title: Cdc14ab KO time 5

status: Public on Oct 31 2022

type: SRA

city: Madrid

first: Osvaldo

last: Graña

state: Comunidad de Madrid

address: C/ Melchor Fernández Almagro, 3

department: Structural Biology

country: Spain

institute: CNIO

library_source: transcriptomic

data_processing:
Data were processed with cellranger-arc-2.0.0, Loupe Browser 6, and scanpy 1.7.2
Genome_build: mm10
Supplementary_files_format_and_content: raw, feature and matrix files

molecule: polyA RNA

organism: Mus musculus

source_name: mESC Cdc14ab KO, 5 days in N2B27

growth_protocol: mESCs were grown over feeders in LIF-containing DMEM. Medium was changed every day

extract_protocol:
ESCs in LIF-containing media (T0) or after 5 days (T5) in neural differentiation media were washed twice with PBS, trypsinized and counted. Dead cells were removed with Dead Cell Removal kit (Miltenyi Biotec). Cells were counted again and 1 million cells were centrifuged at 300 g 10 min at 4oC in PBS 0.04% BSA. Cells were treated with 0.1 U/l of DNAse I (Invitrogen) 5 min in ice. Cells were washed in PBS 0.04% BSA and centrifuged 10 min at 300 g twice. Cells were incubated 2 min with 100 l Lysis Buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP40, 0.01% Digitonin, 1% BSA, 1 mM DTT, 1 U/l RNase inhibitor) in ice for nuclei extraction. After incubation, nuclei were washed in 1 ml of Wash Buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 1 mM DTT, 1 U/l RNase inhibitor) and centrifuged 5 min at 500 g. Washing was repeated two more times and nuclei were filtered in 40 m Flowmi Cell Strainer, counted and assessed for integrity.
Cell nuclei were loaded onto a Chromium Next GEM Chip J (10x Genomics) for a target recovery of ~5000 nuclei per condition, and processed into a 10x Chromium Controller as described in the manufacturer's protocol (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression, CG000338 Rev A). Generation of gel beads in emulsion (GEMs), barcoding, pre-amplification PCR and ATAC library construction were all performed as recommended by the manufacturer.
snGEX

treatment_protocol: Prior extraction, ESCs were grown on gelatin-coated plates at low density to remove feeders. For differentiation induction, LIF-containing medium was replaced with N2B27 with growing factors EGF and FGF2. Medium was changed every 2 days.

tag: genotype

value: Cdc14ab KO

tag: cell type

value: embryonic stem cells from mouse blastocysts

tag: treatment

value: Neural differentiation media 5 days

tag: clone/replicate

value: clone 3


title: Wild-type time 5

source_name: mESC wild-type, 5 days in N2B27

value: wild type


title: Wild-type time 0

source_name: mESC wild-type not differentiated

value: LIF-containing ESC media


title: Cdc14ab KO time 0

source_name: mESC Cdc14ab KO not differentiated


title: Wild-type time 5 [ATAC-Seq]

description: mESC wild-type, 5 days in N2B27

library_source: genomic

data_processing:
Data were processed with cellranger-arc-2.0.0, Loupe Browser 6, and scanpy 1.7.2
Genome_build: mm10
Supplementary_files_format_and_content: BED files with ATAC peaks

molecule: genomic DNA

source_name: embryonic stem cells from mouse blastocysts

extract_protocol:
ESCs in LIF-containing media (T0) or after 5 days (T5) in neural differentiation media were washed twice with PBS, trypsinized and counted. Dead cells were removed with Dead Cell Removal kit (Miltenyi Biotec). Cells were counted again and 1 million cells were centrifuged at 300 g 10 min at 4oC in PBS 0.04% BSA. Cells were treated with 0.1 U/l of DNAse I (Invitrogen) 5 min in ice. Cells were washed in PBS 0.04% BSA and centrifuged 10 min at 300 g twice. Cells were incubated 2 min with 100 l Lysis Buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% NP40, 0.01% Digitonin, 1% BSA, 1 mM DTT, 1 U/l RNase inhibitor) in ice for nuclei extraction. After incubation, nuclei were washed in 1 ml of Wash Buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA, 1 mM DTT, 1 U/l RNase inhibitor) and centrifuged 5 min at 500 g. Washing was repeated two more times and nuclei were filtered in 40 m Flowmi Cell Strainer, counted and assessed for integrity.
Cell nuclei were loaded onto a Chromium Next GEM Chip J (10x Genomics) for a target recovery of ~5000 nuclei per condition, and processed into a 10x Chromium Controller as described in the manufacturer's protocol (Chromium Next GEM Single Cell Multiome ATAC + Gene Expression, CG000338 Rev A). Generation of gel beads in emulsion (GEMs), barcoding, pre-amplification PCR and ATAC library construction were all performed as recommended by the manufacturer.
snATAC


title: Wild-type time 0 [ATAC-Seq]

description: mESC wild-type not differentiated


title: Cdc14ab KO time 5 [ATAC-Seq]

description: mESC Cdc14ab KO, 5 days in N2B27


title: RB-CR101_S3 - NFE2 CUT&RUN replicate 2

city: Oxford

first: Robert

middle: A

last: Beagrie

address: Headley Way

department: Molecular Haematology Unit

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

data_processing:
Library strategy: CUT&RUN
Reads were aligned to the mm9 and mm10 builds of the mouse genome using bowtie v2.4.1.
PCR duplicates were removed using samtools v1.10
BigWig files were generated from genome coverage using DeepTools 3.4.3 and a scaling factor of 1000/[number of reads mapped to eColi genome]
Genome_build: mm9, mm10
Supplementary_files_format_and_content: BigWig

source_name: Primary haematopoietic/erythroid progenitor cells

growth_protocol: Primary erythroid progenitor cells were isolated from fetal livers, which were freshly isolated at e12.5-e13.5 from C57BL/6 mouse embryos. 5-15 livers were pooled together for each experimental replicate, mechanically dissociated in staining buffer (PBS, 0.2% BSA, 5 mM Glucose) and strained through a 30-um strainer. Cells were immunostained at 4 °C in the presence of rabbit IgG (200 ug/ml, Jackson Laboratories 015-000-003) to block Fc receptors. To enrich for early erythroid progenitors, cells were first stained with 5 ug/ml biotin-conjugated anti-Ter119 (BD 553672) for 30 min, before magnetic depletion using streptavidin nanobeads (BioLegend Mojosort 480016) following the manufacturer’s instructions. Cells were then incubated with 0.5 ug/ml APC-conjugated streptavidin (BD 553672), 0.33 ug/ml PE-Cy7-conjugated anti-CD71 (BioLegend 113811) and a panel of 5 FITC-conjugated lineage antibodies (anti-CD41, anti-CD45R, anti-CD3e, anti-CD11b and anti-Ly-6G/6C, all at 1 ug/ml; BD 553848, 553087, 553061, 557396, and 553126, respectively) for 45 min. Cells were then resuspended in FACS running buffer (staining buffer plus 2 mM EDTA). 0.66 ug/ml Hoechst was added immediately prior to sorting in order to distinguish live cells. Cells were sorted into Eppendorf tubes containing 500 ul RPMI supplemented with 10% FCS using a BD FACSAria Fusion machine with a 100 uM nozzle size.

extract_protocol:
CUT&RUN was carried out following the protocol given in Skene & Henikoff, 2017. Briefly, Concanavalin A magnetic beads were activated by washing twice in binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). 100000 FACS-sorted erythroblasts were washed twice in 1.5 ml of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and one Roche Complete Protease Inhibitor tablet) then resuspended in 200 ul wash buffer, mixed with 10 ul activated bead suspension and rotated for 5-10 min at RT. Tubes were then placed in a magnetic rack, the wash buffer was replaced with 200 ul of antibody buffer (wash buffer plus 0.02% digitonin, 2 mM EDTA and 1 ul anti-NFE2 Rabbit polyclonal antibody (Novus; GTX102698)) and the tubes rotated for 2 hours at 4 C. Tubes were then placed on a magnetic rack and the cells were washed once with digitonin buffer (wash buffer plus 0.02% digitonin) before being resuspended in 200 ul digitonin buffer. pA-MNase enzyme (a kind gift of the Henikoff lab) was added to each tube to a final concentration of 700 ng/ml and the tubes rotated for 1 hour at 4 C. Tubes were then placed on a magnetic rack and the cells were washed twice with digitonin buffer before being resuspended in 150 ul digitonin buffer. Digestion was initiated by the addition of 3 ul 100 mM CaCl2 to each sample and was allowed to proceed whilst tubes incubated on ice for 30 minutes before being quenched with 50 ul 4x stop buffer (680 mM NaCl, 40 mM EDTA, 8 mM EGTA, 0.04% digitonin, 0.1 mg/ml of RNase A, 0.1 mg/ml glycogen). Tubes were incubated for 10 min at 37 C, then centrifuged for 5 min at 4 C at 16,000 xg. The supernatant was moved to fresh tubes, mixed with 1 ul of 20% SDS and 1.5 ul of 20 mg/ml proteinase K, then incubated for 10 min at 70 C. DNA was purified by phenol-chloroform extraction and ethanol precipitation, then libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.
Libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.

tag: developmental stage

tag: tissue

value: Primary erythroid progenitor cells isolated from fetal liver

tag: immunophenotype

value: Lin- CD71:high Ter119:high

tag: strain

tag: antibody


title: RB-CR89_S3 - NFE2 CUT&RUN replicate 1


title: RB-CR107_S4 - NFE2 CUT&RUN replicate 2

value: Lin- CD71:med Ter119:high


title: Cdc14ab KO time 0 [ATAC-Seq]

description: mESC Cdc14ab KO not differentiated


title: RB-CR94_S4 - NFE2 CUT&RUN replicate 1


title: RB-CR100_S2 - NFE2 CUT&RUN replicate 2

value: Lin- CD71:high Ter119:med


title: RB-CR85_S1 - NFE2 CUT&RUN replicate 1

value: Lin- CD71:high Ter119-


title: RB-CR87_S2 - NFE2 CUT&RUN replicate 1


title: RB-CR98_S1 - NFE2 CUT&RUN replicate 2


title: RB-CR97_S0 CD71 medium - NFE2 CUT&RUN replicate 2

value: Lin- CD71:med Ter119-


title: RB-CR86_S1 - IgG CUT&RUN replicate 1

extract_protocol:
CUT&RUN was carried out following the protocol given in Skene & Henikoff, 2017. Briefly, Concanavalin A magnetic beads were activated by washing twice in binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). 100000 FACS-sorted erythroblasts were washed twice in 1.5 ml of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and one Roche Complete Protease Inhibitor tablet) then resuspended in 200 ul wash buffer, mixed with 10 ul activated bead suspension and rotated for 5-10 min at RT. Tubes were then placed in a magnetic rack, the wash buffer was replaced with 200 ul of antibody buffer (wash buffer plus 0.02% digitonin, 2 mM EDTA and 1 ul Rabbit IgG antibody (Millipore; 12-370)) and the tubes rotated for 2 hours at 4 C. Tubes were then placed on a magnetic rack and the cells were washed once with digitonin buffer (wash buffer plus 0.02% digitonin) before being resuspended in 200 ul digitonin buffer. pA-MNase enzyme (a kind gift of the Henikoff lab) was added to each tube to a final concentration of 700 ng/ml and the tubes rotated for 1 hour at 4 C. Tubes were then placed on a magnetic rack and the cells were washed twice with digitonin buffer before being resuspended in 150 ul digitonin buffer. Digestion was initiated by the addition of 3 ul 100 mM CaCl2 to each sample and was allowed to proceed whilst tubes incubated on ice for 30 minutes before being quenched with 50 ul 4x stop buffer (680 mM NaCl, 40 mM EDTA, 8 mM EGTA, 0.04% digitonin, 0.1 mg/ml of RNase A, 0.1 mg/ml glycogen). Tubes were incubated for 10 min at 37 C, then centrifuged for 5 min at 4 C at 16,000 xg. The supernatant was moved to fresh tubes, mixed with 1 ul of 20% SDS and 1.5 ul of 20 mg/ml proteinase K, then incubated for 10 min at 70 C. DNA was purified by phenol-chloroform extraction and ethanol precipitation, then libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.
Libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.

value: IgG


title: RB-CR90_S3 - IgG CUT&RUN replicate 1


title: RB-CR88_S3 - NFE2 CUT&RUN replicate 1


title: RB-CR99_S1 - IgG CUT&RUN replicate 2


title: RB-CR84_S0 CD71 medium - NFE2 CUT&RUN replicate 1


title: RB-CR83_S0 CD71 low - NFE2 CUT&RUN replicate 1

value: Lin- CD71- Ter119-


title: RB-CR95_Lin+ - NFE2 CUT&RUN replicate 2

value: Lin+ CD71- Ter119-


title: RB-CR96_S0 CD71 low - NFE2 CUT&RUN replicate 2


title: RB-CR82_Lin+ - NFE2 CUT&RUN replicate 1


title: RB-CR176_S3 - H3K4me3 CUT&RUN replicate 1

data_processing:
Library strategy: CUT&RUN
Reads were aligned to the mm9 and mm10 builds of the mouse genome using bowtie v2.4.1.
PCR duplicates were removed using samtools v1.10
Contaminating reads mapping to chr11:32270389-32273090 (mm10) were removed
BigWig files were generated from genome coverage using DeepTools 3.4.3 and a scaling factor of 1000/[number of reads mapped to eColi genome]
Genome_build: mm9, mm10
Supplementary_files_format_and_content: BigWig

extract_protocol:
CUT&RUN was carried out following the protocol given in Skene & Henikoff, 2017. Briefly, Concanavalin A magnetic beads were activated by washing twice in binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). 100000 FACS-sorted erythroblasts were washed twice in 1.5 ml of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and one Roche Complete Protease Inhibitor tablet) then resuspended in 200 ul wash buffer, mixed with 10 ul activated bead suspension and rotated for 5-10 min at RT. Tubes were then placed in a magnetic rack, the wash buffer was replaced with 200 ul of antibody buffer (wash buffer plus 0.02% digitonin, 2 mM EDTA and 1 ul anti-H3K4me3 Rabbit polyclonal antibody (Millipore; 07-473)) and the tubes rotated for 2 hours at 4 C. Tubes were then placed on a magnetic rack and the cells were washed once with digitonin buffer (wash buffer plus 0.02% digitonin) before being resuspended in 200 ul digitonin buffer. pA-MNase enzyme (a kind gift of the Henikoff lab) was added to each tube to a final concentration of 700 ng/ml and the tubes rotated for 1 hour at 4 C. Tubes were then placed on a magnetic rack and the cells were washed twice with digitonin buffer before being resuspended in 150 ul digitonin buffer. Digestion was initiated by the addition of 3 ul 100 mM CaCl2 to each sample and was allowed to proceed whilst tubes incubated on ice for 30 minutes before being quenched with 50 ul 4x stop buffer (680 mM NaCl, 40 mM EDTA, 8 mM EGTA, 0.04% digitonin, 0.1 mg/ml of RNase A, 0.1 mg/ml glycogen). Tubes were incubated for 10 min at 37 C, then centrifuged for 5 min at 4 C at 16,000 xg. The supernatant was moved to fresh tubes, mixed with 1 ul of 20% SDS and 1.5 ul of 20 mg/ml proteinase K, then incubated for 10 min at 70 C. DNA was purified by phenol-chloroform extraction and ethanol precipitation, then libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.
Libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.


title: RB-CR175_S2 - H3K4me3 CUT&RUN replicate 1

extract_protocol:
CUT&RUN was carried out following the protocol given in Skene & Henikoff, 2017. Briefly, Concanavalin A magnetic beads were activated by washing twice in binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). 50000 FACS-sorted erythroblasts were washed twice in 1.5 ml of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and one Roche Complete Protease Inhibitor tablet) then resuspended in 200 ul wash buffer, mixed with 10 ul activated bead suspension and rotated for 5-10 min at RT. Tubes were then placed in a magnetic rack, the wash buffer was replaced with 200 ul of antibody buffer (wash buffer plus 0.02% digitonin, 2 mM EDTA and 1 ul anti-H3K4me3 Rabbit polyclonal antibody (Millipore; 07-473)) and the tubes rotated for 2 hours at 4 C. Tubes were then placed on a magnetic rack and the cells were washed once with digitonin buffer (wash buffer plus 0.02% digitonin) before being resuspended in 200 ul digitonin buffer. pA-MNase enzyme (a kind gift of the Henikoff lab) was added to each tube to a final concentration of 700 ng/ml and the tubes rotated for 1 hour at 4 C. Tubes were then placed on a magnetic rack and the cells were washed twice with digitonin buffer before being resuspended in 150 ul digitonin buffer. Digestion was initiated by the addition of 3 ul 100 mM CaCl2 to each sample and was allowed to proceed whilst tubes incubated on ice for 30 minutes before being quenched with 50 ul 4x stop buffer (680 mM NaCl, 40 mM EDTA, 8 mM EGTA, 0.04% digitonin, 0.1 mg/ml of RNase A, 0.1 mg/ml glycogen). Tubes were incubated for 10 min at 37 C, then centrifuged for 5 min at 4 C at 16,000 xg. The supernatant was moved to fresh tubes, mixed with 1 ul of 20% SDS and 1.5 ul of 20 mg/ml proteinase K, then incubated for 10 min at 70 C. DNA was purified by phenol-chloroform extraction and ethanol precipitation, then libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.
Libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.


title: RB-CR174_S1 - H3K4me3 CUT&RUN replicate 1


title: RTCR30_S4 - H3K4me1 CUT&RUN replicate 1

extract_protocol:
CUT&RUN was carried out following the protocol given in Skene & Henikoff, 2017. Briefly, Concanavalin A magnetic beads were activated by washing twice in binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). 100000 FACS-sorted erythroblasts were washed twice in 1.5 ml of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and one Roche Complete Protease Inhibitor tablet) then resuspended in 200 ul wash buffer, mixed with 10 ul activated bead suspension and rotated for 5-10 min at RT. Tubes were then placed in a magnetic rack, the wash buffer was replaced with 200 ul of antibody buffer (wash buffer plus 0.02% digitonin, 2 mM EDTA and 1 ul anti-H3K4me1 Rabbit polyclonal antibody (Abcam; ab8895)) and the tubes rotated for 2 hours at 4 C. Tubes were then placed on a magnetic rack and the cells were washed once with digitonin buffer (wash buffer plus 0.02% digitonin) before being resuspended in 200 ul digitonin buffer. pA-MNase enzyme (a kind gift of the Henikoff lab) was added to each tube to a final concentration of 700 ng/ml and the tubes rotated for 1 hour at 4 C. Tubes were then placed on a magnetic rack and the cells were washed twice with digitonin buffer before being resuspended in 150 ul digitonin buffer. Digestion was initiated by the addition of 3 ul 100 mM CaCl2 to each sample and was allowed to proceed whilst tubes incubated on ice for 30 minutes before being quenched with 50 ul 4x stop buffer (680 mM NaCl, 40 mM EDTA, 8 mM EGTA, 0.04% digitonin, 0.1 mg/ml of RNase A, 0.1 mg/ml glycogen). Tubes were incubated for 10 min at 37 C, then centrifuged for 5 min at 4 C at 16,000 xg. The supernatant was moved to fresh tubes, mixed with 1 ul of 20% SDS and 1.5 ul of 20 mg/ml proteinase K, then incubated for 10 min at 70 C. DNA was purified by phenol-chloroform extraction and ethanol precipitation, then libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.
Libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.


title: RB-CR172_S0 CD71 low - H3K4me3 CUT&RUN replicate 1


title: RB-CR171_Lin+ - H3K4me3 CUT&RUN replicate 1


title: RTCR29_S3 - H3K4me1 CUT&RUN replicate 1


title: RTCR28_S2 - H3K4me1 CUT&RUN replicate 1


title: RTCR26_S0 CD71 medium - H3K4me1 CUT&RUN replicate 1


title: RTCR27_S1 - H3K4me1 CUT&RUN replicate 1


title: RTCR25_S0 CD71 low - H3K4me1 CUT&RUN replicate 1


title: RTCR3_S0 CD71 medium - H3K27me3 CUT&RUN replicate 3

data_processing:
Library strategy: CUT&RUN
Reads were aligned to the mm9 and mm10 builds of the mouse genome using bowtie v2.4.1.
PCR duplicates were removed using samtools v1.10
Contaminating reads mapping to chr11:32270389-32273090 or chr11:32250933-32251253(mm10) were removed
BigWig files were generated from genome coverage using DeepTools 3.4.3 and a scaling factor of 1000/[number of reads mapped to eColi genome]
Genome_build: mm9, mm10
Supplementary_files_format_and_content: BigWig

extract_protocol:
CUT&RUN was carried out following the protocol given in Skene & Henikoff, 2017. Briefly, Concanavalin A magnetic beads were activated by washing twice in binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). 100000 FACS-sorted erythroblasts were washed twice in 1.5 ml of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and one Roche Complete Protease Inhibitor tablet) then resuspended in 200 ul wash buffer, mixed with 10 ul activated bead suspension and rotated for 5-10 min at RT. Tubes were then placed in a magnetic rack, the wash buffer was replaced with 200 ul of antibody buffer (wash buffer plus 0.02% digitonin, 2 mM EDTA and 1 ul anti-H3K27me3 Rabbit polyclonal antibody (Millipore; 07-449)) and the tubes rotated for 2 hours at 4 C. Tubes were then placed on a magnetic rack and the cells were washed once with digitonin buffer (wash buffer plus 0.02% digitonin) before being resuspended in 200 ul digitonin buffer. pA-MNase enzyme (a kind gift of the Henikoff lab) was added to each tube to a final concentration of 700 ng/ml and the tubes rotated for 1 hour at 4 C. Tubes were then placed on a magnetic rack and the cells were washed twice with digitonin buffer before being resuspended in 150 ul digitonin buffer. Digestion was initiated by the addition of 3 ul 100 mM CaCl2 to each sample and was allowed to proceed whilst tubes incubated on ice for 30 minutes before being quenched with 50 ul 4x stop buffer (680 mM NaCl, 40 mM EDTA, 8 mM EGTA, 0.04% digitonin, 0.1 mg/ml of RNase A, 0.1 mg/ml glycogen). Tubes were incubated for 10 min at 37 C, then centrifuged for 5 min at 4 C at 16,000 xg. The supernatant was moved to fresh tubes, mixed with 1 ul of 20% SDS and 1.5 ul of 20 mg/ml proteinase K, then incubated for 10 min at 70 C. DNA was purified by phenol-chloroform extraction and ethanol precipitation, then libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.
Libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.


title: RB-CR111_S1 - H3K27me3 CUT&RUN replicate 1


title: RB-CR114_S4 - H3K27me3 CUT&RUN replicate 1


title: RB-CR112_S2 - H3K27me3 CUT&RUN replicate 1


title: RTCR7_S4 - H3K27me3 CUT&RUN replicate 3


title: RTCR24_Lin+ - H3K4me1 CUT&RUN replicate 1


title: RTCR6_S3 - H3K27me3 CUT&RUN replicate 3


title: RB-CR113_S3 - H3K27me3 CUT&RUN replicate 1


title: RTCR8_S3 - IgG CUT&RUN replicate 3


title: RTCR5_S2 - H3K27me3 CUT&RUN replicate 3


title: RB-CR180_S1 - H3K27me3 CUT&RUN replicate 2


title: RB-CR179_S0 CD71 medium - H3K27me3 CUT&RUN replicate 2


title: RB-CR110_S0 CD71 medium - H3K27me3 CUT&RUN replicate 1


title: RTCR2_S0 CD71 low - H3K27me3 CUT&RUN replicate 3


title: RB-CR178_S0 CD71 low - H3K27me3 CUT&RUN replicate 2


title: RB-CR109_S0 CD71 low - H3K27me3 CUT&RUN replicate 1


title: RTCR1_Lin+ - H3K27me3 CUT&RUN replicate 3


title: RB-CR173_S0 CD71 medium - H3K4me3 CUT&RUN replicate 1


title: RB-CR108_Lin+ - H3K27me3 CUT&RUN replicate 1


title: RB-CR121_S4 - H3K27ac CUT&RUN replicate 1

extract_protocol:
CUT&RUN was carried out following the protocol given in Skene & Henikoff, 2017. Briefly, Concanavalin A magnetic beads were activated by washing twice in binding buffer (20 mM HEPES-KOH pH 7.9, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). 100000 FACS-sorted erythroblasts were washed twice in 1.5 ml of wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine and one Roche Complete Protease Inhibitor tablet) then resuspended in 200 ul wash buffer, mixed with 10 ul activated bead suspension and rotated for 5-10 min at RT. Tubes were then placed in a magnetic rack, the wash buffer was replaced with 200 ul of antibody buffer (wash buffer plus 0.02% digitonin, 2 mM EDTA and 1 ul anti-H3K27ac Rabbit monoclonal antibody (Millipore; MABE647)) and the tubes rotated for 2 hours at 4 C. Tubes were then placed on a magnetic rack and the cells were washed once with digitonin buffer (wash buffer plus 0.02% digitonin) before being resuspended in 200 ul digitonin buffer. pA-MNase enzyme (a kind gift of the Henikoff lab) was added to each tube to a final concentration of 700 ng/ml and the tubes rotated for 1 hour at 4 C. Tubes were then placed on a magnetic rack and the cells were washed twice with digitonin buffer before being resuspended in 150 ul digitonin buffer. Digestion was initiated by the addition of 3 ul 100 mM CaCl2 to each sample and was allowed to proceed whilst tubes incubated on ice for 30 minutes before being quenched with 50 ul 4x stop buffer (680 mM NaCl, 40 mM EDTA, 8 mM EGTA, 0.04% digitonin, 0.1 mg/ml of RNase A, 0.1 mg/ml glycogen). Tubes were incubated for 10 min at 37 C, then centrifuged for 5 min at 4 C at 16,000 xg. The supernatant was moved to fresh tubes, mixed with 1 ul of 20% SDS and 1.5 ul of 20 mg/ml proteinase K, then incubated for 10 min at 70 C. DNA was purified by phenol-chloroform extraction and ethanol precipitation, then libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.
Libraries were prepared using the Ultra-II DNA library prep kit (NEB) following the manufacturer's protocol with 13 PCR cycles.


title: RB-CR120_S3 - H3K27ac CUT&RUN replicate 1


title: RB-CR177_Lin+ - H3K27me3 CUT&RUN replicate 2


title: RB-CR122_S3 - IgG CUT&RUN replicate 1


title: RB-CR168_S1 - H3K27ac CUT&RUN replicate 2


title: RB-CR118_S1 - H3K27ac CUT&RUN replicate 1


title: RB-CR166_S0 CD71 low - H3K27ac CUT&RUN replicate 2


title: RB-CR167_S0 CD71 medium - H3K27ac CUT&RUN replicate 2


title: RB-CR117_S0 CD71 medium - H3K27ac CUT&RUN replicate 1


title: RB-CR119_S2 - H3K27ac CUT&RUN replicate 1


title: RB-CR116_S0 CD71 low - H3K27ac CUT&RUN replicate 1


title: RB-CR165_Lin+ - H3K27ac CUT&RUN replicate 2


title: RB-CR115_Lin+ - H3K27ac CUT&RUN replicate 1


title: Liver biopsy - F - Indiv_s124

type: RNA

city: Toulouse

first: Hervé

last: Guillou

address: 180 Chemin de Tournefeuille

department: ToxAlim

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE v3 microarray (8X60K, Design 072363  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 072363_D_F_20150612). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);} We selected the spots with a minimal weight of 1 for 5 out of 80 microarrays. At this step, 38582 spots out of 62976 were selected.  The mean signal of the 32 first samples, 24 next and 24 last ones were substracted to individuals signals to correct the batch effect of the 3 serials (characteristics:WashBatch) observed during the microarray washing procedure. Data were then stored in an ExpressionSet object and normalized by the quantile method using the normalize.quantiles function from the preprocessCore R library. Replicated probes on the array (identical ProbeName) were resolved by taking the median normalized signal of each set of replicated probes. The resulting matrix has 35909 rows each corresponding to a unique ProbeName (provided as data Matrix).

molecule: total RNA

organism: Homo sapiens

source_name: Liver biopsy

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: All patients gave written consent and liver samples were frozen and stored at - 80 ° C at the Biological Resource Center of the Toulouse University Hospital.

extract_protocol: RNAs were extracted from liver samples in males and females mice using the method Chomczynski P and Sacchi N (1987) with Tri-reagent (Sigma Aldrich).

treatment_protocol: For the present study, patients who met the following criteria were selected: age over 18, signed informed consent, liver biopsy puncture (PBH) performed by the transjugular route. Patients with one or more of the following criteria were excluded from the analysis: women hysterectomized before 50 years with unknown hormonal status, Turner's syndrome, hormone treatments other than than contraceptive pill and hormone replacement therapy, immunosuppressive treatments, steatosic treatments (methotrexate, tamoxifen, corticosteroids, amiodarone), patient under guardianship or curatorship, and liver biopsy performed during bariatric surgery.

value: liver

tag: diagnosis

value: NAFLD

tag: gender

value: F

tag: washbatch


title: Liver biopsy - F - Indiv_s5


title: Liver biopsy - F - Indiv_s64


title: Liver biopsy - F - Indiv_s93


title: Liver biopsy - M - Indiv_s17

value: M


title: Liver biopsy - M - Indiv_s119


title: Liver biopsy - M - Indiv_s37


title: Liver biopsy - M - Indiv_s67


title: Liver biopsy - F - Indiv_s126


title: Liver biopsy - F - Indiv_s40


title: Liver biopsy - F - Indiv_s21


title: Liver biopsy - M - Indiv_s28


title: Liver biopsy - M - Indiv_s101


title: Liver biopsy - M - Indiv_s120


title: Liver biopsy - M - Indiv_s139


title: Liver biopsy - M - Indiv_s6


title: Liver biopsy - F - Indiv_s27


title: Liver biopsy - M - Indiv_s118


title: Liver biopsy - M - Indiv_s22


title: Liver biopsy - M - Indiv_s122


title: Liver biopsy - F - Indiv_s20


title: Liver biopsy - F - Indiv_s116


title: Liver biopsy - M - Indiv_s137


title: Liver biopsy - M - Indiv_s76


title: Liver biopsy - M - Indiv_s46


title: Liver biopsy - M - Indiv_s2


title: Liver biopsy - F - Indiv_s80


title: Liver biopsy - F - Indiv_s98


title: Liver biopsy - M - Indiv_s91


title: Liver biopsy - M - Indiv_s55


title: Liver biopsy - M - Indiv_s90


title: Liver biopsy - M - Indiv_s41


title: Liver biopsy - F - Indiv_s69


title: Liver biopsy - F - Indiv_s71


title: Liver biopsy - M - Indiv_s7


title: Liver biopsy - M - Indiv_s128


title: Liver biopsy - F - Indiv_s107


title: Liver biopsy - M - Indiv_s50


title: Liver biopsy - F - Indiv_s106


title: Liver biopsy - M - Indiv_s131


title: Liver biopsy - M - Indiv_s79


title: Liver biopsy - F - Indiv_s66


title: Liver biopsy - M - Indiv_s97


title: Liver biopsy - F - Indiv_s134


title: Liver biopsy - M - Indiv_s42


title: Liver biopsy - M - Indiv_s94


title: Liver biopsy - M - Indiv_s135


title: Liver biopsy - F - Indiv_s129


title: Liver biopsy - F - Indiv_s136


title: Liver biopsy - F - Indiv_s127


title: Liver biopsy - M - Indiv_s132


title: Liver biopsy - M - Indiv_s18


title: Liver biopsy - F - Indiv_s117


title: Liver biopsy - M - Indiv_s58


title: Liver biopsy - F - Indiv_s77


title: Liver biopsy - M - Indiv_s121


title: Liver biopsy - M - Indiv_s35


title: Liver biopsy - M - Indiv_s89


title: Liver biopsy - M - Indiv_s100


title: Liver biopsy - M - Indiv_s75


title: Liver biopsy - M - Indiv_s111


title: Liver biopsy - M - Indiv_s115


title: Liver biopsy - F - Indiv_s108


title: Liver biopsy - M - Indiv_s109


title: Liver biopsy - M - Indiv_s68


title: Liver biopsy - M - Indiv_s36


title: Liver biopsy - F - Indiv_s48


title: Liver biopsy - M - Indiv_s99


title: Liver biopsy - F - Indiv_s138


title: AFCs, Lv-Ctrl, 1

city: Xining

first: Liu

last: Chenhao

state: Qinghai

address: Xinqiao Street

department: Orthopedic

country: China

institute: Qinghai Provincial People's Hospital

data_processing:
Illumina Novaseq 6000 platform was used to sequence short sequences
DESeq2 was used to differentiao gene analysis.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes TPM values for each Sample

organism: Rattus norvegicus

source_name: AFCs, Mechanical stretch, Lv-Ctrl

growth_protocol: AFCs were maintained in F12/DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C°

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Total RAN > 1μg(concentration>35ng/μL)was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Apoptosis was induced by mechanical stretch. AFCs were treated with pLVX-shRNA-Puro and pLVX-shRNA-Puro-Piezo1.

value: Sprague Dawley

value: Anulus fibrosus cells

value: Ctrl

value: Mechanical stretch


title: AFCs, Lv-Piezo1, 3

source_name: AFCs, Mechanical stretch, Lv-Piezo

value: Piezo1 knock down


title: AFCs, Lv-Ctrl, 3


title: AFCs, Lv-Piezo1, 4


title: AFCs, Lv-Piezo1, 2


title: AFCs, Lv-Piezo1, 1


title: AFCs, Lv-Ctrl, 2


title: AFCs, Lv-Ctrl, 4


title: Liver biopsy - M - Indiv_s26


title: Liver biopsy - F - Indiv_s130


title: Liver biopsy - F - Indiv_s110


title: Liver biopsy - F - Indiv_s123


title: Sham surgery rat#3, biological rep3

city: hangzhou

first: yueqin

last: cai

state: zhejiang

address: 548 Binwen Road, Binjiang District

institute: zhejiang chinese medical university

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
All transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64). After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Assembly: GCA_015227675.2
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: kidney

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: kidney

value: WT

value: Sham surgery


title: UUO surgery rat#2, biological rep2

value: UUO surgery


title: Adenine group rat#3, biological rep3

value: Adenine group


title: UUO surgery rat#3, biological rep3


title: Liver biopsy - M - Indiv_s72


title: Liver biopsy - M - Indiv_s30


title: Liver biopsy - M - Indiv_s125


title: Adenine group rat#1, biological rep1


title: UUO surgery rat#1, biological rep1


title: Liver biopsy - F - Indiv_s61


title: Liver biopsy - F - Indiv_s104


title: Control group rat#3, biological rep3

value: Control group


title: Sham surgery rat#1, biological rep1


title: Sham surgery rat#2, biological rep2


title: Liver biopsy - F - Indiv_s33


title: UAC3

city: Jiamusi

first: Fan

last: Wu

address: Southwest Gang Street

institute: Jiamusi University

data_processing:
A cDNA library constructed by technology from the pooled RNA from condylar cartilage samples of SD rat was sequenced run with Illumina Novaseq TM 6000 sequence platform.
Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads. Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis
Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9). The parameters were as  follows:1) removing reads containing adapters;2) removing reads containing polyA and polyG;3) removing reads containing more than 5% of unknown nucleotides (N);4) removing low quality reads containing more than 20% of low quality (Q-value≤20) bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, 0.11.9). including the Q20, Q30 and GC-content of the clean data.
Assembly: rattus norvegicus ensembl V101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: condylar cartilage

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer's procedure. Then 10 ug of total RNA was extracted according to the RNA-Seq sample preparation kit for constructing sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: condylar cartilage

value: Sprague-Dawley

value: unilateral anterior crossbite, 8 weeks


title: CONT_3

value: control, 8weeks


title: UAC2


title: Adenine group rat#2, biological rep2


title: ligamentum flavum , ossified ,rep 1

city: Jinan

first: Dachuan

last: Wang

state: Shandong

address: Jingwu Weiqi Road NO.324

institute: Shandong provincial hospital

description:
treat 1
B01

data_processing:
Paired reads were harvested from Illumina HiSeq 4000 sequencer with quality controlled by Q30. After 3’ adaptor-trimming and the removal of low quality reads by Cutadapt software (v1.9.3), clean reads of all libraries were aligned to the reference genome (UCSC HG19) by Hisat2 software (v2.0.4). ExomePeak software was used for identifying RNA m6A-modified regions (m6A peaks) with FDR (false discovery rate) < 0.05. As previously reported, the common methylated RNAs (CMRs) were defined as RNAs containing at least one m6A peak in all samples, while the specific methylated RNAs (SMRs) were the RNAs with m6A modification only in one sample, and m6A peaks of SMRs were defined as specific m6A peaks. Biological process, molecular function and cellular component analysis were performed for the enrichment of differentially methylated genes, CMRs and SMRs.
Assembly: hg19  Supplementary files format and content: Number of raw junction read  Library strategy: m6A-Seq

source_name: ligamentum flavum

extract_protocol:
Trizol reagent (Invitrogen) was applied to extract total RNA.
MeRIP-Seq was performed by Cloudseq Biotech Inc. (Shanghai, China) according to the published procedure with proper adjustments. Briefly, the fragmented RNA was incubated with m6A polyclonal antibody (Synaptic Systems, 202003) in IPP buffer at 4°C for 2 hours. Then the mixture was immune-precipitated by incubation with protein-A beads (Thermo Fisher) at 4°C for an additional 2 hours. Then, bound RNA was eluted from the beads with N6-methyladenosine (BERRY & ASSOCIATES, PR3732) in IPP buffer and then extracted with Trizol reagent (Thermo Fisher) following the manufacturer's instruction. Purified RNA was used for RNA-seq library generation with NEBNext® UltraTM RNA Library Prep Kit (NEB). Both the input sample without immunoprecipitation and the m6A IP samples were subjected to 150 bp paired-end sequencing on Illumina HiSeq sequencer. In addition, the q-PCR was performed to detect the level of m6A using purified RNA fragments

value: ligamentum flavum


title: ligamentum flavum , ossified ,rep 3

description:
treat 3
B03


title: ligamentum flavum ,non ossified ,rep 3

description:
control 3
A03


title: ligamentum flavum , ossified ,rep 2

description:
treat 2
B02


title: hESC_EPI, d3

city: Cambridge

first: Vincent

last: Knight-Schrijver

address: Wellcome-MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Puddicombe Way

institute: University Of Cambridge

library_source: transcriptomic single cell

data_processing:
Files were de-multiplexed using bcl2fastq by CRUK sequencing facilities.
FASTQ files were aligned using Cellranger version 3.0.2 against the human reference genome GRCh38 using default parameters.
Cells were called in Cellranger version 3.0.2.
Barcodes were filtered in R retaining only cells with between 1000 and 15000 UMIs, over 400 unique features, and under 15 % content of mitochondrial RNA.
A further processing step was carried out in the associated article: “A single-cell comparison of adult and foetal human epicardium defines the age-associated changes in epicardial activity”. Where 300 cells were sampled from each timepoint after the QC steps to run a simplified analysis.
Assembly: GRCh38
Supplementary files format and content: Firstly for each time point the untouched filtered output from Cellranger is provided in three standard 10X files “features.tsv.gz”, “barcodes.tsv.gz”, and “matrix.mtx.gz”.
Supplementary files format and content: Secondly, a single R data storage file formatted as a Seurat object is provided (“hESC.so.rds”), which contains a random sample of 1800 cells after QC (300 cells from each time point). This dataset and analysis is referred to in the initial publication associated with this data.

source_name: hESC-epicardium

growth_protocol: Differentiation of epicardium was carried out by L. Gambardella according to our previously published protocols (Iyer et al., 2015). Briefly, hESCs were initially differentiated into lateral plate mesoderm (LM) in the presence of FGF2 and BMP4. The LM is then exposed to WNT3A, BMP4 and retinoic acid resulting in hESC-EPI after 8 to 9 days.

extract_protocol:
Cells were harvested on days 1, 2, 3, 4, 8, and 9 of differentiation after the LM stage by re-suspension in PBS.
Samples were submitted for 10x library preparation for 3’ single cell sequencing using V3 chemistry at the CRUK Cambridge institute.

value: hESC-epicardium

tag: cell line

tag: time

value: Day 3


title: hESC_EPI, d4

value: Day 4


title: hESC_EPI, d9

value: Day 9


title: hESC_EPI, d1

value: Day 1


title: hESC_EPI, d2

value: Day 2


title: hESC_EPI, d8

value: Day 8


title: ligamentum flavum ,non ossified ,rep 1

description:
control 1
A01


title: UAC1


title: CONT_2


title: Control group rat#1, biological rep1

value: kidney

value: WT


title: CONT_1


title: Control group rat#2, biological rep2


title: CUDC+ABT-2

city: Lake Orion

first: Katie

middle: Hege

last: Hurrish

state: MI

address: 2902 Regency Dr.

country: USA

institute: Wayne State University School of Medicine

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC hg19) with hisat2 software (v2.0.4).
Then, HTSeq software (v0.9.1) was used to get the raw count, and edgeR was used to perform normalization, then differentially expressed mRNAs were identified by p-value and fold change.
GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs.
Assembly: UCSC hg19
Supplementary files format and content: The FASTQ format is the standard file format for high-throughput sequencing, and is the original sequencing file with quality scores produced by the sequencer.
Supplementary files format and content: The BAM format is the binary form of the high-throughput sequencing standard alignment file format SAM format, which requires special software to open. Here, we can import the bam file into IGV for visualization.

source_name: AML

extract_protocol:
RNA high throughput sequencing was performed by Cloud-Seq Biotech (Shanghai, China).
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts,USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads.

value: AML

value: leukemia

value: CUDC-907, 10 hours and ABT-199, 1 hour


title: CUDC-25nM-2

value: CUDC-907 25 nM, 10 hours


title: CUDC-25nM-3


title: CUDC-25nM-1


title: ABT-500nM-3

value: ABT-199 500 nM, 1 hour


title: ABT-500nM-2


title: ligamentum flavum ,non ossified ,rep 2

description:
control 2
A02


title: Control3


title: ABT-500nM-1


title: Control1


title: Control2


title: CUDC+ABT-3


title: CRISPR-KO-screen GeCKO V2 libB representation control

city: La Jolla

first: Paola

last: Benaglio

state: CA

address: 9500 Gilman Drive #0761

department: Pediatrics

institute: University of California San Diego

description:
CRISPR-KO-screen of  EndoC_betaH1 with GeCKO V2 library B - representation control
CRISPR-KO-screen_results.csv

data_processing:
Adaptor sequences ggaaaggacgaaacaccg and gttttagagctagaaatagca flanking the 19-20 base pair of sgRNA sequences were trimmed using cutadapt. Trimmed sequencing reads were aligned to the reference sgRNA library using bowtie2, and sgRNA counting was performed using MAGeCK. Statistical significance of guide RNA representation in control and cytokine treated datasets was estimated with the mle subcommand in the MAGeCK package. An effect (beta) for each gene from this analysis was extracted as an indicator of enrichment (positive beta) or depletion (negative beta) of sgRNAs targeting this gene in the cytokine-treated cells. miRNA genes and genes with less that 3 sgRNA guides were excluded from further analysis.
Assembly: hg19
Supplementary files format and content: Matrix tables with raw gene or peak counts for every gene/peak and every sample
Supplementary files format and content: Co-accessible sites are provided for beta cells and annotated with gene promter within a 5kb window
Supplementary files format and content: List of islet candidate regulatory elements coordinates annotated with cell type and cytokine response
Supplementary files format and content: List of final barcodes and cell type assignments of the snATAC experiments
Library strategy: Targeted-DNA-Seq

source_name: EndoC_betaH1 cell line

growth_protocol: EndoC-βH1 cells were cultured at 9×104 cells/cm2 of cell culture surface area pre-coated with ECM (Sigma) and Fibronectin (Sigma). Cell culture media containing DMEM (Gibco), 2% BSA (Sigma), 3.5× 10-4% 2-mercaptoethanol (Gibco), 0.12% Nicotinamide (Calbiochem), 5.5 ng/mL transferrin (Sigma), 6.7pg/mL Sodium Selenite (Sigma) and 1% Penicillin-Streptomycin (Gibco) were refreshed every 2 days. Cells were passaged weekly using 0.25% Trypsin-EDTA, which was quenched with an equal volume of FBS and two volumes of IMDM media (Gibco).

extract_protocol:
Genomic DNA from 60M cells per condition was purified with a Quick-gDNA™ MidiPrep kit (Zymo Research).
sgRNA library were amplified from the genomic DNA using a two-step nested PCR method modified from a previous published protocol (PMID: 28417999). Amplicons from the first step of PCR were gel purified and subjected to a second round of PCR to add Illumina sequencing adaptors and TruSeq indexes. Sequencing library amplified from the second round of PCR were size-selected and purified with a magnetic bead-based SPRIselect reagent (Beckman Coulter), and subjected to HiSeq4000 Illumina NGS platform using a single read (SR75) method.

treatment_protocol: EndoC-βH1 cells were expanded to a total of 300 million cells before spin-inoculated with the lentiviral human GeCKO-V2 library at an MOI=0.3. To enrich for successfully transduced cells, a 3-day puromycin (5 μg/mL, Sigma) selection was performed 48 hours after the spin-inoculation and 60M (500X genome coverage) cells were harvested as a representation control. The rest of the cells were kept in the culture condition for an additional 14 days with puromycin (1 μg/mL) to achieve sufficient gene deletion and treated with either 0.1% BSA or a combination 0.5 ng/mL IL1β (PerroTech), 1 ng/mL TNFα (PerroTech) and 10 ng/mL IFNγ (PerroTech) for 72 hours.

value: no treatment

tag: experiment label

value: representation control

tag: transduced vectors

value: GeCKO V2 libB


title: CUDC+ABT-1


title: CRISPR-KO-screen GeCKO V2 libB Rep3 untreat 72h

description:
CRISPR-KO-screen of  EndoC_betaH1 with GeCKO V2 libB replicate3 treatment: no treatment for 72h
CRISPR-KO-screen_results.csv

tag: treatment duration

value: untreat

value: GeCKO V2 libB Rep3


title: CRISPR-KO-screen GeCKO V2 libA Rep3 untreat 72h

description:
CRISPR-KO-screen of  EndoC_betaH1 with GeCKO V2 libA replicate3 treatment: no treatment for 72h
CRISPR-KO-screen_results.csv

value: GeCKO V2 libA Rep3


title: CRISPR-KO-screen GeCKO V2 libB Rep2 untreat 72h

description:
CRISPR-KO-screen of  EndoC_betaH1 with GeCKO V2 libB replicate2 treatment: no treatment for 72h
CRISPR-KO-screen_results.csv

value: GeCKO V2 libB Rep2


title: CRISPR-KO-screen GeCKO V2 libB Rep1 untreat 72h

description:
CRISPR-KO-screen of  EndoC_betaH1 with GeCKO V2 libB replicate1 treatment: no treatment for 72h
CRISPR-KO-screen_results.csv

value: GeCKO V2 libB Rep1


title: CRISPR-KO-screen GeCKO V2 libB Rep1 3cyt-hi 72h

description:
CRISPR-KO-screen of  EndoC_betaH1 with GeCKO V2 libB replicate1 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 72h
CRISPR-KO-screen_results.csv


title: CRISPR-KO-screen GeCKO V2 libB Rep3 3cyt-hi 72h

description:
CRISPR-KO-screen of  EndoC_betaH1 with GeCKO V2 libB replicate3 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 72h
CRISPR-KO-screen_results.csv


title: CRISPR-KO-screen GeCKO V2 libA Rep2 untreat 72h

description:
CRISPR-KO-screen of  EndoC_betaH1 with GeCKO V2 libA replicate2 treatment: no treatment for 72h
CRISPR-KO-screen_results.csv

value: GeCKO V2 libA Rep2


title: CRISPR-KO-screen GeCKO V2 libA Rep1 untreat 72h

description:
CRISPR-KO-screen of  EndoC_betaH1 with GeCKO V2 libA replicate1 treatment: no treatment for 72h
CRISPR-KO-screen_results.csv

value: GeCKO V2 libA Rep1


title: CRISPR-KO-screen GeCKO V2 libB Rep2 3cyt-hi 72h

description:
CRISPR-KO-screen of  EndoC_betaH1 with GeCKO V2 libB replicate2 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 72h
CRISPR-KO-screen_results.csv


title: CRISPR-KO-screen GeCKO V2 libA representation control

description:
CRISPR-KO-screen of  EndoC_betaH1 with GeCKO V2 library A - representation control
CRISPR-KO-screen_results.csv

value: GeCKO V2 libA


title: CRISPR-KO-screen GeCKO V2 libA Rep2 3cyt-hi 72h

description:
CRISPR-KO-screen of  EndoC_betaH1 with GeCKO V2 libA replicate2 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 72h
CRISPR-KO-screen_results.csv


title: CRISPR-KO-screen GeCKO V2 libA Rep3 3cyt-hi 72h

description:
CRISPR-KO-screen of  EndoC_betaH1 with GeCKO V2 libA replicate3 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 72h
CRISPR-KO-screen_results.csv


title: RNA Isl.12534700 3cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
RNA-seq of islet SAMN12534700 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 24h
Bulk_RNASeq_count.matrix.txt

data_processing:
We used STAR to align paired-end RNA-Seq reads to hg19 genome with a splice junction database built from Gencode v19 annotation. Gene expression values were quantified using RSEM. Genes were filtered for >0.1 TPM on average per sample. We identified differentially expressed genes between each cytokine treatment and untreated conditions using DESeq2.
Assembly: hg19
Supplementary files format and content: Matrix tables with raw gene or peak counts for every gene/peak and every sample
Supplementary files format and content: Co-accessible sites are provided for beta cells and annotated with gene promter within a 5kb window
Supplementary files format and content: List of islet candidate regulatory elements coordinates annotated with cell type and cytokine response
Supplementary files format and content: List of final barcodes and cell type assignments of the snATAC experiments

source_name: Pancreatic islets

growth_protocol: Human islet samples were enriched using a dithizone stain and cultured in CMRL 1066 supplemented with 10% FBS, 1X pen-strep, 8mM glucose, 2mM L-glutamine, 1mM sodium pyruvate, 10mM HEPES, and 250ng/mL Amphotericin B.

extract_protocol:
RNA was isolated using the RNeasy Mini system from Qiagen. Approximately 500-1000 islets were used per sample. RNA quality was assessed using a 2200 TapeStation to confirm RNA integrity.
Ribodepleted total RNA libraries were prepared and sequenced by the UCSD Institute for Genomic Medicine on an Illumina HiSeq 4000 using paired end reads of 100bp.

treatment_protocol: For cytokine-treated samples, human cytokines were added to the culture media for the indicated duration and concentration as follows: for high doses, 10ng/mL and IFN-g, 0.5ng/mL IL-1B (2 cytokines), with 1ng/mL TNF-α where indicated (3 cytokines); for low doses, 0.2ng/mL IFN-g and 0.01ng/mL IL-1B (2 cytokines), with 0.02ng/mL TNF-α where indicated (3 cytokines).

value: Pancreatic islets

tag: source id


title: RNA Isl.12534700 untreat 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
RNA-seq of islet SAMN12534700 treatment: untreated for 24h
Bulk_RNASeq_count.matrix.txt


title: CRISPR-KO-screen GeCKO V2 libA Rep1 3cyt-hi 72h

description:
CRISPR-KO-screen of  EndoC_betaH1 with GeCKO V2 libA replicate1 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 72h
CRISPR-KO-screen_results.csv


title: RNA Isl.12534700 2cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
RNA-seq of islet SAMN12534700 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β (high dose) for 24h
Bulk_RNASeq_count.matrix.txt


title: RNA Isl.1200521 2cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
RNA-seq of islet SAMN1200521 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β (high dose) for 24h
Bulk_RNASeq_count.matrix.txt


title: RNA Isl.1200521 3cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
RNA-seq of islet SAMN1200521 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 24h
Bulk_RNASeq_count.matrix.txt


title: RNA Isl.1200521 untreat 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
RNA-seq of islet SAMN1200521 treatment: untreated for 24h
Bulk_RNASeq_count.matrix.txt


title: RNA Isl.10977276 untreat 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
RNA-seq of islet SAMN10977276 treatment: untreated for 24h
Bulk_RNASeq_count.matrix.txt


title: RNA Isl.10977276 3cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
RNA-seq of islet SAMN10977276 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 24h
Bulk_RNASeq_count.matrix.txt


title: RNA Isl.10977276 2cyt-lo 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
RNA-seq of islet SAMN10977276 treatment: 0.2 ng/mL IFN-γ, 0.01 ng/mL IL-1β (low dose) for 24h
Bulk_RNASeq_count.matrix.txt


title: RNA Isl.10977276 3cyt-lo 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
RNA-seq of islet SAMN10977276 treatment: 0.2 ng/mL IFN-γ, 0.01 ng/mL IL-1β, 0.02 ng/mL TNF-α (low dose) for 24h
Bulk_RNASeq_count.matrix.txt


title: RNA Isl.10977276 2cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
RNA-seq of islet SAMN10977276 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β (high dose) for 24h
Bulk_RNASeq_count.matrix.txt


title: RNA Isl.10861888 untreat 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
RNA-seq of islet SAMN10861888 treatment: untreated for 24h
Bulk_RNASeq_count.matrix.txt


title: RNA Isl.10861888 3cyt-lo 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
RNA-seq of islet SAMN10861888 treatment: 0.2 ng/mL IFN-γ, 0.01 ng/mL IL-1β, 0.02 ng/mL TNF-α (low dose) for 24h
Bulk_RNASeq_count.matrix.txt


title: RNA Isl.10861888 3cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
RNA-seq of islet SAMN10861888 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 24h
Bulk_RNASeq_count.matrix.txt


title: RNA Isl.10861888 2cyt-lo 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
RNA-seq of islet SAMN10861888 treatment: 0.2 ng/mL IFN-γ, 0.01 ng/mL IL-1β (low dose) for 24h
Bulk_RNASeq_count.matrix.txt


title: ATAC Isl.12889245 untreat 72h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN12889245 treatment: untreated for 72h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt

data_processing:
FASTQ reads were trimmed using Trim Galore and aligned to the hg19 reference genome with BWA mem. We marked duplicate reads with Picard, and filtered, sorted, indexed, and aligned reads using samtools with flags ‘-q 30’, ‘-f 3’, ‘-F 3332’. Mitochondrial reads were also removed. We generated a consensus ATAC-seq peaks list by merging reads from all experiments and calling peaks using MACS2 with parameters ‘--extsize 200 --keep-dup all --shift -100 --nomodel’. The peaks were filtered to remove sites found in less than three individual samples and the ENCODE hg19 blacklist v2. A count matrix of reads from each sample mapping to the consensus peaks was created using featureCounts and used for differential accessibility analysis using DESeq2.
Assembly: hg19
Supplementary files format and content: Matrix tables with raw gene or peak counts for every gene/peak and every sample
Supplementary files format and content: Co-accessible sites are provided for beta cells and annotated with gene promter within a 5kb window
Supplementary files format and content: List of islet candidate regulatory elements coordinates annotated with cell type and cytokine response
Supplementary files format and content: List of final barcodes and cell type assignments of the snATAC experiments

extract_protocol:
Cells were collected from culture and homogenized in permeabilization buffer consisting of 5% BSA, 0.2% IGEPAL-CA630, 1mM DTT, and 1X cOmplete EDTA-free protease inhibitor (Sigma) in 1X PBS. Isolated nuclei were resuspended in 1X TDE1 buffer (Illumina) and quantified using a Countess II Automated Cell Counter (Thermo).
Approximately 50,000 nuclei were tagmented in a 25uL reaction volume using 2.5uL TDE1 (Illumina). Transposition reactions were carried out for 30 minutes at 37C in a thermal cycler. Tagmentation reactions were cleaned up using a 2X reaction volume of Ampure XP beads (Beckman Coulter) and used to prepare libraries using the Nextera XT Dual-Indexed primer system (Nextera) and NEBNext High-Fidelity PCR Master Mix (New England Biolabs). Libraries were sequenced on an Illumina HiSeq 4000 using paired end reads of 100bp.


title: RNA Isl.10861888 2cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
RNA-seq of islet SAMN10861888 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β (high dose) for 24h
Bulk_RNASeq_count.matrix.txt


title: ATAC Isl.12889245 untreat 48h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN12889245 treatment: untreated for 48h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.12889245 untreat 6h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN12889245 treatment: untreated for 6h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.12889245 3cyt-hi 6h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN12889245 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 6h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.12889245 3cyt-hi 72h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN12889245 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 72h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.12889245 untreat 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN12889245 treatment: untreated for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.12889245 3cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN12889245 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.12889245 3cyt-hi 48h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN12889245 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 48h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.12833535 untreat 6h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN12833535 treatment: untreated for 6h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.12833535 untreat 48h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN12833535 treatment: untreated for 48h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.12833535 3cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN12833535 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.12833535 3cyt-hi 48h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN12833535 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 48h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.10977276 untreat 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN10977276 treatment: untreated for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.12833535 untreat 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN12833535 treatment: untreated for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.10977276 2cyt-lo 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN10977276 treatment: 0.2 ng/mL IFN-γ, 0.01 ng/mL IL-1β (low dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.10977276 3cyt-lo 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN10977276 treatment: 0.2 ng/mL IFN-γ, 0.01 ng/mL IL-1β, 0.02 ng/mL TNF-α (low dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.10079665 3cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN10079665 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.10079665 untreat 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN10079665 treatment: untreated for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.12833535 3cyt-hi 6h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN12833535 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 6h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.10079665 3cyt-lo 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN10079665 treatment: 0.2 ng/mL IFN-γ, 0.01 ng/mL IL-1β, 0.02 ng/mL TNF-α (low dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.10079665 2cyt-lo 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN10079665 treatment: 0.2 ng/mL IFN-γ, 0.01 ng/mL IL-1β (low dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.12833535 3cyt-hi 72h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN12833535 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 72h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.10977276 2cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN10977276 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β (high dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.10079665 2cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN10079665 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β (high dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.9767462 untreat 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN09767462 treatment: untreated for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.9767462 2cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN09767462 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β (high dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.9479768 untreat 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN09479768 treatment: untreated for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.R284 untreat 24h

description:
ATAC-seq of islet R284 treatment: untreated for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.R284 3cyt-lo 24h

description:
ATAC-seq of islet R284 treatment: 0.2 ng/mL IFN-γ, 0.01 ng/mL IL-1β, 0.02 ng/mL TNF-α (low dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.9479768 2cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN09479768 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β (high dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.R284 3cyt-hi 24h

description:
ATAC-seq of islet R284 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.R284 2cyt-hi 24h

description:
ATAC-seq of islet R284 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β (high dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.R284 2cyt-lo 24h

description:
ATAC-seq of islet R284 treatment: 0.2 ng/mL IFN-γ, 0.01 ng/mL IL-1β (low dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: H_Exp: HCC cell line [HBx overexpression]

city: Haikou

last: Luzheng

address: Hainan General Hospital

department: Department of Hepatobiliary and Pancreatic Surgery

institute: The Affiliated Hainan Hospital of Hainan Medical University （Hainan General Hospital）

description: HCC cell lines with HBx overexpression (HepG2 H6679)

data_processing:
The original image data file obtained by Illumina Hiseq recognition was transformed into the  original sequencing sequence (Sequenced Reads) base on the CASAVA(latest version) base recognition  (Base Calling) analysis
Firstly, Cutadapt was used to remove the reads that contained adaptor contamination, low-quality bases, and undetermined bases. Sequence quality was then verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
We utilized Bowtie2 and Hisat2 to map reads to the genome of species. The remaining reads (unmapped reads) were still mapped to the genome using tophat-fusion. Expression abundance of known transcripts in different samples was calculated by FPKM （Fragments Per Kilobase of exon model per Million mapped reads）.
Initially, CIRCExplorer and CIRI were used to denovo assemble the mapped reads to circRNAs. After that, back splicing reads were identified in unmapped reads using tophat-fusion. All samples generated unique circRNAs. We normalized the back-spliced reads (support for circRNA) by read length and number of mapped reads (spliced reads per billion mapping, denoted as SRPBM), which permits quantitative comparisons between back splicing from different RNA-seq data.
Genome_build: GRCH38

source_name: HCC cell lines

growth_protocol: All cell lines were authenticated by short tandem repeat (STR) profiling and mycoplasma contamination negative test. All cell lines were cultured at 37 °C in a 5% CO2 humidified chamber, and grown in RPMI1640 (Gibco, USA) , medium with 10% fetal bovine serum(FBS,Gibco,USA). The CM was prepared when cells were grown at 90% confluence in the medium with 10%FBS, the medium was changed without FBS, and cells were cultured for a further 48 h. Then the supernatant was removed and centrifuged at 1,500× g for 10 min at 4 ℃ to remove cell debris. CM was aliquoted and stored at -80℃ for further experiments.

extract_protocol:
A total of two samples from parental HepG2-H5298 and HepG2-H6679 cells were used for RNA extraction, performed as above (Trizol reagents, Invitrogen).
The RNA amount and purity of each sample were quantified using NanoDropND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed using Agilent 2100 with RIN number >7.0. Approximately 5 µg of total RNA was used to deplete ribosomal RNA according to the manuscript of Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, CA, USA). After removing ribosomal RNAs, the left RNAs were fragmented into small pieces using divalent cations under high temperatures. After digestion, reverse transcription, and amplification with PCR, cDNA was obtained, and the average insert size for the final cDNA library was 300 bp (±50 bp). At last, we performed a paired-end sequencing on an IlluminaHiseq 4000 (Illumina) following the vendor's recommended protocol.

treatment_protocol: with HBx overexpression (HepG2 H6679)

value: HepG2 H6679

tag: cell type

value: Hepatocellular carcinoma (HCC)

value: with HBx overexpression (HepG2 H6679)


title: H_Ctrl: HCC cell line [empty vector]

description: HCC cell lines with empty vector control

value: HepG2 H5298

tag: treatment

value: with empty vector control


title: ATAC Isl.10977276 3cyt-hi 24h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN10977276 treatment: 10 ng/mL IFN-γ, 0.5 ng/mL IL-1β, 1 ng/mL TNF-α (high dose) for 24h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt


title: ATAC Isl.12833535 untreat 72h

description:
The SAMN# names correspond to the bio-repository Integrated Islet Distribution Program  IDs
ATAC-seq of islet SAMN12833535 treatment: untreated for 72h
Islet_cytokine_responsive_cCREs.xlsx
Bulk_ATACSeq_count.matrix.txt

value: no treatment


title: AMs, CD11c-Cre_Tfam-fl/fl, 3wks, rep4

first: Stefanie

middle: K

last: Wculek

address: C. de Melchor Fernández Almagro, 3

institute: Centro Nacional de Investigaciones Cardiovasculares Carlos III

description:
SW8
sex: Cell pool of 3-5 male and/or female mice

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2 pipeline.
Sequencing adaptor contamination was removed from reads using Cutadapt v1.7.1.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.3.1.
Data were then processed with a pipeline that used Bioconductor package LIMMA for normalization (TMM method) and differential expression analysis.
Assembly: GRCm38 assembly, Ensembl gene build 99
Supplementary files format and content: NormCounts.txt: Tab-delimited text file includes ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

source_name: Lung

extract_protocol:
Total RNA was harvested using the RNeasy Micro kit with DNase digestion (Qiagen) following the manufacturers’ instructions. 200 ng of total RNA was used for the construction of sequencing libraries.
NEBNext Ultra II Directional RNA library Prep Kit for Illumina.

treatment_protocol: Lungs were harvested from untreated 3-week-old Tfam-fl/fl or CD11c-Cre Tfam-fl/fl male or female mice and minced and incubated for 20 min in HBSS (Gibco) under presence of 0.25 mg/ml Liberase TL (Sigma) and 50 μg/ml DNaseI (Sigma) with shaking at 37 °C. To obtain single cell suspensions, lungs were squeezed through a 70 or 100 μm cell strainer (Corning) and cell suspensions were subjected for 5 min to Red Blood Cell Lysis Buffer (Sigma), washed with FACS buffer [3% heat-inactivated Fetal Bovine Serum (FBS), 0.5mM EDTA (both Sigma) in PBS (Gibco)] and re-filtered through a 40 μm cell strainer. Lung single cell suspensions were incubated with mouse CD11c MicroBeads UltraPure and loaded onto LS columns (all Miltenyi Biotec) and the positive fraction collected according to manufacturers’ instructions before fluorescent staining. Then, single cell suspensions were incubated for 20 min at 4 °C in PBS with 2% heat inactivated-FBS and 0.5 mM EDTA (Sigma) with FcR block anti-mouse CD16/CD32 (2.4G2, Tonbo Biosciences) and fluorochrome-conjugated antibodies anti-mouse CD45 (clone 30-F11), anti-mouse F4/80 (clone BM8) and anti-mouse CD11c (clone HL3). DAPI (Sigma) was used to exclude dead cells. Cells were flow-sorted using the FACSAria II cell sorter running FACSDiva software (BD Biosciences).

value: Lung

value: CD45+ F4/80+ CD11c+ FACS-sorted Alveolar Macrophages

tag: genotype

value: CD11c-Cre Tfam-fl/fl (KO)

value: Untreated

tag: age

value: 3 weeks

tag: pool

value: 3-5 male and/or female mice


title: AMs, CD11c-Cre_Tfam-fl/fl, 3wks, rep2

description:
SW4
sex: Cell pool of 3-5 male and/or female mice

tag: tissue


title: AMs, Tfam-fl/fl, 3wks, rep2

description:
SW3
sex: Cell pool of 3-5 male and/or female mice

value: Tfam-fl/fl (WT)


title: AMs, CD11c-Cre_Tfam-fl/fl, 3wks, rep3

description:
SW6
sex: Cell pool of 3-5 male and/or female mice


title: AMs, Tfam-fl/fl, 3wks, rep3

description:
SW5
sex: Cell pool of 3-5 male and/or female mice


title: AMs, Tfam-fl/fl, 3wks, rep1

description:
SW1
sex: Cell pool of 3-5 male and/or female mice


title: AMs, CD11c-Cre_Tfam-fl/fl, 3wks, rep1

description:
SW2
sex: Cell pool of 3-5 male and/or female mice


title: TRA89 [NPp53MutAllo TRA-1]

city: New York

first: Juan

middle: M

last: Arriaga

state: NY

address: 1425 Madison Ave

department: Oncological Sciences, Urology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Libraries were sequenced using Illumina HiSeq2500/4000 or NovaSeq6000 at Columbia Genome Center, or Genewiz. We multiplex samples in each lane, which yields targeted number of single-end/paired-end 100bp or 150bp reads for each sample, as a fraction of 280-400 million reads for the whole lane.
Reads were pseudo-aligned to mouse reference genome version GRCm38 mm10, using kallisto v0.44.0 (Bray et al., 2016) with sequence-based bias correction.
Genome_build: Mouse: UCSC/mm10
Supplementary_files_format_and_content: Tab-delimited text files include kallisto estimated counts for each gene in each sample
Supplementary_files_format_and_content: Gemms_counts.xlsx: Includes 19 NPK samples from GSE143815

source_name: Mouse prostate allograft

extract_protocol:
RNA was prepared from snap-frozen tissues the using MagMAX-96 total RNA isolation kit and only RNA samples having between >200 ng and 1 ug and with an RNA integrity number (RIN) > 8 were used.
Libraries were prepared by the Columbia Genome Center or Genewiz. Poly-A pull-down was used to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required). Libraries were prepared using TruSeq RNA library prep kit v2 or TruSeq Stranded mRNA library prep kit.

value: Mouse prostate allograft

value: Nkx3.1CreERT2/+; Ptenflox/flox; Trp53LSL-R27H/flox; R26R+/+

value: Trametinib

tag: mouse id

tag: use

value: Pharmacodynamics


title: TRA90 [NPp53MutAllo TRA-2]


title: PAN86 [NPp53MutAllo PANO-2]

value: Panobinostat


title: CLO93 [NPp53MutAllo CLO-3]

value: Clofarabine


title: TRA92 [NPp53MutAllo TRA-3]


title: CLO91 [NPp53MutAllo CLO-2]


title: CLO88 [NPp53MutAllo CLO-1]


title: PAN87 [NPp53MutAllo PANO-3]


title: PAN85 [NPp53MutAllo PANO-1]


title: BOR84 [NPp53MutAllo BOR-3]

value: Bortezomib


title: Liver biopsy - M - Indiv_s56

value: liver

tag: diagnosis

value: NAFLD

value: M


title: BOR83 [NPp53MutAllo BOR-2]


title: AMs, Tfam-fl/fl, 3wks, rep4

description:
SW7
sex: Cell pool of 3-5 male and/or female mice

value: Lung


title: VEH78 [NPp53MutAllo Veh-3]

value: Vehicle


title: TEM79 [NPp53MutAllo TEM-1]

value: Temsirolimus


title: BOR82 [NPp53MutAllo BOR-1]


title: VEH77 [NPp53MutAllo Veh-2]


title: 403M_0h

city: qingdao

first: qiaoling

last: song

address: Xiang Gang East Road NO.23

institute: Ocean University of China

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated.
Sequencing data contains a number of connectors, low-quality Reads, so we use Cutadapt (v1.15) software to filter the sequencing data to get high quality sequence(Clean Data)for further analysis .
In data mapping analysis ,The reference genome and gene annotation files were downloaded from genome website. The filtered reads were mapping to the reference genome using HISAT2(http://ccb.jhu.edu/software/hisat2/index.shtml )， the default mismatch was no more than 2. The alignment region distribution of mapped reads was calculated.
Firstly , we use HTSeq(0.9.1) statistics to compare the Read Count values on each gene as the original expression of the gene, and then used FPKM to standardize the expression.
Then we used DESeq (1.30.0)to analyze the genes of difference expression with screened conditions as follows: expression difference multiple |log2FoldChange| > 1, significant P-value < 0.05.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file with raw gene counts for every gene and every sample

source_name: BMDM

growth_protocol: Bone marrow were isolated and routinely generated by 7-day M-CSF treatment.

extract_protocol:
Total RNA was isolated by using a TRIzol Reagent according to the manufacturer’s instructions (Invitrogen), genomic DNA was removed using DNase I (TaKara), and
1 μg of this RNA was used for high-throughput sequencing using Illumina Hiseq 4000 sequencers.

treatment_protocol: no treatment

tag: strain

value: bone marrow

value: 8 weeks


title: TEM80 [NPp53MutAllo TEM-2]


title: TEM81 [NPp53MutAllo TEM-3]


title: WTM_0h


title: VEH76 [NPp53MutAllo Veh-1]


title: Ctrl_Microglia_rep2

city: los angeles

first: lin

last: Pan

address: 2203 glendon avenue

department: Psychiatry

institute: UCLA

data_processing:
STAR package was used to map reads to mouse genome mm10
HTSEQ was used to obtain raw counts from Sequencing reads.
EdgeR‐Limma‐Voom packages in R  were used to calculate Reads per Kilobase per Million Mapped Reads (RPKM) values from raw counts.
DESeq2 package was used to analyze the Differential gene expression.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with RPKM for every gene and every sample

source_name: brain

extract_protocol:
whole brains except olfactory bulb and cerebelum were removed from p17 mice. Different glia cell types were enriched using immunopanning method. CD45 was used to purify microglia. GalC hybrydoma was used to purify Differentiated oligodendrocytes. O4 hybrodoma was used to purify oligodendrocyte precursor cells. Hepacam was used to purify astrocytes. Total RNAs were collected using Qiagen miRNeasy kit.
cDNAs were generated using the Nugen Ovation V2 kit (Nugen), then fragmented using the Covaris sonicator. Sequencing libraries were prepared using the Next Ultra RNA Library Prep kit (New England Biolabs) with 12 cycles of PCR amplification.

value: Microglia

value: ibot+/-


title: Ctrl_Microglia_rep1


title: Pdibot_Microglia_rep1


title: Ctrl_Microglia_rep3


title: Pdibot_Microglia_rep3


title: Pdibot_Astrocyte_rep2

value: Astrocytes


title: Pdibot_Astrocyte_rep3


title: Pdibot_Microglia_rep2


title: Ctrl_Astrocyte_rep3


title: Pdibot_Astrocyte_rep1


title: Ctrl_Astrocyte_rep2


title: Ctrl_OPC_rep2

value: Oligodendrocyte precursor cells


title: Pdibot_OPC_rep1


title: Pdibot_OPC_rep3


title: Pdibot_OPC_rep2


title: Ctrl_OPC_rep1


title: Ctrl_Astrocyte_rep1


title: Pdibot_OLG_rep2

value: Differentiated oligodendrocytes


title: Ctrl_OPC_rep3


title: Pdibot_OLG_rep1


title: Ctrl_OLG_rep3


title: STIM1 knockout larval brain bio rep1

city: Bangalore

first: Jsmine

last: Kaur

state: Karnatka

address: GKVK Campus

department: Biological Sciences

country: India

institute: NCBS

data_processing:
FASTQC was used to check the quality and adapter contamination
Sequence reads were mapped to Dm6 assembly using HISAT2. Sorting of the output BAM was done using Samtools. This served as an input for htseq-count.
The raw counts were then used as an input in DESeq2 to obtain differentially expressed genes using default thresholds.
Assembly: Dm6
Supplementary files format and content: matrix.txt.control_vs_treated.DESeq2.DE_results.txt represents FPKMs.  The htseq.txt files represent raw counts.

organism: Drosophila melanogaster

extract_protocol:
RNA was harvested using trizol.
cDNA was obtained using low input TAKARA kit with 10ng RNA. Libraries were formed using Nextera XT library prep kit (Illumina)

tag: developmental stage

value: larval

value: brain


title: STIM1 knockout larval brain bio rep2


title: WT larval brain bio rep4

value: WT/CS


title: WT larval brain bio rep3


title: Pdibot_OLG_rep3


title: Ctrl_OLG_rep1


title: STIM1 knockout larval brain bio rep3


title: WT larval brain bio rep2


title: Ctrl_OLG_rep2


title: WT larval brain bio rep1


title: STIM1 knockout larval brain bio rep4


title: lncap_LNCAPPS5A_H5_Ryuvidine_0.18_24

city: New York City

first: Alessandro

last: Vasciaveo

address: 1130 Saint Nicholas Ave., 910

department: Department of Systems Biology

institute: Columbia University

data_processing:
Sequencing was performed in a Hi Seq 2500 sequencer (Illumina) and base calling was performed with Illumina HCS software.
RNASeq reads were mapped for each well to the human reference genome assembly 38 using the STAR aligner (Dobin et al., 2013), version 2.5.2b
Individual counts files were combined across genes and ERCC2 spike-in counts removed, yielding the raw counts file for each cell-line experiment.
Assembly: hg38
Supplementary files format and content: 2 semicolon delinated text files (for 2 cell-lines) with raw gene counts for every gene and every sample

source_name: prostate cancer

extract_protocol:
Cells are lysed for PLATE-Seq in Buffer TCL (Qiagen) supplemented with 2-mercaptoethanol in 96-well plates. We transfer 30 μl of cell lysate from each well to a 96-well plate with oligo(dT) grafted to the wells (mRNA TurboCapture Plate, Qiagen) and added 1 μl of 1:100 dilution of ERCC Ex-Fold Spike-Ins (ThermoFisher) to a subset of the sample wells. The plate is then centrifuged at 295 × g for 1 min to eliminate air bubbles followed by incubation for 90 min at room temperature with shaking at 200 rpm. Lysate is then removed from the oligo(dT) capture plate and wells are washed three times with Buffer TCW (Qiagen) using the 96 CO-RE Head of a Hamilton Microlab STAR automated liquid handling system. After drying the plate, mRNA is then eluted by adding 30 μl of elution buffer (nuclease-free water supplemented with 0.4 U μl−1 SUPERaseIN (ThermoFisher)), incubation at 65 °C for 5 min, and incubation at room temperature for 5 min. mRNA samples are then transferred to a new PCR plate (Hard-Shell PCR plate, 96-well, Bio-Rad) using sterile-filter 96-well, 50 μl tips on the Hamilton STAR. To anneal primers for reverse transcription, 3 μl of 100 μM adapter-linked oligo(dT) primers are added to each well along with 10 μl of 5× ProtoScript RT Buffer (New England BioLabs) with the Hamilton STAR CO-RE Head and 1000 μl channel pipetting system (see Supplementary Table 2 for “PLATEseq_oligodTBC” sequences). The plate is then heated to 94 °C for 2 min and placed immediately on ice for 5 min. The remaining components of the reverse transcription master mix including 0.5 mM of each dNTP, 10 mM DTT, 35.8 U of Protoscript II Reverse Transcriptase (New England BioLabs), and water are then added to bring the final reaction volume to 50 μl per well. The plate is then centrifuged at 295 × g for 1 min and incubated at 42 °C for 2 h. At this point, the samples can optionally be frozen at −80 °C. To remove excess primer, 1 μl of a fourfold dilution of Exonuclease I (New England BioLabs) is added to each sample. The Exonculease I reaction is incubated at 25 °C for 1 h. To hydrolyze the RNA, we add 20 μl of a 1:1 mixture of 1 M sodium hydroxide and 0.5 M EDTA to each well and incubate at 65 °C for 15 min. The wells are then pooled together into a single tube to which 80 μl of 12 M hydrochloric acid are added to neutralize the sample. At this point, the pooled sample can optionally be frozen at −80 °C. The pooled, neutralized sample is purified and concentrated using a Qiagen MinElute column using a vacuum apparatus according to the manufacturer’s instructions, and pooled cDNA is eluted in 15 μl of nuclease-free water. For second-strand synthesis, 1 μl of 10 mM dNTP mixture and 1 μl of 100 mM adapter-linked random hexamer primers are added to the pooled cDNA sample. The mixture is then heated to 70 °C for 2 min and immediately placed on ice for 5 min. Next, 2 μl of NEB Buffer 2 (New England BioLabs) and 1 μl of Klenow large fragment DNA polymerase (New England BioLabs) are added and the reaction is incubated at room temperature for 30 min. The reaction is then stopped by addition of EDTA to a final concentration of 50 μM the double-stranded cDNA is purified with two rounds of bead clean-up using AMPure XP beads (Beckman Counter) at a 1:1 bead-to-sample ratio. Finally, the double-stranded cDNA pool is amplified by PCR using Phusion DNA Polymerase (New England BioLabs)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cell-lines were treated at a 48-hour IC20 for each drug and RNA was collected at 24 hours to minimize cell-death.

value: Ryuvidine

tag: cell line

value: LNCaP

tag: provider

value: ATCC

tag: vendor id

tag: Sex

value: male


title: lncap_LNCAPPS5A_G11_UNTREATED_0_24

value: UNTREATED


title: lncap_LNCAPPS5A_G12_Thapsigargin_0.01_24

value: Thapsigargin


title: lncap_LNCAPPS5A_H2_Ro 106-9920_1.5_24


title: lncap_LNCAPPS5A_H3_NNC 05-2090 hydrochloride_3.5_24

value: NNC 05-2090 hydrochloride


title: lncap_LNCAPPS5A_G3_PHA 665752_4.5_24


title: lncap_LNCAPPS5A_G8_BNTX maleate salt hydrate_0.5_24

value: BNTX maleate salt hydrate


title: lncap_LNCAPPS5A_G9_AC-93253 iodide_0.03_24

value: AC-93253 iodide


title: lncap_LNCAPPS5A_H4_Scriptaid_0.5_24

value: Scriptaid


title: lncap_LNCAPPS5A_G10_Podophyllotoxin_0.02_24

value: Podophyllotoxin


title: lncap_LNCAPPS5A_H1_SB 216641 hydrochloride_3.5_24

value: SB 216641 hydrochloride


title: lncap_LNCAPPS5A_G7_Bay 11-7085_3_24


title: lncap_LNCAPPS5A_G5_JK 184_0.09_24


title: lncap_LNCAPPS5A_G6_Etonitazenyl isothiocyanate_4_24

value: Etonitazenyl isothiocyanate


title: lncap_LNCAPPS5A_G2_FIT_4_24

value: FIT


title: lncap_LNCAPPS5A_G4_AT 101_1.5_24


title: lncap_LNCAPPS5A_G1_RS 17053 hydrochloride_2_24

value: RS 17053 hydrochloride


title: lncap_LNCAPPS5A_F12_Tetraethylthiuram disulfide_0.11_24

value: Tetraethylthiuram disulfide


title: lncap_LNCAPPS5A_F11_DMSO_0_24

value: DMSO


title: lncap_LNCAPPS5A_F10_beta-Lapachone_1_24

value: beta-Lapachone


title: lncap_LNCAPPS5A_F9_Emetine dihydrochloride hydrate_0.035_24

value: Emetine dihydrochloride hydrate

value: LNCaP


title: lncap_LNCAPPS5A_F8_Brefeldin A_0.05_24

value: Brefeldin A

value: ATCC

value: male


title: lncap_LNCAPPS5A_F6_UNTREATED_0_24

value: UNTREATED


title: lncap_LNCAPPS5A_F7_CP-100356 monohydrochloride_2_24

value: CP-100356 monohydrochloride


title: lncap_LNCAPPS5A_F5_SN 38_0.075_24

value: SN 38


title: lncap_LNCAPPS5A_F2_GR 127935 hydrochloride_2.5_24

value: GR 127935 hydrochloride


title: lncap_LNCAPPS5A_F4_BIBU 1361 dihydrochloride_1.5_24

value: BIBU 1361 dihydrochloride


title: lncap_LNCAPPS5A_E12_Vincristine_0.025_24

value: Vincristine


title: lncap_LNCAPPS5A_F1_Metaphit_2.5_24

value: Metaphit


title: lncap_LNCAPPS5A_E10_Niclosamide_1_24

value: Niclosamide


title: lncap_LNCAPPS5A_E9_Diphenyleneiodonium chloride_0.04_24

value: Diphenyleneiodonium chloride


title: lncap_LNCAPPS5A_E11_DMSO_0_24


title: lncap_LNCAPPS5A_E7_Cantharidin_1_24

value: Cantharidin


title: lncap_LNCAPPS5A_E2_WIN 64338 hydrochloride_2_24

value: WIN 64338 hydrochloride


title: lncap_LNCAPPS5A_D12_CP-31398 dihydrochloride hydrate_2_24

value: CP-31398 dihydrochloride hydrate


title: lncap_LNCAPPS5A_E4_SNAP 5089_3_24

value: SNAP 5089


title: lncap_LNCAPPS5A_E5_Astemizole_2_24

value: Astemizole

value: LNCaP


title: lncap_LNCAPPS5A_D11_Terfenadine_2_24

value: Terfenadine

value: ATCC


title: lncap_LNCAPPS5A_E8_Calcimycin_0.5_24

value: Calcimycin

value: male


title: lncap_LNCAPPS5A_D8_Benserazide hydrochloride_4.5_24

value: Benserazide hydrochloride


title: lncap_LNCAPPS5A_E6_UNTREATED_0_24

value: UNTREATED


title: lncap_LNCAPPS5A_D9_(S)-(+)-Camptothecin_0.035_24

value: (S)-(+)-Camptothecin


title: lncap_LNCAPPS5A_E1_Pyrrolidinedithiocarbamate ammonium_1_24

value: Pyrrolidinedithiocarbamate ammonium


title: lncap_LNCAPPS5A_D7_Chelerythrine chloride_1_24

value: Chelerythrine chloride


title: lncap_LNCAPPS5A_E3_ER 27319 maleate_0.5_24

value: ER 27319 maleate


title: lncap_LNCAPPS5A_D6_DMSO_0_24

value: DMSO


title: lncap_LNCAPPS5A_D10_Parthenolide_0.5_24

value: Parthenolide


title: lncap_LNCAPPS5A_D4_IMD 0354_2_24


title: lncap_LNCAPPS5A_D5_NSC632839_2_24


title: lncap_LNCAPPS5A_D3_Ro 31-8220 mesylate_0.5_24

value: Ro 31-8220 mesylate


title: lncap_LNCAPPS5A_C12_Sanguinarine chloride_0.5_24

value: Sanguinarine chloride


title: lncap_LNCAPPS5A_D1_Tetrindole mesylate_3_24

value: Tetrindole mesylate


title: lncap_LNCAPPS5A_D2_UNTREATED_0_24


title: lncap_LNCAPPS5A_F3_JTC 801_0.5_24

value: JTC 801


title: lncap_LNCAPPS5A_C11_Quinacrine dihydrochloride_1.5_24

value: Quinacrine dihydrochloride

value: LNCaP


title: lncap_LNCAPPS5A_C10_Ivermectin_2_24

value: Ivermectin

value: ATCC


title: lncap_LNCAPPS5A_C9_2_3-Dimethoxy-1_4-naphthoquinone_3-Dimethoxy-1_4-naphthoquinone_0.5_24

value: male


title: lncap_LNCAPPS5A_C7_Anisomycin_0.06_24

value: Anisomycin


title: lncap_LNCAPPS5A_C8_Bromoacetyl alprenolol menthane_2.5_24

value: Bromoacetyl alprenolol menthane


title: lncap_LNCAPPS5A_C5_CGK 733_3_24

value: CGK 733


title: lncap_LNCAPPS5A_C4_Bax channel blocker_1.5_24

value: Bax channel blocker


title: lncap_LNCAPPS5A_C6_DMSO__24


title: lncap_LNCAPPS5A_C2_UNTREATED_0_24

value: UNTREATED


title: lncap_LNCAPPS5A_B12_Wiskostatin_2_24

value: Wiskostatin


title: lncap_LNCAPPS5A_B5_CGP 71683 hydrochloride_5_24

value: CGP 71683 hydrochloride


title: lncap_LNCAPPS5A_C3_ZK 93423_2.5_24


title: lncap_LNCAPPS5A_C1_IPAG_0.5_24

value: IPAG


title: lncap_LNCAPPS5A_B7_(R)-CR8_0.23_24


title: lncap_LNCAPPS5A_B9_NSC 95397_1_24


title: lncap_LNCAPPS5A_B3_NSC 663284_1.5_24


title: lncap_LNCAPPS5A_B6_DIPPA hydrochloride_2_24

value: DIPPA hydrochloride


title: lncap_LNCAPPS5A_B10_L-703_606 oxalate salt hydrate_2.5_24

value: L-703_606 oxalate salt hydrate


title: lncap_LNCAPPS5A_B11_Stattic_1.5_24

value: Stattic


title: lncap_LNCAPPS5A_B4_Lylamine hydrochloride_1.5_24

value: Lylamine hydrochloride


title: lncap_LNCAPPS5A_B2_DMSO_0_24

value: DMSO


title: lncap_LNCAPPS5A_B1_HEAT hydrochloride_1.5_24

value: HEAT hydrochloride

value: LNCaP


title: lncap_LNCAPPS5A_A10_NNC 55-0396_4.5_24

value: ATCC


title: lncap_LNCAPPS5A_A12_PAC-1_2_24

value: male


title: lncap_LNCAPPS5A_A11_Auranofin_0.5_24

value: Auranofin


title: lncap_LNCAPPS5A_B8_CGP-74514A hydrochloride_0.5_24

value: CGP-74514A hydrochloride


title: lncap_LNCAPPS5A_A9_Ellipticine_1_24

value: Ellipticine


title: lncap_LNCAPPS5A_A3_(R)-(-)-Niguldipine hydrochloride_2.5_24

value: (R)-(-)-Niguldipine hydrochloride


title: lncap_LNCAPPS5A_A8_Z-L-Phe chloromethyl ketone_1.5_24

value: Z-L-Phe chloromethyl ketone


title: lncap_LNCAPPS5A_A6_SU 3327_1.5_24


title: lncap_LNCAPPS5A_A7_SR 33805 oxalate_2.5_24

value: SR 33805 oxalate


title: lncap_LNCAPPS5A_A2_DMSO_0_24


title: lncap_LNCAPPS4B_G12_PP-121_0.0011_24


title: lncap_LNCAPPS5A_A1_3'-Fluorobenzylspiperone maleate_3.5_24

value: 3'-Fluorobenzylspiperone maleate


title: lncap_LNCAPPS4B_E12_LAQ824_0.01_24


title: lncap_LNCAPPS4B_H12_PI-103_0.0002_24