title: MU_ZT18_2_SCN

city: Lausanne

first: Cédric

last: Gobet

address: EPFL

country: Switzerland

institute: EPFL

data_processing:
STAR was used to map RNA-seq reads onto a chimeric genome consisting of the Mus musculus (GRCm38/mm10) and Homo sapiens (GRCh39/hg38 ) reference sequences and to quantify the number of uniquely mapped reads per gene and organism.
Assembly: Chimeric Mus musculus (GRCm38/mm10) and Homo sapiens (GRCh38/hg19 ) genome
Supplementary files format and content: Raw read count (unique mapping) for mouse (and human) genes in Liver, ARC, Muscle and SCN mouse tissues. Tab-delimited.

source_name: Suprachiasmatic Nucleus

growth_protocol: Fah-/-, Rag2-/-, Il2rg-/- mice (FRG) were crossed with non-obese diabetic mouse strain to create FRGN mice (Yecuris,Tualatin, OR, USA), whose livers can be fully repopulated with human or murine hepatocytes. Human liver tissue and hepatocytes were obtained through the Liver Tissue Cell Distribution System, and the studies were exempted by IRB 0411142 since no human subjects were involved (University of Pittsburgh). Human and murine hepatocytes were transplanted via splenic injections that allowed to repopulate the mouse liver by maintaining on 2-(2-nitro-4- fluoromethylbenzoyl) cyclohexane -1,3-dione (CuRx™ Nitisinone (NTBC)  in the drinking water, a medication that prevents hepatocyte death when FAH deficiency is present.

extract_protocol:
RNA was isolated from tissues using the RNeasy kit from QIAGEN according to the manufacturer’s recommendations
cDNA was prepared following the NEBNext® Ultra™ II Directional RNA Library Prep Kit protocol

treatment_protocol: Engraftment is sustained over the life of the animal with an appropriate regimen of Nitisinone (20-0026) and prophylactic treatment of Sulfamethoxazole (SMX) / Trimethoprin (TMP) antibiotics (20-0037). Due to the impaired immune system of these stains, they are susceptible to respiratory infections. Mice received prophylactic antibiotic treatment cycles in order to minimize respiratory infections. Treatments with a combination of SMX/TMP for 5 days twice a month greatly reduces the occurrence of common respiratory infections as well as subsequent secondary infections. The final concentration of SMX/TMP drinking water is 640µg/ml, 128 µg/ml (TMP) (CuRx™ SMX/TMP Antibiotic Cat# 20-0037, Yecuris corporation) and 3% Dextrose (Sigma-Aldrich ref D9434). The homozygous deletion of fah in FRGN mice which produces a fumaryloacetoacetate dehydrogenase deficiency that disrupts tyrosine metabolism, leading to buildup of hepatotoxic metabolite, fumarylacetoacetate.  With the administration of 2-(2-nitro-4- fluoromethylbenzoyl) cyclohexane -1,3-dione (CuRx™ Nitisinone (NTBC) Cat# 20-0026), the intracellular accumulation of furmarylacetoacetate is blocked and the mice live normal immune deficient mouse lifespans. Mice are cycling on 8mg/l NTBC treatment with SMX/TMP antibiotic and 3% of Dextrose for 3 days every 5 weeks. To maintain hydration of the mice during the extended period off Nitisinone, it is best to use sterile drinking water that contains 3% Dextrose. Because the dextrose provides an opportunistic environment for bacterial growth, new containers of sterile dextrose water need to be prepared every week as described previously (Azuma et al., 2007). Ten weeks old male mice FRGN® repopulated with human hepatocytes (Hu-FRGN®) and FRGN® repopulated with murine hepatocytes (Mu-FRGN®) (Cat#10-0013 and Cat#10-0009, YECURIS corporation, Oregon, USA) were fed a Pico Lab High Energy Mouse Diet 5LJ5 (LabDiet). Only mice with human hepatocyte repopulation >70% (corresponding to circulating levels of human albumin >3.5 mg/mL) were used in this study.

value: Suprachiasmatic Nucleus

tag: time

value: FRGN

value: control liver muranized


title: 14C_M_667

status: Public on May 25 2023

type: SRA

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

country: USA

institute: HHMI-Salk-Institute

library_source: genomic

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

molecule: genomic DNA

organism: Mus musculus

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: PCG

tag: age

tag: strain


title: MU_ZT14_2_SCN

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: genotype

tag: treatment


title: 14C_M_665


title: 14C_M_663


title: 14C_M_662


title: 14C_M_661


title: MU_ZT10_2_SCN


title: neclei isolated from LPS-treated mouse tongue epithelium

city: Philadelphia

first: Hong

last: Wang

address: 3500 Market Street

institute: Monell Chemical Senses Center

library_source: genomic single cell

data_processing:
Demultiplexed raw base call files generated from sequencing were processed using the 10x Genomics Cell Ranger ATAC pipeline (version 1.2.0).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: circumvallate papillae

extract_protocol:
To isolate the nuclei for scATAC-seq, the peeled tongue epithelia from PBS- and LPS-treated mice were prepared. Six mice per group were used. Epithelia from the circumvallate papillae were cut off and rinsed in calcium-free Tyrode’s buffer (140 mM NaCl, 5 mM KCl, 10 mM HEPES, 1 mM MgCl2, 10 mM glucose, 10 mM Na-pyruvate, 2 mM EGTA, pH 7.4). Circumvallate epithelia were then transferred to a solution containing 0.25% trypsin-EDTA (Fisher Scientific) and incubated at 37˚C for 15 min. Cold Opti-MEM with 10% fetal bovine serum (FBS) (Thermo Fisher Scientific) was added to the mixture, and cells were further dissociated by gentle pipetting. Cells were centrifuged, rinsed with cold Opti-MEM with 10% FBS, passed through a 40 µm cell strainer, and rinsed once with wash buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 1% bovine serum albumin (BSA), and 0.1% Tween-20). Dissociated cells were then resuspended in 0.1x Lysis buffer (10 mM Tris-HCl, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.9% BSA, 0.01% Tween-20, 0.01% NP40, 0.001% digitonin) and incubated on ice for 5 min. Cell lysis was monitored by staining with trypan blue solution (0.4%; Thermo Fisher Scientific). Nuclei were rinsed with wash buffer, centrifuged, resuspended in 1x nuclei buffer (10x Genomics), and counted. About 4000 nuclei per group were used for downstream ATAC-seq procedures.
The chromatin transposition reaction, nuclei partitioning, barcoding, and library construction were carried out using 10x Genomics Chromium scATAC reagent kits, following the manufacturer’s protocols. High-throughput sequencing was also performed at the NGSC using Illumina HiSeq 4000 instruments.
Cell Ranger ATAC 1.2.0

tag: developmental stage

value: adult

value: circumvallate papillae

value: LPS


title: 14C_M_659


title: 14C_M_660


title: 14C_M_657


title: 14C_M_656


title: 14C_M_654


title: NNN_69_5hmc

city: Bethesda

first: Chuanyuan

last: Chen

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Library strategy: Nano-hmC-Seal
The 5hmC and RNA-seq reads were then mapped to the UCSC hg19 reference genome by STAR-2.5.3 software
The de-duplication of 5hmC was performed using the parameter "-tbp 5" in makeTagDirectory of HOMER software
the gene raw counts matrix was generated by the HOMER's analyzeRepeats
Genome_build: hg19
Supplementary_files_format_and_content: txt

organism: Homo sapiens

source_name: bone marrow

extract_protocol:
mRNA was extracted from 1µg of total RNA by using Dynabeads mRNA Direct kit (Ambion). Nano-hmC-Seal was performed as previously described with minor changes. 9 Libraries were prepared with KAPA Hyperplus kit (KAPA KK8515) using extracted genomic DNA from patient peripheral blood or bone marrow cells.
20 ng of mRNA were used for library construction by using TruSeq stranded mRNA sample preparation kit (Illumina). For 5hmC, Briefly, 50ng genomic DNA in 14µl H2O was fragmented at 37 °C for 20 minutes by addition of 2µl of 10x KAPA Fragmentation Buffer and 4µl of KAPA Fragmentation Enzyme. The fragmented DNA was end-polished at 65 °C for 30 minutes by adding 2.8µl of End Repair & A-Tailing Buffer and 1.2µl of End Repair & A-Tailing Enzyme Mix. 3µl of 1.5µM Adapter (Bioo Scientific NOVA-514103) was added followed by 12µl of Ligation Buffer and 4µl DNA Ligase. The mixture was incubated at 20 °C for 1 hour. Libraries were then purified by DNA Clean and Concentrator kit (Zymo D4013) and eluted in 20µl H2O. β-GT labeling was then performed by addition of 0.85µl self-synthesized 3mM N3-UDG and 2.5µl of T4-βGT (Thermo EO0831) at 37 °C for 2 hours. Azide labeled DNA libraries were then purified by DNA Clean and Concentrator kit (Zymo D4013) and eluted in 30µl H2O. Libraries were further biotinylated by addition of 1µl 4.5mM (Sigma 760749) DBCO-PEG4-Biotin and incubated at 37 °C for 2 hours. Biotinylated DNA libraries were then purified by DNA Clean and Concentrator kit (Zymo D4013) and eluted in 30µl H2O. The biotinylated DNA was further enriched by 5 µl of M-270 Streptavidin beads (Thermo 65305) and incubated at room temperature for 30 minutes. The beads were washed 3 times with Wash Buffer (5 mM Tris-HCl (pH 7.5); 0.5 mM EDTA; 1 M NaCl; 0.05% Tween 20) and resuspended in 20µl H2O. Libraries were amplified with on-bead PCR by addition of 5µl Primer Mix (KAPA KK8515) and 25µl of Enzyme Mix (KAPA KK8515) with following condition (98 ˚C 30 s ;98 ˚C 15 s ;60 ˚C 30 s; 72 ˚C 30 s; Repeat 14 cycles; 72 ˚C 1 min). Post-amplification cleanup was performed by adding 0.9x Ampure beads (Beckman Coulter A63880); beads were washed twice with 80% ethanol and eluted in 50µl H2O.

tag: disease state

value: AML

value: bone marrow

tag: therapy

value: AZA

tag: patient


title: NNN_71_5hmc


title: NNN_68_5hmc


title: NNN_43_5hmc


title: NNN_37_5hmc


title: NNN_42_5hmc


title: MU_ZT14_1_SCN


title: MU_ZT22_2_SCN


title: MU_ZT18_1_SCN


title: MU_ZT06_2_SCN


title: MU_ZT02_2_SCN


title: MU_ZT10_1_SCN


title: 14C_M_664


title: 14C_M_653


title: NNN_40_5hmc


title: NNN_72_5hmc


title: MU_ZT06_1_SCN


title: 14C_M_651


title: 14C_M_652


title: NNN_47_5hmc


title: 14C_M_650


title: MU_ZT22_1_SCN


title: 14C_M_658


title: 14C_M_655


title: NNN_39_5hmc


title: 14C_M_648


title: 14C_M_649


title: 14C_M_647


title: MU_ZT02_1_SCN


title: 14C_M_646


title: NNN_8_5hmc


title: 14C_M_645


title: 14C_M_641


title: CCC_33_5hmc

source_name: peripheral blood

value: peripheral blood

value: HiDAC-Mito


title: 14C_M_644


title: 14C_M_642


title: CCC_32_5hmc


title: HU_ZT22_2_SCN

value: liver humanized


title: HU_ZT14_2_SCN


title: HU_ZT10_2_SCN


title: 14C_M_643


title: 14C_M_639


title: CCC_31_5hmc


title: 14C_M_640


title: HU_ZT18_2_SCN


title: 14C_M_638


title: HU_ZT02_2_SCN


title: CCC_29_5hmc


title: 14C_M_636


title: HU_ZT18_1_SCN


title: 14C_M_637


title: 14C_M_635


title: 14C_M_634


title: CCC_27_5hmc


title: 14C_M_633


title: HU_ZT14_1_SCN


title: CCC_26_5hmc


title: NNN_7_5hmc


title: HU_ZT06_1_SCN


title: CCC_23_5hmc


title: 14C_M_632


title: CCC_24_5hmc


title: 14C_M_631


title: 14C_M_630


title: 14C_M_628


title: 14C_M_629


title: 14C_M_627


title: CCC_22_5hmc


title: 14C_M_625


title: CCC_19_5hmc


title: 14C_M_626


title: MU_ZT14_2_ARC

source_name: Arcuate Nucleus

value: Arcuate Nucleus


title: CCC_21_5hmc

source_name: unknown

value: unknown


title: HU_ZT10_1_SCN


title: 14C_M_622


title: CCC_18_5hmc


title: MU_ZT18_2_ARC


title: 14C_M_621


title: 14C_M_623


title: 14C_M_620


title: 14C_M_624


title: 14C_M_619


title: MU_ZT02_2_ARC


title: MU_ZT06_2_ARC


title: 14C_M_618


title: HU_ZT02_1_SCN


title: 14C_M_617


title: MU_ZT10_2_ARC


title: 14C_M_616


title: CCC_15_5hmc


title: CCC_14_5hmc


title: 14C_M_614


title: MU_ZT18_1_ARC


title: 14C_M_613


title: 14C_M_612


title: CCC_13_5hmc


title: CCC_12_5hmc


title: 14C_M_611


title: MU_ZT22_2_ARC


title: MU_ZT14_1_ARC


title: 14C_M_610


title: MU_ZT10_1_ARC


title: CCC_10_5hmc


title: 14C_M_608


title: CCC_16_5hmc


title: CCC_8_5hmc


title: 14C_M_607


title: 14C_M_606


title: 14C_M_609


title: 14C_M_605


title: MU_ZT06_1_ARC


title: CCC_5_5hmc


title: MU_ZT22_1_ARC


title: 14C_M_615


title: MU_ZT02_1_ARC


title: 14C_M_602


title: HU_ZT22_2_ARC


title: 14C_M_603


title: 14C_M_600


title: CCC_1_5hmc


title: HU_ZT14_2_ARC


title: 14C_M_599


title: CCC_2_5hmc


title: CCC_4_5hmc


title: HU_ZT02_2_ARC


title: PB_152_5hmc

value: AZA-HiDAC-Mito


title: BM_152_5hmc


title: 14C_M_604


title: HU_ZT10_2_ARC


title: 14C_M_597


title: PB_150_5hmc


title: 14C_M_594


title: 14C_M_596


title: 14C_M_601


title: 14C_M_593


title: 14C_M_598


title: 14C_M_595


title: BM_150_5hmc


title: HU_ZT18_1_ARC


title: HU_ZT14_1_ARC


title: 14C_M_589


title: 14C_M_590


title: HU_ZT18_2_ARC


title: 14C_M_592


title: HU_ZT06_1_ARC


title: 14C_M_588


title: PB_144_5hmc


title: PB_143_5hmc


title: 14C_M_591


title: 14C_M_583


title: HU_ZT02_1_ARC


title: 14C_M_584


title: BM_144_5hmc


title: 14C_M_582


title: BM_143_5hmc


title: BM_142_5hmc


title: BM_141_5hmc


title: MU_ZT22_2_MUSCLE

source_name: Skeletal Muscle

value: Skeletal Muscle


title: PB_135_5hmc


title: MU_ZT18_2_MUSCLE


title: 14C_M_579


title: 14C_M_578


title: MU_ZT22_1_MUSCLE


title: 14C_M_576


title: 14C_M_577


title: 14C_M_581


title: 14C_M_575


title: MU_ZT18_1_MUSCLE


title: PB_133_5hmc


title: 14C_M_573


title: 14C_M_574


title: 14C_M_586


title: HU_ZT10_1_ARC


title: 14C_M_580


title: BM_135_5hmc


title: BM_133_5hmc


title: MU_ZT10_2_MUSCLE


title: MU_ZT14_1_MUSCLE


title: BM_130_5hmc


title: BM_128_5hmc


title: 14C_M_568


title: 14C_M_572


title: 14C_M_569


title: 14C_M_570


title: 14C_M_571


title: MU_ZT06_2_MUSCLE


title: MU_ZT10_1_MUSCLE


title: BM_126_5hmc


title: MU_ZT06_1_MUSCLE


title: BM_122_5hmc


title: MU_ZT02_2_MUSCLE


title: BM_123_5hmc


title: 14C_M_561


title: 14C_M_567


title: 14C_M_564


title: 14C_M_566


title: MU_ZT14_2_MUSCLE


title: 14C_M_563


title: 14C_M_565


title: 14C_M_560


title: 14C_M_558


title: 14C_M_559


title: MU_ZT02_1_MUSCLE


title: HU_ZT22_2_MUSCLE


title: 14C_M_556


title: 14C_M_562


title: 14C_M_555


title: PB_120_5hmc


title: 14C_M_553


title: HU_ZT18_3_MUSCLE


title: HU_ZT22_1_MUSCLE


title: BM_116_5hmc


title: PB_118_5hmc


title: 14C_M_551


title: 14C_M_550


title: 14C_M_554


title: 14C_M_549


title: BM_115_5hmc


title: HU_ZT18_2_MUSCLE


title: 14C_M_548


title: HU_ZT14_1_MUSCLE


title: 14C_M_547


title: HU_ZT18_1_MUSCLE


title: BM_113_5hmc


title: 14C_M_557


title: HU_ZT14_2_MUSCLE


title: BM_114_5hmc


title: BM_121_5hmc


title: 14C_M_545


title: 14C_M_544


title: PB_108_5hmc


title: 14C_M_543


title: HU_ZT10_2_MUSCLE


title: 14C_M_542


title: BM_110_5hmc


title: 14C_M_541


title: 14C_M_552


title: 14C_M_540


title: HU_ZT10_1_MUSCLE


title: BM_108_5hmc


title: PB_107_5hmc


title: HU_ZT06_3_MUSCLE


title: HU_ZT06_2_MUSCLE


title: PB_106_5hmc


title: HU_ZT02_3_MUSCLE


title: BM_107_5hmc


title: BM_106_5hmc


title: PB_98_5hmc


title: PB_97_5hmc


title: HU_ZT02_2_MUSCLE


title: MU_liver_ZT6_2_S24

source_name: Liver

value: Liver


title: BM_95_5hmc


title: 14C_M_535


title: 14C_M_527


title: 14C_M_528


title: 14C_M_529


title: 14C_M_538


title: 14C_M_526


title: 14C_M_531


title: 14C_M_533


title: 14C_M_532


title: 14C_M_539


title: 14C_M_537


title: 14C_M_536


title: 14C_M_534


title: 14C_M_525


title: 14C_M_530


title: 14C_M_524


title: HU_ZT06_1_MUSCLE

value: FRGN


title: BM_91_5hmc


title: 14C_M_523


title: 14C_M_546


title: MU_liver_ZT2_2_S21

value: control liver muranized


title: HU_ZT02_1_MUSCLE


title: PB_92_5hmc


title: 14C_M_520

value: PCG


title: 14C_M_521


title: 14C_M_522


title: MU_liver_ZT2_1_S26


title: 14C_M_519


title: PB_90_5hmc


title: MU_liver_ZT6_1_S3


title: MU_liver_ZT22_2_S12


title: MU_liver_ZT18_1_S15


title: BM_90_5hmc


title: 14C_M_516


title: 14C_M_518


title: 14C_M_517


title: 14C_M_255


title: 14C_M_515


title: 14C_M_254


title: MU_liver_ZT14_2_S4


title: 14C_M_513


title: MU_liver_ZT22_1_S18


title: 14C_M_253


title: PB_88_5hmc


title: PB_84_5hmc


title: BM_88_5hmc


title: MU_liver_ZT14_1_S11


title: 14C_M_252


title: 14C_M_251


title: BM_82_5hmc


title: MU_liver_ZT10_2_S27


title: 14C_M_248


title: 14C_M_249


title: 14C_M_250


title: 14C_M_512


title: BM_92_5hmc


title: MU_liver_ZT18_2_S8


title: MU_liver_Zt10_1_S7


title: HU_liver_ZT6_3_S20


title: PB_77_5hmc


title: HU_liver_ZT6_1_S5


title: BM_77_5hmc


title: PB_73_5hmc


title: HU_liver_ZT2_3_S17


title: 14C_M_244


title: 14C_M_243


title: 14C_M_242


title: BM_73_5hmc


title: HU_liver_ZT2_2_S22


title: 14C_M_241


title: PB_76_5hmc


title: PB_80_5hmc


title: HU_liver_ZT2_1_S1


title: 14C_M_247


title: 14C_M_246


title: PB_72_5hmc


title: 14C_M_240


title: HU_liver_ZT22_2_S14


title: BM_80_5hmc


title: 14C_M_245


title: HU_liver_ZT6_2_S25


title: BM_76_5hmc


title: HU_liver_ZT22_1_S19


title: BM_72_5hmc


title: HU_liver_ZT18_3_S23


title: MCF7, rep2

city: Taipei

first: Trees-Juen

last: Chuang

address: 128 Academia Road, Section 2, Nankang

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

data_processing:
RNA-seq read wre aligned to GRCh38 genome using STAR.
Expressions of genes and isoforms(read count, FPKM, TPM) were calculated using RSEM.
Assembly: hg38
Supplementary files format and content: txt (read count, FPKM, and TPM)

source_name: cell line

growth_protocol: MCF-7 cells were culture in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FBS and 1% penicillin-streptomycin at 37oC and placed in a humidified atmosphere containing 5% CO2

extract_protocol: Total RNA (10 mg) was harvested from MCF7 using TRI reagent (Ambion) for cDNA library preparation. Enrichment of mRNA by depletion of ribosomal RNA was performed using a RiboMinus transcriptome isolation kit (Invitrogen). RiboMinus RNA (1 mg) was then fragmented using RNase III for 10 min and cleaned up using a RiboMinus concentration module (Invitrogen).

value: cell line

tag: cell line

tag: cell type

value: human breast cancer


title: 14C_M_237


title: 14C_M_239


title: PB_74_5hmc


title: HU_liver_ZT18_2_S10


title: PC9/p53EV DMSO rep1 [EV_UN_1]

city: Fukuoka

first: RITSU

last: IBUSUKI

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Respiratory Medicine

country: Japan

institute: Kyushu University

data_processing:
MGI DNBseq-G400 FAST was used to perform the amplicons deep sequencing following the standard operation protocol. The sequence format was 150bp pair read for all samples.
All sequencing reads were trimmed low-quality bases and adapters with Trimmomatic (v.0.38) .
Raw counts for each gene were estimated in each sample using RSEM version 1.3.0 and Bowtie 2. Calculation of the log fold-change (log FC) and p-value were performed using edgeR.
Assembly: hg38
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

source_name: Lung cancer cell line

growth_protocol: Cells were cultured (1 × 10^6 cells into a 12 well plate) for 24 hours before treatment on uncoated plastic in RPMI 1640 (Gibco, Carlsbad, CA, USA) supplemented with 10 % fetal bovine serum and 1 % penicillin–streptomycin (Gibco) .

extract_protocol:
Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Hilden, Germany) , in accordance with the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols MGIEasy RNA Directional Library Prep Set (MGI).

treatment_protocol: 600nM osimertinib or DMSO as a control for 24 hours

value: Lung adenocarcinoma cells

value: TP53 null


title: PC9/p53R248Q DMSO rep1 [R248Q_UN_1]

value: TP53 GOF mutation


title: 14C_M_236


title: 5-3, RNA-seq rep3 [VS279]

first: Vinutha

last: Balachandra

address: 10 Center Drive

department: National Cancer Institute, Genetics Branch

institute: National Institute for Health

data_processing:
Basecalls were performed using bcl2fastq for NextSeq output.
RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using cudadapt v1.18, discarding reads left with < 20 bp
RNA-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2-2.4.2.
Assembly: hg38

molecule: polyA RNA

source_name: squamous cell carcinoma of head and neck

growth_protocol: Cells were grown in DMEM medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin and 2nM L-glutamine.

extract_protocol:
RNA was extracted using the Direct-zol RNA miniprep kit (Zymo Research, Irvine, CA).
Libraries were constructed according to the Illumina TruSeq Stranded mRNA Library Prep kit (cat# 20020594).

treatment_protocol: Cells were treated with human IFN-β at 1000U/ml (R&D systems Inc, 8499-IF-010/CF) for 24h prior to cell collection.

value: SMYD3 KO 5-3

value: human IFN-β (R&D systems Inc, 8499-IF-010/CF) for 24h prior to collection


title: PC9/p53R248Q osimertinib rep2 [R248Q_24h_2]


title: PC9/p53EV osimertinib rep1 [EV_24h_1]


title: PC9/p53EV DMSO rep2 [EV_UN_2]


title: PC9/p53R248Q osimertinib rep1 [R248Q_24h_1]


title: PB_71_5hmc

value: AML

value: peripheral blood


title: PC9/p53R248Q DMSO rep2 [R248Q_UN_2]


title: 5-3, RNA-seq rep2 [VS278]

value: squamous cell carcinoma of head and neck


title: PC9/p53EV osimertinib rep2 [EV_24h_2]


title: 14C_M_234


title: BM_74_5hmc

value: bone marrow


title: HU_liver_ZT14_2_S6

value: liver humanized


title: HU_liver_ZT18_1_S16


title: 5-3, RNA-seq rep1 [VS277]


title: BM_71_5hmc

value: AZA-HiDAC-Mito


title: HN6, RNA-seq rep3 [VS267]


title: 14C_M_233


title: 14C_M_238


title: HU_liver_ZT14_1_S13

value: Liver


title: PB_69_5hmc


title: HN6, RNA-seq rep2 [VS266]


title: 14C_M_232


title: HN6, RNA-seq rep1 [VS265]


title: PB_68_5hmc


title: HU_liver_ZT10_2_S2

value: FRGN


title: 14C_M_231


title: 14C_M_230


title: 14C_M_229


title: PB_67_5hmc


title: BM_69_5hmc


title: HU_liver_ZT10_1_S9


title: 14C_M_228


title: BM_68_5hmc


title: PB_65_5hmc


title: 14C_M_226


title: BM_67_5hmc


title: 14C_M_227


title: BM_65_5hmc


title: 14C_M_225


title: 14C_M_224


title: PB_66_5hmc


title: MKL1 cells treated with vehicle (DMSO) [MKL1_C1]

city: Long Beach

first: Ling

last: Gao

email: ling.gao@va.gov, lingg3@hs.uci.edu

state: California

address: 5901 E.7th Street

institute: Department of Veterans Affairs

data_processing:
Rsubread for alignment
Sequence reads were mapped to GRCh38 reference human genome
Read count extraction was carried out using featureCounts() function
Differential analysis on raw data and sample distance calculations on normalized data performed using DESeq2
Assembly: hg38
Supplementary files format and content: consolidated tab-delimited text file represents raw counts for each sample

source_name: MKL1 cells treated with vehicle (DMSO)

growth_protocol: Suspension cultures were maintained in RPMI-1640 media supplemented with 10% Fetal bovine serum, penicillin-streptomycin (100 U/ml) and L-glutamine (4mM), at 37C in a humidified atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). >1.0 ug of total RNA was evaluated for quality using Agilent Bioanalyzer Nano RNA chip prior to library construction
RNA libraries for RNA-seq were prepared using Illumina TruSeq stranded mRNA following manufacturer's protocols.

treatment_protocol: Cells were treated with 10µM Domatinostat (Selleck Chem, S7555) or vehicle control (DMSO) for 24h

value: Merkel cell carcinoma cell line

value: MCPyV positive

value: DMSO


title: MKL1 cells treated with 10µM Domatinostat [MKL1_D1]

value: Domatinostat (10µM)


title: 14C_M_223

value: PCG


title: MKL1 cells treated with vehicle (DMSO) [MKL1_C2]


title: PB_64_5hmc


title: PB_61_5hmc


title: 14C_M_222


title: mCPBA_TFEA_pH_7.4_1

city: West Haven

first: Matthew

last: Simon

state: Connecticut

address: 300 Heffernan Dr, 300 Hefferna Dr

institute: Yale University

description:
For tdf files, reads are filtered for number of T-to-C mutations (0-5+) and strandedness (min/pos). For counts dataframe (counts_data.csv.gz), the columns indicate the sample name, aligner used to aign the data (aligner), aligner settings used (settings), gene, transcript, whether the read in intronic (intronic), number of T-to-C mutations, the the number of reads in the group (n). For the bakR data (bakR_kdeg_data.csv.gz), thew columns indicate the sample, transcript, first-order rate constant of RNA degradation with drop out (kdeg_DO), first-order rate constant of RNA degradation with improved handling (kdeg_IH), the log2 fold change in the first-order rate constant between drop out and improved handling conditions (L2FC_kdeg), and the adjusted p-value for the log2 fold change.
counts_data.csv.gz
bakR_kdeg_data.csv.gz

data_processing:
Adpter sequences were trimmed from raeds using Cutadapt.
PCR duplicates were remvoed using fastuniq.
Reads were aligned to the GRCh38 genome using HISAT2, STAR, or HISAT-3N with default parameters or more lenient parameters to reduce mismatch penalties. For HISAT2 moderately lenients paramers are --mp 4,2 and very lenient parameters are --mp 1,0. For STAR moderately lenients paramers are --outFilterMismatchNmax 20 and very lenient parameters are --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 1 --outFilterLread 0.05.
Reads were processed using Picard tools, including FixMateInformation, SortSam and BuildBamIndex
Reads were filtered for those that aligned uniquely, with MAPQ ≥ 2, and without insertions.
HTSeq-count was used to identify mapped reads in UCSC transcripts (union mode).
T-to-C mutations were identified using a custom script (available on Bitbucket). Only mutations at positions with a base quality score of greater than 40 that were at least three nt from the end of the read were counted. Reads were excluded where there were greater than five T-to-C mutations and these mutations did not account for at least one third of the observed mutations (NM tag).
SNP sites were filtered from our data in two ways: 1, bcftools was used to identify T-to-C SNP sites in control samples, and these sites were excluded from analysis; 2, sites exhibiting high T-to-C mutation rates in non-s4U treated controls were excluded from analysis.
STAR aligner was used to make genome-coverage tracks (inputAlignmentsFromBam mode, outWigType tdf), and tracks were normalized using DESeq2 (estimateSizeFactors).
Tracks were converted to binary format using IGVtools (toTDF).
Half-life estimates from NR-seq data were estimated using an R package, bakR.
Assembly: GRCh38
Supplementary files format and content: Processed data files include tdf files to visualize sequencing data in IGV, a table of read counts and T-to-C mutation counts by gene from NR-seq, and a table of transcript first-orde rate constants by gene from NR-seq data estimated by the bakR R package and the log2 fold change in the measured constant between drop out and improved handling conditions.
Library strategy: NRRNA-seq

growth_protocol: 293T were grown in Dulbecco’s Modified Essential Media supplemented with 10% fetal bovine serum (Gibco) and Pen/Strep (50 U/ml).

extract_protocol:
RNA was harvested with Trizol reagent, followed by chloroform extraction and isopropanol precipitation. For all nucleotide recoding RNA sequencing (NR-seq) methods, genomic DNA was depleted using Turbo DNAse, followed by cleanup with RNAclean beads. RNA for NR-seq was treated with nucleotide conversion chemistry as described in Schofield et al. Nature Methods 2018, Riml et al. Angew Chem Int Ed Engl 2017, or Herzog et al. Nat Methods 2017.
NR-seq libraries were generated following standard protocols using the SMARTer Stranded Total RNA-Seq Kit-Pico Input Mammalian, V2 (Takara Bio USA, cat. 634413).

treatment_protocol: 293T cells were treated with 100 μM s4U for 2 hours or untreated as unlabeled controls.

value: cell line

value: HEK 293T

value: Human embryonic kidnerycells

value: WT

tag: s4u labelling

value: 2 hr 100 100 μM 4-thiouridine

tag: chemistry

value: mCPBA + TFEA pH 7.4

tag: handling

value: Improved handling conditions


title: mCPBA_TFEA_pH_7.4_2


title: mCPBA_NH3_pH_8.8_2

value: mCPBA + NH3 pH 8.8


title: mCPBA_NH3_pH_8.8_1


title: NaIO4_TFEA_pH_7.4_1

value: NaIO4 + TFEA pH 7.4


title: 14C_M_221


title: NaIO4_TFEA_pH_7.4_2


title: PB_60_5hmc

value: AML

value: peripheral blood

value: AZA-HiDAC-Mito


title: MKL1 cells treated with 10µM Domatinostat [MKL1_D2]

value: Merkel cell carcinoma cell line


title: mCPBA_TFEA_pH_5.2_2

value: mCPBA + TFEA pH 5.2


title: 14C_M_220


title: mCPBA_TFEA_pH_5.2_1


title: PB_57_5hmc


title: A549sgNegTSGT1_1

city: San Francisco

first: Alex

middle: G

last: Lee

address: 1550 4th Street

institute: UCSF

data_processing:
FASTQC (0.11.8) was used to get the QC results.
The raw count table was generated using MAGeCK program, a model-based Analysis of Genome-wide CRISPR-Cas9 Knockout. The sub-command count ask MAGeCK to generate sgRNA count table using the fastq files and the sgRNA information (including sgRNA id, sequence and gene target) as input.
Assembly: no alignment necessary
Supplementary files format and content: tab delimited text file

source_name: Neg, Control, T1

growth_protocol: Cells were cultured in RPMI medium with 10% serum and passaged when confluent. During the screen, the pooled libraries were maintained at 1,000 cells per sgRNA.

extract_protocol:
DNA was extracted using Qiagen’s Blood Maxi Kit, sgRNA cassettes were PCR-amplified from genomic DNA (T0 and end points) using NEB Q5 DNA Polymerase in order to add deep sequencing adapters and sample barcodes. Finally, sgRNA compositions was analyzed by deep sequencing using HiSeq4000 SE65 technology (Illumina).
The sgRNA library was synthetized as a single oligo pool (Twist Bioscience), PCR-amplified and cloned into the lentiviral vector pMB160, derived from pLG20 (gift from Luke Gilbert, UCSF).

treatment_protocol: Cells were transfected with sgRNA oligos using Lipofectamine RNAiMAX (following manufacture's instructions).

value: epithelial cell

tag: timepoint

tag: disease

value: lung carcinoma


title: A549sgUHRF1TSGT1_2

source_name: UHRF1 pertrub, T1


title: A549sgNegTSGT1_2


title: NaIO4_NH3_pH_8.8_1

value: NaIO4 + NH3 pH 8.8


title: A549sgUHRF1TSGT0_2

source_name: UHRF1 pertrub, T0


title: A549sgUHRF1TSGT0_1


title: A549TSGlibT0

source_name: Control, T0


title: A549sgUHRF1TSGT1_1


title: 14C_M_219

tag: brain region

value: PCG


title: A549sgNegTSGT0_2

source_name: Neg Control, T0


title: PB_55_5hmc

tag: time


title: TUC_IH_2

value: cell line

value: HEK 293T

value: OsO4 + NH3


title: NaIO4_NH3_pH_8.8_2

value: Human embryonic kidnerycells

value: WT

value: 2 hr 100 100 μM 4-thiouridine


title: 14C_M_218

source_name: C57BL/6J Male P56 Mouse Brain

tag: age

tag: strain


title: BM_55_5hmc

tag: tissue

value: bone marrow


title: 14C_M_217


title: A549sgNegTSGT0_1


title: TUC_IH_1

tag: genotype

value: Improved handling conditions


title: input

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

description: input DNA

data_processing:
Basecalls performed using BaseCall version 1.1.2
ChIP-seq reads were aligned to the mm9 genome assembly using SOAPaligner/soap2 version 2.21 with the following configurations：-v 2 -s 35 -m 50 -x 600
Data were filtered using the following specifications：Sequenced reads with adaptor sequence or low-quality sequence (we define the low quality read as the percentage of base which quality is lesser than 5 is greater than 50% in a read) are discarded
Peaks were called using macs2 version 2.1.0 with the following setting: --bw 200 -g mm -s 49 -p 1e-5 -m 10 30
Genome_build: hg19
Supplementary_files_format_and_content: Bw files were transformed from wig files generated using macs2

source_name: CCMCL1 MCL cells

growth_protocol: We harvested mouse brains at indicated ages and cross-linked with 1% paraformaldehyde.

extract_protocol:
After isolation of nucleus with lysis buffer (50 mM HEPES-KOH, 135 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% TritonX100), the chromatin was digested with micrococcal nuclease. The pellet was resuspended with IP buffer (50 mM Tris-HCl, 100 mM NaCl, 10 mM EDTA, 0.1% SDS, and 1% TritonX100) and the nuclear membrane was broken with sonication. IP was performed with respective antibody overnight at  cold room. The antibody-antigen was precipitated with magnetic beads. The ChIPed DNA was eluted and extracted with DNA extraction kit (MN #740609.250).
Libraries were made using KAPA Hyper Prep kit (KAPABiosystems #KR0961) following manufacturer’s instructions. Briefly, 30 ng from each immunoprecipitated or Input DNA, were end-repaired, phosphorylated, A-tailed and ligated to adaptors (Roche SeqCap Adapter kit A #07141530001). Ligated products were size selected with 0.8X SPRI beads to obtain 250~350 bp of DNA. After purification, 8-cycle PCR amplification reaction was performed. PCR product was cleaned by the use of 1X SPRI beads. Final product was resuspended in 30 ul of Tris buffer.

value: blood

value: Mature B cell

value: Mantle cell lymphoma

tag: chip antibody


title: 14C_M_216


title: PB_58_5hmc

tag: disease state

value: AML

value: peripheral blood

value: AZA-HiDAC-Mito


title: TUC_IH_NF

value: Unlabelled, -s4U control


title: NNN_71_RNA

data_processing:
The 5hmC and RNA-seq reads were then mapped to the UCSC hg19 reference genome by STAR-2.5.3 software
The de-duplication of 5hmC was performed using the parameter "-tbp 5" in makeTagDirectory of HOMER software
the gene raw counts matrix was generated by the HOMER's analyzeRepeats
Genome_build: hg19
Supplementary_files_format_and_content: txt

source_name: bone marrow

tag: therapy

value: AZA


title: TUC_DO_2

value: Drop out conditions


title: 14C_M_215

value: PCG


title: PB_54_5hmc

source_name: peripheral blood

tag: patient


title: TUC_DO_1

value: cell line

tag: cell line

value: HEK 293T


title: NNN_68_RNA


title: NNN_72_RNA


title: BM_58_5hmc


title: BM_54_5hmc


title: BM_57_5hmc


title: PB_53_5hmc


title: 14C_M_213


title: 14C_M_212


title: 14C_M_211


title: PB_51_5hmc


title: TUC_DO_NF

tag: cell type

value: Human embryonic kidnerycells

value: OsO4 + NH3


title: NNN_42_RNA


title: NNN_40_RNA


title: 14C_M_209


title: 14C_M_210


title: SLAM_IH_2

value: WT

tag: s4u labelling

value: 2 hr 100 100 μM 4-thiouridine

value: Iodoacetimide alkylation


title: BM_53_5hmc

value: bone marrow


title: BM_51_5hmc


title: SLAM_IH_1

tag: chemistry

value: Improved handling conditions


title: NNN_47_RNA


title: SLAM_DO_1

tag: handling


title: PB_48_5hmc


title: NNN_39_RNA


title: 14C_M_208


title: NNN_69_RNA


title: 14C_M_214


title: SLAM_DO_2


title: 14C_M_207


title: NNN_8_RNA


title: PB_47_5hmc


title: NNN_37_RNA


title: SLAM_IH_NF


title: SLAM_DO_NF


title: BM_48_5hmc


title: NNN_7_RNA


title: BM_47_5hmc


title: 14C_M_205


title: TL_IH_1

value: NaIO4 + TFEA  pH 5.2


title: CCC_8_RNA

value: AML

value: HiDAC-Mito


title: TL_IH_NF


title: BM_45_5hmc

value: AZA-HiDAC-Mito


title: TL_IH_2


title: CCC_5_RNA


title: BM_43_5hmc


title: 14C_M_203


title: PB_42_5hmc

value: peripheral blood


title: CCC_33_RNA


title: TL_DO_1


title: 14C_M_201


title: 14C_M_206


title: VD3VPA_3

city: Yokohama

first: Shoen

last: Kume

address: Kanagawa, Yokohama City Midori Ward Nagatsutacho4259-B1 Building 812

department: Life Science and Technology

institute: Tokyo Institute of Technology

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.  In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.   At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly.  Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 2 reads were aligned to the reference genome using Hisat2 v2.0.5.  We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.  And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.  FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).  DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution.  The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate.  Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected.  GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.   KEGG is a database resource for understanding high-level functions and 3 utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/).  We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.  The Reactome database brings together the various reactions and biological pathways of human model species.  Reactome pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. The DO (Disease Ontology) database describes the function of human genes and diseases.  DO pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes.   The DisGeNET database integrates human disease-related genes. DisGeNET pathways with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. We used clusterProfiler software to test the statistical enrichment of differentially expressed genes in the Reactome pathway, the DO pathway, and the DisGeNET pathway.
Gene Set Enrichment Analysis (GSEA) is a computational approach to determine if a pre-defined Gene Set can show a significant consistent difference between two biological states.  The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were tested to see if they were enriched at the top or bottom of the list.  Gene set enrichment analysis can include subtle expression changes. We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO, KEGG, Reactome, DO and DisGeNET data sets were used for GSEA independently.
Differential gene expression analysis was performed using the Subio platform (Subio).
Assembly: GRCh38.p13

extract_protocol:
RNA was extracted using the Cica Geneus RNA Prep Kit (Kanto Chemical) and DNase I (Qiagen) treatment was performed according to the manufacturer’s instructions.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.   Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.   Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.   Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-).   Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.   Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities.   After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization.   In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).   Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor- ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR.   Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.   At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system (with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection).  The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions.   After cluster generation, the library preparations were sequenced on an Illumina platform (Novaseq 6000PE150) and paired-end reads were generated.カキハ オクッテイタダイタ ガイヨウニ シュッテン ヨウ ヨウカクニン オソラク コンカイハ

value: human iPS cells

tag: differentiation stage

value: iPSC-derived Enterocytes

tag: treatment

value: From D15 to D23 under M3 with 100 uM VPA and 1 uM VD3


title: TL_DO_NF

value: cell line

value: Unlabelled, -s4U control

value: Drop out conditions


title: VD3VPA_2


title: CCC_32_RNA


title: 14C_M_200

tag: brain region

value: PCG


title: PB_38_5hmc

tag: time


title: VD3VPA_1


title: 14C_M_199

tag: age


title: PB_37_5hmc


title: CCC_29_RNA


title: CCC_31_RNA


title: CCC_27_RNA


title: BM_38_5hmc


title: VPA_3

value: From D15 to D23 under M3 with 100 uM VPA and without VD3


title: PB_25_5hmc


title: VPA_2


title: CCC_4_RNA

value: unknown


title: VPA_1


title: 14C_M_204

tag: strain


title: 14C_M_202


title: TL_DO_2

tag: tissue

value: HEK 293T

value: Human embryonic kidnerycells

value: WT

value: 2 hr 100 100 μM 4-thiouridine


title: 14C_M_198


title: 14C_M_197


title: 14C_M_196


title: CCC_26_RNA

value: AML

value: bone marrow


title: PB_24_5hmc

value: AZA-HiDAC-Mito


title: CCC_24_RNA

value: HiDAC-Mito


title: PB_40_5hmc

value: peripheral blood


title: 14C_M_195


title: BM_25_5hmc


title: CCC_23_RNA


title: 14C_M_194


title: VD3_2

value: human iPS cells

value: iPSC-derived Enterocytes

value: From D15 to D23 under M3 with 1 uM VD3


title: VD3_3


title: VD3_1


title: CCC_22_RNA


title: BM_24_5hmc


title: PB_23_5hmc


title: 14C_M_193


title: CCC_21_RNA


title: 14C_M_192


title: CCC_19_RNA


title: 14C_M_127


title: PB_22_5hmc


title: Control_1

value: From D15 to D23 under M3 without VD3


title: CCC_18_RNA


title: Control_2


title: BM_23_5hmc


title: 14C_M_126


title: PB_19_5hmc


title: 14C_M_125


title: CCC_15_RNA


title: CCC_16_RNA


title: BM_22_5hmc


title: Takara ASI

description: Takara ASI

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts.   In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.   At the same time, Q20, Q30 and GC content of the clean data were calculated.   All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.   Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure.   STAR exhibits better alignment precision and sensitivity than other RNA-seq aligners for both experimental and simulated data.
HTSeq was used to count the read numbers mapped of each gene.   And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.   RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Differential gene expression analysis was performed using the Subio platform (Subio).
Assembly: GRCh38.p13
Supplementary files format and content: RNAseq1_subioexportedprocesseddata.xlsx representing Raw Signal (count) and Processed Signal (RPKM).

source_name: Adult Small Intestine

extract_protocol:
RNA was extracted using the RNeasy micro-kit (Qiagen, Germany) or Cica Geneus RNA Prep Kit (Kanto Chemical) and DNase I (Qiagen) treatment was performed according to the manufacturer’s instructions.
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.   Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.   Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.   Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-).   Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.   Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities.   After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization.   In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).   Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor- ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR.   Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.   At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.  The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions.   After cluster generation, the library preparations were sequenced on an Illumina platform (Novaseq 6000PE150) and paired-end reads were generated.
Novaseq 6000PE150

value: Adult Small Intestine

value: Intestinal cells


title: PB_18_5hmc


title: D23, -VD3, rep 3

description: D23 -VD3 3


title: Biochain ASI

description: Biochain ASI


title: CCC_14_RNA


title: 14C_M_124

value: PCG


title: 14C_M_123


title: BM_15_5hmc


title: CCC_13_RNA


title: 14C_M_122


title: Control_3


title: BM_13_5hmc


title: CCC_12_RNA


title: 14C_M_121


title: PB_12_5hmc


title: CCC_10_RNA


title: CCC_1_RNA


title: 14C_M_120


title: PB_11_5hmc


title: PB_6_5hmc


title: 14C_M_119


title: D23, -VD3, rep 1

description: D23 -VD3 1


title: D23, -VD3, rep 2

description: D23 -VD3 2


title: D23, +VD3, rep 2

description: D23 +VD3 2

value: From D15 to D23 under M3 with VD3


title: PB_97_RNA


title: D15, rep 3

description: D15 3

value: iPSC-derived Intestinal Progenitor (D15)


title: PB_5_5hmc


title: 14C_M_118


title: BM_6_5hmc


title: 14C_M_117


title: D15, rep 2

description: D15 2


title: PB_92_RNA


title: D15, rep 1

description: D15 1


title: BM_5_5hmc


title: PB_91_RNA


title: 14C_M_116


title: PB_4_5hmc


title: 14C_M_115


title: D23, +VD3, rep 3

description: D23 +VD3 3


title: 14C_M_113


title: BM_4_5hmc


title: PB_84_RNA


title: D23, +VD3, rep 1

description: D23 +VD3 1


title: PB_83_RNA


title: PB_93_RNA


title: BM_2_5hmc


title: PB_64_RNA


title: PB_3_5hmc


title: 14C_M_111


title: 14C_M_110


title: PB_6_RNA


title: 14C_M_109


title: PB_5_RNA


title: D10, rep 3

description: D10 3

value: iPSC-derived Intestinal Progenitor (D10)


title: 14C_M_108


title: BM_3_5hmc


title: PB_88_RNA


title: PB_1_5hmc


title: Caco2, rep 3

description: Caco2 3

source_name: Colon

value: Colon

value: Epithelial cells


title: D0, rep 3

description: D0 3

value: Undifferentiated (D0)


title: D10, rep 2

description: D10 2


title: BM_1_5hmc

value: AML

value: bone marrow


title: D10, rep 1

description: D10 1


title: D0, rep 2

description: D0 2


title: 14C_M_107


title: PB_38_RNA

value: AZA-HiDAC-Mito


title: D0, rep 1

description: D0 1


title: PB_2_5hmc

value: peripheral blood


title: Caco2, rep 2

description: Caco2 2


title: 14C_M_112


title: PB_37_RNA


title: 14C_M_106


title: Pooled BCR Library 8 for Donors HDL153, HDL141, HDL142

city: New York

first: Peter

middle: A

last: Sims

address: 3960 Broadway, Lasker 203AC

institute: Columbia University

description: JoshGC.bcr.filtered_contig_annotations.csv.gz

data_processing:
Quantification of scRNA-seq library pools was performed by pseudoalignment to the human transcriptome (Gencode v24 annotation derived from GRCh38) using kallisto  v0.46.2 in “BUS” mode. ADT barcodes were extracted from demultiplexed fastq files using custom scripts (https://github.com/simslab/DropSeqPipeline8). Hashtag barcodes from cell-identifying barcodes containing >1,000 unique transcripts were demultiplexed using the Hashsolo  with default parameters. scBCR-seq data were demultiplexed and aligned with VDJ cassette and variable sequencing identification using Cell Ranger VDJ v7.0.1 using the GRCh38/Ensembl v7.0.0 annotation from 10x Genomics.
Assembly: GRCh38/Gencode v24
Supplementary files format and content: CITE-seq/scRNA-seq files are tab-delimited count matrices where each column is a cell and each row is a feature (antibody or gene). There is a header indicating the cell-identifying barcode, hashtag, and sample-of-origin for each cell (column). The header is formatted as barcode_donor_hashtag_tissue.
Supplementary files format and content: scBCR-seq files are csv filtered contig files output from Cell Ranger VDJ that contain the VDJ cassettes, nucleotide/amino acid sequences of variable regions, cell-identifying barcode, hashtag, and sample-of-origin for each cell.
Library strategy: BCR-seq

source_name: mixture of lung lymph node, mesenteric lymph node, lung

extract_protocol:
Lung and lymph nodes were mechanically and enzymatically digested into single-cell suspensions as described in Szabo et al, Nature Communications, 2019. B cells were enriched by FACS using antibodies against CD45, CD33, CD66b, CD3, and CD19 to isolate CD45+/CD66b-/CD33-/CD3-/CD19+ cells from each tissue. Enriched B cell populations from each sample were resuspended in PBS/FBS/EDTA and stained with 3 uL of a unique TotalSeq C DNA-barcoded hashtag for 30 minutes on ice. Cells were then washed, counted, and pooled in PBS/FBS to ensure equal nunbers of live cells from each sample.
CITE-seq/scBCR-seq libraries were constructed using the Chromium Next GEM Single Cell 5’ Reagent Kit v2 (10x Genomics) with both a 5’ Feature Barcode Kit (10x Genomics) for antibody-derived tag (ADT) amplification and a Chromium Single Cell Human BCR Amplification Kit (10x Genomics) for targeted BCR amplification, according to the manufacturer’s instructions.

value: B cells

tag: antibodies/tags


title: PB_157_RNA


title: Caco2, rep 1

description: Caco2 1


title: 14C_M_105


title: Pooled BCR Library 7 for Donors HDL153, HDL141, HDL142

value: mixture of lung lymph node, mesenteric lymph node, lung


title: PB_156_RNA


title: PB_152_RNA


title: 14C_M_104


title: 14C_M_103


title: PB_135_RNA


title: Pooled BCR Library 5 for Donors HDL153, HDL141, HDL142


title: Caco-2 cells, antibiotic, rep2

city: Woluwe-Saint-Lambert

first: Laure

last: Elens

address: Avenue Emmanuel Mounier 72

department: LDRI

country: Belgium

institute: UCLouvain

description:
cells were treated for 48h
atb2_1

data_processing:
Fastq files were processed using a standard RNAseq pipeline including Trimmomatic-0.38 (Bolger et al.) to remove low quality reads.
Hisat2-2.1.0 (Kim et al.) to align reads to the human genome (GRCh38), and gene expression levels were evaluated using featureCounts from subread-2.0.0 (Liao et al.) and Homo_sapiens.GRCh38.105.chr.gtf.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts values for each sample

source_name: gastrointestinal

growth_protocol:
Caco-2 cells were maintained in DMEM (high glucose, high glutamine) supplemented with 10% fetal bovine serum (FBS), 1% antibiotic-antimycotic, and 1% nonessential amino acids, in 5% CO2 at 37°C.
Caco-2 cells were seeded in plates and growth for 48h before treatment.

extract_protocol:
RNA was harvested using Tripure reagent. At least 0.5ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Immunia TruSeq Stranded Total RNA with Ribo-Zero.

treatment_protocol:
Treatment were then added for 48 additional hours before RNA extraction (treatment constitutes 10% of the medium).
Treatment was either PBS (vehicle), faecal water from control mice, faecal water from antibiotics-treated mice, or antibiotic cocktail.
Antibiotic cocktail was composed of neomycin (1 g/L), vancomycin (0.5 g/L) and meropenem (0.25 g/L).

value: gastrointestinal

tag: genotype

value: wildtype

value: antibiotics


title: Caco-2 cells, antibiotic, rep3

description:
cells were treated for 48h
atb3_1


title: 14C_M_102


title: PB_118_RNA

tag: disease state


title: Caco-2 cells, antibiotic, rep1

description:
cells were treated for 48h
atb1_1


title: Pooled BCR Library 4 for Donors HDL153, HDL141, HDL142


title: Caco-2 cells, faecal water antibiotic, rep8

description:
cells were treated for 48h
FW_atb8_1

value: faecal water, antibiotic mice


title: 14C_M_100

value: PCG


title: Pooled BCR Library 3 for Donors HDL153, HDL141, HDL142


title: PB_120_RNA

tag: therapy


title: 14C_M_101


title: 14C_M_99


title: BM_98_RNA

tag: patient


title: Caco-2 cells, faecal water antibiotic, rep7

description:
cells were treated for 48h
FW_atb7_1

tag: cell line


title: Pooled BCR Library 2 for Donors HDL153, HDL141, HDL142

tag: cell type


title: Pooled BCR Library 1 for Donors HDL153, HDL141, HDL142


title: 14C_M_98


title: BM_97_RNA


title: Pooled BCR Library 6 for Donors HDL153, HDL141, HDL142


title: Caco-2 cells, antibiotic, rep4

description:
cells were treated for 48h
atb4_1


title: Caco-2 cells, faecal water antibiotic, rep3

description:
cells were treated for 48h
FW_atb3_1


title: Caco-2 cells, faecal water antibiotic, rep4

description:
cells were treated for 48h
FW_atb4_1


title: BM_92_RNA


title: 14C_M_96


title: 14C_M_97


title: Caco-2 cells, faecal water antibiotic, rep2

description:
cells were treated for 48h
FW_atb2_1


title: PR-Set7 mutant, replicate 1

city: Grand Forks

first: Gbolahan

last: Bamgbose

state: ND

address: 501 N Columbia Rd

department: Biomedical Sciences

institute: University of North Dakota

data_processing:
Paired-end reads were quality-checked using FastQC (version. 0.11.9), groomed with fastp (version 0.23.2) and reads were mapped to the Drosophila genome (dm6) using RNA STAR (version 2.7.8a). Reads of annotated genes were counted using featureCounts (2.0.1). Differential expression analysis was performed with DESeq2  (Version 1.34.0), with Log2 fold change of at least 1 (absolute) considered significant (FDR < 0.05).
Assembly: dm6
Supplementary files format and content: tab-delimited text file of normalized counts

organism: Drosophila melanogaster

source_name: Third-instar larvae

growth_protocol: All animals were raised in a 25°C incubator.

extract_protocol:
10 third instar larvae was used for each biological replicate. RNA was harvested using Rneasy mini plus kit (Qiagen).
mRNA was enriched via Poly(A) selection. Novogene libraries were prepared using NEB's Ultra II RNA library kit

value: Third-instar larvae

value: PR-Set7 mutant


title: 14C_M_95


title: PR-Set7 mutant, replicate 3


title: BM_90_RNA


title: Caco-2 cells, faecal water antibiotic, rep1

description:
cells were treated for 48h
FW_atb1_1


title: BM_89_RNA


title: Caco-2 cells, faecal water control, rep8

description:
cells were treated for 48h
FW_ctl8_1

value: faecal water, control mice


title: 14C_M_94


title: Mutant H3T3A, scRNA-seq

city: Baltimore

first: Daniel

last: Ringwalt

address: 3400N Charles St

department: Biology

institute: Johns Hopkins University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: Dmel_r6.47
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Midgut

extract_protocol:
15 intestines dissected per sample were digested in water bath (37C, 15 minutes); short vortexes every two minutes. Cells were then filtered with a 40 μm filter, pelleted using a centrifuge, washed with HBSS, and resuspended in 20 μL of HBSS.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics).

value: Midgut

value: H3T3A-mCherry transgene


title: AW-YFP, replicate 3

data_processing:
The quality of FASTQ files (raw reads) were checked using FastQC (version. 0.11.9) and trimmed with fastp (version 0.23.2). Trimmed FASTQ files were aligned to the Drosophila genome (dm6) using Bowtie2 (version 2.4.5) to generate bam files. Unmapped and low-quality reads were discarded from bam files (<=20 mapQuality) using BamTools. Duplicate reads were identified and removed from mapped reads using Picard MarkDuplicates (http://broadinstitute.github.io/picard/). Deeptools MultiBamSummary was used to determine reproducibility of ChIP-Seq reads. MACS2 (Version 2.2.7.1) was used to narrowPeaks against pooled control using default settings. MACS2 bedGraph pileups were used to generate bigWig using using bedgraph-to-bigWig (UCSC, version 357).
Assembly: dm6
Supplementary files format and content: bigWig of AW and Control.

extract_protocol:
75 wandering third-instar larvae (3 biological replicates per genotype) were collected in a 2ml DNA LoBind Eppendorf tube and washed twice with 1ml 1X PBS. The larvae were homogenized in ice-cold lysis buffer (200ul 1X protease inhibitor cocktail, 250ul PMSF, 800ul 1X PBS, 1ul Tween 20) using a pellet pestle. The homogenized lysate was supplemented with 244.5ul of 11% formaldehyde to a final concentration of 1.8% and the samples were crosslinked for 15 minutes at room temperature on a rotator. Glycine was added to a final concentration of 500mM to quench the fixative on ice for 5 minutes at room temperature. The larval debris was pelleted at 1,000g for 3 minutes and the supernatant was removed. The pellet was resuspended in 1ml sonication buffer (0.5% SDS, 20mM Tris pH 8.0, 2mM EDTA, 0.5mM EGTA, 0.5mM PMSF, 1X protease inhibitor cocktail) and chromatin was fragmented to 300 – 500bp Bioruptor sonicator (UCD-200) for 20 cycles (30 seconds high frequency sonication, 1.5 sec pause) in a cold room. The sonicated material was pelleted at 10,000g for 10 minutes at 4°C, supernatant was collected, then fragment size was checked prior to immunoprecipitation. The sonicated chromatin was pre-cleared and incubated with anti-GFP antibody overnight (TP-401, Torrey Pines Biolabs) 4°C overnight. The immunoprecipitated chromatin was then collected with pre-washed Protein A agarose beads for 2 hours. The beads were sequentially washed with the following buffers: 1 low salt buffer wash (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCL pH 8.0, 150mM NaCl), 3 high salt buffer washes (0.1% SDS, 1% Triton X-100, 2mM EDTA, 20mM Tris-HCL pH 8.0, 500mM NaCl), 1 LiCL wash (2mM EDTA, 20mM Tris-HCl pH 8.0, 0.25M LiCl, 1% NP-40) and 2 TE buffer washers before elution. Bound chromatin on beads was eluted twice at room temperature using 250ul of freshly prepared ChIP elution buffer (1% SDS, 100mM NaHCO3) for 15 minutes and reverse-crosslinked overnight. The eluates were then treated with RNase A and proteinase K prior to DNA extraction via phenol-chloroform extraction and ethanol precipitation. Libraries were made and sequenced at Novogene.
Libraries were made using NEBNext Ultra II DNA Library Prep Kit at Novogene

tag: chip antibody

value: anti-GFP (TP-401, Torrey Pines Biolabs)


title: Caco-2 cells, faecal water antibiotic, rep6

description:
cells were treated for 48h
FW_atb6_1


title: Wild-type H3, scRNA-seq

description: 10x Genomics

value: H3-mCherry transgene


title: 14C_M_93

data_processing:
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Assembly: mm10
Supplementary files format and content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column
Library strategy: snmC-seq3

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: Caco-2 cells, faecal water control, rep7

description:
cells were treated for 48h
FW_ctl7_1


title: BM_95_RNA

value: AML

value: bone marrow


title: BM_84_RNA

value: AZA-HiDAC-Mito


title: 14C_M_92


title: PR-Set7 mutant, replicate 2


title: Caco-2 cells, faecal water control, rep6

description:
cells were treated for 48h
FW_ctl6_1


title: BM_83_RNA


title: 14C_M_91


title: AW-YFP, replicate 1


title: Caco-2 cells, faecal water control, rep4

description:
cells were treated for 48h
FW_ctl4_1


title: AW_Control, replicate 3


title: BM_80_RNA


title: 14C_M_90


title: BM_88_RNA


title: AW_Control, replicate 2


title: 14C_M_89


title: Caco-2 cells, faecal water control, rep2

description:
cells were treated for 48h
FW_ctl2_1


title: BM_76_RNA


title: AW-YFP, replicate 2


title: AW_Control, replicate 1


title: 14C_M_88


title: Caco-2 cells, faecal water control, rep1

description:
cells were treated for 48h
FW_ctl1_1


title: BM_72_RNA


title: 14C_M_87


title: ZNII-YFP, replicate 3

data_processing:
The quality of FASTQ files (raw reads) were checked using FastQC (version. 0.11.9) and trimmed with fastp (version 0.23.2). Trimmed FASTQ files were aligned to the Drosophila genome (dm6) using Bowtie2 (version 2.4.5) to generate bam files. Unmapped and low-quality reads were discarded from bam files (<=20 mapQuality) using BamTools. Duplicate reads were identified and removed from mapped reads using Picard MarkDuplicates (http://broadinstitute.github.io/picard/). Deeptools MultiBamSummary was used to determine reproducibility of ChIP-Seq reads. MACS2 (Version 2.2.7.1) was used to narrowPeaks against pooled control using default settings. MACS2 bedGraph pileups were used to generate bigWig using using bedgraph-to-bigWig (UCSC, version 357).
Assembly: dm6
Supplementary files format and content: bigWig of ZNII and Control.


title: Caco-2 cells, control PBS, rep3

description:
cells were treated for 48h
ctl3_1

value: vehicle PBS


title: BM_67_RNA


title: Caco-2 cells, control PBS, rep4

description:
cells were treated for 48h
ctl4_1


title: 14C_M_86


title: BM_66_RNA


title: 14C_M_85


title: Caco-2 cells, control PBS, rep2

description:
cells were treated for 48h
ctl2_1


title: ZNII_Control, replicate 3


title: BM_82_RNA


title: ZNII-YFP, replicate 2


title: ZNII-YFP, replicate 1


title: 14C_M_84


title: BM_65_RNA


title: Caco-2 cells, faecal water control, rep3

description:
cells were treated for 48h
FW_ctl3_1


title: BM_64_RNA


title: Caco-2 cells, control PBS, rep1

description:
cells were treated for 48h
ctl1_1


title: ZNII_Control, replicate 2


title: BM_58_RNA


title: ZNII_Control, replicate 1


title: Pooled GEX Library 8 for Donors HDL153, HDL141, HDL142

description: JoshGC.gex.matrix.txt.gz

data_processing:
Quantification of scRNA-seq library pools was performed by pseudoalignment to the human transcriptome (Gencode v24 annotation derived from GRCh38) using kallisto  v0.46.2 in “BUS” mode. ADT barcodes were extracted from demultiplexed fastq files using custom scripts (https://github.com/simslab/DropSeqPipeline8). Hashtag barcodes from cell-identifying barcodes containing >1,000 unique transcripts were demultiplexed using the Hashsolo  with default parameters. scBCR-seq data were demultiplexed and aligned with VDJ cassette and variable sequencing identification using Cell Ranger VDJ v7.0.1 using the GRCh38/Ensembl v7.0.0 annotation from 10x Genomics.
Assembly: GRCh38/Gencode v24
Supplementary files format and content: CITE-seq/scRNA-seq files are tab-delimited count matrices where each column is a cell and each row is a feature (antibody or gene). There is a header indicating the cell-identifying barcode, hashtag, and sample-of-origin for each cell (column). The header is formatted as barcode_donor_hashtag_tissue.
Supplementary files format and content: scBCR-seq files are csv filtered contig files output from Cell Ranger VDJ that contain the VDJ cassettes, nucleotide/amino acid sequences of variable regions, cell-identifying barcode, hashtag, and sample-of-origin for each cell.

value: mixture of lung lymph node, mesenteric lymph node, lung

value: B cells


title: Pooled GEX Library 7 for Donors HDL153, HDL141, HDL142

description: JoshGC.gex.matrix.txt.gz


title: 14C_M_82


title: 14C_M_83


title: BM_57_RNA


title: Pooled GEX Library 6 for Donors HDL153, HDL141, HDL142

description: JoshGC.gex.matrix.txt.gz


title: 14C_M_81


title: 14C_M_80


title: BM_55_RNA


title: Pooled GEX Library 5 for Donors HDL153, HDL141, HDL142

description: JoshGC.gex.matrix.txt.gz


title: Pooled GEX Library 4 for Donors HDL153, HDL141, HDL142

description: JoshGC.gex.matrix.txt.gz


title: BM_54_RNA


title: 14C_M_79


title: 14C_M_78


title: Pooled GEX Library 3 for Donors HDL153, HDL141, HDL142

description: JoshGC.gex.matrix.txt.gz


title: 14C_M_77


title: BM_48_RNA


title: ZNI_Control, replicate 1

data_processing:
The quality of FASTQ files (raw reads) were checked using FastQC (version. 0.11.9) and trimmed with fastp (version 0.23.2). Trimmed FASTQ files were aligned to the Drosophila genome (dm6) using Bowtie2 (version 2.4.5) to generate bam files. Unmapped and low-quality reads were discarded from bam files (<=20 mapQuality) using BamTools. Duplicate reads were identified and removed from mapped reads using Picard MarkDuplicates (http://broadinstitute.github.io/picard/). Deeptools MultiBamSummary was used to determine reproducibility of ChIP-Seq reads. MACS2 (Version 2.2.7.1) was used to narrowPeaks against pooled control using default settings. MACS2 bedGraph pileups were used to generate bigWig using using bedgraph-to-bigWig (UCSC, version 357).
Assembly: dm6
Supplementary files format and content: bigWig of ZNI and Control.


title: Pooled GEX Library 2 for Donors HDL153, HDL141, HDL142

description: JoshGC.gex.matrix.txt.gz


title: 14C_M_76


title: Pooled GEX Library 1 for Donors HDL153, HDL141, HDL142

description: JoshGC.gex.matrix.txt.gz


title: ZNI_Control, replicate 2


title: ZNI-YFP, replicate 2


title: ZNI_Control, replicate 3


title: ZNI-YFP, replicate 1


title: ZNI-YFP, replicate 3


title: Pooled ADT Library 8 for Donors HDL153, HDL141, HDL142

description: JoshGC.adt.matrix.txt.gz

library_source: other

data_processing:
Quantification of scRNA-seq library pools was performed by pseudoalignment to the human transcriptome (Gencode v24 annotation derived from GRCh38) using kallisto  v0.46.2 in “BUS” mode. ADT barcodes were extracted from demultiplexed fastq files using custom scripts (https://github.com/simslab/DropSeqPipeline8). Hashtag barcodes from cell-identifying barcodes containing >1,000 unique transcripts were demultiplexed using the Hashsolo  with default parameters. scBCR-seq data were demultiplexed and aligned with VDJ cassette and variable sequencing identification using Cell Ranger VDJ v7.0.1 using the GRCh38/Ensembl v7.0.0 annotation from 10x Genomics.
Assembly: GRCh38/Gencode v24
Supplementary files format and content: CITE-seq/scRNA-seq files are tab-delimited count matrices where each column is a cell and each row is a feature (antibody or gene). There is a header indicating the cell-identifying barcode, hashtag, and sample-of-origin for each cell (column). The header is formatted as barcode_donor_hashtag_tissue.
Supplementary files format and content: scBCR-seq files are csv filtered contig files output from Cell Ranger VDJ that contain the VDJ cassettes, nucleotide/amino acid sequences of variable regions, cell-identifying barcode, hashtag, and sample-of-origin for each cell.
Library strategy: ADT-seq

molecule: protein

value: TotalSeqC Universal Cocktail, TotalSeqC HTO1-9


title: BM_47_RNA


title: 14C_M_75


title: DZNI-YFP, replicate 3

description: DZNI.bigwig

data_processing:
The quality of FASTQ files (raw reads) were checked using FastQC (version. 0.11.9) and trimmed with fastp (version 0.23.2). Trimmed FASTQ files were aligned to the Drosophila genome (dm6) using Bowtie2 (version 2.4.5) to generate bam files. Unmapped and low-quality reads were discarded from bam files (<=20 mapQuality) using BamTools. Duplicate reads were identified and removed from mapped reads using Picard MarkDuplicates (http://broadinstitute.github.io/picard/). Deeptools MultiBamSummary was used to determine reproducibility of ChIP-Seq reads. MACS2 (Version 2.2.7.1) was used to narrowPeaks against pooled control using default settings. MACS2 bedGraph pileups were used to generate bigWig using using bedgraph-to-bigWig (UCSC, version 357).
Assembly: dm6
Supplementary files format and content: bigWig of DZNI and Control.


title: 14C_M_74


title: DZNI-YFP, replicate 2

description: DZNI.bigwig


title: Pooled ADT Library 7 for Donors HDL153, HDL141, HDL142

description: JoshGC.adt.matrix.txt.gz


title: DZNI-YFP, replicate 1

description: DZNI.bigwig


title: Pooled ADT Library 6 for Donors HDL153, HDL141, HDL142

description: JoshGC.adt.matrix.txt.gz


title: BM_36_RNA


title: 14C_M_73


title: BM_43_RNA


title: BM_53_RNA


title: DNZNI_Control, replicate 3


title: BM_51_RNA


title: 14C_M_72


title: BM_3_RNA


title: 14C_M_71


title: DNZNI_Control, replicate 2


title: Pooled ADT Library 4 for Donors HDL153, HDL141, HDL142

description: JoshGC.adt.matrix.txt.gz


title: Pooled ADT Library 5 for Donors HDL153, HDL141, HDL142

description: JoshGC.adt.matrix.txt.gz


title: BM_25_RNA


title: DNZNI_Control, replicate 1


title: BM_24_RNA


title: 14C_M_70


title: BM_45_RNA


title: PARP1-YFP, replicate 2

data_processing:
The quality of FASTQ files (raw reads) were checked using FastQC (version. 0.11.9) and trimmed with fastp (version 0.23.2). Trimmed FASTQ files were aligned to the Drosophila genome (dm6) using Bowtie2 (version 2.4.5) to generate bam files. Unmapped and low-quality reads were discarded from bam files (<=20 mapQuality) using BamTools. Duplicate reads were identified and removed from mapped reads using Picard MarkDuplicates (http://broadinstitute.github.io/picard/). Deeptools MultiBamSummary was used to determine reproducibility of ChIP-Seq reads. MACS2 (Version 2.2.7.1) was used to narrowPeaks against pooled control using default settings. MACS2 bedGraph pileups were used to generate bigWig using using bedgraph-to-bigWig (UCSC, version 357).
Assembly: dm6
Supplementary files format and content: bigWig of PARP1 and Control.


title: BM_157_RNA


title: PARP1-YFP, replicate 3


title: 14C_M_69


title: 14C_M_67


title: Pooled ADT Library 1 for Donors HDL153, HDL141, HDL142

description: JoshGC.adt.matrix.txt.gz


title: Pooled ADT Library 3 for Donors HDL153, HDL141, HDL142

description: JoshGC.adt.matrix.txt.gz


title: Pooled ADT Library 2 for Donors HDL153, HDL141, HDL142

description: JoshGC.adt.matrix.txt.gz


title: PARP1-YFP, replicate 1


title: BM_152_RNA


title: BM_150_RNA


title: JEKO-sgFOXO1.2

description: TPMcounts.csv

data_processing:
Illumina bcl2fastq2 v2.17 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the UCSC mm9 mouse reference genome using tophat v2.0.11.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Assembly: hg19
Supplementary files format and content: CSV file including gene id, TPM value of each gene in each sample

source_name: JEKO1 MCL cells

growth_protocol: Cells were acttively growing in RPMI1640 media witth 10% FBS and 1% antibiotics.

extract_protocol:
Total RNA was extracted with NuceloSpin RNA extraction kit (MN#740955.250) followed by manufacturer's instructions. Briefly, the brains were lysed with 350 uL of lysis buffer (RA) and cleaned with Nucleospin filter. Added the 70% EtOH to bound RNA to RNA column. After digest genomic DNA with DNase, the columns were washed with provided wash solutions and eluted RNA with 30 uL of RNase free water. The RNA concentrations were determined with NanoDrop.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 96 hr prior to the lysis of cells were infected with lentivirus particles encoding respective sgRNA.

value: B cell lymphoma

tag: developmental stage

value: Mantle cell lymphoma

tag: tumor origin

value: Mature B cell

value: sgFOXO1.2 infected


title: 14C_M_65

value: PCG


title: JEKO-MOCK

description: TPMcounts.csv

value: vehicle treated


title: Control, replicate 2

value: Third-instar larvae


title: 14C_M_66


title: BM_144_RNA

extract_protocol:
mRNA was extracted from 1µg of total RNA by using Dynabeads mRNA Direct kit (Ambion). Nano-hmC-Seal was performed as previously described with minor changes. 9 Libraries were prepared with KAPA Hyperplus kit (KAPA KK8515) using extracted genomic DNA from patient peripheral blood or bone marrow cells.
20 ng of mRNA were used for library construction by using TruSeq stranded mRNA sample preparation kit (Illumina). For 5hmC, Briefly, 50ng genomic DNA in 14µl H2O was fragmented at 37 °C for 20 minutes by addition of 2µl of 10x KAPA Fragmentation Buffer and 4µl of KAPA Fragmentation Enzyme. The fragmented DNA was end-polished at 65 °C for 30 minutes by adding 2.8µl of End Repair & A-Tailing Buffer and 1.2µl of End Repair & A-Tailing Enzyme Mix. 3µl of 1.5µM Adapter (Bioo Scientific NOVA-514103) was added followed by 12µl of Ligation Buffer and 4µl DNA Ligase. The mixture was incubated at 20 °C for 1 hour. Libraries were then purified by DNA Clean and Concentrator kit (Zymo D4013) and eluted in 20µl H2O. β-GT labeling was then performed by addition of 0.85µl self-synthesized 3mM N3-UDG and 2.5µl of T4-βGT (Thermo EO0831) at 37 °C for 2 hours. Azide labeled DNA libraries were then purified by DNA Clean and Concentrator kit (Zymo D4013) and eluted in 30µl H2O. Libraries were further biotinylated by addition of 1µl 4.5mM (Sigma 760749) DBCO-PEG4-Biotin and incubated at 37 °C for 2 hours. Biotinylated DNA libraries were then purified by DNA Clean and Concentrator kit (Zymo D4013) and eluted in 30µl H2O. The biotinylated DNA was further enriched by 5 µl of M-270 Streptavidin beads (Thermo 65305) and incubated at room temperature for 30 minutes. The beads were washed 3 times with Wash Buffer (5 mM Tris-HCl (pH 7.5); 0.5 mM EDTA; 1 M NaCl; 0.05% Tween 20) and resuspended in 20µl H2O. Libraries were amplified with on-bead PCR by addition of 5µl Primer Mix (KAPA KK8515) and 25µl of Enzyme Mix (KAPA KK8515) with following condition (98 ˚C 30 s ;98 ˚C 15 s ;60 ˚C 30 s; 72 ˚C 30 s; Repeat 14 cycles; 72 ˚C 1 min). Post-amplification cleanup was performed by adding 0.9x Ampure beads (Beckman Coulter A63880); beads were washed twice with 80% ethanol and eluted in 50µl H2O.


title: 14C_M_64


title: Control, replicate 1


title: BM_143_RNA


title: BM_142_RNA


title: JEKO-sgFOXO1.1

description: TPMcounts.csv

value: sgFOXO1.1 infected


title: BM_156_RNA


title: Parp mutant, replicate 2

data_processing:
Paired-end reads were quality-checked using FastQC (version. 0.11.9), groomed with fastp (version 0.23.2) and reads were mapped to the Drosophila genome (dm6) using RNA STAR (version 2.7.8a). Reads of annotated genes were counted using featureCounts (2.0.1). Differential expression analysis was performed with DESeq2  (Version 1.34.0), with Log2 fold change of at least 1 (absolute) considered significant (FDR < 0.05).
Assembly: dm6
Supplementary files format and content: tab-delimited text file of normalized counts for each sample

value: Parp mutant


title: JEKO-sgROSA

description: TPMcounts.csv

value: sgROSA infected


title: BM_141_RNA

data_processing:
The 5hmC and RNA-seq reads were then mapped to the UCSC hg19 reference genome by STAR-2.5.3 software
The de-duplication of 5hmC was performed using the parameter "-tbp 5" in makeTagDirectory of HOMER software
the gene raw counts matrix was generated by the HOMER's analyzeRepeats
Genome_build: hg19
Supplementary_files_format_and_content: txt

value: AML


title: CKO4, bone shaft, post natal day 7

city: Xi'an

first: Chao

last: Zheng

address: Changle west road

country: China

institute: Fourth Military Medical University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm38
Supplementary files format and content: Expression matrix, including FPKM values for each sample, in Excel format.

source_name: Bone shaft

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: Bone shaft

value: Col2.3kb-Cre; Slc26a2 fl/fl


title: JEKO-cpd10

description: TPMcounts.csv

value: cpd10 treated


title: Parp mutant, replicate 3


title: CKO1, bone shaft, post natal day 7


title: CCMCL1-MOCK

description: TPMcounts.csv


title: Control, replicate 3

value: anti-GFP (TP-401, Torrey Pines Biolabs)


title: CKO2, bone shaft, post natal day 7


title: BM_135_RNA

value: bone marrow

value: AZA-HiDAC-Mito


title: CCMCL1-sgPAX5.2

description: TPMcounts.csv

value: B cell lymphoma

value: sgPAX5.2 infected


title: WT, replicate 3

value: Wildtype


title: BM_133_RNA


title: WT, replicate 2


title: CCMCL1-sgPAX5.1

description: TPMcounts.csv

value: Mantle cell lymphoma

value: Mature B cell

value: sgPAX5.1 infected


title: Control4, bone shaft, post natal day 7

value: Col2.3kb-Cre; Slc26a2 fl/+


title: BM_130_RNA


title: Parp mutant, replicate 1

value: Third-instar larvae


title: 14C_M_68

value: PCG


title: CCMCL1-sgIRF4.2

description: TPMcounts.csv

value: sgIRF4.2 infected


title: Control3, bone shaft, post natal day 7


title: BM_128_RNA

value: AML


title: CKO3, bone shaft, post natal day 7

value: Bone shaft


title: WT, replicate 1


title: Control2, bone shaft, post natal day 7


title: CCMCL1-cpd10

description: TPMcounts.csv


title: BM_126_RNA


title: CCMCL1-sgEBF1.2

description: TPMcounts.csv

value: sgEBF1.2 infected


title: BM_123_RNA


title: BM_122_RNA


title: BM_116_RNA


title: BM_113_RNA


title: BM_110_RNA


title: CCMCL1-sgIRF4.1

description: TPMcounts.csv

value: sgIRF4.1 infected


title: Control1, bone shaft, post natal day 7


title: Osteoarthritis, Superficial zone cells, Biol rep 1

first: Ikue

last: Tosa

state: New York

department: College of Dental Medicine

data_processing:
MultiQC (1.13) for quality check. Trim Galore (0.6.7) for adapter and quality trimming.
First time read alignment with STAR (2.7.9a) with parameters of: --chimSegmentMin 10 --alignEndsType Local --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --alignIntronMin 70 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1  --outSAMstrandField intronMotif --outFilterType BySJout --twopassMode Basic.
Mapping restuls from the first time read alignment then passed to StringTie (2.1.0) for reference-based (OryCun2.0 Eensembl release-105) de novo transcriptome assembly with parameters of: -m 100 -a 5 -j 0.1 -c 0.5 -f 0.005
Finally, trimmed sequence reads were mapped to de novo transcriptome assembly using Salmon software (1.1.0).
The estimated TPM and read counts from Salmon software was converted to gene-level following the DESeq2 (1.26.0) manual.
Assembly: OryCun2.0
Supplementary files format and content: excel file include TPM and read counts for each sample

organism: Oryctolagus cuniculus

source_name: Temporomandibular Joint

extract_protocol:
Total RNA was extracted from tissue samples using RNeasy Micro kit (Qiagen).
QIAseq FastSelect rRNA HMR Kit (Qiagen) was used for rRNA depletion, followed by library preparation using NEBNext Ultra II Directional RNA Library Prep Kit (NEB).

treatment_protocol: Temporomandibular joint osteoarthritis was surgically induced using a disc perforation model. An incision was created superior to the zygomatic process. The disc was retracted posteriorly and a periosteal elevator was placed under the disc to protect the condyle from secondary injury. A punch biopsy was used to create a 2.5 mm in the posterior-lateral TMJ disc and the perforated disc tissue was removed. No disc attachments were severed and the disc reduced to its normal anatomical location.

value: Temporomandibular Joint

value: Superficial zone cells

value: WT

value: Osteoarthritis


title: Osteoarthritis, Superficial zone cells, Biol rep 2


title: Osteoarthritis, Condylar cartilage cells, Biol rep 2

value: Condylar cartilage cells


title: Control, Condylar cartilage cells, Biol rep 2

value: Control


title: Control, Condylar cartilage cells, Biol rep 3


title: Osteoarthritis, Condylar cartilage cells, Biol rep 1


title: Osteoarthritis, Condylar cartilage cells, Biol rep 3


title: Osteoarthritis, Superficial zone cells, Biol rep 3


title: BM_107_RNA

value: bone marrow

value: AZA-HiDAC-Mito


title: MZ_1h2

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
Illumina Casava1.7 software used for basecalling.
RSEM (Li and Dewey 2011) was used to align RNA-Seq reads to the human genome and to quantify transcript abundance
EBSeq (Leng, Dawson et al. 2013) was used to compare the aligned reads from multiple conditions to find differentially expressed genes in wild type using a cutoff of FDR <0.05.
Comparisons between Fo and MZ activated samples were carried out DESeq2 (Love, Huber et al. 2014).
Differentially expressed genes were identified using DESeq2
Two filtering steps were followed to define differentially expressed genes in cells with modified NF-kB expression.
First, all differentially changed genes were selected based on an FDR <0.05 after DESeq2 analysis; Second, only those genes were selected that were more than 2-fold up or down-regulated in wild samples after anti-IgM treatment.
All samples were normalized to 1 million aligned reads for visualization.
Marginal zone (MZ), Follicular (FO) splenic B sample sequences were aligned to mouse genome assembly mm10
Assembly: mm10
Supplementary files format and content: .txt are matrix files containing raw counts

source_name: spleen

growth_protocol: B cells were cultured in RPMI 1640 medium supplemented with 10% FBS (HyClone), Penicillin-Streptomycin-Glutamine (Invitrogen), and 2-mercaptoethanol for 30 minutes

extract_protocol:
Total RNA was isolated using the RNeasy micro Kit (74004, QIAGEN)
RNA libraries were prepared for sequencing by processing 10ng total RNA with SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (634412, Takara Bio)

treatment_protocol: Two replicates were treated with 10μg/ml goat anti-mouse IgM Fab`2 for 0 hours (unstimulated), 1 hour, 4 hours or 18 hours, dead cell removal was performed on 18hr samples

value: B cell

value: 10μg/ml goat anti-mouse IgM Fab`2 1 hour


title: MZ_18h1

value: 10μg/ml goat anti-mouse IgM Fab`2 18 hours


title: MZ_1h1


title: Control, Condylar cartilage cells, Biol rep 1


title: MZ_4h1

value: 10μg/ml goat anti-mouse IgM Fab`2 4 hours


title: MZ_0h2


title: MZ_4h2


title: BM_114_RNA


title: BM_106_RNA


title: MZ_0h1


title: Control, Superficial zone cells, Biol rep 3


title: BM_1_RNA


title: IgG

data_processing:
Basecalls performed using BaseCall version 1.1.2
ChIP-seq reads were aligned to the Hg19 genome assembly using SOAPaligner/soap2 version 2.21 with the following configurations：-v 2 -s 35 -m 50 -x 600
Data were filtered using the following specifications：Sequenced reads with adaptor sequence or low-quality sequence (we define the low quality read as the percentage of base which quality is lesser than 5 is greater than 50% in a read) are discarded
Peaks were called using macs2 version 2.1.0 with the following setting: --bw 200 -g mm -s 49 -p 1e-5 -m 10 30
Assembly: hg19
Supplementary files format and content: Bw files were transformed from wig files generated using macs2

growth_protocol: We treated CCMCL1 cells  and cross-linked with 1% paraformaldehyde.

value: blood

value: Mature B cell

tag: disease

value: Mantle cell lymphoma

value: rabbit IgG, Cell signaling technology

tag: sample type

value: IgG control


title: CCMCL1-sgFOXO1.2 [CM.FOXO1_2]

description: TPMcounts.csv

value: B cell lymphoma

tag: treatment

value: sgFOXO1.2 infected


title: CCMCL1-sgROSA [CM.ROSA]

description: TPMcounts.csv

value: sgROSA infected


title: CCMCL1-sgFOXO1.1 [CM.FOXO1_1]

description: TPMcounts.csv

value: sgFOXO1.1 infected


title: H3K27Ac-sgROSA

value: abcam #ab4729

value: H3K27Ac ChIP


title: H3K27Ac-sgFOXO1


title: H3K27Ac-cpd10 48hr


title: H3K4me1

value: abcam #ab8895

value: H3K4me1 ChIP


title: H3K27Ac-vehicle


title: CCMCL1-sgEBF1.1

description: TPMcounts.csv

value: sgEBF1.1 infected


title: FO_18h2

value: B cell


title: Control, Superficial zone cells, Biol rep 1

value: Temporomandibular Joint

value: Superficial zone cells

value: WT

value: Control


title: MCF7, rep1

data_processing:
RNA-seq read wre aligned to GRCh38 genome using STAR.
Expressions of genes and isoforms(read count, FPKM, TPM) were calculated using RSEM.
Assembly: hg38
Supplementary files format and content: txt (read count, FPKM, and TPM)

source_name: cell line

extract_protocol: Total RNA (10 mg) was harvested from MCF7 using TRI reagent (Ambion) for cDNA library preparation. Enrichment of mRNA by depletion of ribosomal RNA was performed using a RiboMinus transcriptome isolation kit (Invitrogen). RiboMinus RNA (1 mg) was then fragmented using RNase III for 10 min and cleaned up using a RiboMinus concentration module (Invitrogen).

value: cell line

value: human breast cancer


title: Control, Superficial zone cells, Biol rep 2


title: FO_18h1

value: 10μg/ml goat anti-mouse IgM Fab`2 18 hours


title: MZ_18h2


title: FO_4h2

value: 10μg/ml goat anti-mouse IgM Fab`2 4 hours


title: FO_4h1


title: FO_1h2

value: 10μg/ml goat anti-mouse IgM Fab`2 1 hour


title: TOTAL, rep3

last: Bortvin

address: 3520 San Martin drive

department: Embryology

institute: Carnegie Institution for Science

description:
repName_collapsed_counts_upper_quantile_norm.txt
IP_comb_vs_TOTAL_comb_DESeq2.txt
TOTAL_3

data_processing:
For genomic repeats analysis, reads were mapped to mouse mm10 reference genome using STAR v2.6.0c, option --outFilterMultimapNmax 100. The obtained .bam file was used as input for Telescope v1.0.3. The updated counts were collapsed to single repeat subfamilies using a custom Perl script and normalized using EBSeq v1.26.0. Normalized genomic repeat counts for all samples are provided in the table "repName_collapsed_counts_upper_quantile_norm.txt".
For coding genes analysis, reads were mapped to mouse mm10 using STAR v2.6.0c. Counts were normalized using DESeq2 v1.24.0.
Assembly: mm10
Supplementary files format and content: tab-delimited text files, including normalized collapsed counts for genomic repeats and DESeq2 output files for coding genes

source_name: Testis

extract_protocol:
Freshly dissected testes were collected in ice-cold PBS and homogenized in Lysis buffer containing 100 mM KCl, 20 mM Tris-HCl pH 7.5, 2 mM MgCl2, 0.3% NP-40, Halt protease and phosphatase inhibitors (Thermo Fisher), RNasin Ribonuclease Inhibitor (Promega) in nuclease-free water. Lysates were clarified by centrifugation, supernatants were recovered and EDTA was added at a final concentration of 10 mM. Extracts (TOTAL) were further fractionated by 10-50% sucrose gradient ultracentrifugation; fractions 5, 6, 7 and 8 were pooled and used as INPUT for either anti-L1 ORF1p co-immunoprecipitations (IP) or incubations with Beads Only (BO). RNA from TOTAL, INPUT, IP and BO samples was purified using TRIzol reagent and treated with TURBO DNase (Invitrogen).
Libraries were generated using the TruSeq Stranded Total RNA kit (Illumina), with Ribo-Zero rRNA depletion.

tag: time

value: 3 months

value: Testis

tag: antibody

value: Mael-/-


title: TOTAL, rep1

description:
repName_collapsed_counts_upper_quantile_norm.txt
IP_comb_vs_TOTAL_comb_DESeq2.txt
TOTAL_1

tag: strain


title: Human Ast biol rep 3

city: Daejeon

first: C Justin

address: 55, Expo-ro, Doryong-dong, Yuseong-gu

department: Center for Cognition and Sociality

country: South Korea

institute: Institute for Basic Science

description: mRNA libraries prepared using Ultra RNA library prep kit (NEBNEXT, #E7530)

data_processing:
BCL files obtained from Illumina HiSeq2500 were converted to fastq and demultiplexed based on the index primer sequences. The data was imported to Partek Genomic Suite (Flow ver 10.0.21.0328; Copyright 2009, Partek Inc., St. Louis, MO, USA), where further processing was carried out.
Read quality was checked for each sample using FastQC (Flow version 10.0.21.0328)
High-quality reads were aligned using STAR (2.7.3a)
Aligned reads were quantified to the human genome assembly GRCh37 (hg19, NCBI), quantified using hg19 - RefSeq transcript 93 and normalised to obtain fragments per kilobase million (FPKM) values of positively detected and quantified genes in each biological replicate.
Alternately spliced variants for the genes were also detected during quantification, and normalised to obtain FPKM values of the splice variants.
Assembly: hg19
Supplementary files format and content: Processed data files include normalised FPKM values for positively identified genes (HumanAst_Gene_FPKM.txt)
Supplementary files format and content: Processed data files include normalised FPKM values for altrernately spliced variants of positively identified genes (HumanAst_Transcript_FPKM.txt)

source_name: Brain

growth_protocol: Human astrocyte cultures were grown in Dulbecco’s modified Eagle’s medium (DMEM, Corning) supplemented with 4.5 g/L glucose, L-glutamine, sodium pyruvate, 10% heat-inactivated fetal bovine serum, and 1000 units/ml of penicillin–streptomycin. Cultures were maintained at 37oC in a humidified atmosphere containing 5% CO2.

extract_protocol:
Total RNA was isolated from the cell culture using Rnasy Mini Kit (Qiagen, #74104).
1μg of total RNA was enriched for Poly-mRNA (Dynabeads mRNA purification kit, Invitrogen) and reverse transcribed to double-stranded cDNA. The cDNA was end-repaired, adenylated and ligated to Illumina indices prior to 14 cycles of PCR amplification (Ultra RNA library prep kit, NEBNext). Sequencing was performed using 20pM libraries hybridized to  a 2x100 paired-end flow cell in HiSeq2500 (Illumina).

treatment_protocol: Cells were grown and passaged as required. 2 days before RNA isolation, cells were seeded onto a 60mm diameter culture dish and allowed to grow to 70% confluency before washing with Dulbecco's modified Phosphate buffered Saline and proceeding to RNA extraction.

tag: tissue

value: Brain

value: Immortalised human astrocytes (fetal) SV40 [abm T0280]

value: Fetal astrocytes

value: Naive


title: Human Ast biol rep 4


title: Human Ast biol rep 2


title: Human Ast biol rep 1


title: FO_1h1

value: B cell


title: hBMECs CRISPR library C Round 3

city: Nanjing

first: Zhe

last: Ma

state: JS

address: Tonwei Road No.1

institute: nanjing agricultural university

description:
PCR amplicon
Data was analysed with MAGeCK, processed data was in different sheets of Table S3
Sheet Name: Replicate_C_Round_3.sgrna_summa

data_processing:
Reads were trimmed with Cutadapt 4.1
MAGeCK was used for data analysis
Supplementary files format and content: The output file was Table S3.XLSX
Library strategy: Amplicon-seq

source_name: hBMECs

extract_protocol:
Genomic DNA was obtained from the input library and after each of the three rounds of screening with the Blood and Cell Culture DNA Maxi Kit.
The sequenced samples was genereted by PCR with primers containing P7 or P5 adaptor

value: hBMECs

value: Endothelial cells

value: CRISPR muntant library

value: Treated with SzM protein from streptococcus equi ssp. zooepidemicus


title: FO_0h2


title: INPUT, rep2

description:
repName_collapsed_counts_upper_quantile_norm.txt
IP_comb_vs_INPUT_comb_DESeq2.txt
INPUT_2