title: 16_B M ATG RA

description:
Group F
sample name: 16

value: lung

value: Male


title: RBG19996_Young_MSC-L_024

status: Public on Nov 02 2022

type: SRA

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health

country: China

institute: Shanghai Jiao Tong University School of Medicine

library_source: transcriptomic

data_processing:
Reads were mapped to the Mus musculus genome (EMSEMBL GRCm38.p4 Release 81) and ERCC sequences using GSNAP (version 2015-09-29) with parameters: -A sam –B 5 –t 24 –n 1 –Q –N 1.
HTseq-count (PMID: 25260700) was used to count reads mapped to each gene, with parameters: –s no.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: HT-Seq counts / gene counts (.txt)

molecule: total RNA

organism: Mus musculus

source_name: endosteum and central marrow

extract_protocol:
Single endosteal and central marrow stromal cells were directly sorted into individual wells of a 96-well PCR plate containing 2.3 µl of 0.2% Triton-X100 (Sigma-Aldrich, 93443) and 1U of Superase-In RNase Inhibitor (Ambion). Of note, information regarding expression of surface markers was recorded for each cell. Cells were frozen immediately at -80C until further processing. After thawing on ice, 2 µl of annealing mixture (1 µM oligodT –IDT-, 5mM each dNTPs and a dilution 1:6,000,000 of ERCC RNA Spike-In Mix -Invitrogen-) was added followed by incubation at 72C for 3 minutes. Then 5.7 µl of Reverse Transcription mix (3.5 U/µl of Maxima H minus retrotranscriptase –ThermoFisher-, 0.88 U/µl of Superase-In RNase Inhibitor, 1.75X Maxima RT Buffer, 3.5 µM TSO – Qiagen- and 13.15% PEG 8000 –Sigma-Aldrich-) was added and the mixture was incubated at 42 C for 90 min, followed by 70 C for 15 min. cDNA was further amplified by adding 40 µl of PCR mix (0.03 U/µl of Terra PCR direct polymerase –Takara Bio-, 1.25X Terra PCR Direct Buffer, 0.25 µM IS PCR primer –IDT-). PCR was as follows: 3 min at 98 °C for initial denaturation followed by 21 cycles of 15 s at 98 °C, 30 s at 65 °C, 4 min at 68 °C. Final elongation was performed for 10 min at 72 °C.  Sequences of oligodT, TSO and IS PCR primers were as previously described (PMID: 24385147).
Following preamplification, all samples were purified using Ampure XP beads (Beckman Coulter) at a ratio of 1:0.6 with a final elution in 25 µl of EB Buffer (Qiagen). The cDNA was then quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher). Size distributions were checked on high-sensitivity DNA chips (Agilent Bioanalyzer). Samples were used to construct Nextera XT libraries (Illumina) from 100 pg of preamplified cDNA. Libraries were purified and size selected (0.5X-0.7X) using Ampure XP beads. Then, libraries were quantified using KAPA qPCR quantification kit (KAPA Biosystems), pooled and sequenced in an Illumina HiSeq 4000 instrument.

tag: cell population

value: mesenchymal and endothelial cells

value: MSC-L

tag: age

value: Young


title: 15_B M SAL RA

city: Sheridan

first: Kenneth

middle: L

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

country: USA

institute: Bioinformatic Solutions LLC

description:
Group E
sample name: 15

data_processing:
Quality trim to a minimum of Q15
Map to the mm10 genome using GSNAP version 2012-07-20 using the commandline: gsnap -d mm10_total -v mm10_total.snp138 --use-splicing=mm10_total.ensembl.splicesites --max-mismatches=0.06 -i2 -n2 -Q --gunzip --force-xs-dir --nofails -B5 -t${num_processors} --read-group-id=$j --read-group-name=$j --read-group-library=$j --read-group-platform=illumina -A sam $outfile_R1 $outfile_R2 | samtools view -bS -@ ${num_processors} - | samtools sort -@ ${num_processors} -o ./Illumina_data/${j}.sorted.bam -; samtools index ./Illumina_data/${j}.sorted.bam
sort and index using SAMTOOLS
call FPKM using CUFFLINKS
Assembly: mm10
Supplementary files format and content: Excel file containing FPKM values

source_name: Lung Tissue

extract_protocol:
Total RNA was extracted with Qiagen Rneasy Mini Kit
Illumina directional mRNA prep; HiSeq2000 using 2x150bp format

treatment_protocol: Adult mice were exposued to either a single I.P injection of saline or 25mg/kg of ATG. Mice were these placed in either room air or hyperoxia (>95%) oxygen for 96hrs. Following exposure mice were dosed with ketamine/xylazine for euthanazia; and lung tissue was collected. ~20ug of tissue was collected for transcriptomics, which was snap frozen at the time of colelction. Stored in -70C until time of processing for RNA-sequencing.

tag: tissue

tag: strain

tag: Sex

tag: atg treatment

value: Saline

tag: air treatment

value: Room Air


title: Monocytes_STm_5

city: Rehovot

first: Ziv

last: Shulman

address: Herzl St 234

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were trimmed using Cutadapt
Reads were aligned to the genome using STAR
Quantification was done using htseq-count as previously described in R. Kohen, BMC Bioinformatics, 2019.
Genome_build: mm10
Supplementary_files_format_and_content: Excel file with Deseq2 output

molecule: polyA RNA

source_name: Monocytes

growth_protocol: Fresh cells were sorted for RNA preparation

extract_protocol:
mRNA was extracted from sorted cells using mRNA direct kit (Invitrogen) and mRNA from each sample was barcoded during reverse transcription and pooled.
Libraries were prepared using a bulk adaptation of the previously described protocol (Keren-Shaul et al. Nat. Protoc, 2019 and Jaitin et al. Science, 2014).Following Agencourt Ampure XP bead cleanup (Beckman Coulter), the pooled samples underwent second strand synthesis and were linearly amplified by T7 in vitro transcription. The resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with Illumina sequences during ligation, RT, and PCR.  Libraries were quantified by Qubit and TapeStation as well as by qPCR for the ACTB gene as previously described. Sequencing was done using a Nextseq 75 cycle high output kit (Illumina; paired end sequencing).

treatment_protocol: Mice were orally infected with Salmonella Typhimurium for 3 days or injected with 50 microgram LPS twice and analysed on day 3. Peyer's patches were harvested and cells were sorted into lysis buffer (invitrogen Dynabeads kit) for RNA extraction.

tag: cell type

value: Ly6G- CD11b+ Ly6Chi Sca-1+

tag: mouse strain

tag: genotype

value: wild type

tag: treatment

value: STm infected


title: Monocytes_STm_4


title: ABZM00701: DNMT3B_4.2 [MARS_scRNA]

first: Amos

last: Tanay

address: Herzl

data_processing:
Read-1 files were mapped to the mm9 genome assembly using Bowtie2 (default parameters)
Demultiplexing and UMI counting were based on 8bp of UMI and 7bp of cell-barcodes in Read-2, and performed using the pipeline described in Jaitin et al. 2014

source_name: Cell Bank Riken BioResource Research Center)

growth_protocol: Mouse embryonic stem cells (mESCs) were maintained under standard conditions. Cells were fed with fresh medium every day and were split every 2 days.

extract_protocol:
RNA capture for scRNA MARSseq: single-cells were FACS-sorted directly into barcoded lysis solution in 384-well MARS-seq plates, which were immediately transfered and kep at -80C. lysis solution contained UPW, 2nM poly-dT barcodes,  0.1%triton and RNAse inhibitors.
cDNA MARS-seq library preparation: scRNA MARS-seq library prepartion was performed as described in Jaitin et al. 2014. For bulk MARS-seq, only differences were were using set of 348 barcoded oligos, which allowed to pool the 384 well plate into VBLOCK KIT reservoir by centrifuge, later in the process. The step of klenow heat inactivation was removed. The volumes of the first RT and Exonuclease I reaction mix were scaled down to 1 and 0.5 μl respectively. Each reaction mix was dispensed by MANTISR (FORMULATRIX).

treatment_protocol: For the epigenetic reset, mESC were cultured in Neurobasal and DMEM-F12 (WITHOUT HEPES) medium (1:1), supplemented with N2B27, 20 ng/ml recombinant human LIF and 2i for two to three passages. Embryoid bodies were established in 25 μl hanging drops on a cover of low-adherent bacterial culture dish, allowing 500 cells/drop to aggregate for 48 hours. After two days 48-56 EBs were pooled into 10 cm low adherent bacterial culture dish.

tag: cell line/mouse line

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

tag: batch index

value: GATC


title: Monocytes_STm_3


title: Monocytes_STm_1


title: 12_H M ATG HYP

description:
Group D
sample name: 12

value: Aurothioglucose

value: Hyperoxia


title: RBG19999_Young_MSC-L_026


title: 11_H M ATG HYP

description:
Group D
sample name: 11


title: ABZM00647: DNMT3A_7F.2 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: AGTC


title: 13_B M SAL RA

description:
Group E
sample name: 13


title: RBG19993_Young_MSC-L_023


title: ABZM00649: DNMT3B_7F.2 [MARS_scRNA]

value: TTGG


title: ABZM00648: DNMT3B_7F.1 [MARS_scRNA]

value: CATG


title: Monocytes_STm_2


title: ABZM00650: J1_WT_4.1 [MARS_scRNA]

source_name: J1 (SCRC1010, ATCC)

value: J1 (SCRC1010, ATCC)

value: ACAG


title: ABZM00646: DNMT3A_7F.1 [MARS_scRNA]

value: ATGC


title: RBG19988_Old_AEC_040

value: mesenchymal and endothelial cells

value: AEC

value: Old


title: RBG19998_Young_MSC-L_025

value: MSC-L

value: Young


title: RBG19991_Young_MSC-L_022


title: 10_H M ATG HYP

description:
Group D
sample name: 10

value: lung

value: Male


title: 14_B M SAL RA

description:
Group E
sample name: 14

value: Saline

value: Room Air


title: ABZM00645: DNMT3B_6.5 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: CTCG


title: RBG19987_Old_AEC_039


title: ABZM00642: DNMT3B_6.4 [MARS_scRNA]

value: GATC


title: Monocytes_Control_1

value: Ly6G- CD11b+ Ly6Chi

value: wild type

value: untreated


title: 8_H M SAL HYP

description:
Group C
sample name: 8

value: Hyperoxia


title: Monocytes_Control_3

value: Ly6G- CD11b+ Ly6Chi Sca-1+


title: RBG19986_Old_AEC_038

value: mesenchymal and endothelial cells


title: GCB1_LPS_4

source_name: B cells

value: PP GC B cell (B220+, CD138-, FAS+, CD38-)

value: LPS treated


title: RBG19985_Old_AEC_037

value: AEC

value: Old


title: ABZM00641: DNMT3A_6.9 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: GCAT


title: 7_H M SAL HYP

description:
Group C
sample name: 7

value: lung

value: Male

value: Saline


title: 9_H M SAL HYP

description:
Group C
sample name: 9


title: GCB1_LPS_3


title: GCB1_LPS_2


title: Monocytes_Control_2


title: 5_H M ATG RA

description:
Group B
sample name: 5

value: Aurothioglucose

value: Room Air


title: 6_H M ATG RA

description:
Group B
sample name: 6


title: RBG19983_Old_AEC_035


title: RBG19982_Old_AEC_034


title: 4_H M ATG RA

description:
Group B
sample name: 4


title: ABZM00633: DNMT3A_4.12 [MARS_scRNA]

value: GTAG


title: 3_H M SAL RA

description:
Group A
sample name: 3


title: GCB1_STm_4

value: wild type

value: STm infected


title: GCB1_STm_3


title: RBG19980_Old_AEC_032


title: ABZM00630: DNMT3A_4.11 [MARS_scRNA]

value: AGGG


title: ABZM00629: DNMT3B_3.11 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: TCCG


title: RBG19979_Old_AEC_031

value: mesenchymal and endothelial cells


title: GCB1_STm_2

value: PP GC B cell (B220+, CD138-, FAS+, CD38-)


title: 2_H M SAL RA

description:
Group A
sample name: 2


title: RBG19984_Old_AEC_036

value: AEC


title: 1_H M SAL RA

description:
Group A
sample name: 1


title: ABZM00626: DNMT3B_3.10 [MARS_scRNA]

value: GCGC


title: RBG19978_Old_AEC_030

value: Old


title: ABZM00638: DNMT3A_6.8 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: AAGT


title: ABZM00637: DNMT3B_4.8 [MARS_scRNA]

value: GCTG


title: DMSO rep3

city: Heidelberg

first: Sören

last: Meyer

address: Im Neuenheimer Feld 669

country: Germany

institute: University Hospital Heidelberg

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using Kalisto
TPM values were calculated using a Kalisto.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample.

source_name: infarct area, heart 48h post I/R

extract_protocol:
Hearts were removed and the infarted area was identified and seperated for RNA extraction using Trizol reagent. Ribosomal RNA was depleted using RiboZero (Illumina, San Diego, USA). RNA-seq libraries were generated using TrueSeq RNA Access Library Prep Kit (Illumina, San Diego, USA). Sequencing was performed on HiSeq2000 sequencer (Illumina, San Diego, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: heart

value: 12 weeks

tag: agent

value: DMSO

tag: time

value: 48h post I/R


title: DMSO rep2


title: ABZM00625: DNMT3A_3.6 [MARS_scRNA]

value: AAAC


title: ABZM00634: DNMT3B_4.7 [MARS_scRNA]

value: TAAG


title: RBG19977_Old_AEC_029


title: RBG19981_Old_AEC_033


title: DMSO rep1


title: RBG19976_Old_AEC_028


title: GCB1_STm_1

value: wild type

value: STm infected


title: ABZM00622: DNMT3A_3.5 [MARS_scRNA]

value: TCTA


title: RBG19989_Young_MSC-L_021

value: mesenchymal and endothelial cells

value: MSC-L

value: Young


title: GCB1_LPS_1

value: PP GC B cell (B220+, CD138-, FAS+, CD38-)

value: LPS treated


title: GCB1_Control_7


title: RBG19975_Old_AEC_027

value: AEC

value: Old


title: LGK974 rep3


title: RBG19974_Old_AEC_026


title: GCB1_Control_4

value: untreated


title: GCB1_Control_3


title: ABZM00621: DNMT3B_2.6 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: TGAT


title: LGK974 rep2

value: heart

value: 12 weeks


title: LGK974 rep1

value: 48h post I/R


title: GCB1_Control_6


title: RBG19973_Old_AEC_025


title: GCB1_Control_2


title: RBG19972_Old_AEC_024


title: ABZM00653: DNMT3A_4.1 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center


title: ABZM00619: DNMT3A_2.5 [MARS_scRNA]

value: CTAC


title: ABZM00618: DNMT3A_2.4 [MARS_scRNA]

value: ACAG


title: RBG19971_Old_AEC_023


title: ABZM00617: DNMT3B_1.6 [MARS_scRNA]

value: TTGG


title: GCB1_Control_1

value: wild type


title: GCB1_Control_5


title: GFPpos time 28 rep 2

city: San Francisco

first: Peng

last: Tien

state: CA

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco

description:
H2B-eGFP
7252-GFPpos

data_processing:
FASTQC for  quality control, Cuadapt and Sickle for triming adaptors
reads were aligned and mapped using HISAT and Stringtie
DESeq was use to call differential gene expression, in Rstudio
Genome_build: UCSC mus musculus mm10

source_name: lung

extract_protocol:
Whole lung was dissected from the adult mouse and tracheally perfused with a digestion cocktail of Collagenase Type I (225 U/ml, Thermo Fisher), Dispase (15 U/ml, Thermo Fisher) and Dnase (50 U/ml, Sigma) and removed from the chest. The lung was further diced with razor blades and the mixture was incubated for 45 mins at 37 ºC and vortexed intermittently. The mixture was then washed with FACS buffer (2% FBS in DMEM-F12). The mixture was passed through a 70 µm cell strainer and resuspended in RBC lysis buffer, before passing through a 40 µm cell strainer. Cells suspensions were incubated with the appropriate antibodies in FACS buffer for 30 min at 4 ºC and washed with FACS buffer. DAPI (0.2 µg/ml) was used to exclude dead cells. Doublets and dead cells were excluded based on forward scatter, side scatter and DAPI fluorescence. CD45-Epcam-CD31-PDGFRa+GFP- or CD45-Epcam-CD31-PDGFRa+GFP+ cells were sorted . Cells were sorted into FACS buffer. FACS analysis was performed by FACSDiva (BD Biosciences). The RNA was extracted by PicoPure RNA Isolation Kit (Applied Biosystems) from the sorted cells, and the amount and quality of extracted RNA was measured by RNA 6000 Pico Kit (Agilent). The Bulk RNA-seq was done in GENEWIZ.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Naphthalene was dissolved in corn oil at 300mg/ml at 37C nutating for 1 hour and administered intraperitoneally once at 200mg/kg. Corn oil was injected to solvent control animals.

value: Lung mesenchyme

tag: genotype/variation

value: CD45-Epcam-CD31-PDGFRa+GFP+ (p16INK4a+)

value: lung

tag: developmental stage

value: adult

value: 28 days post Naphthalene injury


title: GFPpos time 28 rep 3

description:
H2B-eGFP
7229-GFPpos


title: RBG19969_Old_AEC_021

tag: cell population

value: mesenchymal and endothelial cells

value: AEC

value: Old


title: P665InoculatedRep3Time2

city: Cordoba

first: Sara

last: Fondevilla

state: Cordoba

address: Avda. Menéndez Pidal s/n

country: Spain

institute: Instituto de Agricultura Sostenible-CSIC

description:
P665inoc2.3
MACE-seq

data_processing:
Libraries were sorted according to their respective index.
Duplicates obtained during PCR amplifications were identified and eliminated by TrueQuant technology.
Reads were filtered for quality and homopolymer.
Sequencing adapter primers and cDNA synthesis primers were eliminated.
Reads were mapped against a custom transcriptome using SOAP2.2 software.
DEseq2 package was used for normalization and differential expression analysis.
Assembly: Transcriptome.fa
Supplementary files format and content: all_comparisons_merged.txt: Tab-delimited text file includes normalized and raw abundance measurements data for each sample.

organism: Lathyrus oleraceus

source_name: Leaves

extract_protocol:
RNA was extracted using TRISure (Bioline, London, UK).
Around 5 μg of total RNA was used to construct MACE libraries using the “MACE-Kit” (GenXPro GmbH, Frankfurt am Main, Germany) following the supplier’s manual.

treatment_protocol:
Half of the plants were inoculated with Peyronellaea pinodes applying a suspension of 5 x 10^5 spores per milliliter.
The other half of the plants were maintained in the same conditions but they were not inoculated.

value: Leaves

tag: phenotype

value: Resistant to P. pinodes

value: Inoculated with P. pinodes

tag: time point

value: 48 hours


title: GFPpos time 28 rep 1

description:
H2B-eGFP
7186-GFPpos

tag: tissue


title: RBG19970_Old_AEC_022

tag: age


title: ABZM00620: DNMT3B_2.5 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: ATCA


title: GFPneg time 28 rep 3

description:
H2B-eGFP
7229-GFPneg

value: CD45-Epcam-CD31-PDGFRa+GFP- (p16INK4a-)


title: ABZM00615: DNMT3A_1.6 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: AGTC


title: ABZM00616: DNMT3B_1.5 [MARS_scRNA]

value: CATG


title: P665InoculatedRep2Time2

description:
P665inoc2.2
MACE-seq


title: P665InoculatedRep1Time2

description:
P665inoc2.1
MACE-seq


title: P665InoculatedRep3Time1

description:
P665inoc1.3
MACE-seq

value: 24 hours


title: RBG19968_Old_MSC-S_039

value: MSC-S


title: ABZM00613: DNMT3B_0.8 [MARS_scRNA]

value: GTAG


title: RBG19967_Old_MSC-S_038


title: RBG19966_Old_MSC-S_037


title: GFPneg time 28 rep 1

description:
H2B-eGFP
7186-GFPneg

value: Lung mesenchyme

value: lung

value: adult

value: 28 days post Naphthalene injury


title: ABZM00612: DNMT3B_0.7 [MARS_scRNA]

value: CGAG


title: P665InoculatedRep1Time1

description:
P665inoc1.1
MACE-seq

value: Leaves

value: Resistant to P. pinodes


title: RBG19965_Old_MSC-S_036

value: mesenchymal and endothelial cells

value: Old


title: GFPpos time 14 rep 3

description:
H2B-eGFP
7353-GFPpos

value: CD45-Epcam-CD31-PDGFRa+GFP+ (p16INK4a+)

value: 14 days post Naphthalene injury


title: P665InoculatedRep2Time1

description:
P665inoc1.2
MACE-seq

value: Inoculated with P. pinodes


title: P665ControlRep3Time2

description:
P665contr2.3
MACE-seq

value: Non inoculated

value: 48 hours


title: RBG19964_Old_MSC-S_035


title: ABZM00611: DNMT3A_0.6 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: CTGA


title: GFPpos time 14 rep 1

description:
H2B-eGFP
7152-GFPpos


title: GFPpos time 14 rep 2

description:
H2B-eGFP
7224-GFPpos


title: P665ControlRep2Time2

description:
P665contr2.2
MACE-seq


title: RBG19963_Old_MSC-S_034

value: MSC-S


title: ABZM00608: DNMT3B_3.8 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: GGTA


title: P665ControlRep1Time2

description:
P665contr2.1
MACE-seq


title: ABZM00609: DNMT3B_3.9 [MARS_scRNA]

value: TCCG


title: ABZM00614: DNMT3A_1.5 [MARS_scRNA]

value: TAAG


title: RBG19962_Old_MSC-S_033


title: GFPneg time 28 rep 2

description:
H2B-eGFP
7252-GFPneg

value: Lung mesenchyme

value: CD45-Epcam-CD31-PDGFRa+GFP- (p16INK4a-)

value: lung

value: adult

value: 28 days post Naphthalene injury


title: RBG19961_Old_MSC-S_032

value: mesenchymal and endothelial cells

value: Old


title: P665ControlRep3Time1

description:
P665contr1.3
MACE-seq

value: Leaves

value: Resistant to P. pinodes

value: 24 hours


title: GFPneg time 14 rep 2

description:
H2B-eGFP
7224-GFPneg

value: 14 days post Naphthalene injury


title: ABZM00607: DNMT3A_3.4 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: TTTC


title: P665ControlRep1Time1

description:
P665contr1.1
MACE-seq

value: Non inoculated


title: ABZM00610: DNMT3A_0.5 [MARS_scRNA]

value: AGGG


title: P665ControlRep2Time1

description:
P665contr1.2
MACE-seq


title: GFPneg time 14 rep 1

description:
H2B-eGFP
7152-GFPneg


title: GFPpos time 7 rep 3

description:
H2B-eGFP
7352-GFPpos

value: CD45-Epcam-CD31-PDGFRa+GFP+ (p16INK4a+)

value: 7 days post Naphthalene injury


title: ABZM00606: DNMT3A_3.3 [MARS_scRNA]

value: GCGC


title: ABZM00605: DNMT3B_2.4 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: AAAC


title: GFPneg time 14 rep 3

description:
H2B-eGFP
7353-GFPneg

value: Lung mesenchyme

value: CD45-Epcam-CD31-PDGFRa+GFP- (p16INK4a-)

value: lung

value: adult


title: GFPpos time 7 rep 2

description:
H2B-eGFP
7308-GFPpos


title: RBG19959_Old_MSC-S_030

value: mesenchymal and endothelial cells

value: MSC-S

value: Old


title: MessireInoculatedRep3Time2

description:
Messireinoc2.3
MACE-seq

value: Leaves

value: Messire

value: Susceptible to P. pinodes

value: Inoculated with P. pinodes

value: 48 hours


title: GFPpos time 7 rep 1

description:
H2B-eGFP
7156-GFPpos

value: CD45-Epcam-CD31-PDGFRa+GFP+ (p16INK4a+)


title: ABZM00604: DNMT3B_2.3 [MARS_scRNA]

value: CGCC


title: MessireInoculatedRep2Time2

description:
Messireinoc2.2
MACE-seq


title: RBG19957_Old_MSC-S_028


title: RBG19958_Old_MSC-S_029


title: MessireInoculatedRep1Time2

description:
Messireinoc2.1
MACE-seq


title: ABZM00603: DNMT3A_2.3 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: ACTT


title: GFPneg time 7 rep 2

description:
H2B-eGFP
7308-GFPneg

value: 7 days post Naphthalene injury


title: MessireInoculatedRep3Time1

description:
Messireinoc1.3
MACE-seq

value: 24 hours


title: GFPneg time 7 rep 3

description:
H2B-eGFP
7352-GFPneg

value: Lung mesenchyme

value: CD45-Epcam-CD31-PDGFRa+GFP- (p16INK4a-)


title: ABZM00602: DNMT3B_1.4 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: TCTA


title: RBG19956_Old_MSC-S_027

value: mesenchymal and endothelial cells

value: MSC-S


title: GFPneg time 7 rep1

description:
H2B-eGFP
7156-GFPneg

value: lung

value: adult


title: RBG19955_Old_MSC-S_026

value: Old


title: MessireInoculatedRep1Time1

description:
Messireinoc1.1
MACE-seq

value: Leaves

value: Messire

value: Susceptible to P. pinodes

value: Inoculated with P. pinodes


title: ABZM00601: DNMT3B_1.3 [MARS_scRNA]

value: TGAT


title: ABZM00600: DNMT3A_1.4 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: ATCA


title: RBG19954_Old_MSC-S_025


title: MessireInoculatedRep2Time1

description:
Messireinoc1.2
MACE-seq

value: 24 hours


title: RBG19960_Old_MSC-S_031


title: GFPpos time 0 rep 3

description:
H2B-eGFP
7347-GFPpos

value: Lung mesenchyme

value: CD45-Epcam-CD31-PDGFRa+GFP+ (p16INK4a+)

value: Solvent


title: ABZM00599: DNMT3A_1.3 [MARS_scRNA]

value: CTAC


title: RBG19953_Old_MSC-S_024

value: mesenchymal and endothelial cells


title: GFPpos time 0 rep 2

description:
H2B-eGFP
7217-GFPpos


title: ABZM00598: DNMT3B_0.6 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: ACAG


title: MessireControlRep2Time2

description:
Messirecontr2.2
MACE-seq

value: Non inoculated

value: 48 hours


title: RBG19952_Old_MSC-S_023

value: MSC-S

value: Old


title: MessireControlRep3Time2

description:
Messirecontr2.3
MACE-seq

value: Leaves

value: Messire

value: Susceptible to P. pinodes


title: GFPpos time 0 rep 1

description:
H2B-eGFP
7153-GFPpos

value: lung

value: adult


title: RBG19951_Old_MSC-S_022


title: GFPneg time 0 rep 3

description:
H2B-eGFP
7347-GFPneg

value: CD45-Epcam-CD31-PDGFRa+GFP- (p16INK4a-)


title: ABZM00597: DNMT3B_0.5 [MARS_scRNA]

value: TTGG


title: MessireControlRep1Time2

description:
Messirecontr2.1
MACE-seq


title: GFPneg time 0 rep 2

description:
H2B-eGFP
7217-GFPneg

value: Lung mesenchyme


title: ABZM00596: DNMT3A_0.4 [MARS_scRNA]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center

value: CATG


title: RBG19950_Old_MSC-S_021

value: mesenchymal and endothelial cells


title: GFPneg time 0 rep1

description:
H2B-eGFP
7153-GFPneg

value: Solvent


title: MessireControlRep3Time1

description:
Messirecontr1.3
MACE-seq

value: 24 hours


title: ABZM00594: DKO16_7.3 [MARS_scRNA]

source_name: Dr. Masaki Okano

value: ATGC


title: ABZM00595: DNMT3A_0.3 [MARS_scRNA]

value: AGTC


title: RBG19949_Old_MSC-S_020

value: MSC-S


title: ABZM00593: DKO16_7.2 [MARS_scRNA]

value: CTCG


title: MessireControlRep1Time1

description:
Messirecontr1.1
MACE-seq

value: Leaves

value: Non inoculated


title: RBG19948_Young_AEC_040

value: AEC

value: Young


title: E18.5-CC11-Zac1LMOI

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description:
Primary pre-hypertrophic chondrocytes
PolyA RNA
Processed data file: Log2RPM_E18.5-CC.txt

data_processing:
Library strategy: SMART-seq2
Libraries were sequenced with 2x50bp paired-end reads on a HiSeq2000 platform.
Reads were trimmed using Trim Galore v0.4.2 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. They were mapped to the mouse GRCm38 genome assembly using HISAT2. BAM files were imported to Seqmonk v36.0 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Raw read counts per transcript were calculated using the RNA-Seq quantitation pipeline using non-stranded counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: Log2RPM_E18.5-CC.txt: Quantitated RNA-Seq data file is tab delimited and contains the following columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) mRNA ID (Ensembl) (7) Description (Ensembl); (12-17) log2 RPM value.

source_name: Embryonic day E18.5 costal chondrocytes

extract_protocol:
[tissue collection] Ribcages were collected from E18.5 embryos, cleared from skin and soft tissues as much as possible and digested overnight with 0.25% trypsin, 0.2% collagenase II at 37°C. The homogenates were passed through 70µm cell strainer to make single cells and then prepared for cell sorting as previously described (Belluoccio, D., et al. 2010). Briefly, the cells were incubated with conjugated antibodies anti-CD24a and/or CD200 to separate the different chondrocyte types and Dapi was used for live cells; subsequently the cells were sorted using the inFlux v7 Sorter USB. Pre-hypertrophic costal chondrocytes (Cd24a+, Cd200+) were used for mRNA-seq libraries.
Total RNA was extracted from around 2000 E18.5 costal chondrocytes cells using TRIsure reagent. PolyA RNA was used for library construction.
Six Zac1LOM and 5 Zac1MOI biological replicates mRNA-seq libraries were prepared using the SMART-seq2 method as previously described (Picelli, S., et al. 2014).

value: Costal Chondrocytes

value: Embryonic day E18.5

value: wild type


title: TAM112 grains, 14DAP, rep2

city: College Station

first: Sakiko

last: Okumoto

state: TX

address: 370 OLSEN BLVD MS 2474

institute: TAMU

data_processing:
Alignment with HiSAT2
reads were counted using FeatureCounts in Subread package
Assembly: IWGSC RefSeq assembly v1.1
Supplementary files format and content: CSV, containing raw read counts for all twelve samples

organism: Triticum aestivum

source_name: grains

growth_protocol: Wheat (Triticum aestivum cv. TAM11447) plants were grown in 2018 at Texas A&M Research and Extension Center in Bushland, TX (35° 06′ N, 102° 27′ W). Standard agronomic practices were performed according to Texas A&M AgriLife extension recommendations. Spikes at five and 14 days after flowering were harvested and stored in liquid N2.

extract_protocol:
The powdered grain tissues have been extracted with 100mM Tris pH 8.0, 150mM LiCl, 50nM EDTA, 1.5% sodium dodecyl sulfate (SDS), 1.5% 2-mercaptoethanol, and phenol/chl/IAA. The supernatant is further extracted with Trizol, precipitated with isoproanol, then purified using Qiagen® RNeasy Plant Kit.
RNA library was constructed using NEXTFLEX Rapid Directional RNA-Seq Kit 2.0, following the manufacturer's protocol.

tag: cultivar

value: grains

tag: Stage


title: TAM112 grains, 14DAP, rep3


title: ABZM00592: DKO16_7.1 [MARS_scRNA]

value: GGAC


title: TAM112 grains, 14DAP, rep1


title: RBG19947_Young_AEC_039


title: E18.5-CC10-Zac1LMOI

tag: cell type


title: RBG19944_Young_AEC_036


title: TAM112 grains, 5 DAP, rep3


title: RBG19946_Young_AEC_038


title: E18.5-CC9-Zac1LMOI


title: E18.5-CC8-Zac1LMOI


title: MessireControlRep2Time1

description:
Messirecontr1.2
MACE-seq

value: Messire

value: Susceptible to P. pinodes


title: ABZM00590: DKO16_6.1 [MARS_scRNA]

value: GATC


title: ABZM00591: DKO16_6.2 [MARS_scRNA]

value: GTCC


title: ABZM00589: DKO16_5.2 [MARS_scRNA]

value: GCAT


title: RBG19943_Young_AEC_035

value: mesenchymal and endothelial cells


title: TAM112 grains, 5 DAP, rep2


title: ABZM00588: DKO16_5.1 [MARS_scRNA]

value: CGGT


title: RBG19942_Young_AEC_034


title: TAM112 grains, 5 DAP, rep1


title: E18.5-CC6-Zac1LOM

value: Zac1 biallelic expressing


title: ABZM00587: DKO16_4.2 [MARS_scRNA]

value: TAGA


title: E18.5-CC4-Zac1LOM_Rep2


title: RBG19945_Young_AEC_037


title: RBG19941_Young_AEC_033


title: TAM111 grains, 14 DAP, rep3


title: E18.5-CC4-Zac1LOM_Rep1


title: RBG19940_Young_AEC_032


title: TAM111 grains, 14 DAP, rep2


title: E18.5-CC3-Zac1LOM_Rep2


title: RBG19939_Young_AEC_031


title: TAM111 grains, 14 DAP, rep1


title: ABZM00585: DKO16_3.2 [MARS_scRNA]

value: GCTG


title: RBG19937_Young_AEC_029

value: AEC


title: ABZM00583: DKO16_0.2 [MARS_scRNA]

value: GCCA


title: ABZM00584: DKO16_3.1 [MARS_scRNA]

value: AGCT


title: ABZM00586: DKO16_4.1 [MARS_scRNA]

value: AAGT


title: ABZM00582: DKO16_0.1 [MARS_scRNA]

value: TAAG


title: TAM111 grains, 5 DAP, rep3

value: grains


title: RBG19938_Young_AEC_030

value: Young


title: E18.5-CC2-Zac1LOM_Rep1

value: Costal Chondrocytes

value: Embryonic day E18.5


title: TAM111 grains, 5 DAP, rep1


title: RBG19936_Young_AEC_028


title: E18.5-CC2-Zac1LOM_Rep2


title: E18.5-CC5-Zac1LOM


title: RBG19935_Young_AEC_027


title: ABZM00581: J1_WT_0.5 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: GTAG


title: E18.5-CC1-Zac1LOM_Rep2


title: ABZM00580: J1_WT_0.4 [MARS_scRNA]

value: CGAG


title: RBG19934_Young_AEC_026

value: mesenchymal and endothelial cells


title: E18.5-CC1-Zac1LOM_Rep1


title: Cow 3, visceral adipose tissue (VAT), snRNA-seq

city: Lexington

first: Shavahn

middle: C

last: Loux

state: KY

address: 1400 Nicholasville

department: Veterinary Science

institute: University of Kentucky

library_source: transcriptomic single cell

data_processing:
Data analysis was performed using the scRNA-Seq package Seurat v3.1.4 (Stuart et al., 2019) in the R environment (version 4.1.3), following recommended practice for scRNA-Seq analysis, including quality control, normalization, and scaling of data, feature selection, dimensionality reduction, clustering, and visualization of data. Data quality control was performed by: (1) removing genes observed in fewer than 3 cells to avoid random noise; (2) filtering nuclei with a minimum gene count of 300 and a maximum of 6,000 genes; and (3) setting a threshold of <15% for mitochondrial gene expression. In Seurat, data was normalized using the “NormalizeData” function while “CellCycleScoring” was used to classify nuclei regarding cell cycle stage and assign respective scores to each nucleus. Variability was regressed out the by difference between G2M and S phase score based on the gene expression of cell cycle genes by scaling and centering the residuals as implemented in the function “ScaleData”. Using the “FindVariableFeatures” function in Seurat, we identified 8,000 highly variable genes. The scaled and normalized expression data of respective genes served as input for a principal component analysis (PCA), and the top 30 dimensions were used to plot the variability between cells in a two-dimensional diagram by means of the Uniform Manifold Approximation and Projection (UMAP) procedure to reduce the dimensionality of the data.
Supplementary files format and content: RDS file

organism: Bos taurus

source_name: Adipose tissue (visceral)

extract_protocol:
Visceral adipose tissue (VAT) was collected from greater omentum and subcutaneous adipose tissue (SAT) from the right flank of the same three lactating Holstein dairy cows in a local abattoir. Samples were snap frozen in liquid nitrogen, transported to the laboratory, and stored at -80°C until further processing. Nuclei isolation from bovine VAT and SAT was adapted from a previous protocol with brain tissue (Krishnaswami et al., 2016). Briefly, 500 mg samples of frozen VAT or SAT were washed with sterile RNase free cold 1X PBS (10XPBS buffer, pH 7.4, Invitrogen, Cat. No. AM9625 diluted 1:10 with Nuclease-free water, Invitrogen, Cat. No. AM9932), then minced with a scalpel using a petri dish on ice. Samples were homogenized in a precooled 15 mL glass dounce homogenizer (10 strokes with pestle A followed by 15 strokes with pestle B) with 1.5 mL of homogenization buffer composed by 5 mM MgCl2 (Invitrogen, Cat. No. AM9530G), 10 mM Tris Buffer (pH 8.0) (Invitrogen, Cat. No. AM9855G), 25 mM KCl (Invitrogen, Cat. No. AM9640G), 250 mM sucrose (Sigma-Aldrich, Cat. No. S0389-500g), 1X protease inhibitor (Roche, Cat. No. 11836170001), 1 µM DL-Dithiothreitol solution (DTT, Sigma-Aldrich, Cat. No. 646563-10X), 0.4 U/µL Ribolock RNase Inhibitor (40 U/μL) (ThermoScientific, Cat. No. EO0381), 0.2 U/µL Superasin (20 U/µL) (Invitrogen, Cat. No. AM2696), and 0.1% Triton X-100 (Sigma-Aldrich, Cat. No. T8787-100ML). Samples were then strained with pre-wet 100 µm and 40 µm filters into a 50 mL conical tube. Next, each sample was transferred to two 1.5 mL pre-chilled microcentrifuge RNase free tubes and centrifuged at 500 × g, 4°C for 5 min. Supernatant was pipetted off leaving approximately 50 µL, which was resuspended in 500 µL of 1% BSA-PBS (Bovine serum albumin, Sigma-Aldrich, Cat. No. A7030-10G) including 0.2 U/μL of Ribolock RNase Inhibitors. Before proceeding with fluorescence activated cell sorting (FACS), a subsample of nuclei was used to assess the overall quality of the nuclei by staining with trypan blue and visualized by phase-contrast light microscopy. To enable sorting of nuclei, we immune-stained the nuclei sample with propidium iodide (PI) (Invitrogen, Cat. No. V13241, 10 ug/mL) in a 1:100 dilution, leaving approximately 20-30 µL of sample to be used as unstained control. Each sample was transferred into a pre-coated 5 mL polystyrene flow cytometry tube and sorted using a 100 µM nozzle in a BD FACSAria II Cell Sorter (BD Biosciences, Franklin Lakes, NJ, USA). Sorting strategy included doublet discrimination and selection of intact nuclei by sub-gating on PI stanning. PI+ nuclei was sorted directly into a 1.5 mL microcentrifuge tube containing 20 µL of 1% BSA-PBS and 0.2 U/μL of Ribolock RNase Inhibitors. After nuclei isolation, samples were centrifuged at 100 × g, 4°C for 6 min, and the supernatant was pipetted off leaving approximately 50 µL of resuspended nuclei sample. Single nuclei suspensions were subjected to final nuclei counting on an automated cell counter (Countess 2, Life Technologies Inc., Carlsbad, CA, USA) and diluted to a concentration of 700-1,000 nuclei/µL.
3’ single nuclei libraries were generated following manufacturer's user guide: 10X Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index). Final library quality was resolved using DS 5000 HS assay kit using Tape Station 4200 (Agilent Technologies, Santa Clara, CA, USA). The libraries were quantified using Qubit dsDNA HS assay kit on Qubit Fluorometer version 2.0 (Life Technologies Inc., Carlsbad, CA, USA). Pooled libraries were subjected to 150 bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq 6000). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files and the CellRanger Pipeline (10X Genomics) was used to align reads and generate count matrices

tag: breed

value: Holstein

value: Adipose tissue (visceral)


title: Cow 3, subcutaneous adipose tissue (SAT), snRNA-seq

source_name: Adipose tissue (subcutaneous)

value: Adipose tissue (subcutaneous)


title: E18.5-CC3-Zac1LOM_Rep1

value: Zac1 biallelic expressing


title: ABZM00579: J1_P12P2_sdEB6_3 [MARS_scRNA]

value: CTGA


title: RBG19933_Young_AEC_025

value: AEC


title: TAM111 grains, 5 DAP, rep2


title: Cow 2, visceral adipose tissue (VAT), snRNA-seq


title: ABZM00578: J1_P12P2_sdEB6_2 [MARS_scRNA]

value: AGGG


title: RBG19932_Young_AEC_024


title: RBG19931_Young_AEC_023


title: ABZM00577: J1_P12P_2sdEB6_2 [MARS_scRNA]

value: TCCG


title: RBG19930_Young_AEC_022


title: ABZM00576: J1_P12P2_sdEB6_1.2 [MARS_scRNA]

value: GGTA


title: RBG19929_Young_AEC_021


title: Cow 1, visceral adipose tissue (VAT), snRNA-seq


title: ABZM00574: J1_P10P2_dEB6_CXCR4neg_EPCAMpos.2 [MARS_scRNA]

value: GCGC


title: Cow 1, subcutaneous adipose tissue (SAT), snRNA-seq


title: ABZM00575: J1_P12P2_sdEB6_1.1 [MARS_scRNA]

value: TTTC


title: RBG19928_Young_MSC-S_040

value: MSC-S

value: Young


title: Cow 3, bulk RNA sequencing, visceral adipose tissue (VAT)

data_processing:
For bulk RNA sequencing data, FASTQ reads were trimmed for quality and adapters with TrimGalore 0.4.3 and mapped to bovine genome ARS-UCD1.2 with STAR-2.7.2a (Dobin et al., 2012) in the two-pass mode, quantMode GeneCounts including the following specifications (--outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignEndsType Local --chimOutType WithinBAM --twopassMode Basic --twopass1readsN -1). Annotation was performed using Ensembl v106.  Normalization of expression values was performed using gene length corrected trimmed mean of M-values (GeTMM) (Smid et al., 2018). Differentially expressed genes were identified One-Way ANOVA between VAT and SAT samples based upon a robust Benjamini-Hochberg corrected false discovery rate (FDR) P value < 0.05 (JMP 14 Pro).
Supplementary files format and content: xls

extract_protocol:
Visceral adipose tissue (VAT) was collected from greater omentum and subcutaneous adipose tissue (SAT) from the right flank of the same three lactating Holstein dairy cows in a local abattoir. Samples were snap frozen in liquid nitrogen, transported to the laboratory, and stored at -80°C until further processing. Nuclei isolation from bovine VAT and SAT was adapted from a previous protocol with brain tissue (Krishnaswami et al., 2016). Briefly, 500 mg samples of frozen VAT or SAT were washed with sterile RNase free cold 1X PBS (10XPBS buffer, pH 7.4, Invitrogen, Cat. No. AM9625 diluted 1:10 with Nuclease-free water, Invitrogen, Cat. No. AM9932), then minced with a scalpel using a petri dish on ice. Samples were homogenized in a precooled 15 mL glass dounce homogenizer (10 strokes with pestle A followed by 15 strokes with pestle B) with 1.5 mL of homogenization buffer composed by 5 mM MgCl2 (Invitrogen, Cat. No. AM9530G), 10 mM Tris Buffer (pH 8.0) (Invitrogen, Cat. No. AM9855G), 25 mM KCl (Invitrogen, Cat. No. AM9640G), 250 mM sucrose (Sigma-Aldrich, Cat. No. S0389-500g), 1X protease inhibitor (Roche, Cat. No. 11836170001), 1 µM DL-Dithiothreitol solution (DTT, Sigma-Aldrich, Cat. No. 646563-10X), 0.4 U/µL Ribolock RNase Inhibitor (40 U/μL) (ThermoScientific, Cat. No. EO0381), 0.2 U/µL Superasin (20 U/µL) (Invitrogen, Cat. No. AM2696), and 0.1% Triton X-100 (Sigma-Aldrich, Cat. No. T8787-100ML). Samples were then strained with pre-wet 100 µm and 40 µm filters into a 50 mL conical tube. Next, each sample was transferred to two 1.5 mL pre-chilled microcentrifuge RNase free tubes and centrifuged at 500 × g, 4°C for 5 min. Supernatant was pipetted off leaving approximately 50 µL, which was resuspended in 500 µL of 1% BSA-PBS (Bovine serum albumin, Sigma-Aldrich, Cat. No. A7030-10G) including 0.2 U/μL of Ribolock RNase Inhibitors. Before proceeding with fluorescence activated cell sorting (FACS), a subsample of nuclei was used to assess the overall quality of the nuclei by staining with trypan blue and visualized by phase-contrast light microscopy. To enable sorting of nuclei, we immune-stained the nuclei sample with propidium iodide (PI) (Invitrogen, Cat. No. V13241, 10 ug/mL) in a 1:100 dilution, leaving approximately 20-30 µL of sample to be used as unstained control. Each sample was transferred into a pre-coated 5 mL polystyrene flow cytometry tube and sorted using a 100 µM nozzle in a BD FACSAria II Cell Sorter (BD Biosciences, Franklin Lakes, NJ, USA). Sorting strategy included doublet discrimination and selection of intact nuclei by sub-gating on PI stanning. PI+ nuclei was sorted directly into a 1.5 mL microcentrifuge tube containing 20 µL of 1% BSA-PBS and 0.2 U/μL of Ribolock RNase Inhibitors. After nuclei isolation, samples were centrifuged at 100 × g, 4°C for 6 min, and the supernatant was pipetted off leaving approximately 50 µL of resuspended nuclei sample. Single nuclei suspensions were subjected to final nuclei counting on an automated cell counter (Countess 2, Life Technologies Inc., Carlsbad, CA, USA) and diluted to a concentration of 700-1,000 nuclei/µL.
Total RNA from adipose tissue was extracted using the RNeasy Lipid Tissue Mini kit (Qiagen, Cat. No. 74804) and RNA quality was determined using RNA Screen Tape (Agilent). Samples with RNA integrity number (RIN) greater than 7 were used in the subsequent steps. Messenger RNA purification, RNA fragmentation, double stranded cDNA, and adaptor ligation were generated using llumina Stranded mRNA Prep kit according to the manufacture’s protocol (Illumina, Cat. No. 20040534). PCR enriched libraries were quantified using the Quant-iT PicoGreen™ dsDNA Assay Kit (Invitrogen, Cat. No. P11496) and equimolar indexed libraries were pooled. Pooled libraries were checked using the Agilent Tapestation 2200 and quantified by qPCR. The libraries were then diluted to 250 pM and spiked with 1% phiX libraries (Illumina control). The transcriptome sequencing was performed on the barcoded stranded RNA-Seq libraries using Illumina NovaSeq 6000 flow cell, paired-end reads (2 × 50 bp) targeting at least 30 million reads per sample.


title: P20-T3-Zac1LOM

data_processing:
Libraries were sequenced with 2x50bp paired-end reads on a HiSeq2000 platform.
Reads were trimmed using Trim Galore v0.4.2 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence.  They were mapped to the mouse GRCm38 genome assembly using TopHat v2.1.0. BAM files were imported to Seqmonk v36.0 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). Raw read counts per transcript were calculated using the RNA-Seq quantitation pipeline using opposite-stranded counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: Quantitated RNA-Seq data file is tab delimited and contains the following columns: (1) mRNA name (Ensembl); (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) No value; (7) Feature; (8) mRNA ID (Ensembl); (9) Description (Ensembl); (10) Type; (11) Orientation; (12) Distance; (13-18) log2 RPM value

extract_protocol:
[tissue collection] Tongues were collected from either wild type or Zac1o knockout mice, expressing Zac1 gene biallelically, (Veselovska et al. 2015) at E13.5, P0 or P20.
Total RNA was extracted from E13.5 tongues using the AllPrep DNA/RNA extraction kit (Qiagen) and from P0 and P20 tongues using TRIsure reagent (Bioline).The RNA was treated with Ribo-Zero rRNA Removal Kit (Illumina) before library constraction
Three biological replicate RNA-seq libraries were made per genotype, each from 300 ng total RNA, using the dUTP-based strand-specific method as previously described (Veselovska et al. 2015), with 10 cycles of PCR amplification.

value: Tongue

value: Postnatal day P20


title: P20-T1-Zac1MOI

value: wild type


title: P20-T2-Zac1MOI


title: P20-T2-Zac1LOM


title: Cow 3, bulk RNA sequencing, subcutaneous adipose tissue (SAT)


title: ABZM00573: J1_P10P2_dEB6_CXCR4neg_EPCAMpos.1 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: AAAC


title: RBG19927_Young_MSC-S_039

value: mesenchymal and endothelial cells


title: P20-T3-Zac1MOI


title: P0-T3-Zac1MOI

value: Postnatal day P0


title: Cow 2, bulk RNA sequencing, visceral adipose tissue (VAT)

value: Holstein

value: Adipose tissue (visceral)


title: RBG19926_Young_MSC-S_038


title: P0-T3-Zac1LOM

value: Zac1 biallelic expressing


title: Cow 2, bulk RNA sequencing, subcutaneous adipose tissue (SAT)

value: Adipose tissue (subcutaneous)


title: RBG19925_Young_MSC-S_037


title: P0-T2-Zac1MOI


title: Cow 1, bulk RNA sequencing, visceral adipose tissue (VAT)


title: ABZM00570: J1_P10P2_dEB6_CXCR4pos_EPCAMneg.2 [MARS_scRNA]

value: TCTA


title: ABZM00571: J1_P10P2_dEB6_CXCR4pos_EPCAMpos.1 [MARS_scRNA]

value: ACTT


title: RBG19924_Young_MSC-S_036


title: Cow 1, bulk RNA sequencing, subcutaneous adipose tissue (SAT)


title: P20-T1-Zac1LOM


title: P0-T1-Zac1MOI


title: RBG19923_Young_MSC-S_035


title: P0-T1-Zac1LOM


title: ABZM00569: J1_P10P2_dEB6_CXCR4pos_EPCAMneg.1 [MARS_scRNA]

value: TGAT


title: RBG19922_Young_MSC-S_034


title: Pu-seq, RNASEH2A-mAID (the control line of POLA1-Y865F cells), rep 3

city: Tokyo

first: Yasukazu

last: Daigaku

address: 3-8-31 Ariake Koto-ku

department: Cancer institute

country: Japan

institute: Japanese Foundation for Cancer Research

description:
pol-usage_alpha_rep3_watson_w1000_MA30_BT5.bw
pol-usage_alpha_rep3_crick_w1000_MA30_BT5.bw
initiation-index_rep3_w1000_MA30-15.bw
fork-index_rightward_rep3_w1000_MA30-15.bw
fork-index_leftward_rep3_w1000_MA30-15.bw
coupling-index-rightward_rep3_w1000_MA30.bw
coupling-index-leftward_rep3_w1000_MA30.bw

library_source: genomic

data_processing:
Raw reads were aligned to GRCh38 using Bowtie2 (version 2.3.5).
Those which aligned to multiple genomic locations with the same mismatch scores (AS and XS scores as outputted by Bowtie2) were excluded a custom Perl script: sam-dup-align-exclude-v2.pl (available at the GitHub site: https://github.com/yasukasu/sam-dup-align-excludesam-to-bincount).
The position of the 5′ end of each R1 read (which corresponds to the 5′ end of ssDNA hydrolysed by alkali treatment) was determined, and the number of reads in 1-kb bins across the genome were counted separately for the Watson and Crick strands using a custom Perl script: pe-sam-to-bincount.pl (available at the GitHub site: https://github.com/yasukasu/sam-to-bincountsam-dup-align-exclude).
This generated the four data sets for the analysis of one polymerase. In case of Polε: at the chromosome coordinate x, Nwε(x), is the count for RNASEH2-mAID POLE1-M630F on the Watson strand; Ncε(x) is the count for RNASEH2-mAID POLE1-M630F on the Crick strand; Nw+(x) is the count for RNASEH2-mAID POL+ on the Watson strand; Nc+(x) is the count for RNASEH2-mAID POL+ on the Crick strand.
The datasets were normalised using the total number of reads: e.g. N’wε(x) = Nwε(x)/∑ Nwε for the Polε mutant on the Watson strand (where N’ indicates normalisation). These normalised data were used to calculate relative polymerase usage: e.g. Ew(x) = N’wε(x)/N’w+(x) for usage of Polε on the Watson strand; Ec(x) = N’cε(x)/N’c+(x) for usage of Polε on the Crick strand. The equivalent analysis was performed to yield usage of Polα on Watson and Crick strand: Aw(x) and Ac(x). When these data were plotted or used for further analysis (below) they were smoothed using moving average of 2m+1, where m is an arbitrary number the value of which is given in the relevant context. Thus the data point for each bin is an average of 2m+1 bins: the point of origin and the m bins either side(when the file name cotain MA3, m=3).
The difference between each neighbouring data point of polymerase usage was calculated as ΔEw(x), ΔEc(x), ΔAw(x) and ΔAc(x) with Ew(x), Ec(x), Aw(x) and Ac(x) which were smoothed using the value m = 30. These differential data were further smoothed by application of a moving average with value m = 15. At each location where all four polymerase profiles exhibit consistent patterns for initiating bidirectional replication forks (ΔEw(x)>0 ∩ ΔEc(x)<0 ∩ ΔAw(x)<0 ∩ ΔAc(x)>0) or patterns consistent with the merging of two forks (ΔEw(x)<0 ∩ ΔEc(x)>0 ∩ ΔAw(x)>0 ∩ ΔAc(x)<0) an initiation index was defined as: Ini(x) = ΔEw(x) - ΔEc(x) - ΔAw(x) + ΔAc(x). This data was subjected to Z-score normalisation (mean = 0, standard deviation = 1) and Z(0) were subtracted to maintain the original + or – information, which represent increased levels of replication initiation and termination in the cell population respectively. Fork index (Fk) was similarly calculated, but separately for rightward and leftward moving forks. For example, locations of rightward fork initiation are where ΔdEw(x)>0 ∩ ΔdAc(x)>0. Similarly, positions of rightward moving fork termination are where ΔEw(x)<0 ∩ ΔAc(x)<0. At these positions Fk was calculated as Fk-R(x) = ΔEw(x) + ΔAc(x) to give the fork index of rightward moving forks. The equivalent was performed for leftward moving forks: location initiation is are where ΔEc(x)<0 ∩ ΔAw(x)<0 and termination where ΔEc(x)>0 ∩ ΔAw(x)>0). The index for these locations was calculated as Fk-L(x) = - dEc(x) - dAw(x). These data were subjected to Z-scores normalisation and Z(0) subtracted.
The data of polymerase usage: Ew(x), Ec(x), Aw(x) and Ac(x) were smoothed using the value m = 30. To establish a separate coupling index (CI) for both leftward and rightward forks, the lagging strand profile was subtracted from the leading strand profile. For rightward moving forks: CI-R = (Ew(x) - Ac(x))/(Ew(x) + Ac(x)), for leftward moving forks:  CI-L = (Ec(x) - Aw(x))/(Ec(x) + Aw(x)).
Assembly: GRCh38
Supplementary files format and content: bigWig format files for polymerase usage, initiation index, fork index and coupling index
Library strategy: Pu-seq

molecule: genomic DNA

organism: Homo sapiens

source_name: cultured cells

growth_protocol: For AID2 system, cells were treated with 5Ph-IAA for 48hr

extract_protocol:
DNA was prepared using  the QIAGEN Blood & Cell Culture DNA Kits (100/G)
25 μg of genomic DNA was alkali treated in 0.3 M NaOH at 55 °C for 2 hr, then loaded onto a 1.5% agarose gel and run for 1 hr 40 min at 100 V. The gel was stained with acridine orange (final concentration 5 μg/ml) for 2 hr at room temperature with gentle shaking followed by overnight destaining in water. Fragments of 300–2000 bp were excised from the gel and isolated with a gel-extraction kit (Macherey-Nagel, NucleoSpin Gel and PCR Clean-up, #740609). Library preparation was performed as previously described in Daigaku et al Nat Struct Mol Biol 2015 (doi:10.1038/nsmb.2962).

tag: cell line


title: Cow 2, subcutaneous adipose tissue (SAT), snRNA-seq


title: Pu-seq, RNASEH2A-mAID POLA1-Y865F, rep 3

value: HCT116 CMV-OsTIR(F74G)::AAVS1(bi) RNASEH2A-mAID-Clover(bi) POLA1-Y865F(bi)


title: ABZM00568: J1_WT_4.8 [MARS_scRNA]

value: ATCA


title: Pu-seq, Pu-seq, RNASEH2A-mAID POLE1-M630F, rep 3

description:
pol-usage_epsilon_rep3_watson_w1000_MA30_BT5.bw
pol-usage_epsilon_rep3_crick_w1000_MA30_BT5.bw
initiation-index_rep3_w1000_MA30-15.bw
fork-index_rightward_rep3_w1000_MA30-15.bw
fork-index_leftward_rep3_w1000_MA30-15.bw
coupling-index-rightward_rep3_w1000_MA30.bw
coupling-index-leftward_rep3_w1000_MA30.bw

growth_protocol: For the AID system, cells were treated with doxycycline and auxinole for 24 hrs to induce OsTIR1 without background degradation and this medium was replaced with medium containg doxycycline and IAA. The cells were incubated for  further 48hr.

value: HCT116 Tet-OsTIR::AAVS1(bi) RNASEH2A- mAID-Clover::hygR(bi) POLE1-L630F(bi)


title: RBG19921_Young_MSC-S_033

value: MSC-S

value: Young


title: RBG19920_Young_MSC-S_032


title: ABZM00567: J1_WT_4.7 [MARS_scRNA]

value: CTAC


title: E13.5-T3-Zac1MOI

value: Tongue

value: Embryonic day E13.5

value: wild type


title: ABZM00572: J1_P10P2_dEB6_CXCR4pos_EPCAMpos.2 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: CGCC


title: ABZM00566: TKO_6.6 [MARS_scRNA]

value: TKO_Cell Bank Riken BioResource Research Center

value: ACAG


title: E13.5-T3-Zac1LOM

value: Zac1 biallelic expressing


title: RBG19919_Young_MSC-S_031

value: mesenchymal and endothelial cells


title: ABZM00565: TKO_6.5 [MARS_scRNA]

value: TTGG


title: Pu-seq, RNASEH2A-mAID (the control line of POLE1-M630F cells), rep 3


title: P0-T2-Zac1LOM

value: Postnatal day P0


title: E13.5-T2-Zac1LOM


title: RBG19918_Young_MSC-S_030


title: ABZM00563: J1_WT_6.8 [MARS_scRNA]

value: AGTC


title: E13.5-T1-Zac1MOI


title: Pu-seq, RNASEH2A-mAID (the control line of POLE1-M630F cells), rep 2

growth_protocol: For the AID system , cells were treated with doxycycline and auxinole for 24 hrs to induce OsTIR1 without background degradation and this medium was replaced with medium containg doxycycline and IAA. The cells were incubated for further 48hr.


title: RBG19917_Young_MSC-S_029


title: ABZM00558: J1_WT_7_g.8 [MARS_scRNA]

value: CGGT


title: E13.5-T1-Zac1LOM


title: PC9OR cells, biol rep 1

city: Xian

first: Yubo

address: Yanta Road

department: Medicine

institute: Xian Jiaotong University

data_processing:
the clean reads were obtained by filtering out rRNA, adaptor and low-quality reads using SOAP (1.5.2, parameters : -l 15 -q 0.2 -n 0.05 -i)
sequence data are mapped to Genome Reference Consortium Human Build 37(GRCh37) using Bowtie2 (2.2.5; parameters : -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 1 -k 200)
The counts and FPKM data were obtained using RSEM (1.2.12, parameters:--forward-prob 0)
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include expected count and RPKM values for each Sample

source_name: Lung

growth_protocol: PC9 cells and PC9OR were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using TRIzol (Invitrogen) and then qualified using Agilent 2100 bioanalyzer (Agilent). About 0.2µg RNA was used to construct sequencing libraries
TruSeq® Stranded kit (illumina) was used to prepare RNA libraries according to manufactory’s guide.

value: Lung

value: lung adenocarcinoma cells

tag: genotype

value: WT

value: osimertinib resistant


title: RBG19915_Young_MSC-S_027

value: MSC-S

value: Young


title: ABZM00556: J1_WT_7_g.6 [MARS_scRNA]

tag: cell line/mouse line

value: AAGT


title: ABZM00557: J1_WT_7_g.7 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

tag: batch index

value: TAGA


title: RBG19914_Young_MSC-S_026


title: PEACH.PPV.GRR

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

description:
smallRNA
D2

data_processing:
Illumina adapter removal: To remove Illumina adapters in 50 nt short reads, in FASTQ format, the sequence of the first 8 nucleotides of the adapter used (TGAATTC) was searched and, when detected, reads were 3’ truncated at that position. Remaining sequences, between 18 and 42 nt were considered “smallRNAs” (sRNAs)
sRNA count and filtering: For each sample, a table of unique sRNA sequences and their number of occurrences per sample (raw counts), was prepared. Only sRNA sequences appearing 3 or more times in, at least one sample, were considered for ulterior analysis. At the end, a total of 1,248,316 unique 18-42 nt sRNAs remained
Annotation of sRNAs with miRBase: Each sRNA was compared with mature miRNAs from miRBase. Only exact matches were considered. Raw counts of these known miRNAs were used to calculate normalization factors.
Normalization of sRNA counts based on known miRNA counts: To make sRNA abundances comparable between samples, raw count of each sRNA in each sample was multiplied by the average raw counts of known miRNAs detected in the previuos step, for all samples, and divided by the average sRNA raw counts of that sample
Differential expression of sRNAs: To detect differentially expressed sRNAs between two samples (experiment vs control) DEGexp function of DEGseq package was used. Normalized counts, as calculated in the previous step, were used as expression values. For each sRNA, log2(fold changes) an q-values were obtained
Genome_build: Peach v2.0.a1 (v2.1) https://www.rosaceae.org/species/prunus_persica/genome_v2.0.a1
Supplementary_files_format_and_content: Text-tabulated table containing more than 1 000 000 rows (one per smallRNA detected) with smallRNA sequences and their abundances in each sample

organism: Prunus persica

source_name: Leaf

growth_protocol: Plants were subjected to growth cycles in the greenhouse and rest periods in cold chamber. Leaf samples were collected after cycle 2 pooling leaves from 5 different plants

extract_protocol:
RNA was extracted using RNeasy Plant Mini Kit (Qiagen) and RNA samples were sent to the Centre for Genomic Regulation (CRG, Barcelona, Spain) for library preparation and RNA sequencing
The cDNA libraries of miRNA were prepared using the TruSeq Small RNA Library Preparation Kit of Illumina (following the manufactures protocol), cDNA libraries were sequenced using an Illumina GAII machine to perform 50 bp single sequencing

treatment_protocol: Control (A) and PPV-infected “GF305” peaches (B), “GF305” peach grafted with “Garrigues” almond (C and F), PPV-infected “GF305” peach grafted with “Garrigues” almond (D and G) and “GF305” peach grafted with “Garrigues” almond and the inoculated with PPV (E)

value: Leaf

tag: infection

value: PPV-infected

tag: grafted

value: Grafted

tag: treatment

value: GF305 infected with PPV and then grafted with Garrigues


title: E13.5-T2-Zac1MOI

value: Tongue

value: Embryonic day E13.5

tag: genotype/variation

value: wild type


title: Pu-seq, RNASEH2A-mAID POLA1-Y865F, rep2

description:
The ribonucletide incorporation into genomic DNA in RNASEH2A-mAID POLA1-Y865F
pol-usage_alpha_rep2_watson_w1000_MA30_BT5.bw
pol-usage_alpha_rep2_crick_w1000_MA30_BT5.bw
initiation-index_rep2_w1000_MA30-15.bw
fork-index_rightward_rep2_w1000_MA30-15.bw
fork-index_leftward_rep2_w1000_MA30-15.bw
coupling-index-rightward_rep2_w1000_MA30.bw
coupling-index-leftward_rep2_w1000_MA30.bw

data_processing:
Library strategy: Pu-seq
Raw reads were aligned to GRCh38 using Bowtie2 (version 2.3.5).
Those which aligned to multiple genomic locations with the same mismatch scores (AS and XS scores as outputted by Bowtie2) were excluded a custom Perl script: sam-dup-align-exclude-v2.pl (available at the GitHub site: https://github.com/yasukasu/sam-dup-align-excludesam-to-bincount).
The position of the 5′ end of each R1 read (which corresponds to the 5′ end of ssDNA hydrolyzed by alkali treatment) was determined, and the number of reads in 1-kb bins across the genome were counted separately for the Watson and Crick strands using a custom Perl script: pe-sam-to-bincount.pl (available at the GitHub site: https://github.com/yasukasu/sam-to-bincountsam-dup-align-exclude).
This generated the four data sets for the analysis of one polymerase. In case of Polε: at the chromosome coordinate x, Nwε(x), is the count for RNASEH2-mAID POLE1-M630F on the Watson strand; Ncε(x) is the count for RNASEH2-mAID POLE1-M630F on the Crick strand; Nw+(x) is the count for RNASEH2-mAID POL+ on the Watson strand; Nc+(x) is the count for RNASEH2-mAID POL+ on the Crick strand.
The datasets were normalized using the total number of reads: e.g. N’wε(x) = Nwε(x)/∑ Nwε for the Polε mutant on the Watson strand (where N’ indicates normalization). These normalized data were used to calculate relative polymerase usage: e.g. Ew(x) = N’wε(x)/N’w+(x) for usage of Polε on the Watson strand; Ec(x) = N’cε(x)/N’c+(x) for usage of Polε on the Crick strand. The equivalent analysis was performed to yield usage of Polα on Watson and Crick strand: Aw(x) and Ac(x). When these data were plotted or used for further analysis (below) they were smoothed using moving average of 2m+1, where m is an arbitrary number the value of which is given in the relevant context. Thus the data point for each bin is an average of 2m+1 bins: the point of origin and the m bins either side(when the file name cotain MA3, m=3).
The difference between each neighboring data point of polymerase usage was calculated as ΔEw(x), ΔEc(x), ΔAw(x) and ΔAc(x) with Ew(x), Ec(x), Aw(x) and Ac(x) which were smoothed using the value m = 30. These differential data were further smoothed by application of a moving average with value m = 15. At each location where all four polymerase profiles exhibit consistent patterns for initiating bidirectional replication forks (ΔEw(x)>0 ∩ ΔEc(x)<0 ∩ ΔAw(x)<0 ∩ ΔAc(x)>0) or patterns consistent with the merging of two forks (ΔEw(x)<0 ∩ ΔEc(x)>0 ∩ ΔAw(x)>0 ∩ ΔAc(x)<0) an initiation index was defined as: Ini(x) = ΔEw(x) - ΔEc(x) - ΔAw(x) + ΔAc(x). This data was subjected to Z-score normalization (mean = 0, standard deviation = 1) and Z(0) were subtracted to maintain the original + or – information, which represent increased levels of replication initiation and termination in the cell population respectively. Fork index (Fk) was similarly calculated, but separately for rightward and leftward moving forks. For example, locations of rightward fork initiation are where ΔdEw(x)>0 ∩ ΔdAc(x)>0. Similarly, positions of rightward moving fork termination are where ΔEw(x)<0 ∩ ΔAc(x)<0. At these positions Fk was calculated as Fk-R(x) = ΔEw(x) + ΔAc(x) to give the fork index of rightward moving forks. The equivalent was performed for leftward moving forks: location initiation is are where ΔEc(x)<0 ∩ ΔAw(x)<0 and termination where ΔEc(x)>0 ∩ ΔAw(x)>0). The index for these locations was calculated as Fk-L(x) = - dEc(x) - dAw(x). These data were subjected to Z-scores normalization and Z(0) subtracted.
The data of polymerase usage: Ew(x), Ec(x), Aw(x) and Ac(x) were smoothed using the value m = 30. To establish a separate coupling index (CI) for both leftward and rightward forks, the lagging strand profile was subtracted from the leading strand profile. For rightward moving forks: CI-R = (Ew(x) - Ac(x))/(Ew(x) + Ac(x)), for leftward moving forks:  CI-L = (Ec(x) - Aw(x))/(Ec(x) + Aw(x)).
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig format files for polymerase usage, initiation index, fork index and coupling index

source_name: HCT116 cells

value: HCT116 CMV-OsTIR(F74G)::AAVS1(bi) RNASEH2A-mAID-Clover(bi) POLA1-Y865F(bi)

tag: system


title: ABZM00555: J1_WT_7_g.5 [MARS_scRNA]

value: GCTG


title: PEACH.GRR

description:
smallRNA
C

value: Not infected

value: GF305 grafted with Garrigues


title: ABZM00564: J1_WT_6.9 [MARS_scRNA]

value: CATG


title: RBG19913_Young_MSC-S_025

source_name: endosteum and central marrow

tag: cell population

value: mesenchymal and endothelial cells

value: MSC-S


title: PEACH.PPV

description:
smallRNA
B1

value: Graftless

value: GF305 infected with PPV


title: ABZM00550: J1_WT_6.7 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: CGAG


title: PC9OR cells, biol rep 2

value: Lung

value: lung adenocarcinoma cells

value: WT

tag: phenotype

value: osimertinib resistant


title: Pu-seq, RNASEH2A-mAID POLA1-Y865F, rep1

description:
The ribonucletide incorporation into genomic DNA in RNASEH2A-mAID POLA1-Y865F
pol-usage_alpha_rep1_watson_w1000_MA30_BT5.bw
pol-usage_alpha_rep1_crick_w1000_MA30_BT5.bw
initiation-index_rep1_w1000_MA30-15.bw
fork-index_rightward_rep1_w1000_MA30-15.bw
fork-index_leftward_rep1_w1000_MA30-15.bw
coupling-index-rightward_rep1_w1000_MA30.bw
coupling-index-leftward_rep1_w1000_MA30.bw


title: RBG19911_Young_MSC-S_023

value: Young


title: RBG19912_Young_MSC-S_024


title: RBG19916_Young_MSC-S_028


title: Pu-seq, RNASEH2A-mAID (the control line of POLA1-Y865F cells), rep2

description:
The ribonucletide incorporation into genomic DNA in RNASEH2A-mAID (the control line of POLA1-Y865F cells)
pol-usage_alpha_rep2_watson_w1000_MA30_BT5.bw
pol-usage_alpha_rep2_crick_w1000_MA30_BT5.bw
initiation-index_rep2_w1000_MA30-15.bw
fork-index_rightward_rep2_w1000_MA30-15.bw
fork-index_leftward_rep2_w1000_MA30-15.bw
coupling-index-rightward_rep2_w1000_MA30.bw
coupling-index-leftward_rep2_w1000_MA30.bw


title: PEACH

description:
smallRNA
A1

tag: tissue

value: Leaf

value: Wild Type GF305


title: PC9 cells, biol rep 2

value: control


title: ABZM00549: J1_WT_6.6 [MARS_scRNA]

value: CTGA


title: ABZM00548: J1_WT_6.5 [MARS_scRNA]

value: AGGG


title: PEACH.GRR.PPV

description:
smallRNA
E2

value: PPV-infected

value: Grafted

value: GF305 grafted with Garrigues and then infected with PPV


title: RBG19910_Young_MSC-S_022

value: mesenchymal and endothelial cells

value: MSC-S

tag: age


title: Pu-seq, RNASEH2A-mAID (the control line of POLA1-Y865F cells), rep1

description:
The ribonucletide incorporation into genomic DNA in RNASEH2A-mAID (the control line of POLA1-Y865F cells)
pol-usage_alpha_rep1_watson_w1000_MA30_BT5.bw
pol-usage_alpha_rep1_crick_w1000_MA30_BT5.bw
initiation-index_rep1_w1000_MA30-15.bw
fork-index_rightward_rep1_w1000_MA30-15.bw
fork-index_leftward_rep1_w1000_MA30-15.bw
coupling-index-rightward_rep1_w1000_MA30.bw
coupling-index-leftward_rep1_w1000_MA30.bw


title: PC9 cells, biol rep 1


title: ABZM00547: J1_WT_6.4 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: TCCG


title: RBG19909_Young_MSC-S_021


title: Early-T-III

city: Seville

middle: Pablo

last: Couso

address: Carretera de Utrera, Km 1

institute: Centro Andaluz de Biologia del Desarrollo

description: Early Embryo Replicate T RiboSeq sample III

data_processing:
Sequencing reads were clipped, trimmed and aligned to an rRNA, snoRNA, snRNA & tRNA reference using Bowtie, discarding the alignments and collecting unaligned reads (Ingolia et al 2012).
Unaligned reads were mapped to the whole genome of Drosophila melanogaster FlyBase (Release 6.13) using HISAT2, default setiings.
Profiles of ribosome footprints  were constructed by quantifying the number of footprint reads aligned at each position within the feature (ORF) of interest. Ribosome density was computed by scaling read counts for each feature-by-feature length and by the total number of genome-aligned reads, using Rsamtool package (http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html).
For framing analyses, all ribosome footprints were aligned to a custom transcriptome assembly consisting of every ORF studied in its -18 and +15 mRNA context.
Assembly: FB2016_05 Dmel (Release r6.13)
Supplementary files format and content: Excel file includes RPKM values for all lncORFs in all samples (lncORF_table_2022.xlsx)
Library strategy: Ribo-seq

molecule: cytoplasmic RNA

organism: Drosophila melanogaster

source_name: Embryo

growth_protocol: Wild-type Drosophila melanogaster flies (Oregon-R) were grown in standard cages with molasses egg-laying plates containing yeast paste.

extract_protocol:
We purified mRNAs in polysomes, away from monosomes (80S), ribosomal subunits (40S, 60S). Footprinting was performed overnight at 4°C with RNaseI (Invitrogen), stopped with SUPERase·In TM RNase inhibitor (Invitrogen) and precipitated. mRNA from total cytoplasmic lysate, was purified using oligo (dT) Dynabeads (Invitrogen) and fragmented by alkaline hydrolysis.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
NEBNext Small RNA Library Prep Set for Illumina (NEB, E7300), rRNA depleted using biotinylated DNA fragments and oligos from rRNAs and going through one round of subtractive hybridization using MyOne Streptavidin C1 Dynabeads (Invitrogen). After ethanol precipitation, samples were processed as NEB guidelines.
We purified mRNAs in polysomes, away from monosomes (80S), ribosomal subunits (40S, 60S). Footprinting was performed overnight at 4°C with RNaseI (Invitrogen), stopped with SUPERase·In TM RNase inhibitor (Invitrogen) and precipitated. mRNA from total cytoplasmic lysate, was purified using oligo (dT) Dynabeads (Invitrogen) and fragmented by alkaline hydrolysis.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Embryo

tag: developmental stage

value: Early

value: wild-type

tag: embryo replicate

value: T


title: RBG18925_Old_MSC-L_020

data_processing:
Reads were mapped to the Mus musculus genome (EMSEMBL GRCm38.p4 Release 81) and ERCC sequences using GSNAP (version 2015-09-29) with parameters: -A sam –B 5 –t 24 –n 1 –Q –N 1.
HTseq-count (PMID: 25260700) was used to count reads mapped to each gene, with parameters: –s no.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: HT-Seq counts / gene counts (.txt)

value: MSC-L

value: Old


title: Pu-seq, RNASEH2A-mAID POLE1-M630F, rep1

description:
The ribonucletide incorporation into genomic DNA in RNASEH2A-mAID POLE1-M630F
pol-usage_epsilon_rep1_watson_w1000_MA30_BT5.bw
pol-usage_epsilon_rep1_crick_w1000_MA30_BT5.bw
initiation-index_rep1_w1000_MA30-15.bw
fork-index_rightward_rep1_w1000_MA30-15.bw
fork-index_leftward_rep1_w1000_MA30-15.bw
coupling-index-rightward_rep1_w1000_MA30.bw
coupling-index-leftward_rep1_w1000_MA30.bw

value: HCT116 Tet-OsTIR::AAVS1(bi) RNASEH2A- mAID-Clover::hygR(bi) POLE1-L630F(bi)

value: AID


title: Pu-seq, RNASEH2A-mAID (the control line of POLE1-M630F cells)

description:
The ribonucletide incorporation into genomic DNA in RNASEH2A-mAID (the control line of POLE1-M630F cells)
pol-usage_epsilon_rep1_watson_w1000_MA30_BT5.bw
pol-usage_epsilon_rep1_crick_w1000_MA30_BT5.bw
pol-usage_epsilon_rep2_watson_w1000_MA30_BT5.bw
pol-usage_epsilon_rep2_crick_w1000_MA30_BT5.bw
initiation-index_rep1_w1000_MA30-15.bw
initiation-index_rep2_w1000_MA30-15.bw
fork-index_rightward_rep1_w1000_MA30-15.bw
fork-index_leftward_rep1_w1000_MA30-15.bw
fork-index_rightward_rep2_w1000_MA30-15.bw
fork-index_leftward_rep2_w1000_MA30-15.bw
coupling-index-rightward_rep1_w1000_MA30.bw
coupling-index-leftward_rep1_w1000_MA30.bw
coupling-index-rightward_rep2_w1000_MA30.bw
coupling-index-leftward_rep2_w1000_MA30.bw

growth_protocol: For the AID system , cells were treated with doxycycline and auxinole for 24 hrs to induce OsTIR1 without background degradation and this medium was replaced with medium containg doxycycline and IAA. The cells were incubated for  further 48hr.


title: E18.5-CC7-Zac1LMOI

tag: cell type

value: Costal Chondrocytes

value: Embryonic day E18.5

value: wild type


title: ABZM00542: J1_WT_5.8 [MARS_scRNA]

value: CGCC


title: Early-T-II

description: Early Embryo Replicate T RiboSeq sample II


title: Early-T-mRNA-II

description: Early Embryo Replicate T mRNA sample II

data_processing:
Sequencing reads were clipped, trimmed and aligned to an rRNA, snoRNA, snRNA & tRNA reference using Bowtie, discarding the alignments and collecting unaligned reads (Ingolia et al 2012).
Unaligned reads were mapped to the whole genome of Drosophila melanogaster FlyBase (Release 6.13) using HISAT2, default setiings.
Profiles of ribosome footprints  were constructed by quantifying the number of footprint reads aligned at each position within the feature (ORF) of interest. Ribosome density was computed by scaling read counts for each feature-by-feature length and by the total number of genome-aligned reads, using Rsamtool package (http://www.bioconductor.org/packages/release/bioc/html/Rsamtools.html).
For framing analyses, all ribosome footprints were aligned to a custom transcriptome assembly consisting of every ORF studied in its -18 and +15 mRNA context.
Assembly: FB2016_05 Dmel (Release r6.13)
Supplementary files format and content: Excel file includes RPKM values for all lncORFs in all samples (lncORF_table_2022.xlsx)

extract_protocol:
We purified mRNAs in polysomes, away from monosomes (80S), ribosomal subunits (40S, 60S). Footprinting was performed overnight at 4°C with RNaseI (Invitrogen), stopped with SUPERase·In TM RNase inhibitor (Invitrogen) and precipitated. mRNA from total cytoplasmic lysate, was purified using oligo (dT) Dynabeads (Invitrogen) and fragmented by alkaline hydrolysis.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
NEBNext Small RNA Library Prep Set for Illumina (NEB, E7300)
We purified mRNAs in polysomes, away from monosomes (80S), ribosomal subunits (40S, 60S). Footprinting was performed overnight at 4°C with RNaseI (Invitrogen), stopped with SUPERase·In TM RNase inhibitor (Invitrogen) and precipitated. mRNA from total cytoplasmic lysate, was purified using oligo (dT) Dynabeads (Invitrogen) and fragmented by alkaline hydrolysis.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.


title: ABZM00541: J1_WT_5.7 [MARS_scRNA]

value: ACTT


title: RBG18924_Old_MSC-L_019

extract_protocol:
Single endosteal and central marrow stromal cells were directly sorted into individual wells of a 96-well PCR plate containing 2.3 µl of 0.2% Triton-X100 (Sigma-Aldrich, 93443) and 1U of Superase-In RNase Inhibitor (Ambion). Of note, information regarding expression of surface markers was recorded for each cell. Cells were frozen immediately at -80C until further processing. After thawing on ice, 2 µl of annealing mixture (1 µM oligodT –IDT-, 5mM each dNTPs and a dilution 1:6,000,000 of ERCC RNA Spike-In Mix -Invitrogen-) was added followed by incubation at 72C for 3 minutes. Then 5.7 µl of Reverse Transcription mix (3.5 U/µl of Maxima H minus retrotranscriptase –ThermoFisher-, 0.88 U/µl of Superase-In RNase Inhibitor, 1.75X Maxima RT Buffer, 3.5 µM TSO – Qiagen- and 13.15% PEG 8000 –Sigma-Aldrich-) was added and the mixture was incubated at 42 C for 90 min, followed by 70 C for 15 min. cDNA was further amplified by adding 40 µl of PCR mix (0.03 U/µl of Terra PCR direct polymerase –Takara Bio-, 1.25X Terra PCR Direct Buffer, 0.25 µM IS PCR primer –IDT-). PCR was as follows: 3 min at 98 °C for initial denaturation followed by 21 cycles of 15 s at 98 °C, 30 s at 65 °C, 4 min at 68 °C. Final elongation was performed for 10 min at 72 °C.  Sequences of oligodT, TSO and IS PCR primers were as previously described (PMID: 24385147).
Following preamplification, all samples were purified using Ampure XP beads (Beckman Coulter) at a ratio of 1:0.6 with a final elution in 25 µl of EB Buffer (Qiagen). The cDNA was then quantified using the Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher). Size distributions were checked on high-sensitivity DNA chips (Agilent Bioanalyzer). Samples were used to construct Nextera XT libraries (Illumina) from 100 pg of preamplified cDNA. Libraries were purified and size selected (0.5X-0.7X) using Ampure XP beads. Then, libraries were quantified using KAPA qPCR quantification kit (KAPA Biosystems), pooled and sequenced in an Illumina HiSeq 4000 instrument.

value: mesenchymal and endothelial cells


title: S2-Control

description: S2 Control mRNA sample 1


title: S2-Poly

description: S2 Polysome RiboSeq sample

extract_protocol:
We purified mRNAs in polysomes, away from monosomes (80S), ribosomal subunits (40S, 60S). Footprinting was performed overnight at 4°C with RNaseI (Invitrogen), stopped with SUPERase·In TM RNase inhibitor (Invitrogen) and precipitated. mRNA from total cytoplasmic lysate, was purified using oligo (dT) Dynabeads (Invitrogen) and fragmented by alkaline hydrolysis.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
NEBNext Small RNA Library Prep Set for Illumina (NEB, E7300), rRNA depleted using biotinylated DNA fragments and oligos from rRNAs and going through two consecutive rounds of subtractive hybridization using MyOne Streptavidin C1 Dynabeads (Invitrogen). After ethanol precipitation, samples were processed as NEB guidelines.
We purified mRNAs in polysomes, away from monosomes (80S), ribosomal subunits (40S, 60S). Footprinting was performed overnight at 4°C with RNaseI (Invitrogen), stopped with SUPERase·In TM RNase inhibitor (Invitrogen) and precipitated. mRNA from total cytoplasmic lysate, was purified using oligo (dT) Dynabeads (Invitrogen) and fragmented by alkaline hydrolysis.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: fraction

value: polysome


title: RBG18923_Old_MSC-L_018


title: ABZM00540: J1_WT_5.6 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: TCTA


title: RBG18922_Old_MSC-L_017


title: ABZM00539: J1_WT_5.5 [MARS_scRNA]

value: TGAT


title: RBG18921_Old_MSC-L_016


title: After_6

city: Moscow

first: Pavel

last: Makhnovsky

address: 76A Khoroshevskoye shosse

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

data_processing:
Adapter sequences and low quality reads were trimmed using the Timmomatic tool (v0.36) (options:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:35)
High-quality reads were aligned to the reference human GRCh38.p13 primary assembly genome using HISAT v2.1.0
Uniqe reads were counted for known exons of each gene using Rsubread package (R) and Ensembl annotation (GRCh38.101)
TPM values calculated using kallisto v0.44.0
Assembly: GRCh38.p13 primary genome assembly
Supplementary files format and content: tab-delimited text files: DESeq2.txt — differential expression analysis, Read_counts.txt — uniquely aligned read counts for genes

source_name: musculus soleus

extract_protocol:
A frozen muscle sample (~10-15 mg) was lysed by the RLT buffer (Qiagen, Germany) using a drill homogenizer and total RNA was extracted by a silica spin column (CleanRNA Standard, Evrogen, Russia). RNA concentration and integrity were evaluated by a fluorimetric assay (Qubit 4, ThermoScientific, USA) and capillary electrophoresis (TapeStation, Agilent, Germany), respectively.
Strand-specific libraries were prepared by the NEBNext Ultra II Directional RNA Library Preparation kit (NEB, USA)

treatment_protocol: Six healthy females (25-39 years old [range]; median height 1.64 m and interquartile range [1.62-1.70] m; body mass 64.9 [60.8-67.9] kg; BMI 22.39 [20.19-24.59] kg/m2) were exposed to 3 days of “dry” immersion. Samples from the soleus muscle were taken prior to and after “dry” immersion from the left leg using a modified Bergström biopsy needle with manual suction under local anesthesia (2 ml 2% lidocaine). Both biopsies were taken on the 10-th day of the menstrual cycle.

value: musculus soleus

tag: Sex

value: female

tag: individual

value: 3-day dry immersion

tag: time point

value: after treatment


title: Pu-seq, RNASEH2A-mAID POLE1-M630F, rep2

description:
The ribonucletide incorporation into genomic DNA in RNASEH2A-mAID POLE1-M630F
pol-usage_epsilon_rep2_watson_w1000_MA30_BT5.bw
pol-usage_epsilon_rep2_crick_w1000_MA30_BT5.bw
initiation-index_rep2_w1000_MA30-15.bw
fork-index_rightward_rep2_w1000_MA30-15.bw
fork-index_leftward_rep2_w1000_MA30-15.bw
coupling-index-rightward_rep2_w1000_MA30.bw
coupling-index-leftward_rep2_w1000_MA30.bw

tag: cell line


title: Before_5

value: No treatment

value: before treatment


title: S2-Mono

description: S2 Monosome RiboSeq sample

value: monosome

tag: genotype

value: wild-type


title: Late-B-mRNA-II

description: Late Embryo Replicate B mRNA sample II

value: Embryo

value: Late

value: B


title: ABZM00535: J1_WT_4.6 [MARS_scRNA]

data_processing:
Read-1 files were mapped to the mm9 genome assembly using Bowtie2 (default parameters)
Demultiplexing and UMI counting were based on 8bp of UMI and 7bp of cell-barcodes in Read-2, and performed using the pipeline described in Jaitin et al. 2014

source_name: J1 (SCRC1010, ATCC)

extract_protocol:
RNA capture for scRNA MARSseq: single-cells were FACS-sorted directly into barcoded lysis solution in 384-well MARS-seq plates, which were immediately transfered and kep at -80C. lysis solution contained UPW, 2nM poly-dT barcodes,  0.1%triton and RNAse inhibitors.
cDNA MARS-seq library preparation: scRNA MARS-seq library prepartion was performed as described in Jaitin et al. 2014. For bulk MARS-seq, only differences were were using set of 348 barcoded oligos, which allowed to pool the 384 well plate into VBLOCK KIT reservoir by centrifuge, later in the process. The step of klenow heat inactivation was removed. The volumes of the first RT and Exonuclease I reaction mix were scaled down to 1 and 0.5 μl respectively. Each reaction mix was dispensed by MANTISR (FORMULATRIX).

tag: cell line/mouse line

tag: batch index

value: TTGG


title: ABZM00534: J1_WT_4.5 [MARS_scRNA]

value: CATG


title: Late-T-II

description: Late Embryo Replicate T RiboSeq sample II

value: T


title: Mid-T-II

description: Mid Embryo Replicate T RiboSeq sample II

value: Mid


title: Before_4

tag: treatment


title: ABZM00533: J1_WT_4.4 [MARS_scRNA]

value: J1 (SCRC1010, ATCC)

value: AGTC


title: RBG18919_Old_MSC-L_014

value: mesenchymal and endothelial cells

value: MSC-L

value: Old


title: ABZM00532: DNMT3B_7_g.5 [MARS_scRNA]

source_name: Cell Bank Riken BioResource Research Center)

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: TAGA


title: RBG18918_Old_MSC-L_013


title: After_3

value: musculus soleus

value: female

value: 3-day dry immersion

value: after treatment


title: RBG18917_Old_MSC-L_012


title: Before_6

value: No treatment

value: before treatment


title: ABZM00531: DNMT3B_7_g.4 [MARS_scRNA]

value: AAGT


title: After_5


title: Before_3


title: RBG18916_Old_MSC-L_011


title: RBG18920_Old_MSC-L_015


title: ABZM00529: TKO_7_g.3 [MARS_scRNA]

value: TKO_Cell Bank Riken BioResource Research Center

value: AGCT


title: Before_2


title: RBG18914_Old_MSC-L_009


title: After_2


title: After_4


title: After_1


title: ABZM00528: TKO_7_g.2 [MARS_scRNA]

value: GCCA


title: Before_1


title: RBG18913_Old_MSC-L_008


title: RBG18912_Old_MSC-L_007


title: ABZM00527: TKO_7_g.1 [MARS_scRNA]

value: TAAG


title: ABZM00526: DNMT3B_6.3 [MARS_scRNA]

value: GTAG


title: ABZM00525: DNMT3B_6.2 [MARS_scRNA]

value: CGAG


title: RBG18911_Old_MSC-L_006

value: mesenchymal and endothelial cells

value: MSC-L


title: ABZM00530: DNMT3B_7_g.3 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: GCTG


title: RBG18915_Old_MSC-L_010

value: Old


title: ABZM00523: TKO_6.4 [MARS_scRNA]

value: AGGG


title: RBG18910_Old_MSC-L_005


title: ABZM00524: DNMT3B_6.1 [MARS_scRNA]

value: CTGA


title: RBG18909_Old_MSC-L_004


title: RBG18908_Old_MSC-L_003


title: ABZM00522: TKO_6.3 [MARS_scRNA]

value: TCCG


title: Bc14h1

city: Changchun

first: Shouan

last: Liu

address: Xi-An-Da Road 5333

institute: Jilin University

description: Botrytis cinerea treated samples replicate 1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Panax ginseng

source_name: Botrytis cinerea treated rep1

growth_protocol: The 2-year old ginseng root were grown in soil under a microbe free climate chamber with the 10 h light and 14 h dark. After germination, the plants were watered once a week and kept growing for about one month.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The B. cinerea B05.10 was grown in PDA (200 g potato, 20 g glucose, 20 g agar and 1 L water) plate to produce the conidia spores. For incubation, the ginseng leaves were spray infected with 5*105 spores mL-1. The buffer without any spores were sprayed as untreated control (CK). All leaves were harvest at 14 hours and frozen at -80℃ for RNA sequencing.

value: leaf

value: Botrytis cinerea treated

value: 2 year old


title: Bc14h3

description: Botrytis cinerea treated samples replicate 3

source_name: Botrytis cinerea treated rep3


title: Bc14h2

description: Botrytis cinerea treated samples replicate 2

source_name: Botrytis cinerea treated rep2


title: CK3

description: uninfected control samples replicate 3

source_name: CK rep3

value: uninfected control


title: ABZM00521: TKO_6.2 [MARS_scRNA]

value: TKO_Cell Bank Riken BioResource Research Center

value: GGTA


title: CK1

description: uninfected control samples replicate 1

source_name: CK rep1


title: RBG18907_Old_MSC-L_002


title: RBG18906_Old_MSC-L_001


title: Flower, stage 5 rep3

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for base calling.
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, Q30and 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 Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat 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.
HTSeq v0.6.1 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 stages (three biological replicates per stage) was performed using the DESeq R package (1.18.0). DESeq 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 <0.01 found by DESeq were assigned as differentially expressed
Supplementary_files_format_and_content: FPKMs

organism: Tulipa gesneriana

source_name: flower

extract_protocol:
The flowers of Tulipa gesneriana at different stages were collected for RAN isolation following the standard Qiagen RNeasy mini kit protocol. RNA purity and integrity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: flower

value: late senescence

value: WT


title: RBG18885_Young_MSC-L_020

address: 227 Chongqing South Road

value: mesenchymal and endothelial cells

value: Young


title: Flower, stage 5 rep2


title: ABZM00518: DNMT3B_5.6 [MARS_scRNA]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center

value: AAAC


title: RBG18884_Young_MSC-L_019

value: MSC-L


title: CK2

description: uninfected control samples replicate 2

source_name: CK rep2


title: Flower, stage 5 rep1


title: ABZM00517: DNMT3B_5.5 [MARS_scRNA]

value: CGCC


title: RBG18883_Young_MSC-L_018


title: Flower, stage 4 rep3

value: early senescence


title: ABZM00520: TKO_6.1 [MARS_scRNA]

value: TTTC


title: RBG18882_Young_MSC-L_017


title: ABZM00516: DNMT3B_4.6 [MARS_scRNA]

value: ACTT


title: ABZM00519: DNMT3B_5.7 [MARS_scRNA]

value: GCGC


title: Flower, stage 4 rep2


title: ABZM00515: DNMT3B_4.5 [MARS_scRNA]

value: TCTA


title: RBG18881_Young_MSC-L_016


title: Flower, stage 4 rep1


title: ABZM00514: DNMT3B_4.4 [MARS_scRNA]

value: TGAT


title: ABZM00513: TKO_5.7 [MARS_scRNA]

value: TKO_Cell Bank Riken BioResource Research Center

value: ATCA


title: Flower, stage 3 rep3

value: flower

value: full blooming


title: Flower, stage 3 rep2

value: WT


title: ABZM00512: TKO_5.6 [MARS_scRNA]

value: CTAC


title: Wild-type worms_rep2

type: RNA

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: wild-type

hyb_protocol: The fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies). In brief, the 600ng of labeled cRNA sample were fragmented at 60ºC for 30min and hybridized to the GXP array (8X60K, AMADID: 84944) format. Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies) and scanned using the Agilent Microarray Scanner (AgilentTechnologies).

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Caenorhabditis elegans

source_name: C.elegans Genetic Centre

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as templatefor cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP (Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-2000. 600ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to an Agilent Gene Expression Microarray 8X60K. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

growth_protocol: Worms were grown on OP50 containing plates using standard methods (Brenner, 1974).

extract_protocol: RNA isolation was carried as described by (Inada and Pleiss, 2010). The quantity and purity of the RNA was assessed by using the Nanodrop Spectrophotometer (Thermo Scientific; ND-2000) and the integrity of the RNA was analyzed on the Bioanalyzer (Agilent; 2100). We considered RNA to be of good quality based on the 260/280 and 260/230 values (Nanodrop) and also RNA integrity number (RIN) (Bioanalyzer).

treatment_protocol: Worms were harvested at L3 stage by washing with M9 buffer in a microcentrifuge tube.

value: wild type


title: RBG18878_Young_MSC-L_013

city: Shanghai

first: Xiaonan

last: Wang

institute: Shanghai Jiao Tong University School of Medicine

value: mesenchymal and endothelial cells

value: Young


title: Flower, stage 3 rep1


title: RBG18879_Young_MSC-L_014

value: MSC-L


title: RBG18880_Young_MSC-L_015


title: Wild-type worms_rep1

description: wild-type


title: Wild-type worms

description: wild-type


title: RBG18877_Young_MSC-L_012


title: ABZM00511: TKO_5.5 [MARS_scRNA]

value: ACAG


title: ABZM00510: TKO_4.6 [MARS_scRNA]

value: TTGG


title: RBG18876_Young_MSC-L_011


title: Flower, stage 2 rep3

value: partial blooming


title: Flower, stage 2 rep2


title: ABZM00509: TKO_4.5 [MARS_scRNA]

value: CATG


title: RBG18875_Young_MSC-L_010


title: Flower, stage 2 rep1


title: ubl-5 knockout worms-4

description: Homozygous lethal deletion chromosome balanced by bli-4- and GFP-marked translocation. Heterozygotes are WT with pharyngeal GFP signal, and segregate WT GFP, arrested hT2 aneuploids, and non-GFP gk3358 homozygotes (early larval arrest).

value: larval(L3) arrest


title: RBG18874_Young_MSC-L_009


title: ABZM00508: TKO_4.4 [MARS_scRNA]

value: AGTC


title: ubl-5 knockout worms-3_rep1


title: ABZM00507: DKO_7.3 [MARS_scRNA]

source_name: Dr. Masaki Okano

value: CGAG


title: ubl-5 knockout worms-2


title: ABZM00506: DKO_7.2 [MARS_scRNA]

value: CTGA


title: Flower, stage 1 rep1

value: buds


title: ubl-5 knockout worms-3_rep2


title: Flower, stage 1 rep3

value: flower


title: ABZM00505: DKO_7.1 [MARS_scRNA]

value: AGGG


title: RBG18873_Young_MSC-L_008


title: GK4_A

type: genomic

city: Shenzhen

first: Yueyuan

last: Zheng

state: China

address: Zhenyuan Road, 628

institute: The Seventh Affiliated Hospital of Sun Yat-sen University

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

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

data_processing: The SeSAME package was used to extract the DNA methylation value of each probe using the openSesame function. Recommended general masking probes were removed according to the annotation file of Infinium DNA methylation arrays. Differentially methylated probes were identified by the limma package (version 3.46.0) with adjusted p-value < 0.05, absolute delta methylation change > 0.2.

label: Cy5 and Cy3

source_name: GEJ TP53/CDKN2A KO organoid 4

label_protocol: Standard Illumina Protocol

growth_protocol: Organoid were embeded in Matrigel and maintained in aDME/F12 based organoid condtion medium

extract_protocol: Genomic DNA was extracted from organoids using Qiagen DNeasy Blood & Tissue kits

value: TP53/CDKN2A KO


title: Flower, stage 1 rep2

value: WT


title: GK2_A

source_name: GEJ TP53/CDKN2A KO organoid 2


title: GK2_B


title: GK3_A

source_name: GEJ TP53/CDKN2A KO organoid 3


title: ubl-5 knockout worms-1