mRNA


title: F5_W1_1_D4

description:
Old2neg_D4
Sample barcode: N479Barcode_704.515
mRNA


title: G11_W4_1_O22

description:
Young2neg_O22
Sample barcode: N479Barcode_727.511
mRNA


title: F6_W1_1_E4

description:
Old2neg_E4
Sample barcode: N479Barcode_704.505
mRNA


title: H2_W4_1_B23

description:
Young2neg_B23
Sample barcode: N479Barcode_728.513
mRNA


title: F7_W4_1_O21

description:
Young2pos_O21
Sample barcode: N479Barcode_726.511
mRNA


title: D11_W4_1_K20

description:
Young2pos_K20
Sample barcode: N479Barcode_724.508
mRNA


title: A3_W1_1_C1

description:
Old2pos_C1
Sample barcode: N479Barcode_701.503
mRNA


title: H4_W1_1_J5

description:
Old2neg_J5
Sample barcode: N479Barcode_705.518
mRNA


title: B2_W1_1_N1

description:
Old2neg_N1
Sample barcode: N479Barcode_701.521
mRNA


title: G7_W4_1_K22

description:
Young2neg_K22
Sample barcode: N479Barcode_727.508
mRNA


title: D4_W4_1_D20

description:
Young2neg_D20
Sample barcode: N479Barcode_724.515
mRNA


title: E1_W4_1_M20

description:
Young2pos_M20
Sample barcode: N479Barcode_724.510
mRNA


title: G5_W4_1_I22

description:
Young2pos_I22
Sample barcode: N479Barcode_727.507
mRNA


title: A3_W4_1_O17

description:
Young2pos_O17
Sample barcode: N479Barcode_721.511
mRNA


title: A2_W1_1_B1

description:
Old2pos_B1
Sample barcode: N479Barcode_701.513
mRNA


title: G6_W1_1_A5

description:
Old2pos_A5
Sample barcode: N479Barcode_705.502
mRNA


title: F8_W4_1_P21

description:
Young2pos_P21
Sample barcode: N479Barcode_726.522
mRNA


title: D5_W1_1_H3

description:
Old2neg_H3
Sample barcode: N479Barcode_703.517
mRNA


title: A7_W4_1_C18

description:
Young2neg_C18
Sample barcode: N479Barcode_722.503
mRNA


title: A11_W1_1_K1

description:
Old2neg_K1
Sample barcode: N479Barcode_701.508
mRNA


title: G7_W1_1_B5

description:
Old2neg_B5
Sample barcode: N479Barcode_705.513
mRNA


title: F7_W1_1_F4

description:
Old2pos_F4
Sample barcode: N479Barcode_704.516
mRNA


title: E10_W4_1_F21

description:
Young2neg_F21
Sample barcode: N479Barcode_726.516
mRNA


title: B5_W1_1_A2

description:
Old2neg_A2
Sample barcode: N479Barcode_702.502
mRNA


title: BEAS-2B cells treated with 60 nm of silica nanoparticles, biological rep3


title: B12_W1_1_G2

description:
Old2pos_G2
Sample barcode: N479Barcode_702.506
mRNA


title: C12_W1_1_C3

description:
Old2neg_C3
Sample barcode: N479Barcode_703.503
mRNA


title: B6_W4_1_N18

description:
Young2neg_N18
Sample barcode: N479Barcode_722.521
mRNA


title: B11_W1_1_F2

description:
Old2pos_F2
Sample barcode: N479Barcode_702.516
mRNA


title: G3_W4_1_G22

description:
Young2pos_G22
Sample barcode: N479Barcode_727.506
mRNA


title: G1_W1_1_L4

description:
Old2pos_L4
Sample barcode: N479Barcode_704.520
mRNA


title: B4_W1_1_P1

description:
Old2neg_P1
Sample barcode: N479Barcode_701.522
mRNA


title: C5_W1_1_L2

description:
Old2pos_L2
Sample barcode: N479Barcode_702.520
mRNA


title: G4_W1_1_O4

description:
Old2pos_O4
Sample barcode: N479Barcode_704.511
mRNA


title: E9_W4_1_E21

description:
Young2neg_E21
Sample barcode: N479Barcode_726.505
mRNA


title: H3_W4_1_C23

description:
Young2neg_C23
Sample barcode: N479Barcode_728.503
mRNA


title: D4_W1_1_G3

description:
Old2neg_G3
Sample barcode: N479Barcode_703.506
mRNA


title: D12_W1_1_O3

description:
Old2pos_O3
Sample barcode: N479Barcode_703.511
mRNA


title: A1_W4_1_M17

description:
Young2pos_M17
Sample barcode: N479Barcode_721.510
mRNA


title: G1_W4_1_E22

description:
Young2pos_E22
Sample barcode: N479Barcode_727.505
mRNA


title: E2_W4_1_N20

description:
Young2pos_N20
Sample barcode: N479Barcode_724.521
mRNA


title: D6_W4_1_F20

description:
Young2neg_F20
Sample barcode: N479Barcode_724.516
mRNA


title: A1_W1_1_A1

description:
Old2pos_A1
Sample barcode: N479Barcode_701.502
mRNA


title: G5_W1_1_P4

description:
Old2pos_P4
Sample barcode: N479Barcode_704.522
mRNA


title: C6_W1_1_M2

description:
Old2pos_M2
Sample barcode: N479Barcode_702.510
mRNA


title: F9_W1_1_H4

description:
Old2pos_H4
Sample barcode: N479Barcode_704.517
mRNA


title: E4_W4_1_P20

description:
Young2pos_P20
Sample barcode: N479Barcode_724.522
mRNA


title: A4_W4_1_P17

description:
Young2pos_P17
Sample barcode: N479Barcode_721.522
mRNA


title: C8_W1_1_O2

description:
Old2neg_O2
Sample barcode: N479Barcode_702.511
mRNA


title: F1_W1_1_P3

description:
Old2neg_P3
Sample barcode: N479Barcode_703.522
mRNA


title: F10_W4_1_B22

description:
Young2pos_B22
Sample barcode: N479Barcode_727.513
mRNA


title: F3_W1_1_B4

description:
Old2neg_B4
Sample barcode: N479Barcode_704.513
mRNA


title: C7_W1_1_N2

description:
Old2neg_N2
Sample barcode: N479Barcode_702.521
mRNA


title: H11_W1_1_A6

description:
Old2pos_A6
Sample barcode: N479Barcode_706.502
mRNA


title: A8_W4_1_D18

description:
Young2neg_D18
Sample barcode: N479Barcode_722.515
mRNA


title: C12_W4_1_P19

description:
Young2neg_P19
Sample barcode: N479Barcode_723.522
mRNA


title: B10_W4_1_B19

description:
Young2pos_B19
Sample barcode: N479Barcode_723.513
mRNA


title: A5_W4_1_A18

description:
Young2pos_A18
Sample barcode: N479Barcode_722.502
mRNA


title: D8_W4_1_H20

description:
Young2pos_H20
Sample barcode: N479Barcode_724.517
mRNA


title: F4_W4_1_L21

description:
Young2neg_L21
Sample barcode: N479Barcode_726.520
mRNA


title: D9_W4_1_I20

description:
Young2pos_I20
Sample barcode: N479Barcode_724.507
mRNA


title: C10_W1_1_A3

description:
Old2neg_A3
Sample barcode: N479Barcode_703.502
mRNA


title: H2_W1_1_H5

description:
Old2neg_H5
Sample barcode: N479Barcode_705.517
mRNA


title: B4_W4_1_L18

description:
Young2neg_L18
Sample barcode: N479Barcode_722.520
mRNA


title: B7_W1_1_C2

description:
Old2pos_C2
Sample barcode: N479Barcode_702.503
mRNA


title: C2_W1_1_I2

description:
Old2pos_I2
Sample barcode: N479Barcode_702.507
mRNA


title: B9_W4_1_A19

description:
Young2pos_A19
Sample barcode: N479Barcode_723.502
mRNA


title: G11_W1_1_E5

description:
Old2neg_E5
Sample barcode: N479Barcode_705.505
mRNA


title: G9_W4_1_M22

description:
Young2neg_M22
Sample barcode: N479Barcode_727.510
mRNA


title: A9_W4_1_E18

description:
Young2neg_E18
Sample barcode: N479Barcode_722.505
mRNA


title: E12_W4_1_H21

description:
Young2neg_H21
Sample barcode: N479Barcode_726.517
mRNA


title: B11_W4_1_C19

description:
Young2pos_C19
Sample barcode: N479Barcode_723.503
mRNA


title: F11_W1_1_J4

description:
Old2pos_J4
Sample barcode: N479Barcode_704.518
mRNA


title: H6_W1_1_L5

description:
Old2neg_L5
Sample barcode: N479Barcode_705.520
mRNA


title: H7_W1_1_M5

description:
Old2pos_M5
Sample barcode: N479Barcode_705.510
mRNA


title: B10_W1_1_E2

description:
Old2pos_E2
Sample barcode: N479Barcode_702.505
mRNA


title: C4_W1_1_K2

description:
Old2pos_K2
Sample barcode: N479Barcode_702.508
mRNA


title: D6_W1_1_I3

description:
Old2neg_I3
Sample barcode: N479Barcode_703.507
mRNA


title: D2_W1_1_E3

description:
Old2neg_E3
Sample barcode: N479Barcode_703.505
mRNA


title: D3_W4_1_C20

description:
Young2neg_C20
Sample barcode: N479Barcode_724.503
mRNA


title: A12_W1_1_L1

description:
Old2neg_L1
Sample barcode: N479Barcode_701.520
mRNA


title: G8_W1_1_C5

description:
Old2neg_C5
Sample barcode: N479Barcode_705.503
mRNA


title: F12_W1_1_K4

description:
Old2pos_K4
Sample barcode: N479Barcode_704.508
mRNA


title: H8_W4_1_H23

description:
Young2pos_H23
Sample barcode: N479Barcode_728.517
mRNA


title: H1_W1_1_G5

description:
Old2neg_G5
Sample barcode: N479Barcode_705.506
mRNA


title: D7_W4_1_G20

description:
Young2pos_G20
Sample barcode: N479Barcode_724.506
mRNA


title: D10_W1_1_M3

description:
Old2pos_M3
Sample barcode: N479Barcode_703.510
mRNA


title: F2_W1_1_A4

description:
Old2neg_A4
Sample barcode: N479Barcode_704.502
mRNA


title: A10_W4_1_F18

description:
Young2neg_F18
Sample barcode: N479Barcode_722.516
mRNA


title: G10_W4_1_N22

description:
Young2neg_N22
Sample barcode: N479Barcode_727.521
mRNA


title: C1_W4_1_E19

description:
Young2pos_E19
Sample barcode: N479Barcode_723.505
mRNA


title: D5_W4_1_E20

description:
Young2neg_E20
Sample barcode: N479Barcode_724.505
mRNA


title: E11_W4_1_G21

description:
Young2neg_G21
Sample barcode: N479Barcode_726.506
mRNA


title: B5_W4_1_M18

description:
Young2neg_M18
Sample barcode: N479Barcode_722.510
mRNA


title: H6_W4_1_F23

description:
Young2neg_F23
Sample barcode: N479Barcode_728.516
mRNA


title: C4_W4_1_H19

description:
Young2pos_H19
Sample barcode: N479Barcode_723.517
mRNA


title: B9_W1_1_D2

description:
Old2pos_D2
Sample barcode: N479Barcode_702.515
mRNA


title: C3_W1_1_J2

description:
Old2pos_J2
Sample barcode: N479Barcode_702.518
mRNA


title: C9_W1_1_P2

description:
Old2neg_P2
Sample barcode: N479Barcode_702.522
mRNA


title: C7_W4_1_K19

description:
Young2neg_K19
Sample barcode: N479Barcode_723.508
mRNA


title: A5_W1_1_E1

description:
Old2pos_E1
Sample barcode: N479Barcode_701.505
mRNA


title: A6_W4_1_B18

description:
Young2pos_B18
Sample barcode: N479Barcode_722.513
mRNA


title: D2_W4_1_B20

description:
Young2neg_B20
Sample barcode: N479Barcode_724.513
mRNA


title: F11_W4_1_C22

description:
Young2pos_C22
Sample barcode: N479Barcode_727.503
mRNA


title: H5_W4_1_E23

description:
Young2neg_E23
Sample barcode: N479Barcode_728.505
mRNA


title: E6_W4_1_B21

description:
Young2pos_B21
Sample barcode: N479Barcode_726.513
mRNA


title: A12_W4_1_H18

description:
Young2neg_H18
Sample barcode: N479Barcode_722.517
mRNA


title: B7_old_hipp_P12

description:
Old1pos_P12
Sample barcode: N459Barcode_715.522
mRNA


title: B3_W1_1_O1

description:
Old2neg_O1
Sample barcode: N479Barcode_701.511
mRNA


title: H2_old_hipp_N14

description:
Old1neg_N14
Sample barcode: N459Barcode_718.521
mRNA


title: B11_young_hipp_M7

description:
Young1pos_M7
Sample barcode: N459Barcode_707.510
mRNA


title: E11_young_hipp_O9

description:
Young1neg_O9
Sample barcode: N459Barcode_711.511
mRNA


title: B8_young_hipp_J7

description:
Young1pos_J7
Sample barcode: N459Barcode_707.518
mRNA


title: D3_young_hipp_M8

description:
Young1neg_M8
Sample barcode: N459Barcode_710.510
mRNA


title: G10_old_hipp_J14

description:
Old1neg_J14
Sample barcode: N459Barcode_718.518
mRNA


title: D12_old_hipp_I13

description:
Old1pos_I13
Sample barcode: N459Barcode_716.507
mRNA


title: D8_young_hipp_B9

description:
Young1pos_B9
Sample barcode: N459Barcode_711.513
mRNA


title: G7_old_hipp_I14

description:
Old1neg_I14
Sample barcode: N459Barcode_718.507
mRNA


title: B3_W4_1_K18

description:
Young2neg_K18
Sample barcode: N479Barcode_722.508
mRNA


title: G2_young_hipp_M10

description:
Young1pos_M10
Sample barcode: N459Barcode_712.510
mRNA


title: H1_young_hipp_H11

description:
Young1neg_H11
Sample barcode: N459Barcode_714.517
mRNA


title: D6_young_hipp_P8

description:
Young1neg_P8
Sample barcode: N459Barcode_710.522
mRNA


title: G6_old_hipp_H14

description:
Old1pos_H14
Sample barcode: N459Barcode_718.517
mRNA


title: B5_young_hipp_G7

description:
Young1neg_G7
Sample barcode: N459Barcode_707.506
mRNA


title: D7_old_hipp_F13

description:
Old1pos_F13
Sample barcode: N459Barcode_716.516
mRNA


title: A7_young_hipp_M6

description:
Young1neg_M6
Sample barcode: N459Barcode_706.510
mRNA


title: H5_W1_1_K5

description:
Old2neg_K5
Sample barcode: N479Barcode_705.508
mRNA


title: D10_young_hipp_D9

description:
Young1pos_D9
Sample barcode: N459Barcode_711.515
mRNA


title: E12_young_hipp_P9

description:
Young1neg_P9
Sample barcode: N459Barcode_711.522
mRNA


title: F6_young_hipp_E10

description:
Young1neg_E10
Sample barcode: N459Barcode_712.505
mRNA


title: C3_young_hipp_A8

description:
Young1pos_A8
Sample barcode: N459Barcode_710.502
mRNA


title: B12_W4_1_D19

description:
Young2pos_D19
Sample barcode: N479Barcode_723.515
mRNA


title: D9_young_hipp_C9

description:
Young1pos_C9
Sample barcode: N459Barcode_711.503
mRNA


title: A12_old_hipp_J12

description:
Old1neg_J12
Sample barcode: N459Barcode_715.518
mRNA


title: F2_young_hipp_B10

description:
Young1neg_B10
Sample barcode: N459Barcode_712.513
mRNA


title: F7_old_hipp_C14

description:
Old1pos_C14
Sample barcode: N459Barcode_718.503
mRNA


title: F11_young_hipp_J10

description:
Young1pos_J10
Sample barcode: N459Barcode_712.518
mRNA


title: C2_young_hipp_P7

description:
Young1pos_P7
Sample barcode: N459Barcode_707.522
mRNA


title: B3_old_hipp_M12

description:
Old1neg_M12
Sample barcode: N459Barcode_715.510
mRNA


title: C1_young_hipp_O7

description:
Young1pos_O7
Sample barcode: N459Barcode_707.511
mRNA


title: G8_young_hipp_C11

description:
Young1neg_C11
Sample barcode: N459Barcode_714.503
mRNA


title: A7_old_hipp_G12

description:
Old1neg_G12
Sample barcode: N459Barcode_715.506
mRNA


title: B10_old_hipp_A13

description:
Old1pos_A13
Sample barcode: N459Barcode_716.502
mRNA


title: D6_old_hipp_E13

description:
Old1neg_E13
Sample barcode: N459Barcode_716.505
mRNA


title: C7_young_hipp_E8

description:
Young1neg_E8
Sample barcode: N459Barcode_710.505
mRNA


title: G6_young_hipp_A11

description:
Young1pos_A11
Sample barcode: N459Barcode_714.502
mRNA


title: C11_young_hipp_I8

description:
Young1neg_I8
Sample barcode: N459Barcode_710.507
mRNA


title: G1_young_hipp_L10

description:
Young1pos_L10
Sample barcode: N459Barcode_712.520
mRNA


title: A3_old_hipp_E12

description:
Old1pos_E12
Sample barcode: N459Barcode_715.505
mRNA


title: A1_young_hipp_G6

description:
Young1pos_G6
Sample barcode: N459Barcode_706.506
mRNA


title: H10_old_hipp_A15

description:
Old1pos_A15
Sample barcode: N459Barcode_719.502
mRNA


title: B12_old_hipp_B13

description:
Old1pos_B13
Sample barcode: N459Barcode_716.513
mRNA


title: G11_young_hipp_F11

description:
Young1neg_F11
Sample barcode: N459Barcode_714.516
mRNA


title: B2_old_hipp_L12

description:
Old1neg_L12
Sample barcode: N459Barcode_715.520
mRNA


title: C4_young_hipp_B8

description:
Young1pos_B8
Sample barcode: N459Barcode_710.513
mRNA


title: G4_young_hipp_O10

description:
Young1pos_O10
Sample barcode: N459Barcode_712.511
mRNA


title: E6_old_hipp_L13

description:
Old1pos_L13
Sample barcode: N459Barcode_716.520
mRNA


title: E10_young_hipp_N9

description:
Young1neg_N9
Sample barcode: N459Barcode_711.521
mRNA


title: E11_old_hipp_N13

description:
Old1neg_N13
Sample barcode: N459Barcode_716.521
mRNA


title: D11_old_hipp_H13

description:
Old1pos_H13
Sample barcode: N459Barcode_716.517
mRNA


title: A11_young_hipp_A7

description:
Young1neg_A7
Sample barcode: N459Barcode_707.502
mRNA


title: C9_young_hipp_G8

description:
Young1neg_G8
Sample barcode: N459Barcode_710.506
mRNA


title: H3_old_hipp_O14

description:
Old1neg_O14
Sample barcode: N459Barcode_718.511
mRNA


title: H7_young_hipp_N11

description:
Young1pos_N11
Sample barcode: N459Barcode_714.521
mRNA


title: A1_old_hipp_C12

description:
Old1pos_C12
Sample barcode: N459Barcode_715.503
mRNA


title: A2_old_hipp_D12

description:
Old1pos_D12
Sample barcode: N459Barcode_715.515
mRNA


title: G12_old_hipp_L14

description:
Old1neg_L14
Sample barcode: N459Barcode_718.520
mRNA


title: D10_old_hipp_G13

description:
Old1pos_G13
Sample barcode: N459Barcode_716.506
mRNA


title: B1_old_hipp_K12

description:
Old1neg_K12
Sample barcode: N459Barcode_715.508
mRNA


title: E6_young_hipp_K9

description:
Young1pos_K9
Sample barcode: N459Barcode_711.508
mRNA


title: F1_young_hipp_A10

description:
Young1neg_A10
Sample barcode: N459Barcode_712.502
mRNA


title: G5_old_hipp_G14

description:
Old1pos_G14
Sample barcode: N459Barcode_718.506
mRNA


title: B9_young_hipp_K7

description:
Young1pos_K7
Sample barcode: N459Barcode_707.508
mRNA


title: F2_old_hipp_P13

description:
Old1neg_P13
Sample barcode: N459Barcode_716.522
mRNA


title: G2_old_hipp_F14

description:
Old1pos_F14
Sample barcode: N459Barcode_718.516
mRNA


title: E7_old_hipp_M13

description:
Old1neg_M13
Sample barcode: N459Barcode_716.510
mRNA


title: G12_young_hipp_G11

description:
Young1neg_G11
Sample barcode: N459Barcode_714.506
mRNA


title: D12_young_hipp_F9

description:
Young1pos_F9
Sample barcode: N459Barcode_711.516
mRNA


title: G3_young_hipp_N10

description:
Young1pos_N10
Sample barcode: N459Barcode_712.521
mRNA


title: E9_young_hipp_M9

description:
Young1neg_M9
Sample barcode: N459Barcode_711.510
mRNA


title: E5_young_hipp_J9

description:
Young1pos_J9
Sample barcode: N459Barcode_711.518
mRNA


title: H10_young_hipp_A12

description:
Young1pos_A12
Sample barcode: N459Barcode_715.502
mRNA


title: B5_old_hipp_N12

description:
Old1neg_N12
Sample barcode: N459Barcode_715.521
mRNA


title: E1_old_hipp_J13

description:
Old1pos_J13
Sample barcode: N459Barcode_716.518
mRNA


title: D2_old_hipp_D13

description:
Old1neg_D13
Sample barcode: N459Barcode_716.515
mRNA


title: B12_young_hipp_N7

description:
Young1pos_N7
Sample barcode: N459Barcode_707.521
mRNA


title: E1_young_hipp_G9

description:
Young1pos_G9
Sample barcode: N459Barcode_711.506
mRNA


title: A4_young_hipp_J6

description:
Young1pos_J6
Sample barcode: N459Barcode_706.518
mRNA


title: H5_old_hipp_P14

description:
Old1neg_P14
Sample barcode: N459Barcode_718.522
mRNA


title: B6_old_hipp_O12

description:
Old1neg_O12
Sample barcode: N459Barcode_715.511
mRNA


title: E3_young_hipp_I9

description:
Young1pos_I9
Sample barcode: N459Barcode_711.507
mRNA


title: H6_young_hipp_M11

description:
Young1neg_M11
Sample barcode: N459Barcode_714.510
mRNA


title: B7_young_hipp_I7

description:
Young1pos_I7
Sample barcode: N459Barcode_707.507
mRNA


title: G1_old_hipp_E14

description:
Old1pos_E14
Sample barcode: N459Barcode_718.505
mRNA


title: E3_old_hipp_K13

description:
Old1pos_K13
Sample barcode: N459Barcode_716.508
mRNA


title: C12_young_hipp_J8

description:
Young1neg_J8
Sample barcode: N459Barcode_710.518
mRNA


title: B4_young_hipp_F7

description:
Young1neg_F7
Sample barcode: N459Barcode_707.516
mRNA


title: H11_old_hipp_B15

description:
Old1pos_B15
Sample barcode: N459Barcode_719.513
mRNA


title: B3_young_hipp_E7

description:
Young1neg_E7
Sample barcode: N459Barcode_707.505
mRNA


title: H1_old_hipp_M14

description:
Old1neg_M14
Sample barcode: N459Barcode_718.510
mRNA


title: D2_young_hipp_L8

description:
Young1neg_L8
Sample barcode: N459Barcode_710.520
mRNA


title: F7_young_hipp_F10

description:
Young1pos_F10
Sample barcode: N459Barcode_712.516
mRNA


title: G9_young_hipp_D11

description:
Young1neg_D11
Sample barcode: N459Barcode_714.515
mRNA


title: B2_young_hipp_D7

description:
Young1neg_D7
Sample barcode: N459Barcode_707.515
mRNA


title: F5_young_hipp_D10

description:
Young1neg_D10
Sample barcode: N459Barcode_712.515
mRNA


title: G11_old_hipp_K14

description:
Old1neg_K14
Sample barcode: N459Barcode_718.508
mRNA


title: G10_young_hipp_E11

description:
Young1neg_E11
Sample barcode: N459Barcode_714.505
mRNA


title: D1_young_hipp_K8

description:
Young1neg_K8
Sample barcode: N459Barcode_710.508
mRNA


title: E2_young_hipp_H9

description:
Young1pos_H9
Sample barcode: N459Barcode_711.517
mRNA


title: C10_young_hipp_H8

description:
Young1neg_H8
Sample barcode: N459Barcode_710.517
mRNA


title: H8_young_hipp_O11

description:
Young1pos_O11
Sample barcode: N459Barcode_714.511
mRNA


title: H9_young_hipp_P11

description:
Young1pos_P11
Sample barcode: N459Barcode_714.522
mRNA


title: A8_young_hipp_N6

description:
Young1neg_N6
Sample barcode: N459Barcode_706.521
mRNA


title: F1_old_hipp_O13

description:
Old1neg_O13
Sample barcode: N459Barcode_716.511
mRNA


title: H4_young_hipp_K11

description:
Young1neg_K11
Sample barcode: N459Barcode_714.508
mRNA


title: H3_young_hipp_J11

description:
Young1neg_J11
Sample barcode: N459Barcode_714.518
mRNA


title: D1_old_hipp_C13

description:
Old1neg_C13
Sample barcode: N459Barcode_716.503
mRNA


title: A2_young_hipp_H6

description:
Young1pos_H6
Sample barcode: N459Barcode_706.517
mRNA


title: H5_young_hipp_L11

description:
Young1neg_L11
Sample barcode: N459Barcode_714.520
mRNA


title: F3_young_hipp_C10

description:
Young1neg_C10
Sample barcode: N459Barcode_712.503
mRNA


title: B10_young_hipp_L7

description:
Young1pos_L7
Sample barcode: N459Barcode_707.520
mRNA


title: G7_young_hipp_B11

description:
Young1neg_B11
Sample barcode: N459Barcode_714.513
mRNA


title: F8_young_hipp_G10

description:
Young1pos_G10
Sample barcode: N459Barcode_712.506
mRNA


title: G5_young_hipp_P10

description:
Young1pos_P10
Sample barcode: N459Barcode_712.522
mRNA


title: A3_young_hipp_I6

description:
Young1pos_I6
Sample barcode: N459Barcode_706.507
mRNA


title: A10_old_hipp_H12

description:
Old1neg_H12
Sample barcode: N459Barcode_715.517
mRNA


title: A10_young_hipp_P6

description:
Young1neg_P6
Sample barcode: N459Barcode_706.522
mRNA


title: F10_young_hipp_I10

description:
Young1pos_I10
Sample barcode: N459Barcode_712.507
mRNA


title: A12_young_hipp_B7

description:
Young1neg_B7
Sample barcode: N459Barcode_707.513
mRNA


title: H2_young_hipp_I11

description:
Young1neg_I11
Sample barcode: N459Barcode_714.507
mRNA


title: C5_young_hipp_C8

description:
Young1pos_C8
Sample barcode: N459Barcode_710.503
mRNA


title: A6_old_hipp_F12

description:
Old1pos_F12
Sample barcode: N459Barcode_715.516
mRNA


title: F9_young_hipp_H10

description:
Young1pos_H10
Sample barcode: N459Barcode_712.517
mRNA


title: C8_young_hipp_F8

description:
Young1neg_F8
Sample barcode: N459Barcode_710.516
mRNA


title: Z23X: cR-H9-EOS XAV939->E8 d23

city: Cambridge

first: Giuliano

middle: Giuseppe

last: Stirparo

state: Cambridgeshire

address: 418 Cambridge Science Park Milton Rd

country: United Kingdom

institute: Cerevance ltd

description:
Z23X
lane1_Z23X_TACTAGTC_merged_L001_Aligned_COUNT

data_processing:
STAR alignment
htseq-count (-a 20)
Genome_build: hg38 (annotation GRCh38_87)

source_name: hPSC

extract_protocol:
Total RNA, ReliaPrep kit (Promega)
rRNA was depleted using Illumina's Ribozero HMR kit following the manufacturers protocol. The libraries are then prepared using the KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, Roche). The libraries were sequenced on HiSeq 2500.

treatment_protocol: 2 lines of human naïve pluripotent stem cells (embryo-derived HNES1 and chemically reset cR-H9-EOS) were cultured in N2B27 and 2uM XAV939 for 10 days. After that the cells were split into two conditions: N2B27 + 2uM XAV939 + 3ng/ml Activin A + 10ng/ml FGF2 (XAF), or E8 medium, for extended maintenance. The experiment was performed in biological triplicates for each cell line. RNAseq was performed with the cells on day 0, 1, 2, 3, 7, 10, when the cells were cultured in XAV939; and one time point after transfer to maintenance conditions, at not less than 22 days of culture from the start of the experiment. Conventional hES cell line H9-EOS, which was a parental line for the chemically reset cR-H9-EOS was used as a control (in biological triplicate).

value: chemically reset cR-H9-EOS

value: chemically reset hPSC after formative transition

tag: day of formative transition


title: Z23E: cR-H9-EOS XAV939->XAF d23

description:
Z23E
lane1_Z23E_TTCAGCTC_merged_L001_Aligned_COUNT


title: H9-4: H9-EOS conventional hES

description:
H9-4
lane1_H9-ctrl4_TTACTCGC_merged_L001_Aligned_COUNT

value: H9-EOS (parental line for cR-H9-EOS)

value: conventional hPSC


title: H9-3: H9-EOS conventional hES

description:
H9-3
lane1_H9-ctrl3_TATGTGGC_merged_L001_Aligned_COUNT


title: B6_young_hipp_H7

description:
Young1neg_H7
Sample barcode: N459Barcode_707.517
mRNA


title: H9-1: H9-EOS conventional hES

description:
H9-1
lane1_H9-ctrl1_TGTCTATC_merged_L001_Aligned_COUNT


title: D11_young_hipp_E9

description:
Young1pos_E9
Sample barcode: N459Barcode_711.505
mRNA


title: A9_young_hipp_O6

description:
Young1neg_O6
Sample barcode: N459Barcode_706.511
mRNA


title: F6_old_hipp_B14

description:
Old1neg_B14
Sample barcode: N459Barcode_718.513
mRNA


title: C6_young_hipp_D8

description:
Young1pos_D8
Sample barcode: N459Barcode_710.515
mRNA


title: Z10: cR-H9-EOS XAV939 d10

description:
Z10
lane1_Z10_TCAGATTC_merged_L001_Aligned_COUNT

value: chemically reset hPSC during formative transition


title: Z7: cR-H9-EOS XAV939 d7

description:
Z7
lane1_Z7_TATGCCAG_merged_L001_Aligned_COUNT


title: D5_young_hipp_O8

description:
Young1neg_O8
Sample barcode: N459Barcode_710.511
mRNA


title: Z2: cR-H9-EOS XAV939 d2

description:
Z2
lane1_Z2_TCATTGAG_merged_L001_Aligned_COUNT


title: Z3: cR-H9-EOS XAV939 d3

description:
Z3
lane1_Z3_TGGCTCAG_merged_L001_Aligned_COUNT


title: D7_young_hipp_A9

description:
Young1pos_A9
Sample barcode: N459Barcode_711.502
mRNA


title: Z1: cR-H9-EOS XAV939 d1

description:
Z1
lane1_Z1_TGTATGCG_merged_L001_Aligned_COUNT


title: Z0: cR-H9-EOS XAV939 d0

description:
Z0
lane1_Z0_TCCAGTCG_merged_L001_Aligned_COUNT

value: chemically reset hPSC


title: F12_young_hipp_K10

description:
Young1pos_K10
Sample barcode: N459Barcode_712.508
mRNA


title: X28X: cR-H9-EOS XAV939->E8 d28

description:
X28X
lane1_X28X_TCAGGAGG_merged_L001_Aligned_COUNT


title: E7_young_hipp_L9

description:
Young1neg_L9
Sample barcode: N459Barcode_711.520
mRNA


title: F5_old_hipp_A14

description:
Old1neg_A14
Sample barcode: N459Barcode_718.502
mRNA


title: F11_old_hipp_D14

description:
Old1pos_D14
Sample barcode: N459Barcode_718.515
mRNA


title: X7: cR-H9-EOS XAV939 d7

description:
X7
lane1_X7_TACTTCGG_merged_L001_Aligned_COUNT


title: X2: cR-H9-EOS XAV939 d2

description:
X2
lane1_X2_TTGGTATG_merged_L001_Aligned_COUNT


title: H11_young_hipp_B12

description:
Young1pos_B12
Sample barcode: N459Barcode_715.513
mRNA


title: X3: cR-H9-EOS XAV939 d3

description:
X3
lane1_X3_TGAACTGG_merged_L001_Aligned_COUNT


title: A6_young_hipp_L6

description:
Young1pos_L6
Sample barcode: N459Barcode_706.520
mRNA


title: X1: cR-H9-EOS XAV939 d1

description:
X1
lane1_X1_TAACGCTG_merged_L001_Aligned_COUNT


title: W28X: cR-H9-EOS XAV939->E8 d28

description:
W28X
lane1_W28X_TAGTCTTG_merged_L001_Aligned_COUNT


title: W10: cR-H9-EOS XAV939 d10

description:
W10
lane1_W10_TGTGGTTG_merged_L001_Aligned_COUNT


title: Myh6-Cre; TRalphaAMI_2

city: San Francisco

first: Guo

middle: N

last: Huang

state: CA

address: 555 Mission Bay Blvd S, CVRB 352V

department: Cardiovascular Research Institute

institute: University of California, San Francisco

data_processing:
Sequenced reads with quality less than 20 were removed after trimming adapter and remove reads less than 15bp with cutadapt(v1.9), STAR(v2.5.2b) --outFilterMismatchNoverLmax 0.04 used to map filtered reads to mm10 reference
Gene count matrix was generated with featureCounts(v1.5.1) and then convert to RPKM with read count / length in kbp * 1m
Genome_build: mm10
Supplementary_files_format_and_content: TXT: RAW COUNT and RPKM

source_name: Myh6-Cre; TRalphaAMI_P14 heart

extract_protocol:
Hearts were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.  Illumina TruSeq RNA Library Prep Kit v2 (Cat#RS-122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: mixed (ICR; C57BL/6)

tag: genotype/variation

value: Myh6-Cre; TRalphaAMI

value: postnatal day 14 (P14)

value: heart


title: W27E: cR-H9-EOS XAV939->XAF d27

description:
W27E
lane1_W27E_TTCCATTG_merged_L001_Aligned_COUNT


title: Myh6-Cre; TRalphaAMI_1


title: Myh6-Cre; TRalphaAMI_3


title: B1_young_hipp_C7

description:
Young1neg_C7
Sample barcode: N459Barcode_707.503
mRNA


title: X10: cR-H9-EOS XAV939 d10

description:
X10
lane1_X10_TCTCACGG_merged_L001_Aligned_COUNT


title: D4_young_hipp_N8

description:
Young1neg_N8
Sample barcode: N459Barcode_710.521
mRNA


title: A5_young_hipp_K6

description:
Young1pos_K6
Sample barcode: N459Barcode_706.508
mRNA


title: A11_old_hipp_I12

description:
Old1neg_I12
Sample barcode: N459Barcode_715.507
mRNA


title: X0: cR-H9-EOS XAV939 d0

description:
X0
lane1_X0_TCGAAGTG_merged_L001_Aligned_COUNT


title: X27E: cR-H9-EOS XAV939->XAF d27

description:
X27E
lane1_X27E_TAAGTTCG_merged_L001_Aligned_COUNT


title: W7: cR-H9-EOS XAV939 d7

description:
W7
lane1_W7_TCCTCAAT_merged_L001_Aligned_COUNT


title: W3: cR-H9-EOS XAV939 d3

description:
W3
lane1_W3_TACAGGAT_merged_L001_Aligned_COUNT


title: D24E: HNES1 XAV939->XAF d24

description:
D24E
lane1_D24E_TTGACTCT_merged_L001_Aligned_COUNT

value: embryo-derived HNES1

value: embryo-derived naive hPSC after formative transition


title: W1: cR-H9-EOS XAV939 d1

description:
W1
lane1_W1_TTCCTGCT_merged_L001_Aligned_COUNT


title: D25X: HNES1 XAV939->E8 d25

description:
D25X
lane1_D25X_TGCATAGT_merged_L001_Aligned_COUNT


title: TRalphaAMI_2

source_name: TRalphaAMI_P14 heart

value: TRalphaAMI


title: TN_24_5

first: Joni

last: Nikkanen

address: 555 Mission Bay Blvd S

institute: UCSF

description: Sample 8_5

data_processing:
Reads with 7 or longer repeats of A nucleotides were clipped before the A repeat
Reads were trimmed using Trimmomatic; parameters: leading:15, trailing:15, minLen: 35
Reads were aligned using Kallisto with 100 bootsraps. Parameters: --single -l 100 -s 20
Differential gene expression analysis was performed using Sleuth in R.
Gene 'ENSMUSG00000075014' was removed from analysis as an outlier.
Genome_build: Mouse number 6_3 did not responde to LPS-treatment and was therefore removed from the analysis

source_name: Liver

extract_protocol:
Liver was removed, flash frozen in liquid nitrogen and RNA was harvested using Bioline RNA Extraction kit.
We adapted Cel-Seq2 protocol to sequence RNA transcripts in livers of mice treated with LPS. Cel-Seq2 was performed using reverse-transcription primers that contained anchored polyT, a 6 base pair unique barcode, a 6-base pair UMI (unique molecular identifier), the 5’ Illumina adaptor as used in the Illumina small RNA kit, and a T7 promoter. Instead of single cells, total RNA isolated from liver was used for linear mRNA amplification.A total of 10 ng of RNA was used for library preparation, and the aRNA was converted to cDNA with 3’ RNA adaptors sequences (RPI) found in the TruSeq Small RNA Library Prep Pooling Guide. A total of 11 cycles of PCR were performed with an elongation time of 30 seconds. Following cDNA cleanup and dilution, samples were multiplexed and sequenced on Illumina Nextseq 500 using Mid Output v2 Kit.
Cel-Seq2 (modified for tissue)

tag: strain

value: liver

tag: ambient temp

tag: time post-lps injection

value: 24 hours


title: TN_24_3

description: Sample 8_3


title: TN_24_2

description: Sample 8_2


title: D2: HNES1 XAV939 d2

description:
D2
lane1_D2_TCTGCTGT_merged_L001_Aligned_COUNT

value: embryo-derived naive hPSC during formative transition


title: RNApolII in situ ChIA-PET, Wild type cultured NSC (TR2)

city: Milano

first: Federico

last: Zambelli

address: Via Giovanni Celoria 26

department: Department of Biosciences

country: Italy

institute: University of Milan

library_source: genomic

data_processing:
Linker detection from paired-end FASTQ reads using in-house program (ChIA-PET Utilities, CPU)
Map to genome using hybrid bwa mem and bwa aln and take best alignment from both results (implemented in CPU suite )
Pairing the mapped reads and collecting PETs (CPU pair module)
Deduplicating PETs (CPU dedup module)
Clustering PETs into interactions (CPU cluster module)
Callling significant interactions from the PET clusters using (based on ChiaSig software but rewritten for efficiency and scallability on deep sequencing data)
Genome_build: mm9
Supplementary_files_format_and_content: ChiaSig output, significant interactions with PET count >=2

molecule: genomic DNA

source_name: Wild type cultured NSC (TR2)

growth_protocol: P0 brain-derived NSC cultures were obtained from dissected telencephalon of individual Sox2-deleted mice, or wild type controls, and individually grown, as described in (Favaro et al., 2009) and (Zhang et al., 2013). Cells were grown in parallel for two passages in 10 ng/ml Epidermal Growth Factor (EGF) and 10 ng/ml basic Fibroblast Growth Factor (bFGF), followed by cell dissociation and expansion in the presence of EGF, but not bFGF, for 3-4 more passages, as described in Zhang et al. (2013), for optimal maintenance of mutant NSC (Favaro et al., 2009).  The culture of Sox2-deleted NSC was performed in parallel with that of wild type NSC (Zhang Y et al., Nature 2013, 504:306-10).

extract_protocol:
For the in situ RNAPolII ChIA-PET, 10 million for formaldehyde crosslinked cells were suspended with 100  μl 0.55% SDS and incubated at RT for 10 min, 62°C for 10 min and 37°C for 10 min to permeabilize nuclei, which was followed by adding 25 μl 20% TritonX-100 with an incubation of 30 min at 37°C to quench SDS, and then 50 μl of blunt-end four-cutter AluI (cat# R0137L, NEB), 50 μl 10 × CutSmart buffer and 275 μl H2O incubating at 37°C overnight for in situ digestion. After pelleted and washed once with 1 ml 1× CutSmart buffer, the nuclei were suspended in 500 μl A tailing solution composed of 50 μl 10 × CutSmart buffer, 10 μl BSA (cat#B9000S, NEB), 10 μl 10 mM dATP (cat#N0440S, NEB), 10 μl Klenow (3’-5’ exo-) (cat#M0202L, NEB), and 420 μl H2O and incubated at RT for 1 hr.  The in situ proximity ligation with biotinylated bridge linker was performed by adding 200 μl 5 × ligation buffer (cat#B6058S, NEB), 6 μl Bridge linker (200 ng/ul), 10 μl T4 DNA ligase (cat#M0202L, NEB) and 284 μl H2O and incubating at 16°C overnight.
The nuclei with in situ proximity ligation were then subjected to sonication and chromatin immunoprecipitation with anti-RNApolII antibody (8WG16, cat# 920102, Biolegend, San Diego, CA), Tn5 tagmentation, biotin selection, PETs were amplified by PCR and sequenced.

treatment_protocol: Neurospheres were partially dissociated by mild pipetting and then crosslinked as in Zhang Y et al., 2013, Nature 504:306-10; see GEO submission ….

value: mixed C57BL/6 x DBA

value: forebrain-derived neural stem cells (NSCs)

value: wild type

tag: passages

value: passage 3 to 7

tag: chip antibodies

value: RNAPII monoclonal antibody (8WG16, cat# 920102, Biolegend, San Diego, CA)


title: D3: HNES1 XAV939 d3

description:
D3
lane1_D3_TTGGAGGT_merged_L001_Aligned_COUNT

tag: cell type


title: RNApolII in situ ChIA-PET, Wild type cultured NSC (TR3)

source_name: Wild type cultured NSC (TR3)


title: D10: HNES1 XAV939 d10

description:
D10
lane1_D10_TGATACGT_merged_L001_Aligned_COUNT


title: TRalphaAMI_1

tag: tissue


title: W2: cR-H9-EOS XAV939 d2

description:
W2
lane1_W2_TAGTGACT_merged_L001_Aligned_COUNT

value: chemically reset cR-H9-EOS

value: chemically reset hPSC during formative transition


title: C22E: HNES1 XAV939->XAF d22

description:
C22E
lane1_C22E_TCCGTCTT_merged_L001_Aligned_COUNT


title: W0: cR-H9-EOS XAV939 d0

description:
W0
lane1_W0_TGCGATCT_merged_L001_Aligned_COUNT

value: chemically reset hPSC


title: RNApolII in situ ChIA-PET, Sox2-deleted cultured NSC (TR3)

source_name: Sox2-deleted cultured NSC (TR3)


title: D1: HNES1 XAV939 d1

description:
D1
lane1_D1_TTCTGTGT_merged_L001_Aligned_COUNT


title: RNApolII in situ ChIA-PET, Sox2-deleted cultured NSC (TR2)

source_name: Sox2-deleted cultured NSC (TR2)


title: C10: HNES1 XAV939 d10

description:
C10
lane1_C10_TCTCGGTT_merged_L001_Aligned_COUNT


title: C22X: HNES1 XAV939->E8 d22

description:
C22X
lane1_C22X_TAAGCGTT_merged_L001_Aligned_COUNT


title: TN_24_1

description: Sample 8_1


title: TRalphaAMI_3

value: mixed (ICR; C57BL/6)


title: RT_24_5

description: Sample 7_5


title: TN_24_4

description: Sample 8_4


title: D0: HNES1 XAV939 d0

description:
D0
lane1_D0_TGTACCTT_merged_L001_Aligned_COUNT

value: embryo-derived naive hPSC


title: RT_24_4

description: Sample 7_4


title: D7: HNES1 XAV939 d7

description:
D7
lane1_D7_TCGAGCGT_merged_L001_Aligned_COUNT


title: RT_24_3

description: Sample 7_3


title: RT_24_2

description: Sample 7_2


title: C3: HNES1 XAV939 d3

description:
C3
lane1_C3_CTTGTACT_merged_L001_Aligned_COUNT


title: C7: HNES1 XAV939 d7

description:
C7
lane1_C7_TGGTTGTT_merged_L001_Aligned_COUNT


title: C2: HNES1 XAV939 d2

description:
C2
lane1_C2_GGCTACAG_merged_L001_Aligned_COUNT


title: TN_12_4

description: Sample 6_5

value: 12 hours


title: TN_12_2

description: Sample 6_2


title: A25X: HNES1 XAV939->E8 d25

description:
A25X
lane1_A25X_CAGATCTG_merged_L001_Aligned_COUNT

value: embryo-derived HNES1


title: TN_12_3

description: Sample 6_4


title: C1: HNES1 XAV939 d1

description:
C1
lane1_C1_TAGCTTGT_merged_L001_Aligned_COUNT


title: C0: HNES1 XAV939 d0

description:
C0
lane1_C0_GATCAGCG_merged_L001_Aligned_COUNT


title: RT_24_1

description: Sample 7_1


title: RT_12_5

description: Sample 5_5


title: A10: HNES1 XAV939 d10

description:
A10
lane1_A10_GCCAATGT_merged_L001_Aligned_COUNT


title: A7: HNES1 XAV939 d7

description:
A7
lane1_A7_ACAGTGGT_merged_L001_Aligned_COUNT


title: RT_12_1

description: Sample 5_1


title: RT_12_3

description: Sample 5_3


title: A2: HNES1 XAV939 d2

description:
A2
lane1_A2_TTAGGCAT_merged_L001_Aligned_COUNT


title: A0: HNES1 XAV939 d0

description:
A0
lane1_A0_ATCACGTT_merged_L001_Aligned_COUNT


title: TN_12_1

description: Sample 6_1


title: RT_12_4

description: Sample 5_4


title: TN_4_3

description: Sample 4_3

value: 4 hours


title: A1: HNES1 XAV939 d1

description:
A1
lane1_A1_CGATGTTT_merged_L001_Aligned_COUNT


title: A22E: HNES1 XAV939->XAF d22+

description:
A22E
lane1_A25E_ACTTGATG_merged_L001_Aligned_COUNT

value: embryo-derived naive hPSC after formative transition


title: TN_4_4

description: Sample 4_4

value: liver


title: RT_12_2

description: Sample 5_2


title: Termination period of calcification in low strength group [LST-3]

city: Wuhan

first: Desheng

last: Qi

address: Shizishan Street No.1

department: College of Animal Nutrition and Feed Science

institute: Huazhong Agricultural University

description:
LST-3
HSTvsLST.DEG.fasta; HSTvsLST.html

data_processing:
The corresponding sequence reads were mapped to the chicken genome in Ensembl using Bowtie2/Tophat2 (http://tophat.cbcb.umd.edu).
Genes with ׀fold change׀> 1.5 and padj < 0.05 were identified as DEGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to analyze the functions of DEGs.
Genome_build: Galgal4 (GCA_000002315.2)
Supplementary_files_format_and_content: raw_counts.txt
Supplementary_files_format_and_content: nomalized_counts.txt
Supplementary_files_format_and_content: fasta: Differential expression genes.
Supplementary_files_format_and_content: html: KEGG path

organism: Gallus gallus

source_name: laying hen

extract_protocol:
Total RNA was isolated using the Trizol Reagent, after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer. Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit(Illumina, USA).
First strand cDNA was synthesized using random oligonucleotides and SuperScript II. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 200 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

treatment_protocol: The uterine samples were taken from the laying hens which laying hard and weak-shell eggs during calcification periods respectively.

tag: breed

value: Hy-Line Brown

value: Uterus

value: 42 weeks

tag: eggshell strength group

value: low strength

tag: egg calcification period

value: Termination


title: TN_4_2

description: Sample 4_2


title: Termination period of calcification in low strength group [LST-2]

description:
LST-2
HSTvsLST.DEG.fasta; HSTvsLST.html


title: A3: HNES1 XAV939 d3

description:
A3
lane1_A3_TGACCACT_merged_L001_Aligned_COUNT

value: embryo-derived naive hPSC during formative transition


title: TN_4_1

description: Sample 4_1


title: Termination period of calcification in low strength group [LST-1]

description:
LST-1
HSTvsLST.DEG.fasta; HSTvsLST.html


title: Growth period of calcification in low strength group [LSG-3]

description:
LSG-3
HSGvsLSG.DEG.fasta; HSGvsLSG.html

value: Growth


title: RT_4_3

description: Sample 3_3


title: Initiation period of calcification in low strength group [LSI-3]

description:
LSI-3
HSIvsLSI.DEG.fasta; HSIvsLSI.html

value: Initiation


title: RT_4_1

description: Sample 3_1


title: TN_0_5

description: Sample 2_5

value: 0 hours


title: TN_0_4

description: Sample 2_4


title: TN_0_3

description: Sample 2_3


title: Growth period of calcification in low strength group [LSG-1]

description:
LSG-1
HSGvsLSG.DEG.fasta; HSGvsLSG.html


title: Initiation period of calcification in low strength group [LSI-2]

description:
LSI-2
HSIvsLSI.DEG.fasta; HSIvsLSI.html


title: Growth period of calcification in high strength group [HSG-3]

description:
HSG-3
HSGvsLSG.DEG.fasta; HSGvsLSG.html

value: high strength


title: Termination period of calcification in high strength group [HST-2]

description:
HST-2
HSTvsLST.DEG.fasta; HSTvsLST.html


title: Termination period of calcification in high strength group [HST-3]

description:
HST-3
HSTvsLST.DEG.fasta; HSTvsLST.html


title: TN_0_1

description: Sample 2_1


title: RT_0_3

description: Sample 1_3


title: RT_0_1

description: Sample 1_1


title: RT_0_2

description: Sample 1_2


title: TN_0_2

description: Sample 2_2


title: RT_4_2

description: Sample 3_2


title: Growth period of calcification in high strength group [HSG-1]

description:
HSG-1
HSGvsLSG.DEG.fasta; HSGvsLSG.html


title: Growth period of calcification in high strength group [HSG-2]

description:
HSG-2
HSGvsLSG.DEG.fasta; HSGvsLSG.html


title: Initiation period of calcification in low strength group [LSI-1]

description:
LSI-1
HSIvsLSI.DEG.fasta; HSIvsLSI.html


title: RT_4_4

description: Sample 3_4


title: Initiation period of calcification in high strength group [HSI-1]

description:
HSI-1
HSIvsLSI.DEG.fasta; HSIvsLSI.html


title: RT_0_4

description: Sample 1_4


title: Mt3 Stox2 promoter 4Cseq

description:
Restriction enyzmes: RE1 NlaIII, RE2 Csp6I
Viewpoint: chr8:48372281-48372611

data_processing:
Library strategy: 4C-seq
BCL2fastq version 2.18.0.12 was used to demultiplex data and convert BCL files generated by Illumina (Nextseq) system to fastq files.
Sequenced reads were trimmed for view-point specific primer sequence (reverse complement), and masked for low-quality calls with Cutadapt version 1.8.3; parameters: -q 30 --trim-n -e 0.1 --minimum-length 15.
4cker pipeline is used to process the reads. First, reduced genome reference files containing reference sequence flanking RE1 sites were made for specific RE1 and read length (following https://github.com/rr1859/R.4Cker). Second, bowtie index files were then built. Third, the reads were aligned to the reduced genome using bowtie2 with default parameters. Software: bedtools, oligoMatch from kent tools, and bowtie2.
BedGraph generation: the mapped reads, which contain restriction enzyme (RE) fragments, were quantified similar to 4cker suggestion (cat mapped.sam| grep -v "^@" | awk '$5 > 39 {print $3}'| grep "^chr" | sort | uniq -c | sed -e 's/_\|:\| \|-/\t/g' | awk '{print $2"\t"$3"\t"$4"\t"$1 }').
Analysis was performed with 4cker library in R: library(R.4Cker) and the normalized 4C count bedGraph files from cisAnalysis (parameter k=10) were generated and deposited here.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: bedGraph files

source_name: Mutant cultured fP0 forebrain NSC

growth_protocol: P0 brain-derived NSC cultures were obtained from dissected forebrain of wild type and Sox2-deleted P0 mice, and grown, as described in (Favaro et al., Nat. Neurosci. 2009, 12:1248-56) and (Zhang et al., Nature 2013). Cells were grown in parallel for two passages in 10 ng/ml Epidermal Growth Factor (EGF) and 10 ng/ml basic Fibroblast Growth Factor (bFGF), followed by cell dissociation and expansion in the presence of EGF, but not bFGF, for 3-4 more passages, as described in Zhang et al. (2013), for optimal maintenance of mutant NSC (Favaro et al., 2009). The culture of Sox2-deleted NSC was performed in parallel with that of wild type NSC (Zhang Y et al., Nature 2013, 504:306-10). The background of mice was C57BL/6/DBA (as in Favaro et al., 2009).

extract_protocol:
The extraction procedures were performed as described in Stadhouders et al., 2013.
4C-seq libraries were prepared as described in Stadhouders et al., 2013. Briefly, nine regions of seven genes were chosen as viewpoints based on their relevance to brain development, presence of interaction detected by the ChIA-PET analysis and observed differential connectivity between wild type and mutant cells. The primers were designed using Primer Designer for 4C Viewpoints (https://mnlab.uchicago.edu/4Cpd/). Depending on the locus of interest, we used one of the three different 4 base cutters, DpnII (NEB), Csp6I (Thermo Scientific) or NlaIII (NEB), for the first or second rounds of restriction enzyme digestion. The primer sequences, viewpoint regions and the restriction enzyme used for each viewpoint were listed in Table S11 of the publication. Briefly, ten million cells from each individual mouse were crosslinked with 1% formaldehyde and lysed with the lysis buffer (50 mM Tris–HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TX-100 and 1 x complete protease inhibitor) using a douncer. The collected nuclei were digested with 600 U of the first enzyme followed by ligation with 100 U T4 DNA ligase (Roche). 600 mg Proteinase K (Invitrogen) and 300 mg RNase A (Invitrogen) were added and incubated sequentially, respectively. Following the phenol-chloroform purification, the samples were treated with a second round of digestion using the second enzyme and self-ligated with 200 U T4 DNA ligase (Roche). The phenol-chloroform purified self-ligation products were used as templates for 4C-PCR. 200 μl PCR reactions using 500 ng of 4C template were performed for 28 cycles for each viewpoint and pooled together. The PCR products were purified using AMPure beads (Beckman-Coulter) according to the manufacturer’s instructions and pooled for sequencing on the Illumina NextSeq 500.

treatment_protocol: Cells from individual brain cultures were fixed with 1% formaldehyde solution in 10 million cells aliquots for subsequent 4Cseq analysis. Briefly, cells from each individual mouse culture were crosslinked with 1% formaldehyde and snap-frozen in 10 million cells aliquots. Cells (one aliquot) were then lysed with the lysis buffer (50 mM Tris–HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% NP-40, 1% TX-100 and 1 x complete protease inhibitor) using a douncer. The collected nuclei were digested with 600 U of the first enzyme followed by ligation with 100 U T4 DNA ligase (Roche). 600 mg Proteinase K (Invitrogen) and 300 mg RNase A (Invitrogen) were added and incubated sequentially, respectively. Following the phenol-chloroform purification, the samples were treated with a second round of digestion using the second enzyme and self-ligated with 200 U T4 DNA ligase (Roche). The phenol-chloroform purified self-ligation products were used as templates for 4C-PCR. 200 μl PCR reactions using 500 ng of 4C template were performed for 28 cycles for each viewpoint and pooled together. The PCR products were purified using AMPure beads (Beckman-Coulter) according to the manufacturer’s instructions and pooled for sequencing on the Illumina NextSeq 500.

value: forebrain-derived neural stem cells

value: passage 3 to 7

tag: viewpoint

value: Stox2 promoter


title: Growth period of calcification in low strength group [LSG-2]

description:
LSG-2
HSGvsLSG.DEG.fasta; HSGvsLSG.html


title: Initiation period of calcification in high strength group [HSI-3]

description:
HSI-3
HSIvsLSI.DEG.fasta; HSIvsLSI.html


title: Initiation period of calcification in high strength group [HSI-2]

description:
HSI-2
HSIvsLSI.DEG.fasta; HSIvsLSI.html


title: Wt1 Stox2 promoter 4Cseq

source_name: Wild type cultured fP0 forebrain NSC

value: Wild type


title: Mt3 Tcf4 promoter 4Cseq

description:
Restriction enyzmes: RE1 DpnII, RE2 Csp6I
Viewpoint: chr18:69504831-69505556

value: Tcf4 promoter


title: Mt1 Stox2 promoter 4Cseq


title: Wt2 Stox2 promoter 4Cseq


title: Wt3 Stox2 promoter 4Cseq


title: Mt2 Tcf4 promoter 4Cseq


title: Termination period of calcification in high strength group [HST-1]

description:
HST-1
HSTvsLST.DEG.fasta; HSTvsLST.html


title: Mt1 Tcf4 promoter 4Cseq


title: Mt2 Stox2 promoter 4Cseq


title: Mt2 Kat2b promoter 4Cseq

description:
Restriction enyzmes: RE1 DpnII, RE2 Csp6I
Viewpoint: chr17: 53707484-53707872

value: Kat2b promoter


title: Mt1 Kat2b promoter 4Cseq


title: Wt3 Kat2b promoter 4Cseq


title: Mt3 Kat2b promoter 4Cseq


title: Wt3 Tcf4 promoter 4Cseq


title: Wt2 Tcf4 promoter 4Cseq


title: Wt1 Tcf4 promoter 4Cseq


title: Wt2 Kat2b promoter 4Cseq


title: Wt1 Kat2b promoter 4Cseq


title: Mt3 Olig2 promoter 4Cseq

description:
Restriction enyzmes: RE1 DpnII, RE2 Csp6I
Viewpoint: chr16:91223837-91224410

value: Olig2 promoter


title: Mt1 Olig2 promoter 4Cseq


title: Mt2 Olig2 promoter 4Cseq


title: mRNA_BreastCancer_rep52

city: Koto

first: Nobuyuki

last: Fukui

state: Tokyo

country: Japan

institute: Japanese Foundation For Cancer Research

hyb_protocol: After fragmentation, cRNA was hybridized with Affymetrix Hybridization,Wash, and Stain Kit on Affymetrix Human Genome GeneChip U133 Plus 2.0 array following manufactuer's instruction.

scan_protocol: GeneChip was scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Data was processed with RMA using Affymetrix Expression Console software.

source_name: mRNA from fresh frozen breast tumor tissue

label_protocol: Biotinylated cRNA was prepared with Affymetrix GeneChip 3'IVT Plus kit  according to the manufactuer's instruction.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy mini kit following manufacturer's instruction.

tag: gender

value: female


title: mRNA_BreastCancer_rep60


title: mRNA_BreastCancer_rep58


title: mRNA_BreastCancer_rep61


title: mRNA_BreastCancer_rep57


title: mRNA_BreastCancer_rep55


title: mRNA_BreastCancer_rep49


title: Wt3 Olig2 promoter 4Cseq

tag: strain/background


title: mRNA_BreastCancer_rep59

tag: age


title: mRNA_BreastCancer_rep56


title: mRNA_BreastCancer_rep50


title: mRNA_BreastCancer_rep51


title: mRNA_BreastCancer_rep53


title: mRNA_BreastCancer_rep48


title: Wt2 Olig2 promoter 4Cseq


title: mRNA_BreastCancer_rep46


title: mRNA_BreastCancer_rep45


title: Wt1 Olig2 promoter 4Cseq


title: Mt3 Olig1 promoter 4Cseq

description:
Restriction enyzmes: RE1 DpnII, RE2 Csp6I
Viewpoint: chr16:91270415-91270745

value: Olig1 promoter


title: Mt1 Olig1 promoter 4Cseq


title: Mt2 Olig1 promoter 4Cseq


title: Wt2 Olig1 promoter 4Cseq


title: Wt3 Olig1 promoter 4Cseq


title: Wt1 Olig1 promoter 4Cseq


title: Mt3 Sox3 promoter 4Cseq

description:
Restriction enyzmes: RE1 NlaIII, RE2 DpnII
Viewpoint: chrX:58144663-58145390

value: Sox3 promoter


title: Mt2 Sox3 promoter 4Cseq

description:
Restriction enyzmes: RE1 NlaIII, RE2 DpnII
Viewpoint: chrX:58144663-58145389


title: Mt1 Sox3 promoter 4Cseq

description:
Restriction enyzmes: RE1 NlaIII, RE2 DpnII
Viewpoint: chrX:58144663-58145388


title: Wt3 Sox3 promoter 4Cseq


title: mRNA_BreastCancer_rep43


title: mRNA_BreastCancer_rep42


title: mRNA_BreastCancer_rep38


title: mRNA_BreastCancer_rep44


title: mRNA_BreastCancer_rep39


title: mRNA_BreastCancer_rep47


title: dDRIP-seq_seedllings_rep1

city: Nanjing

first: Fang

last: Yuan

state: Jiangsu

address: No.1, Weigang Street, Xuanwu District, Nanjing

institute: NanJing Argricultural University

data_processing:
Library strategy: dDRIP-seq
The raw data sets were trimmed adapter sequences and removed low-quality bases by Trim Galore version 0.4.3.
dDRIP_seq: Clean reads were aligned to the rice reference genome (MSU 7.0) with Bowtie1. We distinguished the strand specific reads using flags of SAM files. The direction of the nascent RNA strand associated with R-loops is concordant with the direction of R2 reads (R2 of the pair-end reads) aligned to the genome. We then extracted unique mappable wR-loops reads by flags of R2 reads equal to 163, and cR-loops reads by flags of R2 reads equal to 147.
dDRIP-seq: Unique mappable reads corresponding to w/c R-loops were used for R-loop peak calling using MACS2(Zhang et al. 2008). The parameter was set with macs2 callpeak --keep-dup 1 -g 3.8e+8 -B --extsize 200 -q 0.01 --nomodel --SPMR
NBS-seq:  Low-quality reads and adapters were removed from the raw data by using Trim Galore. The clean data were mapped to the rice reference genome (MSU7.0) by using Bismark (Krueger and Andrews 2011). Uniquely mappable reads were used for calculating the methylated cytosines using the bismark methylation_extractor program.
Genome_build: MSU7.0
Supplementary_files_format_and_content: bed files were generated using MACS2
Supplementary_files_format_and_content: CX_report.txt files were generated using Bismark

organism: Oryza sativa

source_name: seedlings

growth_protocol: rice cultivar “Nipponbare” seeds were grown in a greenhouse with temperature ranging from 30-34℃with a 12h/12h light-dark cycle for two weeks. Two-week-old rice seedlings were collected and ground into a fine powder in liquid nitrogen, which were used for nuclei isolation and genomic DNA preparation in the downstream assays.For calli induction, the same “Nipponbare” seeds were sterilized and cultured in rice calli induction medium (NB basal medium plus vitamin, glutamine, proline, casein hydrolysate, sucrose, and phytogel as well as 3 mg/L 2,4-D at pH 5.8) in growth chamber at 28°C–29°C with dark conditions. Three-week-old calli were collected and ground into a fine powder in liquid nitrogen, which were used for for nuclei isolation and genomic DNA preparation using the same method as for the seedling tissue above.

extract_protocol:
Briefly,the purified nuclei were used for extraction of high quality genomic DNA using three rounds of phenol, phenol:chloroform, and chloroform extraction coupling with ethanol precipitation. The purified genomic DNA was fragmented into main sizes between 200-500bp using sonication. The 5μg sonicated DNA with or without RNase H treatment was purified using Qiaquick PCR purification kit and incubated with 30μl of well characterized S9.6 antibody bound Dynalbeads overnight at 4℃ in IP buffer (10mM NaPO4, 140mM NaCl,0.05%Triton X-100). After washing with IP buffer three times, Dynalbeads was eluted with elution buffer (50mM Tris-HCl pH8.0, 10mM EDTA, 0.5% SDS) two times with 250μl at 65℃ for 15 mins each. Antibody bound DNA was finally purified using phenol-chloroform extraction and pelleted with ethanol. Air-dried DNA was resuspended in 20 μl of 10 mM Tris-HCl (pH 8.0).
dDRIP-seq: Directional DRIP-seq libraries were prepared using DRIPed DNA above followed the published protocol with minor modifications(Wang et al. 2011). The library preparation directly started from the second strand synthesis step by skipping preparation of mRNA fragments and the first cDNA synthesis steps. The dUTP incorporated second-strand DNA was synthesized using DNA polymerase I. The remaining steps were exactly following the published protocol mentioned above. The final DRIP-seq library was QCed and sequenced using Illumina Hiseq2500 platform.
NBS-seq: The non-denatured sonicated genomic DNA, the same as the one used in dDRIP experiment, was used for bisulfite treatment using EZ DNA methylation-gold kit purchased from ZYMO research. The bisulfite reaction and purification f bisulfite treated DNA was exactly followed the manual. The final purified DNA was used for BS-seq library preparation using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina purchased from NEB (Cat#: E7645S)

tag: cultivar

value: Nipponbare

value: seedlings

tag: replicate

value: biological replicate1

value: two weeks

tag: growth temperature

tag: antibody


title: NBS-seq_seedlings

data_processing:
The raw data sets were trimmed adapter sequences and removed low-quality bases by Trim Galore version 0.4.3.
dDRIP_seq: Clean reads were aligned to the rice reference genome (MSU 7.0) with Bowtie1. We distinguished the strand specific reads using flags of SAM files. The direction of the nascent RNA strand associated with R-loops is concordant with the direction of R2 reads (R2 of the pair-end reads) aligned to the genome. We then extracted unique mappable wR-loops reads by flags of R2 reads equal to 163, and cR-loops reads by flags of R2 reads equal to 147.
dDRIP-seq: Unique mappable reads corresponding to w/c R-loops were used for R-loop peak calling using MACS2(Zhang et al. 2008). The parameter was set with macs2 callpeak --keep-dup 1 -g 3.8e+8 -B --extsize 200 -q 0.01 --nomodel --SPMR
NBS-seq:  Low-quality reads and adapters were removed from the raw data by using Trim Galore. The clean data were mapped to the rice reference genome (MSU7.0) by using Bismark (Krueger and Andrews 2011). Uniquely mappable reads were used for calculating the methylated cytosines using the bismark methylation_extractor program.
Genome_build: MSU7.0
Supplementary_files_format_and_content: bed files were generated using MACS2
Supplementary_files_format_and_content: CX_report.txt files were generated using Bismark


title: mRNA_BreastCancer_rep40


title: EZH2-Input-CrePlus

first: Brian

last: Huntly

address: Hills Road

department: Department of Haematology

institute: University of Cambridge

data_processing:
Chip Seq pipeline: Adapter sequences were trimmed for all reads and mapped against mm10 reference genome using Bowtie2. Uniquely mapped reads were retained and peaks were called using SICER with W200 and G600 parameters.
Genome_build: mm10
Supplementary_files_format_and_content: BigWig and BED files

source_name: Lin- BM progenitors (HSPCs)

extract_protocol:
Lineage negative bone marrow cells were used. Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibodies.
ChIP-Seq libraries were prepared for sequencing using a TruSeq ChIP Sample Prep Kit (Illumina) and standard Illumina protocols

tag: strain

tag: genotype

value: EZH2 KO


title: mRNA_BreastCancer_rep36


title: mRNA_BreastCancer_rep41


title: mRNA_BreastCancer_rep54


title: EZH2-Input-CreMinus

value: EZH2 WT


title: Mt1 c-Fos enhancer (3-prime) 4Cseq

description:
Restriction enyzmes: RE1 Csp6II, RE2 NlaIII
Viewpoint: chr12:86827970-86829043

tag: genotype/variation

tag: passages

value: c-Fos enhancer (3')


title: mRNA_BreastCancer_rep32


title: mRNA_BreastCancer_rep37


title: mRNA_BreastCancer_rep34


title: mRNA_BreastCancer_rep35


title: Wt1 c-Fos enhancer (3-prime) 4Cseq

tag: cell type

value: forebrain-derived neural stem cells


title: Mt3 c-Fos promoter 4Cseq

description:
Restriction enyzmes: RE1 NlaIII, RE2 Csp6I
Viewpoint: chr12:86814272-86814992

value: passage 3 to 7

value: c-Fos promoter


title: mRNA_BreastCancer_rep31


title: Wt1 Sox3 promoter 4Cseq

value: Wild type


title: mRNA_BreastCancer_rep30


title: Wt2 Sox3 promoter 4Cseq


title: Mt2 c-Fos promoter 4Cseq


title: Mt1 c-Fos promoter 4Cseq


title: H3k4me3-CrePlus2

data_processing:
Chip Seq pipeline: Adapter sequences were trimmed for all reads and mapped against mm10 reference genome using Bowtie2. Uniquely mapped reads were retained and peaks were called using SICER with W200 and G600 parameters.
RNA Seq pipeline: Rads were trimmed for adaptor sequence.Paired end reads were aligned to mm10 genome STAR version 2.4.0. To generate the bigwig file, we first extended each read to 200 bp along 5' end and generated bedgraph file using genomeCoverageBed and converted to bigwig using the wigToBigwig software
Genome_build: mm10
Supplementary_files_format_and_content: BigWig and BED files

tag: chip antibody

value: H3K4me3 (Diagenode, C15410003)


title: H3k4me3-CrePlus1


title: Wt3 c-Fos promoter 4Cseq


title: mRNA_BreastCancer_rep33


title: H3k4me3-CreMinus1


title: H3k4me3-CreMinus2


title: Wt2 c-Fos promoter 4Cseq


title: EZH2-H3K27me3-CrePlus1

value: H3K27me3 (Millipore, 07-449)


title: Wt1 c-Fos promoter 4Cseq


title: Mt1 c-Fos enhancer (5-prime) 4Cseq

description:
Restriction enyzmes: RE1 NlaIII, RE2 DpnII
Viewpoint: chr12:86796901-86797329

value: c-Fos enhancer (5')


title: EZH2-H3K27me3-CreMinus2


title: Wt1 c-Fos enhancer (5-prime) 4Cseq


title: Stag3/Rec8_doublemutant_input_replicate_1

city: Bar Harbor

first: Mary Ann

last: Handel

state: ME

address: 600 Main Street

department: Research

institute: The Jackson Laboratory

description: Single Stranded DNA Sequencing (SSDS)

data_processing:
Fastq files for paired-end sequenced DMC1 samples were trimmed using Trimmomatic (v0.32) and subsequently parsed for detection and selection of paired reads having homology at the 5’ and 3’ ends as established by protocols for single strand DNA enrichment.
These selected paired-end reads represent the detectable single stranded DNA reads. Selected reads were aligned to mm10 genome using BWA (0.5.10-tpx) and bam files were parsed for detection and subsequent selection of single ended reads containing true genomic sequence versus fill-in sequence at the homologous region.
Fastq files were created containing only the single ended, single stranded DNA reads for subsequent alignments. Peaks were called utilizing MACS 2.0 with the read extension parameter set to 800 in order to force pileups.
The fourth column in each bedGraph file represents the strength of the peak. Peak strength is defined as the number of tags per peak as calculated by the coverageBed algorithm in the BEDTools suite.
Genome_build: mm10
Supplementary_files_format_and_content: MACS callpeak

source_name: Input S3R8K_testis_SSDS_1

growth_protocol: Germ cells were extracted from 8 weeks old testis of euthanized mice and subjected to immunoprecipitation.

extract_protocol:
To determine the sites and frequencies of double-stranded breaks in mouse spermatocytes ChIP was performed on 2-month old testis samples using anti-DMC1 antibody which specifically recognizes single-stranded end protruding from germ cell-specific double-stranded ends as per Brick et. al. 2012. Germ cells were isolated from the desired genotypes using Dounce Homogenizer, crosslinked, sonicated and immunoprecipitated with anti-DMC1(C-20) antibody.
The libraries were prepared using adapters from TruSeq DNA LT sample prep kit. Libraries were prepared according to the prescribed protocols and amplified for 12 cycles. Size selection of library fragments of 150 - 250 bp was performed after PCR amplification. SSDS samples were denatured and quickly renatured before adapter ligation. The amount of DNA after PCR is low to reduce background. Important comments:  The samples were run on Bioanalyzer for quality control. Libraries were sequenced on an Illumina® HiSeq 2500, with 75 bp paired-end reads.

tag: tissue

value: Testis


title: Rec8_mutant_input_replicate_2

description: Single Stranded DNA Sequencing (SSDS)

source_name: Input R8K_testis_SSDS_2


title: EZH2-H3K27Ac-CrePlus1

value: H3K27Ac (Abcam, ab4729)


title: EZH2-H3K27Ac-CreMinus2


title: EZH2-H3K27Ac-CreMinus1


title: Rec8_mutant_input_replicate_1

description: Single Stranded DNA Sequencing (SSDS)

source_name: Input R8K_testis_SSDS_1


title: B6N_input_replicate_2

description: Single Stranded DNA Sequencing (SSDS)

source_name: Input B6N_testis_SSDS_2

value: Wildtype


title: B6N_input_replicate_3

description: Single Stranded DNA Sequencing (SSDS)

source_name: Input B6N_testis_SSDS_3


title: EZH2-WT2

source_name: Murine Lineage negative bone marrow cells

extract_protocol:
Total RNA was extracted from bone marrow cells using an AllPrep DNA/RNA Mini Kit as per manufacturer’s protocol.
RNA-seq libraries were prepared for sequencing using standard Illumina protocols


title: Stag3/Rec8_doublemutant_ChIP_replicate_1

description: Single Stranded DNA Sequencing (SSDS)

source_name: Anti-DMC1 S3R8K_testis_SSDS_1

value: Anti-DMC1 (C-20); vendor:Santa Cruz; sc-8973


title: EZH2-WT1


title: EZH2-KO2


title: Rec8_mutant_ChIP_replicate_2

description: Single Stranded DNA Sequencing (SSDS)

source_name: Anti-DMC1 R8K_testis_SSDS_2


title: Rec8_mutant_ChIP_replicate_1

description: Single Stranded DNA Sequencing (SSDS)

source_name: Anti-DMC1 R8K_testis_SSDS_1


title: EZH2-H3K27me3-CrePlus2


title: EZH2-KO1


title: Stag3_mutant_ChIP_replicate_2

description: Single Stranded DNA Sequencing (SSDS)

source_name: Anti-DMC1 S3K_testis_SSDS_2

value: Stag3 -/-


title: MLL-CreMinus2

source_name: Murine leukaemia cells


title: MLL-CrePlus2


title: AML-ETO-CRE-PLUS2


title: MLL-CreMinus1


title: MLL-CrePlus1


title: Stag3_mutant_ChIP_replicate_1

description: Single Stranded DNA Sequencing (SSDS)

source_name: Anti-DMC1 S3K_testis_SSDS_1


title: EZH2-H3K27me3-CreMinus1


title: AML-ETO-CRE-MINUS2


title: MLL-EZH2Inhibitor_M3_GSK

treatment_protocol: 24 hours treatment with DMSO or GSK343(10uM)

tag: treatment


title: AML-ETO-CRE-MINUS1


title: MLL-EZH2Inhibitor_M2_GSK


title: EZH2-H3K27Ac-CrePlus2


title: MLL-EZH2Inhibitor_M1_GSK


title: MLL-EZH2Inhibitor_M2_DMSO

value: DMSO


title: MLL-EZH2Inhibitor_M1_DMSO


title: miR-15-16_cKO_4

first: John

middle: D

last: Gagnon

address: 513 Parnasus Ave.

department: Microbiology & Immunology

data_processing:
Base calling: Illumina HiSeq 4000
Sequence alignment: Sequence alignment was performed using STAR_2.4.2a. Genome alignments were restricted to those reads that mapped uniquely to an annotated transcriptome provided by Ensembl.
Expression analysis: Mappings were aggregated on a per-gene basis as raw input for the program DESeq2 v1.14.0.
Genome_build: mm10
Supplementary_files_format_and_content: Processed files include plus and minus strand BigWig files for each sample as well as pooled replicates reads per million (RPM) normalized.

source_name: CD4+ T cells

growth_protocol: CD4+ T cells from the spleen and lymph nodes of mice were enriched by Dynabead positive selection (Invitrogen, L3T4). Cells were stimulated with anti-CD3 and anti-CD28 for 3 days then rested with 20 units/ml recombinant IL-2 (National Cancer Institute) for an additional 2 days.

extract_protocol:
5,000,000 cells from each sample were lysed in Trizol (Life Technologies) and RNA isolated using miRNeasy Micro Kit (QIAGEN) with on-column Dnase digestion.
RNA sequencing libraries were generated using the TruSeq PolyA kit (illumina). Libraries were sequenced on the HiSeq 4000 to generate single-end 50bp reads per the manufacturer's instructions (Illumina).

value: CD4+ T cells

value: miR-15/16fl/fl CD4-Cre


title: miR-15-16_cKO_5


title: miR-15-16_cKO_3


title: miR-15-16_cKO_1


title: miR-15-16_cKO_2


title: miR-15-16_FL_4


title: miR-15-16_FL_2


title: MDA231-DOXO-EV

city: Duarte

first: Xiwei

last: Wu

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

institute: City of Hope National Medical Center

data_processing:
Sequenced reads were adapter trimmed and mapped onto human genome version hg19 using Bowtie v1 software and the expression level of mature miRNAs in the miRBase human miRNA database v15 was summarized.
Normalization and identification of differentially expressed miRNAs between groups were carried out using Bioconductor package “edgeR”.
Genome_build: hg19
Supplementary_files_format_and_content: miRNA expression counts in text format

source_name: Extracellular vesicles

growth_protocol: MDA-MB-231 cells were grown in DMEM plus 10% fetal bovine serum (FBS).  To collect extracellular vesicles (EV), conditioned medium was first prepared by incubating cells grown at sub-confluence in growth medium containing EV-depleted FBS (prepared by overnight ultracentrifugation of medium-diluted sera at 100,000 ×g at 4 °C) for 48 h, and pre-cleared by centrifugation at 500 ×g for 15 min and then at 10,000 ×g for 20 min.  EVs were pelleted by ultracentrifugation at 110,000 ×g for 70 min, and washed in PBS under the same ultracentrifugation conditions.

extract_protocol:
TRIZOL LS reagent (Thermo Fisher Scientific) was used to extract total RNA from EVs following the manufacturer’s protocol.  RNA pellet was dissolved in RNase-free water, and subjected to library construction and deep sequencing.
Each sample was independently subjected to library preparation and deep sequencing.  All small RNAs of 15–52 nts were selected and sequenced using the Illumina system, following the manufacturer’s protocol (Illumina Inc., San Diego, CA).  Library preparation, as well as cluster generation and deep sequencing, was performed according to the 5' ligation-dependent (5′ monophosphate-dependent) manufacturer’s protocol (Digital Gene Expression for small RNA; Illumina).  Small RNAs were size-selected between 17 and 52 nt according to the single-stranded DNA marker in the small RNA sequencing kit (Illumina).  The library was quantified using picoGreen and qPCR.  Sequencing was performed on a Genome Analyzer IIx (Illumina), and image processing and base calling were conducted using Illumina’s pipeline.

treatment_protocol: Cells were treated with docetaxel (DTX; 4 nM), doxorubicin (DOXO; 125 nM), or PBS for 48 h in growth medium containing EV-depleted FBS.

tag: cell line

value: doxorubicin (DOXO)

tag: sample type

value: Extracellular vesicles

tag: molecule subtype

value: miRNA


title: MDA231-DTX-EV

value: docetaxel (DTX)


title: MDA231-PBS-EV

value: PBS


title: miR-15-16_FL_1


title: miR-15-16_FL_3


title: AML-ETO-CRE-PLUS1

value: EZH2 KO


title: MLL-EZH2Inhibitor_M3_DMSO

value: EZH2 WT


title: FLC27_XDGP: Fibrolamellar carcinoma

first: Praveen

last: Sethupathy

description: small RNA

data_processing:
Small RNA-seq data was processed using the approach described in Kanke et al. (J. Integr. Bioinform, 2016)
Reads were trimmed using Cutadapt/1.1.2
Trimmed reads were mapped to the hg19 reference genome using Bowtie/1.1.0 without mismatches. These perfectly aligned reads represent miRNA loci.
Imperfectly aligned reads were re-mapped to miRNA loci using SHRiMP/2.2.2
Read counts were normalized using RPMMM (reads per million mapped to miRNAs)
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files include RPMMM (reads per million mapped to miRNAs) values for each sample

source_name: Fibrolamellar carcinoma

extract_protocol:
RNA was extracted from mouse livers using the Norgen Total RNA Purification kit.
Libraries were prepared using TriLink CleanTag Small RNA Library Prep kit protocol per manufacturer's instructions by the the Genome Sequencing Facility of the Greehey Children’s Cancer Research Institute at the University of Texas Health Science Center at San Antonio. Single end sequencing was performed on an Illumina HiSeq2000.

value: liver

tag: tumor type

value: Metastasis


title: FLC26_OAOE: Fibrolamellar carcinoma

description: small RNA


title: FLC26_ICBQ_Normal: non-malignant liver

description: small RNA

source_name: Non-malignant liver

value: Normal (non-malignant)


title: FLC27_BWSX_Normal: non-malignant liver

description: small RNA


title: FLC26_YJEE: Fibrolamellar carcinoma

description: small RNA

value: Primary


title: FLC27_BDCH: Fibrolamellar carcinoma

description: small RNA


title: 75 % hmC model + 25% non hmC model, 5hmc Jump-seq

city: Chicago

first: Yuwen

last: Liu

state: IL

address: 900 East 57th Street. KCDB building. Room 10250

department: Human Genetics

institute: University of Chicago

data_processing:
Library strategy: Jump-seq
For each 50 bp Illumina sequencing read, umi_tools were used to trim the first 8 bases which constitute a unique molecular identi-fier (UMI) and attach the UMI information to the name of each read.
The UMI sequence of each read was used later to remove PCR duplicates (reads starting at the same genomic location and sharing a same UMI sequence are likely to arise from one DNA fragment with a hydroxymethylated site, thus need to be collapsed and count-ed as one read).
After extracting UMI, cutadapt was used to retain reads with a Jump-Seq barcode “NNNNNNN” (The Jump barcode used for each library used in this study could be found in Table S4) and to trim the barcode from each of these retained reads.
We also used cutadapt to remove the bases that match the invariant adaptor sequence at the 3’end of each read.
Bowtie was used to map the reads to the mouse genome (mm9) not allowing any mismatch in the first 35 bp of each read. Only uniquely mapped reads were kept and processed with umi_tools to remove PCR duplicates based on the UMI sequence of each read.
Use a Binomial model to call peaks. Since reads are generated from 5hmC (unknown), it is more appropriate and reasonable to check the distribution of reads over C (known), rather than over every possible base. To avoid multiple counting of one read, the 5' end of every reads could be used when calling the coverage, instead of the entire length of the reads.
Genome_build: mm9
Supplementary_files_format_and_content: .txt files are tab-delimited text files of peaks called for each library; .5prime.bed files include information for the 5'prime end positions (the landing location) of reads for each library.

source_name: synthesized oligo spike-in

growth_protocol: mESCs were cultured in feeder-free gelatin-coated plates in Dulbecco’s Modified Eagle Medium (DMEM) (Invitrogen Cat. No. 11995) supplemented with 20% FBS (GIBCO), 2 mM L-glutamine (GIBCO), 0.1 mM 2-mercaptoethanol (Sigma), 1 × nonessential amino acids (GIBCO), 1,000 units/ml LIF (Millipore Cat. No. ESG1107), 1 × pen/strep (GIBCO), 3 mM CHIR99021 (Stemgent), and 1 mM PD0325901 (Stemgent). mESCs were passaged every other day with Trispin (GIBCO) and seeded on gelatin-coated plates. Cells were kept under standard 37 ℃ and 5% CO2 conditions.

extract_protocol:
mESCs genomic DNA was purified using Quick-DNA™ Microprep Plus Kit (Zymo Research). The Tn5 reaction protocol has been described previously1. In brief, genomic DNA was fragmented and tagmented by mixing 4 µL 5 × TAPS-MgCl2-PEG 8,000 (for DNA < 1 ng) or 5 × TAPS-MgCl2-DMF, 1 µL of the assembled Tn5 and adaptor complex, genomic DNA and suitable volume of H2O up to 20 µL. Buffer used were: TAPS-MgCl2-PEG 8,000 (50 mM TAPS-NaOH, pH 8.5, 25 mM MgCl2, 40% PEG 8,000) or 5 × TAPS-MgCl2-DMF (50 mM TAPS-NaOH, pH 8.5, 25 mM MgCl2, 50% DMF). For 48 ng genomic DNA, 1 µL of 2-fold diluted Tn5 is sufficient; for 24 ng genomic DNA, Tn5 needs to be diluted 4 folds and for less genomic DNA, Tn5 should be diluted accordingly. For 600 pg genomic DNA or 100 cells, Tn5 should be diluted 320 folds and added 1 µL into the reaction. The reactions were incubated for 7 min at 55℃, and Tn5 was inactivated for 7 min at 55℃ after adding 1 µL proteinase K (Thermo Fisher Scientific). Typically, all the genomic DNA was converted to fragments of average size 200-300 bp. The fragmented DNA was purified by DNA Clean & Concentrator™-5 kit (Zymo Research) and eluted into H2O. T4 bacteriophage β-GT and Tet was prepared as previously described3,4. The 5-hmC labeling reactions were performed in a 20 μL solution containing 50 mM HEPES buffer (pH 8.0), 25 mM MgCl2, tagmented genomic DNA (100-500 bp), 100 μM UDP-6-N3-Glu, and 1 μM wild-type β-GT. The reactions were incubated for 1 h at 37 °C. In the case of 5mC, the strategy of coupling Tet oxidation with β-GT was used5: 5hmC base is protected by transferring a regular glucose from UDP-glucose using β-GT, followed by purifica-tion with DNA Clean & Concentrator™-5 kit (Zymo Research). After the azide-glucose transfer reaction, the DNA substrates were purified by Clean & Concentrator™-5 kit (Zymo Research) and reconstituted in H2O. The click chemistry was performed with addi-tion of 0.8 nmol dibenzocyclooctyne modified Jump P5 probe into the DNA solution, and the reaction mixture was incubated for 24 h at 37 °C.
The click products were incubated with Dynabeads™ MyOne™ Streptavidin C1 (Thermo Fisher Scientific) in 1 × B & W Buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2 M NaCl) at RT for 20min (the click reactions with different barcoded Jump P5 probe could be pooled together for purification), followed by extensively washing steps: 1 × B & W Buffer 1 time, 0.15 M NaOH 1 time, 0.1 M NaOH twice, 1 × B & W Buffer with 200M Tris-HCl pH 7.5 one time, H2O three times and finally the beads were resuspended in 6 µL H2O and 2 µL of 5 × Sequenase Reaction Buffer for annealing (the loop shape Jump probe formed hairpin to initiate primer ex-tension). The reaction was heated at 95 °C and slowly ramped to 4 °C in Thermocycler. 1 µL Sequenase Version 2.0 DNA Polymer-ase (Thermo Fisher Scientific) and 1 µL dNTP (NEB) were added in the annealed solution, incubated at 37 °C for 2 h. Then 1 µL USER® Enzyme (NEB) was added to cleave at the dU linker region to release the newly synthesized strand. The 11 µL Jump prod-ucts were subjected to library construction with limited cycle amplification. Next-generation sequencing (NGS) libraries were gen-erated using NEBNext® Ultra™ II Q5® Master Mix (NEB), NEBNext® Multiplex Oligos for Illumina® (NEB) for NEB kit compat-ible Jump P7 adaptor and Jump P5 probe and Illumina Nextera DNA oligo sets for Nextera DNA kit compatible Jump P7 adaptor and Jump P5 probe.

treatment_protocol: Hyperactive Tn5 was produced following the published protocol with some details modified1,2. In brief, pTXB1-Tn5 plasmid (Catalog # 60240, Addgene) was transformed into C3013 cells (NEB). 6 L culture was grown at 37 ℃ to OD600 ~ 1. The culture was then cooled to 16 ℃ and IPTG was added to 0.1 mM. After continued growth for additional 16 h at 16 ℃, cells were harvested and lysed by French press in lysis buffer (25 mM Tris, pH = 8.0, 0.7 M NaCl, 0.1% Triton X-100). Then the lysate was centrifuged at 13,000 rpm for 30 min, followed by adding 10% PEI (Sigma) to remove E. coli DNA. The supernatant was loaded on a chitin column (NEB), followed by extensively wash by lysis buffer and 36 h cleavage with 100 mM DTT. The elution was purified by Source 15S column using Buffer A: 20 mM Tris 7.5 and Buffer B: 20 mM Tris 7.5, 200 mM NaCl. Tn5 comes out at conduction ~ 30. Collected fractions were pooled and subjected to gel filtration with gel filtration buffer (20 mM HEPES-KOH pH 7.6, 200 mM NaCl, 0.1 mM EDTA, 1 mM DTT). Finally, the 3-step purified Tn5 was concentrated to OD280 = 3.0 and stored at -80 ℃ after adding 1.1 vol 100% glycerol and 0.33 vol of 2 × Tn5 dialysis buffer (20 mM HEPES-KOH pH = 7.6, 200 mM NaCl, 0.2 mM EDTA, 2 mM DTT, 20% glycerol). For assembly, oligonucleotides (Jump-P7 adapter and Tn5 bottom adaptor) were resuspended in 1 × TE (pH = 8.0) to a final concentration of 100 µM each. Equimolar amounts of Jump-P7 adapter and Tn5 bottom adaptor were mixed, denatured at 95 ℃ for 10 min and slowly cooled down to anneal. One vol Tn5 was added 0.143 vol annealed adaptor, mixed gently but thoroughly and the Tn5-adaptor complex was incubated for 60 min at RT and stored at -80 ℃.

value: Mouse Embryonic Stem Cells


title: FLC25_UYHR: Fibrolamellar carcinoma

address: T7 006 Vet Research Tower

institute: Cornell University

description: small RNA


title: FLC23_RVBN: Fibrolamellar carcinoma

description: small RNA


title: NT2: RA-21-2

city: Athens

first: Wentao

last: Li

state: GA

address: 500 D. W Brooks Drive

department: Environmental Health Science

institute: University of Georgia

data_processing:
Reads from RNA-seq were aligned using STAR.
Read counts for each gene were obtained using FeatureCounts
Likelihood ratio test for differential expression analysis across all time points were carried out using DESeq2
p-values were adjusted by the Benjamini-Hochberg procedure
Genome_build: hg19
Supplementary_files_format_and_content: CSV files contain the read counts and RPKM for each gene.

source_name: NT2 cells

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM, Gibco, USA) supplemented with 10% fetal bovine serum (FBS, Sigma-Aldrich, USA) at 37 ºC in a 5% CO2 humidified incubator.

extract_protocol:
Total RNA was then isolated using RNA Reagent (Invitrogen) and PureLink RNA Mini Kit (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For induction of NT2 cells into neurons, 10 mM all-trans retinoic acid (RA) (Sigma), dissolved in DMSO, was added into the culture medium at a final concentration of 10 µM. Bone morphogenetic protein-2 (BMP-2) (GenScript) at a final concentration of 30 ng/ml was firstly used to test the muscle cell induction, and then 40 ng/ml BMP-2 was used in later experiments. As a negative control, DMSO was added into the culture medium for a final concentration of 0.1%. NT2 cells were treated with differentiation induction agents or DMSO for up to 21 days and the culture medium was changed every 2 days.

value: RA

tag: treatment time (d)


title: NT2: RA-21-1


title: FLC20_ZDNV: Fibrolamellar carcinoma

description: small RNA


title: 25 % hmC model + 75% non hmC model, 5hmc Jump-seq


title: 5 % hmC model + 95% non hmC model, 5hmc Jump-seq


title: 50 % hmC model + 50% non hmC model, 5hmc Jump-seq


title: 1 % hmC model + 99% non hmC model, 5hmc Jump-seq


title: FLC18_MKZC: Fibrolamellar carcinoma

description: small RNA


title: NT2: RA-10-1


title: 0.6ng 5hmc Jump-seq rep2

source_name: Mouse Embryonic Stem Cells


title: 0 % hmC model + 100% non hmC model, 5hmc Jump-seq


title: 100 % hmC model + 0% non hmC model, 5hmc Jump-seq


title: 0.6ng 5hmc Jump-seq rep1


title: FLC18_FXYQ: Fibrolamellar carcinoma

description: small RNA


title: <100 um B29 group

city: Rochester

first: Ching-Ho

last: Chang

address: 60 Crittenden Blvd, Apt 709

department: Biology

institute: U of Rochester

description: SAMPLE 2

data_processing:
The data were analyzed using R package limma v.3.34.9.
The data were normalised using normexp background correction and quantile normalization by control probes with limma in R

source_name: pancreatic islets

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: BALB/c mice were purchased from the Jackson Laboratory. The University Committee on Animal Resources at the University of Rochester approved all mouse experiments.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy mini kit according to the protocol provided with the kit. Quality control was performed by Yale Center for Genome Analysis (YCGA; New Haven, CT).

treatment_protocol: BALB/c mice were intraperitoneally injected four times with 25 ug of serpin B13 mAb or control mAb (total dose of 100 ug) every other day at 2 weeks old and sacrificed two weeks after the last injection (5 weeks old).

value: BALB/c

tag: age

value: 5 weeks old

value: pancreatic islets

value: serpin B13 mAb (clone:B29)


title: >200 um IgG group

description: SAMPLE 5

value: control mAb (IgG)


title: 100~200 um IgG group

description: SAMPLE 3


title: 100~200 um B29 group

description: SAMPLE 4


title: FLC17_WCKN: Fibrolamellar carcinoma

city: Ithaca

description: small RNA


title: <100 um IgG group

description: SAMPLE 1


title: 2.4ng 5hmc Jump-seq rep4


title: 2.4ng 5hmc Jump-seq rep3


title: 2.4ng 5hmc Jump-seq rep2


title: NT2: RA-5-1