title: PKBuffer Brain PBS sample #1 [BB1P1]

tag: genotype


title: PKBuffer Liver LPS sample #2 [BLI2L2]

status: Public on Mar 31 2022

type: SRA

city: Seattle

first: Karol

last: Bomsztyk

state: WA

address: 850 Republican St

department: UW Medicine South Lake Union

country: USA

institute: University of Washington

description: 2mg sample from frozen organ in CryoTray

library_source: transcriptomic

data_processing:
Illumina RTA version 3.9.25
Index for alignment was built using the 'buildindex'  function from the Bioconductor 'Rsubread' (version 2.3.2) package. Index was assembled from the NCBI Genome Reference Consortium Mouse Build 39 (GRCm39) RefSeq assembly
Reads were aligned and counted in RStudio using the Bioconductor ‘RSubread’ (version 2.8.2) package. Alignment was done with the ‘align’ function on the paired gzFASTQ files creating sorted BAM files. Align commands:  type = "rna", input_format = "gzFASTQ", output_format = "BAM", sortReadsByCoordinates = TRUE, PE_orientation = "fr"
‘featureCounts’ function was used with the NCBI GRCm39 RefSeq Annotation and the commands: isGTFAnnotationFile=TRUE, countMultiMappingReads = FALSE, strandSpecific = 2, isPairedEnd=TRUE.
Assembly: mm39
Supplementary files format and content: tab deliminted text files include raw gene counts and gene annotation for each sample.
Supplementary files format and content: .csv table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol:
1-2mg samples of frozen tissue were sampled with the CryoCore and put into separate wells of a 96 well plates.  100ul of either PIXUL PK Buffer or TRIZOL buffer wer added to the wells and then all samples were sonicated in PIXUL sonicator (Matchstick Technologies, Inc Kirkland WA and Active Motif Carlsbad, CA). Samples are processed for 30 seconds in PIXUL with settings: Pulse=50, PRF=1.0 Burst=20.  TRIZOL samples then received additional 100ul of TRIZOL and followed manufacturers protocol for RNA isolation.  PIXUL PK Buffer samples are immediately incubated (After sonication) in the same PIXUL plate at 95C for 20 minutes, and then put on ice for 5 minutes. Cooled samples are centrifuged in a plate centrifuge for 10 minutes at 4,200g and 4C and then put back on ice. 60ul of clear supernatant (without any floating residue) from each well is carefully transferred via pipette to a new semi-skirted 96 well PCR plate on ice. Isolation of nucleic acids with 1.8x SPRI beads is done as per the Omega Bio-tek protocol (Norcross, GA) with a two-minute final SPRI bead drying time and final elution to 50ul of ultrapure ddH2O and then put samples on ice. Finally, DNase I and RNAse Out are added to the eluted RNA samples and DNase I digestion is done as per the manufacturer’s protocol.
Sequencing libraries were prepared using Zymo-Seq RiboFree Total RNA Library Kit with starting RNA between 205-480ng and libraries amplified between 13-14 cycles of PCR as per manufacturers protocol. Libraries were diluted as per Illumina NextSeq2000 Sequencing System Guide to a final pooled loading concentration of 650pM in resuspension buffer (RSB) plus Tween 20 with a 10% PhiX spike-in and sequenced in Illumina P2 cartridges on NextSeq 2000 that employed a dual-index, paired-end, 75 base read length (PE75).

treatment_protocol: Female 8–12-week-old C57bl/6 mice were injected intraperitoneally (IP) with 5mg/kg lipopolysaccharide (LPS) in 200ml PBS or with 200ml PBS as control. The specific protocol was approved by Institutional Animal Care and Use Committee (IACUC) at the University of Washington. After 12 hours mice were euthanized by isoflurane overdose and confirmatory cervical dislocation. Brains, hearts, kidneys, and livers were harvested, immediately placed on ice, and then frozen in CryoTrays

tag: tissue

value: Liver

tag: tissue treatment

value: Lipopolysaccharide (LPS) treated

tag: rna isolation buffer

value: PIXUL Proteinase K Buffer

tag: mouse number

value: Female 8-12 week-old C57bl/6


title: PKBuffer Kidney LPS sample #1 [BK1L40]

source_name: Kidney

value: Kidney


title: PKBuffer Heart LPS sample #1 [BH2L30]

source_name: Heart

value: Heart


title: Bmal1-HepWT-ZT6-2

status: Public on Jan 26 2022

city: Lausanne

first: Benjamin

middle: D

last: Weger

state: VD

address: Station 15

department: SV

country: Germany

institute: EPFL

data_processing:
Sequences were aligned to the full reference genome index build with Ensembl annotation to improve accuracy on splices junctions using STAR 2.4.0i
A custom Perl script was used to quantify uniquely mapped reads. For each Ensembl gene, all exons of the respective annotated protein-coding transcripts were considered.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: liver

extract_protocol:
Liver RNAs were extracted as previously described (Gachon et al, 2006) with classical methods using guanidium thiocyanate lysis buffer. Muscle and epididymal white adipose tissue were disrupted and extracted using the tissue lyser II (Qiagen) and the miRNeasy Mini Kit (Qiagen) following the manufacturer's protocol, repectively.
The RNA were quantified with Ribogreen (Life Technologies) and quality assessed on a Fragment Analyzer (Advances Analytical). Sequencing libraries were prepared from 250 ng total RNA using the TruSeq Stranded RNA  Sample Prep Kit v2 (Illumina) with the Ribo-Zero Gold depletion set. The procedure was automated on a Sciclone NGS Workstation (Perkin Elmer). The manufacturer’s protocol was followed, except for the PCR amplification step. The latter was run for 12 cycles with the KAPA HiFi HotStart ReadyMix (Kapa BioSystems). This optimal PCR cycle number has been evaluated using the Cycler Correction Factor method as described previously (Atger et al., PNAS, 2015). Purified libraries were quantified with Picogreen (Life Technologies) and the size pattern was controlled with the DNA High Sensitivity Reagent kit on a LabChip GX (Perkin Elmer). Libraries were then pooled by 18 and each pool was clustered at a concentration of 10 pmol on 4 lanes of  two High Output (8-lane) v3 flow cell (Illumina). Sequencing was performed for 2 x 100 cycles on a HiSeq 2500 following Illumina’s recommendations.

value: liver

tag: strain

value: Alb::Cre_0/0, Bmal1_fl/fl

tag: feeding regimen

value: night restricted feeding

tag: time

value: zeitgeber time zt6

tag: age

value: 8-12 weeks


title: Bmal1-HepWT-ZT6-1


title: Bmal1-HepWT-ZT2-1

value: zeitgeber time zt2


title: Bmal1-HepWT-ZT22-2

value: zeitgeber time zt22


title: Bmal1-HepWT-ZT2-2


title: Bmal1-HepWT-ZT22-1


title: LFS_MB_1R_model_DMSO_negative_control

status: Public on Feb 08 2022

type: RNA

city: Heidelberg

first: Aurélie

last: Ernst

address: Im Neuenheimer Feld 580

institute: DKFZ Heidelberg

hyb_protocol: 6,6 ug of fragmented and labeled ds-cDNA were hybridized for 17 hr at 45°C on Human Clariom™ S Arrays (Applied Biosystems) (according to GeneChip™ 3’ IVT Pico Kit Manual Workflow USER GUIDE).

scan_protocol: Gene Expression Microarrays were scanned using the Affymetrix GeneChip® Scanner 3000 according to GeneChip® Expression Wash, Stain and Scan Manual for Cartridge Arrays.

data_processing: The raw CEL files of the clariom S human expression arrays were imported to R and normalized using the RMA method using the bioconductor package oligo. Expression probes were annotated by the bioconductor transcript annotation database clariomshumantranscriptcluster.db using the bioconductor packageaffycoretools. Sample correction and differential gene expression were performed by bioconductor package limma.

label: biotin

organism: Homo sapiens

source_name: Medulloblastoma 1st relapse from Li-Fraumeni syndrome patient1

label_protocol: The GeneChip™ 3' IVT Pico Kit (Applied Biosystems) is used to generate labeled ds-cDNA  from input amounts of 5ng total RNA.

growth_protocol: LFS_MB_P, LFS_MB_1R, RCMB18 were short-term spheroid cultures derived from human tumor cells from patient-derived xenograft models. All experiments were performed with mycoplasma-free cells. Spheroid cultures from patient-derived xenograft models were prepared by homogenizing the freshly isolated tumors from mice brains by pipetting in NeuroCult™ NS-A Proliferation Kit (STEMCELL Technologies, 05751). Homogenized tissue is then filtered to get single cell suspension. Cells were then centrifuged at 1000 rpm for 5 minutes and pellet was resuspended to get 0.5 million cells per 10 ml growth medium. Growth medium was comprised of 46.75 ml Neurobasal™-A Medium (Invitrogen, 10888022) with 46.75 ml DMEM/F-12 (Invitrogen, 11330057), 1 ml MEM Non-Essential Amino Acids Solution (100X) (Invitrogen, 11140050), 1 ml Sodium Pyruvate (100 mM) (Invitrogen, 11360070), 2.5 ml Hepes buffer (1M) (Invitrogen, 15630080), 1 ml GlutaMAX™ Supplement (Invitrogen, 35050061), 1 ml Penicillin-Streptomycin (Invitrogen, 15140122), 2 ml B-27™ Supplement minus vitamin A (50X) (Invitrogen, 12587001), 40 µl Heparin (50 mg/ml stock) (Sigma, H3149-10KU), 20ng/ml Human FGF rec 154aa (Peprotech, GMP100-18 B), 10 ng/ml EGF (Sigma, E 4127) and 100 µl LIF(Millipore, LIF1010). Spheroids were cultured for 1 weeks in 25 cm2 flask (Greiner, 690195) before drug treatment.

extract_protocol: Total RNA was extracted using the RNeasy mini kit (Qiagen, 74104) according to the manufacturer's instructions.

treatment_protocol: Spheroids were treated with either vehicle control, BGB 290 (IC20), romidepsin (IC20) or BGB 290 (IC20) with romidepsin (IC20) for 24 hours.

tag: cell type

value: Patient derived xenograft spheroids

value: LFS_MB_1R spheroid

tag: treatment

value: DMSO negative control


title: LFS_MB_P_model_DMSO_negative_control

source_name: Medulloblastoma from Li-Fraumeni syndrome patient1

value: LFS_MB_P spheroid


title: RCMB18_model_BGB290_IC20_24hours_single_treatment

source_name: Medulloblastoma from Li-Fraumeni syndrome patient2

value: RCMB18 spheroid

value: BGB290 IC20 for 24hours


title: RCMB18_model_Romidepsin_IC20_24hours_single_treatment

value: romidepsin IC20 for 24hours


title: LFS_MB_1R_model_Romidepsin_IC20_24hours_single_treatment


title: LFS_MB_P_model_BGB290_IC20_24hours_single_treatment


title: LFS_MB_1R_model_Romidepsin_IC20_and_BGB290_IC20_24hours_double_treatment

value: BGB290 IC20 and romidepsin IC20 for 24hours


title: LFS_MB_P_model_Romidepsin_IC20_24hours_single_treatment


title: RCMB18_model_DMSO_negative_control


title: LFS_MB_1R_model_BGB290_IC20_24hours_single_treatment


title: Bmal1-HepWT-ZT18-2

value: zeitgeber time zt18


title: Bmal1-HepWT-ZT18-1


title: Bmal1-HepWT-ZT14-2

value: zeitgeber time zt14


title: LFS_MB_1R [450K]

type: genomic

description:
Bisulfite treated genomic DNA, LFS_MB_1R cancer cell line
3998523031_R02C01 Beta

hyb_protocol: Standard Illumina Protocol Illumina

scan_protocol: Illumina iScan System Illumina iScan System

data_processing:
Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.
Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

molecule: genomic DNA

source_name: Medulloblastoma 1st relapse from Li-Fraumeni syndrome patient 1

label_protocol:
Standard Illumina Protocol
Illumina

growth_protocol:
LFS_MB_P, LFS_MB_1R, LFS_MB_2R and BT084 were short-term spheroid cultures derived from human tumor cells from patient-derived xenograft models. All experiments were performed with mycoplasma-free cells. Spheroid cultures from patient-derived xenograft models were prepared by homogenizing the freshly isolated tumors from mice brains by pipetting in NeuroCult™ NS-A Proliferation Kit (STEMCELL Technologies, 05751). Homogenized tissue is then filtered to get single cell suspension. Cells were then centrifuged at 1000 rpm for 5 minutes and pellet was resuspended to get 0.5 million cells per 10 ml growth medium. Growth medium was comprised of 46.75 ml Neurobasal™-A Medium (Invitrogen, 10888022) with 46.75 ml DMEM/F-12 (Invitrogen, 11330057), 1 ml MEM Non-Essential Amino Acids Solution (100X) (Invitrogen, 11140050), 1 ml Sodium Pyruvate (100 mM) (Invitrogen, 11360070), 2.5 ml Hepes buffer (1M) (Invitrogen, 15630080), 1 ml GlutaMAX™ Supplement (Invitrogen, 35050061), 1 ml Penicillin-Streptomycin (Invitrogen, 15140122), 2 ml B-27™ Supplement minus vitamin A (50X) (Invitrogen, 12587001), 40 µl Heparin (50 mg/ml stock) (Sigma, H3149-10KU), 20ng/ml Human FGF rec 154aa (Peprotech, GMP100-18 B), 10 ng/ml EGF (Sigma, E 4127) and 100 µl LIF(Millipore, LIF1010). Spheroids were cultured for 3 weeks in 25 cm2 flask (Greiner, 690195) and passaged by trypsinization with 0.05% Trypsin/EDTA once a week. All adherent cells were passaged by trypsinization with 0.25% Trypsin/EDTA. Spheroids were passaged by trypsinization with 0.05% Trypsin/EDTA.     Formulations of culture media for cell lines used in this study were the following:  For UWB1.289 and UWB1.289+BRCA1 cells, 48.5 % RPMI Medium 1640 (Gibco, 21875-034) and 48.5% MEGM media (Lonza, CC-3150) (Supplements were added provided with the kit) with 3% FCS. For UWB1.289+BRCA1, G418 was added to final concentration of 200 µg/ml. For MDA-MB-436 cells, 1X DMEM high glucose (Gibco, 41965-039) with 10% FCS. For KHOS-240S cells, 1X DMEM high glucose (Gibco, 41965-039) with 10% FCS, 1% L-glutamine and 1% MEM Non-essential amino acids (MEM NEAA) (Gibco, 11140-050). For SaOS-2 cells, Roti®-CELL McCoy's 5A (Carl Roth, 9111.1) with 15 % FCS and 1% L-glutamine. For SJSA-1 cells, RPMI Medium 1640 (Gibco, 21875-034) with 10% FCS and 1% L-glutamine. For HD-N33 cells, RPMI Medium 1640 (Gibco, 21875-034) with 10 % FCS and 1% L-glutamine.
NA

extract_protocol:
Extraction of high molecular weight DNA from frozen tumor samples was carried out using Promega ReliaPrep™ gDNA Tissue Miniprep System
Extraction of high molecular weight DNA from frozen tumor samples was carried out using a Qiagen Blood & Cell Culture DNA Midi Kit (Qiagen, Hilden, Germany) after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany).

tag: cell line

tag: tumor

value: Medulloblastoma


title: Bmal1-HepWT-ZT14-1

value: liver

value: Alb::Cre_0/0, Bmal1_fl/fl


title: RCMB18_model_Romidepsin_IC20_and_BGB290_IC20_24hours_double_treatment


title: HD-N33 [450K]

description:
Bisulfite treated genomic DNA, HD-N33 cancer cell line
3999543052_R01C02 Beta

source_name: Neuroblastoma

value: Cancer Cell line


title: Bmal1-HepWT-ZT10-2

value: night restricted feeding

value: zeitgeber time zt10

value: 8-12 weeks


title: Bmal1-HepKO-ZT6-2

value: Alb::Cre_+/0, Bmal1_fl/fl

value: zeitgeber time zt6


title: MB145 (BT084) [450K]

description:
Bisulfite treated genomic DNA, MB145 (BT084) cancer cell line
8622007132_R03C01 Beta

source_name: Medulloblastoma from Li-Fraumeni syndrome patient

value: Patient derived xenograft spheroids


title: Bmal1-HepWT-ZT10-1


title: Bmal1-HepKO-ZT6-1


title: Bmal1-HepKO-ZT14-2


title: Bmal1-HepKO-ZT18-1


title: Bmal1-HepKO-ZT14-1


title: Bmal1-HepKO-ZT22-1

value: zeitgeber time zt22


title: Bmal1-HepKO-ZT22-2


title: Bmal1-HepKO-ZT18-2


title: Bmal1-HepKO-ZT2-2

value: zeitgeber time zt2


title: Bmal1-HepKO-ZT2-1


title: Sample_BmalKO_ob_94_liver_ZT12

extract_protocol:
Liver RNAs were extracted as previously described (Gachon et al, 2006) with classical methods using guanidium thiocyanate lysis buffer. Muscle and epididymal white adipose tissue were disrupted and extracted using the tissue lyser II (Qiagen) and the miRNeasy Mini Kit (Qiagen) following the manufacturer's protocol, repectively.
The RNA were quantified with Ribogreen (Life Technologies) and quality assessed on a Fragment Analyzer (Advances Analytical). Sequencing libraries were prepared from 250 ng total RNA using the TruSeq Stranded RNA  Sample Prep Kit v2 (Illumina) with the Ribo-Zero Gold depletion set. The procedure was automated on a Sciclone NGS Workstation (Perkin Elmer). The manufacturer’s protocol was followed, except for the PCR amplification step. The latter was run for 12 cycles with the KAPA HiFi HotStart ReadyMix (Kapa BioSystems). This optimal PCR cycle number has been evaluated using the Cycler Correction Factor method as described previously (Atger et al., PNAS, 2015). Purified libraries were quantified with Picogreen (Life Technologies) and the size pattern was controlled with the DNA High Sensitivity Reagent kit on a LabChip GX (Perkin Elmer). Libraries were then pooled by 18 and each pool was clustered at a concentration of 10 pmol on 4 lanes of  two High Output (8-lane) v3 flow cell (Illumina). Sequencing was performed for 2 x 100 cycles on a Illumina HiSeq 2500 following Illumina’s recommendations.

tag: genotype bmal1

value: BmalKO

tag: genotype leptin

value: ob

value: AL

tag: zeitgeber time

tag: animal id

value: 20 weeks


title: Sample_BmalKO_ob_98_liver_ZT12


title: Bmal1-HepKO-ZT10-2

tag: genotype


title: LFS_MB_P_model_Romidepsin_IC20_and_BGB290_IC20_24hours_double_treatment

value: LFS_MB_P spheroid

value: BGB290 IC20 and romidepsin IC20 for 24hours


title: LFS_MB_P [450K]

description:
Bisulfite treated genomic DNA, LFS_MB_P cancer cell line
10006823133_R01C01 Beta

source_name: Medulloblastoma from Li-Fraumeni syndrome patient 1

value: Medulloblastoma


title: Bmal1-HepKO-ZT10-1

tag: tissue

value: liver


title: Sample_BmalKO_ob_28_liver_ZT12


title: Sample_BmalKO_ob_24_liver_ZT12


title: Sample_BmalKO_ob_26_liver_ZT12


title: Sample_BmalKO_ob_16_liver_ZT12


title: Sample_BmalWT_wt_89_liver_ZT12

value: BmalWT

value: wt


title: Sample_BmalWT_ob_38_liver_ZT12


title: Sample_BmalWT_ob_13_liver_ZT12


title: Sample_BmalWT_ob_95_liver_ZT12


title: Sample_BmalKO_wt_54_liver_ZT12


title: Sample_BmalKO_wt_25_liver_ZT12


title: Sample_BmalWT_wt_19_liver_ZT12


title: Sample_BmalWT_wt_17_liver_ZT12


title: Sample_BmalKO_wt_60_liver_ZT12


title: Sample_BmalWT_ob_85_liver_ZT12


title: Sample_BmalWT_ob_99_liver_ZT12


title: Sample_BmalWT_wt_14_liver_ZT12


title: Sample_BmalKO_wt_34_liver_ZT12


title: Sample_BmalKO_wt_59_liver_ZT12


title: Sample_BmalKO_wt_51_liver_ZT12


title: Sample_BmalWT_wt_90_liver_ZT12


title: Sample_BmalWT_wt_78_liver_ZT12


title: Sample_BmalKO_ob_235_Muscle_ZT12

value: Muscle


title: UWB1.289 [EPIC]

description:
Bisulfite treated genomic DNA, UWB1.289 cancer cell line
203048410044_R04C01 Beta

source_name: Ovarian carcinoma

value: Cancer Cell line


title: Sample_BmalKO_ob_450_Muscle_ZT12


title: Sample_BmalKO_ob_663_Muscle_ZT12


title: Sample_BmalWT_ob_758_Muscle_ZT12


title: Sample_BmalKO_ob_344_Muscle_ZT12


title: Sample_BmalKO_wt_749_Muscle_ZT12


title: Sample_BmalWT_ob_270_Muscle_ZT12


title: Sample_BmalKO_wt_34_Muscle_ZT12


title: Sample_BmalKO_wt_453_Muscle_ZT12


title: Sample_BmalKO_ob_98_Muscle_ZT12


title: Sample_BmalWT_wt_470_Muscle_ZT12


title: Sample_BmalWT_wt_478_Muscle_ZT12


title: Sample_BmalWT_wt_467_Muscle_ZT12


title: Sample_BmalWT_ob_681_Muscle_ZT12


title: Sample_BmalWT_wt_459_Muscle_ZT12


title: Sample_BmalWT_ob_465_Muscle_ZT12


title: Sample_BmalWT_ob_272_Muscle_ZT12


title: Sample_BmalWT_ob_451_Muscle_ZT12


title: Sample_BmalKO_wt_374_Muscle_ZT12


title: SJSA1 [EPIC]

description:
Bisulfite treated genomic DNA, SJSA1 cancer cell line
203049640078_R08C01 Beta

source_name: Osteosarcoma


title: MDA-MB-436 [EPIC]

description:
Bisulfite treated genomic DNA, MDA-MB-436 cancer cell line
203048410044_R08C01 Beta

source_name: Breast carcinoma


title: Saos_2 [EPIC]

description:
Bisulfite treated genomic DNA, Saos_2 cancer cell line
203048410044_R06C01 Beta


title: Sample_BmalKO_wt_71_Muscle_ZT12


title: UWB1.289+BRCA1 [EPIC]

description:
Bisulfite treated genomic DNA, UWB1.289+BRCA1 cancer cell line
203048410044_R05C01 Beta


title: Sample_BmalWT_wt_373_Muscle_ZT12


title: Sample_BmalKO_wt_159_Muscle_ZT12


title: KHOS-240S [EPIC]

description:
Bisulfite treated genomic DNA, KHOS-240S cancer cell line
203048410044_R07C01 Beta


title: Sample_BmalWT_wt_404_Muscle_ZT12


title: Sample_BmalKO_ob_98_WAT_ZT12

value: WAT


title: LFS_MB_2R [EPIC]

description:
Bisulfite treated genomic DNA, LFS_MB_2R cancer cell line
200889820015_R08C01 Beta

source_name: Medulloblastoma 2nd relapse from Li-Fraumeni syndrome patient 1


title: Sample_BmalKO_ob_344_WAT_ZT12


title: Sample_BmalKO_ob_26_WAT_ZT12


title: Sample_BmalKO_ob_759_WAT_ZT12


title: Sample_BmalKO_ob_16_WAT_ZT12


title: Sample_BmalKO_ob_28_WAT_ZT12


title: Sample_BmalKO_wt_54_WAT_ZT12


title: Sample_BmalKO_wt_34_WAT_ZT12


title: Sample_BmalWT_ob_85_WAT_ZT12


title: Sample_BmalKO_wt_51_WAT_ZT12


title: Sample_BmalWT_wt_404_WAT_ZT12


title: Sample_BmalKO_wt_60_WAT_ZT12


title: Sample_BmalKO_wt_25_WAT_ZT12


title: Sample_BmalWT_ob_38_WAT_ZT12


title: Sample_BmalWT_wt_17_WAT_ZT12


title: Sample_BmalWT_wt_470_WAT_ZT12


title: Sample_BmalWT_ob_99_WAT_ZT12


title: Sample_BmalWT_wt_467_WAT_ZT12


title: Sample_BmalWT_wt_373_WAT_ZT12


title: Sample_BmalWT_wt_19_WAT_ZT12


title: Sample_BmalKO_wt_59_WAT_ZT12


title: P4 X797

status: Public on Jan 20 2022

city: Hangzhou

first: Yishan

last: Chen

address: #866 Yuhangtang Road

country: China

institute: Zhejiang University

data_processing:
Illumina Casava1.7 software used for basecalling.
alignment was conducted with Tophat
The final gene expression data was normalized using Cuffnorm and represented as counts
Genome_build: mm10
Supplementary_files_format_and_content: Csv files include raw counts of each gene from each sample

source_name: articular cartilage

growth_protocol: Mouse chondrocytes were isolated from knee cartilage of C57Bl/6 mice (postnatal 0-4 days) following the previously published method. The digested cells was resuspended and culture with DMEM/F12 medium (Gibico), supplemented with 10% fetal bovine serum, at 37 ¡ãC with 5% CO2. P0 chondrocytes represents the primary chondrocytes having been cultured in vitro less than 24 hours (h). For dedifferentiation model, chondrocytes were passaged after a doubling of cell quantity (seeding density: 24000/cm2; collecting density: 48000/cm2).

extract_protocol:
Single cells were lysated, preamplified and library prepared according C1-HT IFC protocol of Fluidigm Corporation.
Single cells were lysated, preamplified and library prepared according C1-HT IFC protocol of Fluidigm Corporation.

treatment_protocol: We captured 634 in vitro expanded mouse chondrocytes of passage 0, 2, 4 and 8 (19 p0, 369 p2, 187 p4, 59 p8 ) to conduct single cell RNA sequencing and analysis

value: cartilage

tag: passage

value: passage 4


title: P4 X796


title: P4 X798


title: P4 X792


title: P4 X800


title: P4 X793


title: P4 X794


title: P4 X791


title: Sample_BmalWT_ob_465_WAT_ZT12


title: P4 X786


title: P4 X799


title: P4 X789


title: P8 X781

value: passage 8


title: P4 X773


title: P4 X769


title: P4 X770


title: P8 X785


title: P4 X768


title: P8 X765


title: P4 X777


title: P8 X763


title: P4 X762


title: P4 X766


title: P8 X795


title: P8 X759


title: P4 X760


title: P4 X754


title: P4 X761


title: P4 X787


title: P8 X755


title: P4 X771


title: P4 X778


title: P4 X746


title: P4 X747


title: P8 X748


title: P4 X767


title: P4 X745


title: P4 X739


title: P4 X742


title: P4 X764


title: P4 X743


title: P4 X757


title: P4 X734


title: P4 X732


title: P4 X731


title: P4 X727


title: P4 X744


title: P4 X729


title: P4 X740


title: P4 X725


title: P8 X724


title: P4 X726


title: P4 X735


title: P8 X752


title: P8 X722


title: P4 X728


title: P4 X733


title: P4 X730


title: P4 X720


title: P4 X751


title: P4 X741


title: P4 X750


title: P4 X723


title: P4 X721


title: P4 X714


title: P4 X709


title: P4 X718


title: P8 X717


title: P8 X715


title: P8 X710


title: P4 X712


title: P4 X705


title: P8 X703


title: P4 X701


title: P4 X702


title: P4 X685


title: P8 X681


title: P4 X716


title: P8 X680


title: P8 X690


title: P4 X689


title: P4 X678


title: P8 X711


title: P8 X688


title: P8 X687


title: P4 X669


title: P4 X662


title: P4 X686


title: P4 X683


title: P4 X661


title: P8 X684


title: P8 X679


title: P4 X672


title: P4 X682


title: P4 X653


title: P4 X671


title: P4 X706


title: P4 X651


title: P8 X670


title: P4 X656


title: P8 X646


title: P4 X655


title: P8 X648


title: P4 X647


title: P4 X645


title: P8 X644


title: P4 X628


title: P4 X623


title: P4 X622


title: P4 X643


title: P8 X642


title: P8 X640


title: P4 X638


title: P4 X606


title: P4 X668


title: P4 X637


title: P4 X636


title: P4 X639


title: P4 X602


title: P4 X601


title: P4 X633


title: P4 X631


title: P4 X629


title: P8 X620


title: P4 X650


title: P4 X619


title: P4 X599


title: P8 X618


title: P4 X617


title: P4 X615


title: P4 X594


title: P4 X588


title: P8 X605


title: P4 X603


title: P4 X587


title: P4 X634


title: P4 X585


title: P4 X581


title: P8 X632


title: P4 X600


title: P4 X597


title: P4 X598


title: P4 X596


title: P8 X580


title: P4 X590


title: P4 X589


title: P4 X591


title: P4 X592


title: P4 X595


title: P8 X573


title: P4 X569


title: P4 X593


title: P4 X586


title: P4 X561


title: P8 X568


title: P4 X576


title: P4 X579


title: P4 X556


title: P4 X583


title: P8 X557


title: P8 X553


title: P8 X554


title: P8 X555


title: P4 X552


title: P4 X548


title: P4 X546


title: P4 X538


title: P8 X533


title: P4 X549


title: P4 X547


title: P4 X526


title: P4 X544


title: P8 X529


title: P8 X560


title: P4 X562


title: P4 X539


title: P4 X540


title: P4 X551


title: P4 X527


title: P4 X530


title: P4 X532


title: P4 X528


title: P4 X524


title: P4 X523


title: P4 X522


title: P4 X521


title: P8 X520


title: P4 X518


title: P4 X513


title: P4 X516


title: P4 X504


title: P8 X510


title: P4 X509


title: P8 X502


title: P8 X498


title: P8 X493


title: P4 X512


title: P4 X488


title: P4 X481


title: P4 X489


title: P8 X483


title: P4 X482


title: P2 X480

value: passage 2


title: P8 X486


title: P4 X519


title: P2 X477


title: P8 X487


title: P8 X503


title: P4 X491


title: P8 X517


title: P4 X484


title: P2 X476


title: P2 X475


title: P4 X485


title: P2 X479


title: P2 X478


title: P2 X474


title: P2 X473


title: P2 X472


title: P2 X466


title: P2 X467


title: P2 X463


title: P2 X469


title: P2 X468


title: P2 X465


title: P2 X455


title: P2 X459


title: P2 X452


title: P2 X456


title: P2 X461


title: P2 X457


title: P2 X458


title: P2 X462


title: P2 X460


title: P2 X453


title: P2 X451


title: P2 X454


title: P0 X450

value: passage 0


title: P2 X447


title: P2 X470


title: P2 X449


title: P2 X442


title: P2 X443


title: P2 X448


title: P2 X446


title: P2 X445


title: P2 X444


title: P2 X464


title: P2 X441


title: P2 X440


title: P2 X437


title: P2 X438


title: P2 X439


title: P2 X430


title: P2 X435


title: P2 X432


title: P2 X426


title: P2 X434


title: P2 X418


title: P2 X420


title: P2 X433


title: P2 X429


title: P2 X431


title: P2 X424


title: P2 X427


title: P2 X436


title: P2 X421


title: P2 X423


title: P0 X417


title: P2 X419


title: P2 X422


title: P2 X416


title: P0 X413


title: P0 X415


title: P0 X409


title: P2 X412


title: P2 X411


title: P2 X410


title: P2 X425


title: P2 X408


title: P2 X407


title: P2 X406


title: P2 X405


title: P2 X414


title: P2 X402


title: P2 X404


title: P2 X399


title: P2 X401


title: P2 X392


title: P2 X395


title: P2 X396


title: P2 X394


title: P2 X389


title: P2 X391


title: P2 X393


title: P2 X400


title: P2 X397


title: P2 X384


title: P2 X388


title: P2 X381


title: P2 X383


title: P2 X387


title: P2 X390


title: P2 X386


title: P0 X380


title: P2 X385


title: P2 X379


title: P2 X378


title: P2 X377


title: P2 X375


title: P2 X398


title: P2 X374


title: P2 X373


title: P2 X370


title: P2 X382


title: P2 X367


title: P2 X365


title: P2 X366


title: P2 X364


title: P2 X360


title: P2 X358


title: P2 X369


title: P2 X368


title: P2 X362


title: P2 X361


title: P2 X354


title: P2 X356


title: P2 X353


title: P2 X352


title: P2 X363


title: P2 X357


title: P2 X351


title: P2 X350


title: P2 X355


title: P2 X372


title: P2 X348


title: P2 X371


title: P2 X347


title: P2 X346


title: P2 X359


title: P2 X344


title: P2 X343


title: P2 X342


title: P2 X341


title: P2 X340


title: P2 X339


title: P2 X334


title: P2 X335


title: P2 X349


title: P2 X336


title: P2 X338


title: P2 X331


title: P2 X325


title: P2 X330


title: P2 X332


title: P2 X327


title: P2 X324


title: P2 X323


title: P2 X326


title: P2 X345


title: P2 X322


title: P2 X321


title: P2 X320


title: P2 X319


title: P2 X317


title: P2 X318


title: P2 X314


title: P2 X333


title: P2 X316


title: P2 X329


title: P2 X337


title: P2 X328


title: P2 X312


title: P2 X311


title: P2 X313


title: P2 X308


title: P2 X310


title: P2 X303


title: P2 X305


title: P2 X307


title: P2 X304


title: P2 X301


title: P2 X299


title: P2 X296


title: P2 X297


title: P2 X295


title: P2 X306


title: P2 X298


title: P2 X300


title: P2 X294


title: P0 X315


title: P2 X293


title: P2 X292


title: P2 X291


title: P2 X286


title: P0 X290


title: P2 X287


title: P2 X284


title: P2 X289


title: P0 X282


title: P2 X309


title: P2 X283


title: P4 X272


title: P4 X271


title: P8 X247


title: P4 X249


title: P8 X262


title: P4 X263


title: P8 X274


title: P4 X251


title: P4 X248


title: P4 X244


title: P4 X241


title: P4 X246


title: P2 X239


title: P4 X242


title: P2 X240


title: P4 X245


title: P2 X236


title: P2 X238


title: P2 X235


title: P0 X237


title: P4 X279


title: P2 X234


title: P2 X233


title: P2 X232


title: P2 X285


title: P2 X230


title: P2 X231


title: P2 X228


title: P2 X229


title: P4 X264


title: P4 X243


title: P2 X223


title: P2 X226


title: P2 X224


title: P2 X225


title: P2 X222


title: P2 X219


title: P2 X220


title: P2 X217


title: P2 X215


title: P2 X227


title: P2 X212


title: P0 X218


title: P2 X214


title: P2 X213


title: P2 X216


title: P2 X206


title: P2 X208


title: P2 X205


title: P2 X200


title: P2 X209


title: P0 X202


title: P2 X204


title: P2 X207


title: P2 X201


title: P2 X203


title: P2 X199


title: P2 X198


title: P2 X197


title: P2 X193


title: P2 X192


title: P2 X195


title: P2 X194


title: P2 X221


title: P2 X189


title: P2 X184


title: P2 X186


title: P2 X190


title: P2 X183


title: P2 X188


title: P2 X185


title: P2 X211


title: P2 X177


title: P2 X179


title: P2 X178


title: P2 X170


title: P2 X174


title: P2 X169


title: P2 X181


title: P2 X196


title: P2 X168


title: P2 X180


title: P2 X182


title: P2 X163


title: P2 X162


title: P2 X158


title: P2 X175


title: P2 X160


title: P2 X172


title: P2 X191


title: P2 X176


title: P0 X171


title: P2 X166


title: P2 X187


title: P2 X153


title: P2 X167


title: P2 X164


title: P0 X165


title: P2 X150


title: P2 X152


title: P2 X157


title: P2 X154


title: P2 X146


title: P2 X148


title: P2 X143


title: P2 X142


title: P2 X140


title: P2 X147


title: P2 X159


title: P2 X136


title: P2 X173


title: P2 X139


title: P2 X138


title: P2 X155


title: P2 X151


title: P2 X132


title: P2 X135


title: P2 X130


title: P2 X129


title: P2 X125


title: P2 X134


title: P2 X137


title: P2 X141


title: P2 X121


title: P2 X145


title: P2 X122


title: P4 X120


title: P0 X133


title: P8 X117


title: P2 X131


title: P2 X128


title: P8 X114


title: P2 X144


title: P4 X118


title: P2 X126


title: P4 X108


title: P4 X106


title: P4 X110


title: P4 X119


title: P2 X123


title: P4 X87


title: P4 X103


title: P4 X90


title: P4 X85


title: P2 X124


title: P4 X101


title: P4 X104


title: P8 X84


title: P0 X127


title: P2 X77


title: P4 X111


title: P2 X76


title: P2 X78


title: P2 X75


title: P4 X83


title: P4 X86


title: P4 X81


title: P2 X79


title: P2 X72


title: P0 X73


title: P2 X71


title: P2 X67


title: P2 X74


title: P2 X68


title: P2 X70


title: P2 X69


title: P2 X66


title: P2 X60


title: P2 X63


title: P2 X58


title: P2 X62


title: P2 X64


title: P2 X65


title: P2 X51


title: P2 X50


title: P2 X61


title: P2 X47


title: P2 X56


title: P4 X82


title: P2 X57


title: P2 X59


title: P2 X54


title: P2 X53


title: P2 X43


title: P2 X52


title: P2 X48


title: P2 X44


title: P2 X46


title: P2 X55


title: P2 X42


title: P2 X38


title: P2 X49


title: P2 X40


title: P2 X37


title: P2 X41


title: P2 X36


title: P2 X33


title: P2 X30


title: P2 X32


title: P2 X45


title: P2 X34


title: P2 X31


title: P2 X29


title: P2 X28


title: P2 X27


title: P2 X25


title: P2 X21


title: P2 X26


title: P2 X23


title: P2 X39


title: P2 X24


title: P2 X20


title: P2 X22


title: P2 X19


title: P2 X15


title: P2 X16


title: P2 X17


title: P2 X18


title: P0 X35


title: P2 X13


title: P2 X10


title: P2 X8


title: P2 X7


title: P2 X9


title: P0 X12


title: P2 X6


title: P2 X4


title: P2 X1


title: Single MII oocyte replicate 12

status: Public on Dec 22 2021

city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

country: United Kingdom

institute: University of Cambridge

description:
SLX-17237.D712rna_D502rna.H7FMTDRXX.s
Single MII oocyte replicate 12 from patient 4226ID

data_processing:
Sequencing adapter sequences were removed by Cutadapt (1.7.1)
Mapping of the trimmed reads was by STAR (2.5.0a)
Gene-level counts were then performed using ht-seq-count on the reverse strand(0.6.1p1)
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw gene-level counts in tab-delimited text format

source_name: Single-cell embryo

extract_protocol:
Single-cell oocytes/embryos were thawed and directly lysed using Takara Clontech Smartseq lysis buffer with RNAse inhibitor
Whole transcriptome amplification and library preparation was performed using Takara Clontech Smarter Stranded Total RNA-Seq Kit Pico Input version 2

treatment_protocol: Patients underwent ovarian stimulation according to guidelines of each clinic, where protocols included agonist luteal phase and antagonist suppression.  On the day of mII oocyte retrieval (day 0), oocytes were either cryopreserved by a slow freeze method using propanediol (PROH)  or used to produce embryos by in vitro fertilization or ICSI.  Immediately after fertilization assessment, morphologically normal bipronuclear (2pn) zygotes were cryopreserved using dimethylsulfoxide and stored under liquid nitrogen as appropriate.

tag: patient code

value: Single-cell embryo

value: MII

tag: replicate

tag: barcode


title: P2 X3

tag: strain


title: P2 X5


title: P2 X2


title: Single 2PN embryo replicate 11

description:
SLX-17237.D711rna_D501rna.H7FMTDRXX.s
Single 2PN embryo replicate 11 from patient 88


title: Single MII oocyte replicate 9

description:
SLX-17237.D709rna_D502rna.H7FMTDRXX.s
Single MII oocyte replicate 9 from patient 4265


title: Single 2PN embryo replicate 10

description:
SLX-17237.D710rna_D501rna.H7FMTDRXX.s
Single 2PN embryo replicate 10 from patient 88


title: Single 2PN embryo replicate 12

description:
SLX-17237.D712rna_D501rna.H7FMTDRXX.s
Single 2PN embryo replicate 12 from patient 122


title: Single MII oocyte replicate 11

description:
SLX-17237.D711rna_D502rna.H7FMTDRXX.s
Single MII oocyte replicate 11 from patient 11524


title: Single MII oocyte replicate 10

description:
SLX-17237.D710rna_D502rna.H7FMTDRXX.s
Single MII oocyte replicate 10 from patient 11524


title: Single 2PN embryo replicate 9

description:
SLX-17237.D709rna_D501rna.H7FMTDRXX.s
Single 2PN embryo replicate 9 from patient 130


title: Single MII oocyte replicate 8

description:
SLX-17237.D708rna_D502rna.H7FMTDRXX.s
Single MII oocyte replicate 8 from patient 4265


title: P2 X11


title: Single 2PN embryo replicate 6

description:
SLX-17237.D706rna_D501rna.H7FMTDRXX.s
Single 2PN embryo replicate 6 from patient 70


title: P2 X14


title: Single MII oocyte replicate 6

description:
SLX-17237.D705rna_D502rna.H7FMTDRXX.s
Single MII oocyte replicate 6 from patient 010319S


title: Single 2PN embryo replicate 7

description:
SLX-17237.D707rna_D501rna.H7FMTDRXX.s
Single 2PN embryo replicate 7 from patient 130


title: Single MII oocyte replicate 7

description:
SLX-17237.D707rna_D502rna.H7FMTDRXX.s
Single MII oocyte replicate 7 from patient 4210ID


title: Single 2PN embryo replicate 5

description:
SLX-17237.D704rna_D501rna.H7FMTDRXX.s
Single 2PN embryo replicate 5 from patient Z306-02129


title: Single MII oocyte replicate 5

description:
SLX-17237.D704rna_D502rna.H7FMTDRXX.s
Single MII oocyte replicate 5 from patient 010319S


title: Single 2PN embryo replicate 4

description:
SLX-17237.D703rna_D501rna.H7FMTDRXX.s
Single 2PN embryo replicate 4 from patient H26


title: Single MII oocyte replicate 4

description:
SLX-17237.D703rna_D503rna.H7FMTDRXX.s
Single MII oocyte replicate 4 from patient 4273ID


title: Single 2PN embryo replicate 3

description:
SLX-17237.D702rna_D501rna.H7FMTDRXX.s
Single 2PN embryo replicate 3 from patient H26


title: Single MII oocyte replicate 1

description:
SLX-17237.D701rna_D503rna.H7FMTDRXX.s
Single MII oocyte replicate 1 from patient 4226ID


title: HCT116 cells, NAA40 KnockDown replicate 3

status: Public on Nov 15 2021

city: Cologne

first: Peter

last: Tessarz

state: Nordrhein-Westfalen

address: Joseph-Stelzman-Str 9b

institute: Max Planck Institute

data_processing:
fastq reads were mapped using STAR to hg38 genome and ERCC sequences with Ensembl annotation GRCm38.91
The count matrix generated by featurecounts was analysed for differential expression using limma-voom bioconductor R package
Genome_build: hg38
Supplementary_files_format_and_content: sample (columns) and genes (rows) -wise read count table

source_name: cell culture

growth_protocol: HCT116 CNTRL and KD cells were cultured in McCoy’s 5a medium (Gibco, Invitrogen) supplemented with 10% fetal bovine serum (Gibco, Invitrogen) and 1% penicillin/streptomycin (Gibco, Invitrogen). Cells were grown in a humidified atmosphere at 37oC containing 5% CO2

extract_protocol:
RNA was isolated using Direct-zol and RNA MiniPrep kit from Zymoresearch, according to manufacturer's instructions.
RNA-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CTRL and KD cells were cultured in the presence or absence of 1μg/ml doxycycline for 96 hrs

value: colon cancer cell line HCT116

value: NAA40 KnockDown

value: no doxycycline


title: Single 2PN embryo replicate 8

description:
SLX-17237.D708rna_D501rna.H7FMTDRXX.s
Single 2PN embryo replicate 8 from patient 130


title: Single 2PN embryo replicate 1

description:
SLX-17237.D701rna_D501rna.H7FMTDRXX.s
Single 2PN embryo replicate 1 from patient H26


title: HCT116 cells, NAA40 KnockDown replicate 4


title: HCT116 cells, NAA40 KnockDown replicate 1


title: HCT116 cells, scramble (SCR) control replicate 4

value: SCR control


title: HCT116 cells, doxycycline treated NAA40 KnockDown replicate 3

value: doxycycline


title: HCT116 cells, doxycycline treated NAA40 KnockDown replicate 2


title: HCT116 cells, doxycycline treated NAA40 KnockDown replicate 1


title: HCT116 cells, scramble (SCR) control replicate 3


title: HCT116 cells, scramble (SCR) control replicate 1


title: HCT116 cells, doxycycline treated scramble (SCR) control replicate 4


title: HCT116 cells, doxycycline treated scramble (SCR) control replicate 2


title: MAYO_BP_23

status: Public on Nov 12 2021

city: Dublin

first: Leonie

last: Young

state: Dublin

address: 31A York Street

department: Surgery

country: Ireland

institute: RCSI

data_processing:
Salmon (v.0.91) was used to perform quasi-mapping of sequencing reads, with seqBias and gcBias corrections enabled, using a 31bp k-mer index of the GRCh38.p10 (GENCODE v.27) human reference transcripts, to estimate transcript abundance for each sample
Tximport package was used to import transcript abundance estimates from quant.sf files, generated by Salmon read mapping into R statistical programming environment for gene expression quantification. Transcript abundance estimates were collapsed to gene level gene expression counts. TXI data objects for MAYO and PITT-RCSI RNA-Seq cohort, containing unprocessed Salmon read counts, transcript per million (TPM) and gene length values were combined for subsequent downstream analysis.
Genes with little to no expression across all 90 samples were filtered if gene TPM < 0.5 in at least 10% of all samples (N=90)
Filtered gene level counts were normalized with edgeR calcNormFactors() and cpm() function, where counts per million (CPM): CPM = C * 106/N (counts (C) scaled by the library depth in million units). A log2 transformation was applied to CPM: log2(CPM +1), where 1 is a pseudocount added to prevent negative value counts. Filtered log2 CPM and TPM genes were annotated using biomaRt R package to identify protein coding genes using the ENSEMBL GRCh38 p.10 database.
In order to correct for between RNA-Seq cohort (MAYO, PITT-RCSI) batch driven effect, filtered protein coding gene expression counts were used as input to svaseq R package for batch effect assessment. A multiple linear regression model was fit for each surrogate variable (SV), with the following independent predictors: sequencing batch ID [1,5], disease status (primary breast (P) / brain metastases (M)), estrogen receptor (ER) IHC status (ER+/ER-) and primary tumor histological subtype (DCIS, IDC, ILC, Mixed ILC/IDC). A linear model fitted using SV1 was found to be significantly associated with sequencing batch (P < 0.05; R2 ~0.70).   As such, in order to correct for between RNA-Seq cohort (MAYO, PITT-RCSI) batch driven effect, removeBatchEffect() function in LIMMA package in R, was used with SV1, to adjust gene expression values to account for mean shifts in expression driven by the batch driven effect.
Genome_build: GRCh38.p10 (GENCODE v.27)
Supplementary_files_format_and_content: .xlsx excel spread sheet containing batch corrected log2 TMM normalized CPM proteing coding gene expression values for all 90 samples

source_name: primary breast tumor

extract_protocol: 100 ng of total RNA and a TruSeq Stranded Total RNA (Degraded RNA) v2 RNA Exome Library and TS RNA Access capture protocol (Illumina)

tag: cohort

value: MAYO

tag: patient id

tag: disease state

value: breast cancer

value: primary breast tumor


title: MAYO_BP_24


title: MAYO_BM_23

source_name: brain metastatic tumor

value: brain metastatic tumor


title: Single MII oocyte replicate 3

description:
SLX-17237.D702rna_D503rna.H7FMTDRXX.s
Single MII oocyte replicate 3 from patient 4273ID

tag: cell type


title: HCT116 cells, scramble (SCR) control replicate 2

tag: cell line

tag: treatment


title: HCT116 cells, doxycycline treated scramble (SCR) control replicate 3


title: MAYO_BM_24


title: HCT116 cells, doxycycline treated scramble (SCR) control replicate 1


title: MAYO_BM_20


title: MAYO_BM_22


title: Single MII oocyte replicate 2

description:
SLX-17237.D702rna_D502rna.H7FMTDRXX.s
Single MII oocyte replicate 2 from patient 010319M


title: MAYO_BM_21


title: MAYO_BP_22


title: HCT116 cells, NAA40 KnockDown replicate 2


title: MAYO_BP_21


title: HCT116 cells, doxycycline treated NAA40 KnockDown replicate 4


title: Single 2PN embryo replicate 2

description:
SLX-17237.D701rna_D502rna.H7FMTDRXX.s
Single 2PN embryo replicate 2 from patient 122


title: MAYO_BM_19


title: MAYO_BP_19


title: MAYO_BP_20


title: BCL6 KO_2

status: Public on Nov 05 2021

first: Thomas

last: Ciucci

data_processing:
Basecalling was performed using RTA 1.18.64
Sequencing reads were demultiplexed using Bcl2fastq 1.8.4
Raw RNAseq fastq reads were trimmed with Trimmomatic and aligned to mouse genome using STAR
Gene-assignment and count of RNA reads were performed with Htseq
Genome_build: mm10
Supplementary_files_format_and_content: FPM normalization was performed with the FPM function of the DEseq2 package

source_name: BCL6_7 dpi_GP66+ CD4+ T cells

extract_protocol:
RNA was isolated using the RNeasy Plus Micro kit (Qiagen)
SMARTer Ultra Low Input reagent (Takara) and Nextera XT DNA (Illumina)
Libraries were pooled and  sequenced with paired-end reads of 150bp on a Illumina HiSeq 2500 sequencer (Illumina) to reach 70 million read pairs per sample

tag: strain background

tag: genotype/variation

tag: mouse origin

value: Ox40cre+ Bcl6flox/flox RosaYFP+

value: Spleen

value: GP66:I-Ab+ CD4+


title: BCL6 BLIMP1 DKO_2

source_name: DKO_7 dpi_GP66+ CD4+ T cells

value: BCL6-/- BLIMP1-/-

value: Ox40cre+ Bcl6flox/flox Blimp1flox/flox RosaYFP+


title: WT_2

source_name: WT_7 dpi_GP66+ CD4+ T cells

value: WT

value: Ox40cre+ RosaYFP+


title: BLIMP1 KO_2

source_name: BLIMP1_7 dpi_GP66+ CD4+ T cells

value: Ox40cre+ Blimp1flox/flox RosaYFP+


title: BLIMP1 KO_1


title: WT_1


title: BCL6 KO_1


title: WT (scATAC-Seq)

description: GP66:I-Ab+ CD4+

data_processing:
Basecalling was performed using RTA 2.4.11
Sequencing reads were demultiplexed using Bcl2fastq 2.17
10x data for scRNA samples are run through cellranger ATAC v1.0.1  to produce the fastq files
The fastq files are processed throgh the cellranger count to get differential expression counts.
Genome_build: mm10

source_name: Spleen

extract_protocol:
Single Cell ATACseq per the manufacturer instructions (10X genomics)
Libraries were pooled and  sequenced with paired-end reads of 50x50bp  on a NextSeq500 sequencer (Illumina).


title: BCL6 BLIMP1 DKO  (scATAC-Seq)

description: GP66:I-Ab+ CD4+


title: BCL6 BLIMP1 DKO  (scRNA-Seq)

description: GP66:I-Ab+ CD4+

data_processing:
Basecalling was performed using RTA 2.4.11
Sequencing reads were demultiplexed using Bcl2fastq 2.17
10x data for scRNA samples are run through cellranger v2.2.0  to produce the fastq files
The fastq files are processed throgh the cellranger count to get differential expression counts.
For hashtagged sequencing, samples were demultiplexed based on the expression of barcodes CTTTCGCCAACTCTG for WT, CCCTCTCTGGATTCT for DKO
Genome_build: mm10

extract_protocol:
Single Cell 3 Reagent Kits v2 per the manufacturer instructions (10X genomics)
Libraries were pooled and  sequenced with paired-end reads of 26x57bp  on a NextSeq500 sequencer (Illumina).


title: WT + BCL6 BLIMP1 DKO (scRNA-Seq)

description: GP66:I-Ab+ CD4+

value: WT + BCL6-/- BLIMP1-/-

value: WT + Bcl6flox/flox Blimp1flox/flox RosaYFP+


title: WT (scRNA-Seq)

description: GP66:I-Ab+ CD4+


title: BCL6 KO  (scRNA-Seq)

description: GP66:I-Ab+ CD4+


title: BLIMP1 KO, A (scRNA-Seq)

description: GP66:I-Ab+ CD4+

data_processing:
Basecalling was performed using RTA 2.4.11
Sequencing reads were demultiplexed using Bcl2fastq 2.17
10x data for scRNA samples are run through cellranger v2.2.0 to produce the fastq files
The fastq files are processed throgh the cellranger count to get differential expression counts.
Genome_build: mm10

extract_protocol:
Single Cell 3 Reagent Kits v2 per the manufacturer instructions (10X genomics)
Single Cell 3 Reagent Kits v2 per the manufacturer instructions (10X genomics)
Libraries were pooled and sequenced with paired-end reads of 28x90bp on a Novaseq sequencer (Illumina).


title: BCL6 KO, B (scRNA-Seq)

description: GP66:I-Ab+ CD4+


title: MW_7

status: Public on Sep 23 2021

city: New York

first: Jorge

last: Moscat

state: NY

address: 1188 York Avenue

department: Pathology and Laboratory Medicine

institute: WEILL CORNELL MEDICINE

description: WT

data_processing:
Read data was processed with the BlueBee Genomics Platform (BlueBee, San Mateo, CA).
Reads were aligned using Lexogen Quantseq 2.3.1 FWD UMI pipeline, and differential transcript expression was determined using Lexogen QuantSeq DE 1.3.1 pipeline. Both pipelines are from BluBee Genomics Platform.
Counts were normalized by total number of reads per each samples and multiplied by 10E6.
Genes with 0 counts in all the samples were removed.
Genome_build: Mus musculus - mouse (GRCm38)
Supplementary_files_format_and_content: Counts matrix with gene expression value for all samples.

source_name: Mouse tumor organoids from Liver metastasis of intestinal tumor

growth_protocol: Around 1,000 cells were plated in a drop of cold basement-membrane extract (BME) medium (Cultrex BME Type 2, Amsbio). Then organoids are cultured in advanced DMEM/F12, supplemented with 10 mM HEPES, Glutamax, B-27 without retinoid acid (all Life Technologies), 50 ng/ml recombi- nant human EGF (Peprotech)

extract_protocol:
RNA was harvested using Trizol reagent and purified using Quick-RNA MiniPrep kit (Zymo Research).
Libraries were prepared from 200 ng of total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen, and optional UMIs (Vienna, Austria). Barcoded libraries were pooled, and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego CA).

treatment_protocol: No treatment was applied. Organoids were harvested at ~80% confluency 72h after plating.

value: small intestine

value: sgScbr


title: BCL6 BLIMP1 DKO_1


title: MW_8

description: WT


title: IEC_LKO_rep0

description: Small intestinal tissue from intestinal epithelial cell-specific PKCLambda-KO mouse

library_source: genomic

data_processing:
FASTQ.gz files were concatenated into two files per sample and used as input for Taiji software (https://taiji-pipeline.github.io/documentation/)
Taiji software uses BWA to allign the data to mm10 genome.
Taiji uses samtools, bedGraphToBigWig to generate bigwig files, and MACS2 to call peaks.
Genome_build: mm10
Supplementary_files_format_and_content: processed data file consist of a bigwig file per sample

source_name: Small intestinal epithelial cell

extract_protocol:
Small intestines were isolated using EDTA, frozen on dry ice, and pellet was kept at -80C.
The cell pellet was resuspended in 50 μl lysis buffer and then spun down 500 × g for 10 min at 4 °C. The nuclei pellet was resuspended into 50 μl transposition reaction mixture containing Tn5 transposase from Nextera DNA Library Prep Kit (Illumina) and incubated at 37 °C for 30 min. Then the transposase-associated DNA was purified using MinElute PCR purification kit (QIAGEN). To amplify the library, the DNA was first amplified for 5 cycles using indexing primer from Nextera kit and NEBNext High-Fidelity 2X PCR master mix. To reduce the PCR amplification bias, 5 μl of amplified DNA after the first 5 cycles was used to do qPCR of 20 cycles to decide the number of cycles for the second round of PCR.
The total amplified DNA was size selected to fragments less than 800 bp using SPRI beads. Quantification of the ATAC-seq library was done with QuBit. The size of the pooled library was examined by TapeStation. Barcoded ATAC-seq libraries were pooled and paired end sequenced (sX75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego, CA).

treatment_protocol: No treatment

value: Small intestine

tag: age

value: 8 weeks old

value: Villincre-positive, PKClambda f/f


title: ML_11

description: PKClambdaKO

tag: genotype

value: sgPrkci


title: ML_12

description: PKClambdaKO

tag: tissue


title: ML_10

description: PKClambdaKO


title: IEC_WT_rep0

description: Small intestinal tissue from wild type mouse

value: Villincre-negative, PKClambda f/f


title: MW_9

description: WT


title: d7-Cl13-1 [TCR] + d7-Cl13-2 [TCR]

status: Public on Sep 21 2021

data_processing:
Basecalling was performed using RTA 2.4.11
Sequencing reads were demultiplexed using Bcl2fastq 2.17
The fastq files are processed throgh the cellranger count to get differential expression counts.
For hashtagged sequencing, samples were demultiplexed based on the expression of barcoded antibodies
Barcodes =  d7-Arm-1 None, d7-Arm-2 None, d7-Arm-3 ACCCACCAGTAAGAC, d21-Arm-1 GGTCGAGAGCATTCA, d21-Arm-2 None, d80-Arm-1 None, d80-Arm-2 None, d7-Cl13-1 CTTGCCGCATGTCAT, d7-Cl13-2 AAAGCATTCTTCACG, d21-Cl13-1 None, d21-Cl13-2 CTTTGTCTTTGTGAG
Genome_build: mm10
Supplementary_files_format_and_content: h5; TCR annotation/sequences; GEX barcode/matrix/gene list

extract_protocol:
Single Cell 3' or 5'  Reagent Kits v2 per the manufacturer instructions (10X genomics)
Libraries were pooled and  sequenced with paired-end reads on a Illumina sequencers.

value: Wild-type

value: infected with Clone 13


title: d80-Arm-2 [TCR]

value: Spleen

value: GP66:I-Ab+ CD4+


title: d21-Cl13-2 [TCR]


title: d80-Arm-1 [TCR]


title: BLIMP1 KO  (scRNA-Seq)

description: GP66:I-Ab+ CD4+


title: d7-Arm-3 [TCR] + d21-Arm-1 [TCR]


title: d80-Arm-2 [GEX]

value: infected with LCMV Armstrong


title: d7-Cl13-1 [GEX] + d7-Cl13-2 [GEX]


title: d7-Arm-3 [GEX] + d21-Arm-1 [GEX]


title: d80-Arm-1 [GEX]


title: d7-Arm-2 [GEX]


title: d21-Cl13-1 [GEX]


title: d7-Arm-1 [GEX]


title: d21-Arm-2 [GEX]


title: d7-Arm-2 [TCR]


title: WT_HUDEP2_rep1

status: Public on Sep 13 2021

city: Memphis

first: Yong

last: Cheng

state: Tennessee

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St. Jude Children's Research Hospital

data_processing:
transcript level quantification was calculated using default parameter of Kallisto quant (version 0.43.1)
transcript to gene level quantification was carried out using ensembl gene annotation version 75 for hg19
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include transcript per million (TPM) values for each Sample

growth_protocol: Cells were expanded in StemSpan serum-free expansion medium (SFEM; Stem Cell Technologies) supplemented with 1 µM dexamethasone, 1 µg/mL doxycycline, 50 ng/mL human stem cell factor (SCF), 3 units/mL erythropoietin (EPO), and 1% penicillin–streptomycin

extract_protocol:
quick-RNA MiniPrep from Zymo Research (R1054) was used to extract RNA
TruSeq Stranded mRNA Library Prep Kit (Illumina) was used to create libraries for sequencing

treatment_protocol: CRISPR GFP integration was carried out using 3xNLS Cas9 protein and RL48-hGOLGA4-EGFP plasmid containing GFP expression cassettee

value: Human Umbilical cord blood-Derived Erythroid Progenitor-2 cells

tag: sample type

value: wild-type


title: WT_HUDEP2_rep2

source_name: Human Umbilical cord blood-Derived Erythroid Progenitor-2


title: d7-Arm-1 [TCR]


title: RPA-ChIP_timecourse___control_rep2_060min_RPA-IP

status: Public on Sep 07 2021

city: Martinsried

first: Karl-Uwe

last: Reusswig

address: Am Klopferspitz 18

institute: Max Planck Institute of Biochemistry

data_processing:
Sequencing reads were mapped to the S. cerevisiae reference genome (sacCer3) using bwa mem (v 0.7.17-r1188) with default parameters and conveted to BAM files using samtools (v 1.12)
For strand-specific ChIP-seq, reads were separated by strand using samtools (v 1.12) with option "-f 99" and "-f 147" for reads mapping to the forward strand and option "-f 83" and "-f 163" for reads mapping to the reverse strand.
Data were normalized for sequencing depth and multiple mapping reads were filtered out using bamCoverage from deepTools (v 3.5.1) with the settings "--binSize 50 --minMappingQuality 60 --normalizeUsing CPM" and saved as bigWig-files
Genome_build: sacCer3
Supplementary_files_format_and_content: The bigWig-files represent sequencing-depth normalized coverage (CPM) of chromosomes for EdU-ChIP or forward/reverse strands for RPA-ChIP.

organism: Saccharomyces cerevisiae

source_name: budding yeast cells

growth_protocol: Cells were grown in YP-media supplemented with 2% raffinose and 0.25 mM adenine at 30 °C to log-phase (OD600 0.5-0.7) and synchronized with α-factor (5-10 µg/ml) for 2:30 h. Cell cycle arrest was assessed by microscopy and by measurement of DNA content (flow cytometry).

extract_protocol:
Cells were mechanically lysed and chromating was sheared by sonication to fragments of 200-500 bp. 40% (RPA) or 90%(EdU) of the extracts were used for immunoprecipitation. The purified complexes from RPA-ChIP samples were additionally treated with proteinase K and crosslinks were reversed. DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Libraries for ChIP-seq of EdU-labeled DNA were prepared using NEBNext Ultra II DNA Library Prep kit following the manufacturer's instructions. Libraries for strand-specific ChIP-seq of RPA-bound DNA were prepared using Accel-NGS 1S Plus Library Kit according to the manufacturer's instructions as in Peritore et al. (2021) [PMID:33651987].

treatment_protocol: Replication was induced in G1-arrested cells by adding galactose to the medium (2% final concentration). In the BiFC strains, replication was induced by prolonged arrest in G1 for 5 h. To label newly synthesized DNA for EdU-ChIP, cells were also exposed to 100 µM EdU. For RPA-ChIP, cells were crosslinked with 1% formaldehyde for 16 minutes at room temperature at the indicated timepoints and subsequently quenched with 400 mM glycine.

tag: chip-antibody

value: Agrisera AS07 214 (anti-RFA from S. cerevisiae)

tag: timepoint

value: 60 min release to M (after 2 h G1 arrest and 3 h replication in G1)


title: RPA-ChIP_timecourse___control_rep1_120min_totalDNA

value: 120 min release to M (after 2 h G1 arrest and 3 h replication in G1)


title: RPA-ChIP_timecourse___control_rep2_120min_RPA-IP


title: RPA-ChIP_timecourse___control_rep2_060min_totalDNA


title: RPA-ChIP_timecourse___control_rep2_180min_RPA-IP

value: 180 min release to M (after 2 h G1 arrest and 3 h replication in G1)


title: RPA-ChIP_timecourse___control_rep2_000min_totalDNA

value: 0 min release to M (after 2 h G1 arrest and 3 h replication in G1)


title: RPA-ChIP_timecourse___control_rep2_120min_totalDNA


title: RPA-ChIP_timecourse___control_rep2_000min_RPA-IP


title: RPA-ChIP_timecourse___control_rep1_180min_RPA-IP


title: RPA-ChIP_timecourse___control_rep1_030min_totalDNA

value: 30 min release to M (after 2 h G1 arrest and 3 h replication in G1)


title: RPA-ChIP_timecourse___control_rep2_180min_totalDNA


title: RPA-ChIP_timecourse___control_rep1_060min_RPA-IP


title: RPA-ChIP_timecourse___control_rep1_120min_RPA-IP


title: WT_HUDEP2_rep3


title: d21-Cl13-2 [GEX]


title: RPA-ChIP_timecourse___control_rep2_030min_totalDNA


title: RPA-ChIP_timecourse___control_rep1_060min_totalDNA


title: RPA-ChIP_timecourse___control_rep1_180min_totalDNA


title: RPA-ChIP_timecourse___control_rep2_030min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep2_120min_RPA-IP


title: RPA-ChIP_timecourse___control_rep1_030min_RPA-IP


title: RPA-ChIP_timecourse___control_rep1_000min_RPA-IP


title: RPA-ChIP_timecourse___control_rep1_000min_totalDNA


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep2_180min_totalDNA


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep2_120min_totalDNA


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep2_180min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep1_120min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep1_000min_totalDNA


title: RPA-ChIP_timecourse___bypassCDK_rep2_060min_totalDNA


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep2_000min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep1_180min_totalDNA


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep1_030min_totalDNA


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep1_030min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep2_060min_totalDNA


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep1_060min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep2_030min_totalDNA


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep2_030min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep1_000min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDK_rep2_180min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDK_rep2_180min_totalDNA


title: RPA-ChIP_timecourse___bypassCDK_rep2_120min_totalDNA


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep2_060min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep2_000min_totalDNA


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep1_180min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep1_120min_totalDNA


title: RPA-ChIP_timecourse___bypassCDKandDDK_rep1_060min_totalDNA


title: RPA-ChIP_timecourse___bypassCDK_rep2_060min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDK_rep2_120min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDK_rep2_000min_totalDNA


title: RPA-ChIP_timecourse___bypassCDK_rep1_180min_totalDNA


title: RPA-ChIP_timecourse___bypassCDK_rep1_120min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDK_rep2_030min_totalDNA


title: RPA-ChIP_timecourse___bypassCDK_rep2_030min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDK_rep2_000min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDK_rep1_120min_totalDNA


title: RPA-ChIP_timecourse___bypassCDK_rep1_180min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDK_rep1_000min_totalDNA


title: RPA-ChIP_timecourse___bypassCDK_rep1_030min_RPA-IP


title: RPA-ChIP_timecourse___bypassCDK_rep1_030min_totalDNA


title: RPA-ChIP_rad52___wt-control_rep2_beforeRelease_totalDNA

value: 3 h arrested in G1


title: RPA-ChIP_rad52___wt-control_rep2_releasedToM_totalDNA

value: 3 h arrested in G1 followed by 2 h release to M


title: RPA-ChIP_timecourse___bypassCDK_rep1_060min_totalDNA


title: RPA-ChIP_rad52___wt-control_rep1_beforeRelease_totalDNA


title: RPA-ChIP_rad52___wt-control_rep2_releasedToM_RPA-IP


title: RPA-ChIP_rad52___wt-control_rep1_beforeRelease_RPA-IP


title: RPA-ChIP_rad52___wt-bypassCDKandDDK_rep2_beforeRelease_totalDNA


title: RPA-ChIP_rad52___wt-bypassCDKandDDK_rep2_releasedToM_totalDNA


title: RPA-ChIP_timecourse___bypassCDK_rep1_000min_RPA-IP


title: RPA-ChIP_rad52___wt-control_rep2_beforeRelease_RPA-IP


title: RPA-ChIP_rad52___wt-bypassCDKandDDK_rep1_releasedToM_totalDNA


title: RPA-ChIP_rad52___wt-bypassCDKandDDK_rep2_beforeRelease_RPA-IP


title: RPA-ChIP_rad52___wt-bypassCDKandDDK_rep1_releasedToM_RPA-IP


title: RPA-ChIP_rad52___wt-bypassCDKandDDK_rep1_beforeRelease_RPA-IP


title: RPA-ChIP_rad52___wt-bypassCDKandDDK_rep2_releasedToM_RPA-IP


title: RPA-ChIP_rad52___wt-control_rep1_releasedToM_totalDNA


title: RPA-ChIP_timecourse___bypassCDK_rep1_060min_RPA-IP


title: RPA-ChIP_rad52___rad52-control_rep2_releasedToM_RPA-IP


title: RPA-ChIP_rad52___rad52-control_rep2_beforeRelease_totalDNA


title: RPA-ChIP_rad52___rad52-control_rep1_releasedToM_RPA-IP


title: RPA-ChIP_rad52___rad52-control_rep1_releasedToM_totalDNA


title: RPA-ChIP_rad52___rad52-control_rep2_beforeRelease_RPA-IP


title: RPA-ChIP_rad52___wt-control_rep1_releasedToM_RPA-IP


title: RPA-ChIP_rad52___wt-bypassCDKandDDK_rep1_beforeRelease_totalDNA


title: RPA-ChIP_rad52___rad52-bypassCDKandDDK_rep2_releasedToM_totalDNA


title: RPA-ChIP_rad52___rad52-control_rep1_beforeRelease_totalDNA


title: RPA-ChIP_rad52___rad52-bypassCDKandDDK_rep2_releasedToM_RPA-IP


title: RPA-ChIP_BiFC___control_rep1_releasedToM_totalDNA

value: 5 h arrested in G1 followed by 2 h release to M


title: RPA-ChIP_BiFC___control_rep2_releasedToM_RPA-IP


title: RPA-ChIP_rad52___rad52-control_rep2_releasedToM_totalDNA


title: RPA-ChIP_rad52___rad52-bypassCDKandDDK_rep2_beforeRelease_totalDNA


title: RPA-ChIP_BiFC___control_rep2_releasedToM_totalDNA


title: RPA-ChIP_rad52___rad52-bypassCDKandDDK_rep1_releasedToM_totalDNA


title: RPA-ChIP_BiFC___control_rep2_G1_RPA-IP

value: 5 h arrested in G1


title: RPA-ChIP_BiFC___control_rep1_G1_totalDNA


title: RPA-ChIP_rad52___rad52-bypassCDKandDDK_rep1_releasedToM_RPA-IP


title: RPA-ChIP_BiFC___control_rep1_G1_RPA-IP


title: RPA-ChIP_rad52___rad52-control_rep1_beforeRelease_RPA-IP


title: RPA-ChIP_BiFC___control_rep2_G1_totalDNA


title: RPA-ChIP_rad52___rad52-bypassCDKandDDK_rep1_beforeRelease_RPA-IP


title: RPA-ChIP_rad52___rad52-bypassCDKandDDK_rep1_beforeRelease_totalDNA


title: RPA-ChIP_BiFC___BiFC_rep1_releasedToM_RPA-IP


title: RPA-ChIP_rad52___rad52-bypassCDKandDDK_rep2_beforeRelease_RPA-IP


title: RPA-ChIP_BiFC___BiFC_rep2_releasedToM_RPA-IP


title: RPA-ChIP_BiFC___BiFC_rep2_G1_totalDNA


title: EdU-IP_no_HU___nobypass_rep2_3h_totalDNA

value: Streptavidin (Dynabeads M-280)

value: 3 h replication in G1 in presence of 100 µM EdU


title: RPA-ChIP_BiFC___BiFC_rep2_G1_RPA-IP


title: EdU-IP_no_HU___nobypass_rep2_0h_totalDNA

value: 0 h (G1-arrested)


title: EdU-IP_no_HU___nobypass_rep2_3h_EdU-IP


title: RPA-ChIP_BiFC___BiFC_rep1_G1_RPA-IP


title: RPA-ChIP_BiFC___BiFC_rep2_releasedToM_totalDNA


title: RPA-ChIP_BiFC___control_rep1_releasedToM_RPA-IP


title: EdU-IP_no_HU___nobypass_rep2_0h_EdU-IP


title: EdU-IP_no_HU___nobypass_rep1_0h_totalDNA


title: RPA-ChIP_BiFC___BiFC_rep1_releasedToM_totalDNA


title: EdU-IP_no_HU___nobypass_rep1_3h_EdU-IP


title: EdU-IP_no_HU___nobypass_rep1_0h_EdU-IP


title: EdU-IP_no_HU___control_rep2_0h_totalDNA


title: EdU-IP_no_HU___control_rep1_3h_totalDNA


title: EdU-IP_no_HU___control_rep2_3h_totalDNA


title: EdU-IP_no_HU___bypass-CDKandDDK_rep2_0h_totalDNA


title: EdU-IP_no_HU___control_rep1_0h_EdU-IP


title: RPA-ChIP_BiFC___BiFC_rep1_G1_totalDNA


title: EdU-IP_no_HU___control_rep2_3h_EdU-IP


title: EdU-IP_no_HU___bypass-CDKandDDK_rep2_0h_EdU-IP


title: EdU-IP_no_HU___bypass-CDKandDDK_rep2_3h_EdU-IP


title: EdU-IP_no_HU___bypass-CDKandDDK_rep2_3h_totalDNA


title: EdU-IP_no_HU___control_rep1_0h_totalDNA


title: EdU-IP_no_HU___control_rep1_3h_EdU-IP


title: EdU-IP_no_HU___bypass-CDKandDDK_rep1_3h_totalDNA


title: EdU-IP_no_HU___bypass-CDKandDDK_rep1_0h_totalDNA


title: EdU-IP_no_HU___bypass-CDKandDDK_rep1_0h_EdU-IP


title: EdU-IP_no_HU___bypass-CDKandDDK_rep1_3h_EdU-IP


title: RPA-ChIP_release_HU___wildtype_totalDNA_asynchronous

value: asynchronous


title: EdU-IP_no_HU___nobypass_rep1_3h_totalDNA


title: EdU-IP_no_HU___bypass-CDK_rep2_3h_totalDNA


title: EdU-IP_no_HU___bypass-CDK_rep2_0h_totalDNA


title: EdU-IP_no_HU___bypass-CDK_rep2_3h_EdU-IP


title: RPA-ChIP_release_HU___wildtype_totalDNA_30minReleasedFromG1ToHU

value: released for 30 min to 200 mM HU (after 2 h G1-arrest)


title: RPA-ChIP_release_HU___wildtype_totalDNA_60minReleasedFromG1ToHU

value: released for 60 min to 200 mM HU (after 2 h G1-arrest)


title: EdU-IP_no_HU___control_rep2_0h_EdU-IP


title: EdU-IP_no_HU___bypass-CDK_rep2_0h_EdU-IP


title: EdU-IP_no_HU___bypass-CDK_rep1_3h_totalDNA


title: RPA-ChIP_release_HU___wildtype_totalDNA_120minReleasedFromG1ToHU

value: released for 120 min to 200 mM HU (after 2 h G1-arrest)


title: EdU-IP_no_HU___bypass-CDK_rep1_3h_EdU-IP


title: RPA-ChIP_release_HU___wildtype_RPA-IP_asynchronous

value: Agrisera AS07 214 (anti-RFA from S. cerevisiae)


title: RPA-ChIP_release_HU___wildtype_RPA-IP_60minReleasedFromG1ToHU


title: RPA-ChIP_release_HU___wildtype_RPA-IP_30minReleasedFromG1ToHU


title: EdU-IP_HU___control_rep1_totalDNA

value: 3 h replication in G1 in presence of 100 µM EdU and 60 mM HU


title: EdU-IP_no_HU___bypass-CDK_rep1_0h_totalDNA


title: RPA-ChIP_release_HU___wildtype_RPA-IP_120minReleasedFromG1ToHU


title: EdU-IP_no_HU___bypass-CDK_rep1_0h_EdU-IP


title: EdU-IP_HU___bypass-CDKandDDK_rep2_totalDNA


title: EdU-IP_HU___bypass-CDKandDDK_rep1_totalDNA


title: EdU-IP_HU___control_rep1_EdU-IP


title: EdU-IP_HU___bypass-CDKandDDK_rep2_EdU-IP


title: EdU-IP_HU___control_rep2_totalDNA


title: EdU-IP_HU___bypass-CDK_rep1_totalDNA


title: EdU-IP_HU___control_rep2_EdU-IP


title: EdU-IP_HU___bypass-CDK_rep1_EdU-IP


title: M13

status: Public on Aug 11 2021

city: Philadelphia

first: Dwight

middle: Edward

last: Stambolian

state: PA

address: 422 Curie Blvd.

department: Opthalmalogy

institute: University of Pennsylvania

data_processing:
Gene count matrix was normalized and transformed into a natural log scale
Z-scores calculated across cells within each batch to further standardize log-transformed expression values.
Highly variable genes selected using 'filter_genes_dispersion' function from the Scanpy package.
Cell clustered into distinct cell types using DESC (a deep embedding clustering algorithm).
Genome_build: HG38
Supplementary_files_format_and_content: txt file (gene x cell)

source_name: retina

extract_protocol:
The human eyeball was immediately removed within 6 hours after death, and placed in cold phosphate buffered saline (PBS). The retina was carefully removed under a dissecting microscope, and the retina tissue was dissociated straightaway using the Papain dissociaton system (Worthington, Lakewood, NJ, USA) following the manufacturer's instructions.
To assess cell viability, cells were stained with 0.4% trypan blue (Mediatech, Inc., Manassas, VA, USA) and counted using a hemocytometer. Sc-RNA seq was carried out on the viable cells using Chromium 10x Genomics as per the manufacturer's recommendations.

tag: race

value: Caucasian

value: retina


title: P13


title: EdU-IP_HU___bypass-CDKandDDK_rep1_EdU-IP

tag: strain


title: EdU-IP_HU___bypass-CDK_rep2_EdU-IP


title: M14


title: P14


title: KNLH70

status: Public on Jul 09 2021

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
Raw sequencing data were demultiplexed, aligned to the joint human (GRCh38) and mouse (mm10) genome,  and UMI-collapsed using CellRanger. Cells with more than 25% of mouse gene counts were discarded. In the remaining cells, mouse gene counts were discarded.
Supplementary_files_format_and_content: count table

molecule: polyA RNA

source_name: Pancreatic islets

extract_protocol:
Nuclei were  lysed in droplets using the 10X Chromium instrument.
Reverse transcription was performed in droplet and library construction was performed according to the 10X Chromium Single Cell 3' Reagent Kit.

value: Pancreatic islets

tag: run

tag: donor

tag: barcode suffix


title: P12


title: M12


title: KNLH34

tag: cell type


title: P11


title: KNLH36


title: M11


title: KNLH35


title: H3K27ME3 Old Sample 2

status: Public on Jul 08 2021

description:
Old2_H3K27ME3
H3K27ME3_rpkm_table.txt

data_processing:
Library strategy: CUT&RUN
fastq reads were mapped to mm10 genome using bowtie2 and duplicates were then removed using MarkDuplicates program of Picard Tools. For mapping spike-in fragments to yeast, the --no-overlap --no-dovetail options and map to a repeat-masked version of the spike-in genome to avoid cross-mapping of the experimental genome to that of the spike-in DNA.
The peaks were then called using chromstaR package in differential mode between Young and Old for each histone mark.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *_rpkm_table.txt: Tab-separated text files of peaks called by chromstaR in differential mode.

growth_protocol: MSCs from young and old mice were exclusively cultured under 2% O2 in αMEM media supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
For CUT&RUN libraries 300K cells / sample were washed twice with 1.5ml Wash Buffer (20mM MHEPES, 150mM NaCl, 0,5mM Spermidine) and incubated with 200ul activated Concavalin A beads for 10minutes at RT. Cell-bead suspension was resuspended in 100ul antibody buffer (20mM MHEPES, 150mM NaCl, 0,5mM Spermidine, 0,05% Digitonin, 2mM EDTA) which was then divided into two 50ul tubes, and in each one of those 1ul of H3K27ac or H3K27me3 antibodies was added (antibody dilution 1:50 / antibody incubation O/N at 4C). Cell-bead suspension was then washed twice with Digitonin Buffer (20mM MHEPES, 150mM NaCl, 0,5mM Spermidine, 0,05% Digitonin) and 2.5 ul of EpiCypher CUTANA pAG-MNase were added in 50ul Digitonin Buffer, for 10 minutes. After washing samples twice with Digitonin buffer, 3ul of 100mm CaCl2 were added in 150ul of Digitoning buffer. Samples were incubated for 2hours at 4C. To stop the reaction 100ul of the STOP buffer (340mM NaCl, 20mm EDTA, 4mM EGTA, 0,02%Digitonin, 50ug/ml RNase A, 50ug/ml Glycogen, yeast genomic DNA) were added in each tube. Samples were incubated at 37C for 10minutes at 500rpm and after centrifugation, liquid was collected, DNA was purified using Zymo DNA clean concentrator kit and DNA was eluted in 10ul elution buffer.
For library construction we followed a modified Ford et al., protocol (https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-7-312). In brief, we first blunted DNA ends by incubating ChIP-ed DNA for 30 minutes at 20C with T4 DNA ligase buffer (without ATP), 5 µl ATP 10 mM, 2 µl dNTPs 10 mM, 0,5 µl End-Repair-Enzyme-Mix(5µl T4 DNA Polymerase,1µl Klenow fragment, 5µl T4 PNK) in 17.5ul H2O. DNA was then cleaned-up using Ampure XP beads and was next subjected to poly-A addition at the 3'ends of DNA fragments. For addition of "A" bases, 2 µl NEB buffer2 10X, 1 µl dATP 4mM and 0,5 µl Klenow 3’ to 5’ exo minus 5 U/µl were added to each sample. Samples were incubated for 30 minutes at 37°C and 5 minutes at 70°, for inactivation. Next, adapters were ligated to each ChIP - sample by adding 27,25 µl 2X Quick ligase buffer, 2,5 µl annealed NEXTflex adapters, 3,75 µl H2O and 1 µl Quick Ligase (2000 U/µl NEB). Ligation reaction was incubated 15 minutes at RT and 15 minutes at 30°C and was then stopped by addition of 5,5 µl EDTA 0,5M pH 8.0. DNA samples were cleaned up by Ampure XP beads and libraries were amplified by PCR after addition of 1 µl PCR primer Mix and 20 µl HiFi HotStart 2X Kapa Mixm, as following: 45 seconds at 98°C/ 15 seconds at 98°C - 30 seconds at 63°C - 30 seconds at 72°C (12x) / 60 seconds at 72°C. DNA was cleaned up by Ampure XP beads and purified using Zymo DNA concentrator kit. Quantity of the libraries was assessed by measuring DNA concentration in Qubit library quality was assessed by running samples on the TapeStation.

value: mesenchymal stem cells

value: 18-22 months

tag: antibody


title: H3K27AC Old Sample 3

description:
Old3_H3K27AC
H3K27AC_rpkm_table.txt


title: H3K27ME3 Old Sample 1

description:
Old1_H3K27ME3
H3K27ME3_rpkm_table.txt


title: H3K27ME3 Young Sample 1

description:
Young1_H3K27ME3
H3K27ME3_rpkm_table.txt

value: 3-5 months


title: H3K27ME3 Young Sample 3

description:
Young3_H3K27ME3
H3K27ME3_rpkm_table.txt


title: H3K27AC Old Sample 2

description:
Old2_H3K27AC
H3K27AC_rpkm_table.txt


title: EdU-IP_HU___bypass-CDK_rep2_totalDNA


title: H3K27AC Young Sample 3

description:
Young3_H3K27AC
H3K27AC_rpkm_table.txt


title: Old sample_2 batch C

data_processing:
fastq reads were processed with the zUMIs pipeline. Reads were mapped on mm10 genome with Ensembl annotation GRCm38.91
Automated downsampled count matrix generated by zUMIs pipeline was analysed for differential expression using R platform
Genome_build: mm10
Supplementary_files_format_and_content: sample (columns) and genes (rows) -wise read count table


title: H3K27AC Young Sample 2

description:
Young2_H3K27AC
H3K27AC_rpkm_table.txt


title: H3K27AC Young Sample 1

description:
Young1_H3K27AC
H3K27AC_rpkm_table.txt


title: Old sample_3 batch C


title: Young sample_1 batch B


title: Old sample_2 batch B


title: Old sample_1 batch B


title: H3K27ME3 Old Sample 3

description:
Old3_H3K27ME3
H3K27ME3_rpkm_table.txt


title: Young sample_4 batch A


title: Young sample_3 batch A


title: Old sample_1 batch C


title: H3K27ME3 Young Sample 2

description:
Young2_H3K27ME3
H3K27ME3_rpkm_table.txt


title: ATAC-seq_Young sample_2

data_processing:
fastq reads were mapped to mm10 genome using bowtie2 and duplicates were then removed using MarkDuplicates program of Picard Tools.
The peaks were then called using chromstaR package in differential mode between Young and Old.
The called peaks were then used in nucleoATAC for nucleosome positioning. The peaks were split into mono, di, tri and nucleosome free regions using standard insert length for each.
Genome_build: mm10

growth_protocol: MSCs from young and old mice were cultured exclusively under 2% O2 in αMEM media supplemented with 10% FBS and 1% penicillin/streptomycin.

extract_protocol:
Nuclei were isolated by cell resuspension in ice-cold lysis buffer (10mM Tris-HCl ph=7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 1X protease inhibitor cocktail) and centrifugation at 4oC for 5min. The nuclear pellet was then resuspended in ice-cold 1X TD Ilumina buffer.
Libraries were prepared using Nextera PCR primers and the NEBNext High-Fidelity PCR Master Mix


title: ATAC-seq_Young sample_1


title: Young sample_1 batch A


title: H3K27AC Old Sample 1

description:
Old1_H3K27AC
H3K27AC_rpkm_table.txt


title: ATAC-seq_Old sample_1


title: ATAC-seq_Old sample_2


title: Young sample_2 batch A


title: H3AC Young Sample 2

data_processing:
Library strategy: CUT&RUN
fastq reads were mapped to mm10 genome using bowtie2 and duplicates were then removed using MarkDuplicates program of Picard Tools. For mapping spike-in fragments to yeast, the --no-overlap --no-dovetail options and map to a repeat-masked version of the spike-in genome to avoid cross-mapping of the experimental genome to that of the spike-in DNA.
The peaks were then called using chromstaR package in differential mode with 8 states combination across Young, Old and acetate treated Old.
Genome_build: mm10
Supplementary_files_format_and_content: H3AC_rpkm_table.txt (Tab-separated text file of peaks called by chromstaR in differential mode.)

growth_protocol: MSCs from young and old mice were exclusively cultured under 2% O2 in αMEM media supplemented with 10% FBS and 1% penicillin/streptomycin. We used control young and old MSCs, as well as old MSCs treated for 3 days with 5mM sodium acetate.

extract_protocol:
For H3ac CUT&RUN libraries ~100K cells / sample were washed twice with 1.5ml Wash Buffer (20mM MHEPES, 150mM NaCl, 0,5mM Spermidine) and incubated with 200ul activated Concavalin A beads for 10minutes at RT. Cell-bead suspension was resuspended in 50ul antibody buffer (20mM MHEPES, 150mM NaCl, 0,5mM Spermidine, 0,05% Digitonin, 2mM EDTA) in which 1ul of the H3ac antibody was added (antibody dilution 1:50 / antibody incubation O/N at 4C). Cell-bead suspension was then washed twice with Digitonin Buffer (20mM MHEPES, 150mM NaCl, 0,5mM Spermidine, 0,05% Digitonin) and 2.5 ul of EpiCypher CUTANA pAG-MNase were added in 50ul Digitonin Buffer, for 10 minutes. After washing samples twice with Digitonin buffer, 3ul of 100mm CaCl2 were added in 150ul of Digitoning buffer. Samples were incubated for 2hours at 4C. To stop the reaction 100ul of the STOP buffer (340mM Nacl, 20mm EDTA, 4mM EGTA, 0,02%Digitonin, 50ug/ml RNase A, 50ug/ml Glycogen, yeast genomic DNA) were added in each tube. Samples were incubated at 37C for 10minutes at 500rpm and after centrifugation, liquid was collected, DNA was purified using Zymo DNA clean concentrator kit and DNA was eluted in 10ul elution buffer.
For library construction we followed a modified Ford et al, protocol (https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-7-312). In brief, we first blunted DNA ends by incubating ChIP-ed DNA for 30 minutes at 20C with T4 DNA ligase buffer (without ATP), 5 µl ATP 10 mM, 2 µl dNTPs 10 mM, 0,5 µl End-Repair-Enzyme-Mix(5µl T4 DNA Polymerase,1µl Klenow fragment, 5µl T4 PNK) in 17.5ul H2O. DNA was then cleaned-up using Ampure XP beads and was next subjected to poly-A addition at the 3'ends of DNA fragments. For addition of "A" bases, 2 µl NEB buffer2 10X, 1 µl dATP 4mM and 0,5 µl Klenow 3’ to 5’ exo minus 5 U/µl were added to each sample. Samples were incubated for 30 minutes at 37°C and 5 minutes at 70°, for inactivation. Next, adapters were ligated to each ChIP - sample by adding 27,25 µl 2X Quick ligase buffer, 2,5 µl annealed NEXTflex adapters, 3,75 µl H2O and 1 µl Quick Ligase (2000 U/µl NEB). Ligation reaction was incubated 15 minutes at RT and 15 minutes at 30°C and was then stopped by addition of 5,5 µl EDTA 0,5M pH 8.0. DNA samples were cleaned up by Ampure XP beads and libraries were amplified by PCR after addition of 1 µl PCR primer Mix and 20 µl HiFi HotStart 2X Kapa Mixm, as following: 45 seconds at 98°C/ 15 seconds at 98°C - 30 seconds at 63°C - 30 seconds at 72°C (12x) / 60 seconds at 72°C. DNA was cleaned up by Ampure XP beads and purified using Zymo DNA concentrator kit. Quantity of the libaries was assessed by measuring DNA concentration in Qubit library quality was assessed by running samples on the TapeStation.

treatment_protocol: The old MSCs were treated for 3 days with 5mM sodium acetate.

tag: treatment

value: No treatment


title: Young sample_2 batch B


title: H3AC Old Acetate Sample 2

value: Acetate treatment


title: H3AC Old Sample 2


title: H3AC Old Acetate Sample 1


title: H3AC Young Sample 1


title: H3AC Old Sample 1


title: 31_1

status: Public on Jun 11 2021

first: Sander

middle: M

last: Houten

address: 1425 Madison Avenue, Box 1498

department: Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

description: RNA isolation batch 2

data_processing:
Illumina HiSeq2500 for base caling
Read alignment. STAR (release 2.5.1b)
gene-level read quantification via featureCounts v1.5.3
Genome_build: mouse genome mm10 (GRCm38.75)
Supplementary_files_format_and_content: text file containing raw gene counts for each sample

source_name: heart

extract_protocol:
RNA was isolated using QIAzol lysis reagent followed by purification using the RNeasy kit (Qiagen)
mRNA-focused cDNA libraries were generated using Illumina reagents (polyA capture), and samples were run on an Illumina HiSeq 2500 sequencer to yield a read depth of approximately 70 million 100 nucleotide single-end reads per samples.

value: mixed (mostly C57BL/6N with some 129)

value: heart

tag: Sex

value: male

value: Acadl Het / Acadvl wt

tag: diet

value: chow


title: 31_5

description: RNA isolation batch 2

value: Acadl Het / Acadvl KO


title: 28_1

description: RNA isolation batch 1


title: 32_2

description: RNA isolation batch 1


title: 38_2

description: RNA isolation batch 1

value: Acadl wt / Acadvl wt


title: 38_3

description: RNA isolation batch 1


title: 32_1

description: RNA isolation batch 2

value: Acadl KO / Acadvl wt


title: 23_2

description: RNA isolation batch 1

value: Acadl KO / Acadvl Het


title: 25_3

description: RNA isolation batch 1


title: 27_1

description: RNA isolation batch 2

value: Acadl Het / Acadvl Het


title: 37_1

description: RNA isolation batch 1


title: 30_1

description: RNA isolation batch 2


title: 25_2

description: RNA isolation batch 2


title: 30_2

description: RNA isolation batch 1


title: 36_3

description: RNA isolation batch 2


title: 8_3

description: RNA isolation batch 2


title: 28_3

description: RNA isolation batch 2


title: 27_2

description: RNA isolation batch 2


title: 26_3

description: RNA isolation batch 2


title: 26_4

description: RNA isolation batch 2


title: 25_1

description: RNA isolation batch 2


title: HepG2_siControl_10min-EU-RNA_rep2

status: Public on Jun 02 2021

city: Chicago

first: Li-Sheng

last: Zhang

state: IL

address: 929 E 57th St Rm E313

department: Department of Chemistry

institute: The University of Chicago

data_processing:
The sequencing data was all trimmed with cutadapt tool to remove adapters and low-quality reads (length shorter than 18). Reads were processed with BBMap tool (https://sourceforge.net/projects/bbmap/) to remove PCR duplicates, and then further trimmed the random barcode using cutadapt tool and remove low-quality reads again. Reads were then aligned to the relevant genome (human-hg19) using Tophat2 (version 2.1.1) and bowtie2 (version 2.3.5.1) with at most three mismatches. The generated .bam files were split into positive strand and negative strand using Samtools, and then sorted. The total reads coverage at each position was calculated by fine-tuned bam-readcount (https://github.com/genome/bam-readcount).
Library strategy: DAMM-seq
Genome_build: hg19

growth_protocol: Human HepG2 cell line used in this study were all purchased from ATCC (the American Type Culture Collection). HepG2 cell line was maintained in DMEM (GIBCO, 11995), supplemented with 10% FBS and 1% 100X Pen/Strep (GIBCO). All cells were cultured at 37°C under 5.0% CO2, at Heracell™ VIOS 160i incubator (Thermo Scientific).

extract_protocol:
Then after 10-min or 20-min or 30-min, wash the cells with cold DPBS once and add TRIzol reagent immediately to lyse the cells. Cellular total RNA was extracted by the standard protocol of TRIzol reagent. Then EU-labeled RNA was enriched and purified by Click-iT™ Nascent RNA Capture Kit, for gene expression analysis.
THe EU-labeled RNA was fragmented into 40-70 nt using RNA Fragmentation Reagent (AM8740, Invitrogen) following the manufacturer’s protocol and Oligo Clean & Concentrator (Zymo Research). Then the library construction procedures will be conducted with T4 PNK end repair, RNA 3’-adapter ligation, HIV RT reverse transcription, cDNA 3’-adapter ligation and PCR amplification respectively, according to standard steps in section “DAMM-seq for methylated site detection”. All libraries were sequenced on Illumina NovaSeq 6000 with single-end 100 bp read length.

treatment_protocol: Typical 10-cm plates of human HepG2 cells were prepared for 48-hour ALKBH7 knockdown. AllStars negative control siRNA from Qiagen (1027281) was used as control siRNA (siControl). Human ALKBH7 siRNA was ordered from Qiagen with catalog number as Hs_SPATA11_3 FlexiTube siRNA (SI00730793). Transfection was achieved by using Lipofectamine RNAiMAX (Invitrogen) for siRNA. After 48-hour siRNA knockdown, add new warm medium containing 0.5 mM EU, followed by putting back to cell incubator immediately.

tag: treatment group

value: siControl


title: HepG2_siALKBH7_10min-EU-RNA_rep2


title: HepG2_ALKBH7-KO_10min-EU-RNA_rep1


title: 24_2

description: RNA isolation batch 2


title: HepG2_siControl_10min-EU-RNA_rep1


title: HepG2_ALKBH7-KO_10min-EU-RNA_rep2


title: HepG2_siALKBH7_10min-EU-RNA_rep1


title: HepG2_WT_30min-EU-RNA_rep2

value: wild-type


title: HepG2_WT_30min-EU-RNA_rep1


title: HepG2_WT_20min-EU-RNA_rep2


title: HepG2_WT_10min-EU-RNA_rep2


title: HepG2_WT_20min-EU-RNA_rep1


title: HepG2_WT_10min-EU-RNA_rep1


title: icSHAPE_siALKBH7_Pulldown-rep1

description:
cell culture
Sample 47
icSHAPE_ReadsCoverage_mt-RNA_H-strand.xlsx,  icSHAPE_ReadsCoverage_mt-RNA_L-strand.xlsx

data_processing:
Library strategy: icSHAPE
The sequencing data was all trimmed with cutadapt tool to remove adapters and low-quality reads (length shorter than 18). Reads were processed with BBMap tool (https://sourceforge.net/projects/bbmap/) to remove PCR duplicates, and then further trimmed the random barcode using cutadapt tool and remove low-quality reads again. Reads were then aligned to the relevant genome (human-hg19) using Tophat2 (version 2.1.1) and bowtie2 (version 2.3.5.1) with at most three mismatches. The generated .bam files were split into positive strand and negative strand using Samtools, and then sorted. The total reads coverage at each position was calculated by fine-tuned bam-readcount (https://github.com/genome/bam-readcount). The generated bam-readcount results were used for calculating enrichment folds of the flexible region icSHAPE peak.
Genome_build: hg19
Supplementary_files_format_and_content: icSHAPE_ReadsCoverage_mt-RNA_H-strand.xlsx,  icSHAPE_ReadsCoverage_mt-RNA_L-strand.xlsx

extract_protocol:
. Forty 15-cm plates of HepG2 cells were prepared for 48-hour knockdown (siControl, siALKBH7, 5 plates per replicate). Upon the completion of knockdown, cells were collected by cell lifter in 5 mL cold DPBS and merged into one 50 mL centrifuge tube. The cell suspension was spun at 300g at 4 °C for 2 min to produce the cell pellet. For the cell pellet corresponding to one of four replicates in each case (4 of siControl or 4 of siALKBH7), add 500 uL control solution (450 uL DPBS + 50 uL DMSO) into two replicates of each case respectively, and add 500 uL NAI-N3 solution (450 uL DPBS + 50 uL 1.0 M NAI-N3 in DMSO) into other two replicates of each case respectively. Then incubate the resuspended solution at 37 ℃ for 5 min, followed by centrifuge at 300g for 2 min. Remove the supernatant carefully and wash the cell pellet with cold DPBS once, followed by centrifuge at 300g for 2 min again.   The cell pellet was resuspended with 1 mL NP-40 lysis buffer prepared in 10 mL volume: 50 mM HEPES pH 7.5, 150 mM NaCl, 2 mM EDTA, 10 mM MgCl2, 0.5% NP-40, plus 50 uL TURBO™ DNase (2 U/µL, AM2238, Invitrogen) and 500 uL SUPERase•In™ RNase Inhibitor (20 U/μL, AM2694, Invitrogen). Incubate the cell suspension at 4 °C for 30 minutes, followed by a spin at 16,000g at 4 °C for 5 min. The supernatant was transferred to a new Eppendorf tube and keep 10 uL of that as input with TRIzol added. The 1 mL lysate was dilute to 5 mL with IP wash buffer and then 250 uL of J2-Dynabeads was added for an incubation at 4 °C for 2 hours. The magnetic beads were washed once with 1 ml of IP wash buffer and transferred into a new Eppendorf tube by 500 µL of IP wash buffer. The beads were further washed twice by 1 mL of IP wash buffer, and J2-bound dsRNA was extracted with TRIzol reagent.
Dilute the harvested dsRNA in 17 uL RNase-free water (for both DMSO-treated and NAI-N3 treated samples), and then add 2 uL of 2 mM sDIBO-biotin together with 1 uL SUPERase•In™ RNase Inhibitor. Incubate at 37 °C for 1 hour and purify RNA through Oligo Clean & Concentrator (Zymo Research). Dilute the purified RNA with 17 uL RNase-free water and add 2 uL RNA Fragmentaion Buffer (NEBNext® Magnesium RNA Fragmentation Module), followed by heating at 95 °C for 3 min. Put all samples onto ice immediately and add 2 uL Stop Buffer. RNA purification was performed for the 4 samples from DMSO treated case using Oligo Clean & Concentrator (Zymo Research), to afford “input” samples. For other 4 samples from NAI-N3 treated case, mix the RNA solution with 20 uL freshly-prepared C1 beads suspension (10 uL Dynabeads™ MyOne™ Streptavidin C1 beads washed twice with 200 uL 1X B&W buffer and stored in 20 uL 2X B&W buffer based on the manufacturer’s protocol). After the incubation of 30 min at 4 °C, wash the beads three times with icSHAPE wash buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 0.05% NP40), followed by proteinase K digestion at 55 °C for 30 min. The harvested RNA (serving as “pulldown”, from NAI-N3 treated) was purified by Oligo Clean & Concentrator (Zymo Research), and sent for library construction together with “input” samples using SMARTer Stranded Total RNA-Seq Kit v2 (Takara). All libraries were sequenced on Illumina Illumina NovaSeq 6000 with single-end 100 bp read length.

treatment_protocol: siRNA knockdown and plasmid transfection. Typical 15-cm plates of human HepG2 cells were prepared for 48-hour ALKBH7 knockdown. AllStars negative control siRNA from Qiagen (1027281) was used as control siRNA (siControl). Human ALKBH7 siRNA was ordered from Qiagen with catalog number as Hs_SPATA11_3 FlexiTube siRNA (SI00730793). Transfection was achieved by using Lipofectamine RNAiMAX (Invitrogen) for siRNA.

tag: cell line

value: Pulldown

tag: rna fraction

value: mitochondrial dsRNA


title: icSHAPE_siALKBH7_Pulldown-rep2

description:
cell culture
Sample 48
icSHAPE_ReadsCoverage_mt-RNA_H-strand.xlsx,  icSHAPE_ReadsCoverage_mt-RNA_L-strand.xlsx

tag: genotype


title: icSHAPE_siALKBH7_Input-rep2

description:
cell culture
Sample 44
icSHAPE_ReadsCoverage_mt-RNA_H-strand.xlsx,  icSHAPE_ReadsCoverage_mt-RNA_L-strand.xlsx

value: Input


title: icSHAPE_siControl_Pulldown-rep2

description:
cell culture
Sample 46
icSHAPE_ReadsCoverage_mt-RNA_H-strand.xlsx,  icSHAPE_ReadsCoverage_mt-RNA_L-strand.xlsx


title: icSHAPE_siControl_Input-rep1

description:
cell culture
Sample 41
icSHAPE_ReadsCoverage_mt-RNA_H-strand.xlsx,  icSHAPE_ReadsCoverage_mt-RNA_L-strand.xlsx


title: icSHAPE_siALKBH7_Input-rep1

description:
cell culture
Sample 43
icSHAPE_ReadsCoverage_mt-RNA_H-strand.xlsx,  icSHAPE_ReadsCoverage_mt-RNA_L-strand.xlsx


title: 24_1

description: RNA isolation batch 2

tag: tissue