title: PBAT_GKAQ_WT_54_1a

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

country: United Kingdom

institute: Altos Labs

data_processing:
library strategy: BS-seq (PBAT)
Raw FastQ files were processed with Trim Galore, then mapped to the mouse GRCm38 genome. Mapping of ChIP-seq data was done using Bowtie2, RNA-seq data was mapped using HISAT2 v2.1.0 guided by known splice sites, BS-seq data with Bismark v0.19.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: ChIP-seq report: 10kb running windows (N=272,566) were quantified as reads per kilobase per million (RPKM). Windows were filtered to exclude mapping artefacts, defined as RPKM>6 in at least one replicate set of 10% input libraries (N=408).
Supplementary_files_format_and_content: RNA-seq report: Log transformed read count quantitation per million reads of oocyte genes (Veselovska et al. 2015  doi: 10.1186/s13059-015-0769-z)
Supplementary_files_format_and_content: Bismark coverage report: A Bismark coverage file.

source_name: oocyte

growth_protocol: GV oocytes were collected from overies of mice aged 22-25 days

extract_protocol:
Oocytes were collected by manual dissection in M2 medium
RNA-seq libraries were prepared as described (Hanna et al. 2019  doi: 10.1186/s13059-019-1833-x)
ChIP-seq libraries were prepared using ULI-nChIP, as previously described (Hanna et al. 2018 doi: 10.1038/s41594-017-0013-5). Antibodies were added using 250ng/reaction for both anti-H3K9me2 (mouse monoclonal, Abcam, ab1220) and anti-IgG (rabbit polyclonal, Diagenode, EB-070-010). Library preparation was completed with a MicroPlex Library Preparation kit v2 (Diagenode) with Sanger eight-base indices for multiplexing. Relative enrichment over input was quantified using the library concentrations determined by Bioanalyzer High Sensitivity DNA Analysis (Agilent).
Low input bisulphite (BS)-seq libraries were prepared by post-bisulphite adapter tagging as previously described (Hanna et al. 2018 doi: 10.1038/s41594-017-0013-5)

value: oocyte

tag: genotype

value: Control


title: 2_3_2_S21

status: Public on Dec 02 2022

type: SRA

city: Bergen

first: Bjørn Tore

last: Gjertsen

address: Klinisk institutt 2 Postboks 7804

department: Clinical science

country: Norway

institute: University of Bergen

description: library: P9

library_source: transcriptomic

data_processing:
Hisat2 alignment against Grch38.p10
Featurecount
Supplementary files format and content: count.table.txt tab separated count file

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

extract_protocol:
PB samples at pre-treatment, 4 - and 24 hours after start of treatment for RNA sequencing was sampled in BC Vacutainer CPTTM Mononuclear cell preparation tubes with sodium heparin. Mononuclear cells were prepared by density gradient separation (Lymphoprep, Axis-shield). For RNA sequencing, approximately 1x10^6 cells were dissolved in TRIzolTM Reagent (Thermo Fisher) and stored at -80°C until analysis.
Illumina TruSeq Stranded Total RNA

tag: disease state

value: acute myeloid leukemia (AML)

tag: tissue

value: Whole blood

tag: cell type

value: PBMC

value: Normal

tag: treatment

value: Daunorubicine + Cytarabine

tag: time


title: 2_5_0_S16

description: library: P11

value: Trisomy 10

value: Pre-treatment


title: 2_9_1_S23

description: library: P15


title: 2_9_2_S26

description: library: P15


title: 2_9_0_S20

description: library: P15


title: PBAT_GKAQ_WT_45_2d

department: Bioinformatics

library_source: genomic

molecule: genomic DNA

organism: Mus musculus


title: PBAT_GKAQ_WT_52_1h


title: PBAT_GKAQ_DKO_51_1f

value: G9a-Glp cDKO


title: 2_3_1_S18

description: library: P9


title: 2_15_0_S17

description: library: P24


title: PBAT_GKAQ_WT_45_2e


title: PBAT_GKAQ_DKO_46_2k


title: PBAT_G9a_WT_10_2H


title: PBAT_G9a_WT_8_1C


title: 2_18_0_S18

description: library: P27


title: 2_3_0_merged

description: library: P9


title: PBAT_G9a_WT_10_2E


title: 1_8_2_merged

description: library: P4


title: 1678571_MW119_P8_Input

city: Memphis

first: Shannon

last: McKinney-Freeman

state: TN

address: 262 Danny Thomas Place

department: Department of Hematology

country: USA

institute: St. Jude Children’s Research Hospital

data_processing:
BWA mem mapping to mm9
Multi-mapped reads were removed using samtools
Peaks were called using MACS2
Genome_build: mm9
Supplementary_files_format_and_content: bigwiggle

growth_protocol: Nfix+/+ and Nfix-/- HPC5 cells were maintained in Iscove’s modified Dulbecco’s media with GlutaMax (IMDM) (Gibco; Carlsbad, CA) supplemented with 5% fetal bovine serum (FBS) (Atlanta Biologicals; Flowery Branch, GA), 1.5x10−4 M monothiolglycerol (MTG) (Sigma-Aldrich; St. Louis, MO), 100 ng/mL murine stem cell factor (SCF) (PeproTech; Rocky Hill, NJ) and 10 ng/mL human interleukin-6 (hIL-6) (PeproTech; Rocky Hill, NJ).

extract_protocol: 20 million Nfix+/+ and Nfix-/- HPC5 cells were fixed with 1% formaldehyde (Sigma-Aldrich; St. Louis, MO) for 10 minutes at room temperature with gentle stirring. Fixing was quenched with 2M glycine (Sigma-Aldrich; St. Louis, MO) and further stirring for five minutes at room temperature. Cells were collected by centrifugation and snap frozen for storage at -80°C. Cells were then resuspended in buffer L1 (50mM HEPES pH 7.5, 140mM NaCl, 1mM EDTA pH 8.0, 10% glycerol, 0.5% NP40, 0.25% Triton X-100) supplemented with one Protease Inhibitor tablet (Roche; Basel, Switzerland). During lysis, samples were kept on ice for 10 minutes with gentle agitation every two minutes. Samples were centrifuged at 1693 rcf for 10 minutes at 4°C in a swing bucket rotor. Supernatant was removed and cells were resuspended in buffer L2 (200mM NaCl, 1mM EDTA pH 8.0, 0.5mM EGTA, 10mM Tris pH8.0) supplemented with one Protease Inhibitor tablet (Roche; Basel Switzerland). Samples were rocked at room temperature for 10 minutes. Nuclei were isolated by centrifugation at 1693 rcf for 10 minutes at 4°C. Supernatant was carefully removed and 1X RIPA buffer was added to samples. Nuclei were sonicated using a cell disruptor (SFX250) (Branson Ultrasonics Corporation; Brookefield, CT). Lysate was clarified with centrifugation at 18879 rcf for 15 minutes at 4°C. The supernatant was carefully transferred to a 15mL conical vial. Samples were incubated with protein A/G sepharose beads (Pierce; Waltham, MA) overnight to preclear supernatant. 20µg of anti-PU.1 (sc-390405, Santa Cruz; Dallas, TX), and anti-NFIX (clone: 7B5.3) antibodies were also pre-bound to protein A/G agarose beads (Pierce; Waltham, MA) for overnight incubation. Pre-cleared chromatin was centrifuged at 1000 rcf for three minutes at 4°C. Pre-cleared chromatin was added to respective antibody-bead complex in Eppendorf tubes while some pre-cleared chromatin was reserved for input. Samples were rotated at 4°C for four hours. After incubation, samples were centrifuged at 5418 rcf for five minutes at 4°C. Supernatant was aspirated and beads were washed with various buffers: once with IP Wash Buffer I (20mM Tris pH8.0, 50mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), twice with IP High Salt Wash Buffer (20mM Tris pH8.0, 500mM NaCl, 2mM EDTA, 1% Triton X-100, 0.1% SDS), once with IP Wash Buffer II (10mM Tris pH8.0, 250mM LiCl, 1mM EDTA, 1% NP-40, 1% deoxycholic acid), and twice with TE buffer. DNA:protein complexes from beads were eluted twice with freshly made elution buffer (1% SDS, 100mM sodium bicarbonate). To reverse crosslinking, 5M NaCl (final concentration 370mM), 10mg/mL RNase (final concentration 0.45mg/mL), and 20mg/mL proteinase-K (final concentration 0.26mg/mL) were added to eluates and input samples. Incubate samples at 37°C for 30 minutes, 45°C for 30 minutes, and 65°C overnight. DNA was eluted using the Qiagen MinElute (Hilden, Germany) kit following manufacturer’s protocol except DNA was eluted in 28uL with provided EB buffer. DNA was quantified using the Quant-iT PicoGreen assay (Life Technologies; Carlsbad, CA) Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific; Waltham, MA) or SpectraMax Quant AccuBlue Pico dsDNA assay kit (Molecular Devices; San Jose, CA). Libraries were prepared with KAPA HyperPrep Library Preparation Kits (KK8504) (Roche; Basel, Switzerland). Libraries were analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent Technologies; Santa Clara, CA), 5300 Fragment Analyzer System HS Large Fragment Kit (Agilent Technologies; Santa Clara, CA), 4200 TapeStation D1000 ScreenTape assay (Agilent Technologies; Santa Clara, CA) or Caliper LabChip GX DNA High Sensitivity Reagent Kit (PerkinElmer; Waltham, MA). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (Life Technologies; Carlsbad, CA) or low pass sequencing with a MiSeq nano kit (Illumina; San Diego, CA). Single read 50 cycle sequencing was performed on a NovaSeq 6000 (Illumina; San Diego, CA) or NextSeq 550 (Illumina; San Diego, CA).

tag: cell line

tag: antibody

value: input


title: 1_8_0_S24

description: library: P4


title: PBAT_G9a_KO_8_1H

value: G9a cKO


title: PBAT_GKAQ_DKO_46_2m


title: 1_71_1_merged

description: library: P20

value: inv (3) MECOM


title: Ad_b_IP [mmRe_IP]

city: Guangzhou

first: SHUYI

last: CHEN

state: Guangdong

address: 54 S. Xianlie Rd

department: State Key Laboratory of Ophthalmology

country: China

institute: Zhongshan Ophthalmic Center, SYSU

data_processing:
library strategy: meRIP-seq
raw data was processed through in-house perl scripts to get rid of low quality data (containing adapter, polyN and Q<20)
clean reads were aligned to the mouse reference genome (mm10) using BWA mem v0.7.12
peak calling was performed using MACS2 v2.1.0 peak finding algorithm. A q value of enrichment of 0.05 was used.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

extract_protocol:
TRIzol
MeRIP-seq libraries were constructed following the protocol described in Dominissini D et al., Nat. Prot. 2012, 8: 176

tag: strain

tag: age

value: adult

value: retina


title: PBAT_G9a_KO_10_2F


title: Ad_b_Inp [mmRe_Inp]


title: PBAT_G9a_KO_10_1


title: Ad_a_IP


title: 2_1_0_S1

description: library: P6

value: Inv (16) CBFB/MYH11


title: 1_71_0_S25

description: library: P20


title: Ad_a_Inp


title: p0_b_IP


title: p0_b_Inp


title: 1_68_2_S11

description: library: P16


title: 1_68_0_S10

description: library: P16


title: GKAQ55_1e_DKO_RNAseq

data_processing:
Raw FastQ files were processed with Trim Galore, then mapped to the mouse GRCm38 genome. Mapping of ChIP-seq data was done using Bowtie2, RNA-seq data was mapped using HISAT2 v2.1.0 guided by known splice sites, BS-seq data with Bismark v0.19.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: ChIP-seq report: 10kb running windows (N=272,566) were quantified as reads per kilobase per million (RPKM). Windows were filtered to exclude mapping artefacts, defined as RPKM>6 in at least one replicate set of 10% input libraries (N=408).
Supplementary_files_format_and_content: RNA-seq report: Log transformed read count quantitation per million reads of oocyte genes (Veselovska et al. 2015  doi: 10.1186/s13059-015-0769-z)
Supplementary_files_format_and_content: Bismark coverage report: A Bismark coverage file.


title: p0_a_IP


title: 1_8_1_merged

description: library: P4


title: p0_a_Inp


title: PBAT_G9a_WT_10_1


title: GKAQ57_1f_WT_RNAseq


title: 1_67_2_S12

description: library: P14


title: p6_b_IP

data_processing:
Library strategy: MeRIP-seq
Raw data was processed through in-house perl scripts to get rid of low quality data (containing adapter, polyN and Q<20).
Clean reads were aligned to the mouse reference genome (mm10) using BWA mem v0.7.12.
Peak calling was performed using MACS2 v2.1.0 peak finding algorithm. A q value of enrichment of 0.05 was used.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig

source_name: retina

extract_protocol:
TRIzol
MeRIP-seq libraries were constructed following the protocol described in Dominissini D et al., Nat. Prot. 2012, 8: 176.

value: Retina

value: Postnatal day 6


title: 1_67_0_S8

description: library: P14


title: PBAT_G9a_KO_10_2G

value: oocyte


title: 1_71_2_S6

description: library: P20

value: acute myeloid leukemia (AML)


title: p6_a_input


title: p6_a_IP


title: GKAQ55_1b_WT_RNAseq

value: Control


title: GKAQ51_1c_DKO_RNAseq


title: Ctrl_1

data_processing:
Basecalls performed using CASAVA.
Clean reads were aligned to the mouse reference genome (mm10) using Hisat2.
featureCounts was used to count the reads numbers mapped to each gene.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: gene_count.txt: Tab-delimited text file includes read counts for each gene.

extract_protocol:
TRIzol
NEBNext UltraTM RNA library Prep Kit for Illumina following manufacturer's protocol.

value: Postnatal day 7


title: Ctrl_3


title: GKAO115_4d_KO_RNAseq


title: 1_66_0_S14

description: library: P34

value: Whole blood

value: PBMC


title: 1_66_2_S15

description: library: P34

value: Daunorubicine + Cytarabine (dose reduced)


title: 1_62_2_S22

description: library: P7

value: Daunorubicine + Cytarabine


title: Ctrl_2


title: Ctrl_4


title: CKO_4

value: Mettl3 knockout


title: CKO_2


title: GKAO115_3g_WT_RNAseq


title: GKAO109_4d_WT_RNAseq


title: 1_62_0_S16

description: library: P7

value: Pre-treatment


title: H343

city: Houston

first: Chunru

last: Lin

state: TX

address: 1515 Holcombe Boulevard

department: Department of Molecular and Cellular Oncology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.1.0 with default parameters
Fragments per kilobase million (FPKM) were calculated by edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM

source_name: HEART

extract_protocol:
Tumor, heart, kidney, skeletal muscle, liver and lung tissues were collected and flash frozen in liquid nitrogen. Total RNA was extracted using TRIzol. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HEART

value: ICB


title: CKO_3


title: 1_55_2_S13

description: library: P23

value: Normal


title: CKO_1


title: H345


title: p6_b_input


title: GKAO109_4c_KO_RNAseq

value: G9a cKO


title: H344


title: 1_55_1_merged

description: library: P23


title: H341

value: IgG control


title: GKAQ54_1e_WT_RNAseq


title: H340


title: H338


title: GKAO115_4c_KO_RNAseq


title: 1_55_0_S5

description: library: P23


title: M344

source_name: MUSCLE

value: MUSCLE


title: M347


title: M345


title: 1_53_2_S11

description: library: P5


title: 1_53_1_merged

description: library: P5


title: 1_62_1_S19

description: library: P7

value: Inv (16) CBFB/MYH11


title: M340


title: Human differentiated IEO (2% oxygen)

city: Trondheim

first: Gunnar

middle: Andreas

last: Walaas

address: Prinsesse Kristinas gate 1

department: Department of Clinical and Molecular Medicine

institute: Norwegian University of Science and Technology

library_source: transcriptomic single cell

data_processing:
Illumina bcl2fastq v2.20.0.422 software used for basecalling.
cellranger-6.0.2 pipeline was used to generate UMI read counts
Assembly: GRCh38
Supplementary files format and content: Cellranger type output of UMI counts in the sparse matrix mtx format and row and column name in separate files

source_name: Colon organoids

growth_protocol: Human colonic stem cells were plated in matrigel with a medium containing WNT-3a, advanced DMEM and R-spondin in addition to Noggin, Nictotinamide, N-Acetyl-L-Cysteine, A-83-01, SB202190, EGF and Gastrin. Initialy during establishment of the organoids the medium was supplemented with Y-27632. In paralell, the IEOs were incubated in 2% and 20% oxygen.

extract_protocol:
IEOs were enzymatically and mechanically dissociated into a single cell suspension of PBS + 0.05% BSA. Ten thousand cells were loaded onto the platform for each sample.
scRNA-sequencing was performed using a Chromium Controller and the Chromium Single Cell 3' Reagent Kit (10X Genomics, USA), according to manufacturer protocols. Briefly, cells and barcoded gel beads were isolated in partitioning oil droplets (GEMs) using 10X Genomics Chromium Controller instrument. Reverse transcription was performed, resulting in cDNA tagged with a cell barcode and unique molecular index (UMI). Next, GEMs were broken and cDNA amplified. Prior to sequencing, the libraries were quantitated by quantitative polymerase chain reaction using the KAPA Library Quantification Kit–Illumina/ABI Prism® (Kapa Biosystems, Wilmington, MA, USA) and validated using the Agilent High Sensitivity DNA Kit on a bioanalyzer. Libraries were normalized and pooled to 2.3 pM subjected to clustering. Sequencing was performed on a NextSeq500 HO flowcell (Illumina, San Diego, CA, USA), for 26 cycles for Read 1 (cell barcode and UMI read), 8 cycles for index read and 56 cycles for Read 2 (transcript read), according to the manufacturer's instructions. Base calling was done on the NextSeq500 instrument by RTA 2.4.6. FASTQ files were generated using bcl2fastq2 Conversion Software v2.20.0.422 (Illumina, Inc. San Diego, CA, USA).

treatment_protocol: The undifferentiated colonoids remained in the growth medium, while  differentiation was induced, in half of the samples, by reducing the WNT-3a concentration, removing Nicotinamide and SB202190 while adding DAPT

value: Colon

value: Intestinal epithelial organoid

value: Healthy

tag: treatment 1

value: Differentiated

tag: treatment 2

value: 2% oxygen


title: Human undifferentiated IEO (2% oxygen)

value: Undifferentiated


title: M339


title: Human differentiated IEO (20% oxygen)

value: 20% oxygen


title: Human undifferentiated IEO (20% oxygen)


title: M338


title: 1_53_0_S3

description: library: P5

value: acute myeloid leukemia (AML)

value: Whole blood

value: PBMC


title: LV344

source_name: LIVER

value: LIVER


title: 1_5_2_merged

description: library: P2

value: Daunorubicine + Cytarabine


title: GKAO109_4b_WT_RNAseq

value: oocyte

value: Control


title: LV343

value: ICB


title: LV341

value: IgG control


title: 1_5_1_merged

description: library: P2

value: Inv (16) CBFB/MYH11


title: 3266_Undifferentiated

data_processing:
Illumina bcl2fastq v2.20.0.422 software used for basecalling.
FASTQ files were filtered and trimmed (fastp v0.20.0)
Transcript counts were generated using quasi mapping to the GRCh38 transcriptome (Salmon v1.3.0)
Assembly: GRCh38
Supplementary files format and content: Tab seprated file with count and normalized counts

growth_protocol: Human colonic stem cells were plated in matrigel with a medium containing WNT-3a, advanced DMEM and R-spondin in addition to Noggin, Nictotinamide, N-Acetyl-L-Cysteine, A-83-01, SB202190, EGF and Gastrin. Initialy during establishment of the organoids the medium was supplemented with Y-27632

extract_protocol:
Colonoids were collected with cell recovery solution, washed with PBS/0.1% BSA twice, snap frozen in liquid nitrogen, and stored at -80 ᵒC. Rneasy kit was used as per manufacturer's instructions.
RNA sequencing libraries were generated for 54 RNA samples, using SENSE mRNA-Seq library prep kit V2, according to manufacturer’s instructions (Lexogen GmbH, Vienna, Austria). In brief, 500 ng of total RNA was prepared and incubated with magnetic beads coated with oligo-dT, then all other RNAs except mRNA were removed by washing. Library preparation was then initiated by random hybridization of starter/stopper heterodimers to the poly(A) RNA still bound to the magnetic beads. These starter/stopper heterodimers contain Illumina-compatible linker sequences. A single-tube reverse transcription and ligation reaction extends the starter to the next hybridized heterodimer, where the newly synthesized cDNA insert was ligated to the stopper. Second-strand synthesis was performed to release the library from the beads. The resulting double-stranded library was purified and amplified (15 PCR cycles) after adding the adaptors and indexes. Finally, libraries were quantitated by qPCR using KAPA Library Quantification Kit (Kapa Biosystems, Inc., MA, USA) and validated using Agilent High Sensitivity DNA Kit on a Bioanalyzer (Agilent Technologies, CA, USA). The size range of the DNA fragments were measured to be in the range of 160-400 bp with average library size 236 bp.  Prior to sequencing, the libraries were quantitated by quantitative polymerase chain reaction using the KAPA Library Quantification Kit–Illumina/ABI Prism® (Kapa Biosystems, Wilmington, MA, USA) and validated using the Agilent High Sensitivity DNA Kit on a bioanalyzer. Libraries were normalized to 2.6 pM subjected to clustering. Single read sequencing was performed for 86 cycles on a NextSeq500 HO flowcell (Illumina, San Diego, CA, USA), according to the manufacturer's instructions. Base calling was done on the NextSeq500 instrument by RTA 2.4.6. FASTQ files were generated using bcl2fastq2 Conversion Software v2.20.0.422 (Illumina, Inc. San Diego, CA, USA).    Acknowledgment  The library prep, sequencing and the sequencing related bioinformatics analysis were performed in close collaboration with the Genomics Core Facility (GCF), Norwegian University of Science and Technology (NTNU). GCF is funded by the Faculty of Medicine and Health Sciences at NTNU and Central Norway Regional Health Authority.”

treatment_protocol: Differentiation was induced on day 10 in half of the organoids. The undifferentiated colonoids remained in the growth medium, while the differentiation was induced by reducing the WNT-3a concentration, removing Nicotinamide and SB202190 while adding DAPT

value: Colon


title: LV340


title: LV345


title: 3266_Differentiated

value: Intestinal epithelial organoid


title: 3264_undifferentiated

value: Healthy


title: LV339


title: T346

source_name: TUMOR

value: TUMOR


title: 1_5_0_merged

description: library: P2

value: Pre-treatment


title: T345


title: 1_49_2_S13

description: library: P33

value: Normal

value: Daunorubicine + Cytarabine (dose reduced)


title: 3264_Differentiated

value: Differentiated


title: T344


title: 9001_Undifferentiated

value: Undifferentiated


title: T340


title: T338


title: 9001_Differentiated


title: T339


title: LG347

source_name: LUNG

value: LUNG


title: LG342


title: LG345


title: LG339


title: LG343


title: LG338


title: Genome_Wide_CRISPR_Screen_U937_SNRNP200_High

city: South San Francisco

first: Simon

middle: J

last: Hogg

state: California

address: 1000 Gateway Boulevard

department: Oncology Discovery Research

institute: AbbVie

data_processing:
FASTQ files were trimmed using cutadapt (version 2.5) to remove sequences dervied from the sgRNA expression vector to yield the 20 b.p. sgRNA sequence using the following parameters: -g TGTGGAAAGGACGAAACACCG -a GTTTTAGAGCTAGAAATAGCAAG --maximum-length 20.
sgRNA counts were generated using MaGeCk (version 0.5.9.4) count command using options for read-depth normalization (--norm-method total).
Pairewise statistical comparisons were computed using MaGeCK test command using default parameters.
Assembly: HG19
Supplementary files format and content: Counts matrix of non-normalized sgRNA counts
Library strategy: CRISPR/Cas9 screen

source_name: Histiocytic Lymphoma

growth_protocol: K-562 and U-937 cells expressing Cas9 cDNA were transduced with the genome-scale Brunello sgRNA library (77,441 sgRNAs) at a low multiplicity of infection to ensure only 1 viral integration per cell. Transduced cells were then selected and expanded in the presence of Puromycin for 3 days to isolate sgRNA transduced cells.

extract_protocol:
Cell pellets were lysed and genomic DNA was extracted using the QIAamp DNA Mini Kit (Qiagen) and quantified by Qubit (ThermoScientific). gRNAs amplicons were amplified by PCR using TaKaRa ExTaq® DNA Polymerase (Takara) to add Illumina sequencing adapters and multiplexing barcodes.
Amplicons were quantified by Qubit and Bioanalyzer (Agilent), multiplexed, and sequenced on an Illumina NextSeq 500 to obtain 75b.p. single-end reads.

treatment_protocol: K-562 and U-937 cells were stained for cell surface SNRNP200 expression using antibodies, then populations of SNRNP200 high or low cells (representing the top or bottom ~10%) were isolated using fluorescence activated cell sorting (FACS). A population of bulk, unselected cells (i.e. not subjected to selectino pressure by flow cytometry) were also collected for each cell line.

tag: genetic perturbation

value: Cas9 expression by cDNA

tag: crispr sgrna library

value: Human sgRNA library Brunello in lentiCRISPRv6

tag: selection pressure

value: SNRNP200 High sorted by fluorescence activated cell sorting


title: Genome_Wide_CRISPR_Screen_U937_Unselected

value: Human sgRNA library Brunello in lentiCRISPRv5

value: Bulk unsorted population


title: K346

source_name: KIDNEY

value: KIDNEY

value: ICB


title: delthrW_rich_rep3

city: Ploen

first: Jenna

last: Gallie

address: August-Thienemann Strasse 2

country: Germany

description: mature tRNA

data_processing:
Library strategy: YAMAT-Seq
Sorted into 30 samples using the unique, 6-bp Illumina indices. 0 mismatches allowed.
Per sample: reads between 80 and 151 bp were extracted (in Geneious v11.1.4)
Per sample: 80-151 bp reads were aligned to a set of 49 reference tRNA sequences (all unique primary sequences predicted in the MG1655 genome by GtRNAdb2.0). This was done using Geneious version 11.1.4 (assembly parameters: up to 10% mismatches or gaps of <3 bp per read, up to 5 ambiguities per read, no assignment of reads that map equally well to more than one reference sequence, and no iterations)
Per sample: read numbers for the (up to) 49 contigs were used in pairwise comparisons with DESeq2 (in R version 3.6.0)
Assembly: The 49 tRNA sequence reference file was derived from the MG1655 genome sequence (RefSeq: NZ_CP009685.1) using GtRNAdb2.0 (http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/bacteria/Esch_coli_K_12_MG1655_3/eschColi_K_12_MG1655_3-tRNAs.fa)
Supplementary files format and content: Two excel workbooks. (1) "aligned_reads_redundancy.xlsx" contains a summary of the data for all 30 samples, plus a spreadsheet for each of the 10 strain-medium combinations, each listing the of the number of reads aligned to each reference sequence in each replicate. (2) "deseq_comparisons_redundancy.xlsx" contains the DESeq2 output for pairwise comparisons between strain-medium combinations of interest.

organism: Escherichia coli K-12

source_name: liquid cell culture

growth_protocol: Samples were streaked from cyrogenically frozen stocks (-80˚C; glycerol saline) onto standard LB agar plates, and grown at 37˚C overnight. For each sample listed below, a single colony of the relevant genotype was chosen and grown in liquid rich LB culture overnight (all samples; 37˚C, shaking). 150 ul of grown overnight culture was transferred into either (i) 15 ml fresh RLB (rich medium samples), or (ii) 15 ml fresh M9+0.05% galactose (poor medium samples). Cultures were grown at 37˚C (shaking) to mid-exponential phase (roughly 3 hours and OD600 of ~0.5-0.7 for RLB; 8-10 hours and OD600 ~0.2-0.3 for M9+Gal). Samples of each culture were used to calculate cfu/ml and measure OD600 (to demonstrate culture growth) at various time points.

extract_protocol:
Per sample: 4 ml (RLB) or 12 ml (M9+Gal) aliquots of mid-exponential phase culture were taken, and total RNA extracted (TRIzol Max Bacterial RNA isolation kit; Life Technologies).
The YAMAT-seq method is an adaptation of that published for human cell lines (Shigematsu et al., 2017; doi:10.1093/nar/gkx005 ) and adapted for use in the bacterium Pseudomonas fluorescens in (Ayan et al., 2020; doi:10.7554/eLife.57947).  Briefly, for each sample, 5 ug total RNA was subjected to tRNA deacylation treatment by exposure to hydrochloric acid. Hybrid DNA/RNA Y-shaped adapters (Eurofins) were ligated to exposed 5'-CCA-3' tRNA ends using T4 RNA ligase 2 (New England Biolabs). Ligation products were reverse transcribed into cDNA (SuperScript III reverse transcriptase; Thermo Fisher), and amplified PCR (Phusion; Thermo Fisher). One of 30 sample-specific indices (Illumina) was added to each of the 30 reactions. The quality and quantity of each PCR product was checked using an Agilent DNA 7500 kit on a Bioanalyzer (Agilent), and samples combined in equimolar amounts into a single tube. The mixture was run on a 5 % polyacrylaminde gel (Bio-Rad Laboratories), and the group of bands ranging between ~180 bp and ~280 bp excised. DNA was extracted in deionized water overnight, and agarose removed by centrifugation through filter paper. DNA quality and quantity was checked with a Quant-iT dsDNA BR Assay kit (Invitrogen) on a Fluorescence Nanodrop. High throughput sequencing was performed at the Max Planck Institute for Evolutionary Biology (Ploen, Germany). Single-end, 150 bp reads were generated with a NextSeq 550 Output v2.5 kit (Illumina).

tag: strain type

value: engineered

value: {delta}thrW

tag: growth medium

value: rich (Rich LB)


title: K344


title: delthrW_rich_rep2

institute: Max Planck Institute for Evolutionary Biology

description: mature tRNA

tag: genotype


title: delthrW_poor_rep3

description: mature tRNA

value: poor (M9 with 0.05 % galactose)


title: K343


title: Genome_Wide_CRISPR_Screen_K562_Unselected

source_name: Chronic Myelogenous Leukemia

value: Human sgRNA library Brunello in lentiCRISPRv2


title: Genome_Wide_CRISPR_Screen_K562_SNRNP200_High

value: Human sgRNA library Brunello in lentiCRISPRv3


title: delthrW_rich_rep1

description: mature tRNA


title: delthrW_poor_rep2

description: mature tRNA


title: 1_49_0_S12

description: library: P33

tag: disease state

value: acute myeloid leukemia (AML)

value: Whole blood

value: PBMC

value: Normal

value: Pre-treatment


title: K342

tag: tissue

value: IgG control


title: Ring1bKO-G2

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

country: Spain

institute: GENyO

data_processing:
For CaptureC, paired-end reads were aligned to mm10 and filtered for HiC artefacts using HiCUP (Wingett S, et al. (2015)) and Bowtie2 (Langmead and Salzberg, 2012) with fragment filter set to 100-800bp. Read counts of reads aligning to captured gene promoters and interaction scores (=significant interactions) were then called by CHiCAGO (Cairns et al., 2016).
For visualisation of CaptureC data weighted pooled read counts from chicago data files were normalized to total read count aligning to captured gene promoters in the sample and further to the number of promoters in the respective capture experiment. Bigwig files were generated from these normalized read counts.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: Capture-C

growth_protocol: FUCCI-Ring1bfl/fl mESCs were cultured in 5% CO2 at 37 ºC on 0.1% gelatin-coated dishes in DMEM KO (Gibco) media supplemented with 10% FCS, leukaemia-inhibiting factor (LIF), penicillin/streptomycin (Biowest), L-glutamine (Biowest) and 2-mercaptoethanol (Gibco) and hygromycin B (InvivoGen) as described previously (Asenjo et al, 2020)

extract_protocol:
Chromatin extraction and fixation was carried out from 2x106 cells from G1 and G2-sorted FUCCI-Ring1bfl/fl and FUCCI-Ring1b-/- cells. Cells were resuspended in 1.86 ml of complete medium and fixed with formaldehyde (1.89%) and incubated for 10 minutes on a rotating wheel at room temperature. The fixation reaction was stopped by adding cold glycine (final concentration 150 mM). Fixated cells were centrifuged (5 min 1000 rpm 4°C) and washed 1x with cold PBS. After centrifugation, cells were resuspended in cold lysis buffer (10 mM Tris pH 8, 10 mM NaCl, 0.2% NP-40, 1x protease inhibitors (Roche)) and incubated for 20 min on ice. Subsequently, the pellet was centrifuged (5 min, 1800 rpm, 4°C) and resuspended in 200 μl of lysis buffer. Next steps were carry out as described previously in (Dimitrova et al., 2021)
2-4 µg DNA from each sample were adaptor-ligated and indexed using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) and NEBNext Multiplex Oligos for Illumina (New England Biolabs). The libraries were amplified with 7 PCR cycles using Herculase II Fusion Polymerase kit (Agilent). Libraries hybridisation was performed as described previously (Dimitrova et al., 2021)

treatment_protocol: Treatment with 800 nM 4-hydroxytamoxifen (Tmx, Sigma) for 48 hours and collected for downstream analyses 24 hours later (72 hours total). 4-thiouridine labelling during 1 hour 37ºC. Cell-cycle sorting using an Aria Fusion cell sorter.

tag: cell-type

value: Mouse embryonic stem cells

value: Derived from male blastocysts in (Endoh et al 2008)

tag: developmental stage


title: K340

tag: treatment


title: Ring1bflfl-G2


title: delthrW_poor_rep1

description: mature tRNA


title: Genome_Wide_CRISPR_Screen_U937_SNRNP200_Low

tag: cell line

value: Cas9 expression by cDNA

value: Human sgRNA library Brunello in lentiCRISPRv7

value: SNRNP200 Low sorted by fluorescence activated cell sorting


title: delglyU_rich_rep3

description: mature tRNA

value: engineered

value: {delta}glyU


title: delglyU_rich_rep2

description: mature tRNA

value: rich (Rich LB)


title: Genome_Wide_CRISPR_Screen_K562_SNRNP200_Low

value: Human sgRNA library Brunello in lentiCRISPRv4


title: delglyU_rich_rep1

description: mature tRNA


title: Ring1bflfl-G1


title: KFR / Rh4 / RMS

city: Zürich

first: Sara

middle: Giulia

last: Danielli

state: Zürich

address: Steinwiesstrasse 75

department: Department of Oncology

country: Switzerland

institute: University Children's Hospital

description: Cells stained with TotalSeq™-B0251 anti-human Hashtag 1 Antibody (barcode sequence: GTCAACTCTTTAGCG)

data_processing:
Illumina sequencing reads were processed (de-multiplexing features and cellular barcodes, read alignment to the reference human genome GRCh38, and gene expression matrix generation) using the 10X Genomics Cell Ranger software Suite (version 3.0.1). Each gene expression matrix was then analyzed independently using Seurat R package (version 3.2.2)28 in R (version 3.6.1), with some modifications to the standard pipeline. We first de-multiplexed gene expression matrices based on hashtag oligonucleotide (HTOs) enrichment. To do so, we added HTO data as a new independent assay to the RNA data and used centered log-ratio (CLR) transformation to normalize HTO raw counts. Cells were de-multiplexed using Seurat’s HTODemux function with default parameters. We assigned sample identities based on the maximal HTO signal and on the antibody sequence used for staining.
De-multiplexed samples were analyzed independently. Low quality cells, identified as cells with <200 or >8000 genes, total number of transcripts (UMIs) <1000 or >50000, and/or percentage UMIs mapping to mitochondrial genes >15%, were removed. After log-normalizing the data, we assigned cell cycle scores per single-cell, using Seurat’s CellCycleScoring function, and scaled the expression of each gene regressing out the number of UMIs and the percentage UMIs mapping to mitochondrial genes. We then performed principal component analysis (PCA) to denoise the data and, based on elbow plots and the percentage of explained variance, selected the number of principal components (PCs) to consider for downstream analysis. We then built a shared nearest neighbor graph and used the Louvain algorithm for clustering (resolution of 0.2-0.3) the cell subpopulation. Single cells were visualized as uniform manifold approximation and projection (UMAP) plots. Differential expression analysis was performed using Seurat’s FindAllMarkers function only considering genes with >log2(0.25) fold-change and expressed in at least 5% of cells in the cluster.
Assembly: hg38
Supplementary files format and content: RDS Seurat objects containing single-cell RNA-seq data from each sample after quality filtering

molecule: polyA RNA

source_name: Rhabdomyosarcoma

extract_protocol:
Dissociated PDX tumor cells were cultured as primary cultures for a low number of passages before sequencing.For sequencing, cells were detached from the plates and washed 1x with PBS. Cells from different primary cultures or cell lines or experimental conditions were independently stained with a different oligonucleotide-tagged antibody (TotalseqTM-B hashtag antibodies) according to the manufacturer’s protocol and pooled together in equal proportion before sequencing in a single lane. In brief, 1-2 M cells were resuspended in 50 uL Cell Staining Buffer (Biolegend, 420201) and blocked with 5 µl of Human TruStain FcX™ (Biolegend, 422301) for 10 min at 4°C. Cells were then stained with 1.5 ug of TotalseqTM-B hashtag antibodies (Biolegend, 394631, 394633; 394635, 394637, 394639, 394641, 394643, 394645) in a total volume of 100 uL Cell Staining Buffer (Biolegend, 420201). After 30 min incubation on ice, cells were washed 3 times, pooled together, and resuspended in medium at a final concentration of 1000 cells/μl. Cells were stained with trypan blue and counted manually with a hemocytometer to determine their concentration. Viability was confirmed to be >85% before loading onto chip.
Cells were processed for library preparation according to the 10X Genomics Chromium Single Cell 3′ v3 workflow. Cell volume was adjusted to yield a recovery of ~10,000 cells and loaded onto the 10X Genomics Single Cell A Chip. Library quality and concentration were assessed using High-Sensitivity D5000 ScreenTape (Agilent).

value: Rhabdomyosarcoma

tag: cell type

value: KFR cell line

value: no


title: Ring1b-MBL-KO-Input

data_processing:
bcl2fastq v2.18.0.12 used for basecalling
Cutadapt 1.9.1 with parameters -q 20 -m 30 used for quality-trimming sequences
STAR_2.5.2b used for aligning sequences to mm9 reference genome
Samtools 1.3.1 used to discard alignments with quality < 200 and to sort bam files
bamCoverage 3.5.0 used to normalize with BPM method a with default parameters.
Assembly: mm9
Supplementary files format and content: Bigwig files containing Reads per Million (RPM) values.

source_name: FUCCI-mESCs

growth_protocol: FUCCI-mESCs were cultured in 5% CO2 at 37 ºC on 0.1% gelatin-coated dishes in DMEM KO (Gibco) media supplemented with 10% FCS, leukaemia-inhibiting factor (LIF), penicillin/streptomycin (Biowest), L-glutamine (Biowest) and 2-mercaptoethanol (Gibco)  and hygromycin B (InvivoGen) as described previously (Asenjo et al. 2020)

extract_protocol:
ChIP assays were mainly performed as described previously (Asenjo et al, 2020).
ChIP-seq libraries were generated from 1-5 ng of immunoprecipitated DNA with the NEBNext Ultra DNA Library Prep kit for Illumina according to manufacturer’s instructions.

treatment_protocol: Cell-cycle sorting using an Aria Fusion cell sorter

tag: strain

value: Mixed background:129/Sv / C57BL/C6


title: delglyU_poor_rep3

description: mature tRNA

value: poor (M9 with 0.05 % galactose)


title: delglyU_poor_rep1

description: mature tRNA


title: delglyU_poor_rep2

description: mature tRNA


title: eRMS-8.1 (Berlin 13454) / eRMS-8.2 (Berlin 13870) / eRMS-8.3 (Berlin 13933)

value: PDX primary culture


title: eRMS-2.1 (Rh71) / eRMS-2.2 (Rh74) / eRMS-3.2 (Mast139)


title: Ring1b-G2-Input


title: Ring1b-MBL-WT-Input


title: delleuVPQ_rich_rep2

description: mature tRNA

value: {delta}leuVPQ


title: aRMS-1 (IC-pPDX-104) / aRMS-2 (IC-pPDX-29) / aRMS-3 (IC-pPDX-35)


title: RH4/KFR shSCR/shP3F1

value: Rh4 cell type


title: aRMS-4 (Mast118) / aRMS-5 (Berlin13304)


title: Ring1b-S-Input

value: Mouse embryonic stem cells


title: Ring1b-MBL-KO

description: ChIP-seq

data_processing:
bcl2fastq v2.18.0.12 used for basecalling
Cutadapt 1.9.1 with parameters -q 20 -m 30 used for quality-trimming sequences
STAR_2.5.2b used for aligning sequences to mm9 reference genome
Samtools 1.3.1 used to discard alignments with quality < 200 and to sort bam files
BamCompare 3.1.3 used to normalize with BPM method and to apply a smoothing of 10 bp. For ChIP-Seq samples, signal from input samples was sustracted to the samples signal. For RNA-Seq samples, signal from the reverse strand was sustracted to the signal in the forward strand.
genome build: mm9
processed data files format and content: Bigwig files containing Reads per Million (RPM) with a 10 bp smoothing. ChIP-Seq signal was normalized against input signal. For RNA-Seq, signal in forward strand has positive values, while signal in reverse strand has negative values.


title: Ring1b-G1-Input


title: delleuVPQ_rich_rep3

description: mature tRNA


title: Ring1b-MBL-WT

description: ChIP-seq


title: HeLa, GD, rep2

city: Hefei

first: Xiaolin

last: Wang

address: Huangshan Road

institute: USTC

description:
Linear_RNAs.txt.gz
CircRNA_RNAs.txt.gz

data_processing:
The adaptors were trimmed with Cutadapt to obtain clean reads. The data quality was then checked with FastQC and the low-quality (Q value ≤ 20) reads were removed.
Reads were aligned to the human reference genome (hg19) with Bowtie2 (-v 1). For linear RNAs including lncRNAs and mRNAs, the corresponding reads were counted with BEDtools and read per million (RPM) was used to calculate levels for lncRNAs and mRNAs.
For circRNA prediction, find_circ and CIRI2 were applied to identify high-confidence back-spliced junctions (BSJs).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include reads for each Sample

source_name: HeLa cells

extract_protocol:
Total RNA was extracted by TRIzol reagent (Invitrogen, 15596026) according to the manufacturer’s instructions.
Libraries were constructed by the TruSeq Ribo Profile Library Prep Kit (Illumina, RPHMR12126) according to the manufacturer’s instructions.

value: HeLa cells

value: human cervical carcinoma cells

value: WT

value: Glucose deprivation for 6h


title: K338

value: KIDNEY

value: IgG control


title: Ring1b-G2

description: ChIP-seq


title: delleuVPQ_rich_rep1

description: mature tRNA

value: engineered

value: rich (Rich LB)


title: HeLa, TG, rep2

description:
Linear_RNAs.txt.gz
CircRNA_RNAs.txt.gz

value: 300 nM TG  for 6 h


title: delleuVPQ_poor_rep2

description: mature tRNA


title: delleuVPQ_poor_rep3

description: mature tRNA


title: delleuVPQ_poor_rep1

description: mature tRNA


title: delglyVXY_rich_rep3

description: mature tRNA

value: {delta}glyVXY


title: Ring1b-S

description: ChIP-seq


title: Ring1b-G1

description: ChIP-seq


title: HeLa, TG, rep1

description:
Linear_RNAs.txt.gz
CircRNA_RNAs.txt.gz


title: HeLa, Ctrl, rep2

description:
Linear_RNAs.txt.gz
CircRNA_RNAs.txt.gz

value: Mock


title: 8_Control_IgG_ChIPseq

data_processing:
library strategy: ULI-nChIP-seq
Raw FastQ files were processed with Trim Galore, then mapped to the mouse GRCm38 genome. Mapping of ChIP-seq data was done using Bowtie2, RNA-seq data was mapped using HISAT2 v2.1.0 guided by known splice sites, BS-seq data with Bismark v0.19.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: ChIP-seq report: 10kb running windows (N=272,566) were quantified as reads per kilobase per million (RPKM). Windows were filtered to exclude mapping artefacts, defined as RPKM>6 in at least one replicate set of 10% input libraries (N=408).
Supplementary_files_format_and_content: RNA-seq report: Log transformed read count quantitation per million reads of oocyte genes (Veselovska et al. 2015  doi: 10.1186/s13059-015-0769-z)
Supplementary_files_format_and_content: Bismark coverage report: A Bismark coverage file.

value: oocyte

value: Control

tag: chip antibody

value: IgG


title: HeLa, Ctrl, rep1

description:
Linear_RNAs.txt.gz
CircRNA_RNAs.txt.gz


title: 7_DKO_input_ChIPseq

value: G9a-Glp cDKO

value: input


title: delglyVXY_poor_rep3

description: mature tRNA

value: poor (M9 with 0.05 % galactose)


title: Donor a3, IL-2, pH 6.5

city: Lille

first: Suman

last: Mitra

address: 1 Place de Verdun

country: France

institute: INSERM

data_processing:
Clean sequence reads were obtained by removing bad quality reads from raw data using fastp. Reads were removed when containing adapter, when containing more than 10% of uncertain nucleotides (N) in either R1 or R2 read or when containing more than 50 percent low quality nucleotides (Base Quality less than 5).
Trimmed sequence reads were mapped to hg38 using STAR v2.6.1d (mismatch = 2)
Read count extraction and normalization were performed using FeatureCounts v1.5.0-p3
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include raw count values for each sample

source_name: CD8+ T cells

growth_protocol: Human T cells were cultured in RPMI 1640 with GlutaMAX (Gibco, 61870036) supplemented with 10% FBS, minimum non-essential amino acids, 1 mM sodium pyruvate, and penicillin/streptomycin. When the pH of the media was adjusted to conduct short or long-term experiments, HCl was used to acidify the media and 20 mM HEPES pH 6.5 was added to maintain stable the pH at 6.5 in the presence of 5% CO2. An equivalent amount of HEPES pH 7.5 was added to the media at pH 7.5. Cells were cultured in the presence of 5% CO2 at 37°C.

extract_protocol:
RNA of human CD8+ T cells was purified using Quick-RNA Microprep kit (Zymo Research)
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext ® Ultra TM RNA  Library Prep Kit for Illumina ® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was  purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand  Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis  was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of  3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in  length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-  ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and  Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system

treatment_protocol: Activated human CD8+ T cells were rested O/N, transferred in complete media pH 7.5 or 6.5 and stimulated for 4 h with 10 nM IL-2 or Switch-2

value: CD8+ T cells


title: 6_Control_IgG_ChIPseq

source_name: oocyte


title: Donor a3, unstim, pH 7.5

value: unstim, pH 7.5


title: HeLa, GD, rep1

description:
Linear_RNAs.txt.gz
CircRNA_RNAs.txt.gz

value: HeLa cells

value: human cervical carcinoma cells

value: WT


title: 5_DKO_input_ChIPseq


title: Donor a3, IL-2, pH 7.5


title: delglyVXY_poor_rep2

description: mature tRNA


title: delglyVXY_poor_rep1

description: mature tRNA


title: 5_DKO_H3K9me2_ChIPseq


title: Donor a3, unstim, pH 6.5

value: unstim, pH 6.5


title: eRMS-1.1 (Rh70) / eRMS-1.2 (Rh73) / eRMS-4 (IC-pPDX-82)

value: Rhabdomyosarcoma

value: PDX primary culture

value: no


title: mouse breast cancer multiome scATAC-seq raw data late stage biological replicate 3

city: Stanford

first: Michael

last: Januszyk

state: CA

address: 257 Campus Dr

institute: Stanford University

description:
Processed data available on GSM6543827
Raw data associated with this sample contains only scATAC-seq data.

data_processing:
Data generated using the 10X Multiome platform were processed using 10X’s cellranger-arc toolkit in Linux per the manufacturer’s instructions. This included (1) an ATAC matrix computer step of barcode processing, read trimming, read alignment, duplicate marking, peak calling, and peak-barcode matrix generation using either the mm10 mouse or GRCh38 human reference genome; (2) a gene expression (GEX) Matrix Computer step of read trimming, genome alignment, transcriptome alignment, UMI correction, and UMI counting; and joint cell calling. Downstream secondary analysis for ATAC and GEX included dimensionality reduction, clustering, peak annotation, transcription factor analysis, differential expression analysis, differential accessibility analysis, and feature linkage as described above using the Seurat, Signac, and ArchR toolkits.
Library strategy: multiome-seq

source_name: endogenous breast tumors

extract_protocol:
Tumor tissue specimens from mouse or human specimens was minced on ice. The tissue was then digested for 3x 30 minutes in a 37C water bath agitator in 0.5 mg/mL collagenase (collagenase type IV, ThermoFisher) digest buffer in Medium 199 (HyClone, GE Healthcare) consisting of 5% fetal bovine serum (Gibco FBS, ThermoFisher), DNase I (Worthington), Poloxamer 188 (Cat. P5556-100ML, Sigma), HEPES, and CaCl2. The digest was quenched with quench media (DMEM (Gibco DMEM, ThermoFisher) with 15% FBS), then centrifuged at 300 x G for 5 minutes at 4C, resuspended in quench media, and filtered through 100, 70, and 40m cell strainers (Falcon cell strainer, ThermoFisher). Red blood cell lysis was performed using Hybri-Max (Sigma) per the manufacturer's protocol. Cells were counted and re-suspended for further processing.
Multiome was then performed at the Stanford Genomics Facility (SGF) using the 10x Genomics platform. The relevant protocols were followed per manufacturer’s guidelines. Nuclei isolation was pursued as for scATAC-seq sequencing using 0.1x lysis buffer with 3-minute incubation.
Final libraries were analyzed on an Agilent Bioanalyzer High Sensitivity DNA chip for qualitative control purposes. Libraries were sequenced on a HiSeq 4000 Illumina platform targeting 50,000 reads per cell.

value: endogenous breast tumors

value: all cells (unsorted)

value: black 6


title: Donor a3, Switch-2, pH 7.5

value: Switch-2, pH 7.5


title: WT_rich_rep3

description: mature tRNA

value: MG1655 wildtype (wt)

value: wt

value: rich (Rich LB)


title: 4_Control_H3K9me2_ChIPseq

extract_protocol:
Oocytes were collected by manual dissection in M2 medium
RNA-seq libraries were prepared as described (Hanna et al. 2019  doi: 10.1186/s13059-019-1833-x)
ChIP-seq libraries were prepared using ULI-nChIP, as previously described (Hanna et al. 2018 doi: 10.1038/s41594-017-0013-5). Antibodies were added using 250ng/reaction for both anti-H3K9me2 (mouse monoclonal, Abcam, ab1220) and anti-IgG (rabbit polyclonal, Diagenode, EB-070-010). Library preparation was completed with a MicroPlex Library Preparation kit v2 (Diagenode) with Sanger eight-base indices for multiplexing. Relative enrichment over input was quantified using the library concentrations determined by Bioanalyzer High Sensitivity DNA Analysis (Agilent).
Low input bisulphite (BS)-seq libraries were prepared by post-bisulphite adapter tagging as previously described (Hanna et al. 2018 doi: 10.1038/s41594-017-0013-5)

value: oocyte

value: Control


title: WT_rich_rep1

description: mature tRNA


title: delglyVXY_rich_rep1

description: mature tRNA

value: engineered

value: {delta}glyVXY


title: WT_rich_rep2

description: mature tRNA


title: mouse breast cancer multiome scATAC-seq raw data late stage biological replicate 1

description:
Processed data available on GSM6543825
Raw data associated with this sample contains only scATAC-seq data.


title: delglyVXY_rich_rep2

description: mature tRNA


title: mouse breast cancer multiome scATAC-seq raw data early stage biological replicate 3

description:
Processed data available on GSM6543824
Raw data associated with this sample contains only scATAC-seq data.


title: Donor a2, IL-2, pH 7.5

value: CD8+ T cells


title: 7_DKO_H3K9me2_ChIPseq

value: G9a-Glp cDKO


title: 3_G9a-KO_input_ChIPseq

value: G9a cKO

value: input


title: 2_Control_input_ChIPseq


title: Donor a2, IL-2, pH 6.5


title: Donor a2, unstim, pH 7.5

value: unstim, pH 7.5


title: mouse breast cancer multiome scATAC-seq raw data early stage biological replicate 2

description:
Processed data available on GSM6543823
Raw data associated with this sample contains only scATAC-seq data.


title: WT_poor_rep3

description: mature tRNA

value: poor (M9 with 0.05 % galactose)


title: WT_poor_rep2

description: mature tRNA


title: 4_Control_input_ChIPseq


title: mouse breast cancer multiome scATAC-seq raw data early stage biological replicate 1

description:
Processed data available on GSM6543822
Raw data associated with this sample contains only scATAC-seq data.

value: endogenous breast tumors


title: WT_poor_rep1

description: mature tRNA


title: 3_G9a-KO_H3K9me2_ChIPseq


title: mouse breast cancer multiome scATAC-seq raw data late stage biological replicate 2

description:
Processed data available on GSM6543826
Raw data associated with this sample contains only scATAC-seq data.

value: all cells (unsorted)


title: Donor a2, Switch-2, pH 7.5


title: Donor a2, unstim, pH 6.5

value: unstim, pH 6.5


title: Donor a3, Switch-2, pH 6.5

value: Switch-2, pH 6.5


title: mouse breast (non-cancer) multiome scATAC-seq raw data biological replicate 3

description:
Processed data available on GSM6543821
Raw data associated with this sample contains only scATAC-seq data.

value: black 6


title: Donor a2, Switch-2, pH 6.5


title: 2_Control_H3K9me2_ChIPseq


title: Donor a1, IL-2, pH 7.5


title: 1_G9a-KO_input_ChIPseq


title: WT heart 7dpa

city: Pittsburgh

last: Tsang

state: PA

address: 3501 Fifth Ave. BST3-5062

department: Cell Biology

institute: University of Pittsburgh

data_processing:
fastq files were analyzed using CLC genomics workbench 20.0
sequence reads were mapped onto Danio rerio GRC.z11
EDGE test was performed using CLC genomics workbench
Assembly: Danio rerio GRC.z11
Supplementary files format and content: Zuppo et al 7dpa vs. uninj.xlsx

organism: Danio rerio

source_name: Heart

growth_protocol: Zebrafish adult at 6 months -1year of age

extract_protocol:
Adutls hearts were injured through ventricular resection and allowed to recover until 7 days post amputation.
Ventricles were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent and Quiagen RNeasy micro kit (Cat# 74004).

value: Heart

value: AB*

tag: time point


title: mouse breast (non-cancer) multiome scATAC-seq raw data biological replicate 1

description:
Processed data available on GSM6543819
Raw data associated with this sample contains only scATAC-seq data.


title: WT_4 [CM-2]

city: Dallas

first: Ralf

last: Kittler

state: Texas

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: Pure CM nuclei was used for RNA-Seq library prep protocol

data_processing:
library strategy: Nuclear RNA-Seq
Reads were mapped to mm10 assembly using tophat
Transcripts were called and quantified using cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values

source_name: Whole heart

extract_protocol:
Whole mouse hearts were harvested at P28. Pure CM Nuclei were isolated using 2.2M sucrose cushion for all samples. MAN-IP was performed for 3 CCS compartment specific Cre driver lines. For the 3 Cre driver lines, microdissection was performed to enrich for tissue of interest and obtain specific cell-type nuclei (SAN, AVN, and VCS). CCS specific nuclei were pooled from multiple hearts to ensure enough starting nuclear RNA for good quality library preparation
The nuclei suspension (CM nuclei from whole heart, CCS enriched nuclei, etc.) was mixed with equal volume of DNA/RNA Shield (2X concentrate provided in ZR-Duet DNA/RNA MiniPrep Plus kit, #D7003), and RNA was extracted using the same kit following the instruction manual. Qubit quantification was used to estimate RNA concentration. Next, RNA was concentrated to 10µl volume using the RNA Clean and Concentrator-5 Kit (Zymo Research, #R1015). RNA sequencing libraries were made using the TruSeq Stranded Total RNA with Ribo-Zero Human/Mouse/Rat kit (Illumina) according to manufacturer instructions. The resulting RNAseq libraries' quality and concentration were assessed using a 2100 Bioanalyzer with the High Sensitivity DNA Kit (Agilent) and a Qubit Fluorometer with the Qubit dsDNA HS Assay Kit (Life Technologies). RNA-seq libraries were generated from ribosomal depleted RNA and were sequenced on a HiSeq 2500 (50 bp, Illumina).

tag: strain background

tag: genotype/variation

value: WT

tag: age

value: heart

tag: sample type

value: Pure Cardiomyocyte (CM) nuclei (from 2.2M sucrose cushion) from whole WT P28 mouse heart

tag: replicate

value: Biological replicate-2


title: Atoh8 KD_DDC_Day17_RNA-seq Rep1

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

data_processing:
Quality control was checked by fastqc
Sequence reads were trimmed for adaptor sequence/low-quality sequence using trim_galore
Trimmed sequence reads were mapped to GrCM38/mm10 using hisat2-2.10
Read count extraction were performed using htseq-count and FPKM normalization were performed using Cufflinks v.2.2.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: liver

extract_protocol:
Livers were removed, flash frozen on dry ice, total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions.  RNA libraries were prepared for sequencing using standard Illumina protocols.
1.3 ug of total RNA was used for the construction of sequencing libraries.

value: hepatocyte

value: ATOH8 knockdown

value: 0.1% DDC diet for 17 days


title: dusp6 mutant heart 7dpa

value: dusp6 pt30a/pt30a


title: 1_G9a-KO_H3K9me2_ChIPseq

value: oocyte

value: G9a cKO


title: 4393_9_TL628_moDC_ACTTGAA

city: Leiden

first: Yanling

last: Xiao

country: Netherlands

institute: LUMC

description: DC subset unique comp. list (moDC).txt

data_processing:
TopHat software (version 2.1.0).
Read counts were normalized using Limma (Version 3.22.7) and count per million (CPM) were calculated
Differential-expression analysis and Hierarchical clustering were performed using Limma (Version 3.22.7).
For the 'DC subset unique comp. list (*).txt' files, from Column B-M are the raw counts, and from column N-Y are the normalized counts.
Assembly: Homo sapiens GRCh37.66
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

source_name: PBMC

extract_protocol:
Total RNA isolation was performed according to manufacturer’s protocol using the RNeasy MinElute Cleanup Kit (Qiagen).
Strand-specific cDNA libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina) according to the manufacturer’s protocol. The libraries were analyzed for size and quantity of complementary DNAs (cDNAs) on a 2100 Bioanalyzer using a 7500 chip (Agilent), diluted and pooled in equimolar ratios into a multiplex sequencing pool. The libraries were sequenced as 65 base single reads on a HiSeq2500 with V4 chemistry (Illumina).

value: PBMC

value: dendritic cells

tag: cell subset

value: moDC (CD11c+CD14+CD1c+CD206+)


title: C_4 [VCS-2]

description: Myc-IP enriched Cntn2+ nuclei was used for RNA-Seq library prep protocol

source_name: His Bundle/Purkinje Fiber system (VCS) in heart

value: Cntn2-Cre/+; R26RSun1-Myc-Egfp/+

value: 2.2M sucrose cushion-purified nuclei followed by Myc antibody mediated MAN-IP to enrich for Cntn2+ nuclei


title: Atoh8 KD_DDC_Day17_RNA-seq Rep3

tag: genotype


title: WT_3 [CM-1]

value: Biological replicate-1


title: Atoh8 KD_DDC_Day17_RNA-seq Rep2


title: mouse breast (non-cancer) multiome scATAC-seq raw data biological replicate 2

description:
Processed data available on GSM6543820
Raw data associated with this sample contains only scATAC-seq data.

value: endogenous breast tumors

value: all cells (unsorted)

value: black 6


title: Donor a1, IL-2, pH 6.5

value: CD8+ T cells


title: Donor a1, unstim, pH 7.5

value: unstim, pH 7.5


title: WT_DDC_Day17_RNA-seq Rep3

value: hepatocyte

value: WT


title: 4393_10_TL628_cDC2_GATCAGA

description: DC subset unique comp. list (cDC2).txt

value: cDC2 (CD11c+CD14-CD1c+)


title: WT_DDC_Day17_RNA-seq Rep2

value: 0.1% DDC diet for 17 days


title: C_3 [VCS-1]

value: heart


title: 4393_11_TL628_cDC1_TAGCTTA

description: DC subset unique comp. list (cDC1).txt


title: 4393_12_TL628_pDC_GGCTACA

description: DC subset unique comp. list (pDC).txt


title: 4393_5_TL608_moDC_GTCCGCA

description: DC subset unique comp. list (moDC).txt


title: S_4 [SAN-2]

description: Myc-IP enriched Shox2+ nuclei was used for RNA-Seq library prep protocol

source_name: Sino-Atrial Node(SAN) of the heart

value: Shox2-Cre/+; R26RSun1-Myc-Egfp/+

value: 2.2M sucrose cushion-purified nuclei followed by Myc antibody mediated MAN-IP to enrich for Shox2+ nuclei

value: Biological replicate-2


title: Donor a1, unstim, pH 6.5

value: unstim, pH 6.5


title: S_3 [SAN-1]


title: WT_DDC_Day17_RNA-seq Rep1


title: Donor a1, Switch-2, pH 7.5

value: Switch-2, pH 7.5


title: Donor a1, Switch-2, pH 6.5

value: Switch-2, pH 6.5


title: 4393_6_TL608_cDC2_GTGAAAC

description: DC subset unique comp. list (cDC2).txt

value: PBMC

value: dendritic cells


title: G_4 [AVN-2]

description: Myc-IP enriched Gjd3+ nuclei was used for RNA-Seq library prep protocol

source_name: Atrioventricular Node (AVN) in heart

value: Gjd3-Cre/+; R26RSun1-Myc-Egfp/+

value: 2.2M sucrose cushion-purified nuclei followed by Myc antibody mediated MAN-IP to enrich for Gjd3+ nuclei


title: CD8 TILs, Switch-2, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/6.1/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Subcutaneous melanoma

extract_protocol:
Mice were sacrificed the day after the end of the therapy and tumors were excised and tumor infiltrating lymphocytes were enriched using lymphocyte M density gradient protocol. Then MagniSort mouse CD8 T cell enrichment kit (ThermoFisher, 8804-6822-74) was used to enrich for CD8+ TILs from the cell suspension. An equal amount of cell from each biological replicates (n=3) was pooled together and stained using Zombie aqua Fixable viability kit, anti-mouse CD3 PerCP-Cy5.5, and anti-mouse CD8 PE (Biolegend, 100708). Live CD3+CD8+ cells were sorted and used for scRNA-seq. 13,000 cells were loaded on 10x Genomics Chromium system.
Library was performed according to the manufacter’s instructions (Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) protocol, 10x Genomics).

value: CD8+ T cells

value: Subcutaneous melanoma

value: 6-8 weeks old


title: AOXGrSt_3

city: Madison

first: Mehdi

last: Kabbage

state: WI

address: 1630 Linden Drive

institute: UW Madison

data_processing: alignments with HISAT2 to the reference

organism: Sclerotinia sclerotiorum

source_name: hyphae

extract_protocol:
Flash frozen in liquid nitrogen and subjected to RNA extraction using a Maxwell RSC Plant RNA kit.
mRNA Enrichment

treatment_protocol: WT (1980) and ΔSsAOX S. sclerotiorum was grown in 1% glucose minimal media (GMM) for three days, before being transferred to fresh 1% GMM containing 1% soybean stem extract. Cultures were grown for an additional 4 hours before being flash frozen in liquid nitrogen and subjected to RNA extraction using a Maxwell RSC Plant RNA kit.

value: hyphae

value: dSsAOX

value: 1% glucose minimal media with 1% soybean stem extract


title: CD8 TILs, IL-2, scRNAseq

description: 10x Genomics


title: 4393_7_TL608_cDC1_ATCACGA

description: DC subset unique comp. list (cDC1).txt

value: WT


title: 4393_8_TL608_pDC_TTAGGCA

description: DC subset unique comp. list (pDC).txt


title: CD8 TILs, PBS, scRNAseq

description: 10x Genomics

value: PBS


title: AT-S2 [SAN-2]

description:
Myc-IP enriched Shox2+ nuclei was used for OMNI-ATAC library prep protocol
AT_S_2_S8

data_processing:
Adapters were trimmed using Cutadapt
Reads were mapped to mouse genome using bowtie
Low quality reads were filtered using samtools
Removed duplicates using picard
Peaks were called using Homer
Genome_build: mm10
Supplementary_files_format_and_content: ATAC-seq signal in bigwig format

source_name: Sino-Atrial Node(SAN) in the heart

extract_protocol:
Whole mouse hearts were harvested at P28. Pure CM Nuclei were isolated using 2.2M sucrose cushion for all samples. MAN-IP was performed for 3 CCS compartment specific Cre driver lines. For the 3 Cre driver lines, microdissection was performed to enrich for tissue of interest and obtain specific cell-type nuclei (SAN, AVN, and VCS).
We used 2 independent (pooled tissue from same genotypes) biological replicates per experimental sample for library construction. To generate ATAC-Seq libraries, we followed the improved ATAC-Seq version called Omni-ATAC from Howard Chang lab (Corces et al., 2017). Very briefly, in this study, upon counting the nuclei using Countess II FL (using DAPI light cube) Automated Cell Counter, 50000 nuclei were pelleted in ATAC-Resuspension Buffer (recipe published in the same study) containing 0.1% Tween-20. The supernatant was carefully discarded. Nuclei pellet was incubated with transposase in the transposition mixture following the above-mentioned protocol. Transposed DNA was cleaned with Zymo DNA Clean and Concentrator-5 Kit (#D4014). This was followed by pre-amplification of transposed fragments, qPCR amplification, followed by KAPA library quantification to determine additional cycles for the final PCR amplification (none to very few additional cycles were required upon following the Omni-ATAC protocol). After final amplification, the ATAC-Seq library was cleaned with Zymo DNA Clean and Concentrator-5 Kit (#D4014) and submitted for Tape Station and Qubit analysis. 4nM of each ATAC-Seq library was used for paired-end sequencing on an Illumina NextSeq 500 Mid Output (130 M) flow cell. Image analysis and base calling were performed with Sanger/Illumina 1.9 pipeline.

value: Shox2-Cre/+; R26RSun1-Myc-Egfp/+

value: heart

value: 2.2M sucrose cushion-purified nuclei followed by Myc antibody mediated MAN-IP to enrich for Shox2+ nuclei


title: AOXGrSt_1


title: 4393_1_TL571_moDC AGTCAAC

description: DC subset unique comp. list (moDC).txt

value: moDC (CD11c+CD14+CD1c+CD206+)


title: G_3 [AVN-1]

value: Biological replicate-1


title: AOXGrSt_2


title: MUT_14DPA_R2

city: Santander

first: Marian

last: Ros

address: 22nd Albert Einstein St.

institute: IBBTEC-CSIC-SODERCAN

description: 6xAmputated HL central digits 14 DPA MUT rep2

data_processing:
4 lanes used for each sample
Basic read quality check was performed using FastQC
RNA-seq reads were mapped with STAR (v.2.7.8a) against the mouse reference genome GRCm39 using the ENCODE parameters
Genes were quantified with RSEM version 1.3.0 with default parameters using the gencode annotation version M27
BigWig files were generated from bam files
Assembly: Gencode M27 primary assembly gtf
Supplementary files format and content: .txt files for each Sample contain estimated counts, FPKM and TPM
Supplementary files format and content: BigWig files for each Sample containing mapped read signals

source_name: 14 DPA blastema

extract_protocol:
RNeasy Plus Mini Kit (QIAGEN, Ref. 74134), manufacturer´s protocol, total RNA was used for the construction of sequencing libraries.
Illumina Stranded total RNA library preparation kit

value: 14 DPA blastema

value: mixed CD1 C57Bl/6 background

value: 35 days

value: MUT


title: WTGrSt_3


title: AT-S1 [SAN-1]

description:
Myc-IP enriched Shox2+ nuclei was used for OMNI-ATAC library prep protocol
AT_S_1_S7


title: AT-C1 [VCS-1]

description:
Myc-IP enriched Cntn2+ nuclei was used for OMNI-ATAC library prep protocol
AT_C_1_S5

value: Cntn2-Cre/+; R26RSun1-Myc-Egfp/+

value: 2.2M sucrose cushion-purified nuclei followed by Myc antibody mediated MAN-IP to enrich for Cntn2+ nuclei


title: WTGrSt_2


title: WT_14DPA_R1

description: 6xAmputated HL central digits 14 DPA WT rep2


title: AT-G2 [AVN-2]

description:
Myc-IP enriched Gjd3+ nuclei was used for OMNI-ATAC library prep protocol
AT_G_2_S4

value: Gjd3-Cre/+; R26RSun1-Myc-Egfp/+

value: 2.2M sucrose cushion-purified nuclei followed by Myc antibody mediated MAN-IP to enrich for Gjd3+ nuclei

value: Biological replicate-2


title: 4393_4_TL571_pDC_CCGTCCC

description: DC subset unique comp. list (pDC).txt

value: PBMC

value: dendritic cells


title: 4393_3_TL571_cDC1_ATGTCAG

description: DC subset unique comp. list (cDC1).txt

value: WT


title: 4393_2_TL571_cDC2_AGTCAAC

description: DC subset unique comp. list (cDC2).txt

value: cDC2 (CD11c+CD14-CD1c+)


title: M5_1 rep3

description: mature tRNA

data_processing:
Sorted into 24 samples using the unique, 6-bp Illumina indices. 0 mismatches allowed.
Per sample: reads between 80 and 151 bp were extracted (in Geneious v11.1.4)
Per sample: 80-151 bp reads were aligned to a set of 42 reference tRNA sequences (all unique primary sequences predicted in the SBW25 genome by GtRNAdb). This was done using Geneious version 11.1.4 (assembly parameters: up to 10% mismatches or gaps of <3 bp per read, up to 5 ambiguities per read, no assignment of reads that map equally well to more than one reference sequence, and no iterations)
Per sample: read numbers for the 42 contigs were used in pairwise comparisons with DESeq2 (in R version 3.6.0)
Genome_build: The 42 tRNA sequence reference file was derived from the SBW25 genome sequence (NCBI accession number: NC_012660.1) using GtRNAdb (http://gtrnadb.ucsc.edu/GtRNAdb2/genomes/bacteria/Pseu_fluo_SBW25/pseuFluo_SBW25-tRNAs.fa)
Supplementary_files_format_and_content: 24 text files: the raw read numbers aligned to the 42 reference sequences. One file per sample.
Supplementary_files_format_and_content: Two excel workbooks. "aligned_reads_multicopy.xlsx" contains a summary of the data for all 24 samples, plus a spreadsheet for each of the 8 strains listing the of the number of reads aligned to each reference sequence in each replicate. "deseq2_comparisons_multicopy.xlsx"  contains the DESeq2 output for pairwise comparisons between strains of interest.

organism: Pseudomonas fluorescens

source_name: liquid cell culture

growth_protocol: Samples were grown from single colonies in liquid culture overnight (28˚C, shaking). A small volume of grown culture was inoculated into fresh medium and grown to mid-exponential phase (approx. 5-7 hours, 28˚C, shaking).

extract_protocol:
Per sample: 1.5 ml aliquots of mid-exponential phase culture were taken, and total RNA extracted (TRIzol Max Bacterial RNA isolation kit; Life Technologies).
The YAMAT-seq method is an adaptation of that published for human cell lines (Shigematsu et al., 2017; doi:10.1093/nar/gkx005 ) and adapted for use in Pseudomonas fluorescens in (Ayan et al., 2020; doi:10.7554/eLife.57947).  Briefly, for each sample, 5 ug total RNA was subjected to tRNA deacylation treatment by exposure to hydrochloric acid. Hybrid DNA/RNA Y-shaped adapters (Eurofins) were ligated to exposed 5'-CCA-3' tRNA ends using T4 RNA ligase 2 (New England Biolabs). Ligation products were reverse transcribed into cDNA (SuperScript III reverse transcriptase; Thermo Fisher), and amplified PCR (Phusion; Thermo Fisher). One of 24 sample-specific indices (Illumina) was added to each of the 24 reactions. The quality and quantity of each PCR product was checked using an Agilent DNA 7500 kit on a Bioanalyzer (Agilent), and samples combined in equimolar amounts into a single tube. The mixture was run on a 5 % polyacrylaminde gel (Bio-Rad Laboratories), and the group of bands ranging between ~180 bp and ~250 bp excised. DNA was extracted in deionized water overnight, and agarose removed by centrifugation through filter paper. DNA quality and quantity was checked with a Quant-iT dsDNA BR Assay kit (Invitrogen) on a Fluorescence Nanodrop. High throughput sequencing was performed at the Max Planck Institute for Evolutionary Biology (Ploen, Germany). Single-end, 150 bp reads were generated with a NextSeq 550 Output v2.5 kit (Illumina).

tag: strain type

value: engineered then evolved

tag: evolution day


title: WT_14DPA_R2

description: 6xAmputated HL central digits 14 DPA WT rep1

tag: tissue


title: MUT_14DPA_R3

description: 6xAmputated HL central digits 14 DPA MUT rep3


title: AT-C2 [VCS-2]

description:
Myc-IP enriched Cntn2+ nuclei was used for OMNI-ATAC library prep protocol
AT_C_2_S6

value: heart


title: WTGrSt_1

value: hyphae

value: 1% glucose minimal media with 1% soybean stem extract


title: AT-G1 [AVN-1]

description:
Myc-IP enriched Gjd3+ nuclei was used for OMNI-ATAC library prep protocol
AT_G_1_S3

value: Biological replicate-1


title: NAM_MCL1_DTEP_3

city: Tampa

first: Jianguo

last: Tao

state: Florida

address: 12902 Magnolia Dr

institute: Moffitt Cancer Center

data_processing:
RNA sequencing was performed on HiSeq 2500v4 high output (50-bp, single-end reads)
Tophat2 was used to align the Fasq files.
TPM values were calculated and normalized using Cuffnorm
Genes that had a p < 0.05 and at least a two-fold change were considered to be significantly altered between treatments.
Cutoff value for expressed genes was TPM value equal to or higher than 1.
Genome_build: hg38
Supplementary_files_format_and_content: TPM values were shown in "MCL_DTEP_TPM.csv" file

source_name: Mantle cell lympohoma

growth_protocol: SU-DHL16, Namalwa, EJ-1, and BJAB cells were grown in RPMI-1640 medium with 10% FBS and Namalwa and SU-DHL16 cells were treated with 2uM S63845 for approximately 6 months.Drug-resistant variants (Namlwa-DTEP and SU-DHL16-DTEP) were maintained in drug free media for 1 week before utilized in experiments. MCL cells exposed to DMSO were maintained in parallel and used for comparison with their respective drug-resistant cell lines

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini (Qiagen Cat# 74134)
Library prep was conducted using TruSeq Stranded mRNA Library Prep Kit (Illumina Cat #RS-122-2101/2) according to the manufacturer’s instructions

value: Namalwa

tag: group

value: DTEP

tag: s63845 sensitivity

value: resistant


title: MUT_12DPA_R3

description: 6xAmputated HL central digits 12 DPA MUT rep3

source_name: 12 DPA blastema

value: 12 DPA blastema

value: mixed CD1 C57Bl/6 background

value: 33 days

value: MUT


title: NAM_MCL1_DTEP_2

tag: cell line

tag: treatment


title: AT-WT-2 [CM-2]

description:
Pure CM nuclei was used for OMNI-ATAC library prep protocol
AT_WT_2_S2

value: Pure Cardiomyocyte (CM) nuclei (from 2.2M sucrose cushion) from whole WT P28 mouse heart

value: Biological replicate-2


title: MUT_14DPA_R1

description: 6xAmputated HL central digits 14 DPA MUT rep1

value: 14 DPA blastema

tag: strain

value: 35 days


title: M1_1 rep3

description: mature tRNA


title: AT-WT-1 [CM-1]

description:
Pure CM nuclei was used for OMNI-ATAC library prep protocol
AT_WT_1_S1

value: WT


title: NAM_MCL1_DTEP_1


title: NAM_PAR_3

value: Parental

value: naïve

value: DMSO


title: dEGEG rep3

description: mature tRNA

value: engineered

value: {delta}EGEG


title: MUT_12DPA_R1

description: 6xAmputated HL central digits 12 DPA MUT rep1


title: WT_12DPA_R2

description: 6xAmputated HL central digits 12 DPA WT rep2


title: Total_RNA_NIP_Rep2_36hr_CPA

city: New York

first: Shuvadeep

last: Maity

state: NY

address: 12 waverly place

department: Center for Genomics and Systems Biology

institute: New york University

data_processing:
We used Picard tools (Illumina Basecalls to Fastq version 2.17.11) and demultiplexing pheniqs (https://github.com/biosails/pheniqs,  develoiped by NYU )  for basecalling.
Sequenced reads were trimmed to remove the adapter sequence and for quality control using fastx-toolkit v 0.0.14 with parameters -t 20 -l 20. Multiple fastq files from the same sample were merged.
Reads were mapped to abundant sequences to remove ribosomal rDNA, adapter contaminants, PhiX, and polyA/C sequences using bowtie2 2.3.2 with default settings.
Remaining reads were mapped to GRCm38 - mm10 using tophat v2.1.1 with parameter  settings:--no-coverage-search -G genecode mm10 basic.gtf .
Aligned reads were filtered for unique mapping and length: RNA >25.
Read counts were generated using htseq v0.6.1p1 and parameters: --stranded=reverse intersection-nonempty --format=bam.
Genome_build: mm10
Supplementary_files_format_and_content: txt and count data

source_name: Cranial Motor neuron differntiated from mouse embryonic stem cells

growth_protocol: The total RNA was derived from two different motor neurons (spinal motor neuron -NIL, cranial motor neuron-NIP). We differentiated and maintained neurons under standard motor neuron medium condition, i.e  in Neurobasl medium (Gibco) with 2% fetal bovine serum (ThermoFisher Scientific), B27, L-glutamine, BME and different combinations of growth factores described previously (D An et al 2019) at 37℃ and 5% CO2.

extract_protocol:
For RNA seq, we extracted the total RNA from day2 motor neurons after 12, 36 hrs of treatment 20uM CPA. The media was then removed and the cells were washed with 10 ml chilled PBS. Following removal of the PBS, 800 ul of lysis Buffer (Qiagen RNeasy Mini Kit) was added and the cells were  scraped off the plate and transferred to a pre-chilled eppendorf tube, recovering ~1 ml of lysate per sample. We processed the lysate according to the Qiagen RNeasy kit extraction protocol. We also performed in-column DNAse digestion using RNAse-Free DNase (Qiagen). The total RNA was then used for RNAseq library following KAPA RNA HyperPrep Kit with RiboErase (HMR) protocol. We used Agilent TapeStation to confirm the  quality and quantity of total RNA and sequence library during different stages of RNAseq library preparation.
RNA libraries for RNA seq were prepared according to the KAPA RNA HyperPrep Kit with  RiboErase (HMR) protocol.

treatment_protocol: Day 2 motor neurons were treated with 20uM cyclopiazonic acid (CPA) to induce ER stress. We treated samples for 0, 6, 12 hrs prior to collection.

value: Cyclopiazonic acid (CPA) 36 hr


title: M3_1 rep3

description: mature tRNA

value: engineered then evolved


title: NAM_PAR_2

value: Namalwa


title: Total_RNA_NIP_Rep2_12hr_CPA

value: Cranial Motor neuron differntiated from mouse embryonic stem cells

value: Cyclopiazonic acid (CPA) 12 hr


title: W1_1 rep3

description: mature tRNA

value: evolved wildtype (control)


title: mWT_Antibody_Capture

city: Memphis

first: Shannon

last: McKinney-Freeman

address: 262 Danny Thomas Place

institute: St. Jude Children’s Research Hospital

description:
CITE-seq
manual_label.RData

library_source: other

data_processing:
Single cell data was analyzed using cellranger count. Transcriptome database was cellranger-mm10-3.0.0.
The weighted nearest-neighbor UMAP and cell clusters were generated using Seurat (v4.0.4) following the reference guide of “WNN analysis of CITE-seq, RNA+ADT”
Differential gene expression analysis was done using FindMarkers with “slot=data, logfc.threshold=0.2, test.used=wilcox, pseudocount.use=1”. Genes were further filtered by FDR<=0.01, which was calculated using the Benjamini-Hochberg method in R.
Genome_build: mm10
Supplementary_files_format_and_content:Rdata

molecule: other

extract_protocol:
BM was extracted from femurs, pelvic bones, tibias and spines of TAM-treated Nfixflox/floxRosa26CreERT2+/+ and Nfixflox/floxRosa26CreERT2+/T mice via crushing
c-Kit+ cells were isolated via magnetic enrichment using anti-CD117 microbeads (Miltenyi Biotec, Carlsbad, CA) and an autoMACs magnetic cell separator (Miltenyi Biotec, Carlsbad, CA). For c-Kit+ cells, HSPC (Lineage-Sca-1+cKit+) and LT-HSC (Lineage-Sca-1+c-Kit+CD48-CD150+) isolation, cells were stained with anti-Lineage BV605 cocktail, anti-Sca-1-PerCPCy5.5 (E13-161.7), anti-c-Kit-APCe780 (2B8), anti-CD48-Alexa Fluor 700 (HM48-1), anti-CD150-PE-Cy7 (TC15-12F12.2). For CMP (Lineage-Sca-1-c-Kit+CD34+CD16/32med) isolation, cells were stained with anti-Lineage BV605 cocktail, anti-Sca-1-PerCP-Cy5.5 (E13-161.7), anti-c-Kit-APCe780 (2B8), anti-CD34-FITC (RAM34) and anti-CD16/32-Alexa Fluor 700 (2.4G2). In addition to FACS antibodies, cells were labeled with CITE-seq antibodies (see Supplementary Table S1). 4′,6-diamidino-2-phenylindole (DAPI) (Sigma-Aldrich, St. Louis, MO) was used for dead cell exclusion. All cell isolations were performed using cell sorting on FACSAria III (BD Biosciences, San Jose, CA). Post cell sorting, 7000 Lineage-cKit+ BM, 1000 HSPC, 1000 CMP, and 1000 LT-HSC were pooled together for 10x genomics

value: Bone Marrow


title: WT_12DPA_R1

description: 6xAmputated HL central digits 12 DPA WT rep1

value: 12 DPA blastema

value: mixed CD1 C57Bl/6 background

value: 33 days


title: mNFIXko_Antibody_Capture

description:
CITE-seq
manual_label.RData


title: SBW25 rep3

description: mature tRNA

value: SBW25 (wildtype)


title: rWT rep3

description: mature tRNA

value: engineered wildtype (control)

value: rWT


title: M5_1 rep2

description: mature tRNA


title: BJAB_2

value: BJAB

value: Parental

value: resistant


title: mNFIXko_Gene_Expression

description:
CITE-seq
manual_label.RData


title: BJAB_1


title: BJAB_3


title: Total_RNA_NIP_Rep2_0hr

value: No Cyclopiazonic acid (CPA)


title: MUT_12DPA_R2

description: 6xAmputated HL central digits 12 DPA MUT rep2

value: MUT


title: M3_1 rep2

description: mature tRNA

value: engineered then evolved


title: mWT_Gene_Expression

description:
CITE-seq
manual_label.RData


title: Total_RNA_NIL_Rep2_36hr_CPA

source_name: Spinal Motor neuron differntiated from mouse embryonic stem cells

value: Cyclopiazonic acid (CPA) 36 hr


title: Total_RNA_NIP_Rep2_36hr

value: Cranial Motor neuron differntiated from mouse embryonic stem cells

value: No Cyclopiazonic acid (CPA) 36 hr


title: EJ1_PAR_3

value: naïve

value: DMSO


title: M1_1 rep2

description: mature tRNA


title: NAM_PAR_1

value: Namalwa


title: EJ1_PAR_2


title: Total_RNA_NIP_Rep2_12hr

value: No Cyclopiazonic acid (CPA) 12 hr


title: dglyGCC rep2

description: mature tRNA

value: engineered

value: {delta}glyGCC


title: Mu

city: Guangzhou

first: Shuyi

last: Chen

address: #7 Jinsui Rd, Zhujiang Newtown

institute: Zhongshan Ophthlamic Center

data_processing:
cellranger (v3.1.0) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 3.1, https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Genome_build: mm10_Ensembl92
Supplementary_files_format_and_content: MTX file and TSV file contain counts for each barcodes and genes

source_name: retina

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3.1 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols.

treatment_protocol: retinas were dissected, and digested into single cells using papain.

value: Mettl3-conditional knockout

value: retina


title: Total_RNA_NIL_Rep2_36hr

value: Spinal Motor neuron differntiated from mouse embryonic stem cells


title: Total_RNA_NIL_Rep2_12hr_CPA

value: Cyclopiazonic acid (CPA) 12 hr


title: Ctrl

value: Ctrl


title: SU16_MCL1_DTEP_3

value: DTEP

value: resistant


title: artesunate-treated ECM mice brain-4

first: Ziyi

last: Pan

address: NO.12, Airport Road, Baiyun District

institute: Guangzhou University of Chinese Medicine

data_processing:
Illumina software used for basecalling.
Trimmomatic software were used to filtering data
Quality distribution plot and base content distribution were generated by FASTQC
STAR software is used to align clean reads to reference genome.
Read counts for individual transcripts of each sample were produced with HTSeq-count
Genome_build: mm10
Supplementary_files_format_and_content: text files include read counts and FPKM values for each Sample
Supplementary_files_format_and_content: text files include differiential genes statistic between two group for all samples

source_name: artesunate-treated ECM

growth_protocol: The mice are kept in an SPF barrier environment, free to drink and eat

extract_protocol:
brains were removed and protected by RNAlater, total RNA was extracted by Trizol (Thermo Fisher Scientific,15596018), RNA purity and concentration were evaluated by using the Nanodrop ND-2000 spectrophotometer (ThermoFisher Scientific, Waltham, MA, USA). RNA purity and integrity were determined by 1% agarose gel electrophoresis for 16 minutes at 180V voltage. RNA integrity were confirmed by using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
RNA libraries were prepared for using NEBNext UltraTM RNA Library Prep Kit（NEB #E7490）

treatment_protocol: four replicate per group,normal mice, experimental cerebral malaria mice and artesunate-treated ECM mice for 4 days.

value: brain

value: 6 weeks old

value: wild type


title: artesunate-treated ECM mice brain-3


title: SU16_MCL1_DTEP_2


title: EJ1_PAR_1

value: Parental


title: dEGEG rep2

last: Gallie

institute: Max Planck Institute for Evolutionary Biology

description: mature tRNA

value: {delta}EGEG


title: Total_RNA_NIL_Rep2_0hr

value: No Cyclopiazonic acid (CPA)


title: Total_RNA_NIL_Rep2_12hr


title: Total_RNA_NIP_Rep1_36hr

value: Cranial Motor neuron differntiated from mouse embryonic stem cells

value: No Cyclopiazonic acid (CPA) 36 hr


title: W1_1 rep2

description: mature tRNA

value: evolved wildtype (control)


title: artesunate-treated ECM mice brain-2


title: Total_RNA_NIP_Rep1_36hr_CPA

value: Cyclopiazonic acid (CPA) 36 hr


title: M5_1 rep1

description: mature tRNA

value: engineered then evolved


title: artesunate-treated ECM mice brain-1


title: SU16_PAR_3

value: naïve

value: DMSO


title: ECM mice brain-4

source_name: experimental cerebral malaria (ECM)


title: SU16_PAR_2


title: ECM mice brain-3


title: Total_RNA_NIP_Rep1_12hr

value: No Cyclopiazonic acid (CPA) 12 hr


title: Total_RNA_NIP_Rep1_12hr_CPA

value: Cyclopiazonic acid (CPA) 12 hr


title: M3_1 rep1

description: mature tRNA


title: SU16_PAR_1


title: M1_1 rep1

description: mature tRNA


title: Total_RNA_NIP_Rep1_0hr


title: rWT rep2

description: mature tRNA

value: engineered wildtype (control)

value: rWT


title: ECM mice brain-2

value: brain


title: dglyGCC rep1

description: mature tRNA

value: engineered

value: {delta}glyGCC


title: scl28-3 root sample #3

city: Rosario

first: Ramiro

last: Rodriguez

address: Ocampo y Esmeralda

country: Argentina

institute: IBR

data_processing:
Reads were aligned using hisat2 version 2.0.0-beta
Gene counts were generated using htseq-count version 0.6.1p1
Counts were processed in edgeR
Genome_build: TAIR10 release of the Arabidopsis genome
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each gene in each sample

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Plants were grown in continuous light at 21°C in Petri plates containing Murashige and Skoog solid medium (1 × Murashige and Skoog salts, 1% sucrose, 2.3 mM MES (pH 5.8 adjusted with KOH), 1% agar).

extract_protocol:
RNA was isolated from root tips (∼2 mm) using RNeasy plant mini kit (QIAGEN, http://www.qiagen.com). Approximately 300 root tips from 6-days-old plants were collected for each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: organ

value: root


title: dEGEG rep1

city: Ploen

first: Jenna

address: August-Thienemann Strasse 2

description: mature tRNA

value: {delta}EGEG


title: SU16_MCL1_DTEP_1

value: DTEP

value: resistant


title: ECM mice brain-1

value: 6 weeks old

value: wild type


title: scl28-3 root sample #2


title: control mice brain-4

source_name: control


title: SBW25 rep2

description: mature tRNA

value: SBW25 (wildtype)


title: Total_RNA_NIL_Rep1_36hr

value: Spinal Motor neuron differntiated from mouse embryonic stem cells

value: No Cyclopiazonic acid (CPA) 36 hr


title: W1_1 rep1

description: mature tRNA

value: evolved wildtype (control)


title: scl28-3 root sample #1


title: control mice brain-3


title: rWT rep1

description: mature tRNA


title: control mice brain-2


title: SBW25 rep1

description: mature tRNA


title: Total_RNA_NIL_Rep1_12hr

value: No Cyclopiazonic acid (CPA) 12 hr


title: control mice brain-1


title: Total_RNA_NIL_Rep1_0hr

value: No Cyclopiazonic acid (CPA)


title: MARC-PEDV-IP-2

status: Public on Dec 01 2022

city: Hangzhou

first: Yaowei

last: Huang

address: 866 Yuhangtang Rd

institute: Zhejiang University

description: MARC-PEDV.bed

data_processing:
The adapters and low quality bases were removed by using cutadapt (v1.15)
The Fastq files were aligned to the reference genome (hg38,chlSab2 and PEDV) using TopHat (v2.1.1)
The m6A peak calling method was modified from published work.The longest isoform of each gene was scanned using a 100-bp sliding window with 10-bp steps. We excluded windows with read counts less than 1/20 of the top window in both the input and m6A-IP sample to reduce bias from potentially inaccurate gene structure annotation and the arbitrary use of the longest isoform.
For each gene, the read counts in each window were normalized by the median count of all windows of that gene. The differential windows between the input and IP samples were identified with a negative binomial model by using the edgeR package.
Sequence motifs on m6A peaks were identified by HOMER
Genome_build: hg38, chlSab2 and PEDV

organism: Chlorocebus aethiops

source_name: monkey kidney epithelial cells

growth_protocol: S10-3 and MARC-145 cells were grown in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics at 37 °C.

extract_protocol:
Total RNA was extracted form Mock or PEDV-infected samples using TRIzol reagent, and then mRNA was purified using the GenElute mRNA miniprep kit (Sigma) and fragmented by ZnCl2.Fragmented mRNA was incubated with anti-m6A antibody (Synaptic Systems).
Sample eluted RNA and input control libraries were constructed using a TruSeq stranded mRNA sample preparation kit (Illumina) according to the manufacturer’s instructions.
MeRIP-seq

treatment_protocol: Cells were uninfected or infected with PEDV (MOI=0.1) for 24 hours

tag: cell type

value: monkey kidney epithelial cells

tag: antibody

value: Anti-m6A antibody

value: PEDV infection for 24hpi


title: Wild type root sample #1

tag: genotype/variation


title: MARC-PEDV-IP-1

description: MARC-PEDV.bed


title: MARC-PEDV-Input-2

description: MARC-PEDV.bed


title: Total_RNA_NIL_Rep1_36hr_CPA

value: Cyclopiazonic acid (CPA) 36 hr


title: MARC-Ctrl-IP-2

description: MARC-Ctrl.bed

value: No treatment


title: MARC-PEDV-Input-1

description: MARC-PEDV.bed


title: MARC-Ctrl-Input-2

description: MARC-Ctrl.bed


title: MARC-Ctrl-Input-1

description: MARC-Ctrl.bed


title: MARC-Ctrl-IP-1

description: MARC-Ctrl.bed


title: HAP1 cells, Control-4

city: Middlebury College

first: Amanda

last: Crocker

state: Vermont

address: 276 Bicentennial Way

department: Neuroscience

institute: Middlebury College

description:
DNBseq Platform
RawHTseqCounts_ALL.txt
NormCountsDeseq2HTseqCountsStrict.txt

data_processing:
SOAPnuke v.1.5.2 was used to filter reads with adapters, reads with unknown bases more than 10%, low quality reads (the percentage of base which quality is lesser than 15 is greater than 50% in a read)
HiSat2 used for allignment using hg38 build and Homo Sapien GRCh38 NCBI GTF file. Htseq-Counts was used for gene counts. Deseq2 was used for normalization and differential expression analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited files containing either raw counts from Htseq-Counts or normalized counts from DESeq2

growth_protocol: Wild type or gene-edited HAP1 cells (SLC25A1 and SLC25A4) were grown in IMDM supplemented with 10% FBS and 100 µg/ml penicillin and streptomycin at 37°C in a 10% CO2 incubator. Cells were grown on 10cm tissue culture dishes to 85% confluency. Cells were placed on ice, washed 3 times with ice cold PBS (Corning, 21-040), and then incubated with PBS with 10mM EDTA for 30 minutes at 4°C. Mechanical agitation with a 10ml pipette was used to remove cells from plates. The collected cells were then centrifuged at 800xg for 5 minutes at 4°C. Following centrifugation, the supernatant was removed and the pellet was washed with ice cold PBS. The resuspended pellet was then spun at 16,100 x g for 5 minutes. The supernatant was aspirated away and the remaining pellet was flash frozen on dry ice for at least 5 minutes and stored at -80°C until further use.

extract_protocol:
The poly-A containing mRNA molecules were purified using poly-T oligo attached magnetic beads.
Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification. We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library. DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the DNBseq platform for the following data analysis study. For this step, the DNBseq platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.

treatment_protocol: No treatments were applied

value: C631 (RRID:CVCL_Y019)

value: WT

value: Parental Wildtype Line


title: Total_RNA_NIL_Rep1_12hr_CPA

value: Cyclopiazonic acid (CPA) 12 hr


title: HAP1 cells, Control-3


title: HAP1 cells, Control-2


title: Wild type root sample #3

value: root


title: HAP1 cells, C3-3

value: HZGHC001753c010 (RRID:CVCL_TM05)

value: SLC25A1 KO

value: CRISPR/Cas9-Edited Knockout Cell Line


title: HAP1 cells, C3-4


title: HAP1 cells, C11-4

value: HZGHC000778c011 (RRID:CVCL_TM45)

value: SLC25A4 KO


title: HAP1 cells, C11-3


title: HAP1 cells, C11-1


title: Wild type root sample #2

value: wild type


title: HAP1 cells, C3-2