title: MYOG.FL.5.1.B11.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
MYOG_FL_cycle4_Protein5_B11_S1175_L007

value: MYOG


title: NCOA3.DBD.1.1.C8.cycle3

status: Public on Oct 28 2020

type: SRA

city: La Jolla

first: Yunjiang

last: Qiu

state: CA

address: 9500 Gilman Drive

country: USA

institute: University of California, San Diego

description:
processed data file:
pbs.obs_pval05.tsv
NCOA3_DBD_cycle3_Protein1_C8_S32_L001

library_source: genomic

data_processing:
ChIP-seq: Reads were aligned using BWA MEM with either single-end or pair-end model to the hg19 reference genome. Reads with low mapping quality (mapq<10) were filtered out, and PCR duplicates were removed using Picard tool. MACS2 were then applied to call peaks and generate signals to view in the genome browser.
STARR-seq:STARR-seq reads were aligned to the oligo libraries using BWA with default parameters. Read counts for each oligos were then counted using custom scripts. Counts for technical replicates were merged. Oligos were filtered to keep only oligos covered by more than 25 reads in the input library and more than five reads in at least three libraries.
Hi-C:Briefly, each end of read pairs were aligned separately using BWA MEM to the hg19 reference genome with default parameters. Chimeric read ends were further processed to keep only the five-prime alignment. Read ends with low mapping quality (mapq<10) were removed, and remaining read ends were paired using custom scripts. PCR duplicates were removed using Picard tool (http://broadinstitute.github.io/picard). Aligned reads were further transformed to the juicer format and processed into hic format using juicebox tool. Chromatin loops were called using Hiccups with default parameters.
WGS:Reads from whole genome sequencing (WGS) were aligned using BWA MEM in pair-end model with default parameters. PCR duplicates were removed using Picard tools (http://broadinstitute.github.io/picard). Variants were then called according to the GATK best practice pipeline using GATK 3.6-0.
RNA-seq:Reads were aligned to the hg19 reference genome using STAR 2.4.2a with default parameters in pair-end model. Only uniquely aligned reads were kept for further analysis. Cufflinks 2.2.1 was used to compute FPKM for each gene.
SELEX:Sequencing data of each HT-SELEX cycle was aligned to the oligo library using BWA. More specific details to identify pbSNPs can be found in methods of associated manuscript.
Genome_build: hg19
Supplementary_files_format_and_content:
ChIP-seq: Peak files in narrowPeak format and signal files in bigWig format for each samples were provided.
STARR-seq:Counts for each STARR-seq experiments were provided.
Hi-C:Juicebox hic format contains contact matrices in multiple resolutions and list of loops in text format were provided.
WGS:VCF file for all variants and phased variants in HepG2 cells were provided.
RNA-seq:Text files including FPKM values for all genes in each sample were provided.
SELEX:Text file summarizing measurements of allelic TF binding to all SNPs tested was included.

molecule: genomic DNA

organism: synthetic construct

source_name: Synthesized DNA

growth_protocol: The HEK293T cells (ATCC, CRL-3216) and HepG2 (ATCC, HB-8065) cells were cultured under normal condition with 5% CO2 at 37°C.

extract_protocol:
ChIP-seq:   Briefly, the cells were crossed linked with 1% formaldehyde at ambient temperature for 10 min. The reaction was quenched by 125mM glycine for 5 min at room temperature. Cells were washed with PBS and treated with hypotonic buffer (20mM Hepes pH7.9, 10mM KCl, 1mM EDTA, 10% Glycerol and 1mM DTT with additional protease inhibitor (Roche)) to isolate nuclei. The nuclei were suspended with RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate with protease inhibitor) and sonicated using Covaris S220 Focused-ultrasonicator. Fragmented chromatin was pre-cleared with protein G conjugated sepharose beads (GE). Antibodies were used to pull down the respective proteins and their associated chromatin. Washes with different concentration of NaCl were performed. The enriched protein-DNA complexes were reverse crosslinked at 65°C over night with proteinase K (NEB). DNA was purified with Qiagen MinElute kit. STARR-seq:  The plasmid pool was transfected into HEK293T or HepG2 cell lines using Fugene HD and continued culturing for 48 hours before harvest. Total RNA was extracted with RNeasy kit (Qiagen, 74104) and mRNA was enriched with poly(dT)25 Dynabeads (Invitrogen, 61002). First strand cDNA was synthesized using a specific primer (5’-CAAACTCATCAATGTATCTTATCATG) with high High-Capacity cDNA Reverse Transcription kit (ThermoFisher Scientific, 4368814). The nested PCR was used to amplify the SNP specific fragments from cDNA, first using two reporter-specific PCR primers (5’-GGGCCAGCTGTTGGGGTGTCCAC & 5’-CTTATCATGTCTGCTCGAAGC) and then generic primers used in HT-SELEX. DNA was purified with AMPure beads.   Hi-C:  Briefly, the human islets were washed with cold PBS and cut into small pieces. For HepG2 cells, the cells were trypsinized and washed with PBS. The chromatin was cross-linked with 1% formaldehyde (Sigma) at ambient temperature for 10 min and quenched with 125mM glycine for 5 min. PBS washed tissue was homogenized with loose fitting douncer for 30 strokes before centrifugation to isolate the nuclei. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n. The single strand overhang was filled with biotinylated-14-ATP (Life Tech.) using Klenow DNA polymerase (NEB). Different from tradition Hi-C, with in situ protocol the ligation was performed when the nuclear membrane was still intact. DNA was ligated for 4h at 16 °C using T4 ligase (NEB). Protein was degraded by proteinase K (NEB) treatment at 55 °C for 30 min. The crosslinking was reversed with 500 mM of NaCl and heated at 68 °C o/n. DNA was purified and sonicated to 300-700 bp small fragments. Biotinylated DNA was selected with Dynabeads My One T1 Streptavidin beads (Life Tech.). Sequencing library was prepared on beads and intensive wash was performed between different reactions.  Whole genome sequencing:  The genomic DNA was extracted using Qiagen kit (cat. no. 69506). The DNA was then fragmented with Covaris S220 ultrasonicator to 300-500 bp long.  RNA-seq:  The total RNA was isolated using Qiagen RNeasy mini kit. The sequencing library was prepared using Truseq illumine RNA Library Prep Kit v2 (cat. #RS-122-2001).  SELEX:  Briefly, the E. coli expressed 6xHis-tagged TF proteins were immobilized to Ni sepharose beads (GE, 17-5318-01) in Promega binding buffer (10mM Tris pH7.5, 50mM NaCl, 1mM MgCl2, 4% glycerol, 0.5mM EDTA, 5µg/ml poly-dIdC). Oligos from input or previous HT-SELEX cycles were added into the protein beads mixture and incubated at ambient temperature for 30 min. After binding, the beads were consecutively washed for 12 times with the Promega binding buffer. After final wash, TE (10mM Tris pH 8.0, 1mM EDTA) was used to re-suspend the beads and for PCR amplification. The PCR products from each HT-SELEX cycle were purified (Qiagen, 28004).
ChIP-seq:
Briefly, the cells were crossed linked with 1% formaldehyde at ambient temperature for 10 min. The reaction was quenched by 125mM glycine for 5 min at room temperature. Cells were washed with PBS and treated with hypotonic buffer (20mM Hepes pH7.9, 10mM KCl, 1mM EDTA, 10% Glycerol and 1mM DTT with additional protease inhibitor (Roche)) to isolate nuclei. The nuclei were suspended with RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate with protease inhibitor) and sonicated using Covaris S220 Focused-ultrasonicator. Fragmented chromatin was pre-cleared with protein G conjugated sepharose beads (GE). Antibodies were used to pull down the respective proteins and their associated chromatin. Washes with different concentration of NaCl were performed. The enriched protein-DNA complexes were reverse crosslinked at 65°C over night with proteinase K (NEB). DNA was purified with Qiagen MinElute kit. STARR-seq:
The plasmid pool was transfected into HEK293T or HepG2 cell lines using Fugene HD and continued culturing for 48 hours before harvest. Total RNA was extracted with RNeasy kit (Qiagen, 74104) and mRNA was enriched with poly(dT)25 Dynabeads (Invitrogen, 61002). First strand cDNA was synthesized using a specific primer (5’-CAAACTCATCAATGTATCTTATCATG) with high High-Capacity cDNA Reverse Transcription kit (ThermoFisher Scientific, 4368814). The nested PCR was used to amplify the SNP specific fragments from cDNA, first using two reporter-specific PCR primers (5’-GGGCCAGCTGTTGGGGTGTCCAC & 5’-CTTATCATGTCTGCTCGAAGC) and then generic primers used in HT-SELEX. DNA was purified with AMPure beads.
Hi-C:
Briefly, the human islets were washed with cold PBS and cut into small pieces. For HepG2 cells, the cells were trypsinized and washed with PBS. The chromatin was cross-linked with 1% formaldehyde (Sigma) at ambient temperature for 10 min and quenched with 125mM glycine for 5 min. PBS washed tissue was homogenized with loose fitting douncer for 30 strokes before centrifugation to isolate the nuclei. Nuclei were isolated and directly applied for digestion using 4 cutter restriction enzyme MboI (NEB) at 37 °C o/n. The single strand overhang was filled with biotinylated-14-ATP (Life Tech.) using Klenow DNA polymerase (NEB). Different from tradition Hi-C, with in situ protocol the ligation was performed when the nuclear membrane was still intact. DNA was ligated for 4h at 16 °C using T4 ligase (NEB). Protein was degraded by proteinase K (NEB) treatment at 55 °C for 30 min. The crosslinking was reversed with 500 mM of NaCl and heated at 68 °C o/n. DNA was purified and sonicated to 300-700 bp small fragments. Biotinylated DNA was selected with Dynabeads My One T1 Streptavidin beads (Life Tech.). Sequencing library was prepared on beads and intensive wash was performed between different reactions.
Whole genome sequencing:
The genomic DNA was extracted using Qiagen kit (cat. no. 69506). The DNA was then fragmented with Covaris S220 ultrasonicator to 300-500 bp long.
RNA-seq:
The total RNA was isolated using Qiagen RNeasy mini kit. The sequencing library was prepared using Truseq illumine RNA Library Prep Kit v2 (cat. #RS-122-2001).
SELEX:
Briefly, the E. coli expressed 6xHis-tagged TF proteins were immobilized to Ni sepharose beads (GE, 17-5318-01) in Promega binding buffer (10mM Tris pH7.5, 50mM NaCl, 1mM MgCl2, 4% glycerol, 0.5mM EDTA, 5µg/ml poly-dIdC). Oligos from input or previous HT-SELEX cycles were added into the protein beads mixture and incubated at ambient temperature for 30 min. After binding, the beads were consecutively washed for 12 times with the Promega binding buffer. After final wash, TE (10mM Tris pH 8.0, 1mM EDTA) was used to re-suspend the beads and for PCR amplification. The PCR products from each HT-SELEX cycle were purified (Qiagen, 28004).

treatment_protocol: Fugene HD (Promega, E2311) was used for plasmid transfection. Specifically, 2 µg of STARR-seq plasmids were mixed with 5 µl of transfection reagents for transfection into 300,000 cells cultured in a single well of 6-well plate. For siRNA transfection, HiPerfect transfection was used following the manufacture guidance. For each experiment, 50 nM of siRNA was used with 5 ul of HiPerfect reagent to make the transfection complex for 1-3×104 cells. Cells were continued to be cultured for 72 hours. The siRNAs targeting human HLF (cat. #GS3131) and MAFG (cat. #GS4097) were commercially available from Qiagen. Silencer negative control siRNA was commercially manufactured and order from Thermo Fisher (cat. #AM4635).

tag: library strategy

value: SELEX

tag: tf

tag: tf type

value: DBD (DNA binding domain)

tag: cycle

tag: plate

tag: molecule subtype

value: Synthesized DNA


title: GCM1.DBD.4.0.B9.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
GCM1_DBD_cycle3_Protein4_B9_S309_L002


title: USF1.FL.7.1.D6.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
USF1_FL_cycle3_Protein7_D6_S1002_L006

value: FL (Full Length)


title: GATA2.DBD.2.0.H3.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
GATA2_DBD_cycle4_Protein2_H3_S567_L003


title: TEAD2.FL.6.0.F2.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
TEAD2_FL_cycle3_Protein6_F2_S926_L005


title: FOXQ1.DBD.2.0.A10.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
FOXQ1_DBD_cycle3_Protein2_A10_S106_L001


title: ESR2.DBD.1.1.C10.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
ESR2_DBD_cycle4_Protein1_C10_S418_L003


title: NFIB.FL.6.0.E10.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
NFIB_FL_cycle3_Protein6_E10_S922_L005

value: NFIB


title: CREM.DBD.1.1.E8.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
CREM_DBD_cycle3_Protein1_E8_S56_L001

value: CREM


title: TP73L.DBD.3.1.A9.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
TP73L_DBD_cycle3_Protein3_A9_S201_L002


title: ZNF597.FL.6.0.C2.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
ZNF597_FL_cycle4_Protein6_C2_S1274_L007


title: MAFA.DBD.2.0.A1.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
MAFA_DBD_cycle4_Protein2_A1_S481_L003

value: MAFA


title: ZNF323.FL.7.1.G10.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
ZNF323_FL_cycle3_Protein7_G10_S1042_L006


title: RFX2.DBD.2.0.B5.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
RFX2_DBD_cycle4_Protein2_B5_S497_L003


title: OLIG3.DBD.3.1.H4.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
OLIG3_DBD_cycle4_Protein3_H4_S664_L004


title: MEIS2.DBD.3.1.A3.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
MEIS2_DBD_cycle4_Protein3_A3_S579_L004


title: ZNF138.FL.8.0.H4.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
ZNF138_FL_cycle3_Protein8_H4_S1144_L006


title: POU3F2.DBD.4.0.A2.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
POU3F2_DBD_cycle4_Protein4_A2_S674_L004


title: ELF1.FL.6.0.D4.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
ELF1_FL_cycle3_Protein6_D4_S904_L005


title: CTCF.DBD.3.1.A4.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
CTCF_DBD_cycle3_Protein3_A4_S196_L002

value: CTCF


title: USF1.DBD.1.1.G1.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
USF1_DBD_cycle4_Protein1_G1_S457_L003


title: PPARG.FL.8.0.H3.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
PPARG_FL_cycle3_Protein8_H3_S1143_L006

value: PPARG


title: SPIB.FL.5.1.C5.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
SPIB_FL_cycle3_Protein5_C5_S797_L005

value: SPIB


title: MSC.DBD.3.1.D11.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
MSC_DBD_cycle3_Protein3_D11_S239_L002

value: MSC


title: GRHL1.DBD.4.0.G11.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
GRHL1_DBD_cycle3_Protein4_G11_S371_L002


title: MSC.FL.5.1.B9.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
MSC_FL_cycle4_Protein5_B9_S1173_L007


title: MAFF.FL.6.0.B3.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
MAFF_FL_cycle3_Protein6_B3_S879_L005

value: MAFF


title: MAFF.DBD.1.1.H5.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
MAFF_DBD_cycle4_Protein1_H5_S473_L003


title: CTCF.DBD.3.1.A4.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
CTCF_DBD_cycle4_Protein3_A4_S580_L004


title: NFKB2.DBD.3.1.A8.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
NFKB2_DBD_cycle4_Protein3_A8_S584_L004


title: GFI1.DBD.2.0.F6.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
GFI1_DBD_cycle4_Protein2_F6_S546_L003


title: VENTX.FL.5.1.F2.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
VENTX_FL_cycle3_Protein5_F2_S830_L005

value: VENTX


title: PPARD.DBD.3.1.F3.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
PPARD_DBD_cycle4_Protein3_F3_S639_L004

value: PPARD


title: DLX2.FL.5.1.E11.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
DLX2_FL_cycle4_Protein5_E11_S1211_L007


title: HSF4.DBD.2.0.D9.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
HSF4_DBD_cycle4_Protein2_D9_S525_L003


title: EBF2.DBD.1.1.C6.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
EBF2_DBD_cycle3_Protein1_C6_S30_L001


title: BHLHE23.DBD.1.1.B4.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
BHLHE23_DBD_cycle4_Protein1_B4_S400_L003


title: IRF3.FL.6.0.C12.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
IRF3_FL_cycle4_Protein6_C12_S1284_L007


title: HESX1.FL.7.1.D8.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
HESX1_FL_cycle3_Protein7_D8_S1004_L006


title: ELF3.FL.6.0.G4.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
ELF3_FL_cycle4_Protein6_G4_S1324_L007


title: BCL6B.DBD.2.0.F12.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
BCL6B_DBD_cycle4_Protein2_F12_S552_L003


title: NCOA3.DBD.1.1.C8.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
NCOA3_DBD_cycle4_Protein1_C8_S416_L003


title: ISX.DBD.1.1.B11.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
ISX_DBD_cycle4_Protein1_B11_S407_L003

value: ISX


title: ZSCAN4.DBD.4.0.D4.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
ZSCAN4_DBD_cycle3_Protein4_D4_S328_L002


title: TP73.DBD.2.0.E1.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
TP73_DBD_cycle4_Protein2_E1_S529_L003


title: SIX2.FL.7.1.D12.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
SIX2_FL_cycle3_Protein7_D12_S1008_L006


title: MEF2C.FL.6.0.E9.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
MEF2C_FL_cycle3_Protein6_E9_S921_L005


title: ZBTB26.FL.6.0.F7.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
ZBTB26_FL_cycle4_Protein6_F7_S1315_L007


title: NHLH1.FL.7.1.C4.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
NHLH1_FL_cycle3_Protein7_C4_S988_L006


title: HMX1.DBD.1.1.E3.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
HMX1_DBD_cycle3_Protein1_E3_S51_L001


title: POU3F4.DBD.2.0.C9.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
POU3F4_DBD_cycle4_Protein2_C9_S513_L003


title: HOXB4.DBD.2.0.E3.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
HOXB4_DBD_cycle4_Protein2_E3_S531_L003


title: POU5F1.FL.8.0.F3.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
POU5F1_FL_cycle3_Protein8_F3_S1119_L006


title: HOXA9.DBD.4.0.D7.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
HOXA9_DBD_cycle3_Protein4_D7_S331_L002


title: ESRRA.DBD.1.1.E2.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
ESRRA_DBD_cycle4_Protein1_E2_S434_L003

value: ESRRA


title: RBPJ.DBD.2.0.F3.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
RBPJ_DBD_cycle3_Protein2_F3_S159_L001

value: RBPJ


title: NKX6_2.DBD.1.1.D12.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
NKX6_2_DBD_cycle3_Protein1_D12_S48_L001

value: SELEX


title: NFAT5.DBD.3.1.A12.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
NFAT5_DBD_cycle3_Protein3_A12_S204_L002

value: DBD (DNA binding domain)


title: IRF3.DBD.3.1.C5.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
IRF3_DBD_cycle4_Protein3_C5_S605_L004

value: Synthesized DNA


title: PDX1.DBD.1.1.H9.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
PDX1_DBD_cycle4_Protein1_H9_S477_L003


title: FOXB1.DBD.1.1.G7.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
FOXB1_DBD_cycle4_Protein1_G7_S463_L003


title: ATF3.DBD.3.1.B7.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
ATF3_DBD_cycle3_Protein3_B7_S211_L002


title: MSX1.FL.5.1.A1.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
MSX1_FL_cycle3_Protein5_A1_S769_L005

value: FL (Full Length)


title: KLF14.DBD.4.0.C5.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
KLF14_DBD_cycle4_Protein4_C5_S701_L004


title: NPAS4.DBD.1.1.A1.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
NPAS4_DBD_cycle4_Protein1_A1_S385_L003


title: HOXB9.DBD.4.0.D12.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
HOXB9_DBD_cycle3_Protein4_D12_S336_L002


title: TEAD2.FL.5.1.E5.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
TEAD2_FL_cycle3_Protein5_E5_S821_L005


title: EGR2.FL.6.0.F3.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
EGR2_FL_cycle4_Protein6_F3_S1311_L007


title: NKX6_1.DBD.8.0.G5.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
NKX6_1_DBD_cycle3_Protein8_G5_S1133_L006


title: TFAP2B.DBD.4.0.A7.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
TFAP2B_DBD_cycle4_Protein4_A7_S679_L004


title: NR2F6.FL.5.1.C11.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
NR2F6_FL_cycle3_Protein5_C11_S803_L005


title: GLI3.DBD.2.0.C12.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
GLI3_DBD_cycle3_Protein2_C12_S132_L001


title: SPIB.FL.7.1.A10.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
SPIB_FL_cycle3_Protein7_A10_S970_L006


title: EVX2.DBD.2.0.E5.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
EVX2_DBD_cycle4_Protein2_E5_S533_L003


title: STARR-seq Input

description:
processed data file:
starr_seq.count.tsv
JY_180

value: STARR-seq

tag: sample type

value: STARR-seq Input


title: PAX8.DBD.1.1.F9.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
PAX8_DBD_cycle4_Protein1_F9_S453_L003


title: ELF5.DBD.4.0.E3.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
ELF5_DBD_cycle4_Protein4_E3_S723_L004


title: PAX9.DBD.2.0.B9.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
PAX9_DBD_cycle4_Protein2_B9_S501_L003


title: ATOH7.DBD.1.1.A9.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
ATOH7_DBD_cycle4_Protein1_A9_S393_L003


title: BHLHB8.DBD.4.0.B10.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
BHLHB8_DBD_cycle4_Protein4_B10_S694_L004


title: RFXDC2.DBD.8.0.B3.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
RFXDC2_DBD_cycle3_Protein8_B3_S1071_L006


title: SOX8.FL.5.1.G7.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
SOX8_FL_cycle3_Protein5_G7_S847_L005


title: PPARG.FL.8.0.G8.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
PPARG_FL_cycle3_Protein8_G8_S1136_L006


title: DEAF1.DBD.3.1.D3.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
DEAF1_DBD_cycle3_Protein3_D3_S231_L002


title: SOX10.FL.7.1.H8.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
SOX10_FL_cycle3_Protein7_H8_S1052_L006


title: OTX1.DBD.3.1.E9.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
OTX1_DBD_cycle4_Protein3_E9_S633_L004


title: UBP1.DBD.4.0.D8.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
UBP1_DBD_cycle4_Protein4_D8_S716_L004


title: ZNF740.DBD.4.0.C9.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
ZNF740_DBD_cycle4_Protein4_C9_S705_L004


title: ZSCAN16.FL.5.1.H2.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
ZSCAN16_FL_cycle3_Protein5_H2_S854_L005


title: HSF1.DBD.2.0.D7.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
HSF1_DBD_cycle4_Protein2_D7_S523_L003


title: NEUROD2.FL.5.1.B8.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
NEUROD2_FL_cycle4_Protein5_B8_S1172_L007


title: SCRT2.DBD.4.0.C8.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
SCRT2_DBD_cycle3_Protein4_C8_S320_L002


title: HHEX.DBD.3.1.F1.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
HHEX_DBD_cycle3_Protein3_F1_S253_L002

value: HHEX


title: HOXD3.FL.6.0.A6.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
HOXD3_FL_cycle4_Protein6_A6_S1254_L007


title: PRRX2.FL.5.1.B1.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
PRRX2_FL_cycle3_Protein5_B1_S781_L005


title: TEAD1.FL.8.0.D5.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
TEAD1_FL_cycle3_Protein8_D5_S1097_L006


title: FOXM1.FL.8.0.H1.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
FOXM1_FL_cycle3_Protein8_H1_S1141_L006


title: BATF.FL.8.0.E8.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
BATF_FL_cycle3_Protein8_E8_S1112_L006

value: BATF


title: FEV.DBD.1.1.G5.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
FEV_DBD_cycle3_Protein1_G5_S77_L001

value: FEV


title: HEY1.FL.6.0.H10.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
HEY1_FL_cycle3_Protein6_H10_S958_L005


title: GATA3.FL.6.0.F5.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
GATA3_FL_cycle3_Protein6_F5_S929_L005


title: HSF2.FL.7.1.E10.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
HSF2_FL_cycle3_Protein7_E10_S1018_L006


title: SPIB.DBD.3.1.G1.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
SPIB_DBD_cycle3_Protein3_G1_S265_L002

value: SPIB


title: ISL1.FL.6.0.H7.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
ISL1_FL_cycle3_Protein6_H7_S955_L005


title: FOXO6.DBD.2.0.B10.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
FOXO6_DBD_cycle3_Protein2_B10_S118_L001


title: LIN28B.FL.5.1.D10.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
LIN28B_FL_cycle4_Protein5_D10_S1198_L007


title: HMX2.FL.7.1.F11.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
HMX2_FL_cycle3_Protein7_F11_S1031_L006


title: RORB.DBD.4.0.G8.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
RORB_DBD_cycle3_Protein4_G8_S368_L002

value: RORB


title: PKNOX1.DBD.3.1.C12.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
PKNOX1_DBD_cycle3_Protein3_C12_S228_L002


title: ALX3.FL.5.1.A12.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
ALX3_FL_cycle4_Protein5_A12_S1164_L007


title: MLX.FL.6.0.A12.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
MLX_FL_cycle3_Protein6_A12_S876_L005

value: MLX


title: LBX2.DBD.2.0.B11.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
LBX2_DBD_cycle3_Protein2_B11_S119_L001


title: CDX1.DBD.2.0.E4.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
CDX1_DBD_cycle3_Protein2_E4_S148_L001


title: CREB3L1.FL.6.0.D10.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
CREB3L1_FL_cycle4_Protein6_D10_S1294_L007


title: LHX4.FL.8.0.D8.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
LHX4_FL_cycle3_Protein8_D8_S1100_L006


title: DUXA.DBD.2.0.C4.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
DUXA_DBD_cycle4_Protein2_C4_S508_L003

value: DUXA


title: IRF9.FL.5.1.C9.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
IRF9_FL_cycle4_Protein5_C9_S1185_L007


title: ARX.DBD.1.1.H2.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
ARX_DBD_cycle3_Protein1_H2_S86_L001

value: ARX


title: NR2F6.DBD.3.1.H7.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
NR2F6_DBD_cycle3_Protein3_H7_S283_L002


title: NR4A3.DBD.1.1.D2.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
NR4A3_DBD_cycle4_Protein1_D2_S422_L003


title: MEOX2.FL.6.0.G9.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
MEOX2_FL_cycle3_Protein6_G9_S945_L005


title: EVX1.DBD.1.1.H10.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
EVX1_DBD_cycle4_Protein1_H10_S478_L003


title: HOXC8.FL.5.1.A10.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
HOXC8_FL_cycle4_Protein5_A10_S1162_L007


title: LHX9.DBD.2.0.E2.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
LHX9_DBD_cycle4_Protein2_E2_S530_L003


title: CDC5L.DBD.3.1.D8.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
CDC5L_DBD_cycle3_Protein3_D8_S236_L002


title: ZNF282.DBD.2.0.F11.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
ZNF282_DBD_cycle3_Protein2_F11_S167_L001


title: ALX1.FL.6.0.G12.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
ALX1_FL_cycle4_Protein6_G12_S1332_L007


title: PAX7.DBD.2.0.E10.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
PAX7_DBD_cycle3_Protein2_E10_S154_L001


title: HOXA11.DBD.3.1.B1.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
HOXA11_DBD_cycle3_Protein3_B1_S205_L002


title: MYBL1.DBD.4.0.B11.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
MYBL1_DBD_cycle4_Protein4_B11_S695_L004


title: PKNOX1.FL.6.0.D5.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
PKNOX1_FL_cycle3_Protein6_D5_S905_L005


title: DLX3.FL.6.0.A4.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
DLX3_FL_cycle3_Protein6_A4_S868_L005


title: SNAI2.FL.7.1.B1.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
SNAI2_FL_cycle3_Protein7_B1_S973_L006


title: NoProtein.NA.8.0.H7.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
NoProtein_NA_cycle3_Protein8_H7_S1147_L006

value: NoProtein


title: RFX6.FL.8.0.G12.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
RFX6_FL_cycle3_Protein8_G12_S1140_L006


title: SOX11.DBD.1.1.B3.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
SOX11_DBD_cycle4_Protein1_B3_S399_L003


title: NKX2_5.FL.6.0.A5.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
NKX2_5_FL_cycle3_Protein6_A5_S869_L005


title: FOXL2.FL.5.1.G4.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
FOXL2_FL_cycle3_Protein5_G4_S844_L005


title: HSF4.DBD.2.0.D9.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
HSF4_DBD_cycle3_Protein2_D9_S141_L001


title: ZBTB33.DBD.3.1.F7.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
ZBTB33_DBD_cycle3_Protein3_F7_S259_L002


title: HOXA2.FL.7.1.F12.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
HOXA2_FL_cycle3_Protein7_F12_S1032_L006


title: GATA5.FL.5.1.H5.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
GATA5_FL_cycle3_Protein5_H5_S857_L005


title: ZNF77.DBD.8.0.G4.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
ZNF77_DBD_cycle3_Protein8_G4_S1132_L006


title: HOXD13.DBD.2.0.E12.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
HOXD13_DBD_cycle4_Protein2_E12_S540_L003


title: CLOCK.DBD.1.1.G3.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
CLOCK_DBD_cycle3_Protein1_G3_S75_L001

value: CLOCK


title: ZNF581.DBD.4.0.D1.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
ZNF581_DBD_cycle4_Protein4_D1_S709_L004


title: RARG.FL.5.1.G12.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
RARG_FL_cycle4_Protein5_G12_S1236_L007

value: RARG


title: NR2E1.FL.5.1.C10.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
NR2E1_FL_cycle3_Protein5_C10_S802_L005

value: SELEX


title: ex vivo stimulated donor 100

city: San Framcisco

first: Steven

middle: A

last: Yukl

state: California

address: 4150 Clement Street

institute: San Francisco VA Medical Center - University of California San Francisco

description:
All_genes_Yukl_Telwatte_0875
BioJupies_ex-vivo-cells

library_source: transcriptomic

data_processing:
FASTQC qualtity control of raw sequencing reads
Alignment to standard reference genome using STAR
Gene-level abundance measurements
Differential expression analyzed using BioJupies (Torre et al 2018)
Genome_build: human NCBI genome build 36
Supplementary_files_format_and_content: txt files were generated using STAR and BioJupies; rows contain gene/transcript names and columns contain different parameters (fold-change, p-value, FDR, etc)

molecule: total RNA

organism: Homo sapiens

source_name: peripheral CD4+ T cells

growth_protocol: Resting-cell model following Lassen et al. 2012 protocol. Wild-type model following Matins et al. 2016 protocol, using Nelfinavir and AMD-3100 instead of Nelfinavir and Raltegravir as antiretroviral drugs. Ex vivo peripheral CD4+ T cells culture and activated following Yukl et al 2018 protocol.

extract_protocol:
RNA was extracted by TriReagent, following manufacturers instructions
TruSeq stranded Total mRNA kit (Illumina) library prepared by UCSF Functional Genomics Core Facility
TruSeq stranded Total mRNA with Ribo-Zero Globin (Illumina)

treatment_protocol: Stimulation with anti-CD3/CD28

tag: cell model

value: HIV-infected ART-suppressed individual

tag: individual

value: donor 100

tag: treatment

value: stimulated (anti-CD3/CD28)

tag: cell type

value: peripheral CD4+ T cells


title: ex vivo unstimulated donor 100

value: unstimulated


title: ex vivo stimulated donor 94

value: donor 94


title: ZNF140.DBD.3.1.B2.cycle3

description:
processed data file:
pbs.obs_pval05.tsv
ZNF140_DBD_cycle3_Protein3_B2_S206_L002

value: DBD (DNA binding domain)

value: Synthesized DNA


title: ZIC3.FL.5.1.H11.cycle4

description:
processed data file:
pbs.obs_pval05.tsv
ZIC3_FL_cycle4_Protein5_H11_S1247_L007

value: FL (Full Length)


title: wild-type model stimulated donor B98

description:
All_genes_Yukl_Telwatte_0875
BioJupies_wild-type-model

value: wild-type model

value: donor B98


title: ex vivo unstimulated donor 94


title: wild-type model unstimulated donor B98


title: wild-type model unstimulated donor B97

value: donor B97


title: resting-cell model stimulated donor RR13

description:
All_genes_Yukl_Telwatte_0779
BioJupies_resting-model

value: resting-cell model

value: donor RR13


title: wild-type model stimulated donor B97


title: resting-cell model unstimulated donor RR13


title: HepG2 RNA MAFG KD 6

description:
processed data file:
MAFG-6.fpkm.tsv
RZY828

molecule: polyA RNA

value: RNA-seq

tag: cell line/type

value: MAFG siRNA

value: polyA RNA


title: resting-cell model stimulated donor RR11

value: donor RR11


title: HepG2 RNA HLF KD 1

description:
processed data file:
HLF-D1.fpkm.tsv
RZY830

value: HLF siRNA


title: HepG2 RNA MAFG KD 5

description:
processed data file:
MAFG-5.fpkm.tsv
RZY827


title: HepG2 RNA HLF KD 2

description:
processed data file:
HLF-D2.fpkm.tsv
RZY831


title: HepG2 RNA MAFG KD 3

description:
processed data file:
MAFG-3.fpkm.tsv
RZY825


title: resting-cell model unstimulated donor RR11


title: HepG2 RNA HiPerfect

description:
processed data file:
HiPerfect.fpkm.tsv
RZY833

value: HiPerfect reagent


title: HepG2 RNA Negative

description:
processed data file:
Negative.fpkm.tsv
RZY834

value: Negative control siRNA


title: A0002 Hi-C

description:
processed data file:
Islet.hic
Islet.loops.txt
JY-63

source_name: A0002 Islet

value: Hi-C

value: Islet

value: genomic DNA


title: A0004 Hi-C

description:
processed data file:
Islet.hic
Islet.loops.txt
JY-64

source_name: A0004 Islet


title: HepG2 RNA Control

description:
processed data file:
HepG2-WT.fpkm.tsv
RZY832


title: HepG2 Hi-C

description:
processed data file:
HepG2.hic
HepG2.loops.txt
JY334-1


title: HEK293T STARR-seq Rep3 AB

description:
processed data file:
starr_seq.count.tsv
JY_189

value: STARR-seq


title: HepG2 WGS

description:
processed data file:
HepG2.recalibrated_variants.vcf
HepG2.phased_variants.vcf
JY-193-1

value: Whole Genome Sequencing


title: A0010 Hi-C

description:
processed data file:
Islet.hic
Islet.loops.txt
JY-344-3

source_name: A0010 Islet


title: HEK293T STARR-seq Rep1 AB

description:
processed data file:
starr_seq.count.tsv
JY_187


title: HEK293T STARR-seq Rep3 ssIII

description:
processed data file:
starr_seq.count.tsv
JY_186


title: HEK293T STARR-seq Rep2 ssIII

description:
processed data file:
starr_seq.count.tsv
JY_185


title: HepG2 STARR-seq Rep1 AB

description:
processed data file:
starr_seq.count.tsv
JY_190


title: HepG2 STARR-seq Rep2 AB

description:
processed data file:
starr_seq.count.tsv
JY_191


title: HEK293T STARR-seq Rep1 ssIII

description:
processed data file:
starr_seq.count.tsv
JY_184


title: HepG2 STARR-seq Rep3 AB

description:
processed data file:
starr_seq.count.tsv
JY_192


title: HepG2 STARR-seq Rep3 ssIII

description:
processed data file:
starr_seq.count.tsv
JY_183


title: HepG2 STARR-seq Rep1 ssIII

description:
processed data file:
starr_seq.count.tsv
JY_181


title: HepG2 STARR-seq Rep2 ssIII

description:
processed data file:
starr_seq.count.tsv
JY_182


title: HepG2 Input for ATF3 and CEBPA

description: Input for ATF3 and CEBPA

data_processing:
Reads were aligned using BWA MEM with either single-end or pair-end model to the hg19 reference genome. Reads with low mapping quality (mapq<10) were filtered out, and PCR duplicates were removed using Picard tool.
MACS2 were then applied to call peaks and generate signals to view in the genome browser.
Genome_build: hg19
Peak files in narrowPeak format and signal files in bigWig format for each samples were provided.

growth_protocol: The HepG2 (ATCC, HB-8065) cells were cultured under normal condition with 5% CO2 at 37°C.

extract_protocol:
Briefly, the cells were crossed linked with 1% formaldehyde at ambient temperature for 10 min. The reaction was quenched by 125mM glycine for 5 min at room temperature. Cells were washed with PBS and treated with hypotonic buffer (20mM Hepes pH7.9, 10mM KCl, 1mM EDTA, 10% Glycerol and 1mM DTT with additional protease inhibitor (Roche)) to isolate nuclei. The nuclei were suspended with RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate with protease inhibitor) and sonicated using Covaris S220 Focused-ultrasonicator. Fragmented chromatin was pre-cleared with protein G conjugated sepharose beads (GE). Antibodies were used to pull down the respective proteins and their associated chromatin. Washes with different concentration of NaCl were performed. The enriched protein-DNA complexes were reverse crosslinked at 65 C over night with proteinase K (NEB). DNA was purified with Qiagen MinElute kit.
Sequencing library was prepared using an in-house kit, including end-repair, “A” addition and adapter ligation. The library was sequenced with illumina HiSeq 4000 for 50bp single read or 100bp pair-end, acquiring 10-30 million reads.

tag: chip antibody


title: Fat-H-1

status: Public on Oct 26 2020

city: Karaj

first: Abolfazl

last: Bahrami

address: Daneshgah

department: Biology

country: Iran

institute: University of Tehran

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to bostau8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: bosTau8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

organism: Gallus gallus

source_name: Fat

extract_protocol:
Tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Fat

tag: fertility

value: high


title: B483J baseline Nasopharyngeal swab

status: Public on Oct 23 2020

city: Fajara

first: Karim

last: MANE

address: Atlantic Boulevard

department: Statistics and Bioinformatics

country: Gambia

institute: MRCG @ LSHTM

description:
190411_NB502007_0228_AH7TM5BGXB-71_CAGATG_S71_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

data_processing:
After sequencing, the raw reads were filtered. Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads.
Reads in fastq were mapped to human Homo_sapiens.GRCh38.fasta using DART v1.3.3.
Reads in BAM files were deduplicated using the umi_tools dedup command. Then optical duplicates were also removed using the Picard MarkDuplicates tools.
Reads Per Kilobase of exon per Megabase of library size (RPKM), Transcripts Per Megabase of library size (TPM), Counts Per Megabase of library size (CPM), Reads Per Kilobase of library size (RPK) were calculated using the Rsubread R package. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Homo_sapiens.GRCh38 (http://hgdownload.cse.ucsc.edu/goldenPath/hg38)
Supplementary_files_format_and_content: Tab-delimited text files include RPKM, TPM, CPM, RPK, raw counts values for each Sample.

source_name: Nasopharyngeal swab

extract_protocol:
Total RNA was extracted using the Lexogen SPLIT RNA Extraction kit.
Libraries were constructed using the Lexogen QuantSeq kit FWD HT.

value: Nasopharyngeal secretion

tag: age

value: 37 months

tag: virus status

value: Viruses negative


title: D421K baseline Nasopharyngeal swab

description:
190411_NB502007_0228_AH7TM5BGXB-72_GTAGAA_S72_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 31 months

value: Viruses positive


title: D434A baseline Nasopharyngeal swab

description:
190411_NB502007_0228_AH7TM5BGXB-70_AACCGA_S70_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 45 months


title: B210A baseline Nasopharyngeal swab

description:
190411_NB502007_0228_AH7TM5BGXB-65_AAGCTC_S65_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 25 months


title: B172C baseline Nasopharyngeal swab

description:
190411_NB502007_0228_AH7TM5BGXB-67_TCGTTC_S67_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 51 months


title: B490H baseline Nasopharyngeal swab

description:
190411_NB502007_0228_AH7TM5BGXB-64_CAGGAC_S64_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 27 months


title: HEK293T STARR-seq Rep2 AB

description:
processed data file:
starr_seq.count.tsv
JY_188

tag: library strategy

value: polyA RNA


title: D428B baseline Nasopharyngeal swab

description:
190405_NB502007_0224_AH7J2LBGXB-08_TGTGCA_S8_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 26 months


title: D132H baseline Nasopharyngeal swab

description:
190405_NB502007_0224_AH7J2LBGXB-07_CTAGTC_S7_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 43 months


title: D415C baseline Nasopharyngeal swab

description:
190411_NB502007_0228_AH7TM5BGXB-66_GACGAT_S66_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 33 months


title: A208B baseline Nasopharyngeal swab

description:
190405_NB502007_0224_AH7J2LBGXB-01_CAGCGT_S1_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 32 months


title: A212B baseline Nasopharyngeal swab

description:
190405_NB502007_0224_AH7J2LBGXB-02_GATCAC_S2_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: Not Available


title: A457G baseline Nasopharyngeal swab

description:
190405_NB502007_0224_AH7J2LBGXB-06_GTGTAG_S6_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: B136J baseline Nasopharyngeal swab

description:
190405_NB502007_0224_AH7J2LBGXB-04_TGCACG_S4_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 28 months


title: A444J baseline Nasopharyngeal swab

description:
190404_NB502007_0223_AH7VTFBGXB-25_TTTATG_S25_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 35 months


title: A447D baseline Nasopharyngeal swab

description:
190404_NB502007_0223_AH7VTFBGXB-27_CAAGCA_S27_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: Nasopharyngeal secretion

value: 38 months


title: A420J baseline Nasopharyngeal swab

description:
190404_NB502007_0223_AH7VTFBGXB-23_CACACT_S23_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 39 months

value: Viruses negative


title: D137G baseline Nasopharyngeal swab

description:
190404_NB502007_0223_AH7VTFBGXB-24_CCGCAA_S24_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: D111K baseline Nasopharyngeal swab

description:
190404_NB502007_0223_AH7VTFBGXB-20_TATGTC_S20_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 36 months


title: D408C baseline Nasopharyngeal swab

description:
190404_NB502007_0223_AH7VTFBGXB-19_ATACTG_S19_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: Viruses positive


title: B423F baseline Nasopharyngeal swab

description:
190404_NB502007_0223_AH7VTFBGXB-21_GAGTCC_S21_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: A427A baseline Nasopharyngeal swab

description:
190404_NB502007_0223_AH7VTFBGXB-12_ATGAAC_S12_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: HepG2 Input for HOXB4,PEA3,MAFF/G/K,HLF,HNF1B,HOXA13,IRF3, and TGIF2LX


title: D414H baseline Nasopharyngeal swab

description:
190404_NB502007_0223_AH7VTFBGXB-22_GGAGGT_S22_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: A126K baseline Nasopharyngeal swab

description:
190404_NB502007_0223_AH7VTFBGXB-11_TTAACT_S11_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 42 months


title: B099K baseline Nasopharyngeal swab

description:
190404_NB502007_0223_AH7VTFBGXB-10_CGGTTA_S10_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 37 months


title: A116C baseline Nasopharyngeal swab

description:
190404_NB502007_0223_AH7VTFBGXB-09_TCAGGA_S9_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 27 months


title: B488A baseline Nasopharyngeal swab

description:
190403_NB502007_0222_AH7T7LBGXB-48_AATAGC_S48_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 52 months


title: A211D baseline Nasopharyngeal swab

description:
190405_NB502007_0224_AH7J2LBGXB-05_ACATTA_S5_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: B152D baseline Nasopharyngeal swab

description:
190403_NB502007_0222_AH7T7LBGXB-17_TCTTAA_S17_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: B151E baseline Nasopharyngeal swab

description:
190403_NB502007_0222_AH7T7LBGXB-44_ACAGAT_S44_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 40 months


title: B160H baseline Nasopharyngeal swab

description:
190403_NB502007_0222_AH7T7LBGXB-28_GCTCGA_S28_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 50 months


title: A439J baseline Nasopharyngeal swab

description:
190403_NB502007_0222_AH7T7LBGXB-18_GTCAGG_S18_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: A134F baseline Nasopharyngeal swab

description:
190404_NB502007_0223_AH7VTFBGXB-29_GCGAAT_S29_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: A467H baseline Nasopharyngeal swab

description:
190403_NB502007_0222_AH7T7LBGXB-14_AATCCG_S14_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 29 months


title: B476K baseline Nasopharyngeal swab

description:
190403_NB502007_0222_AH7T7LBGXB-04_TGCACG_S4_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 49 months


title: A433D baseline Nasopharyngeal swab

description:
190403_NB502007_0222_AH7T7LBGXB-13_CCTAAG_S13_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: A146G baseline Nasopharyngeal swab

description:
190403_NB502007_0222_AH7T7LBGXB-12_ATGAAC_S12_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: A410F baseline Nasopharyngeal swab

description:
190403_NB502007_0222_AH7T7LBGXB-16_TACCTT_S16_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 26 months


title: B156H baseline Nasopharyngeal swab

description:
190402_NB502007_0221_AH7J2YBGXB-47_GCATGG_S47_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 28 months


title: B197B baseline Nasopharyngeal swab

description:
190402_NB502007_0221_AH7J2YBGXB-39_CAACAG_S39_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 25 months


title: B181C baseline Nasopharyngeal swab

description:
190402_NB502007_0221_AH7J2YBGXB-94_AGAATC_S94_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: Nasopharyngeal secretion


title: A139C baseline Nasopharyngeal swab

description:
190402_NB502007_0221_AH7J2YBGXB-46_CTCCAT_S46_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: D133H baseline Nasopharyngeal swab

description:
190402_NB502007_0221_AH7J2YBGXB-40_GATTGT_S40_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: A215K baseline Nasopharyngeal swab

description:
190402_NB502007_0221_AH7J2YBGXB-32_CGAAGG_S32_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 24 months


title: D123E baseline Nasopharyngeal swab

description:
190402_NB502007_0221_AH7J2YBGXB-31_ACCTAC_S31_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: B207A baseline Nasopharyngeal swab

description:
190402_NB502007_0221_AH7J2YBGXB-23_CACACT_S23_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: A200J baseline Nasopharyngeal swab

description:
190402_NB502007_0221_AH7J2YBGXB-38_ACCGTG_S38_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: B411J baseline Nasopharyngeal swab

description:
190402_NB502007_0221_AH7J2YBGXB-16_TACCTT_S16_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 54 months


title: D413K baseline Nasopharyngeal swab

description:
190402_NB502007_0221_AH7J2YBGXB-08_TGTGCA_S8_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 41 months


title: A484G baseline Nasopharyngeal swab

description:
190402_NB502007_0221_AH7J2YBGXB-07_CTAGTC_S7_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: Viruses negative


title: A464E baseline Nasopharyngeal swab

description:
190402_NB502007_0221_AH7J2YBGXB-24_CCGCAA_S24_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: D120D baseline Nasopharyngeal swab

description:
190403_NB502007_0222_AH7T7LBGXB-36_CGCAAC_S36_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 31 months

value: Viruses positive


title: D405J baseline Nasopharyngeal swab

description:
190401_NB502007_0220_AH3J5YBGXB-37_TGGCGA_S37_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 43 months


title: B204D baseline Nasopharyngeal swab

description:
190401_NB502007_0220_AH3J5YBGXB-51_CACTAA_S51_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 36 months


title: A101A baseline Nasopharyngeal swab

description:
190403_NB502007_0222_AH7T7LBGXB-20_TATGTC_S20_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 47 months


title: B221F baseline Nasopharyngeal swab

description:
190401_NB502007_0220_AH3J5YBGXB-35_GTTACC_S35_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 37 months


title: B478J baseline Nasopharyngeal swab

description:
190401_NB502007_0220_AH3J5YBGXB-29_GCGAAT_S29_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: B173D baseline Nasopharyngeal swab

description:
190401_NB502007_0220_AH3J5YBGXB-21_GAGTCC_S21_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: B205G baseline Nasopharyngeal swab

description:
190401_NB502007_0220_AH3J5YBGXB-27_CAAGCA_S27_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: A108G baseline Nasopharyngeal swab

description:
190401_NB502007_0220_AH3J5YBGXB-22_GGAGGT_S22_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 50 months


title: A144E baseline Nasopharyngeal swab

description:
190401_NB502007_0220_AH3J5YBGXB-19_ATACTG_S19_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: A450A baseline Nasopharyngeal swab

description:
190401_NB502007_0220_AH3J5YBGXB-14_AATCCG_S14_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 27 months


title: B106E baseline Nasopharyngeal swab

description:
190401_NB502007_0220_AH3J5YBGXB-11_TTAACT_S11_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 35 months


title: A440E baseline Nasopharyngeal swab

description:
190401_NB502007_0220_AH3J5YBGXB-13_CCTAAG_S13_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: D430G baseline Nasopharyngeal swab

description:
190401_NB502007_0220_AH3J5YBGXB-06_GTGTAG_S6_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: B149A baseline Nasopharyngeal swab

description:
190401_NB502007_0220_AH3J5YBGXB-05_ACATTA_S5_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: B191J baseline Nasopharyngeal swab

description:
190402_NB502007_0221_AH7J2YBGXB-30_TGGATT_S30_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 55 months


title: A176F baseline Nasopharyngeal swab

description:
190329_NB502007_0219_AH7JHLBGXB-49_GTGCCA_S49_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 30 months


title: D426C baseline Nasopharyngeal swab

description:
190329_NB502007_0219_AH7JHLBGXB-50_TCGAGG_S50_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 26 months


title: D419E baseline Nasopharyngeal swab

description:
190329_NB502007_0219_AH7JHLBGXB-41_CTCTCG_S41_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: Nasopharyngeal secretion

value: 34 months


title: A213H baseline Nasopharyngeal swab

description:
190329_NB502007_0219_AH7JHLBGXB-34_TTGGTA_S34_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 28 months


title: B220C baseline Nasopharyngeal swab

description:
190329_NB502007_0219_AH7JHLBGXB-42_TGACAC_S42_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: Not Available


title: B441C baseline Nasopharyngeal swab

description:
190329_NB502007_0219_AH7JHLBGXB-33_AGATAG_S33_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: B155B baseline Nasopharyngeal swab

description:
190329_NB502007_0219_AH7JHLBGXB-26_AACGCC_S26_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 57 months

value: Viruses negative


title: D117A baseline Nasopharyngeal swab

description:
190329_NB502007_0219_AH7JHLBGXB-10_CGGTTA_S10_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: D129B baseline Nasopharyngeal swab

description:
190401_NB502007_0220_AH3J5YBGXB-43_AAGACA_S43_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: D124C baseline Nasopharyngeal swab

description:
190329_NB502007_0219_AH7JHLBGXB-09_TCAGGA_S9_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: B154G baseline Nasopharyngeal swab

description:
190329_NB502007_0219_AH7JHLBGXB-17_TCTTAA_S17_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: Viruses positive


title: A474C baseline Nasopharyngeal swab

description:
190329_NB502007_0219_AH7JHLBGXB-03_ACCAGT_S3_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: B443G baseline Nasopharyngeal swab

description:
190329_NB502007_0219_AH7JHLBGXB-18_GTCAGG_S18_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: A196A baseline Nasopharyngeal swab

description:
190329_NB502007_0219_AH7JHLBGXB-02_GATCAC_S2_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: A463B baseline Nasopharyngeal swab

description:
190329_NB502007_0219_AH7JHLBGXB-01_CAGCGT_S1_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).


title: MFA of oriC ins1 <delta>mks::mukFEB cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep

status: Public on Oct 21 2020

city: Gif-sur-Yvette

first: Virginia

last: Lioy

address: 1 Avenue de la Terrasse

department: Genome Biology

country: France

institute: Institute for Integrative Biology of the Cell (I2BC)

data_processing:
3C-seq libraries were processed using the 3C-seq pipeline available at (https://github.com/koszullab/).
Removal of PCR duplicates based on the 20 first bp of the read containing a 6 nt random tag (home made script).
Iterative alignment, Min-leght=20, step=5, bowtie2 --very-sensitive
Filtering, Mapping quality=30, no ambiguous reads.
Assignment to restriction fragment.
Removal of un-informative events (uncuts, loops etc) as described in Cournac et al. BMC 2012.
Binning at 10kb.
Genome_build: Custom reference genome: Pseudomonas aeruginosa PAO1_mksIN.fasta.
Supplementary_files_format_and_content: 628x628 normalized contact matrix in txt format for the 3C-seq data.
Supplementary_files_format_and_content: Marker frequency analysis (MFA) processed data is presented as 1kb binned data in txt format.

organism: Pseudomonas aeruginosa PAO1

source_name: oriC ins1 <delta>mks::mukFEB cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

growth_protocol: Strains were grown overnight in LB, diluted 300 times in minimal medium A supplemented with 0.25% citrate and grown at 30°C until they reach an OD600 comprised between 0.05 and 0.1.

extract_protocol:
3C libraries were generated as described previously (Lioy and Boccard 2018). Briefly, 100 ml of culture was crosslinked with fresh formaldehyde for 30 minutes (5% final concentration) at room temperature (RT) followed by 30 minutes at 4°C. Formaldehyde was quenched with a final concentration of 0.25 M glycine for 20 minutes at 4°C. Fixed cells were collected by centrifugation, frozen on dry ice and stored at -80°C until use. Frozen pellets of ≈ 1-2 x 10e9 cells were defrosted, suspended in 600 µl Tris 10 mM EDTA 0.5 mM (TE) (pH 8) with 4 µl of lysozyme (35 U/µl; Tebu Bio), and incubated at RT for 20 minutes. SDS was added to the mix (final concentration 0.5%) and the cells incubated for 10 minutes at RT. 50µl of lysed cells were transferred to a tube containing 450µL of digestion mix (1X NEB 1 buffer, 1% triton X-100). This process was repeated 11 times (total 12 tubes with 500 µl). 100 units of HpaII were added to 10 tubes. All the tubes were then incubated for 2 hours at 37°C. To stop the digestion reaction, 8 tubes were immediately centrifuged during 20 min at 20,000 g, and pellets were suspended in 500ul of sterile water. The digested DNA (4 ml in total) was split in 4 aliquots, and diluted in 8 ml ligation buffer (1X ligation buffer NEB without ATP, 1 mM ATP, 0.1 mg/ml BSA, 125 Units of T4 DNA ligase 5 U/µl). Ligation was performed at 16°C for 4 hours, followed by incubation overnight (ON) at 65°C with 100 µl of proteinase K (20 mg/ml) and 100ul EDTA 500 mM. DNA was then precipitated with an equal volume of 3 M Na-Acetate (pH 5.2) and two volumes of iso-propanol. After one hour at -80°C, DNA was pelleted, suspended in 500µl 1X TE buffer. The remaining 4 tubes (2 tubes with HpaII and 2 tubes without restriction enzyme that were also incubated at 37°C with the resto of tubes) were directly incubated with 50 µl of proteinase K (20mg/ml) overnight at 65°C. Finally, all the tubes were transferred into 2 ml centrifuge tubes, extracted twice with 400 µl phenol-chloroform pH 8.0, precipitated, washed with 1 ml cold ethanol 70% and diluted in 30 µl 1X TE buffer in presence of RNase A (1 mg/ml). Tubes containing the ligated DNA (3C libraries), the digested DNA or the non-digested DNA were pooled into 3 different tubes and the efficiency of the 3C preparation was assayed by running a 1% agarose gel. 3C libraries were quantified on gel using QuantityOne software (BioRad).
Approximately 5 µg of a 3C library was suspended in water (final volume 130 µL) and sheared using a Covaris S220 instrument (Duty cycle 5, Intensity 5, cycles/burst 200, time 60 sec for 4 cycles). The DNA was purified using Qiaquick® PCR purification kit, DNA ends were prepared for adapter ligation following standard protocols (see Cournac 2016). Custom-made adapters (Marbouty 2015) were ligated overnight at 4°C. Ligase was inactivated by incubating the tubes at 65°C for 20 minutes. To purify DNA fragments ranging in size from 400 to 900 pb, a PippinPrep apparatus (SAGE Science) was used. For each library, one PCR reaction of 12 cycles was performed (using 2 µL of 3C library, 0.2 µM Illumina primers PE1.0 and PE2.0 and xx units of Taq Phusion [Finnzymes]). The PCR product was purified on Qiagen MinElute columns and primers dimers were removed from the 3C library by using AMPure XP beads following manufacturer’s protocol (Beckman Coulter). Finally, libraries were subject to paired-end sequencing on an Illumina sequencer (NextSeq).

tag: genotype/variation

value: PAO1 oriC ins1 Dmks::mukFEB


title: MFA of oriC ins1 <delta>mks::mukFEB cells in exponential phase minimal medium A supplemented with 0.25% citrate


title: MFA of oriC ins1 <delta>smc cells in exponential phase minimal medium A supplemented with 0.25% citrate

source_name: oriC ins1 <delta>smc cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

value: PAO1 oriC ins1 mksEFIN Dsmc


title: MFA of oriC ins1 <delta>mks cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep

source_name: oriC ins1 <delta>mks cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

value: PAO1 oriC ins1


title: MFA of oriC ins1 <delta>mks cells in exponential phase minimal medium A supplemented with 0.25% citrate


title: MFA of oriC ins1 cells in exponential phase minimal medium A supplemented with 0.25% citrate

source_name: oriC ins1 cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

value: PAO1 oriC ins1 mksEFIN


title: MFA of oriC ins1 cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep


title: 3C-seq of oriC ins1 <delta>smc cells in exponential phase minimal medium A supplemented with 0.25% citrate

data_processing:
Library strategy: 3C-seq
3C-seq libraries were processed using the 3C-seq pipeline available at (https://github.com/koszullab/).
Removal of PCR duplicates based on the 20 first bp of the read containing a 6 nt random tag (home made script).
Iterative alignment, Min-leght=20, step=5, bowtie2 --very-sensitive
Filtering, Mapping quality=30, no ambiguous reads.
Assignment to restriction fragment.
Removal of un-informative events (uncuts, loops etc) as described in Cournac et al. BMC 2012.
Binning at 10kb.
Genome_build: Custom reference genome: Pseudomonas aeruginosa PAO1_mksIN.fasta.
Supplementary_files_format_and_content: 628x628 normalized contact matrix in txt format for the 3C-seq data.
Supplementary_files_format_and_content: Marker frequency analysis (MFA) processed data is presented as 1kb binned data in txt format.


title: A429H baseline Nasopharyngeal swab

description:
190329_NB502007_0219_AH7JHLBGXB-25_TTTATG_S25_R1_001
Virus status (negative or positive) was determined after vaccination, but on samples taken prior to vaccination (but on the same day).

value: 43 months


title: MFA of oriC ins1 <delta>smc cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep


title: 3C-seq of oriC ins1 <delta>mks cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep


title: 3C-seq of <delta>smc parS-330 cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep

source_name: <delta>smc parS-330 cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

value: PAO1 DparS parS -330 DrrnD mksEFIN Dsmc


title: 3C-seq of oriC ins1 cells in exponential phase minimal medium A supplemented with 0.25% citrate


title: 3C-seq of <delta>mks parS-330 cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep

source_name: <delta>mks parS-330 cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

value: PAO1 DparS parS -330 DrrnD


title: 3C-seq of <delta>mks parS-330 cells in exponential phase minimal medium A supplemented with 0.25% citrate


title: 3C-seq of <delta>smc parS+550 cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep

source_name: <delta>smc parS+550 cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

value: PAO1 DparS parS+550 mksEFIN Dsmc


title: 3C-seq of parS+550 <delta>mks::mukFEB cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep

source_name: parS+550 <delta>mks::mukFEB cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

value: PAO1 DparS parS+550 Dmks::mukFEB


title: 3C-seq of <delta>smc parS+550 cells in exponential phase minimal medium A supplemented with 0.25% citrate


title: 3C-seq of parS+550 <delta>mks::mukFEB cells in exponential phase minimal medium A supplemented with 0.25% citrate


title: 3C-seq of oriC ins1 <delta>mks cells in exponential phase minimal medium A supplemented with 0.25% citrate


title: 3C-seq of oriC ins1 <delta>smc cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep


title: 3C-seq of <delta>mks parS+550 cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep

source_name: <delta>mks parS+550 cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

value: PAO1 <delta>parS parS+550


title: 3C-seq of <delta>mks parS+550 cells in exponential phase minimal medium A supplemented with 0.25% citrate


title: 3C-seq of parS+550 cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep

source_name: parS+550 cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

value: PAO1 DparS parS+550 mksEFIN


title: 3C-seq of parS+550 cells in exponential phase minimal medium A supplemented with 0.25% citrate


title: 3C-seq of <delta>mks::mukFEB Dsmc cells in exponential phase minimal medium A supplemented with 0.25% citrate

source_name: <delta>mks::mukFEB Dsmc cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

value: PAO1 Dmks::mukFEB Dsmc


title: 3C-seq of <delta>mks::mukFEB Dsmc cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep


title: MFA of WT cells in exponential phase minimal medium A supplemented with 0.25% citrate

source_name: WT cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

value: PAO1 mksEFIN


title: MFA of WT cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep


title: 3C-seq of <delta>mks::mukFEB cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep

source_name: <delta>mks::mukFEB cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

value: PAO1 Dmks::mukFEB


title: 3C-seq of DparS Dsmc cells in exponential phase minimal medium A supplemented with 0.25% citrate

source_name: DparS Dsmc cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

value: PAO1 mksEFIN DparS Dsmc


title: 3C-seq of DparS Dsmc cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep


title: 3C-seq of oriC ins1 cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep


title: 3C-seq of <delta>mks::mukFEB cells in exponential phase minimal medium A supplemented with 0.25% citrate


title: 3C-seq of <delta>smc parS-330 cells in exponential phase minimal medium A supplemented with 0.25% citrate


title: 3C-seq of DparA cells in exponential phase minimal medium A supplemented with 0.25% citrate

value: PAO1 mksEFIN DparA


title: 3C-seq of parS-330 cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep

source_name: parS-330 cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

value: DparS parS -330 DrrnD mksEFIN


title: 3C-seq of DparS123 cells in exponential phase minimal medium A supplemented with 0.25% citrate

value: PAO1 mksEFIN DparS123


title: 3C-seq of DparS cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep

source_name: DparS cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

value: PAO1 mksEFIN DparS


title: 3C-seq of DparS cells in exponential phase minimal medium A supplemented with 0.25% citrate


title: 3C-seq of Dmks Dsmc cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep

source_name: Dmks Dsmc cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

value: PAO1 Dsmc


title: 3C-seq of Dmks Dsmc cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep2


title: 3C-seq of Dmks cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep

source_name: Dmks cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C


title: 3C-seq of Dmks cells in exponential phase minimal medium A supplemented with 0.25% citrate


title: 3C-seq of Dsmc cells in exponential phase minimal medium A supplemented with 0.25% citrate

source_name: Dsmc cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

value: PAO1 mksEFIN Dsmc


title: 3C-seq of WT cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep


title: 3C-seq of WT cells in exponential phase minimal medium A supplemented with 0.25% citrate


title: 3C-seq of Dsmc cells in exponential phase minimal medium A supplemented with 0.25% citrate-Rep


title: ERY input [1928]

status: Public on Oct 14 2020

city: University Park

first: Ross

last: Hardison

state: PA

address: 303 Wartik Lab

institute: Pennsylvania State University

description:
1928
1909.mm10.broadpeak.gz
1926.mm10.broadpeak.gz

data_processing:
Basecalls using bcl2fastq-1.8.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm10 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle and peaks called using MACS with parameters --format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Filter blacklist regions from peaks, and convert the *peaks.xls file from MACs to broadpeak format (see UCSC Genome Browser for format specs).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWigs, signal from MACS.
Supplementary_files_format_and_content: broadpeaks, peak calls by MACS.

organism: Mus musculus

source_name: ERY cells

extract_protocol:
Lysates were prepared from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq samples were prepared by end repair, 3’ adenylation, and adaptor ligation using Illumina’s TruSeq ChIP-seq Sample Preparation Kit.

value: bone marrow derived progenitor cells

tag: facs cell isolation sort markers

tag: strain

tag: average chromatin size as measured between a 100-500 bp window using the agilent bioanalyzer 7500 chip


title: CFUE input [1986]

description:
1986
1980.mm10.broadpeak.gz

source_name: CFUE cells

value: CD4-, CD8-, IL7Ra-, CD11b-, Ly6g-, CD45R-, Ter119+, CD44+, FSCHigh


title: iMk input [1929]

description:
1929
1908.mm10.broadpeak.gz
1910.mm10.broadpeak.gz

source_name: iMk cells


title: CFUMk input [1985]

description:
1985
1979.mm10.broadpeak.gz

source_name: CFUMk cells


title: GMP input [1983]

description:
1983
1977.mm10.broadpeak.gz

source_name: GMP cells


title: CMP input [1982]

description:
1982
1976.mm10.broadpeak.gz

source_name: CMP cells


title: LSK input [1296]

description:
1296
1295.mm10.broadpeak.gz
1927.mm10.broadpeak.gz

source_name: LSK cells


title: hESC-HNF1A-HET: ES_797402

status: Public on Oct 13 2020

city: New York

first: Dieter

last: Egli

state: New York

address: 701 West 168th Street

institute: Columbia University

description: Differentiation day 25. Experiment number A34. Genotype HNF1A HET

data_processing:
Single cell RNA-Seq data from total of 309 hESC-derived cells (113 for WT and 158 for KO and 38 for HET) were obtained. Raw reads were aligned to the hg19 reference genome using STAR (2.5.2b) and gene quantification were performed using FeatureCounts (1.5.2).
Quality control was conducted as follows: cells with low mapped reads (<1,000,000), low exon count (<100,000), low exon mapped rate (<0.2), high intergenic mapped rate (>0.3), low detected gene count (<1,000) and with more than 10% Mitochondria genes' count were removed. In addition, genes with <10 non-zero counts across all the cells were eliminated. All the downstream analysis was done with in R-3.4.1. Filtered raw count data were normalized and scaled by Seurat package and only variable genes generated by Seurat were used to do PCA and t-SNE. n=3 for each genotype.
Genome_build: GRCh37
Supplementary_files_format_and_content: .txt files are the processed raw count files of each cell with label information.

source_name: Endocrine cells

growth_protocol: The initial stages of differentiation were conducted in planar culture (d0-d11). For definitive endoderm stage (d1-d3) cells were cultured using STEMdiffTM Definitive Endoderm Differentiation Kit (Stemcell Technologies, 05110). For primitive gut stage (d4-d6), cells were cultured in RPMI containing GlutaMAX (Life Technology, 61870-127), 1% (v/v) Penicillin-Streptomycin (PS) (Thermo Fisher Scientific, 15070-063), 1% (v/v) B27 Serum-Free Supplement (50x) (Life Technology, 17504044) and 50 ng/ml FGF7 (R&D System, 251-KG). For posterior foregut stage (d7-d8), cells were cultured in DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27, 0.25 μM KAAD-Cyclopamine (Stemgent, 04-0028), 2 μM Retinoic acid (Stemgent, 04-0021) and 0.25 μM LDN193189 (Stemgent, 04-0074). For pancreatic progenitor stage (d9-d11), cells were cultured in DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27 and 50 ng/ml EGF (R&D System, 236-EG). Cells were then dissociated using TrypLE™ Express (Life Technology, 12605036) and seeded into low-attachment 96 well-plates (Corning, 7007) (1 well of 6 well-plate to 60 wells of 96-well-plate) for clustering step to form aggregates or clusters of endocrine cells in DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27, 0.25 μM Cyclopamine, 1 μM thyroid hormone (T3) (Sigma, T6397), 10 μM Alk5i, 10 μM Zinc sulfate (Sigma-Aldrich, Z4750) and 10 μg/ml Heparin (Sigma-Aldrich, H3149) for 2 days (d12-d13). For pancreatic endocrine stage (d14-20) cells were cultured using DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27, 100 nM LDN, 1 μM T3, 10 μM Alk5i, 10 μM Zinc sulfate, 10 μg/ml Heparin and 100 nM gamma-secretase inhibitor (DBZ) (EMD Millipore, 565789). For mature pancreatic endocrine stage (d21-d27) cells were cultured using DMEM containing GlutaMax, 1% (v/v) PS, 1% (v/v) B27, 1 μM T3, 10 μM Alk5i, 10 μM Zinc sulfate, 10 μg/ml Heparin, 1 mM N-acetyl cysteine (N-Cys) (Sigma-Aldrich, A9165-5G), 10 μM Trolox (EMD Millipore, 648471-500MG) and 2 μM R428 (Tyrosine kinase receptor AXL inhibitor) (ApexBio, A8329). From d1 to d11 media was changed every day and from d12 to d27 media was changed every other day. All differentiations were done for 27 to 30 days.

extract_protocol:
Around 100 cells per genotype at day 25 of differentiation are dissociated and sorted for GFP using BD FACS Aria II cell sorter.
Human embryonic stem cells with different HNF1A genotypes (WT, KO1, KO2 and HET) were differentiated into islet-like clusters of endocrine cells for 25 days in vitro. Clusters of islet-like cells were dissociated into single cells and insulin producing cells were purified by FACS sorting for INS-GFP. Cells were analyzed by single cell RNA sequencing. There are three WT and three KO.

treatment_protocol: Cells are untreated

value: hES-derived endocrine cells

tag: passages

tag: cell id

tag: clone

tag: genotype

value: HNF1A HET

tag: days

value: Differentiation day 25

tag: batch


title: hESC-HNF1A-HET: ES_797404

tag: cell type


title: MEP input [1984]

description:
1984
1978.mm10.broadpeak.gz

source_name: MEP cells

tag: chip antibody


title: hESC-HNF1A-HET: ES_797403


title: hESC-HNF1A-HET: ES_797398


title: hESC-HNF1A-HET: ES_797399


title: hESC-HNF1A-HET: ES_797401


title: hESC-HNF1A-HET: ES_797400


title: 3C-seq of Dmks Dsmc cells in exponential phase minimal medium A supplemented with 0.25% citrate


title: hESC-HNF1A-HET: ES_797396


title: hESC-HNF1A-HET: ES_797393


title: hESC-HNF1A-HET: ES_797394


title: hESC-HNF1A-HET: ES_797391


title: hESC-HNF1A-HET: ES_797395


title: hESC-HNF1A-HET: ES_797390


title: hESC-HNF1A-HET: ES_797388


title: hESC-HNF1A-HET: ES_797389


title: hESC-HNF1A-HET: ES_797387


title: hESC-HNF1A-HET: ES_797385


title: hESC-HNF1A-HET: ES_797386


title: hESC-HNF1A-HET: ES_797384


title: hESC-HNF1A-HET: ES_797397


title: hESC-HNF1A-HET: ES_797382


title: hESC-HNF1A-HET: ES_797383


title: hESC-HNF1A-HET: ES_797379


title: hESC-HNF1A-HET: ES_797380


title: hESC-HNF1A-HET: ES_797378


title: hESC-HNF1A-HET: ES_797381


title: hESC-HNF1A-HET: ES_797377


title: hESC-HNF1A-HET: ES_797376


title: hESC-HNF1A-HET: ES_797392


title: hESC-HNF1A-HET: ES_797375


title: hESC-HNF1A-HET: ES_797374


title: hESC-HNF1A-HET: ES_797370


title: hESC-HNF1A-HET: ES_797373


title: hESC-HNF1A-HET: ES_797371


title: PDX-biopsy - middle layer - rep2

status: Public on Oct 11 2020

city: Rockville

first: David

last: Morse

state: Maryland

address: 9800 Medical Center Drive

department: National Center for Advancing Translational Sciences

institute: National Institutes of Health

description:
inDrops Transcriptome libraries
biopsy_middle_TR2_ACTCTAGG

data_processing:
For Raw Fastq Files: R1 biological read, R2 first half of the gel barcode, R3 library index, and R4 second half of the gel barcode (8 cycles) and the UMI (6 cycles).
indropv3 filtering and demultiplexing
indropv3 identify abundant barcodes
indropv3 quantify expression
indropv3 sort
indropv3 aggregate
demultiplexed and sorted fastq files for each sample are provided as output from the indop pipeline
Matrices are coverted into 10X format and loaded into R for processing
Genome_build: Homo_sapiens.GRCh38.85 and Mus_musculus.GRCm38.85
Supplementary_files_format_and_content: processed data provided in a sparse raw counts matrix
Supplementary_files_format_and_content: barcodes.tsv, genes.tsv, matrix.mtx

source_name: PDX-biopsy - middle layer

growth_protocol: spheroids were cultured in 96-well ultra-low attachemnt plates for 14 days; Organoids were derived from patient ascites and miantained in a matrigel solution; PDX tumors were derived from patient ascites and grown subcutaneously in mice.

extract_protocol: Indrop v3

treatment_protocol: samples were stained using the SEEP protocol, dissociated using accutase (spheroid/organoid) or gentleMACS (PDX biopsy), and sorted by fluorescent intensity via FACS.

tag: tissue

value: biopsy of PDX solid tumor

value: ascites-derived HGSOC cells

tag: layer

value: middle

tag: disease state

value: HGSOC


title: hESC-HNF1A-HET: ES_797368


title: hESC-HNF1A-HET: ES_797369


title: PDX-biopsy - surface layer - rep2

description:
inDrops Transcriptome libraries
biopsy_surface_TR2_TCTTACGC

source_name: PDX-biopsy - surface layer

value: surface


title: hESC-HNF1A-HET: ES_797367


title: PDX-biopsy - center layer - rep1

description:
inDrops Transcriptome libraries
biopsy_central_TR1_ATAGAGAG

source_name: PDX-biopsy - center layer

value: center


title: ascited-derived organoid - surface layer - rep1

description:
inDrops Transcriptome libraries
organoid_surface_TR1_AGAGGATA

value: Ascited-derived organoids


title: tumor spheroid - surface layer - rep3

description:
inDrops Transcriptome libraries
spheroid_surface_BR2_S8

source_name: tumor spheroid - surface layer

value: PEO1 cell spheroids


title: ascited-derived organoid - middle layer - rep2

description:
inDrops Transcriptome libraries
organoid_middle_TR2_TCGCTATG

source_name: ascited-derived organoid - middle layer


title: ascited-derived organoid - surface layer - rep2

description:
inDrops Transcriptome libraries
organoid_surface_TR2_TCAGCGAA


title: tumor spheroid - surface layer - rep4

description:
inDrops Transcriptome libraries
spheroid_surface_BR2_TR2_S17


title: tumor spheroid - surface layer - rep1

description:
inDrops Transcriptome libraries
spheroid_surface_BR1_S7


title: ascited-derived organoid - center layer - rep1

description:
inDrops Transcriptome libraries
organoid_central_TR1_GCGATCTA

source_name: ascited-derived organoid - center layer


title: tumor spheroid - surface layer - rep2

description:
inDrops Transcriptome libraries
spheroid_surface_BR1_TR2_S16


title: ascited-derived organoid - middle layer - rep1

description:
inDrops Transcriptome libraries
organoid_middle_TR1_ATAGAGAG


title: ascited-derived organoid - center layer - rep2

description:
inDrops Transcriptome libraries
organoid_central_TR2_TGGTAACG


title: tumor spheroid - inside layer - rep4

description:
inDrops Transcriptome libraries
spheroid_inner_BR2_TR2_S13

source_name: tumor spheroid - inside layer

value: inside


title: tumor spheroid - outside layer - rep2

description:
inDrops Transcriptome libraries
spheroid_outer_BR1_TR2_S14

source_name: tumor spheroid - outside layer

value: outside


title: tumor spheroid - inside layer - rep3

description:
inDrops Transcriptome libraries
spheroid_inner_BR2_S4


title: tumor spheroid - inside layer - rep1

description:
inDrops Transcriptome libraries
spheroid_inner_BR1_S3


title: tumor spheroid - center layer - rep4

description:
inDrops Transcriptome libraries
spheroid_central_BR2_TR2_S11

source_name: tumor spheroid - center layer


title: tumor spheroid - inside layer - rep2

description:
inDrops Transcriptome libraries
spheroid_inner_BR1_TR2_S12


title: tumor spheroid - outside layer - rep1

description:
inDrops Transcriptome libraries
spheroid_outer_BR1_S5


title: PDX-biopsy - middle layer - rep1

description:
inDrops Transcriptome libraries
biopsy_middle_TR1_AGAGGATA


title: tumor spheroid - center layer - rep2

description:
inDrops Transcriptome libraries
spheroid_central_BR1_TR2_S10


title: PDX-biopsy - surface layer - rep1

description:
inDrops Transcriptome libraries
biopsy_surface_TR1_CTCCTTAC


title: tumor spheroid - center layer - rep1

description:
inDrops Transcriptome libraries
spheroid_central_BR1_S1


title: hESC-HNF1A-HET: ES_797372

description: Differentiation day 25. Experiment number A34. Genotype HNF1A HET


title: MsmegUvrD10minR1

status: Public on Oct 06 2020

city: Chapel Hill

first: Yanyan

last: Yang

state: NC

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

institute: University of North Carolina  at Chapel Hill

data_processing:
adaptor trimming
filtering reads based on length
alignment
read filtering based on nucleotide composition
strand separation
gene coverage count
Genome_build: M. smegmatis wild type strain MC2155 (GCA_000015005.1 was downloaded from EnsemblBacteria)
Supplementary_files_format_and_content: bigwig

organism: Mycolicibacterium smegmatis

source_name: Mycolicibacterium smegmatis MC2 155

extract_protocol: We apply XR-seq in Mycolicibacterium smegmatis MC2 155, the cells were were grown with shaking at 37 °C in Luria Broth containing 0.5% (w/vol) Tween 80. Exponentially growing cells were transferred to R150 tissue culture dishes in volumes of 15 mL and were irradiated at an OD600 of ∼0.6 at room temperature with 100 J/m2. dishes were then incubated for 10 min at room temperature, and then cells were harvested, chilled, and maintained on ice. Excision products were then isolated using a modified Hirt procedure that employs shearing to assist cell lysis.  Cells were pelleted at 4 °C, resuspended in ice-cold TE [Tris (10 mM)-EDTA (1 mM) (pH 8.0)], transferred to ice cold Eppendorf tubes, and pelleted at 4 °C, and the supernatants were removed. Pellets were then resuspended with 360 μL of ice-cold TE. Then, 50 μL of room temperature 10% (wt/vol) SDS was added, and cells were lysed by passage through a 26G needle 40 times followed by incubation at room temperature for 20 min. A 120-μL volume of room temperature NaCl (5 M) was then added, tubes were gently mixed, and suspensions were incubated at 4 °C overnight. After centrifuging at high speed for 1 h in a microfuge at 4 °C, supernatants (about 480 μL each) were taken, and each was mixed with and incubated with 12 μL of RNaseA (R4642; Sigma) for 1 h at 37 °C, and then with 12 μL of proteinase K (P8107S; NEB) for 1.5 h at 60 °C. Samples were then extracted twice with phenol/chloroform/isoamyl alcohol and precipitated with ethanol. Samples were immunoprecipitated with an anti-CPD antibody and then ligated to adapters and processed for sequencing (XR-seq). XR-seq libraries were pooled and then sequenced on the HiSeq 2500Rapid Run platform at the UNC-Chapel Hill High-Throughput Sequencing Facility.

tag: treatment

value: UV

value: uvrD-


title: MsmegWT5minR1

value: wild type


title: PDX-biopsy - center layer - rep2

description:
inDrops Transcriptome libraries
biopsy_central_TR2_AGCTAGAA


title: tumor spheroid - outside layer - rep4

description:
inDrops Transcriptome libraries
spheroid_outer_BR2_TR2_S15


title: tumor spheroid - outside layer - rep3

description:
inDrops Transcriptome libraries
spheroid_outer_BR2_S6


title: APP/PS1 rep2

status: Public on Oct 05 2020

city: shanghai

first: song

last: chenghuan

address: south chongqing road

country: China

institute: shanghai jiaotong university

data_processing:
Solexa Pipeline Version 1.8 software was used for image processing and base recognition.
The sequencing quality of reads was evaluated with FastQC software. Hisat2 software was used for comparison to the reference genome.
Transcriptional abundance estimation was performed using StringTie software with reference to official database annotation information.
Ballgown was used for FPKM calculation.
Genome_build: mm9
Supplementary_files_format_and_content: *_mRNA.txt: Tab-delimited text files include abundance measurements.
Supplementary_files_format_and_content: *_circRNA.txt: Tab-delimited text files include abundance measurements.

source_name: Hippocampus

extract_protocol:
Hippocampus were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: age

value: 6 months

value: Hippocampus


title: APP/PS1 rep1


title: WT rep1

value: Wild type


title: WT rep3


title: APP/PS1 rep3


title: tumor spheroid - center layer - rep3

description:
inDrops Transcriptome libraries
spheroid_central_BR2_S2


title: WT rep2


title: Breast cancer_BH0505-8

type: RNA

city: New Taipei

first: Chih-Cheng

last: Chien

address: No 2, Ln 59, Jian-Cheng Rd, Sijhih Dist

country: Taiwan

institute: Sijhih Cathay General Hospital

description: Gene expression data from breast cancer tissues.

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45 °C on GeneChip® Human Genome U133 Plus 2.0 expression arrays (Affymetrix, Inc., Santa Clara, CA).

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000.

data_processing: Scanned images processed by GeneChip® Operating Software and Affymetrix’s Microarray Suite software to generate detection p values. The Robust Multichip Average (RMA) algorithm, which consisted three steps of background adjustment, quantile normalization, and final summarization, was applied for perfect match probe signals within the study.

label: biotin

source_name: Breast cancer tumor tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 8 ug total RNA.

extract_protocol: Total RNA was extracted from frozen specimens using TRIzol® reagent (Invitrogen, Carlsbad, CA). RNA was purified using RNeasy® mini kits (Qiagen, Valencia, CA) and RNA integration was checked by gel electrophoresis.

treatment_protocol: Breast cancer samples were prospectively collected during surgery. Cancerous breast tissues were snap-frozen and stored in liquid nitrogen at -80 °C with RNAlaterTM reagent (Qiagen, Germantown, MD) within 30 minutes after surgery. Frozen samples were cut into 1~2-mm thick slices, and slices with more than 90% of cancer content were selected for microarray experiment.

value: Breast

tag: dcis

value: With DCIS

tag: comed-dcis

value: Comedo DCIS

tag: microcalcification

value: Without microcalcification

tag: relapse status

value: non-relapse

tag: survival time (years)

tag: er

value: negative

tag: pr

tag: grade

tag: her2 status

value: overexpression

tag: predicted risk

value: low


title: 3C-seq of parS-330 cells in exponential phase minimal medium A supplemented with 0.25% citrate

source_name: parS-330 cells in exponential phase minimal medium A supplemented with 0.25% citrate as carbon source at 30°C

tag: genotype/variation

value: DparS parS -330 DrrnD mksEFIN


title: Breast cancer_BH0533-4

value: Without DCIS

value: Non-comedo DCIS

value: positive

value: normal

value: high


title: Breast cancer_BH0505-9

value: With microcalcification


title: Breast cancer_BH0478-6


title: Breast cancer_BH0485-3


title: Breast cancer_BH0505-5


title: Breast cancer_BH0485-8

value: relapse


title: Breast cancer_BH0478-4


title: Breast cancer_BH0485-7


title: Breast cancer_BH0485-9


title: Breast cancer_Breast Cancer 121T


title: Breast cancer_BH0485-4


title: Breast cancer_BH0485-10


title: Breast cancer_BH0485-5


title: Breast cancer_BH0533-2


title: Breast cancer_BH0533-1


title: Breast cancer_BH0478-5


title: Breast cancer_BH0505-3


title: Breast cancer_Breast Cancer 108T


title: Breast cancer_BH0478-3


title: Breast cancer_BH0470-5


title: Breast cancer_BH0470-3


title: Breast cancer_BH0470-1


title: Breast cancer_BH0533-5


title: Breast cancer_Breast Cancer 119T


title: Breast cancer_BH0485-6


title: Breast cancer_BH0470-2


title: Breast cancer_BH0470-6


title: Breast cancer_BH0533-3


title: Breast cancer_BH0434-1


title: Breast cancer_BH0396-5


title: Breast cancer_BH0396-7


title: Breast cancer_BH0396-4


title: Breast cancer_BH0394-9


title: Breast cancer_BH0430-2


title: Breast cancer_BH0394-8


title: Breast cancer_BH0396-2


title: Breast cancer_BH0394-10


title: Breast cancer_BH0396-6


title: Breast cancer_BH0394-5


title: Breast cancer_BH0396-3


title: Breast cancer_BH0396-10


title: Breast cancer_BH0354-2


title: Breast cancer_BH0394-3


title: Breast cancer_BH0354-3


title: Breast cancer_BH0394-7


title: Breast cancer_BH0394-2


title: Breast cancer_BH0354-4


title: Breast cancer_BH0354-1


title: Breast cancer_BH0394-6


title: Breast cancer_BH0394-4


title: Breast cancer_BH0394-1


title: Breast cancer_BH0396-1


title: Breast cancer_BH0344-7


title: Breast cancer_BH0344-9


title: Breast cancer_BH0344-4


title: Breast cancer_BH0344-3


title: Breast cancer_BH0344-10


title: Breast cancer_BH0344-2


title: Breast cancer_154T


title: Breast cancer_BH0312-10


title: Breast cancer_BH0312-6


title: Breast cancer_153T


title: Breast cancer_BH0312-13


title: Breast cancer_BH0312-12


title: Breast cancer_BH0312-9


title: Breast cancer_140T


title: Breast cancer_BH0312-7


title: Breast cancer_BH0312-3


title: Breast cancer_142T


title: Breast cancer_BH0312-8


title: Breast cancer_151T


title: Breast cancer_BH0312-11


title: Breast cancer_129T


title: Breast cancer_135T


title: Breast cancer_136T


title: Breast cancer_134T


title: Breast cancer_76 cancer


title: Breast cancer_111T


title: Breast cancer_90T


title: Breast cancer_120T


title: Breast cancer_128T


title: Breast cancer_72 cancer


title: Breast cancer_75 cancer


title: Breast cancer_70 cancer


title: Breast cancer_69 cancer


title: Breast cancer_78 cancer2


title: Breast cancer_66 cancer


title: Breast cancer_64 cancer


title: Breast cancer_28 camcer


title: Breast cancer_59 cancer


title: Breast cancer_58 cancer


title: Breast cancer_62 cancer


title: Breast cancer_48 cancer


title: Breast cancer_65 cancer


title: Breast cancer_13 cancer


title: Breast cancer_14 cancer


title: Breast cancer_22 cancer


title: Breast cancer_10 cancer


title: Breast cancer_12 cancer


title: Breast cancer_15 cancer


title: Breast cancer_BH0312-4