title: 3C-seq control for rifampicin treatment of SMChigh cells and parSopt at –9kb in exp phase in SMG at 37°C

source_name: 3C-seq control for rifampicin treatment of SMChigh cells and parSopt at –9kb in exponential phase in SMG at 37°C.

extract_protocol:
3C-seq  3C libraries were prepared as previously described (Marbouty et al., 2015). Minimal media (SMG) was used instead of LB. Briefly, cells were grown in 400 ml of SMG medium to exponential phase (OD = 0.022-0.030) and fixed with fresh formaldehyde (3% final concentration) for 30 minutes at RT, followed by 30 minutes at 4°C and quenched for 30 minutes with 0.25 M glycine at 4°C. Fixed cells were harvested by filtering, washed in fresh SMG, frozen in liquid nitrogen and stored at -80°C until further use.    For time-course experiments 2 l preculture was first grown until mid-exponential phase (OD = 0.022-0.030) and next, appropriate culture volumes were added to fresh pre-warmed SMG so that at given time points 2 x 200 ml of culture at mid-exponential could be collected (two technical replicates). The cultures were induced with 2 mM theophylline or 1 mM IPTG, depending on the promoter used, Ptheo or Pspank, respectively. Due to characteristics of the theophylline switch, the pre-culture as well as induction was performed at 30°C.     Frozen pellets were resuspended in 600 µl 1x TE and incubated at RT for 20 minutes with 4 µl of Ready-lyze lysozyme (35U/ul, Tebu Bio). Next, SDS was added to a final concentration of 0.5% and incubated at RT for 10 minutes.   50 µl of lysed cells were aliquoted to 8 tubes containing 450 µl of digestion mix (1x NEB 1 buffer, 1% triton X-100, and 100 U HpaII enzyme (NEB)) and incubated at 37°C for 3 hours with constant shaking. Digested DNA was collected by centrifugation, diluted into 4 tubes containing 8 ml of ligation mix (1x ligation buffer: 50 mM Tris-HCl, 10 mM MgCl2, 10 mM DTT), 1 mM ATP, 0.1 mg/ml BSA, 125 U T4 DNA ligase 5 U/ml) and incubated at 16°C for 4 hours. Ligation reaction was followed by O/N decrosslinking at 65°C in the presence of 250 µg/ml proteinase K (Eurobio) and 5 mM EDTA.  DNA was precipitated with 1 volume of isopropanol and 0.1 Volume of 3 M sodium acetate (pH 5.2, Sigma) at -80°C for 1 hour. After centrifugation, the DNA pellet was resuspended in 1x TE at 30°C for 20 minutes. Next, DNA was extracted once with 400 µl phenol-chloroform-isoamyl alcohol solution and precipitated with 1.5 volume cold 100% ethanol in the presence of 0.1 volume 3 M sodium acetate at -80°C for 30 minutes. The pellet was collected and resuspended in 30 µl TE with RNaseA at 37°C for 30 minutes. All tubes were pooled and the resulting 3C library was quantified on gel using ImageJ.     ChIP-seq  ChIP samples were prepared as described previously (Bürmann et al., 2017). Briefly, cells were cultured in 200 ml of minimal media (SMG) at 37°C until mid-exponential phase (OD=0.022-0.030) and fixed with buffer F (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 0.5 mM EGTA pH 8.0, 1 mM EDTA pH 8.0, 10% (w/v) formaldehyde) for 30 minutes at RT with occasional shaking. Cells were harvested by filtration and washed in PBS. Each sample was adjusted for 2 OD units (2 ml at OD600 = 1) and resuspended in TSEMS lysis buffer (50 mM Tris pH 7.4, 50 mM NaCl, 10 mM EDTA pH 8.0, 0.5 M sucrose and PIC (Sigma), 6 mg/ml lysozyme from chicken egg white (Sigma)). After 30 minutes of incubation at 37°C with vigorous shaking protoplasts were washed again in 2 ml TSEMS, resuspended in 1 ml TSEMS, split into 3 aliquots, pelleted and, after flash freezing, stored at -80°C until further use.    For time-course experiments 1 l preculture was first grown until mid-exponential phase (OD = 0.022-0.030) and next, appropriate culture volumes were added to fresh pre-warmed SMG so that at given time points 200 ml of culture at mid-exponential could be processed. The cultures were induced with 2 mM theophylline (Ptheo promoter). Due to characteristics of the theophylline switch, the pre-culture as well as induction was performed at 30°C.     For IP of samples for ChIP-seq, each pellet was resuspended in 1 ml of buffer L (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1% (v/v) Triton X-100, 0.1% (w/v) Na-deoxycholate, 0.1 mg/ml RNaseA and PIC (Sigma)) and transferred to milliTUBE 1ml AFA Fiber and sonicated in a Covaris E220 water bath sonicator for 5 minutes at 4°C, 100 W, 200 cycles, 10% load and water level 5. Next, lysates were transferred into 2 ml tubes and centrifuged 10 minutes at 21000g at 4°C. 800 µl of supernatant was used for IP and 200 µl was kept as WCE (whole cell extract).     For IP, first, antibody serum was incubated with Protein G coupled Dynabeads (Invitrogen) in 1:1 ratio for 2.5 hours at 4°C with rotation. Next, beads were washed in buffer L and 50 µl were aliquoted to each sample tube. Samples were incubated for 2 hours at 4°C with rotation, followed by a series of washes with buffer L, buffer L5 (buffer L containing 500 mM NaCl), buffer W (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% (v/v) NP-40, 0.5% (w/v) sodium deoxycholate, 1 mM EDTA pH 8.0) and buffer TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0). Finally, the beads were resuspended in 520 µl buffer TES (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% (w/v) SDS). 300 µl of TES and 20 µl of 10% SDS were also added to WCE. Both tubes were incubated O/N at 65°C with vigorous shaking to reverse formaldehyde crosslinks.    Following rabbit polyclonal antibodies were used:  For anti-scpB ChIP time-course experiment COD3 BsScpB-His6.  For other anti-scpB ChIP experiments COD33 BsScpB-His6.  For anti-parB ChIP experiments COD11 BsParB-His.  All were manufactured by Eurogentec.    Phenol-chloroform extraction was performed to purify the decrosslinked DNA. Samples were transferred to screw cap 1.5-ml tubes and first mixed vigorously with 500 µl of phenol equilibrated with buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). After centrifugation (10 minutes, RT, 13000 rpm), 450 µl of the aqueous phase was transferred to a new screw cap tube and mixed with equal volume of chloroform, followed by centrifugation. 400ul of aqueous phase was recovered for DNA precipitation with 2.5x volume of 100 % ethanol, 0.1x volume of 3M NaOAc and 1.2 µl of GlycoBlue and incubated for 20 minutes at -20°C. Next, samples were centrifuged for 10 minutes at 20000 g at RT and pellets obtained pellets were resuspended in 10 µl of EB (Qiagen) shaking at 55°C for 10 minutes and finally purified with a PCR purification kit, eluting in 50 uL EB.
3C-seq  1 ug of 3C library was suspended in water (final volume 130 µl) and sonicated using Covaris S220 (following manufacturers recommendations to obtain 500 bp target size). Next, DNA was purified with Qiagen PCR purification kit, eluted in 40 µl EB and quantified using NanoDrop. 1 ug of DNA was processed according to manufacturer instructions (Paired-End DNA sample Prep Kit – Illumina – PE-930-1001), except that DNA was ligated to custom-made adapters for 4 hours at RT, followed by inactivation step at 65°C for 20 minutes. DNA was purified with 0.75x AMPure beads and 3 µl were used for 50 µl PCR reaction (12 cycles). Amplified libraries were purified on Qiagen columns and pair end sequenced on an Illumina platform (HiSeq4000 or NextSeq).     ChIP-seq  For deep sequencing, the DNA libraries were prepared by Genomic Facility at CIG, UNIL, Lausanne. Briefly, the DNA was fragmented by sonication (Covaris S2) to fragment sizes ranging from 220–250 bp. DNA libraries were prepared using the Ovation Ultralow Library Systems V2 Kit (NuGEN) including 15 cycles of PCR amplification. Five to ten million single end sequence reads were obtained on a HiSeq2500 (Illumina) with 150-bp read length

tag: genotype

value: 1A700, [delta]7-parS(parS359+), smc::ermB, [delta]amyE::smc::CAT, qoxD-specR::scpAB-ywcE


title: 3C-seq for rifampicin treatment of SMChigh cells and parSopt at –9kb in exp phase in SMG at 37°C

status: Public on Jul 30 2021

type: SRA

city: Lausanne

first: Anna

last: Anchimiuk

state: Vaud

address: UNIL-Sorge District

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

library_source: genomic

data_processing:
ChIP-seq data was trimmed using Trimmomatic-0.39 (SE -phred33, ILLUMINACLIP:TruSeq3-SE:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36), mapped with bowtie2 using --very-sensitive-local setting, sorted with samtools and obtained .bam files were further imported to SeqMonk for Read Count Quantitation.
Sequencing data from 3C-seq experiments was demultiplexed, adapters trimmed, and PCR duplicates removed using custom scripts. If additional sequencing was performed, it is indicated in the sample name as '_reseq' and the data was pooled prior to mapping. Next, data was processed as described at https://github.com/axelcournac/3C_tutorial.
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-local
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.
3C-seq: binning at 10kb. ChIP-seq: binning at 1kb.
Genome_build: NC_000964 (1A700) or NC_022898 (PY79)
Supplementary_files_format_and_content: 422x422 (for 1A700 strains) and 404x404 (for PY79 strains) normalized contact matrix in txt format for the 3C-seq data. '_pooled' in processed data file name contains a matrix resulting from processing data from sample which was resequenced and both fastq files were combined. Read Count Quantitation and generation of Probe Report in .txt format with SeqMonk (used All Reads, Correct for total read count, Correcct for Milion Reads) for the ChIP-seq data.

molecule: genomic DNA

organism: Bacillus subtilis

source_name: 3C-seq for rifampicin treatment of SMChigh cells and parSopt at –9kb in exponential phase in SMG at 37°C.

growth_protocol: strains were grown overnight in SMG, diluted to OD600 0.004 in fresh SMG and grown at 30 or 37°C until reached an OD600 between 0.022-0.026


title: 3C-seq for rifampicin treatment of SMChigh cells and parSopt at -304kb and –9kb in exp phase in SMG at 37°C

source_name: 3C-seq for rifampicin treatment of SMChigh cells and parSopt at -304kb and –9kb in exponential phase in SMG at 37°C.

value: 1A700, [delta]6-parS (mtparS334 to parS359), smc::ermB, [delta]amyE::smc::CAT, qoxD-specR::scpAB-ywcE


title: F6-3-1 [Bisulfite-Seq]

city: Copenhagen

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
1) Reads were trimmed using Trim Galore!  v0.4.3 with the --rrbs flag.
2) Trimmed reads were mapped to mm10 (GENCODE vM13) and methylation levels estimated using Bismark v0.18.1 and Bowtie2 v2.2.5 on default settings.
3) The SNPs (dbSNP build 142) with major allele frequency 0.95 at most in autosomal chromosomes were filtered out.
4) CpGs with coverage larger than 10 times the 95-percentile of coverage in each sample are filtered out.
5) Differential methylation analysis was performed by edgeR v3.24.0 using "(sequencing) pool" as a covariate for maternal and paternal lines separately. CpGs with minimum 8 counts were considered for differential methylation analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Coverage (cov) files contain the coverage per sample (data processing step 2)

organism: Mus musculus

source_name: Quadricep

extract_protocol:
Allprep® DNA/RNA/miRNA Universal Kit (Qiagen) according to the manufacturer’s instructions
DNA samples were incubated with MpsI enzyme (NEB #R0106L). Bisulfite conversion was performed using the EZ DNA methylation lightening Kit (Zymo Research). The DNA was then PCR amplified and ligated to TruSeq (Illumina) sequencing adapters. Libraries were subjected to 75-bp single-end sequencing on NextSeq 2500 (Illumina ).

treatment_protocol:
Study 1: Female mice (C57BL/6, 8 weeks old) were subjected to either normal chow (NC) diet (n = 4) or 60% high-fat (HF) diet (Research Diets, NJ; n = 8) for 6 weeks. For mating, a lean male mouse (C57BL/6, 14 weeks old) was placed in the cage with 2 female mice. Once confirmed pregnant (by vaginal plug), the male mouse was removed and the female mice were housed individually in cages equipped with running wheels, which were locked for the sedentary groups. The groups were defined as normal chow, sedentary (NC-Sed), maternal high-fat diet, sedentary (M-HF-Sed) and maternal high-fat diet, exercise (M-HF-Ex).
Study 2: Male mice (C57BL/6, 8 weeks old) were subjected to either normal chow (NC) diet (n = 4) or 60% high-fat (HF) diet (Research Diets, NJ; n = 4) for 6 weeks. Male mice were then mated with lean female mice (C57BL/6, 14 weeks old) and once confirmed pregnant (by vaginal plug), the male mouse was removed, and the female mice were house individually with running wheels as described above. The groups were defined as normal chow, sedentary (NC-Sed), paternal high-fat diet, sedentary (P-HF-Sed) and paternal high-fat diet, exercise (P-HF-Ex).
In both studies, all groups were provided normal chow with sedentary activity from the day after birth and thereafter.  Adult offspring were humanely euthanized at 10 months of age and quadricep muscle collected. Study 1 and 2 were conducted in parallel allowing the NC-Sed group to serve as the control group for both studies.

tag: diet

value: high fat

tag: treatment

value: Ex

tag: parent

value: P

tag: group

value: PHE

tag: pool

value: D


title: F6-1-5 [Bisulfite-Seq]

value: normal chow

value: Sed

value: MP

value: NCS


title: 3C-seq for rifampicin treatment with wtSmc and parSopt at -304kb and –9kb in exp phase in SMG at 37°C

source_name: 3C-seq for rifampicin treatment of cells with wtSmc and parSopt at -304kb and –9kb in exponential phase in SMG at 37°C.

value: 1A700, [delta]6-parS (mtparS334 to parS359), smc::ermB


title: F5-3-4 [Bisulfite-Seq]

value: M

value: MHE

value: B


title: 3C-seq control for rifampicin treatment of SMChigh cells in exp phase in SMG at 37°C

source_name: 3C-seq control for rifampicin treatment of SMChigh cells in exponential phase in SMG at 37°C.

value: 1A700, [delta]amyE::smc::CAT, qoxD-specR::scpAB-ywcE, trpC2


title: 3C-seq for rifampicin treatment of SMChigh cells in exp phase in SMG at 37°C

source_name: 3C-seq for rifampicin treatment of SMChigh cells in exponential phase in SMG at 37°C.


title: m1_div5_ATACseq

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

country: USA

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm10 version of the mouse genome using Bowtie-1.1.1
For each sample peaks of accessibility were identified and annotated using MACS2 with the default settings
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files are normalized to reads per peak million (rpm) using R/Bioconductor

source_name: IRF4-sufficient B cells from division 5

extract_protocol:
Cells were FACS sorted into FACS buffer and tagmentation for ATAC-seq performed.
10,000 cells were centrifuged for 10 minutes at 500xg, and tagmentation was performed by resuspending cells in 25 ul of Tagmentation mix (1X TD buffer (10 mM TAPS-NaOH pH 8.1, 5 mM MgCl2, 10% DMF), 2.5 μl Tn5 transposase, 0.1% Tween 20 and 0.02% Digitonin) and then incubated for 1 h at 37°C. DNA was purified and amplified into a sequencing library with KAPA HiFi Polymerase and the Nextera Indexing Kit Primers (Illumina, Inc).

treatment_protocol: Splenic naive IRF4-sufficent and -deficient B cells were isolated (Miltenyi CD43- isolation kit), CTV-labeled, and 15 million cells were transferred into mMT hosts. One day later host mice were challenged with LPS, and three days post-LPS challenge cells were isolated in discrete division by the indicated markers.

tag: Sex

value: Female

tag: sorting markers

tag: genotype/variation

value: Cd19+/+ Irf4fl/fl

tag: tissues for b cell isolation and recovered from hosts

value: Spleen

tag: host

value: uMT

tag: stimulation

value: LPS

tag: days post-lps inoculation of host


title: 3C-seq control for rifampicin treatment of SMChigh cells and parSopt at -304kb and –9kb in exp phase in SMG at 37°C

source_name: 3C-seq control for rifampicin treatment of SMChigh cells and parSopt at -304kb and –9kb in exponential phase in SMG at 37°C.

value: 1A700, [delta]6-parS (mtparS334 to parS359), smc::ermB, [delta]amyE::smc::CAT, qoxD-specR::scpAB-ywcE


title: 3C-seq control for rifampicin treatment with Smc-CC425 and parSopt at -304kb and –9kb in exp phase in SMG at 37°C

source_name: 3C-seq control for rifampicin treatment of cells with Smc-CC425 and parSopt at -304kb and –9kb in exponential phase in SMG at 37°C.


title: 3C-seq for rifampicin treatment with Smc-CC425 and parSopt at -304kb and –9kb in exp phase in SMG at 37°C

source_name: 3C-seq for rifampicin treatment of cells with Smc-CC425 and parSopt at -304kb and –9kb in exponential phase in SMG at 37°C.


title: F5-3-1 [Bisulfite-Seq]

value: high fat

value: Ex


title: 3C-seq of cells with wtSmc and parS334 (at -304kb) inactivated in exponential phase in SMG at 37°C

extract_protocol:
3C-seq:
3C libraries were prepared as previously described (Marbouty et al., 2015). Minimal media (SMG) was used instead of LB. Briefly, cells were grown in 400 ml of SMG medium to exponential phase (OD = 0.022-0.030) and fixed with fresh formaldehyde (3% final concentration) for 30 minutes at RT, followed by 30 minutes at 4°C and quenched for 30 minutes with 0.25 M glycine at 4°C. Fixed cells were harvested by filtering, washed in fresh SMG, frozen in liquid nitrogen and stored at -80°C until further use.
For time-course experiments 2 l preculture was first grown until mid-exponential phase (OD = 0.022-0.030) and next, appropriate culture volumes were added to fresh pre-warmed SMG so that at given time points 2 x 200 ml of culture at mid-exponential could be collected (two technical replicates). The cultures were induced with 2 mM theophylline or 1 mM IPTG, depending on the promoter used, Ptheo or Pspank, respectively. Due to characteristics of the theophylline switch, the pre-culture as well as induction was performed at 30°C.
Frozen pellets were resuspended in 600 µl 1x TE and incubated at RT for 20 minutes with 4 µl of Ready-lyze lysozyme (35U/ul, Tebu Bio). Next, SDS was added to a final concentration of 0.5% and incubated at RT for 10 minutes.
50 µl of lysed cells were aliquoted to 8 tubes containing 450 µl of digestion mix (1x NEB 1 buffer, 1% triton X-100, and 100 U HpaII enzyme (NEB)) and incubated at 37°C for 3 hours with constant shaking. Digested DNA was collected by centrifugation, diluted into 4 tubes containing 8 ml of ligation mix (1x ligation buffer: 50 mM Tris-HCl, 10 mM MgCl2, 10 mM DTT), 1 mM ATP, 0.1 mg/ml BSA, 125 U T4 DNA ligase 5 U/ml) and incubated at 16°C for 4 hours. Ligation reaction was followed by O/N decrosslinking at 65°C in the presence of 250 µg/ml proteinase K (Eurobio) and 5 mM EDTA.
DNA was precipitated with 1 volume of isopropanol and 0.1 Volume of 3 M sodium acetate (pH 5.2, Sigma) at -80°C for 1 hour. After centrifugation, the DNA pellet was resuspended in 1x TE at 30°C for 20 minutes. Next, DNA was extracted once with 400 µl phenol-chloroform-isoamyl alcohol solution and precipitated with 1.5 volume cold 100% ethanol in the presence of 0.1 volume 3 M sodium acetate at -80°C for 30 minutes. The pellet was collected and resuspended in 30 µl TE with RNaseA at 37°C for 30 minutes. All tubes were pooled and the resulting 3C library was quantified on gel using ImageJ.
ChIP-seq:
ChIP samples were prepared as described previously (Bürmann et al., 2017). Briefly, cells were cultured in 200 ml of minimal media (SMG) at 37°C until mid-exponential phase (OD=0.022-0.030) and fixed with buffer F (50 mM Tris-HCl pH 7.4, 100 mM NaCl, 0.5 mM EGTA pH 8.0, 1 mM EDTA pH 8.0, 10% (w/v) formaldehyde) for 30 minutes at RT with occasional shaking. Cells were harvested by filtration and washed in PBS. Each sample was adjusted for 2 OD units (2 ml at OD600 = 1) and resuspended in TSEMS lysis buffer (50 mM Tris pH 7.4, 50 mM NaCl, 10 mM EDTA pH 8.0, 0.5 M sucrose and PIC (Sigma), 6 mg/ml lysozyme from chicken egg white (Sigma)). After 30 minutes of incubation at 37°C with vigorous shaking protoplasts were washed again in 2 ml TSEMS, resuspended in 1 ml TSEMS, split into 3 aliquots, pelleted and, after flash freezing, stored at -80°C until further use.
For time-course experiments 1 l preculture was first grown until mid-exponential phase (OD = 0.022-0.030) and next, appropriate culture volumes were added to fresh pre-warmed SMG so that at given time points 200 ml of culture at mid-exponential could be processed. The cultures were induced with 2 mM theophylline (Ptheo promoter). Due to characteristics of the theophylline switch, the pre-culture as well as induction was performed at 30°C.
For IP of samples for ChIP-seq, each pellet was resuspended in 1 ml of buffer L (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1% (v/v) Triton X-100, 0.1% (w/v) Na-deoxycholate, 0.1 mg/ml RNaseA and PIC (Sigma)) and transferred to milliTUBE 1ml AFA Fiber and sonicated in a Covaris E220 water bath sonicator for 5 minutes at 4°C, 100 W, 200 cycles, 10% load and water level 5. Next, lysates were transferred into 2 ml tubes and centrifuged 10 minutes at 21000g at 4°C. 800 µl of supernatant was used for IP and 200 µl was kept as WCE (whole cell extract).
For IP, first, antibody serum was incubated with Protein G coupled Dynabeads (Invitrogen) in 1:1 ratio for 2.5 hours at 4°C with rotation. Next, beads were washed in buffer L and 50 µl were aliquoted to each sample tube. Samples were incubated for 2 hours at 4°C with rotation, followed by a series of washes with buffer L, buffer L5 (buffer L containing 500 mM NaCl), buffer W (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% (v/v) NP-40, 0.5% (w/v) sodium deoxycholate, 1 mM EDTA pH 8.0) and buffer TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0). Finally, the beads were resuspended in 520 µl buffer TES (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1% (w/v) SDS). 300 µl of TES and 20 µl of 10% SDS were also added to WCE. Both tubes were incubated O/N at 65°C with vigorous shaking to reverse formaldehyde crosslinks.
Following rabbit polyclonal antibodies (manufactured by Eurogentec) were used:
For anti-scpB ChIP time-course experiment COD3 BsScpB-His6
For other anti-scpB ChIP experiments COD33 BsScpB-His6
For anti-parB ChIP experiments COD11 BsParB-His
Phenol-chloroform extraction was performed to purify the decrosslinked DNA. Samples were transferred to screw cap 1.5-ml tubes and first mixed vigorously with 500 µl of phenol equilibrated with buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). After centrifugation (10 minutes, RT, 13000 rpm), 450 µl of the aqueous phase was transferred to a new screw cap tube and mixed with equal volume of chloroform, followed by centrifugation. 400ul of aqueous phase was recovered for DNA precipitation with 2.5x volume of 100 % ethanol, 0.1x volume of 3M NaOAc and 1.2 µl of GlycoBlue and incubated for 20 minutes at -20°C. Next, samples were centrifuged for 10 minutes at 20000 g at RT and pellets obtained pellets were resuspended in 10 µl of EB (Qiagen) shaking at 55°C for 10 minutes and finally purified with a PCR purification kit, eluting in 50 uL EB.
3C-seq
1 ug of 3C library was suspended in water (final volume 130 µl) and sonicated using Covaris S220 (following manufacturers recommendations to obtain 500 bp target size). Next, DNA was purified with Qiagen PCR purification kit, eluted in 40 µl EB and quantified using NanoDrop. 1 ug of DNA was processed according to manufacturer instructions (Paired-End DNA sample Prep Kit – Illumina – PE-930-1001), except that DNA was ligated to custom-made adapters for 4 hours at RT, followed by inactivation step at 65°C for 20 minutes. DNA was purified with 0.75x AMPure beads and 3 µl were used for 50 µl PCR reaction (12 cycles). Amplified libraries were purified on Qiagen columns and pair end sequenced on an Illumina platform (HiSeq4000 or NextSeq).
ChIP-seq
For deep sequencing, the DNA libraries were prepared by Genomic Facility at CIG, UNIL, Lausanne. Briefly, the DNA was fragmented by sonication (Covaris S2) to fragment sizes ranging from 220–250 bp. DNA libraries were prepared using the Ovation Ultralow Library Systems V2 Kit (NuGEN) including 15 cycles of PCR amplification. Five to ten million single end sequence reads were obtained on a HiSeq2500 (Illumina) with 150-bp read length

tag: strain/genotype information

value: 1A700, Δ1-parS(mtparS334)


title: F4-2-1 [Bisulfite-Seq]

value: normal chow

value: Sed

value: D


title: 3C-seq for rifampicin treatment with Smc-CC425 and parS at –9kb in exp phase in SMG at 37°C

source_name: 3C-seq for rifampicin treatment of cells with Smc-CC425 and parS at –9kb in exponential phase in SMG at 37°C.

value: PY79:[delta]7-parS, parAB::specR, smc(1-476 SpnSmc(398-768) 695-1186) ftsY::ermB


title: 3C-seq of cells with wtSmc and parS334 (at -304kb) mutated to parSopt in exponential phase in SMG at 37°C

value: 1A700, mtparS334 to parS359


title: 3C-seq of cells with Smc-CC334, Spn hinge+CC100 in exponential phase in SMG at 37°C


title: 3C-seq control for rifampicin treatment with wtSmc and parS at –9kb in exp phase in SMG at 37°C

source_name: 3C-seq control for rifampicin treatment of cells with wtSmc and parS at –9kb in exponential phase in SMG at 37°C.

value: PY79:[delta]7-parS, parAB::kanR


title: 3C-seq for rifampicin treatment with wtSmc and parS at –9kb in exp phase in SMG at 37°C

source_name: 3C-seq for rifampicin treatment of cells with wtSmc and parS at –9kb in exponential phase in SMG at 37°C.


title: 3C-seq control for rifampicin treatment with Smc-CC425 and parS at –9kb in exp phase in SMG at 37°C

source_name: 3C-seq control for rifampicin treatment of cells with Smc-CC425 and parS at –9kb in exponential phase in SMG at 37°C.


title: F4-2-4 [Bisulfite-Seq]

value: MP

value: NCS

value: C


title: F4-1-7 [Bisulfite-Seq]

value: P

value: PHS


title: 3C-seq for rifampicin treatment with Smc-CC425 in exp phase in SMG at 37°C

source_name: 3C-seq for rifampicin treatment of cells with Smc-CC425 in exponential phase in SMG at 37°C.


title: F4-1-5 [Bisulfite-Seq]

value: B


title: 3C-seq of SMChigh cells and parSopt at -304kb and -9kb in exponential phase in SMG at 37°C

source_name: 3C-seq of SMChigh cells and parSopt at -304kb and –9kb in exponential phase in SMG at 37°C

value: 1A700, Δ6-parS (mtparS334 to parS359), smc::ermB, ΔamyE::smc::CAT, qoxD-specR::scpAB-ywcE


title: 3C-seq time course of wtSmc and parS at -304kb and –9kb cells in exponential phase in SMG at 37°C [BSG4427_t20_3C]

value: 1A700, Δ6-parS (mtparS334 to parS359), ΔparB::kanR, smc::specR, ΔamyE::(Pspank-optRBS-parB(mtparS)-lacI)::CAT


title: 3C-seq of SMChigh cells and parSopt at –304kb in exponential phase in SMG at 37°C

value: 1A700, Δ7-parS(parS334->359+), parAB::kanR, smc::ermB, ΔamyE::smc::CAT, qoxD-specR::scpAB-ywcE


title: 3C-seq of cells with Smc-CC296 in exponential phase in SMG at 37°C


title: 3C-seq of cells with Smc-CC257 in exponential phase in SMG at 37°C


title: 3C-seq of cells with Smc-CC334, Spn hinge in exponential phase in SMG at 37°C

value: 1A700, smc(Streptococcus pneumoniae hinge) ftsY::ermB, trpC2


title: F4-1-4 [Bisulfite-Seq]

value: high fat


title: 3C-seq of SMChigh cells and parSopt at -9kb in exponential phase in SMG at 37°C

source_name: 3C-seq of SMChigh cells and parSopt at –9kb in exponential phase in SMG at 37°C

value: 1A700, Δ7-parS(parS359+), smc::ermB, ΔamyE::smc::CAT, qoxD-specR::scpAB-ywcE


title: VC203

type: RNA

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: 1 µg of purified cRNA from samples and reference were hybridized on the oligo glass two-color array using Agilent Technologies SurePrint G3 Human Gene Expression Microarrays 4X44K v2. The dye-swap replication procedure was applied.

scan_protocol: Images were scanned using an Agilent C dual-laser microarray scanner and analyzed by the Agilent Feature Extraction (FE) Software (Agilent Technologies).

data_processing: The LIMMA (LInear Models for Microarray Analysis) package was used to analyze gene expression profile of oropharynx squamous cell carcinoma samples. Raw intensity values were background subtracted (method = normexp, offset = 50) and normalized using the loess method, for the within array normalizaton, and Aquantile, for the between array normalization. Duplicated probes were averaged. Then, Cy3 and Cy5 channels were separated using the separate channel analysis of two-color data, available within the Limma package.

molecule: total RNA

organism: Homo sapiens

label_protocol: Five hundred ng of total RNA of each sample and of Universal Reference (Human Universal Reference Total RNA; Clontech, Mountain View, CA) were amplified by the Amino Allyl MessageAmp I aRNA Kit (Ambion, Austin, TX), as previously described [20]. Labeling was performed using cyanine 3 (IRIS 3) and cyanine 5 (IRIS 5) (Molecular Targeting Technologies, Inc).

extract_protocol: Briefly, fresh frozen tissues were fragmented through mechanical homogenization by using TissueLyser LT (Qiagen) and addition of TRI Reagent (Sigma Aldrich). Total RNA extraction and isolation was performed by using the Absolutely RNA miRNA kit (Agilent Technologies) following the manufacturer’s instructions. The quality of total RNA was assessed by capillary electrophoresis with Bioanalyzer 2100 (Agilent Technologies); Purity and quantity of total RNA were assessed using NanoDrop spectrophotometer (NanoDrop Thermo Scientific).

tag: tissue

value: Oropharynx squamous cell carcinoma

tag: hpv status

value: Negative

tag: survival

value: deceased

source_name: Ref

value: Universal Reference


title: 3C-seq control for rifampicin treatment with wtSmc and parSopt at -304kb and –9kb in exp phase in SMG at 37°C

source_name: 3C-seq control for rifampicin treatment of cells with wtSmc and parSopt at -304kb and –9kb in exponential phase in SMG at 37°C.

tag: genotype

value: 1A700, [delta]6-parS (mtparS334 to parS359), smc::ermB


title: 3C-seq time course of wtSmc and parS at -304kb and –9kb cells in exponential phase in SMG at 37°C [BSG4427_t10_3C]


title: 3C-seq control for rifampicin treatment with Smc-CC425 in exp phase in SMG at 37°C

source_name: 3C-seq control for rifampicin treatment of cells with Smc-CC425 in exponential phase in SMG at 37°C.


title: 3C-seq control for rifampicin treatment of wt cells in exp phase in SMG at 37°C

source_name: 3C-seq control for rifampicin treatment of wt cells in exponential phase in SMG at 37°C.

value: PY79:smc::tet, parAB::kanR


title: 3C-seq of wt cells in exp phase in SMG at 37°C

source_name: 3C-seq of wt cells in exponential phase in SMG at 37°C.


title: 3C-seq time course of wtSmc and parS at –9kb cells in exponential phase in SMG at 37°C [BSG4152_t15_3C]

value: 1A700, Δ7-parS(parS359+), ΔparB::kanR, smc::specR, ΔamyE::(Pspank-optRBS-parB(mtparS)-lacI)::CAT


title: 3C-seq of SMChigh cells in exponential phase in SMG at 37°C

value: 1A700, ΔamyE::smc::CAT, qoxD-specR::scpAB-ywcE, trpC2


title: 3C-seq time course of wtSmc and parS at -304kb and –9kb cells in exponential phase in SMG at 37°C [BSG4427_t0_3C]


title: F4-1-1 [Bisulfite-Seq]

source_name: Quadricep

tag: diet

value: Sed

value: P

value: C


title: 3C-seq of cells with wtSmc and parSopt at -304kb and +328kb in exponential phase in SMG at 37°C

value: 1A700, Δ6-parS(parS334->359+), parAB::kanR, smc::ermB, ΔamyE::parS-359 + tetO qPCR primer seq::cat


title: 3C-seq time course of wtSmc and parS at –9kb cells in exponential phase in SMG at 37°C [BSG4152_t10_3C]


title: 3C-seq time course of wtSmc and parS at -304kb and –9kb cells in exponential phase in SMG at 37°C [BSG4427_t15_3C]

value: 1A700, Δ6-parS (mtparS334 to parS359), ΔparB::kanR, smc::specR, ΔamyE::(Pspank-optRBS-parB(mtparS)-lacI)::CAT


title: F2-4-7 [Bisulfite-Seq]

tag: treatment

value: PHS

value: D


title: F2-4-4 [Bisulfite-Seq]

value: high fat

tag: parent


title: Heart KO Rep5

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: age 12 w, male

library_source: transcriptomic

data_processing:
trimmed with trim_galore version 0.6.4. Parameters: --length 26 --phred33
Tophat with Parameters: -p 16 -g 1 --segment-length 25 -i 30 -I 3000
Get raw counts with featureCounts (R package Rsubread version 2.1.5)
RPKM Normalization was performed with the returnRPKM function (systemPipeR package version 1.22)
Genome_build: mm10 from UCSC
Supplementary_files_format_and_content: RPKM values and raw counts

source_name: left ventricle

extract_protocol:
Hearts were rapidly removed, RNA extracted using Trizol
RNA libraries were prepared for sequencing using standard BGISeq-500 protocols

value: KO

tag: strain

value: heart


title: F2-4-1 [Bisulfite-Seq]

tag: group

tag: pool

value: A


title: F2-3-7 [Bisulfite-Seq]

value: B


title: 3C-seq of SMChigh cells and parSopt at –304kb in exponential phase in SMG at 37°C_rep

value: 1A700, Δ7-parS(parS334->359+), parAB::kanR, smc::ermB, ΔamyE::smc::CAT, qoxD-specR::scpAB-ywcE


title: Heart KO Rep3

description: age 12 w, male


title: 3C-seq time course of wtSmc and parS at -304kb and -9kb cells in exponential phase in SMG at 37°C [t25]

source_name: 3C-seq time course of wtSmc and parS at -304kb and –9kb cells in exponential phase in SMG at 37°C


title: 3C-seq of SMChigh cells and parSopt at -304kb and -9kb in exponential phase in SMG at 37°C_rep

value: 1A700, Δ6-parS (mtparS334 to parS359), smc::ermB, ΔamyE::smc::CAT, qoxD-specR::scpAB-ywcE


title: 3C-seq time course of wtSmc and parS at -9kb cells in exponential phase in SMG at 37°C [t25]

source_name: 3C-seq time course of wtSmc and parS at –9kb cells in exponential phase in SMG at 37°C


title: 3C-seq of cells with wtSmc and parSopt at -9kb and +328kb in exponential phase in SMG at 37°C_rep

source_name: 3C-seq of cells with wtSmc and parSopt at –9kb and +328kb in exponential phase in SMG at 37°C

value: 1A700, Δ6-parS(parS359+), smc::specR, ΔamyE::parS-359 + tetO qPCR primer seq::cat


title: 3C-seq of cells with wtSmc and parSopt at -9kb and +328kb in exponential phase in SMG at 37°C


title: 3C-seq of cells with wtSmc and parSopt at -304kb and -9kb in exponential phase in SMG at 37°C_rep

source_name: 3C-seq of cells with wtSmc and parSopt at -304kb and –9kb in exponential phase in SMG at 37°C

value: 1A700, Δ6-parS (mtparS334 to parS359), smc::ermB


title: Heart KO Rep2

description: age 12 w, male


title: 3C-seq of cells with wtSmc and parSopt at -304kb and -9kb in exponential phase in SMG at 37°C


title: F2-2-7 [Bisulfite-Seq]

value: Ex

value: PHE


title: 3C-seq time course of wtSmc and parS at –9kb cells in exponential phase in SMG at 37°C [BSG4152_t20_3C]

value: 1A700, Δ7-parS(parS359+), ΔparB::kanR, smc::specR, ΔamyE::(Pspank-optRBS-parB(mtparS)-lacI)::CAT


title: F3-4-8 [Bisulfite-Seq]

value: M

value: MHE


title: 3C-seq of cells with wtSmc and parSopt at +328kb in exponential phase in SMG at 37°C_rep

value: 1A700, Δ7-parS, parAB::kanR, smc::specR, ΔamyE::parS-359 + tetO qPCR primer seq::cat


title: 3C-seq of SMChigh cells and parSopt at -9kb in exponential phase in SMG at 37°C_rep

value: 1A700, Δ7-parS(parS359+), smc::ermB, ΔamyE::smc::CAT, qoxD-specR::scpAB-ywcE


title: 3C-seq time course of wtSmc and parS at –9kb cells in exponential phase in SMG at 37°C [BSG4152_t0_3C]


title: F2-1-7 [Bisulfite-Seq]

value: P


title: Heart KO Rep1

description: age 12 w, male


title: 3C-seq of SMChigh cells in exponential phase in SMG at 37°C_rep

value: 1A700, ΔamyE::smc::CAT, qoxD-specR::scpAB-ywcE, trpC2


title: F2-1-2 [Bisulfite-Seq]

value: high fat

value: D


title: Heart WT  Rep5

description: age 12 w, male

value: WT

value: heart


title: 3C-seq of cells with wtSmc and parSopt at -304kb and +328kb in exponential phase in SMG at 37°C_rep

value: 1A700, Δ6-parS(parS334->359+), parAB::kanR, smc::ermB, ΔamyE::parS-359 + tetO qPCR primer seq::cat


title: Heart KO Rep4

description: age 12 w, male

value: KO


title: F1-4-5 [Bisulfite-Seq]

value: C


title: 3C-seq of cells with Smc-CC425 and parSopt at -304kb in exponential phase in SMG at 37°C_rep

value: 1A700, Δ7-parS(parS334->359+), parAB::kanR, smc::ermB


title: 3C-seq of cells with Smc-CC425 and parSopt at -304kb in exponential phase in SMG at 37°C


title: Blood_RO_B3

city: Raebareli

first: SANJAY

last: YADAV

state: UTTAR PRADESH

address: All India Institute of Medical Sciences Dalmau Road, Munshiganj,

country: India

institute: AIIMS RAEBARLI

description: Rotenone 3

data_processing:
The raw data was analyzed by ExpressionSuite software and Relative quantification of miRNAs expression was calculated by -ΔΔCt method, selecting U87 level as endogenous control. software performs all deltadeltaCt based fold-change calculations and performed student t-test to calculate p-value from the uploaded raw threshold cycle data .
ExpressionSuite software- Computed normalized signal intensity

label: FAM-NFQ

organism: Rattus norvegicus

source_name: Peripheral blood

label_protocol: A TaqMan Custom RT pool primer (Cat#A25630) of 112 miRNAs was used for cDNA synthesis by reverse transcription. Reverse transcription of mature miRNAs was carried out by using a TaqMan miRNA Reverse Transcription kit reagents (Cat# 4366596) from Thermo Fischer, USA. In short, the reaction mixture contained MultiScribe reverse transcriptase 75 units, RT buffer 1X, OpenArray Custom RT primers 1X, RNase inhibitor 2 units, 3mM MgCl2, 2.0mM deoxynucleotide triphosphates (dNTPs) and 100ng of RNA input limiting 7.5µl the final reaction volume. Thermal cycling of Reverse transcription process was repeated for additional 39 cycles of 16°C for 2 minutes, 42°C for 1 minute and 50°C for 1 second. . In Preamplification, a total 25 µl reaction volume including 2.5µl custom preamp primer pools mixed with 12.5µl of preamp master mix and 2.5µl cDNA and additional nuclease-free water add to reach the final volume. The thermal cycling condition used for preamplification were 95°C for 10 min, 55°C for 2 min, 72°C for 2 min and 12 cycles of 95°C/15 sec, 60°C/4 min. At the end of cycling, preamplification products were incubated at 99.90C for 10 min. for inactivation of enzymes. Preamplification products were diluted (1 to 40) in 0.1X Tris-EDTA buffer. The diluted preamplification products mixed with 2x TaqMan OpenArray Real-Time PCR Master Mix (Cat#4462159) and pipette on OpenArray plates by OpenArray AccuFill System from Thermo Fisher Scientific and run the preamplification product as described manufacturer on QuantStudio 12K Flex RT-PCR machine from Thermo Fisher Scientific, USA

growth_protocol: All the animals were kept under the standard condition (light/dark cycle: 12/12 h, temp: 22˚C, with ad libitum commercial pellet diet and water) and cared for in according to guidelines of CSIR- IITR Institutional Animal Ethics Committee (IAEC).

extract_protocol: Ribopure Blood RNA Isolation Kit by Thermo Fisher was utilized to extract the RNA (including small RNAs) as suggested protocol by manufacturer protocol.

treatment_protocol: Wistar rats were intraperitoneally injected 2.5mg/kg body weight for 2 months (60 days). Control animals received intraperitoneal injection of the vehicle only.

tag: agent

value: Rotenone

tag: Sex

value: Male

value: Wistar albino

value: Blood

tag: developmental stage

value: 12 week


title: F1-4-4 [Bisulfite-Seq]

value: normal chow

value: Sed

value: MP

value: NCS

value: B


title: 3C-seq of cells with wtSmc and parSopt at +328kb in exponential phase in SMG at 37°C

value: 1A700, Δ7-parS, parAB::kanR, smc::specR, ΔamyE::parS-359 + tetO qPCR primer seq::cat


title: Heart WT  Rep3

description: age 12 w, male

value: WT


title: 3C-seq of cells with Smc-CC425 and parSopt at -304kb and -9kb in exponential phase in SMG at 37°C

source_name: 3C-seq of cells with Smc-CC425 and parSopt at -304kb and –9kb in exponential phase in SMG at 37°C


title: Blood_RO_B2

description: Rotenone 2


title: Heart WT  Rep4

description: age 12 w, male

value: heart


title: F1-3-7 [Bisulfite-Seq]

value: D


title: Blood_RO_B1

description: Rotenone 1


title: Heart WT  Rep1

description: age 12 w, male


title: F1-3-3 [Bisulfite-Seq]


title: Blood_VC_B3

description: Control 3

value: Control


title: 3C-seq time course t40 of Smc-CC425 and parS at -9kb cells in exponential phase in SMG at 30°C

source_name: 3C-seq time course t40 of Smc-CC425 and parS at –9kb cells in exponential phase in SMG at 30°C

value: PY79:Δ7-parS(parS359+), ΔparB::kanR, smc(1-476 SpnSmc(398-768) 695-1186) ftsY::ermB, amyE::(PhbsB short 5'UTR-theo E+ -parB (mtparS))::CAT


title: Heart WT  Rep2

description: age 12 w, male


title: F1-3-1 [Bisulfite-Seq]

value: A


title: F7-4-4

data_processing:
Reads were mapped to mm10 with STAR v2.5.2b and gene read coverages were computed with featureCounts v1.5.2 using GENCODE vM13 annotation
Differentially expressed genes were identified using DESeq2 v1.11.8 for maternal and paternal lines separately.
Genome_build: mm10
Supplementary_files_format_and_content: Text file in tab separated format with gene coverages in units of normalized read counts

extract_protocol:
Total RNA was extracted from skeletal muscle with TRIzol (Invitrogen, Madison, WI, USA) according to the manufacturer’s instructions.
RNA was checked for quality using the Bioanalyser instrument (Agilent Technologies) and subject to the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol (Illumina). Libraries were subjected to 100-bp single-end sequencing on HiSeq 2500 (Illumina).

value: high-fat diet

value: Ex

value: M

value: MHE


title: Blood_VC_B2

description: Control 2

value: Male

value: Wistar albino

value: Blood

value: 12 week


title: 3C-seq time course t20 of Smc-CC425 and parS at -9kb cells in exponential phase in SMG at 30°C

source_name: 3C-seq time course t20 of Smc-CC425 and parS at –9kb cells in exponential phase in SMG at 30°C


title: 3C-seq time course t30 of Smc-CC425 and parS at -9kb cells in exponential phase in SMG at 30°C

source_name: 3C-seq time course t30 of Smc-CC425 and parS at –9kb cells in exponential phase in SMG at 30°C


title: Blood_VC_B1

description: Control 1


title: F7-2-4

value: Sed

value: MHS


title: F7-2-1


title: mLST8-knockout H1299 cells reconstituted with mLST8-E303D mutant [303-3]

city: Shanghai

first: Yingji

last: Chen

address: 2005 Songhu Road

department: School of Life Science

country: China

institute: Fudan University

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data).
The reference genomes and the annotation file were downloaded from ENSEMBL database. Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0. HISAT2 is the successor to TopHat2, which uses a modified BWT algorithm to convert reference genomes to index for faster speed and fewer resources.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample,FPKM could eliminate the effect of sequencing depth and gene length on gene expression levels.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

growth_protocol: H1299 cells were maintained in DMEM with 10% (v/v) FBS

extract_protocol:
NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530L, NEB, USA) was used with 2 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: untreated

tag: cell type

value: Human non-small cell lung cancer cells

tag: genotype/variation

value: mLST8-E303D mutant


title: mLST8-knockout H1299 cells reconstituted with mLST8-E303D mutant [303-2]


title: 3C-seq time course t60 of wtSmc and parS at -9kb cells in exponential phase in SMG at 30°C

source_name: 3C-seq time course t60 of wtSmc and parS at –9kb cells in exponential phase in SMG at 30°C

value: PY79:Δ7-parS(parS359+), ΔparB::kanR, amyE::(PhbsB short 5'UTR-theo E+ -parB (mtparS))::CAT


title: 3C-seq time course t0 of Smc-CC425 and parS at -9kb cells in exponential phase in SMG at 30°C

source_name: 3C-seq time course t0 of Smc-CC425 and parS at –9kb cells in exponential phase in SMG at 30°C


title: 3C-seq time course t60 of Smc-CC425 and parS at -9kb cells in exponential phase in SMG at 30°C

source_name: 3C-seq time course t60 of Smc-CC425 and parS at –9kb cells in exponential phase in SMG at 30°C


title: F6-3-4

value: P

value: PHE


title: 3C-seq time course t40 of wtSmc and parS at -9kb cells in exponential phase in SMG at 30°C

source_name: 3C-seq time course t40 of wtSmc and parS at –9kb cells in exponential phase in SMG at 30°C


title: F7-1-3


title: F6-1-5

value: normal chow

value: MP

value: NCS


title: mLST8-knockout H1299 cells reconstituted with mLST8-wild type [WT-2]

value: mLST8-wild type


title: F5-3-4

value: high-fat diet

value: Ex

value: M


title: 3C-seq time course t30 of wtSmc and parS at -9kb cells in exponential phase in SMG at 30°C

source_name: 3C-seq time course t30 of wtSmc and parS at –9kb cells in exponential phase in SMG at 30°C


title: mLST8-knockout H1299 cells reconstituted with mLST8-wild type [WT-1]


title: 3C-seq time course t20 of wtSmc and parS at -9kb cells in exponential phase in SMG at 30°C

source_name: 3C-seq time course t20 of wtSmc and parS at –9kb cells in exponential phase in SMG at 30°C


title: 3C-seq time course t0 of wtSmc and parS at -9kb cells in exponential phase in SMG at 30°C

source_name: 3C-seq time course t0 of wtSmc and parS at –9kb cells in exponential phase in SMG at 30°C


title: 3C-seq of cells with Smc-CC253 and parS at -9kb in exponential phase in SMG at 37°C

source_name: 3C-seq of cells with Smc-CC253 and parS at –9kb in exponential phase in SMG at 37°C


title: F4-1-1

source_name: Quadricep

value: PHS


title: F3-4-8

value: MHE


title: mLST8-knockout H1299 cells reconstituted with mLST8-E303D mutant [303-1]


title: mLST8-knockout H1299 cells reconstituted with mLST8-wild type [WT-3]


title: F2-4-7


title: Cortical brain organoids_batch 2, scRNA-seq

city: San Francisco

first: Chang

last: Kim

address: 505 Parnassus Ave

institute: UCSF

data_processing:
cellranger-3.0.0 count
Multi-seq demultiplexing was used to remove doublets and assign cells
Genome_build: Human reference, GRCh38 (Ensembl 93)
Supplementary_files_format_and_content: Count matrix of cellranger count after doublet removal

source_name: Org_MG_batch 2

growth_protocol: Cerebral organoids were generated based on a previously published method (Pasca, Sloan et al. 2015)

extract_protocol:
Cells were enzymatically and mechanically digested and useds with the standard 10X Genomics scRNAseq pipeline
RNA libraries were prepared for sequencing using standard 10X Genomics protocols

treatment_protocol: Primary microglia engrafted into organoids at week5 and cultured for additional 5 weeks

tag: sample type

value: Cortical brain organoids

value: iPSC-derived

tag: age

value: week 10

tag: cell line

value: mixed samples (Lines 28126, 1323-4, YH10)

value: mixed samples (with and without microglia)


title: Cortical brain organoids_batch 1, scRNA-seq

source_name: Org_MG_batch 1


title: 3C-seq of cells with Smc-CC421 and parS at -9kb in exponential phase in SMG at 37°C

source_name: 3C-seq of cells with Smc-CC421 and parS at –9kb in exponential phase in SMG at 37°C

tag: strain/genotype information


title: S5: mouse_sepsis_24h_rep5

city: chongqing

first: Liying

last: Zou

address: 136 Zhongshan 2nd

institute: Children's Hspital of ChongQing Medical University

description: gene expression after 24h in septic mouse lung

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression(8*60K)for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: C57BL/6 mice (male) at 6-8 weeks old were raised under specific pathogen-free conditions in a mouse facility, with food and water ad libitum.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions

treatment_protocol: Briefly, anesthesia was induced using an intraperitoneal injection of pentobarbital sodium 50 mg/kg and the mouse cecum was exposed by a 2-cm laparotomy under aseptic con-ditions. A 21-gauge needle performed two through-and-through punctures in the medial between the end of the cecum and the ligation site. Some feces was then extruded through the punctures. We then repositioned the cecum in the peritoneal cavity and sutured the incision. The sham-operated group mice underwent the same process without puncture and ligation. All mice were resuscitated with Saline at 5 ml/100 g was used to resuscitate the mice.

tag: tissue

value: lung

value: male


title: F2-3-7

value: Sed

value: P


title: iPSC-derived microglia cells, scRNA-seq

source_name: iMG

growth_protocol: Cells shipped from manufacturer

treatment_protocol: FBS-free culture conditions for 8 days

value: iPSC-derived microglia cells

value: Fujifilm Cellular Dynamics  1279


title: S4: mouse_sepsis_24h_rep4


title: 3C-seq of cells with Smc-CC425 and parS at -9kb in exponential phase in SMG at 37°C

source_name: 3C-seq of cells with Smc-CC425 and parS at –9kb in exponential phase in SMG at 37°C


title: F2-1-2

value: PHE


title: S6: mouse_sepsis_24h_rep6


title: S3: mouse_sepsis_24h_rep3


title: Head_tumor_6

city: Wuhan

first: Chen-Yu

last: Wang

state: Hubei

address: 299 Bayi Road, Wuchang District

institute: Wuhan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2-align-s version 2.2.0 with parameters -p 16
The gene expression level was calculated by Cufflinks (v 2.2.1).
Fragments Per Kilobase of exon model per Million mapped fragments(FPKM) 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 Fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Matrix table with raw gene counts for every gene and every sample

source_name: tumor tissue

extract_protocol:
Tissues were harvested and total RNA was extracted with RNA extraction kit (Aidlab) according to the manufacturer’s manual.
RNA-seq library was constructed by using Illumina TruSeq library construction kit (Vazyme, ND606). 4 µg total RNA was used for each sample according to the manufacturer’s instruction.

treatment_protocol: After five sequential days of tamoxifen treatments by oral gavage

value: tumor


title: 3C-seq of cells with Smc-CC431 and parS at -9kb in exponential phase in SMG at 37°C

source_name: 3C-seq of cells with Smc-CC431 and parS at –9kb in exponential phase in SMG at 37°C


title: S2: mouse_sepsis_24h_rep2


title: MCC26_DOXpos_2

city: Boston

first: Yoshihiro

last: Morimoto

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana Farber Cancer Institute

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Genome_build: GRCh38.74
Supplementary_files_format_and_content: MCC26_Cuff_Gene_Counts.csv

molecule: polyA RNA

growth_protocol: MCC26 cells were cultured in RPMI 1640 medium (Corning, Corning, NY, USA) supplemented with 10% FBS and 2 mM glutamine.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

treatment_protocol: Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline.

tag: cell line background

value: Merkel cell carcinoma

tag: phenotype

value: puromycin resistance

value: 500 ng/ml doxycycline


title: S1: mouse_sepsis_24h_rep1


title: C6: mouse_control_24h_rep6


title: C5: mouse_control_24h_rep5

description: gene expression after 24h in mouse lung


title: Head_tumor_4


title: C3: mouse_control_24h_rep3

description: gene expression after 24h in mouse lung


title: F1-4-5

tag: diet

value: high-fat diet

tag: treatment

value: Ex


title: MCC26_DOXpos_1


title: 3C-seq of cells with Smc-CC425 and parS at -9kb in exponential phase in SMG at 37°C_rep


title: F1-3-7

value: normal chow

tag: parent

value: MP

value: NCS


title: 3C-seq of cells with Smc-CC435 and parS at -9kb in exponential phase in SMG at 37°C

source_name: 3C-seq of cells with Smc-CC435 and parS at –9kb in exponential phase in SMG at 37°C


title: MCC26_DOXpos_3


title: MCC26_DOXneg_3

value: 0.1% DMSO as the vehicle control


title: F1-3-1

tag: group


title: Head_normal_5

source_name: normal tissue

value: normal


title: 3C-seq of cells with wtSmc and parS at -9kb in exponential phase in SMG at 37°C_rep

source_name: 3C-seq of cells with wtSmc and parS at –9kb in exponential phase in SMG at 37°C

value: 1A700, Δ7-parS(parS359+), smc::specR


title: C2: mouse_control_24h_rep2

description: gene expression after 24h in mouse lung

tag: strain

value: lung

value: male


title: MCC26_DOXneg_2


title: C1: mouse_control_24h_rep1

description: gene expression after 24h in mouse lung


title: C4: mouse_control_24h_rep4

description: gene expression after 24h in mouse lung


title: Head_tumor_2


title: Head_normal_3


title: 3C-seq of cells with Smc-CC253 in exponential phase in SMG at 37°C_rep


title: 3C-seq of cells with wtSmc and parS at -9kb in exponential phase in SMG at 37°C


title: 3C-seq of cells with Smc-CC253 in exponential phase in SMG at 37°C


title: Head_tumor_6_INPUT

data_processing:
Sequenced reads were trimmed for adaptor sequence using cutadapt version 1.18 , and masked for low-complexity or low-quality sequence
ChIP-seq reads were aligned to the mm10 genome assembly using  with bowtie2-align-s version 2.3.5.1
peaks were called using macs2 2.1.1.20160309 with the following setting -p 1E-10 --nomodel --keep-dup all --SPMR --extsize 147 --broad --broad-cutoff 1E-10
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using deeptools 3.1.3; Scores represent RPKM

growth_protocol: Tgfbr1/Pten 2cKO mice was generated as previously described (20). Tgfbr1 cKO mice (mixed genetic strains of FVB/N, C57BL/6, 129SV/J and CD1) were crossed with the Ptenflox/flox mouse line (genetic strain 129SV/J) to generate mice heterozygous for both Tgfbr1 flox and Pten foxp with K14-CreERtam (K14-CreERtam;Tgfbr1f/+;Ptenf/+)

extract_protocol:
Lysates were clarified from MNase digested nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed by VATHS Univer_x0002_sal DNA Library Prep Kit for Illumina (Vazyme ND604). Briefly, 50 μL of purified ChIP DNA (8–10 ng) was end-repaired for dA tailing, followed by adaptor ligation.Libraries were sequenced by Illumina  Hi-seq X Ten platform with pair-end reads of 150 bp.

tag: chip antibody


title: Head_normal_1


title: MKL-1/tet-MUC1shRNA day5 [MKL1_DOXpos_3]

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Genome_build: GRCh38.74
Supplementary_files_format_and_content: Cuff_Gene_Counts.csv

source_name: MKL-1/tet-MUC1shRNA day5

growth_protocol: MKL-1 cells were cultured in RPMI 1640 medium (Corning, Corning, NY, USA) supplemented with 10% FBS and 2 mM glutamine.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNasy plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.


title: Head_tumor_6_H3K4me1


title: MCC26_DOXneg_1


title: 3C-seq of cells with Smc-CC425 in exponential phase in SMG at 37°C_rep


title: MKL-1/tet-MUC1shRNA day5 [MKL1_DOXpos_2]


title: 3C-seq of cells with Smc-CC421 in exponential phase in SMG at 37°C


title: Head_tumor_6_H3K27ac

value: H3K27ac (Abcam Ab4729)


title: MKL-1/tet-MUC1shRNA day5 [MKL1_DOXpos_1]


title: MKL-1/tet-MUC1shRNA day5 [MKL1_DOXneg_2]


title: 3C-seq of cells with Smc-CC425 in exponential phase in SMG at 37°C


title: 3C-seq of cells with Smc-CC431 in exponential phase in SMG at 37°C


title: 3C-seq of wt cells in exponential phase in SMG at 37°C

value: 1A700, smc ftsY::ermB, trpC2


title: Head_tumor_2_INPUT


title: 3C-seq of cells with Smc-CC435 in exponential phase in SMG at 37°C


title: Head_tumor_2_H3K4me1


title: 7thdaypi-rep2-H

city: Riverside

first: Heba

middle: A. H. M.

last: Zaghloul

state: CA

address: 900 University Ave

department: Entomology

institute: University of California, Riverside

data_processing:
Illumina adapter sequences were removed and low quality sequencing reads removed using Trimmomatic software
Ribosomal contaminant sequences were removed using sortMeRNA software
Reads were aligned to reference genome using Bowtie2 software
Transcript expression was estimated using custom written Perl scripts and reported as log base2 transformed RPKMs
Reads assembled into contig using Trinity software, contigs were oriented and further assembled using CAR software
Supplementary_files_format_and_content: Transcript expression values are reported as log2 transformed RPKM values in Microsoft Excel spreadsheet format, contig assembly sequences are reported as a plain text file

organism: Trichoplusia ni

source_name: TnAV 7th day infected Trichoplusia ni caterpillar (Hemolymph)

extract_protocol:
Total RNA was collected from healthey or TnAV-6a1 variant infected (third or early fourth instars) Trichoplusia ni larval hemolymph or fat body, epidermis and tracheal matrix tissues using TRIzol (Invitrogen), followed by using 5 ug total RNA as the starting material for DNase-treatment by RNA Clean and Concentrator TM-5 kit (ZYMO RESEARCH).
After the DNase-treatment of total RNA, the mRNA was isolated from each sample using the NEB NextPoly(A) mRNA magnetic isolation module kit (New England Biolabs). The cDNA libraries were then prepared following the manufacturer's instructions of NEBNext® Ultra™ Directional RNA Library Prep Kit (New England Biolabs) for Illumina®. For each time point in the two tissues under study we sequenced two biological replicates.

tag: virus name/genotype

value: Trichoplusia ni ascovirus-6a1 variant

value: Hemolymph


title: MKL-1/tet-MUC1shRNA day3 [MKL1_DOXpos_1]

source_name: MKL-1/tet-MUC1shRNA day3

value: Merkel cell carcinoma


title: MKL-1/tet-MUC1shRNA day3 [MKL1_DOXpos_2]

value: puromycin resistance


title: 48hpi-rep2-H

source_name: TnAV 48h infected Trichoplusia ni caterpillar (Hemolymph)


title: MKL-1/tet-MUC1shRNA day3 [MKL1_DOXneg_3]


title: 48hpi-rep1-H


title: Head_normal_5_INPUT


title: Head_tumor_4_INPUT

value: tumor


title: 24hpi-rep2-H

source_name: TnAV 24h infected Trichoplusia ni caterpillar (Hemolymph)


title: 24hpi-rep1-H


title: 7thdaypi-rep1-H


title: Head_normal_5_H3K27ac


title: MKL-1/tet-MUC1shRNA day5 [MKL1_DOXneg_3]


title: Head_tumor_2_H3K27ac


title: MKL-1/tet-MUC1shRNA day5 [MKL1_DOXneg_1]


title: Head_normal_3_INPUT


title: Head_tumor_4_H3K4me1


title: MKL-1/tet-MUC1shRNA day3 [MKL1_DOXpos_3]

value: 500 ng/ml doxycycline


title: 12hpi-rep2-H

source_name: TnAV 12 h infected Trichoplusia ni caterpillar (Hemolymph)


title: Head_tumor_4_H3K27ac


title: 12hpi-rep1-H

source_name: TnAV 12h infected Trichoplusia ni caterpillar (Hemolymph)


title: Head_normal_3_H3K4me1


title: Head_normal_3_H3K27ac


title: MKL-1/tet-MUC1shRNA day3 [MKL1_DOXneg_2]


title: Head_normal_1-INPUT


title: 6hpi-rep2-H

source_name: TnAV 6h infected Trichoplusia ni caterpillar (Hemolymph)


title: Head_normal_5_H3K4me1


title: Head_normal_1-H3K4me1


title: 6hpi-rep1-H


title: MKL-1/tet-MUC1shRNA day3 [MKL1_DOXneg_1]


title: WNT16_rep3

first: Qihua

last: Le

address: No. 83 Fen Yang Rd

department: Department of Ophthalmology

institute: Eye, Ear, Nose & Throat Hospital of Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
Clean reads were separately aligned to reference genome with orientation mode using HISAT2 (http://ccb.jhu.edu/software/hisat2/index.shtml)[1] software. The mapped reads of each sample were assembled by StringTie(https://ccb.jhu.edu/software/stringtie/index.shtml? t=example) in a reference-based approach
To identify DEGs (differential expression genes), the expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/)  was used to quantify gene abundances.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: cornea

extract_protocol:
Total RNA was extracted from human limbal epithelial stem cells using TRIzol® Reagent. A total of 1μg RNA was used to prepare RNA-seq transcriptome library using TruSeqTM RNA sample preparation kit (Illumina, San Diego, CA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Corneaoscleral

tag: Sex

value: female

tag: genotype

value: WNT16-treated  human limbal epithelial stem cells


title: WNT16_rep2


title: Cntl_rep1

value: Wild type human limbal epithelial stem cells


title: Head_normal_1-H3K27ac


title: 0hr-rep2-H

source_name: Uninfected 0h, Trichoplusia ni caterpillar (Hemolymph)


title: Cntl_rep2


title: WNT16_rep1


title: 0hr-rep1-H


title: EAT 143

city: London

first: Paula

last: Longhi

address: William Harvey Research Institute

country: United Kingdom

institute: Queen Mary, University of London

description: RawCounts.tsv

data_processing:
Pseudo-alignment and count abundance via salmon v1.4.0
Import to R via tximport v1.16.1
Normalisation of raw counts via DESeq2v1.28.1
n/a
n/a
Genome_build: GENCODE v37
Supplementary_files_format_and_content: TSV; raw count

source_name: EPICARDIAL ADIPOSE TISSUE

extract_protocol:
Total RNA was extracted from the adipose tissue using QIAzol (QIAGEN) and the RNeasy Lipid Tissue Mini Kits (QIAGEN) following the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: metabolic status

value: Type 2 diabetic

value: Epicardial adipose tissue (EAT)


title: EAT 152

description: RawCounts.tsv


title: 48hpi-rep2-FET

source_name: TnAV 48h infected Trichoplusia ni caterpillar (Fat body, Epidermis and Tracheal matrix)

value: Fat body, epidermis, and tracheal matrix


title: EAT 129

description: RawCounts.tsv


title: 48hpi-rep1-FET


title: MED5-3HA_kin28as_DMSO_R1

city: Bloomington

first: Gabriel

middle: E

last: Zentner

state: IN

address: 915 E 3rd St

department: Biology

institute: Indiana University

data_processing:
Alignment by Bowtie 2
Unmapped and low quality reads were removed using Samtools with parameters “-F 2048 -f 2”
Duplicated reads were removed using Samtools with parameters “fixmate -m”
BAM files were converted to BED files using robtools (version 1.0 available at https://github.com/francoisrobertlab/robtools)
Coverage for each base pair was computed using genomeCoverageBed from BEDTools (version 2.27.1) and normalized to 1 million reads.
Genome_build: UCSC sacCer3
Supplementary_files_format_and_content: bigWig

organism: Saccharomyces cerevisiae

growth_protocol: ATP analog sensitive kin28as strains were pre-cultured in yeast nitrogen base (YNB) medium lacking uracil before inoculation in yeast extract-peptone-dextrose (YPD) medium

extract_protocol:
ChIP-seq done as in Jeronimo et al. 2016 [PMID:27773677]
Library preparation done as described in Jeronimo et al. 2019 [PMID:31365865]

treatment_protocol: 6μM of 1-Naphthyl PP1 (NA-PP1; Tocris Bioscience) or DMSO for 15 min at 30°C prior to crosslinking

tag: chip tag

tag: background

value: DMSO


title: MED8-3HA_kin28as-med16D_DMSO_R2


title: 24hpi-rep2-FET

source_name: TnAV 24h infected Trichoplusia ni caterpillar (Fat body, Epidermis and Tracheal matrix)


title: MED8-3HA_kin28as-med16D_DMSO_R1


title: EAT 127

description: RawCounts.tsv


title: Cntl_rep3


title: MED8-3HA_kin28as_DMSO_R2


title: 24hpi-rep1-FET


title: EAT 112

description: RawCounts.tsv


title: MED8-3HA_kin28as_DMSO_R1


title: EAT 133

description: RawCounts.tsv

value: Obese/overweight


title: noTag_kin28as-med16D_DMSO_R2

value: noTag


title: 12hpi-rep1-FET

source_name: TnAV 12h infected Trichoplusia ni caterpillar (Fat body, Epidermis and Tracheal matrix)


title: 12hpi-rep2-FET

source_name: TnAV 12 h infected Trichoplusia ni caterpillar (Fat body, Epidermis and Tracheal matrix)


title: noTag_kin28as-med16D_DMSO_R1


title: 6hpi-rep2-FET

source_name: TnAV 6h infected Trichoplusia ni caterpillar (Fat body, Epidermis and Tracheal matrix)


title: EAT 128

description: RawCounts.tsv


title: EAT 100

description: RawCounts.tsv


title: 6hpi-rep1-FET


title: MED5-3HA_kin28as-med16D_NAPP1_R2

value: 15 mins of 6uM NaPP1 in DMSO


title: EAT 74

description: RawCounts.tsv


title: MED5-3HA_kin28as_NAPP1_R2


title: MED5-3HA_kin28as-med16D_NAPP1_R1


title: 48hr-rep1-FET

source_name: Uninfected 48h, Trichoplusia ni caterpillar (Fat body, Epidermis and Tracheal matrix)

value: Trichoplusia ni ascovirus-6a1 variant


title: MED5-3HA_kin28as_NAPP1_R1


title: 48hr-rep2-FET


title: 24hr-rep2-FET

source_name: Uninfected 24h,Trichoplusia ni caterpillar (Fat body, Epidermis and Tracheal matrix)


title: EAT 38

description: RawCounts.tsv

value: Lean


title: 0hr-rep2-FET

source_name: Uninfected 0h, Trichoplusia ni caterpillar (Fat body, Epidermis and Tracheal matrix)


title: EAT 150

description: RawCounts.tsv


title: EAT 122

description: RawCounts.tsv


title: EAT 132

description: RawCounts.tsv


title: 24hr-rep1-FET

source_name: Uninfected 24h, Trichoplusia ni caterpillar (Fat body, Epidermis and Tracheal matrix)


title: MED8-3HA_kin28as-med16D_NAPP1_R2


title: MED8-3HA_kin28as-med16D_NAPP1_R1


title: 0hr-rep1-FET


title: MED8-3HA_kin28as_NAPP1_R2


title: MED8-3HA_kin28as_NAPP1_R1


title: EAT 117

description: RawCounts.tsv


title: noTag_kin28as-med16D_NAPP1_R2


title: EAT 115

description: RawCounts.tsv


title: EAT P96

description: RawCounts.tsv


title: EAT P56

description: RawCounts.tsv


title: noTag_kin28as_DMSO_R2


title: noTag_kin28as-med16D_NAPP1_R1


title: noTag_kin28as_NAPP1_R2


title: noTag_kin28as_NAPP1_R1


title: NCAD_PAT_2

first: Kailei

last: Shi

address: Yanan west road NO.168

institute: Huadong Hospital Affiliated to Fudan University

description:
gene_counts_and_FPKM.txt
12PeriWAT

data_processing:
The original image data files obtained from high-throughput sequencing are transformed into original RAW Reads by Base Calling analysis after image processing
Raw Reads were deposited in FASTQ file format
For each FASTQ file, the software FASTQC was used to evaluate the quality of the sequencing results.
The sequence was filtered using FASTP software and then called clean reads
The clean reads was aligned by HisAT2. Its matching algorithm is Spliced Maping algorithm
Counts in each gene segment were counted using Stringtie software, then normalized with the TMM (mean of M values) algorithm, and finally FPKM value of each gene was calculated.
Genome_build: GRCh38.91

source_name: pericardial adipose tissue of Contral patients

extract_protocol:
We took a sample of PAT (1.0 g) adjacent to the pericardial surface during surgery. The adipose sections collected from 5 CAD and 4 control patients were kept in 10% formalin for histological analysis. The other adipose tissues were immediately snap-frozen in liquid nitrogen (–80°C). Five CAD and 4 control adipose tissue samples underwent RNA sequencing.
Paired-end libraries were synthesized using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following the TruSeq™ RNA sample preparation guide. Briefly, the poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Thereafter, the mRNA was fragmented into small pieces using divalent cations under 94°C for 8 min. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers. Subsequently, the second strand cDNA was synthesized using DNA Polymerase I and RNase H. These cDNA fragments then underwent an end repair process, the addition of a single ‘A’ base, and ligation of the adapters. The products were purified and enriched with PCR to generate the final cDNA library. Clean libraries were quantified using a Qubit® 2.0 Fluorometer (Life Technologies, USA), and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and evaluate the mole concentration. Cluster was generated using cBot with the library diluted to 10 pM and then was sequenced using the Illumina NovaSeq 6000 (Illumina, USA).

value: pericardial adipose tissue

tag: disease status

value: control patients undergoing valve replacement or valve repair


title: NCAD_PAT_3

description:
gene_counts_and_FPKM.txt
17PeriWAT


title: NCAD_PAT_4

description:
gene_counts_and_FPKM.txt
20PeriWAT


title: CAD_PAT_5

description:
gene_counts_and_FPKM.txt
22PeriWAT

source_name: pericardial adipose tissue of Coronary artery disease patients

value: CAD patients undergoing coronary artery bypass grafting (CABG)


title: MED5-3HA_kin28as-med16D_DMSO_R1


title: CAD_PAT_4

description:
gene_counts_and_FPKM.txt
19PeriWAT


title: NCAD_PAT_1

description:
gene_counts_and_FPKM.txt
3PeriWAT


title: CAD_PAT_3

description:
gene_counts_and_FPKM.txt
18PeriWAT


title: noTag_kin28as_DMSO_R1


title: MED5-3HA_kin28as_DMSO_R2


title: PC3 treated with KR-37524, rep2

city: Daejeon

first: Gyutae

last: Lim

state: Not US or Canada

address: 141 Gajeong-ro, Yuseong-gu

country: South Korea

institute: KRICT

description: Gene expression data from PC3

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing:
Array data export processing and analysis was performed using Affymetrix® GeneChip Command Console® Software (AGCC)
Normalized signal of Affymetrix Power Tools analysis (summarization, background correction, normalization)

label: biotin

source_name: PC3, human prostate adenocarcinoma cells

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: Six sheets of each cell line were seeded in a 60mm dish and incubated for 24 hours.

extract_protocol: After 6 hours, the medium was removed and cells were obtained by treatment with 1ml of TRIzol. Cells were disrupted by pipetting and stored in a deep freezer.

treatment_protocol: After 24 hours, DMSO and KR-37524 were diluted 1000-fold in medium and the cells were treated.

tag: cell line

value: human prostate

tag: cell type

value: human prostate adenocarcinoma cells


title: CAD_PAT_2

description:
gene_counts_and_FPKM.txt
14PeriWAT

tag: tissue


title: CAD_PAT_1

description:
gene_counts_and_FPKM.txt
13PeriWAT


title: PC3 treated with DMSO, rep1

description: Gene expression data from PC3


title: PC3 treated with DMSO, rep2

description: Gene expression data from PC3


title: PC3 treated with DMSO, rep3

description: Gene expression data from PC3


title: PC3 treated with KR-37524, rep3

description: Gene expression data from PC3


title: MED5-3HA_kin28as-med16D_DMSO_R2


title: Apoe4_rep4

city: Lexington

first: Timothy

middle: S

last: McClintock

state: Kentucky

address: 800 Rose street

department: Department of Physiology

institute: University of Kentucky

data_processing:
fastq files were aligned to version 79 of mouse reference genome GRCm38 using the STAR aligner.
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
read counts were normalized as FPKM in DESeq2
Differentially expressed transcripts ( £5% Padj value) were identified by DESeq2 Package
Genome_build: version 79 of mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 result that includes Log2FC and Padj values

source_name: Olfactory Epithelium

growth_protocol: No culture experiment

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
mRNA library  preparation (poly A  enrichment), Sequencing Platform & Strategy: NovaSeq 6000 PE150

treatment_protocol: No treatment

tag: background strain

value: Olfactory Epithelium

tag: age

value: 6 months

value: untreated


title: Apoe4_rep5

tag: treatment


title: Apoe4_rep6


title: SS6 blood

city: Farmington

first: Youzhi

last: Cheng

state: Connecticut

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: University of Connecticut Health Center

description: mRNA, ADT

data_processing:
Library strategy: ECCITE-seq
FASTQ files generated from the 10X libraries were processed using the count module of Cell Ranger pipeline, v3.0.1 (10X Genomics). FASTQ files from the TCR α/β and TCR γ/δ libraries were processed using the vdj module of Cell Ranger pipeline, v3.0.1 (10X Genomics). For ADT libraries and HTO libraries, the tag quantification pipeline v.1.3.2, available at https://github.com/Hoohm/CITE-seq-Count, was used to tally up the counts from reads. A Hamming distance of 1 was used as criteria for read sequence matches to pre-assigned barcode sequences. All reads from the 5’ mRNA, TCR α/β and TCR γ/δ libraries were aligned to the GRCh38 reference. For an ECCITE-seq experiment, raw UMI gene expression (GEX), TCR α/β, TCR γ/δ clonotype, ADT and HTO count matrices were obtained. Samples were then demultiplexed by their HTO using Seurat HTODemux with positive quantile parameter set to 0.999.
Scrublet (v 0.2.1) was further used to identify and remove intra-sample cell duplicates. We parameterized the model using a 7% expected doublet rate, 30 principal components (default) and a minimum gene variability of the 85th percentile (default). We performed further manual thresholding by using a doublet score of 0.2.
Count matrices for all modalities were loaded into a Seurat v3 object (Seurat v3.0.2) and Seurat functions were used for normalization, visualization and downstream processing. For gene expression data, we normalized the count data using LogNormalize, and scaled the resulting normalized values using ScaleData. For all other modalities (ADT, HTO, TCR α/β, TCR γ/δ), we normalized the count data using CLR (margin = 2), and scaled the resulting normalized values using ScaleData.
Genome_build: hg38
Supplementary_files_format_and_content: *clonotypeAB.tsv.gz: CDR3 sequence of the alpha and/or beta chain of the T-Cell Receptor (TCR)
*clonotypeGD.tsv.gz: CDR3 sequence of the gamma and/or delta chain of the TCR
*TCRb.tsv.gz: CDR3 sequence of the beta chain of the TCR
*TCRg.tsv.gz: CDR3 sequence of the gamma chain of the TCR
*ADT.tsv.gz: Antibody derived tag counts
*GEX.tsv.gz: gene expression counts
*HTO.tsv.gz: hashtag oligo counts

source_name: Peripheral blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from the blood of patients and healthy controls by gradient centrifugation using Ficoll-Paquetm PLUS (GE Healthcare) and Sepmate-50 tubes (Stemcell). Buffy coat PBMCs were collected and washed twice with PBS 2% FBS. Skin biopsies were digested in 0.25mg/ml of Liberase TL and 0.5 mg/ml DNase (Sigma) diluted in RPMI and incubated for 1.5 hours at 37°C. Skin dissociated cells were filtered through a 70-uM cell strainer. All cells from single cell suspensions were cryopreserved in freezing medium (40% RPMI 1640, 50% FBS and 10% DMSO). Cryopreserved PBMCs and skin dissociated cells were thawed for 1-2 minutes in a 37o C water bath, washed twice in warm PBS 2% FBS and re-suspended in complete media (RPMI 1640 supplemented with 10% FBS and 2mM L-Glut) on the day of the experiments.
All experiments were performed using the 10x genomics V(D)J solution which incorporates scRNA-seq with additional profiling of protein surface markers . Antibody oligo counts are listed in the ADT and HTO tables. Stained cells from each sample were pooled and loaded into the 10X Chromium Single Cell Immune Profiling workflow according to the manufacturer’s instructions . Additional modifications included:   (1) Addition of 2 pmol of TotalSeq-C BioLegend protein-tag additive (CTCGTGGGCTCGGAGATGTGTATAAGAGACG) during cDNA amplification PCR for pools stained with TotalSeq-C antibodies.  (2)  N7NY_xx indexing primers, as described in Mimitou et al., 2019, were used along with SI-PCR primer to make libraries for TotalSeq-C antibodies.   Libraries were pooled and sequenced on Illumina NovaSeq 6000, MiSeq or HiSeq 2500.

value: PBMCs

tag: disease state

value: SS

value: M


title: MCF7 treated with DMSO, rep2

description: Gene expression data from MCF7

source_name: MCF7, human breast carcinoma cells

value: human breast

value: human breast carcinoma cells

value: DMSO


title: MCF7 treated with KR-37524, rep3

description: Gene expression data from MCF7


title: MCF7 treated with DMSO, rep3

description: Gene expression data from MCF7


title: PC3 treated with KR-37524, rep1

description: Gene expression data from PC3


title: Apoe4_rep2


title: Apoe4_rep3


title: SS5 blood

description: mRNA, ADT

value: F


title: MCF7 treated with KR-37524, rep1

description: Gene expression data from MCF7


title: MCF7 treated with KR-37524, rep2

description: Gene expression data from MCF7


title: MFIV1 skin

description: mRNA, ADT

source_name: skin biopsy

value: skin dissociated cells

value: leukemic MF


title: MCF7 treated with DMSO, rep1

description: Gene expression data from MCF7


title: A549 treated with DMSO, rep3

description: Gene expression data from A549

source_name: A549, human lung carcinoma cells

value: human lung

value: human lung carcinoma cells


title: Apoe3_rep4


title: MFIV1 blood

description: mRNA, ADT


title: SS4 skin

description: mRNA, ADT


title: Apoe3_rep2


title: SS3 skin

description: mRNA, ADT


title: A549 treated with DMSO, rep2

description: Gene expression data from A549


title: SS3 blood

description: mRNA, ADT


title: Apoe4_rep1


title: A549 treated with KR-37524, rep2

description: Gene expression data from A549


title: A549 treated with KR-37524, rep3

description: Gene expression data from A549


title: Apoe3_rep3


title: SS4 blood

description: mRNA, ADT


title: SS2 blood

description: mRNA, ADT


title: A549 treated with KR-37524, rep1

description: Gene expression data from A549


title: SS1 skin

description: mRNA, ADT


title: WT-Piwi-IP_3_3

city: Bethesda

first: Pavol

last: Genzor

state: MD

address: 6720A Rockledge Drive, Suite 100

department: ACESO

institute: Henry M Jackson Foundation

description:
Piwi-associated RNA (piRNA)
size-selected piRNAs with 10 UMIs

data_processing:
Fastq files were trimmed using cutadapt (v2.3) to remove the 5` and 3` adapters and keep 10 unique molecular identifiers (UMI) - 8N's at 5` end and 2N's at 3` end.
Fastq files were processed in R using custom script where sequences were collapsed by UMI to remove PCR duplicates, UMI's were trimmed,  and sequences shorter than 18-nt in length were removed. To reduce the file size while retaining all the information, the sequences were collapsed and individual sequence abundance was recorded in fasta header. Fasta header is comprised of sample name that is followed by a unique alphanumeric string containing sequence ID number (S) and abundance count (M) and have following structure: SAMPLE_XY - S[UniqueSequenceID]M[SequenceAbundance]. Fasta header "FH-Piwi-IP_1_1-S32M12" can be split into sample name ("FH-Piwi-IP_1_1") and unique string ("S32M12")  that can be further split into unique sequence ID ("S32") and abundance count of this particular sequence ("M12"). Please see UNIQSEQS.fa processed files. These files are deposited for the convenient, fast download and analysis.
UNIQSEQS.fasta files were aligned to genome comprised of the structural RNAs (tRNA, rRNA, snRNA, snoRNA) using STAR (v2.5.2b), the unmapped sequences were collected and mapped to the dm6 genome using the same aligner. The obtained .bam files were analyzed in R using custom scripts.
piRNA quantification was performed by determining the number of cells per sample (S1-S8) using molecular counts of the callibrator oligoes in the UNIQSEQS.fasta files. MiRNAs were quantified by mapping to miR Base (Release 22.1). PiRNAs were quantified by considering seqeunces in 24 - 29-nt size range.
Genome_build: dm6 (Drosophila melanogaster)
Supplementary_files_format_and_content: xlsx: piRNA_quantification; fasta: custom trimmed and filtered unique sequence files

organism: Drosophila melanogaster

source_name: OSC cell line

growth_protocol: OSC cell culture was grown as described in protocols described here: https://dgrc.bio.indiana.edu/product/View?product=288

extract_protocol:
piRNAs: RNA was extracted from the OSC cell lysate by immunoprecipitating PIWI proteins using anti-Flag antibody beads or custom made fly anti-Piwi antibodies. Total small RNAs: RNA was extracted from the cells usign PureLink miRNA Isolation kit (Thermo Fisher Scientific, K157001)
piRNA libraries: Imunoprecipitated RNA was ligated to 3` adapter containing unique indexes and two random bases (2N), and ligation products in 48 to 58-nt size range (equivalent to 19 - 29-nt long initial fragments) were recovered from Urea PAGE gel. Purified fragments were then ligated to 5` adapter containing eight random bases (8N) and purified on Urea PAGE gel again by selecting fragments in 82 - 92-nt size range. Final fragments were PCR amplified to add sequencing adapters. Total small RNAs libraries: A pellet of one million cells was used to purifiy small RNAs using PureLink miRNA Isolation kit (Thermo Fisher Scientific, K157001) and were spiked with a mix of 26 nt-long synthetic RNA callibrator sequences. RNA was ligated to 3` adapter containing unique indexes and two random bases (2N), and ligation products in 48 to 58-nt size range (equivalent to 19 - 29-nt long initial fragments) were recovered from Urea PAGE gel. Purified fragments were then ligated to 5` adapter containing eight random bases (8N) and PCR ampliffied to add sequencing adapters.

value: ovarian somatic sheet cells (OSC)

value: WT

tag: ip antibody

value: rabbit anti-DmPiwi #2, custom made, Primm_201410-00003 KCA/14

value: GTTCAGAGTTCTACAGTCCGACGATCNNNNNNNN

value: NNATCGACTGGAATTCTCGGGTGCCAAGG


title: D3T_WT_2_TFH_2

city: Beijing

first: Hai

last: Qi

state: Non-US/Non-Canadian

address: Shuangqing Road

institute: Tsinghua University

data_processing:
Sequenced reads were mapped to mm10 whole genome using HISAT2 version 2.2.1 by Daehwan Kim (infphilo@gmail.com, www.ccb.jhu.edu/people/infphilo)
For each sample, the number of reads mapping to GTF reference  were calculated using htseq-count (Part of the 'HTSeq' framework, version 0.12.4.)
Transcripts Per Kilobase of exon model per Million mapped reads  (TPM) were calculated . In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: .csv files include TPM values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CXCR5hiPD-1hi TFH cells

extract_protocol:
SMART-Seq2 protocol for single-cell analysis was adapted and optimized for analyzing ~200 cells
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: lymph nodes

value: CXCR5hiPD-1hi TFH cells

tag: time

value: 3 days after activation in vivo by NP-OVA immunization


title: D3T_WT_1_TFH_2


title: D3T_WT_3_TFH_1


title: D3T_WT_2_TFH_1


title: D3T_WT_3_TFH_2


title: HC blood

description: mRNA, ADT

value: PBMCs

value: Healthy control

value: M


title: HC skin

description: mRNA, ADT


title: SS1 blood

description: mRNA, ADT

value: SS


title: Apoe3_rep1

value: Olfactory Epithelium

value: 6 months

value: untreated


title: D3T_WT_1_TFH_1


title: A549 treated with DMSO, rep1

description: Gene expression data from A549

value: human lung

value: DMSO


title: SS2 skin

description: mRNA, ADT

value: skin dissociated cells


title: A375 treated with DMSO, rep1

description: Gene expression data from A375

source_name: A375, human skin malignant melanoma cells

value: human skin

value: human skin malignant melanoma cells


title: A375 treated with DMSO, rep2

description: Gene expression data from A375


title: A375 treated with KR-37524, rep3

description: Gene expression data from A375


title: ChIP-Rx Input R8

city: Innsbruck

first: Univ.-Prof. Dr. Andreas

last: Mayer

address: Innrain 80/82

department: Institute for Genomics and RNomics

country: Austria

institute: Biocenter, Medical University Innsbruck

data_processing:
For ChIP-Rx, we aligned the sequencing reads to a joined reference genome which we assembled from human (hg38/GRCh38) and the spiked-in mouse (mm10/GRCm38)
reference genomes using Bowtie2 v2.3.5.1 (Langmead and Salzberg, 2012) in paired-end mode with '-k 1'.
We extracted the raw density from human for the protein of interest using bedtools (Quinlan and Hall, 2010) in the 'genomecov -bg' mode.
Genome_build: Human (hg38/GRCh38) and the spiked-in mouse (mm10/GRCm38)
Supplementary_files_format_and_content: bigWig files were generated using ‘bedGraphToBigWig’; Scores represent Reads per Million (RPM) or the fold-enrichment 'FE' signal over the matched input control.

source_name: bone marrow, CML

growth_protocol: K562 dTAG-BRD4 cells were cultured in RPMI containing 10% FBS, 5% penicillin-streptomycin. NIH3T3 cells, which were used as spike-ins, were grown in DMEM containing 10% FBS , 5% penicillin-streptomycin. K562 dTAG-BRD4 cells were plated at 5 x 10^5 cells/ml, NIH3T3 were plated at 2 x 10^6 cells/T75 flask every two days.

extract_protocol:
K562 dTAG-BRD4 cells were crosslinked with 1% formaldehyde for 5 min at room temperature, NIH3T3 cells were crosslinked for 8 min. After combining NIH3T3 and K562 dTAG-BRD4 cells in a ratio of 1:5, cells were lysed as described by Baluapuri et al. (2019), followed by sonication using a Covaris E220evolution at intensity 4, duty cycle 5%, 200 cycles per burst for 20 min. Lysates were pre-cleared by centrifugation. Lysates and antibodies coupled to Dynabeads Protein G (Thermo Fisher Scientific) were incubated at 4°C overnight with rotation. Afterwards, the beads were washed with buffers prepared according to Baluapuri et al. (2019). DNA fragments were purified using the ChIP DNA Clean & Concentrator kit (Zymo).
Libraries were constructed from 6 to 30 ng DNA using the NEBNext Ultra II DNA kit (NEB) according to the manufacturer's instructions. After purifying the amplified libraries with AMPure XP beads (Beckman Coulter), fragments of 200 to 500 bp were extracted from an 8% TBE gel. Library quality and quantity were assessed using BioAnalyzer HS DNA (Agilent) and Qubit dsDNA HS (Thermo Fisher) assays, respectively.

treatment_protocol: K562 dTAG-BRD4 cells at a concentration of 1 x 10^6/ml were treated with 500 nM dTAG7 or DMSO for 2 h.

value: K562 dTAG-BRD4

value: BRD4 degradation

tag: antibody

value: no antibody


title: D3T_HET_3_TFH_2

value: lymph nodes

value: CXCR5hiPD-1hi TFH cells


title: A375 treated with KR-37524, rep1

description: Gene expression data from A375


title: A375 treated with DMSO, rep3

description: Gene expression data from A375


title: WT-Piwi-IP_3_1

value: ovarian somatic sheet cells (OSC)

value: WT

value: rabbit anti-DmPiwi #2, custom made, Primm_201410-00003 KCA/14

value: GTTCAGAGTTCTACAGTCCGACGATCNNNNNNNN

value: NNATCGACTGGAATTCTCGGGTGCCAAGG


title: WT-Piwi-IP_3_2


title: A375 treated with KR-37524, rep2

description: Gene expression data from A375


title: D3T_HET_3_TFH_1

value: 3 days after activation in vivo by NP-OVA immunization


title: D3T_HET_2_TFH_2


title: ChIP-Rx Pol II Ser2-P dTAG7 2h Rep 1

value: Pol II CTD Ser2-P, Active Motif, 61083, 8 µg

tag: matched input

value: ChIP-Rx Input R8


title: ChIP-Rx Pol II Ser2-P DMSO 2h Rep 1

value: control


title: WT-Piwi-IP_2_3

tag: genotype

value: NNAGTGTCTGGAATTCTCGGGTGCCAAGG


title: WT-Piwi-IP_2_2


title: D3T_HET_2_TFH_1


title: ChIP-Rx Input R7


title: ChIP-Rx Input R6


title: D3T_HET_1_TFH_2


title: ChIP-Rx Input R5


title: ChIP-Rx Input R4


title: WT-Piwi-IP_2_1


title: WT-Piwi-IP_1_3

value: NNTAGTCGTGGAATTCTCGGGTGCCAAGG


title: WT-Piwi-IP_1_1


title: ChIP-Rx Input R3


title: ChIP-Rx Input R2


title: D3B_WT_4

source_name: NP+IgDlowB220+ pre-GC B cells

value: NP+IgDlowB220+ pre-GC B cells

value: helped by CD4-Cre OT-II T cells


title: D3B_WT_2


title: D3B_WT_3


title: FH-Piwi-IP_3_3

value: 3xFH-Piwi / WT

value: anti-Flag M2 magnetic beads, Millipore Sigma, M8823

value: NNCTGTAGTGGAATTCTCGGGTGCCAAGG


title: CAPTURE-3C-seq_HUDEP2_BCL11A_KO_beta3

city: Memphis

first: Jian

last: Xu

state: Tennessee

address: 262 Danny Thomas Place, MS 345

department: Pathology

institute: St. Jude Children's Research Hospital

description:
3C DNA
The combined sample represents all three beta samples. In our study, all the replicates (beta1,2,3) were combined for downstream data analysis, so only the processed data files for the combined datasets have been provided. However, all sample files were uploaded to make them available to the research community.

data_processing:
Sequencing reads were aligned to human genome assembly hg19 using Bowtie2 v2.2.8 with default parameters. The reads with low mapping quality and duplicate reads were removed after the alignment with the Picard command-line tools.
After preprocessing and filtering, we generated the list of count numbers of read pairs from the bait region to any chromosomal regions. A pair of reads that located within two different regions is considered an interaction between them.
The interaction significance between the bait region and another chromosomal region was calculated by a Bayesian-Mixture Model. The PETs from bait region to any chromosomal regions were reported in Pairwise interaction format (https://eg.readthedocs.io/en/latest/text.html#longrange).
Genome_build: hg19
Supplementary_files_format_and_content: Pairwise Interaction Format

source_name: HUDEP2 BCL11A KO cells

growth_protocol: HUDEP-2 cells were maintained in expansion medium: StemSpan SFEM (STEMCELL Technologies) with 50 ng/ml SCF, 3 IU/ml EPO, 10-6 M dexamethasone, 1 ug/ml doxycycline, and passaged every three days.

extract_protocol:
10 ng of 3C DNA was processed for library generation using the NEBNext Ultra II DNA Library prep kit following the manufacturer’s protocol (New England Biolabs). Raw reads that aligned to exactly one location in the reference human genome (hg19) were retained for downstream data analysis.
CAPTURE-3C-seq

value: BCL11A knockout


title: CAPTURE-3C-seq_HUDEP2_BCL11A_KO_beta2


title: CAPTURE-3C-seq_HUDEP2_BCL11A_KO_combined


title: ChIP-Rx Input R1

value: K562 dTAG-BRD4

value: BRD4 degradation

value: no antibody


title: FH-Piwi-IP_3_2

value: ovarian somatic sheet cells (OSC)

value: GTTCAGAGTTCTACAGTCCGACGATCNNNNNNNN


title: D3B_HET_4

value: lymph nodes

value: helped by CD4-CrexBcl6fl/+ OT-II T cells

value: 3 days after activation in vivo by NP-OVA immunization


title: FH-Piwi-IP_2_3

value: NNTAGCGATGGAATTCTCGGGTGCCAAGG


title: FH-Piwi-IP_3_1


title: ChIP-Rx CstF64 dTAG7 2h Rep 2

value: CstF64, Bethyl, A301-092A, 10 µg

value: ChIP-Rx Input R5


title: CAPTURE-3C-seq_HUDEP2_combined

source_name: HUDEP2 cells

value: wild-type (WT)


title: ChIP-Rx CstF64 dTAG7 2h Rep 1

value: ChIP-Rx Input R6


title: D3T_HET_1_TFH_1

value: CXCR5hiPD-1hi TFH cells


title: D3B_WT_1

value: NP+IgDlowB220+ pre-GC B cells

value: helped by CD4-Cre OT-II T cells


title: FH-Piwi-IP_2_2

value: 3xFH-Piwi / WT

value: anti-Flag M2 magnetic beads, Millipore Sigma, M8823


title: ChIP-Rx CstF64 DMSO 2h Rep 2

value: K562 dTAG-BRD4

value: control


title: WT-Piwi-IP_1_2

value: ovarian somatic sheet cells (OSC)

value: WT

value: rabbit anti-DmPiwi #2, custom made, Primm_201410-00003 KCA/14

value: NNTAGTCGTGGAATTCTCGGGTGCCAAGG


title: CAPTURE-3C-seq_HUDEP2_beta2


title: D3B_HET_2

value: lymph nodes

value: helped by CD4-CrexBcl6fl/+ OT-II T cells

value: 3 days after activation in vivo by NP-OVA immunization


title: D3B_HET_3


title: FH-Piwi-IP_2_1

value: GTTCAGAGTTCTACAGTCCGACGATCNNNNNNNN

value: NNTAGCGATGGAATTCTCGGGTGCCAAGG


title: ChIP-Rx CstF64 DMSO 2h Rep 1

value: CstF64, Bethyl, A301-092A, 10 µg

value: ChIP-Rx Input R6


title: CAPTURE-3C-seq_HUDEP2_beta1

value: wild-type (WT)


title: CAPTURE-3C-seq_HUDEP2_BCL11A_KO_beta1

value: BCL11A knockout


title: D3B_HET_1

value: NP+IgDlowB220+ pre-GC B cells


title: FH-Piwi-IP_1_2

value: 3xFH-Piwi / WT

value: anti-Flag M2 magnetic beads, Millipore Sigma, M8823

value: NNGCGATATGGAATTCTCGGGTGCCAAGG


title: s10-CD3posCD45RAneg-TR3

city: Graz

first: Silvia

last: Fibi-Smetana

state: Styria

address: Stremayrgasse 16

department: Biomedical Informatics

institute: Graz University of Technology

description: hospitalized patient s10, technical replicate 3

data_processing:
RNA-Seq data was processed using published Drop-seq pipeline (v1.0) to obtain the count table
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: blood

extract_protocol:
Blood sampling 2 weeks after positive SARS-CoV-2-RNA results, stained samples were sorted for CD3+ CD45RA- population (memory T cells), RNA-isolation via TCL-lysis buffer and 2-mercaptoethanol
Library preparation according to Parekh et. Al 2016, Nature Scientific Reports

tag: diagnosis

value: memory T cell

tag: group

value: hospitalized

tag: sample name as in counts.txt.gz

value: TTTACA


title: ChIP-Rx CPSF73 DMSO 2h Rep 2

value: K562 dTAG-BRD4

value: control

value: CPSF73, Bethyl, A301-091A, 10 µg

value: ChIP-Rx Input R7


title: ChIP-Rx CPSF73 dTAG7 2h Rep 1

value: BRD4 degradation


title: m43-CD3posCD45RAneg-TR3

description: not hospitalized patient m43, technical replicate 3

value: not hospitalized

value: TAGTAA