title: CC-seq of Human: WT, Async, VP16, Rep4

city: Brighton

first: William

last: Gittens

state: I am not in the U.S. or Canada

address: Science Park Road

department: Genome Damage and Stability Centre

institute: University of Sussex

description:
CC-seq map of Top2-DNA CCs
WG34_RPE1_WT_Asyn_VP16

data_processing:
Paired end reads that passed filter were aligned to hg19 using bowtie2 (options: -X 1000 --no-discordant --very-sensitive --mp 5,1 --np 0), using MAPQ10 settings
SAM files processed via terminalMapper (Perl, v5.22.1; https://github.com/Neale-Lab) that computes the coordinates of the protein-linked 5’-terminal nucleotide.
PCR duplicates, where Read1 and Read2 position were identical, were removed.
Data were filtered to remove known ultra-high signal regions and repeat regions
Genome_build: hg19
Supplementary_files_format_and_content: FullMap files containing sparsely-formatted, 1bp histograms detailing the total number of Watson (+) and  Crick (-) hits for all mapped base-pairs. 4-column format (Chr, Pos, Watson, Crick).

source_name: cell culture

growth_protocol: Human hTERT RPE-1 cells (normal diploid karyotype, immortalized non-cancer) were obtained from ATCC and cultured at 37 ˚C, 5% CO2 and 3% O2 in Dulbecco’s Modified Eagle’s Medium DMEM/F-12 (Sigma), supplemented with 10% Fetal Calf Serum (FCS) and 90 Units/ml Penicillin-Streptomycin. For asynchronous  cell populations, RPE-1 cells were seeded at a density of (3.5x103 cells/cm2l) and incubated for 72 h at 37 ˚C, to ensure subconfluent log-phase growth (~70% confluency)  at the time of the experiment. For G1 cell populations, WT and TOP2B-/- RPE-1 cells were seeded at a density of 5x103 cells/cm2 and incubated for 48 h at 37 ˚C in DMEM/F12 containing 10% FCS, prior to a further 24 h incubation in DMEM/F12 medium containing no FCS to ensure complete G1-phase arrest (verified by FACs)

extract_protocol:
1.5x107 RPE-1 cells were treated as described above, pelleted by centrifugation, washed once with 15 ml ice-cold PBS, and resuspended in three aliquots of 400 µL ice-cold PBS.  1 ml ice-cold ethanol was added to 400 µL cell suspensions in microcentrifuge tubes in order to rapidly denature proteins in situ, mixed, incubated for 10 min on ice, and pelleted by centrifugation. The supernatant was thoroughly removed by aspiration, prior to addition of 200 µL 1x STE buffer (2% SDS, 0.5 M Tris pH 8.1, 10 mM EDTA, 0.05% bromophenol blue), cell disruption using a pestle (VWR), addition of a further 400 µL 1x STE buffer, and incubation for 10 min at 65 ˚C. Samples were cooled on ice and 500 µL Phenol-Chloroform-isoamyl alcohol (25:24:1; Sigma) was added. The mixtures were emulsified by shaking and pipetting 5 times with a 1 ml micropipette, prior to phase separation by centrifugation at 20,000 g for 20 min. By minimising mechanical shearing of the lysate prior to phenol chloroform extraction, peptides that are covalently linked to high molecular weight DNA segregate into the aqueous phase alongside other purified nucleic acids. Free protein, coated in SDS, will partition to the interphase. 500 µL of the aqueous phase was removed to a clean microcentrifuge tube, taking care not to disturb the interphase, and nucleic acids were precipitated with 1 ml ice-cold ethanol, pelleted by centrifugation, washed with ice-cold 70% ethanol, and dissolved in TE buffer overnight at 4 ˚C. Samples were then incubated with 0.2 mg/ml RNase A (Sigma) for 1 h at 37 ˚C; nucleic acids were precipitated with 1 ml ethanol, pelleted by centrifugation, washed twice with 70% ethanol and dissolved in TE overnight. Aliquots of nonproteolysed DNA  were combined to a total of 1 ml and sonicated to an average fragment size of 300-400 bp with Covaris (duty cycle: 10%, intensity/peak power incidence: 75W, cycles/burst: 200, time: 15 min). 1 ml of sonicated sample was diluted to reduce viscosity by addition of 1 ml TE. Triton-X100, N-Lauroylsarcosine sodium salt and NaCl were then added to complete the binding buffer (final concentrations: 0.3 M NaCl, 0.2% Triton-X100, 0.1% N-Lauroylsarcosine sodium salt). Each sample was divided over several Miniprep (QIAGEN) silica-fibre membrane spin columns, such that the total DNA loaded to each was approximately 20 µg. Under these high salt conditions, protein, but not nucleic acids, bind to the silica membrane, leading to selective retention of any covalent complexes (CCs). The flowthrough was reapplied to the column to improve yield. Columns were washed 6 times with 600 µL of TEN (10 mM Tris, 1 mM EDTA, 0.3 M NaCl) per 1 min wash to remove any residual non-CC DNA fragments, prior to elution with 100 µL TES (10 mM Tris, 1 mM EDTA, 0.5% SDS). The SDS detergent in the elution buffer releases interactions between protein and silica, thereby releasing bound CCs.
Eluted products were pooled to 500 µL in TES and incubated with 1 mg/ml Proteinase K (Sigma) for 30 min at 60 ˚C, prior to overnight ethanol precipitation at -80 ˚C with 1.41 ml ethanol, 0.2 mg/ml glycogen and 200 mM NaOAc. The DNA-glycogen precipitate was pelleted by centrifugation at 20,000 g for 1 hr at 4 ˚C, washed once with 1.5 ml 70% ethanol, and re-pelleted by centrifugation. The supernatant was aspirated and the pellet was air-dried for 10 min at RT, prior to solubilisation in 52 µL 10 mM Tris-HCl. DNA concentration was measured in a 2 µL sample with the Qubit (ThermoFisher) and High Sensitivity reagents.  The remaining 50 µL was used as input for one round of end repair and adapter ligation with NEBNext Ultra II DNA Library Preparation kit (NEB), according to manufacturer’s instructions, except for the use of a custom P7 adapter (see table).  The use of custom adapters is to allow differentiation of the sheared end (P7 adapter) from the Top2/Spo11 end (P5 adapter). After ligation of the P7 adapter, DNA was isolated with AMPure XP beads (Beckman Coulter) according to manufacturer’s instructions (beads:input of 78:90) and eluted in 50 µL 10 mM Tris-HCl. Samples were diluted 2-fold with 50 µL Tdp2 reaction buffer (100 mM TrisOAc, 100 mM NaOAc, 2 mM MgOAc, 2 mM DTT, 200 µg/ml BSA) and incubated with 3 µL of 10 µM recombinant human TDP2, for 1 h at 37 ˚C. DNA was isolated again with AMPure XP beads (beads:input of 103:103) and eluted in 52 µL 10 mM Tris-HCl. Next, a second round of adapter ligation was conducted using adapter P5 (see table), without prior end repair in order to prevent dephosphorylation of DNA 3’-phosphate termini which may be generated by TDP2 activity on 3’-CCs. After ligation of the P5 adapter to the Top2/Spo11-cleaved end, DNA was isolated with AMPure XP beads (beads:input of 78:90) and eluted in 17 µL 10 mM Tris-HCl. DNA concentration was measured in 2 µL using the Qubit. The remaining 15 µL was used as template for the PCR step of the NEBNext Ultra II PCR step using universal primer (P5 end) and indexed primers for multiplexing (P7 end), according to manufacturer's instructions. PCR reactions were diluted with 50 µL 10 mM Tris-HCl, DNA was isolated with AMPure XP beads (beads:input of 84:100) and eluted in 30 µL 1 mM Tris-HCl pH 8.1. Samples were then subjected to 200-600 bp size selection using the BluePippin (Sage Science), prior to quantification of molarity using the Bioanalyzer (Agilent).

treatment_protocol: For the "VP16" condition,   cells were preincubated with 5 µM MG132 (Sigma) for 90 min, trypsinised and incubated in suspension with  5 µM MG132 and 100 µM VP16 (Sigma) for 20 min at 37 ˚C. For the "UT" condition,  cells were preincubated with 5 µM MG132 (Sigma) for 90 min, trypsinised and incubated in suspension with  5 µM MG132 and for 20 min at 37 ˚C.

value: WT

tag: cell phase

value: Asynchronous

tag: treatment


title: CC-seq of Human: WT, Async, VP16, Rep3

status: Public on Sep 28 2019

type: SRA

country: United Kingdom

description:
CC-seq map of Top2-DNA CCs
WG24_RPE1_WT_Asyn_VP16

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

tag: genotype


title: CC-seq of Human: WT, Async, UT, Rep3

description:
CC-seq map of Top2-DNA CCs
WG23_RPE1_WT_Asyn_UT

value: UT


title: CC-seq of Human: WT, Async, UT, Rep2

description:
CC-seq map of Top2-DNA CCs
WG15_RPE1_WT_Asyn_UT


title: K562_WT_D10_2

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

description:
quantseq_counts.txt
1c2

library_source: transcriptomic

data_processing:
Basecalls performed using RTA version 2.4.11
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were aligned to the human genome (G1k V37), or mouse genome (MM10) using HiSAT2 and reads were assigned to genes using htseq-count.
Differential expression was calculated using either limma, voom or DESeq2
Genome_build: mm10, hg19
Supplementary_files_format_and_content: tab-delimited text files of gene counts for each Sample

molecule: total RNA

source_name: erythroleukemia

growth_protocol:
[Culture Media]  RPMI-1640 supplemented with 2 mM Glutamax, 100 IU/mL Penicillin, 100 µg/mL Streptomycin and 10% HI-FCS
All cell lines were cultured in 5% CO2 at 37ºC

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit. RNA concentration was quantified with a NanoDrop spectrophotometer (Thermo Scientific).
Libraries were prepared using QuantSeq 3’ mRNA-seq Library Prep kit (Lexigen).

tag: disease state

value: erythroleukemia

tag: time

value: Day 10

tag: replicate


title: K562_EED_KO_D10_1

description:
quantseq_counts.txt
4c1


title: gastric cancer tissues from Pdx-1-Cre;Cdh1F/+;Trp53F/F;Smad4F/F mice 2

type: RNA

city: Seoul

first: Jun Won

last: Park

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Veterinary Pathology

country: South Korea

institute: Seoul National University

hyb_protocol: According to the standard Affymetrix protocol

scan_protocol: Affymetrix GeneChip® Scanner 3000 7G

data_processing: The data were analyzed with Expression Console™ Software 1.3.1 using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

organism: Mus musculus

growth_protocol: monitoring mice

extract_protocol: Trizol reagent according to the manufacturer's instructions.

treatment_protocol: No treatment

tag: tissue

value: gastric cancer tissues

tag: strain/genotype

tag: histology

value: diffuse-type gastric cancer


title: K562_EED_KO_D7_3

description:
quantseq_counts.txt
4a3

value: Control

value: Day 7


title: K562_WT_D10_3

description:
quantseq_counts.txt
1c3


title: K562_EED_KO_D7_2

description:
quantseq_counts.txt
4a2


title: K562_EED_KO_IFN_D7_2

description:
quantseq_counts.txt
4b2

value: IFNg


title: CC-seq of Human: WT, Async, UT, Rep1

description:
CC-seq map of Top2-DNA CCs
WG11_RPE1_WT_Asyn_UT


title: K562_EED_KO_D7_1

description:
quantseq_counts.txt
4a1


title: K562_WT_D10_1

description:
quantseq_counts.txt
1c1


title: K562_WT_IFN_D7_2

description:
quantseq_counts.txt
1b2


title: K562_WT_IFN_D7_1

description:
quantseq_counts.txt
1b1


title: K562_WT_D7_3

description:
quantseq_counts.txt
1a3


title: K562_WT_D7_2

description:
quantseq_counts.txt
1a2


title: K562_WT_IFN_D7_3

description:
quantseq_counts.txt
1b3


title: CC-seq of Human: WT, Async, VP16, Rep2

description:
CC-seq map of Top2-DNA CCs
WG16_RPE1_WT_Asyn_VP16


title: K562-IRF1_input_Control

data_processing:
Basecalls performed using RTA version 2.4.11
Bcl2fastq (Illumina) was used to convert BCL files to Fastq files
Reads were aligned to the human genome (GRCh37) or mouse genome (GRCm38), combined with fly genome (BDGP5) or a modified Tasmanian devil genome (Devil_ref v7.0) with BWA-mem.
Peak calling was performed with MACS2 with default parameters with deeptools for normalisation
Genome_build: mm10, hg19, devil v7.0
Supplementary_files_format_and_content: bed files of peaks called by MACS2

source_name: erythroleukaemia

growth_protocol:
[Culture Media]  RPMI-1640 supplemented with 2 mM Glutamax, 100 IU/mL Penicillin, 100 µg/mL Streptomycin and 10% HI-FCS
All cell lines were cultured in 5% CO2 at 37ºC with the exception of C5065 cells, which were cultured in 5% CO2 at 35ºC.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 15 min at room temperature, and cross-linking was stopped by the addition of 0.125 M glycine. Cells were lysed in 1% SDS, 10 mM EDTA, 50 mM Tris-HCl, pH 8.0, and protease inhibitors. Lysates were sonicated in a Covaris ultrasonicator to achieve a mean DNA fragment size of 500 bp. Samples were diluted 1:10 in modified  RIPA buffer (1% Triton X-100, 0.1% deoxycholate, 90 mM NaCl, 10 mM Tris-HCl, pH 8.0, and  protease inhibitors) and incubated rotating with antibody for a minimum of 12 h at 4 °C.  Protein A Dynabeads (Life Technologies) were used to bind the antibody and associated chromatin. After washing and elution from the beads, samples were reverse cross-linked overnight and purified with QIAquick PCR purification kits (Qiagen).
Sequencing libraries were prepared from eluted DNA using Rubicon ThruPLEX DNA-seq kit.

value: erythroleukaemia

tag: chip antibody


title: K562-IRF1_input_EPZ


title: K562_EED_KO_D10_2

description:
quantseq_counts.txt
4c2


title: K562_WT_D7_1

description:
quantseq_counts.txt
1a1


title: K562-input_Control


title: K562-IRF1_ChIP_EPZ

value: IRF1 (D5E4, Cell Signaling)


title: K562-IRF1_ChIP_Control


title: K562-input_EPZ


title: K562_EED_KO_IFN_D7_1

description:
quantseq_counts.txt
4b1


title: K562-H3K4me3_ChIP_EPZ

value: H3K4me3 (ab8580, Abcam)


title: K562-H3K27me3_ChIP_Control

value: H3K27me3 (C37B11, Cell Signaling)


title: K562-H3K4me3_ChIP_Control


title: K562-H3K27ac_ChIP_Control

value: H3K27ac (ab4729, Abcam)


title: K562-H3K27me3_ChIP_EPZ


title: HC_S973 [MRE-seq]

city: Houston

first: Lisha

last: Zhu

state: TX

address: 7000 fannin st

country: USA

institute: UT Health Science Center at Houston

data_processing:
MeDIP-seq reads were aligned to the human genome hg19 using Burrows-Wheeler Alignment ( BWA) with default parameters in bwa mem, MRE-seq reads were aligned to the human genome hg19 using BWA with default parameters in bwa aln and bwa samse
R package repMnM was applied to obtain the DMRs between UAD and HC which combined the information of MeDIP-Seq and MRE-Seq together, the whole geome region was binned to 500bp bins and each bin was tested for differential methylation between ADU and HC. repMnM resulted DMRs of 500 length between ADU and HC.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph

source_name: neutrophils

growth_protocol: Peripheral blood mononuclear cells were separated from neutrophils and red blood cells by density-gradient centrifugation. Red cells were removed from neutrophils by hypotonic lysis. Neutrophils were then immediately stored at -80C.

extract_protocol: Library preparation followed the protocol (Li D, Zhang B, Xing X, Wang T. Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Methods. 2015 Jan 15;72:29-40. doi: 10.1016/j.ymeth.2014.10.032.)

treatment_protocol: High-quality, intact genomic DNA  was extracted using an optimized method (Li D, Zhang B, Xing X, Wang T. Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation. Methods. 2015 Jan 15;72:29-40. doi: 10.1016/j.ymeth.2014.10.032.).

tag: cell type

value: neutrophils

tag: disease type

value: healthy


title: HC_S972 [MRE-seq]


title: K562_EED_KO_IFN_D7_3

description:
quantseq_counts.txt
4b3


title: K562-H3K27ac_ChIP_EPZ


title: HC_S809 [MRE-seq]


title: HC_S971 [MRE-seq]


title: HC_S808 [MRE-seq]


title: ADU_S833 [MRE-seq]

value: Juvenile Idiopathic Arthritis


title: ADU_S913 [MRE-seq]


title: ADU_S920 [MRE-seq]


title: HC_S973 [MeDIP-seq]


title: ADU_S1014 [MRE-seq]


title: ADU_S819 [MRE-seq]


title: HC_S972 [MeDIP-seq]


title: HC_S809 [MeDIP-seq]


title: ADU_S917 [MeDIP-seq]


title: ADU_S920 [MeDIP-seq]


title: HC_S808 [MeDIP-seq]


title: ADU_S913 [MeDIP-seq]


title: CC-seq of Human: WT, Async, VP16, Rep1

description:
CC-seq map of Top2-DNA CCs
WG12_RPE1_WT_Asyn_VP16

value: WT

value: Asynchronous


title: ADU_S833 [MeDIP-seq]


title: RP-116_IFNg + EZH2i_m-4b

description:
counts_filtered_anno.txt
m-4b

source_name: SCLC

growth_protocol:
[Culture Media]  DMEM/F12 with 15 mM HEPES, supplemented with 2 mM Glutamax, 100 IU/mL Penicillin, 100 µg/mL Streptomycin, 4 μg/mL Hydrocortisone, 5 ng/mL EGF, 5 mL of Insulin-Transferrin-Selenium  solution and  10% HI-FCS
All cell lines were cultured in 5% CO2 at 37ºC

value: SCLC

value: IFNg + EZH2i


title: RP-116_IFNg + EZH2i_m-4c

description:
counts_filtered_anno.txt
m-4c


title: RP-116_IFNg + EZH2i_m-4a

description:
counts_filtered_anno.txt
m-4a


title: ADU_S1014 [MeDIP-seq]


title: RP-116_EZH2i_m-3a

description:
counts_filtered_anno.txt
m-3a


title: RP-116_EZH2i_m-3b

description:
counts_filtered_anno.txt
m-3b


title: ADU_S819 [MeDIP-seq]


title: RP-116_IFNg_m-2b

description:
counts_filtered_anno.txt
m-2b


title: RP-116_IFNg_m-2a

description:
counts_filtered_anno.txt
m-2a


title: RP-116_EZH2i_m-3c

description:
counts_filtered_anno.txt
m-3c


title: Col-0_18days_after_pollination_total_rep2

city: Wageningen

first: Leónie

last: Bentsink

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

hyb_protocol: GeneChip® 3' IVT Express kit (cat. # 901229) was used for hybridisation, washing and staining of the cartridges.

scan_protocol: Scanning of the arrays was performed using the Affimetrix 3000G scanner.

data_processing: The GeneChip data were analyzed using the R statistical programming environment and Bioconductor packages. The data were normalized using the RMA algorithm. The P values were adjusted for multiple testing with the Benjamini and Hochberg method to control for false positives.

organism: Arabidopsis thaliana

source_name: Col-0 seeds

label_protocol: RNA was processed and cRNA synthesized according to the 3’ GeneChips OneCycle kit.

growth_protocol: For the transcriptome and  transcriptome analyses Col-0 were grown in a randomized complete block design with three replicates. Each replicate consisted of a bulk of eight plants. The precise growth conditions used were described by (El-Lithy et al., Genetics, 2006). Plant were harvested at specified developmental stages.

extract_protocol: The total RNA and polysomal RNA were purified with TriPure Isolation Reagent (Roche, Basel, Switzerland), further purified using RNeasy Mini spin columns (Qiagen, Hilden, Germany) and dissolved in RNase-free H2O for further analyses.

treatment_protocol: RNA was extracted from seeds developed at each stages with three biological replicates for each time point.

tag: developmental stage

value: 18 DAP

value: seeds

tag: ecotype

tag: rna type

value: Total RNA


title: RP-116_Control_m-1c

description:
counts_filtered_anno.txt
m-1c

value: Control


title: RP-116_Control_m-1b

description:
counts_filtered_anno.txt
m-1b


title: RP116-input_Control

source_name: small cell lung cancer

growth_protocol:
[Culture Media]  DMEM/F12 with 15 mM HEPES, supplemented with 2 mM Glutamax, 100 IU/mL Penicillin, 100 µg/mL Streptomycin, 4 μg/mL Hydrocortisone, 5 ng/mL EGF, 5 mL of Insulin-Transferrin-Selenium  solution and  10% HI-FCS
All cell lines were cultured in 5% CO2 at 37ºC with the exception of C5065 cells, which were cultured in 5% CO2 at 35ºC.

value: small cell lung cancer


title: RP-116_Control_m-1a

description:
counts_filtered_anno.txt
m-1a


title: HC_S971 [MeDIP-seq]


title: ADU_S917 [MRE-seq]


title: RP116-H3K27ac_ChIP_Control


title: RP116-H3K4me3_ChIP_Control


title: RP116-H3K27me3_ChIP_EPZ


title: RP116-H3K27me3_ChIP_Control


title: RP116-input_EPZ


title: RP116-H3K27ac_ChIP_EPZ


title: RP-116_IFNg_m-2c

description:
counts_filtered_anno.txt
m-2c

value: IFNg


title: Cnp1_mhf2D_cen1_inactive_wt_spore_11

city: Hangzhou

first: Min

last: Lu

state: Zhejiang

address: Yuhangtang road 866

country: China

institute: Zhejiang University, Life Sciences Institute

data_processing:
Quality control performed using FASTX-Toolkit.
ChIP-seq reads were trimmed to ensure uniformity using FASTX-Toolkit.
ChIP-seq reads were aligned to the S. pombe genome assembly ASM294v.2.22 using Burrows-Wheeler Aligner (BWA)’s default parameters, which randomly assigned the ChIP-seq reads to the repetitive DNA sequences.
Model-based Analysis of ChIP-seq (MACS) was used for peak calling. Briefly, the mapped reads were filtered to keep one tag at the same location (--keep-dup) and were normalized by sequencing depth in million reads (-B --SPMR). The mapped reads were extended to the size of 146 bp to define the nucleosome positions (--shift 73 --extsize 146). Others were set as the default parameters.
Genome_build: S. pombe genome ASM294v.2.22
Supplementary_files_format_and_content: bdg files were generated using MACS.

organism: Schizosaccharomyces pombe

source_name: fission yeast haploid cells

growth_protocol: Single colonies of each strains  were struck and cultured in YES medium at 29 °C. The cell cultures were harvested when the optical density (OD) reached aound 1.

extract_protocol:
Cells were digested with Zymolase and lysed, the chromatin lysates were treated with micrococcal nuclease to digest chromatin into mononucleosomes. The histone-DNA complexes were isolated with antibody.
Libraries of DNA were prepared using KAPA library preparation kit following the accompanied instructions.

value: mhf2+ (carrying the inactivated Centromere 1)

tag: cell growth stage

value: log phase

tag: temperature condition

value: 29 °C

value: Cnp1 (gift from Robin Allshire lab)


title: Cnp1_mhf2D_cen1_inactive_wt_spore_9


title: H3K9me2_mhf2D_cen1_inactive_wt_spore_18

value: mhf2+ (carrying Cnp1 spreading)


title: RP116-H3K4me3_ChIP_EPZ

tag: treatment

value: H3K4me3 (ab8580, Abcam)


title: H3K9me2_mhf2D_cen1_inactive_wt_spore_14


title: H3K9me2_mhf2D_cen1_inactive_wt_spore_12


title: H3K9me2_mhf2D_cen1_inactive_wt_spore_16


title: Cnp1_wt_cen_spreading_ura4_4

value: mhf2+ (carrying the spreading of Cnp1)

value: fission yeast haploid cells


title: Cnp1_clr4D_cen_active_1

value: clr4{delta} (carrying no inactivated Centromere 1/2/3)


title: H3K9me2_wt_cen_spreading_ura4_5


title: Cnp1_wt_cen1_inactive_clr4D_transformation_1

value: mhf2+clr4{delta} (carrying the inactivated Centromere 1)


title: H3K9me2_wt_cen2_inactive_ura4_2

value: mhf2+ (carrying the inactivated Centromere 2)


title: Cnp1_wt_cen_spreading_ura4_5


title: Cnp1_mhf2D_cen2_inactive_clr4D_transformation_1

value: mhf2{delta}clr4{delta} (carrying the inactivated Centromere 2)


title: Cnp1_wt_cen_spreading_ura4_3


title: Cnp1_wt_cen_spreading_ura4_2


title: H3K9me2_wt_cen2_inactive_ura4_3


title: Cnp1_mhf2D_cen1_inactive_wt_spore_10

value: mhf2{delta} (carrying the inactivated Centromere 1)


title: Cnp1_wt_cen2_inactive_ura4_3


title: Cnp1_wt_cen_spreading_ura4_1


title: Cnp1_wt_cen2_inactive_ura4_1


title: Cnp1_wt_cen2_inactive_ura4_2


title: Cnp1_wt_cen1_inactive_ura4_7


title: Cnp1_wt_cen1_inactive_ura4_6


title: H3K9me2_mhf2D_cen1_inactive_wt_spore_17


title: H3K9me2_mhf2D_cen1_inactive_wt_spore_13


title: Cnp1_wt_cen1_inactive_ura4_5


title: Cnp1_wt_cen1_inactive_ura4_4


title: Cnp1_wt_cen1_inactive_ura4_2


title: Cnp1_wt_cen1_inactive_ura4_3


title: Cnp1_wt_cen1_inactive_ura4_1


title: Cnp1_mhf2D_cen1_inactive_wt_spore_18


title: Cnp1_mhf2D_cen1_inactive_wt_spore_17


title: Cnp1_mhf2D_cen1_inactive_wt_spore_14


title: Cnp1_mhf2D_cen1_inactive_wt_spore_13


title: Cnp1_mhf2D_cen1_inactive_wt_tetrad_1_1


title: Cnp1_mhf2D_cen1_inactive_wt_tetrad_1_2


title: Cnp1_wt_cen1_inactive_wt_tetrad_2_3


title: Cnp1_wt_cen1_inactive_wt_tetrad_2_1


title: Cnp1_wt_cen1_inactive_wt_tetrad_2_4


title: Cnp1_wt_cen1_inactive_wt_tetrad_1_4


title: Cnp1_wt_cen1_inactive_wt_tetrad_2_2


title: H3K9me2_mhf2D_cen1_inactive_wt_spore_15


title: Cnp1_wt_cen1_inactive_wt_tetrad_1_3


title: Cnp1_wt_cen1_inactive_wt_tetrad_1_2


title: Cnp1_wt_cen1_inactive_wt_tetrad_1_1


title: Cnp1_mhf2D_cen2_inactive_0

value: mhf2{delta} (carrying the inactivated Centromere 2)


title: Cnp1_mhf2_wt_cen1_inactive_0


title: Cnp1_haploid_mhf2_wt_3

value: mhf2+ (meiotic progeny of mhf2{delta}/+)


title: Cnp1_mhf2D_cen1_inactive_clr4D_tetrad_1_3

value: mhf2[delta]clr4[delta] (carrying the inactivated Centromere 2)


title: Cnp1_mhf2D_cen1_inactive_clr4D_tetrad_1_4

value: mhf2+clr4+ (carrying the inactivated Centromere 1)


title: Cnp1_mhf2D_cen1_inactive_wt_spore_15


title: Cnp1_haploid_wip1_wt_1

value: wip1+ (meiotic progeny of wip1{delta}/+)


title: Cnp1_mhf2_wt_cen2_inactive_0

value: log phase


title: Cnp1_haploid_mhf1_wt_1

value: mhf1+ (meiotic progeny of mhf1{delta}/+)


title: Cnp1_mhf2D_cen1_inactive_wt_tetrad_1_4

value: mhf2+ (carrying the inactivated Centromere 1)

value: Cnp1 (gift from Robin Allshire lab)


title: Cnp1_mhf2D_cen1_inactive_wt_tetrad_1_3


title: Cnp1_mhf2D_cen1_inactive_clr4D_tetrad_1_1


title: H3K9me2_mhf2D_cen1_inactive_wt_spore_10

value: mhf2[delta] (carrying the inactivated Centromere 1)


title: Cnp1_mhf2D_cen1_inactive_clr4D_tetrad_1_2


title: H3K9me2_mhf2D_cen1_inactive_wt_spore_11


title: H3K9me2_mhf2D_cen1_inactive_wt_spore_9


title: Cnp1_mhf2D_cen1_inactive_wt_tetrad_2_3


title: Cnp1_mhf2D_cen1_inactive_wt_tetrad_2_1


title: Cnp1_mhf2D_cen1_inactive_wt_tetrad_2_2


title: H3K9me2_wt_cen1_inactive_wt_tetrad_2_3


title: Cnp1_mhf2D_cen1_inactive_wt_tetrad_2_4


title: H3K9me2_mhf2D_cen1_inactive_wt_tetrad_1_4


title: H3K9me2_wt_cen1_inactive_wt_tetrad_2_4


title: Cnp1_haploid_mhf2_wt_1


title: H3K9me2_mhf2D_cen1_inactive_wt_tetrad_1_2


title: H3K9me2_wt_cen1_inactive_wt_tetrad_2_1


title: H3K9me2_mhf2D_cen1_inactive_wt_tetrad_1_3


title: CC_P38_10

city: NICE

first: PASQUALE

last: PENSIERI

address: PARC VALROSE

department: SCIENCES NATURELLES

country: France

institute: INSTITUT BIOLOGIE VALROSE

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Alignment : Reads were mapped onto mm10 assembly of mouse genome using STAR v.2.5.3a
Quantification : Gene Expression was quantified using HTSeq v.0.6.1p1 (union mode) and Ensembl release 93 annotations.
Genome_build: mm10
Supplementary_files_format_and_content: Tabulated text file containing raw read counts in each sample.

growth_protocol: All mice used for this experiment were raised according to the EUROPEAN COMMUNITIES COUNCIL DIRECTIVE of the 22 September 2010 (2010/63/EEC) and to the guideline declared in our Project of Aniaml Experimentation

extract_protocol:
Total RNA was extracted by full retinas using a Tri Reagent (T9424 Sigma) solution according to the manufacturer's protocol
RNA-Seq libraries were generated from 500 ng of total RNA using TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

treatment_protocol: A single dose of a solution tamoxifen/corn oil was injected intraperitonally (5ul/gram of weight of a 10mg/ul stock solution) to promote an efficient KO

value: retina

tag: genotype/variation

value: Otx2 KO

tag: cell type in which ablation occurs

value: photoreceptor

tag: days after ko induction


title: H3K9me2_wt_cen1_inactive_wt_tetrad_1_4

tag: genotype


title: CC_P38_11


title: CC_P34_8


title: CC_P38_12


title: CC_P34_9


title: CC_P34_7


title: H3K9me2_mhf2D_cen1_inactive_wt_tetrad_1_1


title: Cnp1_mhf2D_cen1_inactive_wt_spore_12

value: mhf2+ (carrying Cnp1 spreading)

value: fission yeast haploid cells


title: H3K9me2_wt_cen1_inactive_wt_tetrad_1_3


title: CC_P32_6


title: H3K9me2_wt_cen1_inactive_wt_tetrad_1_2


title: H3K9me2_wt_cen1_inactive_wt_tetrad_2_2


title: CC_P32_4


title: H3K9me2_mhf2_wt_cen2_inactive_1

value: mhf2+ (carrying the inactivated Centromere 2)


title: H3K9me2_mhf2_wt_cen1_inactive_1


title: CC_P30_3

value: control


title: Cnp1_mhf2_wt_cen2_inactive_1


title: K562_EED_KO_D10_3

description:
quantseq_counts.txt
4c3

tag: disease state

value: erythroleukemia

tag: cell line

tag: time

value: Day 10

tag: replicate


title: CC_P30_2

tag: tissue


title: Cnp1_mhf2D_cen2_inactive_1

value: mhf2[delta] (carrying the inactivated Centromere 2)

tag: chip antibody


title: CC_P30_1


title: Cnp1_mhf2_wt_cen1_inactive_1


title: Cnp1_mhf2D_cen1_inactive_1


title: Cnp1_haploid_mhf2D_cen3_inactive_3

value: mhf2[delta] (meiotic progeny of mhf2[delta]/+, carrying the inactivated Centromere 3)


title: CC-seq of Human: top2b-/-, Async, VP16, Rep2

description:
CC-seq map of Top2-DNA CCs
WG28_RPE1_top2b_Asyn_VP16

tag: cell phase

value: Asynchronous


title: Cnp1_haploid_mhf2D_cen2_inactive_2

value: mhf2[delta] (meiotic progeny of mhf2[delta]/+, carrying the inactivated Centromere 2)

value: log phase


title: CC-seq of Human: top2b-/-, G1, UT, Rep2

description:
CC-seq map of Top2-DNA CCs
WG25_RPE1_top2b_G1_UT

value: UT


title: CC-seq of Human: top2b-/-, G1, VP16, Rep2

description:
CC-seq map of Top2-DNA CCs
WG26_RPE1_top2b_G1_VP16


title: CC-seq of Human: WT, Async, VP16, Rep3 (b)

description:
CC-seq map of Top2-DNA CCs
WG24b_RPE1_WT_Asyn_VP16

value: WT


title: CC-seq of Human: top2b-/-, Async, UT, Rep2

description:
CC-seq map of Top2-DNA CCs
WG27_RPE1_top2b_Asyn_UT


title: Cnp1_haploid_mhf2D_cen2_inactive_1

value: Cnp1 (gift from Robin Allshire lab)


title: CC-seq of Human: WT, G1, VP16, Rep2

description:
CC-seq map of Top2-DNA CCs
WG22_RPE1_WT_G1_VP16


title: Cnp1_haploid_mhf1D_cen3_inactive_1

value: mhf1[delta] (meiotic progeny of mhf1[delta]/+, carrying the inactivated Centromere 3)


title: Cnp1_haploid_mhf2D_cen3_inactive_2


title: CC-seq of Human: WT, Async, UT, Rep3 (b)

description:
CC-seq map of Top2-DNA CCs
WG23b_RPE1_WT_Asyn_UT


title: CC_P32_5

value: retina

value: Otx2 KO


title: D. melanogaster  L-DOPA 3

city: Middletown

first: Joseph

last: Coolon

state: CT

address: 52 Lawn Avenue Biology Department

department: Biology

institute: Wesleyan University

description: Lanno_et_al_2019_melanogaster_cuffdiff.txt

data_processing:
FASTQC on each of the 6 raw fastq files
Bowtie2 alignment using the D. sechellia, D. simulans, and D. melanogaster reference genomes available at the time of analysis (Drosophila_sechellia.dsec_caf1.dna.toplevel.fa, Drosophila_simulans.ASM75419v3.dna.toplevel.fa, Drosophila_melanogaster.BDGP6.dna.toplevel.fa)
Cuffdiff for quantification and differential expression analysis using the D. sechellia, D. simulans, and D. melanogaster reference genomes available at the time of analysis (Drosophila_sechellia.dsec_caf1.dna.toplevel.fa, Drosophila_simulans.ASM75419v3.dna.toplevel.fa, Drosophila_melanogaster.BDGP6.dna.toplevel.fa) and gene files available at the time of analysis (Drosophila_sechellia.dsec_caf1.42.gff3, Drosophila_simulans.ASM75419v3.42.gff3, Drosophila_melanogaster.BDGP6.95.gff3) with geometric library normalization
Genome_build: Drosophila_sechellia.dsec_caf1.dna.toplevel.fa
Genome_build: Drosophila_simulans.ASM75419v3.dna.toplevel.fa
Genome_build: Drosophila_melanogaster.BDGP6.dna.toplevel.fa
Supplementary_files_format_and_content: Tab-delimited Cuffdiff output in text format

organism: Drosophila melanogaster

source_name: Whole adults

growth_protocol: Flies were reared on cornmeal medium using a 16:8 light:dark cycle at 20 degrees Celsius

extract_protocol:
Total RNA was extracted from whole female adults using Promega SV Total RNA Isolation System
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Flies were exposed to 10mg/mL L-DOPA mixed into instant Drosophila food or control food for a period of 24 hours

tag: strain

value: whole adult fly


title: CC-seq of Human: WT, G1, UT, Rep2

description:
CC-seq map of Top2-DNA CCs
WG21_RPE1_WT_G1_UT


title: Cnp1_haploid_mhf2D_cen1_inactive_1

value: mhf2[delta] (meiotic progeny of mhf2[delta]/+, carrying the inactivated Centromere 1)


title: D. melanogaster  L-DOPA 2


title: Cnp1_haploid_wip1D_cen2_inactive_1

value: wip1[delta] (meiotic progeny of wip1[delta]/+, carrying the inactivated Centromere 2)


title: Cnp1_haploid_mhf2D_cen3_inactive_1


title: anti-SOX17 TCam-2 #3

city: Bonn

first: Sina

last: Jostes

address: Venusberg Campus 1

department: Department of Developmental Pathology

country: Germany

institute: Institute of Pathology

description: processed data file: SOX17_peakfile.xlsx

data_processing:
Reads were mapped to the human genome (hg38) using CLC Genomics Workbench 12 (Qiagen, Hilden, Germany).
Peak-calling was performed using HOMER (Hypergeometric Optimization of Motif EnRichment) Software (http://homer.ucsd.edu/homer/).
TDF file of merged SOX17 ChIP-seq data for visualization in IGV genome browser.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *_peakfile.xlsx: annotated HOMER peak files (SOX2/SOX17 vs. 2% Input control); Includes only peaks that were identified in all three biological replicates.
TCam-2_SOX17_merged.bam.tdf (for GSM3741719; GSM3741721; GSM3741723); 2102EP_SOX2_merged.bam.tdf (for GSM3741713; GSM3741715; GSM3741717)

source_name: Human testicular germ cell tumour cell line

growth_protocol: TCam-2 cells were cultured in RPMI medium (Thermo Fisher Scientific, Waltham, USA). 2102EP cells were cultured in DMEM medium (Thermo Fisher Scientific). Both media were supplemented with 10% FBS (Thermo Fisher Scientific), 1% penicillin / streptomycin (PAN, Aidenbach, Germany) and 200 mM L-glutamine (PAN).

extract_protocol:
For chromatin preparation of cell lines, 1 x 10e7 cells / immunoprecipitation were fixed for 30 minutes (min) at room temperature (RT) using Diagenode Crosslink Gold (Diagenode, Liège, Belgium). After two washing steps with PBS (Thermo Fisher Scientific) cells were additionally fixed for 10 min in 1% formaldehyde (Applichem, Darmstadt, Germany) and then processed according to the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology, Leiden, Netherlands).
ChIP-seq libraries were generated using the MicroPlex Library Preparation Kit v2 (Diagenode).

tag: cell type

value: Seminoma-like cells


title: hPSC-EC

city: Kyoto

first: Rio

last: Sugimura

state: KYOTO

address: 53 Shogoin

country: Japan

institute: CiRA

data_processing:
Sequencing was performed on an Illumina HiSeq 2500 platform in a 75-base single-end mode.
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat v2.0.13 in combination with Bowtie2 ver. 2.2.3 and SAMtools ver. 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) was calculated using Cufflinks version 2.2.1.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM

source_name: endothelial cells

growth_protocol: endothelial cells were cultured in alpha-MEM supplimented with 15% FBS, 1% insulin-transferrin, 5ng/mL IL7, 10ng/mL FLT-3L, 50ng/mL L-ascorbic acid, 1% L-glut, Pen/Strep.

extract_protocol:
Total RNA was extracted using ISOGEN according to the manufacturer’s protocol.
Library preparation was performed using a TruSeq stranded mRNA sample prep kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Endothelial cells were seeded on 50 ug/mL fibronectin-coat

tag: culture

value: Trans-well cultured with human bone marrow CD34+ cells

value: human pluripotent stem cell-derived endothelial cells


title: anti-SOX17 TCam-2 #2


title: HUVEC

value: endothelial cells


title: 2% Input TCam-2 #3


title: D. melanogaster  L-DOPA 1


title: CC-seq of Human: top2b-/-, G1, VP16, Rep1

description:
CC-seq map of Top2-DNA CCs
WG18_RPE1_top2b_G1_VP16


title: CC-seq of Human: top2b-/-, Async, UT, Rep1

description:
CC-seq map of Top2-DNA CCs
WG19_RPE1_top2b_Asyn_UT


title: Cnp1_haploid_mhf1D_cen2_inactive_1

value: mhf1[delta] (meiotic progeny of mhf1[delta]/+, carrying the inactivated Centromere 2)

tag: cell growth stage


title: 2% Input TCam-2 #2


title: D. melanogaster  Control 3


title: CC-seq of Human: top2b-/-, G1, UT, Rep1

description:
CC-seq map of Top2-DNA CCs
WG17_RPE1_top2b_G1_UT


title: anti-SOX17 TCam-2 #1


title: D. melanogaster  Control 2


title: CC-seq of Human: WT, Async, VP16, Rep2 (b)

description:
CC-seq map of Top2-DNA CCs
WG16b_RPE1_WT_Asyn_VP16

value: Asynchronous


title: D. melanogaster Control 1


title: 2% Input TCam-2 #1


title: CC-seq of Human: WT, Async, UT, Rep2 (b)

description:
CC-seq map of Top2-DNA CCs
WG15b_RPE1_WT_Asyn_UT


title: H3K9me2_haploid_mhf2_wt_3

value: mhf2+ (meiotic progeny of mhf2[delta]/+)

tag: temperature condition


title: H3K9me2_haploid_mhf2_wt_2

value: log phase


title: anti-SOX2 2102EP #3

description: processed data file: SOX2_peakfile.xlsx

value: Embryonal carcinoma-like cells


title: CC-seq of Human: top2b-/-, Async, VP16, Rep1

description:
CC-seq map of Top2-DNA CCs
WG20_RPE1_top2b_Asyn_VP16

tag: treatment


title: CC-seq of Human: WT, G1, VP16, Rep1

description:
CC-seq map of Top2-DNA CCs
WG14_RPE1_WT_G1_VP16

value: WT


title: Adult flies, Space 3 (Space bacteria injected)

city: Moffett Field

first: Rachel

middle: Rene

last: Gilbert

state: CA

department: Space Biosciences

institute: NASA Ames Research Center

description: Space 3

data_processing:
Transcript abundance estimates from the demultiplexed raw sequenced reads were made using kallisto (default settings, version 0.42.4) and the D melanogaster reference transcriptome build  r6.13
Differential expression analysis between space and ground bacteria conditions was performed using sleuth (version 0.30.0) wald test. All other settings default
Transcripts with q-values < 0.05 were considered significantly differentially expressed.
Genome_build: Transcriptome_build: flybase dmel_r6.13
Supplementary_files_format_and_content: spacevsgroundWaldTest.csv

molecule: polyA RNA

source_name: 2 whole organisms pooled

growth_protocol: Flies were cultivated at 25 °C and 50% relative humidity on standard fly food with 12 hour light-dark cycles. To generate synchronized 2 to 3 day old F1 flies, adult flies were allowed to lay for 48 hours in a bottle, then parent flies were discarded, and the bottles with eggs were allowed to grow into adult flies at 25 °C. Flies were collected on day 2 and allowed to mature for 24 hours after collection before injections of the bacteria samples.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit with 2-mercaptoethanol added in triplicate from 2 pooled adult (2-3 day old female) Drosophila melanogaster (w1118) per treatment, with 4 total treatment groups (no injection control, sham injection with PBS, ground bacteria-injected, and space bacteria-injected)
indexed, polyA+ RNA libraries were prepared for sequencing using standard Illumina protocols at the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley

treatment_protocol: 2-3 day old flies were injected in the ventral abdominal segment with 100 nL of sample (no injection control, sham injection with PBS, ground bacteria-injected, and space bacteria-injected). RNA was extracted from live flies 18 hours post-injection.

value: Space sample injected

tag: age

value: 2-3 day old adult

tag: Sex

value: female


title: H3K9me2_haploid_mhf1_wt_2

value: mhf1+ (meiotic progeny of mhf1[delta]/+)


title: Adult flies, Space 2 (Space bacteria injected)

description: Space 2


title: H3K9me2_haploid_mhf1_wt_1


title: anti-SOX2 2102EP #2

description: processed data file: SOX2_peakfile.xlsx


title: Adult flies, Space 1 (Space bacteria injected)

description: Space 1


title: H3K9me2_haploid_wip1_wt_2

value: wip1+ (meiotic progeny of wip1[delta]/+)


title: Adult flies, Ground 3 (Ground bacteria injected)

description: Ground 3

value: Ground sample injected


title: 2% Input 2102EP #2

description: processed data file: SOX2_peakfile.xlsx


title: Cnp1_haploid_wip1D_cen1_inactive_1

value: wip1[delta] (meiotic progeny of wip1[delta]/+, carrying the inactivated Centromere 1)

value: Cnp1 (gift from Robin Allshire lab)


title: H3K9me2_haploid_wip1_wt_1


title: Adult flies, Ground 2 (Ground bacteria injected)

description: Ground 2


title: anti-SOX2 2102EP #1

description: processed data file: SOX2_peakfile.xlsx


title: H3K9me2_haploid_mhf2_wt_1


title: Adult flies, Sham 3 (PBS injection)

description: Sham 3

value: Sham


title: Adult flies, Ground 1 (Ground bacteria injected)

description: Ground 1


title: H3K9me2_diploid_heterozygous_mhf2D_1

source_name: fission yeast diploid cells

value: mhf2[delta]/+ (heterozygous deletion diploid)


title: ADT_0BCZH_input IP

description: ADT sample 0BCZH input

data_processing:
ChIP-seq reads were aligned to the human genome using Burrows-Wheeler Alignment ( BWA) with default parameters in bwa aln and bwa samse
Broad peaks were called using MACS version 2 with the following settings:-B --broad --nomodel --extsize 150 -q 0.01 --broad-cutoff 0.05
Genome_build: hg19
Supplementary_files_format_and_content: BROADPEAK file reports peaks with FDR q <0.05

source_name: active disease, treated

extract_protocol:
Peripheral blood mononuclear cells (PBMC) were separated from neutrophils and red blood cells by density-gradient centrifugation. Red cells were removed from neutrophils by hypotonic lysis. Neutrophils were crosslinked using 1% formaldehyde in 10 ml PBS for 10 min at room temperature. Crosslinking was quenched by adding 1× glycine.
ChIP was performed following the protocol (Cell Signaling Technologies, Inc.). DNA-sequencing was conducted using the Illumina HiSeq 2500.

value: neutrophils

value: Juvenile Idiopathic Arthritis


title: CC-seq of Human: WT, G1, UT, Rep1

description:
CC-seq map of Top2-DNA CCs
WG13_RPE1_WT_G1_UT

value: UT


title: ADT_0BCZH_H3K4me1_ChIPSeq

description: ADT sample 0BCZH H3K4me1

value: Anti-Histone H3 (mono methyl K4) antibody - ChIP Grade (ab8895)


title: Adult flies, Sham 2 (PBS injection)

description: Sham 2


title: H3K9me2_sim3D_1

growth_protocol: Single colonies of each strains  were struck and cultured in YES medium at 29 °C unless specific temperature conditions were indicated (e.g., 26 °C). The cell cultures were harvested when the optical density (OD) reached aound 1.

value: log phase


title: Adult flies, Sham 1 (PBS injection)

description: Sham 1


title: H3K9me2_ams2D_1


title: ADT_0BCZH_H3K27ac_ChIPSeq

description: ADT sample 0BCZH H3K27ac

value: Anti-Histone H3 (acetyl K27) antibody - ChIP Grade (ab4729)


title: H3K9me2_mis18_ts_36_1

value: 26 C shifted to 36 C for 6 h


title: Adult flies, Control 3 (no injection)

description: Control 3

value: Control


title: H3K9me2_mis18_ts_26_1


title: 2% Input 2102EP #3

description: processed data file: SOX2_peakfile.xlsx

value: Embryonal carcinoma-like cells


title: Adult flies, Control 2 (no injection)

description: Control 2

value: 2-3 day old adult

value: female


title: gastric cancer tissues from Pdx-1-Cre;Cdh1F/F;Trp53F/F mice 1

label_protocol: According to the standard Affymetrix protocol

extract_protocol: AllPrep DNA/RNA/Protein Mini Kit according to the manufacturer's instructions.

value: gastric cancer tissues

tag: strain/genotype

value: Pdx-1-Cre;Cdh1F/F;Trp53F/F mice

tag: histology

value: diffuse-type gastric cancer


title: gastric cancer tissues from Pdx-1-Cre;Cdh1F/F;Trp53F/F mice 3


title: gastric cancer tissues from Pdx-1-Cre;Cdh1F/+;Trp53F/F;Smad4F/F mice 4


title: gastric cancer tissues from Pdx-1-Cre;Cdh1F/F;Trp53F/F mice 2


title: 2% Input 2102EP #1

description: processed data file: SOX2_peakfile.xlsx


title: ADT_0B9MX_input IP

description: ADT sample 0B9MX input

tag: disease state


title: gastric cancer tissues from Pdx-1-Cre;Cdh1F/+;Trp53F/F;Smad4F/F mice 2


title: Adult flies, Control 1 (no injection)

description: Control 1


title: H3K9me2_mis16_ts_36_1

tag: genotype


title: ADT_0B9MX_H3K27ac_ChIPSeq

description: ADT sample 0B9MX H3K27ac


title: H3K9me2_mis16_ts_26_1


title: ADT_0BC75_input IP

description: ADT sample 0BC75 input


title: normal gastric epithelium from Pdx1-1-Cre-negative mice 4

value: normal gastric epithelium

value: Pdx1-1-Cre-negative mice

value: normal


title: H3K9me2_mhf2D_2

tag: biological replicate


title: ADT_0BC75_H3K4me1_ChIPSeq

description: ADT sample 0BC75 H3K4me1

value: neutrophils


title: H3K9me2_mhf2D_1


title: ADT_0BC75_H3K27ac_ChIPSeq

description: ADT sample 0BC75 H3K27ac

value: Juvenile Idiopathic Arthritis


title: H3K9me2_cnp3Dfta6D_2


title: H3K9me2_cnp3Dfta6D_1


title: Leaf, YORK.09.10

city: Los Angeles

first: Alayna

last: Mead

address: 4140 Terasaki Life Sciences Building 610 Charles E. Young Drive East

department: Ecology and Evolutionary Biology

institute: University of California, Los Angeles

data_processing:
Raw sequences were converted from qseq to fastq format and reads failing the Illumina quality filter were removed. Used “convert_qseq_to_fastq.py” script here: github.com/alaynamead/RNAseq_scripts
Reads were demultiplexed, allowing for a 1-base mismatch in the barcode sequence. Used “demultiplexer.py” script here: github.com/alaynamead/RNAseq_scripts
Cutadapt 2.3 was used to trim adapters (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT) and low quality ends using a cutoff quality score of 27 (-q27,27) and reads shorter than 30 bp after trimming were removed (--minimum-length 30).
Reads were mapped to the Quercus lobata genome v3.0 using STAR 2.7.1.
Reads which mapped to multiple locations within the genome (quality score < 255) were removed using Samtools 1.9.
The Picard 2.20.3 MarkDuplicates function was used to identify duplicate reads, and the sequencing-platform artifact duplicates were removed.
The number of reads mapping to each gene was obtained using the HTSeq 0.11.1 htseq-count function.
Genome_build: Quercus lobata genome v3.0 (NCBI  accession # LRBV00000000)
Supplementary_files_format_and_content: Raw counts of sequenced reads for each gene.

organism: Quercus lobata

source_name: leaf

growth_protocol: Acorns were planted in the UCLA Plant Growth Center on December 20, 2017. Seedlings were watered as needed and periodically sprayed with fungicide to control powdery mildew. Experiment began when seedlings were 5 months old.

extract_protocol:
Leaf tissues were flash frozen in liquid nitrogen and ground using a Mixer Mill MM301 (Retsch, Germany). Powdered tissues were transferred to cold 2mL tubes and 1.8 mL of cold RNA Extraction Buffer + DTT was added. RNA Extraction Buffer consists of 8 M Urea, 3 M LiCl, 1% polyvinylpyrrolidone K-60, 5 mM DTT (added just before use, 1M stock). The tubes were then vortexed for 30 seconds, incubated at 4°C for 30 minutes, then centrifuged at 4°C for 30 minutes at 20,000 rcf. The supernatant was discarded and the pellet was used as the starting material for the Spectrum Plant Total RNA kit, protocol A, adding 750uL of Binding Solution, and performing on-column DNase I digestion.
RNAseq libraries were constructed using the TruSeq RNA Library Prep Kit v2 following the Low Sample (LS) Protocol in the TruSeq RNA Sample Preparation v2 Guide.

treatment_protocol: Treated seedlings were sprayed with a solution of 50 µM 5-Azacytidine in TWEEN 20; control seedlings were sprayed with TWEEN 20. Seedlings were sprayed for 27 days.

value: control

tag: family

tag: individual


title: CC-seq of S. cerevisiae Spo11: sae2, meiosis, BioRep3, TechRep1

description:
3_MJ315_sae2_6h
CC-seq map of Spo11-DNA CCs.

data_processing:
Library strategy: CC-seq
Paired end reads that passed filter were aligned to Cer3H4L2 (https://github.com/Neale-Lab) using bowtie2 (options: -X 1000 --no-discordant --very-sensitive --mp 5,1 --np 0), using MAPQ0 settings.
SAM files processed via terminalMapper (Perl, v5.22.1; https://github.com/Neale-Lab) that computes the coordinates of the protein-linked 5’-terminal nucleotide.
Data were filtered to exclude long terminal repeats, retrotransposons, telomeres, and the rDNA.
Genome_build: Cer3H4L2 (https://github.com/Neale-Lab)
Supplementary_files_format_and_content: FullMap files containing sparsely-formatted, 1bp histograms detailing the total number of Watson (+) and Crick (-) hits for all mapped base-pairs. 4-column format (Chr, Pos, Watson, Crick).

organism: Saccharomyces cerevisiae

growth_protocol: Cells were grown overnight to saturation in 4 ml YPD medium (1% yeast extract, 2% peptone, 2% glucose supplemented with 0.5 mM adenine and 0.4 mM uracil) at 30 ˚C, then diluted to OD600 0.2 in 200 ml YPA medium (1% yeast extract, 2% peptone, 1% potassium acetate) and grown vigorously for 15 h at 30 ˚C.

extract_protocol:
1x10e9 yeast cells were treated as described above, then spheroplasted in 1.5 ml spheroplasting buffer (1 M sorbitol, 50 mM NaHPO4 buffer pH 7.2, 10 mM EDTA) containing 200 μg/ml Zymolyase 100T (AMS Biotech) and 1% β-mercaptoethanol (Sigma) for 20 min at 37 ˚C. 2 µL Protease Inhibitor Cocktail and 2 µL Pefabloc (Sigma) were added before splitting into five aliquots of 400 µL. 1 ml ice-cold ethanol was added to 400 µL cell suspensions in microcentrifuge tubes in order to rapidly denature proteins in situ, mixed, incubated for 10 min on ice, and pelleted by centrifugation. The supernatant was thoroughly removed by aspiration, prior to addition of 200 µL 1x STE buffer (2% SDS, 0.5 M Tris pH 8.1, 10 mM EDTA, 0.05% bromophenol blue), cell disruption using a pestle (VWR), addition of a further 400 µL 1x STE buffer, and incubation for 10 min at 65 ˚C. Samples were cooled on ice and 500 µL Phenol-Chloroform-isoamyl alcohol (25:24:1; Sigma) was added. The mixtures were emulsified by shaking and pipetting 5 times with a 1 ml micropipette, prior to phase separation by centrifugation at 20,000 g for 20 min. By minimising mechanical shearing of the lysate prior to phenol chloroform extraction, peptides that are covalently linked to high molecular weight DNA segregate into the aqueous phase alongside other purified nucleic acids. Free protein, coated in SDS, will partition to the interphase. 500 µL of the aqueous phase was removed to a clean microcentrifuge tube, taking care not to disturb the interphase, and nucleic acids were precipitated with 1 ml ice-cold ethanol, pelleted by centrifugation, washed with ice-cold 70% ethanol, and dissolved in TE buffer overnight at 4 ˚C. Samples were then incubated with 0.2 mg/ml RNase A (Sigma) for 1 h at 37 ˚C; nucleic acids were precipitated with 1 ml ethanol, pelleted by centrifugation, washed twice with 70% ethanol and dissolved in TE overnight. Aliquots of nonproteolysed DNA were combined to a total of 1 ml and sonicated to an average fragment size of 300-400 bp with Covaris (duty cycle: 10%, intensity/peak power incidence: 75W, cycles/burst: 200, time: 15 min). 1 ml of sonicated sample was diluted to reduce viscosity by addition of 1 ml TE. Triton-X100, N-Lauroylsarcosine sodium salt and NaCl were then added to complete the binding buffer (final concentrations: 0.3 M NaCl, 0.2% Triton-X100, 0.1% N-Lauroylsarcosine sodium salt). Each sample was divided over several Miniprep (QIAGEN) silica-fibre membrane spin columns, such that the total DNA loaded to each was approximately 20 µg. Under these high salt conditions, protein, but not nucleic acids, bind to the silica membrane, leading to selective retention of any covalent complexes (CCs.). The flowthrough was reapplied to the column to improve yield. Columns were washed 6 times with 600 µL of TEN (10 mM Tris, 1 mM EDTA, 0.3 M NaCl) per 1 min wash to remove any residual non-CC DNA fragments, prior to elution with 100 µL TES (10 mM Tris, 1 mM EDTA, 0.5% SDS). The SDS detergent in the elution buffer releases interactions between protein and silica, thereby releasing bound CCs..
Eluted products were pooled to 500 µL in TES and incubated with 1 mg/ml Proteinase K (Sigma) for 30 min at 60 ˚C, prior to overnight ethanol precipitation at -80 ˚C with 1.41 ml ethanol, 0.2 mg/ml glycogen and 200 mM NaOAc. The DNA-glycogen precipitate was pelleted by centrifugation at 20,000 g for 1 hr at 4 ˚C, washed once with 1.5 ml 70% ethanol, and re-pelleted by centrifugation. The supernatant was aspirated and the pellet was air-dried for 10 min at RT, prior to solubilisation in 52 µL 10 mM Tris-HCl. DNA concentration was measured in a 2 µL sample with the Qubit (ThermoFisher) and High Sensitivity reagents. The remaining 50 µL was used as input for one round of end repair and adapter ligation with NEBNext Ultra II DNA Library Preparation kit (NEB), according to manufacturer’s instructions, except for the use of a custom P7 adapter (see table). The use of custom adapters is to allow differentiation of the sheared end (P7 adapter) from the Top2/Spo11 end (P5 adapter). After ligation of the P7 adapter, DNA was isolated with AMPure XP beads (Beckman Coulter) according to manufacturer’s instructions (beads:input of 78:90) and eluted in 50 µL 10 mM Tris-HCl. Samples were diluted 2-fold with 50 µL Tdp2 reaction buffer (100 mM TrisOAc, 100 mM NaOAc, 2 mM MgOAc, 2 mM DTT, 200 µg/ml BSA) and incubated with 3 µL of 10 µM recombinant human TDP2, for 1 h at 37 ˚C. DNA was isolated again with AMPure XP beads (beads:input of 103:103) and eluted in 52 µL 10 mM Tris-HCl. Next, a second round of adapter ligation was conducted using adapter P5 (see table), without prior end repair in order to prevent dephosphorylation of DNA 3’-phosphate termini which may be generated by TDP2 activity on 3’-CCs. After ligation of the P5 adapter to the Top2/Spo11-cleaved end, DNA was isolated with AMPure XP beads (beads:input of 78:90) and eluted in 17 µL 10 mM Tris-HCl. DNA concentration was measured in 2 µL using the Qubit. The remaining 15 µL was used as template for the PCR step of the NEBNext Ultra II PCR step using universal primer (P5 end) and indexed primers for multiplexing (P7 end), according to manufacturer's instructions. PCR reactions were diluted with 50 µL 10 mM Tris-HCl, DNA was isolated with AMPure XP beads (beads:input of 84:100) and eluted in 30 µL 1 mM Tris-HCl pH 8.1. Samples were then subjected to 200-600 bp size selection using the BluePippin (Sage Science), prior to quantification of molarity using the Bioanalyzer (Agilent).

treatment_protocol: Cells were then washed with water, resuspended in 200 ml sporulation medium (2% potassium acetate supplemented with diluted amino acids), incubated vigorously for 6 h at 30 ˚C.

value: meiosis


title: Cnp1_mhf2D_cen1_inactive_wt_spore_16

value: mhf2+ (carrying Cnp1 spreading)

value: log phase

tag: chip antibody

value: Cnp1 (gift from Robin Allshire lab)

tag: tissue

value: fission yeast haploid cells


title: CC-seq of S. cerevisiae Spo11: sae2, meiosis, BioRep5, TechRep1

description:
7B_MJ315_sae2_6h
CC-seq map of Spo11-DNA CCs.

tag: strain

tag: cell phase


title: CC-seq of S. cerevisiae Spo11: sae2, meiosis, BioRep4, TechRep1

description:
5_MJ315_sae2_6h
CC-seq map of Spo11-DNA CCs.


title: Leaf, YORK.09.08


title: Leaf, YORK.09.03


title: normal gastric epithelium from Pdx1-1-Cre-negative mice 2


title: gastric cancer tissues from Pdx-1-Cre;Cdh1F/+;Trp53F/F;Smad4F/F mice 3


title: gastric cancer tissues from Pdx-1-Cre;Cdh1F/+;Trp53F/F;Smad4F/F mice 1


title: CC-seq of S. cerevisiae Spo11: sae2, meiosis, BioRep5, TechRep2

description:
7C_MJ315_sae2_6h
CC-seq map of Spo11-DNA CCs.


title: CC-seq of S. cerevisiae Spo11: sae2, meiosis, BioRep2, TechRep1

description:
2A_MJ315_sae2_6h
CC-seq map of Spo11-DNA CCs.


title: normal gastric epithelium from Pdx1-1-Cre-negative mice 1


title: H3K9me2_cnp3D_1


title: Leaf, YORK.09.37


title: ADU_0B9ZK_H3K27ac_ChIPSeq

description: ADU sample 0B9ZK H3K27ac

source_name: active disease, untreated

tag: cell type

value: Anti-Histone H3 (acetyl K27) antibody - ChIP Grade (ab4729)


title: H3K9me2_fta6D_1

tag: cell growth stage


title: normal gastric epithelium from Pdx1-1-Cre-negative mice 3


title: Leaf, LAY.15.34


title: ADU_0BA0X_input IP

description: ADU sample 0BA0X input


title: CC-seq of S. cerevisiae Spo11: sae2, meiosis, BioRep1, TechRep1

description:
1_MJ315_sae2
CC-seq map of Spo11-DNA CCs.


title: Leaf, LAY.15.30


title: CC-seq of S. cerevisiae Spo11: sae2spo11y-f, meiosis, BioRep1, TechRep1

description:
1B_MJ319_sae2spo11YF_6h
CC-seq map of Spo11-DNA CCs.


title: ADU_0B9ZK_input IP

description: ADU sample 0B9ZK input


title: ADU_0B9ZK_H3K4me1_ChIPSeq

description: ADU sample 0B9ZK H3K4me1

value: Anti-Histone H3 (mono methyl K4) antibody - ChIP Grade (ab8895)


title: sum1[delta]-KO rep2

description: Sum1 knockout replicate 2

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 Kluyveromyces lactis whole genome using tophat v2.0.10 default parameters
Fragments Per Kilobase of exon per million fragments mapped (FPKM) were calculated using cuffnorm v2.2.1.
Genome_build: Kluyveromyces lactis
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Kluyveromyces lactis

source_name: Rusche laboratory

growth_protocol: Overnight cultures grown in YPD were diluted to an OD of 0.3 in YPD. The cultures were incubated at 30C with shaking until an OD of 1

extract_protocol:
Hot phenol treatment was used to harvest total RNA. Turbo Dnase (Life technologies) was used to remove DNA. Samples were concentrated using a Qaigen RNA column.
RNA samples were processed for sequencing using the TruSeq non-stranded RNA Library Prep Kit (Illumina), and 50 bp single end sequencing was performed on an Illumina HiSeq 2500 machine at SUNY Buffalo gemonics core facility.

treatment_protocol: 10 OD of cells were harvested by centrifugation and washed in AE buffer (50mM NaOAc pH 5.3 and 10mM EDTA).

value: early log phase yeast cells

value: MATa sum1[delta] hmr[delta] hml[delta]


title: ADU_0BA0X_H3K4me1_ChIPSeq

description: ADU sample 0BA0X H3K4me1


title: H3K9me2_sim4_ts_36_1

tag: temperature condition

value: 26 C shifted to 36 C for 6 h


title: Leaf, LAY.15.09

tag: treatment


title: Leaf, LAY.15.03


title: H3K9me2_mal2_ts_36_1


title: sum1[delta]-KO rep1

description: Sum1 knockout replicate 1


title: Leaf, HV.11.40


title: sir4[delta]-KO rep1

description: Sir4 knockout replicate 1

value: MATa sir4[delta] hmr[delta] hml[delta]


title: sir4[delta]-KO rep2

description: Sir4 knockout replicate 2


title: ADU_0BA0X_H3K27ac_ChIPSeq

description: ADU sample 0BA0X H3K27ac


title: Leaf, HV.11.34


title: H3K9me2_mal2_ts_26_1


title: Leaf, HV.11.33


title: H3K9me2_mis15_ts_26_1


title: sir2[delta]-KO rep1

description: Sir2 knockout replicate 1

value: MATa sir2[delta] hmr[delta] hml[delta]


title: sir2[delta]-KO rep2

description: Sir2 knockout replicate 2


title: Leaf, HV.11.05


title: WT rep1

description: Wildtype replicate 1

value: MATa SIR2 hmr[delta] hml[delta]


title: H3K9me2_mis12_ts_36_1


title: D. sechellia L-DOPA 3

organism: Drosophila sechellia

value: whole adult fly


title: H3K9me2_mis12_ts_26_1


title: H3K9me2_sim4_ts_26_1


title: H3K9me2_nuf2_ts_36_1


title: D. simulans L-DOPA 3

organism: Drosophila simulans


title: D. sechellia L-DOPA 2


title: D. simulans L-DOPA 2


title: H3K9me2_nuf2_ts_26_1


title: D. simulans L-DOPA 1


title: DFT-input

organism: Sarcophilus harrisii

source_name: facial tumor

value: facial tumor

tag: cell line


title: DFT-H3K27ac_ChIP

value: H3K27ac (ab4729, Abcam)


title: D. sechellia L-DOPA 1


title: WT rep2

description: Wildtype replicate 2


title: D. simulans Control 3


title: D. sechellia Control 3


title: D. sechellia Control 2


title: D. simulans Control 2


title: DFT-H3K27me3_ChIP

value: H3K27me3 (C37B11, Cell Signaling)


title: DFT-H3K4me3_ChIP

value: H3K4me3 (ab8580, Abcam)


title: D. sechellia Control 1


title: D. simulans Control 1


title: H3K9me2_mis15_ts_36_1


title: CTX_SST_1

status: Public on Sep 27 2019

city: Boston

middle: Aurel

last: Nagy

state: Massachusetts

address: 220 Longwood Ave

department: Department of Neurobiology

institute: Harvard Medical School

data_processing:
ATAC-seq alignment: All ATAC-seq libraries were sequenced on the Nextseq 500 benchtop DNA sequencer (Illumina). Seventy-five base pair (bp) single-end reads were obtained for all datasets. ATAC-seq experiments were sequenced to a minimum depth of 20 million (M) reads. Reads for all samples were aligned to the mouse genome (GRCm38/mm10, December 2011) using default parameters for the Subread (subread-1.4.6-p3, (Liao et al., 2013)) alignment tool after quality trimming with Trimmomatic v0.33 (Bolger et al., 2014) with the following command: java -jar trimmomatic-0.33.jar SE -threads 1 -phred33 [FASTQ_FILE] ILLUMINACLIP:[ADAPTER_FILE]:2:30:10 LEADING:5 TRAILING:5 SLIDINGWINDOW:4:20 MINLEN:45. Nextera adapters were trimmed out for ATAC-seq data. Duplicates were removed with samtools rmdup. To generate UCSC genome browser tracks for ATAC-seq visualization, BEDtools was used to convert output bam files to BED format with the bedtools bamtobed command. Published mm10 blacklisted regions (Consortium, 2012) were filtered out using the following command: bedops –not-element-of 1 [BLACKLIST_BED]. Filtered BED files were scaled to 20 M reads and converted to coverageBED format using the BEDtools genomecov command. bedGraphToBigWig (UCSC-tools) was used to generate bigWIG files for the UCSC genome browser.
ATAC-seq peak calling and quantification: Two independent peak calling algorithms were employed to ensure robust, reproducible peak calls. First, tag directories were created using HOMER makeTagDirectory for each replicate, and peaks were called using default parameters for findPeaks with -style factor. MACS2 was also called using default parameters on each replicate. The summit files output by MACS2 were converted to bed format and each summit extended bidirectionally to achieve a total length of 300 bp. As the ATAC-seq peak calls would ultimately be used to narrow down potential regulatory elements for screening of a limited subset, we applied the overly stringent requirement that a peak be called by both approaches in a given replicate for its inclusion in the final peak list for that sample. Peaks identified in any sample in this way were aggregated to produce a final superset of 323,369 regulatory elements called as accessible in at least one cell type. The featurecounts package was used to obtain ATAC-seq read counts for each of these accessible putative GREs.
indrop processing: The published inDrops mapping pipeline (github.com/indrops/indrops) was used to assign reads to cells. To map viral sequences, a custom annotated transcriptome was generated using the indrops pipeline build_index command supplied with the following newly generated reference files: a custom genome with one additional contig comprising a shared 5' sequence (gcatcgataccgagcgcgcgatcgc), the given 10 bp barcode, and a shared 3' sequence (tcgagagatctgtgatagcggc) was appended to the GRCm38.dna_sm.primary_assembly.fa genome file for each cloned GRE. These sequences were also appended GRCm38.88.gtf gene annotation file, with all sequences assigned the same gene_id and gene_name, but unique transcript_id, transcript_name, and protein_id. After inDrops pipeline mapping and cell deconvolution, the pysam package was used to extract the 'XB' and 'XU' tags, which contain cell barcode and UMI sequences, respectively, from every read that mapped uniquely to any one of the custom viral contigs (i.e. requiring the read map to the 10 bp barcode with at most 1 mismatch) in the inDrops pipeline-output bam files. These barcode-UMI combinations were condensed to generate a final cell x GRE barcode UMI counts table for each sample.
Genome_build: mm10 (GRCm38) with GRCm38.88.gtf; for PESCA screen, custom mm10 build with viral contigs used
Supplementary_files_format_and_content: 180319_PESCA.yaml: YAML file for indrops pipeline mapping of these samples; 180320_[SAMPLE_ID]_WITH_BARCODES.counts.tsv.gz: cells by UMIFM counts tables for each sample, with viral barcode counts; macs_homer_intersect_[SAMPLE_ID].bed: bed peak files showing peaks that survived intersection filter between MACS2 and HOMER peak calling approaches for each sample, with 4th column containing MACS2 -log10(pvalue); atac_master_binary_peak_table.csv: list of genomic coordinates for all peaks called in any of the input ATAC datasets, as well as binary table showing whether a peak was called in each replicate of SST, PV, or VIP ATAC-seq experiments; atac_master_counts.csv: featureCounts derived, unnormalized table of reads detected within each ATAC-seq peak for SST, PV, and VIP ATAC-seq experiments; annotated_gres.csv: list of 287 elements cloned into PESCA screen, as well as genomic annotation, closest TSS, and GRE sequence

source_name: cortex

extract_protocol: We crossed Sst-IRES-Cre (The Jackson Laboratory Stock # 013044), Vip-IRES-Cre (The Jackson Laboratory Stock # 010908) and Pv-Cre (The Jackson Laboratory Stock # 017320) with SUN1-2xsfGFP-6xMYC (The Jackson Laboratory Stock # 021039) and used adult (6-12 wk old) male and female F1 progeny. Nuclear purifications were performed from whole cortex of adult mice as previously described using anti-GFP antibodies (Fisher G10362). Isolated nuclei were gently resuspended in cold L1 buffer (50 mM Hepes pH 7.5, 140 mM NaCl, 1 mM EDTA, 1 mM EGTA, 0.25% Triton X-100, 0.5% NP40, 10% Glycerol, protease inhibitors), and pelleted at 800g for 5 minutes at 4°C. DNA libraries were prepared from the nuclei using the Nextera DNA Library Prep Kit (Illumina) according to manufacturer’s protocols.  The final libraries were purified using the Qiagen minelute kit and sequenced on a Nextseq 500 benchtop DNA sequencer (Illumina). 2 replicates were generated and sequenced for each mouse strain.

tag: virus

value: uninjected

tag: age

tag: Sex

value: male


title: CTX_SST_2


title: CTX_VIP_1


title: CTX_VIP_2


title: CTX_PV_1


title: 6-19

source_name: visual cortex

extract_protocol: For PESCA screening we used adult (6-10 wk) C57BL/6J (The Jackson Laboratory, Stock # 000664) mice. Animals were anesthetized with isofluorane (1–3% in air) and placed on a stereotactic instrument (Kopf) with a 37°C heated pad. The PESCA library (AAV9, 1.9 x 1013 genome copies/mL) was stereotactically injected in V1 (800 nL per site at 25 nL/min) using a sharp glass pipette (25-45 μm diameter) that was left in place for 5 min prior to and 10 min following injection to minimize backflow. Two injections were performed per animal at coordinates 3.0 and 3.7 mm posterior, 2.5 mm lateral relative to bregma, and 0.6 mm ventral relative to the brain surface. Individual rAAV-GRE constructs were stereotactically injected at a titer of 1 x 1011 genome copies/mL. (250 nL per site at 25 nL/min).  All injections were performed at two depths (0.4 and 0.7 mm ventral relative to the brain surface) to achieve broader infection across cortical layers. The injection coordinates relative to bregma were 3.0 or 3.7 mm posterior, 2.5 or -2.5 mm lateral. Single-nuclei suspensions were generated as described previously(1)  , with minor modifications. V1 was dissected and placed into a Dounce with homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH, pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors). The sample was homogenized using a tight pestle with 10 stokes. IGEPAL solution (5%, Sigma) was added to a final concentration of 0.32%, and 5 additional strokes were performed. The homogenate was filtered through a 40-μm filter, and OptiPrep (Sigma) added to a final concentration of 25% iodixanol.  The sample was layered onto an iodixanol gradient and centrifuged at 10,000g for 18 minutes as previously described1,2  . Nuclei were collected between the 30% and 40% iodixanol layers and diluted to 80,000-100,000 nuclei/mL for encapsulation. All buffers contained 0.15% RNasin Plus RNase Inhibitor (Promega) and 0.04% BSA. Single nuclei were captured and barcoded whole-transcriptome libraries prepared using the inDrops platform as previously described(5, 6), collecting five libraries of approximately 3,000 nuclei from each animal. For enrichment of virally-derived transcripts, a fraction (3 μL) of the amplified RNA intermediate was reverse transcribed with random hexamers without prior fragmentation. PCR was next used to amplify virally derived transcripts. The forward primer was designed to introduce the R1 sequence and anneal to a sequence uniquely present 5’ of the viral-barcode sequence present in the viral transcripts (5’- GCATCGATACCGAGCGC). The reverse primer was designed to anneal to a sequence present 5’ of the cell-barcode (5’- GGGTGTCGGGTGCAG). The result of the PCR is preferential amplification of the viral-derived transcripts, while simultaneously retaining the cell-barcode sequence necessary to assign each transcript to a particular cell/nucleus. Following PCR amplification (18 cycles, Hot Start High-Fidelity Q5 polymerase) all the libraries were indexed, pooled, and sequenced on a Nextseq 500 benchtop DNA sequencer (Illumina).

value: SST PESCA AAV9


title: Normal 2

city: Changsha

first: Feng

last: Zhang

state: Hunan

address: 139 Renmin Middle Road, Furong District

institute: The Second Xiangya Hospital

description: lncRNA expression data from donator's trabecular meshwork

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human IncRNA Arrays, and incubated for 17 hours at 65℃ in an Agilent Hybridization Oven

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (G2505C)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 4 out of 8 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Pathway analysis and GO analysis were applied to determine the roles of these differentially expressed mRNAs played in these biological pathways or GO terms. Hierarchical Clustering and combined analysis were performed using in-house scripts

source_name: Normal

label_protocol: 1ug RNA used for labeling and were performed according to the Agilent One-Color Mircroarray-Based Gene Expression Analysis Protocol (Agilent Technology)

growth_protocol: Normal Controls and POAG patients' trabecular meshwork

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

treatment_protocol: Trabecular meshwork from surgery were collected and preseved at -80℃

tag: diagnosis

value: Normal

value: Trabecular meshwork

tag: gender

value: Male


title: Normal 3


title: POAG 4

description: lncRNA expression data from POAG patient's trabecular meshwork

source_name: POAG

value: POAG

value: Female


title: POAG 2


title: Normal 1


title: Normal 4


title: POAG 1


title: CTX_PV_2


title: POAG 3


title: H3K9me2_wt_cen1_inactive_wt_tetrad_1_1

tag: genotype

value: log phase


city: Chicago

first: Riyue

last: Bao

state: IL

address: 900 E 57 Street

department: Center for Research Informatics

institute: University of Chicago

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM224.MS_naive_active.E6, Clinically active relapsing/remitting MS, long-term treatment (8MU)

hyb_protocol: The fragmented and labeled single stranded cDNA was hybridized to Human Clariom D array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin in an Affymetrix Fluidics Station 450 according to Affymetrix  GeneChip WT Plus Reagent Kit guide (Thermo Fisher Scientific, Inc).

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL. intensity files were generated by GeneChip Command Console Software (AGCC, Thermo Fisher Scientific, Inc).  The Cel. files were then used to analyze the data with TAC console (Affymetrix).

data_processing: Raw CEL files were imported, log2-transformed, and normalized using GC Correction and Space Transformation Robust Multi-array Average (GC-STT-RMA) algorithms in Affymetrix Power Tools (APT, version 1·17·0).

source_name: Human peripheral blood mononuclear cells

label_protocol: 250 ng of total RNA was used to generate double stranded cDNA and cRNA. 5.5ug of single stranded cDNA synthesized from cRNA was fragmented and biotin labeled according to Affymetrix  GeneChip WT Plus Reagent Kit manual (Thermo Fisher Scientific, Inc).

growth_protocol: mononuclear cells, extracted on ficoll gradients

extract_protocol: Total RNA extracted, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN).  Before affymetrix genechip Human ClariomD microarray analysis, the quality and quantity of each RNA sample were checked using a 2100 BioAnalyzer (Agilent, inc). High-quality RNA (RNA integrity number>9.0) was used for whole transcript microarray analysis

treatment_protocol: Blood obtained before, and 4 and 24  h after, in vivo injection of 8 or 16 million units (250 or 500 micrograms)) of interferon-b, subcutaneous.

value: peripheral blood mononuclear cells


description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM210.MS_naive_stable.D2, Clinically stable relapsing/remitting MS,.0u, long-term treatment (8MU)


description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM219.MS_naive_active.E1, Clinically active relapsing/remitting MS, long-term treatment (8MU)


description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM213.MS_naive_stable.D5, Clinically stable relapsing/remitting MS,.0u, long-term treatment (8MU)


description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM215.MS_naive_stable.D7, Clinically stable relapsing/remitting MS,.0u, long-term treatment (8MU)


description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM221.MS_naive_active.E3, Clinically active relapsing/remitting MS, long-term treatment (8MU)


description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM222.MS_naive_active.E4, Clinically active relapsing/remitting MS, long-term treatment (8MU)


description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM216.MS_naive_stable.D8, Clinically stable relapsing/remitting MS,.0u, long-term treatment (8MU)


description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM225.MS_naive_active.E7, Clinically active relapsing/remitting MS, long-term treatment (8MU)


description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM226.MS_naive_active.E8, Clinically active relapsing/remitting MS, long-term treatment (8MU)


description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM227.MS_naive_active.E9, Clinically active relapsing/remitting MS, long-term treatment (8MU)


description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM218.MS_naive_stable.D10, Clinically stable relapsing/remitting MS,.0u, long-term treatment (8MU)


description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM220.MS_naive_active.E2, Clinically active relapsing/remitting MS, long-term treatment (8MU)


title: SM202.Healthy_Control.C2

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM202.Healthy_Control.C2


title: SM204.Healthy_Control.C4

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM204.Healthy_Control.C4


title: SM208.Healthy_Control.C8

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM208.Healthy_Control.C8


description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM212.MS_naive_stable.D4, Clinically stable relapsing/remitting MS,.0u, long-term treatment (8MU)


title: SM207.Healthy_Control.C7

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM207.Healthy_Control.C7


title: SM206.Healthy_Control.C6

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM206.Healthy_Control.C6


description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM209.MS_naive_stable.D1, Clinically stable relapsing/remitting MS,.0u, long-term treatment (8MU)


title: SM203.Healthy_Control.C3

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM203.Healthy_Control.C3


title: SM201.Healthy_Control.C1

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM201.Healthy_Control.C1


title: SM200.Partial_Responder.B15, Clinically stable MS, 16MU IFN-beta (500 ug), 24  h after IFN-beta injection

description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM200.Partial_Responder.B15, Clinically stable MS, 16MU (16 million units IFN-b (500 ug)), 24  h after IFN-b injection


description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM211.MS_naive_stable.D3, Clinically stable relapsing/remitting MS,.0u, long-term treatment (8MU)


description:
Total RNA was extracted from each sample, reverse-transcribed, and amplified using the RNeasy Reagent Kit (QIAGEN, Valencia, CA).  Quantitation and integrity of total RNA samples was measured by Agilent 2100 Bioanalyzer. RNA Integrity Number was calculated based on the entire electrophoretic trace of the RNA sample to evaluate the presence or absence of degradation products. Samples were randomized and then 100 ng RNA was hybridized to GeneChip® Human Transcriptome Arrays (HTA) 2·0 according to manufacturer’s instructions (Affymetrix, Santa Clara, CA). One sample with only 60 ng of RNA was assayed with no degradation in signal. HTA identify a broad dynamic range of expression in protein-coding RNAs, long non-coding RNAs (lncRNA, >200bp), and other RNA biotypes, and detect very low-level signals such as lncRNAs and RNAs coding for cytokines and neuroprotective genes.
SM223.MS_naive_active.E5, Clinically active relapsing/remitting MS, long-term treatment (8MU)