title: WT EBd7 CD71+ H3K27ac 1

description:
Chromatin from purified CD71+ erythroid cells derived from differentiated WT mES cells, ChIPed for H3K27ac, sample 1
Genome-wide library of ChIPed chromatin


title: WT EBd7 CD71+ CTCF 2

status: Public on Sep 22 2021

type: SRA

city: Oxford

first: Mira

middle: Tony

last: Kassouf

state: England

address: John Radcliffe Hospital, Headly way

department: Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Chromatin from purified CD71+ erythroid cells derived from differentiated WT mES cells, ChIPed for CTCF, sample 2
Genome-wide library of ChIPed chromatin

library_source: genomic

data_processing:
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Alignment to the genome (Bowtie) maintaining strict read order
Removal of PCR duplicates;
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions
Genome_build: mm9
Supplementary_files_format_and_content: BigWig

molecule: genomic DNA

organism: Mus musculus

source_name: E14TG2a.IV mES derived Erythroid cells

extract_protocol:
To produce CD71+ erythroid cells in vitro from differentiated mESCs (WT or mutant): 24h prior to differentiation, mESCs were induced by passaging into IMDM base media, trypsinised and plated in differentiation media (IMDM suplemented serum and other reagents and growth factors) in either triple vent petri dishes (Thermo Fisher) or flat-bottom 96-well plates (Thermo Fisher) at 3x104 cells in 10 cm dishes or 250 cells per well of a 96-well plate for up to seven days without disruption. EBs were harvested and disaggregated in 0.25% trypsin for 3 minutes at 37°C. CD71-positive cells were isolated by magnetic column separation (LS Column, Miltenyi), according to the manufacturer’s instructions. Briefly, cells (from disaggregated EBs) were labelled with anti-mouse CD71-FITC (eBioscience 11-0711-85; 1:200) in staining buffer (PBS with 10% FCS; 500 ul per 10^7 cells) for 20 minutes at 4°C, washed, then incubated with MACS anti-FITC separation microbeads (Miltenyi; 10 ul  per 10^7 cells, following the manufacturer’s instructions) and bead-labelled cells were retained by LS columns. Cells were then processed for ChIP-Seq as in Hay D et al, Nature Genetics, 2016.
Cells were fixed with 1% Formaldehyde, lysed, sonicated and immunoprecipitated with the antibody of interest (CTCF: Merck Millipore 07-729 at 5ug/ml, H3K27ac: Abcam ab4729 at 0.5ug/ml, H3K4me1: Abcam ab8895 at 0.3ug/ml, H3K4me3: Abcam ab8580 at 2.5ug/ml). Libraries were prepared using the NEB Ultra II library preparation kit according to manufacturer’s instructions. Samples were sequenced using 40 bp paired end reads on the NextSeq platform
The strategy was to characterise the chromatin state of the CD71+ erythroid cells (WT and mutant) derived from mESC-EB in vitro differentitation system by isolating and analysing DNA regions bound by the antibodies of interest, genome-wide.

tag: cell type

value: E14TG2a.IV mES derived Erythroid cells

tag: strain

tag: chip antibody

value: CTCF:Merck Millipore 07-729 at 5ug/ml


title: WT EBd7 CD71+ H3K4me3 1

description:
Chromatin from purified CD71+ erythroid cells derived from differentiated WT mES cells, ChIPed for H3K4me3, sample 1
Genome-wide library of ChIPed chromatin

value: H3K4me3:Abcam ab8580 at 2.5ug/ml


title: D3839 EBd7 CD71+ CTCF 1

description:
Chromatin from purified CD71+ erythroid cells derived from differentiated mutant mES cells deleted for two CTCF sites at the Alpha Globin locus at positions (HS38 and HS39.5), ChIPed for CTCF, sample 1
Genome-wide library of ChIPed chromatin


title: WT EBd7 CD71+ R1 Capture sample 3 (WT_EB11_Enhancers)

description: sequences enriched from a 3C library for their interaction with the Capture point in the Alpha Globin locus as detailed in the sample name

data_processing:
Library strategy: Capture-C-seq
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (dpnIIPE.pl)
Alignment to the genome (Bowtie) maintaining strict read order
Removal of PCR duplicates; Parsing of informative reads and mapping to restriction enzyme fragments (CCanalyser2.pl)
Combining data from multiple replicates (custom scripts)
Removal of ploidy regions and off target capture (custom scripts)
Analysis in R to normalise between tracks using the total number of informative interactions
Genome_build: mm9
Supplementary_files_format_and_content: Custom combined data format (restriction enzyme fragment \t sample 1 \t sample 2 \t etc.)

source_name: Chromatin from purified CD71+ erythroid cells derived from differentiated WT mES cells, alpha globin enhancer sequence R1 as Capture point, sample 3

extract_protocol:
To produce CD71+ erythroid cells in vitro from differentiated mESCs (WT or mutant D3839 which is a mouse ESC line where mouse alpha globon HS38 and HS39.5 indicating CTCF sites/5' boundary elements have been deleted): 24h prior to differentiation, mESCs were induced by passaging into IMDM base media, trypsinised and plated in differentiation media (IMDM suplemented serum and other reagents and growth factors) in either triple vent petri dishes (Thermo Fisher) or flat-bottom 96-well plates (Thermo Fisher) at 3x104 cells in 10 cm dishes or 250 cells per well of a 96-well plate for up to seven days without disruption. EBs were harvested and disaggregated in 0.25% trypsin for 3 minutes at 37°C. CD71-positive cells were isolated by magnetic column separation (LS Column, Miltenyi), according to the manufacturer’s instructions. Briefly, cells (from disaggregated EBs) were labelled with anti-mouse CD71-FITC (eBioscience 11-0711-85; 1:200) in staining buffer (PBS with 10% FCS; 500 ul per 10^7 cells) for 20 minutes at 4°C, washed, then incubated with MACS anti-FITC separation microbeads (Miltenyi; 10 ul  per 10^7 cells, following the manufacturer’s instructions) and bead-labelled cells were retained by LS columns. Cells were then processed for Capture-C as in Davies J et al, Nature Methods.
The protocol used for generation of the 3C libraries was similar to previous methods with minor modifications. Briefly, cells were crosslinked with 2% formaldehyde (10 minutes, room temperature); quenched with cold glycine; washed in phosphate buffered saline; resuspended in cold lysis buffer (tris 10mM, NaCl 10mM, NP40 0.2%, complete proteinase inhibitor (Roche)) and snap frozen to -80.  Cells were thawed on ice, washed in milliq dH2O and Dounce homogenised on ice (x 40 strokes). Cells were then resuspended with 0.25% SDS and restriction enzyme buffer and incubated at 37C for 1h at 1400rpm on a Comfort Thermomixer (Eppendorf) followed by a further incubation of 1h following the addition of triton X100 (final concentration 1.67%). An overnight digestion was performed using Dpn II (500U /ml (NEB) at 37C / 1400 rpm). The digested chromatin was ligated overnight (Fermentas HC Ligase final concentration 10U/ml) at 16 degrees at 1400 rpm on the Thermomixer.  The samples were then decrosslinked overnight at 65C with Proteinase K (Roche) followed by a 30 min incubation at 37C with RNAse (Roche). Phenol/Chloroform extraction was then performed followed by an Ethanol precipitation and a wash with 70% Ethanol. Digestion efficiencys were assessed by gel electrophoresis (1% agarose) and RT-PCR (Taqman), which showed digestion efficiencies in excess of 80%.  DNA content of the Dpn II 3C libraries were quantitated using a Qubit fluorometer (Life technologies) and 5-10ug of each library was sheared using a Covaris S2 in milliq dH2O. Covaris settings used were: duty cycle 10%, Intensity 5, Cycles/burst 200, Time 6 cycles of 60seconds, Set Mode Frequency sweeping Temperature 4 to 7 degrees. Following shearing DNA was purified using AMPureXP beads (Agencourt) and DNA quality assessed on a Bioanalyser 2100 using a DNA High Sensitivity Chip (Agilent). DNA end repair and adapter ligation was performed using the NEB Next or NEB Ultra II DNA sample preparation reagent kits, depending on the amount of DNA available, using the standard protocol.  Biotinylated capture oligonucleotides were designed to the ends of the viewpoint fragments.  Where possible 1-2ug of each adapter ligated library were hybridized with the biotinylated capture oligonucleotides, using  the Nimblegen SeqCap reagents and an adapted protocol.  The quality of the resultant captured library was assessed by Agilent tapestation or bioanalyser (D1000). The resulting libraries were sequenced using Illumina Next-Seq.
The experimental strategy was to generate very high complexity randomly sonicated 3C libraries with ligated Illumina sequencing adaptors (ideally with several hundred thousand fold coverage).  Oligonucleotide capture technology was then used to pull down the restricion fragments containing the viewpoints of interest and their interacting partners, which were subsequently idendified by high throughput sequencing.  The power of the technique is that multiple samples and genes can be analysed simultaneously by using differently indexed samples.

tag: analysis

value: Alpha Globin Locus


title: WT EBd7 CD71+ H3K4me1 2

description:
Chromatin from purified CD71+ erythroid cells derived from differentiated WT mES cells, ChIPed for H3K4me1, sample 2
Genome-wide library of ChIPed chromatin

value: H3K4me1:Abcam ab8895 at 0.3ug/ml


title: WT EBd7 CD71+ CTCF 1

description:
Chromatin from purified CD71+ erythroid cells derived from differentiated WT mES cells, ChIPed for CTCF, sample 1
Genome-wide library of ChIPed chromatin


title: WT EBd7 CD71+ R1 Capture sample 2 (WT_EB9_Enhancers)

source_name: Chromatin from purified CD71+ erythroid cells derived from differentiated WT mES cells, alpha globin enhancer sequence R1 as Capture point, sample 2


title: WT EBd7 CD71+ R1 Capture sample 1(WT_EB8_Enhancers)

source_name: Chromatin from purified CD71+ erythroid cells derived from differentiated WT mES cells, alpha globin enhancer sequence R1 as Capture point, sample 1


title: APHSpleen_Ter119_ATAC_3

description:
Ter119+ erythroid cells purified from the spleen of a WT Phenylhydrazine APH-treated mice, sample 3
Genome-wide library of transposed elements

data_processing:
Trim_galore (to remove sequencing adaptors)
Alignment to the genome Bowtie 1 standard parameters with -m set to 2
Removal of PCR duplicates;
plot density of alignments in a moving 300bp window with an moving increment of 30 bp
Genome_build: mm9
Supplementary_files_format_and_content: BigWig

source_name: mouse derived Erythroid cells

extract_protocol:
Spleen from WT APH-treated mice are disaggregated and cells stained with ter119-PE antibody then incubated with anti-PE MACS beads (Miltenyi) and purified using LS columns (Miltenyi), all following manufacturor's instructions.
To produce CD71+ erythroid cells in vitro from differentiated mESCs (WT or mutant): 24h prior to differentiation, mESCs were induced by passaging into IMDM base media, trypsinised and plated in differentiation media (IMDM suplemented serum and other reagents and growth factors) in either triple vent petri dishes (Thermo Fisher) or flat-bottom 96-well plates (Thermo Fisher) at 3x104 cells in 10 cm dishes or 250 cells per well of a 96-well plate for up to seven days without disruption. EBs were harvested and disaggregated in 0.25% trypsin for 3 minutes at 37°C. CD71-positive cells were isolated by magnetic column separation (LS Column, Miltenyi), according to the manufacturer’s instructions. Briefly, cells (from disaggregated EBs) were labelled with anti-mouse CD71-FITC (eBioscience 11-0711-85; 1:200) in staining buffer (PBS with 10% FCS; 500 ul per 10^7 cells) for 20 minutes at 4°C, washed, then incubated with MACS anti-FITC separation microbeads (Miltenyi; 10 ul  per 10^7 cells, following the manufacturer’s instructions) and bead-labelled cells were retained by LS columns. Cells were then processed for ATAC-Seq as in (Buenrostro et al, 2013).
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013). 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen). Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). Due to the broad range of DNA fragment sizes found in these libraries, quantitation with the Qubit for DNA concentration was found to be highly variable and was omitted. The libraries were quantified using the universal library quantification kit (KAPA Biosystems). Samples were sequenced using: 75bp paired end reads (MiSeq platform) or 40 bp paired end reads (NextSeq platform).
The strategy was to survey regions of open chromatin in our cell population of interest (CD71+ EB-derived cells) as they mark regulatory genomic regions. The modified Tn5 can in one step identify open chromatin fragments, cut, and ligate adaptors. The fragments can then be multiplexed and sequenced

value: mouse derived Erythroid cells

value: Genome-wide


title: APHSpleen_Ter119_ATAC_2

description:
Ter119+ erythroid cells purified from the spleen of a WT Phenylhydrazine APH-treated mice, sample 2
Genome-wide library of transposed elements


title: E105Blood_ATAC_3

description:
circulating blood derived from mouse embryos at embryonic day E10.5, from one litter, sample 3
Genome-wide library of transposed elements

extract_protocol:
Circulating blood is collected from bled embryos at E10.5
To produce CD71+ erythroid cells in vitro from differentiated mESCs (WT or mutant): 24h prior to differentiation, mESCs were induced by passaging into IMDM base media, trypsinised and plated in differentiation media (IMDM suplemented serum and other reagents and growth factors) in either triple vent petri dishes (Thermo Fisher) or flat-bottom 96-well plates (Thermo Fisher) at 3x104 cells in 10 cm dishes or 250 cells per well of a 96-well plate for up to seven days without disruption. EBs were harvested and disaggregated in 0.25% trypsin for 3 minutes at 37°C. CD71-positive cells were isolated by magnetic column separation (LS Column, Miltenyi), according to the manufacturer’s instructions. Briefly, cells (from disaggregated EBs) were labelled with anti-mouse CD71-FITC (eBioscience 11-0711-85; 1:200) in staining buffer (PBS with 10% FCS; 500 ul per 10^7 cells) for 20 minutes at 4°C, washed, then incubated with MACS anti-FITC separation microbeads (Miltenyi; 10 ul  per 10^7 cells, following the manufacturer’s instructions) and bead-labelled cells were retained by LS columns. Cells were then processed for ATAC-Seq as in (Buenrostro et al, 2013).
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013). 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen). Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). Due to the broad range of DNA fragment sizes found in these libraries, quantitation with the Qubit for DNA concentration was found to be highly variable and was omitted. The libraries were quantified using the universal library quantification kit (KAPA Biosystems). Samples were sequenced using: 75bp paired end reads (MiSeq platform) or 40 bp paired end reads (NextSeq platform).
The strategy was to survey regions of open chromatin in our cell population of interest (CD71+ EB-derived cells) as they mark regulatory genomic regions. The modified Tn5 can in one step identify open chromatin fragments, cut, and ligate adaptors. The fragments can then be multiplexed and sequenced


title: Basal_1

city: Singapore

first: Yoshiaki

last: Ito

state: Select...

address: 14 Medical Drive #12-01

country: Singapore

institute: National University of Singapore

description: Sample 5

library_source: transcriptomic

data_processing:
Raw reads were aligned to mouse reference genome version GRCm38 gencode M23 (downloaded from https://www.gencodegenes.org/) using STAR aligner version 2.7.1a with default parameters (Dobin et al., Bioinformatics 2013)
Read counts per gene were generated using featureCounts function in the subread package version 2.0.0. (Liao et al., Nucleic Acids Res 2013)
RPKM values were calculated using cpm function of the edgeR R package (Robinson et al., Bioinformatics 2010)
Genome_build: mm10
Supplementary_files_format_and_content: RPKM

molecule: total RNA

source_name: Mammary gland

extract_protocol:
Mammary gland was dissected from 6-8 weeks old mice (used 4 mice for each experiment), and cut in pieces of 1 mm^3. To isolate mammary glands, tissue was incubated in enzyme digestion buffer (Advanced DMEM/F12 (Thermo Fisher Scientific), 2 mg/ml Collagenase Type VIII (Merck), 5 μg/ml Insulin (Merck), 50 μg/ml Gentamicin (Thermo Fisher Scientific), 20 mg/ml Trypsin (Thermo Fisher Scientific), 5 % Fatal bovine serum (FBS) (Biowest)) at 37 oC for 30 min, and centrifuged at 500 G for 10 minutes. After removing fat fraction, the pellet was re-suspended in TrypLE Express (Thermo Fisher Scientific) with 10 μM Y-27632 (Miltenyi Biotec) and incubated at 37 oC for 10 minutes. DMEM/F12 with 10 % FBS was added in cell suspension, and cell suspension was filtered through 30 μm cell-strainer (Miltenyi Biotec). After centrifugation, the pellet was resuspended in HBSS (Merck) with 2% FBS, and incubated with PE-Cy7-conjugated anti-CD24 (clone M1/69, BD Pharmingen), APC-conjugated anti-CD29 (clone eBioHMb1-1, Thermo Fisher Scientific), PE-conjugated anti-CD45 (clone 30-F11, Thermo Fisher Scientific), PE-conjugated anti-CD31 (clone MEC 13.3, BD Pharmingen), PE-conjugated anti-CD140a (clone APA5, Thermo Fisher Scientific) and APC-Cy7- conjugated anti-CD326 (Ep-CAM) (clone G8.8, BioLegend) at 4 oC for 30 minutes. After wash in HBSS with 2% FBS, the cells were resuspended in HBSS with 2% FBS and 1 μg/ml DAPI (Merck). Cells were sorted on FACS Aria with FACS DiVa software (BD Bioscience), and were collected in HBSS with 2% FBS. RNA was isolated from sorted epithelial cells, organoids or MCF7 cells using NucleoSpin RNA XS (Macherey-Nagel) or RNeasy mini kit according to the manufacturer’s instructions.
RNA were sent to Beijing Genomics Institute (BGI) for transcriptome library preparation and sequencing.

tag: tissue

value: Mammary gland

value: Basal epithelial cells

tag: genotype

value: Wildtype

tag: age

value: 6-8 weeks

tag: numbers

value: 3 mice

tag: facs antibody

tag: cell population

value: CD24low/CD29high epithelial cells


title: Luminal_4

description: Sample 4

value: Luminal epithelial cells

value: PE-Cy7-conjugated anti-CD24 (clone M1/69, BD Pharmingen), APC-conjugated anti-CD29 (clone eBioHMb1-1, Thermo Fisher Scientific), PE-conjugated anti-CD45 (clone 30-F11, Thermo Fisher Scientific), PE-conjugated anti-CD31 (clone MEC 13.3, BD Pharmingen), PE-conjugated anti-CD140a (clone APA5, Thermo Fisher Scientific) and APC-Cy7- conjugated anti-CD326 (Ep-CAM) (clone G8.8, BioLegend)

value: CD24high/CD29low epithelial cells


title: E105Blood_ATAC_2

description:
circulating blood derived from mouse embryos at embryonic day E10.5, from one litter, sample 2
Genome-wide library of transposed elements


title: APHSpleen_Ter119_ATAC_1

description:
Ter119+ erythroid cells purified from the spleen of a WT Phenylhydrazine APH-treated mice, sample 1
Genome-wide library of transposed elements

extract_protocol:
Spleen from WT APH-treated mice are disaggregated and cells stained with ter119-PE antibody (BD Biosciences at a working concentration of 2ug/ml) then incubated with anti-PE MACS beads (Miltenyi) and purified using LS columns (Miltenyi), all following manufacturor's instructions.
To produce CD71+ erythroid cells in vitro from differentiated mESCs (WT or mutant): 24h prior to differentiation, mESCs were induced by passaging into IMDM base media, trypsinised and plated in differentiation media (IMDM suplemented serum and other reagents and growth factors) in either triple vent petri dishes (Thermo Fisher) or flat-bottom 96-well plates (Thermo Fisher) at 3x104 cells in 10 cm dishes or 250 cells per well of a 96-well plate for up to seven days without disruption. EBs were harvested and disaggregated in 0.25% trypsin for 3 minutes at 37°C. CD71-positive cells were isolated by magnetic column separation (LS Column, Miltenyi), according to the manufacturer’s instructions. Briefly, cells (from disaggregated EBs) were labelled with anti-mouse CD71-FITC (eBioscience 11-0711-85; 1:200) in staining buffer (PBS with 10% FCS; 500 ul per 10^7 cells) for 20 minutes at 4°C, washed, then incubated with MACS anti-FITC separation microbeads (Miltenyi; 10 ul  per 10^7 cells, following the manufacturer’s instructions) and bead-labelled cells were retained by LS columns. Cells were then processed for ATAC-Seq as in (Buenrostro et al, 2013).
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013). 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen). Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). Due to the broad range of DNA fragment sizes found in these libraries, quantitation with the Qubit for DNA concentration was found to be highly variable and was omitted. The libraries were quantified using the universal library quantification kit (KAPA Biosystems). Samples were sequenced using: 75bp paired end reads (MiSeq platform) or 40 bp paired end reads (NextSeq platform).
The strategy was to survey regions of open chromatin in our cell population of interest (CD71+ EB-derived cells) as they mark regulatory genomic regions. The modified Tn5 can in one step identify open chromatin fragments, cut, and ligate adaptors. The fragments can then be multiplexed and sequenced


title: Luminal_3

description: Sample 3


title: WT EBd7 CD71+ H3K4me1 1

description:
Chromatin from purified CD71+ erythroid cells derived from differentiated WT mES cells, ChIPed forH3K4me1, sample 1
Genome-wide library of ChIPed chromatin


title: E105Blood_ATAC_1

description:
circulating blood derived from mouse embryos at embryonic day E10.5, from one litter, sample 1
Genome-wide library of transposed elements


title: D3839_EB_CD71_ATAC_2

description:
Purified CD71+ erythroid cells derived from Embryoid Bodies (EBs) resulting from mES in vitro differentiation of mutant mES cells deleted for two CTCF sites at the Alpha Globin locus at positions (HS38 and HS39.5), sample 2
Genome-wide library of transposed elements

extract_protocol:
To produce CD71+ erythroid cells in vitro from differentiated mESCs (WT or mutant): 24h prior to differentiation, mESCs were induced by passaging into IMDM base media, trypsinised and plated in differentiation media (IMDM suplemented serum and other reagents and growth factors) in either triple vent petri dishes (Thermo Fisher) or flat-bottom 96-well plates (Thermo Fisher) at 3x104 cells in 10 cm dishes or 250 cells per well of a 96-well plate for up to seven days without disruption. EBs were harvested and disaggregated in 0.25% trypsin for 3 minutes at 37°C. CD71-positive cells were isolated by magnetic column separation (LS Column, Miltenyi), according to the manufacturer’s instructions. Briefly, cells (from disaggregated EBs) were labelled with anti-mouse CD71-FITC (eBioscience 11-0711-85; 1:200) in staining buffer (PBS with 10% FCS; 500 ul per 10^7 cells) for 20 minutes at 4°C, washed, then incubated with MACS anti-FITC separation microbeads (Miltenyi; 10 ul  per 10^7 cells, following the manufacturer’s instructions) and bead-labelled cells were retained by LS columns. Cells were then processed for ATAC-Seq as in (Buenrostro et al, 2013).
Assay for transposition of active chromatin sequencing (ATAC-Seq) was performed as previously published (Buenrostro, 2013). 60000-80000 cells were used per biological replicate. Cells were lysed and nuclei were isolated prior to transposition with Tn5 transposase (Nextera, Illumina) for 30 minutes at 37°C. DNA was purified using a MinElute kit (Qiagen). Libraries were amplified and barcoded using the NEBNext 2xMastermix (NEB) and the custom primers as published in Buenrostro et al., 2013. ATAC-Seq libraries profiles were visualized using D1000 tape on the Tapestation (Agilent). Due to the broad range of DNA fragment sizes found in these libraries, quantitation with the Qubit for DNA concentration was found to be highly variable and was omitted. The libraries were quantified using the universal library quantification kit (KAPA Biosystems). Samples were sequenced using: 75bp paired end reads (MiSeq platform) or 40 bp paired end reads (NextSeq platform).
The strategy was to survey regions of open chromatin in our cell population of interest (CD71+ EB-derived cells) as they mark regulatory genomic regions. The modified Tn5 can in one step identify open chromatin fragments, cut, and ligate adaptors. The fragments can then be multiplexed and sequenced


title: D3839_EB_CD71_ATAC_1

description:
Purified CD71+ erythroid cells derived from Embryoid Bodies (EBs) resulting from mES in vitro differentiation of mutant mES cells deleted for two CTCF sites at the Alpha Globin locus at positions (HS38 and HS39.5), sample 1
Genome-wide library of transposed elements


title: Luminal_1

description: Sample 1


title: Luminal_2

description: Sample 2


title: Eyecup Tmem135 FUN025/FUN025 rep4

city: Madison

first: Akihiro

last: Ikeda

state: Wisconsin

address: 5322 Genetics Biotechnology Center, 425 Henry Mall

department: Medical Genetics

country: USA

institute: University of Wisconsin-Madison

data_processing:
QC raw sequences with FastQC v0.11.8
trimmed 5' adaptor (cut 9 bases) with trimmomatic v0.39
QC raw sequences with FastQC v0.11.8
mapped sequences with HISAT2 v2.1.0
sorted by chromosome with samtools sort v 1.9
count mapped sequences with featureCounts v2.0.0
Genome_build: GRCm38
Supplementary_files_format_and_content: raw counts

source_name: Eyecup

extract_protocol:
Posterior eyecups without the neural retina were collected and pooled from individual 2.5-month-old WT, Tmem135FUN025/+, and Tmem135FUN025/FUN025 mice of both genders between 11:00 and 1:00 PM. Samples were immediately flash frozen. Total RNA was extracted from eyecups with an RNeasy Plus Universal Mini kit (Qiagen, Hilden, Germany) following the Manufacturer’s instructions.
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Ipswich, MA, USA) following manufacturer’s instructions.


title: Eyecup Tmem135 FUN025/FUN025 rep5


title: 96W_EB_CD71_ATAC_2

description:
Purified CD71+ erythroid cells derived from differentiated WT mES cells into Embryoid Bodies (EBs), pooled from wells of 96W plates, sample 2
Genome-wide library of transposed elements


title: 96W_EB_CD71_ATAC_1

description:
Purified CD71+ erythroid cells derived from differentiated WT mES cells into Embryoid Bodies (EBs), pooled from wells of 96W plates, sample 1
Genome-wide library of transposed elements


title: Eyecup Tmem135 FUN025/FUN025 rep3


title: Eyecup Tmem135 FUN025/FUN025 rep2


title: 96W_EB_CD71_ATAC_3

description:
Purified CD71+ erythroid cells derived from differentiated WT mES cells into Embryoid Bodies (EBs), pooled from wells of 96W plates, sample 3
Genome-wide library of transposed elements


title: Basal_2

description: Sample 6


title: EB_CD71Ter119_ATAC_2

description:
Purified double positive CD71+ ter119+ erythroid cells derived from in vitro differentiation of WT mES cells into Embryoid Bodies (EBs), sample 2
Genome-wide library of transposed elements


title: EB_CD71Ter119_ATAC_3

description:
Purified double positive CD71+ ter119+ erythroid cells derived from in vitro differentiation of WT mES cells into Embryoid Bodies (EBs), sample 3
Genome-wide library of transposed elements


title: Eyecup Tmem135 FUN025/+ rep6


title: EB_CD71Ter119_ATAC_1

description:
Purified double positive CD71+ ter119+ erythroid cells derived from in vitro differentiation of WT mES cells into Embryoid Bodies (EBs), sample 1
Genome-wide library of transposed elements


title: Eyecup Tmem135 FUN025/+ rep5


title: EB_CD71_ATAC_3

description:
Purified CD71+ erythroid cells derived from in vitro differentiationof WT mES cells into Embryoid Bodies (EBs), sample 3
Genome-wide library of transposed elements


title: EB_CD71_ATAC_2

description:
Purified CD71+ erythroid cells derived from in vitro differentiationof WT mES cells into Embryoid Bodies (EBs), sample 2
Genome-wide library of transposed elements


title: Eyecup Tmem135 FUN025/+ rep4


title: EB_CD71_ATAC_1

description:
Purified CD71+ erythroid cells derived from in vitro differentiationof WT mES cells into Embryoid Bodies (EBs), sample 1
Genome-wide library of transposed elements


title: Eyecup Tmem135 FUN025/+ rep3


title: Eyecup Tmem135 FUN025/+ rep2


title: E14_mESC_ATAC_1

description:
wildtype mouse Embryonic Stem Cells (mESC)
Genome-wide library of transposed elements

source_name: E14TG2a.IV mouse ES cells

value: E14TG2a.IV mouse ES cells


title: Eyecup Tmem135 FUN025/+ rep1


title: E14_mESC_ATAC_3


title: E14_mESC_ATAC_2


title: Eyecup WT rep3


title: CLP PCV 2

city: Malmö

first: Milladur

last: Rahman

state: Skane

address: Jan Waldenströmsg. 35 hus 91 plan 10

department: Department of Clinical Sciences, Malmö

country: Sweden

institute: Lund University

data_processing:
The sequencing data was analyzed using the following pipeline: ‘Demultiplexing’ using the bcl2fastq2 software, ‘Raw Quality Control’ (QC) using FastQC, ‘Read Mapping and QC’ was done using HISAT2 software, and the reference genome sequence was from the Ensemble database, the Mouse 38, and the annotation (GTF) was from the release 93, ‘Expression Counts’ was performed using the StringTie software and finally ‘Differentially Expressed Genes (DEGs)’ analysis was performed using DESeq2
Genome_build: mouse m38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Lung

extract_protocol:
Total RNA was isolated from the sorted cells with RNeasy Plus Micro kit (Qiagen) and the quality of RNA was checked by Bioanalyzer RNA 6000 pico assay (Agilent, California, USA).
Sequence library was prepared using SMARTer® Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (634411, Takara Bio USA, Inc.). After library preparation and quality check, the double-stranded-cDNA was sequenced on NextSeq 500 (SY-415-1001, Illumina) using (read one-index reads-read two, bp): 75-8-8-75 setup.

value: Lung endothelial cells

value: post capillary venules (PCV)

value: 8-10 week

value: WT type

tag: Sex

value: male

tag: procedure

value: 4h after CLP surgery


title: Eyecup WT rep4


title: CLP PCV 3


title: CLP PCV 1


title: Eyecup Tmem135 FUN025/FUN025 rep1


title: Sham PCV 3

value: 4h after sham surgery


title: Knockout 1-E161

city: Philadelphia

first: Mark

last: Kahn

state: PA

address: 3400 Civic Center Blvd

department: Cardiovascular Institute

institute: University of Pennsylvania

data_processing:
Illumina software used for basecalling.
CellRanger used for raw processing
Seurat R-package used for further analysis
Genome_build: mm10
Supplementary_files_format_and_content: A xlsx spreadsheet containing normalized expression of genes based on cluster and group

source_name: Kidney Cortex

extract_protocol:
Kidneys were perfused with HBSS and stored in RNALater at -80C. A 2 mm3 section of tissue was rinsed briefly with PBS and minced before adding 1 mL of lysis buffer containing 20 mM Tris-HCl (pH 8), 320 mM sucrose, 5 mM CaCl2, 3 mM MgAc2,  0.1 mM EDTA, and 0.1% TritonX-100. The tissue was initially dissociated by pipetting up and down ~10X with a p-1000 tip and then being passed through a 25G syringe ~10X. The tissue was incubated on ice for 10 minutes and then passed through a 30 µm CellTrics filter. Nuclei were pelleted by centrifugation (5 min, 500g, 4°C) and washed with PBS after removal of supernatant. Nuclei were pelleted again and resuspended in 1 mL of PBS containing 0.04% BSA and RNAse inhibitor (0.2u/µL) before counting by hemocytometer.  Nuclei were then diluted and prepared using the 10X Chromium System according to the manufacturer’s instructions (10X Genomics).
RNA libraries were prepared for sequencing using standard 10X Genomics and Illumina protocols

value: Podocin-Cre Klf4 fl/fl

value: FVB/N

value: kidney cortex

tag: rna fraction

value: nuclear RNA

tag: preparation

value: Single nuclei


title: Control 1-A151

value: Klf4 fl/fl


title: Sham PCV 2


title: Knockout 3

data_processing:
Illumina software used for basecalling.
FastQC to perform Quality Controls and generate QC report for the input RNA-seq data
STAR for the read alignment
featureCounts for assigning reads to genes
edgeR Bioconductor package were used to compute CPM and RPKM
Genome_build: mm10
Supplementary_files_format_and_content: one xlsx file contains RPKM values for all 6 samples

source_name: Isolated Kidney Glomeruli

extract_protocol:
Mice were perfused with HBSS containing 2.5 mg/ml iron oxide and 0.1% BSA. At the end of perfusion, kidneys were removed, decapsulated, minced into 1-mm3 pieces, and digested in HBSS containing 1 mg/ml collagenase A and 100 U/ml deoxy- ribonuclease I. Digested tissue was then passed through a 100-mm cell strainer and collected by centrifugation. The pel- let was resuspended in 2 ml of HBSS, and glomeruli were collected using a magnet. The purity of glomerular was veri- fied under microscopy. Total RNA was isolated from kidney glomeruli of mice using the RNAeasy kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Kidney Glomeruli


title: Knockout 2


title: Eyecup WT rep1


title: Knockout 1


title: CLP capEC 3

value: capillaries (capEc)


title: CLP capEC 2


title: Control 2


title: Sham capEC 3


title: CLP capEC 1


title: Control 3


title: Sham capEC 2


title: Eyecup WT rep2


title: WT_mESCs_KLF5.5_V5_ChIPSeq

city: Berkeley

first: Robert

last: Tjian

state: CA

address: University of California, Berkeley 450 Li Ka Shing #3370

department: MCB

institute: UC Berkeley

data_processing:
Base-calling performed with CASAVA by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley
ChIP-seq reads quality control performed with FastQC (version 0.10.1)
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie (version 0.12.8) with the following configurations: -n 2 -m 1
ChIP-Seq peaks were called using MACS2 (version 2.1.0.20140616) with the following configurations: -t <sample.bam>  -c <input.bam> -f BAM -g mm --nomodel --extsize 250
bigWig coverage files were generated with deepTools (version 2.4.1) with the following configurations: bamCoverage -of bigwig --binSize 50 --normalizeTo1x 2150570000 --extendReads 250 --ignoreDuplicates
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-seq: tdf files were generated using igvtools (igvtools count -w 50 -e 200) / txt files are Partek detected enriched regions RAD23B vs. IgG); RNA-seq: text files contain CuffDiff results

source_name: Mouse embryonic stem cells derived from C57B6/J mice

extract_protocol:
Cell pellets were thawed in ice and resuspended in cell lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, and 0.5% NP-40, 1 ml/15 cm plate) and incubated for 10 min on ice. Lysates were then centrifuged for 10 min at 4000 rpm. Nuclear pellets were resuspended in 6 volumes of sonication buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 0.1% SDS), incubated on ice for 10 min, and sonicated to obtain DNA fragments below 2000 bp in length (Covaris S220 sonicator, 20% Duty factor, 200 cycles/burst, 100 peak incident power, 32 cycles of 20" on and 40" off).  Sonicated lysates were cleared by centrifugation and 800 μg of chromatin was diluted in RIPA buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl) to a final concentration of 0.8 μg/μl, precleared with Protein A sepharose (GE Healthcare) for 2 hours at 4°C and immunoprecipitated overnight with 8 μg of antibodies. 4% of the precleared chromatin was saved as input.  Immunoprecipitated DNA was purified with the Qiagen QIAquick PCR Purification Kit, eluted in 60 μl of water and used for library preparation.
Libraries were prepared with the Illumina ChIP-seq DNA sample preparation kit according to manufacturer instructions (for input DNA we used only 150 ng of DNA)

treatment_protocol: Cells were cross-linked for 5 minutes at room temperature with 1% formaldehyde-containing medium; cross-linking was stopped by PBS-glycine (0.125 M final). Cells were washed twice with ice-cold PBS, scraped, centrifuged for 10 min at 4000 rpm, 4 'C and pellets flash-frozen in liquid nitrogen and stored at - 80 'C until lysed.

value: embryonic stem cells

value: wild type, overexpressing V5-KLF5

value: anti-  V5 (Invitrogen R960-25)


title: Sham PCV 1

value: Lung endothelial cells

value: post capillary venules (PCV)


title: Tri-4C-GLN_TT2

city: HONG KONG

first: Danny

last: Leung

state: HONG KONG

address: Clear Water Bay

country: China

institute: HONG KONG UNIV OF SCIENCE & TECHNOLOGY

data_processing:
The reverse reads resulting from paired-end sequencing were firstly processed by “fastx_barcode_splitter” function and by “fastx_trimmer” function of Fastx-Toolkit, in order to obtain read pairs derived from targeted anchor.
Bowtie was used to align the resulted forward and reverse reads to mm10 assembly separately.
The resulted SAM files were converted into BAM and BED files with SAMTools and BEDTools
The PCR duplicates which shared the same coordinates of the sonicated end  from forward reads were removed.
Finally, the resulted BED file was converted into BigWig format for visualization with the UCSC genome browser
Genome_build: mm10
Supplementary_files_format_and_content: WGS: BigWig files were generated by UCSC utilites; Scores represent raw reads number.
Supplementary_files_format_and_content: Tri-4C: BigWig files were generated by UCSC utilites; Scores represent RPKM in 500bp bins.

source_name: Embryonic stem cell

growth_protocol: mESCs were grown on 0.1% gelatinized plate supplemented with 15% certified FBS (Life Technologies), 20mM HEPES, 0.1mM non-essential amino acids, 0.1mM 2-mercaptoethanol, 100U/ml penicillin, 0.05mM streptomycin, 1U/ul Leukemia-inhibitory factor(LIF) and 2mM glutamine. Cells were passage at 80% confluency.

extract_protocol:
Tri-4C was performed with modifications from a pre-print protocol (BioRxiv doi: https://doi.org/10.1101/743005). Briefly, 1 x 107 crosslinked mESCs were resuspended in cold lysis buffer (10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630 (Sigma)) with 1x protease inhibitors followed by incubation on ice for 15 minutes and centrifuge at 4°C. The pellet was then washed with cold lysis buffer and resuspended in 0.5% SDS (Sigma). After incubated at 62°C for 7 minutes, 10% Triton X-100 (Sigma) was added to obtain the nuclei. Subsequently, in situ digestion was done overnight with MboI (NEB), CviQI (NEB), and NlaIII (NEB) endonucleases. The digested chromatin was washed twice to remove remaining enzyme. End blunting was performed by adding dNTP (Invitrogen), DNA polymerase I Klenow (NEB) and T4 DNA polymerase (NEB) followed by incubation at 37°C for 1 hour with rotation. Blunt end ligation was then carried out by adding T4 ligase buffer (NEB), 10% Triton X-100 (Sigma), BSA (NEB) and T4 ligase (NEB) followed by rotating at room temperature for 4 hours. The chromatin was then resuspended in 1 x T4 ligase buffer (NEB) with Proteinase K and SDS and incubated at 65°C for reverse crosslinking. The resulting DNA was purified by phenol-chloroform extraction and sonicated with Covaris S220 at 140 watts for 80 seconds. The fragmented DNA was size-selected using 0.40x/1.0x of Ampure XP beads (Beckman Coulter) and eluted in 10mM Tris-HCl. Subsequently, the sonicated fragment ends were repaired and A-tailed followed by purification with 1.0x of Ampure XP beads (Beckman Coulter).
The A-tailed DNA fragments were then ligated with pre-annealed Y-shape adaptor and purified twice with 1.0x of Ampure XP beads (Beckman Coulter). Size distribution of final preamplification libraries was determined by Fragment analyzer with the DNF 474 kit. To amplify the Tri-4C library targeting the designated anchor, nested PCR was conducted for 14 cycles in the first round and 14 cycles in the second round.

treatment_protocol: Cells were crosslinked using 1% formaldehyde for 10minutes at room temperature then quenched with glycine.

tag: strain background

tag: cell line

value: wild type

value: Embryonic stem cell


title: WT_mESCs_KLF5.5_IgG_ChIPSeq

value: Mouse normal IgG (Jackson ImmunoResearch 015-000-003)


title: WT_mESCs_KLF5.5_input


title: D3_input


title: RNAseq_J1_GLN_PB1

data_processing:
Reads were aligned to mouse reference genome mm10 using STAR and uniquely mapped reads were included in further analysis
The output file was subsequently converted into BigWig file by homemade scripts and uploaded to UCSC genome browser to visualize
Meanwhile, generated BAM file was used to calculate Fragments Per Kilobase per Million reads (FPKM) of genes with RSEM
BigWig files were generated by STAR v2.5.3a and UCSC utilites; Scores represent RPM signal for piled up genomic alignments

molecule: polyA RNA

extract_protocol:
Total RNA were extracted using Rneasy Mini Kit (Qiagen) according to manufacturer protocols.
RNA-seq libraries were prepared by Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Vazyme) and QIAseq Stranded RNA Library Kits (Qiagen) according to manufacturer protocols.

tag: chip-seq antibody

value: GLN KI with PiggyBac


title: Dmxr1, rep2

city: Bangalore

first: Aditi

last: Gupta

state: Karnataka

address: FE-15, Biological Sciences Building, Indian Institute of Science

department: Biochemistry

country: India

institute: Indian Institute of Science

description: Sample T2

data_processing:
demultiplexing and base call to fastq conversion using illumina’s bcl2fastq v2.19.0.316
Adapter trimming using fastp 0.19.6
Read alignment to reference GCA_900235035.1_ASM90023503v1 using bowtie2
Counts per gene were obtained using featureCounts v1.6.4
Differential expression analysis was performed using DESeq2.
Genome_build: GCA_900235035.1_ASM90023503v1
Supplementary_files_format_and_content: read counts per gene in excel file

organism: Komagataella pastoris

growth_protocol: cells cultured in YNBE media for 14 hours

extract_protocol:
RNeasy Mini Kit Qiagen
NEBNext Ultra II RNA Library Prep Kit for Illumina was used to prepare the library after depleting rRNA from the total RNA  using RiboMinus™ Transcriptome Isolation Kit, bacteria.

tag: auxotroph

value: Histidine auxotroph

tag: antibiotic resistance

value: ZeocinTM

value: Deletion mutant of Mxr1


title: RNAseq_TT2_Klhdc4_KD_scramble_shRNA_1

tag: cell type

tag: strain

value: control


title: RNAseq_J1_GLN_PB14


title: GS115, rep2

description: Sample C2

value: Wild Type


title: RNAseq_TT2_Klhdc4_KD_shRNA_1

value: Klhdc4 KD


title: RNAseq_TT2_GLN_KD_scramble_shRNA_1


title: RNAseq_TT2_GLN_KD_scramble_shRNA_2


title: Dmxr1, rep1

description: Sample T1


title: GS115, rep1

description: Sample C1


title: Control 1

value: Klf4 fl/fl

value: FVB/N

tag: tissue

value: Kidney Glomeruli


title: Sham capEC 1

value: capillaries (capEc)

value: 8-10 week

tag: genotype

value: WT type

value: male

value: 4h after sham surgery


title: RNAseq_TT2_GLN_KO_C13_P5

value: Embryonic stem cell

value: GLN KO


title: Rvb2-G_IP_2

city: La Jolla

first: Brian

middle: Matthew

last: Zid

state: California

address: 9500 Gilman Drive

department: Chemistry and Biochemistry

institute: University of California San Diego

description: Rvb2 IP-2; 10-min glucose starvation

data_processing:
QC by FastQC
The reads were mapped to S288C S. cerevisiae genome using Bowtie2
The mapped reads were then sorted, indexed and converted into BAM files using SAMtools
Duplicated reads were removed using Picard Tools
deepTools was used to calculate and plot the enrichment of Rvb1/Rvb2 on genome and selected genes
BEDtools was used to calculate the coverage of regions of interest
Genome_build: S288C S. cerevisiae
Supplementary_files_format_and_content: csv. read counts on -500 bp to TSS and TSS to +500 bp

organism: Saccharomyces cerevisiae

source_name: W303 budding yeast

growth_protocol: Cells grew at 30C for ~18 hours to reach an OD660 around 0.4 (log-phase)

extract_protocol:
Cells were lysed by beadbeating. Lysates were sonicated and TAP-tagged proteins of interest were isolated by rabbit IgG
NextSeq 500 SR 75 cycles

treatment_protocol: Cells were washed once by synthetic medium lacking glucose (SC-G) and resuspended in the same volume of SC-G medium

tag: treatment

value: 10-min glucose starvation

tag: antibody

value: Rabbit IgG targeting TAP-tag


title: RNAseq_TT2_GLN_KD_shRNA_2

value: GLN KD


title: Pgk1-G_IP_1

description: Pgk1 IP-1; 10-min glucose starvation


title: RNAseq_TT2_GLN_KD_shRNA_1


title: RNAseq_TT2_GLN_KO_C43_P5


title: Tri-4C-GLN_J1

value: wild type


title: Rvb2-G_IP_1

description: Rvb2 IP-1; 10-min glucose starvation


title: D3_V5_ChIPSeq

value: embryonic stem cells

tag: chip antibody

value: anti-  V5 (Invitrogen R960-25)


title: Rvb2-G_input

description: Rvb2 input; 10-min glucose starvation

value: none (input)


title: RNAseq_TT2_GLN_KO_C43_P3


title: RNAseq_TT2_Klhdc4_KD_shRNA_2

value: Klhdc4 KD


title: Rvb1-G_IP_1

description: Rvb1 IP-1; 10-min glucose starvation


title: Rvb1-G_IP_2

description: Rvb1 IP-2; 10-min glucose starvation


title: RNAseq_TT2_rep2


title: Pgk1-G_IP_2

description: Pgk1 IP-2; 10-min glucose starvation


title: RNAseq_J1_rep2


title: RNAseq_TT2_rep1


title: Rvb1-G_input

description: Rvb1 input; 10-min glucose starvation


title: Pgk1-G_input

description: Pgk1 input; 10-min glucose starvation


title: ChIPseq_Input_TT2

data_processing:
Reads were aligned to GRCm38/mm10 genome assembly by Bowtie v1.2 with parameters -v 3 -m 1 --best --strata.
Duplicates were then removed by Picard MarkDuplicates v2.9.0.
Input-subtracted reads per kilobase per million (RPKM) values per 100bp bin were generated as previously described (Hawkins et al., 2010).
BigWig files were generated by UCSC utilites; Scores represent input-subtracted RPKM for each 100bp bin.

extract_protocol:
Chromatin were extracted by lysing the cells and fragmented with sonication. The histone-DNA complexes were then isolated with antibodies.
ChIP libraries were prepared for sequencing using KAPA Hyper Prep Kit (Roche) according to manufacturer protocol


title: COLO320DM_RNA

city: Stanford

first: Howard

middle: Y

last: Chang

address: CCSR 2130, 269 Campus Drive

department: Center for Personal Dynamic Regulomes

institute: Stanford University

description: RNA-seq library

data_processing:
Paired-end reads were aligned to the hg19 genome using STAR-Fusion (version 1.6.0) and the genome build GRCh37_gencode_v19_CTAT_lib_Mar272019.plug-n-play.
Read counts obtained using featureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: text file with raw read counts

organism: Homo sapiens

source_name: COLO320-DM cells

growth_protocol: Cells were maintained in RPMI (Life Technologies, #11875-119) supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin.

extract_protocol:
RNA was extracted using RNeasy Plus mini Kit (QIAGEN 74136). Genomic DNA was removed from samples using the TURBO DNA-free kit (ThermoFisher, Cat# AM1907).
RNA-seq libraries were prepared using the TruSeq Stranded mRNA Library Prep (Illumina, Cat# 20020595) following the manufacturer’s protocol.

treatment_protocol: COLO320-DM cells were transfected with Alt-R S.p. Cas9 Nuclease V3 (IDT, Cat# 1081058) complexed with a non-targeting control sgRNA (Synthego) with a Gal4 sequence following Synthego’s RNP transfection protocol using the Neon Transfection System (ThermoFisher, Cat# MPK5000).


title: ChIPseq_H3K27ac_J1_PB14

value: H3K27ac (Active Motif:39133)

value: GLN KI with PiggyBac


title: ChIPseq_H3K27ac_J1_PB1


title: RNAseq_J1_rep1


title: ChIPseq_H3K27ac_TT2


title: ChIPseq_Input_J1


title: RNAseq_TT2_GLN_KO_C13_P3


title: ATAC-Seq frontal_cortex_UMB4540_rep1

city: San Diego

first: Bing

last: Ren

address: 9500 Gilman Dr

data_processing:
For each sequenced single nucleus ATAC-Seq library, we obtained four FASTQ files, two for paired end DNA reads and two for the combinatorial indexes for i5 and T7 (768 and 364 indices, respectively). We selected all reads with up to 2 mismatches per i5 and T7 index (Hamming distance between each pair of indices is 4) and integrated the concatenated barcode at the beginning of the read name in the demultiplexed FASTQ files.
snATAC-seq reads were aligned to the GRCh38 genome assembly using BWA version 0.7.17-r1188 with the following parameters: "mem -M -k 32 -t 8".
Aligned reads were name sorted and filtered using Samtools version 1.9 with the following parameters: "-f 2 -F 0x70c -q 30".
Duplicated paired-end fragments were removed for each nucleic and nucleic were filtered based on stringent quality control criteria including an enrichment of reads at transcription start sites (TSS enrichment; TSSe) greater than 7-fold, and a minimum of > 1,000 mapped paired-end fragments per nucleus.
Nuclei were further filtered for potential doublets using a version of Scrublet modified for single cell ATAC-seq.
For each sample, we generated a cell by bin (5kb) count matrix and used it for the initial clustering analysis.
Nuclei from all samples were pooled and subjected to clustering analysis using the Taiji pipeline (https://taiji-pipeline.github.io/).
Genome_build: GRCh38
Supplementary_files_format_and_content: bigwig files were generated using bedGraphToBigWig. Score represents RPKM.
Supplementary_files_format_and_content: Fragment files were generated using the Taiji pipeline (https://taiji-pipeline.github.io/). Column 1: chromosome; Column 2: adjusted start position; Column 3: adjusted end position. Column 4: cell barcode; Column 5: the total number of read pairs associated with this fragment (including unique and all duplicate read pairs).
Supplementary_files_format_and_content: metadata.tsv.gz: tab-delimited text files containing final clustering result and metadata of nucleic from all samples

source_name: frontal cortex

extract_protocol:
Nuclei were extracted from flash frozen tissue either by manual pulverization via mortar and pestle while submerged in liquid nitrogen, or homogenization in a gentleMACS M-tube (Miltenyi) on a gentleMACS Octo Dissociator (Miltenyi) using the “Protein_01_01” protocol in MACS buffer (5 mM CaCl2, 2 mM EDTA, 1X protease inhibitor (Roche, 05-892-970-001), 300 mM MgAc, 10 mM Tris-HCL pH 8, 0.6 mM DTT) and pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf).
Extracted nuclei were permeabilized either in 1 mL Nuclear Permeabilization Buffer (1X PBS, 5% Bovine Serum Albumin, 0.2% IGEPAL CA-630 (Sigma), 1 mM DTT, 1X Protease inhibitor), or 1 mL OMNI Buffer (10mM Tris-HCL (pH 7.5), 10mM NaCl, 3mM MgCl2, 0.1% Tween-20 (Sigma), 0.1% IGEPAL-CA630 (Sigma) and 0.01% Digitonin (Promega) in water). After resuspension in permeabilization buffer, nuclei were rotated at 4 ˚C for 5 minutes before being pelleted with a swinging bucket centrifuge (500 x g, 5 min, 4°C; 5920R, Eppendorf). After centrifugation, permeabilized nuclei were resuspended in 500 μL high salt tagmentation buffer (36.3 mM Tris-acetate (pH = 7.8), 72.6 mM potassium-acetate, 11 mM Mg-acetate, 17.6% DMF) and counted using a hemocytometer. Concentration was adjusted to 2,000 nuclei/9 μl, and 2,000 nuclei were dispensed into each well of a 96-well plate per sample (96 tagmentation wells/sample, samples were processed in batches of 2-4 samples). For tagmentation, 1 μL barcoded Tn5 transposomes were added using a BenchSmart™ 96 (Mettler Toledo), mixed five times, and incubated for 60 min at 37 °C with shaking (500 rpm). To inhibit the Tn5 reaction, 10 µL of 40 mM EDTA (final 20mM) were added to each well with a BenchSmart™ 96 (Mettler Toledo) and the plate was incubated at 37 °C for 15 min with shaking (500 rpm). Next, 20 µL of 2x sort buffer (2 % BSA, 2 mM EDTA in PBS) were added using a BenchSmart™ 96 (Mettler Toledo). All wells were combined into a separate FACS tube for each sample, and stained with Draq7 at 1:150 dilution (Cell Signaling). Using a SH800 (Sony), 20 nuclei per sample were sorted per well into eight 96-well plates (total of 768 wells) containing 10.5 µL EB (25 pmol primer i7, 25 pmol primer i5, 200 ng BSA (Sigma)). Preparation of sort plates and all downstream pipetting steps were performed on a Biomek i7 Automated Workstation (Beckman Coulter). After addition of 1 µL 0.2% SDS, samples were incubated at 55 °C for 7 min with shaking (500 rpm). 1 µL 12.5% Triton-X was added to each well to quench the SDS. Next, 12.5 µL NEBNext High-Fidelity 2× PCR Master Mix (NEB) were added and samples were PCR-amplified (72 °C 5 min, 98 °C 30 s, (98 °C 10 s, 63 °C 30 s, 72°C 60 s) × 12 cycles, held at 12 °C). After PCR, all wells were combined. Libraries were purified according to the MinElute PCR Purification Kit manual (Qiagen) using a vacuum manifold (QIAvac 24 plus, Qiagen) and size selection was performed with SPRISelect reagent (Beckmann Coulter, 0.55x and 1.5x). Libraries were purified one more time with SPRISelect reagent (Beckman Coulter, 1.5x). Libraries were quantified using a Qubit fluorimeter (Life technologies) and a nucleosomal pattern of fragment size distribution was verified using a Tapestation (High Sensitivity D1000, Agilent). Libraries were sequenced on a NextSeq500 or HiSeq4000 sequencer (Illumina) using custom sequencing primers with following read lengths: 50 + 10 + 12 + 50 (Read1 + Index1 + Index2 + Read2).
OTHER: single cell ATAC-seq

tag: sample type

value: normal

tag: biosample

value: flash-frozen tissue

tag: donor age (years)

tag: donor sex

tag: race

value: Caucasian

tag: case of death

value: Unkown


title: ATAC-Seq frontal_cortex_UMB4540_rep2

value: male


title: ATAC-Seq uterus_SM-A87A2

source_name: uterus

value: female

value: asian

value: cerebral vascular accident


title: ATAC-Seq vagina_SM-A9HOS

source_name: vagina


title: ATAC-Seq uterus_SM-IOBHX


title: ChIPseq_H3K27ac_J1

value: Embryonic stem cell

tag: cell line


title: ATAC-Seq thyroid_SM-C1MKY

source_name: thyroid

value: white

value: anoxia


title: ATAC-Seq thyroid_SM-JF1O4


title: ATAC-Seq stomach_SM-JF1O3

source_name: stomach


title: CLP+MLT4_heart

city: Nanjing

first: Zhiguang

last: Shi

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

institute: Nanjing Medical 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 v2.1.0 with default parameters
Read counts were calculated using Htseq-count with default parameters
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene counts for each Sample

source_name: heart

extract_protocol:
Samples were collected and flash-frozen in liquid nitrogen and, then treated by Trizol in -80℃ until RNA extraction. Extracting total RNA from tissues by Trizol. 1.5% agarose gels were used to monitor the RNA degradation and contamination. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). The next RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 3.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Library preparation for RNA sequencing. A total amount of 1μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer (5X).First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system(Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with sizeselected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 System.

value: Heart

value: CLP+MLT


title: sst_mef2c_cr_rep2

city: Cambridge

first: Kathryn

last: Allaway

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Disease

institute: Broad Institute

data_processing:
Library strategy: CUT&RUN
CUT&RUN data were processed as described in Zhu et al., 2019 (PMID: 31500663). Briefly, paired-end reads were trimmed with Trimmomatic to remove adaptor sequences. Trimmed reads were then aligned to the mm10 genome using Bowtie2 with the –dovetail setting enabled. PCR duplicates, multiple mapped reads, and reads overlapping with the blacklist regions were excluded from downstream analyses.
To ensure all libraries were compared at the same read depth, BAM files were downsampled to 8.5 million reads before peak calling.  For each sample, peaks were called and bigwig files were generated using MACS2 (-f BAMPE -g mm -q 0.05 -B) (v.2.2.7.1; https://github.com/taoliu/MACS)
Genome_build: mm10
Supplementary_files_format_and_content: .bed files containing locations of called peaks for each sample.
Supplementary_files_format_and_content: .bw files containing bigwigs showing genome-wide signal for each sample.

source_name: Whole Cortex

extract_protocol:
Nuclear isolation was performed as described in Mo et al., 2015 (PMID: 26087164). The neocortex was dissected from adult Pv-Cre;INTACT and Sst-Cre;INTACT mice in ice-cold buffer HB [0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tricine-KOH pH 7.8, 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, 1X cOmpleteTM, EDTA-free Protease Inhibitor Cocktail (Sigma), and 10 mM Sodium Butyrate]. Cortices were homogenized by a dounce homogenizer in the presence of 0.3% IGEPAL. The homogenate was then filtered through a 30 µm MACS SmartStrainer (Miltenyi Biotec), mixed with working solution [5 volume of OptiPrep + 1 volume of Diluent (150 mM KCl, 30 mM MgCl2, and 120 mM Tricine-KOH pH 7.8)] at a 1:1 ratio, and underlaid with 30% and 40% gradient solution (working solution diluted by buffer HB). Following ultracentrifugation at 10,000g for 18 mins at 4°C, nuclei were collected from the interface of 30% and 40% layers and then resuspended in FACS buffer (1X PBS, 1% BSA, 1X Protease Inhibitor Cocktail, and 10 mM Sodium Butyrate) for sorting GFP-positive nuclei on a Sony SH800S sorter.
CUT&RUN on sorted nuclei was performed as described in Stroud et al., 2020 (PMID: 32589877). Nuclei were resuspended in CUT&RUN wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.2% Tween 20, 1 mg/ml BSA, 0.5 mM Spermidine, 1X Protease Inhibitor Cocktail, and 10 mM Sodium Butyrate) and captured with Concanavalin A beads (Bangs Laboratories) at room temperature for 10 mins. Bead-bound nuclei were then incubated with MEF2C antibody (182901-AP, Proteintech, 1:100) in antibody buffer (CUT&RUN wash buffer, 0.1% Triton X-100, and 2 mM EDTA) overnight at 4°C. The next day, beads were washed twice with antibody buffer and then incubated with pA-MNase (0.7 µg/ml) in antibody buffer at 4°C for 1 hour. After two washes with Triton wash buffer (CUT&RUN wash buffer and 0.1% Triton X-100), tethered cleavage was induced by addition of CaCl2 at a final concentration of 3mM on ice for 30 mins. To release protein-DNA complex, nuclei were combined with 2X STOP solution (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.04% Triton X-100, and 50 µg/ml RNase A) at a 1:1 ratio and incubated at 37°C for 20 mins. Solubilized chromatin was separated from bead-bound nuclei on a magnetic rack, supplemented with 0.1% SDS, and then digested with 0.2 mg/ml Proteinase K at 65°C for 1 hour. Released DNA was extracted with phenol chloroform. CUT&RUN libraries were constructed using NEBNext Ultra II DNA Library Prep Kit as described in Liu et al., 2018 (PMID: 29606353). Libraries with different barcodes were pooled and sequenced on NextSeq with NextSeq 500/550 High Output Kit v2 (75 cycles), generating 7-14 million paired-end 42-bp reads per sample.

value: SST+ cortical interneurons

tag: age

value: adult


title: E13_MGE_multi_rna

description: Gene expression (RNA) from the same barcoded cells as ATAC sample

data_processing:
Raw multiomic data was processed using the Cell Ranger ARC v1.0.0 pipeline (10x Genomics). Reads were aligned to the GRCm38 (mm10) mus musculus genome.
Read filtering, alignment, and barcode counting were performed using cellranger-arc count.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv file containing cell barcodes  present in the corresponding expression matrix.
Supplementary_files_format_and_content: features.tsv file containing gene IDs and names present in the corresponding expression matrix.
Supplementary_files_format_and_content: matrix.mtx file is sparse matrix containing feature-barcode matrices.
Supplementary_files_format_and_content: The fragments.tsv.gz file is  a tabular file where each line represents a unique ATAC-seq fragment. Duplicate reads are collapsed into a single fragment record.
Supplementary_files_format_and_content: The per_barcode_metrics.csv file contains QC information associated with each barcode for cell-calling.

source_name: medial ganglionic eminence

extract_protocol:
E13.5 embryos were harvested from timed pregnant CD-1 mice  and the MGE was dissected in ice-cold Leibovitz's L-15 medium. Pooled tissue from several embryos were dissociated using the Neural Tissue Dissociation Kit (T) (Miltyeni Biotec, PN-130-093-231) according to the manufacturer’s instructions. Dissociated cells were then filtered through a 70 um filter, and centrifuged at 300xg for 5 min at 4C. Nuclei then were isolated as described in the 10x Genomics demonstrated protocols ‘Nuclei Isolation from Embryonic Mouse Brain for Single Cell Multiome ATAC + Gene Expression Sequencing ’ for fresh tissue for input to single-cell Multiome library preparation.
Single-cell multiomic (ATAC + Gene Expression) libraries were prepared on the 10x Genomics platform using the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Reagent Bundle (PN-1000285), Chromium Next GEM Chip J Single Cell Kit (PN-1000230), Single Index Kit N Set A (Pn- PN-1000212) and Dual Index Kit TT Set A (PN-1000215) as instructed by the manufacturer. Libraries were sequenced using the Nova-Seq 100 cycle kit (ATAC library) and Next-Seq 150 cycle kit (Gene Expression library) (Illumina) by Broad Institute Genomic Services.
Dual scRNA/scATAC-seq

value: MGE cells


title: ATAC-Seq stomach_SM-JF1NP


title: ChIPseq_Input_J1_PB14

tag: chip-seq antibody

value: GLN KI with PiggyBac


title: ATAC-Seq stomach_SM-IOBHV

value: normal


title: CLP_heart

value: CLP


title: sst_mef2c_cr_rep1


title: CLP+MLT4_kidney

source_name: kidney

extract_protocol:
Samples were collected and flash-frozen in liquid nitrogen and, then treated by Trizol in -80℃ until RNA extraction. Extracting total RNA from tissues by Trizol. 1.5% agarose gels were used to monitor the RNA degradation and contamination. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). The next RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 3.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Library preparation for RNA sequencing. A total amount of 1μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEB Next First Strand Synthesis Reaction Buffer (5X).First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNaseH-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEB Next Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments with right length, the library fragments were purified with AMPure XP system(Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 System.

value: Kidney


title: ChIPseq_Input_J1_PB1


title: pv_mef2c_cr_rep2

value: PV+ cortical interneurons


title: ATAC-Seq stomach_SM-CHLWL

value: flash-frozen tissue

value: male


title: ATAC-Seq thyroid_SM-IOBHW

value: female

value: asian


title: CLP_kidney


title: ATAC-Seq small_intestine_SM-JF1O2

source_name: small intestine terminal ileum

value: cerebral vascular accident


title: pv_mef2c_cr_rep1


title: RNA_KO_345

city: San Antonio

first: Peng

last: Zhang

state: TX

address: 8403 Floyd Curl Drive

institute: UT Health San Antonio

data_processing:
The fastq files were quality controlled by fastqc and trimmed by Trimmomatic
Clean reads were aligned to the reference genome using STAR
The raw read counts of each gene were calculated using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow

extract_protocol:
Total RNA from individual mice was isolated with TRIzol reagent (Invitrogen)
The RNA libraries were prepared with the Illumina TruSeq Strand-Specific mRNA Sample Preparation System and followed by sequencing with a read length of 2 × 75 bp using the Illumina NextSeq 500.

treatment_protocol: BM c-Kit+ cells from Mx1Cre+ Ints11 flox/fox and WT littermates were purified by sorting 4 days after poly(I:C) injection.

value: cKit+ bone marrow cells


title: ATAC-Seq small_intestine_SM-ADA5F

value: white

value: anoxia


title: RNA_KO_339


title: ATAC-Seq skin_sun_exposed_SM-JF1NT

source_name: skin sun exposed


title: RNA_KO_340


title: ATAC-Seq small_intestine_SM-A62GO


title: ATAC-Seq skin_sun_exposed_SM-IQYCP


title: RNA_WT_344


title: psoriasis [P32]

type: genomic

city: Liverpool

first: Christian

last: Hedrich

state: Please select...

address: Department of Women's & Children's Health,University of Liverpool, Alder Hey Children's NHS Foundation Trust,Eaton Road,

description: main analyses

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPICBeadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
R environnment and packages Minfi and ChAMP
matrix processed value definition: Average Beta
matrix signal intensities value definition: Unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: CD8+T cells

label_protocol: Standard Illumina Protocol

growth_protocol: cells obtained from patients PBMCs

extract_protocol: genomic DNA was extracted from sorted CD8+T cells using ZR-Duet DNA/RNA MiniPrep kits (Zymo Research) according to manufacturer instructions

treatment_protocol: no treatment

tag: gender

tag: patient group

value: psoriasis

value: CD8+T cells


title: RNA_WT_343

tag: cell type

tag: strain


title: PsA Patient [P12_after]

department: Department of Women's & Children's Health

description: Before/After treatment analysis

value: PsA Patient

tag: before or after treatment

value: After treatment


title: RNA_WT_341

tag: genotype


title: psoriasis [P33]

description: main analyses


title: psoriasis [P17_after]

description: Before/After treatment analysis


title: ATAC-Seq skin_sun_exposed_SM-ADYHK


title: psoriasis [P2_after]

description: Before/After treatment analysis


title: ATAC-Seq skin_SM-JF1O1

source_name: skin non sun exposed


title: psoriasis [P1_after]

description: Before/After treatment analysis


title: PsA Patient [P31]

description: main analyses


title: ATAC-Seq skin_sun_exposed_SM-IOBHU


title: control [K10]

description: main analyses

value: control


title: PsA Patient [P23]

description: main analyses


title: ATAC-Seq skin_SM-IOBHT

value: normal


title: psoriasis [P5_after]

description: Before/After treatment analysis


title: CD8a_WT_t0_1

type: RNA

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

hyb_protocol: Following fragmentation and end-labelling, 2.07 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Mouse Gene 1.0 ST arrays (Affymetrix) interrogating 28.853 genes represented by approximately 27 probes spread across the full length of the gene.

scan_protocol: The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) and scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0,7 µm.

data_processing: CEL files were further processed with Affymetrix Expression Console software version 1.3.1 to calculate probe set signal intensities using Robust Multi-array Average (RMA) algorithms with default settings.

label: biotin

source_name: CD8a+ conventional dendritic cell from uninfected WT mouse

label_protocol: Biotinylated double strand cDNA targets were prepared from 4 to 20 ng of total RNA using the NuGEN Ovation Pico WTA System V2 Kit followed by the NuGEN Encore Biotin Module Kit according to manufacturer recommendations.

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted from sorted cells with the Qiagen RNeasy PLUS Micro Kit, according to the manufacturer protocol.

treatment_protocol: Mice were untreated or infected for 1.5 days with a salivary gland stock of the Smith strain of MCMV that was administered through intraperitoneal injection.

tag: strain background

tag: genotype/variation

value: WT

value: F

tag: treatment

value: MCMV

tag: treatment duration

tag: tissue

value: spleen

value: CD8a+ conventional dendritic cell


title: CD8a_XCR1_t1_1

source_name: CD8a+ conventional dendritic cell from XCR1-/- mouse infected with MCMV


title: CD8a_WT_t1_1

source_name: CD8a+ conventional dendritic cell from WT mouse infected with MCMV


title: CD8a_XCR1_t1_2


title: CD8a_WT_t0_2


title: input_WT_409

data_processing:
Raw data of each sample was quality controlled by fastqc and trimmed by TrimGalore
clean reads were aligned to mouse reference genome using bowtie2
The raw sam files generated by bowtie2 were sorted and reads on mitochondrion or with low Mapping quality (<30) were filtered using samtools
Sambamba was used to remove PCR duplications
Peak calling was performed with MACS2 with options: -g mm -n test -B -q 0.05
Genome_build: mm10
Supplementary_files_format_and_content: BigWig files were generated using deeptools(bamCoverage --normalizeUsing CPM)
NarrowPeak files were generated using MACS2

extract_protocol:
BM cKit+ were fixed with 1% formaldehyde, lysates were sonicated and the DNA was sheared to an average length of 100 to 300 bp. Histone-DNA complexes were isolated with specific histone modification antibodies.
The ChIP libraries were prepared using the MicroPlex Library Preparation Kit (Diagenode) and sequenced with a read length of 75 bp on an Illumina NextSeq 500 system

treatment_protocol: BM cKit+ cells from Mx1Cre+ Ints11 flox/fox and WT littermates were purified by sorting 4 days after poly(I:C) injection

tag: chip antibody


title: CD8a_WT_t1_2


title: CD8a_XCR1_t0_2

source_name: CD8a+ conventional dendritic cell from uninfected XCR1-/- mouse


title: PsA Patient [P22]

description: main analyses

value: female


title: ATAC-Seq pancreas_SM-JF1O6

source_name: pancreas

tag: sample type

tag: biosample

value: flash-frozen tissue

tag: donor age (years)

tag: donor sex

value: male

tag: race


title: input_KO_399

value: cKit+ bone marrow cells


title: CD8a_XCR1_t0_1

tag: gender


title: control [K4]

description: main analyses

tag: patient group

tag: age


title: psoriasis [P2_before]

description: main analyses and Before/After treatment analysis

value: Before treatment

tag: cell type


title: input_WT_407

tag: strain


title: input_KO_401

tag: genotype


title: control [K9]

description: main analyses


title: PsA Patient [P13]

description: main analyses


title: ATAC-Seq pancreas_SM-JF1NS

value: white

tag: case of death

value: anoxia


title: H3K4me3_KO_401

value: H3K4me3 (diagenode C15410003)


title: PsA Patient [P12_before]

value: PsA Patient

tag: before or after treatment

value: CD8+T cells


title: H3K4me3_KO_399


title: ATAC-Seq pancreas_SM-IOBHS

value: asian

value: cerebral vascular accident


title: ATAC-Seq pancreas_SM-ADRUQ

value: normal


title: ATAC-Seq ovary_SM-IOBHR

source_name: ovary


title: psoriasis [P8]

description: main analyses

value: psoriasis


title: psoriasis [P17_before]


title: psoriasis [P14]

description: main analyses


title: psoriasis [P5_before]


title: H3K4me3_WT_409


title: control [K8]

description: main analyses

value: control


title: control [K1]

description: main analyses


title: control [K11]

description: main analyses


title: H3K4me3_WT_407


title: ATAC-Seq nerve_tibial_SM-IOBHQ

source_name: tibial nerve


title: psoriasis [P16]

description: main analyses


title: ATAC-Seq nerve_tibial_SM-CP2V6


title: ATAC-Seq nerve_tibial_SM-CHLWU


title: H3K27me3_KO_399

value: H3K27me3 (Millipore 07-449)


title: PsA Patient [P10]

description: main analyses


title: H3K27me3_KO_401


title: PsA Patient [P20]

description: main analyses


title: psoriasis [P1_before]


title: ATAC-Seq muscle_SM-JF1O9

source_name: gastrocnemius muscle


title: ATAC-Seq muscle_SM-IOBHP


title: control [K6]

description: main analyses


title: H3K27me3_WT_409


title: H3K27me3_WT_407


title: ATAC-Seq muscle_SM-C1PWV


title: control [K2]

description: main analyses


title: control [K15]

description: main analyses


title: TAC+EMPA-4

city: Bunkyo-ku

first: Goro

last: Katsuumi

state: Tokyo

address: Hongo 2-1-1

country: Japan

institute: Juntendo University

description: TAC-EMPA

data_processing:
These libraries were analyzed on a NextSeq500 with a NextSeq 500/550 High Output Kit v2 (Illumina).
TopHat 2 (version 2.0.13) was used for mapping reads to the reference genome (Ensembl GRCm38/mm10) with annotation data downloaded from the Ensembl Asia website (URL https://asia.ensembl.org/).
Expression of each transcript was quantified as the number of fragments per kilobase of transcript per million fragments mapped (FPKM), and expression was compared among 3 groups by Cuffdiff (included in Cufflinks version 2.2.1).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Heart

extract_protocol:
Total RNA was isolated from tissue samples with an RNeasy Mini Kit (Qiagen, 74104) and its quality was assessed by using the Agilent 2100 Bioanalyzer with the Agilent RNA6000 pico Kit (Agilent Technologies).
The TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) was employed to construct four libraries according to the specifications of the manufacturer.

treatment_protocol: C57BL/6Ncr mice were received Transcerse-Aortic-Constriction(TAC) operation at 12wo and empagliflozin mixed in chow was administered for 5days after 2 weeks passed from TAC operation.

value: Heart

value: 14 weeks old


title: TAC+EMPA-3

description: TAC-EMPA


title: KB01_emb_RNA_rep3

city: New York

first: Jun

last: Kim

state: NY

address: 100 Washington Square East 1009 Silver Center

department: Biology

institute: NYU

data_processing:
Basecalls were performed using CASAVA version 1.8.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using cufflinks version 2.2.0 using default parameters supplying gene annotations. FPKMs values were converted to TPMs.
Raw counts for each gene were generated using htseq-count version 0.6.1p1 using default parameters.
Genome_build: WS220
Supplementary_files_format_and_content: TPM text file contains the TPM values for each gene for each replicate
Supplementary_files_format_and_content: Tab-delimited text files include DESEQ2 outputs
Supplementary_files_format_and_content: RNAseq counts text file contains the raw counts for each gene for each of the replicates

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: For mixed embryo collections, asynchronus parents were heat shocked at 35C for 30 minutes and were then allowed to recover at RT for 2 hours. Adult worms were then bleached and embryos were collected.

extract_protocol:
RNA was extracted by freeze cracking by freezing in liquid nitrogen and thawing at 37C water bath five times. RNA was isolated according to the manufacturer's (Invitrogen) Trizol extraction protocol. Purified total RNA was cleaned up through Qiagen RNeasy column. mRNA was purified from .5-10 ug of total RNA using Sera-Mag Oligo(dT) beads (ThermoScientific). cDNA preparation was done in the presence of dUTP to prepare stranded RNA-seq libraries as in PMID:19620212
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Packed embryos were resuspended in 10V of Trizol and frozen at -80C.

tag: developmental stage

value: mixed embryo


title: KB01_emb_RNA_rep2


title: KB01_emb_RNA_rep1


title: ATAC-Seq mammary_tissue_SM-JF1NV

source_name: breast mammary tissue

value: flash-frozen tissue

value: female


title: ATAC-Seq muscle_SM-ADA6L


title: psoriasis [P15]

description: main analyses


title: TAC+EMPA-1

description: TAC-EMPA


title: MK14_emb_RNA_rep3


title: ATAC-Seq lung_SM-JF1NZ

source_name: lung


title: ATAC-Seq lung_SM-ACCPU

value: male


title: ATAC-Seq mammary_tissue_SM-IOBHL


title: MK14_emb_RNA_rep1


title: MK14_emb_RNA_rep2


title: TAC-3

description: TAC-control


title: TAC-1

description: TAC-control


title: LS_ext549_emb_RNA_N2_HS_rep3

value: N2, heat shock

value: wild type


title: G19

city: Guangzhou

first: Yan

last: Li

state: Guangdong

address: Industrial Road No.253, Guangzhou, Guangdong, 510282, China

department: Department of Neurosurgery

institute: Zhujiang Hospital

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction.Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 3 out of 16 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses.

source_name: anaplastic glioma

label_protocol: The enriched circular RNAs were amplified and transcribed into Cy3 fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: Frozen tissues from glioma and normal patients were cryo pulverized using biopulverizer (Biospec) and homogenized with TRIzol (Invitrogen Life Technologies) by Mini-Bead-Beater-16 (Biospec). RNA was collected from each sample based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.

treatment_protocol: All samples were seperated and preserved at -80 degrees Celsius in 30 minutes after surgical resection.

value: brain glioma sample

value: Female

tag: who grade

value: II


title: G17

source_name: diffuse astrocytoma

tag: tissue

value: Male


title: ATAC-Seq lung_SM-A8WNH

value: asian

value: cerebral vascular accident


title: C4-2R Combo Rep3

city: Lexington

first: Xiaoqi

last: Liu

address: 760 press Ave

department: Toxicology & Cancer Biology

institute: University of Kentucky

data_processing:
Data quality control (minimum Phred score 30, minimum read length 50 bp) was performed was performed using TrimGalore toolkit (version 0.4.4).
Quality trimmed reads were mapped to human reference genome (GRCh38) downloaded from Ensembl (https://www.ensembl.org) database, using the STAR aligner (version 2.5.4b).
Reads aligned to each gene feature were counted via HTSeq package.
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts file describing the counts of the reads aligned to each gene feature in each replicate.

source_name: Prostate

extract_protocol:
RNA extraction, library preparations, and sequencing reactions were conducted at GENEWIZ, LLC. (South Plainfield, NJ, USA) as follows:  Total RNA was extracted from cell pellet samples using Qiagen RNeasy Plus Universal mini kit following manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s instructions (NEB, Ipswich, MA, USA).

value: Prostate

tag: treatment

value: Media was changed and cells were treated with DMSO every 24 hours for 72 hours


title: ATAC-Seq heart_lv_SM-JF1NY

source_name: heart left ventricle

tag: sample type

value: normal


title: TAC-2

description: TAC-control

value: Heart


title: MK60_VC199_Larvae_rep4

growth_protocol: Larvae were collected after overnight embryo hatching and growth for 24 hours on NGM plates.

treatment_protocol: Packed larvae were resuspended in 10V of Trizol and frozen at -80C.


title: C4-2R 500 nM Decitabine Rep3


title: LS_ext536_emb_RNA_N2_HS_rep2


title: TAC+EMPA-2

description: TAC-EMPA

value: 14 weeks old


title: ATAC-Seq liver_SM-A8WNZ

source_name: liver

tag: biosample


title: MK46_VC199_Larvae_rep3


title: C4-2R Combo Rep2


title: MK19MK27_VC199_Larvae_rep2


title: G8

source_name: oligodendroglioma


title: C4-2R 500 nM Decitabine Rep1


title: C4-2R Combo Rep1


title: G7

source_name: glioblastoma multiforme

value: IV


title: G11

source_name: anaplastic oligodendroglioma

value: III


title: ATAC-Seq heart_lv_SM-IOBHO

value: flash-frozen tissue

tag: donor age (years)

value: female


title: ATAC-Seq esophagus_muscularis_SM-IQYD1

source_name: esophagus muscularis

tag: donor sex

value: male

value: white

value: anoxia


title: C4-2R DMSO Rep3


title: ATAC-Seq heart_atrial_appendage_SM-JF1NX

source_name: heart right atrial appendage

tag: race


title: ATAC-Seq lung_SM-A62E9


title: ATAC-Seq heart_atrial_appendage_SM-IOBHN


title: ATAC-Seq esophagus_muscularis_SM-IOBHM


title: C4-2R 500 nM Decitabine Rep2


title: SEA86_VC199_emb_rep4

growth_protocol: For mixed embryo collections, asynchronus parents were bleached and embryos collected.

value: mixed embryo


title: SEA77_VC199_emb_rep3


title: G16

value: brain glioma sample

tag: gender


title: G10

value: Male


title: G6


title: LS_ext534_emb_RNA_N2_HS_rep1

value: N2, heat shock

value: wild type


title: G3


title: G1

value: Female


title: G5

source_name: ganglioglioma

value: II


title: ATAC-Seq esophagus_muscularis_SM-A8CPH

value: normal


title: SHS-mock2

city: Athens

first: Ralph

middle: A

last: Tripp

state: GA

address: 113B, Animal Health Research Center

department: Department of Infectious Diseases

institute: University of Georgia

data_processing:
Reads were trimmed to remove adaptor sequences and then analyzed for miRNA differential expression using Chimira (Vitsios and Enright, 2015) and OASIS 2.0 (Rahman et al., 2018a). Read counts were normalized to a total number of reads per sample and then differential expression was calculated using DESeq2 (Love et al., 2014).
Genome_build: hg38
Supplementary_files_format_and_content: Read counts

source_name: neuronal cells

growth_protocol: Human SHSY5Y (SHS) neuroblastoma cells (ATCC CRL 2266) were grown in DMEM (Sigma, St. Louis, MO) containing 10% FBS (Atlanta Biologicals, Atlanta, GA). SHS cells were maintained at 37°C, 5% CO2.

extract_protocol:
Total RNA from mock-treated or virus-infected SHS cells was isolated using RNAzol RT (MRC, Cincinnati, OH) per the manufacturer’s instructions and divided into small and large RNA fractions, and quantified using a Qubit fluorimeter-based RNA assay (Invitrogen Life Tech, Carlsbad, CA).
Illumina next-generation sequencing (NGS) libraries were constructed using a TruSeq® small RNA library (Illumina, San Diego, CA). Briefly, small RNA from mock-treated SHS cells (n=2/group), or RSV- or MeV-infected SHS cells (n=3/group) was isolated at 12 hpi or 24 hpi and ligated with 3’ and 5’ RNA adaptors using T4 RNA ligase 2 (Epicenter Biotechnologies, Madison, WI) at 28°C for 60 min.  Ligated RNA was reverse transcribed using proprietary reverse primers and the first-strand cDNA was amplified with a combination of a proprietary forward primer and reverse primers containing unique index bar codes per the manufacturer’s instructions.  Amplicons were run on a Tapestation 2200 (Agilent, Santa Clara, CA) high-sensitivity DNA chip to visualize products. Indexed samples were pooled per the manufacturer’s protocol and electrophoresed on a 6% TBE-urea PAGE gel. Bands corresponding to 147bp and 157bp corresponding to adaptor-ligated mature miRNA and other non-coding RNAs were cut-out and cDNAs were precipitated. Libraries were validated on a Tapestation 2200 (Agilent) using a high-sensitivity DNA chip.  Libraries were denatured for 5 min using 5M NaOH and loaded onto a MiSeq (Agilent) for sequencing by synthesis.

treatment_protocol: RSV strain A2 (ATCC CCL 81) was propagated in Vero cells  (Oshansky et al., 2009; Dahiya and Atreya, 2014). Briefly, 80% confluent Vero cells were infected (MOI = 1.0) for 1 h at 37°C, 5% CO2. After infection, 2% FBS was added to the DMEM, and the cells were incubated for 3 days until syncytia were evident. On the day of harvest, the cells were removed and centrifuged at 500 xg for 15 min at 4°C.  The WT MV strain Dublin-3267 of MeV was grown in Vero cells expressing human CD150 (SLAM),  a high-affinity receptor for MeV (Tatsuo et al., 2000).

tag: cell line

tag: agent

value: mock


title: ATAC-Seq esophagus_mucosa_SM-A9VPA

source_name: esophagus mucosa

value: asian

value: cerebral vascular accident


title: ATAC-Seq esophagus_mucosa_SM-A9HOR


title: LNCaP DMSO Rep3

value: Prostate

value: Media was changed and cells were treated with DMSO every 24 hours for 72 hours


title: MK11_VC199_Larvae_rep1


title: C4-2R DMSO Rep1


title: C4-2R DMSO Rep2


title: ATAC-Seq esophagus_muscularis_SM-CSSCV

value: flash-frozen tissue

value: female


title: 24h-MeV3

value: Measles virus

tag: time point


title: LNCaP DMSO Rep2


title: 24h-MeV2


title: NBT7

source_name: cortical brain

value: brain normal sample

tag: age


title: SEA70_VC199_emb_rep2

source_name: whole worms

tag: strain

value: mixed embryo

tag: genotype


title: Para_rubber_tree_sapling_ethrel_treated_48hr_rep3

city: Tsukuba

first: Nobutaka

last: Mitsuda

state: Ibaraki

address: Central 6 Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology

hyb_protocol: Hybridized using Gene Expression Hybridization kit (Agilent) and washed by Gene Expression wash pack (Agilent).

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Agilent Feature Extraction Software (v 9.1.3.1) was used for background subtraction. After that, signal of each probe was divided by median value of filter-passed probes.

organism: Hevea brasiliensis

source_name: Para rubber tree (Hevea brasiliensis) clone PB260 6-week-old sapling treated with Ethrel for 48 hours

label_protocol: 200 ng of total RNA was used for labeling procedure using Low Input Qick Amp Labeling kit (One-color) (Agilent).

growth_protocol: All plants were grown on soil in greenhouse at BPPT, Indonesia.

extract_protocol: The ground sample was homogenized in cetyltrimethylammonium bromide (CTAB) reagent containing 2% (w/v) CTAB, 2.5% (w/v) PVP-40, 100 mM Tris-HCl (pH 7.5), 25 mM EDTA (pH 8.0), 2 M NaCl, and 2% 2-mercaptoethanol, then treated with chloroform:isoamyl alcohol (24:1, v/v). The aqueous phase was incubated with 3 M LiCl at 4°C overnight, then RNA was precipitated and the solution was centrifuged at 13 000 rpm for 20 min at 4°C. The pellet was purified with the Plant RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions. To degrade genomic DNA, the RNA was treated with recombinant DNase I (TAKARA Bio).

treatment_protocol: Stem region 2–5 cm below the shoot apex was swabbed with either 2.5% Ethrel (containing 24% ethephon; Bayer CropScience, Inc.) or distilled water (mock control) using small brushes at around 09:00 in the greenhouse.

value: Wild type clone PB260

value: Ethrel

tag: treatment duration

value: 48 hours


title: ATAC-Seq esophagus_mucosa_SM-AZPYJ

value: male

value: white

tag: case of death

value: anoxia


title: C4-2 DMSO Rep3


title: NBT3

value: Female

tag: who grade


title: NBT6

tag: tissue

value: Male


title: SHS-mock1

value: mock


title: G2

source_name: anaplastic astrocytoma

value: brain glioma sample

value: III


title: C4-2 DMSO Rep2

value: Prostate

tag: treatment

value: Media was changed and cells were treated with DMSO every 24 hours for 72 hours


title: NBT1


title: 12h-MeV3


title: SEA51SEA58_VC199_emb_rep1

tag: developmental stage


title: ATAC-Seq esophagus_ge_junction_SM-IOERG

source_name: esophagus gastroesophageal junction

tag: sample type

value: normal

tag: biosample

value: flash-frozen tissue

value: female

value: asian

value: cerebral vascular accident


title: ATAC-Seq colon_transverse_SM-ACCQ1

source_name: transverse colon

tag: donor age (years)

tag: donor sex


title: C4-2 DMSO Rep1

source_name: Prostate


title: 12h-MeV1

value: Measles virus


title: ATAC-Seq esophagus_ge_junction_SM-CTD24

tag: race


title: 24h-MeV1

tag: cell line


title: 24h-RSV3

tag: agent

value: Respiratory Syncytial Virus


title: ATAC-Seq colon_sigmoid_SM-JF1O8

source_name: sigmoid colon

value: male


title: D2_Nor_10X

first: Xin

address: 132 Daxuecheng Outer Ring E Rd

department: School of Medicine

institute: Sun Yat-sen University

data_processing:
Sequencing data from 10X genomics was processed by CellRanger (v3.1.0, 10X Genomics) software with defualt parameters. Reads were aligned to GRCh38 reference genome (v3.1.0, 10X Genomics).
Genome_build: GRCh38
Supplementary_files_format_and_content: h5 files were generated using the CellRanger package (10X Genomics).

source_name: H1 ESC derived hematopoietic cells in vitro

extract_protocol:
The single cell suspension was washed twice with 1x PBS + 0.04% BSA.   The cell number and concentration was confirmed with TC20™ Automated Cell Counter  Approximately Number (5000, etc.) cells were subjected immediately onto the 10XGenomics Chromium Controller machine for Gel Beads-in-Emulsion (GEM) generation.  mRNA was prepared using 10x Genomics Chromium Single Cell 3’ reagent kit (V2 chemistry).  During this step, cells were partitioned into the GEMs along with Gel Beads coated with oligos. These oligos provide poly-dT sequences to capture mRNAs released after cell lysis inside the droplets, as well as cell-specific and transcript-specific barcodes (16 bp 10X Barcode and 10 bp Unique Molecular Identifier (UMI), respectively).   After RT-PCR, cDNA was recovered, purified and amplified to generate sufficient quantities for library preparation.
RNA libraries were prepared for sequencing using standard 10x Genomics protocols.Library quality and concentration were assessed using Agilent Bioanalyzer 2100.  Libraries were run on the Hiseq X for Illumina PE150 sequencing.

tag: Stage

value: day 2


title: LNCaP DMSO Rep1


title: D4_Nor_10X

value: day 4


title: ATAC-Seq colon_transverse_SM-A9HOW


title: Para_rubber_tree_sapling_ethrel_treated_24hr_rep2

source_name: Para rubber tree (Hevea brasiliensis) clone PB260 6-week-old sapling treated with Ethrel for 24 hours

value: Wild type clone PB260

value: Ethrel

value: 24 hours


title: Para_rubber_tree_sapling_ethrel_treated_6hr_rep3

source_name: Para rubber tree (Hevea brasiliensis) clone PB260 6-week-old sapling treated with Ethrel for 6 hours

value: 6 hours


title: Para_rubber_tree_sapling_ethrel_treated_24hr_rep3


title: ATAC-Seq colon_transverse_SM-A9VP4


title: 12h-MeV2

tag: time point


title: Para_rubber_tree_sapling_ethrel_treated_6hr_rep2


title: Para_rubber_tree_sapling_ethrel_treated_6hr_rep1


title: Para_rubber_tree_sapling_ethrel_treated_48hr_rep1

value: 48 hours


title: Para_rubber_tree_sapling_ethrel_treated_24hr_rep1


title: ATAC-Seq colon_transverse_SM-BZ2ZS


title: D0_H1_Nor_10X

source_name: H1 ESC

value: day 0


title: Para_rubber_tree_sapling_ethrel_treated_48hr_rep2


title: D6_Nor_10X

value: day 6


title: HeLa-TFIP11-iCLIP_GGTT

city: New Orleans

first: Tina

middle: M

last: O'Grady

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

data_processing:
Data were demultiplexed using iCount demultiplex
Reads with the same index from different sequencing lanes were pooled
Reads were mapped to GRCh37 (Ensembl 75) reference chromosomes using iCount mapstar
cDNA were counted using iCount xlsites
Significant CLIP peaks were computed using iCount peaks
Genome_build: hg19
Supplementary_files_format_and_content: bedgraphs of significant binding site peaks (two separate indexes/libraries)

source_name: HeLa

growth_protocol: Cell were maintained in DMEM + 10% heat-inactivated FBS, at 37°C with 5% CO2

extract_protocol:
Cells were lysed, incubated 5 min at 37°C and centrifuged at 1200 rpm for 15min at 4°C. The supernatant was incubated with RNase T1 for 5 min at 37°C. To immunoprecipitate TFIP11, lysate was incubated with Dynabeads coupled with rabbit anti-TFIP11 antibody (Proteintech #66114-Ig) for 2h at 4°C with rotation and washed five times with wash buffer (50mM Tris-HCl pH 7.4, 1M NaCl, 1% NP40, 0.1% SDS, 0.5% DOC). After dephosphorylation of RNA 3’ ends, RNAs binding TFIP11 were ligated with ϒATP-P32-associated linker and these RNA-protein complexes were separated by SDS-PAGE, transferred to a nitrocellulose membrane and visualized by autoradiography. Protein was digested with proteinase K from the membrane. Immunoprecipitated RNA was eluted from the nitrocellulose membrane with phenol-chloroform and precipitated with absolute ethanol. RNAs were separated with 6% acrylamide/urea gel.
Library construction was performed essentially as described in Huppertz et al. (PMID 24184352). Purified and 3'end tagged RNA (L3 linker) from TFIP11 complexes were reverse transcribed using specific reverse primer for each independent iCLIP experiments. CDNA were purified on 6% acrylamide/urea gel, circularized using Circligase II (Epicentre), and linearized using a specific DNA primer and BamH1 restriction enzyme. Linearized DNA was amplified by PCR to generate the iCLIP libraries using primer P3 (CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT) and P5 (AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT) for Illumina-type library construction. Libraries were controled on Agilent Bioanalyzer chip and quantified using Qbit. Libraries are stranded.

treatment_protocol: Cells were cross linked with UV at 400 mJ/cm2 and harvested with cold PBS.

value: HeLa

tag: rip antibody

value: anti-TFIP11  (Proteintech #66114-Ig)


title: 12h-RSV2


title: HeLa-TFIP11-iCLIP_TTGT